updated progress bars

R/options.R

@@ -30,10 +30,12 @@
 #' @examples
 #' morts<-morts(data=events,type="mort",ID="ID",station="Station.Name",
 #' method="any")
+#' head(morts)
 #'
 #' # If station change not identified yet:
 #' morts_bw<-backwards(data=events,morts=morts,ID="ID",
 #' station="Station.Name",res.start="ResidenceStart")
+#' head(morts_bw)
 #'
 #' # Identify station change first:
 #' station.change<-stationchange(data=events,type="mort",
@@ -42,6 +44,7 @@
 #' morts_bw<-backwards(data=events,morts=morts,ID="ID",
 #' station="Station.Name",res.start="ResidenceStart",
 #' stnchange=station.change)
+#' head(morts_bw)
 backwards<-function(data,morts,ID,station,res.start,stnchange=NULL){
  if (any(data[[station]]=="Break")){
  warning("Either a station name was 'Break' or data included seasonal
@@ -137,13 +140,19 @@ backwards<-function(data,morts,ID,station,res.start,stnchange=NULL){
 #' @export
 #'
 #' @examples
-#' drift.events<-drift(data=events,type="mort",ID="ID",
-#' station="Station.Name",ddd=ddd,from.station="From",to.station="To")
+#' # With no drift:
+#' head(events)
+#'
+#' drift.events<-drift(data=events[events$ID=="A",],type="mort",ID="ID",
+#' station="Station.Name",ddd=ddd,from.station="From",to.station="To",
+#' progress.bar=FALSE)
+#' head(drift.events)
 #'
 #' # With cutoff:
-#' drift.events<-drift(data=events,type="mort",ID="ID",
+#' drift.events<-drift(data=events[events$ID=="A",],type="mort",ID="ID",
 #' station="Station.Name",ddd=ddd,from.station="From",to.station="To",
-#' cutoff=1,cutoff.units="days")
+#' cutoff=1,cutoff.units="days",progress.bar=FALSE)
+#' head(drift.events)
 drift<-function(data,type,ID,station,res.start="auto",res.end="auto",
  residences="auto",units="auto",ddd,from.station,to.station,
  cutoff=NULL,cutoff.units=NULL,progress.bar=TRUE){
@@ -301,7 +310,7 @@ drift<-function(data,type,ID,station,res.start="auto",res.end="auto",
 #' residence events that is within the period of interest will be retained,
 #' and `residences` will be recalculated, using specified `units`.
 #' Default is `TRUE`.
-#' @param progressbar option to display progress bar as function is run. Default
+#' @param progress.bar option to display progress bar as function is run. Default
 #' is TRUE.
 #'
 #' @return a dataframe in the same format as the input data, with residence
@@ -311,16 +320,19 @@ drift<-function(data,type,ID,station,res.start="auto",res.end="auto",
 #' @examples
 #' # Seasons in format dd-mm
 #' season.events<-season(data=events,type="mort",ID="ID",
-#' station="Station.Name",season.start="01-06",season.end="31-10")
+#' station="Station.Name",season.start="01-06",season.end="31-10",
+#' progress.bar=FALSE)
+#' head(season.events)
 #'
 #' # Seasons in format YYYY-mm-dd HH:MM:SS
 #' season.start<-c("2003-06-15","2004-06-21")
 #' season.end<-c("2003-10-15","2004-10-30")
 #' season.events<-season(data=events,type="mort",ID="ID",
-#' station="Station.Name",season.start=season.start,season.end=season.end)
+#' station="Station.Name",season.start=season.start,season.end=season.end,progress.bar=FALSE)
+#' head(season.events)
 season<-function(data,type="mort",ID,station,res.start="auto",res.end="auto",
  residences="auto",units="auto",season.start,
- season.end,overlap=TRUE,progressbar=TRUE){
+ season.end,overlap=TRUE,progress.bar=TRUE){
 
  if (type %in% c("actel","vtrack")){
  data<-extractres(data=data,type=type)
@@ -423,11 +435,11 @@ season<-function(data,type="mort",ID,station,res.start="auto",res.end="auto",
  data.season<-data[0,]
 
