Adding filter options for sibreport anlaysis #687

R/check_params.R

@@ -30,7 +30,7 @@ check_params = function(params_sleep = c(), params_metrics = c(),
   #-----------------------------------------------------------------------------------------
   if (length(params_sleep) > 0) { # Check class of sleep parameters
     numeric_params = c("anglethreshold", "timethreshold", "longitudinal_axis", "possible_nap_window", "possible_nap_dur",
-                       "colid", "coln1", "def.noc.sleep", "nnights", "sleepefficiency.metric")
+                       "colid", "coln1", "def.noc.sleep", "nnights", "sleepefficiency.metric", "possible_nap_edge_acc")
     boolean_params = c("ignorenonwear", "constrain2range", "HASPT.ignore.invalid",
                        "relyonguider", "sleeplogidnum")
     character_params = c("HASPT.algo", "HASIB.algo", "Sadeh_axis", "nap_model",

R/g.part5.analyseRest.R

@@ -1,8 +1,16 @@
 g.part5.analyseRest = function(sibreport = NULL, dsummary = NULL,
                                 ds_names = NULL, fi = NULL, di = NULL,
-                                time = NULL, tz = NULL, possible_nap_dur = NULL) {
+                                time = NULL, tz = NULL, possible_nap_dur = 0,
+                               possible_nap_edge_acc = Inf) {
   # Only consider sib episodes with minimum duration
-  longboutsi = which((sibreport$type == "sib" & sibreport$duration >= possible_nap_dur) |
+  if (length(grep(pattern = "mean_acc_1min", x = colnames(sibreport))) > 0) {
+    sibreport$acc_edge = pmax(sibreport$mean_acc_1min_before, sibreport$mean_acc_1min_after)
+  } else {
+    sibreport$acc_edge = 0
+  }
+  longboutsi = which((sibreport$type == "sib" &
+                        sibreport$duration >= possible_nap_dur[1] &
+                        sibreport$acc_edge <= possible_nap_edge_acc) |
                        (sibreport$type != "sib" & sibreport$duration >= 1))
   # for qc purposes:
   dsummary[di,fi] = length(longboutsi)

R/load_params.R

@@ -26,7 +26,8 @@ load_params = function(group = c("sleep", "metrics", "rawdata",
                         sleeplogsep = NULL, sleepwindowType = "SPT",
                         possible_nap_window = c(9, 18),
                         possible_nap_dur = c(15, 240),
-                        nap_model = c(), sleepefficiency.metric = 1)
+                        nap_model = c(), sleepefficiency.metric = 1,
+                        possible_nap_edge_acc = Inf)
   }
   if ("metrics" %in% group) {
     params_metrics = list(do.anglex = FALSE, do.angley = FALSE, do.anglez = TRUE,

man/GGIR.Rd

@@ -1104,7 +1104,10 @@ GGIR(mode = 1:5,
         wake times). If 2, sleep efficiency is calculated as detected nocturnal
         sleep time divided by detected duration in sleep period time plus sleep latency (where
         sleep latency refers to the difference between log-derived sleep onset and 
-        accelerometer-detected sleep onset).
+        accelerometer-detected sleep onset).}
+        
+      \item{possible_nap_edge_acc}{
+        Minimum acceleration before or after the SIB for the nap to be considered.
       }
     }
   }
@@ -1293,7 +1296,9 @@ GGIR(mode = 1:5,
         In \link{g.part4}: To indicate whether to generate report for the sustained 
         inactivity bouts (SIB). If set to TRUE and when an advanced sleep diary is
         available in part 4 then part 5 will use this to generate summary statistics
-        on the overlap between self-reported nonwear and napping with SIB}
+        on the overlap between self-reported nonwear and napping with SIB. Here,
+        SIB cna be filter based on argument possible_nap_edge_acc and the first value
+        of possible_nap_dur}
 
       \item{do.visual}{
         Boolean (default = TRUE).

man/g.part5.analyseRest.Rd

@@ -10,7 +10,9 @@
 \usage{
   g.part5.analyseRest(sibreport = NULL, dsummary = NULL,
                                 ds_names = NULL, fi = NULL,
-                                di = NULL, time = NULL, tz = NULL)
+                                di = NULL, time = NULL, tz = NULL,
+                                possible_nap_dur = 0,
+                                possible_nap_edge_acc = Inf)
 }
 \arguments{
   \item{sibreport}{
@@ -35,6 +37,13 @@
   \item{tz}{
     Timezone database name
   }
+  \item{possible_nap_dur}{
+    Minimum sib duration to be considered. For self-reported naps/nonwear
+    there is a minimum duration of 1 epoch.
+  }
+  \item{possible_nap_edge_acc}{
+    Maximum acceleration before or after the SIB for it to be considered.
+  }
 }
 \value{
   List with updated objects dsummary, ds_names, fi, and di

man/g.part5_analyseSegment.Rd

@@ -19,8 +19,7 @@
                                   add_one_day_to_next_date,
                                   lightpeak_available,
                                   tail_expansion_log,
-                                  foldernamei, sibreport = NULL,
-                                  possible_nap_dur = NULL)
+                                  foldernamei, sibreport = NULL)
 }
 \arguments{
   \item{indexlog}{
@@ -87,10 +86,6 @@
   \item{sibreport}{
     Sibreport object as passed on from \link{g.part5}
   }
-  \item{possible_nap_dur}{
-    Minimum sib duration to be considered. For self-reported naps/nonwear
-    there is a minimum duration of 1 epoch.
-  }
 }
 \value{
   List with objects: indexlog, timeList, and the matrix with the prelimenary results

tests/testthat/test_load_check_params.R

@@ -10,7 +10,7 @@ test_that("load_params can load parameters", {
 
   # Test length of objects
   expect_equal(length(params), 8)
-  expect_equal(length(params$params_sleep), 21)
+  expect_equal(length(params$params_sleep), 22)
   expect_equal(length(params$params_metrics), 41)
   expect_equal(length(params$params_rawdata), 37)
   expect_equal(length(params$params_247), 20)