Re: [R] Use nparcomp function from nparcomp library to run post hoc

From: Jun Shen <jun.shen.ut_at_gmail.com>
Date: Sat, 30 Apr 2011 08:48:43 -0500

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 <dwinsemius_at_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 <djmuser_at_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.ut_at_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_at_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_at_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
>
>

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