Files in brouwern/FACavian

An R implementation and extension of full-annual cycle (FAC) model of Runge & Marra *2005)

.DS_Store

.Rbuildignore

.gitignore

DESCRIPTION

FACavian.Rcheck/00check.log

FACavian.Rproj

LICENSE

LICENSE.md

NAMESPACE

NEWS.md R/FACavian-package.R R/RandVitalRateResponseSurface.R R/eq01buildW0vect.R R/eq02buildW1Mat.R R/eq03buildW2Mat.R R/eq04_Bfc.R R/eq05_Bfk.R R/eq06_Bmc.R R/eq07_Bmk.R R/eq08_Bmd.R R/eq09_Pcgg.R R/eq10_Pcgp.R R/eq11_Pcpg.R R/eq12_Pcpp.R R/eq13_Pkgg.R R/eq14_Pkgp.R R/eq15_Pkpg.R R/eq16_Pkpp.R R/eq17buildB0Vect.R R/eq18AbuildRvect.R R/eq18BbuildPmat.R R/eq19AbuildFmat.R R/eq19BbuildMinMat.R R/eq20buildSbmat.R R/eq21buildSfmat.R R/eq22buildSymat.R R/eq23_stack_Ai.R R/eq24_comp_loop.R R/eq24_competition.R R/eq24_make_gamma_vec.R R/eq25_comp_constrain.R R/eq26_alloc_winter_P.R R/eq27_post_comp_pooling.R R/error_check_B0.R R/error_check_P_test.R R/error_check_Pxxx.R R/error_check_Y1_sex_ratio.R R/error_check_build_Ptest_df.R R/error_check_param_set.R R/error_check_summer.R R/make_FAC_df.R R/make_multiFAC_df.R R/param_grid.R R/param_ranges.R R/param_seqs.R R/param_seqs2.R R/param_set.R R/plot_Fig28_3.R R/plot_Fig28_4.R R/plot_Fig28_4_IBM.R R/plot_Fig28_5.R R/plot_Fig28_6.R R/plot_runFAC.R R/r_vitals.R R/runFAC.R R/runFAC_check_equilibrium.R R/runFAC_finalize_output.R R/runFAC_multi.R R/runFAC_multi_finalize_output.R R/runFAC_store_pop_state_i.R R/step0_set_up.R R/step1_winter_survival.R R/step3_substepA1_hab_acquire_IB.R R/step3_substepA1_hab_acquire_RM.R R/step3_substepA2_mate_acquire_IB.R R/step3_substepA2_mate_acquire_RM.R R/step5_winter_habitat_acquisition.R R/test_P.R R/test_P_df_maker.R R/test_dat_P.R README.md

