update after adding example dataset

R/data.R

@@ -102,3 +102,27 @@ NULL
 #'@usage data(seasons)
 #'@format A data frame with 5 rows (years) and 2 variables.
 NULL
+
+#'Example of new acoustic telemetry detection data
+#'
+#'These are fabricated detection data to demonstrate the use of the review
+#'function.
+#'
+#'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 new.data
+#'@usage data(new.data)
+#'@format A data frame with 35 rows (observations) and 3 variables.
+NULL

R/mort.R

@@ -351,8 +351,8 @@ morts<-function(data,type="mort",ID,station,res.start="auto",res.end="auto",
  morts[nrow(morts)+1,]<-res.temp[j[k],]
  }
  }
+ setTxtProgressBar(pb,i)
  }
- setTxtProgressBar(pb,i)
  }
  }
 
@@ -367,47 +367,49 @@ morts<-function(data,type="mort",ID,station,res.start="auto",res.end="auto",
  for (i in 1:nrow(sc2)){
  res.temp<-data.morts[data.morts[[ID]]==sc2[[ID]][i],]
  res.temp<-res.temp[order(res.temp[[res.start]]),]
- repeat {
- if (res.temp[[station]][nrow(res.temp)]=="Break"){
- res.temp<-res.temp[-nrow(res.temp),]
- }
- else {break}
- }
- if (any(res.temp[[station]]=="Break")){
- # Need two values, and determine which is lower
- # Value 1: difftime between end of most recent residence and station change (sc2)
- dt1<-difftime(res.temp[[res.end]][nrow(res.temp)],
- sc2[[res.start]][i],
- units=units)
- # Value 2: difftime between end of most recent residence and most recent break
- k<-(which(res.temp[[res.start]]==max(res.temp[[res.start]][res.temp[[station]]=="Break"])))+1
- dt2<-difftime(res.temp[[res.end]][nrow(res.temp)],
- res.temp[[res.start]][k],
- units=units)
- comp<-min(dt1,dt2)
- }
- else {
- comp<-difftime(res.temp[[res.end]][nrow(res.temp)],
- sc2[[res.start]][i],
- units=units)
- }
- # If the cumulative residence at the most recent station is longer than the
- # threshold of max.rescml
- if (comp>max.rescml){
- # If the ID is already in morts
- if (sc2[[ID]][i] %in% morts[[ID]]){
- # Identify which row
- j<-which(morts[[ID]]==sc2[[ID]][i])
- # If the residence currently in res.morts ocurred later
- # than the cumulative residence period
- if (morts[[res.start]][j]>sc2[[res.start]][i]){
- # Adjust the start time to the earlier date
- morts[j,]<-sc2[i,]
+ if (nrow(res.temp)>0){
+ repeat {
+ if (res.temp[[station]][nrow(res.temp)]=="Break"){
+ res.temp<-res.temp[-nrow(res.temp),]
  }
+ else {break}
+ }
+ if (any(res.temp[[station]]=="Break")){
+ # Need two values, and determine which is lower
+ # Value 1: difftime between end of most recent residence and station change (sc2)
+ dt1<-difftime(res.temp[[res.end]][nrow(res.temp)],
+ sc2[[res.start]][i],
+ units=units)
+ # Value 2: difftime between end of most recent residence and most recent break
+ k<-(which(res.temp[[res.start]]==max(res.temp[[res.start]][res.temp[[station]]=="Break"])))+1
+ dt2<-difftime(res.temp[[res.end]][nrow(res.temp)],
+ res.temp[[res.start]][k],
+ units=units)
+ comp<-min(dt1,dt2)
  }
- # If the ID is not yet in morts
  else {
- morts[nrow(morts)+1,]<-sc2[i,]
+ comp<-difftime(res.temp[[res.end]][nrow(res.temp)],
+ sc2[[res.start]][i],
+ units=units)
+ }
+ # If the cumulative residence at the most recent station is longer than the
+ # threshold of max.rescml
+ if (comp>max.rescml){
+ # If the ID is already in morts
+ if (sc2[[ID]][i] %in% morts[[ID]]){
+ # Identify which row
+ j<-which(morts[[ID]]==sc2[[ID]][i])
+ # If the residence currently in res.morts ocurred later
+ # than the cumulative residence period
+ if (morts[[res.start]][j]>sc2[[res.start]][i]){
+ # Adjust the start time to the earlier date
+ morts[j,]<-sc2[i,]
+ }
+ }
+ # If the ID is not yet in morts
+ else {
+ morts[nrow(morts)+1,]<-sc2[i,]
+ }
  }
  }
  setTxtProgressBar(pb,i)
@@ -679,7 +681,7 @@ infrequent<-function(data,type="mort",ID,station,res.start="auto",
  }
  }
  else {
- inf.morts[nrow(inf.morts)+1,]<-res.temp[1,]
+ inf.morts[nrow(inf.morts)+1,]<-res.temp[j,]
  }
  }
  }

