Re: [R] Formatting multi-way ANOVA output for spectra analysis
Dear Robert,
Although you don't say so, it sounds as if you may be using the Anova()
function in the car package, which is what the R Commander uses for ANOVA. If
so, in most cases, Anova() returns an object of class c("anova", "data.frame"),
which can be manipulated as a data frame. To see this, try something like
str(Anova(your.model))
You should be able to extract, manipulate, and graph whatever components of the
object interest you.
I hope this helps,
John
-
John Fox
Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
Web: https://socialsciences.mcmaster.ca/jfox/
> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Robert D.
> Bowers M.A.
> Sent: Wednesday, July 25, 2018 1:12 PM
> To: r-help@r-project.org
> Subject: [R] Formatting multi-way ANOVA output for spectra analysis
>
> I've studied R a little bit, although I haven't used it in some time (except
> via
> RCommander). I'm working on my dissertation project and have
> spectrometer data that I need to evaluate. I need to find a way to simplify
> the
> output from multi-way ANOVA so I can reduce the areas of the spectrum to
> only those where there are significant differences between sites. (A
> preliminary study on a too-small sample size indicates that certain areas of
> the spectrum can distinguish between sites. This project is the next step.)
>
> The dataset is comprised of analyses done on samples from five separate
> locations, with 50 samples taken from each site. The output of the
> spectrometer per sample is values for 2048 individual wavelengths, in a
> spreadsheet with the wavelength as the first column. Since I'm doing the
> analysis wavelength-by-wavelength, I've transposed the data and broke the
> data for the project down into smaller spreadsheets (so that R can perform
> ANOVA on each wavelength).
>
> The problem is, I can do ANOVA now on each wavelength, but I don't need a
> full output table for each... I just need to know if there is significant
> variation
> between any of the sites at that wavelength, based on 95% confidence level
> (or better). If I could get some sort of simple chart (or a single line in a
> spreadsheet), that would help to narrow down the areas of the spectrum that I
> need to focus on to evaluate the results of the tests.
>
> I've been reading information about ANOVA, but have found very little that is
> clear about formatting the output - and I don't need to rehash all of the
> math. I just need to find out how to hack down the output to just the part I
> need (if possible). Once that's done, I can decide what wavelengths are
> valuable for future tests and simplify the process.
>
> Thanks for any help given!
>
> Bob
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html
> and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Batch mode questions.
On Wed, 25 Jul 2018, David Winsemius wrote: # create a list from these files list.filenames<-list.files(pattern=".CSV$") # This gets a list of all CSV files It would get all the files with all caps "CSV" anywhere within the file name, but it would not get any files with an extension ".csv", nor would it exclude a file named "somethingCSV" . The pattern argument is interpreted as a regex pattern and the meaning of a period is different. Better for this purpose would be: list.files(pattern="\\.(csv|CSV)$") I suppose this criticism might be platform-specific if the filesystem were caps-agnostic, but mine is not. David, I saw that and noted that since linux separates meaning between upper- and lower-case letters it would need to be modified is there were any *.CSV files in the directory. Same type of problem occurs when file names have spaces in them. Regards, Rich __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Batch mode questions.
> On Jul 25, 2018, at 2:54 PM, Rich Shepard wrote: > > On Wed, 25 Jul 2018, Shawn Way wrote: > >> To get you start, here's a script I used to combine any number of files >> into one data.frame. >> >> library(knitr) >> library(tidyverse) >> library(xlsx) >> library(xtable) >> library(lubridate) >> >> # create a list from these files >> list.filenames<-list.files(pattern=".CSV$") # This gets a list of all CSV >> files It would get all the files with all caps "CSV" anywhere within the file name, but it would not get any files with an extension ".csv", nor would it exclude a file named "somethingCSV" . The pattern argument is interpreted as a regex pattern and the meaning of a period is different. Better for this purpose would be: list.files(pattern="\\.(csv|CSV)$") I suppose this criticism might be platform-specific if the filesystem were caps-agnostic, but mine is not. -- David. >> >> data <- list.filenames %>% >> map(read_csv) %>% # This reads all the files in order >> reduce(rbind) # This combines the data into one data frame > > Thanks, Shawn. I'm reading up on functions and will look at using a > function within either a Rscript or source'd script. > > It's about time I learn to automate repeated, tedious tasks in R. > > Much appreciated, > > Rich > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. David Winsemius Alameda, CA, USA 'Any technology distinguishable from magic is insufficiently advanced.' -Gehm's Corollary to Clarke's Third Law __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Batch mode questions.
On Wed, 25 Jul 2018, Shawn Way wrote: To get you start, here's a script I used to combine any number of files into one data.frame. library(knitr) library(tidyverse) library(xlsx) library(xtable) library(lubridate) # create a list from these files list.filenames<-list.files(pattern=".CSV$") # This gets a list of all CSV files data <- list.filenames %>% map(read_csv) %>% # This reads all the files in order reduce(rbind) # This combines the data into one data frame Thanks, Shawn. I'm reading up on functions and will look at using a function within either a Rscript or source'd script. It's about time I learn to automate repeated, tedious tasks in R. Much appreciated, Rich __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Unable to Change Library Paths in R 3.5.1 in Windows 10
Pemissions settings on your target directory (which is a Windows not an R issue)?? -- Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Wed, Jul 25, 2018 at 1:17 PM, Jack Pincus wrote: > I just installed R 3.5.1 on a new Windows 10 computer. R tries to set a > personal library to C:/Users/jackp/OneDrive/Documents/R/win-lib/3.5. I > want to store R packages on my local hard drive, not OneDrive. I tried > placing the line of code:.libPaths(c(.libPaths(), > "C:/Users/jackp/Documents/R/win-lib/3.5")) at the top of Rprofile located > in C:/Program Files/R/R3.5.1/library/base?R but it does not recognize > libraries in my personal library. Any suggestions how to fix this > problem. Also, is there a reason that R tries to default to OneDrive in > Windows 10. I also had a OneDrive folder in Windows 8.1 but could set R to > recognize a personal library on C:/Users/jackp/Documents. > Thanks in advance, > Jack > [[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/ > posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Unable to Change Library Paths in R 3.5.1 in Windows 10
I just installed R 3.5.1 on a new Windows 10 computer. R tries to set a personal library to C:/Users/jackp/OneDrive/Documents/R/win-lib/3.5. I want to store R packages on my local hard drive, not OneDrive. I tried placing the line of code:.libPaths(c(.libPaths(), "C:/Users/jackp/Documents/R/win-lib/3.5")) at the top of Rprofile located in C:/Program Files/R/R3.5.1/library/base?R but it does not recognize libraries in my personal library. Any suggestions how to fix this problem. Also, is there a reason that R tries to default to OneDrive in Windows 10. I also had a OneDrive folder in Windows 8.1 but could set R to recognize a personal library on C:/Users/jackp/Documents. Thanks in advance, Jack [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A couple of batch mode questions
On Wed, 25 Jul 2018, Bert Gunter wrote: Eric may have more to say, but the straightforward answer is: use functions to do what you want and pass any file specific info to them as parameters of function calls. Bert, I was considering that functions would be the way to go. The functions can call other functions in addition to doing calculations. Thanks for re-inforcing that approach, Rich __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A couple of batch mode questions
Eric may have more to say, but the straightforward answer is: use functions to do what you want and pass any file specific info to them as parameters of function calls. If this seems arcane to you, then you have some homework to do, as using functions is a (maybe the) central programming paradigm in R. Numerous tutorials elaborate on this. If I have misunderstood, my apologies, and just disregard. Cheers, Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Wed, Jul 25, 2018 at 1:02 PM, Rich Shepard wrote: > On Wed, 25 Jul 2018, Eric Berger wrote: > > You should be able to do all this within R. From what you have written I >> don't see a compelling reason to use scripts at the shell level. >> > > Eric, > > The source() help page's last example calls a set of scripts to run > sequentially. I assume this is used to run the same .R script on each file, > with any file-specific variables used in each one. Perhaps I'm not seeing > how to pass parameters to the script call with source() so that the same .R > script can be automagically run for each imput file name. In my newness to > this it appears Rscript allows running the same script substituting inpu > file names based on arguments on the Rscript command line. > > Regards, > > Rich > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posti > ng-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A couple of batch mode questions
