Rcapture-package {Rcapture} | R Documentation |
Estimation of abundance and other demographic parameters for closed populations, open populations and the robust design in capture-recapture experiments using loglinear models.
Package: | Rcapture |
Type: | Package |
Version: | 1.2-0 |
Date: | 2009-04-27 |
License: | GPL |
DESCRIPTION OF THE ACCEPTED DATA SET FORMATS
A capture-recapture data set is given to the various Rcapture functions through the X
argument. X
must be a numeric matrix. The arguments dfreq
and dtype
indicate the format of the matrix. Each have two possible values, meaning that a total of four data set formats are possible with Rcapture.
1- If dfreq=FALSE
and dtype="hist"
, the default, X
has one row per unit captured in the experiment. Each row is an observed capture history. It must contain only zeros and ones; the number one indicates a capture. In this case, the number of columns in the table represents the number of capture occasions in the experiment (noted t). Here is a fictive example of a data set of this type for t=2:
1 1
1 1
1 0
1 0
1 0
1 0
0 1
2- If dfreq=TRUE
and dtype="hist"
, X
contains one row per capture history followed by its frequency. In that case, X
has t+1 columns. As for the format presented previously, the first t columns of X
, identifying the capture histories, must contain only zeros and ones. The number one indicates a capture. In this format, the example data set is represented by the following matrix:
1 1 2
1 0 4
0 1 1
3- If dfreq=FALSE
and dtype="nbcap"
, X
is simply a vector of numbers of captures. The length of the vector is n, the number of captured units. In this format, the example data set looks like:
2 2 1 1 1 1 1
4- If dfreq=TRUE
and dtype="nbcap"
, X
is a 2 columns matrix. The first column contains the numbers of captures, the second columns contains the observed frequencies. In this format, the example data is:
2 2
1 5
Only few functions have the dtype
argument. Functions without dtype
argument accept only a data matrix X
of the form dtype="hist"
. So the first two formats listed above are the most commun.
Formats with dtype="nbcap"
are useful for experiments with a large number of capture occasions t. Often, no units will be caugth a large number of times, and the data set will contain no observations for t captures. Therefore, the number of capture occasions t cannot be deduced from X
as it can be when dtype="hist"
. So if one gives a data matrix X
with dtype="nbcap"
, one must also provide t
, the number of capture occasions, as an additional argument.
For now, the data formats with dtype="nbcap"
are not generalized to the robust design. So dtype
is not an argument of the robustd.0
function.
Sophie Baillargeon Sophie.Baillargeon@mat.ulaval.ca and
Louis-Paul Rivest Louis-Paul.Rivest@mat.ulaval.ca
Baillargeon, S. and Rivest, L.P. (2007) Rcapture: Loglinear models for capture-recapture in R. Journal of Statistical Software, 19(5), http://www.jstatsoft.org/v19/i05.
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Rivest, L.P. and Levesque, T. (2001) Improved log-linear model estimators of abundance in capture-recapture experiments. Canadian Journal of Statistics, 29, 555–572.
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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.
Rivest, L.P. (2008) Why a time effect often has a limited impact on capture-recapture estimates in closed populations. Canadian Journal of Statistics, 36(1), 75–84.