Dear David/Dennis, Thanks. I have 'mvtnorm' and 'multicomp' installed on R 2.10.1. After I installed R 2.13.0, I copied the whole library from R 2.10.1 to R 2.13.0. That should do it? Then when I tried to load 'nparcomp' in 2.13.0, I got the error saying "Error: package 'mvtnorm' is not installed for 'arch=i386'". What does arch=i386 mean?
So I downgraded to 2.12.2, no luck. Now I am on 2.12.1 and it is working. But I have some other packages (e.g. plyr, Hmisc) cannot be loaded on 2.12.1 and I got a similar error. I have a .First function to load all these packages when R is started every time. Error: package 'Hmisc' is not installed for 'arch=i386' So the question is how we know which version of R we should use to make all packages work. Thanks again. By the way, I am on Windows XP. Jun On Sat, Apr 30, 2011 at 6:12 AM, David Winsemius <dwinsem...@comcast.net>wrote: > > On Apr 29, 2011, at 7:17 PM, Jun Shen wrote: > > Hi, Dennis, >> >> Thanks for the reply. I tried to upgrade to R 2.13.0. Then when I tried to >> load the library(nparcomp), I got an error >> >> Error: package 'mvtnorm' is not installed for 'arch=i386' >> >> What does that mean? Thanks. >> >> > You can see from Dennis' console output that 4 other packages are loaded > when nparcomp is loaded. You have apparently not installed all of the needed > packages for the new version of R. There is an argument to the > install.packages function that will check for dependencies. Or perhaps you > need to set that option in a GUI interface. > > -- > David. > > > > Jun >> >> On Fri, Apr 29, 2011 at 5:49 PM, Dennis Murphy <djmu...@gmail.com> wrote: >> >> Hi: >>> >>> Is this the function nparcomp() in the nparcomp package or the one >>> from the mutoss package? When using functions from packages, it is >>> useful to indicate the package name. I'm assuming you're using the >>> nparcomp package, because your code worked for me when that package >>> was loaded: >>> >>> library(nparcomp) >>>> >>> Loading required package: multcomp >>> Loading required package: mvtnorm >>> Loading required package: survival >>> Loading required package: splines >>> >>>> >>>> nparcomp(Ulceration~Group,data=test,type='Dunnett',control='Non-treated') >>>> >>> >>> Nonparametric Multiple Comparison Procedure based on relative >>> contrast effects , Type of Contrast : Dunnett >>> NOTE: >>> *-------------------Weight Matrix------------------* >>> - Weight matrix for choosen contrast based on all-pairs comparisons >>> >>> *-----------Analysis of relative effects-----------* >>> - Simultaneous Confidence Intervals for relative effects p(i,j) >>> with confidence level 0.95 >>> - Method = Multivariate Delta-Method (Logit) >>> - p-Values for H_0: p(i,j)=1/2 >>> >>> *----------------Interpretation--------------------* >>> p(a,b) > 1/2 : b tends to be larger than a >>> *--------------Mult.Distribution-------------------* >>> - Equicoordinate Quantile >>> - Global p-Value >>> *--------------------------------------------------* >>> $weight.matrix >>> >>> < snipped for brevity - all zeros > >>> >>> $Data.Info >>> Sample Size >>> 1 Duoderm 24 >>> 2 Fibrase 24 >>> 3 Kollagenase 24 >>> 4 Non-treated 24 >>> 5 Stimulen 24 >>> 6 Vehicle 24 >>> >>> $Analysis.of.relative.effects >>> Comparison rel.effect confidence.interval t.value >>> 1 p(Non-treated,Duoderm) 0.5 [ 0.499 ; 0.501 ] 0 >>> 2 p(Non-treated,Fibrase) 0.5 [ 0.499 ; 0.501 ] 0 >>> 3 p(Non-treated,Kollagenase) 0.5 [ 0.499 ; 0.501 ] 0 >>> 4 p(Non-treated,Stimulen) 0.5 [ 0.499 ; 0.501 ] 0 >>> 5 p(Non-treated,Vehicle) 0.5 [ 0.499 ; 0.501 ] 0 >>> p.value.adjusted p.value.unadjusted >>> 1 1 1 >>> 2 1 1 >>> 3 1 1 >>> 4 1 1 >>> 5 1 1 >>> >>> $Mult.Distribution >>> Quantile p.Value.global >>> 1 2.568766 1 >>> >>> $Correlation >>> [1] NA >>> >>> A graphic also appears indicating zero effect, which is what one would >>> expect since Ulceration = 5 for every observation in the data frame. >>> >>> sessionInfo() >>>> >>> R version 2.13.0 (2011-04-13) >>> Platform: x86_64-pc-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] splines stats graphics grDevices utils datasets methods >>> [8] base >>> >>> other attached packages: >>> [1] nparcomp_1.0-1 multcomp_1.2-5 survival_2.36-9 mvtnorm_0.9-999 >>> [5] sos_1.3-0 brew_1.0-6 plyr_1.5.2 >>> >>> loaded via a namespace (and not attached): >>> [1] tcltk_2.13.0 tools_2.13.0 >>> >>> Check your version of R and the nparcomp package against this. If you >>> have an older version of R or nparcomp, perhaps an upgrade is >>> sufficient to fix the problem. >>> >>> HTH, >>> Dennis >>> >>> On Fri, Apr 29, 2011 at 2:49 PM, Jun Shen <jun.shen...@gmail.com> wrote: >>> >>>> Dear list, >>>> >>>> I tried to use the nparcomp to run some post hoc non-parametric >>>> >>> comparison >>> >>>> and got and error. >>>> >>>> Error in uniroot(pfct, interval = interval) : >>>> f() values at end points not of opposite sign >>>> >>>> Appreciate any comments. >>>> >>>> the command line: >>>> >>>> nparcomp(Ulceration~Group,data=test,type='Dunnett',control='Non-treated') >>>>> >>>> >>>> >>>> Jun >>>> =================================================================== >>>> data as follows >>>> >>>> structure(list(Group = c("Duoderm", "Duoderm", "Duoderm", "Duoderm", >>>> "Duoderm", "Duoderm", "Duoderm", "Duoderm", "Duoderm", "Duoderm", >>>> "Duoderm", "Duoderm", "Duoderm", "Duoderm", "Duoderm", "Duoderm", >>>> "Duoderm", "Duoderm", "Duoderm", "Duoderm", "Duoderm", "Duoderm", >>>> "Duoderm", "Duoderm", "Fibrase", "Fibrase", "Fibrase", "Fibrase", >>>> "Fibrase", "Fibrase", "Fibrase", "Fibrase", "Fibrase", "Fibrase", >>>> "Fibrase", "Fibrase", "Fibrase", "Fibrase", "Fibrase", "Fibrase", >>>> "Fibrase", "Fibrase", "Fibrase", "Fibrase", "Fibrase", "Fibrase", >>>> "Fibrase", "Fibrase", "Kollagenase", "Kollagenase", "Kollagenase", >>>> "Kollagenase", "Kollagenase", "Kollagenase", "Kollagenase", >>>> >>> "Kollagenase", >>> >>>> "Kollagenase", "Kollagenase", "Kollagenase", "