Files in atredennick/community_synchrony
Calculates syunchrony and stability metrics from time series data
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/community_synchrony.R
R/crowding_functions.R
R/import_regression_params_fxns.R
R/import_regression_params_fxns_yrlycomp.R
R/ipm_kernel_vitalrate_fxns.R
R/ipm_kernel_vitalrate_fxns_yrly.R
R/recruitment_function.R
R/recruitment_function_yrlycomp.R
R/run_ipm.R
R/vital_rate_regression_functions.R
R/vital_rate_regression_functions_yrlycomp.R
README.md
community_synchrony.Rproj
data/Arizona/BOER/BOER_buf5_dorm1.csv
data/Arizona/BOER/BOER_genet_xy.csv
data/Arizona/BOER/BOERassign_genets.csv
data/Arizona/BOER/BOERgenets.pdf
data/Arizona/BOER/growDnoNA.csv
data/Arizona/BOER/quadratCover.csv
data/Arizona/BOER/recArea.csv
data/Arizona/BOER/recSize.csv
data/Arizona/BOER/survD.csv
data/Arizona/BORO/BORO_buf5_dorm1.csv
data/Arizona/BORO/BORO_genet_xy.csv
data/Arizona/BORO/BOROassign_genets.csv
data/Arizona/BORO/BOROgenets.pdf
data/Arizona/BORO/growDnoNA.csv
data/Arizona/BORO/quadratCover.csv
data/Arizona/BORO/recArea.csv
data/Arizona/BORO/recSize.csv
data/Arizona/BORO/survD.csv
data/Climate/ClimateIdaho.csv
data/Crowding/crowd_grow_list.RDS
data/Crowding/crowd_survival_list.RDS
data/Idaho/ARTR/ARTR_buf5_dorm2.csv
data/Idaho/ARTR/ARTR_genet_distances.csv
data/Idaho/ARTR/ARTR_genet_xy.csv
data/Idaho/ARTR/assign_genetsARTR.csv
data/Idaho/ARTR/growDnoNA.csv
data/Idaho/ARTR/quadratCover.csv
data/Idaho/ARTR/recArea.csv
data/Idaho/ARTR/recSize.csv
data/Idaho/ARTR/survD.csv
data/Idaho/HECO/HECO_buf5_dorm2.csv
data/Idaho/HECO/HECO_buf5_dorm2_old.csv
data/Idaho/HECO/HECO_genet_distances.csv
data/Idaho/HECO/HECO_genet_xy.csv
data/Idaho/HECO/assign_genetsHECO.csv
data/Idaho/HECO/growDnoNA.csv
data/Idaho/HECO/quadratCover.csv
data/Idaho/HECO/recArea.csv
data/Idaho/HECO/recSize.csv
data/Idaho/HECO/survD.csv
data/Idaho/POSE/POSE_buf5_dorm2.csv
data/Idaho/POSE/POSE_genet_distances.csv
data/Idaho/POSE/POSE_genet_xy.csv
data/Idaho/POSE/POSEassign_genets.csv
data/Idaho/POSE/POSEgenets.pdf
data/Idaho/POSE/growDnoNA.csv
data/Idaho/POSE/quadratCover.csv
data/Idaho/POSE/recArea.csv
data/Idaho/POSE/recSize.csv
data/Idaho/POSE/survD.csv
data/Idaho/PSSP/PSSP_buf5_dorm1.csv
data/Idaho/PSSP/PSSP_buf5_dorm2.csv
data/Idaho/PSSP/PSSP_genet_distances.csv
data/Idaho/PSSP/PSSP_genet_xy.csv
data/Idaho/PSSP/PSSP_obs_cover.pdf
data/Idaho/PSSP/RecrPerArea.csv
data/Idaho/PSSP/assign_genets_PSSP.csv
data/Idaho/PSSP/distance_histogram.pdf
data/Idaho/PSSP/genets.pdf
data/Idaho/PSSP/growDnoNA.csv
data/Idaho/PSSP/quadratCover.csv
data/Idaho/PSSP/recArea.csv
data/Idaho/PSSP/recSize.csv
data/Idaho/PSSP/survD.csv
data/Kansas/BOCU/BOCU_buf5_dorm1.csv
data/Kansas/BOCU/BOCU_genet_distances.csv
