Re: [R] Error with Source()
Normally is a missing comma in a function command list. Ciao! mario On 10-Nov-11 19:02, jim holtman wrote: You have a syntax error in your script. Take a look around line 884 On Thu, Nov 10, 2011 at 9:27 AM, ftoninif_ton...@hotmail.com wrote: Hi everybody, I started to receive a weird message in R that I have never seen before...also I haven't found anything on google or on this forum about it. Whenever I use the command source(...) to point to one of my scripts, I get the following message: Error in source(myfunctions.R) : myfunctions.R:884:9: unexpected symbol 883: 884: cond ^ I am using the same commands as I did in the past and it was working...I started to receive this error (not sure if it has to do with it or not) after trying to create a batch file to run one of my .R scripts with double-click. That batch file worked...but as soon as I use the source() command it does not work any more. Any help is appreciated! Thanks Francesco -- View this message in context: http://r.789695.n4.nabble.com/Error-with-Source-tp4023794p4023794.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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. -- Ing. Mario Valle Data Analysis and Visualization Group| http://www.cscs.ch/~mvalle Swiss National Supercomputing Centre (CSCS) | Tel: +41 (91) 610.82.60 v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82 __ R-help@r-project.org mailing list 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.
Re: [R] proportional area venn diagrams?
On 11/12/2011 01:26 AM, Michael Friendly wrote: In http://finzi.psych.upenn.edu/R/Rhelp02a/archive/14637.html some rudimentary R functions were given for drawing proportional area venn diagrams with area of each intersection ~ the count in a 2 x 2 x 2 table. I'm interested in this, for another application: showing the correlations among Y, X1, X2 using area ~ r^2 of each pair (sometimes called a Ballantine diagram). Before I attempt to hack the code given in that post, are there any packages/functions that do venn diagrams with proportional areas? Rseek turned up quite a view venn-like functions, but I couldn't find any that drew them with proportional areas. Hi Michael, The intersectDiagram function (plotrix) does not draw a Venn diagram, but it does display areas proportional to the number of elements in each intersection. It can also do partial diagrams using the new include argument once the original diagram has been displayed, allowing the user to explore the effect of removing sets or attributes from the diagram. Jim __ R-help@r-project.org mailing list 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.
Re: [R] Second-order effect in Parametric Survival Analysis
On Nov 13, 2011, at 12:51 AM, ryusuke wrote: Thank you Dr. David. I try to summarize it. Assumes x and z are two covariates: x = dummy variable (1 or 0) z = factors (people name) x*z = x + z + x*z Actually I said = x + z + x:z And interaction formula of a two level dummy with a multi-level factor would produce and intercept (which would be for the first person's name), a coefficient for each of other names at level zero, a dummy coefficient (for the first person), and interaction coefficients of each person at the 1-level. therefore this is not a 2nd-order interactions, it should be (for an exponential survival regression):- h(t|(X=x,Z=z)) = exp(Beta0 + XZBeta1) If Beta1 is not a vector in this instance, with a distinct value for each(x,z) pairing, then I am unable to make sense out of that model. The questin remains however whether you are also expecting Beta0 to also be distinct for each specific combination of covariates. #--- I believe there is no 2nd-order interactions survival regression as I searched over www.rseek.org. While I tried to read through the codes of survreg(), I stuck (cannot understand) at survreg6.c survreg6.c apply C Language which involves Cholesky decomposition multi-matrix (first-order interactions) calculation. 1) chinv2.c 2) cholesky3.c 3) chsolve2.c (only solve the equations of first-order interactions) That level of implementation should be addressed to a person with higher levels of knowledge: Therneau or Lumley are the two names that immediately come to mind. If someone gives some idea or suggestion on these? Thank you. Best, Ryusuke -- View this message in context: http://r.789695.n4.nabble.com/Second-order-effect-in-Parametric-Survival-Analysis-tp4034318p4036005.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list 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.
Re: [R] identify duplicate from more than one column
On Nov 13, 2011, at 1:19 AM, Joshua Wiley wrote:
Hi Carlos,
Here is one option:
## read in your data
dat - read.table(textConnection(
obs unithome zsex age
1 015029 18 11 053
2 015029 18 12 049
3 015029 01 11 038
4 015029 01 12 033
5 015029 02 11 036
6 015029 02 12 033
7 015029 03 11 023
8 015029 03 12 019
9 015029 04 12 045
10 015029 05 12 047),
header = TRUE, stringsAsFactors = FALSE)
closeAllConnections()
## create a unique ID for matching unit and home
I would have used the 'interaction' function. And I would have read
the data in with colClasses to preserve the labeling of the household
information:
dat - read.table(textConnection(
+ obs unithome zsex age
+ 1 015029 18 11 053
+ 2 015029 18 12 049
+ 3 015029 01 11 038
+ 4 015029 01 12 033
+ 5 015029 02 11 036
+ 6 015029 02 12 033
+ 7 015029 03 11 023
+ 8 015029 03 12 019
+ 9 015029 04 12 045
+ 10 015029 05 12 047),
+ header = TRUE, stringsAsFactors = FALSE, colClasses=c(rep(factor,
4), numeric))
closeAllConnections()
## create a unique ID for matching unit and home
dat
obs unit home z sex age
11 015029 18 1 1 053
22 015029 18 1 2 049
33 015029 01 1 1 038
44 015029 01 1 2 033
55 015029 02 1 1 036
66 015029 02 1 2 033
77 015029 03 1 1 023
88 015029 03 1 2 019
99 015029 04 1 2 045
10 10 015029 05 1 2 047
dat$together - with(dat, interaction(unit, home) )
dat$togeth.n - as.numeric(dat$together)
dat
obs unit home z sex age together togeth.n
11 015029 18 1 1 053 015029.186
22 015029 18 1 2 049 015029.186
33 015029 01 1 1 038 015029.011
44 015029 01 1 2 033 015029.011
55 015029 02 1 1 036 015029.022
66 015029 02 1 2 033 015029.022
77 015029 03 1 1 023 015029.033
88 015029 03 1 2 019 015029.033
99 015029 04 1 2 045 015029.044
10 10 015029 05 1 2 047 015029.055
I'm assuming that the numbering of the unit/household pairings is
somewhat arbitrary. The I would set to missing all of the non-couple
households:
is.na(dat$togett.n) - !as.logical( ave(dat$sex, dat$together,
FUN=function(x) 1 %in% x 2 %in% x) )
dat
obs unit home z sex age together togett.n
11 015029 18 1 1 053 015029.186
22 015029 18 1 2 049 015029.186
33 015029 01 1 1 038 015029.011
44 015029 01 1 2 033 015029.011
55 015029 02 1 1 036 015029.022
66 015029 02 1 2 033 015029.022
77 015029 03 1 1 023 015029.033
88 015029 03 1 2 019 015029.033
99 015029 04 1 2 045 015029.04 NA
10 10 015029 05 1 2 047 015029.05 NA
I actually think it would be better to use the fully labeled
together variable rather than the numeric version. It retains its
data heritage better.
--
David.
dat$mID - with(dat, paste(unit, home, sep = ''))
## somewhat messy way of creating a couple number
## for each mID, if there is more than 1 row, and more than 1 sex
## it creates a couple id, otherwise 0
i - 0L
dat$couple - with(dat, unlist(lapply(split(sex, mID), function(x) {
i - i + 1L
if (length(x) 1 length(unique(x)) 1) {
rep(i, length(x))
} else 0L
})))
## view results
dat
obs unit home z sex age mID couple
11 15029 18 1 1 53 1502918 1
22 15029 18 1 2 49 1502918 1
33 150291 1 1 38 150291 2
44 150291 1 2 33 150291 2
55 150292 1 1 36 150292 3
66 150292 1 2 33 150292 3
77 150293 1 1 23 150293 4
88 150293 1 2 19 150293 4
99 150294 1 2 45 150294 0
10 10 150295 1 2 47 150295 0
See these functions for more details:
?ave # where I got my idea
?split
?lapply
?`-`
Cheers,
Josh
On Sat, Nov 12, 2011 at 8:16 PM, jour4life jour4l...@gmail.com
wrote:
Hi all,
I've searched everywhere to try to find out how to do this and have
had no
luck. I am trying to construct identifiers for couples in a dataset.
Essentially, I want to identify couples using more than one column as
identifiers. Take for instance:
obs
Re: [R] LOESS function Newton optimization
On Jul 12, 2011, at 7:53 PM, KenjiPsyD wrote: I have a question about running an optimization function on an existing LOESS function defined in R. I have a very large dataset (1 million observations) and have run a LOESS regression. Now, I want to run a Newton-Raphson optimization to determine the point at which the slope change is the greatest. I am relatively new to R and have tried several permutations of the maxNR and nlm functions with no success. For example, I used the nlm function as follows: LOESS - loess(Y ~ X) optim - nlm(function(x) LOESS(x))... I don't see how that would be examining slopes. However, this doesn't seem to work. In the examples I see online, the function in nlm and maxNR are user defined, instead of the output of another function (i.e., my LOESS regression). Is it possible to run this type of optimization function on my Loess function? cars.lo - loess(dist ~ speed, cars) is.function( cars.lo) [1] FALSE If you want to make it a function, there is approxfun in the stats package. car.fun - approxfun(x=cars.lo$x, cars.lo$fitted) plot(dist~speed, data=cars) curve(car.fun, add=TRUE) Some functions require that a function be offered that takes x as its argument. car.fun(x=5) Error in car.fun(x = 5) : unused argument(s) (x = 5) If that is the case with your optimization routine then you can create one with: car.funx - function(x) car.fun(x) car.funx(x=5) [1] 8.095681 -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list 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.
Re: [R] dev.new() within a loop
Hello David,
On Nov 13, 2011, at 5:20 AM, David Winsemius wrote:
However, when executing plot_raw which invokes dev.new(..) all windows come
out blank whereas if I execute each file outside of a loop then I can see
the plots properly.
Perhaps ...(you did not say what package this plot_raw function comes from)
... Read the FAQ about why lattice plot don't print. (It applies to all grid
based plotting functions.)
plot_raw is my own function which just calls ggplot2. So basically I am not
using Lattice.
What can I do differently to avoid the new windows coming back empty?
Thanks in advance,
Best regards,
Giovanni
plot_raw - function(data,connect=TRUE,y_break=500,y_top=-1,label=) {
dev.new()
title - paste(label, sep=)
if (y_top == -1) {
y_top - max(data$Y)
}
if (!decouple) {
# add fake group
data$Workload - 'All'
}
p -
ggplot(data,aes(x=Time,y=Y,group=Workload,shape=Workload,colour=Workload)) +
geom_point(fill=white, size=3) +
scale_y_continuous(breaks=seq(0,max(data$Y),y_break), limits=c(0, y_top)) +
scale_y_continuous(breaks=seq(0,y_limit_top(data$Y,data$se),
y_break_step(data$Y,data$se)),
limits=c(0, y_limit_top(data$Y,data$se))) +
opts(title=title) + theme_bw() +
scale_x_continuous(breaks=data$Time, labels=as.character(data$Time))
if (connect) {
p + geom_line()
} else {
p
}
}
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error in drawing
Dear all,
Thanks. I will add it to my list. Sincerely, Guy Nason
On 10 Nov 2011, at 04:34, R. Michael Weylandt wrote:
It's not a problem with your data or use of the functions -- rather I
think there's just a little bug in the package (and I've cc'd the
maintainer):
draw.wd leads to a call of draw.default(type = l) which in turn
leads to plot(type = l). However, since draw.default doesn't have a
type argument, it gets taken as part of the special ... operator which
leads to a conflict when it runs into the other type = l in
plot.default that comes from plot(type = l) in draw.default (I hope
that's clear -- the problem is that at the end of the stack,
plot.default gets handed type = l twice).
For now, you can add this code to your script before you use draw and
it should be fine.
draw.wd - function (wd, ...)
{
if (IsEarly(wd)) {
ConvertMessage()
stop()
}
filter - wd$filter
draw.default(filter.number = filter$filter.number, family =
filter$family, ...)
}
Hopefully the maintainer can let us know if I've missed something or
can make a change in the package (it shouldn't be too hard).
Michael
On Wed, Nov 9, 2011 at 9:53 PM, Gyanendra Pokharel
gyanendra.pokha...@gmail.com wrote:
I am sorry Michael, the data lidar is in the pacakge SemiPar.
On Wed, Nov 9, 2011 at 9:46 PM, Gyanendra Pokharel
gyanendra.pokha...@gmail.com wrote:
lidar data is in the package faraway
On Wed, Nov 9, 2011 at 8:50 PM, R. Michael Weylandt
michael.weyla...@gmail.com wrote:
Your code is not reproducible. Where is the lidar data coming from?
Michael
On Wed, Nov 9, 2011 at 2:29 PM, Gyanendra Pokharel
gyanendra.pokha...@gmail.com wrote:
I have got following error in drawing wavelet fitting. can some one
help?
library(faraway)
data(lidar)
newlidar-lidar[c(1:128),]
library(wavethresh)
wds - wd(newlidar$logratio)
draw(wds)
Error in plot.default(x = x, y = zwr, main = main, sub = sub, xlab =
xlab,
:
formal argument type matched by multiple actual arguments
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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.
--
Professor Guy Nason
Head of School
School of Mathematics
University of Bristol
http://www.stats.bris.ac.uk/~magpn
PA: Helen Craven
helen.cra...@bristol.ac.uk, +44 (0) 117 928 7978
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and provide commented, minimal, self-contained, reproducible code.
[R] Indirect references
Hi All, I would like to work with symbols referenced by strings: I would like to manipulate data/symbols referencing to them by the string name of the symbol. An example will be clearer. Let's I get a time series through quantmod getSymbols(GLD) This will create a new symbol GLD with the relevant data. I have tried to rename the column names as follows: colnames(get(GLD)) - c(open, close, low, high, volume, adjusted) will give the following error: Error in colnames(GLD)- c(open, close, low, high, volume, : target of assignment expands to non-language object I am confused as to how to do this. (the intent of this is to maintain a list of tickers in string format and loop through them at ease to do whatever treatment) Thanks for your help, Emmanuel __ R-help@r-project.org mailing list 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.
Re: [R] dev.new() within a loop {SOLVED]
In a private communication this poster has indicated that he
eventually found the answer by Googling the question. (The solution
was as described in the FAQ.)
--
David.
On Nov 13, 2011, at 5:21 AM, Giovanni Azua wrote:
Hello David,
On Nov 13, 2011, at 5:20 AM, David Winsemius wrote:
However, when executing plot_raw which invokes dev.new(..) all
windows come out blank whereas if I execute each file outside of a
loop then I can see the plots properly.
Perhaps ...(you did not say what package this plot_raw function
comes from) ... Read the FAQ about why lattice plot don't print.
(It applies to all grid based plotting functions.)
plot_raw is my own function which just calls ggplot2. So basically I
am not using Lattice.
What can I do differently to avoid the new windows coming back empty?
