import.rm: Import summary statistics from removal experiments for...

In DistanceDevelopment/WiSP: Wildlife Simulation Package (wisp)

Description

Import data from actual field data for analysis with the removal estimator of Wisp.

Usage

import.rm(catch)

Arguments

catch

Vector of catch statistics, with length equal to number of sampling occasions

Value

Object of class sample.rm that can be submitted to point.est.rm for abundance estimation

Author(s)

David Borchers, [e-mail]

References

Borchers, Buckland, and Zucchini (2002), Estimating animal abundance: closed populations. Chapter 5 http://www.ruwpa.st-and.ac.uk/estimating.abundance

See Also

generate.sample.rm, point.est.rm

Examples

#  an external file containing data to be read (called 'egdat.txt')
#------------------------------------------
#Habitat	Year	Season	Block	occ1	occ2	occ3	occ4	occ5	occ6	occ7	occ8	occ9
#Forest	2001	Summer	A	4	1	3	2	0	1	2	0	0
#Forest	2001	Summer	B	4	3	3	0	1	0	0	0	0
#Forest	2001	Summer	C	6	3	2	2	1	0	0	2	1
#Forest	2001	Summer	D	3	1	2	2	0	0	1	1	0
#Forest	2001	Summer	E	1	1	2	1	0	0	0	0	0
#Forest	2001	Winter	F	3	4	0	1	0	1	0	0	0
#Forest	2001	Winter	G	1	2	1	1	0	0	0	0	0
#Forest	2001	Winter	H	3	1	2	0	1	0	0	0	0
#Forest	2001	Winter	A	3	2	2	1	0	1	0	1	0
#Forest	2001	Winter	B	4	3	2	0	2	1	1	0	0
#------------------------------------------
# need to put file egdat.txt into working directory before executing next line:
rdat = read.table(file="egdat.txt",header=TRUE,sep="\t")

# Each row of rdat is a separate removal method survey data
# Here's some code to import the caputre columns of any given 
# row (row=1 here) of the file, convert it to a WiSP object and estimate abundance
row <- 1 # choose row
occasions <- 5:13 # cols with capture occasion data (need to set this manually)
max.occ <- length(occasions) # max number occasions in rdat
catch <- rdat[row,occasions] # get capture history rows
catch <- as.vector(catch[!is.na(catch)]) # remove missing values at end of row and convert to vector
#
# So now catch is a vector containing just the removal data from a single survey
samp <- import.rm(catch) # convert to wisp object
est <- point.est.rm(samp) # estimate abundance
summary(est)
plot(est)

DistanceDevelopment/WiSP documentation built on Sept. 18, 2020, 2:55 p.m.