| 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)