Thanks in advance,
Best regards,
Giovanni
plot_raw -
function(data,connect=TRUE,y_break=500,y_top=-1,label=) {
dev.new()
title - paste(label, sep=)
if (y_top == -1) {
y_top - max(data$Y)
}
if (!decouple) {
# add fake group
data$Workload - 'All'
}
p -
ggplot
(data,aes(x=Time,y=Y,group=Workload,shape=Workload,colour=Workload)) +
geom_point(fill=white, size=3) +
scale_y_continuous(breaks=seq(0,max(data$Y),y_break), limits=c(0,
y_top)) +
scale_y_continuous(breaks=seq(0,y_limit_top(data$Y,data$se),
y_break_step(data$Y,data$se)),
limits=c(0, y_limit_top(data$Y,data$se))) +
opts(title=title) + theme_bw() +
scale_x_continuous(breaks=data$Time, labels=as.character(data
$Time))
if (connect) {
p + geom_line()
} else {
p
}
}
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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.
David Winsemius, MD
West Hartford, CT
__
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and provide commented, minimal, self-contained, reproducible code.
[R] 2^k experiment generator
Hello, While looking for info on 2^k experimental design and anova I remember I saw somewhere there was a function to generate all the experiments. I can't find the function anymore can anyone suggest? The function takes as input the factors and levels and generates all the experiments. I know I can do it myself using recursion but I want to avoid 1) reinventing the wheel and 2) making mistakes while at it. TIA, Best regards, Giovanni __ R-help@r-project.org mailing list 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.
Re: [R] dev.new() within a loop
On Nov 13, 2011, at 3:23 PM, David Winsemius wrote: Please read both my comments and the FAQ more carefully . You are inadequately considering the information that has been offered to you. Ok you wanted to make sure I have to read the FAQ well I didn't have to :) Googling using your suggestion found relevant matches and now it works. Where does this resistance to reading the FAQ come from? It is not resistance, the FAQ is very helpful for basic general questions but it can not cover all details. Sometimes it is very hard to find a specific detailed answer within a general FAQ. I have read the FAQ, what makes you think I didn't before? I just could not find the information I was looking for. I had to wrap the ggplot call within a print for my loop to work which is IMHO one of the most obfuscated use-cases for using print I have bumped into. It is a case of isolating the functional aspects of the plot-construction process from the side-effects of interacting with a graphics device. So every user-defined function that try to plot anything has to be wrapped inside a print just in case it ever gets called from within a loop That is not how I understand it. One reason is so there is an object in the workspace that can be later modified. And I suspect the authors (and I am not one of them) imagined that there may be multiple steps in creation of the object, not all of which should result in a plot appearing if this is being done programatically. This is especially appropriate (it would seem to me) for the ggplot plotting model, which adds a variety of layers to a core object. It is also imagined that you may be sending this object to one of a variety of devices. Ok bottom line is always wrap the plot call whatever it is within a print for the just in case. Cheers, Giovanni __ R-help@r-project.org mailing list 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.
Re: [R] 2^k experiment generator
Check out the Task View on Experimental Design: http://cran.at.r-project.org/web/views/ExperimentalDesign.html but perhaps packages rsm or qualityTools have what you want. Bryan *** Bryan Hanson Professor of Chemistry Biochemistry DePauw University On Nov 13, 2011, at 9:25 AM, Giovanni Azua wrote: Hello, While looking for info on 2^k experimental design and anova I remember I saw somewhere there was a function to generate all the experiments. I can't find the function anymore can anyone suggest? The function takes as input the factors and levels and generates all the experiments. I know I can do it myself using recursion but I want to avoid 1) reinventing the wheel and 2) making mistakes while at it. TIA, Best regards, Giovanni __ R-help@r-project.org mailing list 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 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.
Re: [R] 2^k experiment generator
Never mind, found it, it is the expand.grid function. On Nov 13, 2011, at 3:25 PM, Giovanni Azua wrote: Hello, While looking for info on 2^k experimental design and anova I remember I saw somewhere there was a function to generate all the experiments. I can't find the function anymore can anyone suggest? The function takes as input the factors and levels and generates all the experiments. I know I can do it myself using recursion but I want to avoid 1) reinventing the wheel and 2) making mistakes while at it. TIA, Best regards, Giovanni __ R-help@r-project.org mailing list 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.
Re: [R] Indirect references
On 11-11-13 8:10 AM, Back2Numbers wrote: Hi All, I would like to work with symbols referenced by strings: I would like to manipulate data/symbols referencing to them by the string name of the symbol. An example will be clearer. Let's I get a time series through quantmod getSymbols(GLD) This will create a new symbol GLD with the relevant data. I have tried to rename the column names as follows: colnames(get(GLD))- c(open, close, low, high, volume, adjusted) will give the following error: Error in colnames(GLD)- c(open, close, low, high, volume, : target of assignment expands to non-language object I am confused as to how to do this. The syntax colnames(x) - y is a little misleading. It doesn't really modify the object x, it creates a new object then assigns it to x. You can't assign something to get(GLD), so you get the error. The easiest way to do this is not to try to do what quantmod does. Just create new objects and return them from your function. E.g. obj - GLD x - get(obj) colnames(x) - c(open, close, low, high, volume, adjusted) and now x has the names you want. Duncan Murdoch __ R-help@r-project.org mailing list 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] New PLYR issue
Issue with PLYR.
Now using R 2.14 and this data and plyr command line worked with 2.13
I am also loading the same saved data that worked previously, but now
some issue.
library(plyr)
UNESCO - dget('C:/Carbon-GJ/BZE_ecosys.robj')
df2 - ddply(df, UNESCO, summarise, total_ha = sum(Ha))
*Error in if (empty(.data)) return(.data) :
missing value where TRUE/FALSE needed*
Clueless
Ideas suggestions?
Some change in PLYR?
Bruce
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[R] issue using package sos
Issue with sos package I am now using R 2.14 and the sos package did work with 2.13 library(sos) Loading required package: brew Attaching package: 'sos' The following object(s) are masked from 'package:JGR': installPackages The following object(s) are masked from 'package:utils': library(sos); findFn(random forest) found 253 matches; retrieving 13 pages 2 3 4 5 6 7 8 9 10 11 12 13 ++ the first part looks as it used to int he past...but now I have the follow errors? URL Error no protocol: null/doc/html/packages.html Click OK then another box pops up URL Error unkonwn protocl: c Clicked OK Then the help window opens Top line isted is C:\Documents~\temp\RtmpE3Letk\fileaa2 When I select the other tab packages .. it is blank. As always clueless in Belize, Bruce __ R-help@r-project.org mailing list 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.
Re: [R] dev.new() within a loop
On Nov 13, 2011, at 9:35 AM, Giovanni Azua wrote:
On Nov 13, 2011, at 3:23 PM, David Winsemius wrote:
Please read both my comments and the FAQ more carefully . You are
inadequately considering the information that has been offered to
you.
Ok you wanted to make sure I have to read the FAQ well I didn't
have to :) Googling using your suggestion found relevant matches
and now it works.
Where does this resistance to reading the FAQ come from?
It is not resistance, the FAQ is very helpful for basic general
questions but it can not cover all details. Sometimes it is very
hard to find a specific detailed answer within a general FAQ. I have
read the FAQ, what makes you think I didn't before? I just could not
find the information I was looking for.
I told you which FAQ to read. It's only a few sentences. And it very
specifically and I think clearly covers the problem you asked about. I
do not know why you had to google it if you really did read that
particular FAQ.
I had to wrap the ggplot call within a print for my loop to work
which is IMHO one of the most obfuscated use-cases for using print
I have bumped into.
It is a case of isolating the functional aspects of the plot-
construction process from the side-effects of interacting with a
graphics device.
So every user-defined function that try to plot anything has to be
wrapped inside a print just in case it ever gets called from
within a loop
That is not how I understand it. One reason is so there is an
object in the workspace that can be later modified. And I suspect
the authors (and I am not one of them) imagined that there may be
multiple steps in creation of the object, not all of which should
result in a plot appearing if this is being done programatically.
This is especially appropriate (it would seem to me) for the ggplot
plotting model, which adds a variety of layers to a core object. It
is also imagined that you may be sending this object to one of a
variety of devices.
Ok bottom line is always wrap the plot call whatever it is within a
print for the just in case.
That is true when you are using grid-based graphic. It is going to
return a NULL in the case of base graphics calls.
This is the function:
print.ggplot
function (x, newpage = is.null(vp), vp = NULL, ...)
{
set_last_plot(x)
if (newpage)
grid.newpage()
if (is.null(vp)) {
grid.draw(ggplotGrob(x, ...))
}
else {
if (is.character(vp))
seekViewport(vp)
else pushViewport(vp)
grid.draw(ggplotGrob(x, ...))
upViewport()
}
}
environment: namespace:ggplot2
--
David Winsemius, MD
West Hartford, CT
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and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] Roxygen2: version 2.2
# Roxygen2
The premise of `roxygen2` is simple: describe your functions in
comments next to where their definitions and `roxygen2` will process
your source code and comments to produce R compatible Rd files.
Here's a simple example from the `stringr` package:
#' The length of a string (in characters). #' #' @param
string input character vector #' @return numeric vector giving
number of characters in each element of the #' character vector.
Missing string have missing length. #' @keywords character #'
@seealso \code{\link{nchar}} which this function wraps #' @export
#' @examples #' str_length(letters) #' str_length(c(i,
like, programming, NA)) str_length - function(string) {
string - check_string(string)
nc - nchar(string, allowNA = TRUE) is.na(nc) -
is.na(string) nc }
When you `roxygenise` your package these comments will be
automatically transformed to the Rd file you need to pass `R CMD
check`:
\name{str_length} \alias{str_length} \title{The length of a
string (in characters).} \usage{str_length(string)} \arguments{
\item{string}{input character vector} } \description{
The length of a string (in characters). }
\seealso{\code{\link{nchar}} which this function wraps}
\value{numeric vector giving number of characters in each element of
the character vector. Missing string have missing length.}
\keyword{character} \examples{ str_length(letters)
str_length(c(i, like, programming, NA)) }
roxygen2 2.2
NEW FEATURES
* Package docType will automatically add package alias, if needed. (Fixes #4)
* Data docType will automatically add `datasets` keyword, default usage, and
default format. (Fixes #5). Data docType automatically added to data
objects.
* New `@encoding` tag for manually setting non-ASCII encodings when needed.
(Fixes #7)
BUG FIXES
* `write.description()` now tries much harder to respect
users' original DESCRIPTION field formatting instead of forcibly
re-wrapping certain fields at 60 characters.
* `@details` and `@description` now work correctly
* `@useDynLib` now works correctly:
@useDynLib packageName routine1 routine2
produces
useDynLib(packageName, routine1)
useDynLib(packageName, routine2)
in the NAMESPACE file, instead of separate (wrong) useDynLib statements as
before.
* All namespace import directives now behave in the same way as the export
directives, producing multiple single directives instead one multiple
directive: `@importClassesFrom pkg a b` now produces
`importClassesFrom(pkg, a)` and `importClassesFrom(pkg, b)`
* In example files included with `@example` you can now use infix operators
(e.g. %*%) or other things with %, because they will be preceded by a
backslash in the Rd file. This behaviour was already in place for examples
directly included with `@examples`.
* Aliases are no longer quoted, and % is escaped with a backslash (Fixes #24).
Names also have % escaped (Fixes #50)
* Replacement functions (e.g. `foo-`) now get correct usage statements:
`foo() - value` instead of `foo()-value`. (Fixes #38)
* Functions with no arguments now correctly get usage statements (Fixes #35)
* Indentation in examples now preserved (Fixes #27)
* roxygen2 will replace characters that are not valid in filenames with a
character substitute, e.g. `[]` becomes `sub`, `-` becomes `set` (Fixes #6)
* Usage strings use non-breaking spaces to prevent string default values
containing whitespace to be split across multiple lines. This may cause
problems in the unlikely event that you have default value containing a
non-breaking space (`\uA0') (Fixes #21)
* Functions with quoted names now get correct usage statements (Fixes #41)
* Objects that no longer exist are not documented (Fixes #42)
* Errors now display file name and line number of roxygen block to help you
find the problem. Thanks to code contributions from Renaud Gaujoux. (Fixes
#13)
* Documentation with no untagged text but with `@title`, `@description` and
`@details` tags now produces correct output.
--
Assistant Professor / Dobelman Family Junior Chair
Department of Statistics / Rice University
http://had.co.nz/
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Re: [R] issue using package sos
Neotropical bat risk assessments neotropical.bats at gmail.com writes: Issue with sos package I am now using R 2.14 and the sos package did work with 2.13 library(sos) Loading required package: brew Attaching package: 'sos' The following object(s) are masked from 'package:JGR': installPackages The following object(s) are masked from 'package:utils': library(sos); findFn(random forest) found 253 matches; retrieving 13 pages 2 3 4 5 6 7 8 9 10 11 12 13 ++ Have you tried it from within base R/R-Gui (it looks like you're using JGR)? findFn() doesn't work from within RStudio, and I can imagine there's a similar situation with JGR. At least trying it would eliminate one possibility. Results of sessionInfo() would be helpful ... __ R-help@r-project.org mailing list 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.
Re: [R] New PLYR issue
Not reproducible. Read the posting guide. Provide enough data to reproduce the
problem.
---
Jeff NewmillerThe . . Go Live...
DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. 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.
Neotropical bat risk assessments neotropical.b...@gmail.com wrote:
Issue with PLYR.
Now using R 2.14 and this data and plyr command line worked with 2.13
I am also loading the same saved data that worked previously, but now
some issue.
library(plyr)
UNESCO - dget('C:/Carbon-GJ/BZE_ecosys.robj')
df2 - ddply(df, UNESCO, summarise, total_ha = sum(Ha))
*Error in if (empty(.data)) return(.data) :
missing value where TRUE/FALSE needed*
Clueless
Ideas suggestions?
Some change in PLYR?
