Merge pull request wadpac#45 from jhmigueles/master

About issue wadpac#9

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") {
+g.part3 = function(metadatadir=c(),f0,f1,anglethreshold = 5,timethreshold = 5, 
+                   metric="ENMO",ignorenonwear=FALSE,overwrite=FALSE,desiredtz="Europe/London") {
   # description: function to apply sleep detection functions to milestone data generated by g.part1
   #------------------------------------
   # create output directory if it does not exist
@@ -58,7 +58,7 @@ g.part3 = function(metadatadir=c(),f0,f1,anglethreshold = 5,
       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)
-        SLE = g.sib.det(M,IMP,I,twd=c(-12,12),timethreshold=timethreshold,anglethreshold=anglethreshold,desiredtz=desiredtz)
+        SLE = g.sib.det(M,IMP,I,twd=c(-12,12),timethreshold=timethreshold,anglethreshold=anglethreshold,metric=metric,desiredtz=desiredtz)
         L5list = SLE$L5list
         if (length(SLE$output) > 0 & SLE$detection.failed == FALSE) {
           id = as.character(unlist(strsplit(I$filename,"_"))[1])
@@ -77,4 +77,4 @@ g.part3 = function(metadatadir=c(),f0,f1,anglethreshold = 5,
   SI = sessionInfo()
 
   save(SI,file=paste(metadatadir,"/results/QC/sessioninfo_part3.RData",sep=""))
-}
+}

man/g.part3.Rd

@@ -11,7 +11,7 @@ them as nocturnal sleep or day time sustained inactivity periods.
 Typical users should work with function g.shell.GGIR only.
 }
 \usage{
-g.part3(metadatadir=c(),f0,f1,anglethreshold = 5,timethreshold = 5,
+g.part3(metadatadir=c(),f0,f1,anglethreshold = 5,timethreshold = 5,metric="ENMO",
   ignorenonwear=FALSE,overwrite=FALSE,desiredtz="Europe/London")
 }
 \arguments{
@@ -37,6 +37,9 @@ g.part3(metadatadir=c(),f0,f1,anglethreshold = 5,timethreshold = 5,
   default = 5. This can be specified as multiple thresholds, each of 
   which will be implemented. For example, timethreshold = c(5,10)
   }
+  \item{metric}{
+    Which one of the metrics do you want to consider to analyze L5. The metric of interest need to be calculated in M (see \link{g.part1})
+  }
   \item{ignorenonwear}{
   If TRUEE then ignore detected monitor non-wear periods to avoid 
   confusion between monitor non-wear time and sustained inactivity 
@@ -85,4 +88,4 @@ g.part3(metadatadir=metadatadir,anglethreshold=5,timethreshold=5,overwrite=FALSE
 \item van Hees VT, Sabia S, et al. (2015) A novel, open access method to
 assess sleep duration using a wrist-worn accelerometer, PLoS ONE, November 2015
 }
-}
+}