reformat migration.R to 80c

R/check.R

@@ -987,8 +987,8 @@ checkReport <- function(report){
 #'
 #' @keywords internal
 #'
-checkFirstDetBackFromRelease <- function(movements, tag, bio, detections, arrays, spatial, GUI, save.tables.locally, n) {
-  event(type = "debug", "Running checkFirstDetBackFromRelease.")
+checkFirstMove <- function(movements, tag, bio, detections, arrays, spatial, GUI, save.tables.locally, n) {
+  event(type = "debug", "Running checkFirstMove.")
   # NOTE: The NULL variables below are actually column names used by data.table.
   # This definition is just to prevent the package check from issuing a note due unknown variables.
   Valid <- NULL

R/explore.R

@@ -450,7 +450,7 @@ explore <- function(
                                     dist.mat = dist.mat, GUI = GUI, save.tables.locally = save.tables.locally)
       }
     } else { # nocov start
-      output <- overrideValidityChecks(moves = movements[[tag]], tag = tag, detections = detections.list[[tag]],
+      output <- overrideChecks(moves = movements[[tag]], tag = tag, detections = detections.list[[tag]],
                                        GUI = GUI, save.tables.locally = save.tables.locally, n = counter)
     } # nocov end
     return(output)

R/helper.R

@@ -1,3 +1,79 @@
+#' Parse argument and its value as a string
+#' 
+#' used to store the calls of the main actel functions as a string
+#' 
+#' @param arg the argument to be parsed
+#' @param arg_val an optional argument, to use as the value of the argument
+#'        used in "arg". Used when arg is, in itself, a complex object provided
+#'        by the user. E.g. a datapack, or an argument of preload.
+#' 
+#' @return A string showing the argument and its value, as it would have been
+#'         inputted into the R console.
+#' 
+#' @keywords internal
+#' 
+parse_arg <- function(arg,  arg_val) {
+  output <- paste0(deparse(substitute(arg)), " = ")
+
+  if (!missing(arg_val)) {
+    return(paste0(output, arg_val))
+  }
+  if (is.null(arg)) {
+    return(paste0(output, "NULL"))
+  }
+
+  if (is.character(arg)) {
+    a <- "'"
+    b <- "', '"
+  } else {
+    a <- ""
+    b <- ", "
+  }
+  if (is.list(arg)) {
+      output <- paste0(output, parse_list(arg))
+  } else {
+    if (length(arg) == 1) {
+      output <- paste0(output, a, arg, a)
+    } else {
+      output <- paste0(output, "c(", a, paste0(arg, collapse = b), a, ")")
+    }
+  }
+  return(output)
+}
+
+#' Helper to parse list arguments
+#' 
+#' Used inside [parse_arg()] to properly parse list arguments
+#' 
+#' @inheritParams parse_arg
+#' 
+#' @return A string showing the list as it would have been
+#'         inputted into the R console.
+#' 
+#' @keywords internal
+#' 
+parse_list <- function(arg) {
+  aux <- sapply(1:length(arg), function(i) {
+    if (is.character(arg[[i]])) {
+      a <- "'"
+      b <- "', '"
+    } else {
+      a <- ""
+      b <- ", "
+    }
+    name_i <- names(arg)[i]
+    content <- paste(arg[[i]], collapse = b)
+    if (length(arg[[i]]) == 1) {
+      output_i <- paste0("'", name_i,"' = ", a, content, a)
+    } else {
+      output_i <- paste0("'", name_i,"' = c(", a, content, a, ")")
+    }
+    return(output_i)
+  })
+  output <- paste0("list(", paste0(aux, collapse = ", "), ")")
+  return(output)
+}
+
 #' collapse event indexes into ranges
 #'
 #' @param x a numerical vector

R/residency.R

@@ -473,7 +473,7 @@ residency <- function(
                                     dist.mat = dist.mat, GUI = GUI, save.tables.locally = save.tables.locally)
       }
     } else {
-      output <- overrideValidityChecks(moves = movements[[tag]], tag = tag, detections = detections.list[[tag]], # nocov
+      output <- overrideChecks(moves = movements[[tag]], tag = tag, detections = detections.list[[tag]], # nocov
                                        GUI = GUI, save.tables.locally = save.tables.locally, n = counter) # nocov
     }
     return(output)
@@ -494,12 +494,21 @@ residency <- function(
 
     aux <- sectionMovements(movements = movements[[i]], spatial = spatial, valid.dist = attributes(dist.mat)$valid)
 
-    aux <- checkMinimumN(movements = aux, tag = tag, min.total.detections = 0, # don't run the minimum total detections check here.
+    if (!is.null(aux)) {
+      # don't run the minimum total detections check here (i.e. set it to 0);
+      # that's already done when compiling the array movements.
+      aux <- checkMinimumN(movements = aux, tag = tag, min.total.detections = 0,
                          min.per.event = min.per.event[2], n = counter)
 
-    output <- checkSMovesN(secmoves = aux, tag = tag, section.warning = section.warning, section.error = section.error, GUI = GUI,
-                           save.tables.locally = save.tables.locally, n = counter)
-    return(output)
+      output <- checkSMovesN(secmoves = aux, tag = tag,
+                             section.warning = section.warning,
+                             section.error = section.error, GUI = GUI,
+                             save.tables.locally = save.tables.locally,
+                             n = counter)
+      return(output)
+    } else {
+      return(NULL)
+    }
   })
   names(section.movements) <- names(movements)
 

R/user_interaction.R

@@ -869,8 +869,8 @@ transferValidity <- function(from, to) { # nocov start
 #'
 #' @keywords internal
 #'
-overrideValidityChecks <- function(moves, detections, tag, GUI, save.tables.locally, n) { # nocov start
-  event(type = "debug", "Starting overrideValidityChecks.")
+overrideChecks <- function(moves, detections, tag, GUI, save.tables.locally, n) { # nocov start
+  event(type = "debug", "Starting overrideChecks.")
   trigger <- paste0("M: Override has been triggered for tag ", tag,
                     " ", n, ". Entering full manual mode.")