rtrim: Trends and Indices for Monitoring Data
Version 1.0.1

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 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
URL https://github.com/markvanderloo/rtrim
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("rtrim")

Getting started

Package overview
rtrim for TRIM users
TRIM by example
Working with TRIM command files and TRIM data files

Popular man pages

check_observations: Check whether there are sufficient observations to run a...
get_estimation_method: Extract estimation method from 'tof' object
get_overal_imputed_slope: Extract overall imputed slope 'tof' object
overdispersion: Extract overdispersion from trim object
print.trim: print a 'trim' object
rtrim-package: Trend and Indices for Monitoring Data
skylark: Skylark population data
See all...

All man pages Function index File listing

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

Score Source code
as_rtrim Source code
assert_covariate_counts Source code
assert_increasing Source code
assert_plt_model Source code
assert_positive Source code
assert_sufficient_counts Source code
autodelete Source code
check_observations Man page Source code
check_observations.character Man page Source code
check_observations.data.frame Man page Source code
check_observations.trimcommand Man page Source code
check_tcf Source code
coef.trim Man page Source code
coef_m2_covars Source code
coef_m3_covars Source code
convert_path Source code
count_summary Man page Source code
export Source code
export.trim.totals Source code
extract_keyval Source code
get_coef Man page Source code
get_cov_count_errlist Source code
get_deletion Source code
get_estimation_method Man page Source code
get_gof Man page Source code
get_indextab Source code
get_model Man page Source code
get_n_site Man page Source code
get_n_time Man page Source code
get_num Source code
get_oneliner Source code
get_overal_cp_imputed_slope Source code
get_overal_imputed_slope Man page Source code
get_overdispersion Source code
get_serial_correlation Source code
get_str Source code
get_time_indices Man page Source code
get_time_totals Man page Source code
get_version Man page Source code
get_wald Man page Source code
gof Man page Source code
gof.numeric Source code
gof.trim Man page Source code
has_changepoints Source code
has_covariates Source code
icv_read Source code
index Man page Source code
key_regex Source code
ndex Source code
now_what Man page Source code
onLoad Source code
oneliner Source code
overall Man page Source code
overdispersion Man page Source code
parse_formula Source code
pieces_from_changepoints Source code
plot.trim.index Man page Source code
plot.trim.overall Man page Source code
plot.trim.results Source code
pr Source code
print.count.summary Man page Source code
print.tof Source code
print.trim Man page Source code
print.trim.gof Man page Source code
print.trim.overall Man page Source code
print.trim.summary Source code
print.trim.wald Man page Source code
print.trimcommand Man page Source code
print_and_capture Source code
printf Source code
read_icv Source code
read_icv.character Source code
read_icv.trimcommand Source code
read_tcf Man page Source code
read_tdf Man page Source code
read_tdf.character Man page Source code
read_tdf.trimcommand Man page Source code
read_tof Man page Source code
read_vcv Man page Source code
replace_with_space Source code
results Man page Source code
rprintf Source code
rtrim-package Man page
serial_correlation Man page Source code
setNames Source code
set_trim_verbose Man page Source code
shd Source code
shortstr Source code
skylark Man page
skylark2 Man page
snifreport Source code
strip_line Source code
summary.trim Man page Source code
summary.trimbatch Man page Source code
tc_from_char Source code
tdfread Source code
totals Man page Source code
trim Man page Source code
trim.data.frame Man page Source code
trim.formula Man page Source code
trim.trimcommand Man page Source code
trim_estimate Man page Source code
trim_refine Man page Source code
trim_workhorse Man page Source code
trimbatch Source code
trimcommand Man page Source code
vcov.trim Man page Source code
wald Man page Source code
wald.trim Man page Source code