  for (i in 1:length(season.start)){
- if (progressbar==TRUE){
+ if (progress.bar==TRUE){
  print(paste("season/period",i,"of",length(season.start)))
  }
  if (length(tag)>1){
- if (progressbar==TRUE){
+ if (progress.bar==TRUE){
  pb<-txtProgressBar(1,length(tag),style=3)
  }
  }
@@ -471,7 +483,7 @@ season<-function(data,type="mort",ID,station,res.start="auto",res.end="auto",
  }
  data.season<-rbind(data.season,data.temp)
  if (length(tag)>1){
- if (progressbar==TRUE){
+ if (progress.bar==TRUE){
  setTxtProgressBar(pb,j)
  }
  }

R/plot.R

@@ -4,8 +4,7 @@
 #' mortalities. Plotting uses ggplot2. Interactive option also uses plotly.
 #'
 #' @param data a dataframe of residence events. Residence events must include
-#' tag ID, location name, start time, and end time. Residence events must also
-#' include duration if making an interactive plot.
+#' tag ID, location name, start time, and end time.
 #' @param type the method used to generate the residence events. Options are
 #' "mort", "actel", "glatos", "vtrack", or "manual".
 #' @param ID a string of the name of the column in `data` that holds the tag or
@@ -45,7 +44,7 @@
 #' `facet.by="year"`.
 #' @param facet.by option to facet by "season" (as defined with `season.start`
 #' and `season.end`) or "year". Default is "season".
-#' @param progressbar option to display progress bar as function is run. Default
+#' @param progress.bar option to display progress bar as function is run. Default
 #' is TRUE.
 #'
 #' @return a ggplot2 plot. Additional arguments (e.g., formatting axes,
@@ -57,19 +56,21 @@
 #'
 #' @examples
 #' plot<-mortsplot(data=events,type="mort",ID="ID",station="Station.Name")
+#' plot
 #'
 #' # With mortalities plotted over residences:
 #' morts<-morts(data=events,type="mort",ID="ID",station="Station.Name",
-#' method="any")
+#' method="any",progress.bar=FALSE)
 #'
 #' plot<-mortsplot(data=events,type="mort",ID="ID",station="Station.Name",
 #' morts=morts)
+#' plot
 mortsplot<-function(data,type,ID,station,res.start="auto",res.end="auto",
  morts=NULL,singles=TRUE,interactive=FALSE,residences=NULL,
  units=NULL,
  season.start=NULL,season.end=NULL,facet=FALSE,
  facet.axis="x",facet.by="season",
- progressbar=TRUE){
+ progress.bar=TRUE){
 
  if (!requireNamespace("ggplot2", quietly = TRUE)) {
  stop("Package \"ggplot2\" must be installed to use this function.",
@@ -175,7 +176,7 @@ mortsplot<-function(data,type,ID,station,res.start="auto",res.end="auto",
  if (units=="auto"){
  units<-autofield(type=type,field="units",data=data)
  }
- if (progressbar==TRUE){
+ if (progress.bar==TRUE){
  print("Extracting data from the period/season(s) of interest")
  }
  if (is.null(season.start)&is.null(season.end)&facet.by=="year"){
@@ -184,7 +185,7 @@ mortsplot<-function(data,type,ID,station,res.start="auto",res.end="auto",
  }
  data<-season(data=data,type=type,ID=ID,station=station,res.start=res.start,res.end=res.end,
  residences=residences,units=units,season.start=season.start,
- season.end=season.end,overlap=FALSE,progressbar=FALSE)
+ season.end=season.end,overlap=FALSE,progress.bar=progress.bar)
  data<-data[data[[station]]!="Break",]
  if (!is(season.start,"POSIXt")){
  try(season.start<-as.POSIXct(season.start,tz="UTC"),silent=TRUE)

