rtrim: Trends and Indices for Monitoring Data

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.

AuthorPatrick Bogaart, Mark van der Loo, and Jeroen Pannekoek
Date of publication2016-11-28 16:54:05
MaintainerAdriaan Gmelig Meyling <rtrim@cbs.nl>
LicenseEUPL
Version1.0.1
https://github.com/markvanderloo/rtrim

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

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