Re: [R] how to get paste() to output \% so LaTeX will interpret it as a percent sign rather than a comment symbol

[Hadley Wickham]

You're getting confused between the contents of the string and the
printed representation of the string. There's a little bit about this
in R4DS: https://r4ds.hadley.nz/strings#escapes

(or in brief, do writeLines(trailing.7.message))

Hadley

On Fri, Sep 8, 2023 at 7:23 AM Christopher Ryan via R-help
 wrote:
>
> I'm using a .Rnw --> Sweave --> pdflatex workflow on Windows 10, with emacs
> 26.3 and ESS (not sure which version.)
>
> I have this code:
>
> n.tests.7 <- 3 ## for example
> trailing.7.pos.percent <- 12  ## for example
> trailing.7.message <-
> ifelse( n.tests.7 > 0,
> paste("In the past seven days,", n.tests.7, "test results have
> been reported, of which", trailing.7.pos.percent, "\\% were positive"),
> paste("No test results have been reported from these labs in
> the past seven days.") )
>
> Desired outcome in the resulting .tex file is "In the past seven days, 3
> test results have been reported, of which 12\% were positive."
>
> But I get "In the past seven days, 3 test results have been reported, of
> which 12\\% were positive." Which, when compiled in pdflatex,
> unsurprisingly cuts off the sentence at 12
>
> Replacing, in the .Rnw code, the \\% with \% , yields an R error message:
>
> Error: '\%' is an unrecognized escape in character string starting ""\%"
>
> Grateful for any help.
>
> --Chris Ryan
>
> [[alternative HTML version deleted]]
>
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> and provide commented, minimal, self-contained, reproducible code.



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Re: [R] Book Recommendation

[Hadley Wickham]

These days I'd recommend duckdb
(https://cran.r-project.org/web/packages/duckdb/index.html) instead.
It's a similar design to RSQLite (i.e. you don't need a separate
server) but it's designed for the needs of data science.

Hadley

On Tue, Aug 29, 2023 at 9:22 AM Martin Møller Skarbiniks Pedersen
 wrote:
>
> The SQLite is a good database to use.
>
> https://cran.r-project.org/web/packages/RSQLite/vignettes/RSQLite.html
>
> On Mon, Aug 28, 2023, 22:12 Stephen H. Dawson, DSL via R-help <
> r-help@r-project.org> wrote:
>
> >
> > This is an academic course. The effort now is to nail down the former. I
> > am pushing against a local db for the students. I prefer they focus on
> > the get-and-analyze efforts and not db administration efforts.
> >
> >
>
> [[alternative HTML version deleted]]
>
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> and provide commented, minimal, self-contained, reproducible code.



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Re: [R] Book Recommendation

[Hadley Wickham]

You might find this chapter of R for Data Science helpful:
https://r4ds.hadley.nz/databases

Hadley

On Tue, Aug 29, 2023 at 3:47 AM Stephen H. Dawson, DSL via R-help
 wrote:
>
> Good Morning,
>
>
> I am doing some research to develop a new course where I teach. I am
> looking for a book to use in the course content to teach accomplishing
> SQL in R.
>
> Does anyone know of a book on this topic to recommend for consideration?
>
>
> Thank You,
> --
> *Stephen Dawson, DSL*
> /Executive Strategy Consultant/
> Business & Technology
> +1 (865) 804-3454
> http://www.shdawson.com
>
> __
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Re: [R] Merge with closest (not equal) time stamps

[Hadley Wickham]

It sounds like you might want a rolling join, e.g.
https://dplyr.tidyverse.org/reference/join_by.html#rolling-joins.

(And data.table has similar functionality which inspired dplyr)

Hadley

On Mon, Aug 7, 2023 at 9:32 PM Naresh Gurbuxani
 wrote:
>
>
> I have two dataframes, each with a column for timestamp.  I want to
> merge the two dataframes such that each row from first dataframe
> is matched with the row in the second dataframe with most recent but
> preceding timestamp. Here is an example.
>
> option.trades <- data.frame(timestamp = as.POSIXct(c("2023-08-07 10:23:22", 
> "2023-08-07 10:25:33", "2023-08-07 10:28:41")), option.price = c(2.5, 2.7, 
> 1.8))
>
> stock.trades <- data.frame(timestamp = as.POSIXct(c("2023-08-07 10:23:21", 
> "2023-08-07 10:23:34", "2023-08-07 10:24:57", "2023-08-07 10:28:37", 
> "2023-08-07 10:29:01")), stock.price = c(102.2, 102.9, 103.1, 101.8, 101.7))
>
> stock.trades <- stock.trades[order(stock.trades$timestamp),]
>
> library(plyr)
> mystock.prices <- ldply(option.trades$timestamp, function(tstamp) 
> tail(subset(stock.trades, timestamp <= tstamp), 1))
> names(mystock.prices)[1] <- "stock.timestamp"
> myres <- cbind(option.trades, mystock.prices)
>
> This method works. But for large dataframes, it is very slow.  Is there
> a way to speed up the merge?
>
> Thanks,
> Naresh
>
> __
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Re: [R] Off-topic: ChatGPT Code Interpreter

[Hadley Wickham]

> I am not sure what your example means but text to image conversion can be
> done quite easily in many programming environments and does not need an AI
> unless you are using it to hunt for info.  I mean you can open up many Paint
> or Photo programs and look at the menus and often one allows you to write
> using whatever font/size/color/background you want to add a layer on the
> image. There are plenty of free resources on-line that I sometimes use to
> write something in a large fiery font or whatever and when I get the result
> I want, I save it as graphics.

I would recommend you try out one of the many text-to-image AI
services like https://www.midjourney.com/ or
https://openai.com/dall-e-2. These services are much more
sophisticated than you might imagine.

Hadley

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Re: [R] R does not run under latest RStudio

[Hadley Wickham]

I'm not aware of widespread problems, but it's possible that some
combination of OS, RStudio version, and R version might be causing
problems. Unfortunately I don't think there's enough information in
this thread for anyone to tell if that's the case.

Hadley

On Fri, Apr 7, 2023 at 1:18 PM Sorkin, John  wrote:
>
> I have also had difficulty running R in RStudio. Has anyone else had problems?
>  It will be a shame if we need to abandon R Studio. It is a very good IDE.
> John
>
> John David Sorkin M.D., Ph.D.
> Professor of Medicine
> Chief, Biostatistics and Informatics
> University of Maryland School of Medicine Division of Gerontology and 
> Geriatric Medicine
> Baltimore VA Medical Center
> 10 North Greene Street
> GRECC (BT/18/GR)
> Baltimore, MD 21201-1524
> (Phone) 410-605-7119
> (Fax) 410-605-7913 (Please call phone number above prior to 
> faxing)
>
> On Apr 6, 2023, at 5:30 PM, David Winsemius  wrote:
>
> 
> On 4/6/23 03:49, Steven Yen wrote:
> The RStudio list generally does not respond to free version users. I was 
> hoping someone one this (R) list would be kind enough to help me.
>
>
> I don't think that is true. It is perhaps true that you cannot get 
> personalized help from employed staff, but you can certainly submit to the 
> Q forum.
>
>
> --
>
> David
>
>
> Steven from iPhone
>
> On Apr 6, 2023, at 6:22 PM, Uwe Ligges  
> wrote:
>
> No, but you need to ask on an RStudio mailing list.
> This one is about R.
>
> Best,
> Uwe Ligges
>
>
>
>
> On 06.04.2023 11:28, Steven T. Yen wrote:
> I updated to latest RStudio (RStudio-2023.03.0-386.exe) but
> R would not run. Error message:
> Error Starting R
> The R session failed to start.
> RSTUDIO VERSION
> RStudio 2023.03.0+386 "Cherry Blossom " (3c53477a, 2023-03-09) for Windows
> [No error available]
> I also tried RStudio 2022.12.0+353 --- same problem.
> I then tried another older version of RStudio (not sure version
> as I changed file name by accident) and R ran.
> Any clues? Please help. Thanks.
> __
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> and provide commented, minimal, self-contained, reproducible code.
>[[alternative HTML version deleted]]
>
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> and provide commented, minimal, self-contained, reproducible code.
>
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> PLEASE do read the posting guide 
> 

Re: [R] Lazy-load corrupt?

[Hadley Wickham]

This often indicates you need to restart R.
Hadley

On Friday, February 3, 2023, Nick Wray  wrote:

> Hello  When trying to call various packages eg
> library(raster)
> library(sp)
> library(rgdal)
>
> I get this error message:
> Loading required package: sp
> Error: package or namespace load failed for ‘sp’ in get0(name, envir =
> where, mode = "function", inherits = FALSE):
>  lazy-load database 'C:/PROGRA~1/R/R-42~1.1/library/base/R/base.rdb' is
> corrupt
> Error: package ‘sp’ could not be loaded
> In addition: Warning messages:
> 1: package ‘raster’ was built under R version 4.2.2
> 2: package ‘sp’ was built under R version 4.2.2
> 3: In get0(name, envir = where, mode = "function", inherits = FALSE) :
>   restarting interrupted promise evaluation
> 4: In get0(name, envir = where, mode = "function", inherits = FALSE) :
>   internal error -3 in R_decompress1
>
>
> Other packages load fine (and the packages above load OK on my spare
> laptop) but I'm imagining that this means that I have to uninstall my
> current R and reinstall the latest version - but before I go through all
> that can anyone confirm that that is indeed what I need to do or is there
> some other problem?
>
> Thanks Nick Wray
>
> [[alternative HTML version deleted]]
>
> __
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> PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


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Re: [R] interval between specific characters in a string...

[Hadley Wickham]

On Sun, Dec 4, 2022 at 1:22 PM  wrote:
>
> This may be a fairly dumb and often asked question about some functions like 
> strsplit()  that return a list of things, often a list of ONE thing that be 
> another list or a vector and needs to be made into something simpler..
>
> The examples shown below have used various methods to convert the result to a 
> vector but why is this not a built-in option for such a function to simplify 
> the result either when possible or always?
>
> Sure you can subset it with " [[1]]" or use unlist() or as.vector() to coerce 
> it back to a vector. But when you have a very common idiom and a fact that 
> many people waste lots of time figuring out they had a LIST containing a 
> single vector and debug, maybe it would have made sense to have either a 
> sister function like strsplit_v() that returns what is actually wanted or 
> allow strsplit(whatever, output="vector") or something giving the same result.
>
> Yes, I understand that when there is a workaround, it just complicates the 
> base, but there could be a package that consistently does things like this to 
> make the use of such functions easier.

The next version of stringr (currently being processed by CRAN)
provides str_split_1() for exactly this purpose.

Hadley

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Re: [R] interval between specific characters in a string...

[Hadley Wickham]

On Sun, Dec 4, 2022 at 12:50 PM Hervé Pagès  wrote:
>
> On 03/12/2022 07:21, Bert Gunter wrote:
> > Perhaps it is worth pointing out that looping constructs like lapply() can
> > be avoided and the procedure vectorized by mimicking Martin Morgan's
> > solution:
> >
> > ## s is the string to be searched.
> > diff(c(0,grep('b',strsplit(s,'')[[1]])))
> >
> > However, Martin's solution is simpler and likely even faster as the regex
> > engine is unneeded:
> >
> > diff(c(0, which(strsplit(s, "")[[1]] == "b"))) ## completely vectorized
> >
> > This seems much preferable to me.
>
> Of all the proposed solutions, Andrew Hart's solution seems the most
> efficient:
>
>big_string <- strrep("abaaabbabaaabaaab", 50)
>
>system.time(nchar(strsplit(big_string, split="b", fixed=TRUE)[[1]]) + 1)
>#user  system elapsed
>#   0.736   0.028   0.764
>
>system.time(diff(c(0, which(strsplit(big_string, "", fixed=TRUE)[[1]]
> == "b"
>#user  system elapsed
>#  2.100   0.356   2.455
>
> The bigger the string, the bigger the gap in performance.
>
> Also, the bigger the average gap between 2 successive b's, the bigger
> the gap in performance.
>
> Finally: always use fixed=TRUE in strsplit() if you don't need to use
> the regex engine.

You can do a bit better if you are willing to use stringr:

library(stringr)
big_string <- strrep("abaaabbabaaabaaab", 50)

system.time(nchar(strsplit(big_string, split="b", fixed=TRUE)[[1]]) + 1)
#>user  system elapsed
#>   0.126   0.002   0.128

system.time(str_length(str_split(big_string, fixed("b"))[[1]]))
#>user  system elapsed
#>   0.103   0.004   0.107

(And my timings also suggest that it's time for Hervé to get a new computer :P)

It feels like an approach that uses locations should be faster since
you wouldn't have to construct all the intermediate strings.

system.time(pos <- str_locate_all(big_string, fixed("b"))[[1]][,1])
#>user  system elapsed
#>   0.075   0.004   0.080
# I suspect this could be optimised with a little thought making this approach
# faster overall
system.time(c(0, diff(pos))
#>user  system elapsed
#>   0.022   0.006   0.027

Hadley

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Re: [R] help finding a starting point to diagnose inability to install or update packages

[Hadley Wickham]

If this happens again in the future, you might try the development
version of pak:

install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/;)
pak::pak("tidyverse")

pak automatically diagnoses a number of common problems that causes
install.packages() to fail.

Hadley

On Sun, Apr 25, 2021 at 4:51 PM Larry Johnson
 wrote:
>
> It was pointed out to me by Jeff Newmiller that I should have been hitting 
> "reply all" so that others could see the thread and make comment, 
> corrections, or benefit from any solution.
>
> So, I'm going to summarize the end result.
>
> Duncan Murdoch walked me through some diagnostic steps, and what ultimately 
> worked was to run
>
> remove.packages("broom")
> install.packages("broom")
>
> and then repeat that for each of the four packages that attempts to load 
> tidyverse indicated had dependency issues (I know that last sentence was 
> ungrammatical, but you probably get my drift).
>
> I'd still like to know why updating packages in bulk isn't working for me, 
> but I can move ahead for now, and I'll figure out how to fix that later.
>
> So thanks Duncan.
>
>
> Larry Johnson
>
> Editor and Publisher
>
> Cobb County Courier
>
> 404-664-2034
>
> http://cobbcountycourier.com
>
> 
> From: Duncan Murdoch 
> Sent: Sunday, April 25, 2021 12:41 PM
> To: Larry Johnson ; r-help@r-project.org 
> 
> Subject: Re: [R] help finding a starting point to diagnose inability to 
> install or update packages
>
> On 25/04/2021 10:52 a.m., Larry Johnson wrote:
> > Hi. Short version.  tidyverse disappeared from my packages, and won't 
> > install.  The initial failure stated I had an outdated broom package, but 
> > updates are failing too, not just on broom, but on all packages, and there 
> > is no meaningful error output on the installation failures.
> >
> > I typically use RStudio on Fedora 33, but the problem I'm about to describe 
> > occurs whether I use RStudio or the text version.
> >
> > To give you overview, here is the output from sessionInfo:
> >
> >
> >> sessionInfo()
> > R version 4.0.4 (2021-02-15)
> > Platform: x86_64-redhat-linux-gnu (64-bit)
> > Running under: Fedora 33 (Workstation Edition)
> >
> > Matrix products: default
> > BLAS/LAPACK: /usr/lib64/libflexiblas.so.3.0
> >
> > locale:
> >   [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
> >   [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
> >   [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
> >   [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
> >   [9] LC_ADDRESS=C   LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] stats graphics  grDevices datasets  utils methods   base
> >
> > loaded via a namespace (and not attached):
> >   [1] htmlwidgets_1.5.3   colorspace_2.0-0scales_1.1.1
> > compiler_4.0.4
> >   [5] magrittr_2.0.1  R6_2.5.0leaflet_2.0.4.1 
> > htmltools_0.5.1.1
> >   [9] tools_4.0.4 crosstalk_1.1.1 digest_0.6.27   
> > lifecycle_1.0.0
> > [13] munsell_0.5.0   rlang_0.4.10CoprManager_0.3.7.1
> >>
> >
> > After trying complete reinstalls of R, RStudio, and the CRAN repositories 
> > here's the last error messages I've gotten in my attempts to install and 
> > load tidyverse:
> >
> >
> >> install.packages(c("broom", "callr", "cli", "cpp11", "dbplyr", "haven", 
> >> "highr", "knitr", "pillar", "processx", "RcppArmadillo", "reprex", 
> >> "tibble", "tinytex", "vctrs", "viridis", "viridisLite", "withr"))
> > Install system packages...
> >> install.packages("tidyverse")
> > Install system packages...
> >> library(tidyverse)
> > Error: package or namespace load failed for ‘tidyverse’ in loadNamespace(j 
> > <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
> >   namespace ‘broom’ 0.7.5 is being loaded, but >= 0.7.6 is required
> >
> > Attempts to install or update broom fail with no output.
> >
> > I've been searching for similar reports of failure here in these archives, 
> > on the RStudio forums, and on the internet and have found nothing that's a 
> > seamless match.  If I can't find anything I'll check out filing a bug 
> > report (I've never done it with R before).
> >
> > Any help with a starting point in diagnosing this will be appreciated.
>
> Are you using install_github(), or otherwise installing non-CRAN
> versions?  If so, stop doing that. First, run update.packages(ask=FALSE)
> to make sure you are up to date.  Then delete any package that is newer
> than the CRAN version, and reinstall it using the basic install.packages().
>
> Here's code to compare versions:
>
> CRAN <- available.packages()
> here <- installed.packages()
> for (i in seq_len(nrow(here))) {
>if (here[i, "Package"] %in% rownames(CRAN) &&
>package_version(here[i, "Version"]) >
>  package_version(CRAN[here[i, "Package"], "Version"]))
>  cat(here[i, c("Package", "Version")], "\n", sep=" " )
> }
>
> Duncan Murdoch
>
> 

Re: [R] roxygen2 & markdown & math

[Hadley Wickham]

On Tuesday, January 12, 2021, Duncan Murdoch 
wrote:

> On 12/01/2021 1:12 p.m., Sigbert Klinke wrote:
>
>> Hi,
>>
>> thanks a lot, but maybe I was to vague.
>>
>> I do not want to replace \eqn{...} and \deqn{...} by \mjseqn{...} and
>> \mjsdeqn{...}. I would like to use $...$ and $$...$$ as in Rmarkdown to
>> get something better readable.
>>
>
> I think that's a question/suggestion that would have to go to the roxygen2
> team.  They're the ones who convert Markdown into the Rd input format.
> Presumably they could convert $...$ into the appropriate macro using
> Mathjax or not, but I have no idea how difficult that would be.
>

If I remember correctly, I think it would be relatively hard since roxygen2
uses commonmark, which doesn’t include math in its parse tree. It might be
possible to hack something together with regular expressions, but of course
that brings with it the risk of introducing new edge cases that don’t
behave as expected.

Hadley


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Re: [R] How to understand the mentality behind tidyverse and ggplot2?

[Hadley Wickham]

I'd recommend two places to get started:

* https://r4ds.had.co.nz/data-visualisation.html for a quick intro to
ggplot2 (and the rest of the book explains the general tidyverse
philosophy)

* https://ggplot2-book.org for the full details of ggplot2.

Hadley

On Wed, Nov 18, 2020 at 11:37 AM C W  wrote:
>
> Dear R list,
>
> I am an old-school R user. I use apply(), with(), and which() in base
> package instead of filter(), select(), separate() in Tidyverse. The idea of
> pipeline (i.e. %>%) my code was foreign to me for a while. It makes the
> code shorter, but sometimes less readable?
>
> With ggplot2, I just don't understand how it is organized. Take this code:
>
> > ggplot(diamonds, aes(x=carat, y=price)) + geom_point(aes(color=cut)) +
> geom_smooth()
>
> There are three plus signs. How do you know when to "add" and what to
> "add"? I've seen more plus signs.
>
> To me, aes() stands for aesthetic, meaning looks. So, anything related to
> looks like points and smooth should be in aes(). Apparently, it's not the
> case.
>
> So, how does ggplot2 work? Could someone explain this for an old-school R
> user?
>
> Thank you!
>
> [[alternative HTML version deleted]]
>
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> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.



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Re: [R] combine filter() and select()

[Hadley Wickham]

On Wed, Aug 19, 2020 at 10:03 AM Ivan Calandra  wrote:
>
> Dear useRs,
>
> I'm new to the tidyverse world and I need some help on basic things.
>
> I have the following tibble:
> mytbl <- structure(list(files = c("a", "b", "c", "d", "e", "f"), prop =
> 1:6), row.names = c(NA, -6L), class = c("tbl_df", "tbl", "data.frame"))
>
> I want to subset the rows with "a" in the column "files", and keep only
> that column.
>
> So I did:
> myfile <- mytbl %>%
>   filter(grepl("a", files)) %>%
>   select(files)
>
> It works, but I believe there must be an easier way to combine filter()
> and select(), right?

Not in the tidyverse. As others have mentioned, both [ and subset() in
base R allow you to simultaneously subset rows and columns, but
there's no single verb in the tidyverse that does both. This is
somewhat informed by the observation that in data frames, unlike
matrices, rows and columns are not exchangeable, and you typically
want to express subsetting in rather different ways.

Hadley

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Re: [R] Reorganize the data (dplyr or other packages?)

[Hadley Wickham]

> | but they won't receive any new
> | features, and we believe that there
> | are now better approaches to solving
> | the same problem.
>
> Is tidyr::pivot_longer this better
> solution?  It is an easier to understand
> version of the now retired and confusing
> (for me) tidyr::gather which at least
> reigned back in 2018 (was that any good
> compared to reshape?).