_pkgdown.yml

data/test_dat_P.RData

docs/404.html

docs/LICENSE-text.html

docs/LICENSE.html

docs/articles/.DS_Store

docs/articles/Introduction.html

docs/articles/Introduction_files/figure-html/.DS_Store

docs/articles/Runge_and_Marra_notes.html

docs/articles/Sherry_Holmes_notes.html

docs/articles/a-Bio_Intro-FAC_demography.html

docs/articles/a-Bio_Intro-FAC_demography_files/figure-html/.DS_Store

docs/articles/a-Bio_Intro-FAC_demography_files/figure-html/unnamed-chunk-1-1.png

docs/articles/a-Bio_Intro-FAC_demography_files/header-attrs-2.11/header-attrs.js

docs/articles/a-Introduction.html

docs/articles/a-Introduction_FAC_demography.html

docs/articles/a-Introduction_FAC_demography_files/figure-html/.DS_Store

docs/articles/a-Introduction_files/figure-html/.DS_Store

docs/articles/b-model_intro-RM_FAC_model.html

docs/articles/b-model_intro-RM_FAC_model_files/header-attrs-2.11/header-attrs.js

docs/articles/b-overview.html

docs/articles/b-running_a_FAC.html

docs/articles/b-running_a_FAC_files/figure-html/.DS_Store

docs/articles/c-running_multiple_FACs.html

docs/articles/c-running_multiple_FACs_files/figure-html/.DS_Store

docs/articles/c-software_intro_rmFAC.html

docs/articles/c-software_intro_rmFAC_files/header-attrs-2.11/header-attrs.js

docs/articles/c-the_runFAC_command.html

docs/articles/c-the_runFAC_command_files/figure-html/.DS_Store

docs/articles/d-the_runFAC_command.html

docs/articles/d-the_runFAC_command_files/figure-html/.DS_Store

docs/articles/d-the_runFAC_command_files/figure-html/unnamed-chunk-16-1.png

docs/articles/d-the_runFAC_command_files/figure-html/unnamed-chunk-17-1.png

docs/articles/d-the_runFAC_command_files/figure-html/unnamed-chunk-27-1.png

docs/articles/d-the_runFAC_command_files/header-attrs-2.11/header-attrs.js

docs/articles/d-the_runFAC_multi_command.html

docs/articles/d-the_runFAC_multi_command_files/figure-html/.DS_Store

docs/articles/e-make_figure_28_3.html

docs/articles/e-make_figure_28_3_files/figure-html/.DS_Store

docs/articles/e-the_runFAC_multi_command.html

docs/articles/e-the_runFAC_multi_command_files/figure-html/.DS_Store

docs/articles/e-the_runFAC_multi_command_files/figure-html/unnamed-chunk-21-1.png

