Merge pull request #893 from wadpac/issue879_bugVisualization

Issue879 bug visualization
wadpac · Sep 11, 2023 · a990e0f · a990e0f
2 parents 406d939 + 25b32ab
commit a990e0f
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diff --git a/NEWS.md b/NEWS.md
@@ -1,12 +1,13 @@
 # CHANGES IN GGIR VERSION 2.10-3
 
+- Visualreport: Bug fixed extracting the numeric value of the days to exclude in g.plot5 #879
+
 - Part 1: Fixed minor bug to keep calibration data in the data quality report after re-running parts 1 and 2 with overwrite = TRUE and backup.cal.coef = "retrieve" #896
 
 - Part 5: Fix minor bug by which GGIR skipped the last day if measurement finishes before midnight and timewindow = MM #891
 
 - Part 4: Added parameter sleepefficiency.metric to decide if in-bed time (denominator) should be guider_spt or acc_spt + latency #811
 
-
 # CHANGES IN GGIR VERSION 2.10-2
 
 - Part 1: Revision to readability of code (credits: Lena Kushleyeva)

diff --git a/R/g.part2.R b/R/g.part2.R
@@ -227,6 +227,19 @@ g.part2 = function(datadir = c(), metadatadir = c(), f0 = c(), f1 = c(),
           SUM$summary$names_appendedRecordings = names_appendedRecordings
           SUM$summary$overlap_hrs_appendedRecordings = overlap_appendedRecordings
         }
+        # convert daysummary and summary variables to numeric
+        char2num_df = function(df) {
+          # save as numeric columns that can be coerced to numeric
+          df = lapply(df, function(x) tryCatch(as.numeric(as.character(x)), 
+                                               error = function(cond) return(x),
+                                               warning = function(cond) return(x)))
+          # list to data frame
+          df = as.data.frame(df, check.names = FALSE)
+          return(df)
+        }
+        SUM$summary = char2num_df(SUM$summary)
+        SUM$daysummary = char2num_df(SUM$daysummary)
+        # save milestone data
         save(SUM, IMP, tail_expansion_log, file = paste0(metadatadir, ms2.out, "/", RDname)) #IMP is needed for g.plot in g.report.part2
       }
       if (M$filecorrupt == FALSE & M$filetooshort == FALSE) rm(IMP)

diff --git a/R/g.plot5.R b/R/g.plot5.R
@@ -193,15 +193,15 @@ g.plot5 = function(metadatadir = c(), dofirstpage = FALSE, viewingwindow = 1,
           lengthnight = summarysleep_tmp$SptDuration #including wake periods
           nocsleepdur = summarysleep_tmp$SleepDurationInSpt
           sleepefficiency = (nocsleepdur / lengthnight) * 100
-          f01 = as.numeric(P2daysummary_tmp[,c45])
-          f02 = as.numeric(P2daysummary_tmp[,MainMetric])
+          f01 = P2daysummary_tmp[,c45]
+          f02 = P2daysummary_tmp[,MainMetric]
           f05 = matrix(NA, nrow = 2, ncol = length(summarysleep_tmp$SptDuration))
           f05[1,] = summarysleep_tmp$SleepDurationInSpt
           f05[2,] = summarysleep_tmp$SptDuration - summarysleep_tmp$SleepDurationInSpt
           f05_2 = summarysleep_tmp$SptDuration
           f06 = sleepefficiency
           # f07 = P2daysummary_tmp$N.valid.hours # Previously needed when reading csv-report Part 2
-          f07 = as.numeric(P2daysummary_tmp$`N valid hours`)
+          f07 = P2daysummary_tmp$`N valid hours`
           # allocate colours
           CLS = c("white", "black")
           CLS_A = rep(CLS[1], length(days_PA))

diff --git a/tests/testthat/test_chainof5parts.R b/tests/testthat/test_chainof5parts.R
@@ -53,8 +53,8 @@ test_that("chainof5parts", {
   expect_equal(nrow(IMP$metashort), 11280)
   expect_equal(round(mean(IMP$metashort$ENMO), digits = 5), 0.00802, tolerance = 3)
   expect_equal(round(as.numeric(SUM$summary$meas_dur_def_proto_day), digits = 3), 1)
-  expect_equal(SUM$summary$`N valid WEdays`, "1")
-  expect_equal(SUM$summary$`N valid WKdays`, "2")
+  expect_equal(SUM$summary$`N valid WEdays`, 1)
+  expect_equal(SUM$summary$`N valid WKdays`, 2)
 
   # part 2 with strategy = 5
   g.part2(datadir = fn, metadatadir = metadatadir, f0 = 1, f1 = 1,
@@ -67,8 +67,8 @@ test_that("chainof5parts", {
   expect_equal(nrow(IMP$metashort), 11280)
   expect_equal(round(mean(IMP$metashort$ENMO), digits = 5), 0.03398, tolerance = 3)
   expect_equal(round(as.numeric(SUM$summary$meas_dur_def_proto_day), digits = 3), 1)
-  expect_equal(SUM$summary$`N valid WEdays`, "1")
-  expect_equal(SUM$summary$`N valid WKdays`, "2")
+  expect_equal(SUM$summary$`N valid WEdays`, 1)
+  expect_equal(SUM$summary$`N valid WKdays`, 2)
 
   # part 2 with strategy = 2 and iglevels = 1
   g.part2(datadir = fn, metadatadir = metadatadir, f0 = 1, f1 = 1,
@@ -103,7 +103,7 @@ test_that("chainof5parts", {
   expect_equal(round(mean(IMP$metashort$ENMO), digits = 5), 0.02911, tolerance = 3)
   expect_that(round(as.numeric(SUM$summary$meas_dur_dys), digits = 5), equals(1.95833))
   expect_that(ncol(SUM$daysummary), equals(34))
-  expect_equal(SUM$daysummary$`p50_ENMO_mg_0-24hr`, c("17.15", "33",  "0"))
+  expect_equal(SUM$daysummary$`p50_ENMO_mg_0-24hr`, c(17.15, 33,  0))
   expect_equal(round(as.numeric(SUM$daysummary$`p90_ENMO_mg_0-24hr`)), c(44, 54, 41), tolerance = 0)
   expect_equal(mean(as.numeric(SUM$daysummary$`M3_ENMO_mg_0-24hr`)), 89.26, tolerance = 3)
   expect_equal(mean(as.numeric(SUM$daysummary$`M3_q40_ENMO_mg_0-24hr`)), 37.383, tolerance = 3)