Merge pull request #626 from wadpac/issue619_ggirread

Integrate GGIRread and deprecated selectdaysfile functionality
wadpac · Sep 2, 2022 · 5a3402d · 5a3402d
2 parents 214d774 + 1c05543
commit 5a3402d
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diff --git a/CITATION.cff b/CITATION.cff
@@ -12,20 +12,10 @@ authors:
     affiliation: "Activinsights Ltd."
     family-names: Fang
     given-names: Zhou
-  -
-    affiliation: "University of Leicester"
-    family-names: Mirkes
-    given-names: Evgeny
-    orcid: "https://orcid.org/0000-0003-1474-1734"
   -
     affiliation: "University College London"
     family-names: Heywood
     given-names: Joe
-  -
-    affiliation: "MRC Epidemiology Unit"
-    family-names: Zhao
-    given-names: "Jing Hua"
-    orcid: "https://orcid.org/0000-0003-4930-3582"
   -
     affiliation: "Polytechnical University of Catalonia"
     family-names: Joan
@@ -44,10 +34,6 @@ authors:
     affiliation: "Shimmer Ltd"
     family-names: Patterson
     given-names: "Matt"
-  -
-    affiliation: "Axivity Ltd"
-    family-names: Jackson
-    given-names: "Dan"
   -
     affiliation: Inserm
     family-names: Chen
@@ -57,7 +43,7 @@ authors:
     family-names: Manasa
     given-names: "Yerramalla"
 cff-version: "1.0.3"
-date-released: 2022-09-01
+date-released: 2022-09-02
 doi: "10.5281/zenodo.1051064"
 keywords:
   - "activity tracker"
@@ -69,5 +55,5 @@ license: "LGPL-2.0-only"
 message: "If you use this software, please cite it using these metadata."
 repository-code: "https://github.com/wadpac/GGIR"
 title: GGIR
-version: "2.7-5"
+version: "2.7-6"
 ...
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,19 +1,16 @@
 Package: GGIR
 Type: Package
 Title: Raw Accelerometer Data Analysis
-Version: 2.7-5
-Date: 2022-09-01
+Version: 2.7-6
+Date: 2022-09-02
 Authors@R: c(person("Vincent T","van Hees",role=c("aut","cre"),
                   email="[email protected]"),
                   person("Jairo H","Migueles",role="aut"),
                   person("Severine","Sabia",role="ctb"),
                   person("Matthew R","Patterson",role="ctb"),
                   person("Zhou","Fang",role="ctb"),
-                  person("Jing Hua","Zhao",role="ctb"),
                   person("Joe","Heywood",role="ctb"),
-                  person("Evgeny","Mirkes",role="ctb"),
                   person("Joan","Capdevila Pujol",role="ctb"),
-                  person("Dan","Jackson",role="ctb"),
                   person("Lena","Kushleyeva",role="ctb"),
                   person("Mathilde","Chen",role="ctb"),
                   person("Manasa","Yerramalla",role="ctb"),
@@ -30,9 +27,7 @@ URL: https://github.com/wadpac/GGIR/, https://groups.google.com/forum/#!forum/Rp
 BugReports: https://github.com/wadpac/GGIR/issues
 License: LGPL (>= 2.0, < 3) | file LICENSE
 Suggests: testthat, covr, knitr, rmarkdown
-Imports: data.table, Rcpp (>= 0.12.10), foreach, doParallel, signal, zoo, GENEAread, tuneR, unisensR, ineq, read.gt3x, activityCounts, ActCR, methods
