small update to code comment

R/prep_training_data.R

@@ -13,8 +13,8 @@
 #'
 #' @importFrom fdasrvf f_to_srvf horizFPCA jointFPCA vertFPCA optimum.reparam time_warping warp_f_gamma
 #' @importFrom purrr map map2
-#' 
-#' @return List with three objects: 
+#'
+#' @return List with three objects:
 #' \itemize{
 #'   \item alignment: output from fdasrvf::time_warping
 #'   \item fpca_type: type of elastic FPCA method applied
@@ -25,23 +25,48 @@ prep_training_data <- function(f, time, fpca_method, ci = c(-2, -1, 0, 1, 2), op
 
   # Make sure 'fpca_method' is all lower case
   fpca_method = tolower(fpca_method)
-  
+
   # Compute number of training functions
   #N = dim(f)[2]
 
   # Change times to be between 0 and 1
   time = seq(0, 1, length.out = length(time))
 
   # Apply time_warping from fdasrvf to training data
-  aligned <- fdasrvf::time_warping(f = f, time = time, parallel = T, optim_method = optim_method, center = F)
+  # Note: We set the centering to false so that later on, the test data
+  # transformations also also implemented with no centering to achieve
+  # better numerical estimates
+  aligned <-
+    fdasrvf::time_warping(
+      f = f,
+      time = time,
+      parallel = T,
+      optim_method = optim_method,
+      center = F
+    )
 
   # Apply an elastic fPCA to the adjusted aligned training data using fdasrvf
   if (fpca_method == "jfpca") {
-    fpca_res = fdasrvf::jointFPCA(warp_data = aligned, no = length(time), ci = ci, showplot = F)
+    fpca_res = fdasrvf::jointFPCA(
+      warp_data = aligned,
+      no = length(time),
+      ci = ci,
+      showplot = F
+    )
   } else if (fpca_method == "hfpca") {
-    fpca_res = fdasrvf::horizFPCA(warp_data = aligned, no = length(time), ci = ci, showplot = F)
+    fpca_res = fdasrvf::horizFPCA(
+      warp_data = aligned,
+      no = length(time),
+      ci = ci,
+      showplot = F
+    )
   } else if (fpca_method == "vfpca") {
-    fpca_res = fdasrvf::vertFPCA(warp_data = aligned, no = length(time), ci = ci, showplot = F)
+    fpca_res = fdasrvf::vertFPCA(
+      warp_data = aligned,
+      no = length(time),
+      ci = ci,
+      showplot = F
+    )
   } else {
     stop("fpca_method specified incorrectly. Must be 'jfpca', 'vfpca', or 'hfpca'.")
   }