example dataset

DESCRIPTION

@@ -26,3 +26,5 @@ Suggests:
  plotly,
  rmarkdown
 VignetteBuilder: knitr
+Depends: 
+ R (>= 2.10)

R/data.R

@@ -0,0 +1,104 @@
+#'Sample acoustic telemetry detection data
+#'
+#'These detection data were subset from a real acoustic telemetry dataset of Arctic
+#'Char near Kugluktuk, Nunavut. The data were from a project that was a
+#'collaboration between the Kugluktuk Hunters and Trappers Organization, the
+#'University of Waterloo, and Fisheries and Oceans Canada. The data are valuable
+#'to the community of Kugluktuk, and are also sensitive due to their pertinence
+#'to the local fishery for Arctic Char. For this reason, the detections have been
+#'given generic station names and fish IDs so locations and sample information
+#'is anonymous. The year has also been changed, but otherwise, the detections are
+#'real, and therefore have all the challenges and intricacies of biological
+#'data.
+#'
+#'The variables are as follows:
+#'
+#'\itemize{
+#'\item DateTimeUTC. The date and time of each detection, in POSIXct format. The
+#'data are in UTC, as downloaded from the receivers.
+#'\item Station.Name Name of the receiver location.
+#'\item ID Unique ID of the fish.
+#'}
+#'
+#'@docType data
+#'@keywords datasets
+#'@name detections
+#'@usage data(detections)
+#'@format A data frame with 447 627 rows (observations) and 3 variables.
+NULL
+
+#'Sample residence events
+#'
+#'Events generated from the sample detection file provided. Events were generated
+#'using the residences() function in mort.
+#'
+#'The detection data were subset from a real acoustic telemetry dataset of Arctic
+#'Char near Kugluktuk, Nunavut. The data were from a project that was a
+#'collaboration between the Kugluktuk Hunters and Trappers Organization, the
+#'University of Waterloo, and Fisheries and Oceans Canada. The data are valuable
+#'to the community of Kugluktuk, and are also sensitive due to their pertinence
+#'to the local fishery for Arctic Char. For this reason, the detections have been
+#'given generic station names and fish IDs so locations and sample information
+#'is anonymous. The year has also been changed, but otherwise, the detections are
+#'real, and therefore have all the challenges and intricacies of biological
+#'data.
+#'
+#'The variables are as follows:
+#'
+#'\itemize{
+#'\item ResidenceStart. The start time of the residence events, in POSIXct.
+#'\item Station.Name. Name of the receiver location.
+#'\item ID. Unique ID of the fish.
+#'\item ResidenceEnd. The end time of the residence events, in POSIXct.
+#'\item ResidenceLength.days. The duration of the residence events. The units are
+#'days, as indicated by the variable name (which is automatically generated
+#'by mort::residences())
+#'}
+#'
+#'@docType data
+#'@keywords datasets
+#'@name events
+#'@usage data(events)
+#'@format A data frame with 11 487 rows (events) and 5 variables.
+NULL
+
+#'Sample dead drift direction dataframe
+#'
+#'The locations have been given generic station names, due to the sensitive nature
+#'of the dataset. The connections between stations (i.e., which stations are
+#'connected by drift and in which direction) are real.
+#'
+#'The variables are as follows:
+#'
+#'\itemize{
+#'\item From. The station where a tag may drift from.
+#'\item To. The station where a tag may drift to, from the station in From.
+#'}
+#'
+#'@docType data
+#'@keywords datasets
+#'@name ddd
+#'@usage data(ddd)
+#'@format A data frame with 18 rows and 2 variables.
+NULL
+
+#'Ice-free seasons
+#'
+#'The year has been changed, due to the sensitive nature of the dataset. The
+#'years have been changed in the same manner as the detection dates, so
+#'the ice-free dates correspond to the dataset in the same way as the original
+#'dataset.
+#'
+#'The variables are as follows:
+#'
+#'\itemize{
+#'\item Start. The date of ice break-up (the start of the period of interest).
+#'\item End. The date of ice freeze-up (the end of the period of interest).
+#'}
+#'
+#'@docType data
+#'@keywords datasets
+#'@name seasons
+#'@usage data(seasons)
+#'@format A data frame with 5 rows (years) and 2 variables.
+NULL