Bruce
[[alternative HTML version deleted]]
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Re: [R] Myriam Saavedra M. Sc. Questions about maximun radius distance
Myriam fantasmita1948 at yahoo.fr writes: Dear Mr. Baddeley I just graduated from a Masters in Applied Mathematics on Jun19th. My thesis was about spatial distribution /a nalysis of some trees in a part of the Congo Basic Forest. In my thesis I used your spatial package in R, and today I'm doing a more deeper study about how we choise the r distance in Function F(). I would like to be able to understand about value of rmaxdefault as: Mr Baddeley isn't here (probably) -- this is a generic help list for questions on R. ripley - min(diff(W$xrange), diff(W$yrange))/4 rlarge - if (!missing(lambda)) sqrt(1000/(pi * lambda)) else Inf rmax - min(rlarge, ripley) For the ripley's calculation, I found your explanation in the internet but for the rlarge I couldn't find it. Could you explain why it is using the value inside of the sqrt (1000/(pi * lambda)). You've given us just a fragment of a question here -- there's not enough context to work with. We don't know where the variable 'W' came from, although presumably from a Ripley's K calculation ... ? Please read http://tinyurl.com/reproducible-000 , and give us more information (e.g. the link (URL) to the explanation you say you found on the internet). I would also suggest that this question might be better suited for the r-sig-ecol...@r-project.org mailing list ... __ R-help@r-project.org mailing list 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] locator not-interactive
Hello everyone, I have these 2 vectors in a type=s plot ( reported below) I would like to check the value of y at z=seq(0,1440, by=60) I think that I can do it calculating a vector that report the position of the value of y = z for which the difference to z is minimal. But I also guess that there should be a built-in function like locator, that provides, given same x points, the y coordinates. Does it actually exist? Thank you for your help H. x-1:679 and y: [1]2222222222222 233 [17]3333333333333 333 [33]3333334444444 444 [49]4444444444444 444 [65]4444444555556 666 [81]6666666666667 777 [97]7777777777777 778 [113]8888888889999 999 [129]9999999999999 999 [145]999999 10 10 10 10 10 10 12 12 12 12 [161] 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 [177] 12 12 12 12 12 12 12 12 12 12 12 13 13 13 13 13 [193] 13 13 13 13 13 13 13 13 13 18 18 18 18 18 18 18 [209] 18 18 18 18 18 18 18 18 18 18 18 18 18 18 19 19 [225] 19 19 19 19 19 19 19 19 24 24 24 24 24 24 24 25 [241] 25 25 25 25 25 25 25 25 25 25 25 25 25 28 28 28 [257] 28 28 28 28 28 28 28 28 28 28 28 28 28 28 28 28 [273] 28 28 28 28 28 28 29 29 29 29 29 29 29 29 29 29 [289] 29 29 29 29 29 29 29 29 29 29 29 29 30 30 30 30 [305] 30 30 30 30 30 30 30 30 30 30 30 32 32 32 32 32 [321] 32 32 32 32 32 32 32 32 33 33 33 33 33 33 33 33 [337] 33 33 33 33 33 33 33 33 33 33 33 33 33 33 33 33 [353] 33 33 33 33 33 33 33 33 34 34 34 34 34 34 34 37 [369] 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 [385] 37 37 37 44 44 44 44 44 44 44 44 44 44 44 44 44 [401] 44 44 44 44 44 44 44 44 44 44 44 44 44 44 44 44 [417] 44 44 44 44 44 44 45 45 60 60 61 61 61 162 162 162 [433] 162 162 162 162 162 162 162 162 162 162 162 162 162 162 162 162 [449] 162 162 162 162 162 162 162 162 162 162 162 163 163 163 163 163 [465] 163 163 163 163 163 163 163 163 163 163 163 163 163 163 163 163 [481] 163 163 163 163 239 239 239 239 239 239 239 239 239 239 239 239 [497] 239 239 239 239 239 239 239 239 239 239 239 239 239 239 239 239 [513] 239 239 604 604 604 604 604 604 604 604 604 604 604 604 605 605 [529] 605 605 605 605 605 605 605 605 605 605 605 605 605 605 605 605 [545] 605 605 605 605 605 605 605 605 605 605 605 605 605 605 605 605 [561] 606 606 606 606 845 845 845 845 845 845 845 845 845 845 845 845 [577] 845 845 845 845 845 845 845 845 845 845 845 845 845 846 846 846 [593] 846 846 846 846 846 846 846 846 846 846 846 846 846 846 846 846 [609] 846 846 846 846 846 846 846 846 846 846 846 846 846 846 847 847 [625] 847 847 847 847 847 847 847 847 847 847 847 847 847 847 847 847 [641] 929 929 929 929 929 929 929 929 929 929 929 929 929 929 930 930 [657] 930 930 930 930 930 930 930 930 930 930 930 930 930 930 930 930 [673] 933 933 933 933 933 933 1015 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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.
Re: [R] R v2.13.2 - Cannot find Rcmd on path?
On 12.11.2011 15:56, jack306 wrote: Dear all: I could not able to find rcmd using the following path: either R version (2.13.2 or 2.14.0); either rtools version (2.13 or 2.14). My os is winxp. The variables set in path are as follows. c:\Rtools\bin;c:\Rtools\MinGW\bin;C:\Perl\bin; C:\Perl\site\bin; c:\Rtools\bin; C:\Program Files\R\R-2.13.2\bin\i386; C:\Program Files\MiKTeX 2.9\miktex\bin;%SystemRoot%\system32;%SystemRoot%;%SystemRoot%\System32\Wbem;C:\Program Files\Common Files\Roxio Shared\DLLShared\;C:\Program Files\Common Files\Roxio Shared\10.0\DLLShared\;c:\Program Files\Microsoft SQL Server\90\Tools\binn\ Start to clean that up! - remove all blanks not part of paths (i.e. all those between the ; and c: - I am not sure what happens for trailing backslashes. - you won't need c:\Rtools\bin twice - MAke sure there is really a Rcmd.exe (if you reallny need that) in C:\Program Files\R\R-2.13.2\bin\i386 Best, Uwe Ligges After I tried setpath.bat file, it doesn't work either. Thank you, Jixiang Wu -- View this message in context: http://r.789695.n4.nabble.com/R-v2-13-2-Cannot-find-Rcmd-on-path-tp3927126p4034596.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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 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.
Re: [R] With an example - Re: rbind.data.frame drops attributes for factor variables
dataset[ nrow(dataset), ] - c (Male, 5, bad) The above seems to have worked to append a row in place of a rbind(). This method does not drop the custom attributes from the column. Do yo see any issue with this method. Thanks, Sammy On Sat, Nov 12, 2011 at 10:16 PM, David Winsemius dwinsem...@comcast.netwrote: On Nov 12, 2011, at 6:40 PM, Sammy Zee wrote: Thanks David. Besides rbind(), is there any other way to add a row to a data frame so that I do not lose the custom attributes. I have already told you the method that I know of. You don't seem to have taken my poin that it is not a data.frame specific problem but rahter a facor problem. You are welcome to redefine `rbind.data.frame`. The R language is rather flexible in that manner. -- David. Thanks, Sammy On Sat, Nov 12, 2011 at 5:17 PM, David Winsemius dwinsem...@comcast.net wrote: On Nov 12, 2011, at 2:47 PM, Sammy Zee wrote: When I use rbind() or rbind.data.frame() to add a row to an existing dataframe, it appears that attributes for the column of type factor are dropped. See the sample example below to reproduce the problem. Please suggest How I can fix this. Thanks, Sammy a=c(Male, Male, Female, Male) b=c(1,2,3,4) c=c(great, bad, good, bad) dataset- data.frame (gender = a, count = b, answer = c) dataset gender count answer 1 Male 1 great 2 Male 2bad 3 Female 3 good 4 Male 4bad attributes(dataset$answer) $levels [1] bad good great $class [1] factor Now adding some custom attributes to column dataset$answer attributes(dataset$answer)-c(**attributes(dataset$answer),** list(newattr1=custom-attr1)) attributes(dataset$answer)-c(**attributes(dataset$answer),** list(newattr2=custom-attr2)) If you look through the code of rbind.data.frame you see that column values are processed with the 'factor' function. attributes(dataset$answer) $levels [1] bad good great $class [1] factor $newattr1 [1] custom-attr1 $newattr2 [1] custom-attr2 attributes(factor(dataset$**answer)) $levels [1] bad good great $class [1] factor So I think you are out of luck. You will need to restore the special attributes yourself. -- David. attributes(dataset$answer) $levels [1] bad good great $class [1] factor $newattr1 [1] custom-attr1 $newattr2 [1] custom-attr2 However as soon as I add a row to this data frame (dataset) by rbind(), it loses the custom attributes (newattr1 and newattr2) I have just added newrow = c(gender=Female, count = 5, answer = great) dataset - rbind(dataset, newrow) attributes(dataset$answer) $levels [1] bad good great $class [1] factor the two custom attributes are dropped!! Any suggestion why this is happening. On Fri, Nov 11, 2011 at 11:44 AM, Jeff Newmiller jdnew...@dcn.davis.ca.us**wrote: As the doctor says, if it hurts don't do that. A factor is a sequence of integers with a corresponding list of character strings. Factors in two separate vectors can and usually do map the same integer to different strings, and R cannot tell how you want that resolved. Convert these columns to character before combining them, and only convert to factor when you have all of your possibilities present (or you specify them in the creation of the factor vector). --**--** --- Jeff NewmillerThe . . Go Live... Sammy Zee szee2...@gmail.com wrote: Hi all, When I use rbind() or rbind.data.frame() to add a row to an existing dataframe, it appears that attributes for the column of type factor are dropped. I see the following post with same problem. However i did not see any reply to the following posting offering a solution. Could someone please help. http://r.789695.n4.nabble.com/**rbind-data-frame-drops-** attributes-for-factor-**variables-td919575.htmlhttp://r.789695.n4.nabble.com/rbind-data-frame-drops-attributes-for-factor-variables-td919575.html Thanks, Sammy [[alternative HTML version deleted]] ___ David Winsemius, MD West Hartford, CT [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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.
Re: [R] R v2.13.2 - Cannot find Rcmd on path?
On Fri, Oct 21, 2011 at 5:07 PM, Hardy Griesbauer hgriesba...@hotmail.com wrote: Hello, I recently updated to R version 2.13.2. With R version 2.10.0, I often created and installed R packages, however, I cannot do this since updating. In other words, when I type in Rcmd build -binary PACKAGENAME I receive an error message: Rcmd is not recognized as an internal I suspect that this is because Rcmd.exe is no longer installed in the bin folder, but rather, in the x64 folder within bin. Please help! What I've done so far: 1) Downloaded and installed the latest version of Rtools (as of October 21, 2011). 2) During installation of Rtools, I included the following in the path: C:\Progra~1\R\R-2.13.2\bin\x64 and confirmed that this is on the path. 3) Read every help manual I can find, but I can't seem to locate the answer to this problem. Other information: R version 2.13.2 (2011-09-30) Platform: x86_64-pc-mingw32/x64 (64-bit) My windows version: Windows 7 Home Premium Service Pack 1 64-bit OS. There is a batch command Rcmd.bat at http://batchfiles.googlecode.com that when run will find R using the registry and then run the appropriate Rcmd.exe so that you don't need to change your path or any other environment variable. Its a self contained .bat file so just place it anywhere on your existing path. At the Windows console this command will show you your path: path Now try Rcmd.bat build ...whatever... If your path is not already set to find Rcmd.exe then Rcmd.bat can be abbreviated to just Rcmd in the above line. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-help@r-project.org mailing list 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.
Re: [R] Has anyone used SIAR package add on?
On Nov 12, 2011 at 8:29pm Alex wrote: Has anyone used SIAR package add on? I posted a reply to an earlier question from you on this subject. See http://r.789695.n4.nabble.com/Errors-in-SIAR-td4029804.html. In it I note that there are problems with the function from siar (not SIAR) you are using, but that this may not be your problem, that the function calls for matrices (you were using data frames), and that you are unlikely to get further help on this until you post your data (or data that resemble yours). It's not that people don't want to help you, but you have to give them something to work with (see the famous footer of this message). One of the demos in the siar package mostly works, the other one does not. It's possible that there is a minor glitch somewhere, which could easily be fixed, so that given data in the correct format you get a result. Why don't you dput() a subset of your data, so that anyone who is interested in helping you can have a go? If your data set is called myData, and is stored as a data frame, then do something like the following and copy the result of dput() into your next email. Of course, if your data set has many rows then you want to adjust the by argument (increase it). Twenty to thirty rows should be sufficient. myPartData - myData[seq(1, nrow(myDat), by=3), ] dput(myPartData) Regards, Mark. - Mark Difford (Ph.D.) Research Associate Botany Department Nelson Mandela Metropolitan University Port Elizabeth, South Africa -- View this message in context: http://r.789695.n4.nabble.com/Has-anyone-used-SIAR-package-add-on-tp4035014p4036852.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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] cannot load zoo package
Using: Mac OS 10.7.2 R version 2.13.2 I cannot load the zoo package. The install runs fine but when trying to load it i get the following error: /Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Users/ntyhurst/Library/R/2.13/library/zoo/libs/i386/zoo.so': dlopen(/Users/ntyhurst/Library/R/2.13/library/zoo/libs/i386/zoo.so, 6): Library not loaded: @rpath/R.framework/Versions/2.13/Resources/lib/libR.dylib Referenced from: /Users/ntyhurst/Library/R/2.13/library/zoo/libs/i386/zoo.so Reason: image not found Error: package/namespace load failed for 'zoo'/ I appreciate any and all help. thank you. -- View this message in context: http://r.789695.n4.nabble.com/cannot-load-zoo-package-tp4036835p4036835.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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] Generate the distribution
Hi everyone, i really need some help with one task. I simply cant understand what i really have to do. The task is: Generate the distribution of maximum on samples of size 200 from beta with shape parameters 5 and 5 distribution. Plot a histogram of simulated values and overlay at least one distribution curve that you think might be suitable. Im rookie with simulations, so i need yours help. Tnx -- View this message in context: http://r.789695.n4.nabble.com/Generate-the-distribution-tp4036755p4036755.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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.
Re: [R] cannot load zoo package
On Sun, Nov 13, 2011 at 11:23 AM, hawkhandler ntyhu...@gmail.com wrote: Using: Mac OS 10.7.2 R version 2.13.2 I cannot load the zoo package. The install runs fine but when trying to load it i get the following error: /Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Users/ntyhurst/Library/R/2.13/library/zoo/libs/i386/zoo.so': dlopen(/Users/ntyhurst/Library/R/2.13/library/zoo/libs/i386/zoo.so, 6): Library not loaded: @rpath/R.framework/Versions/2.13/Resources/lib/libR.dylib Referenced from: /Users/ntyhurst/Library/R/2.13/library/zoo/libs/i386/zoo.so Reason: image not found Error: package/namespace load failed for 'zoo'/ I appreciate any and all help. thank you. Upgrade R to R 2.14.0 or get an older version of zoo. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-help@r-project.org mailing list 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.
Re: [R] R v2.13.2 - Cannot find Rcmd on path?
On 13.11.2011 17:29, Gabor Grothendieck wrote: On Fri, Oct 21, 2011 at 5:07 PM, Hardy Griesbauer hgriesba...@hotmail.com wrote: Hello, I recently updated to R version 2.13.2. With R version 2.10.0, I often created and installed R packages, however, I cannot do this since updating. In other words, when I type in Rcmd build -binary PACKAGENAME I receive an error message: Rcmd is not recognized as an internal I suspect that this is because Rcmd.exe is no longer installed in the bin folder, but rather, in the x64 folder within bin. Please help! What I've done so far: 1) Downloaded and installed the latest version of Rtools (as of October 21, 2011). 2) During installation of Rtools, I included the following in the path: C:\Progra~1\R\R-2.13.2\bin\x64 and confirmed that this is on the path. 3) Read every help manual I can find, but I can't seem to locate the answer to this problem. Other information: R version 2.13.2 (2011-09-30) Platform: x86_64-pc-mingw32/x64 (64-bit) My windows version: Windows 7 Home Premium Service Pack 1 64-bit OS. There is a batch command Rcmd.bat at http://batchfiles.googlecode.com that when run will find R using the registry and then run the appropriate Rcmd.exe so that you don't need to change your path or any other environment variable. Its a self contained .bat file so just place it anywhere on your existing path. At the Windows console this command will show you your path: path Now try Rcmd.bat build ...whatever... If your path is not already set to find Rcmd.exe then Rcmd.bat can be abbreviated to just Rcmd in the above line. I wonder again and again why you try to obfuscate things by your layer of non portable batchfiles. Typing the path correctly and according to the syntax is required in both cases anyway. Best, Uwe __ R-help@r-project.org mailing list 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.
