Description Usage Arguments Value Author(s) References See Also Examples
View source: R/estimateNmales.R
The function estimateNmales
can be used to obtain estimates of
the number of male capercaillie in each geographic region of the
Pyrenees mountains from a model of the lek count data and a model of
the probability of presence of unknown leks.
The function getTotal
can be used to obtain estimate of the
number of male capercaillie in the whole area.
The function changeRate
can be used to obtain estimate of the
rate of change of the number of males between two periods.
The functions showChangeRate
and distritime
can be used
to plot the posterior distribution of rate of changes between two
periods and the posterior distribution of the number of males for each
period respectively. They rely on the package ggplot2, and can be
combined with other functions from this package (e.g. ggtitle
to add a title, etc.).
The function summary
can be used to display summary statistics
on the number of males in a region of interest (or on the whole
area).
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | estimateNmales(coefsCounts, coefsUL, gridFrame, NKAL, NKIL,
what = c("tot", "kalc", "kilc", "ulc", "ul"))
## S3 method for class 'estimateMales'
print(x, ...)
getTotal(x, ...)
changeRate(object, GR, changeRatePeriods = c(1, 5))
## S3 method for class 'estimateMales'
summary(object, GR, CIlevel = 80,
changeRatePeriods = c(1, 5),
threshold = c(-10, 10), ...)
showChangeRate(object, GR, changeRatePeriods = c(1, 5),
quantiles = c(0.1, 0.5, 0.9))
distritime(x, xlab = "Period",
ylab = "Number of cocks", trim = 0.95)
|
coefsCounts |
object of class |
coefsUL |
object of class |
gridFrame |
A data frame containing the list of grid cells present in the Pyrenees
mountains (see |
NKAL |
A vector of length 5 (the 5 geographic regions) containing the number of known active leks in each geographic region. |
NKIL |
A vector of length 5 (the 5 geographic regions) containing the number of known indeterminate leks in each geographic region. |
what |
character string indicating in which compartment should the number
of males be estimated:
|
object,x |
object of class |
GR |
integer value indicating the number of the geographic region for which a summary is required. If missing, the summary is shown for the whole area. |
CIlevel |
numeric value indicating the level for credible intervals |
changeRatePeriods |
vector of length two indicating the number of the two periods used to calculate the change rate (defaulting to the calculation of the rate between the first and fifth period). |
threshold |
vector of length two indicating the change rate thresholds (in percent) defining a decrease/stability/increase of the population size. |
quantiles |
vector of numeric values indicating which quantile should be shown on the plot. |
xlab |
character string indicating the label for the x axis |
ylab |
character string indicating the label for the y axis |
trim |
numeric value indicating how to trim the distribution to
avoid outliers compressing the display. The |
... |
additional arguments to be passed to other functions. |
An object of class "estimateMales"
, which is a list with 5
components (the 5 regions), each component being a matrix with M rows
(MCMC iterations) and P columns (periods), containing M simulations of
the number of males in each region for each period under the model.
The function getTotal
returns a matrix with M rows (MCMC
iterations) and P columns (periods), containing M simulations of
the number of males on the whole area for each period under the model.
The function changeRate
returns a vector with M elements (MCMC
iterations) containing the M simulations of the rate of change of the
number of males in the region (or on the whole area) between the two
periods indicated in the arguments.
The summary returned by the function summary
can be stored as a
list.
Clement Calenge clement.calenge@ofb.gouv.fr
Calenge C., Menoni E., Milhau B., Foulche K, Chiffard J., Marchandeau S. (in prep.). The participatory monitoring of the capercaillie in the French Pyrenees.
getTotal
for further functions to work with objects of
class "estimateMales"
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ## Number of known active and indeterminate leks
NKAL <- c(14L, 64L, 76L, 48L, 46L)
NKIL <- c(6L, 80L, 102L, 32L, 96L)
## The list of coefficients are stored as datasets
nm <- estimateNmales(coefModelCountDetectBinREY, coefModelULPresence,
gridFrame, NKAL, NKIL)
## Summary for the whole area
summary(nm)
## show the distribution of the number of males
## on the whole area
distritime(getTotal(nm))
## Rate of change between period 1 and 5
showChangeRate(nm)
|
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