R2admb: 'ADMB' to R Interface Functions

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.)

Author
Ben Bolker, Hans Skaug, Jeff Laake
Date of publication
2015-04-13 09:10:09
Maintainer
Ben Bolker <bolker@mcmaster.ca>
License
GPL
Version
0.7.13

View on CRAN

Man pages

admb_version
Query ADMB version
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
extract_gradient
Extract gradients
find_large_cor
Find large correlations
mcmc.control
Control options for MCMC after ADMB fitting
plot.admb_hist
Plot MCMC histogram
R2admb-package
ADMB to R interface functions
read_pars
Read in parameters from an AD Model Builder run
read_plt
Read in ADMB profile file
run.control
set run options for running ADMB via R
setup_admb
Set up AD Model Builder environment variables
write_pin
Write parameter and data files for ADMB

Files in this package

R2admb
R2admb/inst
R2admb/inst/admbtests
R2admb/inst/admbtests/reedfrog.R
R2admb/inst/admbtests/fileswitch.R
R2admb/inst/admbtests/toy1_gen.tpl
R2admb/inst/admbtests/simple.R
R2admb/inst/admbtests/toy1.R
R2admb/inst/admbtests/ReedfrogSizepred0.tpl
R2admb/inst/admbtests/racecond.RData
R2admb/inst/admbtests/README
R2admb/inst/admbtests/toy1.tpl
R2admb/inst/admbtests/deltavar_prof.tpl
R2admb/inst/NEWS.Rd
R2admb/inst/tplfiles
R2admb/inst/tplfiles/glmmadmb.tpl
R2admb/inst/tplfiles/ReedfrogSizepred0.tpl
R2admb/inst/tplfiles/toy1.tpl
R2admb/inst/tplfiles/testversion.tpl
R2admb/inst/doc
R2admb/inst/doc/R2admb.pdf
R2admb/inst/doc/Reedfrog_runs.RData
R2admb/inst/doc/toy1_runs.RData
R2admb/tests
R2admb/tests/stderr_bug.R
R2admb/tests/do_admb.R
R2admb/tests/skate.R
R2admb/tests/amak.R
R2admb/tests/racecond.R
R2admb/tests/inputs
R2admb/tests/inputs/readtest1.bar
R2admb/tests/inputs/n2mvol.tpl
R2admb/tests/inputs/ham5.tpl
R2admb/tests/inputs/pheno.tpl
R2admb/tests/inputs/lidar.tpl
R2admb/tests/inputs/skate.cor
R2admb/tests/inputs/kidney.tpl
R2admb/tests/inputs/socatt.tpl
R2admb/tests/inputs/skate.par
R2admb/tests/inputs/biglog.tpl
R2admb/tests/inputs/rat.tpl
R2admb/tests/inputs/chem-eng.tpl
R2admb/tests/inputs/glmmadmb.tpl
R2admb/tests/inputs/forest.tpl
R2admb/tests/inputs/binomial_w2.tpl
R2admb/tests/inputs/diet.tpl
R2admb/tests/inputs/caest.tpl
R2admb/tests/inputs/truncreg.tpl
R2admb/tests/inputs/orange2.tpl
R2admb/tests/inputs/pella-t.tpl
R2admb/tests/inputs/ham4.tpl
R2admb/tests/inputs/readtest1.dat
R2admb/tests/inputs/vonbr.tpl
R2admb/tests/inputs/spatial.tpl
R2admb/tests/inputs/skate.rep
R2admb/tests/inputs/readtest1.tpl
R2admb/tests/inputs/nbmm.tpl
R2admb/tests/inputs/skate.std
R2admb/tests/inputs/liver_gamma.tpl
R2admb/tests/inputs/vonb.tpl
R2admb/tests/inputs/skate.tpl
R2admb/tests/inputs/sdv.tpl
R2admb/tests/inputs/polio.tpl
R2admb/tests/inputs/logistic.tpl
R2admb/tests/inputs/readtest1.std
R2admb/tests/inputs/orange_cor.tpl
R2admb/tests/inputs/bcb.tpl
R2admb/tests/inputs/catage.tpl
R2admb/tests/inputs/bvprobit.tpl
R2admb/tests/inputs/simple.tpl
R2admb/tests/inputs/union.tpl
R2admb/tests/inputs/finance.tpl
R2admb/tests/inputs/amak.tpl
R2admb/tests/inputs/binomial.tpl
R2admb/tests/inputs/orange.tpl
R2admb/tests/inputs/diet_sk.tpl
R2admb/tests/inputs/nested4.tpl
R2admb/tests/inputs/ratre.tpl
R2admb/tests/inputs/readtest1.par
R2admb/tests/inputs/readtest1.cor
R2admb/tests/is_int.R
R2admb/tests/allinputs.R
R2admb/NAMESPACE
R2admb/R
R2admb/R/extract_gradient.r
R2admb/R/do_admb.r
R2admb/R/write-funs.r
R2admb/R/check_section.R
R2admb/R/R2admb-package.R
R2admb/R/mcmc.control.r
R2admb/R/plot.admb_hist.r
R2admb/R/read-funs.r
R2admb/R/get_version.r
R2admb/R/readfit.R
R2admb/R/utility-funs.R
R2admb/R/std_accessor.r
R2admb/R/find_large_cor.r
R2admb/R/run.control.r
R2admb/R/setup_admb.R
R2admb/R/base-funs.r
R2admb/vignettes
R2admb/vignettes/TODO
R2admb/vignettes/Makefile
R2admb/vignettes/toy1_gen.tpl
R2admb/vignettes/R2admb.Rnw
R2admb/vignettes/R2admb.bib
R2admb/vignettes/Reedfrog_runs.RData
R2admb/vignettes/ReedfrogSizepred0.tpl
R2admb/vignettes/ReedfrogSizepred0_gen.tpl
R2admb/vignettes/ESA1009.bst
R2admb/vignettes/TODO_2
R2admb/vignettes/ReedfrogSizepred.tpl
R2admb/vignettes/toy1.tpl
R2admb/vignettes/Reedfrog_runs.R
R2admb/vignettes/ReedfrogSizepred1.tpl
R2admb/vignettes/auto
R2admb/vignettes/auto/R2admb.el
R2admb/vignettes/Gopher.tpl
R2admb/MD5
R2admb/build
R2admb/build/vignette.rds
R2admb/DESCRIPTION
R2admb/man
R2admb/man/admb_version.Rd
R2admb/man/R2admb-package.Rd
R2admb/man/read_plt.Rd
R2admb/man/mcmc.control.Rd
R2admb/man/find_large_cor.Rd
R2admb/man/plot.admb_hist.Rd
R2admb/man/run.control.Rd
R2admb/man/AIC.admb.Rd
R2admb/man/write_pin.Rd
R2admb/man/read_pars.Rd
R2admb/man/compile_admb.Rd
R2admb/man/do_admb.Rd
R2admb/man/extract_gradient.Rd
R2admb/man/setup_admb.Rd