Re: [R] cannot load zoo package
There was a problem with @rpath within R.app on the Mac. Either starting R within a shell (instead of R.app) or updating R.app should both resolve the problem. See https://stat.ethz.ch/pipermail/r-sig-mac/2011-November/008757.html for details. Z On Sun, 13 Nov 2011, hawkhandler wrote: Using: Mac OS 10.7.2 R version 2.13.2 I cannot load the zoo package. The install runs fine but when trying to load it i get the following error: /Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Users/ntyhurst/Library/R/2.13/library/zoo/libs/i386/zoo.so': dlopen(/Users/ntyhurst/Library/R/2.13/library/zoo/libs/i386/zoo.so, 6): Library not loaded: @rpath/R.framework/Versions/2.13/Resources/lib/libR.dylib Referenced from: /Users/ntyhurst/Library/R/2.13/library/zoo/libs/i386/zoo.so Reason: image not found Error: package/namespace load failed for 'zoo'/ I appreciate any and all help. thank you. -- View this message in context: http://r.789695.n4.nabble.com/cannot-load-zoo-package-tp4036835p4036835.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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 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.
Re: [R] To moderator
No. But it has not been posted either. You got that message because you sent your message to the wrong address. You should have sent it to r-help@r-project.org You had probably sent it to r-help-requ...@r-project.org which would have had the effect that the server would have tried to interpret the contents of you message as commands (e.g. to unsubscribe, change your subscription options, etc.), except that the contents of your message are not meaningful as commands to r-help-request. So you should send your message again, and this time to the correct address! However, since it seems that your email address laf...@dms.umontreal.ca is not subscribed to the list, when you do send it you will receive a notification that it has been held for moderation because it has been posted by a non-member to a members-only list. After a while (depending on when a moderator next looks at the heldmessages) it will be approved and will go out to the list. You can save yourself this trouble by subscribing your email address to the r-help list. Visit: https://stat.ethz.ch/mailman/listinfo/r-help and following the instructions in the section Subscribing to R-help. Hoping this helps, Ted. On 13-Nov-11 17:05:46, Lafaye de Micheaux wrote: Dear moderator, Can you tell me if this means that my email has been rejected? Best Pierre Le 13/11/2011 11:54, r-help-ow...@r-project.org a écrit : The results of your email command are provided below. Attached is your original message. - Unprocessed: I am working on a 64 bits Linux system. I issue the following R commands: rm(list=ls()) # To remove all objects in the workspace. gc() # To free memory. used (Mb) gc trigger (Mb) max used (Mb) Ncells 124250 6.7 35 18.7 35 18.7 Vcells 124547 1.0 786432 6.0 476934 3.7 gc() # I had to do it again, don't know why! used (Mb) gc trigger (Mb) max used (Mb) Ncells 124257 6.7 35 18.7 35 18.7 Vcells 124574 1.0 786432 6.0 476934 3.7 gc() # Just to be sure things have stabilized. used (Mb) gc trigger (Mb) max used (Mb) Ncells 124257 6.7 35 18.7 35 18.7 Vcells 124574 1.0 786432 6.0 476934 3.7 x- as.integer(3) object.size(x) 48 bytes gc() # To free memory. used (Mb) gc trigger (Mb) max used (Mb) Ncells 124255 6.7 35 18.7 35 18.7 Vcells 124550 1.0 786432 6.0 476934 3.7 - Ignored: gc() # I had to do it again, don't know why! used (Mb) gc trigger (Mb) max used (Mb) Ncells 124259 6.7 35 18.7 35 18.7 Vcells 124575 1.0 786432 6.0 476934 3.7 gc() # Just to be sure things have stabilized. used (Mb) gc trigger (Mb) max used (Mb) Ncells 124259 6.7 35 18.7 35 18.7 Vcells 124575 1.0 786432 6.0 476934 3.7 My questions are: 1) Why should I use the command gc() two times before the values displayed do not change anymore? 2) object.size(x) is 48 bytes on my system. As I understand it, this is 8 bytes for storing the value 3L and 40 bytes (on my 64 bits OS) to store the header of x. Am-I right? (Note that I understand it would be the same for x- c(3L,4L)) 3) If 2) is OK, then you can see that Ncells increased by 2 units and Vcells by 1 unit. I think that 1 unit of Vcells = 8 bytes. Is it TRUE? (This is written in help(gc)) And in my mind, 1 unit of Ncells should be 20 bytes, so that: 1 unit of Vcells + 2 units of Ncells = 8 + 2*20 = 48, the size of x as returned by the command object.size(x). BUT, when you look at help(gc), one can read: gc returns a matrix with rows Ncells (_cons cells_), usually 28 bytes each on 32-bit systems and 56 bytes on 64-bit systems, So, can you please help me to undertsand all of this? Thanks in advance. Best regards, Pierre -- Pierre Lafaye de Micheaux Adresse courrier: Département de Mathématiques et Statistique Université de Montréal CP 6128, succ. Centre-ville Montréal, Québec H3C 3J7 CANADA Adresse physique: Département de Mathématiques et Statistique Bureau 4249, Pavillon André-Aisenstadt 2920, chemin de la Tour Montréal, Québec H3T 1J4 CANADA Tél.: (00-1) 514-343-6607 / Fax: (00-1) 514-343-5700 laf...@dms.umontreal.ca http://www.biostatisticien.eu - Done. -- Pierre Lafaye de Micheaux Adresse courrier: Département de Mathématiques et Statistique Université de Montréal CP 6128, succ. Centre-ville Montréal, Québec H3C 3J7 CANADA Adresse physique: Département de Mathématiques et Statistique Bureau 4249, Pavillon André-Aisenstadt 2920, chemin de la Tour Montréal, Québec H3T 1J4 CANADA Tél.: (00-1) 514-343-6607 / Fax: (00-1) 514-343-5700
[R] R development master class: NYC, Dec 12-13
Hi all, I hope you don't mind the slightly off topic email, but I'm going to be teaching an R development master class in New York City on Dec 12-13. The basic idea of the class is to help you write better code, focused on the mantra of do not repeat yourself. In day one you will learn powerful new tools of abstraction, allowing you to solve a wider range of problems with fewer lines of code. Day two will teach you how to make packages, the fundamental unit of code distribution in R, allowing others to save time by allowing them to use your code. To get the most out of this course, you should have some experience programming in R already: you should be familiar with writing functions, and the basic data structures of R: vectors, matrices, arrays, lists and data frames. You will find the course particularly useful if you're an experienced R user looking to take the next step, or if you're moving to R from other programming languages and you want to quickly get up to speed with R's unique features. A couple session outline is available at http://www.eventbrite.com/event/2492641558 Both days will incorporate a mix of lectures and hands-on learning. Expect to learn about a topic and then immediately put it into practice with a small example. Plenty of help will be available if you get stuck. You'll receive a printed copy of all slides, as well as electronic access to the slides, code and data. The material covered in the course is currently being turned into a book. You can access the current draft at https://github.com/hadley/devtools/wiki/. Limited discounts for students (66% off) and academics (33% off) are available - please contact me for details. Find out more and sign up at http://www.eventbrite.com/event/2492641558 Regards, Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-help@r-project.org mailing list 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.
Re: [R] To moderator
My apologies for sending the message with the above subject to R-help. I can only assume that it was the result of mis-mousing! (It should only have gone to the original sendar, and to r-help-owner). Best wishes to all, Ted. E-Mail: (Ted Harding) ted.hard...@wlandres.net Fax-to-email: +44 (0)870 094 0861 Date: 13-Nov-11 Time: 17:38:12 -- XFMail -- __ R-help@r-project.org mailing list 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.
Re: [R] R development master class: NYC, Dec 12-13
What, no discount codes for us?! No seriously, as much as I'm for free enterprise, it feels awkward to see you promote an (expensive!) course in a list where people offer not only their knowledge, but also the tools you use, for free. I ignore whether this goes against posting rules, but even if it doesn't I wouldn't want this awesome resource to become a marketing platform. On Sun, 13 Nov 2011 11:34:35 -0600 Hadley Wickham had...@rice.edu wrote: Hi all, I hope you don't mind the slightly off topic email, but I'm going to be teaching an R development master class in New York City on Dec 12-13. The basic idea of the class is to help you write better code, focused on the mantra of do not repeat yourself. In day one you will learn powerful new tools of abstraction, allowing you to solve a wider range of problems with fewer lines of code. Day two will teach you how to make packages, the fundamental unit of code distribution in R, allowing others to save time by allowing them to use your code. To get the most out of this course, you should have some experience programming in R already: you should be familiar with writing functions, and the basic data structures of R: vectors, matrices, arrays, lists and data frames. You will find the course particularly useful if you're an experienced R user looking to take the next step, or if you're moving to R from other programming languages and you want to quickly get up to speed with R's unique features. A couple session outline is available at http://www.eventbrite.com/event/2492641558 Both days will incorporate a mix of lectures and hands-on learning. Expect to learn about a topic and then immediately put it into practice with a small example. Plenty of help will be available if you get stuck. You'll receive a printed copy of all slides, as well as electronic access to the slides, code and data. The material covered in the course is currently being turned into a book. You can access the current draft at https://github.com/hadley/devtools/wiki/. Limited discounts for students (66% off) and academics (33% off) are available - please contact me for details. Find out more and sign up at http://www.eventbrite.com/event/2492641558 Regards, Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-help@r-project.org mailing list 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 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.
Re: [R] Generate the distribution
Anban nino.zajc at gmail.com writes: [snip] i really need some help with one task. I simply cant understand what i really have to do. [snip] Generate the distribution of maximum on samples of size 200 from beta with shape parameters 5 and 5 distribution. Plot a histogram of simulated values and overlay at least one distribution curve that you think might be suitable. This list is explicitly not intended for homework and this looks a whole like homework. If you can convince us that this is *not* homework, or that your instructor is happy to let you ask questions on the web, I'm sure lots of people here will be happy to help. sincerely Ben Bolker __ R-help@r-project.org mailing list 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.
Re: [R] R v2.13.2 - Cannot find Rcmd on path?
I remember I was torn into pieces a few months back when I made a wishlist here that R adds its bin path to PATH on Windows during installation. People had tons of reasons of objection. Although I do not use these batchfiles (usually I do not actually use Windows), I see there is a motivation behind them: there needs to be an easy way for Windows users to use R in command line (e.g. R CMD build...). You may argue that it is easy to understand PATH and modify it manually, and I will say nothing but thank Windows again. Sorry this seems to be off-topic. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA 2011/11/13 Uwe Ligges lig...@statistik.tu-dortmund.de: On 13.11.2011 17:29, Gabor Grothendieck wrote: On Fri, Oct 21, 2011 at 5:07 PM, Hardy Griesbauer hgriesba...@hotmail.com wrote: Hello, I recently updated to R version 2.13.2. With R version 2.10.0, I often created and installed R packages, however, I cannot do this since updating. In other words, when I type in Rcmd build -binary PACKAGENAME I receive an error message: Rcmd is not recognized as an internal I suspect that this is because Rcmd.exe is no longer installed in the bin folder, but rather, in the x64 folder within bin. Please help! What I've done so far: 1) Downloaded and installed the latest version of Rtools (as of October 21, 2011). 2) During installation of Rtools, I included the following in the path: C:\Progra~1\R\R-2.13.2\bin\x64 and confirmed that this is on the path. 3) Read every help manual I can find, but I can't seem to locate the answer to this problem. Other information: R version 2.13.2 (2011-09-30) Platform: x86_64-pc-mingw32/x64 (64-bit) My windows version: Windows 7 Home Premium Service Pack 1 64-bit OS. There is a batch command Rcmd.bat at http://batchfiles.googlecode.com that when run will find R using the registry and then run the appropriate Rcmd.exe so that you don't need to change your path or any other environment variable. Its a self contained .bat file so just place it anywhere on your existing path. At the Windows console this command will show you your path: path Now try Rcmd.bat build ...whatever... If your path is not already set to find Rcmd.exe then Rcmd.bat can be abbreviated to just Rcmd in the above line. I wonder again and again why you try to obfuscate things by your layer of non portable batchfiles. Typing the path correctly and according to the syntax is required in both cases anyway. Best, Uwe __ R-help@r-project.org mailing list 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 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] How to change the font of any help page
Dear all, when I open the help page of any R function, the help page opens with my default browser. However I am not happy with Font of the help page, which probably set as 'Times new roman'. How can I change this Font style? I want to see any help content with the 'Calibri' font. Is it possible? Thanks and regards, __ R-help@r-project.org mailing list 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.
Re: [R] identify duplicate from more than one column
Thanks Jim and David! It seems like both were great options. Both of your suggestions of pasting both IDs together worked well, keeping the pasting as a character is better. Though, Jim's example was interesting, it gave me the following error: Error in `$-.data.frame`(`*tmp*`, coupleid, value = c(1L, 1L, 2L, 2L, : replacement has 123586 rows, data has 123631 Since this was a large dataframe, I don't know exactly where the error occurred. But, it seems like it was detecting missing values in some of the rows and after checking using the is.na() function, it didn't say that there were any missing values used (i.e. the new mID or sex). What do you guys think may be happening? Thanks, Carlos -- View this message in context: http://r.789695.n4.nabble.com/identify-duplicate-from-more-than-one-column-tp4035888p4037177.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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.
Re: [R] R v2.13.2 - Cannot find Rcmd on path?