Yes, and hopefully :)

library(tidyr)

tab <- structure(list(
date = c("2019M08", "2019M09", "2019M10"),
down = c(0.01709827, 0.02094724, 0.01750911),
uc = c(0.2653882, 0.2265797, 0.245003),
up = c(0.7175136, 0.7524731, 0.7374879)),
class = "data.frame", row.names = c(NA, -3L))

tab %>% pivot_longer(
  down:up,
  names_to = "direction",
  values_to = "percentage"
)
#> # A tibble: 9 x 3
#>   datedirection percentage
#>
#> 1 2019M08 down  0.0171
#> 2 2019M08 uc0.265
#> 3 2019M08 up0.718
#> 4 2019M09 down  0.0209
#> 5 2019M09 uc0.227
#> 6 2019M09 up0.752
#> 7 2019M10 down  0.0175
#> 8 2019M10 uc0.245
#> 9 2019M10 up0.737

Created on 2020-08-17 by the [reprex
package](https://reprex.tidyverse.org) (v0.3.0)



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Re: [R] Reorganize the data (dplyr or other packages?)

[Hadley Wickham]

We previously used the term retired to suggest that the package is
taking it easy and relaxing, but isn't dead. This causes a lot of
confusion so we now call this state "superseded" — we'll continue to
keep reshape2 (and reshape!) on CRAN, but they won't receive any new
features, and we believe that there are now better approaches to
solving the same problem.

Hadley

On Mon, Aug 17, 2020 at 3:58 AM Eric Berger  wrote:
>
> Thanks for this information Thierry. I was not aware.
> The author of the packages is Hadley Wickham. He writes on Github that he
> does plan to make changes necessary to keep the package available on CRAN.
>
>
>
> On Mon, Aug 17, 2020 at 11:23 AM Thierry Onkelinx 
> wrote:
>
> > Yes. However reshape2 is a retired package. The author recommends to use
> > his new package tidyr.
> >
> > ir. Thierry Onkelinx
> > Statisticus / Statistician
> >
> > Vlaamse Overheid / Government of Flanders
> > INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
> > FOREST
> > Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
> > thierry.onkel...@inbo.be
> > Havenlaan 88 bus 73, 1000 Brussel
> > www.inbo.be
> >
> >
> > ///
> > To call in the statistician after the experiment is done may be no more
> > than asking him to perform a post-mortem examination: he may be able to say
> > what the experiment died of. ~ Sir Ronald Aylmer Fisher
> > The plural of anecdote is not data. ~ Roger Brinner
> > The combination of some data and an aching desire for an answer does not
> > ensure that a reasonable answer can be extracted from a given body of data.
> > ~ John Tukey
> >
> > ///
> >
> > <https://www.inbo.be>
> >
> >
> > Op ma 17 aug. 2020 om 09:52 schreef Eric Berger :
> >
> >> Alternatively, melt() from the reshape2 package.
> >>
> >> library(reshape2)
> >> melt(x,id.vars="date",measure.vars=c("down","uc","up"),variable.name
> >> ="direction",value.name="percentage")
> >>
> >> HTH,
> >> Eric
> >>
> >>
> >> On Mon, Aug 17, 2020 at 10:49 AM Thierry Onkelinx via R-help <
> >> r-help@r-project.org> wrote:
> >>
> >>> You are looking for tidyr::pivot_longer()
> >>>
> >>> Best regards,
> >>>
> >>> ir. Thierry Onkelinx
> >>> Statisticus / Statistician
> >>>
> >>> Vlaamse Overheid / Government of Flanders
> >>> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
> >>> AND
> >>> FOREST
> >>> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
> >>> thierry.onkel...@inbo.be
> >>> Havenlaan 88 bus 73, 1000 Brussel
> >>> www.inbo.be
> >>>
> >>>
> >>> ///
> >>> To call in the statistician after the experiment is done may be no more
> >>> than asking him to perform a post-mortem examination: he may be able to
> >>> say
> >>> what the experiment died of. ~ Sir Ronald Aylmer Fisher
> >>> The plural of anecdote is not data. ~ Roger Brinner
> >>> The combination of some data and an aching desire for an answer does not
> >>> ensure that a reasonable answer can be extracted from a given body of
> >>> data.
> >>> ~ John Tukey
> >>>
> >>> ///
> >>>
> >>> <https://www.inbo.be>
> >>>
> >>>
> >>> Op ma 17 aug. 2020 om 09:35 schreef John :
> >>>
> >>> > Is there any quick way (dplyr?) to arrange the data
> >>> >  date  down   uc   up
> >>> > 2019M08   0.01709827 0.2653882 0.7175136
> >>> > 2019M09   0.02094724 0.2265797 0.7524731
> >>> > 2019M10   0.01750911 0.2450030 0.7374879
> >>> >
> >>> > to
> >>> >  date  direction  percentage
> >>> > 2019M08   down 0.01709827
> >>> > 2019M09   down 0.02094724
> >>> > 2019M10   down 0.01750911
> >>> > 2019M08   uc 0.2653882
>

Re: [R] A better scales::dollar() ?

[Hadley Wickham]

You can get pretty close with label_number_si():

pounds <- scales::label_number_si(prefix = "£")
pounds(10 ^ (0:7))
#> [1] "£1""£10"   "£100"  "£1K"   "£10K"  "£100K" "£1M"   "£10M"

Created on 2019-12-09 by the [reprex
package](https://reprex.tidyverse.org) (v0.3.0.9001)

Hadley

On Fri, Dec 6, 2019 at 5:51 AM POLWART, Calum (COUNTY DURHAM AND
DARLINGTON NHS FOUNDATION TRUST) via R-help 
wrote:
>
> I'm writing a quite large document in Rmarkdown which has financial data in 
> it.  I format that data using scales::dollar() currently something like this:
>
> >
> > require (scales)
> > x = 10
> > cat (dollar (x, prefix ="£", big.mark=","))
>
> £100,000
>
> But actually, I'd quite like to get £100k out in that instance so I'd do:
>
> > cat (dollar (x/10^3, prefix ="£", suffix="k" ))
>
> £100k
>
> But x could be 100 or 10,000,000.  I want some form of 'automatic' version 
> that might give me something like:
>
> >
> > require (scales)
> > y = 0:7
> > x = 1^y
> > dollar(x, prefix="£")
> [1] "£1"  "£10" "£100""£1,000"  "£10,000" 
> "£100,000""£1,000,000"  "£10,000,000"
>
> But what I want is more like:
>
> £1.00  £10.00  £100  £1k  £10k  £100k  £1m  £10m
>
> I'm sure I can write something as a little function, but before I do - is 
> there something already out there?
>
> I have a similar need to format milligrams through to kilograms.
>
>
> 
>
> This message may contain confidential information. If ...{{dropped:27}}

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Re: [R] Supplying names to vars() in ggplot2.

[Hadley Wickham]

See this new vignette in dev ggplot2:
https://ggplot2.tidyverse.org/dev/articles/ggplot2-in-packages.html

Hadley

On Saturday, November 16, 2019, Rolf Turner  wrote:

>
> I need to call ggplot() from another function with the names of the
> faceting variables supplied as arguments to the calling function.  These
> names (which are names of columns in the relevant data frame)
> are given as character arguments, say "rowName" and "colName".
> Suppose that rowName is equal to "clyde" and colName is equal to "irving".
>
> I'd like to do something like
>
> ... + facet_grid(row=vars(rowName), col=vars(colName)) + ...
>
> but this does not work.  For instance, vars(rowName) gives
>
> [[1]]
>> 
>> expr: ^rowName
>> env:  global
>>
>
> I'd like to get the same thing as if I said vars(clyde) which gives
>
> >
>>
>> [[1]]
>> 
>> expr: ^clyde
>> env:  global
>>
>
> There *must* be some magic arcane incantation that I can apply to rowName
> (and colName) to get what I want.  Mustn't there?
>
> I tried things like vars(as.name(rowName)) --- nope, no help at all.
>
> Can anyone help me out?
>
> cheers,
>
> Rolf Turner
>
> --
> Honorary Research Fellow
> Department of Statistics
> University of Auckland
> Phone: +64-9-373-7599 ext. 88276
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posti
> ng-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


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Re: [R] Why I can not get work the "tidyverse" and "corrr" libraries

[Hadley Wickham]

On Wed, Apr 17, 2019 at 1:06 PM Jeff Newmiller  wrote:
>
> From reading
>
> > namespace ‘rlang’ 0.3.0 is already loaded, but >= 0.3.1 is required
>
> it would seem that you need to upgrade your rlang package...

Typically this indicates you need to restart R.

Hadley

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Re: [R] Unable to install ggplot2

[Hadley Wickham]

rlang works with R 3.1 and up, but it does require compilation from
source, which I suspect is the root cause of this problem.

Hadley

On Wed, Mar 6, 2019 at 5:36 PM peter dalgaard  wrote:
>
> Also, R seems to be version 3.2.x i.e. 3-4 years old. Earliest rlang is anno 
> 2017 as far as I can tell.
>
> -pd
>
> > On 6 Mar 2019, at 19:22 , Norberto Hernandez  
> > wrote:
> >
> > I have the same issue with ggplot2 and the rlang package, you need to
> > have the most updated version of the rlang library in order to get
> > installed ggplot2
> >
> > Regards
> > Norberto
> >
> > El mar., 5 mar. 2019 a las 14:24, Jeff Newmiller
> > () escribió:
> >>
> >> Please post the text version of the error in the future... your picture is 
> >> almost unreadable. Also, if it is actually important that you are using 
> >> RStudio then your question probably doesn't belong here. Also, if the 
> >> problem is a faulty contributed package then you will need to contact the 
> >> package maintainer as the Posting Guide mentioned below says.
> >>
> >> I don't know why the dependency is not being handled correctly, but my 
> >> suggestion would be to install the rlang package first, and once that is 
> >> installed try installing ggplot2. Read the errors... it says there is a 
> >> problem with the rlang package.
> >>
> >> On March 5, 2019 10:04:41 AM PST, Kamalika Ray  
> >> wrote:
> >>> Hi,
> >>> I have been trying to install the ggplot2 package but I am unable to do
> >>> so. My Mac OS version is 10.7.4 and I have downloaded the
> >>> R-Studio-1.1.463.
> >>> I have attached the screenshot of the error message which appears.
> >>>
> >>> Please help!
> >>>
> >>> Thank you,
> >>> Kamalika
> >>> India
> >>
> >> --
> >> Sent from my phone. Please excuse my brevity.
> >>
> >> __
> >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide 
> >> http://www.R-project.org/posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
> --
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Office: A 4.23
> Email: pd@cbs.dk  Priv: pda...@gmail.com
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.



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Re: [R] RMarkdown vignettes v. Jupyter notebooks?

[Hadley Wickham]

I'd highly recommend Yihui's extensive write up:
https://yihui.name/en/2018/09/notebook-war/

Hadley
On Thu, Oct 11, 2018 at 4:08 AM Spencer Graves
 wrote:
>
> Hello:
>
>
>What are the differences between Jupyter notebooks and RMarkdown
> vignettes?
>
>
>I'm trying to do real time monitoring of the broadcast quality of
> a radio station, and it seems to me that it may be easier to do that in
> Python than in R.[1]  This led me to a recent post to
> "python-l...@python.org" that mentioned "Jupyter, Mathematica, and the
> Future of the Research Paper"[2] by Paul Romer, who won the 2018 Nobel
> Memorial Prize in Economics only a few days ago.  In brief, this article
> suggests that Jupyter notebooks may replace publication in refereed
> scientific journals as the primary vehicle for sharing scientific
> research, because they make it so easy for readers to follow both the
> scientific and computational logic and test their own modifications.
>
>
>A "Jupyter Notebook Tutorial: The Definitive Guide"[3] suggested
> I first install Anaconda Navigator.  I got version 1.9.2 of that.  It
> opens with options for eight different "applications" including
> JupyterLab 0.34.9, Jupyter Notebook 5.6.0, Spyder 3.3.1 (an IDE for
> Python), and RStudio 1.1.456.
>
>
>This leads to several questions:
>
>
>  1.  In general, what experiences have people had with
> Jupyter Notebooks, Anaconda Navigator, and RMarkdown vignettes in
> RStudio, and the similarities and differences?  Do you know any
> references that discuss this?
>
>
>  2.  More specifically, does it make sense to try to use
> RStudio from within Anaconda Navigator, or is one better off using
> RStudio as a separate, stand alone application -- or should one even
> abandon RStudio and run R instead from within a Jupyter Notebook? [I'm
> new to this topic, so it's possible that this question doesn't even make
> sense.]
>
>
>Thanks,
>Spencer Graves
>
>
> [1] If you have ideas for how best to do real time monitoring of
> broadcast quality of a radio station, I'd love to hear them.  I need
> software that will do that, preferably something that's free, open
> source.  The commercial software I've seen for this is not adequate for
> my purposes, so I'm trying to write my own.  I have a sample script in
> Python that will read a live stream from a radio tuner and output a
> *.wav of whatever length I want, and I wrote Python eight years ago for
> a similar real time application.  I'd prefer to use R, but I don't know
> how to get started.
>
>
> [2] 2018-04-13:
> "https://paulromer.net/jupyter-mathematica-and-the-future-of-the-research-paper;.
> This further cites a similar article in The Atlantic from 2018-04-05:
> "www.theatlantic.com/science/archive/2018/04/the-scientific-paper-is-obsolete/556676".
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Extract function parameters from a R expression

[Hadley Wickham]

You need to recursively walk the parse tree/AST. See, e.g.,
https://adv-r.hadley.nz/expressions.html#ast-funs

Hadley

On Wed, Jun 20, 2018 at 10:08 AM, Sigbert Klinke
 wrote:
> Hi,
>
> I have read an R program with
>
> expr <- parse("myRprg.R")
>
> How can I extract the parameters of a specifc R command, e.g. "library"?
>
> So, if myprg.R containes the lines
>
> library("xyz")
> library("abc")
>
> then I would like to get "xyz" and "abc" back from expr.
>
> Thanks in advance
>
> Sigbert
>
> --
> https://hu.berlin/sk
>
>
>
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> and provide commented, minimal, self-contained, reproducible code.
>



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Re: [R] Converting a list to a data frame

[Hadley Wickham]

On Wed, May 2, 2018 at 11:53 AM, Jeff Newmiller
 wrote:
> Another approach:
>
> 
> library(tidyr)
> L <- list( A = data.frame( x=1:2, y=3:4 )
>  , B = data.frame( x=5:6, y=7:8 )
>  )
> D <- data.frame( Type = names( L )
>, stringsAsFactors = FALSE
>)
> D$data <- L
> unnest(D, data)
> #>   Type x y
> #> 1A 1 3
> #> 2A 2 4
> #> 3B 5 7
> #> 4B 6 8
> 

I think a slightly more idiomatic tidyverse solution is dplyr::bind_rows()

l <- list(
  A = data.frame(x = 1:2, y = 3:4),
  B = data.frame(x = 5:6, y = 7:8)
)

dplyr::bind_rows(l, .id = "type")
#>   type x y
#> 1A 1 3
#> 2A 2 4
#> 3B 5 7
#> 4B 6 8

This also has the advantage of returning a data frame when the inputs
are data frames.

Hadley

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Re: [R] Problem installing libxml2 under Homebrew

[Hadley Wickham]

Is there a reason that you can't use the binary provided by CRAN?
That's the easiest way to get xml2.
Hadley

On Sat, Feb 17, 2018 at 1:53 AM, Peter Meilstrup
 wrote:
> i am trying to install xml2 from CRAN, and it is throwing an error
> that it cannot find the libxml2 library configuration.
>
> The thing is that pkg-config seems to be set up correctly:
>
> $ echo $PKG_CONFIG_PATH
> :/usr/local/opt/libxml2/lib/pkgconfig:/usr/local/opt/libxml2/lib/pkgconfig
>
> $ pkg-config --cflags --libs libxml-2.0
> -I/usr/local/Cellar/libxml2/2.9.7/include/libxml2
> -L/usr/local/Cellar/libxml2/2.9.7/lib -lx
>
> Output of install.packages:
>
>> install.packages("xml2")
> --- Please select a CRAN mirror for use in this session ---
> trying URL 'https://cloud.r-project.org/src/contrib/xml2_1.2.0.tar.gz'
> Content type 'application/x-gzip' length 251614 bytes (245 KB)
> ==
> downloaded 245 KB
>
> * installing *source* package ‘xml2’ ...
> ** package ‘xml2’ successfully unpacked and MD5 sums checked
> Found pkg-config cflags and libs!
> Using PKG_CFLAGS=-I/usr/include/libxml2
> Using PKG_LIBS=-L/usr/lib -lxml2 -lz -lpthread -licucore -lm
> - ANTICONF ERROR ---
> Configuration failed because libxml-2.0 was not found. Try installing:
>  * deb: libxml2-dev (Debian, Ubuntu, etc)
>  * rpm: libxml2-devel (Fedora, CentOS, RHEL)
>  * csw: libxml2_dev (Solaris)
> If libxml-2.0 is already installed, check that 'pkg-config' is in your
> PATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-config
> is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
> R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
> 
> ERROR: configuration failed for package ‘xml2’
>
> Homebrew package info:
>
> dekkera:pkgconfig peter$ brew info libxml2 R
> libxml2: stable 2.9.7 (bottled), HEAD [keg-only]
> GNOME XML library
> http://xmlsoft.org
> /usr/local/Cellar/libxml2/2.9.7 (281 files, 10.4MB)
>   Poured from bottle on 2018-02-16 at 22:42:54
> From: https://github.com/Homebrew/homebrew-core/blob/master/Formula/libxml2.rb
> ==> Options
> --HEAD
> Install HEAD version
> ==> Caveats
> This formula is keg-only, which means it was not symlinked into /usr/local,
> because macOS already provides this software and installing another version in
> parallel can cause all kinds of trouble.
>
> If you need to have this software first in your PATH run:
>   echo 'export PATH="/usr/local/opt/libxml2/bin:$PATH"' >> ~/.bash_profile
>
> For compilers to find this software you may need to set:
> LDFLAGS:  -L/usr/local/opt/libxml2/lib
> CPPFLAGS: -I/usr/local/opt/libxml2/include
> For pkg-config to find this software you may need to set:
> PKG_CONFIG_PATH: /usr/local/opt/libxml2/lib/pkgconfig
>
> If you need Python to find bindings for this keg-only formula, run:
>   echo /usr/local/opt/libxml2/lib/python2.7/site-packages >>
> /usr/local/lib/python2.7/site-packages/libxml2.pth
>   mkdir -p /Users/peter/Library/Python/2.7/lib/python/site-packages
>   echo 'import site;
> site.addsitedir("/usr/local/lib/python2.7/site-packages")' >>
> /Users/peter/Library/Python/2.7/lib/python/site-packages/homebrew.pth
>
> R: stable 3.4.3 (bottled)
> Software environment for statistical computing
> https://www.r-project.org/
> /usr/local/Cellar/R/3.4.0_1 (2,246 files, 59.1MB)
>   Poured from bottle on 2017-05-20 at 17:10:29
> /usr/local/Cellar/R/3.4.1_2 (2,114 files, 55.3MB)
>   Poured from bottle on 2017-09-19 at 03:23:33
> /usr/local/Cellar/R/3.4.2 (2,111 files, 55.1MB)
>   Poured from bottle on 2017-11-13 at 22:23:36
> /usr/local/Cellar/R/3.4.3 (2,110 files, 55.1MB)
>   Poured from bottle on 2017-12-02 at 23:20:16
> /usr/local/Cellar/R/3.4.3_1 (3,773 files, 115.4MB)
>   Built from source on 2018-02-08 at 22:01:49 with: --with-x11
> --with-cairo --with-java
> From: https://github.com/Homebrew/homebrew-core/blob/master/Formula/r.rb
> ==> Dependencies
> Build: pkg-config ✔
> Required: gcc ✔, gettext ✔, jpeg ✔, libpng ✔, pcre ✔, readline ✔, xz ✔
> Optional: openblas ✔
> ==> Requirements
> Optional: java ✔
> ==> Options
> --with-java
> Build with java support
> --with-openblas
> Build with openblas support
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.



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Re: [R] Fwd: Wanted to learn R Language

[Hadley Wickham]

Or try haven::read_xpt(): http://haven.tidyverse.org/reference/read_xpt.html

Hadley

On Thu, Nov 30, 2017 at 3:13 PM, Jim Lemon  wrote:
> Hi SAS_learner,
> Have a look at the read.xport function in the foreign package.
>
> Jim
>
> On Fri, Dec 1, 2017 at 7:50 AM, SAS_learner  wrote:
>> Hello all ,
>>
>> I am a SAS user for a while and wanted to learn to program in R . My
>> biggest hurdle to start, is to get the data (I work in clinical domain
>> ) that too inside VPN secured access. The only way I can learn during
>> my work time is create my own data frames and create programs that can
>> be used for data ( either SDTM or AdAM data ) validation or checking
>> Table counts . For this I need to imitate the clinical data structure
>> . If there is any place or a package that help to start. I have couple
>> of dummy SAS datasets in my work area , but not sure how can I can
>> access them . Can anybody help me . Thanks ahead .
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
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> and provide commented, minimal, self-contained, reproducible code.



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Re: [R] To implement OO or not in R package, and if so, how to structure it?

[Hadley Wickham]

> Did you read this?
> https://cran.r-project.org/doc/contrib/Leisch-CreatingPackages.pdf
>
> Maybe it could give you some insight in how to create package.

That resource is ~9 years old. There are more modern treatments
available. You can read mine at http://r-pkgs.had.co.nz.

Hadley


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Re: [R] To implement OO or not in R package, and if so, how to structure it?

[Hadley Wickham]

I just finished the first draft of the chapters on OO programming for
the 2nd edition of "Advanced R": https://adv-r.hadley.nz - you might
find them helpful.