On Wed, 25 Jul 2018, Eric Berger wrote: You should be able to do all this within R. From what you have written I don't see a compelling reason to use scripts at the shell level. Eric, The source() help page's last example calls a set of scripts to run sequentially. I assume this is used to run the same .R script on each file, with any file-specific variables used in each one. Perhaps I'm not seeing how to pass parameters to the script call with source() so that the same .R script can be automagically run for each imput file name. In my newness to this it appears Rscript allows running the same script substituting inpu file names based on arguments on the Rscript command line. Regards, Rich __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A couple of batch mode questions
You should be able to do all this within R. >From what you have written I don't see a compelling reason to use scripts at the shell level. Best, Eric On Wed, Jul 25, 2018 at 9:41 PM, Rich Shepard wrote: > On Wed, 25 Jul 2018, Eric Berger wrote: > > 1. For R scripts you should also consider the package littler developed by >> Dirk Eddelbuettel, Highly recommended. For info >> http://dirk.eddelbuettel.com/code/littler.html or the github repository. >> > > Eric, > > I'll definintely look at that package. > > 2. Scripts can be useful both for short calculations, extending the shell, >> or for large R jobs that are not interactive and can run unsupervised. >> e.g. I have a script that is run automatically on a daily schedule. It >> performs a number of calculations and updates a database with the results. >> > > My immediate need is to import 30 data files, change factors into dates > and datetimes, print a summary, then plot a PDF scatterplot. This is why I > need to learn Rscript. I should be able to wrap that in a bash shell > script's for ... do loop that runs the Rscript for all *.dat files in the > directory. > > Much appreciated, > > > Rich > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posti > ng-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Formatting multi-way ANOVA output for spectra analysis
In general, analysis functions in R return objects. When returned alone on an interactive console the default print method for that object gets printed. However, you can put it into a variable with the <- assignment operator, and use the str function to see what values are inside the object, and use the summary object to obtain another object with certain computed values depending on the analysis object. It might make sense to use a model analysis for this data... I don't know how you are handling variation in gross irradiance between measurements. Anyway, this can get involved and you haven't provided sample data or code so this starts to get off topic (which is R, not statistics) pretty quick. On July 25, 2018 10:11:55 AM PDT, "Robert D. Bowers M.A." wrote: >I've studied R a little bit, although I haven't used it in some time >(except via RCommander). I'm working on my dissertation project and >have spectrometer data that I need to evaluate. I need to find a way >to >simplify the output from multi-way ANOVA so I can reduce the areas of >the spectrum to only those where there are significant differences >between sites. (A preliminary study on a too-small sample size >indicates that certain areas of the spectrum can distinguish between >sites. This project is the next step.) > >The dataset is comprised of analyses done on samples from five separate > >locations, with 50 samples taken from each site. The output of the >spectrometer per sample is values for 2048 individual wavelengths, in a > >spreadsheet with the wavelength as the first column. Since I'm doing >the analysis wavelength-by-wavelength, I've transposed the data and >broke the data for the project down into smaller spreadsheets (so that >R >can perform ANOVA on each wavelength). > >The problem is, I can do ANOVA now on each wavelength, but I don't need > >a full output table for each... I just need to know if there is >significant variation between any of the sites at that wavelength, >based >on 95% confidence level (or better). If I could get some sort of >simple >chart (or a single line in a spreadsheet), that would help to narrow >down the areas of the spectrum that I need to focus on to evaluate the >results of the tests. > >I've been reading information about ANOVA, but have found very little >that is clear about formatting the output - and I don't need to rehash >all of the math. I just need to find out how to hack down the output >to >just the part I need (if possible). Once that's done, I can decide >what >wavelengths are valuable for future tests and simplify the process. > >Thanks for any help given! > >Bob > >__ >R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide >http://www.R-project.org/posting-guide.html >and provide commented, minimal, self-contained, reproducible code. -- Sent from my phone. Please excuse my brevity. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A couple of batch mode questions
On Wed, 25 Jul 2018, Eric Berger wrote: 1. For R scripts you should also consider the package littler developed by Dirk Eddelbuettel, Highly recommended. For info http://dirk.eddelbuettel.com/code/littler.html or the github repository. Eric, I'll definintely look at that package. 2. Scripts can be useful both for short calculations, extending the shell, or for large R jobs that are not interactive and can run unsupervised. e.g. I have a script that is run automatically on a daily schedule. It performs a number of calculations and updates a database with the results. My immediate need is to import 30 data files, change factors into dates and datetimes, print a summary, then plot a PDF scatterplot. This is why I need to learn Rscript. I should be able to wrap that in a bash shell script's for ... do loop that runs the Rscript for all *.dat files in the directory. Much appreciated, Rich __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A couple of batch mode questions
On Wed, 25 Jul 2018, MacQueen, Don wrote: From my perspective, which is a unix-alike perspective, Rscript makes R useable in exactly the same way as other unix style scripting languages such as perl, tcsh, bash, etc. This is useful, and a good thing. If I remember (and understood) correctly, it is why Rscript was introduced, later in R's history than BATCH. Don, As a linux-only user for more than two decades I really appreciate the value of running scripts from the command line. For a current project, after extracting 29 years of data from PDF forms I ran them through a bash shell script (passing the name of the source file as $1) that calls two sed and six awk scripts. The output is ready to be read into R. If I want to pass custom parameters to the script (script-specific parameters of my own that I put on the command line), the syntax for either supplying them or parsing them might be different. I'm not sure, since I don't do this very often, and never use CMD BATCH. But it would be worth checking. This is what I need to work out now for Rscript: how to set positional or named parameters on the command line with the source file name and the R data.frame name. Thanks for your comments. Best regards, Rich __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] initiate elements in a dataframe with lists
If you need to make a list of long but unknown length you can save time by
adding the items to an environment, with names giving the order, then
converting the environment to a list when you are done filling the
environment. E.g.,
> makeData
function (container, n)
{
for (i in seq_len(n)) container[[sprintf("%06x", i)]] <- seq_len(i%%5)
container
}
> # use an environment
> system.time(E <- makeData(new.env(parent=emptyenv()), 10^5))
user system elapsed
0.380.000.38
> # convert environment to a list
> system.time(EL <- as.list(E, sorted=TRUE))
user system elapsed
0.620.000.62
> # use a list
> system.time(L <- makeData(list(), 10^5))
user system elapsed
142.561.46 153.78
> all.equal(EL, L)
[1] TRUE
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Wed, Jul 25, 2018 at 10:43 AM, Jeff Newmiller
wrote:
> The code below reeks of a misconception that lists are efficient to add
> items to, which is a confusion with the computer science term "linked
> list". In R, a list is NOT a linked list... it is a vector, which means
> the memory used by the list is allocated at the time it is created, and
> REALLOCATED when a new item is added. The only reason you should use a list
> is because you expect to put values of different types or shapes into it,
> which does not appear to apply in this use case.
>
> In R, you should make a valiant effort to create things right the first
> time, and if that doesn't work then preallocate the space you will need in
> the vectors you are working with. Since you have a need to store a variable
> number of elements in each intersectX element, the column needs to be a
> list but the elements of that list can perfectly well be character vectors.
