Fixed infrequent, prep for CRAN

.Rbuildignore

@@ -7,3 +7,6 @@
 ^pkgdown$
 ^\.github$
 ^working$
+^cran-comments\.md$
+^doc$
+^Meta$

.gitignore

@@ -5,3 +5,5 @@
 working/
 pkgdown/
 inst/doc
+/doc/
+/Meta/

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: mort
-Title: mort: Identifying potential mortalities and expelled tags in aquatic acoustic telemetry arrays
+Title: Identifying Potential Mortalities and Expelled Tags in Aquatic Acoustic Telemetry Arrays
 Version: 0.0.1
 Authors@R: c(
- person("Rosie", "Smith", , "[email protected]", role = c("aut", "cre"),
+ person("Rosie", "Smith", , "[email protected]", role = c("aut", "cre", "cph"),
  comment = c(ORCID = "0000-0003-2675-4452")),
  person("Heidi", "Swanson", role = "fnd")
  )
@@ -24,7 +24,9 @@ Suggests:
  ggplot2,
  knitr,
  plotly,
- rmarkdown
+ rmarkdown,
+ testthat (>= 3.0.0)
 VignetteBuilder: knitr
 Depends: 
- R (>= 2.10)
+ R (>= 3.5.0)
+Config/testthat/edition: 3

R/helper.R

@@ -165,7 +165,6 @@ extractres<-function(data,type){
 }
 
 
-
 #' Compare specified to default units
 #' @description Compare specified units to package default units and issue
 #' a warning if there is no match.
@@ -204,3 +203,95 @@ unitcheck<-function(type,units,data){
  }
 }
 
+
+#' Convert units of time
+#' @description Convert a period of time into different units.
+#'
+#' @param unit1 Initial units of the period of time.
+#' @param unit2 Desired units of the period of time.
+#' @param val1 Period of time, in the units of `unit1`
+#'
+#' @return A numeric value of the period time in the desired units (`unit2`).
+#' @keywords internal
+#' @noRd
+#'
+#' @examples
+#' unitconvert("secs","mins",60)
+#' unitconvert("weeks","hours",1)
+unitconvert<-function(unit1,unit2,val1){
+ if (unit1=="secs"){
+ if (unit2=="mins"){
+ val.new<-val1/60
+ }
+ if (unit2=="hours"){
+ val.new<-val1/60/60
+ }
+ if (unit2=="days"){
+ val.new<-val1/60/60/24
+ }
+ if (unit2=="weeks"){
+ val.new<-val1/60/60/24/7
+ }
+ }
+ else if (unit1=="mins"){
+ if (unit2=="secs"){
+ val.new<-val1*60
+ }
+ if (unit2=="hours"){
+ val.new<-val1/60
+ }
+ if (unit2=="days"){
+ val.new<-val1/60/24
+ }
+ if (unit2=="weeks"){
+ val.new<-val1/60/24/7
+ }
+ }
+ else if (unit1=="hours"){
+ if (unit2=="secs"){
+ val.new<-val1*60*60
+ }
+ if (unit2=="mins"){
+ val.new<-val1*60
+ }
+ if (unit2=="days"){
+ val.new<-val1/24
+ }
+ if (unit2=="weeks"){
+ val.new<-val1/24/7
+ }
+ }
+ else if (unit1=="days"){
+ if (unit2=="secs"){
+ val.new<-val1*60*60*24
+ }
+ if (unit2=="mins"){
+ val.new<-val1*60*24
+ }
+ if (unit2=="hours"){
+ val.new<-val1*24
+ }
+ if (unit2=="weeks"){
+ val.new<-val1/7
+ }
+ }
+ else if (unit1=="weeks"){
+ if (unit2=="secs"){
+ val.new<-val1*60*60*24*7
+ }
+ if (unit2=="mins"){
+ val.new<-val1*60*24*7
+ }
+ if (unit2=="hours"){
+ val.new<-val1*24*7
+ }
+ if (unit2=="days"){
+ val.new<-val1*7
+ }
+ }
+ else{
+ stop("Units are not supported. Units must be 'secs', 'mins', 'hours', 'days', or 'weeks'.")
+ }
+
+ val.new
+}