+Imports: data.table, foreach, doParallel, signal, zoo, GENEAread, tuneR, unisensR, ineq, read.gt3x, activityCounts, ActCR, methods, GGIRread
 Depends: stats, utils, R (>= 3.5.0)
-NeedsCompilation: yes
-LinkingTo: Rcpp
 VignetteBuilder: knitr
-ByteCompile: yes
+
diff --git a/NAMESPACE b/NAMESPACE
@@ -9,18 +9,16 @@ export(g.analyse, g.calibrate,
        chartime2iso8601, g.abr.day.names,
        g.applymetrics, g.create.sp.mat, g.detecmidnight,
        g.dotorcomma, g.downsample,
-       getFirstTimestamp, getStartEndNumeric,
-       getStartEnd, g.extractheadervars,
-       g.getidfromheaderobject, g.getM5L5,
+       getFirstTimestamp, g.extractheadervars,
+       g.getM5L5,
        g.getstarttime, g.loadlog,
        g.plot5, g.readaccfile,
        g.report.part2, g.report.part4,
        g.report.part5, g.sib.det,
        g.sib.plot, g.wavread,
        g.weardec, isfilelist,
        iso8601chartime2POSIX, is_this_a_dst_night,
-       POSIXtime2iso8601, numUnpack,
-       resample, is.ISO8601,
+       POSIXtime2iso8601, is.ISO8601,
        updateBlocksize, g.IVIS,
        createConfigFile, identify_levels,
        g.sib.sum, datadir2fnames,
@@ -54,5 +52,3 @@ importFrom("stats", "aggregate.data.frame", "weighted.mean",
 import(data.table)
 importFrom("methods", "is")
 importFrom("utils", "available.packages", "packageVersion")
-useDynLib(GGIR, .registration = TRUE)
-importFrom(Rcpp, sourceCpp)
diff --git a/R/GGIR.R b/R/GGIR.R
@@ -130,12 +130,9 @@ GGIR = function(mode = 1:5, datadir = c(), outputdir = c(),
   # Print GGIR header to console
   GGIRversion = ""
   SI = sessionInfo()
-  try(expr = {GGIRversion = SI$loadedOnly$GGIR$Version}, silent = TRUE)
-  if (length(GGIRversion) == 0) {
-    try(expr = {GGIRversion = SI$otherPkgs$GGIR$Version}, silent = TRUE)
-  }
+  GGIRversion = SI$otherPkgs$GGIR$Version
   if (length(GGIRversion) == 0) GGIRversion = "could not extract version"
-  GGIRversion = paste0(" ",GGIRversion)
+  # GGIRversion = paste0(" ",GGIRversion)
   rm(SI)
   cat(paste0("\n   GGIR version: ",GGIRversion,"\n"))
   cat("\n   Do not forget to cite GGIR in your publications via a version number and\n")
@@ -206,9 +203,11 @@ GGIR = function(mode = 1:5, datadir = c(), outputdir = c(),
                           "dopart4", "dopart5", "fnames", "useRDA", "metadatadir", "ci", "config",
                           "configfile", "filelist", "outputfoldername", "numi", "logi",
                           "conv2logical", "conv2num", "SI", "params", "argNames", "dupArgNames",
-                          "print_console_header", "configfile_csv", "myfun", "ex", "dir2fn", "fnamesfull") == FALSE)]
+                          "print_console_header", "configfile_csv", "myfun", "ex", "dir2fn", "fnamesfull",
+                          "GGIRversion") == FALSE)]
   config.parameters = mget(LS)
   config.matrix = as.data.frame(createConfigFile(config.parameters))
+  config.matrix$context[which(config.matrix$context == "")] = "not applicable"
   if (dir.exists(metadatadir)) {
     write.csv(config.matrix, file = paste0(metadatadir, "/config.csv"), row.names = FALSE)
   } else {

