[R] package ‘contingency.tables’ is not available (for R version 2.15.2)
I am trying to create contingency tables (to evaluate prior to performing Pearson's Chi-Squared test for independence). I would like to see column and row totals as well as expected and observed values and cell counts. I tried to use the package contingency. tables but get the following warning: package contingency.tables is not available (for R versions 2.15.2) Is there something comparable or was this replaced with something else for later versions of R. Any help would be appreciated so that I may create a contigencey table like this. Thank you. ** *Joanna * [[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] package ‘contingency.tables’ is not available (for R version 2.15.2)
Thank you. I actually ended up using: CrossTable(mdt) Cell Contents |-| | N | | Chi-square contribution | | N / Row Total | | N / Col Total | | N / Table Total | |-| Total Observations in Table: 8 | | Blue | Green | Red | Row Total | -|---|---|---|---| A | 1 | 0 | 1 | 2 | | 0.083 | 0.500 | 0.083 | | | 0.500 | 0.000 | 0.500 | 0.250 | | 0.333 | 0.000 | 0.333 | | | 0.125 | 0.000 | 0.125 | | -|---|---|---|---| G | 1 | 0 | 1 | 2 | | 0.083 | 0.500 | 0.083 | | | 0.500 | 0.000 | 0.500 | 0.250 | | 0.333 | 0.000 | 0.333 | | | 0.125 | 0.000 | 0.125 | | -|---|---|---|---| H | 1 | 0 | 1 | 2 | | 0.083 | 0.500 | 0.083 | | | 0.500 | 0.000 | 0.500 | 0.250 | | 0.333 | 0.000 | 0.333 | | | 0.125 | 0.000 | 0.125 | | -|---|---|---|---| W | 0 | 2 | 0 | 2 | | 0.750 | 4.500 | 0.750 | | | 0.000 | 1.000 | 0.000 | 0.250 | | 0.000 | 1.000 | 0.000 | | | 0.000 | 0.250 | 0.000 | | -|---|---|---|---| Column Total | 3 | 2 | 3 | 8 | | 0.375 | 0.250 | 0.375 | | -|---|---|---|---| and expected.counts - (apply(mdt,1,sum) %o% apply(mdt,2,sum))/sum(mdt) print(expected.counts) Blue Green Red A 0.75 0.5 0.75 G 0.75 0.5 0.75 H 0.75 0.5 0.75 W 0.75 0.5 0.75 to get the info I needed. Regards, Joanna On Mon, Mar 4, 2013 at 2:15 PM, Milan Bouchet-Valat nalimi...@club.frwrote: Le lundi 04 mars 2013 à 12:37 -0600, Joanna Papakonstantinou a écrit : I am trying to create contingency tables (to evaluate prior to performing Pearson's Chi-Squared test for independence). I would like to see column and row totals as well as expected and observed values and cell counts. I tried to use the package contingency. tables but get the following warning: package contingency.tables is not available (for R versions 2.15.2) Is there something comparable or was this replaced with something else for later versions of R. Any help would be appreciated so that I may create a contigencey table like this. I'm not aware of the existence of such a package, but base R provides most of what you need, and other packages offer even more. See e.g. http://www.statmethods.net/stats/frequencies.html Regards -- ** *Joanna Papakonstantinou, Ph.D.* [[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] cutreeDynamic error
Thank you, Peter. This worked. I appreciate your time and help. Regards, Joanna On Wed, Feb 27, 2013 at 1:21 AM, Peter Langfelder peter.langfel...@gmail.com wrote: On Tue, Feb 26, 2013 at 8:34 AM, Joanna Papakonstantinou joanna.p...@gmail.com wrote: So I realized I had to convert my dd.daisy to a matrix and used: ddmatrix.daisy-as.matrix(dd.daisy) and then I passed that in as the distM: cutreeDynamic(as.hclust(dd.diana), cutHeight = NULL, minClusterSize = 2, method = hybrid, distM = ddmatrix.daisy,deepSplit = (ifelse(method==hybrid, 1, FALSE)),maxCoreScatter = NULL, minGap = NULL, maxAbsCoreScatter = NULL, minAbsGap = NULL,useMedoids = FALSE, maxDistToLabel = cutHeight,respectSmallClusters = TRUE, verbose = 2, indent = 0) However, now I am getting a different error: Detecting clusters... ..cutHeight not given, setting it to 0.847 === 99% of the (truncated) height range in dendro. Error in ifelse(method == hybrid, 1, FALSE) : object 'method' not found Anny suggestions on how to fix this? Yes, leave out the 'deepSplit = (ifelse(method==hybrid, 1, FALSE))' from the call. This is not really a cutreeDynamic problem, it is a perhaps somewhat confusing aspect of R language. If you don't specify deepSplit, its default value will be evaluated within the function 'interior' where the variable 'method' is defined. If you do specify deepSplit, the expression that you specify is evaluated from 'outside' the function where the variable 'method' is undefined. Thus, the seemingly same expression can lead to two different results. In fact, you may want to leave out all arguments for which you are using a default value, it will make your call shorter and less prone to the type of error you just experienced. HTH, Peter -- ** *Joanna Papakonstantinou, Ph.D.* [[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] cutreeDynamic error
I am having difficulty getting the dynamic tree cut package to work.