>
> x <- data.frame( TYPE=c("DEL", "DEL", "DUP", "TRA", "INV", "TRA")
>, CHRA=c("chr1", "chr1", "chr1", "chr1", "chr2", "chr2")
>, POSA=c(10, 15, 120, 340, 100, 220)
>, CHRB=c("chr1", "chr1", "chr1", "chr2", "chr2", "chr1")
>, POSB=c(30, 100, 300, 20, 200, 320)
>, stringsAsFactors = FALSE
>)
> compareRng <- function( chr1, pos1, chr2, pos2, delta ) {
> ( chr1 == chr2
> & ( pos2 - delta ) < pos1
> & pos1 < ( pos2 + delta )
> )
> }
> makeIntersectX <- function( n, chrlabel, poslabel, delta ) {
> lgclidx <- rep( TRUE, nrow( x ) )
> lgclidx[ n ] <- FALSE
> x[[ chrlabel ]][ compareRng( x[[ chrlabel ]][ n ]
> , x[[ poslabel ]][ n ]
> , x[[ chrlabel ]]
> , x[[ poslabel ]]
> , delta
> )
> & lgclidx
> ]
> }
>
> x$intersectA <- lapply( seq.int( nrow( x ) )
> , makeIntersectX
> , chrlabel = "CHRA"
> , poslabel = "POSA"
> , delta = 10L
> )
> x$intersectB <- lapply( seq.int( nrow( x ) )
> , makeIntersectX
> , chrlabel = "CHRB"
> , poslabel = "POSB"
> , delta = 21L
> )
>
>> x
>>
> TYPE CHRA POSA CHRB POSB intersectA intersectB
> 1 DEL chr1 10 chr1 30 chr1
> 2 DEL chr1 15 chr1 100 chr1
> 3 DUP chr1 120 chr1 300 chr1
> 4 TRA chr1 340 chr2 20
> 5 INV chr2 100 chr2 200
> 6 TRA chr2 220 chr1 320 chr1
>
> Note that depending on what you plan to do beyond this point, it might
> actually be more performant to use a data frame with repeated rows instead
> of list columns... but I cannot tell from what you have provided.
>
> On Wed, 25 Jul 2018, Bogdan Tanasa wrote:
>
> Dear Thierry and Juan, thank you for your help. Thank you all.
>>
>> Now, if I would like to add an element to the empty list, how shall I do :
>> for example, shall i = 2, and j = 1, in a bit of more complex R code :
>>
>> x <- data.frame(TYPE=c("DEL", "DEL", "DUP", "TRA", "INV", "TRA"),
>> CHRA=c("chr1", "chr1", "chr1", "chr1", "chr2", "chr2"),
>> POSA=c(10, 15, 120, 340, 100, 220),
>> CHRB=c("chr1", "chr1", "chr1", "chr2", "chr2", "chr1"),
>> POSB=c(30, 100, 300, 20, 200, 320))
>>
>> x$labA <- paste(x$CHRA, x$POSA, sep="_")
>> x$labB <- paste(x$CHRB, x$POSB, sep="_")
>>
>> x$POSA_left <- x$POSA - 10
>> x$POSA_right <- x$POSA + 10
>>
>> x$POSB_left <- x$POSB - 10
>> x$POSB_right <- x$POSB + 10
>>
>> x$intersectA <- rep(list(list()), nrow(x))
>> x$intersectB <- rep(list(list()), nrow(x))
>>
>> And we know that for i = 2, and j = 1, the condition is TRUE :
>>
>> i <- 2
>>
>> j <- 1
>>
>> if ( (x$CHRA[i] == x$CHRA[j] ) &&
>> (x$POSA[i] > x$POSA_left[j] ) &&
>> (x$POSA[i] < x$POSA_right[j] ) ){
>> x$intersectA[i] <- c(x$intersectA[i], x$labA[j])}
>>
>> the R code does not work. Thank you for your kind help !
>>
>> On Wed, Jul 25, 2018 at 12:26 AM, Thierry Onkelinx <
>> thierry.onkel...@inbo.be
>>
>>> wrote:
>>>
>>
>> Dear Bogdan,
>>>
>>>
Re: [R] initiate elements in a dataframe with lists
Dear Jeff, it is a precious help and a fabulous suggestion. I will slowly
go over the R code that you have sent. Thanks a lot !
On Wed, Jul 25, 2018 at 10:43 AM, Jeff Newmiller
wrote:
> The code below reeks of a misconception that lists are efficient to add
> items to, which is a confusion with the computer science term "linked
> list". In R, a list is NOT a linked list... it is a vector, which means
> the memory used by the list is allocated at the time it is created, and
> REALLOCATED when a new item is added. The only reason you should use a list
> is because you expect to put values of different types or shapes into it,
> which does not appear to apply in this use case.
>
> In R, you should make a valiant effort to create things right the first
> time, and if that doesn't work then preallocate the space you will need in
> the vectors you are working with. Since you have a need to store a variable
> number of elements in each intersectX element, the column needs to be a
> list but the elements of that list can perfectly well be character vectors.
>
> x <- data.frame( TYPE=c("DEL", "DEL", "DUP", "TRA", "INV", "TRA")
>, CHRA=c("chr1", "chr1", "chr1", "chr1", "chr2", "chr2")
>, POSA=c(10, 15, 120, 340, 100, 220)
>, CHRB=c("chr1", "chr1", "chr1", "chr2", "chr2", "chr1")
>, POSB=c(30, 100, 300, 20, 200, 320)
>, stringsAsFactors = FALSE
>)
> compareRng <- function( chr1, pos1, chr2, pos2, delta ) {
> ( chr1 == chr2
> & ( pos2 - delta ) < pos1
> & pos1 < ( pos2 + delta )
> )
> }
> makeIntersectX <- function( n, chrlabel, poslabel, delta ) {
> lgclidx <- rep( TRUE, nrow( x ) )
> lgclidx[ n ] <- FALSE
> x[[ chrlabel ]][ compareRng( x[[ chrlabel ]][ n ]
> , x[[ poslabel ]][ n ]
> , x[[ chrlabel ]]
> , x[[ poslabel ]]
> , delta
> )
> & lgclidx
> ]
> }
>
> x$intersectA <- lapply( seq.int( nrow( x ) )
> , makeIntersectX
> , chrlabel = "CHRA"
> , poslabel = "POSA"
> , delta = 10L
> )
> x$intersectB <- lapply( seq.int( nrow( x ) )
> , makeIntersectX
> , chrlabel = "CHRB"
> , poslabel = "POSB"
> , delta = 21L
> )
>
>> x
>>
> TYPE CHRA POSA CHRB POSB intersectA intersectB
> 1 DEL chr1 10 chr1 30 chr1
> 2 DEL chr1 15 chr1 100 chr1
> 3 DUP chr1 120 chr1 300 chr1
> 4 TRA chr1 340 chr2 20
> 5 INV chr2 100 chr2 200
> 6 TRA chr2 220 chr1 320 chr1
>
> Note that depending on what you plan to do beyond this point, it might
> actually be more performant to use a data frame with repeated rows instead
> of list columns... but I cannot tell from what you have provided.
>
>
> On Wed, 25 Jul 2018, Bogdan Tanasa wrote:
>
> Dear Thierry and Juan, thank you for your help. Thank you all.