R/options.R

@@ -218,12 +218,12 @@ drift<-function(data,type,ID,station,res.start="auto",res.end="auto",
  else {
  for (k in 1:length(j)){
  if ((res.temp[[station]][j[k]+1] %in%
- ddd[[to.station]][ddd[[from.station]]==res.temp[[station]][j[k]]])&
+ ddd[[to.station]][ddd[[from.station]]==res.temp[[station]][[j[k]]][length(res.temp[[station]][[j[k]]])]])&
  difftime(res.temp[[res.start]][j[k]+1],
  res.temp[[res.end]][j[k]],
  units=cutoff.units)<cutoff){
  res.temp[[res.start]][j[k]+1]<-res.temp[[res.start]][j[k]]
- res.temp[[station]][j[k]+1]<-res.temp[[station]][j[k]]
+ res.temp[[station]][[j[k]+1]]<-append(res.temp[[station]][[j[k]]],res.temp[[station]][[j[k]+1]])
  del<-c(del,j[k])
  }
  }
@@ -286,6 +286,8 @@ 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
+#' is TRUE.
 #'
 #' @return a dataframe in the same format as the input data, with residence
 #' events limited to the period(s) of interest.
@@ -297,7 +299,7 @@ drift<-function(data,type,ID,station,res.start="auto",res.end="auto",
 #' season.end="31-10")}
 season<-function(data,type="mort",ID,station,res.start="auto",res.end="auto",
  residences="auto",units="auto",season.start,
- season.end,overlap=TRUE){
+ season.end,overlap=TRUE,progressbar=TRUE){
 
  if (type %in% c("actel","vtrack")){
  data<-extractres(data=data,type=type)
@@ -400,9 +402,13 @@ season<-function(data,type="mort",ID,station,res.start="auto",res.end="auto",
  data.season<-data[0,]
 
  for (i in 1:length(season.start)){
- print(paste("season/period",i,"of",length(season.start)))
+ if (progressbar==TRUE){
+ print(paste("season/period",i,"of",length(season.start)))
+ }
  if (length(tag)>1){
- pb<-txtProgressBar(1,length(tag),style=3)
+ if (progressbar==TRUE){
+ pb<-txtProgressBar(1,length(tag),style=3)
+ }
  }
  for (j in 1:length(tag)){
  data.temp<-data[0,]
@@ -444,7 +450,9 @@ season<-function(data,type="mort",ID,station,res.start="auto",res.end="auto",
  }
  data.season<-rbind(data.season,data.temp)
  if (length(tag)>1){
- setTxtProgressBar(pb,j)
+ if (progressbar==TRUE){
+ setTxtProgressBar(pb,j)
+ }
  }
  }
  }

R/plot.R

@@ -45,6 +45,8 @@
 #' `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
+#' is TRUE.
 #'
 #' @return a ggplot2 plot. Additional arguments (e.g., formatting axes,
 #' legend, aes, manual colour scales) can be added as for any ggplot2 plot.
@@ -60,7 +62,8 @@ 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"){
+ facet.axis="x",facet.by="season",
+ progressbar=TRUE){
 
  if (!requireNamespace("ggplot2", quietly = TRUE)) {
  stop("Package \"ggplot2\" must be installed to use this function.",
@@ -134,8 +137,26 @@ mortsplot<-function(data,type,ID,station,res.start="auto",res.end="auto",
  }
  }
 