R/residences.R

@@ -13,6 +13,8 @@
 #' @param ID a string of the name of the column in `data` that holds the tag or sample IDs.
 #' @param datetime a string of the name of the column in `data` that holds the date and time.
 #' @param station a string of the name of the column in `data` that holds the station name or receiver location.
+#' @param progress.bar option to display progress bar as residences are generated.
+#' Default is TRUE.
 #'
 #' @return A data frame with one row for each residence event, including date/time of
 #' residence start, date/time of residence end, and duration of residence event. All
@@ -23,10 +25,12 @@
 #' @importFrom utils setTxtProgressBar txtProgressBar
 #'
 #' @examples
-#' res.events<-residences(data=detections,ID="ID",station="Station.Name",
-#' datetime="DateTimeUTC",cutoff=1,units="days")
+#' head(detections)
+#' res.events<-residences(data=detections[1:500,],ID="ID",station="Station.Name",
+#' datetime="DateTimeUTC",cutoff=1,units="days",progress.bar=FALSE)
+#' head(res.events)
 
-residences<-function(data,ID,station,datetime,cutoff,units){
+residences<-function(data,ID,station,datetime,cutoff,units,progress.bar=TRUE){
  # Create list of unique IDs
  tag<-unique(na.omit(data[[ID]]))
 
@@ -51,7 +55,9 @@ residences<-function(data,ID,station,datetime,cutoff,units){
  # Set up res
  res<-cbind(data[0,],ResidenceEnd=as.POSIXct(as.character()))
 
- pb<-txtProgressBar(1,length(tag),style=3)
+ if (progress.bar==TRUE){
+ pb<-txtProgressBar(1,length(tag),style=3)
+ }
  for (i in 1:length(tag)){
  # Subset by ID
  res.sub<-data[data[[ID]]==tag[i],]
@@ -109,7 +115,9 @@ residences<-function(data,ID,station,datetime,cutoff,units){
  break
  }
  }
- setTxtProgressBar(pb,i)
+ if (progress.bar==TRUE){
+ setTxtProgressBar(pb,i)
+ }
  }
  colnames(res)[colnames(res)==datetime]<-"ResidenceStart"
  attributes(res$ResidenceStart)$tzone<-attributes(data[[datetime]])$tzone

R/review.R

@@ -4,7 +4,7 @@
 #' alive.
 #'
 #' @param morts a dataframe with previously flagged mortalities. Format does
-#' not need to match `new.data`, but the names and formats of `ID`, `station`,
+#' not need to match `new.data` exactly, but the names and formats of `ID`, `station`,
 #' and `res.start` fields must match in all input dataframes.
 #' @param new.data a dataframe of new residence events (i.e., generated from
 #' detection data that were not included in earlier `mort` analyses).
@@ -37,6 +37,8 @@
 #' @param residences an optional character string with the name of the column
 #' in `morts` and `new.data` that holds the duration of the residence events.
 #' Only needed if drift is applied.
+#' @param progress.bar option to display progress bar as function and called
+#' functions are run. Default is TRUE.
 #'
 #' @return A dataframe with one row for each tag ID from `morts`
 #' with a station/location change that was identified
@@ -49,13 +51,14 @@
 #'
 #' @examples
 #' morts<-morts(data=events,type="mort",ID="ID",station="Station.Name",
-#' method="any")
+#' method="any",progress.bar=FALSE)
 #'
 #' undead<-review(morts=morts,new.data=new.data,
-#' type="mort",ID="ID",station="Station.Name")
+#' type="mort",ID="ID",station="Station.Name",progress.bar=FALSE)
 review<-function(morts,new.data,old.data=NULL,type,ID,station,res.start="auto",
  res.end=NULL,residences=NULL,units=NULL,
- ddd=NULL,from.station=NULL,to.station=NULL){
+ ddd=NULL,from.station=NULL,to.station=NULL,
+ progress.bar=TRUE){
 
  if (type %in% c("actel","vtrack")){
  new.data<-extractres(data=new.data,type=type)
@@ -199,7 +202,7 @@ review<-function(morts,new.data,old.data=NULL,type,ID,station,res.start="auto",
  res.start=res.start,res.end=res.end,
  ddd=ddd,from.station=from.station,to.station=to.station,
  residences=residences,
- units=units)
+ units=units,progress.bar=progress.bar)
  for (i in 1:nrow(morts)){
  res.temp<-data[data[[ID]]==morts[[ID]][i],]
  j<-1