rtrim: Trends and Indices for Monitoring Data

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The TRIM model is widely used for estimating growth and decline of animal populations based on (possibly sparsely available) count data. The current package is a reimplementation of the original TRIM software developed at Statistics Netherlands by Jeroen Pannekoek. See <https://www.cbs.nl/en-gb/society/nature-and-environment/indices-and-trends--trim--> for more information about TRIM.

Author
Patrick Bogaart, Mark van der Loo, and Jeroen Pannekoek
Date of publication
2016-11-28 16:54:05
Maintainer
Adriaan Gmelig Meyling <rtrim@cbs.nl>
License
EUPL
Version
1.0.1
URLs

View on CRAN

Man pages

check_observations
Check whether there are sufficient observations to run a...
coef.trim
Extract TRIM model coefficients.
count_summary
Compute a summary of counts
get_coef
Extract model coefficients from 'tof' object
get_estimation_method
Extract estimation method from 'tof' object
get_gof
Extract goodness of fit from 'tof' object
get_model
Extract model type from 'tof' object
get_n_site
Extract nr of times from 'tof' object
get_n_time
Extract nr of sites from 'tof' object
get_overal_imputed_slope
Extract overall imputed slope 'tof' object
get_time_indices
Extract time indices from 'tof' object
get_time_totals
Extract time totals from 'tof' object
get_version
Extract TRIM version used for output
get_wald
Extract Wald test parameters from 'tof' object
gof
Extract TRIM goodness-of-fit information.
index
Extract time-indices from trim output
now_what
Give advice on further refinement of TRIM models
overall
Compute overall slope
overdispersion
Extract overdispersion from trim object
plot.trim.index
Plot time-indices from trim output
plot.trim.overall
Plot overall slope
print.count.summary
print a count summary
print.trim
print a 'trim' object
print.trimcommand
print a trimcommand object
print.trim.gof
Print method for 'trim.gof'
print.trim.overall
Print an object of class trim.overall
print.trim.wald
Print an object of class trim.wald
read_tcf
Read a TRIM command file
read_tdf
Read TRIM data files
read_tof
Read a TRIM3 output file
read_vcv
Read a TRIM3 variance-covariance output file
results
collect observed, modelled, and imputed counts from TRIM...
rtrim-package
Trend and Indices for Monitoring Data
serial_correlation
Extract serial correlation from TRIM object
set_trim_verbose
Set verbosity of trim model functions
skylark
Skylark population data
summary.trim
Summary information for a TRIM job
summary.trimbatch
summarize a trimbatch object
totals
Extract time-totals from TRIM output
trim
Estimate TRIM model parameters
trimcommand
Create a trimcommand object
trim_estimate
TRIM estimation function
trim_refine
TRIM stepwise refinement
trim_workhorse
TRIM workhorse function
vcov.trim
Extract variance-covariance matrix from TRIM output
wald
Test significance of TRIM coefficients with the Wald test