+ if (is(data[[station]],"list")){
+ data$station2<-as.character(NA)
+ for (i in 1:nrow(data)){
+ if (length(data[[station]][[i]])==1){
+ data$station2[i]<-data[[station]][[i]][1]
+ }
+ else {
+ stn.temp<-unique(data[[station]][[i]])
+ stn.temp<-stn.temp[order(stn.temp)]
+ stn.temp<-paste("Drift",paste(stn.temp,collapse=" "))
+ stn.temp<-gsub(" ","-",stn.temp)
+ data$station2[i]<-stn.temp
+ }
+ }
+ station<-"station2"
+ }
+
  if (!is.null(season.start)|
- !is.null(season.end)){
+ !is.null(season.end)|
+ facet.by=="year"){
  if (is.null(residences)){
  residences<-autofield(type=type,field="residences",data=data)
  }
@@ -148,10 +169,16 @@ mortsplot<-function(data,type,ID,station,res.start="auto",res.end="auto",
  if (units=="auto"){
  units<-autofield(type=type,field="units",data=data)
  }
- print("Extracting data from the period/season(s) of interest")
+ if (progressbar==TRUE){
+ print("Extracting data from the period/season(s) of interest")
+ }
+ if (is.null(season.start)&is.null(season.end)&facet.by=="year"){
+ season.start<-"01-01"
+ season.end<-"31-12"
+ }
  data<-season(data=data,type=type,ID=ID,station=station,res.start=res.start,res.end=res.end,
  residences=residences,units=units,season.start=season.start,
- season.end=season.end,overlap=FALSE)
+ season.end=season.end,overlap=FALSE,progressbar=FALSE)
  data<-data[data[[station]]!="Break",]
  if (!is(season.start,"POSIXt")){
  try(season.start<-as.POSIXct(season.start,tz="UTC"),silent=TRUE)
@@ -349,11 +376,13 @@ mortsplot<-function(data,type,ID,station,res.start="auto",res.end="auto",
  if (facet==TRUE){
  if (!is.null(data$Year)&facet.axis=="y"){
  plot<-plot+
- ggplot2::facet_grid(Year~.,scales="free",space="free_y")
+ ggplot2::facet_grid(Year~.,scales="free",space="free_y")+
+ scale_x_datetime(date_labels = "%b %d")
  }
  else if (!is.null(data$Year)&facet.axis=="x"){
  plot<-plot+
- ggplot2::facet_grid(.~Year,scales="free",space="free_x")
+ ggplot2::facet_grid(.~Year,scales="free",space="free_x")+
+ scale_x_datetime(date_labels = "%b %d")
  }
  else if (!is.null(data$Season)){
  plot<-plot+

R/review.R

@@ -72,8 +72,10 @@ review<-function(morts,new.data,old.data=NULL,type,ID,station,res.start="auto",
  stop("ID and station must be specified (i.e., cannot be 'auto') for format='mort'")
  }
 
- if (!(type %in% c("manual","actel"))&units!="auto"){
- unitcheck(type=type,units=units,data=data)
+ if (!is.null(ddd)){
+ if (!(type %in% c("manual","actel"))&units!="auto"){
+ unitcheck(type=type,units=units,data=data)
+ }
  }
 
  # Fill in auto fields

R/stationchange.R

@@ -288,6 +288,8 @@ resmax<-function(data,ID,station,res.start,
 #' @param units units of the duration of the residence events in `data`.
 #' @param stnchange a dataframe with the start time and location of the most
 #' recent station or location change. Must use the same column names as `data`.
+#' @param progressbar option to display progress bar as function is run. Default
+#' is TRUE.
 #'
 #' @return a dataframe with the cumulative residence information for each
 #' period where an animal was consecutively detected at a single station/location.
@@ -300,10 +302,12 @@ resmax<-function(data,ID,station,res.start,
 #' res.start="StartUTC",res.end="EndUTC",residences="ResidencesLength.days",
 #' units="days",stnchange=station.change)}
 resmaxcml<-function(data,ID,station,res.start,res.end,
- residences,units,stnchange){
+ residences,units,stnchange,progressbar=TRUE){
  res.maxcml<-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]&
@@ -388,7 +392,9 @@ resmaxcml<-function(data,ID,station,res.start,res.end,
  else {break}
  }
  }
- setTxtProgressBar(pb,i)
+ if (progressbar==TRUE){
+ setTxtProgressBar(pb,i)
+ }
  }
 