For what it's worth: the fix was to put the x64 folder FIRST in the path. -Original Message- From: xieyi...@gmail.com [mailto:xieyi...@gmail.com] On Behalf Of Yihui Xie Sent: November-13-11 10:16 AM To: Uwe Ligges Cc: Gabor Grothendieck; r-help@r-project.org; Hardy Griesbauer Subject: Re: [R] R v2.13.2 - Cannot find Rcmd on path? I remember I was torn into pieces a few months back when I made a wishlist here that R adds its bin path to PATH on Windows during installation. People had tons of reasons of objection. Although I do not use these batchfiles (usually I do not actually use Windows), I see there is a motivation behind them: there needs to be an easy way for Windows users to use R in command line (e.g. R CMD build...). You may argue that it is easy to understand PATH and modify it manually, and I will say nothing but thank Windows again. Sorry this seems to be off-topic. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA 2011/11/13 Uwe Ligges lig...@statistik.tu-dortmund.de: On 13.11.2011 17:29, Gabor Grothendieck wrote: On Fri, Oct 21, 2011 at 5:07 PM, Hardy Griesbauer hgriesba...@hotmail.com wrote: Hello, I recently updated to R version 2.13.2. With R version 2.10.0, I often created and installed R packages, however, I cannot do this since updating. In other words, when I type in Rcmd build -binary PACKAGENAME I receive an error message: Rcmd is not recognized as an internal I suspect that this is because Rcmd.exe is no longer installed in the bin folder, but rather, in the x64 folder within bin. Please help! What I've done so far: 1) Downloaded and installed the latest version of Rtools (as of October 21, 2011). 2) During installation of Rtools, I included the following in the path: C:\Progra~1\R\R-2.13.2\bin\x64 and confirmed that this is on the path. 3) Read every help manual I can find, but I can't seem to locate the answer to this problem. Other information: R version 2.13.2 (2011-09-30) Platform: x86_64-pc-mingw32/x64 (64-bit) My windows version: Windows 7 Home Premium Service Pack 1 64-bit OS. There is a batch command Rcmd.bat at http://batchfiles.googlecode.com that when run will find R using the registry and then run the appropriate Rcmd.exe so that you don't need to change your path or any other environment variable. Its a self contained .bat file so just place it anywhere on your existing path. At the Windows console this command will show you your path: path Now try Rcmd.bat build ...whatever... If your path is not already set to find Rcmd.exe then Rcmd.bat can be abbreviated to just Rcmd in the above line. I wonder again and again why you try to obfuscate things by your layer of non portable batchfiles. Typing the path correctly and according to the syntax is required in both cases anyway. Best, Uwe __ R-help@r-project.org mailing list 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 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] Understand Ncells and Vcells, from gc()
Dear all, I am working on a 64 bits Linux system. I issue the following R commands: rm(list=ls()) # To remove all objects in the workspace. gc() # To free memory. used (Mb) gc trigger (Mb) max used (Mb) Ncells 124250 6.7 35 18.7 35 18.7 Vcells 124547 1.0 786432 6.0 476934 3.7 gc() # I had to do it again, don't know why! used (Mb) gc trigger (Mb) max used (Mb) Ncells 124257 6.7 35 18.7 35 18.7 Vcells 124574 1.0 786432 6.0 476934 3.7 gc() # Just to be sure things have stabilized. used (Mb) gc trigger (Mb) max used (Mb) Ncells 124257 6.7 35 18.7 35 18.7 Vcells 124574 1.0 786432 6.0 476934 3.7 x - as.integer(3) object.size(x) 48 bytes gc() # To free memory. used (Mb) gc trigger (Mb) max used (Mb) Ncells 124255 6.7 35 18.7 35 18.7 Vcells 124550 1.0 786432 6.0 476934 3.7 gc() # I had to do it again, don't know why! used (Mb) gc trigger (Mb) max used (Mb) Ncells 124259 6.7 35 18.7 35 18.7 Vcells 124575 1.0 786432 6.0 476934 3.7 gc() # Just to be sure things have stabilized. used (Mb) gc trigger (Mb) max used (Mb) Ncells 124259 6.7 35 18.7 35 18.7 Vcells 124575 1.0 786432 6.0 476934 3.7 My questions are: 1) Why should I use the command gc() two times before the values displayed do not change anymore? 2) object.size(x) is 48 bytes on my system. As I understand it, this is 8 bytes for storing the value 3L and 40 bytes (on my 64 bits OS) to store the header of x. Am-I right? (Note that I understand it would be the same for x - c(3L,4L)) 3) If 2) is OK, then you can see that Ncells increased by 2 units and Vcells by 1 unit. I think that 1 unit of Vcells = 8 bytes. Is it TRUE? (This is written in help(gc)) And in my mind, 1 unit of Ncells should be 20 bytes, so that: 1 unit of Vcells + 2 units of Ncells = 8 + 2*20 = 48, the size of x as returned by the command object.size(x). BUT, when you look at help(gc), one can read: ‘gc’ returns a matrix with rows ‘Ncells’ (_cons cells_), usually 28 bytes each on 32-bit systems and 56 bytes on 64-bit systems, So, can you please help me to undertsand all of this? Thanks in advance. Best regards, Pierre -- Pierre Lafaye de Micheaux Adresse courrier: Département de Mathématiques et Statistique Université de Montréal CP 6128, succ. Centre-ville Montréal, Québec H3C 3J7 CANADA Adresse physique: Département de Mathématiques et Statistique Bureau 4249, Pavillon André-Aisenstadt 2920, chemin de la Tour Montréal, Québec H3T 1J4 CANADA Tél.: (00-1) 514-343-6607 / Fax: (00-1) 514-343-5700 laf...@dms.umontreal.ca http://www.biostatisticien.eu __ R-help@r-project.org mailing list 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] Function not found, maybe respective package has to be put in environment?
Hello everybody, I have a problem and would like to start with an example: library(snow) library(tseries) fn - function(x) adf.test(x) clusterApply(cl=cl, x=x , fun=fn) R cannot find the function adf.test() because it is inside the function fn(). This problem does not occur when, for example, fn - function(x) mean(x) holds. Therefore, I think the package tseries has to be put somehow in the environment where also the package stats is because the function mean() works but the function adf.test() not. But how to solve the problem? Remark: The above code is an example to illustrate my problem. My original function is more complex and somewhere inside my function I refer to some other function from the package tsDyn. I hope you can help me. Kind regards, Andy. __ R-help@r-project.org mailing list 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.
Re: [R] Function not found, maybe respective package has to be put in environment?
You have to load tseries on the nodes, not only on the master, i.e.: clusterEvalQ(cl, library(tseries)) Best, Uwe Ligges On 13.11.2011 19:34, Andreas Klein wrote: Hello everybody, I have a problem and would like to start with an example: library(snow) library(tseries) fn- function(x) adf.test(x) clusterApply(cl=cl, x=x , fun=fn) R cannot find the function adf.test() because it is inside the function fn(). This problem does not occur when, for example, fn- function(x) mean(x) holds. Therefore, I think the package tseries has to be put somehow in the environment where also the package stats is because the function mean() works but the function adf.test() not. But how to solve the problem? Remark: The above code is an example to illustrate my problem. My original function is more complex and somewhere inside my function I refer to some other function from the package tsDyn. I hope you can help me. Kind regards, Andy. __ R-help@r-project.org mailing list 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 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.
Re: [R] How to change the font of any help page
Each package comes with its own R.css these days and it can be tweaked by the package. If it is the standard on, it uses your browser's default font for displaying the plain text in the body of a help page. Best, Uwe Ligges On 13.11.2011 19:46, Christofer Bogaso wrote: Dear all, when I open the help page of any R function, the help page opens with my default browser. However I am not happy with Font of the help page, which probably set as 'Times new roman'. How can I change this Font style? I want to see any help content with the 'Calibri' font. Is it possible? Thanks and regards, __ R-help@r-project.org mailing list 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 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.
Re: [R] Kolmogorov-smirnov test
I recently gave a presentation at the 50th Army Operational Research Symposium at Ft Lee describing an implementation of Conover's exact calculation method for the KS test applied to discrete distributions. My implementation was done in Matlab script as opposed to R. Multiple Monte-Carlo trials were most encouraging. Seeing a comparison of the methods of implementation would be interesting. -- View this message in context: http://r.789695.n4.nabble.com/Kolmogorov-smirnov-test-tp3313842p4037287.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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.
Re: [R] R development master class: NYC, Dec 12-13
No seriously, as much as I'm for free enterprise, it feels awkward to see you promote an (expensive!) course in a list where people offer not only their knowledge, but also the tools you use, for free. You might have a point if I taught this course instead of offering knowledge and code for free, but I do it as well. Over the years I have contributed thousands of answers on R-help and hundreds on stackoverflow. I've written dozens of open-source packages and look after several R related mailing lists. I make pre-prints of all my papers available for free, I release all my lecture notes under creative commons licenses and I'm a supporting benefactor of the R foundation (or at least I've submitted the paperwork, I'm not yet listed on the site). What more do you want?! Some of the money I earn from these courses goes to pay for my summer salary and supports student research. It also gives me confidence that if I don't get tenure because I've been writing R packages instead of papers, I can keep doing the work I love. Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-help@r-project.org mailing list 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.
Re: [R] R development master class: NYC, Dec 12-13
Ha! Point publicly acknowledged. Best, A. On Sun, 13 Nov 2011 13:41:36 -0600 Hadley Wickham had...@rice.edu wrote: No seriously, as much as I'm for free enterprise, it feels awkward to see you promote an (expensive!) course in a list where people offer not only their knowledge, but also the tools you use, for free. You might have a point if I taught this course instead of offering knowledge and code for free, but I do it as well. Over the years I have contributed thousands of answers on R-help and hundreds on stackoverflow. I've written dozens of open-source packages and look after several R related mailing lists. I make pre-prints of all my papers available for free, I release all my lecture notes under creative commons licenses and I'm a supporting benefactor of the R foundation (or at least I've submitted the paperwork, I'm not yet listed on the site). What more do you want?! Some of the money I earn from these courses goes to pay for my summer salary and supports student research. It also gives me confidence that if I don't get tenure because I've been writing R packages instead of papers, I can keep doing the work I love. Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-help@r-project.org mailing list 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.
Re: [R] R development master class: NYC, Dec 12-13
Though I can't speak for Alex, I suspect this was a case of him either (1) not realizing you were actually the poster of the original email, or (2) he is relatively new to the woRld and hasn't yet connecting your name to your (enumerable) contributions. Also: Some of the money I earn from these courses goes to pay for my summer salary and supports student research. It also gives me confidence that if I don't get tenure because I've been writing R packages instead of papers, I can keep doing the work I love. If that actually happens, that would be an amazing/colossal (not in a good way) testament to how well the rating system works in academia. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ R-help@r-project.org mailing list 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.
Re: [R] identify duplicate from more than one column
Hi Carlos, Am I Jim? (I ask because there are at least two quite active Jim's on this list and one could have conceivably replied to you offlist). Regarding your error, it is rather difficult to tell without knowing exactly what your data is like and what you did. For _just_ the unit, home, and sex variables that we are working with, could you post the output of str() and summary() ? Something like: str(dat[c(unit, home, sex)]) summary(dat[c(unit, home, sex)]) where you replace 'dat' with your data frame name and the variable with the variable names. Also, please post the exact code you used leading up to the error. I am not certain whether you used mine, David's, or some mix...as near as I can tell, neither David or I used the 'coupleid' variable name, so you at least changed names. Best Regards, Josh On Sun, Nov 13, 2011 at 10:37 AM, jour4life jour4l...@gmail.com wrote: Thanks Jim and David! It seems like both were great options. Both of your suggestions of pasting both IDs together worked well, keeping the pasting as a character is better. Though, Jim's example was interesting, it gave me the following error: Error in `$-.data.frame`(`*tmp*`, coupleid, value = c(1L, 1L, 2L, 2L, : replacement has 123586 rows, data has 123631 Since this was a large dataframe, I don't know exactly where the error occurred. But, it seems like it was detecting missing values in some of the rows and after checking using the is.na() function, it didn't say that there were any missing values used (i.e. the new mID or sex). What do you guys think may be happening? Thanks, Carlos -- View this message in context: http://r.789695.n4.nabble.com/identify-duplicate-from-more-than-one-column-tp4035888p4037177.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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. -- Joshua Wiley Ph.D. Student, Health Psychology Programmer Analyst II, ATS Statistical Consulting Group University of California, Los Angeles https://joshuawiley.com/ __ R-help@r-project.org mailing list 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.
Re: [R] Generate the distribution
Google is an amazing resource for getting information. Try Googling 'simulation in R' - I got several useful hits on the first page. HTH, Dennis On Sun, Nov 13, 2011 at 7:41 AM, Anban nino.z...@gmail.com wrote: Hi everyone, i really need some help with one task. I simply cant understand what i really have to do. The task is: Generate the distribution of maximum on samples of size 200 from beta with shape parameters 5 and 5 distribution. Plot a histogram of simulated values and overlay at least one distribution curve that you think might be suitable. Im rookie with simulations, so i need yours help. Tnx -- View this message in context: http://r.789695.n4.nabble.com/Generate-the-distribution-tp4036755p4036755.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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 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.
Re: [R] R development master class: NYC, Dec 12-13
On Sun, Nov 13, 2011 at 2:55 PM, Steve Lianoglou mailinglist.honey...@gmail.com wrote: Some of the money I earn from these courses goes to pay for my summer salary and supports student research. It also gives me confidence that if I don't get tenure because I've been writing R packages instead of papers, I can keep doing the work I love. If that actually happens, that would be an amazing/colossal (not in a good way) testament to how well the rating system works in academia. I'm not in academia, but government research. I do go through a review very similar to the tenure process. Last time, I was told that I couldn't list my R package and associated papers as a research activity with substantial impact because it was outside my official scope of work. (Even though I wrote it so I could *do* my work.) I have no trouble seeing academic administrators do the same thing. Sarah -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list 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.
Re: [R] R v2.13.2 - Cannot find Rcmd on path?
On Sun, Nov 13, 2011 at 1:38 PM, Hardy Griesbauer hgriesba...@hotmail.com wrote: For what it's worth: the fix was to put the x64 folder FIRST in the path. Of course that only fixes it for now. Every time you upgrade R you have to change it all over again. With the batch files there is nothing to set and therefore nothing to change each time. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-help@r-project.org mailing list 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.
Re: [R] R development master class: NYC, Dec 12-13
On Sun, Nov 13, 2011 at 11:55 AM, Steve Lianoglou mailinglist.honey...@gmail.com wrote: Some of the money I earn from these courses goes to pay for my summer salary and supports student research. It also gives me confidence that if I don't get tenure because I've been writing R packages instead of papers, I can keep doing the work I love. If that actually happens, that would be an amazing/colossal (not in a good way) testament to how well the rating system works in academia. I think there's a broader issue here, that many people (Hadley included, but many many others) who do open source work go seriously underappreciated and underrespected. This is not just in academia. You do not have to read too many emails on R-help or R-devel to see someone complaining about something that is not working or is not working the way it should. Suggestions for improvement are always great, but it seems to me the tone is often very negative considering the amount of time and effort very gifted people put into it and have gotten A) little or no payment B) little recognition from their respective institutions. Makes me wish I was more than a graduate student and had more to give. Josh -- Joshua Wiley Ph.D. Student, Health Psychology Programmer Analyst II, ATS Statistical Consulting Group University of California, Los Angeles https://joshuawiley.com/ __ R-help@r-project.org mailing list 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.
Re: [R] Simulation over data repeatedly for four loops
Perhaps you might want to abstract your code a bit and try something like:
X = rnorm(500) # Some Data
replicate(1e4, mean(sample(X, 500, replace = T)))
Obviously you can set up a loop over your data sets as needed.
Michael
On Sat, Nov 12, 2011 at 6:46 PM, Francesca francesca.panco...@gmail.com wrote:
Dear Contributors,
I am trying to perform a simulation over sample data,
but I need to reproduce the same simulation over 4 groups of data. My
ability with for loop is null, in particular related
to dimensions as I always get, no matter what I try,
number of items to replace is not a multiple of replacement length
This is what I intend to do: replicate this operation for
four times, where the index for the four groups is in the
part of the code: datiPc[[1]][,2].
I have to replicate the following code 4 times, where the
changing part is in the data from which I pick the sample,
the data that are stored in datiPc[[1]][,2].
If I had to use data for the four samples, I would substitute the 1 with a
j and replicate a loop four times, but it never worked.
My desired final outcome is a matrix with 1 observations for each
couple of extracted samples, i.e. 8 columns of 1 observations of means.
db-c()
# Estrazione dei campioni dai dati di PGG e TRUST
estr1 - c();
estr2 - c();
m1-c()
m2-c()
tmp1- data1[[1]][,2];
tmp2- data2[[2]][,2];
for(i in 1:100){
estr1-sample(tmp1, 1000, replace = TRUE)
estr2-sample(tmp2, 1000, replace = TRUE)
m1[i]-mean(estr1,na.rm=TRUE)
m2[i]-mean(estr2,na.rm=TRUE)
}
db-data.frame(cbind(m1,m2))
Thanks for any help you can provide.