Hadley

On Thu, Sep 14, 2017 at 7:58 AM, Alexander Shenkin  wrote:
> Hello all,
>
> I am trying to decide how to structure an R package.  Specifically, do I use
> OO classes, or just provide functions?  If the former, how should I
> structure the objects in relation to the type of data the package is
> intended to manage?
>
> I have searched for, but haven't found, resources that guide one in the
> *decision* about whether to implement OO frameworks or not in one's R
> package.  I suspect I should, but the utility of the package would be aided
> by *collections* of objects.  R, however, doesn't seem to implement
> collections.
>
> Background: I am writing an R package that will provide a framework for
> analyzing structural models of trees (as in trees made of wood, not
> statistical trees).  These models are generated from laser scanning
> instruments and model fitting algorithms, and hence may have aspects that
> are data-heavy.  Furthermore, coputing metrics based on these structures can
> be computationally heavy.  Finally, as a result, each tree has a number of
> metrics associated with it (which may be expensive to calculate), along with
> the underlying data of that tree.  It will be important as well to perform
> calculations across many of these trees, as one would do in a dataframe.
>
> This last point is important: if one organizes data across potentially
> thousands of objects, how easy or hard is it to massage properties of those
> objects into a dataframe for analysis?
>
> Thank you in advance for thoughts and pointers.
>
> Allie
>
> __
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.



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Re: [R] functions from 'base' package are not accessible

[Hadley Wickham]

This was a change in tidyr 0.7.0 that is causing a lot of confusion,
so we are preparing tidyr 0.7.1 which will back this change out.

If you want a work around in the meantime, you can express your
operation a bit more elegantly as:

library(tidyr)

df <- data.frame(v1 = 1:5, somestring = 6:10, v3 = 11:15, v4 = 16:20)
df %>%
  gather(key = var, value = val, somestring:ncol(df)) %>%
  head(2)

Hadley

On Thu, Aug 24, 2017 at 6:32 AM, Eugeny Melamud
 wrote:
> Hi all!
>
> The following code (executed in console)...
> somevar <- data.frame(v1 = 1:5, somestring = 6:10, v3 = 11:15, v4 = 
> 16:20);
> somevar %>% gather(key = var, value = val, which(names(somevar) == 
> "somestring"):length(somevar)) %>% head(2);
> throws...
> Error in which(names(somevar) == "somestring") :
>   could not find function "which"
>
> if I change which(names(somevar) == "somestring") with 0 I'll get
>Error in length(somevar) :
>   could not find function "length"
>
> So it looks like base package is not loaded. Still if type 'which' in console 
> I get
>   function (x, arr.ind = FALSE, useNames = TRUE)
>   {
> wh <- .Internal(which(x))
> if (arr.ind && !is.null(d <- dim(x)))
> arrayInd(wh, d, dimnames(x), useNames = useNames)
> else wh
>   }
>   
>   
>
> base (that contains which function) package is installed. R version is 3.4.1 
> and system is Win8
>
> Where should I look to understand how to fix the problem?
>
> Thank you in advance!
> Eugeny
>
>
> [[alternative HTML version deleted]]
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.



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Re: [R] tidyverse repeating error: "object 'rlang_mut_env_parent' not found"

[Hadley Wickham]

The most likely explanation is you have a new version of dplyr/tibble
and an old version of rlang. Try re-installing rlang.

Hadley

On Mon, Aug 14, 2017 at 9:26 AM, Szumiloski, John
 wrote:
> UseRs,
>
> When doing some data manipulations using the tidyverse, I am repeatedly 
> getting the same error message in now three separate situations.  I can write 
> up a reproducible example, but want to lay out the high-level issues in case 
> someone recognizes exactly what is happening here.
>
> The error is:
>
> Error in mut_env_parent(overscope$.top_env, lexical_env) :
>   object 'rlang_mut_env_parent' not found
>
> and it occurs in three situations:
>
>
> 1)  Using tidyr::nest() on an output from dplyr::group_by()
>
> 2)  Using tibble::tibble() with  =  arguments
>
> 3)  Using dplyr::select() on a tibble to select two columns
>
> Any obvious clues as to what's happening here? The only non-base packages 
> loaded are current tidyverse, forcats, magrittr, readxl and stringr.
>
> Thanks,
> John
> John Szumiloski, Ph.D.
> Principal Scientist, Statistician
> Pharmaceutical Development / Drug Product Science & Technology
> NBR105-1-1411
>
> Bristol-Myers Squibb
> P.O. Box 191
> 1 Squibb Drive
> New Brunswick, NJ
> 08903-0191
>
> (732) 227-7167
>
>
> 
> This message (including any attachments) may contain c...{{dropped:14}}

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Re: [R] Inheritance for S3 classes

[Hadley Wickham]

You might find http://adv-r.hadley.nz/s3.html to be helpful (in
particular, http://adv-r.hadley.nz/s3.html#constructors-1, gives my
advice about subclass constructors)

Hadley

On Mon, Aug 7, 2017 at 7:06 PM, Kym Nitschke  wrote:
> Hi R Users,
>
> I am relatively new to programming in R … so I apologise if my questions 
> appear ‘dumb’.
>
> I am using a package that defines a number of S3 classes. I want to create an 
> S3 child class of one of these classes. The parent class has a contractor 
> with many arguments. I have been having difficulty writing the child class 
> contractor. I have been unable to find a good reference in the internet for 
> writing S3 classes. What I have been able to find out so far is that the 
> child class constructor should call the parent class constructor … which in 
> this case requires passing the argument list with a variable number of 
> arguments (i.e. there are a number of optional arguments) from the child to 
> the parent.
>
> So my first question is … is there an easy way to do this? The match.call 
> function will return a call object .. however the attributes function when 
> used on the call object returns a ‘NULL’.
>
> My second question is … can any one recommend a good reference for object 
> oriented programming in R which includes a comprehensive discussion of the S3 
> class model?
>
> Thanks
>
> Regards,
>
> Kym
> __
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> and provide commented, minimal, self-contained, reproducible code.



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Re: [R] Math ops behaviour with multiple classes

[Hadley Wickham]

On Thu, Jun 8, 2017 at 2:45 PM, Bert Gunter  wrote:
> I think you may be confusing (S3) class and ?mode.

Your point is well made, but to be precise, I think you should talk
about the "type of" an object, not it's mode. mode() is a wrapper
around typeof(), designed (I believe) for S compatibility.

Hadley

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Re: [R] [FORGED] Logical Operators' inconsistent Behavior

[Hadley Wickham]

On Fri, May 19, 2017 at 6:38 AM, S Ellison  wrote:
>> TRUE & FALSE is FALSE but TRUE & TRUE is TRUE, so TRUE & NA could be
>> either TRUE or FALSE and consequently is NA.
>>
>> OTOH FALSE & (anything) is FALSE so FALSE & NA is FALSE.
>>
>> As I said *think* about it; don't just go with your immediate knee-jerk
>> (simplistic) reaction.
>
> Hmm... not sure that was quite fair to the OP. Yes,  FALSE &  == 
> FALSE. But 'NA' does not mean 'anything'; it means 'missing' (see ?'NA'). It 
> is much less obvious that FALSE &  should generate a non-missing 
> value. SQL, for example, generally  takes the view that any expression 
> involving 'missing' is 'missing'.

That's not TRUE ;)

sqlite> select (3 > 2) OR NULL;
1

sqlite> select (4 < 3) AND NULL;
0

Hadley


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Re: [R] Confused about using data.table package,

[Hadley Wickham]

On Sun, Feb 19, 2017 at 3:01 PM, David Winsemius  wrote:
>
>> On Feb 19, 2017, at 11:37 AM, C W  wrote:
>>
>> Hi R,
>>
>> I am a little confused by the data.table package.
>>
>> library(data.table)
>>
>> df <- data.frame(w=rnorm(20, -10, 1), x= rnorm(20, 0, 1), y=rnorm(20, 10, 1),
>> z=rnorm(20, 20, 1))
>>
>> df <- data.table(df)
>
>   df <- setDT(df) is preferred.

Don't you mean just

setDT(df)

?

setDT() modifies by reference.

>>
>> df_3 <- df[, a := x-y] # created new column a using x minus y, why are we
>> using colon equals?
>
> You need to do more study of the extensive documentation. The behavior of the 
> ":=" function is discussed in detail there.

You can get to that documentation with ?":="

Hadley

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Re: [R] Is a list an atomic object? (or is there an issue with the help page of ?tapply ?)

[Hadley Wickham]

On Mon, Feb 20, 2017 at 7:31 AM, Martin Maechler
 wrote:
>> Hervé Pagès 
>> on Tue, 14 Feb 2017 17:10:05 -0800 writes:
>
> > Hi, tapply() will work on any object 'X' that has a length
> > and supports single-bracket subsetting. These objects are
> > sometimes called "vector-like" objects. Atomic vectors,
> > lists, S4 objects with a "length" and "[" method,
> > etc... are examples of "vector-like" objects.
>
> > So instead of saying
>
> >X: an atomic object, typically a vector.
>
> > I think it would be more accurate if the man page was
> > saying something like
>
> >X: a vector-like object that supports subsetting with
> > `[`, typically an atomic vector.
>
> Thank you, Hervé!
>
> Actually (someone else mentioned ?)
> only   length(X) and  split(X, )   need to work,
> and as split() itself is an S3 generic function,  X can be even
> more general... well depending on how exactly you understand
> "vector-like".
>
> So I would go with
>
>X: an R object for which a ‘split’ method exists.  Typically
>   vector-like, allowing subsetting with ‘[’.

I think technically tapply() should be using NROW() check that X and
INDEX are compatible. That would make it more compatible with split()
semantics.

Hadley

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Re: [R] Is a list an atomic object? (or is there an issue with the help page of ?tapply ?)

[Hadley Wickham]

It seems like this should be consistent with split(), since that's
what actually powers the behaviour.

Reading the description for split leads to this rather interesting example:

tapply(mtcars, 1:11, I)

Hadley

On Tue, Feb 14, 2017 at 7:10 PM, Hervé Pagès  wrote:
> Hi,
>
> tapply() will work on any object 'X' that has a length and supports
> single-bracket subsetting. These objects are sometimes called
> "vector-like" objects. Atomic vectors, lists, S4 objects with a "length"
> and "[" method, etc... are examples of "vector-like" objects.
>
> So instead of saying
>
>   X: an atomic object, typically a vector.
>
> I think it would be more accurate if the man page was saying something
> like
>
>   X: a vector-like object that supports subsetting with `[`, typically
>  an atomic vector.
>
> H.
>
>
> On 02/04/2017 04:17 AM, Tal Galili wrote:
>>
>> In the help page of ?tapply it says that the first argument (X) is "an
>> atomic object, typically a vector."
>>
>> However, tapply seems to be able to handle list objects. For example:
>>
>> ###
>>
>> l <- as.list(1:10)
>> is.atomic(l) # FALSE
>> index <- c(rep(1,5),rep(2,5))
>> tapply(l,index,unlist)
>>
>>> tapply(l,index,unlist)
>>
>> $`1`
>> [1] 1 2 3 4 5
>>
>> $`2`
>> [1]  6  7  8  9 10
>>
>>
>> ###
>>
>> Hence, does it mean a list an atomic object? (which I thought it wasn't)
>> or
>> is the help for tapply needs updating?
>> (or some third option I'm missing?)
>>
>> Thanks.
>>
>>
>>
>>
>>
>> Contact
>> Details:---
>> Contact me: tal.gal...@gmail.com |
>> Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
>> www.r-statistics.com (English)
>>
>> --
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
>
>
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Re: [R] Failure to understand namespaces in XML::getNodeSet

[Hadley Wickham]

I think you want

x <- read_xml('
  http://labkey.org/etl/xml;>
  MFIA 9-Plex (CharlesRiver)
')

The collapse argument do what you think it does.

Hadley

On Tue, Jan 31, 2017 at 5:36 PM, Mark Sharp <msh...@txbiomed.org> wrote:
> Hadley,
>
> Thank you. I am able to get the xml_ns_strip() function to work with my file 
> directly so I will likely be able to reach my immediate goal.
>
> However, I still have had no success with understanding the namespace 
> problem. I am not able to use read_xml() using the object I generated for the 
> reproducible example, which is simply a character vector of length 4 having 
> the contents of the XML file as produce by readLines(). I then used dput() to 
> define the structure. The resulting structure apparently is not to the liking 
> of read_xml(). I have reproduced the necessary code here for your 
> convenience. There error is below.
>
> ##
> library(xml2)
> library(stringr)
> with_ns_xml <- c("",
>  "http://labkey.org/etl/xml\;>",
>  "MFIA 9-Plex (CharlesRiver)",
>  "")
> ## without str_c() collapse it complain of a vector of length > 1 also.
> read_xml(str_c(with_ns_xml, collapse = TRUE))
> Error in doc_parse_raw(x, encoding = encoding, base_url = base_url, as_html = 
> as_html,  :
>   Start tag expected, '<' not found [4]
>
> ## produces the following error message.
> Error in doc_parse_raw(x, encoding = encoding, base_url = base_url, as_html = 
> as_html,  :
>   Start tag expected, '<' not found [4]
>
> I have similar issues with xml2::xml_find_all
> xml_find_all(str_c(with_ns_xml, collapse = TRUE), "/WorkSet//Description")
>
> ## Produces the following error message.
> Error in UseMethod("xml_find_all") :
>   no applicable method for 'xml_find_all' applied to an object of class 
> "character"
>
>
>
> R. Mark Sharp, Ph.D.
> msh...@txbiomed.org
>
>
>
>
>
>> On Jan 31, 2017, at 4:27 PM, Hadley Wickham <h.wick...@gmail.com> wrote:
>>
>> See the last example in ?xml2::xml_find_all or use xml2::xml2::xml_ns_strip()
>>
>> Hadley
>>
>> On Tue, Jan 31, 2017 at 9:43 AM, Mark Sharp <msh...@txbiomed.org> wrote:
>>> I am trying to read a series of XML files that use a namespace and I have 
>>> failed, thus far, to discover the proper syntax. I have a reproducible 
>>> example below. I have two XML character strings defined: one without a 
>>> namespace and one with. I show that I can successfully extract the node 
>>> using the XML string without the namespace and fail when using the XML 
>>> string with the namespace.
>>>
>>> Mark
>>> PS I am having the same problem with the xml2 package and am hoping 
>>> understanding one with help with the other.
>>>
>>> ##
>>> library(XML)
>>> ## The first XML text (no_ns_xml) does not have a namespace defined
>>> no_ns_xml <- c("", "",
>>>   "MFIA 9-Plex (CharlesRiver)",
>>>   "")
>>> l_no_ns_xml <-xmlTreeParse(no_ns_xml, asText = TRUE, getDTD = FALSE,
>>>   useInternalNodes = TRUE)
>>> ## The node is found
>>> getNodeSet(l_no_ns_xml, "/WorkSet//Description")
>>>
>>> ## The second XML text (with_ns_xml) has a namespace defined
>>> with_ns_xml <- c("",
>>> "http://labkey.org/etl/xml\;>",
>>> "MFIA 9-Plex (CharlesRiver)",
>>> "")
>>>
>>> l_with_ns_xml <-xmlTreeParse(with_ns_xml, asText = TRUE, getDTD = FALSE,
>>>   useInternalNodes = TRUE)
>>> ## The node is not found
>>> getNodeSet(l_with_ns_xml, "/WorkSet//Description")
>>> ## I attempt to provide the namespace, but fail.
>>> ns <-  "http://labkey.org/etl/xml;
>>> names(ns)[1] <- "xmlns"
>>> getNodeSet(l_with_ns_xml, "/WorkSet//Description", namespaces = ns)
>>>
>>> R. Mark Sharp, Ph.D.
>>> Director of Data Science Core
>>> Southwest National Primate Research Center
>>> Texas Biomedical Research Institute
>>> P.O. Box 760549
>>> San Antonio, TX 78245-0549
>>> Telephone: (210)258-9476
>>> e-mail: msh...@txbiomed.org
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> CONFIDENTIALITY NOTICE: This e-mail and 

Re: [R] Failure to understand namespaces in XML::getNodeSet

[Hadley Wickham]

See the last example in ?xml2::xml_find_all or use xml2::xml2::xml_ns_strip()

Hadley

On Tue, Jan 31, 2017 at 9:43 AM, Mark Sharp  wrote:
> I am trying to read a series of XML files that use a namespace and I have 
> failed, thus far, to discover the proper syntax. I have a reproducible 
> example below. I have two XML character strings defined: one without a 
> namespace and one with. I show that I can successfully extract the node using 
> the XML string without the namespace and fail when using the XML string with 
> the namespace.
>
> Mark
> PS I am having the same problem with the xml2 package and am hoping 
> understanding one with help with the other.
>
> ##
> library(XML)
> ## The first XML text (no_ns_xml) does not have a namespace defined
> no_ns_xml <- c("", "",
>"MFIA 9-Plex (CharlesRiver)",
>"")
> l_no_ns_xml <-xmlTreeParse(no_ns_xml, asText = TRUE, getDTD = FALSE,
>useInternalNodes = TRUE)
> ## The node is found
> getNodeSet(l_no_ns_xml, "/WorkSet//Description")
>
> ## The second XML text (with_ns_xml) has a namespace defined
> with_ns_xml <- c("",
>  "http://labkey.org/etl/xml\;>",
>  "MFIA 9-Plex (CharlesRiver)",
>  "")
>
> l_with_ns_xml <-xmlTreeParse(with_ns_xml, asText = TRUE, getDTD = FALSE,
>useInternalNodes = TRUE)
> ## The node is not found
> getNodeSet(l_with_ns_xml, "/WorkSet//Description")
> ## I attempt to provide the namespace, but fail.
> ns <-  "http://labkey.org/etl/xml;
> names(ns)[1] <- "xmlns"
> getNodeSet(l_with_ns_xml, "/WorkSet//Description", namespaces = ns)
>
> R. Mark Sharp, Ph.D.
> Director of Data Science Core
> Southwest National Primate Research Center
> Texas Biomedical Research Institute
> P.O. Box 760549
> San Antonio, TX 78245-0549
> Telephone: (210)258-9476
> e-mail: msh...@txbiomed.org
>
>
>
>
>
>
>
>
>
> CONFIDENTIALITY NOTICE: This e-mail and any files and/or...{{dropped:10}}
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.



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Re: [R] Assessing the name of an object within an argument

[Hadley Wickham]

You might find http://adv-r.had.co.nz/Computing-on-the-language.html helpful.

Hadley

On Tue, Jan 10, 2017 at 2:49 AM,   wrote:
> Hi All,
>
> I have a function like
>
> my_func <- function(dataset)
> {
>   some operation
> }
>
> Now I would like not only to operate on the dataset (how this is done is
> obvious) but I would like to get the name of the dataset handed over as an
> argument.
>
> Example:
>
> my_func <- function(dataset = iris)
> {
>   print(dataset)  # here I do not want to print the dataset but the name
> of the object - iris in this case - instead
>   # quote() does not do the trick cause it prints "dataset" instead of
> "iris"
>   # as.name() gives an error saying that the object can not coerced to a
> symbol
> }
>
> Is there a way to do this?
>
> Kind regards
>
> Georg
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-help
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> and provide commented, minimal, self-contained, reproducible code.



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Re: [R] ggplot aestetics: beginner question - I am lost in endless possibilites

[Hadley Wickham]

You are going to find your life much easier if you:

* Organise your code so it's easier to read
* Use a consistent naming scheme for your variables
* Learn a bit more about how to modify variables succintly

Here's my rewriting of your script to make it easier to see what's going on.

library(tidyverse)

df <- tibble(
  name = c("Ernie","Ernie","Ernie", "Leon","Leon","Leon"),
  recorded_time = c("03.01.2011","04.01.2011","05.01.2011",
"04.01.2011","05.01.2011","06.01.2011"),
  known_state = c("breeding","moulting","moulting", "breeding","breeding",NA)
)
df$recorded_time <- lubridate::dmy(df$recorded_time)

ggplot(df) +
  geom_tile(
aes(recorded_time, name, fill = known_state),
colour = "black",
height = 0.5
  ) +
  scale_fill_discrete(na.value = "white")

Hadley

On Thu, Dec 15, 2016 at 8:22 PM, Dagmar  wrote:
> # Dear all,
> # I hope someone can help me with this. I am so lost and can't find a
> solution even though I spent hours on searching for a solution of that tiny
> problem.
> # Maybe someone of you could give me hint?
> #This is my string:
> exdatframe <- data.frame(Name=c("Ernie","Ernie","Ernie",
> "Leon","Leon","Leon"),
>   recordedTime=c("03.01.2011","04.01.2011","05.01.2011",
> "04.01.2011","05.01.2011","06.01.2011"),
>knownstate =c("breeding","moulting","moulting",
>  "breeding","breeding",NA))
> exdatframe
>
> exdatframeT <- as.POSIXct
> (strptime(as.character(exdatframe$recordedTime),"%d.%m.%Y"))
> exdatframeT
> exdatframe2 <- cbind(exdatframe, exdatframeT)
> exdatframe2$recordedTime <-NULL
> exdatframe2
> str(datframe)
>
> library(ggplot2)
> ggplot(exdatframe2)+geom_tile(aes(x=exdatframeT,y=Name,fill=knownstate),
> height=0.5)
>
> # Now all I want is:
> # 1) a black outline around the bars. Adding colour="black" like I have
> found elsewere on the internet doesn't work
> # 2) change the colours: E.g. I want white for NAs. I can't find a command
> to describe my wishes.
>
> #?
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-help
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> and provide commented, minimal, self-contained, reproducible code.