>>
>> Now, if I would like to add an element to the empty list, how shall I do :
>> for example, shall i = 2, and j = 1, in a bit of more complex R code :
>>
>> x <- data.frame(TYPE=c("DEL", "DEL", "DUP", "TRA", "INV", "TRA"),
>> CHRA=c("chr1", "chr1", "chr1", "chr1", "chr2", "chr2"),
>> POSA=c(10, 15, 120, 340, 100, 220),
>> CHRB=c("chr1", "chr1", "chr1", "chr2", "chr2", "chr1"),
>> POSB=c(30, 100, 300, 20, 200, 320))
>>
>> x$labA <- paste(x$CHRA, x$POSA, sep="_")
>> x$labB <- paste(x$CHRB, x$POSB, sep="_")
>>
>> x$POSA_left <- x$POSA - 10
>> x$POSA_right <- x$POSA + 10
>>
>> x$POSB_left <- x$POSB - 10
>> x$POSB_right <- x$POSB + 10
>>
>> x$intersectA <- rep(list(list()), nrow(x))
>> x$intersectB <- rep(list(list()), nrow(x))
>>
>> And we know that for i = 2, and j = 1, the condition is TRUE :
>>
>> i <- 2
>>
>> j <- 1
>>
>> if ( (x$CHRA[i] == x$CHRA[j] ) &&
>> (x$POSA[i] > x$POSA_left[j] ) &&
>> (x$POSA[i] < x$POSA_right[j] ) ){
>> x$intersectA[i] <- c(x$intersectA[i], x$labA[j])}
>>
>> the R code does not work. Thank you for your kind help !
>>
>> On Wed, Jul 25, 2018 at 12:26 AM, Thierry Onkelinx <
>> thierry.onkel...@inbo.be
>>
>>> wrote:
>>>
>>
>> Dear Bogdan,
>>>
>>> You are looking for x$intersectA <- vector("list", nrow(x))
>>>
>>> Best regards,
>>>
>>>
>>> ir. Thierry Onkelinx
>>> Statisticus / Statistician
>>>
>>> Vlaamse Overheid / Government of Flanders
>>> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
>>> AND
>>> FOREST
>>> Team Biometrie &
>>> Kwaliteitszorg
>>> / Team Biometrics & Quality Assurance
>>> thierry.onkel...@inbo.be
>>> Havenlaan 88
>>> bus 73,
>>> 1000 Brussel
>>> www.inbo.be
>>>
>>>
>>> ///
>>>
Re: [R] initiate elements in a dataframe with lists
The code below reeks of a misconception that lists are efficient to add
items to, which is a confusion with the computer science term "linked
list". In R, a list is NOT a linked list... it is a vector, which means
the memory used by the list is allocated at the time it is created, and
REALLOCATED when a new item is added. The only reason you should use a
list is because you expect to put values of different types or shapes into
it, which does not appear to apply in this use case.
In R, you should make a valiant effort to create things right the first
time, and if that doesn't work then preallocate the space you will need in
the vectors you are working with. Since you have a need to store a
variable number of elements in each intersectX element, the column needs
to be a list but the elements of that list can perfectly well be character
vectors.
x <- data.frame( TYPE=c("DEL", "DEL", "DUP", "TRA", "INV", "TRA")
, CHRA=c("chr1", "chr1", "chr1", "chr1", "chr2", "chr2")
, POSA=c(10, 15, 120, 340, 100, 220)
, CHRB=c("chr1", "chr1", "chr1", "chr2", "chr2", "chr1")
, POSB=c(30, 100, 300, 20, 200, 320)
, stringsAsFactors = FALSE
)
compareRng <- function( chr1, pos1, chr2, pos2, delta ) {
( chr1 == chr2
& ( pos2 - delta ) < pos1
& pos1 < ( pos2 + delta )
)
}
makeIntersectX <- function( n, chrlabel, poslabel, delta ) {
lgclidx <- rep( TRUE, nrow( x ) )
lgclidx[ n ] <- FALSE
x[[ chrlabel ]][ compareRng( x[[ chrlabel ]][ n ]
, x[[ poslabel ]][ n ]
, x[[ chrlabel ]]
, x[[ poslabel ]]
, delta
)
& lgclidx
]
}
x$intersectA <- lapply( seq.int( nrow( x ) )
, makeIntersectX
, chrlabel = "CHRA"
, poslabel = "POSA"
, delta = 10L
)
x$intersectB <- lapply( seq.int( nrow( x ) )
, makeIntersectX
, chrlabel = "CHRB"
, poslabel = "POSB"
, delta = 21L
)
x
TYPE CHRA POSA CHRB POSB intersectA intersectB
1 DEL chr1 10 chr1 30 chr1
2 DEL chr1 15 chr1 100 chr1
3 DUP chr1 120 chr1 300 chr1
4 TRA chr1 340 chr2 20
5 INV chr2 100 chr2 200
6 TRA chr2 220 chr1 320 chr1
Note that depending on what you plan to do beyond this point, it might
actually be more performant to use a data frame with repeated rows instead
of list columns... but I cannot tell from what you have provided.
On Wed, 25 Jul 2018, Bogdan Tanasa wrote:
Dear Thierry and Juan, thank you for your help. Thank you all.
Now, if I would like to add an element to the empty list, how shall I do :
for example, shall i = 2, and j = 1, in a bit of more complex R code :
x <- data.frame(TYPE=c("DEL", "DEL", "DUP", "TRA", "INV", "TRA"),
CHRA=c("chr1", "chr1", "chr1", "chr1", "chr2", "chr2"),
POSA=c(10, 15, 120, 340, 100, 220),
CHRB=c("chr1", "chr1", "chr1", "chr2", "chr2", "chr1"),
POSB=c(30, 100, 300, 20, 200, 320))
x$labA <- paste(x$CHRA, x$POSA, sep="_")
x$labB <- paste(x$CHRB, x$POSB, sep="_")
x$POSA_left <- x$POSA - 10
x$POSA_right <- x$POSA + 10
x$POSB_left <- x$POSB - 10
x$POSB_right <- x$POSB + 10
x$intersectA <- rep(list(list()), nrow(x))
x$intersectB <- rep(list(list()), nrow(x))
And we know that for i = 2, and j = 1, the condition is TRUE :
i <- 2
j <- 1
if ( (x$CHRA[i] == x$CHRA[j] ) &&
(x$POSA[i] > x$POSA_left[j] ) &&
(x$POSA[i] < x$POSA_right[j] ) ){
x$intersectA[i] <- c(x$intersectA[i], x$labA[j])}
the R code does not work. Thank you for your kind help !
