Issues #42 and #46

R/g.part3.R

@@ -1,5 +1,5 @@
 g.part3 = function(metadatadir=c(),f0,f1,anglethreshold = 5,timethreshold = 5, 
-                   metric="ENMO",ignorenonwear=FALSE,overwrite=FALSE,desiredtz="Europe/London") {
+                   acc.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,timethreshold = 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,metric=metric,desiredtz=desiredtz)
+        SLE = g.sib.det(M,IMP,I,twd=c(-12,12),timethreshold=timethreshold,anglethreshold=anglethreshold,acc.metric=acc.metric,desiredtz=desiredtz)
         L5list = SLE$L5list
         if (length(SLE$output) > 0 & SLE$detection.failed == FALSE) {
           id = as.character(unlist(strsplit(I$filename,"_"))[1])

R/g.part5.R

@@ -1,5 +1,5 @@
 g.part5 = function(datadir=c(),metadatadir=c(),f0=c(),f1=c(),strategy=1,maxdur=7,hrs.del.start=0,hrs.del.end =0,
-                   loglocation= c(),excludefirstlast=FALSE,windowsizes=c(5,900,3600), metric="ENMO",
+                   loglocation= c(),excludefirstlast=FALSE,windowsizes=c(5,900,3600), acc.metric="ENMO",
                    boutcriter.mvpa=0.8,boutcriter.in=0.9,boutcriter.lig=0.8,storefolderstructure=FALSE,
                    threshold.lig = c(40),
                    threshold.mod = c(100),
@@ -122,7 +122,7 @@ g.part5 = function(datadir=c(),metadatadir=c(),f0=c(),f1=c(),strategy=1,maxdur=7
         IMP = g.impute(M,I,strategy=strategy,hrs.del.start=hrs.del.start,
                        hrs.del.end=hrs.del.end,maxdur=maxdur)
         time = IMP$metashort[,1]
-        ACC = IMP$metashort[,metric] * 1000 #note that this is imputed ACCELERATION because we use this for describing behaviour
+        ACC = IMP$metashort[,acc.metric] * 1000 #note that this is imputed ACCELERATION because we use this for describing behaviour
 
         if (length(which(names(IMP$metashort) == "anglez")) == 0) {
           cat("Warning: anglez not extracted. Please check that do.anglez == TRUE")

R/g.sib.det.R

@@ -1,5 +1,5 @@
 g.sib.det = function(M,IMP,I,twd=c(-12,12),anglethreshold = 5,
-                     timethreshold = c(5,10), metric = "ENMO", desiredtz="Europe/London") {
+                     timethreshold = c(5,10), acc.metric = "ENMO", desiredtz="Europe/London") {
   #==============================================================
   # get variables  
   D = IMP$metashort
@@ -36,7 +36,7 @@ g.sib.det = function(M,IMP,I,twd=c(-12,12),anglethreshold = 5,
       cat("metric anglez was not extracted, please make sure that anglez  is extracted")
     }
     angle = as.numeric(as.matrix(D[1:nD,which(colnames(D)=="anglez")]))
-    ACC = as.numeric(as.matrix(D[1:nD,which(colnames(D)==metric)]))
+    ACC = as.numeric(as.matrix(D[1:nD,which(colnames(D)==acc.metric)]))
     night = rep(0,length(angle))
     if (length(which(is.na(angle) ==TRUE)) > 0) {
       if (which(is.na(angle) ==TRUE)[1] == length(angle)) {

inst/NEWS.Rd

@@ -1,6 +1,27 @@
 \name{NEWS}
 \title{News for Package \pkg{GGIR}}
 \newcommand{\cpkg}{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}
+\section{Changes in version 1.5-11 (release date:01-8-2017)}{
+\itemize{
+  \item Codecov badge added to the README file
+  \item Functions added to create dummy accelerometer file (csv) and dummy sleeplog (csv), 
+	needed for testing
+  \item Default IVIS_epochsize_seconds parameter updated from 30 to 3600
+  \item g.part1 messages on the consolo are now condensed printing only the number of the 
+	blocks loaded separated by spaces rather than new lines
+  \item Split g.part5 function into multiple smaller functions
+  \item Replace hard-coded "Europe/London" in g.part5 by desiredtz, to make the function
+	work for users outside the UK
+  \item Data frame output from g.part5 is now tidied up by removing empty rows and columns generated
+  \item Calculation of mean amplitude deviation (MAD) is now implemented in g.part1 by the argument do.mad
+  \item Percentiles and levels in g.part2 are now calculated for all the acceleration metrics selected
+  \item g.part3, g.part4 and g.part5 are now independent on metric ENMO to work, argument acc.metric allows
+	the user to select which metric to use to describe behavior
+  \item Argument dayborder is now included in g.part5 to consider the whole measurement in case the protocol
+	starts after midnight
+  }
+}
+
 \section{Changes in version 1.5-10 (release date:12-7-2017)}{
 \itemize{
   \item Date format recognition improved for Actigraph csv files
@@ -232,4 +253,4 @@
 \itemize{
   \item This was the first version  
 }
-}
+}

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,metric="ENMO",
+g.part3(metadatadir=c(),f0,f1,anglethreshold = 5,timethreshold = 5,acc.metric="ENMO",
   ignorenonwear=FALSE,overwrite=FALSE,desiredtz="Europe/London")
 }
 \arguments{
@@ -37,7 +37,7 @@ g.part3(metadatadir=c(),f0,f1,anglethreshold = 5,timethreshold = 5,metric="ENMO"
   default = 5. This can be specified as multiple thresholds, each of 
   which will be implemented. For example, timethreshold = c(5,10)
   }
-  \item{metric}{
+  \item{acc.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}{

man/g.part5.Rd

@@ -11,7 +11,7 @@ based on bouted periods as well as non-bouted periods.
 \usage{
 g.part5(datadir=c(),metadatadir=c(),f0=c(),f1=c(),strategy=1,maxdur=7,
 hrs.del.start=0,hrs.del.end =0,
-loglocation= c(),excludefirstlast=FALSE,windowsizes=c(5,900,3600), metric="ENMO",
+loglocation= c(),excludefirstlast=FALSE,windowsizes=c(5,900,3600), acc.metric="ENMO",
 boutcriter.mvpa=0.8,boutcriter.in=0.9,boutcriter.lig=0.8,
 storefolderstructure=FALSE,threshold.lig = c(40),threshold.mod = c(100),
 threshold.vig = c(400),timewindow=c("MM","WW"),boutdur.mvpa = c(1,5,10),
@@ -70,7 +70,7 @@ M5L5res = 10,overwrite=FALSE,desiredtz="Europe/London",bout.metric=4,dayborder=0
  \item{windowsizes}{
   see \link{g.getmeta}
   }
- \item{metric}{
+ \item{acc.metric}{
   Which one of the metrics do you want to consider to describe behaviour. The metric of interest need to be calculated in M (see \link{g.part1})
   }
  \item{boutcriter.mvpa}{

man/g.sib.det.Rd

@@ -9,7 +9,7 @@
 }
 \usage{
   g.sib.det(M,IMP,I,twd=c(-12,12),anglethreshold = 5, 
-                     timethreshold = c(5,10), metric = "ENMO", desiredtz="Europe/London")
+                     timethreshold = c(5,10), acc.metric = "ENMO", desiredtz="Europe/London")
 }
 \arguments{
   \item{M}{
@@ -31,7 +31,7 @@
   \item{timethreshold}{
     See \link{g.part3}
   }
-  \item{metric}{
+  \item{acc.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{desiredtz}{