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Re: [R] Unexpected interference between dplyr and plm

[Hadley Wickham]

On Tue, Nov 29, 2016 at 11:52 AM, William Dunlap  wrote:
>>The other option would be to load dplyr first (which would give the waring
>> that >stats::lag was masked) and then later load plm (which should give a
>> further >warning that dplyr::lag is masked). Then the plm::lag function will
>> be found
>>first.
>
> Another option is to write the package maintainers and complain
> that masking core functions is painful for users.

Don't worry; many people have done that.

Hadley

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Re: [R] on ``unfolding'' a json into data frame columns

[Hadley Wickham]

Two quick hints:

* use simplifyDataFrame = FALSE in fromJSON()

* read 
https://jennybc.github.io/purrr-tutorial/ls02_map-extraction-advanced.html
(and https://jennybc.github.io/purrr-tutorial/)

Hadley

On Tue, Nov 29, 2016 at 8:06 AM, Daniel Bastos  wrote:
> Greetings!
>
> In an SQL table, I have a column that contains a JSON.  I'd like easy
> access to all (in an ideal world) of these JSON fields.  I started out
> trying to get all fields from the JSON and so I wrote this function.
>
> unfold.json <- function (df, column)
> {
> library(jsonlite)
> ret <- data.frame()
>
> for (i in 1:nrow(df)) {
> js <- fromJSON(df[i, ][[column]])
> ret <- rbind(ret, cbind(df[i, ], js))
> }
>
> ret
> }
>
> It takes a data frame and a column-string where the JSON is to be
> found.  It produces a new RET data frame with all the rows of DF but
> with new columns --- extracted from every field in the JSON.
>
> (The performance is horrible.)
>
> fromJSON sometimes produces a list that sometimes contains a data frame.
> As a result, I end up getting a RET data frame with duplicated rows.
> Here's what happens.
>
>> nrow(df)
> [1] 1
>
>> nrow(unfold.json(df, "response"))
> [1] 3
> Warning messages:
> 1: In data.frame(CreateUTC = "2016-11-29 02:00:43", Payload = list( :
>   row names were found from a short variable and have been discarded
> 2: In data.frame(..., check.names = FALSE) :
>   row names were found from a short variable and have been discarded
>>
>
> I expected a data frame with 1 row.  The reason 3 rows is produced is
> because in the JSON there's an array with 3 rows.
>
>> fromJSON(df$response)$RawPayload
> [1] 200   1 128
>
> I have also cases where fromJSON(df$response)$Payload$Fields is a data
> frame containing various rows.  So unfold.json produces a data frame
> with these various rows.
>
> So I gave up on this general approach.
>
> (*) My humble approach
>
> For the moment I'm not interested in RawPayload nor Payload$Fields, so I
> nullified them in this new approach.  To improve performance, I guessed
> perhaps merge() would help and I think it did, but this was not at all a
> decision thought out.
>
> unfold.json.fast <- function (df, column)
> {
> library(jsonlite)
> ret <- data.frame()
> if (nrow(df) > 0) {
> for (i in 1:nrow(df)) {
> ls <- fromJSON(df[i, ][[column]])
> ls$RawPayload <- NULL
> ls$Payload$Fields <- NULL
> js <- data.frame(ls)
> ret <- rbind(ret, merge(df[i, ], js))
> }
> }
>
> ret
> }
>
> I'm looking for advice.  How would you approach this problem?
>
> Thank you!
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-help
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> and provide commented, minimal, self-contained, reproducible code.



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Re: [R] Question about ‘The R Project’.

[Hadley Wickham]

>> We have a question about ‘The R Project’.
>>
>> It looks like it’s an open source software, but the document from the 
>> website shows that it’s free of use not free of price.
>>
>> Please, confirm us the if it cost fees to use it for commercial use.
>>
>> If needed, could you inform us the price for it, too?
>>
>> Best regards,
>> Jane Kim.
>>
>
> Can I use R for commercial purposes?
> https://cran.r-project.org/doc/FAQ/R-FAQ.html#Can-I-use-R-for-commercial-purposes_003f
>  
> 
>
> If you mean RStudio you have to pay for commercial use. RStudio and R are 
> different.
> https://www.rstudio.com/pricing/ 

That's not true, as RStudio is also open source.  You don't have to
pay to use it commercially, but you might want to pay to use it
commercial because we provide additional features of use to people in
bigger companies.

Hadley

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Re: [R] workflow getting UTF-8 csv in and out of R on Mac (spreadsheet editor)

[Hadley Wickham]

You can use readr::write_excel_csv() which adds a BOM that forces excel to
read as UTF-8.

Hadley

On Friday, September 2, 2016, Erich Neuwirth 
wrote:

> read_excel in Hadley’s readxl package
> should handle your encoding problems.
> Writing Excel files on a Mac, however, still is somewhat messy.
>
> And you probably should post this kind of question on r-sig-mac
>
>
>
> On 02 Sep 2016, at 13:03, Kai Mx > wrote:
> >
> > Hi all,
> >
> > I am hoping for some advice on how to handle UTF-8 spreadsheet files in a
> > Mac environment - sort of off-topic, but still relevant for hopefully a
> > bunch of people.
> >
> > I am using R on Mac OS 10.10. Sometimes I have the urge to actually look
> at
> > a large spreadsheet on the big screen or make some changes to the tables.
> > Since most of my colleagues live in the M$ Excel - world I tend to use
> > Excel 2011 as well. However, Excel does not handle UTF-8 (which I like
> > because of different system locales).
> > So I actually do a write.csv with file-encoding in macroman, but even
> then
> > Excel won't just open it and I will have to work my way through the
> > import-dialogue.
> >
> > The other way around, it's even worse. I save the spreadsheet as
> macroman,
> > iconv it to utf-8 and then read.csv it to R.
> >
> > It works, but it's just really messy. Is there a (preferably
> light-weight)
> > csv-spreadsheet Editor for Mac OS that you use? Open-Office? I would like
> > NOT to actually buy another Excel version. However, for collaboration, a
> > xls-export would be phenomenal.
> >
> > Thanks!
> >
> > Kai
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org  mailing list -- To UNSUBSCRIBE and
> more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
>

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Re: [R] read.xlsx function crashing R Studio

[Hadley Wickham]

Or readxl.

Hadley

On Mon, Aug 22, 2016 at 5:54 AM, jim holtman  wrote:
> try the openxlsx package
>
>
> Jim Holtman
> Data Munger Guru
>
> What is the problem that you are trying to solve?
> Tell me what you want to do, not how you want to do it.
>
> On Sun, Aug 21, 2016 at 1:30 PM, Kevin Kowitski 
> wrote:
>
>> Hey everyone,
>>
>>I have used read.xlsx in the past rather than XLConnect for importing
>> Excel data to R.  However, I have been finding now that the read.xlsx
>> function has been causing my R studio to Time out.  I thought it might be
>> because the R studio I had was out of date so I installed R studio X64
>> 3.3.1 and reinstalled the xlsx package but it is still failing.  I have
>> been trying to use XLConnect in it's place which has been working, excpet
>> that I am running into memory error:
>>   Error: OutOfMemoryError (Java): GC overhead limit exceeded
>>
>> I did some online searching and found an option to increase memory:
>>   "options(java.parameters = "-Xmx4g" )
>>
>> but it resulted in this new memory Error:
>>
>>  Error: OutOfMemoryError (Java): Java heap space
>>
>> Can anyone provide me with some help on getting the read.xlsx function
>> working?
>>
>> -Kevin
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posti
>> ng-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> [[alternative HTML version deleted]]
>
> __
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> and provide commented, minimal, self-contained, reproducible code.



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Re: [R] lm() silently drops NAs

[Hadley Wickham]

> I think that's a bit too strict for me, so I wrote my own:
>
> na.warn <- function(object, ...) {
>   missing <- complete.cases(object)
>   if (any(missing)) {
> warning("Dropping ", sum(missing), " rows with missing values",
> call. = FALSE)
>   }
>
>   na.exclude(object, ...)
> }

That should, of course, have been:

missing <- !complete.cases(object)

:-/

Hadley

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Re: [R] lm() silently drops NAs

[Hadley Wickham]

On Tue, Jul 26, 2016 at 3:24 AM, Martin Maechler
 wrote:
> I have been asked (in private)

Martin was very polite to not share my name, but it was me :)

> > Hi Martin,
>
> y <- c(1, 2, 3, NA, 4)
> x <- c(1, 2, 2, 1, 1)
>
> t.test(y ~ x)
> lm(y ~ x)
>
> > Normally, most R functions follow the principle that
> > "missings should never silently go missing". Do you have
> > any background on why these functions (and most model/test
> > function in stats, I presume) silently drop missing values?
>
> And I think, the issue and an answer are important enough to be
> public, hence this posting to R-help :
>
> First note that in some sense it is not true that lm(y ~ x) silently drops
> NAs: Everybody who is taught about lm() is taught to look at
>summary( fm )  where  fm <- lm(y ~ x)

Good point - unfortunately the message was a bit subtle for me, and
don't remember being taught to look for it :(

> and that (for the above case)  "says"
>
>  ' (1 observation deleted due to missingness) '
>
> and so is not entirely silent.
>
>
> This goes all back to the idea of having an 'na.action' argument
> which may be a function (a very good idea, "functional
> programming" in a double sense!)... which Chambers et al
> introduced in The White Book (*1) and which I think to remember
> was quite a revolutionary idea; at least I had liked that very much
> once I understood the beauty of passing functions as arguments
> to other functions.
> One problem already back then has been that we already had the
> ---much more primitive but often sufficient--- standard of an
> 'na.rm = FALSE' (i.e. default FALSE) argument.
>
> This has been tought in all good classes/course about statistical
> modeling with S and R ever since ... I had hoped 
> (but it seems I was too optimistic, .. or many students have too
>  quickly forgotten what they were taught ..)
> Notably the white book itself, and the MASS (*2) book do teach
> this.. though possibly not loudly enough.
>
> Two more decisions about this were made back then, as well:
>
>   1) The default for na.action to be na.omit  (==> "silently dropping")
>
>   2) na.action being governed by  options(na.action = ..)
>
> '1)' may have been mostly "historical": I think it had been the behavior of
> other "main stream" statistical packages back then (and now?) *and*
> possibly more importantly, notably with the later (than white book = "S3")
> advent of na.replace, you did want to keep the missing in your
> data frame, for later analysis; e.g. drawing (-> "gaps" in
> plots) so the NA *were* carried along and would not be
> forgotten, something very important in most case.s.
>
> and '2)' is something I personally no longer like very
> much, as it is "killing" the functional paradigm.
> OTOH, it has to be said in favor of that "session wide" / "global" setting
>   options(na.action = *)
> that indeed it depends on the specific data analysis, or even
> the specific *phase* of a data analysis, *what* behavior of NA
> treatment is desired and at the time it was thought smart
> that all methods (also functions "deep down" called by
> user-called functtions) would automatically use the "currently
> desired" NA handling.
>
> There have been recommendations (I don't know exactly where and
> by whom) to always set
>
>options(na.action = na.fail)
>
> in your global .First() or nowadays rather your  Rprofile, and
> I assume that some of the CRAN packages and some of the "teaching
> setups" would do that (and if you do that, the lm() and t.test()
> calls above give an error).

I think that's a bit too strict for me, so I wrote my own:

na.warn <- function(object, ...) {
  missing <- complete.cases(object)
  if (any(missing)) {
warning("Dropping ", sum(missing), " rows with missing values",
call. = FALSE)
  }

  na.exclude(object, ...)
}

That gives me the behaviour I want:

options(na.action = na.warn)

y <- c(1, 2, 3, NA, 4)
x <- c(1, 2, 2, 1, 1)
mod <- lm(y ~ x)
#> Warning: Dropping 4 rows with missing values

predict(mod)
#>   1   2   3   4   5
#> 2.5 2.5 2.5  NA 2.5
resid(mod)
#>12345
#> -1.5 -0.5  0.5   NA  1.5

To me, this would be the most sensible default behaviour, but I
realise it's too late to change without breaking many existing
expectations.

On a related note, I've never really understood why it's called
na.exclude - from my perspective it causes the _inclusion_ of missing
values in the predictions/residuals.

Thanks for the (as always!) informative response, Martin.

Hadley

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Re: [R] Date Time in R

[Hadley Wickham]

I'd recommend reading up on how to create a minimal reproducible
example (e.g. http://r4ds.had.co.nz/exploratory-data-analysis.html).
It is unlikely anyone will be able to help you unless you can reliably
communicate _exactly_ what you're doing. Unlike human languages,
computer languages are extremely strict, and just one wrong character
can make a big difference.

Hadley

On Tue, Jul 26, 2016 at 10:45 AM, Shivi Bhatia  wrote:
> Hi David please see the code and some reproducible data:
> eir$date<- as.Date(eir$date,format = "%m-%d-%y")  then i had used the
> lubridate library to help with the dates:
> install.packages("lubridate")
> library(lubridate)
> eir$date <- mdy(eir$date)
> weekdays <- wdy(eir$date)
> week names <- wdy(eir$date, label = TRUE)
>
> This the output from the file:
>
> structure(list(date = structure(c(NA_real_, NA_real_, NA_real_), class =
> "Date"),
>
> month = structure(c(2L, 2L, 2L), .Label = c("Jun","May"), class = "factor"),
>
> day = c(30L, 30L, 30L),
>
> weekday = structure(c(2L,2L, 2L), .Label = c("Fri", "Mon", "Sat", "Sun",
> "Thu", "Tue","Wed"), class = "factor"),
>
> survey_rating = c(3L, 2L, 3L), query_status = c("Yes", "Don't know","No"),
>
>  a = c("05-30-16", "05-30-16", "05-30-16")), .Names = c("date","month",
> "day", "weekday", "survey_rating"), row.names = c(NA, 3L), class =
> "data.frame")
>
> There are several other variables that i have removed which are not
> relevant in this context.
>
> On Tue, Jul 26, 2016 at 8:55 PM, David L Carlson  wrote:
>
>> Show us the output, don’t just tell us what you are seeing. If the dates
>> are correct in the csv file, show us the structure of the data frame you
>> created with read.csv() and show the command(s) you used to convert the
>> character data to date format. The solution is likely to be simple if you
>> will cut/paste the R console and not just describe what is happening.
>>
>>
>>
>> David C
>>
>>
>>
>> *From:* Shivi Bhatia [mailto:shivipm...@gmail.com]
>> *Sent:* Tuesday, July 26, 2016 10:08 AM
>> *To:* David L Carlson
>>
>> *Subject:* Re: [R] Date Time in R
>>
>>
>>
>> Hi David,
>>
>> This gives the results accurately. The first line shows all the variable
>> names and the rest shows all values stored for each of the variable. Here
>> date is appearing as correct.
>>
>>
>>
>> Thanks, Shivi
>>
>>
>>
>> On Tue, Jul 26, 2016 at 7:39 PM, David L Carlson 
>> wrote:
>>
>> What does this produce?
>>
>> > readLines("YourCSVfilename.csv", n=5)
>>
>> If the data are in Excel, the date format used in .csv files is not always
>> in the same as the format used when viewing dates in the spreadsheet.
>>
>> -
>> David L Carlson
>> Department of Anthropology
>> Texas A University
>> College Station, TX 77840-4352
>>
>>
>>
>> -Original Message-
>> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Shivi
>> Bhatia
>> Sent: Tuesday, July 26, 2016 7:42 AM
>> To: Marc Schwartz
>> Cc: R-help
>> Subject: Re: [R] Date Time in R
>>
>> Thanks Marc for the help. this really helps.
>> I think there is some issue with the data saved in csv format for this
>> variable as when i checked:
>> str(eir$date)- this results in :-
>> Date[1:5327], format: NA NA NA NA NA.
>>
>> Thanks again.
>>
>> On Tue, Jul 26, 2016 at 5:58 PM, Marc Schwartz 
>> wrote:
>>
>> > Hi,
>> >
>> > That eir$date might be a factor is irrelevant. There is an as.Date()
>> > method for factors, which does the factor to character coercion
>> internally
>> > and then calls as.Date.character() on the result.
>> >
>> > Using the example data below:
>> >
>> > eir <- data.frame(date = c("05-30-16", "05-30-16", "05-30-16",
>> >"05-30-16", "05-30-16", "05-30-16"))
>> >
>> > > str(eir)
>> > 'data.frame':   6 obs. of  1 variable:
>> >  $ date: Factor w/ 1 level "05-30-16": 1 1 1 1 1 1
>> >
>> > > eir
>> >   date
>> > 1 05-30-16
>> > 2 05-30-16
>> > 3 05-30-16
>> > 4 05-30-16
>> > 5 05-30-16
>> > 6 05-30-16
>> >
>> > eir$date <- as.Date(eir$date, format = "%m-%d-%y")
>> >
>> > > str(eir)
>> > 'data.frame':   6 obs. of  1 variable:
>> >  $ date: Date, format: "2016-05-30" ...
>> >
>> > > eir
>> > date
>> > 1 2016-05-30
>> > 2 2016-05-30
>> > 3 2016-05-30
>> > 4 2016-05-30
>> > 5 2016-05-30
>> > 6 2016-05-30
>> >
>> > eir$days <- weekdays(eir$date)
>> >
>> > > str(eir)
>> > 'data.frame':   6 obs. of  2 variables:
>> >  $ date: Date, format: "2016-05-30" ...
>> >  $ days: chr  "Monday" "Monday" "Monday" "Monday" ...
>> >
>> > > eir
>> > date   days
>> > 1 2016-05-30 Monday
>> > 2 2016-05-30 Monday
>> > 3 2016-05-30 Monday
>> > 4 2016-05-30 Monday
>> > 5 2016-05-30 Monday
>> > 6 2016-05-30 Monday
>> >
>> >
>> > I would check to be sure that you do not have any typos in your code.
>> >
>> > Regards,
>> >
>> > Marc Schwartz
>> >
>> >
>> > > On Jul 26, 2016, at 6:58 AM, Shivi Bhatia 
>> wrote:
>> 

Re: [R] Build command in library(devtools)

[Hadley Wickham]

The first place to start is to make sure you have the latest version of
devtools. If that doesn't work, please file an issue on devtools' GitHub.

Hadley

On Wednesday, July 20, 2016, Steven Yen  wrote:

> Here is what I found. I had to go back to as early as R 3.0.3 (March,
> 2014) along with Rtools30.exe that works with that version of R, in
> order for devtools to work right. With other/later version of R, I end
> up building a package with
> library(devtools); build("yenlib",binary=F)
> with no error message but the package does not run correctly; or with
> library(devtools); build("yenlib",binary=T)
> which deliver an error that says zip command failed (bevtools calls
> Rtools when binary=T).
>
> Updated versions are good, but what's the use if they do not work for a
> situation like this.
>
> Any help/insight would be appreciated.
>
> On 7/20/2016 10:08 AM, Steven Yen wrote:
> > On 7/19/2016 4:38 PM, John McKown wrote:
> >> On Tue, Jul 19, 2016 at 3:15 PM, Steven Yen  
> >> >>wrote:
> >>
> >> I recently updated my R and RStudio to the latest version and
> >> now the
> >> binary option in the "build" command in devtools stops working.
> >>
> >> I went around and used the binary=F option which worked by I get
> >> the
> >> .tar.gz file instead of the .zip file which I prefer.
> >>
> >> Does anyone understand the following error message:
> >>
> >> status 127
> >> running 'zip' failed
> >>
> >>
> >> ​I'm not totally sure, but I think that means that R cannot find the
> >> "zip" program in order to run it. ​
>
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org  mailing list -- To UNSUBSCRIBE and
> more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.



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Re: [R] About identification of CRAN CHECK machines in logs

[Hadley Wickham]

On Fri, Jun 10, 2016 at 8:27 AM, Marcelo Perlin  wrote:
> I don't know Hadley. But you can see evidence of "something" systematically
> installing the packages in the log data. From my two CRAN packages I noticed
> a high correlation in the number of downloads.
>
> Try the following script, which will pick 5 random packages from CRAN and
> calculate the correlation matrix between their differenced number of
> downloads. To avoid spurious correlations,  I removed the weekends since we
> can expect some seasonality and also the zero entries. Its crude, I know,
> but it does shows some positive associations between the number of
> installations of the packages.

Which is not at all surprising:

* there are very strong seasonal patterns
* there are big jumps after releases of new versions of R
* some people like to have all packages installed locally

This is an intrinsic problem with download data. There's no way to
tell if a downloader is really using your package or not.

Hadley

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Re: [R] About identification of CRAN CHECK machines in logs

[Hadley Wickham]

On Thu, Jun 9, 2016 at 9:24 AM, Marcelo Perlin  wrote:
> Hi,
>
> I recently released two packages (RndTexExams and GetTDData) in CRAN and
> I'm trying to track the number of downloads and location of users.
>
> I wrote a simple script to download and analyze the log files in http://cran
> -logs.rstudio.com.
> I realized, however, that during the release of a new version of the
> packages there is a spike in the number of downloads. I believe that the
> CRAN checks are included in the number of installations of the package in
> the log files.

I don't think that's true. Why would CRAN be installing the package
from a mirror?