R/mort.R

@@ -570,16 +570,16 @@ morts<-function(data,type="mort",ID,station,res.start="auto",res.end="auto",
 #' ## Recent example
 #' inf_recent<-infrequent(data=events,type="mort",ID="ID",
 #' station="Station.Name",method="recent",
-#' threshold=0.5,threshold.units="hours",
+#' threshold=72,threshold.units="hours",
 #' recent.period=52,recent.units="weeks",
 #' progress.bar=FALSE)
 #' head(inf_recent)
 #'
 #' ## User-defined example
 #' inf_defined<-infrequent(data=events,type="mort",ID="ID",
 #' station="Station.Name",method="defined",
-#' threshold=0.5,threshold.units="hours",
-#' start="2019-10-01",end="2020-06-01",
+#' threshold=12,threshold.units="hours",
+#' start="2006-06-15",end="2006-10-15",
 #' progress.bar=FALSE)
 #' head(inf_defined)
 infrequent<-function(data,type="mort",ID,station,res.start="auto",
@@ -699,6 +699,10 @@ infrequent<-function(data,type="mort",ID,station,res.start="auto",
  if (is.null(recent.units)){
  stop("recent.units is not specified")
  }
+ # Convert threshold units if threshold units and residence units do not match
+ if (units!=threshold.units){
+ threshold<-unitconvert(unit1=threshold.units,unit2=units,val1=threshold)
+ }
  print("Identifying mortalities from infrequent detections")
  if (progress.bar==TRUE){
  pb<-txtProgressBar(1,length(tag),style=3)
@@ -713,28 +717,29 @@ infrequent<-function(data,type="mort",ID,station,res.start="auto",
  j<-min(which(difftime(res.temp[[res.end]][nrow(res.temp)],
  res.temp[[res.end]],
  units=recent.units)<=recent.period))
+ res.temp<-res.temp[j:nrow(res.temp),]
  if (is.null(ddd)){
  if (nrow(res.temp)>=1&
- length(unique(res.temp[[station]][j:nrow(res.temp)]))==1&
+ length(unique(res.temp[[station]]))==1&
  sum(res.temp[[residences]])<threshold){
  if (tag[i] %in% inf.morts[[ID]]){
- j<-which(inf.morts[[ID]]==tag[i])
- if (res.temp[[res.start]][1]<inf.morts[[res.start]][j]){
- inf.morts[j,]<-res.temp[1,]
+ k<-which(inf.morts[[ID]]==tag[i])
+ if (res.temp[[res.start]][1]<inf.morts[[res.start]][k]){
+ inf.morts[k,]<-res.temp[1,]
  if (!is.null(morts.prev)&backwards==TRUE){
- new.morts<-c(new.morts,j)
+ new.morts<-c(new.morts,k)
  }
  }
  }
  else {
- inf.morts[nrow(inf.morts)+1,]<-res.temp[j,]
+ inf.morts[nrow(inf.morts)+1,]<-res.temp[1,]
  }
  }
  }
  else {
  if (nrow(res.temp)>0&
  sum(res.temp[[residences]])<threshold){
- res.temp.drift<-drift(data=res.temp[j:nrow(res.temp),],
+ res.temp.drift<-drift(data=res.temp,
  type=type,ID=ID,station=station,
  res.start=res.start,res.end=res.end,
  residences=residences,units=units,ddd=ddd,
@@ -857,6 +862,10 @@ infrequent<-function(data,type="mort",ID,station,res.start="auto",
  if (!is(end,"POSIXt")){
  stop("end is not in the format YYYY-mm-dd HH:MM:SS")
  }
+ # Convert threshold units if threshold units and residence units do not match
+ if (units!=threshold.units){
+ threshold<-unitconvert(unit1=threshold.units,unit2=units,val1=threshold)
+ }
  if (progress.bar==TRUE){
  pb<-txtProgressBar(1,length(tag),style=3)
  }