R installed TreEvo missing functions

[Daniel Gates]

Greetings again everyone,

I have another question, I was able to load the TreEvo code from svn,
pull out the package and successfully install the package and all
dependencies into the file with all the R packages as well as open it
using library(TreEvo). Unfortunately, when I tried running small
amounts of code from the example Barb sent out earlier I discovered R
had only loaded a subset of the functions from the source code.

Below is the list of the functions I have:

> ls("package:TreEvo")
[1] "BCP" "CredInt"
"fitContinuous.hacked"
[4] "getSimulationSplits" "HPD"
"meanFromPrior"
[7] "mutateState" "pairings"
"PairwiseESS"
[10] "PairwiseKS" "parentOffspringPlots"
"plotPosteriors"
[13] "plotPosteriors_abc" "plotPrior"
"presentABCOutput"
[16] "pullFromPrior" "simulateData"
"summarizeTaxonStates"
[19] "summaryStatsLong" "ThreeD.ABCplots"

So things like boxcoxplsSummary, convertTaxonFrameToGeigerData doRuns
doSimulations etc... all are not recognized commands. Anyone have any
ideas what's happening? I have pretty much just pulled the code
straight from the svn, built it using the bash command:
R CMD BUILD

and then installed it using:
R CMD INSTALL

Thanks!

[Barb Banbury]

It might have to do with those functions not being exported in the NAMESPACE file. Do you have a list handy of exactly which ones are missing? Then I can easily update the file (otherwise I have to go through and see what is missing).  If you don't have it handy, then no worries I can do it the long way.    

Barb

[dga...@huskers.unl.edu]

It looks like these are the 20 in the namespace file:

  "BCP"                  "CredInt"
"fitContinuous.hacked"
   "getSimulationSplits"  "HPD"
"meanFromPrior"
  "mutateState"          "pairings"
"PairwiseESS"
  "PairwiseKS"           "parentOffspringPlots"
"plotPosteriors"
  "plotPosteriors_abc"   "plotPrior"
"presentABCOutput"
  "pullFromPrior"        "simulateData"
"summarizeTaxonStates"
  "summaryStatsLong"     "ThreeD.ABCplots"

I think that leaves (you may want to double check):

abcmodels.extrinsic.R
abcmodels.intrinsic.R
boxcoxplsSummary.R
convertTaxonFrameToGeigerData.R
doRun_abc.R
doRun.R
doSimulation.R
doSimulationForPlotting.R
SetMethods.R



Thanks!

-Dan

---

From: treevo-...@googlegroups.com [treevo-...@googlegroups.com] on behalf of Barb Banbury [darwin...@gmail.com]
Sent: Tuesday, May 08, 2012 7:47 PM
To: treevo-...@googlegroups.com
Subject: Re: R installed TreEvo missing functions

[Barb Banbury]

Ok, hopefully it is fixed for you.  It isn't as simple as just adding those file names to the NAMESPACE file, since there are hidden functions within those files and setMethods can't be part of exports either for some s4 reason I don't fully understand.  

Anyway, if it is still acting up tomorrow let me know and I will continue to chip away at it.  

Barb

---

From: treevo-discuss@googlegroups.com [treevo-discuss@googlegroups.com] on behalf of Barb Banbury [darwin...@gmail.com]

Sent: Tuesday, May 08, 2012 7:47 PM

To: treevo-discuss@googlegroups.com