Hadley

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Re: [R] httr package syntax (PUT)

[Hadley Wickham]

On Wed, Jun 1, 2016 at 7:16 PM, Jared Rodecker  wrote:
> Greetings fellow R users.
>
> I'm struggling with the syntax of submitting a PUT request
>
> I'm trying to insert a few PUT requests into some legacy R code that I have
> that performs daily ETL on a small database. These requests will add users
> to an email mailing list in MailChimp.
>
>
> I have been able to get my GET requests formatted into syntax that R
> (specifically the httr package) accepts:
>
> GET("
> https://us10.api.mailchimp.com/3.0/lists/list_id_X/members/MEMBER_HASH_###;,
> query = list(apikey = 'XX'))
>
>
> However when I try to do something similar for PUT requests this simple
> syntax isn't working - you can't just pass the API KEY and/or requested
> parameters directly through the URL. I get a 401 error if I use the same
> syntax I used for GET.
>
>
> I believe that I need to use the CONFIG option to pass the API key (either
> using AUTHENTICATE or ADD_HEADERS) and the requested parameters in the BODY
> to get the PUT request to work but I can't get the syntax to work - this
> gives a 400 error:
>
>
> auth <- authenticate("anystring", "XX", type = "basic")
>
> parms <- '[{"email_address" : "some_u...@domain.com", "status_if_new" :
> "subscribed"}]'
>
> PUT("
> https://us10.api.mailchimp.com/3.0/lists/list_id_X/members/MEMBER_HASH_###
> ",config=auth,body=parms,encode="json")
>
>
> If anyone can point me to a more flushed out example that would be
> amazing...but even just some tips on how to get more info on my error
> message to help me troubleshoot my syntax would also be a big help.  I've
> also been trying to get httpput (from the RCurl package) but also
> struggling with the syntax there.

If you use verbose() you should be able to see what the problem is -
httr does the json encoding for you. You want:

params <- list(email_address = "some_u...@domain.com", status_if_new =
"subscribed")
PUT("https://us10.api.mailchimp.com/3.0/lists/list_id_X/members/MEMBER_HASH_###;,
   config = auth,
   body = params,
   encode = "json"
)

Hadley

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Re: [R] with vs. attach

[Hadley Wickham]

On Mon, May 9, 2016 at 7:12 AM, peter dalgaard  wrote:
>
> On 09 May 2016, at 02:46 , Bert Gunter  wrote:
>
>> ... To be clear, Hadley or anyone else should also feel free to set me
>> straight, preferably publicly, but privately if you prefer.
>
> Not really to "set anyone straight", but there are some subtleties with mode 
> call objects versus expression objects and formulas to be aware of.
>
> E.g.,
>
>> a <- 2
>> do.call("print", list(a*pi))
> [1] 6.283185
>> do.call("print", list(quote(a*pi)))
> [1] 6.283185
>> do.call("print", list(expression(a*pi)))
> expression(a * pi)
>> do.call("print", list(~a*pi))
> ~a * pi
>
> Thing is, if you insert a call object into a parse tree, nothing is there to 
> preserve its nature as an unevaluated expression. Similarly, in
>
>> call("print", quote(a*pi))
> print(a * pi)
>
> the result is identical to quote(print(a * pi)), so when evaluated, quoting 
> is not seen by print().
>
> As far as I understand, this is also the reason that for math in ggplot, you 
> may need as.expression(bquote()).
>
> In general, I think that a number of things in R had been more cleanly 
> implemented using formulas/expression objects than using substitution and 
> lazy evaluation, notably subset and offset arguments in lm/glm. It would have 
> been so much cleaner to have
>
> lm(math ~ age, data = foo, subset = ~ sex=="1")
>
> than the current situation where lm internally chops its own head off and 
> substitutes with model.frame, then evaluates the call to model.frame() which 
> in turn does eval(substitute(subset), data, env). Of course, at the time, ~ 
> was intended specifically for Wilkinson Rogers type formulas; "abusing" it 
> for other kinds of expressions is something of an afterthought.

Yeah, to my mind, the cool thing about formulas is that they provide a
concise way to capture an environment and an expression, and then
Wilkinson Rogers are just a special case.

It's obvious impossible to go back and change how lm() etc works now,
but I'm reasonably confident that lazyeval provides a strong
foundation going forward. The quasiquotation stuff is particularly
important - and unquote-splice makes it possible to do things that are
impossible with bquote().  (Of course, unquote-splice could be added
to bquote(), but I think you'll still run into issues with
environments)

Hadley


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Re: [R] with vs. attach

[Hadley Wickham]

On Sun, May 8, 2016 at 7:28 PM, Bert Gunter  wrote:
> Jeff:
>
> That's easy to do already with substitute(), since you can pass around
> an unevaluated expression (a parse tree) however you like. As I read
> it, (admittedly quickly) what it's main feature is that it allows you
> more control over the environment in which the expression is finally
> evaluated -- as well as permitting nested expression evaluation fairly
> easily.
>
> But maybe we're saying the same thing ...  IMHO I think Hadley has
> gone overboard here, worrying about rarely important issues, as you
> seem to be intimating also.

These are absolutely critical issues that crop up as soon as other
people want to write functions that use your functions that use NSE.

Hadley

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Re: [R] with vs. attach

[Hadley Wickham]

You may want to read http://rpubs.com/hadley/157957, which captures my
latest thinking (and tooling) around this problem. Feedback is much
appreciated.

Hadley

On Fri, May 6, 2016 at 2:14 PM, David Winsemius  wrote:
>
>> On May 6, 2016, at 5:47 AM, Spencer Graves 
>>  wrote:
>>
>>
>>
>> On 5/6/2016 6:46 AM, peter dalgaard wrote:
>>> On 06 May 2016, at 02:43 , David Winsemius  wrote:
>>>
> On May 5, 2016, at 5:12 PM, Spencer Graves 
>  wrote:
>
> I want a function to evaluate one argument
> in the environment of a data.frame supplied
> as another argument.  "attach" works for
> this, but "with" does not.  Is there a way
> to make "with" work?  I'd rather not attach
> the data.frame.
>
>
> With the following two functions "eval.w.attach"
> works but "eval.w.with" fails:
>
>
> dat <- data.frame(a=1:2)
> eval.w.attach <- function(x, dat){
>  attach(dat)
>  X <- x
>  detach()
>  X
> }
>
> eval.w.with <- function(x, dat){
>  with(dat, x)
> }
>
> eval.w.attach(a/2, dat) # returns c(.5, 1)
 How about using eval( substitute( ...))?

 eval.w.sub <- function(expr, datt){
   eval( substitute(expr), env=datt)
 }
 eval.w.sub(a/2, dat)
 #[1] 0.5 1.0


>>> Actually, I think a better overall strategy is to say that if you want to 
>>> pass an expression to a function, then pass an expression object (or a call 
>>> object or maybe a formula object).
>>>
>>> Once you figure out _how_ your eval.w.attach works (sort of), you'll get 
>>> the creeps:
>>>
>>> Lazy evaluation causes the argument x to be evaluated after the attach(), 
>>> hence the evaluation environment of an actual argument is being temporarily 
>>> modified from inside a function.
>>>
>>> Apart from upsetting computer science purists, there could be hidden 
>>> problems: One major issue is that  values in "dat" could be masked by 
>>> values in the global environment, another issue is that an error in 
>>> evaluating the expression will leave dat attached. So at a minimum, you 
>>> need to recode using on.exit() magic.
>>>
>>> So my preferences go along these lines:
>>>
 dat <- data.frame(a=1:2)
 eval.expression <- function(e, dat) eval(e, dat)
 eval.expression(quote(a/2), dat)
>>> [1] 0.5 1.0
 eval.expression(expression(a/2), dat)
>>> [1] 0.5 1.0
>>>
 eval.formula <- function(f, dat) eval(f[[2]], dat)
 eval.formula(~a/2, dat)
>>> [1] 0.5 1.0
>>
>> Hi, Peter:
>>
>>
>>  I don't like eval.expression or eval.formula, because they don't 
>> automatically accept what I naively thought should work and require more 
>> knowledge of the user.  What about David's eval.w.sub:
>>
>>
>> a <- pi
>> dat <- data.frame(a=1:2)
>> eval.w.sub <- function(a, Dat){
>>  eval( substitute(a), env=Dat)
>> }
>> > eval.w.sub(a/2, dat)
>> [1] 0.5 1.0
>
> I liked eval.expression and tested it with a bquote(...) argument to see if 
> that would succeed. It did, but it didn't return what you wanted for `a/2`, 
> so I tried seeing if a "double eval wuold deliver both yours and my desired 
> results:
>
>  eval.w.sub <- function(a, Dat){
>   eval( eval(substitute(a),Dat), env=Dat)
>  }
> x=2
>  eval.w.sub( a/2, dat)
> [1] 0.5 1.0
>  eval.w.sub( bquote(2*a*.(x) ), dat)
> [1] 4 8
>
> We are here retracing the path the Hadley took in some of his ggplot2 design 
> decsions. Unfortunately for me those NSE rules often left me confused about 
> what should and shouldn't be 'quoted' in the as-character sense and what 
> should be quote()-ed or "unquoted" in the bquote() sense.
> --
>
>>
>>
>>
>>  This produces what's desired in a way that seems simpler to me.
>>
>>
>>  By the way, I really appreciate Peter's insightful comments:
>>
>>
>> eval.w.attachOops <- function(x, Dat){
>>  attach(Dat)
>>  X <- x
>>  detach()
>>  X
>> }
>> > eval.w.attachOops(a/2, dat)
>> The following object is masked _by_ .GlobalEnv:
>>
>>a
>>
>> [1] 1.570796
>> > eval.w.attachOops(b/2, dat)
>> The following object is masked _by_ .GlobalEnv:
>>
>>a
>>
>> Error in eval.w.attachOops(b/2, dat) : object 'b' not found
>> > search()
>> [1] ".GlobalEnv""Dat"   "package:graphics"
>> [4] "package:grDevices" "package:utils" "package:datasets"
>> [7] "package:methods"   "Autoloads" "package:base"
>> > objects(2)
>> [1] "a"
>>
>> *** NOTES:
>>
>>
>>  1.  This gives a likely wrong answer with a warning if "a" exists in 
>> .GlobalEnv, and leaves "Dat" (NOT "dat") attached upon exit.
>>
>>
>>
>>  2.  A stray "detach()" [not shown here] detached "package:stats".  oops.
>>
>>
>> *** Using "on.exit" fixes the problem with failure to detach but not the 
>> likely wrong answer:
>>
>>
>> detach()
>> search()
>> eval.w.attachStillWrong <- function(x, dat){
>>  attach(dat)
>>  

Re: [R] installation of dplyr

[Hadley Wickham]

You normally see these errors when compiling on a vm that has very
little memory.
Hadley

On Tue, Apr 19, 2016 at 2:47 PM, Ben Tupper  wrote:
> Hello,
>
> I am getting a fresh CentOS 6.7 machine set up with all of the goodies for R 
> 3.2.3, including dplyr package. I am unable to successfully install it.  
> Below I show the failed installation using utils::install.packages() and then 
> again using devtools::install_github().  Each yields an error similar to the 
> other but not quite exactly the same - the error messages sail right over my 
> head.
>
> I can contact the package author if that would be better, but thought it best 
> to start here.
>
> Thanks!
> Ben
>
> Ben Tupper
> Bigelow Laboratory for Ocean Sciences
> 60 Bigelow Drive, P.O. Box 380
> East Boothbay, Maine 04544
> http://www.bigelow.org
>
>> sessionInfo()
> R version 3.2.3 (2015-12-10)
> Platform: x86_64-redhat-linux-gnu (64-bit)
> Running under: CentOS release 6.7 (Final)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
>  [9] LC_ADDRESS=C   LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
>
>
>
> 
> #   utils::install.packages()
> 
>
>> install.packages("dplyr", repo = "http://cran.r-project.org;)
> Installing package into ‘/usr/lib64/R/library’
> (as ‘lib’ is unspecified)
> trying URL 'http://cran.r-project.org/src/contrib/dplyr_0.4.3.tar.gz'
> Content type 'application/x-gzip' length 655997 bytes (640 KB)
> ==
> downloaded 640 KB
>
> * installing *source* package ‘dplyr’ ...
> ** package ‘dplyr’ successfully unpacked and MD5 sums checked
> ** libs
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c RcppExports.cpp -o 
> RcppExports.o
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c address.cpp -o address.o
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c api.cpp -o api.o
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c arrange.cpp -o arrange.o
> In file included from ../inst/include/dplyr.h:131,
>  from arrange.cpp:1:
> ../inst/include/dplyr/DataFrameSubsetVisitors.h: In constructor 
> ‘dplyr::DataFrameSubsetVisitors::DataFrameSubsetVisitors(const 
> Rcpp::DataFrame&, const Rcpp::CharacterVector&)’:
> ../inst/include/dplyr/DataFrameSubsetVisitors.h:40: warning: ‘column’ may be 
> used uninitialized in this function
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c between.cpp -o between.o
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c bind.cpp -o bind.o
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4 -m64 -mtune=generic  -c combine_variables.cpp -o 
> combine_variables.o
> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR 
> -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" 
> -I"/usr/lib64/R/library/BH/include"   -fpic  -O2 -g -pipe -Wall 
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4 

Re: [R] simple question on data frames assignment

[Hadley Wickham]

== is also vectorised, and you're better off with TRUE and FALSE
rather than 1 and 0, so I'd recommend:

colordata$response <- colordata$color == 'blue'

Hadley

On Thu, Apr 7, 2016 at 6:52 AM, David Barron  wrote:
> ifelse is vectorised, so just use that without the loop.
>
> colordata$response <- ifelse(colordata$color == 'blue', 1, 0)
>
> David
>
> On 7 April 2016 at 12:41, Michael Artz  wrote:
>
>> Hi I'm not sure how to ask this, but its a very easy question to answer for
>> an R person.
>>
>> What is an easy way to check for a column value and then assigne a new
>> column a value based on that old column value?
>>
>> For example, Im doing
>>  colordata <- data.frame(id = c(1,2,3,4,5), color = c("blue", "red",
>> "green", "blue", "orange"))
>>  for (i in 1:nrow(colordata)){
>>colordata$response[i] <- ifelse(colordata[i,"color"] == "blue", 1, 0)
>>  }
>>
>> which works,  but I don't want to use the for loop I want to "vecotrize"
>> this.  How would this be implemented?
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.



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Re: [R] Updating github R packages

[Hadley Wickham]

It will be included in the next version of devtools - it's totally
do-able, but no one has done it yet.

Hadley

On Wed, Feb 17, 2016 at 6:44 PM, Jeff Newmiller
 wrote:
> AFAIK the answer is no. That would be one of the main drawbacks of depending 
> on github for packages. It isn't really a package repository so much as it is 
> a herd of cats.
> --
> Sent from my phone. Please excuse my brevity.
>
> On February 16, 2016 6:43:02 PM PST, "Hoji, Akihiko"  wrote:
>>Hi,
>>
>>Is there a way to update a R package and its dependencies,  installed
>>from the github repo by a simple command equivalent to
>>“update_packages()”?
>>
>>Thanks.
>>
>>
>>__
>>R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>https://stat.ethz.ch/mailman/listinfo/r-help
>>PLEASE do read the posting guide
>>http://www.R-project.org/posting-guide.html
>>and provide commented, minimal, self-contained, reproducible code.
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.



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Re: [R] vjust unresponsive (ggplot2)

[Hadley Wickham]

vjust was always a hack that I never thought should work. The margins
parameter is the correct way to solve this problem as of ggplot2 2.0.0.

Hadley

On Tuesday, December 22, 2015, Nordlund, Dan (DSHS/RDA) 
wrote:

> Ista,
>
> You are correct, I was not at the latest release of ggplot2.  I updated to
> the latest version and am now seeing the same result as you and the OP.  So
> it does look like an issue with the latest version of ggplot2.
>
> Dan
>
> Daniel Nordlund, PhD
> Research and Data Analysis Division
> Services & Enterprise Support Administration
> Washington State Department of Social and Health Services
>
>
> > -Original Message-
> > From: Ista Zahn [mailto:istaz...@gmail.com ]
> > Sent: Tuesday, December 22, 2015 10:48 AM
> > To: Nordlund, Dan (DSHS/RDA)
> > Cc: r-help@r-project.org 
> > Subject: Re: [R] vjust unresponsive (ggplot2)
> >
> > Hi Dan,
> >
> > Chances are that you haven't yet upgraded to ggplot2 version 2.0. unit
> (as
> > well as arrow and alpha) are now re-exported from ggplot2.
> >
> > Using the latest release I also see that vjust doesn't seem to do
> anything.
> >
> > Best,
> > Ista
> >
> > On Tue, Dec 22, 2015 at 1:37 PM, Nordlund, Dan (DSHS/RDA)
> > > wrote:
> > > Are you sure it is not working for you?  Your example code did not
> work for
> > me at all until I removed the plot .margin  parameter (unit wasn't
> > recognized).  Once I did that hjust and vjust worked as expected.
> However,
> > values between .1 and .9 for vjust don't really move the axis title very
> much
> > so it may not be real noticeable.  Try a value like 2 or 3, just to make
> sure you
> > easily see the change in position before concluding that nothing is
> > happening.
> > >
> > > Dan
> > >
> > > Daniel Nordlund, PhD
> > > Research and Data Analysis Division
> > > Services & Enterprise Support Administration Washington State
> > > Department of Social and Health Services
> > >
> > >
> > > -Original Message-
> > > From: R-help [mailto:r-help-boun...@r-project.org ] On
> Behalf Of Ryan
> > > Utz
> > > Sent: Tuesday, December 22, 2015 10:00 AM
> > > To: r-help@r-project.org 
> > > Subject: [R] vjust unresponsive (ggplot2)
> > >
> > > Hi all,
> > >
> > > I cannot for the life of me get my axis titles to adjust vertically in
> a ggplot.
> > I've seen several posts about this and have tried everything:
> > > keeping vjust within 0 and 1, adjusting the margins, etc. hjust is
> behaving
> > just as it should but vjust just mocks me in silence. No error message is
> > produced.
> > >
> > > Here's a sample code:
> > >
> > > x=data.frame(sample(1:10))
> > > x[,2]=sample(1:10)
> > >
> > > ggplot(data=x,aes(x=V2,y=V2))+theme(axis.title.y=element_text(vjust=.1
> > > ,hjust=0.6),
> > > plot.margin=unit(c(1,1,2,2),'cm'))
> > >
> > > No matter what I put into vjust, nothing happens. Am I missing
> something
> > obvious??
> > >
> > > Thanks ahead of time for any help,
> > > Ryan
> > >
> > >
> > > --
> > >
> > > Ryan Utz, Ph.D.
> > > Assistant professor of water resources
> > > *chatham**UNIVERSITY*
> > > Home/Cell: (724) 272-7769
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > __
> > > R-help@r-project.org  mailing list -- To UNSUBSCRIBE
> and more, see
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> > >
> > > __
> > > R-help@r-project.org  mailing list -- To UNSUBSCRIBE
> and more, see
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> __
> R-help@r-project.org  mailing list -- To UNSUBSCRIBE and
> more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


-- 
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Re: [R] Make a box-whiskers plot in R with 5 variables, color coded.

[Hadley Wickham]

On Tue, Dec 15, 2015 at 9:55 AM, Martin Maechler
 wrote:
>
>
>[]
>
> > You are missing the closing bracket on the boxplot()
> > command.  Just finish with a ')'
>
> Hmm... I once learned
>
>  '()' =: parenthesis/es
>  '[]' =: bracket(s)
>  '{}' =: brace(s)
>
> Of course, I'm not a native English speaker, and my teacher(s) /
> teaching material may have been biased ... but, as all three
> symbol pairs play an important role in R, I think it would be
> really really helpful,  if we could agree on using the same
> precise English here.
>
> I'm happy to re-learn, but I'd really like to end up with three
> different simple English words, if possible.
> (Yes, I know and have seen/heard "curly braces", "round
>  parentheses", ... but I'd hope we can do without the extra adjective.)

I think this is what Americans are taught, but I can never remember
which is which. I use round brackets, square brackets, and squiggly
brackets, which are memorable, and even if you're not familiar with
the terms you can easily understand what I mean.

Hadley

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Re: [R] Make a box-whiskers plot in R with 5 variables, color coded.

[Hadley Wickham]

On Wed, Dec 16, 2015 at 9:34 AM, Hadley Wickham <h.wick...@gmail.com> wrote:
> On Tue, Dec 15, 2015 at 9:55 AM, Martin Maechler
> <maech...@stat.math.ethz.ch> wrote:
>>
>>
>>[]
>>
>> > You are missing the closing bracket on the boxplot()
>> > command.  Just finish with a ')'
>>
>> Hmm... I once learned
>>
>>  '()' =: parenthesis/es
>>  '[]' =: bracket(s)
>>  '{}' =: brace(s)
>>
>> Of course, I'm not a native English speaker, and my teacher(s) /
>> teaching material may have been biased ... but, as all three
>> symbol pairs play an important role in R, I think it would be
>> really really helpful,  if we could agree on using the same
>> precise English here.
>>
>> I'm happy to re-learn, but I'd really like to end up with three
>> different simple English words, if possible.
>> (Yes, I know and have seen/heard "curly braces", "round
>>  parentheses", ... but I'd hope we can do without the extra adjective.)
>
> I think this is what Americans are taught, but I can never remember
> which is which. I use round brackets, square brackets, and squiggly
> brackets, which are memorable, and even if you're not familiar with
> the terms you can easily understand what I mean.