On Wed, Jul 25, 2018 at 12:26 AM, Thierry Onkelinx
wrote:
Dear Bogdan,
You are looking for x$intersectA <- vector("list", nrow(x))
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be
Havenlaan 88
bus 73,
1000 Brussel
www.inbo.be
///
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
///
2018-07-25 8:55 GMT+02:00 Bogdan Tanasa :
Dear all,
Re: [R] A couple of batch mode questions
Some additional comments that might be relevant to people interested in these topics. 1. For R scripts you should also consider the package littler developed by Dirk Eddelbuettel, Highly recommended. For info http://dirk.eddelbuettel.com/code/littler.html or the github repository. 2. Scripts can be useful both for short calculations, extending the shell, or for large R jobs that are not interactive and can run unsupervised. e.g. I have a script that is run automatically on a daily schedule. It performs a number of calculations and updates a database with the results. 3. When creating a large-ish R project that will run as a script, I still break the task into smaller tasks which are implemented as R scripts which are source()'ed into the batch job. The smaller R scripts are usually developed and debugged in an interactive environment, such as RStudio. Best, Eric On Wed, Jul 25, 2018 at 7:36 PM, MacQueen, Don via R-help < r-help@r-project.org> wrote: > From my perspective, which is a unix-alike perspective, Rscript makes R > useable in exactly the same way as other unix style scripting languages > such as perl, tcsh, bash, etc. This is useful, and a good thing. If I > remember (and understood) correctly, it is why Rscript was introduced, > later in R's history than BATCH. > > Scripts run using Rscript can be (slightly) more self-contained, which I > suppose might or might not be an advantage, depending on one's needs: > > To run an R script using Rscript, I type >./myRscript.r > at the command line (less typing), whereas with batch mode, it has to be >R CMD BATCH myRscript.r > (more typing) but if I want any R options applied, such as --no-restore or > --no-save, I include them within the script when using Rscript, but have to > put them on the command line outside the script when using BATCH. > > One can actually execute an R command at the shell prompt using Rscript, > which can't be done with BATCH: > > [296]% Rscript -e 3+4 > [1] 7 > [298]% Rscript -e 'sqrt(2)' > [1] 1.414214 > > If I want to pass custom parameters to the script (script-specific > parameters of my own that I put on the command line), the syntax for either > supplying them or parsing them might be different. I'm not sure, since I > don't do this very often, and never use CMD BATCH. But it would be worth > checking. > > -Don > > -- > Don MacQueen > Lawrence Livermore National Laboratory > 7000 East Ave., L-627 > Livermore, CA 94550 > 925-423-1062 > Lab cell 925-724-7509 > > > > On 7/25/18, 8:22 AM, "R-help on behalf of Rich Shepard" < > r-help-boun...@r-project.org on behalf of rshep...@appl-ecosys.com> wrote: > > On Wed, 25 Jul 2018, Bert Gunter wrote: > > > "Within R one can use source() to run a batch file of R commands, > while R > > CMD BATCH and Rscript are run from the command line. Is this > correct?" > > > > Yes. > > Bert, > >Thanks for confirming. > > > I think your query answers your query: You use Rscript when you want > to use > > R in the command environment, perhaps as part of an analytical > pipeline; > > and you source an R file when you want to work within R. > >That's a given. Why would I prefer Rscript over R CMD BATCH, or > vice-versa? I did not see much difference between the two in their help > files. > > Regards, > > Rich > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/ > posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/ > posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Formatting multi-way ANOVA output for spectra analysis
I've studied R a little bit, although I haven't used it in some time (except via RCommander). I'm working on my dissertation project and have spectrometer data that I need to evaluate. I need to find a way to simplify the output from multi-way ANOVA so I can reduce the areas of the spectrum to only those where there are significant differences between sites. (A preliminary study on a too-small sample size indicates that certain areas of the spectrum can distinguish between sites. This project is the next step.) The dataset is comprised of analyses done on samples from five separate locations, with 50 samples taken from each site. The output of the spectrometer per sample is values for 2048 individual wavelengths, in a spreadsheet with the wavelength as the first column. Since I'm doing the analysis wavelength-by-wavelength, I've transposed the data and broke the data for the project down into smaller spreadsheets (so that R can perform ANOVA on each wavelength). The problem is, I can do ANOVA now on each wavelength, but I don't need a full output table for each... I just need to know if there is significant variation between any of the sites at that wavelength, based on 95% confidence level (or better). If I could get some sort of simple chart (or a single line in a spreadsheet), that would help to narrow down the areas of the spectrum that I need to focus on to evaluate the results of the tests. I've been reading information about ANOVA, but have found very little that is clear about formatting the output - and I don't need to rehash all of the math. I just need to find out how to hack down the output to just the part I need (if possible). Once that's done, I can decide what wavelengths are valuable for future tests and simplify the process. Thanks for any help given! Bob __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] initiate elements in a dataframe with lists
Dear Thierry and Juan, thank you for your help. Thank you all.
Now, if I would like to add an element to the empty list, how shall I do :
for example, shall i = 2, and j = 1, in a bit of more complex R code :
x <- data.frame(TYPE=c("DEL", "DEL", "DUP", "TRA", "INV", "TRA"),
CHRA=c("chr1", "chr1", "chr1", "chr1", "chr2", "chr2"),
POSA=c(10, 15, 120, 340, 100, 220),
CHRB=c("chr1", "chr1", "chr1", "chr2", "chr2", "chr1"),
POSB=c(30, 100, 300, 20, 200, 320))
x$labA <- paste(x$CHRA, x$POSA, sep="_")
x$labB <- paste(x$CHRB, x$POSB, sep="_")
x$POSA_left <- x$POSA - 10
x$POSA_right <- x$POSA + 10
x$POSB_left <- x$POSB - 10
x$POSB_right <- x$POSB + 10
x$intersectA <- rep(list(list()), nrow(x))
x$intersectB <- rep(list(list()), nrow(x))
And we know that for i = 2, and j = 1, the condition is TRUE :
i <- 2
j <- 1
if ( (x$CHRA[i] == x$CHRA[j] ) &&
(x$POSA[i] > x$POSA_left[j] ) &&
(x$POSA[i] < x$POSA_right[j] ) ){
x$intersectA[i] <- c(x$intersectA[i], x$labA[j])}
the R code does not work. Thank you for your kind help !
On Wed, Jul 25, 2018 at 12:26 AM, Thierry Onkelinx wrote:
> Dear Bogdan,
>
> You are looking for x$intersectA <- vector("list", nrow(x))
>
> Best regards,
>
>
> ir. Thierry Onkelinx
> Statisticus / Statistician
>
> Vlaamse Overheid / Government of Flanders
> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
> FOREST
> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
> thierry.onkel...@inbo.be
> Havenlaan 88
> bus 73,
> 1000 Brussel
> www.inbo.be
>
>
> ///
> To call in the statistician after the experiment is done may be no more
> than asking him to perform a post-mortem examination: he may be able to say
> what the experiment died of. ~ Sir Ronald Aylmer Fisher
> The plural of anecdote is not data. ~ Roger Brinner
> The combination of some data and an aching desire for an answer does not
> ensure that a reasonable answer can be extracted from a given body of data.
> ~ John Tukey
>
> ///
>
>
>
> 2018-07-25 8:55 GMT+02:00 Bogdan Tanasa :
>
>> Dear all,
>>
>> assuming that I do have a dataframe like :
>>
>> x <- data.frame(TYPE=c("DEL", "DEL", "DUP", "TRA", "INV", "TRA"),
>> CHRA=c("chr1", "chr1", "chr1", "chr1", "chr2", "chr2"),
>> POSA=c(10, 15, 120, 340, 100, 220),
>> CHRB=c("chr1", "chr1", "chr1", "chr2", "chr2", "chr1"),
>> POSB=c(30, 100, 300, 20, 200, 320)) ,
>>
>> how could I initiate another 2 columns in x, where each element in these 2
>> columns is going to be a list (the list could be updated later). Thank
>> you !
>>
>> Shall I do,
>>
>> for (i in 1:dim(x)[1]) { x$intersectA[i] <- list()}
>>
>> for (i in 1:dim(x)[1]) { x$intersectB[i] <- list()}
>>
>> nothing is happening. Thank you very much !
