wi: Computation of Selection Ratios for Habitat Selection Studies.

Description

These functions compute the resource selection ratios (wi) for design I, II and III data types, with resources defined by several categories. Basic tests are also provided.

Usage

widesI(u, a, avknown = TRUE, alpha = 0.05)
widesII(u, a, avknown = TRUE, alpha = 0.05)
widesIII(u, a, avknown = TRUE, alpha = 0.05)
print.wiI(x, ...)
print.wiII(x, ...)
print.wiIII(x, ...)
plot.wi(x, caxis = 0.7, clab = 1, ylog = FALSE, errbar = c("CI", "SE"),
        main = "Manly selectivity measure", noorder = TRUE, ...)

Arguments

for widesI, a vector with named elements describing the sample of used resource units. For widesII and widesIII a matrix or a data frame giving the number of used resource units for each animal (in ro

for widesI and widesII, a vector with named elements describing the sample or the proportion of available resource units. For widesIII a matrix or a data frame giving the number or the proportion of a

avknown

logical. TRUE if the available proportions are known, and FALSE if they are estimated

alpha

the threshold value for the tests and confidence intervals

an object of class wi

caxis

character size on axes to be passed to par("cex.axis")

clab

character size of axes labels to be passed to par("cex.lab")

ylog

logical. If TRUE, the selection ratios are plotted on a log scale

errbar

a character string. Type of error bars: either "CI" for confidence intervals or "SE" for standard errors

main

a character string. The title of the graph

noorder

logical. If TRUE, the habitat categories are ordered on the graph in decreasing order of their preference. If FALSE, they are not ordered (i.e. they are in the same order as the columns in used and available<

...

additionnal arguments to be passed to the function plot

Value

widesI returns a list of the class wiI. widesII returns a list of class wiII. widesIII returns a list of class wiIII. These objects are all inheriting from the class wi. They have the following components:
used.propthe proportion of use for each resource type.
avail.propthe proportion of available resources.
withe Manly selectivity measure (selection ratio: used/available).
se.withe standard error of the selection ratios.
comparisonsa list with the following components:[object Object],[object Object],[object Object],[object Object]
profilethe profile of preferences: resource types are sorted so that the left type is the most preferred and the right type is the most avoided. Habitats for which the selection ratios are not significant are connected by a line.
alphathe parameter alpha of this function.
avknownthe parameter avknown of this function.
se.usedonly for designs I, the standard error of the proportion of use.
se.availonly for designs I, the standard error of the available proportion.
chisquwionly for designs I, the results of Chi-Square tests of the hypothesis that the selection ratios are in average equals to zero.
Bionly for designs I, equals to wi/sum(wi).
Khi2Ponly for designs I, test of random resource use (Pearson statistic).
Khi2Lonly for designs I, test of random resource use (Log-likelihood statistic).
Khi2L1only for designs II, test of identical use of habitat by all animals.
Khi2L2only for designs II, test of overall habitat selection.
Khi2L2MinusL1only for designs II, test of hypothesis that animals are on average using resources in proportion to availability, irrespective of whether they are the same or not (= Khi2L2 - Khi2L1).
wijonly for designs II and III, a matrix with the selection ratios for all animals and all resource categories.
ICwiupperonly for designs II and III, the upper limit of the confidence intervals on the selection ratios.
ICwiloweronly for designs II and III, the lower limit of the confidence intervals on the selection ratios.
Khi2Ljonly for designs III, the test of habitat selection for each animal.
Khi2Lonly for designs III, the global test of overall habitat selection.

Details

widesI may be used to explore resource selection by animals, when designs I are involved (habitat use and availability are measured at the population level - animals are not identified). The function tests habitat selection with the Khi2 of Pearson and log-likelihood Khi2 (recommended, see Manly et al. 2003). The Manly selectivity measure (selection ratio = used/available) is computed, the preference / avoidance is tested for each habitat, and the differences between selection ratios are computed and tested. widesII computes the selection ratios with design II data (same availability for all animals, but use measured for each one). Tests of identical habitat use for all animals, and of habitat selection are also provided. widesIII computes the selection ratios for design III data (when the use and the availability are measured for each animal - see examples on the wild boar below). Habitat selection is tested using a Chi-square for each animal, and the overall habitat selection is also tested.

References

Manly B.F.J., McDonald L.L., Thomas, D.L., McDonald, T.L. & Erickson, W.P. (2003) Resource selection by animals - Statistical design and Analysis for field studies. Second edition London: Kluwer academic publishers. Thomas D. L. and Taylor E. J. (1990) Study designs and tests for comparing resource use and availability. Journal of Wildlife Management, 54, 322--330.

Examples

Run this code

############################
## Example of moose (Manly et al., 2003, p.52)
## Known available proportions on design I data
moose.avail <- c(0.34, 0.101, 0.104, 0.455)
moose.used <- c(25, 22, 30, 40)
names(moose.used) <- c("InBurnInterior",
                     "InBurnEdge",
                     "OutOfBurnEdge",
                     "OutOfBurnFurther")
names(moose.avail) <- names(moose.used)
## Computation of wi
(wiRatio <- widesI(moose.used, moose.avail))

## plot the values of the selection ratios
opar <- par(mfrow=c(2,2))
plot(wiRatio)

par(opar)




############################
## Example of Elk (Manly et al., 2003, p.62)
## Estimated available proportions on design I data
elk.avail <- c(15, 61, 84, 40)
elk.used <- c(3, 90, 181, 51)
names(elk.used) <- c("0%", "1-25%", "26-75%", ">75%")
names(elk.avail) <- names(elk.used)
## Computation of wi
(wiRatio <- widesI(elk.used, elk.avail, avknown=FALSE))

## plot the values of the selection ratios
opar <- par(mfrow=c(2,2))
plot(wiRatio)

par(opar)




############################
## Example of Bighorn (Manly et al., 2003, p.67)
## Known available proportions on design II data
data(bighorn)
## Computation of wi
(wi <- widesII(bighorn$used, bighorn$availT, alpha = 0.1))

## plot the values of the selection ratios
opar <- par(mfrow=c(2,2))
plot(wi)



############################
## Example of Bighorn (Manly et al., 2003, p.74)
## Estimated available proportions on design II data
## Computation of wi
(wi <- widesII(bighorn$used, bighorn$availE, avknown = FALSE, alpha = 0.1))

## plot the values of the selection ratios
plot(wi)

par(opar)


############################
## Example of Wild boar
## Estimated available proportions on design III data
data(puechdesIII)
used <- puechdesIII$used
available <- puechdesIII$available

## calculation of the selectio ratios
## with sampled availability
(i <- widesIII(used,available, avknown = FALSE, alpha = 0.1))

opar <- par(mfrow = c(2,2))
plot(i)

par(opar)

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