Merge pull request #52 from jhmigueles/Time-detection-g.part5

Time detection in g.part5
wadpac · Oct 8, 2017 · fc78c74 · fc78c74
2 parents 72fae88 + 8ab1e26
commit fc78c74
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Showing 2 changed files with 19 additions and 3 deletions.
diff --git a/R/g.part5.R b/R/g.part5.R
@@ -170,6 +170,13 @@ g.part5 = function(datadir=c(),metadatadir=c(),f0=c(),f1=c(),strategy=1,maxdur=7
               }
               s0 = which(timebb == gik.ons[g])[1]
               s1 = which(timebb == gik.end[g])[1]
+              #Change 1 - 03/10/2017
+              if ( timebb[s0] != as.character(timebb[s0])){
+                    timebb = as.character(timebb)
+                    s0 = which(timebb == gik.ons[g])[1]
+                    s1 = which(timebb == gik.end[g])[1]
+                }
+              #End of change 1
               if (is.na(s0) == TRUE) s0 = which(timebb == paste(gik.ons[g]," 00:00:00",sep=""))[1]
               if (is.na(s1) == TRUE) s1 = which(timebb == paste(gik.end[g]," 00:00:00",sep=""))[1]
               s0 = s0 + pr0 - 1
@@ -279,6 +286,14 @@ g.part5 = function(datadir=c(),metadatadir=c(),f0=c(),f1=c(),strategy=1,maxdur=7
               }
               if (is.na(s0) == TRUE) s0 = which(timebb == paste(w0c," 00:00:00",sep=""))[1]
               if (is.na(s1) == TRUE) s1 = which(timebb == paste(w1c," 00:00:00",sep=""))[1]
+              #Change 2 - 03/10/2017
+               if ( timebb[s0] != as.character(timebb[s0])){
+                    timebb = as.character(timebb)
+                    timebb = as.character(timebb)
+                    if (is.na(s0) == TRUE) s0 = which(timebb == w0c)[1]
+                    if (is.na(s1) == TRUE) s1 = which(timebb == w1c)[1]
+                }
+              #End of change 2
               # }
               if (length(s1) != 0 & length(s0) != 0 & is.na(s0) == FALSE & is.na(s1) == FALSE) {
                 diur[s0:s1] = 1

diff --git a/R/g.shell.GGIR.R b/R/g.shell.GGIR.R
@@ -131,6 +131,7 @@ g.shell.GGIR = function(mode=c(1,2),datadir=c(),outputdir=c(),studyname=c(),f0=1
   if (length(which(ls() == "closedbout")) == 0)  closedbout = FALSE
   if (length(which(ls() == "IVIS_windowsize_minutes")) == 0)  IVIS_windowsize_minutes=60
   if (length(which(ls() == "IVIS_epochsize_seconds")) == 0)  IVIS_epochsize_seconds=30
+  if (length(which(ls() == "acc.metric")) == 0) acc.metric = "ENMO"
 
 
   # # specific for part 5
@@ -197,7 +198,7 @@ g.shell.GGIR = function(mode=c(1,2),datadir=c(),outputdir=c(),studyname=c(),f0=1
     cat(paste0(rep('_',options()$width),collapse=''))
     cat("\nPart 3\n")
     if (f1 == 0) f1 = length(dir(paste(metadatadir,"/meta/basic",sep="")))
-    g.part3(metadatadir=metadatadir,f0=f0,
+    g.part3(metadatadir=metadatadir,f0=f0, acc.metric = acc.metric,
             f1=f1,anglethreshold=anglethreshold,timethreshold=timethreshold,
             ignorenonwear=ignorenonwear,overwrite=overwrite,desiredtz=desiredtz)
   }
@@ -220,9 +221,9 @@ g.shell.GGIR = function(mode=c(1,2),datadir=c(),outputdir=c(),studyname=c(),f0=1
     cat("\nPart 5\n")
     if (f1 == 0) f1 = length(dir(paste(metadatadir,"/meta/ms4.out",sep="")))
     g.part5(datadir=datadir,metadatadir=metadatadir,f0=f0,f1=f1,strategy=strategy,maxdur=maxdur,
-            hrs.del.start=hrs.del.start,
+            hrs.del.start=hrs.del.start, 
             hrs.del.end=hrs.del.end,
-            loglocation=loglocation,excludefirstlast=excludefirstlast,
+            loglocation=loglocation,excludefirstlast=excludefirstlast, acc.metric=acc.metric,
             windowsizes=windowsizes,boutcriter.in=boutcriter.in,boutcriter.lig=boutcriter.lig,
             boutcriter.mvpa=boutcriter.mvpa,storefolderstructure=storefolderstructure,
             threshold.lig = threshold.lig,