I should mention that all three terms have accompanying arm motions ;)

Hadley

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Re: [R] stopifnot with logical(0)

[Hadley Wickham]

On Sat, Dec 12, 2015 at 1:51 PM, Martin Maechler
<maech...@stat.math.ethz.ch> wrote:
>>>>>> Hadley Wickham <h.wick...@gmail.com>
>>>>>> on Sat, 12 Dec 2015 08:08:54 -0600 writes:
>
> > On Sat, Dec 12, 2015 at 3:54 AM, Martin Maechler
> > <maech...@stat.math.ethz.ch> wrote:
> >>>>>>> Henrik Bengtsson <henrik.bengts...@gmail.com> on
> >>>>>>> Fri, 11 Dec 2015 08:20:55 -0800 writes:
> >>
> >> > On Fri, Dec 11, 2015 at 8:10 AM, David Winsemius
> >> <dwinsem...@comcast.net> wrote:
> >> >>
> >> >>> On Dec 11, 2015, at 5:38 AM, Dario Beraldi
> >> <dario.bera...@gmail.com> wrote:
> >> >>>
> >> >>> Hi All,
> >> >>>
> >> >>> I'd like to understand the reason why
> >> stopifnot(logical(0) == x) doesn't >>> (never?) throw an
> >> exception, at least in these cases:
> >> >>
> >> >> The usual way to test for a length-0 logical object is
> >> to use length():
> >> >>
> >> >> x <- logical(0)
> >> >>
> >> >> stopifnot( !length(x) & mode(x)=="logical" )
> >>
> >> > I found
> >>
> >> > stopifnot(!length(x), mode(x) == "logical")
> >>
> >> > more helpful when troubleshooting, because it will tell
> >> you whether > it's !length(x) or mode(x) == "logical"
> >> that is FALSE.  It's as if you > wrote:
> >>
> >> > stopifnot(!length(x)) > stopifnot(mode(x) == "logical")
> >>
> >> > /Henrik
> >>
> >> Yes, indeed, thank you Henrik --- and Jeff Newmiller
> >> who's nice humorous reply added other relevant points.
> >>
> >> As author stopifnot(), I do agree with Dario's "gut
> >> feeling" that stopifnot() "somehow ought to do the right
> >> thing" in cases such as
> >>
> >> stopifnot(dim(x) == c(3,4))
> >>
> >> which is really subtle version of his cases {But the gut
> >> feeling is wrong, as I argue from now on}.
>
> > Personally, I think the problem there is that people
> > forget that == is vectorised, and for a non-vectorised
> > equality check you really should use identical:
>
> > stopifnot(identical(dim(x), c(3,4)))
>
> You are right "in theory"  but practice is less easy:
> identical() tends to be  too subtle for many users ... even
> yourself (;-), not really of course!),  Hadley, in the above case:
>
> Your stopifnot() would *always* stop, i.e., signal an error
> because typically all dim() methods return integer, and c(3,4)
> is double.
> So, if even Hadley gets it wrong so easily, I wonder if its good
> to advertize to always use  identical() in such cases.
> I indeed would quite often use identical() in such tests, and
> you'd too and would quickly find and fix the "trap" of course..
> So you are mostly right also in my opinion...

Ooops, yes - but you would discover this pretty quickly if you weren't
coding in a email client ;)

I wonder if R is missing an equality operator for this case. Currently:

* == is suboptimal because it's vectorised
* all.equal is suboptimal because it returns TRUE or a text string
* identical is suboptimal because it doesn't do common coercions

Do we need another function (equals()?) that uses the same coercion
rules as == but isn't vectorised? (Like == it would only work with
vectors, so you'd still need identical() for (e.g.) comparing
environments)

Hadley

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Re: [R] stopifnot with logical(0)

[Hadley Wickham]

>> I wonder if R is missing an equality operator for this case. Currently:
>>
>> * == is suboptimal because it's vectorised
>> * all.equal is suboptimal because it returns TRUE or a text string
>> * identical is suboptimal because it doesn't do common coercions
>>
>> Do we need another function (equals()?) that uses the same coercion
>> rules as == but isn't vectorised? (Like == it would only work with
>> vectors, so you'd still need identical() for (e.g.) comparing
>> environments)
>
> I don't think so.  We already have all(), so all(x == y) would do what you
> want.

But that recycles, which is what we're trying to avoid here.

Hadley

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Re: [R] stopifnot with logical(0)

[Hadley Wickham]

On Sat, Dec 12, 2015 at 3:54 AM, Martin Maechler
 wrote:
>> Henrik Bengtsson 
>> on Fri, 11 Dec 2015 08:20:55 -0800 writes:
>
> > On Fri, Dec 11, 2015 at 8:10 AM, David Winsemius 
>  wrote:
> >>
> >>> On Dec 11, 2015, at 5:38 AM, Dario Beraldi  
> wrote:
> >>>
> >>> Hi All,
> >>>
> >>> I'd like to understand the reason why stopifnot(logical(0) == x) 
> doesn't
> >>> (never?) throw an exception, at least in these cases:
> >>
> >> The usual way to test for a length-0 logical object is to use length():
> >>
> >> x <- logical(0)
> >>
> >> stopifnot( !length(x) & mode(x)=="logical" )
>
> > I found
>
> > stopifnot(!length(x), mode(x) == "logical")
>
> > more helpful when troubleshooting, because it will tell you whether
> > it's !length(x) or mode(x) == "logical" that is FALSE.  It's as if you
> > wrote:
>
> > stopifnot(!length(x))
> > stopifnot(mode(x) == "logical")
>
> > /Henrik
>
> Yes, indeed, thank you Henrik  --- and Jeff Newmiller who's nice
> humorous reply added other relevant points.
>
> As author stopifnot(), I do agree with Dario's  "gut feeling"
> that stopifnot()  "somehow ought to do the right thing"
> in cases such as
>
>stopifnot(dim(x) == c(3,4))
>
> which is really subtle version of his cases
> {But the gut feeling is wrong, as I argue from now on}.

Personally, I think the problem there is that people forget that == is
vectorised, and for a non-vectorised equality check you really should
use identical:

stopifnot(identical(dim(x), c(3,4)))

Hadley

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Re: [R] Weird behaviour function args in ellipses

[Hadley Wickham]

On Fri, Dec 11, 2015 at 1:13 PM, Duncan Murdoch
 wrote:
> On 11/12/2015 1:52 PM, Mario José Marques-Azevedo wrote:
>>
>> Hi Duncan and David,
>>
>> Thank you for explanation. I'm really disappointed with this R "resource".
>> I think that partial match, mainly in function args, must be optional and
>> not default. We can have many problems and lost hours find errors (it
>> occur
>> with me). I tried to find a solution to disable partial match, but it
>> seems
>> that is not possible. Program with hacks for this will be sad.
>
>
> Nowadays with smart editors, I agree that partial matching isn't really
> necessary.  However, R has been around for 20 years, and lots of existing
> code depends on it.   Eventually you'll get to know the quirks of the
> design.

And if you really dislike this behavour, you can at least warn on it:

options(
  warnPartialMatchArgs = TRUE,
  warnPartialMatchAttr = TRUE,
  warnPartialMatchDollar = TRUE
)

Hadley

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[R] R Consortium projects

[Hadley Wickham]

Hi all,

I'm very pleased to announce that the Infrastructure Steering
Committee (ISC) of the R consortium is calling for proposals:

https://www.r-consortium.org/about/isc/proposals

In brief:

* We want to fund projects that help the R community, broadly construed.

* Currently, we are mostly focussed on funding people who have the
  skills to solve a problem. In the future, we will explore how to
  match up people with skills and people with problems.

* Proposals are due Jan 10.

Please let me know if you have any questions!

Hadley Wickham
Chair, ISC

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Re: [R] Achieve independent fine user control of ggplot geom settings when using groups in multiple geom's

[Hadley Wickham]

I'd recommend reading the ggplot2 book - learning more about how
scales work in ggplot2 will help you understand why this isn't
possible.
Hadley

On Thu, Oct 29, 2015 at 6:31 PM, sbihorel
 wrote:
> Thank for your reply,
>
> I may accept your point about the mapping consistency when the different
> geom's use the same data source. However, as pointed out in my example code,
> this does not have to be the case. Hence my question about the geom-specific
> control of group-dependent graphical settings.
>
> Sebastien
>
>
> On 10/29/2015 4:49 PM, Jeff Newmiller wrote:
>>
>> I think a fundamental design principle of ggplot is that mapping of values
>> to visual representation are consistent within a single plot, so reassigning
>> color mapping for different elements would not be supported.
>>
>> That being said, it is possible to explicitly control specific attributes
>> within a single geom outside of the mapping, though this usually does break
>> mappings in the legend.
>>
>> ---
>> Jeff NewmillerThe .   .  Go
>> Live...
>> DCN:Basics: ##.#.   ##.#.  Live
>> Go...
>>Live:   OO#.. Dead: OO#..  Playing
>> Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
>> /Software/Embedded Controllers)   .OO#.   .OO#.
>> rocks...1k
>>
>> ---
>> Sent from my phone. Please excuse my brevity.
>>
>> On October 29, 2015 11:27:55 AM MST, sbihorel
>>  wrote:
>>>
>>> Thank you for your reply.
>>>
>>> I do not have anything specific data/geom/grouping in mind, rather a
>>> framework in which users would just pile of each other layer after
>>> layer
>>> of geom each defined with specific settings. A minimum realistic
>>> scenario would a geom_point followed by a geom_smooth or a geom_path
>>> using different colors...
>>>
>>> Sebastien
>>>
>>> On 10/29/2015 1:34 PM, Ista Zahn wrote:

 I would say in a word, 'no'. What you seem to be implying is that you
 want multiple color scales, multiple shape scales, etc. As far as I
 know there is no support for that in ggplot2.

 Perhaps if you show us what you're actually trying to accomplish
 someone can suggest a solution or at least a work-around.

 Best,
 Ista

 On Thu, Oct 29, 2015 at 12:26 PM, sbihorel
  wrote:
>
> Hello,
>
> Before I get to my question, I want to make clear that the topic of
>>>
>>> my
>
> present post is similar to posts I recently submitted to the list.
>>>
>>> Although
>
> I appreciate the replies I got, I believe that I did not correctly
>>>
>>> frame
>
> these previous posts to get to the bottom of things.
> I also want to make clear that the code example that I have inserted
>>>
>>> in this
>
> post is meant to illustrate my points/questions and does not reflect
>>>
>>> a
>
> particular interest in the data or the sequence of ggplot geom's
>>>
>>> used
>
> (except otherwise mentioned). Actually, I purposefully used junk
>>>
>>> meaningless
>
> data, geom's sequence, and settings, so that we agree the plot is
>>>
>>> ugly and
>
> that we, hopefully, don't get hang on specifics and start discussing
>>>
>>> about
>
> the merit of one approach vs another.
>
> So here are my questions:
>
> 1- Can a user independently control the settings of each geom's used
>>>
>>> in a
>
> ggplot call sequence when grouping is required?
>
> By control, I mean: user defines the graphical settings (groups,
>>>
>>> symbol
>
> shapes, colors, fill colors, line types, size scales, and alpha) and
>>>
>>> does
>
> not let ggplot choose these settings from some theme default.
> By independently, I mean: the set of graphical settings can be
>>>
>>> totally
>
> different from one group to the next and from one geom to the next.
>
> If this fine control can be achieved, how would you go about it
>>>
>>> (please, be
>
> assured that I already spent hours miserably failing to get to
>>>
>>> anything
>
> remotely productive, so your help would be really appreciated)?
>
> library(dplyr)
> library(tidyr)
> library(ggplot2)
> set.seed(1234)
> dummy <- data.frame(dummy = numeric())
> data <- data.frame(x1 = rep(-2:2, each = 80) + rnorm(4000, sd =
>>>
>>> 0.1),
>
>  g1 = rep(1:4, each = 1000))
> data <- data %>% mutate(y1 = -x1^2 + 2*x1 - 2 + g1 + rnorm(4000, sd
>>>
>>> = 0.25))
>
> data2 <- data %>% select(x2=x1, y2=y1, g2=g1) %>% mutate(x2=-x2)
> data3 <- data.frame(x3 = sample(seq(-2, 2, by = 0.1), 20, replace 

Re: [R] Control of x-axis variable ordering in ggplot

[Hadley Wickham]

You have two problems:

* geom_line() always draws from right-to-left
* you're defining colour outside of the plot in a very non-ggplot2 way.

Here's how I'd do it:

library(ggplot2)
data <- data.frame(
  x = rep(1:4, each = 25),
  y = rep(1:25, times = 4),
  g = rep(1:4, each = 25)
)
data$x <- data$x + 0.005 * data$y ^ 2 - 0.1 * data$y + 1

ggplot(data, aes(x, y, colour = factor(g))) +
  geom_point() +
  geom_path()


Alsonotethatcodeismucheasiertoreadifyouusespaces;)

Hadley

On Thu, Oct 22, 2015 at 8:46 PM, sbihorel
 wrote:
> Hi,
>
> Given a certain data.frame, the lattice xyplot function will plot the data
> as.is and join the data point in the order of the data frame. It is my
> (probably flawed) understanding that, using the same data frame, ggplot
> orders the data by increasing order of the x-axis variable. Can one control
> this behavior?
>
> Thanks
>
> Sebastien
>
> Code example
>
> library(lattice)
> library(ggplot2)
>
>
> data <- data.frame(x=rep(1:4,each=25),
>y=rep(1:25,times=4),
>g=rep(1:4,each=25))
> data$x <- data$x + 0.005*(data$y)^2-0.1*data$y+1
>
> col <- 3:7
>
> xyplot(y~x,data=data,groups=g,type='l',col=col)
>
> ggplot(data, aes(x,y,group=g)) + geom_point(colour=col[data$g]) +
>   geom_line(colour=col[data$g])
>
> __
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Re: [R] retaining characters in a csv file

[Hadley Wickham]

The problem is that quotes in csv files are commonly held to me
meaningless (i.e. they don't automatically force components to be
strings).

Earlier this morning I committed a fix to readr so that numbers
starting with a sequence of zeros are read as character strings. You
may want to try out the dev version: https://github.com/hadley/readr.

Hadley

On Tue, Sep 22, 2015 at 5:00 PM, Therneau, Terry M., Ph.D.
 wrote:
> I have a csv file from an automatic process (so this will happen thousands
> of times), for which the first row is a vector of variable names and the
> second row often starts something like this:
>
> 5724550,"000202075214",2005.02.17,2005.02.17,"F", .
>
> Notice the second variable which is
>   a character string (note the quotation marks)
>   a sequence of numeric digits
>   leading zeros are significant
>
> The read.csv function insists on turning this into a numeric.  Is there any
> simple set of options that
> will turn this behavior off?  I'm looking for a way to tell it to "obey the
> bloody quotes" -- I still want the first, third, etc columns to become
> numeric.  There can be more than one variable like this, and not always in
> the second position.
>
> This happens deep inside the httr library; there is an easy way for me to
> add more options to the read.csv call but it is not so easy to replace it
> with something else.
>
> Terry T



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Re: [R] Unexpected/undocumented behavior of 'within': dropping variable names that start with '.'

[Hadley Wickham]

The problem is that within.data.frame calls as.list.environment with
the default value of all.names = FALSE. I doubt this is a deliberate
feature, and is more likely to be a minor oversight.

Hadley

On Sun, Sep 20, 2015 at 11:49 AM, Brian  wrote:
> Dear List,
>
> Somewhere I missed something, and now I'm really missing something!
>
>> d.f <- data.frame(.id = c(TRUE, FALSE, TRUE), dummy = c(1, 2, 3), a =
> c(1, 2, 3), b = c(1, 2, 3) + 1)
>  > within(d.f, {d = a + b})
>dummy a b d
>  1 1 1 2 3
>  2 2 2 3 5
>  3 3 3 4 7
>  > d.f <- data.frame(.id = c(TRUE, FALSE, TRUE), .dummy = c(1, 2, 3), a
> = c(1, 2, 3), b = c(1, 2, 3) + 1)
>  > within(d.f, {d = a + b})
>a b d
>  1 1 2 3
>  2 2 3 5
>  3 3 4 7
>
> Could somebody please explain to me why this does this? I think could be
> considered a feature (for lots of calculations within a data frame you
> don't have to remove all extra variables at the end).  I just wish it
> was documented.
>
> Cheers,
> Brian
>
>
> sessionInfo()
>  R version 3.1.0 (2014-04-10)
>  Platform: x86_64-pc-linux-gnu (64-bit)
>
>  locale:
>   [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
>   [9] LC_ADDRESS=C   LC_TELEPHONE=C
>  [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
>  attached base packages:
>  [1] splines   grid  stats graphics  grDevices utils datasets
>  [8] methods   base
>
>  other attached packages:
>   [1] scales_0.2.4   plyr_1.8.3 reshape2_1.4
> ccchDataProc_0.7
>   [5] ccchTools_0.6  xtable_1.7-4   tables_0.7.79  Hmisc_3.14-5
>   [9] Formula_1.1-2  survival_2.37-7ggplot2_1.0.1
> IDPmisc_1.1.17
>  [13] lattice_0.20-29myRplots_1.1   myRtools_1.2   meteoconv_0.1
>  [17] pixmap_0.4-11  RColorBrewer_1.0-5 maptools_0.8-30sp_1.1-1
>  [21] mapdata_2.2-3  mapproj_1.2-2  maps_2.3-9 chron_2.3-45
>  [25] MASS_7.3-35
>
>  loaded via a namespace (and not attached):
>   [1] acepack_1.3-3.3 cluster_1.15.2  colorspace_1.2-4
>   [4] compiler_3.1.0  data.table_1.9.4digest_0.6.4
>   [7] foreign_0.8-61  gtable_0.1.2labeling_0.3
>  [10] latticeExtra_0.6-26 munsell_0.4.2   nnet_7.3-8
>  [13] proto_0.3-10Rcpp_0.12.0 rpart_4.1-8
>  [16] stringr_0.6.2   tools_3.1.0
>  > within
>  function (data, expr, ...)
>  UseMethod("within")
>  
>  
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
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> and provide commented, minimal, self-contained, reproducible code.



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Re: [R] ggplot2 scale_shape_manual with large numbers instead of shapes

[Hadley Wickham]

Something like this?

df - data.frame(
  x = runif(30),
  y = runif(30),
  z = factor(1:30)
)

ggplot(df, aes(x, y)) +
  geom_point(aes(shape = z), size = 5) +
  scale_shape_manual(values = c(letters, 0:9))

Hadley

On Thu, Aug 27, 2015 at 4:48 PM, Marian Talbert mtalb...@usgs.gov wrote:
 I'm trying to produce a plot with climate data in which colors describe one
 aspect of the data (emissions scenario) and numbers rather than shapes show
 the model used (there are 36 models for one emissions scenario and 34 for
 the other).  I'm trying to use numbers rather than symbols because there are
 36 climate models and thus not enough symbols.  Numbering seems more
 consistent than some combo of letters and symbols.  I couldn't figure out
 how to define my own shapes as numbers 1 to 36 using scale_shape_manual so
 I'm adding the numbers with annotate.  The problem is that I'd like a second
 legend linking the numbering to the long model names but am having a hard
 time with this.  I've created a toy example below to make this more clear.
 p1 below was my original plot and I'd like p2 only with the second legend
 linking numbers to long model names any suggestions?

 library(ggplot2)


 Dat-data.frame(Temp=c(rnorm(36,0,1),rnorm(36,1.5,1)),Precp=c(rnorm(36,0,1),rnorm(36,1,1)),

 model=factor(rep(paste(LongModelName,c(letters,1:10),sep=_),times=2)),
   Emissions=factor(rep(c(RCP 4.5,RCP 8.5),each=36)))
  EmissionsCol-c(goldenrod2,red)
  Pquants - aggregate(Dat$Precp,list(RCP=Dat$Emissions),
quantile,c(.25,.5,.75),na.rm=TRUE)
  Tquants - aggregate(Dat$Temp,list(RCP=Dat$Emissions),
quantile,c(.25,.5,.75),na.rm=TRUE)
  Quants-data.frame(Emissions=Tquants$RCP,Tmin=Tquants[[2]][,1],
   TMedian=Tquants[[2]][,2],Tmax=Tquants[[2]][,3],

 Pmin=Pquants[[2]][,1],PMedian=Pquants[[2]][,2],Pmax=Pquants[[2]][,3])

 #Original Plot
 Labels-Dat$model
  p1 - ggplot()+geom_point(Dat,mapping=aes(x=Temp,y=Precp,colour=Emissions),
  size=.1)+
  scale_colour_manual(values=c(#EEB422BE,#FFBE),guide=none)+
   annotate(text, label=Labels, x=Dat$Temp,
 y=Dat$Precp,colour=c(#EEB422BE,#FFBE)[Dat$Emissions]) +
   guides(fill=guide_legend(reverse=TRUE))+theme(axis.title =
 element_text(size = 2)) +

 geom_segment(data=Quants,mapping=aes(x=Tmin,y=PMedian,xend=Tmax,yend=PMedian),size=2,colour=black)+

 geom_segment(data=Quants,mapping=aes(x=TMedian,y=Pmin,xend=TMedian,yend=Pmax),size=2,colour=black)+

 geom_segment(data=Quants,mapping=aes(x=Tmin,y=PMedian,xend=Tmax,yend=PMedian,colour=Emissions),size=1)+

 geom_segment(data=Quants,mapping=aes(x=TMedian,y=Pmin,xend=TMedian,yend=Pmax,colour=Emissions),size=1)+

 geom_point(data=Quants,mapping=aes(x=TMedian,y=PMedian,fill=Emissions),size=6,pch=21,colour=black)+
   scale_fill_manual(values=EmissionsCol)
 p1

 #with numbers instead of model names
 Labels-as.numeric(factor(Dat$model))
  p2-
 ggplot()+geom_point(Dat,mapping=aes(x=Temp,y=Precp,colour=Emissions),size=.1)+
  scale_colour_manual(values=c(#EEB422BE,#FFBE),guide=none)+
   annotate(text, label=Labels, x=Dat$Temp,
 y=Dat$Precp,colour=c(#EEB422BE,#FFBE)[Dat$Emissions])+
   guides(fill=guide_legend(reverse=TRUE))+theme(axis.title =
 element_text(size = 2)) +

 geom_segment(data=Quants,mapping=aes(x=Tmin,y=PMedian,xend=Tmax,yend=PMedian),size=2,colour=black)+

 geom_segment(data=Quants,mapping=aes(x=TMedian,y=Pmin,xend=TMedian,yend=Pmax),size=2,colour=black)+

 geom_segment(data=Quants,mapping=aes(x=Tmin,y=PMedian,xend=Tmax,yend=PMedian,colour=Emissions),size=1)+

 geom_segment(data=Quants,mapping=aes(x=TMedian,y=Pmin,xend=TMedian,yend=Pmax,colour=Emissions),size=1)+

 geom_point(data=Quants,mapping=aes(x=TMedian,y=PMedian,fill=Emissions),size=6,pch=21,colour=black)+
   scale_fill_manual(values=EmissionsCol)

 p2





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Re: [R] Issues with RPostgres

[Hadley Wickham]

On Thu, Aug 27, 2015 at 3:46 PM, John McKown
john.archie.mck...@gmail.com wrote:
 On Thu, Aug 27, 2015 at 2:29 PM, Abraham Mathew mathewanalyt...@gmail.com
 wrote:

 I have a user-defined function that I'm using alongside a postgresql
 connection to
 summarize some data. I've connected to the local machine with no problem.
 However,
 the connection keeps throwing the following error when I attempt to use it.
 Can anyone point
 to what I could be doing wrong.

  ds_summary(con, test, vars=c(Age), y=c(Class))
 Error in postgresqlNewConnection(drv, ...) :
   RS-DBI driver: (could not connect postgres@localhost on dbname test
 )


 con is the connection


 It would be helpful to see the assignment to con as well as any other
 assignments related to this. If you are using the DBI package, then what I
 am talking about would be something like:

 drv-dbDriver(PgSQL)
 con-dbConnect(drb,user=...,password=...,dbname=test');

FWIW the best way to create a connection is:

library(DBI)
con - dbConnect(RPostgreSQL::PostgreSQL(), ...)

