set daysleep_offset default value

DESCRIPTION

@@ -13,7 +13,8 @@ Authors@R: c(person("Vincent T","van Hees",role=c("aut","cre"),
                   person("Joan","Capdevila Pujol",role="ctb"),
                   person("Jairo H","Migueles",role="ctb"),
                   person("Matthew R","Patterson",role="ctb"),
-                  person("Dan","Jackson",role="ctb"))
+                  person("Dan","Jackson",role="ctb"),
+                  person("Lena","Kushleyeva",role="ctb"))
 Maintainer: Vincent T van Hees <v.vanhees@accelting.com>
 Description: A tool to process and analyse data collected with wearable raw acceleration sensors as described in Migueles and colleagues (JMPB 2019), and van Hees and colleagues (JApplPhysiol 2014; PLoSONE 2015). The package has been developed and tested for binary data from 'GENEActiv' <https://www.activinsights.com/> and GENEA devices (not for sale), .csv-export data from  'Actigraph' <https://actigraphcorp.com> devices, and .cwa and .wav-format data from 'Axivity' <https://axivity.com>. These devices are currently widely used in research on human daily physical activity. Further, the package can handle accelerometer data file from any other sensor brand providing that the data is stored in csv format and has either no header or a two column header. Also the package allows for external function embedding.
 URL: https://github.com/wadpac/GGIR/, https://groups.google.com/forum/#!forum/RpackageGGIR

R/g.IVIS.R

@@ -1,5 +1,5 @@
-g.IVIS = function(Xi, epochsizesecondsXi = 5, IVIS_epochsize_seconds=c(), IVIS_windowsize_minutes = 60, IVIS.activity.metric = 1) {
-  if (!is.null(IVIS_epochsize_seconds)) {
+g.IVIS = function(Xi, epochsizesecondsXi = 5, IVIS_epochsize_seconds=NA, IVIS_windowsize_minutes = 60, IVIS.activity.metric = 1) {
+  if (!is.na(IVIS_epochsize_seconds)) {
     warning("Argument IVIS_epochsize_seconds has been depricated")
   }
   IVIS_epochsize_seconds = IVIS_windowsize_minutes*60

R/g.part1.R

@@ -582,11 +582,11 @@ g.part1 = function(datadir=c(),outputdir=c(),f0=1,f1=c(),windowsizes = c(5,900,3
   }
   if (do.parallel == TRUE) {
     on.exit(parallel::stopCluster(cl))
-    for (oli in 1:length(output_list)) { # logged error and warning messages
-      if (is.null(unlist(output_list[oli])) == FALSE) {
-        cat(paste0("\nErrors and warnings for ",fnames[oli]))
-        print(unlist(output_list[oli])) # print any error and warnings observed
-      }
+  }
+  for (oli in 1:length(output_list)) { # logged error and warning messages
+    if (is.null(unlist(output_list[oli])) == FALSE) {
+      cat(paste0("\nErrors and warnings for ",fnames[oli]))
+      print(unlist(output_list[oli])) # print any error and warnings observed
     }
   }
 }

R/g.part2.R

@@ -6,7 +6,7 @@ g.part2 = function(datadir=c(),metadatadir=c(),f0=c(),f1=c(),strategy = 1, hrs.d
                    boutcriter = 0.8,ndayswindow=7,idloc=1,do.imp=TRUE,storefolderstructure = FALSE,
                    overwrite=FALSE,epochvalues2csv=FALSE,mvpadur=c(1,5,10),selectdaysfile=c(),
                    window.summary.size=10,dayborder=0,bout.metric=2,closedbout=FALSE,desiredtz="",
-                   IVIS_windowsize_minutes = 60, IVIS_epochsize_seconds = c(), iglevels = c(),
+                   IVIS_windowsize_minutes = 60, IVIS_epochsize_seconds = NA, iglevels = c(),
                    IVIS.activity.metric=2, TimeSegments2ZeroFile=c(), qM5L5  = c(), do.parallel = TRUE,
                    myfun=c(), MX.ig.min.dur=10) {
   snloc= 1
@@ -77,7 +77,7 @@ g.part2 = function(datadir=c(),metadatadir=c(),f0=c(),f1=c(),strategy = 1, hrs.d
   }
   t1 = Sys.time() # copied here
   if (do.parallel == TRUE) {
-    cat(paste0('\n Busy processing ... see ',metadatadir,'/ms2', ' for progress\n'))
+    cat(paste0('\n Busy processing ... see ', metadatadir, ms2.out, ' for progress\n'))
   }
 
