More coverage and typos

R/Analyse_SAR.OSLdata.R

@@ -145,7 +145,7 @@ Analyse_SAR.OSLdata <- function(
   set,
   dtype,
   keep.SEL = FALSE,
-  info.measurement = "unkown measurement",
+  info.measurement = "unknown measurement",
   output.plot = FALSE,
   output.plot.single = FALSE,
   cex.global = 1,

R/RLum.Data.Curve-class.R

@@ -105,7 +105,7 @@ setAs("list", "RLum.Data.Curve",
       function(from,to){
 
         new(to,
-            recordType = "unkown curve type",
+            recordType = "unknown curve type",
             curveType = NA_character_,
             data = matrix(unlist(from), ncol = 2),
             info = list())
@@ -124,7 +124,7 @@ setAs("data.frame", "RLum.Data.Curve",
       function(from,to){
 
               new(to,
-                  recordType = "unkown curve type",
+                  recordType = "unknown curve type",
                   curveType = NA_character_,
                   data = as.matrix(from),
                   info = list())
@@ -144,7 +144,7 @@ setAs("RLum.Data.Curve", "data.frame",
 setAs("matrix", "RLum.Data.Curve",
       function(from,to){
         new(to,
-            recordType = "unkown curve type",
+            recordType = "unknown curve type",
             curveType = NA_character_,
             data = from,
             info = list())

R/RLum.Data.Image-class.R

@@ -86,7 +86,7 @@ setClass(
 setAs("data.frame", "RLum.Data.Image",
       function(from,to){
         new(to,
-            recordType = "unkown curve type",
+            recordType = "unknown curve type",
             curveType = "NA",
             data = array(unlist(from), dim = c(nrow(from),ncol(from),1)),
             info = list())
@@ -110,7 +110,7 @@ setAs("RLum.Data.Image", "data.frame",
 setAs("matrix", "RLum.Data.Image",
       function(from,to){
         new(to,
-            recordType = "unkown curve type",
+            recordType = "unknown curve type",
             curveType = "NA",
             data = array(from, c(nrow(from), ncol(from), 1)),
             info = list())
@@ -131,7 +131,7 @@ setAs("RLum.Data.Image", "matrix",
 setAs("array", "RLum.Data.Image",
       function(from, to){
         new(to,
-            recordType = "unkown curve type",
+            recordType = "unknown curve type",
             curveType = "NA",
             data = from,
             info = list())
@@ -149,7 +149,7 @@ setAs("list", "RLum.Data.Image",
         array_list <- lapply(from, function(x) array(unlist(as.vector(x)), c(nrow(x), ncol(x), 1)))
 
         new(to,
-            recordType = "unkown curve type",
+            recordType = "unknown curve type",
             curveType = "NA",
             data = array(unlist(array_list),
                          c(nrow(array_list[[1]]), ncol(array_list[[1]]), length(array_list))),

R/Second2Gray.R

@@ -135,7 +135,7 @@ Second2Gray <- function(
 
     if(dose.rate@originator != "calc_SourceDoseRate"){
 
-      stop("[Second2Gray()]  Wrong originator for dose.rate 'RLum.Results' object.")
+      stop("[Second2Gray()] Wrong originator for dose.rate 'RLum.Results' object.")
 
     }else{
 

R/analyse_Al2O3C_CrossTalk.R

@@ -121,6 +121,10 @@ analyse_Al2O3C_CrossTalk <- function(
 
   ##modify on request
   if(!is.null(method_control)){
+    if (!is.list(method_control)) {
+      stop("[analyse_Al2O3C_CrossTalk()] 'method_control' is expected ",
+           "to be a list", call. = FALSE)
+    }
     method_control_settings <- modifyList(x = method_control_settings, val = method_control)
 