docs/articles/e-the_runFAC_multi_command_files/figure-html/unnamed-chunk-8-1.png

docs/articles/e-the_runFAC_multi_command_files/header-attrs-2.11/header-attrs.js

docs/articles/f-make_figure_28_3.html

docs/articles/f-make_figure_28_3_files/figure-html/.DS_Store

docs/articles/f-make_figure_28_3_files/figure-html/unnamed-chunk-4-1.png

docs/articles/f-make_figure_28_3_files/header-attrs-2.11/header-attrs.js

docs/articles/f-make_figure_28_4.html

docs/articles/f-make_figure_28_4_files/figure-html/.DS_Store

docs/articles/g-make_figure_28_4.html

docs/articles/g-make_figure_28_4_files/figure-html/.DS_Store

docs/articles/g-make_figure_28_4_files/figure-html/unnamed-chunk-7-1.png

docs/articles/g-make_figure_28_4_files/header-attrs-2.11/header-attrs.js

docs/articles/g-make_figure_28_5.html

docs/articles/g-make_figure_28_5_files/figure-html/.DS_Store

docs/articles/h-make_figure_28_5.html

docs/articles/h-make_figure_28_5_files/figure-html/.DS_Store

docs/articles/h-make_figure_28_5_files/figure-html/unnamed-chunk-8-1.png

docs/articles/h-make_figure_28_5_files/header-attrs-2.11/header-attrs.js

docs/articles/h-make_figure_28_6.html

docs/articles/i-make_figure_28_6.html

docs/articles/i-make_figure_28_6_files/figure-html/unnamed-chunk-7-1.png

docs/articles/i-make_figure_28_6_files/header-attrs-2.11/header-attrs.js

docs/articles/index.html

docs/articles/make_figure_28_5.html

docs/articles/make_figure_28_5_files/figure-html/.DS_Store

docs/articles/p-software_checks.html

docs/articles/p-software_checks_files/header-attrs-2.11/header-attrs.js

docs/articles/p-tests.html

docs/articles/paper-notes.html

docs/articles/relevant_literature.html

docs/articles/running_a_FAC.html

docs/articles/running_a_FAC_files/figure-html/.DS_Store

docs/articles/running_multiple_FACs.html

docs/articles/running_multiple_FACs_files/figure-html/.DS_Store

docs/articles/v-Sherry_Holmes_notes.html

docs/articles/v-Sherry_Holmes_notes_files/header-attrs-2.11/header-attrs.js

docs/articles/w-annotated_bib.html

docs/articles/w-annotated_bib_files/header-attrs-2.11/header-attrs.js

docs/articles/x-creating_a_package.html

docs/articles/x-creating_a_package_files/header-attrs-2.11/header-attrs.js

docs/articles/y-building_a_package.html

docs/articles/y-building_a_package_files/header-attrs-2.11/header-attrs.js

docs/articles/y-creating_a_package.html

docs/articles/z-MANUSCRIPT.html

docs/articles/z-MANUSCRIPT_files/header-attrs-2.11/header-attrs.js

docs/articles/z-TODO.html

docs/articles/z-TODO_files/header-attrs-2.11/header-attrs.js

docs/articles/z-build_and_rebuild_package.html

docs/articles/z-build_and_rebuild_package_files/header-attrs-2.11/header-attrs.js

