[R] beta binomial distribution installation

[Eric Berger]

Hi Amany,
I had no trouble installing TailRank and bioconductor using the link Rhydwyn
 provided.
I was curious about your statement that TailRank uses a different
parameterization for the betabinomial distribution than rmutil.
I looked at the documentation for the two packages and the transformation
to go from one to the other is straightforward.
If you want, you can do the following.
Let (N,u,v) be the parameters used in TailRank and (N,m,s) the parameters
used in rmutil. The correspondence is:

N = N, m  = u/(u+v), s = u+v.

This means you can define functions such as:

mypbb <- function(x,N,u,v) { rmutil::pbetabinom(x,N,u/(u+v),u+v) }   # CDF
myqbb <- function(x,N,u,v) { rmutil:qbetabinom{x,N,u/(u+v),u+v) }  #
inverse CDF

HTH,
Eric





On Wed, Nov 1, 2017 at 6:09 PM, Amany Abdel-Karim <ABDELKARIM2 at msn.com>
wrote:

> Hello,
>
> Thank you for your response. I need to install RankTail package since it
> contains the beta binomial distribution, CDF and inverse CDF in the usual
> form which I need to use. However rmutil package contain unusual forms for
> these functions. So it is easier for me to deal with the forms are
> contained in RankTail.
>
> I tried to install  bioconductor package, using the following commands
> but I still got the following errors:
>
>
>  (1) I tried biocLite() and then library ("TailRank"), I got the following
> errors.
>
> > biocLite()Error in biocLite() : could not find function "biocLite"> library("TailRank")Loading required package: oompaBaseError: package or namespace load failed for ‘TailRank’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
>  there is no package called ‘Biobase’In addition: Warning messages:1: package ‘TailRank’ was built under R version 3.4.2 2: package ‘oompaBase’ was built under R version 3.4.2
>
>
> (2) I tried to write the command biocLite(), then biocLite("TailRank"), I got the following errors:
>
> > biocLite()Error in biocLite() : could not find function "biocLite"> biocLite("ilRank")Error in biocLite("ilRank") : could not find function "biocLite"> biocLite()Error in biocLite() : could not find function "biocLite"> biocLite("TailRank")Error in biocLite("TailRank") : could not find function "biocLite"
>
> >
>
>
> Also, I checked under packages on the right side of the R window and I
> found TailRank , Description is Tail-Rank statistic, and version is 3.1.3.
> So, I tried to write the following code in the console window to check if
> the package works:
>
> > N<-20> u<-3> v<-10> p<-u/u+v> x<-0:N
>
> > yy<-dbb(x,N,u,v)
>
>
> I got the following error:Error in dbb(x, N, u, v) : could not find function "dbb"
>
> >
>
> I am confused because if the package TailRank is already there, why the
> pervious code does not work to calculate dbb (x,N,u,v) and I got error? If
> I do not have the package, would you please let me know the right commands
> I should write in the script window to install TaiRank because the commands
> I used (which I mentioned at the beginning of the email did not work and
> gave errors). I appreciate your help since I am a new user of R.
>
>
> Amany
>
>
>
> ------------------------------
>
> *From:* Eric Berger <ericjberger at gmail.com>
> *Sent:* Wednesday, November 1, 2017 2:42 AM
> *To:* MCGUIRE, Rhydwyn
> *Cc:* Amany Abdel-Karim; R-help at stat.math.ethz.ch
> *Subject:* Re: [R] beta binomial distribution installation
>
> Hi,
> I did a quick search for other packages that provide the beta binomial
> distribution and found "rmutil".
>
> > install.packages("rmutil")
>
> The package has the CDF (pbetabinom) and inverse CDF (qbetabinom) among
> other functions.
>
> HTH,
> Eric
>
>
>
> On Wed, Nov 1, 2017 at 7:50 AM, MCGUIRE, Rhydwyn <
> rmcgu at doh.health.nsw.gov.au> wrote:
>
>> Hi there,
>>
>> It looks like you also need the bioconductor package biobase, I found
>> instructions for downloading that package here:
>> www.bioconductor.org/install
>>
>> Good luck.
>>
>> Cheers,
>> Rhydwyn
>>
>> -----Original Message-----
>> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Amany
>> Abdel-Karim
>> Sent: Wednesday, 1 November 2017 2:13 PM
>> To: R-help at stat.math.ethz.ch
>> Subject: [R] beta binomial distribution installation
>>
>> Hello,
>>
>> I  tried to install package TailRank using the command install.packages
>> (RankTail) and library (TailRank) but I got the following errors. So, how
>> can I install TaiRank in Rstudio to have se beta-binomial distribution, CDF
>> and inverse CDG of  beta-binomal?
>>
>> The commands I used are:
>>
>> > install.packages("TailRank")
>>
>> Installing package into C:/Users/stator-guest/Documents/R/win-library/3.4
>>
>> (as lib is unspecified)
>>
>> Warning in install.packages :
>>
>>   dependency Biobase is not available
>>
>> trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/TailRank_3
>> .1.3.zip'
>>
>> Content type 'application/zip' length 331270 bytes (323 KB)
>>
>> downloaded 323 KB
>>
>>
>>
>> package TailRank successfully unpacked and MD5 sums checked
>>
>>
>>
>> The downloaded binary packages are in
>>
>>             C:\Users\stator-guest\AppData\Local\Temp\RtmpoVx40V\download
>> ed_packages
>>
>> > library(TailRank)
>>
>> Error: package or namespace load failed for TailRank in loadNamespace(i,
>> c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
>>
>>  there is no package called Biobase
>>
>> In addition: Warning message:
>>
>> package TailRank was built under R version 3.4.2
>>
>>
>>
>>
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