Given the data table myddtable
LengthPlaceColorAge5HRed224ABlue205WGreen243GRed222GBlue236WGreen255ARed194H
Blue23
I created a similarity matrix using DAISY and Gower metric and specified
Place and Color columns as characters (since they are categorical variables)
dd.daisy-daisy(myddtable, metric = gower, stand = FALSE, type =
list(character=c(Place,Color)))
Then I clustered using DIANA
dd.diana-diana(dd.daisy)
I am trying to cutreeDynamic {dynamicTreeCut} as follows
cutreeDynamic(dd.diana, cutHeight = 2, minClusterSize = 1, method =
hybrid,+ distM = dd.daisy,+ deepSplit =
(ifelse(method==hybrid, 1, FALSE)),+ maxCoreScatter =
NULL, minGap = NULL,+ maxAbsCoreScatter = NULL,
minAbsGap = NULL,+ maxDistToLabel = cutHeight,+
respectSmallClusters = TRUE, + verbose = 2, indent
= 0)
But get the following error:
Warning in if (class(dendro) != hclust) stop(Argument dendro must
have class hclust.) :
the condition has length 1 and only the first element will be
usedError in cutreeDynamic(dd.diana, cutHeight = 2, minClusterSize =
1, method = hybrid, :
Argument dendro must have class hclust.
Is this trying to tell me I cannot use this with DIANA but only with hclust
because I thought it could be used with any of the hierarchical methods?
I hope someone can please tell me what I am doing wrong.
Thank you.
--
**
*Joanna Papakonstantinou, Ph.D.*
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[R] cutreeDynamic error
So I realized I had to convert my dd.daisy to a matrix and used: ddmatrix.daisy-as.matrix(dd.daisy) and then I passed that in as the distM: cutreeDynamic(as.hclust(dd.diana), cutHeight = NULL, minClusterSize = 2, method = hybrid, distM = ddmatrix.daisy,deepSplit = (ifelse(method==hybrid, 1, FALSE)),maxCoreScatter = NULL, minGap = NULL, maxAbsCoreScatter = NULL, minAbsGap = NULL,useMedoids = FALSE, maxDistToLabel = cutHeight,respectSmallClusters = TRUE, verbose = 2, indent = 0) However, now I am getting a different error: Detecting clusters... ..cutHeight not given, setting it to 0.847 === 99% of the (truncated) height range in dendro. Error in ifelse(method == hybrid, 1, FALSE) : object 'method' not found Anny suggestions on how to fix this? Joanna [[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] How to define variables as categorical using Gower with Daisy
Thank you for pointing me to ?dissimilarity.object. I now see that N = Nominal (factor) and I = Interval scaled (numeric). Regards. On Sun, Feb 24, 2013 at 2:36 PM, Peter Ehlers ehl...@ucalgary.ca wrote: On 2013-02-24 07:57, Joanna Papakonstantinou wrote: I am using the iris dataset that contains mixed variables (some columns are numeric and some categorical). iris Sepal.Length Sepal.Width Petal.Length Petal.WidthSpecies 15.1 3.5 1.4 0.2 setosa 24.9 3.0 1.4 0.2 setosa 34.7 3.2 1.3 0.2 setosa 44.6 3.1 1.5 0.2 setosa . . . I am trying to use the Gower metric so that I may specify that some columns contain categorical data. iris.clust-daisy(iris, metric = gower, stand = FALSE, type = list(factor=Species)) But it is saying that the types= I, I, I, I, N so obviously it is not reading the variable types correctly. I don't know why you say that. Look at ?dissimilarity.object to see what 'I' and 'N' mean. If you read the help page for ?daisy carefully, you'll see that your command is equivalent to iris.clust(iris) i.e. you need not specify the metric etc. BTW, your specification of 'type' indicates that you may have looked at the help page a bit too hastily. Could someone please tell me how to specify the variable types correctly? Thank you. Joanna Peter Ehlers -- ** *Joanna Papakonstantinou, Ph.D.* [[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] Argument dendro must have class hclust - cutreeDynamic error
I am having difficulty getting the dynamic tree cut package to work.
