add mergeFitbitData and allign with mergePHBdata #68

wadpac · Sep 30, 2024 · 671a663 · 671a663
1 parent 3eab460
commit 671a663
Show file tree

Hide file tree

Showing 10 changed files with 140 additions and 60 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,7 +1,9 @@
 export(readGenea, readAxivity, readGENEActiv, 
        GENEActivReader, resample, readWav, 
        readActiGraphCount, readActiwatchCount,
-       readActicalCount, mergePHBfilePairs)
+       readActicalCount, readPHBCount,
+       readFitbit, mergePHBdata,
+       mergeFitbitData)
 useDynLib(GGIRread, .registration = TRUE)
 importFrom(Rcpp, sourceCpp)
 importFrom(data.table, fread)

diff --git a/R/mergeFitbitData.R b/R/mergeFitbitData.R
@@ -0,0 +1,22 @@
+mergeFitbitData = function(filenames = NULL, desiredtz = "", configtz = NULL) {
+  if (length(filenames) < 2) {
+    stop("Provide at least two filenames")
+  }
+  cnt = 1
+  while (cnt <= length(filenames)) {
+    D = readFitbit(filename = filenames[cnt], desiredtz = desiredtz, configtz = configtz)
+    if (cnt == 1) {
+      data = D
+    } else {
+      if (length(intersect(x = data$dateTime, D$dateTime)) == 0) {
+        warning(paste0("Time series do not intersect for files ",
+                       basename(filenames[cnt]), " and ", basename(filenames[cnt - 1])),
+                call. = FALSE)
+      }
+
+      data = merge(data, D, by = "dateTime", all = TRUE)
+    }
+    cnt = cnt + 1
+  }
+  return(data)
+}
diff --git a/R/mergePHBfilePairs.R → R/mergePHBdata.R b/R/mergePHBfilePairs.R → R/mergePHBdata.R
@@ -1,4 +1,4 @@
-mergePHBfilePairs = function(filenames = NULL,
+mergePHBdata = function(filenames = NULL,
                              timeformat = "%m/%d/%Y %H:%M:%S",
                              desiredtz = "", configtz = NULL,
                              timeformatName = "timeformat") {

