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

Functions

check_observations Man page
check_observations.character Man page
check_observations.data.frame Man page
check_observations.trimcommand Man page
coef.trim Man page
count_summary Man page
get_coef Man page
get_estimation_method Man page
get_gof Man page
get_model Man page
get_n_site Man page
get_n_time Man page
get_overal_imputed_slope Man page
get_time_indices Man page
get_time_totals Man page
get_version Man page
get_wald Man page
gof Man page
gof.trim Man page
index Man page
now_what Man page
overall Man page
overdispersion Man page
plot.trim.index Man page
plot.trim.overall Man page
print.count.summary Man page
print.trim Man page
print.trimcommand Man page
print.trim.gof Man page
print.trim.overall Man page
print.trim.wald Man page
read_tcf Man page
read_tdf Man page
read_tdf.character Man page
read_tdf.trimcommand Man page
read_tof Man page
read_vcv Man page
results Man page
rtrim-package Man page
serial_correlation Man page
set_trim_verbose Man page
skylark Man page
skylark2 Man page
summary.trim Man page
summary.trimbatch Man page
totals Man page
trim Man page
trimcommand Man page
trim.data.frame Man page
trim_estimate Man page
trim.formula Man page
trim_refine Man page
trim.trimcommand Man page
trim_workhorse Man page
vcov.trim Man page
wald Man page
wald.trim Man page

Files

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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