extract_histories: Convert Unique Event Identifier Event Data into Multiple...

In fellstat/shinyrecap: Shiny User Interface for Multiple Source Capture Recapture Models

Convert Unique Event Identifier Event Data into Multiple Source Capture Recapture Histories

Description

Convert Unique Event Identifier Event Data into Multiple Source Capture Recapture Histories

Usage

extract_histories(datasets, count_name, cov_names = c())

Arguments

datasets	An ordered list of capture event datasets. The first j-1 columns of the jth dataset should be a 0 or 1 indicator of beng captured in a previous event.
count_name	The name of the column holding the counts of the number of individuals.
cov_names	A character vector of column names for covariates to stratify by.

Value

A dataframe. The first length(datasets) columns of which contain all possible permutations of capture histories. The "__count__" column contains the number of observed cases. Other columns are the stratifying covariates.

Examples

# First sample
dat1 <- data.frame(
  count=c(55,43),
  c1=c("m","f"),
  stringsAsFactors = FALSE
)

# Second sample
dat2 <- data.frame(
  id1=c(1,0,1,0),
  count=c(10,11,5,12),
  c1=c("m","m","f","f"),
  stringsAsFactors = FALSE
)

# Third Sample
dat3 <- data.frame(
  id1=c(1,0,1,0,1,0,1,0),
  id2=c(1,1,1,1,0,0,0,0),
  count=c(2,3,4,3,2,30,4,30),
  c1=c("m","m","f","f","m","m","f","f"),
  stringsAsFactors = FALSE
)

# Fourth Sample
dat4 <- data.frame(
  id1=c(1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0),
  id2=c(1,1,1,1,0,0,0,0,1,1,1,1,0,0,0,0),
  id3=c(1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0),
  count=c(1,1,1,1,0,1,0,0,1,1,1,1,1,0,1,10),
  c1=c("m","m","f","f","m","m","f","f","m","m","f","f","m","m","f","f"),
  stringsAsFactors = FALSE
)

# Combine 4 capture recatpure events together
datasets <- list(dat1,dat2,dat3,dat4)

# Get four sample capture recapture histories from unique event observations
extract_histories(datasets, "count")

# Stratify by a covariate
extract_histories(datasets, "count", cov_names="c1")

# Two sample capture recapture
extract_histories(datasets[1:2], "count", cov_names="c1")

fellstat/shinyrecap documentation built on Jan. 7, 2023, 10:51 p.m.