   # check whether we are indevelopment mode:
@@ -221,11 +221,11 @@ g.part2 = function(datadir=c(),metadatadir=c(),f0=c(),f1=c(),strategy = 1, hrs.d
   }
   if (do.parallel == TRUE) {
     on.exit(parallel::stopCluster(cl))
-    for (oli in 1:length(output_list)) { # logged error and warning messages
-      if (is.null(unlist(output_list[oli])) == FALSE) {
-        cat(paste0("\nErrors and warnings for ",fnames[oli]))
-        print(unlist(output_list[oli])) # print any error and warnings observed
-      }
+  }
+  for (oli in 1:length(output_list)) { # logged error and warning messages
+    if (is.null(unlist(output_list[oli])) == FALSE) {
+      cat(paste0("\nErrors and warnings for ",fnames[oli]))
+      print(unlist(output_list[oli])) # print any error and warnings observed
     }
   }
 }

R/g.part3.R

@@ -47,7 +47,7 @@ g.part3 = function(metadatadir=c(),f0,f1,anglethreshold = 5,timethreshold = 5,
   }
   t1 = Sys.time() # copied here
   if (do.parallel == TRUE) {
-    cat(paste0('\n Busy processing ... see ', metadatadir,'/ms3', ' for progress\n'))
+    cat(paste0('\n Busy processing ... see ', metadatadir,'/meta/ms3.out', ' for progress\n'))
   }
   # check whether we are indevelopment mode:
   GGIRinstalled = is.element('GGIR', installed.packages()[,1])
@@ -126,11 +126,11 @@ g.part3 = function(metadatadir=c(),f0,f1,anglethreshold = 5,timethreshold = 5,
   }
   if (do.parallel == TRUE) {
     on.exit(parallel::stopCluster(cl))
-    for (oli in 1:length(output_list)) { # logged error and warning messages
-      if (is.null(unlist(output_list[oli])) == FALSE) {
-        cat(paste0("\nErrors and warnings for ",fnames[oli]))
-        print(unlist(output_list[oli])) # print any error and warnings observed
-      }
+  }
+  for (oli in 1:length(output_list)) { # logged error and warning messages
+    if (is.null(unlist(output_list[oli])) == FALSE) {
+      cat(paste0("\nErrors and warnings for ",fnames[oli]))
+      print(unlist(output_list[oli])) # print any error and warnings observed
     }
   }
 }

R/g.part5.R

@@ -114,7 +114,7 @@ g.part5 = function(datadir=c(),metadatadir=c(),f0=c(),f1=c(),strategy=1,maxdur=7
   }
   t0 = t1 = Sys.time() # copied here
   if (do.parallel == TRUE) {
-    cat(paste0('\n Busy processing ... see ',metadatadir,'/ms5', ' for progress\n'))
+    cat(paste0('\n Busy processing ... see ', metadatadir, ms5.out, ' for progress\n'))
   }
   # check whether we are in development mode:
   GGIRinstalled = is.element('GGIR', installed.packages()[,1])
@@ -774,11 +774,11 @@ g.part5 = function(datadir=c(),metadatadir=c(),f0=c(),f1=c(),strategy=1,maxdur=7
                                 }
   if (do.parallel == TRUE) {
     on.exit(parallel::stopCluster(cl))
-    for (oli in 1:length(output_list)) { # logged error and warning messages
-      if (is.null(unlist(output_list[oli])) == FALSE) {
-        cat(paste0("\nErrors and warnings for ",fnames.ms3[oli]))
-        print(unlist(output_list[oli])) # print any error and warnings observed
-      }
+  }
+  for (oli in 1:length(output_list)) { # logged error and warning messages
+    if (is.null(unlist(output_list[oli])) == FALSE) {
+      cat(paste0("\nErrors and warnings for ",fnames.ms3[oli]))
+      print(unlist(output_list[oli])) # print any error and warnings observed
     }
   }
 }

R/g.shell.GGIR.R

@@ -37,7 +37,7 @@ g.shell.GGIR = function(mode=1:5,datadir=c(),outputdir=c(),studyname=c(),f0=1,f1
     # if (length(which(mode == 0)) > 0) dopart0 = TRUE
     if (length(which(mode == 1)) > 0) dopart1 = TRUE
     if (length(which(mode == 2)) > 0) dopart2 = TRUE
-    if (length(which(mode == 3)) > 0) dopart3 = TRUE; do.anglez = TRUE
+    if (length(which(mode == 3)) > 0) { dopart3 = TRUE; do.anglez = TRUE }
     if (length(which(mode == 4)) > 0) dopart4 = TRUE
     if (length(which(mode == 5)) > 0) dopart5 = TRUE
   }
@@ -97,7 +97,7 @@ g.shell.GGIR = function(mode=1:5,datadir=c(),outputdir=c(),studyname=c(),f0=1,f1
           } else if (numi == TRUE) {
             txt = paste(as.character(config[ci,1]),"=",as.numeric(config[ci,2]),"",sep="")
           } else if (numi == FALSE & logi == FALSE) {
-            if (length(config[ci,2]) > 0) {
+            if (length(config[ci,2]) > 0 & !is.na(config[ci,2])) {
               if (config[ci,2] == 'c()') {
                 if (config[ci,1] == "def.no.sleep") def.no.sleep = c()
                 if (config[ci,1] == "backup.cal.coef") backup.cal.coef = c()
@@ -206,7 +206,7 @@ g.shell.GGIR = function(mode=1:5,datadir=c(),outputdir=c(),studyname=c(),f0=1,f1
   if (exists("ndayswindow") == FALSE)  ndayswindow = 7
   if (exists("do.imp") == FALSE) do.imp = TRUE
   if (exists("IVIS_windowsize_minutes") == FALSE)  IVIS_windowsize_minutes=60
-  if (exists("IVIS_epochsize_seconds") == FALSE)  IVIS_epochsize_seconds=c()
+  if (exists("IVIS_epochsize_seconds") == FALSE)  IVIS_epochsize_seconds=NA
   if (exists("mvpadur") == FALSE)  mvpadur = c(1,5,10) # related to part 2 (functionality to anticipate part 5)
   if (length(mvpadur) != 3) {
     mvpadur = c(1,5,10)