Given the data table myddtable
LengthPlaceColorAge5HRed224ABlue205WGreen243GRed222GBlue236WGreen255ARed194H
Blue23
I created a similarity matrix using DAISY and Gower metric and specified
Place and Color columns as characters (since they are categorical variables)
dd.daisy-daisy(myddtable, metric = gower, stand = FALSE, type =
list(character=c(Place,Color)))
Then I clustered using DIANA
dd.diana-diana(dd.daisy)
I am trying to cutreeDynamic {dynamicTreeCut} as follows
cutreeDynamic(dd.diana, cutHeight = 2, minClusterSize = 1, method =
hybrid,+ distM = dd.daisy,+ deepSplit =
(ifelse(method==hybrid, 1, FALSE)),+ maxCoreScatter =
NULL, minGap = NULL,+ maxAbsCoreScatter = NULL,
minAbsGap = NULL,+ maxDistToLabel = cutHeight,+
respectSmallClusters = TRUE, + verbose = 2, indent
= 0)
But get the following error:
Warning in if (class(dendro) != hclust) stop(Argument dendro must
have class hclust.) :
the condition has length 1 and only the first element will be
usedError in cutreeDynamic(dd.diana, cutHeight = 2, minClusterSize =
1, method = hybrid, :
Argument dendro must have class hclust.
Is this trying to tell me I cannot use this with DIANA but only with hclust?
Please tell me what I am doing wrong.
Thank you.
*Joanna *
[[alternative HTML version deleted]]
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[R] How to define variables as categorical using Gower with Daisy
I am using the iris dataset that contains mixed variables (some columns are numeric and some categorical). iris Sepal.Length Sepal.Width Petal.Length Petal.WidthSpecies 15.1 3.5 1.4 0.2 setosa 24.9 3.0 1.4 0.2 setosa 34.7 3.2 1.3 0.2 setosa 44.6 3.1 1.5 0.2 setosa . . . I am trying to use the Gower metric so that I may specify that some columns contain categorical data. iris.clust-daisy(iris, metric = gower, stand = FALSE, type = list(factor=Species)) But it is saying that the types= I, I, I, I, N so obviously it is not reading the variable types correctly. Could someone please tell me how to specify the variable types correctly? Thank you. Joanna [[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] Fwd: difficulty defining variables as categorical using Gower with DAISY
I am using the iris dataset that contains mixed variables (some columns are numeric and some categorical). iris Sepal.Length Sepal.Width Petal.Length Petal.WidthSpecies 15.1 3.5 1.4 0.2 setosa 24.9 3.0 1.4 0.2 setosa 34.7 3.2 1.3 0.2 setosa 44.6 3.1 1.5 0.2 setosa . . . I am trying to use the Gower metric so that I may specify that some columns contain categorical data. iris.clust-daisy(iris, metric = gower, stand = FALSE, type = list(factor=Species)) But it is saying that the type= I, I, I, I, N so obviously it is not reading the variable types correctly. Could someone please tell me how to specify the types correctly? Thank you. ** Joanna Papakonstantinou, Ph.D. [[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] Error in setwd(outDir) : cannot change working directory
I only thought one was missing since it kept giving me error that it wasn't
set. But all seems to working OK so I guess I don't need to create anything.
