R2admb: ADMB to R interface functions
Version 0.7.5.3

A series of functions to call AD Model Builder (i.e., compile and run models) from within R, read the results back into R as "admb" objects, and provide standard accessors (i.e. coef(), vcov(), etc.)

Browse man pages Browse package API and functions Browse package files

AuthorBen Bolker, Hans Skaug, Jeff Laake
Date of publication2012-10-28 14:04:55
MaintainerBen Bolker <bolker@mcmaster.ca>
LicenseGPL
Version0.7.5.3
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("R2admb", repos="http://R-Forge.R-project.org")

Man pages

AIC.admb: Standard accessor functions for ADMB model fits
compile_admb: Compile ADMB files, run, read output
do_admb: Compile and/or run an ADMB model, collect output
mcmc.control: Control options for MCMC after ADMB fitting
pin_write: Write parameter and data files for ADMB
R2admb-package: ADMB to R interface functions
read_pars: Read in parameters from an AD Model Builder run
run.control: set run options for running ADMB via R
setup_admb: Set up AD Model Builder environment variables

Functions

AIC.admb Man page Source code
R2admb Man page
R2admb-package Man page
check_section Source code
clean_admb Man page Source code
coef.admb Man page Source code
compile_admb Man page Source code
confint.admb Man page Source code
dat_write Man page
deviance.admb Man page Source code
do_admb Man page Source code
drop_calcs Source code
get_names Source code
indent Source code
logLik.admb Man page Source code
mcmc.args Source code
mcmc.control Man page Source code
numfmt Source code
numfmt2 Source code
numfmt3 Source code
plot.admb_hist Source code
print.admb Source code
print.summary.admb Source code
proc_var Source code
read_admb Man page Source code
read_admbbin Source code
read_chunk Source code
read_hst Source code
read_pars Man page Source code
read_plt Source code
read_psv Man page Source code
read_tpl Source code
rep_pars Source code
reptoRlist Source code
rhist Source code
run.control Man page Source code
run_admb Man page Source code
setup_admb Man page Source code
stdEr Man page Source code
stdEr.admb Man page Source code
str_contains Source code
strip_comments Source code
summary.admb Source code
test_OScase Source code
vcov.admb Man page Source code
write_dat Man page
write_pin Man page

Files

R
R/admb-funs.R
R/setup_admb.R
R/check_section.R
R/do_admb.R
NAMESPACE
tests
tests/inputs
tests/inputs/orange2.tpl
tests/inputs/readtest1.bar
tests/inputs/bcb.tpl
tests/inputs/glmmadmb.tpl
tests/inputs/lidar.tpl
tests/inputs/n2mvol.tpl
tests/inputs/ratre.tpl
tests/inputs/ham5.tpl
tests/inputs/readtest1.std
tests/inputs/readtest1.par
tests/inputs/nbmm.tpl
tests/inputs/binomial.tpl
tests/inputs/orange.tpl
tests/inputs/truncreg.tpl
tests/inputs/readtest1.tpl
tests/inputs/readtest1.dat
tests/inputs/catage.tpl
tests/inputs/polio.tpl
tests/inputs/finance.tpl
tests/inputs/readtest1.cor
tests/inputs/diet.tpl
tests/inputs/chem-eng.tpl
tests/inputs/pheno.tpl
tests/inputs/binomial_w2.tpl
tests/inputs/diet_sk.tpl
tests/inputs/nested4.tpl
tests/inputs/caest.tpl
tests/inputs/forest.tpl
tests/inputs/biglog.tpl
tests/inputs/pella-t.tpl
tests/inputs/vonb.tpl
tests/inputs/logistic.tpl
tests/inputs/rat.tpl
tests/inputs/bvprobit.tpl
tests/inputs/socatt.tpl
tests/inputs/vonbr.tpl
tests/inputs/orange_cor.tpl
tests/inputs/ham4.tpl
tests/inputs/kidney.tpl
tests/inputs/liver_gamma.tpl
tests/inputs/spatial.tpl
tests/inputs/simple.tpl
tests/inputs/amak.tpl
tests/inputs/sdv.tpl
tests/inputs/union.tpl
tests/amak.R
tests/alltpl.R
tests/is_int.R
inst
inst/NEWS.Rd
inst/admbtests
inst/admbtests/reedfrog.R
inst/admbtests/ReedfrogSizepred0.tpl
inst/admbtests/toy1.R
inst/admbtests/fileswitch.R
inst/admbtests/README
inst/admbtests/toy1.tpl
inst/admbtests/simple.R
inst/tplfiles
inst/tplfiles/ReedfrogSizepred0.tpl
inst/tplfiles/toy1.tpl
inst/doc
inst/doc/R2admb.Rnw
inst/doc/R2admb.pdf
inst/doc/Reedfrog_runs.RData
TODO.md
vignettes
vignettes/R2admb-ranefs.pdf
vignettes/R2admb-mcdensplot.pdf
vignettes/R2admb-mctraceplot.pdf
vignettes/R2admb-mchistplot.pdf
vignettes/R2admb-profpic.pdf
vignettes/R2admb-fig1.pdf
vignettes/gopherdat.RData
vignettes/ReedfrogSizepred.tpl
vignettes/Reedfrog_runs.R
vignettes/Gopher.tpl
vignettes/ReedfrogSizepred0.tpl
vignettes/ReedfrogSizepred0_gen.tpl
vignettes/TODO
vignettes/R2admb.bib
vignettes/toy1.tpl
vignettes/Makefile
vignettes/Reedfrog_runs.RData
vignettes/toy1_runs.RData
vignettes/ESA1009.bst
vignettes/R2admb.Rnw
DESCRIPTION
ChangeLog
man
man/mcmc.control.Rd
man/do_admb.Rd
man/AIC.admb.Rd
man/R2admb-package.Rd
man/pin_write.Rd
man/read_pars.Rd
man/run.control.Rd
man/setup_admb.Rd
man/compile_admb.Rd
BinaryFiles
R2admb documentation built on May 21, 2017, 1:11 a.m.