diff --git a/README.md b/README.md
@@ -10,8 +10,8 @@ Brand | Device name | File extension | Data type | GGIRread function
 Axivity Ltd https://axivity.com/ | AX3 and AX6 | .cwa | raw gravitational units |readAxivity
 ActivInsights Ltd https://activinsights.com/ | GENEActiv Original and Sleep | .bin | raw gravitational units  | readGENEActiv
 Unilever Discover Ltd | Genea (no longer manufactured) | .bin | raw gravitational units | readGenea
-ActiGraph | ??? | .csv | count data | readActigraph
-Actiwatch | ??? | .csv and .awd | count data | readActiwatch
-Actical | ??? | .csv | count data | readActical.R
-Philips Health Band | ??? | .xlsx | count data | mergePHBfilePairs.R
-Fitbit | ??? | .json | sleep, steps or calories data | readFitbit.R
+ActiGraph | ??? | .csv | count data | readActigraphCount
+Actiwatch | ??? | .csv and .awd | count data | readActiwatchCount
+Actical | ??? | .csv | count data | readActicalCount
+Philips Health Band | ??? | .xlsx | count data | readPHBCount
+Fitbit | ??? | .json | sleep, steps or calories data | readFitbit
diff --git a/inst/testfiles/calories-1995-06-23_Fitbit.json b/inst/testfiles/calories-1995-06-23_Fitbit.json
@@ -1,142 +1,142 @@
 [{
-  "dateTime" : "06/23/95 00:00:00",
+  "dateTime" : "06/24/95 16:00:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:01:00",
+  "dateTime" : "06/24/95 16:01:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:02:00",
+  "dateTime" : "06/24/95 16:02:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:03:00",
+  "dateTime" : "06/24/95 16:03:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:04:00",
+  "dateTime" : "06/24/95 16:04:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:05:00",
+  "dateTime" : "06/24/95 16:05:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:06:00",
+  "dateTime" : "06/24/95 16:06:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:07:00",
+  "dateTime" : "06/24/95 16:07:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:08:00",
+  "dateTime" : "06/24/95 16:08:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:09:00",
+  "dateTime" : "06/24/95 16:09:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:10:00",
+  "dateTime" : "06/24/95 16:10:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:11:00",
+  "dateTime" : "06/24/95 16:11:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:12:00",
+  "dateTime" : "06/24/95 16:12:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:13:00",
+  "dateTime" : "06/24/95 16:13:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:14:00",
+  "dateTime" : "06/24/95 16:14:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:15:00",
+  "dateTime" : "06/24/95 16:15:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:16:00",
+  "dateTime" : "06/24/95 16:16:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:17:00",
+  "dateTime" : "06/24/95 16:17:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:18:00",
+  "dateTime" : "06/24/95 16:18:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:19:00",
+  "dateTime" : "06/24/95 16:19:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:20:00",
+  "dateTime" : "06/24/95 16:20:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:21:00",
+  "dateTime" : "06/24/95 16:21:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:22:00",
+  "dateTime" : "06/24/95 16:22:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:23:00",
+  "dateTime" : "06/24/95 16:23:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:24:00",
+  "dateTime" : "06/24/95 16:24:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:25:00",
+  "dateTime" : "06/24/95 16:25:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:26:00",
+  "dateTime" : "06/24/95 16:26:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:27:00",
+  "dateTime" : "06/24/95 16:27:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:28:00",
+  "dateTime" : "06/24/95 16:28:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:29:00",
+  "dateTime" : "06/24/95 16:29:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:30:00",
+  "dateTime" : "06/24/95 16:30:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:31:00",
+  "dateTime" : "06/24/95 16:31:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:32:00",
+  "dateTime" : "06/24/95 16:32:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:33:00",
+  "dateTime" : "06/24/95 16:33:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:34:00",
+  "dateTime" : "06/24/95 16:34:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:35:00",
+  "dateTime" : "06/24/95 16:35:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:36:00",
+  "dateTime" : "06/24/95 16:36:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:37:00",
+  "dateTime" : "06/24/95 16:37:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:38:00",
+  "dateTime" : "06/24/95 16:38:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:39:00",
+  "dateTime" : "06/24/95 16:39:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:40:00",
+  "dateTime" : "06/24/95 16:40:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:41:00",
+  "dateTime" : "06/24/95 16:41:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:42:00",
+  "dateTime" : "06/24/95 16:42:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:43:00",
+  "dateTime" : "06/24/95 16:43:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:44:00",
+  "dateTime" : "06/24/95 16:44:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:45:00",
+  "dateTime" : "06/24/95 16:45:00",
   "value" : "1.48"
 },{
-  "dateTime" : "06/23/95 00:46:00",
+  "dateTime" : "06/24/95 16:46:00",
   "value" : "1.48"
 }]
diff --git a/man/mergeFitbitData.Rd b/man/mergeFitbitData.Rd
@@ -0,0 +1,35 @@
+\name{mergeFitbitData}
+\alias{mergeFitbitData}
+\title{
+  Merge Fitbit json files into one data.frame
+}
+\description{
+  Read and merge Fitbit json files into one data.frame, and
+  give warning if time series do not intersect.
+}
+\usage{
+  mergeFitbitData(filenames = NULL,
+                    desiredtz = "", configtz = NULL)
+}
+\arguments{
+  \item{filenames}{
+    Character vector, specifying the filenames (at least two) to be merged.
+  }
+  \item{desiredtz}{
+    Character, timezone name where the accelerometer was worn. Timezone names are
+    expected to be the timezone database names, e.g. Europe/London. See also:
+    https://en.wikipedia.org/wiki/List_of_tz_database_time_zones
+  }
+  \item{configtz}{
+    Character, timezone name where the accelerometer was configured. Leave NULL
+    if equal to desiredtz. Timezones name are expected to be the timezone database
+    names, e.g. Europe/London. See also:
+    https://en.wikipedia.org/wiki/List_of_tz_database_time_zones
+  }
+}
+\value{
+  Merged data from the two or more files.
+}
+\author{
+  Vincent T van Hees <v.vanhees@accelting.com>
+}
diff --git a/man/mergePHBfilePairs.Rd → man/mergePHBdata.Rd b/man/mergePHBfilePairs.Rd → man/mergePHBdata.Rd
@@ -1,5 +1,5 @@
-\name{mergePHBfilePairs}
-\alias{mergePHBfilePairs}
+\name{mergePHBdata}
+\alias{mergePHBdata}
 \title{
   Merge Philips Health Band xlsx file pairs into one csv file
 }
@@ -9,7 +9,7 @@
   xlsx file to csv.
 }
 \usage{
-  mergePHBfilePairs(filenames = NULL,
+  mergePHBdata(filenames = NULL,
                     timeformat = "\%m/\%d/\%Y \%H:\%M:\%S",
                     desiredtz = "", configtz = NULL,
                     timeformatName = "timeformat")