Kollagenase", >>>> >>> "Kollagenase", >>> >>>> "Kollagenase", "Kollagenase", "Kollagenase", "Kollagenase", >>>> >>> "Kollagenase", >>> >>>> "Kollagenase", "Kollagenase", "Kollagenase", "Kollagenase", >>>> >>> "Kollagenase", >>> >>>> "Kollagenase", "Non-treated", "Non-treated", "Non-treated", >>>> >>> "Non-treated", >>> >>>> "Non-treated", "Non-treated", "Non-treated", "Non-treated", >>>> >>> "Non-treated", >>> >>>> "Non-treated", "Non-treated", "Non-treated", "Non-treated", >>>> >>> "Non-treated", >>> >>>> "Non-treated", "Non-treated", "Non-treated", "Non-treated", >>>> >>> "Non-treated", >>> >>>> "Non-treated", "Non-treated", "Non-treated", "Non-treated", >>>> >>> "Non-treated", >>> >>>> "Stimulen", "Stimulen", "Stimulen", "Stimulen", "Stimulen", "Stimulen", >>>> "Stimulen", "Stimulen", "Stimulen", "Stimulen", "Stimulen", "Stimulen", >>>> "Stimulen", "Stimulen", "Stimulen", "Stimulen", "Stimulen", "Stimulen", >>>> "Stimulen", "Stimulen", "Stimulen", "Stimulen", "Stimulen", "Stimulen", >>>> "Vehicle", "Vehicle", "Vehicle", "Vehicle", "Vehicle", "Vehicle", >>>> "Vehicle", "Vehicle", "Vehicle", "Vehicle", "Vehicle", "Vehicle", >>>> "Vehicle", "Vehicle", "Vehicle", "Vehicle", "Vehicle", "Vehicle", >>>> "Vehicle", "Vehicle", "Vehicle", "Vehicle", "Vehicle", "Vehicle" >>>> ), Ulceration = c(5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, >>>> 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, >>>> 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, >>>> 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, >>>> 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, >>>> 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, >>>> 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, >>>> 5, 5, 5), Inflamation = c(3, 4, 3, 2, 3, 3, 4, 4, 2, 2, 3, 3, >>>> 3, 3, 3, 3, 3, 4, 3, 3, 3, 4, 3, 3, 2, 3, 3, 4, 3, 3, 2, 4, 4, >>>> 4, 4, 4, 4, 4, 3, 3, 4, 3, 5, 3, 3, 4, 4, 3, 3, 2, 4, 2, 3, 3, >>>> 4, 3, 4, 3, 3, 4, 3, 4, 2, 3, 3, 4, 2, 3, 4, 3, 2, 3, 3, 3, 2, >>>> 3, 2, 2, 2, 2, 4, 3, 2, 3, 3, 4, 3, 3, 4, 3, 4, 2, 4, 3, 4, 2, >>>> 4, 3, 4, 3, 2, 2, 2, 2, 3, 2, 3, 2, 4, 3, 2, 4, 4, 4, 2, 2, 3, >>>> 3, 2, 4, 3, 2, 3, 2, 2, 2, 4, 2, 3, 2, 3, 2, 3, 3, 3, 4, 3, 3, >>>> 4, 4, 2, 3, 2, 3), Fibroplasia = c(4, 4, 4, 4, 4, 3, 4, 4, 4, >>>> 3, 4, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 2, 4, 4, 3, >>>> 2, 4, 4, 4, 4, 4, 4, 3, 3, 3, 4, 3, 3, 3, 4, 3, 4, 4, 4, 4, 4, >>>> 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 3, 3, 3, 4, 4, 3, 4, 4, 4, 3, 4, >>>> 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, >>>> 4, 4, 3, 4, 4, 3, 4, 3, 2, 3, 3, 4, 3, 3, 4, 4, 3, 3, 3, 4, 3, >>>> 3, 4, 4, 4, 4, 4, 4, 4, 3, 4, 4, 4, 3, 3, 4, 4, 4, 4, 4, 3, 4, >>>> 3, 4, 4, 4, 4, 4, 4, 4, 4), Fibrosis.and.Adexnal.Atrophy = c(4, >>>> 4, 4, 3, 4, 4, 4, 4, 4, 3, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, >>>> 4, 4, 3, 4, 3, 4, 4, 3, 3, 4, 4, 4, 4, 4, 4, 4, 3, 3, 4, 3, 4, >>>> 4, 4, 3, 4, 3, 3, 3, 3, 3, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 3, 3, >>>> 4, 4, 3, 3, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 4, 4, >>>> 4, 4, 3, 4, 4, 4, 3, 4, 3, 4, 3, 4, 4, 3, 4, 3, 2, 3, 3, 4, 4, >>>> 3, 4, 4, 3, 3, 3, 4, 3, 3, 4, 4, 4, 4, 4, 4, 4, 3, 4, 4, 4, 4, >>>> 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4), Inflammation = c(2, >>>> 2, 2, 1, 1, 1, 2, 3, 1, 2, 1, 1, 1, 1, 2, 1, 2, 2, 1, 1, 2, 1, >>>> 1, 1, 1, 1, 1, 1, 1, 2, NA, 1, 1, 1, 2, 2, 2, 1, 2, 1, 1, 2, >>>> 1, 1, 2, 1, 1, 2, 1, 1, 2, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, >>>> 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, >>>> 1, 1, 1, 1, NA, 2, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 1, >>>> 2, 1, 2, 2, 1, 1, 2, 1, 2, 2, 1, 1, 2, 1, 1, 1, 2, 1, 2, 1, 2, >>>> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 2, 2), Fibroplasia.1 >>>> = >>>> c(4, >>>> 4, 4, 4, 4, 3, 4, 4, 4, 3, 4, 3, 3, 3, 4, 4, 4, 4, 3, 3, 3, 3, >>>> 4, 4, 4, 4, 3, 3, 4, 3, NA, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, >>>> 3, 3, 4, 4, 4, 4, 3, 3, 3, 3, 4, 4, 4, 3, 4, 3, 4, 4, 4, 4, 3, >>>> 3, 4, 4, 4, 3, 4, 3, 4, 4, 3, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, >>>> 4, 3, 3, 3, NA, 4, 4, 4, 4, 3, 4, 3, 3, 3, 3, 3, 4, 2, 4, 3, >>>> 4, 4, 3, 4, 4, 2, 3, 2, 3, 3, 3, 3, 4, 4, 4, 4, 3, 3, 3, 3, 3, >>>> 4, 3, 3, 4, 4, 4, 4, 3, 3, 4, 3, 3, 4, 4, 4, 4, 3, 4, 4), Fibrosis = >>>> c(3, >>>> 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, >>>> 3, 3, 3, 3, 3, 3, 3, 3, NA, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, >>>> 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, >>>> 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, >>>> 3, 3, 3, 3, NA, 3, 3, 3, 3, 3, 2, 2, 3, 3, 3, 3, 3, 2, 3, 3, >>>> 3, 3, 3, 3, 3, 2, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, >>>> 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3), Total = c(25, >>>> 26, 25, 22, 24, 22, 26, 27, 23, 21, 24, 21, 22, 23, 25, 24, 25, >>>> 26, 23, 23, 24, 24, 24, 24, 21, 24, 20, 24, 24, 22, 12, 25, 25, >>>> 25, 26, 26, 26, 24, 22, 21, 24, 22, 24, 22, 25, 23, 25, 24, 22, >>>> 21, 24, 21, 24, 24, 25, 23, 25, 23, 24, 24, 24, 24, 20, 21, 24, >>>> 26, 21, 22, 25, 23, 21, 24, 23, 24, 23, 22, 23, 23, 22, 23, 25, >>>> 23, 23, 24, 24, 24, 23, 22, 17, 25, 25, 21, 25, 22, 25, 19, 24, >>>> 23, 22, 23, 21, 16, 22, 20, 25, 22, 22, 24, 25, 19, 21, 20, 25, >>>> 23, 20, 22, 25, 24, 23, 25, 24, 22, 22, 21, 23, 23, 23, 20, 24, >>>> 23, 24, 23, 23, 22, 24, 23, 23, 24, 26, 25, 23, 23, 24, 25)), .Names = >>>> c("Group", >>>> "Ulceration", "Inflamation", "Fibroplasia", >>>> >>> "Fibrosis.and.Adexnal.Atrophy", >>> >>>> "Inflammation", "Fibroplasia.1", "Fibrosis", "Total"), row.names = c(NA, >>>> 144L), class = "data.frame") >>>> >>>> [[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. >>>> >>>> >>> >> [[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. >> > > David Winsemius, MD > West Hartford, CT > > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.