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posti
>> ng-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] A couple of batch mode questions
From my perspective, which is a unix-alike perspective, Rscript makes R useable in exactly the same way as other unix style scripting languages such as perl, tcsh, bash, etc. This is useful, and a good thing. If I remember (and understood) correctly, it is why Rscript was introduced, later in R's history than BATCH. Scripts run using Rscript can be (slightly) more self-contained, which I suppose might or might not be an advantage, depending on one's needs: To run an R script using Rscript, I type ./myRscript.r at the command line (less typing), whereas with batch mode, it has to be R CMD BATCH myRscript.r (more typing) but if I want any R options applied, such as --no-restore or --no-save, I include them within the script when using Rscript, but have to put them on the command line outside the script when using BATCH. One can actually execute an R command at the shell prompt using Rscript, which can't be done with BATCH: [296]% Rscript -e 3+4 [1] 7 [298]% Rscript -e 'sqrt(2)' [1] 1.414214 If I want to pass custom parameters to the script (script-specific parameters of my own that I put on the command line), the syntax for either supplying them or parsing them might be different. I'm not sure, since I don't do this very often, and never use CMD BATCH. But it would be worth checking. -Don -- Don MacQueen Lawrence Livermore National Laboratory 7000 East Ave., L-627 Livermore, CA 94550 925-423-1062 Lab cell 925-724-7509 On 7/25/18, 8:22 AM, "R-help on behalf of Rich Shepard" wrote: On Wed, 25 Jul 2018, Bert Gunter wrote: > "Within R one can use source() to run a batch file of R commands, while R > CMD BATCH and Rscript are run from the command line. Is this correct?" > > Yes. Bert, Thanks for confirming. > I think your query answers your query: You use Rscript when you want to use > R in the command environment, perhaps as part of an analytical pipeline; > and you source an R file when you want to work within R. That's a given. Why would I prefer Rscript over R CMD BATCH, or vice-versa? I did not see much difference between the two in their help files. Regards, Rich __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] DiagrammeR and grViz
The Export option from the interactive Plots view is a terrible option for any publication-quality graphics. There are many [1] ways to make publication-quality graphics in R, and there can be some operating-system-specific downstream tools considerations that affect what works best for you. I happen to prefer using Rmd/Rnw files (knitr+rmarkdown or knitr+latex) with png format in most cases. You can specify the default resolution/size as well as having special settings for specific images [2]. If this is all new to you, then you might want to read some of the many intros on the web, like [3][4]. [1] help(package="grDevices") [2] https://yihui.name/knitr/options/#plots [3] https://sachsmc.github.io/knit-git-markr-guide/knitr/knit.html [4] https://rmarkdown.rstudio.com/articles_intro.html On July 25, 2018 7:35:26 AM PDT, Evan Kransdorf wrote: >Is anyone using DiagrammeR and grViz? > >I made a nice grViz but when I use RStudio to export quality looks bad >(need high resolution figure). > >I can't quite figure out how to use DiagrammeR to export the grViz I >made. >Any suggestions? > >Thank you, Evan > > [[alternative HTML version deleted]] > >__ >R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide >http://www.R-project.org/posting-guide.html >and provide commented, minimal, self-contained, reproducible code. -- Sent from my phone. Please excuse my brevity. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A couple of batch mode questions [ANSWERED]
On Wed, 25 Jul 2018, Rich Shepard wrote: That's a given. Why would I prefer Rscript over R CMD BATCH, or vice-versa? I did not see much difference between the two in their help files. Digging deeper into the Web I read that R CMD BATCH is an older approach to automating R processing from the command line and Rscript is the newer approach. My question's answered. Rich __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] SQL Database
https://rviews.rstudio.com/2017/10/18/database-queries-with-r/ Cheers, Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Wed, Jul 25, 2018 at 7:57 AM, Doran, Harold wrote: > I'm doing some work now to learn which SQL database package is the most > optimal for the task I am working on. There are many packages, and I'm > reviewing the documentation on some of them now. I am seeking advice from > those of you who might suggest a package to use for the task I am currently > working with. > > The work is currently as follows. My users currently use another tool to > extract tables from a server, save those tables as .csv files, and then > those csv files are read into R and stuff is done on the data in those > files. This adds overhead that can be bypassed if users instead can > directly access the database from within R and grab the tables they need > and then those tables are data frames in the R session and available to do > stuff. > > The sequence of work (I think) I just this: > > Step 1: Connect to the remote server (connection string and authenticate > the user) > Step 2: Have a SQL query statement that grabs the tables from the remote > server > Step 3: Close the connection > > The two packages I have narrowed my studies to are Dbplyr and RODBC, both > of which seem to be similar. > > Any experiences out there to suggest these two packages are in fact right > for this task, or would there be other packages that might be more optimal > for this? > > Thanks, > Harold > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/ > posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A couple of batch mode questions
On Wed, 25 Jul 2018, Bert Gunter wrote: "Within R one can use source() to run a batch file of R commands, while R CMD BATCH and Rscript are run from the command line. Is this correct?" Yes. Bert, Thanks for confirming. I think your query answers your query: You use Rscript when you want to use R in the command environment, perhaps as part of an analytical pipeline; and you source an R file when you want to work within R. That's a given. Why would I prefer Rscript over R CMD BATCH, or vice-versa? I did not see much difference between the two in their help files. Regards, Rich __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] SQL Database
I'm doing some work now to learn which SQL database package is the most optimal for the task I am working on. There are many packages, and I'm reviewing the documentation on some of them now. I am seeking advice from those of you who might suggest a package to use for the task I am currently working with. The work is currently as follows. My users currently use another tool to extract tables from a server, save those tables as .csv files, and then those csv files are read into R and stuff is done on the data in those files. This adds overhead that can be bypassed if users instead can directly access the database from within R and grab the tables they need and then those tables are data frames in the R session and available to do stuff. The sequence of work (I think) I just this: Step 1: Connect to the remote server (connection string and authenticate the user) Step 2: Have a SQL query statement that grabs the tables from the remote server Step 3: Close the connection The two packages I have narrowed my studies to are Dbplyr and RODBC, both of which seem to be similar. Any experiences out there to suggest these two packages are in fact right for this task, or would there be other packages that might be more optimal for this? Thanks, Harold __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A couple of batch mode questions
"Within R one can use source() to run a batch file of R commands, while R CMD BATCH and Rscript are run from the command line. Is this correct?" Yes. I think your query answers your query: You use Rscript when you want to use R in the command environment, perhaps as part of an analytical pipeline; and you source an R file when you want to work within R. Cheers, Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Wed, Jul 25, 2018 at 7:41 AM, Rich Shepard wrote: > Within R one can use source() to run a batch file of R commands, while R > CMD BATCH > and Rscript are run from the command line. Is this correct? > > Given these choices, when would I want to run a script within R using > source(), and when would it be better for me to run it from the command > line? > > Reading Appendix B.4 Scripting with R in R-info.pdf, ?Rscipt, and ?BATCH > I > get the impression that 'R CMD BATCH' reads from a named file and writes > output to a named file and Rscript reads/writes to stdin/stdout using > redirection. What are the pros and cons of each? When (or why) would I > select one over the other? > > TIA, > > Rich > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posti > ng-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] A couple of batch mode questions
Within R one can use source() to run a batch file of R commands, while R CMD BATCH and Rscript are run from the command line. Is this correct? Given these choices, when would I want to run a script within R using source(), and when would it be better for me to run it from the command line? Reading Appendix B.4 Scripting with R in R-info.pdf, ?Rscipt, and ?BATCH I get the impression that 'R CMD BATCH' reads from a named file and writes output to a named file and Rscript reads/writes to stdin/stdout using redirection. What are the pros and cons of each? When (or why) would I select one over the other? TIA, Rich __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] DiagrammeR and grViz
Is anyone using DiagrammeR and grViz? I made a nice grViz but when I use RStudio to export quality looks bad (need high resolution figure). I can't quite figure out how to use DiagrammeR to export the grViz I made. Any suggestions? Thank you, Evan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] initiate elements in a dataframe with lists
Hi Bogdan,
Does the following do what you expect?
x$intersectA[[i]] <- c(x$intersectA[[i]], x$labA[j])
Note the difference between `[[` and `[`
On Wed, Jul 25, 2018 at 9:26 AM, Bogdan Tanasa wrote:
> Dear Thierry and Juan, thank you for your help. Thank you very much.
