Package: cesr 1.0.5

cesr: Trend analysis of Constant Effort Site ringing data

Functions for reading EuroCES data in Euring format to produce annual indices of abundance, productivity and survival. Designed to primarily analyse data from schemes with 10-12 visits per year following methods used by the BTO. Use read.ces() to read in data, extract.data() and index() to do abundance/productivity trends and extract.ch() and mark.ces() to estimate survival probabilities.

Authors:Rob Robinson <[email protected]>

cesr_1.0.5.tar.gz
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cesr.pdf |cesr.html✨
cesr/json (API)
NEWS

# Install 'cesr' in R:

install.packages('cesr', repos = c('https://btorobrob.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/btorobrob/cesr/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

cesnames - Species names translation
ukdata - A sample CES dataset

On CRAN:

cpp

2.16 score 1 stars 29 scripts 25 exports 37 dependencies

Last updated 3 days agofrom:f6e8a92cc9. Checks:1 OK, 11 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 25 2025
R-4.5-win-x86_64	WARNING	Mar 25 2025
R-4.5-mac-x86_64	WARNING	Mar 25 2025
R-4.5-mac-aarch64	WARNING	Mar 25 2025
R-4.5-linux-x86_64	WARNING	Mar 25 2025
R-4.4-win-x86_64	WARNING	Mar 25 2025
R-4.4-mac-x86_64	WARNING	Mar 25 2025
R-4.4-mac-aarch64	WARNING	Mar 25 2025
R-4.4-linux-x86_64	WARNING	Mar 25 2025
R-4.3-win-x86_64	WARNING	Mar 25 2025
R-4.3-mac-x86_64	WARNING	Mar 25 2025
R-4.3-mac-aarch64	WARNING	Mar 25 2025

Exports:ces.table extract.ch extract.counts extract.coverage extract.data extract.sites get.euring index load.boxplot map.ces mark.ces plot_scheme plot_trend plot.ces print.ces readBTO readces save.boxplot select.data setceslang siteplot sitereport summary.ces transient_plot writeces

Dependencies:boot cli coda data.table expm fansi generics glue lattice lifecycle lme4 magrittr maps MASS Matrix matrixcalc mgcv minqa msm mvtnorm nlme nloptr pillar pkgconfig plyr rbibutils Rcpp RcppEigen Rdpack reformulas reshape rlang RMark survival tibble utf8 vctrs

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Trend analysis of Constant Effort Site ringing data	cesr-package cesr
Create a table of results for a list of species	ces.table
Species names translation	cesnames
Check ringing details	check_rings
Get adult capture history data for an individual species	extract.ch
Get species data from a CES datset	extract.counts
Identify CES sites covered in each year	extract.coverage
Get data on an individual species	extract.data
Extracts CES site information	extract.sites
Find a Euring code number	get.euring
Calculate indices of abundance and productivity from CES data	index
Load CES boxplot dataset	load.boxplot
Map CES Sites	map.ces
Estimate adult survival from CES data.	mark.ces
Plot CES trend	plot_trend
Plot CES Objects	plot.ces
Print methods for CES objects	print.ces
Read in CES data	readBTO readces
Save CES boxplot dataset	save.boxplot
Subsets a CES dataset	select.data
Set language for printing species names	setceslang
Summary plot of site-specific captures	siteplot
Site reporting summary	sitereport
Summarizing CES objects	summary.ces
Visualise capture frequency	transient_plot
A sample CES dataset	ukdata
Write CES data to a file	writeces