import.chdata: Import capture-recapture data sets from space or...

In RMark: R Code for Mark Analysis

Import capture-recapture data sets from space or tab-delimited files

Description

A relatively flexible function to import capture history data sets that include a capture (encounter) history read in as a character string and an arbitrary number of user specified covariates for the analysis.

Usage

import.chdata(
  filename,
  header = TRUE,
  field.names = NULL,
  field.types = NULL,
  use.comments = TRUE
)

Arguments

filename	file name and path for file to be imported; fields in file should be space or tab-delimited
header	TRUE/FALSE; if TRUE first line is name of variables
field.names	vector of field names if header=FALSE; first field should always be ch - capture history remaining number of fields and their names are arbitrary
field.types	vector identifying whether fields (beyond ch) are numeric ("n") or factor ("f") or should be skipped ("s")
use.comments	if TRUE values within /* and */ on data lines are used as row.names for the RMark dataframe. Only use this option if they are unique values.

Details

This function was written both to be a useful tool to import data and as an example for more specific import functions that a user may want to write for data files that do not satisfy the requirements of this function. In particular this function will not handle files with fixed-width format files that do not contain appropriate tab or space delimiters between the fields. It also requires that the first field is the capture (encounter) history which is named "ch" and is a character string. The remaining fields are arbitrary in number and type and are user defined based on the arguments to the functions. Variables that will be used for grouping should be defined with the field.type="f". Numeric individual covariates (e.g., weight) should be input as field.type="n". Fields in the file that should not be imported should be assigned field.type="s". The examples below illustrate different uses of the calling arguments to import several different data sets that meet the modest requirements of this function.

If you specify a frequency for the encounter history, the field name must be freq. If you use any other name or spelling it will not be recognized and the default frequency of 1 will be used for each encounter history. This function should not be used with files structured for input into the MARK interface. To use those types of files, see convert.inp. It is not neccessary to use either function to create a dataframe for RMark. All you need to is create a dataframe that meets the specification of the RMark format. For example, if you are simulating data, you only need to create a dataframe with the fields ch, freq (if differs from 1) and any covariates you want and then you can use process.data on the dataframe.

If you have comments in your data file, they should not have a column header (field name in first row). If use.comments=TRUE the comments are used as row names of the data frame and they must be unique. If use.comments=FALSE and the file contains comments they are stripped out.

Value

A dataframe for use in MARK analysis with obligate ch character field representing the capture (encounter) history and optional covariate/grouping variables.

Author(s)

Jeff Laake

See Also

export.chdata

Examples

# This example is excluded from testing to reduce package check time
pathtodata=paste(path.package("RMark"),"extdata",sep="/")
example.data<-import.chdata(paste(pathtodata,"example.data.txt",sep="/"),
      field.types=c("n","f","f","f"))
edwards.eberhardt<-import.chdata(paste(pathtodata,"edwardsandeberhardt.txt",
      sep="/"),field.names="ch",header=FALSE)
dipper<-import.chdata(paste(pathtodata,"dipper.txt",sep="/"),
      field.names=c("ch","sex"),header=FALSE)

RMark documentation built on Aug. 14, 2022, 1:05 a.m.