docs/articles/z2-building_a_package.html

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/link.svg

docs/news/index.html

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/.DS_Store

docs/reference/FACavian-package.html

docs/reference/RandVitalRateResponseSurface.html

docs/reference/Rplot001.png

docs/reference/eq01buildW0vect.html

docs/reference/eq02buildW1Mat.html

docs/reference/eq02bulidW1Mat.html

docs/reference/eq03buildW2Mat.html

docs/reference/eq04_Bfc.html

docs/reference/eq05_Bfk.html

docs/reference/eq06_Bmc.html

docs/reference/eq07_Bmk.html

docs/reference/eq08_Bmd.html

docs/reference/eq09_Pcgg-1.png

docs/reference/eq09_Pcgg.html

docs/reference/eq10_Pcgp.html

docs/reference/eq11_Pcpg.html

docs/reference/eq12_Pcpp.html

docs/reference/eq13_Pkgg.html

docs/reference/eq14_Pkgp.html

docs/reference/eq15_Pkpg.html

docs/reference/eq16_Pkpp.html

docs/reference/eq17buildB0Vect.html

docs/reference/eq18AbuildRvec.html

docs/reference/eq18BbuildPmat.html

docs/reference/eq19AbuildFmat.html

docs/reference/eq19BbuildMinMat.html

docs/reference/eq20buildSbmat.html

docs/reference/eq21buildSfmat.html

docs/reference/eq22buildSymat.html

docs/reference/eq23_stack_Ai.html

docs/reference/eq24_comp_loop.html

docs/reference/eq24_competition.html

docs/reference/eq24_make_gamma_vec.html

docs/reference/eq25_comp_constrain.html

docs/reference/eq26_alloc_winter_P.html

docs/reference/eq27_post_comp_pooling.html

docs/reference/error_check_B0.html

docs/reference/error_check_P_test.html

docs/reference/error_check_Pxxx.html

docs/reference/error_check_Y1_sex_ratio.html

docs/reference/error_check_build_Ptest_df.html

docs/reference/error_check_param_set.html

docs/reference/error_check_summer.html

docs/reference/index.html

docs/reference/make_FAC_df.html

docs/reference/make_multiFAC_df.html

docs/reference/param_grid.html

docs/reference/param_ranges.html

docs/reference/param_seqs.html

docs/reference/param_seqs2.html

docs/reference/param_set.html

docs/reference/plot_Fig28_3.html

docs/reference/plot_Fig28_4.html

docs/reference/plot_Fig28_4_IBM.html

docs/reference/plot_Fig28_5.html

docs/reference/plot_Fig28_6.html

docs/reference/plot_runFAC.html

docs/reference/r_vitals.html

docs/reference/redstart-package.html

docs/reference/runFAC.html

docs/reference/runFAC_check_equilibrium.html

docs/reference/runFAC_finalize_output.html

docs/reference/runFAC_multi.html

docs/reference/runFAC_multi_finalize_output.html

docs/reference/runFAC_store_pop_state_i.html

docs/reference/step0_set_up.html

docs/reference/step1_winter_survival.html

docs/reference/step3_substepA1_hab_acquire_IB.html

docs/reference/step3_substepA1_hab_acquire_RM.html

docs/reference/step3_substepA2_mate_acquire_IB.html

docs/reference/step3_substepA2_mate_acquire_RM.html

docs/reference/step5_winter_habitat_acquisition.html

docs/reference/test_P.html

docs/reference/test_P_df_maker.html

docs/reference/test_dat_P.html

inst/Runge_and_Marra_Birds_of_Two_Worlds.pdf man/RandVitalRateResponseSurface.Rd man/eq01buildW0vect.Rd man/eq02buildW1Mat.Rd man/eq03buildW2Mat.Rd man/eq04_Bfc.Rd man/eq05_Bfk.Rd man/eq06_Bmc.Rd man/eq07_Bmk.Rd man/eq08_Bmd.Rd man/eq09_Pcgg.Rd man/eq10_Pcgp.Rd man/eq11_Pcpg.Rd man/eq12_Pcpp.Rd man/eq13_Pkgg.Rd man/eq14_Pkgp.Rd man/eq15_Pkpg.Rd man/eq16_Pkpp.Rd man/eq17buildB0Vect.Rd man/eq18AbuildRvec.Rd man/eq18BbuildPmat.Rd man/eq19AbuildFmat.Rd man/eq19BbuildMinMat.Rd man/eq20buildSbmat.Rd man/eq21buildSfmat.Rd man/eq22buildSymat.Rd man/eq23_stack_Ai.Rd man/eq24_comp_loop.Rd man/eq24_competition.Rd man/eq24_make_gamma_vec.Rd man/eq25_comp_constrain.Rd man/eq26_alloc_winter_P.Rd man/eq27_post_comp_pooling.Rd man/error_check_B0.Rd man/error_check_P_test.Rd man/error_check_Pxxx.Rd man/error_check_Y1_sex_ratio.Rd man/error_check_build_Ptest_df.Rd man/error_check_param_set.Rd man/error_check_summer.Rd man/make_FAC_df.Rd man/make_multiFAC_df.Rd man/param_grid.Rd man/param_ranges.Rd man/param_seqs.Rd man/param_seqs2.Rd man/param_set.Rd man/plot_Fig28_3.Rd man/plot_Fig28_4.Rd man/plot_Fig28_4_IBM.Rd man/plot_Fig28_5.Rd man/plot_Fig28_6.Rd man/plot_runFAC.Rd man/r_vitals.Rd man/redstart-package.Rd man/runFAC.Rd man/runFAC_check_equilibrium.Rd man/runFAC_finalize_output.Rd man/runFAC_multi.Rd man/runFAC_multi_finalize_output.Rd man/runFAC_store_pop_state_i.Rd man/step0_set_up.Rd man/step1_winter_survival.Rd man/step3_substepA1_hab_acquire_IB.Rd man/step3_substepA1_hab_acquire_RM.Rd man/step3_substepA2_mate_acquire_IB.Rd man/step3_substepA2_mate_acquire_RM.Rd man/step5_winter_habitat_acquisition.Rd man/test_P.Rd man/test_P_df_maker.Rd man/test_dat_P.Rd tests/testthat.R tests/testthat/test-my-test.R vignettes/a-Bio_Intro-FAC_demography.Rmd vignettes/b-model_intro-RM_FAC_model.Rmd vignettes/c-software_intro_rmFAC.Rmd vignettes/d-the_runFAC_command.Rmd vignettes/e-the_runFAC_multi_command.Rmd vignettes/f-make_figure_28_3.Rmd vignettes/g-make_figure_28_4.Rmd vignettes/h-make_figure_28_5.Rmd vignettes/i-make_figure_28_6.Rmd vignettes/p-software_checks.Rmd vignettes/v-Sherry_Holmes_notes.Rmd vignettes/w-annotated_bib.Rmd vignettes/x-creating_a_package.Rmd vignettes/y-building_a_package.Rmd vignettes/z-MANUSCRIPT.Rmd vignettes/z-TODO.Rmd vignettes/z-build_and_rebuild_package.Rmd

brouwern/FACavian documentation built on March 23, 2022, 10:07 a.m.