   }
@@ -146,6 +150,14 @@ analyse_Al2O3C_CrossTalk <- function(
 
   ##check irradiation time correction
   if (!is.null(irradiation_time_correction)) {
+
+    if (!is.numeric(irradiation_time_correction) &&
+        !is(irradiation_time_correction, "RLum.Results")) {
+      stop("[analyse_Al2O3C_CrossTalk()] 'irradiation_time_correction' ",
+           "is expected to be a numeric value or an RLum.Results object",
+           call. = FALSE)
+    }
+
     if (is(irradiation_time_correction, "RLum.Results")) {
       if (irradiation_time_correction@originator == "analyse_Al2O3C_ITC") {
         irradiation_time_correction <- get_RLum(irradiation_time_correction)
@@ -164,9 +176,7 @@ analyse_Al2O3C_CrossTalk <- function(
           "[analyse_Al2O3C_CrossTalk()] The object provided for the argument 'irradiation_time_correction' was created by an unsupported function!",
           call. = FALSE
         )
-
       }
-
     }
   }
 

R/analyse_SAR.TL.R

@@ -121,11 +121,14 @@ analyse_SAR.TL <- function(
   ...
 ){
 
+  if (missing("object")) {
+    stop("[analyse_SAR.TL()] No value set for 'object'!", call. = FALSE)
+  }
 
   # Self-call -----------------------------------------------------------------------------------
   if(inherits(object, "list")){
    if(!all(sapply(object, class) == "RLum.Analysis"))
-     stop("[analyse_SAR.TL()] All elements in the input list need to be of class 'RLum.Analysis'!",
+     stop("[analyse_SAR.TL()] All elements in the input list must be of class 'RLum.Analysis'!",
           call. = FALSE)
 
     ##run sequence
@@ -160,13 +163,7 @@ analyse_SAR.TL <- function(
   ##=============================================================================#
   # General Integrity Checks ---------------------------------------------------
 
-  ##GENERAL
-
   ##MISSING INPUT
-  if(missing("object")==TRUE){
-    stop("[analyse_SAR.TL()] No value set for 'object'!", call. = FALSE)
-  }
-
   if(missing("signal.integral.min") == TRUE){
     stop("[analyse_SAR.TL()] No value set for 'signal.integral.min'!", call. = FALSE)
   }
@@ -321,9 +318,7 @@ analyse_SAR.TL <- function(
   LnLxTnTx[,"Name"]<-as.character(LnLxTnTx[,"Name"])
 
   # Calculate Recycling Ratio -----------------------------------------------
-
-  ##Calculate Recycling Ratio
-
+  RecyclingRatio <- NA
   if(length(LnLxTnTx[LnLxTnTx[,"Repeated"]==TRUE,"Repeated"])>0){
 
     ##identify repeated doses
@@ -351,19 +346,14 @@ analyse_SAR.TL <- function(
     ##Just transform the matrix and add column names
     RecyclingRatio<-t(RecyclingRatio)
     colnames(RecyclingRatio)<-temp.ColNames
-
-  }else{RecyclingRatio<-NA}
-
+  }
 
   # Calculate Recuperation Rate ---------------------------------------------
-
-
-  ##Recuperation Rate
+  Recuperation <- NA
   if("R0" %in% LnLxTnTx[,"Name"]==TRUE){
     Recuperation<-round(LnLxTnTx[LnLxTnTx[,"Name"]=="R0","LxTx"]/
                           LnLxTnTx[LnLxTnTx[,"Name"]=="Natural","LxTx"],digits=4)
-  }else{Recuperation<-NA}
-
+  }
 
   # Combine and Evaluate Rejection Criteria ---------------------------------
 
@@ -702,4 +692,3 @@ analyse_SAR.TL <- function(
   return(newRLumResults.analyse_SAR.TL)
 
 }
-

R/analyse_pIRIRSequence.R

@@ -180,6 +180,10 @@ analyse_pIRIRSequence <- function(
   ...
 ){
 
+  if (missing("object")) {
+    stop("[analyse_pIRIRSequence()] No value set for 'object'!")
+  }
+
 # SELF CALL -----------------------------------------------------------------------------------
  if(is.list(object)){
 
