closedp.custom {Rcapture} | R Documentation |
This function is deprecated, please use closedpCI.t
instead.
The closedp.mX
function fits a loglinear model given a design matrix mX
. The closedp.h
function fits Mh or Mth models for which the form of the column for heterogeneity in the design matrix is determined by the user.
closedp.mX(X, dfreq=FALSE, mX, mname="Customized model") closedp.h(X, dfreq=FALSE, m="Mh", h="Poisson", a=2) ## S3 method for class 'closedp.custom': print(x, ...) ## S3 method for class 'closedp.custom': boxplot(x, ...)
X |
The matrix of the observed capture histories (see Rcapture-package for a description of the accepted formats). |
dfreq |
A logical. By default FALSE, which means that X has one row per unit. If TRUE, it indicates that the matrix X contains frequencies in its last column. |
mX |
The design matrix of the loglinear model. In this matrix, the order of the capture histories is as defined in the histpos.t function. |
mname |
A character string specifying the name of the customized model. |
m |
A character string indicating the model to fit, either "Mh"=Mh model or "Mth"=Mth model |
h |
The character string "Poisson" (2^k-1) or a numerical function taking only one argument specifying the form of the column for heterogeneity in the design matrix. |
a |
The value of the exponent's base for a Poisson model. |
x |
An object, produced by the closedp.mX or the closedp.h function, to print or to plot. |
... |
Further arguments passed to or from other methods. |
An intercept is added to the model. Therefore, the mX matrix must not contain a column of ones.
The abundance estimation is calculated as the number of captured units plus the exponential of the intercept. Therefore, these functions are not suited for models with a behavioral effect.
In closedp.h
, the argument h
cannot take the value "Chao" or "Darroch" because these models are already fitted by the closedp
function.
The boxplot.closedp.custom
function produces a boxplot of the pearson residuals of the customized model.
n |
The number of captured units |
results |
A table containing the estimated population size, the standard error of estimation, the deviance, the number of degrees of freedom and the Akaike criteria. |
glm |
The 'glm' object obtained from fitting the model. |
These functions use the glm
function of the stats
package.
Sophie Baillargeon sbaillar@mat.ulaval.ca and Louis-Paul Rivest lpr@mat.ulaval.ca
Rivest, L.P. and Baillargeon, S. (2007) Applications and extensions of Chao's moment estimator for the size of a closed population. Biometrics, 63(4), 999–1006.
data(HIV) mat<-histpos.t(4) mX2<-cbind(mat,mat[,1]*mat[,2]) closedp.mX(HIV,dfreq=TRUE,mX=mX2) data(mvole) period3<-mvole[,11:15] psi <- function(x) { -log(3.5 + x) + log(3.5) } closedp.h(period3, h = psi)