Thank you for your help.
On Wed, Feb 20, 2013 at 7:28 PM, S Ellison s.elli...@lgcgroup.com wrote:
Should I create an output directory somewhere either in Program Files
where
R is installed or in my working directory?
If I wanted to create a writeable test directory I'd put it in my own
workspace, not the program files space.
But why do you think you need to create an output directory?
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Re: [R] duplicate 'row.names' are not allowed
Thank you. I ended up converting the excel file to a csv file and using mytable-read.csv(myfile, header=T) and it worked so I abandoned using the tab delimited txt file. On Wed, Feb 20, 2013 at 9:29 PM, Jim Lemon j...@bitwrit.com.au wrote: On 02/21/2013 07:10 AM, Joanna Papakonstantinou wrote: Some of the names in the columns actually have spaces in them (e.g., S L TX is in one column). So there are really 9. I was able to save the file as a csv file and read.table succesfully. Hi Joanna, As you specified space ( ) as the field delimiter in your initial post, fields with spaces would be read as multiple fields, forcing the first column to be read as row names. I suspect that you changed the delimiter or that read.csv treats this differently from read.delim. I recall having to specify something about row names with read.delim once. Jim -- ** *Joanna Papakonstantinou, Ph.D.* [[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] Error in setwd(outDir) : cannot change working directory
Below is what happened when I ran testInstalledPackages(scope=base,errorsAreFatal=FALSE) Testing examples for package base comparing base-Ex.Rout to base-Ex.Rout.prev ...files differ in number of lines: Testing examples for package tools comparing tools-Ex.Rout to tools-Ex.Rout.save ... 474c474 [1] Matrix nlme vegan mgcv --- [1] Matrix nlme mgcv 619c619 [1] 0cce1e42ef3fb133940946534fcf8896 --- [1] eb723b61539feef013de476e68b5c50a 844c844 [1] R (= 2.15.1) --- [1] R (= 2.14.0) Running specific tests for package tools Running undoc.R Testing examples for package utils comparing utils-Ex.Rout to utils-Ex.Rout.prev ... files differ in number of lines: Running specific tests for package utils Running Sweave-tst.R Warning: running command 'C:/PROGRA~1/R/R-215~1.2/bin/x64/R CMD BATCH --vanilla --no-timing Sweave-tst.R Sweave-tst.Rout LANGUAGE=C' had status 1 Warning: testing 'utils' failed Testing examples for package grDevices comparing grDevices-Ex.Rout to grDevices-Ex.Rout.save ... OK Running specific tests for package grDevices Running ps-tests.R comparing ps-tests.Rout to ps-tests.Rout.save ... OK Running xfig-tests.R comparing xfig-tests.Rout to xfig-tests.Rout.save ... OK Testing examples for package graphics comparing graphics-Ex.Rout to graphics-Ex.Rout.save ... OK Testing examples for package stats comparing stats-Ex.Rout to stats-Ex.Rout.save ... OK Running specific tests for package stats Running NLSstClosest.R Running cmdscale.R Running drop1-polr.R Running ig_glm.R Running ks-test.R comparing ks-test.Rout to ks-test.Rout.save ... OK Running nafns.R Running nls.R comparing nls.Rout to nls.Rout.save ... OK Running offsets.R Running ppr.R Running simulate.R comparing simulate.Rout to simulate.Rout.save ... OK Running smooth.spline.R Running ts-tests.R Testing examples for package datasets comparing datasets-Ex.Rout to datasets-Ex.Rout.save ... OK Testing examples for package methods comparing methods-Ex.Rout to methods-Ex.Rout.prev ... OK Running specific tests for package methods Running S3.R Running basicRefClass.R Running duplicateClass.R Running fieldAssignments.R Running mixinInitialize.R Running namesAndSlots.R Running nextWithDots.R Running refClassExample.R Running testConditionalIs.R Running testGroupGeneric.R Running testIs.R Testing examples for package grid comparing grid-Ex.Rout to grid-Ex.Rout.save ... OK Running specific tests for package grid Running bugs.R Running reg.R Running testls.R comparing testls.Rout to testls.Rout.save ... OK Running units.R Running vignettes for package grid Testing examples for package splines comparing splines-Ex.Rout to splines-Ex.Rout.save ... OK Testing examples