Merge pull request #37 from bhelsel/issue_3536

Update C++ code to resolve issues 20, 34-36

.Rbuildignore

@@ -6,4 +6,5 @@
 ^codecov\.yml$
 ^README\.Rmd$
 ^tests/testthat/test_gcalibrateC\.R$
-^man/figures
+^man/figures
+.vscode/

.gitignore

@@ -3,3 +3,4 @@
 .RData
 .Ruserdata
 .DS_Store
+.vscode/

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: agcounts
 Type: Package
 Title: Calculate 'ActiGraph' Counts from Accelerometer Data
-Version: 0.6.7
+Version: 0.6.8
 Authors@R: c(
     person(c("Brian", "C."), "Helsel", email = "[email protected]", role = c("aut", "cre")),
     person(c("Paul", "R."), "Hibbing", role = "ctb"),

NEWS.md

@@ -1,3 +1,9 @@
+# agcounts 0.6.8
+* Fix issue #20 related to C++ compiling by adding the `Rcpp` plugin for C++ 11.
+* Update C++ code for `gcalibrateC` to resolve issue when there are NaN values in sphere data (issue #35)
+* Resolve issue #36 when `calErrorEnd` never gets below 0.01.
+* Change minloadcrit from 72 to 168 as recommended in issue #34
+
 # agcounts 0.6.7
 * Update `agcalibrate` to speed up function by first converting to a `data.table` before merging with the time stamps.
 * Add parameter `imputeTimeGaps` to `agcalibrate` for users to decide if zeros are added back after calibration.

src/gcalibrate.cpp

@@ -1,3 +1,4 @@
+// [[Rcpp::plugins(cpp11)]]
 #include <RcppArmadillo.h>
 #include <iostream>
 #include <vector>
@@ -91,7 +92,7 @@ Rcpp::List gcalibrateC(Rcpp::Nullable<Rcpp::String> pathname = R_NilValue, Rcpp:
   }
 
   Rcpp::NumericVector ws {5, 900, 3600};
-  int startpage, endpage, blocksize = 12 * ws(2), minloadcrit = 72;
+  int startpage, endpage, blocksize = 12 * ws(2), minloadcrit = 168;
   double NR = ceil((90*pow(10, 6)) / (sf*10)) + 1000; // NR = number of '10' second rows (this is for 10 days at 80 Hz)
   int count = 0; // counter to keep track of the number of seconds that have been read
   double spherecrit = 0.3, sdcriter = 0.013;
@@ -162,7 +163,8 @@ Rcpp::List gcalibrateC(Rcpp::Nullable<Rcpp::String> pathname = R_NilValue, Rcpp:
     if((use > 0) && (use != LD)){
       S = data(Rcpp::Range(use, LD-1), Rcpp::_);
     }
-    data = data(Rcpp::Range(0, use-1), Rcpp::_);
+
+    if(use != 0) data = data(Rcpp::Range(0, use-1), Rcpp::_);    
 
     if(data.nrow() < blocksize * 30){
       LD = 0;
@@ -274,7 +276,9 @@ Rcpp::List gcalibrateC(Rcpp::Nullable<Rcpp::String> pathname = R_NilValue, Rcpp:
 
         for(int i = 0; i < input.nrow(); i++){
           for(int j = 0; j < input.ncol(); j++){
-            closestpoint(i, j) = curr(i, j) / sqrt(rsum[i]);
+            if(curr(i, j) != 0){
+              closestpoint(i, j) = curr(i, j) / sqrt(rsum[i]);
+            }
           }
         }
 
@@ -311,6 +315,7 @@ Rcpp::List gcalibrateC(Rcpp::Nullable<Rcpp::String> pathname = R_NilValue, Rcpp:
 
       if((calErrorEnd < calErrorStart) && (calErrorEnd < 0.01) && (nhoursused > minloadcrit)){
         LD = 0;
+        Rcpp::Rcout << "Recalibration done, no problems detected";
       }
     }
       i += 1;

src/resample_helpers.cpp

@@ -1,3 +1,4 @@
+// [[Rcpp::plugins(cpp11)]]
 #include <Rcpp.h>
 using namespace Rcpp;