@@ -267,14 +271,10 @@ analyse_pIRIRSequence <- function(
 
   ##GENERAL
 
-    ##MISSING INPUT
-    if(missing("object")==TRUE){
-      stop("[analyse_pIRIRSequence()] No value set for 'object'!")
-    }
-
     ##INPUT OBJECTS
     if(is(object, "RLum.Analysis")==FALSE){
-      stop("[analyse_pIRIRSequence()] Input object is not of type 'RLum.Analyis'!")
+      stop("[analyse_pIRIRSequence()] Input object is not of type 'RLum.Analyis'!",
+           call. = FALSE)
     }
 
     ##CHECK ALLOWED VALUES IN SEQUENCE STRUCTURE
@@ -293,20 +293,18 @@ analyse_pIRIRSequence <- function(
 
 # Deal with extra arguments -------------------------------------------------------------------
 
+  ## default values
+  mtext.outer <- "MEASUREMENT INFO"
+  main <- ""
+  log <- ""
+  cex <- 0.7
+
   ##deal with addition arguments
   extraArgs <- list(...)
-
-  mtext.outer <- if("mtext.outer" %in% names(extraArgs)) {extraArgs$mtext.outer} else
-  {"MEASUREMENT INFO"}
-
-  main <- if("main" %in% names(extraArgs)) {extraArgs$main} else
-  {""}
-
-  log <- if("log" %in% names(extraArgs)) {extraArgs$log} else
-  {""}
-
-  cex <- if("cex" %in% names(extraArgs)) {extraArgs$cex} else
-  {.7}
+  mtext.outer <- if ("mtext.outer" %in% names(extraArgs)) extraArgs$mtext.outer
+  main <- if ("main" %in% names(extraArgs)) extraArgs$main
+  log <- if ("log" %in% names(extraArgs)) extraArgs$log
+  cex <- if ("cex" %in% names(extraArgs)) extraArgs$cex
 
 
 # Protocol Integrity Checks --------------------------------------------------
@@ -526,7 +524,7 @@ analyse_pIRIRSequence <- function(
       temp.signal.integral.min <- signal.integral.min[i]
       temp.signal.integral.max <- signal.integral.max[i]
       temp.background.integral.min <- background.integral.min[i]
-      temp.backbround.integral.max <- background.integral.max[i]
+      temp.background.integral.max <- background.integral.max[i]
 
     }else{
 

R/apply_CosmicRayRemoval.R

@@ -34,7 +34,7 @@
 #' @param object [RLum.Data.Spectrum-class] or [RLum.Analysis-class] (**required**): input
 #' object to be treated. This can be also provided as [list]. If an [RLum.Analysis-class] object
 #' is provided, only the [RLum.Data.Spectrum-class] objects are treated. Please note: this mixing of
-#' objects do not work for a list of `RLum.Data` objects.
+#' objects does not work for a list of `RLum.Data` objects.
 #'
 #' @param method [character] (*with default*):
 #' Defines method that is applied for cosmic ray removal. Allowed methods are
@@ -334,14 +334,7 @@ apply_CosmicRayRemoval <- function(
           mtext(side = 3, paste0("Frame: ", x, " (",
                                  colnames(object.data.temp)[x],
                                  ") - no threshold applied!"))
-
-
-
         }
-
-
-
-
       }
 
       ##(9) - return information on the amount of removed cosmic-rays
@@ -366,7 +359,7 @@ apply_CosmicRayRemoval <- function(
 
   }else{
 
-    stop("[apply_CosmicRayRemoval()] Unkown method for cosmic ray removal.")
+    stop("[apply_CosmicRayRemoval()] Unknown method for cosmic ray removal.")
 
