# SPAS

Stratified Petersen Analysis System in R

## Versions and installation

**CRAN** Download the **SPAS**
package

**Github** To install the latest development version
from Github, install the newest version of the **devtools**
package; then run

```
devtools::install_github("cschwarz-stat-sfu-ca/SPAS", dependencies = TRUE,
build_vignettes = TRUE)
```

## Features

This is an R version of the Windoze program SPAS to estimate
population abundance using a Stratified Petersen Estimator (Darroch
1961; Plante et al 1998; Schwarz and Taylor, 1998)

The user is allows to pool rows and/or columns prior to analysis but
the number of rows must be less than or equal to the number of columns
(s <= t). The conditional likelihood formulation of Plante et al
(1998) is used to estimate the parameters.

A good discussion of how to decide on pooling rows/columns is found
in Schwarz and Taylor (1998). The *row.physical.pool* parameter
allows you to choose between physical pooling of rows, or logical
pooling of rows (the underlying data table is unchanged, but capture
probabilities for the pooled rows are forced equal). It is not possible
to do logical pooling of columns and only physical pooling is possible.
See the help() function for details.

If the data are physically pooled prior to analysis, it is not
possible to compare different poolings to see which is most appropriate
using AIC or likelihood ratio tests. If you do logical pooling of rows,
you can compare poolings using AIC or likelihood ratio methods.

Optimization is now done using the TMB package (a relative of ADMB)
which seems to have fixed the convergence issues that plagued earlier
versions of SPAS-R.

## References

Darroch, J. N. (1961). The two-sample capture-recapture census when
tagging and sampling are stratified. Biometrika, 48, 241-260.
https://www.jstor.org/stable/2332748

Plante, N., L.-P Rivest, and G. Tremblay. (1988). Stratified
Capture-Recapture Estimation of the Size of a Closed Population.
Biometrics 54, 47-60. https://www.jstor.org/stable/2533994

Schwarz, C. J., & Taylor, C. G. (1998). The use of the
stratified-Petersen estimator in fisheries management with an
illustration of estimating the number of pink salmon (Oncorhynchus
gorbuscha) that return to spawn in the Fraser River. Canadian Journal of
Fisheries and Aquatic Sciences, 55, 281-296.
https://doi.org/10.1139/f97-238