for package stats4 comparing stats4-Ex.Rout to stats4-Ex.Rout.save ... OK Running specific tests for package stats4 Running confint.R Testing examples for package tcltk comparing tcltk-Ex.Rout to tcltk-Ex.Rout.prev ...OK Testing examples for package compiler comparing compiler-Ex.Rout to compiler-Ex.Rout.prev ... OK Running specific tests for package compiler Running assign.R Running basics.R Running const.R Running envir.R Running jit.R Running loop.R Running switch.R Testing examples for package parallel comparing parallel-Ex.Rout to parallel-Ex.Rout.prev ... OK Running specific tests for package parallel Running Master.R Running vignettes for package parallel I do not really know what any of this means but when I got a graph and no explicit errors returned I just wnet ahead with using the installation. I have not encountered anything wrong while using is so unless there is something you can tell from the above, I guess I will just continue to use the current installation. Many thanks. On Thu, Feb 21, 2013 at 2:36 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Thu, Feb 21, 2013 at 10:46 AM, Joanna Papakonstantinou joanna.p...@gmail.com wrote: I only thought one was missing since it kept giving me error that it wasn't set. But all seems to working OK so I guess I don't need to create anything. No. The first two gave a response of 1 which means they failed. -- ** *Joanna Papakonstantinou, Ph.D.* [[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] Error in setwd(outDir) : cannot change working directory
I installed R on my Windows laptop in C:\Program Files\R\R-2.15.2 and am able to open RGUI (640bit), see packages and run commands. However, when I test the installation and run the basic tests and all the tests on the standard and recommended packages i.e.: library(tools) testInstalledBasic(both) testInstalledPackages(base, errorsAreFatal = FALSE) testInstalledPackages(recommended, errorsAreFatal = FALSE) I am getting errors such as: testInstalledPackages(base,errorsAreFatal=FALSE) Error in setwd(outDir) : cannot change working directory my working driectory is: getwd() [1] C:/Users/jpapa/Documents In which I see R folder as well as the .rData from my last session. what does the wd have to do with the output directory? Do I need to create an output directory? DO I need to setwd(outDir)? do i need to change the wd (for example to the Pogram Files directory where R is installed or to another directory I need to create? if so, how do I do this? i also noticed that i have packages in \library C:/Users/jpapa/Documents/R/win-library/2.15 and in library C:/Program Files/R/R-2.15.2/library. Do all packages need to be in one place? If so, should they be in my Documents or in Program Files? Thank you for your help. ** *Joanna Papakonstantinou, Ph.D.* [[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] Error in setwd(outDir) : cannot change working directory
I am running as administrator. Again, the first 2 tests worked but the 3rd is still giving me an error: testInstalledBasic(basic) running strict specific tests running code in eval-etc.R comparing eval-etc.Rout to eval-etc.Rout.save ...[1] 1 testInstalledBasic(both) running strict specific tests running code in eval-etc.R comparing eval-etc.Rout to eval-etc.Rout.save ...[1] 1 testInstalledPackages(base,errorsAreFatal=FALSE) Error in setwd(outDir) : cannot change working directory So since this my installation was standard, do you just recommend I unistall and resintsall somewhere else? Thank you for your help. On Wed, Feb 20, 2013 at 11:33 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Wed, Feb 20, 2013 at 11:54 AM, Joanna Papakonstantinou joanna.p...