   }
 

R/calc_CosmicDoseRate.R

@@ -260,19 +260,18 @@ calc_CosmicDoseRate<- function(
   ##============================================================================##
 
   if(any(depth < 0) || any(density < 0)) {
-    cat(paste("\nNo negative values allowed for depth and density"))
-    stop(domain=NA)
+    stop("[calc_CosmicDoseRate()] No negative values allowed for ",
+         "depth and density", call. = FALSE)
   }
 
   if(corr.fieldChanges == TRUE) {
     if(is.na(est.age) == TRUE) {
-      cat(paste("\nCorrection for geomagnetic field changes requires",
-                "an age estimate."), fill = FALSE)
-      stop(domain=NA)
+      stop("[calc_CosmicDoseRate()] Correction for geomagnetic field ",
+           "changes requires an age estimate.", call. = FALSE)
     }
     if(est.age > 80) {
-      cat(paste("\nCAUTION: No geomagnetic field change correction for samples",
-                "older >80 ka possible!"), fill = FALSE)
+      cat("\nCAUTION: No geomagnetic field change correction for samples",
+          "older >80 ka possible!")
       corr.fieldChanges<- FALSE
     }
   }

R/calc_FadingCorr.R

@@ -220,11 +220,8 @@ calc_FadingCorr <- function(
       g_value <- as.numeric(get_RLum(g_value)[,c("FIT", "SD")])
 
     }else{
-      try({
-        stop("[calc_FadingCorr()] Unknown originator for the provided RLum.Results object via 'g_value'!",
-             call. = FALSE)
-
-      })
+      message("[calc_FadingCorr()] Error: Unknown originator for the ",
+              "provided RLum.Results object via 'g_value'!")
       return(NULL)
     }
   }
@@ -350,11 +347,11 @@ calc_FadingCorr <- function(
 
       ##otherwise the automatic error value finding
       ##will never work
+      res <- NA
       if(!is(temp,"try-error") && temp$root<1e8) {
-        return(temp$root)
-      } else{
-        return(NA)
+        res <- temp$root
       }
+      return(res)
 
     }, FUN.VALUE = 1))
 

R/calc_FuchsLang2001.R

@@ -14,7 +14,7 @@
 #' **Basic steps of the approach**
 #'
 #' 1. Estimate natural relative variation of the sample using a dose recovery test
-#' 2. Sort the input values ascendantly
+#' 2. Sort the input values in ascending order
 #' 3. Calculate a running mean, starting with the lowermost two values and add values iteratively.
 #' 4. Stop if the calculated `c[v]` exceeds the specified `cvThreshold`
 #'

R/internals_RLum.R

@@ -114,9 +114,9 @@
 #+ .smoothing()      +
 #+++++++++++++++++++++
 
-#' Allows smmoothing of data based on the function zoo::rollmean
+#' Allows smoothing of data based on the function zoo::rollmean
 #'
-#' The function just allows a direct and meaningfull access to the functionality of the zoo::rollmean()
+#' The function just allows a direct and meaningful access to the functionality of the zoo::rollmean()
 #' function. Arguments of the function are only partly valid.
 #'
 #' @param x [numeric] (**required**):

R/merge_Risoe.BINfileData.R

@@ -87,18 +87,17 @@ merge_Risoe.BINfileData <- function(
 
   # Integrity Checks --------------------------------------------------------
   if(length(input.objects) < 2){
-    message("[merge_Risoe.BINfileData()] Nothing done at least two input objects are needed!")
+    message("[merge_Risoe.BINfileData()] Nothing done: at least two input objects are needed!")
     return(input.objects)
 
   }
 
   if(is(input.objects, "character") == TRUE){
     for(i in 1:length(input.objects)){
       if(file.exists(input.objects[i])==FALSE){
-        stop("[merge_Risoe.BINfileData()] File ",input.objects[i]," does not exist!", call. = FALSE)
-
+        stop("[merge_Risoe.BINfileData()] File '", input.objects[i],
+             "' does not exist!", call. = FALSE)
       }
-
     }
 
   }else{
@@ -114,12 +113,8 @@ merge_Risoe.BINfileData <- function(
       }
 
     }else{
-
-      stop("[merge_Risoe.BINfileData()]
-                Input object is not a 'character' nor a 'list'!")
-
+      stop("[merge_Risoe.BINfileData()] Input object is neither a character nor a list!")
     }
-
   }