R/residences.R

@@ -23,8 +23,8 @@
 #' @importFrom utils setTxtProgressBar txtProgressBar
 #'
 #' @examples
-#' \dontrun{residences(data=data,ID="TagID",station="Receiver",
-#'# datetime="DateTimeUTC",cutoff=1,units="days")}
+#' \dontrun{residences(data=detections,ID="TagID",station="Receiver",
+#' datetime="DateTimeUTC",cutoff=1,units="days")}
 
 residences<-function(data,ID,station,datetime,cutoff,units){
  # Create list of unique IDs

R/stationchange.R

@@ -33,6 +33,8 @@
 #' @param to.station a string of the name of the column in `ddd` that contains
 #' the station/location names where drifting detections may move to. Must
 #' be identical to the station/location names in `data`.
+#' @param progressbar option to display progress bar as function is run. Default
+#' is TRUE.
 #'
 #' @return a dataframe with one row for each tag ID, including the date/time of
 #' the residence start at the most recent station or location, the date/time of
@@ -47,7 +49,7 @@
 stationchange<-function(data,type="mort",ID,station,res.start="auto",
  res.end="auto",residences="auto",
  singles=TRUE,drift=FALSE,ddd=NULL,units=NULL,from.station=NULL,
- to.station=NULL){
+ to.station=NULL,progressbar=TRUE){
 
  if (type %in% c("actel","vtrack")&is(data,"list")){
  data<-extractres(data=data,type=type)
@@ -91,7 +93,9 @@ stationchange<-function(data,type="mort",ID,station,res.start="auto",
 
  if (drift==FALSE&
  !is(data[[station]],"list")){
- pb<-txtProgressBar(1,length(tag),style=3)
+ if (progressbar==TRUE){
+ pb<-txtProgressBar(1,length(tag),style=3)
+ }
  for (i in 1:length(tag)){
  res.temp<-data[data[[ID]]==tag[i],]
  # Order by time
@@ -130,7 +134,9 @@ stationchange<-function(data,type="mort",ID,station,res.start="auto",
  else if (nrow(res.temp)==1){
  stn.change[nrow(stn.change)+1,]<-res.temp[1,]
  }
- setTxtProgressBar(pb,i)
+ if (progressbar==TRUE){
+ setTxtProgressBar(pb,i)
+ }
  }
  }
 
@@ -208,6 +214,8 @@ stationchange<-function(data,type="mort",ID,station,res.start="auto",
 #' recent station or location change. Must use the same column names as `data`.
 #' @param drift indicates if drift residence events should be included in
 #' determining the maximum residence duration
+#' @param progressbar option to display progress bar as function is run. Default
+#' is TRUE.
 #'
 #' @return a dataframe with the residence information for the longest residence
 #' for each tag ID that occurred before the most recent station/location change.
@@ -217,10 +225,12 @@ stationchange<-function(data,type="mort",ID,station,res.start="auto",
 #' \dontrun{resmax(data=res.events,ID="TagID",station="Receiver",
 #' res.start="StartUTC",residences="ResidencesLength.days",stnchange=station.change)}
 resmax<-function(data,ID,station,res.start,
- residences,stnchange,drift=FALSE){
+ residences,stnchange,drift=FALSE,progressbar=TRUE){
  res.max<-data[0,]
 
- pb<-txtProgressBar(1,nrow(stnchange),style=3)
+ if (progressbar==TRUE){
+ pb<-txtProgressBar(1,nrow(stnchange),style=3)
+ }
  for (i in 1:nrow(stnchange)){
  # Subset residences for ID i, where res.start < res.start of stnchange
  res.temp<-data[data[[ID]]==stnchange[[ID]][i]&
@@ -245,7 +255,9 @@ resmax<-function(data,ID,station,res.start,
  }
  }
  }
- setTxtProgressBar(pb,i)
+ if (progressbar==TRUE){
+ setTxtProgressBar(pb,i)
+ }
  }
 
  res.max