Merge pull request #50 from PhysicalActivityOpenTools/issue49_minorBugCalibration

Issue49 minor bug calibration

Author: jhmigueles

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: actimetric
 Type: Package
 Title: Classifies Accelerometer Data Into Physical Activity Types
-Version: 0.1.2
+Version: 0.1.3
 Authors@R: c(person("Jairo H","Migueles", role = c("aut","cre"),
                     email = "[email protected]",
                     comment = c(ORCID = "0000-0003-0366-6935")),
@@ -20,7 +20,7 @@ LazyData: true
 Suggests: 
     testthat (>= 3.0.0), randomForest, gsignal, rattle
 Config/testthat/edition: 3
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Depends: 
     R (>= 2.10)
 Imports: 

NEWS.md

@@ -1,3 +1,7 @@
+# actimetric 0.1.3
+
+* Calibration: fix minor bug by which calibration procedure was using time column instead of acceleration columns in data #49
+
 # actimetric 0.1.2
 
 * Documentation: include references to papers, other pieces of code, packages, and authorships #41

R/ReadAndCalibrate.R

@@ -87,7 +87,8 @@ ReadAndCalibrate = function(file, sf, blocksize, blocknumber, inspectfileobject,
     # MODULE 3 - EXTRACT CALIBRATION COEFFICIENTS -----------------------------
     calCoefs = vm.error.st = vm.error.end = NULL
     if (do.calibration == TRUE & iteration == 1) {
-      cal = calibrateRaw(data, sf = sf, verbose = verbose)
+      accCols = which(colnames(data) %in% c("x","y","z"))
+      cal = calibrateRaw(data[, accCols], sf = sf, verbose = verbose)
       if (is.list(cal)) {
         calCoefs = cal$calCoefs; vm.error.st = cal$vm.error.st;
         vm.error.end = cal$vm.error.end

R/featuresTrost2017.R

@@ -43,7 +43,11 @@ featuresTrost2017 = function(data, epoch, sf) {
       k[i, column + 4] = mean(A, trim = 0.05, na.rm = TRUE)
       k[i, column + 5] = sd(A, na.rm = TRUE)
       k[i, column + 6] = sum((A*A), na.rm = TRUE)
-      k[i, column + 7] = cor(Axis[from:(to - 1)], Axis[(from + 1):to], use = "pairwise.complete.obs")
+      if (sd(A, na.rm = TRUE) != 0) { #this avoids warning when no variability (e.g., idle sleep mode in actigraph)
+        k[i, column + 7] = cor(Axis[from:(to - 1)], Axis[(from + 1):to], use = "pairwise.complete.obs")
+      } else {
+        k[i, column + 7] = NA
+      }
       k[i, column + 8] = median(A, na.rm = TRUE)
       k[i, column + 9] = mad(abs(A), na.rm = TRUE)
       k[i, column + 10] = as.vector(quantile(A, c(.10), na.rm = TRUE))