R/g.sib.det.R

@@ -217,6 +217,7 @@ g.sib.det = function(M,IMP,I,twd=c(-12,12),anglethreshold = 5,
         # Estimate Sleep Period Time Window, because this will be used by g.part4 if sleeplog is not available
         tmpANGLE = angle[qqq1:qqq2]
         tmpTIME = time[qqq1:qqq2]
+        daysleep_offset = 0
         inbedout = sptwindow_HDCZA(tmpANGLE,ws3=ws3,constrain2range=constrain2range,
                                    perc = perc, inbedthreshold = inbedthreshold, bedblocksize = bedblocksize,
                                    outofbedsize = outofbedsize)

man/g.IVIS.Rd

@@ -8,7 +8,7 @@
   van Someren.
 }
 \usage{
-  g.IVIS(Xi, epochsizesecondsXi = 5, IVIS_epochsize_seconds = c(),
+  g.IVIS(Xi, epochsizesecondsXi = 5, IVIS_epochsize_seconds = NA,
   IVIS_windowsize_minutes = 60, IVIS.activity.metric = 1)
 }
 \arguments{

man/g.part2.Rd

@@ -21,7 +21,7 @@ do.imp=TRUE,storefolderstructure=FALSE,overwrite=FALSE,
 epochvalues2csv=FALSE, mvpadur=c(1,5,10),selectdaysfile=c(),
 window.summary.size=10,dayborder=0,
 bout.metric=2,closedbout=FALSE,desiredtz="",
-IVIS_windowsize_minutes = 60, IVIS_epochsize_seconds = c(),
+IVIS_windowsize_minutes = 60, IVIS_epochsize_seconds = NA,
 iglevels = c(), IVIS.activity.metric=2, TimeSegments2ZeroFile = c(),
 qM5L5=c(), do.parallel = TRUE, myfun=c(), MX.ig.min.dur=10)
 }

tests/testthat/test_part3_1_night.R

@@ -0,0 +1,44 @@
+library(GGIR)
+context("g.part3")
+test_that("Part 3 identifies 1-night scenario", {
+  skip_on_cran()
+  #=======================
+  # Create a test file for a bit over a day worth of data.
+  # Nmin=2000 is currently the default, but hardcoding it here in case the default changes.
+  create_test_acc_csv(Nmin=2000)
+  fn = "123A_testaccfile.csv"
+  dn = "output_test"
+  if (file.exists(dn)) unlink(dn,recursive=TRUE)
+
+  # g.part# modules report errors and warnings only by printing them out to the console,
+  # so these are not true errors and warnings that would get caught by the testing module.
+  # Instead, grab the console output and parse out any errors we should know about.
+  # 
+  # Note: make sure to call g.shell.GGIR() with do.parallel = FALSE,
+  # otherwise not all console output will be captured.
+
+  out = capture.output(g.shell.GGIR(mode=c(1:3), datadir=fn, outputdir=getwd(), studyname="test", f0=1, f1=1,
+                                    do.report=c(), visualreport=FALSE, viewingwindow=1,
+                                    overwrite=TRUE, do.parallel = FALSE, minimumFileSizeMB=0), 
+                       type = c("output"))
+
+  # There shouldn't be any errors or warnings reported, so if there are any, throw an error.
+  err_idx = grepl("Errors and warnings for", out)
+  for (ii in 1:length(err_idx)) {
+    if (err_idx[ii]) {
+      stop(out[ii:length(err_idx)])
+    }
+  }
+
+  out.file.path = paste(dn, "/meta/ms3.out/", fn, ".RData", sep ="")
+  expect_true(file.exists(out.file.path))
+  load(out.file.path)
+
+  # check that the data file had only one night. The 'night' column should contain only 1s
+  for(i in 1:nrow(sib.cla.sum)) {
+    expect_that(sib.cla.sum$night[i],equals(1))
+  }
+
+  if (file.exists(fn)) file.remove(fn)
+  if (file.exists(dn)) unlink(dn, recursive=TRUE)
+})