RWildbook (version 0.9.3)

markedData: Format Wildbook data for mark-recaputure analysis

Description

Format data from searchWB function in RWildbook package for mark-recapture analysis with marked and RMark packages.

Usage

markedData(data, varname_of_capturetime = "dateInMilliseconds",
  varlist = c("individualID"), start.dates, end.dates = NULL,
  date_format = "%Y-%m-%d", origin = "1970-01-01", removeZeros = TRUE)

Arguments

data

The raw data set from searchWB function in RWildbook package.

varname_of_capturetime

A character object which is the variable name for capture/encounter sighted time.

varlist

A character vector of the names of variables for mark-recapture analysis.

start.dates

A character vector of dates which are the start dates of the capture occasions. The elements should be in the form of date_format.

end.dates

A character vector of dates which are the end dates of the capture occasions. The elements should be in the form of date_format.

date_format

The format for all the arguments of date value.

origin

A point of time which set to be zero in millisecond.

removeZeros

If TRUE (default) then individuals with no captures are removed from the data.

Details

The markedData function format the wildbook data set that users search with the searchWB fucntion for the mark-recapture analysis with mark and RMark package. In marked package, users can process a certain form of data set with process.data function in marked package. The markedData function reutrns data set which can be the input data set of process.data.

Defalut NULL value for end.dates argument

The default value for end.date argument are NULL which means the capture occasion intervals are divided by the elements of start.date argument. In this case, the end date of the last capture occasion is the value of Sys.Date().

The class of output The class of the ouput of markedData is "data.table" and "data.frame". With installing the data.table package, the ouput is a data.table, otherwise it is a data.frame. That means users can process the data with data.table package. Also users can directly process the output with process.data function in marked package.

Examples

# NOT RUN {
# }
# NOT RUN {
## You will need to supply your own login information for whaleshark.org to
## run these examples.

## Load packages
library(marked)

## Extract data for individual A-001 through A-099
data1 <- searchWB(username="username",
                  password="password",
                  baseURL ="whaleshark.org",
                  object="Encounter",
                  individualID=paste0("A-0",rep(0:9,rep(10,10)),rep(0:9,10))[-1])

## Define start and end dates of capture occasions
start.dates1 <- paste0(1998:2016,"-01-01") #Define the start.date value
end.dates1 <- paste0(1998:2016,"-04-01") #Define the end.date value

## Format data for use in marked
markedData1.1 <- markedData(data = data1,
                             varname_of_capturetime = "dateInMilliseconds",
                             varlist = c("individualID"),
                             start.dates = start.dates1,
                             end.dates = NULL,
                             date_format = "%Y-%m-%d",
                             origin = "1970-01-01",
                             removeZeros = TRUE)


## Fit simple CJS model in marked
markedData1.proc=process.data(markedData1.1,model="CJS",begin.time=1)
markedData1.ddl=make.design.data(markedData1.proc)
markedData1.cjs=crm(markedData1.proc,
                    markedData1.ddl,
                    model.parameters=list(Phi=list(formula=~time),p=list(formula=~time)))

## Format data including location as a covariate
markedData1.2 <- markedData(data = data1,
                           varname_of_capturetime = "dateInMilliseconds",
                           varlist = c("individualID","locationID"),
                           start.dates = start.dates1,
                           end.dates = end.dates1,
                           date_format = "%Y-%m-%d",
                           origin = "1970-01-01")
# }
# NOT RUN {
# }