diff --git a/tests/testthat/test_mergeFitbitData.R b/tests/testthat/test_mergeFitbitData.R
@@ -0,0 +1,22 @@
+library(GGIRread)
+context("merge PHB files")
+test_that("merging of PHB files goes correctly", {
+  file1 = system.file("testfiles/steps-1995-06-23_Fitbit.json", package = "GGIRread")
+  file2 = system.file("testfiles/calories-1995-06-23_Fitbit.json", package = "GGIRread")
+  file3 = system.file("testfiles/sleep-1995-06-23_Fitbit.json", package = "GGIRread")
+
+  # apply function to merge the files
+  D = mergeFitbitData(filenames = c(file1, file2),
+                    desiredtz =  "Europe/Amsterdam")
+  expect_equal(nrow(D), 47)
+  expect_equal(ncol(D), 3)
+  expect_equal(sum(D$steps, na.rm = TRUE), 607)
+  expect_equal(sum(D$calories, na.rm = TRUE), 69.56)
+  expect_equal(format(D$dateTime[1]), "1995-06-24 16:00:00")
+
+  # apply function to merge the files
+  expect_warning(mergeFitbitData(filenames = c(file1, file2, file3),
+                      desiredtz =  "Europe/Amsterdam"),
+               regexp = "Time series*")
+})
+
diff --git a/tests/testthat/test_mergePHBfilePairs.R → tests/testthat/test_mergePHBdata.R b/tests/testthat/test_mergePHBfilePairs.R → tests/testthat/test_mergePHBdata.R
@@ -1,11 +1,10 @@
 library(GGIRread)
 context("merge PHB files")
 test_that("merging of PHB files goes correctly", {
-  # prepare folder with test files
   file1 = system.file("testfiles/DataList_AH1234567890_PhilipsHealthBand.xlsx", package = "GGIRread")
   file2 = system.file("testfiles/Sleep_Wake_AH1234567890_PhilipsHealthBand.xlsx", package = "GGIRread")
   # apply function to merge the files
-  D = mergePHBfilePairs(filenames = c(file1, file2),
+  D = mergePHBdata(filenames = c(file1, file2),
                     timeformat = "%m-%d-%Y %H:%M:%S",
                     desiredtz =  "Europe/Amsterdam")
   expect_equal(nrow(D$data), 246)

diff --git a/tests/testthat/test_readFitbit.R b/tests/testthat/test_readFitbit.R
@@ -24,7 +24,7 @@ test_that("Fitbit json is correctly read", {
   D = readFitbit(filename = file, desiredtz =  "Europe/Amsterdam")
   expect_equal(nrow(D), 47)
   expect_equal(ncol(D), 2)
-  expect_equal(format(D$dateTime[1]), "1995-06-23")
+  expect_equal(format(D$dateTime[1]), "1995-06-24 16:00:00")
   expect_equal(sum(D$calories), 69.56)
 })