cesr-package: Trend analysis of Constant Effort Site ringing data

In btorobrob/cesr: Trend analysis of Constant Effort Site ringing data

Trend analysis of Constant Effort Site ringing data

Description

Facilities for reading EuroCES data in Euring format to produce annual indices of productivity, abundance and survival. Primarily designed to analyse data from schemes with 9-12 visits per year following Peach et al. (1996, 1998) and Robinson et al. (2007).

Details

Package:	cesr
Type:	Package
Version:	1.0.2
Date:	2023-06-07
License:	GPL-2
LazyLoad:	yes

Constant Effort Site (CES) ringing data provide a valuable way to monitor changes in abundance, productivity and survival through standardised capture and recapture of individuals. cesr provides some facilities to produce annual trends in abundance and productivity from these data. In order to do this cesr requires CES data organised in a plain text file according to the agreed Euring format (details of which can be found on the Euring website (http://www.euring.org/internal/ces_research_group/euro_ces_meeting_2008_notes.pdf).

The key steps are: (i) to read in the data (with readces);

(ii) generate a table of which plots are covered in which year (with extract.coverage);

(iii) extract data for the species to be analysed (with extract.data), and

(iv) generate the annual abundance/productivity indices (with index).

Adult survival probabilities can be estimated by first using extract.ch then mark.ces. Results can be plotted using plot_trend. More details on how to do each of these can be found in the introductory manual, type

vignette('cesr-intro')

to view it.

Author(s)

Maintainer: Rob Robinson <[e-mail]>

References

• "Peach, W.J., Buckland, S.T. & Baillie, S.R. (1996) The use of constant effort mist-netting to measure between-year changes in the abundance and productivity of common passerines. Bird Study 43:142-156."

• "Peach, W.J., Baillie, S.R. & Balmer, D.E. (1998) Long-term changes in the abundance of passerines in Britain and Ireland as measured by constant effort mist-netting. Bird Study 45:257-275."

• "Robinson, R.A., Freeman, S.N., Balmer, D.E. & Grantham, M.J. (2007) Cetti's Warbler: anatomy of an expanding population. Bird Study 54:230-235."

• "Robinson, R.A., Julliard, R & Saracco, J.F. (2009) Constant effort: studying avian population processes using standardized ringing. Ringing & Migration 24:199-204."

Examples

                                               
## Not run: 
# A sample session might look as follows:
setwd('d:/data/ces')  # set the working directory which contains the data file 
setceslang('English')  # which language for species names? 

alldat <- readces('netherlands.csv')  # read in the data
plot.nl <- extract.coverage(alldat)  # determine which sites covered in which years
sonth.nl <- extract.data(alldat, species=12000,plots=plot.nl)  # extract data for Song Thrush
st.fit0 <- index(sonth.nl, year=2008)  # fit an annual index
st.fit1 <- index(sonth.nl, trend=30)  # fit a simple linear trend

writeces(st.fit0, 'sonthdata.txt')  # write annual indices to a file

## End(Not run)

btorobrob/cesr documentation built on June 9, 2025, 5:39 a.m.