>
> Now, if I would like to add an element to the empty list, how shall I do :
> for example, shall i = 2, and j = 1, in a bit of more complex R code :
>
> x <- data.frame(TYPE=c("DEL", "DEL", "DUP", "TRA", "INV", "TRA"),
> CHRA=c("chr1", "chr1", "chr1", "chr1", "chr2", "chr2"),
> POSA=c(10, 15, 120, 340, 100, 220),
> CHRB=c("chr1", "chr1", "chr1", "chr2", "chr2", "chr1"),
> POSB=c(30, 100, 300, 20, 200, 320))
>
> x$labA <- paste(x$CHRA, x$POSA, sep="_")
> x$labB <- paste(x$CHRB, x$POSB, sep="_")
>
> x$POSA_left <- x$POSA - 10
> x$POSA_right <- x$POSA + 10
>
> x$POSB_left <- x$POSB - 10
> x$POSB_right <- x$POSB + 10
>
> x$intersectA <- rep(list(list()), nrow(x))
> x$intersectB <- rep(list(list()), nrow(x))
>
> And we know that for i = 2, and j = 1, the condition is TRUE :
>
> i <- 2
> j <- 1
>
> if ( (x$CHRA[i] == x$CHRA[j] ) &&
> (x$POSA[i] > x$POSA_left[j] ) &&
> (x$POSA[i] < x$POSA_right[j] ) )
> {
>x$intersectA[i] <- c(x$intersectA[i], x$labA[j])
> }
>
> the R code does not work. Thank you for your kind help !
>
>
>>
>> On Wed, Jul 25, 2018 at 12:26 AM, Thierry Onkelinx <
>> thierry.onkel...@inbo.be> wrote:
>>
>>> Dear Bogdan,
>>>
>>> You are looking for x$intersectA <- vector("list", nrow(x))
>>>
>>> Best regards,
>>>
>>>
>>> ir. Thierry Onkelinx
>>> Statisticus / Statistician
>>>
>>> Vlaamse Overheid / Government of Flanders
>>> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
>>> AND FOREST
>>> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
>>> thierry.onkel...@inbo.be
>>> Havenlaan 88
>>> bus 73,
>>> 1000 Brussel
>>> www.inbo.be
>>>
>>>
>>> ///
>>> To call in the statistician after the experiment is done may be no more
>>> than asking him to perform a post-mortem examination: he may be able to say
>>> what the experiment died of. ~ Sir Ronald Aylmer Fisher
>>> The plural of anecdote is not data. ~ Roger Brinner
>>> The combination of some data and an aching desire for an answer does not
>>> ensure that a reasonable answer can be extracted from a given body of data.
>>> ~ John Tukey
>>>
>>> ///
>>>
>>>
>>>
>>> 2018-07-25 8:55 GMT+02:00 Bogdan Tanasa :
>>>
Dear all,
assuming that I do have a dataframe like :
x <- data.frame(TYPE=c("DEL", "DEL", "DUP", "TRA", "INV", "TRA"),
CHRA=c("chr1", "chr1", "chr1", "chr1", "chr2", "chr2"),
POSA=c(10, 15, 120, 340, 100, 220),
CHRB=c("chr1", "chr1", "chr1", "chr2", "chr2", "chr1"),
POSB=c(30, 100, 300, 20, 200, 320)) ,
how could I initiate another 2 columns in x, where each element in these
2
columns is going to be a list (the list could be updated later). Thank
you !
Shall I do,
for (i in 1:dim(x)[1]) { x$intersectA[i] <- list()}
for (i in 1:dim(x)[1]) { x$intersectB[i] <- list()}
nothing is happening. Thank you very much !
[[alternative HTML version deleted]]
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posti
ng-guide.html
and provide commented, minimal, self-contained, reproducible code.
>>>
>>>
>>
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] initiate elements in a dataframe with lists
Dear Thierry and Juan, thank you for your help. Thank you very much.
Now, if I would like to add an element to the empty list, how shall I do :
for example, shall i = 2, and j = 1, in a bit of more complex R code :
x <- data.frame(TYPE=c("DEL", "DEL", "DUP", "TRA", "INV", "TRA"),
CHRA=c("chr1", "chr1", "chr1", "chr1", "chr2", "chr2"),
POSA=c(10, 15, 120, 340, 100, 220),
CHRB=c("chr1", "chr1", "chr1", "chr2", "chr2", "chr1"),
POSB=c(30, 100, 300, 20, 200, 320))
x$labA <- paste(x$CHRA, x$POSA, sep="_")
x$labB <- paste(x$CHRB, x$POSB, sep="_")
x$POSA_left <- x$POSA - 10
x$POSA_right <- x$POSA + 10
x$POSB_left <- x$POSB - 10
x$POSB_right <- x$POSB + 10
x$intersectA <- rep(list(list()), nrow(x))
x$intersectB <- rep(list(list()), nrow(x))
And we know that for i = 2, and j = 1, the condition is TRUE :
i <- 2
j <- 1
if ( (x$CHRA[i] == x$CHRA[j] ) &&
(x$POSA[i] > x$POSA_left[j] ) &&
(x$POSA[i] < x$POSA_right[j] ) )
{
x$intersectA[i] <- c(x$intersectA[i], x$labA[j])
}
the R code does not work. Thank you for your kind help !
>
> On Wed, Jul 25, 2018 at 12:26 AM, Thierry Onkelinx <
> thierry.onkel...@inbo.be> wrote:
>
>> Dear Bogdan,
>>
>> You are looking for x$intersectA <- vector("list", nrow(x))
>>
>> Best regards,
>>
>>
>> ir. Thierry Onkelinx
>> Statisticus / Statistician
>>
>> Vlaamse Overheid / Government of Flanders
>> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
>> AND FOREST
>> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
>> thierry.onkel...@inbo.be
>> Havenlaan 88
>> bus 73,
>> 1000 Brussel
>> www.inbo.be
>>
>>
>> ///
>> To call in the statistician after the experiment is done may be no more
>> than asking him to perform a post-mortem examination: he may be able to say
>> what the experiment died of. ~ Sir Ronald Aylmer Fisher
>> The plural of anecdote is not data. ~ Roger Brinner
>> The combination of some data and an aching desire for an answer does not
>> ensure that a reasonable answer can be extracted from a given body of data.
>> ~ John Tukey
>>
>> ///
>>
>>
>>
>> 2018-07-25 8:55 GMT+02:00 Bogdan Tanasa :
>>
>>> Dear all,
>>>
>>> assuming that I do have a dataframe like :
>>>
>>> x <- data.frame(TYPE=c("DEL", "DEL", "DUP", "TRA", "INV", "TRA"),
>>> CHRA=c("chr1", "chr1", "chr1", "chr1", "chr2", "chr2"),
>>> POSA=c(10, 15, 120, 340, 100, 220),
>>> CHRB=c("chr1", "chr1", "chr1", "chr2", "chr2", "chr1"),
>>> POSB=c(30, 100, 300, 20, 200, 320)) ,
>>>
>>> how could I initiate another 2 columns in x, where each element in these
>>> 2
>>> columns is going to be a list (the list could be updated later). Thank
>>> you !
>>>
>>> Shall I do,
>>>
>>> for (i in 1:dim(x)[1]) { x$intersectA[i] <- list()}
>>>
>>> for (i in 1:dim(x)[1]) { x$intersectB[i] <- list()}
>>>
>>> nothing is happening. Thank you very much !
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> __
>>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide http://www.R-project.org/posti
>>> ng-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>>
>
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] initiate elements in a dataframe with lists
Thank you Juan. On Wed, Jul 25, 2018 at 12:56 AM, Juan Telleria Ruiz de Aguirre < jtelleria.rproj...@gmail.com> wrote: > Check tidyverse's purrr package: > > https://github.com/rstudio/cheatsheets/raw/master/purrr.pdf > > In the second page of the cheatsheet there is info on how to create list > columns within a data.frame :) > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Query on convergence
Hi
maybe
ii<-TRUE
while(ii) {
do something
if(some condition of two variables is met) {ii <- FALSE}
}
But in R such constructions are seldom necessary.