Best Regards
--
Francesca
--
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Re: [R] R development master class: NYC, Dec 12-13
On 11/13/2011 12:58 PM, Sarah Goslee wrote:
On Sun, Nov 13, 2011 at 2:55 PM, Steve Lianoglou
mailinglist.honey...@gmail.com wrote:
Some of the money I earn from these courses goes to pay for my summer
salary and supports student research. It also gives me confidence that
if I don't get tenure because I've been writing R packages instead of
papers, I can keep doing the work I love.
If that actually happens, that would be an amazing/colossal (not in a
good way) testament to how well the rating system works in academia.
I'm not in academia, but government research. I do go through a review
very similar to the tenure process. Last time, I was told that I couldn't list
my R package and associated papers as a research activity with substantial
impact because it was outside my official scope of work. (Even though I
wrote it so I could *do* my work.) I have no trouble seeing academic
administrators do the same thing.
What can be done to fight that?
Do you publish papers in refereed academic journals, like in
academia?
The ultimate evaluation of the value of publications is the
number of citations to the work. You should be able to go to Science
Citation Index and get reports of the citations to papers you and your
peers have written. With R, I know of two ways to access references.
The simplest is to use the sos package, and then findFn for your name.
Example:
hw. - findFn('{hadley wickham}', 999)
found 517 matches; retrieving 26 pages
2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
summary(hw.)
Call:
findFn(string = {hadley wickham}, maxPages = 999)
Total number of matches: 517
Downloaded 506 links in 24 packages.
Packages with at least 3 matches using pattern
'{hadley%20wickham}'
Package Count MaxScore TotalScore Date
1 ggplot2 2551255 2011-11-04
2 rggobi881 88 2011-04-20
3 reshape541 54 2011-10-07
4 DescribeDisplay233 25 2010-03-24
5helpr201 20 2010-11-05
6 plyr201 20 2011-11-04
7 tourrGui101 10 2011-02-05
8 lvplot 61 6 2010-03-24
9 GGally 42 5 2011-11-04
10 Rd2roxygen 41 4 2011-09-15
11latticeExtra 32 4 2011-11-04
12 hints 31 3 2010-03-24
13 tourr 31 3 2011-09-15
The first few rows are Hadley's packages. The later ones are
other packages that cite him.
Secondly, the information on CRAN for each of Hadley's packages
lists reverse dependencies.
When I look at Science Citation Index for all the papers I've
published, I've been disappointed. When I look at what I've done with
R, it seems that more people have gotten more value from that work than
from the papers I've written. One of the reasons is that papers and
books with companion software is much easier to read and understand,
because walking through R code line by line with examples can answer
many questions that are not easily answered from the printed page alone.
hope this helps.
spencer
p.s. It will be a sad commentary on Rice and the academic tenure system
in the US if Hadley is denied tenure. He has made a major contribution
to the R community and through that to all of humanity through all the
people around the world who use R to help them better understand and
manage their own social, political, and physical environments.
Sarah
--
Spencer Graves, PE, PhD
President and Chief Technology Officer
Structure Inspection and Monitoring, Inc.
751 Emerson Ct.
San José, CA 95126
ph: 408-655-4567
web: www.structuremonitoring.com
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Re: [R] R v2.13.2 - Cannot find Rcmd on path?
On 11-11-13 1:15 PM, Yihui Xie wrote: I remember I was torn into pieces a few months back when I made a wishlist here that R adds its bin path to PATH on Windows during installation. People had tons of reasons of objection. Although I do not use these batchfiles (usually I do not actually use Windows), I see there is a motivation behind them: there needs to be an easy way for Windows users to use R in command line (e.g. R CMD build...). You may argue that it is easy to understand PATH and modify it manually, and I will say nothing but thank Windows again. Sorry this seems to be off-topic. I don't remember any rending and tearing, but I do remember objections to modifying the path during installation. I wouldn't want to write code to do that, because it's hard: - Most people don't want to put R first, because it may hide something important. - Putting it last won't work if an earlier version is already there. So you need to examine the path and correct it, an automatic change is unlikely to be successful. But if you want to write code to do that, just go ahead and do it. Put it in a package, even. Duncan Murdoch Regards, Yihui -- Yihui Xiexieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA 2011/11/13 Uwe Liggeslig...@statistik.tu-dortmund.de: On 13.11.2011 17:29, Gabor Grothendieck wrote: On Fri, Oct 21, 2011 at 5:07 PM, Hardy Griesbauer hgriesba...@hotmail.comwrote: Hello, I recently updated to R version 2.13.2. With R version 2.10.0, I often created and installed R packages, however, I cannot do this since updating. In other words, when I type in Rcmd build -binary PACKAGENAME I receive an error message: Rcmd is not recognized as an internal I suspect that this is because Rcmd.exe is no longer installed in the bin folder, but rather, in the x64 folder within bin. Please help! What I've done so far: 1) Downloaded and installed the latest version of Rtools (as of October 21, 2011). 2) During installation of Rtools, I included the following in the path: C:\Progra~1\R\R-2.13.2\bin\x64 and confirmed that this is on the path. 3) Read every help manual I can find, but I can't seem to locate the answer to this problem. Other information: R version 2.13.2 (2011-09-30) Platform: x86_64-pc-mingw32/x64 (64-bit) My windows version: Windows 7 Home Premium Service Pack 1 64-bit OS. There is a batch command Rcmd.bat at http://batchfiles.googlecode.com that when run will find R using the registry and then run the appropriate Rcmd.exe so that you don't need to change your path or any other environment variable. Its a self contained .bat file so just place it anywhere on your existing path. At the Windows console this command will show you your path: path Now try Rcmd.bat build ...whatever... If your path is not already set to find Rcmd.exe then Rcmd.bat can be abbreviated to just Rcmd in the above line. I wonder again and again why you try to obfuscate things by your layer of non portable batchfiles. Typing the path correctly and according to the syntax is required in both cases anyway. Best, Uwe __ R-help@r-project.org mailing list 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 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 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] sum of squares function
hi, basic question how do i write a function that sums the squares of elements in a vector of any length? thanks Adam -- View this message in context: http://r.789695.n4.nabble.com/sum-of-squares-function-tp4037402p4037402.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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.
Re: [R] identify duplicate from more than one column
Hi Josh, I'm sorry, it was meant for you. I guess for now that error doesn't matter...for now. Essentially, I want to repeat the conditions that state the following, and continue doing so for several variables. At the end of the day, I'm only going to keep the couple ID and remove the duplicates. But, before I do that, I want to see how I can write a line/s that will let me observe both sexes (in the couple) and identify which one has a certain characteristic and apply that to a new variable. For instance, if a male moved residence, but the woman did not, migration = 1, else if a woman moved residence, but not the man, migration = 2, else if both man and woman migrated, then migration = 3, etc... else if both man nor woman did not migrate, then migration = 0 However, in order for me to program this and identify them to construct the variables, I have to ensure that both are in the same couple id, and observe both sexes in the couple before I remove the duplicates. I thought the previous example would help me get at this problem, but it still does not make sense to me. Using the newly created coupleid (Thanks to you guys!) this is what I want to see, where mig = migration: 1 = moved and 0 = did not move: coupleid home z sex agemigmig.new 1 01502918 11 053 13 2 01502918 12 049 13 3 01502901 11 038 02 4 01502901 12 033 12 5 01502902 11 036 13 6 01502902 12 033 13 7 01502903 11 023 00 8 01502903 12 019 00 9 01502904 11 045 02 10 01502905 12 047 12 I hope this makes sense, and thanks again, Josh! Carlos -- View this message in context: http://r.789695.n4.nabble.com/identify-duplicate-from-more-than-one-column-tp4035888p4037652.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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] libary(Rweka) J48 design tree
Hello everybody I'm having some difficulties to design the decision tree algorithm J48. I am using the following code and when I run it gives me the following message plot(m1) Error in plot.Weka_tree(m1) : Plotting of trees with multi-way splits is currently not implemented. #The code library(RWeka) library(randomForest) library(party) if(require(mlbench, quietly = TRUE) require(party, quietly = TRUE)) m1 - J48(income2 ~ age+workclass+native.country, data = dataset) m1 plot(m1) and results #M1 Results workclass = ?: =50K (1433.0/120.0) workclass = Federal-gov: =50K (696.0/281.0) workclass = Local-gov: =50K (1542.0/469.0) workclass = Never-worked: =50K (5.0) workclass = Private: =50K (16939.0/3705.0) workclass = Self-emp-inc | age = 36: =50K (205.0/65.0) | age 36: 50K (652.0/247.0) workclass = Self-emp-not-inc: =50K (1926.0/525.0) workclass = State-gov: =50K (1010.0/262.0) workclass = Without-pay: =50K (13.0/2.0) Number of Leaves : 10 Size of the tree : 12 I tried installing the package RGraphviz, but is not available in CRAN repository. I wonder if there is a package that lets you draw decision trees in a way more effective than the library(party) which the classification algorithms more efficient in R Thanks -- View this message in context: http://r.789695.n4.nabble.com/libary-Rweka-J48-design-tree-tp4037704p4037704.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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] Running totals
I have a table which looks like this: ACC BAL 1 hal -171245.33 2 opn -50487.63 3 pga 213440.38 4 prt 0.18 5 rbs 8292.54 How do I create a column which shows the running totals of the BAL columns? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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.
Re: [R] With an example - Re: rbind.data.frame drops attributes for factor variables
On Nov 13, 2011, at 11:28 AM, Sammy Zee wrote: dataset[ nrow(dataset), ] - c (Male, 5, bad) The above seems to have worked to append a row in place of a rbind(). This method does not drop the custom attributes from the column. Do yo see any issue with this method. Only that it wipes out whatever was in the last row, I suppose you could get around that issue by making a duplicate row: dataset - dataset[ c(1:dataset, nrow(dataset)), ] dataset[ nrow(dataset), ] - c (Male, 5, bad) I generally use NROW rather than nrow but I cannot remember why. -- David. Thanks, Sammy On Sat, Nov 12, 2011 at 10:16 PM, David Winsemius dwinsem...@comcast.net wrote: On Nov 12, 2011, at 6:40 PM, Sammy Zee wrote: Thanks David. Besides rbind(), is there any other way to add a row to a data frame so that I do not lose the custom attributes. I have already told you the method that I know of. You don't seem to have taken my poin that it is not a data.frame specific problem but rahter a facor problem. You are welcome to redefine `rbind.data.frame`. The R language is rather flexible in that manner. -- David. Thanks, Sammy On Sat, Nov 12, 2011 at 5:17 PM, David Winsemius dwinsem...@comcast.net wrote: On Nov 12, 2011, at 2:47 PM, Sammy Zee wrote: When I use rbind() or rbind.data.frame() to add a row to an existing dataframe, it appears that attributes for the column of type factor are dropped. See the sample example below to reproduce the problem. Please suggest How I can fix this. Thanks, Sammy a=c(Male, Male, Female, Male) b=c(1,2,3,4) c=c(great, bad, good, bad) dataset- data.frame (gender = a, count = b, answer = c) dataset gender count answer 1 Male 1 great 2 Male 2bad 3 Female 3 good 4 Male 4bad attributes(dataset$answer) $levels [1] bad good great $class [1] factor Now adding some custom attributes to column dataset$answer attributes(dataset$answer)-c(attributes(dataset $answer),list(newattr1=custom-attr1)) attributes(dataset$answer)-c(attributes(dataset $answer),list(newattr2=custom-attr2)) If you look through the code of rbind.data.frame you see that column values are processed with the 'factor' function. attributes(dataset$answer) $levels [1] bad good great $class [1] factor $newattr1 [1] custom-attr1 $newattr2 [1] custom-attr2 attributes(factor(dataset$answer)) $levels [1] bad good great $class [1] factor So I think you are out of luck. You will need to restore the special attributes yourself. -- David. attributes(dataset$answer) $levels [1] bad good great $class [1] factor $newattr1 [1] custom-attr1 $newattr2 [1] custom-attr2 However as soon as I add a row to this data frame (dataset) by rbind(), it loses the custom attributes (newattr1 and newattr2) I have just added newrow = c(gender=Female, count = 5, answer = great) dataset - rbind(dataset, newrow) attributes(dataset$answer) $levels [1] bad good great $class [1] factor the two custom attributes are dropped!! Any suggestion why this is happening. On Fri, Nov 11, 2011 at 11:44 AM, Jeff Newmiller jdnew...@dcn.davis.ca.uswrote: As the doctor says, if it hurts don't do that. A factor is a sequence of integers with a corresponding list of character strings. Factors in two separate vectors can and usually do map the same integer to different strings, and R cannot tell how you want that resolved. Convert these columns to character before combining them, and only convert to factor when you have all of your possibilities present (or you specify them in the creation of the factor vector). --- Jeff NewmillerThe . . Go Live... Sammy Zee szee2...@gmail.com wrote: Hi all, When I use rbind() or rbind.data.frame() to add a row to an existing dataframe, it appears that attributes for the column of type factor are dropped. I see the following post with same problem. However i did not see any reply to the following posting offering a solution. Could someone please help. http://r.789695.n4.nabble.com/rbind-data-frame-drops-attributes-for-factor-variables-td919575.html Thanks, Sammy [[alternative HTML version deleted]] ___ David Winsemius, MD West Hartford, CT David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list 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.
Re: [R] sum of squares function
Hi Adam, You're in luck, arithmetic operations in R are vectorized so it does not take any extra effort. x - 1:10 sum(x^2) cheers, Josh On Sun, Nov 13, 2011 at 12:20 PM, covfish87 covfis...@hotmail.co.uk wrote: hi, basic question how do i write a function that sums the squares of elements in a vector of any length? thanks Adam -- View this message in context: http://r.789695.n4.nabble.com/sum-of-squares-function-tp4037402p4037402.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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. -- Joshua Wiley Ph.D. Student, Health Psychology Programmer Analyst II, ATS Statistical Consulting Group University of California, Los Angeles https://joshuawiley.com/ __ R-help@r-project.org mailing list 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.
Re: [R] Running totals
Table is not a regular data structure in R so I can't help further without a bit of clarification, but try ?cumsum and ?cbind. Michael On Nov 13, 2011, at 4:18 PM, Mark Carter mcturra2...@yahoo.co.uk wrote: I have a table which looks like this: � ACC��� BAL 1 hal -171245.33 2 opn� -50487.63 3 pga� 213440.38 4 prt�� 0.18 5 rbs��� 8292.54 How do I create a column which shows the running totals of the BAL columns? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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 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.