data/Kansas/BOCU/BOCU_genet_xy.csv
data/Kansas/BOCU/BOCUassign_genets.csv
data/Kansas/BOCU/BOCUgenets.pdf
data/Kansas/BOCU/growDnoNA.csv
data/Kansas/BOCU/quadratCover.csv
data/Kansas/BOCU/recArea.csv
data/Kansas/BOCU/recSize.csv
data/Kansas/BOCU/survD.csv
data/Kansas/BOHI/BOHI_buf5_dorm1.csv
data/Kansas/BOHI/BOHI_genet_distances.csv
data/Kansas/BOHI/BOHI_genet_xy.csv
data/Kansas/BOHI/BOHIassign_genets.csv
data/Kansas/BOHI/BOHIgenets.pdf
data/Kansas/BOHI/growDnoNA.csv
data/Kansas/BOHI/quadratCover.csv
data/Kansas/BOHI/recArea.csv
data/Kansas/BOHI/recSize.csv
data/Kansas/BOHI/survD.csv
data/Kansas/SCSC/K_all.tif
data/Kansas/SCSC/SCSC_buf5_dorm1.csv
data/Kansas/SCSC/SCSC_genet_distances.csv
data/Kansas/SCSC/SCSC_genet_xy.csv
data/Kansas/SCSC/SCSCassign_genets.csv
data/Kansas/SCSC/SCSCgenets.pdf
data/Kansas/SCSC/Thumbs.db
data/Kansas/SCSC/growDnoNA.csv
data/Kansas/SCSC/quadratCover.csv
data/Kansas/SCSC/recArea.csv
data/Kansas/SCSC/recSize.csv
data/Kansas/SCSC/survD.csv
data/Montana/BOGR/BOGR_genet_xy.csv
data/Montana/BOGR/growDnoNA.csv
data/Montana/BOGR/quadratCover.csv
data/Montana/BOGR/recArea.csv
data/Montana/BOGR/recSize.csv
data/Montana/BOGR/survD.csv
data/Montana/BOGR_edited/BOGR_buf5_dorm1_edited.csv
data/Montana/BOGR_edited/BOGR_genet_xy_edited.csv
data/Montana/BOGR_edited/BOGRassign_genets.csv
data/Montana/BOGR_edited/growDnoNA.csv
data/Montana/BOGR_edited/quadratCover.csv
data/Montana/BOGR_edited/readme.txt
data/Montana/BOGR_edited/recArea.csv
data/Montana/BOGR_edited/recArea_quads_not_removed.csv
data/Montana/BOGR_edited/recSize.csv
data/Montana/BOGR_edited/survD.csv
data/Montana/BOGR_edited/suspect_BOGR_quads.csv
data/Montana/BOGR_unedited/BOGR_buf5_dorm1.csv
data/Montana/BOGR_unedited/BOGR_genet_xy.csv
data/Montana/BOGR_unedited/BOGRassign_genets.csv
data/Montana/BOGR_unedited/BOGRgenets.pdf
data/Montana/BOGR_unedited/growDnoNA.csv
data/Montana/BOGR_unedited/quadratCover.csv
data/Montana/BOGR_unedited/recArea.csv
data/Montana/BOGR_unedited/recSize.csv
data/Montana/BOGR_unedited/survD.csv
data/Montana/HECO/HECO_buf5_dorm1.csv
data/Montana/HECO/HECO_genet_xy.csv
data/Montana/HECO/HECOassign_genets.csv
data/Montana/HECO/HECOgenets.pdf
data/Montana/HECO/growDnoNA.csv
data/Montana/HECO/quadratCover.csv
data/Montana/HECO/recArea.csv
data/Montana/HECO/recSize.csv
data/Montana/HECO/survD.csv
data/Montana/PASM/PASM_buf5_dorm1.csv
data/Montana/PASM/PASM_genet_xy.csv
data/Montana/PASM/PASMassign_genets.csv
data/Montana/PASM/PASMgenets.pdf
data/Montana/PASM/growDnoNA.csv
data/Montana/PASM/quadratCover.csv
data/Montana/PASM/recArea.csv
data/Montana/PASM/recSize.csv
data/Montana/PASM/survD.csv
data/Montana/POSE/POSE_buf5_dorm1.csv
data/Montana/POSE/POSE_genet_xy.csv