Files in this package

rtrim
rtrim/inst
rtrim/inst/doc
rtrim/inst/doc/Working_with_tcf.html
rtrim/inst/doc/Skylark_example.html
rtrim/inst/doc/rtrim_for_TRIM_users.R
rtrim/inst/doc/rtrim_for_TRIM_users.html
rtrim/inst/doc/Working_with_tcf.Rmd
rtrim/inst/doc/Skylark_example.R
rtrim/inst/doc/Working_with_tcf.R
rtrim/inst/doc/Skylark_example.Rmd
rtrim/inst/doc/rtrim_for_TRIM_users.Rmd
rtrim/tests
rtrim/tests/testthat.R
rtrim/tests/testthat
rtrim/tests/testthat/test_utils.R
rtrim/tests/testthat/test_tcf.R
rtrim/tests/testthat/test_tdf.R
rtrim/tests/testthat/test_trim.R
rtrim/tests/testthat/outfiles
rtrim/tests/testthat/outfiles/skylark-x2.tcf
rtrim/tests/testthat/outfiles/skylark-1d.out
rtrim/tests/testthat/outfiles/skylark-2b.tcf
rtrim/tests/testthat/outfiles/skylark-minimal.tcf
rtrim/tests/testthat/outfiles/skylark-2b.out
rtrim/tests/testthat/outfiles/skylark-1e.tcf
rtrim/tests/testthat/outfiles/skylark-4c.tcf
rtrim/tests/testthat/outfiles/skylark-1e.out
rtrim/tests/testthat/outfiles/test_skylark_1a_to_2b.R
rtrim/tests/testthat/outfiles/skylark-4e.tcf
rtrim/tests/testthat/outfiles/skylark-1f.out
rtrim/tests/testthat/outfiles/skylark-1a.tcf
rtrim/tests/testthat/outfiles/skylark-1c.tcf
rtrim/tests/testthat/outfiles/skylark-4a.out
rtrim/tests/testthat/outfiles/skylark_wt.dat
rtrim/tests/testthat/outfiles/skylark-4d.tcf
rtrim/tests/testthat/outfiles/skylark-4b.out
rtrim/tests/testthat/outfiles/skylark-1d.tcf
rtrim/tests/testthat/outfiles/skylark-1a.out
rtrim/tests/testthat/outfiles/skylark-4a.tcf
rtrim/tests/testthat/outfiles/skylark-2a.out
rtrim/tests/testthat/outfiles/skylark-x1.tcf
rtrim/tests/testthat/outfiles/skylark-4f.out
rtrim/tests/testthat/outfiles/skylark-4b.tcf
rtrim/tests/testthat/outfiles/skylark-4e.out
rtrim/tests/testthat/outfiles/skylark-x3.tcf
rtrim/tests/testthat/outfiles/skylark-1c.out
rtrim/tests/testthat/outfiles/skylark-model2-f.csv
rtrim/tests/testthat/outfiles/skylark-1b.out
rtrim/tests/testthat/outfiles/skylark-x1.ocv
rtrim/tests/testthat/outfiles/skylark-4f.tcf
rtrim/tests/testthat/outfiles/skylark-1b.tcf
rtrim/tests/testthat/outfiles/skylark-1f.tcf
rtrim/tests/testthat/outfiles/skylark-3a.tcf
rtrim/tests/testthat/outfiles/skylark.dat
rtrim/tests/testthat/outfiles/skylark-2a.tcf
rtrim/tests/testthat/outfiles/skylark-4d.out
rtrim/tests/testthat/outfiles/skylark-4c.out
rtrim/tests/testthat/outfiles/skylark-x2.out
rtrim/tests/testthat/outfiles/skylark_yr.dat
rtrim/tests/testthat/outfiles/skylark-x1.out
rtrim/tests/testthat/outfiles/skylark-x3.out
rtrim/tests/testthat/outfiles/skylark-3a.out
rtrim/tests/testthat/test_checks.R
rtrim/NAMESPACE
rtrim/data
rtrim/data/skylark.RData
rtrim/data/skylark2.RData
rtrim/R
rtrim/R/trim_wald.R
rtrim/R/utils.R
rtrim/R/parse_outfile.R
rtrim/R/read_icv.R
rtrim/R/skylark.R
rtrim/R/trim_index.R
rtrim/R/data_checks.R
rtrim/R/trim_post.R
rtrim/R/read_tcf.R
rtrim/R/trim_workhorse.R
rtrim/R/trim_overall.R
rtrim/R/trim.R
rtrim/R/trim_refine.R
rtrim/R/read_tdf.R
rtrim/R/trim_gof.R
rtrim/R/rtrim-pkg.R
rtrim/vignettes
rtrim/vignettes/Working_with_tcf.Rmd
rtrim/vignettes/Skylark_example.Rmd
rtrim/vignettes/rtrim_for_TRIM_users.Rmd
rtrim/MD5
rtrim/build
rtrim/build/vignette.rds
rtrim/DESCRIPTION
rtrim/man
rtrim/man/vcov.trim.Rd
rtrim/man/get_time_totals.Rd
rtrim/man/print.trim.Rd
rtrim/man/read_tcf.Rd
rtrim/man/get_time_indices.Rd
rtrim/man/read_vcv.Rd
rtrim/man/trimcommand.Rd
rtrim/man/get_wald.Rd
rtrim/man/get_overal_imputed_slope.Rd
rtrim/man/plot.trim.overall.Rd
rtrim/man/get_n_time.Rd
rtrim/man/get_coef.Rd
rtrim/man/coef.trim.Rd
rtrim/man/now_what.Rd
rtrim/man/overall.Rd
rtrim/man/trim_refine.Rd
rtrim/man/skylark.Rd
rtrim/man/index.Rd
rtrim/man/overdispersion.Rd
rtrim/man/trim_workhorse.Rd
rtrim/man/print.trim.wald.Rd
rtrim/man/wald.Rd
rtrim/man/results.Rd
rtrim/man/totals.Rd
rtrim/man/get_version.Rd
rtrim/man/get_gof.Rd
rtrim/man/trim_estimate.Rd
rtrim/man/print.trimcommand.Rd
rtrim/man/check_observations.Rd
rtrim/man/print.count.summary.Rd
rtrim/man/read_tof.Rd
rtrim/man/trim.Rd
rtrim/man/summary.trimbatch.Rd
rtrim/man/serial_correlation.Rd
rtrim/man/set_trim_verbose.Rd
rtrim/man/print.trim.overall.Rd
rtrim/man/plot.trim.index.Rd
rtrim/man/get_n_site.Rd
rtrim/man/count_summary.Rd
rtrim/man/read_tdf.Rd
rtrim/man/print.trim.gof.Rd
rtrim/man/get_model.Rd
rtrim/man/summary.trim.Rd
rtrim/man/get_estimation_method.Rd
rtrim/man/rtrim-package.Rd
rtrim/man/gof.Rd