[Genabel-commits] r935 - in pkg/PredictABEL: . R

Thu Aug 2 17:39:05 CEST 2012

Author: lckarssen
Date: 2012-08-02 17:39:03 +0200 (Thu, 02 Aug 2012)
New Revision: 935

Added:
   pkg/PredictABEL/R/evalCall.R
Modified:
   pkg/PredictABEL/DESCRIPTION
   pkg/PredictABEL/NAMESPACE
   pkg/PredictABEL/R/PredictABEL.R
Log:
In PredictABEL: 
Biggest change is to try to remove the dependency on the PBSmodelling package. This needs to be tested, though. The package now builds OK, only two warnings when running R CMD check. 

- DESCRIPTION: 
  + Removed PBSmodelling from the list of dependencies
  + At request of prof. Ripley use only one maintainer
- NAMESPACE: removed PBSmodelling
- R/PredictABEL.R and R/evalCall.R:
  - Removed the call to resetGraph() from PBSmodelling. I don't think we need it, but more testing is needed. 
  - For now I copied the source code from the evalCall() function directly from the PBSmodelling source. This is OK, since we both are GPLv2. In a future release we should try to rewrite the plotPredictivenessCurve() function.




Modified: pkg/PredictABEL/DESCRIPTION
===================================================================

--- pkg/PredictABEL/DESCRIPTION	2012-07-30 08:24:11 UTC (rev 934)
+++ pkg/PredictABEL/DESCRIPTION	2012-08-02 15:39:03 UTC (rev 935)
@@ -1,11 +1,10 @@
 Package: PredictABEL
 Title: Assessment of risk prediction models
-Version: 1.2-1
-Date: 2012-07-22
+Version: 1.2-2
+Date: 2012-08-02
 Author: Suman Kundu, Yurii S. Aulchenko, A. Cecile J.W. Janssens
-Maintainer: Suman Kundu <s.kundu at erasmusmc.nl>, A. Cecile J.W. Janssens
-        <a.janssens at erasmusmc.nl>
-Depends: R (>= 2.12.0), Hmisc, ROCR, epitools, PBSmodelling
+Maintainer: Suman Kundu <s.kundu at erasmusmc.nl>
+Depends: R (>= 2.12.0), Hmisc, ROCR, epitools
 Suggests: GenABEL
 Description: PredictABEL includes functions to assess the performance of
  risk models. The package contains functions for the various measures that are
@@ -21,8 +20,8 @@
  logistic regression analysis. These logistic regression functions are
  specifically written for models that include genetic variables, but they
  can also be applied to models that are based on non-genetic risk factors only.
- Finally, the package includes function to construct a simulated dataset with 
- genotypes, genetic risks, and disease status for a hypothetical population, which 
+ Finally, the package includes function to construct a simulated dataset with
+ genotypes, genetic risks, and disease status for a hypothetical population, which
  is used for the evaluation of genetic risk models.
 License: GPL (>= 2)
 URL: http://www.genabel.org/packages/PredictABEL

Modified: pkg/PredictABEL/NAMESPACE
===================================================================
--- pkg/PredictABEL/NAMESPACE	2012-07-30 08:24:11 UTC (rev 934)
+++ pkg/PredictABEL/NAMESPACE	2012-08-02 15:39:03 UTC (rev 935)
@@ -8,6 +8,5 @@
 import(
   Hmisc,
   ROCR,
-  epitools,
-  PBSmodelling
+  epitools
 )

Modified: pkg/PredictABEL/R/PredictABEL.R
===================================================================
--- pkg/PredictABEL/R/PredictABEL.R	2012-07-30 08:24:11 UTC (rev 934)
+++ pkg/PredictABEL/R/PredictABEL.R	2012-08-02 15:39:03 UTC (rev 935)
@@ -1187,8 +1187,6 @@
 "plotPredictivenessCurve" <-
   function(predrisk, rangeyaxis, labels, plottitle, xlabel, ylabel, fileplot, plottype)
   {
-    require(PBSmodelling)
-    
     if (missing(plottitle)) {plottitle <- "Predictiveness curve"}
     if (missing(xlabel)) {xlabel <- "Cumulative percentage"}
     if (missing(ylabel)) {ylabel <- "Predicted risks"}
@@ -1210,7 +1208,6 @@
             y <- (1:n)/n
             z <- y >= ylim[1] & y <= ylim[2]
             
-            resetGraph()
             evalCall(plot,
                      argu = list(x = y[z], y = x[z], type = "n",
                        xlab = "", ylab = "", las = 1, mgp = c(0, 0.6, 0),

Added: pkg/PredictABEL/R/evalCall.R
===================================================================
--- pkg/PredictABEL/R/evalCall.R	                        (rev 0)
+++ pkg/PredictABEL/R/evalCall.R	2012-08-02 15:39:03 UTC (rev 935)
@@ -0,0 +1,55 @@
+## The following function was copied from the PBSmodelling R
+## package version 2.64 (downloaded on 2012-08-01 from SVN:
+## http://pbs-modelling.googlecode.com/svn/trunk).
+## The PBSModelling package is has a GPL v2 (or higher) licence
+## according to the DESCRIPTION file, so we can use this copy without
+## problem.
+##
+## Since this is the only part of PBSmodelling PredictABEL depends on,
+## this is the smartest way to remove the PBSmodelling dependency
+## (which itself drags in TCL/TK and other deps at the OS level.)
+##
+## 2012-08-02 L.C. Karssen.
+
+
+##================================================|
+##                 PBS Modelling                  |
+## Support functions (in alphabetic order)--------|
+## Authors:                                       |
+##  Jon T. Schnute <Jon.SchnuteJ at dfo-mpo.gc.ca>   |
+##  Alex Couture-Beil <alex at mofo.ca>              |
+##  Rowan Haigh <Rowan.HaighR at dfo-mpo.gc.ca>      |
+##  Anisa Egeli <>                                |
+##================================================|
+#
+##evalCall-------------------------------2009-03-03
+## Evaluates a function call, resolving conflicting arguments.
+##-----------------------------------------------RH
+evalCall=function(fn,argu,...,envir=parent.frame(),checkdef=FALSE,checkpar=FALSE){
+        fnam=as.character(substitute(fn))
+        fnam.def=paste(fnam,"default",sep=".")
+        base=formals(fnam)
+        if (checkdef && exists(fnam.def)) {
+                defs=formals(fnam.def)
+                udefs=defs[setdiff(names(defs),names(base))]
+                base=c(base,udefs) }
+        base=base[setdiff(names(base),"...")]
+        if (checkpar) {
+                pars=par(); pars=pars[setdiff(names(pars),names(base))] # use only pars not in base
+                forms=c(base,pars) } # all possible formal arguments
+        else forms=base
+#if (fnam=="axis") {browser();return()}
+        #forms=NULL
+        #for (i in names(base)) forms[[i]]=get(i,envir=envir)
+        dots=list(...)
+        argus=argu[setdiff(names(argu),names(dots))]
+        given=c(argus,dots)
+        allow=given[intersect(names(given),names(forms))]
+        strargs=sapply(allow,deparse,width.cutoff=500,simplify=FALSE)
+        strargs=sapply(strargs,paste,collapse="",simplify=FALSE) # collapse multiple strings
+        argspec=character(0)
+        for (i in names(strargs)) argspec=c(argspec,paste(i,"=",strargs[[i]]))
+        expr=paste(fnam,"(",paste(argspec,collapse=","),")",sep="")
+        eval(parse(text=expr))
+        invisible(expr) }
+#-----------------------------------------evalCall