Re: [R] Running totals
Hi Mark, Take a look at ?cumsum and see if this is what you want: ## your data output via dput() (easy to copy and paste from email to R) dat - structure(list(ACC = c(hal, opn, pga, prt, rbs), BAL = c(-171245.33, -50487.63, 213440.38, 0.18, 8292.54)), .Names = c(ACC, BAL ), class = data.frame, row.names = c(1, 2, 3, 4, 5 )) dat$RTotal - cumsum(dat$BAL) dat dat ACCBAL RTotal 1 hal -171245.33 -171245.33 2 opn -50487.63 -221732.96 3 pga 213440.38 -8292.58 4 prt 0.18 -8292.40 5 rbs8292.54 0.14 Hope this helps, Josh On Sun, Nov 13, 2011 at 1:18 PM, Mark Carter mcturra2...@yahoo.co.uk wrote: I have a table which looks like this: ACC BAL 1 hal -171245.33 2 opn -50487.63 3 pga 213440.38 4 prt 0.18 5 rbs 8292.54 How do I create a column which shows the running totals of the BAL columns? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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. -- Joshua Wiley Ph.D. Student, Health Psychology Programmer Analyst II, ATS Statistical Consulting Group University of California, Los Angeles https://joshuawiley.com/ __ R-help@r-project.org mailing list 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] issue plotting TukeyHSD
Hello, When I try to use TukeyHSD in the following way it shows the confidence interval corresponding to the last factor only. throughput.aov - aov(Throughput~No_databases+Partitioning+No_middlewares+Queue_size,data=throughput) plot(TukeyHSD(throughput.aov)) # I expected here to see the confidence intervals for all factors but see only the last. OTOH this one works but then it is unreadable due to the long labels of combined effects in the Y-axis ticks. throughput.aov - aov(Throughput~No_databases*Partitioning*No_middlewares*Queue_size,data=throughput) TIA, Best regards, Giovanni __ R-help@r-project.org mailing list 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] 2^k*r (with replications) experimental design question
Hello, I have one replication (r=1 of the 2^k*r) of a 2^k experimental design in the context of performance analysis i.e. my response variables are Throughput and Response Time. I use the aov function and the results look ok: str(throughput) 'data.frame': 286 obs. of 7 variables: $ Time : int 6 7 8 9 10 11 12 13 14 15 ... $ Throughput: int 42 44 33 41 43 40 37 40 42 37 ... $ No_databases : Factor w/ 2 levels 1,4: 1 1 1 1 1 1 1 1 1 1 ... $ Partitioning : Factor w/ 2 levels sharding,replication: 1 1 1 1 1 1 1 1 1 1 ... $ No_middlewares: Factor w/ 2 levels 2,4: 1 1 1 1 1 1 1 1 1 1 ... $ Queue_size: Factor w/ 2 levels 40,100: 1 1 1 1 1 1 1 1 1 1 ... $ No_clients: Factor w/ 1 level 128: 1 1 1 1 1 1 1 1 1 1 ... head(throughput) Time Throughput No_databases Partitioning No_middlewares Queue_size 16 421 sharding 2 40 27 441 sharding 2 40 38 331 sharding 2 40 49 411 sharding 2 40 5 10 431 sharding 2 40 6 11 401 sharding 2 40 throughput.aov - aov(Throughput~No_databases+Partitioning+No_middlewares+Queue_size,data=throughput) summary(throughput.aov) DfSum Sq Mean Sq F valuePr(F) No_databases 128488651 28488651 53.4981 2.713e-12 *** Partitioning17168771687 0.1346 0.713966 No_middlewares 1 5624454 5624454 10.5620 0.001295 ** Queue_size 1 5089250892 0.0956 0.757443 Residuals 281 149637226 532517 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 This is somehow what I expected and I am happy, it is saying that the Throughput is significatively affected firstly by the number of database instances and secondly by the number of middleware instances. The problem is that I need to integrate multiple replications of this same 2^k so I can also account for experimental error i.e. the _r_ of 2^k*r but I can't see how to integrate the _r_ term into the data and into the aov function parameters. Can anyone advice? TIA, Best regards, Giovanni __ R-help@r-project.org mailing list 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.
Re: [R] 2^k*r (with replications) experimental design question
I'm guessing you have nine replicates of a 2^5 factorial design with a couple of missing values. If so, define a variable to designate the replicates and use it as a blocking factor in the ANOVA. If you want to treat the replicates as a random rather than a fixed factor, then look into the nlme or lme4 packages. HTH, Dennis On Sun, Nov 13, 2011 at 4:33 PM, Giovanni Azua brave...@gmail.com wrote: Hello, I have one replication (r=1 of the 2^k*r) of a 2^k experimental design in the context of performance analysis i.e. my response variables are Throughput and Response Time. I use the aov function and the results look ok: str(throughput) 'data.frame': 286 obs. of 7 variables: $ Time : int 6 7 8 9 10 11 12 13 14 15 ... $ Throughput : int 42 44 33 41 43 40 37 40 42 37 ... $ No_databases : Factor w/ 2 levels 1,4: 1 1 1 1 1 1 1 1 1 1 ... $ Partitioning : Factor w/ 2 levels sharding,replication: 1 1 1 1 1 1 1 1 1 1 ... $ No_middlewares: Factor w/ 2 levels 2,4: 1 1 1 1 1 1 1 1 1 1 ... $ Queue_size : Factor w/ 2 levels 40,100: 1 1 1 1 1 1 1 1 1 1 ... $ No_clients : Factor w/ 1 level 128: 1 1 1 1 1 1 1 1 1 1 ... head(throughput) Time Throughput No_databases Partitioning No_middlewares Queue_size 1 6 42 1 sharding 2 40 2 7 44 1 sharding 2 40 3 8 33 1 sharding 2 40 4 9 41 1 sharding 2 40 5 10 43 1 sharding 2 40 6 11 40 1 sharding 2 40 throughput.aov - aov(Throughput~No_databases+Partitioning+No_middlewares+Queue_size,data=throughput) summary(throughput.aov) Df Sum Sq Mean Sq F value Pr(F) No_databases 1 28488651 28488651 53.4981 2.713e-12 *** Partitioning 1 71687 71687 0.1346 0.713966 No_middlewares 1 5624454 5624454 10.5620 0.001295 ** Queue_size 1 50892 50892 0.0956 0.757443 Residuals 281 149637226 532517 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 This is somehow what I expected and I am happy, it is saying that the Throughput is significatively affected firstly by the number of database instances and secondly by the number of middleware instances. The problem is that I need to integrate multiple replications of this same 2^k so I can also account for experimental error i.e. the _r_ of 2^k*r but I can't see how to integrate the _r_ term into the data and into the aov function parameters. Can anyone advice? TIA, Best regards, Giovanni __ R-help@r-project.org mailing list 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 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.
Re: [R] 2^k*r (with replications) experimental design question
Hi Denis, Thank you again :) what do you exactly mean with blocking factor, that it will be like the others? I'd prefer not to treat the replicates as random but rather account for the experimental error using the replicates. Ahhh I see what you mean, so the experimental error will show up as the SS of my new variable Replicate ... great! Thank you! Best regards, Giovanni On Nov 14, 2011, at 2:38 AM, Dennis Murphy wrote: I'm guessing you have nine replicates of a 2^5 factorial design with a couple of missing values. If so, define a variable to designate the replicates and use it as a blocking factor in the ANOVA. If you want to treat the replicates as a random rather than a fixed factor, then look into the nlme or lme4 packages. HTH, Dennis On Sun, Nov 13, 2011 at 4:33 PM, Giovanni Azua brave...@gmail.com wrote: Hello, I have one replication (r=1 of the 2^k*r) of a 2^k experimental design in the context of performance analysis i.e. my response variables are Throughput and Response Time. I use the aov function and the results look ok: str(throughput) 'data.frame': 286 obs. of 7 variables: $ Time : int 6 7 8 9 10 11 12 13 14 15 ... $ Throughput: int 42 44 33 41 43 40 37 40 42 37 ... $ No_databases : Factor w/ 2 levels 1,4: 1 1 1 1 1 1 1 1 1 1 ... $ Partitioning : Factor w/ 2 levels sharding,replication: 1 1 1 1 1 1 1 1 1 1 ... $ No_middlewares: Factor w/ 2 levels 2,4: 1 1 1 1 1 1 1 1 1 1 ... $ Queue_size: Factor w/ 2 levels 40,100: 1 1 1 1 1 1 1 1 1 1 ... $ No_clients: Factor w/ 1 level 128: 1 1 1 1 1 1 1 1 1 1 ... head(throughput) Time Throughput No_databases Partitioning No_middlewares Queue_size 16 421 sharding 2 40 27 441 sharding 2 40 38 331 sharding 2 40 49 411 sharding 2 40 5 10 431 sharding 2 40 6 11 401 sharding 2 40 throughput.aov - aov(Throughput~No_databases+Partitioning+No_middlewares+Queue_size,data=throughput) summary(throughput.aov) DfSum Sq Mean Sq F valuePr(F) No_databases 128488651 28488651 53.4981 2.713e-12 *** Partitioning17168771687 0.1346 0.713966 No_middlewares 1 5624454 5624454 10.5620 0.001295 ** Queue_size 1 5089250892 0.0956 0.757443 Residuals 281 149637226 532517 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 This is somehow what I expected and I am happy, it is saying that the Throughput is significatively affected firstly by the number of database instances and secondly by the number of middleware instances. The problem is that I need to integrate multiple replications of this same 2^k so I can also account for experimental error i.e. the _r_ of 2^k*r but I can't see how to integrate the _r_ term into the data and into the aov function parameters. Can anyone advice? TIA, Best regards, Giovanni __ R-help@r-project.org mailing list 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 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.
Re: [R] identify duplicate from more than one column
You might find reshape() useful here. Use sex as the 'time' variable so you get a row for each couple containing the age and other data for each member of the couple. That format makes it easy to compare the ages (or migration status, etc.) of members of one couple. You need to define an idvar here, basically a couple identifier and I made it by pasting together the unit and home numbers: dat$unit_home - paste(dat$unit, dat$home, sep=_) reshape(dat, timevar=sex, times=c(1,2), idvar=unit_home, direction=wide) unit_home obs.1 unit.1 home.1 z.1 age.1 obs.2 unit.2 home.2 z.2 age.2 1 15029_18 1 15029 18 153 2 15029 18 149 315029_1 3 15029 1 138 4 15029 1 133 515029_2 5 15029 2 136 6 15029 2 133 715029_3 7 15029 3 123 8 15029 3 119 915029_4NA NA NA NANA 9 15029 4 145 10 15029_5NA NA NA NANA10 15029 5 147 or, to make things clearer, make sex into a factor: dat$sex - factor(dat$sex, levels=1:2, labels=c(M,F)) reshape(dat, timevar=sex, times=c(M,F), idvar=unit_home, direction=wide) unit_home obs.M unit.M home.M z.M age.M obs.F unit.F home.F z.F age.F 1 15029_18 1 15029 18 153 2 15029 18 149 315029_1 3 15029 1 138 4 15029 1 133 515029_2 5 15029 2 136 6 15029 2 133 715029_3 7 15029 3 123 8 15029 3 119 915029_4NA NA NA NANA 9 15029 4 145 10 15029_5NA NA NA NANA10 15029 5 147 reshape() doesn't do a lot of error checking. If you have trios or same-sex couples it will just take the first (I think) of each sex and ignore the rest. If you want to ignore the non-couples, remove rows with any NA's in them. This example is from stats::reshape(). Many people prefer to use the reshape2 or reshape (or reshape3) packages. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of jour4life Sent: Sunday, November 13, 2011 1:47 PM To: r-help@r-project.org Subject: Re: [R] identify duplicate from more than one column Hi Josh, I'm sorry, it was meant for you. I guess for now that error doesn't matter...for now. Essentially, I want to repeat the conditions that state the following, and continue doing so for several variables. At the end of the day, I'm only going to keep the couple ID and remove the duplicates. But, before I do that, I want to see how I can write a line/s that will let me observe both sexes (in the couple) and identify which one has a certain characteristic and apply that to a new variable. For instance, if a male moved residence, but the woman did not, migration = 1, else if a woman moved residence, but not the man, migration = 2, else if both man and woman migrated, then migration = 3, etc... else if both man nor woman did not migrate, then migration = 0 However, in order for me to program this and identify them to construct the variables, I have to ensure that both are in the same couple id, and observe both sexes in the couple before I remove the duplicates. I thought the previous example would help me get at this problem, but it still does not make sense to me. Using the newly created coupleid (Thanks to you guys!) this is what I want to see, where mig = migration: 1 = moved and 0 = did not move: coupleid home z sex agemigmig.new 1 01502918 11 053 13 2 01502918 12 049 13 3 01502901 11 038 02 4 01502901 12 033 12 5 01502902 11 036 13 6 01502902 12 033 13 7 01502903 11 023 00 8 01502903 12 019 00 9 01502904 11 045 02 10 01502905 12 047 12 I hope this makes sense, and thanks again, Josh! Carlos -- View this message in context: http://r.789695.n4.nabble.com/identify-duplicate-from-more-than-one- column-tp4035888p4037652.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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 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,
Re: [R] issue plotting TukeyHSD
On Nov 13, 2011, at 7:22 PM, Giovanni Azua wrote: Hello, When I try to use TukeyHSD in the following way it shows the confidence interval corresponding to the last factor only. throughput.aov - aov(Throughput~No_databases+Partitioning +No_middlewares+Queue_size,data=throughput) plot(TukeyHSD(throughput.aov)) # I expected here to see the confidence intervals for all factors but see only the last. OTOH this one works but then it is unreadable due to the long labels of combined effects in the Y-axis ticks. throughput.aov - aov(Throughput~,data=throughput) If thine name offend thee, pluck it out. names(throughput) [c(No_databases,Partitioning,No_middlewares,Queue_size)] - c(N_db,part,N_midw,Qu_sz) -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list 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.
Re: [R] help with ggplot backgrounds
You are more likely to receive helpful responses if you: a) Provide a reproducible example (e.g. https://github.com/hadley/devtools/wiki/Reproducibility) b) Post to the ggplot2 mailing list. Hadley On Fri, Oct 28, 2011 at 5:03 PM, RanRL rnr...@gmail.com wrote: Hi, I have two questions regarding plotting of this dataset: Product Color StoreA StoreB StoreC Price A Red 4 2 3 78 Blue 5 2 2 78 Greem 4 3 2 80 B Red 3 And so on (Not all products have same colors). I made 2 plots: one is a scatter where x=Price and y=Values (of different stores). The different stores are facet_wrapped, and Color is indicated by point color while Product by point_shape. Second plot is a polar plot of geom_bars with position=dodge for all Products to differentiate the colors. The y value is the value for each store (Price is not represented). My questions: 1. for the first plot, I want to make a background area split into 3, top right is red (indicating high-price/high-values), middle is yellow, the rest is green (these are kind of reverse-log areas, like in heat maps). 2. for the second plot, the red-yellow green are just background geom_rects filled in, but I cant figure out how to specify the xmin and xmax for this (since they are discrete variables). Any help will be appreciated, thanks. -- View this message in context: http://r.789695.n4.nabble.com/help-with-ggplot-backgrounds-tp3949320p3949320.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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. -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-help@r-project.org mailing list 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.
Re: [R] R v2.13.2 - Cannot find Rcmd on path?