diff --git a/R/RcppExports.R b/R/RcppExports.R
diff --git a/R/applyExtFunction.R b/R/applyExtFunction.R
@@ -36,7 +36,7 @@ applyExtFunction = function(data, myfun, sf, ws3,interpolationType=1) {
       # at the moment the function is designed for reading the r3 acceleration channels only,
       # because that is the situation of the use-case we had.
       rawLast = nrow(rawAccel)
-      accelRes = resample(rawAccel, rawTime, timeRes, rawLast, 
+      accelRes = GGIRread::resample(rawAccel, rawTime, timeRes, rawLast, 
                           type=interpolationType) # this is now the resampled acceleration data
       return(accelRes)
     }

diff --git a/R/check_params.R b/R/check_params.R
@@ -63,7 +63,7 @@ check_params = function(params_sleep = c(), params_metrics = c(),
                          "rmc.unit.temp", "rmc.unit.time", "rmc.format.time", 
                          "rmc.origin", "rmc.desiredtz", "rmc.headername.sf", 
                          "rmc.headername.sn", "rmc.headername.recordingid", 
-                         "rmc.header.structure")
+                         "rmc.header.structure", "loadGENEActiv")
     if (is.logical(params_rawdata[["rmc.noise"]])) {
       # Older config files used this, so overwrite with NULL value
       params_rawdata[["rmc.noise"]] = c() 
@@ -98,7 +98,7 @@ check_params = function(params_sleep = c(), params_metrics = c(),
     numeric_params = c("includedaycrit", "ndayswindow", "strategy", "maxdur", "hrs.del.start",
                        "hrs.del.end", "includedaycrit.part5", "minimum_MM_length.part5", "includenightcrit", "max_calendar_days")
     boolean_params = c("excludefirstlast.part5", "do.imp", "excludefirstlast", "excludefirst.part4", "excludelast.part4")
-    character_params = c("selectdaysfile", "data_cleaning_file", "TimeSegments2ZeroFile")
+    character_params = c("data_cleaning_file", "TimeSegments2ZeroFile")
     check_class("cleaning", params = params_cleaning, parnames = numeric_params, parclass = "numeric")
     check_class("cleaning", params = params_cleaning, parnames = boolean_params, parclass = "boolean")
     check_class("cleaning", params = params_cleaning, parnames = character_params, parclass = "character")
@@ -124,6 +124,12 @@ check_params = function(params_sleep = c(), params_metrics = c(),
 
   #-----------------------------------------------------------------------------------
   # Check value combinations and apply corrections if not logical
+  if (length(params_rawdata) > 0) {
+    if (params_rawdata[["loadGENEActiv"]] == "GENEAread") {
+      warning(paste0("\nYou asked GGIR to use package GENEAread instead of GGIRread for reading GENEActiv .bin files.",
+      " Note that this option will be deprecated in the next CRAN release."))
+    }
+  }
   if (length(params_metrics) > 0 & length(params_sleep) > 0) {
     if (length(params_sleep[["def.noc.sleep"]]) != 2) {
       if (params_sleep[["HASPT.algo"]] != "HorAngle") {

diff --git a/R/createConfigFile.R b/R/createConfigFile.R
@@ -80,14 +80,24 @@ createConfigFile = function(config.parameters = c()) {
     }
   }
   SI = sessionInfo()
-  GGIRversion = ""
-  try(expr = {GGIRversion = SI$loadedOnly$GGIR$Version}, silent = TRUE)
-  if (length(GGIRversion) == 0) {
-    try(expr = {GGIRversion = SI$otherPkgs$GGIR$Version}, silent = TRUE)
+  GGIRread_version = GGIRversion = ""
+
+  if ("GGIR" %in% names(SI$otherPkgs)) {
+    GGIRversion = SI$otherPkgs$GGIR$Version
+  } else if ("GGIR" %in% names(SI$loadedOnly)) {
+    GGIRversion = SI$loadedOnly$GGIR$Version
+  }
+  if ("GGIRread" %in% names(SI$otherPkgs)) {
+    GGIRread_version = SI$otherPkgs$GGIRread$Version
+  } else if ("GGIRread" %in% names(SI$loadedOnly)) {
+    GGIRread_version = SI$loadedOnly$GGIRread$Version
   }
   if (length(GGIRversion) == 0) GGIRversion = "Could not retrieve GGIR version"
-  out[nrow(out) - 1,] = c("GGIRversion", GGIRversion, " not applicable")
-  out[nrow(out),] = c("R_version", SI$R.version$version.string, " not applicable")
+  if (length(GGIRread_version) == 0) GGIRread_version = "Could not retrieve GGIRread version"
+
+  out[nrow(out) - 2,] = c("GGIRread_version", GGIRread_version, "not applicable")
+  out[nrow(out) - 1,] = c("GGIRversion", GGIRversion, "not applicable")
+  out[nrow(out),] = c("R_version", SI$R.version$version.string, "not applicable")
   out = out[which(!is.na(out[,1])),]
   out = as.data.frame(out, stringsAsFactors = TRUE)
   row.names(out) <- NULL