data/Montana/POSE/POSEassign_genets.csv
data/Montana/POSE/POSEgenets.pdf
data/Montana/POSE/growDnoNA.csv
data/Montana/POSE/quadratCover.csv
data/Montana/POSE/recArea.csv
data/Montana/POSE/recSize.csv
data/Montana/POSE/survD.csv
data/NewMexico/BOER/BOER_buf5_dorm1.csv
data/NewMexico/BOER/BOER_genet_distances.csv
data/NewMexico/BOER/BOER_genet_xy.csv
data/NewMexico/BOER/BOERassign_genets.csv
data/NewMexico/BOER/BOERgenets.pdf
data/NewMexico/BOER/growDnoNA.csv
data/NewMexico/BOER/quadratCover.csv
data/NewMexico/BOER/recArea.csv
data/NewMexico/BOER/recSize.csv
data/NewMexico/BOER/survD.csv
data/NewMexico/SPFL/SPFL_buf5_dorm1.csv
data/NewMexico/SPFL/SPFL_genet_distances.csv
data/NewMexico/SPFL/SPFL_genet_xy.csv
data/NewMexico/SPFL/SPFLassign_genets.csv
data/NewMexico/SPFL/SPFLgenets.pdf
data/NewMexico/SPFL/growDnoNA.csv
data/NewMexico/SPFL/quadratCover.csv
data/NewMexico/SPFL/recArea.csv
data/NewMexico/SPFL/recSize.csv
data/NewMexico/SPFL/survD.csv
data/alpha_list_growth.csv
data/alpha_list_survival.csv
devel/calc_comp_year_corrs.R
devel/formula.tex
devel/growth_num_compyrs_sig.RDS
devel/inspect_param_corrs.R
devel/lotvol_popmodel.R
devel/make_paramcorr_tables.R
devel/mono_poly_ibm.RDS
devel/plot_abund_v_landscape.R
devel/plot_comp_randeff_cis.R
devel/plot_ibm_sims.R
devel/plot_ipm_sims.R
devel/plot_montana_ipm_yearlycomp.R
devel/plot_timeseries.R
devel/plot_yreffect_corrs.R
devel/prediction_obs_sims_plot.R
devel/randyear_compCIs_growth.png
devel/randyear_compCIs_rec.png
devel/randyear_compCIs_survival.png
devel/recruitment_intercept_comp_cors.pdf
devel/recruitment_num_compyrs_sig.RDS
devel/subset_bogr_data.R
devel/surv_grow_paramcorrs.txt
devel/survival_num_compyrs_sig.RDS
devel/synch_timeseries_test.R
devel/table_spp_interactions.R
devel/test_bogr_quadyrs.R
docs/INTERACTION_TABLES_MASTER.tex
docs/cache/appendix_X1.Rmd
docs/cache/appendix_mathsupport.Rmd
docs/cache/appendix_speciesInteractions.Rmd
docs/cache/appendix_stats.Rmd
docs/cache/appendix_temporalRandomEffects.Rmd
docs/cache/envresp_vs_ipmsynch.png
docs/cache/formatted_fig2.png
docs/cache/ibm_across_landscape_supp_noARTR.png
docs/cache/ibm_sims_fig.png
docs/cache/ipm_pgr_plot.png
docs/cache/prediction_observed.png
docs/cache/synchrony_conceptual_fig.png
docs/components/Montana_yearlycomp_ipmsynch.png
docs/components/all_sims_results.png
docs/components/all_sims_supp_noARTR.png
docs/components/cache/ms_communitySynchrony/__packages
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docs/components/figureS2_simscover.png
docs/components/figureS3_ibmcover.png
docs/components/formatted_figures.key
docs/components/formatted_figures/demographic_variances_cover.png
docs/components/formatted_figures/demographic_variances_pgr.png
