g.part1 can be called with a parameter called strategy, that in g.par…

.Rbuildignore

@@ -0,0 +1,2 @@
+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

@@ -0,0 +1,7 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+src/*.o
+src/*.so
+src/*.dll

GGIR.Rproj

@@ -0,0 +1,17 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

R/g.part3.R

@@ -1,5 +1,5 @@
 g.part3 = function(metadatadir=c(),f0,f1,anglethreshold = 5,
-                   timethreshold = 5,ignorenonwear=FALSE,overwrite=FALSE,desiredtz="Europe/London") {
+                   timethreshold = 5,ignorenonwear=FALSE,overwrite=FALSE,desiredtz="Europe/London",strategy=1) {
   # description: function to apply sleep detection functions to milestone data generated by g.part1
   #------------------------------------
   # create output directory if it does not exist
@@ -57,7 +57,7 @@ g.part3 = function(metadatadir=c(),f0,f1,anglethreshold = 5,
       M = c()
       load(paste(metadatadir,"/meta/basic/",fnames[i],sep=""))
       if (M$filecorrupt == FALSE & M$filetooshort == FALSE) {
-        IMP = g.impute(M,I,strategy=1,hrs.del.start=0,hrs.del.end=0,maxdur=0)
+        IMP = g.impute(M,I,strategy=strategy,hrs.del.start=0,hrs.del.end=0,maxdur=0)
         SLE = g.sib.det(M,IMP,I,twd=c(-12,12),timethreshold=timethreshold,anglethreshold=anglethreshold,desiredtz=desiredtz)
         L5list = SLE$L5list
         if (length(SLE$output) > 0 & SLE$detection.failed == FALSE) {

R/g.part5.R

@@ -38,7 +38,7 @@ g.part5 = function(datadir=c(),metadatadir=c(),f0=c(),f1=c(),strategy=1,maxdur=7
   # specify parameters
   ffdone = fnames.ms5 #ffdone is now a list of files that have already been processed by g.part5
   wdaynames = c("Sunday","Monday","Tuesday","Wednesday","Thursday","Friday","Saturday")
-  nfeatures = 500
+  nfeatures = 1000
   ws3 = windowsizes[1]
   ds_names = rep("",nfeatures)
   di = 1
@@ -110,7 +110,14 @@ g.part5 = function(datadir=c(),metadatadir=c(),f0=c(),f1=c(),strategy=1,maxdur=7
       }
       # load output g.part2
       selp = which(fnames.ms2 == fnames.ms3[i]) # so, fnames.ms3[i] is the reference point for filenames
+       try({
+        hayError=TRUE
       load(file=paste(metadatadir,"/meta/ms2.out/",fnames.ms2[selp],sep=""))
+      hayError=FALSE
+      })
+      if(hayError){
+        stop(paste(metadatadir,"/meta/ms2.out/",fnames.ms2[selp],sep=""))
+      }
       daysummary = SUM$daysummary
       summary = SUM$summary
       # load output g.part4
@@ -763,4 +770,4 @@ g.part5 = function(datadir=c(),metadatadir=c(),f0=c(),f1=c(),strategy=1,maxdur=7
       }
     }
   }
-}
+}

R/g.shell.GGIR.R

@@ -195,7 +195,7 @@ g.shell.GGIR = function(mode=c(1,2),datadir=c(),outputdir=c(),studyname=c(),f0=1
     if (f1 == 0) f1 = length(dir(paste(metadatadir,"/meta/basic",sep="")))
     g.part3(metadatadir=metadatadir,f0=f0,
             f1=f1,anglethreshold=anglethreshold,timethreshold=timethreshold,
-            ignorenonwear=ignorenonwear,overwrite=overwrite,desiredtz=desiredtz)
+            ignorenonwear=ignorenonwear,overwrite=overwrite,desiredtz=desiredtz,strategy=strategy)
   }
   if (dopart4 == TRUE) {
     cat('\n')