Cheers
Petr
> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of tembe-
> atanasio...@ynu.jp
> Sent: Wednesday, July 25, 2018 1:22 PM
> To: r-help@r-project.org
> Subject: [R] Query on convergence
>
> Hello,
>
>
>
> Is there somebody who can demonstrate how to code a while loop that ends
> when a convergence between the values of two or more variables (say vectors)
> is reached? Thank you
>
> Regards
>
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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[R] Query on convergence
Hello, Is there somebody who can demonstrate how to code a while loop that ends when a convergence between the values of two or more variables (say vectors) is reached? Thank you Regards [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] initiate elements in a dataframe with lists
On 07/25/2018 10:23 AM, Ivan Calandra wrote: Just for my understanding: Is a data.frame with list columns still a data.frame? Isn't it then a list? A data.frame is a list of equally sized vectors - that is, each vector must be of the same length. It is not required that the vector is an atomic vector; it can be a list, too. By having equally sized vectors in a list you can arrange the list in a two-dimensional matrix-like format, append row names to them, and you get a data.frame. Principally data.frame(x = 1:3, y = list(1:2, 1:3, 1:4)) should work, but it doesn't, as it was recognized by others, too: https://stackoverflow.com/questions/9547518/create-a-data-frame-where-a-column-is-a-list Cheers, Denes Ivan -- Dr. Ivan Calandra TraCEr, laboratory for Traceology and Controlled Experiments MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution Schloss Monrepos 56567 Neuwied, Germany +49 (0) 2631 9772-243 https://www.researchgate.net/profile/Ivan_Calandra On 25/07/2018 09:56, Juan Telleria Ruiz de Aguirre wrote: Check tidyverse's purrr package: https://github.com/rstudio/cheatsheets/raw/master/purrr.pdf In the second page of the cheatsheet there is info on how to create list columns within a data.frame :) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] initiate elements in a dataframe with lists
At first I was actually thinking about this situation, which cannot work:| data.frame(x = 1:3, y = list(1:2, 1:3, 1:4)) |But I had never thought about this:| df$y <-list(1:2, 1:3, 1:4)| And it actually makes sense. The final requirement here is that all columns must have the same length! I'm not sure though why one would need that. Why not use lists in that case? Thanks! Ivan -- Dr. Ivan Calandra TraCEr, laboratory for Traceology and Controlled Experiments MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution Schloss Monrepos 56567 Neuwied, Germany +49 (0) 2631 9772-243 https://www.researchgate.net/profile/Ivan_Calandra On 25/07/2018 11:56, Juan Telleria Ruiz de Aguirre wrote: >> Just for my understanding: >> Is a data.frame with list columns still a data.frame? Isn't it then a list? > * A data.frame (or tibble) is a list of columns. > * In which each column must be from the same data type, in this case list(). > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] initiate elements in a dataframe with lists
By the way, this also works: dfl <- data.frame(x = 1:3, y = I(list(1:2, 1:3, 1:4))) As indicated in "Advanced R" book: http://adv-r.had.co.nz/Data-structures.html#data-frames __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] initiate elements in a dataframe with lists
> Just for my understanding: > Is a data.frame with list columns still a data.frame? Isn't it then a list? * A data.frame (or tibble) is a list of columns. * In which each column must be from the same data type, in this case list(). __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] initiate elements in a dataframe with lists
Just for my understanding: Is a data.frame with list columns still a data.frame? Isn't it then a list? Ivan -- Dr. Ivan Calandra TraCEr, laboratory for Traceology and Controlled Experiments MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution Schloss Monrepos 56567 Neuwied, Germany +49 (0) 2631 9772-243 https://www.researchgate.net/profile/Ivan_Calandra On 25/07/2018 09:56, Juan Telleria Ruiz de Aguirre wrote: Check tidyverse's purrr package: https://github.com/rstudio/cheatsheets/raw/master/purrr.pdf In the second page of the cheatsheet there is info on how to create list columns within a data.frame :) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] initiate elements in a dataframe with lists
Dear Bogdan,
You are looking for x$intersectA <- vector("list", nrow(x))
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be
///
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
///
2018-07-25 8:55 GMT+02:00 Bogdan Tanasa :
> Dear all,
>
> assuming that I do have a dataframe like :
>
> x <- data.frame(TYPE=c("DEL", "DEL", "DUP", "TRA", "INV", "TRA"),
> CHRA=c("chr1", "chr1", "chr1", "chr1", "chr2", "chr2"),
> POSA=c(10, 15, 120, 340, 100, 220),
> CHRB=c("chr1", "chr1", "chr1", "chr2", "chr2", "chr1"),
> POSB=c(30, 100, 300, 20, 200, 320)) ,
>
> how could I initiate another 2 columns in x, where each element in these 2
> columns is going to be a list (the list could be updated later). Thank you
> !
>
> Shall I do,
>
> for (i in 1:dim(x)[1]) { x$intersectA[i] <- list()}
>
> for (i in 1:dim(x)[1]) { x$intersectB[i] <- list()}
>
> nothing is happening. Thank you very much !
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] initiate elements in a dataframe with lists
Check tidyverse's purrr package: https://github.com/rstudio/cheatsheets/raw/master/purrr.pdf In the second page of the cheatsheet there is info on how to create list columns within a data.frame :) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] initiate elements in a dataframe with lists
Dear all,
assuming that I do have a dataframe like :
x <- data.frame(TYPE=c("DEL", "DEL", "DUP", "TRA", "INV", "TRA"),
CHRA=c("chr1", "chr1", "chr1", "chr1", "chr2", "chr2"),
POSA=c(10, 15, 120, 340, 100, 220),
CHRB=c("chr1", "chr1", "chr1", "chr2", "chr2", "chr1"),
POSB=c(30, 100, 300, 20, 200, 320)) ,
how could I initiate another 2 columns in x, where each element in these 2
columns is going to be a list (the list could be updated later). Thank you !
Shall I do,
for (i in 1:dim(x)[1]) { x$intersectA[i] <- list()}
for (i in 1:dim(x)[1]) { x$intersectB[i] <- list()}
nothing is happening. Thank you very much !
[[alternative HTML version deleted]]
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Re: [R] Using apply function to merge list of data frames
> On 25 Jul 2018, at 08:17, Naresh Gurbuxani
> wrote:
>
> I have a list whose components are data frames. My goal is to construct a
> data frame by merging all the list components. Is it possible to achieve
> this using apply and without a for loop, as used below?
>
> Thanks,
> Naresh
>
> mylist <- list(A = data.frame(date = seq.Date(as.Date('2018-01-01'), by =
> 'week',
> length.out = 5), ret = rnorm(5)),
> B = data.frame(date = seq.Date(as.Date('2018-01-01'), by =
> 'week',
> length.out = 5), ret = rnorm(5)))
>
> mydf <- data.frame(date = seq.Date(as.Date('2018-01-01'), by = 'week',
> length.out = 5))
>
> for(ch in names(mylist)){
>tempdf <- mylist[[ch]]
>names(tempdf)[2] <- paste(names(tempdf)[2], ch, sep = '.')
>mydf <- merge(mydf, tempdf, by = c('date'))}
> _
See if these would help:
on R-help the thread
https://stat.ethz.ch/pipermail/r-help/2018-May/454249.html
and
https://stackoverflow.com/questions/4512465/what-is-the-most-efficient-way-to-cast-a-list-as-a-data-frame?rq=1
Berend
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