docs/components/formatted_figures/environmental_variances_cover.png
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docs/components/formatted_figures/formatted_figure1.png
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docs/components/formatted_figures/synchrony_flowchart_bw.png
docs/components/ibm_sims_across_landscape.png
docs/components/ipm_pgr_plot.png
docs/components/multi_single_rec_param_comparison.png
docs/components/poly_vs_mono_synch.png
docs/components/synchrony_flowchart.png
docs/ms_communitySynchrony.Rmd
docs/ms_communitySynchrony.log
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inst/examples/demo_plot.png
inst/examples/demog_stoch_test.Rmd
inst/examples/demog_stoch_test.pdf
inst/examples/demog_stoch_test.tex
inst/examples/demog_stoch_test_files/figure-latex/figs.pdf
inst/examples/ibm_demogstoch_test.R
inst/examples/idaho_demographic_stoch.pdf
inst/examples/ipm_demostoch_notes.Rmd
inst/examples/ipm_demostoch_notes.pdf
inst/examples/ipm_sims_example.Rmd
inst/examples/synchrony-example.Rmd
inst/examples/vital_rate_fxns_example.Rmd
man/G.Rd
man/S.Rd
man/community_synchrony-package.Rd
man/estimate_crowding.Rd
man/f.Rd
man/format_growth_params.Rd
man/format_recruitment_params.Rd
man/format_survival_params.Rd
man/get_comm_synchrony.Rd
man/get_growth_params.Rd
man/get_ipm_synchrony.Rd
man/get_rpa.Rd
man/get_survival_params.Rd
man/recruit_mcmc.Rd
man/run_ipm.Rd
packrat/init.R
packrat/packrat.lock
packrat/packrat.opts
packrat/src/packrat/packrat_0.4.3.tar.gz
results/allsims_plot_data.RDS
results/calculate_site_metrics.RDS
results/correlation_Rsynch_cv.txt
results/envstoch_predictions.RDS
results/growth_params_list.RDS
results/growth_params_yrlycomp_list.RDS
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results/ibm_sims/ibm_Idaho_fluctnointerexpand4.RDS
results/ibm_sims/ibm_Idaho_fluctnointerexpand5.RDS
results/ibm_sims/ibm_Kansas_constinterexpand1.RDS
results/ibm_sims/ibm_Kansas_constinterexpand2.RDS
results/ibm_sims/ibm_Kansas_constinterexpand3.RDS
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results/ibm_sims_collated.RDS
results/idaho_ibm_demogstoch_only.RDS
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results/idaho_ipm_demogstoch_only_fromPACKAGE.RDS
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results/ipm_comp_nocomp_sims_yearlycomp_Montana.RDS
results/ipm_ibm_covmatdiffs.pdf
results/ipm_yearly_pgr.RDS
results/nt_popvecBIG_ibm.RDS
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results/param_covariance/recruitment_Arizona_BORO_paramcorrs.png
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runscripts/run_ibm.R
runscripts/run_ipm_simulations.R
runscripts/run_ipm_simulations_yrlcomp.R
runscripts/run_ipm_source.R
runscripts/run_ipm_source_yrlycomp.R