The older string based approach is not advised.

Hadley
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Re: [R] How are packages installed with install_github() updated in RStudio?

[Hadley Wickham]

RStudio just calls the same underlying R functions, so it doesn't make
any difference that you're using RStudio.  Currently, there's no
automatic way to update packages installed from github.

Hadley

On Tue, Aug 18, 2015 at 8:14 AM, John Kane jrkrid...@inbox.com wrote:
 Hi Michal,

 Because RStudio seems to use its own method of updating you might be better 
 off asking in their forum.

 John Kane
 Kingston ON Canada


 -Original Message-
 From: prgo...@gmail.com
 Sent: Tue, 18 Aug 2015 10:43:20 +0200
 To: r-help@r-project.org
 Subject: [R] How are packages installed with install_github() updated in
 RStudio?

 Hallo.

 I use RStudio. Because of a bug in the latest CRAN version of dplyr, I
 installed the GitHub version with install_github(). Now I wonder what
 happens when there is a new version. Does RStudio update the packages
 installed from GitHub? If so, does it replace it with the new CRAN
 version,
 or a new GitHub version?

 Many thanks for you answer,
 Michal Kvasnicka

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Re: [R] writing binary data from RCurl and postForm

[Hadley Wickham]

 I think that is because the value returned from postForm has an attribute;
 remove it by casting the return to a vector

   fl - tempfile(fileext=.pdf)
   writeBin(as.vector(postForm(url, binary=TRUE)), fl)


 The httr package might also be a good bet

   writeBin(content(POST(url)), fl)

Or write response directly to disk with

POST(url, write_disk(fl))

Hadley

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Re: [R] dplyr and function length()

[Hadley Wickham]

 No, the effect I described has nothing to do wit USING dplyr. It occurs with
 any (preexisting) data.frame once dplyr is LOADED (require(dplyr). It is
 this silent, sort of backward acting effect that disturbs me.

You're going to need to provide some evidence for that charge: dplyr
does not affect the behaviour of data.frames (only tbl_dfs)

Hadley

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Re: [R] dplyr and function length()

[Hadley Wickham]

 length(df[,1]).

 Both commands will return n.

 However, once dplyr is loaded,

 length(df[,1]) will return a value of 1.

 length(df$m1) and also length(df[[1]]) will correctly return n.

 I know that using length() may not be the most elegant or efficient way to 
 get the value of n. However, what puzzles (and somewhat disturbs) me is that 
 loading of dplyr affects how length() works, without there being a warning 
 or masking message upon loading it.

 Any clarification or comment would be welcome.

 Presumably, dplyr changes how [.data.frame works (by altering the default for 
 drop=, I expect) so that df[,1] is a data frame with 1 variable and not a 
 vector. And yes, that _is_ somewhat disturbing.

It changes the behaviour for [.tbl_df (tbl_df is a very minor
extension of data frame with custom [ and print methods).  This is
partly an experiment to see what happens when you make [ more
consistent - [.tbl_df always returns a data frame, so if you want a
vector you have to use [[.

Hadley

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Re: [R] attributes in dplyr and haven

[Hadley Wickham]

Install the latest version of dplyr? Should be fixed there.
Hadley

On Tue, Aug 4, 2015 at 9:40 AM, Conklin, Mike (GfK)
mike.conk...@gfk.com wrote:
 I read in spss files using haven's read_spss. Each column then gets 
 attributes assigned named
 label - a long description of the variable
 class - labelled
 labels --- answer labels i.e. 1=Male, 2=Female
  example -
 attributes(KPTV[[3]])
 $label
 [1] DERIVED: Survey language

 $class
 [1] labelled

 $labels
 English Spanish
   1   2

 However, if I subset the data.frame  e.g. MassTV-KPTV[row selection logic,] 
 the label attribute disappears

 attributes(MassTV[[3]])
 $labels
 English Spanish
   1   2

 $class
 [1] labelled

 If I use dplyr to filter the data I simply get an ERROR that the label 
 attribute is not supported.

 MassTV-filter(KPTV,KPTV$MNO %in% KPMass$`KPMain$mno`)
 Error: column 'MNO' of type numeric has unsupported attributes: label

 Any ideas on how I can preserve the label attribute (i.e. the long 
 description of the variable name?)

 Thanks for any help,

 Mike

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 Marketing  Data Sciences - North America
 GfK | 8401 Golden Valley Road | Minneapolis | MN | 55427
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Re: [R] ggplot2 - geom_text() with date as x-axis

[Hadley Wickham]

I'm a bit confused what you're trying to accomplish - the mix of
annotate() and geom_text() is confusing. The following code works for
me, and I think might be what you want:

ggplot(ins, aes(td, glucose)) +
  geom_point(colour = red) +
  geom_line(colour = blue) +
  annotate(text, x = texdat, y = 500, label = Glucose, cex = 3)

Hadley

On Thu, Jul 30, 2015 at 10:23 AM, John Kane jrkrid...@inbox.com wrote:
 I am trying to annotate a graph using geom_text() and I seem to be 
 misunderstanding how to use a date in the co-ordinates---or, at least, I 
 think that is the problem. Code is below.

 Can anyone give me a suggestion of where I am going wrong?

 Thanks,
 John

 John Kane
 Kingston ON Canada
 ###===
 ibrary(ggplot2)
 library(lubridate)
 ins  -  structure(list(td = structure(c(1437804720, 1437824100, 1437836220,
 1437851580, 1437863460, 1437878640, 1437890640, 1437904800, 1437918240,
 1437926100, 1437941340, 1437951240), tzone = UTC, class = c(POSIXct,
 POSIXt)), glucose = c(328L, 390L, 358L, 387L, 440L, 328L, 365L,
 450L, 467L, 477L, 408L, 457L), dose = c(NA, 0.5, NA, NA, 0.5,
 NA, NA, 0.5, NA, NA, NA, 0.5)), .Names = c(td, glucose, dose
 ), row.names = c(NA, -12L), class = data.frame)

 anon  - na.omit(ins)  # extract shots

 texdat =  ymd_hm(2015-07-26 20:09)

 glucose  -  ggplot(ins, aes(td, glucose)) + geom_point(colour = red) + 
 geom_line(colour = blue)
 p1  -  glucose + annotate(text, x = texdat, y = 500, label = anon[ ,3 ], 
 cex = 3)
 p1

 # Now the problem
  p2  -  p1 +  geom_text(x = texdat, y = 400 , size = 2,  label= Glucose)
 p2
 ###=

 
 FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks  orcas on your 
 desktop!

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Re: [R] ggplot2 - Specifying Colors Manually

[Hadley Wickham]

Try this:

ggplot(mydf,aes(x)) +
  geom_line(aes(y = y1, colour = y1)) +
  geom_line(aes(y = y2, colour = y2))  +
  scale_color_manual(values = c(y1 = green4, y2 = blue2))

Note that you don't need to use `mydf` and names in the manual scale
should match the values in the aes() calls.
Alsoit'smucheasiertoreadyourcodeifyouusespaces;)

Hadley

On Wed, Jul 22, 2015 at 1:13 PM, Abiram Srivatsa avsriva...@gmail.com wrote:
 Hi,

 Given a data frame, I'm trying to graph multiple lines on one graph, each
 line being a different color and each colored line corresponding to a
 specific name in the legend. Here is a very basic data sample to work with:

  x - seq(0,40,10)
  y1 - sample(1:50,5)
  y2 - sample(1:50,5)

  mydf - data.frame(x,y1,y2)

  p - ggplot(mydf,aes(x=mydf$x)) +
 geom_line(aes(y=mydf$y1,colour=green4)) +
 geom_line(aes(y=mydf$y2,colour=blue2))  +

  scale_color_manual(name=legend,values=c(y1=green4,y2=blue2))


  p


 When I run this, the entire plot is blank. What I WANT to show up is two
 lines, one being the color of green4 and the other being blue2. Besides
 that, I'm trying to associate the colors with the names y1 and y2 in
 the legend, but my codes don't seem to be working.

 I'm very new to R/ggplot2, and I really appreciate any and all help I can
 get.

 Thank you!

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Re: [R] For Hadley Wickham: Need for a small fix in haven::read_spss

[Hadley Wickham]

(FWIW this would've been better send to me directly or filed on
github, rather than sent to R-help)

I think this is more of a problem with the way that you're accessing
the info, than the design of the underlying structure. I'd do
something like this:

attr_default - function(x, which, default) {
  val - attr(x, which)
  if (is.null(val)) default else val
}

sapply(spss1, attr_default, label, NA_character_)

(code untested, but you get the idea)

Hadley

On Mon, Jul 20, 2015 at 8:56 AM, Dimitri Liakhovitski
dimitri.liakhovit...@gmail.com wrote:
 Hadley,

 you've added function labelled to haven, which is great. However, when
 it so happens that in SPSS a variable has no long label, your code
 considers it to be NULL rather than an NA. NULL is correct, but NA
 would probably be better.

 For example, I've read in an SPSS file:

 library(haven)
 spss1 - read_spss(SPSS_Example.sav)

 varnames - names(spss1)
 mylabels - unlist(lapply(spss1, attr, label))

 length(varnames)
 [1] 64

 length(mylabels)
 [1] 62


 Because in this particular dataset there were 2 variables without
 either variable labels or data labels.
 When I run lapply(spss1, attr, label) I see under those 2 variables
 NULL - which is true and valid.
 However,  would it be possible to have instead of NULL an NA? This way
 the length of varnames and mylables would the same and one could put
 them side by side (e.g., in one data frame)?


 Thanks a lot!

 --
 Dimitri Liakhovitski

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Re: [R] Trellis Plots: translating lattice xyplot() to ggplot()

[Hadley Wickham]

I'd recommend starting with a simpler .Rmd or .Rnw file, rather than
using it with lyx. The basic .Rmd file below works for me without any
further adjustments:

# Lattice test

```{r}
library(lattice)
xyplot(mpg ~ wt, data = mtcars)
```


Hadley

On Fri, Jul 10, 2015 at 3:39 PM, Rich Shepard rshep...@appl-ecosys.com wrote:
 On Fri, 10 Jul 2015, Hadley Wickham wrote:

 You shouldn't be explicitly opening a device in a knitr document.


 Hadley,

   Didn't think so.

 I think maybe you should post a minimal document so we can figure out
 what's going wrong.


   Agreed. Attached are the raw data (carlin.csv) and a stripped down LyX
 document with the knitr chunks.

   This is my first attempt to use knitr; I'm reading the knitr book and
 that's where I got the impression that lattice graphics are not supported.

 Rich
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Re: [R] Trellis Plots: translating lattice xyplot() to ggplot()

[Hadley Wickham]

Have you tried explicitly print()ing the lattice graphics in your knitr doc?

Hadley

On Friday, July 10, 2015, Rich Shepard rshep...@appl-ecosys.com wrote:

   Hadley's ggplot2 book is quite old and a new version is in the works, but
 not yet out. I've been using lattice graphics but the knitr package doesn't
 support lattice, only basic plots and ggplot2. My Web searches for Trellis
 plots in ggplot2 equivalent to those in lattice have not been productive.

   I would appreciate a pointer to a resource that would teach me how to
 translate from lattice xyplot() to ggplot2 ggplot().

   This is one such plot needing translation:

 xyplot(value ~ sampdate | variable, data=carlin.1.melt, rm.na = T)

 Rich

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Re: [R] Trellis Plots: translating lattice xyplot() to ggplot()

[Hadley Wickham]

You shouldn't be explicitly opening a device in a knitr document. I think
maybe you should post a minimal document so we can figure out what's going
wrong.

Hadley

On Friday, July 10, 2015, Rich Shepard rshep...@appl-ecosys.com wrote:

 On Fri, 10 Jul 2015, Hadley Wickham wrote:

  Have you tried explicitly print()ing the lattice graphics in your knitr
 doc?


 Hadley,

   Only now. Had not thought of trying this before.

 pdf('carlin-1-descriptive.pdf')
 print(xyplot(value ~ sampdate | variable, data=carlin.1.melt, rm.na = T))

 No error messages, but no graphic, either. Without specifying the pdf
 device, TeX complains it cannot find a graphics device and lists
 bit-mapped,
 ps and svg devices.

   Most likely I do not have the correct syntax.

 Thanks,

 Rich

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Re: [R] : Ramanujan and the accuracy of floating point computations - using Rmpfr in R

[Hadley Wickham]

 It doesn’t appear to me that mpfr was ever designed to handle expressions 
 as the first argument.

 This could be a start. Obviously one would wnat to include code to do other 
 substitutions probably using the all.vars function to pull out the other 
 “constants” and ’numeric’ values to make them of equivalent precision. I’m 
 guessing you want to follow the parse-tree and then testing the numbers for 
 integer-ness and then replacing by paste0( “mpfr(“, val, “L, “, prec,”)” )

 Pre - function(expr, prec){ sexpr - deparse(substitute(expr) )

 Why deparse?  That's almost never a good idea.  I can't try your code (I
 don't have mpfr available), but it would be much better to modify the
 expression than the text representation of it.  For example, I think
 your code would modify strings containing pi, or variables with those
 letters in them, etc.  If you used substitute(expr) without the
 deparse(), you could replace the symbol pi with the call to the Const
 function, and be more robust.


 Really? I did try. I was  fairly sure that someone could do better but I 
 don’t see an open path along the lines you suggest. I’m pretty sure I tried 
 `substitute(expr, list(pi= pi))` when `expr` had been the formal argument and 
 got disappointed because there is no `pi` in the expression `expr`. I 
 _thought_ the problem was that `substitute` does not evaluate its first 
 argument, but I do admit to be pretty much of a klutz with this sort of 
 programming. I don’t think you need to have mpfr installed in order to 
 demonstrate this.

You might want to read http://adv-r.had.co.nz/Expressions.html - it's
my best attempt at explaining how to modify call trees in R.

Hadley

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Re: [R] what constitutes a 'complete sentence'?

[Hadley Wickham]

It might be a line break problem - I think you want:

Description: Functions designed to test for single gene/phenotype
association and
for pleiotropy on genetic and genomic data.

Hadley

On Fri, Jul 3, 2015 at 10:09 AM, Federico Calboli
federico.calb...@helsinki.fi wrote:
 Hi All,

 I am upgrading a package for CRAN, and I get this note:

 checking DESCRIPTION meta-information ... NOTE
 Malformed Description field: should contain one or more complete sentences.

 This is puzzling because:

 cat DESCRIPTION

 ...
 Description: Functions designed to test for single gene/phenotype association 
 and for pleiotropy on genetic and genomic data.
 ...

 In my understanding Functions designed to test for single gene/phenotype 
 association and for pleiotropy on genetic and genomic data.” *is* a complete 
 sentence.  So, what is complete sentence in the opinion of whomever coded 
 that check?

 Best

 F

 --
 Federico Calboli
 Ecological Genetics Research Unit
 Department of Biosciences
 PO Box 65 (Biocenter 3, Viikinkaari 1)
 FIN-00014 University of Helsinki
 Finland

 federico.calb...@helsinki.fi

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Re: [R] what constitutes a 'complete sentence'?

[Hadley Wickham]

In that case, you need to create a minimal reproducible example and make it
publicly available.

Hadley

On Friday, July 3, 2015, Federico Calboli federico.calb...@helsinki.fi
wrote:


  On 3 Jul 2015, at 12:14, Hadley Wickham h.wick...@gmail.com
 javascript:; wrote:
 
  It might be a line break problem - I think you want:
 
  Description: Functions designed to test for single gene/phenotype
  association and
 for pleiotropy on genetic and genomic data.

 Tried this and unfortunately it does not help.

 BW

 F


 
  Hadley
 
  On Fri, Jul 3, 2015 at 10:09 AM, Federico Calboli
  federico.calb...@helsinki.fi javascript:; wrote:
  Hi All,
 
  I am upgrading a package for CRAN, and I get this note:
 
  checking DESCRIPTION meta-information ... NOTE
  Malformed Description field: should contain one or more complete
 sentences.
 
  This is puzzling because:
 
  cat DESCRIPTION
 
  ...
  Description: Functions designed to test for single gene/phenotype
 association and for pleiotropy on genetic and genomic data.
  ...
 
  In my understanding Functions designed to test for single
 gene/phenotype association and for pleiotropy on genetic and genomic data.”
 *is* a complete sentence.  So, what is complete sentence in the opinion of
 whomever coded that check?
 
  Best
 
  F
 
  --
  Federico Calboli
  Ecological Genetics Research Unit
  Department of Biosciences
  PO Box 65 (Biocenter 3, Viikinkaari 1)
  FIN-00014 University of Helsinki
  Finland
 
  federico.calb...@helsinki.fi javascript:;
 
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 http://www.R-project.org/posting-guide.html
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 --
 Federico Calboli
 Ecological Genetics Research Unit
 Department of Biosciences
 PO Box 65 (Biocenter 3, Viikinkaari 1)
 FIN-00014 University of Helsinki
 Finland

 federico.calb...@helsinki.fi javascript:;








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Re: [R] dplyr - counting a number of specific values in each column - for all columns at once

[Hadley Wickham]

On Tue, Jun 16, 2015 at 12:24 PM, Dimitri Liakhovitski
dimitri.liakhovit...@gmail.com wrote:
 Hello!

 I have a data frame:

 md - data.frame(a = c(3,5,4,5,3,5), b = c(5,5,5,4,4,1), c = c(1,3,4,3,5,5),
   device = c(1,1,2,2,3,3))
 myvars = c(a, b, c)
 md[2,3] - NA
 md[4,1] - NA
 md

 I want to count number of 5s in each column - by device. I can do it like 
 this:

 library(dplyr)
 group_by(md, device) %%
 summarise(counts.a = sum(a==5, na.rm = T),
   counts.b = sum(b==5, na.rm = T),
   counts.c = sum(c==5, na.rm = T))

 However, in real life I'll have tons of variables (the length of
 'myvars' can be very large) - so that I can't specify those counts.a,
 counts.b, etc. manually - dozens of times.

 Does dplyr allow to run the count of 5s on all 'myvars' columns at once?

md %%
  group_by(device) %%
  summarise_each(funs(sum(. == 5, na.rm = TRUE)))

Hadley

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Re: [R] Problem with particular file in XML package?

[Hadley Wickham]

I have also seen this problem on a student's windows machine (with R
3.2.0 and on multiple mirrors). It appeared that the package zip
itself was being corrupted (with an error to the tune of downloaded
file size does not agree with actual file size). The most likely
explanation that I could come up with was that a virus checker was
hitting a false positive and mangling the zip file.

Hadley

On Thu, May 28, 2015 at 1:38 AM, Prof Brian Ripley
rip...@stats.ox.ac.uk wrote:
 This really should have been sent to the package maintainer.  But that the
 zip file is corrupt has been reported several times, and does not block
 installation for anyone else, so your (plural) diagnosis is wrong.


 On 28/05/2015 03:56, Gen wrote:

 I have been attempting to install the R devtools package at work.  The
 version of R is 3.1.2 (Pumpkin Helmet).  However, the installation of
 devtools fails because devtools depends on rversions which in turn depends
 upon the XML package (XML_3.98-1.1.tar.gz), and the XML package is not
 importing correctly for us.

 One of our system administrators tried scanning through the files in the
 XML package, and he said that the particular file:
 /src/contrib/XML_3.98-1.1.tar.gz/XML/inst/exampleData/dtd.zip looks
 corrupted.  The actual error message he received was: Archive parsing
 failed!  (Data is corrupted).  For the record, I tried downloading an
 older version of the XML package (XML_3.95-0.1.tar.gz) but that was also
 without success -- this time there was a separate error message about not
 being able to locate xml2-config.  (Perhaps XML_3.95-0.1.tar.gz is just
 not
 compatible with R version 3.1.2?)