diff --git a/R/extract_params.R b/R/extract_params.R
@@ -107,7 +107,7 @@ extract_params = function(params_sleep = c(), params_metrics = c(),
             "config_file_in_outputdir", "imputeTimegaps",
             "argNames", "dupArgNames","do.sgAccEN", "do.sgAnglex", 
             "do.sgAngley", "do.sgAnglez", "frag.classes.spt", "i", 
-            "isna", "tmp", "vecchar", "dupi")
+            "isna", "tmp", "vecchar", "dupi", "GGIRread_version")
           # Find argument in the various parameter objects
           if (newValue[1] != "notfound" & varName %in% ArgNames2Ignore == FALSE) {
             if (varName %in% names(params_general)) {

diff --git a/R/g.analyse.R b/R/g.analyse.R
@@ -1,13 +1,13 @@
 g.analyse =  function(I, C, M, IMP, params_247 = c(), params_phyact = c(),
                       quantiletype = 7, includedaycrit = 16, 
-                      idloc = 1, snloc = 1, selectdaysfile = c(), 
-                      dayborder = 0,  desiredtz = "", myfun = c(), acc.metric = c(), ...) {
+                      idloc = 1, snloc = 1, dayborder = 0,  desiredtz = "", 
+                      myfun = c(), acc.metric = c(), ...) {
 
   #get input variables
   input = list(...)
   expectedArgs = c("I", "C", "M", "IMP", "params_247", "params_phyact", 
                    "quantiletype", "includedaycrit", 
-                   "idloc", "snloc", "selectdaysfile", "dayborder", 
+                   "idloc", "snloc", "dayborder", 
                    "desiredtz", "myfun")
   if (any(names(input) %in% expectedArgs == FALSE) |
       any(!unlist(lapply(expectedArgs, FUN = exists)))) {
@@ -252,7 +252,7 @@ g.analyse =  function(I, C, M, IMP, params_247 = c(), params_phyact = c(),
   #--------------------------------------------------------------
   # Analysis per day
   if (doperday == TRUE) {
-    output_perday = g.analyse.perday(selectdaysfile = selectdaysfile, ndays = ndays,
+    output_perday = g.analyse.perday(ndays = ndays,
                                      firstmidnighti = firstmidnighti, time = time,
                                      nfeatures = nfeatures, midnightsi = midnightsi,
                                      metashort = metashort, averageday = averageday,
@@ -339,11 +339,6 @@ g.analyse =  function(I, C, M, IMP, params_247 = c(), params_phyact = c(),
   } else {
     cosinor_ts = c()
   }
-  if (length(selectdaysfile) > 0) {
-    windowsummary = data.frame(windowsummary,stringsAsFactors = FALSE) # addition for Millenium cohort
-    names(windowsummary) = ws_names
-    invisible(list(summary = filesummary, daysummary = daysummary, windowsummary = windowsummary, cosinor_ts = cosinor_ts))
-  } else {
-    invisible(list(summary = filesummary, daysummary = daysummary, cosinor_ts = cosinor_ts))
-  }
+  invisible(list(summary = filesummary, daysummary = daysummary, cosinor_ts = cosinor_ts))
+
 }