Files

inst
inst/doc
inst/doc/Working_with_tcf.html
inst/doc/Skylark_example.html
inst/doc/rtrim_for_TRIM_users.R
inst/doc/rtrim_for_TRIM_users.html
inst/doc/Working_with_tcf.Rmd
inst/doc/Skylark_example.R
inst/doc/Working_with_tcf.R
inst/doc/Skylark_example.Rmd
inst/doc/rtrim_for_TRIM_users.Rmd
tests
tests/testthat.R
tests/testthat
tests/testthat/test_utils.R
tests/testthat/test_tcf.R
tests/testthat/test_tdf.R
tests/testthat/test_trim.R
tests/testthat/outfiles
tests/testthat/outfiles/skylark-x2.tcf
tests/testthat/outfiles/skylark-1d.out
tests/testthat/outfiles/skylark-2b.tcf
tests/testthat/outfiles/skylark-minimal.tcf
tests/testthat/outfiles/skylark-2b.out
tests/testthat/outfiles/skylark-1e.tcf
tests/testthat/outfiles/skylark-4c.tcf
tests/testthat/outfiles/skylark-1e.out
tests/testthat/outfiles/test_skylark_1a_to_2b.R
tests/testthat/outfiles/skylark-4e.tcf
tests/testthat/outfiles/skylark-1f.out
tests/testthat/outfiles/skylark-1a.tcf
tests/testthat/outfiles/skylark-1c.tcf
tests/testthat/outfiles/skylark-4a.out
tests/testthat/outfiles/skylark_wt.dat
tests/testthat/outfiles/skylark-4d.tcf
tests/testthat/outfiles/skylark-4b.out
tests/testthat/outfiles/skylark-1d.tcf
tests/testthat/outfiles/skylark-1a.out
tests/testthat/outfiles/skylark-4a.tcf
tests/testthat/outfiles/skylark-2a.out
tests/testthat/outfiles/skylark-x1.tcf
tests/testthat/outfiles/skylark-4f.out
tests/testthat/outfiles/skylark-4b.tcf
tests/testthat/outfiles/skylark-4e.out
tests/testthat/outfiles/skylark-x3.tcf
tests/testthat/outfiles/skylark-1c.out
tests/testthat/outfiles/skylark-model2-f.csv
tests/testthat/outfiles/skylark-1b.out
tests/testthat/outfiles/skylark-x1.ocv
tests/testthat/outfiles/skylark-4f.tcf
tests/testthat/outfiles/skylark-1b.tcf
tests/testthat/outfiles/skylark-1f.tcf
tests/testthat/outfiles/skylark-3a.tcf
tests/testthat/outfiles/skylark.dat
tests/testthat/outfiles/skylark-2a.tcf
tests/testthat/outfiles/skylark-4d.out
tests/testthat/outfiles/skylark-4c.out
tests/testthat/outfiles/skylark-x2.out
tests/testthat/outfiles/skylark_yr.dat
tests/testthat/outfiles/skylark-x1.out
tests/testthat/outfiles/skylark-x3.out
tests/testthat/outfiles/skylark-3a.out
tests/testthat/test_checks.R
NAMESPACE
data
data/skylark.RData
data/skylark2.RData
R
R/trim_wald.R
R/utils.R
R/parse_outfile.R
R/read_icv.R
R/skylark.R
R/trim_index.R
R/data_checks.R
R/trim_post.R
R/read_tcf.R
R/trim_workhorse.R
R/trim_overall.R
R/trim.R
R/trim_refine.R
R/read_tdf.R
R/trim_gof.R
R/rtrim-pkg.R
vignettes
vignettes/Working_with_tcf.Rmd
vignettes/Skylark_example.Rmd
vignettes/rtrim_for_TRIM_users.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/vcov.trim.Rd
man/get_time_totals.Rd
man/print.trim.Rd
man/read_tcf.Rd
man/get_time_indices.Rd
man/read_vcv.Rd
man/trimcommand.Rd
man/get_wald.Rd
man/get_overal_imputed_slope.Rd
man/plot.trim.overall.Rd
man/get_n_time.Rd
man/get_coef.Rd
man/coef.trim.Rd
man/now_what.Rd
man/overall.Rd
man/trim_refine.Rd
man/skylark.Rd
man/index.Rd
man/overdispersion.Rd
man/trim_workhorse.Rd
man/print.trim.wald.Rd
man/wald.Rd
man/results.Rd
man/totals.Rd
man/get_version.Rd
man/get_gof.Rd
man/trim_estimate.Rd
man/print.trimcommand.Rd
man/check_observations.Rd
man/print.count.summary.Rd
man/read_tof.Rd
man/trim.Rd
man/summary.trimbatch.Rd
man/serial_correlation.Rd
man/set_trim_verbose.Rd
man/print.trim.overall.Rd
man/plot.trim.index.Rd
man/get_n_site.Rd
man/count_summary.Rd
man/read_tdf.Rd
man/print.trim.gof.Rd
man/get_model.Rd
man/summary.trim.Rd
man/get_estimation_method.Rd
man/rtrim-package.Rd
man/gof.Rd
rtrim documentation built on May 20, 2017, 12:18 a.m.

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