 I tried browsing over to the CRAN checks link for the XML package and
 noticed several red warning messages under the Status column -- not sure
 if that is typical?  Has anyone else had trouble with the XML package
 lately and if so, how did you resolve it?  Would it be possible to remove
 the potentially corrupted file and then re-upload the package source
 XML_3.98-1.1.tar.gz to the CRAN webpage?  Thanks for your
 help/suggestions!

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Re: [R] Rtools 3.3 is not compatible with R 3.2.0.?

[Hadley Wickham]

It's been fixed in the dev version, and I'm planning on submitting to
CRAN in the near future.
Hadley

On Tue, Apr 21, 2015 at 6:01 PM, Shi, Tao shida...@yahoo.com wrote:
 hi list,

 Any updates on this issue?  Thank you very much!

 Tao


 devtools::install_github(rstudio/packrat)
 WARNING: Rtools 3.3 found on the path at c:/Rtools is not compatible with R 
 3.2.0.

 Please download and install Rtools 3.1 from 
 http://cran.r-project.org/bin/windows/Rtools/, remove the incompatible 
 version from your PATH, then run find_rtools().
 Downloading github repo rstudio/packrat@master
 Installing packrat
 C:/PROGRA~1/R/R-32~1.0/bin/x64/R --vanilla CMD INSTALL  \
 C:/Users/tshi/AppData/Local/Temp/Rtmp6VYlhX/devtools25dc273e706c/rstudio-packrat-42b76ad
  --library=C:/Program Files/R/R-3.2.0/library  \
 --install-tests

 * installing *source* package 'packrat' ...
 ** R
 ** inst
 ** tests
 ** preparing package for lazy loading
 ** help
 *** installing help indices
 ** building package indices
 ** testing if installed package can be loaded
 * DONE (packrat)

 find_rtools()
 WARNING: Rtools 3.3 found on the path at c:/Rtools is not compatible with R 
 3.2.0.

 Please download and install Rtools 3.1 from 
 http://cran.r-project.org/bin/windows/Rtools/, remove the incompatible 
 version from your PATH, then run find_rtools().

 sessionInfo()
 R version 3.2.0 (2015-04-16)
 Platform: x86_64-w64-mingw32/x64 (64-bit)
 Running under: Windows 7 x64 (build 7601) Service Pack 1

 locale:
 [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United 
 States.1252LC_MONETARY=English_United States.1252
 [4] LC_NUMERIC=C   LC_TIME=English_United States.1252

 attached base packages:
 [1] stats graphics  grDevices utils datasets  methods   base

 other attached packages:
 [1] devtools_1.7.0   packrat_0.4.3-19

 loaded via a namespace (and not attached):
 [1] httr_0.6.1 tools_3.2.0RCurl_1.95-4.5 stringr_0.6.2  bitops_1.0-6



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Re: [R] library(xlsx) fails with an error: Error: package ‘rJava’ could not be loaded

[Hadley Wickham]

You might want to try readxl instead, as it doesn't have any external
dependencies.
Hadley

On Sat, Apr 18, 2015 at 3:07 PM, John Sorkin
jsor...@grecc.umaryland.edu wrote:
 Windows 7 64-bit
 R 3.1.3
 RStudio 0.98.1103


 I am having difficulty loading and installing the xlsx package. The
 loading occurred without any problem, however the library command
 library(xlsx) produced an error related to rJava. I tried to install
 rJava seperately, re-loaded the xlsx package, and entered the
 library(xlsx) command but received the same error message about rJave.
 Please see terminal messages below. Any suggestion that would allow me
 to load and run xlsx would be appreciated.
 Thank you,
 John


 install.packages(xlsx)
 Installing package into ‘C:/Users/John/Documents/R/win-library/3.1’
 (as ‘lib’ is unspecified)
 trying URL
 'http://cran.rstudio.com/bin/windows/contrib/3.1/xlsx_0.5.7.zip'
 Content type 'application/zip' length 400944 bytes (391 KB)
 opened URL
 downloaded 391 KB


 package ‘xlsx’ successfully unpacked and MD5 sums checked


 The downloaded binary packages are in
 C:\Users\John\AppData\Local\Temp\Rtmp4CO5m7\downloaded_packages
 library(xlsx)
 Loading required package: rJava
 Error : .onLoad failed in loadNamespace() for 'rJava', details:
   call: inDL(x, as.logical(local), as.logical(now), ...)
   error: unable to load shared object
 'C:/Users/John/Documents/R/win-library/3.1/rJava/libs/x64/rJava.dll':
   LoadLibrary failure:  The specified module could not be found.


 Error: package ‘rJava’ could not be loaded
 install.packages(rJava)
 Installing package into ‘C:/Users/John/Documents/R/win-library/3.1’
 (as ‘lib’ is unspecified)
 trying URL
 'http://cran.rstudio.com/bin/windows/contrib/3.1/rJava_0.9-6.zip'
 Content type 'application/zip' length 759396 bytes (741 KB)
 opened URL
 downloaded 741 KB


 package ‘rJava’ successfully unpacked and MD5 sums checked


 The downloaded binary packages are in
 C:\Users\John\AppData\Local\Temp\Rtmp4CO5m7\downloaded_packages
 library(rJava)
 Error : .onLoad failed in loadNamespace() for 'rJava', details:
   call: inDL(x, as.logical(local), as.logical(now), ...)
   error: unable to load shared object
 'C:/Users/John/Documents/R/win-library/3.1/rJava/libs/x64/rJava.dll':
   LoadLibrary failure:  The specified module could not be found.


 Error: package or namespace load failed for ‘rJava’
 library(xlsx)
 Loading required package: rJava
 Error : .onLoad failed in loadNamespace() for 'rJava', details:
   call: inDL(x, as.logical(local), as.logical(now), ...)
   error: unable to load shared object
 'C:/Users/John/Documents/R/win-library/3.1/rJava/libs/x64/rJava.dll':
   LoadLibrary failure:  The specified module could not be found.


 Error: package ‘rJava’ could not be loaded


 John David Sorkin M.D., Ph.D.
 Professor of Medicine
 Chief, Biostatistics and Informatics
 University of Maryland School of Medicine Division of Gerontology and
 Geriatric Medicine
 Baltimore VA Medical Center
 10 North Greene Street
 GRECC (BT/18/GR)
 Baltimore, MD 21201-1524
 (Phone) 410-605-7119
 (Fax) 410-605-7913 (Please call phone number above prior to faxing)


 Confidentiality Statement:
 This email message, including any attachments, is for ...{{dropped:17}}

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Re: [R] misbehavior with extract_numeric() from tidyr

[Hadley Wickham]

On Mon, Apr 20, 2015 at 1:57 PM, arnaud gaboury
arnaud.gabo...@gmail.com wrote:
 On Mon, Apr 20, 2015 at 6:09 PM, William Dunlap wdun...@tibco.com wrote:

 The hyphen without a following digit confuses tidyr::extract_numeric().
 E.g.,
 extract_numeric(23 ft-lbs)
Warning message:
In extract_numeric(23 ft-lbs) : NAs introduced by coercion
[1] NA
 extract_numeric(23 ft*lbs)
[1] 23


 See[0] for the reason on the minus in the regex. It is not a bug but a wish.
 I am honestly very surprised the maintainer decided to go with such a so
 simple solution for negative numbers.

 [0]https://github.com/hadley/tidyr/issues/20

Any heuristic is going to fail in some circumstances. If you want to
be sure it's doing what you want for your use case, write the regular
expression yourself.

Hadley

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Re: [R] open xlsx file using read.xls function of gdata package

[Hadley Wickham]

You might try the readxl package - it's only available on github but it
reads both xlsx and xls. All going well, it should be on its way to CRAN
next week.

Hadley

On Friday, April 3, 2015, Luigi Marongiu marongiu.lu...@gmail.com wrote:

 Dear all,
 I am trying to open excel files using the gdata package. I can do that
 using a .xls file, but the same file, containing the same data,
 formatted in .xlsx gives error (R does not recognize the pattern from
 where to start reading the data).
 Doen anybody knows whether it is possible to read .xlslx with this package?
 Am I missing another package to implement the reading of the .xlsx?
 Thank you
 Luigi

 PS: this is the error I get:
  my.file - array.xlsx
  my.data-read.xls(
 +   my.file,
 +   sheet=sheet x,
 +   verbose=FALSE,
 +   pattern=row name,
 +   na.strings=c(NA,#DIV/0!),
 +   method=tab,
 +   perl=perl
 + )
  Warning message:
 In read.xls(my.file, sheet = sheet x, verbose = FALSE,  :
   pattern not found


 The verbose version runs like this:
 “array.xlsx”
 to tab  file
 “/tmp/Rtmp2tAjzz/filef06102dd018.tab”
 ...

 Executing ' '/usr/bin/perl'
 '/home/gigiux/R/x86_64-pc-linux-gnu-library/3.0/gdata/perl/xls2tab.pl'
  'array.xlsx' '/tmp/Rtmp2tAjzz/filef06102dd018.tab' 'sheet x' '...

 Loading 'array.xlsx'...
 Done.

 Orignal Filename: array.xlsx
 Number of Sheets: 2

 Writing sheet 'sheet x' to file '/tmp/Rtmp2tAjzz/filef06102dd018.tab'
 Minrow=31 Maxrow=17310 Mincol=0 Maxcol=4
   (Ignored 0 blank lines.)

 0

 Done.

 Searching for lines tfntaining pattern  row name ...
 Warning message:
 In read.xls(my.file, sheet = sheet x, verbose = TRUE,  :
   pattern not found
 

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Re: [R] idiom for constructing data frame

[Hadley Wickham]

On Tue, Mar 31, 2015 at 6:42 PM, Sarah Goslee sarah.gos...@gmail.com wrote:
 On Tue, Mar 31, 2015 at 6:35 PM, Richard M. Heiberger r...@temple.edu wrote:
 I got rid of the extra column.

 data.frame(r=seq(8), foo=NA, bar=NA, row.names=r)

 Brilliant!

 After much fussing, including a disturbing detour into nested lapply
 statements from which I barely emerged with my sanity (arguable, I
 suppose), here is a one-liner that creates a data frame of arbitrary
 number of rows given an existing data frame as template for column
 number and name:


 n - 8
 df1 - data.frame(A=runif(9), B=runif(9))

 do.call(data.frame, setNames(c(list(seq(n), r), as.list(rep(NA,
 ncol(df1, c(r, row.names, colnames(df1

 It's not elegant, but it is fairly R-ish. I should probably stop
 hunting for an elegant solution now.

Given a template df, you can create a new df with subsetting:

df2 - df1[rep(NA_real_, 8), ]
rownames(df2) - NULL
df2

This has the added benefit of preserving the types.

Hadley

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Re: [R] Using and abusing %% (was Re: Why can't I access this type?)

[Hadley Wickham]

 I didn't dispute whether '%%' may be useful -- I just pointed out that it
 is slow.  However, it is only part of the problem: 'filter()' and
 'select()', although aesthetically pleasing, also seem to be slow:

 all.states - data.frame(state.x77, Name = rownames(state.x77))

 f1 - function()
 + all.states[all.states$Frost  150, c(Name, Frost)]

 f2 - function()
 + subset(all.states, Frost  150, select = c(Name, Frost))

 f3 - function() {
 + filt - subset(all.states, Frost  150)
 + subset(filt, select = c(Name, Frost))
 + }

 f4 - function()
 + all.states %% subset(Frost  150) %%
 + subset(select = c(Name, Frost))

 f5 - function()
 + select(filter(all.states, Frost  150), Name, Frost)

 f6 - function()
 + all.states %% filter(Frost  150) %% select(Name, Frost)

 mb - microbenchmark(
 + f1(), f2(), f3(), f4(), f5(), f6(),
 + times = 1000L
 + )
 print(mb, signif = 3L)
 Unit: microseconds
  expr min   lq  mean median   uq  max neval   cld
  f1() 115  124  134.8812129  134 1500  1000 a
  f2() 128  141  147.4694145  151 1520  1000 a
  f3() 303  328  344.3175338  348 1740  1000  b
  f4() 458  494  518.0830510  523 1890  1000   c
  f5() 806  848  887.7270875  894 3510  1000d
  f6() 971 1010 1056.5659   1040 1060 3110  1000 e

 So, using '%%', but leaving 'filter()' and 'select()' out of the equation,
 as in 'f4()' is only half as bad as the full 'dplyr' idiom in 'f6()'.  In
 this case, since we're talking microseconds, the speed-up is negligible but
 that *is* beside the point.

When benchmarking it's important to consider both the relative and
absolute difference and to think about how the cost scales as the data
grows - the cost of using using %% is fixed, and 500 µs doesn't seem
like a huge performance penalty to me.

Hadley

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Re: [R] readHTMLTable() in XML package

[Hadley Wickham]

This somewhat simpler rvest code does the trick for me:

library(rvest)
library(dplyr)

i - 1:10
urls - paste0('http://games.crossfit.com/scores/leaderboard.php?stage=5',
  'sort=0division=1region=0numberperpage=100competition=0frontpage=0',
  'expanded=1year=15full=1showtoggles=0hidedropdowns=0showathleteac=1',
  'is_mobile=0page=', i)

results_table - function(url) {
  url %% html %% html_table(fill = TRUE) %% .[[1]]
}

results - lapply(urls, results_table)
out - results %% bind_rows()

Hadley

On Mon, Mar 2, 2015 at 10:00 AM, Doran, Harold hdo...@air.org wrote:
 I'm having trouble pulling down data from a website with my code below as I 
 keep encountering the same error, but the error occurs on different pages.

 My code below loops through a wensite and grabs data from the html table. The 
 error appears on different pages at different times and I'm not sure of the 
 root cause.

 Error in readHTMLTable(readLines(url), which = 1, header = TRUE) :
   error in evaluating the argument 'doc' in selecting a method for function 
 'readHTMLTable': Error in readHTMLTable(readLines(url), which = 1, header = 
 TRUE) :
   error in evaluating the argument 'doc' in selecting a method for function 
 'readHTMLTable':

 library(XML)
 for(i in 1:1000){
 url - 
 paste(paste('http://games.crossfit.com/scores/leaderboard.php?stage=5sort=0page=',
  i, sep=''), 
 'division=1region=0numberperpage=100competition=0frontpage=0expanded=1year=15full=1showtoggles=0hidedropdowns=0showathleteac=1=is_mobile=0',
  sep='')
 tmp - readHTMLTable(readLines(url), which=1, header=TRUE)
 names(tmp) - gsub(\\n, , names(tmp))
 names(tmp) - gsub( +, , names(tmp))
 tmp[] - lapply(tmp, function(x) gsub(\\n, , x))

 if(i == 1){
 dat - tmp
 } else {
 dat - rbind(dat, tmp)
 }
 cat('Grabbing data from page', i, '\n')
 }

 Thanks,
 Harold

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Re: [R] dplyr: producing a good old data frame

[Hadley Wickham]

Hi John,

Just printing the result gives a good indication where the problem lies:

 frm %% rowwise() %% do(MM=max(as.numeric(.)))
Source: local data frame [6 x 1]
Groups: by row

MM
1 dbl[1]
2 dbl[1]
3 dbl[1]
4 dbl[1]
5 dbl[1]
6 dbl[1]

do() is designed to produce scalars (e.g. a linear model), not
vectors, so it doesn't join the results back into a single vector. You
can either fix this yourself with unlist(), or use tidyr::unnest()
which will also handle vectors with length  1.

Hadley

On Mon, Feb 23, 2015 at 2:54 PM, John Posner john.pos...@mjbiostat.com wrote:
 I'm using the dplyr package to perform one-row-at-a-time processing of a data 
 frame:

 rnd6 = function() sample(1:300, 6)
 frm = data.frame(AA=rnd6(), BB=rnd6(), CC=rnd6())

 frm
AA  BB  CC
 1 123  50  45
 2  12  30 231
 3 127 147 100
 4 133  32 129
 5  66 235  71
 6  38 264 261

 The interface is nice and straightforward:

 library(dplyr)
 dplyr_result = frm %% rowwise() %% do(MM=max(as.numeric(.)))

 I've gotten used to the fact that dplyr_result is not a good old vanilla 
 data frame. The as.data.frame() function *seems* to do the trick:

 dplyr_result_2 = as.data.frame(dplyr_result)
 dplyr_result_2
MM
 1 123
 2 231
 3 147
 4 133
 5 235
 6 264

 ... but there's trouble ahead:

 mean(dplyr_result_2$MM)
 [1] NA
 Warning message:
 In mean.default(dplyr_result_2$MM) :
   argument is not numeric or logical: returning NA

 I need to enlist unlist() to get me to my destination:

 mean(unlist(dplyr_result_2$MM))
 [1] 188.8333

 [NOTE: dplyr's as_data_frame() function does a better job than 
 as.data.frame() of indicating that I was headed for trouble. ]

 By contrast, the plyr package's adply() function *does* produce a vanilla 
 data frame:

   library(plyr)
 plyr_result = adply(frm, .margins=1, function(onerowfrm) 
 max(as.numeric(onerowfrm[1,])))
 mean(plyr_result$V1)
 [1] 188.8333

 Is there a good reason for dplyr to require the extra processing? My (naïve 
 ?) recommendation would be to have as_data_frame() produce a vanilla data 
 frame.

 Tx,
 John

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Re: [R] %%

[Hadley Wickham]

On Tue, Feb 17, 2015 at 6:02 PM, Hervé Pagès hpa...@fredhutch.org wrote:
 On 02/17/2015 02:10 PM, Erich Neuwirth wrote:

 AFAIK dplyr imports magrtittr.
 So dplyr ses %% from migrittr, it does not have its own version.

 But it has its own man page so who knows?

If you import and re-export a function from another package, you have
to document it, even if it's already documented elsewhere.

Hadley

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Re: [R] Shiny User Group

[Hadley Wickham]

Maybe https://groups.google.com/forum/#!forum/shiny-discuss ?

Hadley

On Thu, Feb 12, 2015 at 9:07 AM, Doran, Harold hdo...@air.org wrote:
 I found a google user group for shiny, and am curious if there is an SIG as 
 well. Didn't see one in my searches, but looking for an active place to ask 
 questions and share code.

 Thanks.

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Re: [R] Package build help

[Hadley Wickham]

On Sun, Feb 8, 2015 at 5:15 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote:
 On 08/02/2015 4:06 PM, Glenn Schultz wrote:
 Hello All,

 I am in the final stages of building my first package BondLab and the 
 check throughs the following warning.  I think this is namespace thing.  I 
 have not done anything with the namespace at this point.  I am turning my 
 attention to the namespace now.  Am I correct this can be a handled by the 
 namespace?


 I would guess you have imported the lubridate and plyr packages, and
 also defined your own duration() and here() functions, hiding theirs.

You can also see this problem if you have

import(plyr)
import(plyr, here)

etc.

Or with

import(plyr)
import(lubridate)

since I think both provide a here() function.

Hadley

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Re: [R] Passing a Data Frame Name as a Variable in a Function

[Hadley Wickham]

On Thu, Jan 29, 2015 at 11:43 AM, Alan Yong alany...@caltech.edu wrote:
 Much thanks to everyone for their recommendations!  I agree that fishing in 
 the global environment isn't ideal  only shows my budding understanding of R.

 For now, I will adapt Chel Hee's length(eval(parse(text=DFName))[,1]) 
 solution then fully explore Jeff's suggestion to put the data frames into a 
 list.

If you have to go down this route, at least do nrow(get(DFName))

 (1) Add a column to each data frame with a string that is parsed from the 
 appendage of the data frame name, i.e., string is 1001 from data frame 
 object of df.1001; then,
 (2) Bind the rows of all the files.

I'd highly recommend learning a little functional programming such as
the use of lapply (e.g. http://adv-r.had.co.nz/Functionals.html).
Then you can easily do:

csvs - dir(pattern = \\.csv$)
all - lapply(csvs, read.csv)
one - do.call(rbind, all)

to find all the csv files in a directory, load into a list and then
collapse into a single data frame.

You're much better off learning how to do this than futzing around
with named objects in the global environment.

Hadley

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Re: [R] Latest version of Rtools is incompatible with latest version of R !!

[Hadley Wickham]

 Funnily, this problem disappears when I use RTools31.exe. And, I am not the 
 only one facing this issue. A lot of people in my group (in which we all are 
 learning R) are facing the same problem. I am really puzzled as to why 
 RTools32.exe isn't compatible with R 3.1.2 !!
 Thanks again for your time !!Prameet

 You are asking the wrong question.  You should be asking why devtools
 says that Rtools 3.2 is incompatible.

Yes, that was my fault - I hadn't updated devtool's list of Rtools
versions to tell it about 3.2.

I've fixed it in the dev version which can be installed by following
the instructions at
https://github.com/hadley/devtools#updating-to-the-latest-version-of-devtools
 (I'd appreciate it if someone could try this out and let me know if
it doesn't work)

Hadley

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Re: [R] stringr::str_split_fixed query

[Hadley Wickham]

FWIW this is fixed in the dev version of stringr which uses stringi
under the hood:

 stringr::str_split_fixed('ab','',2)
 [,1] [,2]
[1,] a  b
 stringr::str_split_fixed('ab','',3)
 [,1] [,2] [,3]
[1,] a  b  

Hadley

On Wed, Jan 14, 2015 at 12:47 PM, David Barron dnbar...@gmail.com wrote:
 I'm puzzled as to why I get this behaviour with str_split_fixed in the
 stringr package.

 stringr::str_split_fixed('ab','',2)
  [,1] [,2]
 [1,]ab

 stringr::str_split_fixed('ab','',3)
  [,1] [,2] [,3]
 [1,]a  b

 In the first example, I was expecting to get
  [,1] [,2]
 [1,] a   b

 Can someone explain?

 Thanks,
 David

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