  res.maxcml[[residences]]<-difftime(res.maxcml[[res.end]],

README.Rmd

@@ -35,8 +35,6 @@ devtools::install_github("rosieluain/mort")
 ### Package contents
 Please see the package vignettes for more details, as well as guidelines and tips for the following functions.
 
-**Note:** vignettes are under development! We are currently developing a sample dataset, so there are some obvious gaps where there should be figures, tables, etc. These will be completed as soon as the sample dataset is done. 
-
 #### Data preparation and visualization
 
 `residences` condenses detection records into residence events, with a start time, end time, and duration. Residence events are used as the input for all other mort functions. 
@@ -71,27 +69,3 @@ These are functions that may be called by `morts` and/or `infrequent`, depending
 ### Disclaimer
 mort is brand new. Although it is has been tested extensively on a complex dataset, we expect that issues will arise as mort is applied to other datasets and systems. If you run into any issues or have any suggestions for improvements, please post an issue, and we'll see what we can do! 
 
-<!-- ## Example -->
-
-<!-- This is a basic example which shows you how to solve a common problem: -->
-
-<!-- ```{r example} -->
-<!-- library(mort) -->
-<!-- ## basic example code -->
-<!-- ``` -->
-
-<!-- What is special about using `README.Rmd` instead of just `README.md`? You can include R chunks like so: -->
-
-<!-- ```{r cars} -->
-<!-- summary(cars) -->
-<!-- ``` -->
-
-<!-- You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date. `devtools::build_readme()` is handy for this. You could also use GitHub Actions to re-render `README.Rmd` every time you push. An example workflow can be found here: <https://github.com/r-lib/actions/tree/v1/examples>. -->
-
-<!-- You can also embed plots, for example: -->
-
-<!-- ```{r pressure, echo = FALSE} -->
-<!-- plot(pressure) -->
-<!-- ``` -->
-
-<!-- In that case, don't forget to commit and push the resulting figure files, so they display on GitHub and CRAN. -->

README.md

@@ -39,11 +39,6 @@ devtools::install_github("rosieluain/mort")
 Please see the package vignettes for more details, as well as guidelines
 and tips for the following functions.
 
-**Note:** vignettes are under development! We are currently developing a
-sample dataset, so there are some obvious gaps where there should be
-figures, tables, etc. These will be completed as soon as the sample
-dataset is done.
-
 #### Data preparation and visualization
 
 `residences` condenses detection records into residence events, with a
@@ -108,20 +103,3 @@ complex dataset, we expect that issues will arise as mort is applied to
 other datasets and systems. If you run into any issues or have any
 suggestions for improvements, please post an issue, and we’ll see what
 we can do!
-
-<!-- ## Example -->
-<!-- This is a basic example which shows you how to solve a common problem: -->
-<!-- ```{r example} -->
-<!-- library(mort) -->
-<!-- ## basic example code -->
-<!-- ``` -->
-<!-- What is special about using `README.Rmd` instead of just `README.md`? You can include R chunks like so: -->
-<!-- ```{r cars} -->
-<!-- summary(cars) -->
-<!-- ``` -->
-<!-- You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date. `devtools::build_readme()` is handy for this. You could also use GitHub Actions to re-render `README.Rmd` every time you push. An example workflow can be found here: <https://github.com/r-lib/actions/tree/v1/examples>. -->
-<!-- You can also embed plots, for example: -->
-<!-- ```{r pressure, echo = FALSE} -->
-<!-- plot(pressure) -->
-<!-- ``` -->
-<!-- In that case, don't forget to commit and push the resulting figure files, so they display on GitHub and CRAN. -->