Well, I just mean to give the user an option during installation -- like you did in Rtools. I have decided not to argue on this issue any more. Thanks a lot anyway! Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Sun, Nov 13, 2011 at 4:20 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 11-11-13 1:15 PM, Yihui Xie wrote: I remember I was torn into pieces a few months back when I made a wishlist here that R adds its bin path to PATH on Windows during installation. People had tons of reasons of objection. Although I do not use these batchfiles (usually I do not actually use Windows), I see there is a motivation behind them: there needs to be an easy way for Windows users to use R in command line (e.g. R CMD build...). You may argue that it is easy to understand PATH and modify it manually, and I will say nothing but thank Windows again. Sorry this seems to be off-topic. I don't remember any rending and tearing, but I do remember objections to modifying the path during installation. I wouldn't want to write code to do that, because it's hard: - Most people don't want to put R first, because it may hide something important. - Putting it last won't work if an earlier version is already there. So you need to examine the path and correct it, an automatic change is unlikely to be successful. But if you want to write code to do that, just go ahead and do it. Put it in a package, even. Duncan Murdoch Regards, Yihui -- Yihui Xiexieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA __ R-help@r-project.org mailing list 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.
Re: [R] libary(Rweka) J48 design tree
On Sun, 13 Nov 2011, RMSOPS wrote: Hello everybody I'm having some difficulties to design the decision tree algorithm J48. I am using the following code and when I run it gives me the following message plot(m1) Error in plot.Weka_tree(m1) : Plotting of trees with multi-way splits is currently not implemented. The package partykit which recently was released to CRAN should be able to help here: library(partykit) plot(as.party(m1)) Furthermore, write_to_dot(m1, m1.dot) can always be used as described in Kurt Hornik, Christian Buchta, Achim Zeileis (2009) Open-Source Machine Learning: R Meets Weka. Computational Statistics, 24(2), 225-232. doi:10.1007/s00180-008-0119-7 Either use Graphviz directoy on the .dot file or employ Rgraphviz which is hosted at Bioconductor: http://www.Bioconductor.org/packages/release/bioc/html/Rgraphviz.html #The code library(RWeka) library(randomForest) library(party) if(require(mlbench, quietly = TRUE) require(party, quietly = TRUE)) m1 - J48(income2 ~ age+workclass+native.country, data = dataset) m1 plot(m1) and results #M1 Results workclass = ?: =50K (1433.0/120.0) workclass = Federal-gov: =50K (696.0/281.0) workclass = Local-gov: =50K (1542.0/469.0) workclass = Never-worked: =50K (5.0) workclass = Private: =50K (16939.0/3705.0) workclass = Self-emp-inc | age = 36: =50K (205.0/65.0) | age 36: 50K (652.0/247.0) workclass = Self-emp-not-inc: =50K (1926.0/525.0) workclass = State-gov: =50K (1010.0/262.0) workclass = Without-pay: =50K (13.0/2.0) Number of Leaves : 10 Size of the tree : 12 I tried installing the package RGraphviz, but is not available in CRAN repository. I wonder if there is a package that lets you draw decision trees in a way more effective than the library(party) which the classification algorithms more efficient in R Thanks -- View this message in context: http://r.789695.n4.nabble.com/libary-Rweka-J48-design-tree-tp4037704p4037704.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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 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.
Re: [R] Odp: Error in matrix, not ordered vectors or numerical value, and SIAR.
Hi Hello Petr, The demo's don't run either, with the same errors. In that case you shall contact the package maintainer and in a meantime you could try to debug the function yourself if you are in desperate need for the result. Petr Thanks for your help. Best wishes. -- View this message in context: http://r.789695.n4.nabble.com/Error-in- matrix-not-ordered-vectors-or-numerical-value-and-SIAR-tp4024578p4033682.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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 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.
Re: [R] With an example - Re: rbind.data.frame drops attributes for factor variables
dataset[ nrow(dataset), ] - c (Male, 5, bad) The above seems to have worked to append a row in place of a rbind(). This No. It overwrites your last row. You maybe meant dataset[ nrow(dataset)+1, ] - c (Male, 5, bad) Regards Petr method does not drop the custom attributes from the column. Do yo see any issue with this method. Thanks, Sammy On Sat, Nov 12, 2011 at 10:16 PM, David Winsemius dwinsem...@comcast.netwrote: On Nov 12, 2011, at 6:40 PM, Sammy Zee wrote: Thanks David. Besides rbind(), is there any other way to add a row to a data frame so that I do not lose the custom attributes. I have already told you the method that I know of. You don't seem to have taken my poin that it is not a data.frame specific problem but rahter a facor problem. You are welcome to redefine `rbind.data.frame`. The R language is rather flexible in that manner. -- David. Thanks, Sammy On Sat, Nov 12, 2011 at 5:17 PM, David Winsemius dwinsem...@comcast.net wrote: On Nov 12, 2011, at 2:47 PM, Sammy Zee wrote: When I use rbind() or rbind.data.frame() to add a row to an existing dataframe, it appears that attributes for the column of type factor are dropped. See the sample example below to reproduce the problem. Please suggest How I can fix this. Thanks, Sammy a=c(Male, Male, Female, Male) b=c(1,2,3,4) c=c(great, bad, good, bad) dataset- data.frame (gender = a, count = b, answer = c) dataset gender count answer 1 Male 1 great 2 Male 2bad 3 Female 3 good 4 Male 4bad attributes(dataset$answer) $levels [1] bad good great $class [1] factor Now adding some custom attributes to column dataset$answer attributes(dataset$answer)-c(**attributes(dataset$answer),** list(newattr1=custom-attr1)) attributes(dataset$answer)-c(**attributes(dataset$answer),** list(newattr2=custom-attr2)) If you look through the code of rbind.data.frame you see that column values are processed with the 'factor' function. attributes(dataset$answer) $levels [1] bad good great $class [1] factor $newattr1 [1] custom-attr1 $newattr2 [1] custom-attr2 attributes(factor(dataset$**answer)) $levels [1] bad good great $class [1] factor So I think you are out of luck. You will need to restore the special attributes yourself. -- David. attributes(dataset$answer) $levels [1] bad good great $class [1] factor $newattr1 [1] custom-attr1 $newattr2 [1] custom-attr2 However as soon as I add a row to this data frame (dataset) by rbind(), it loses the custom attributes (newattr1 and newattr2) I have just added newrow = c(gender=Female, count = 5, answer = great) dataset - rbind(dataset, newrow) attributes(dataset$answer) $levels [1] bad good great $class [1] factor the two custom attributes are dropped!! Any suggestion why this is happening. On Fri, Nov 11, 2011 at 11:44 AM, Jeff Newmiller jdnew...@dcn.davis.ca.us**wrote: As the doctor says, if it hurts don't do that. A factor is a sequence of integers with a corresponding list of character strings. Factors in two separate vectors can and usually do map the same integer to different strings, and R cannot tell how you want that resolved. Convert these columns to character before combining them, and only convert to factor when you have all of your possibilities present (or you specify them in the creation of the factor vector). --**--** --- Jeff NewmillerThe . . Go Live... Sammy Zee szee2...@gmail.com wrote: Hi all, When I use rbind() or rbind.data.frame() to add a row to an existing dataframe, it appears that attributes for the column of type factor are dropped. I see the following post with same problem. However i did not see any reply to the following posting offering a solution. Could someone please help. http://r.789695.n4.nabble.com/**rbind-data-frame-drops-** attributes-for-factor-**variables-td919575.htmlhttp://r. 789695.n4.nabble.com/rbind-data-frame-drops-attributes-for-factor- variables-td919575.html Thanks, Sammy [[alternative HTML version deleted]] ___ David Winsemius, MD West Hartford, CT [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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 https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
Re: [R] Problem with simple random slope in gam and bam (mgcv package)
Martijn,
This was a problem in summary.gam handling re terms with largish
datasets: I've uploaded a fix for this in mgcv_1.7-11. Hopefully on cran
in the next few days.
best,
Simon
On 09/11/11 12:41, Martijn Wieling wrote:
Dear useRs,
This is the first time I post to this list and I would appreciate any
help available. I've used the excellent mgcv package for a while now
to investigate geographical patterns of language variation, and it has
has always worked without any problems for me. The problem below
occurs using R 2.14.0 (both 32 and 64 bit versions in Windows and the
64 bit version in Unix) and mgcv (both version 1.7-10 and 1.7-6).
In my (simplified) model predicting pronunciation distance I'd like to
include a random slope per Participant for a binary value (IsDem)
which stores a word-specific characteristic. I load the data
(available at http://www.martijnwieling.nl/dat.csv) and run the model
as follows:
library(mgcv) # version 1.7-10, but problem also occurs with earlier versions
(e.g., 1.7-6)
dat = read.csv('dat.csv',header=T) # data available at:
http://www.martijnwieling.nl/dat.csv
dim(dat) # the original dataset is larger, but the problem also occurs in this
subset
[1] 2 4
model = bam(PronDist ~ s(Participant,IsDem,bs=re), data=dat)
print(model) # works fine
summary(model, freq=T) # works fine
summary(model) # the Bayesian p-value estimation does not work:
Error in eigen(B, symmetric = TRUE) : infinite or missing values in 'x'
I obviously am interested in more complex models, but whenever I
include any binary value as a by-word or by-participant random slope I
get the same error. I've tried to locate the error and it appears to
occur in the function pinvXVX in the block which 'deals with the
fractional part of the pinv'.
Any help would be appreciated!
With kind regards,
Martijn Wieling
University of Groningen
http://www.martijnwieling.nl
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--
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Re: [R] R development master class: NYC, Dec 12-13
On Nov 13, 2011, at 20:53 , Alex Ruiz Euler wrote: Ha! Point publicly acknowledged. Best, A. At any rate, R-help has always allowed R-related course announcements, commercial or not. The position has been that as long as it is of interest for R users and not overly intrusive, it is accepted. (Posters need to beware the potential negative publicity from perceived spamming, though.) R developers have been enrolled as teachers for commercial courses (as well as non-commercial or semi-commercial ones) and of course been paid for their work. I don't see a particular problem with someone cutting out the middle man. Peter D. On Sun, 13 Nov 2011 13:41:36 -0600 Hadley Wickham had...@rice.edu wrote: No seriously, as much as I'm for free enterprise, it feels awkward to see you promote an (expensive!) course in a list where people offer not only their knowledge, but also the tools you use, for free. You might have a point if I taught this course instead of offering knowledge and code for free, but I do it as well. -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-help@r-project.org mailing list 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] What is the CADF test criterion=BIC report?
Hello: I am a rookie in using R. When I used the unit root test in CADFtest, I got the different t-test statistics between using criterion=BIC and no using criterion. But when I checked the result with eviews, I find out that no using criterion is correct. Why after using criterion=BIC, I got the different result? Paul data(Canada) ADFt - CADFtest(Canada[,1], max.lag.y = 14, criterion=BIC) summary(ADFt) Augmented DF test ADF test t-test statistic: -1.389086 p-value:0.855681 Max lag of the diff. dependent variable:1.00 Call: dynlm(formula = formula(model), start = obs.1, end = obs.T) Residuals: Min 1Q Median 3Q Max -0.79726 -0.20587 -0.03332 0.23840 0.70460 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) 24.342321 17.435476 1.3960.167 trnd 0.009959 0.006941 1.4350.156 L(y, 1) -0.026068 0.018767 -1.3890.856 L(d(y), 1) 0.615983 0.092632 6.650 7.18e-09 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Residual standard error: 0.3533 on 65 degrees of freedom Multiple R-squared: 0.413, Adjusted R-squared: 0.3859 F-statistic:NA on NA and NA DF, p-value: NA ADFt1 - CADFtest(Canada[,1], max.lag.y =1) summary(ADFt1) Augmented DF test ADF test t-test statistic: -2.7285715 p-value:0.2282588 Max lag of the diff. dependent variable:1.000 Call: dynlm(formula = formula(model), start = obs.1, end = obs.T) Residuals: Min 1Q Median 3Q Max -0.84769 -0.24745 -0.02081 0.24187 0.82344 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) 47.661910 17.439021 2.733 0.00776 ** trnd 0.019217 0.007005 2.743 0.00754 ** L(y, 1) -0.051256 0.018785 -2.729 0.22826 L(d(y), 1) 0.753011 0.075724 9.944 1.61e-15 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Residual standard error: 0.3937 on 78 degrees of freedom Multiple R-squared: 0.5674, Adjusted R-squared: 0.5508 F-statistic:NA on NA and NA DF, p-value: NA __ R-help@r-project.org mailing list 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.
Re: [R] identify duplicate from more than one column
Hi William, This worked like a charm! I was thinking about using reshape(), but was unsure on how to approach it. Though I have a whole lot of variables, I decided to keep only those variables that contained both sexes' characteristics, reshape it into wide format, and merge with the rest of the data later and it worked perfectly. Thanks you guys so much. All ideas were great and I greatly appreciate your help!! Best, Carlos -- View this message in context: http://r.789695.n4.nabble.com/identify-duplicate-from-more-than-one-column-tp4035888p4038380.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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.
Re: [R] rJava .jinit() : Cannot create Java virtual machine (-1)
Hi, I have the same problem in R, and I want to ask you that how to solve the problem. Thank you very much. Wang 2011-11-14 ahwangyuwei [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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] Confused with an error message related to plotrix library in the newer versions of R.
Dear R Users, Greetings! I am confused with an error message related to plotrix library in the newer versions of R. I used to run an R script without fail in the earlier versions (R 2.8.1) of R; but the same script is now throwing up an error message in the newer versions (Now I have R 2.13.0 R 2.14.0). Herewith I am furnishing the same code for your perusal. It would have been better if somebody could look into this matter and explain in detail. require(plotrix) xy.pop - c(17,15,13,11,9,8,6,5,4,3,2,2,1,3) xx.pop - c(17,14,12,11,11,8,6,5,4,3,2,2,2,3) agelabels - c(0-4,5-9,10-14,15-19,20-24,25-29,30-34, 35-39,40-44,45-49,50-54,55-59,60-64,65+) xycol-color.gradient(c(0,0,0.5,0.15),c(0.25,0.5,0.5,1.75),c(0.5,1.5,1,0),18) xxcol-color.gradient(c(0,1,0.5,1),c(0.25,0.5,0.5,1.25),c(0.5,0.25,0.5,1.5),18) par(mar=pyramid.plot(xy.pop,xx.pop,labels=agelabels, labelcex=1.125, main=Population Pyramid -- Malawi, xycol=xycol, xxcol=xxcol)) Much Appreciated, *Prasanth, V.P.* Global Manager Biometrics Delta Technology Management Services Pvt Ltd, Plot No: 13/2, Sector - I, Third Floor, HUDA Techno Enclave, Madhapur, Hyderabad - 500 081. ( : +91-40-3028 2113 È: +91-9848 290025 * : vprasa...@deltaintech.com ** The information contained in this email is confidential and may contain proprietary information. It is meant solely for the intended recipient. Access to this email by anyone else is unauthorized. If you are not the intended recipient, any disclosure, copying, distribution or any action taken or omitted in reliance on this, is prohibited and may be unlawful. No liability or responsibility is accepted if information or data is, for whatever reason corrupted or does not reach its intended recipient. No warranty is given that this email is free of viruses. The views expressed in this email are, unless otherwise stated, those of the author and not those of DELTA Technology and Management Services pvt ltd or its management. DELTA Technology and Management Services pvt ltd reserves the right to monitor intercept and block emails addressed to its users or take any other action in accordance with its email use policy Thank you in advance for your cooperation. ** P Please don't print this e-mail unless you really need to. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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.