@gmail.com wrote: I installed R on my Windows laptop in C:\Program Files\R\R-2.15.2 and am able to open RGUI (640bit), see packages and run commands. However, when I test the installation and run the basic tests and all the tests on the standard and recommended packages i.e.: library(tools) testInstalledBasic(both) testInstalledPackages(base, errorsAreFatal = FALSE) testInstalledPackages(recommended, errorsAreFatal = FALSE) I am getting errors such as: testInstalledPackages(base,errorsAreFatal=FALSE) Error in setwd(outDir) : cannot change working directory my working driectory is: getwd() [1] C:/Users/jpapa/Documents In which I see R folder as well as the .rData from my last session. what does the wd have to do with the output directory? Do I need to create an output directory? DO I need to setwd(outDir)? do i need to change the wd (for example to the Pogram Files directory where R is installed or to another directory I need to create? if so, how do I do this? i also noticed that i have packages in \library C:/Users/jpapa/Documents/R/win-library/2.15 and in library C:/Program Files/R/R-2.15.2/library. Do all packages need to be in one place? If so, should they be in my Documents or in Program Files? Its likely trying to write in the C:\Program Files tree but lacks permission. Run R with Administrator permissions or re-install R elsewhere, e.g. C:\R -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com -- ** *Joanna Papakonstantinou, Ph.D.* [[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] duplicate 'row.names' are not allowed
I am getting an error when trying to import tab delimited .txt file saved from Excel. I have read what is posted on the forums but still am confused. I saved my Excel file (DataTestforR.xlsx) as a tab delimited txt file (DataTestR.txt) on my Desktop. In the RGUI, I tried to import the txt file and got an error myfile-C:\\Users\\jpapa\\Desktop\\DataTestR.txt mydf-read.delim(myfile, header=TRUE,sep= , dec=.) Error in read.table(file = file, header = header, sep = sep, quote = quote, : duplicate 'row.names' are not allowed The first row of my file has column names and the first column of my file has unique identifing names (not duplicated): Cu Sa Na Ci Se NM NPI IPI Seg 0090.00 15.48 1 SOM S L TX 0 0.2 0.2 7-Very 10997.00 64.62 123 B C NJ 0 0.01 0.04 7-Very Please tell me what I am doing wrong. Thank you. ** *Joanna Papakonstantinou, Ph.D.* [[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] Error in setwd(outDir) : cannot change working directory
I ran
testInstalledPackages(scope=base,errorsAreFatal=FALSE)
and it completed (and spit out a graph).
Does this mean I am ok to contunie using this installation of R?
Should I create an output directory somewhere either in Program Files where
R is installed or in my working directory?
Thank you for your time and help.
On Wed, Feb 20, 2013 at 12:20 PM, S Ellison s.elli...@lgcgroup.com wrote:
I am getting errors such as:
testInstalledPackages(base,errorsAreFatal=FALSE)
Error in setwd(outDir) : cannot change working directory
Er, the first parameter in testInstalledPackages() is the output
directory name, not the package name supplied in scope. You probably don;t
have a writeable directory called base
Try
testInstalledPackages(scope=base,errorsAreFatal=FALSE)
S Ellison
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Re: [R] duplicate 'row.names' are not allowed
Some of the names in the columns actually have spaces in them (e.g., S L TX is in one column). So there are really 9. I was able to save the file as a csv file and read.table succesfully. On Wed, Feb 20, 2013 at 2:03 PM, David Winsemius dwinsem...@comcast.netwrote: On Feb 20, 2013, at 10:14 AM, Joanna Papakonstantinou wrote: I am getting an error when trying to import tab delimited .txt file saved from Excel. I have read what is posted on the forums but still am confused. I saved my Excel file (DataTestforR.xlsx) as a tab delimited txt file (DataTestR.txt) on my Desktop. In the RGUI, I tried to import the txt file and got an error myfile-C:\\Users\\jpapa\\Desktop\\DataTestR.txt mydf-read.delim(myfile, header=TRUE,sep= , dec=.) Error in read.table(file = file, header = header, sep = sep, quote = quote, : duplicate 'row.names' are not allowed The first row of my file has column names and the first column of my file has unique identifing names (not duplicated): Cu Sa Na Ci Se NM NPI IPI Seg 0090.00 15.48 1 SOM S L TX 0 0.2 0.2 7-Very I count 11 data columns and nine column names. -- Alameda, CA, USA -- ** *Joanna Papakonstantinou, Ph.D.* [[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.
