Files in cxr

A Toolbox for Modelling Species Coexistence in R

NEWS.md README.md R/RK_project_alpha_global_lambdacov_none_alphacov_none.R R/cxr-package.R R/BH_project_alpha_pairwise_lambdacov_global_alphacov_pairwise.R R/BH_er_lambdacov_global_effectcov_global_responsecov_global.R R/LW_er_lambdacov_global_effectcov_global_responsecov_global.R R/fill_demography_matrix.R R/RK_competitive_ability.R R/cxr_check_input_er.R R/cxr_check_initial_values.R R/cxr_model_template.R R/BH_project_alpha_pairwise_lambdacov_none_alphacov_none.R R/RK_project_alpha_pairwise_lambdacov_none_alphacov_none.R R/LV_project_alpha_pairwise_lambdacov_none_alphacov_none.R R/cxr_pm_multifit.R R/vec_permutation_matrices.R R/LW_species_fitness.R R/BH_pm_alpha_none_lambdacov_none_alphacov_none.R R/summary.R R/species_fitness.R R/cxr_check_pm_input.R R/BH_pm_alpha_pairwise_lambdacov_global_alphacov_global.R R/LW_project_alpha_pairwise_lambdacov_global_alphacov_global.R R/generate_vital_rate_coefs.R R/RK_project_alpha_none_lambdacov_none_alphacov_none.R R/RK_pm_alpha_global_lambdacov_none_alphacov_none.R R/cxr_pm_fit.R R/niche_overlap.R R/LV_er_lambdacov_none_effectcov_none_responsecov_none.R R/RK_pm_alpha_pairwise_lambdacov_global_alphacov_pairwise.R R/BH_pm_alpha_pairwise_lambdacov_global_alphacov_pairwise.R R/neigh_list.R R/LV_er_lambdacov_global_effectcov_global_responsecov_global.R R/RK_species_fitness.R R/LV_pm_alpha_none_lambdacov_none_alphacov_none.R R/cxr_retrieve_er_params.R R/LW_pm_alpha_pairwise_lambdacov_global_alphacov_global.R R/BH_project_alpha_none_lambdacov_none_alphacov_none.R R/LW_pm_alpha_none_lambdacov_none_alphacov_none.R R/densities_to_df.R R/LV_pm_alpha_pairwise_lambdacov_none_alphacov_none.R R/cxr_pm_model_template.R R/BH_pm_alpha_pairwise_lambdacov_none_alphacov_none.R R/competitive_ability.R R/RK_pm_alpha_none_lambdacov_none_alphacov_none.R R/cxr_structural_fitness_diff.R R/salinity_list.R R/RK_pm_alpha_pairwise_lambdacov_none_alphacov_none.R R/cxr_get_init_params.R R/abundance.R R/LW_project_alpha_none_lambdacov_none_alphacov_none.R R/cxr_retrieve_params.R R/LV_pm_alpha_global_lambdacov_none_alphacov_none.R R/BH_er_lambdacov_none_effectcov_none_responsecov_none.R R/fill_transition_matrix.R R/LW_pm_alpha_pairwise_lambdacov_none_alphacov_none.R R/cxr_pm_bootstrap.R R/BH_pm_alpha_global_lambdacov_none_alphacov_none.R R/BH_project_alpha_pairwise_lambdacov_global_alphacov_global.R R/cxr_check_method_boundaries.R R/LV_project_alpha_none_lambdacov_none_alphacov_none.R R/cxr_generate_test_data.R R/RK_project_alpha_pairwise_lambdacov_global_alphacov_global.R R/fill_dispersal_matrix.R R/RK_demographic_ratio.R R/BH_project_alpha_global_lambdacov_none_alphacov_none.R R/cxr_er_bootstrap.R R/BH_species_fitness.R R/LW_project_alpha_pairwise_lambdacov_global_alphacov_pairwise.R R/niche_overlap_SA.R R/fitness_ratio.R R/RK_er_lambdacov_none_effectcov_none_responsecov_none.R R/LV_project_alpha_pairwise_lambdacov_global_alphacov_pairwise.R R/LV_pm_alpha_pairwise_lambdacov_global_alphacov_global.R R/LW_competitive_ability.R R/LV_project_alpha_pairwise_lambdacov_global_alphacov_global.R R/niche_overlap_MCT.R R/RK_pm_alpha_pairwise_lambdacov_global_alphacov_global.R R/LW_demographic_ratio.R R/BH_competitive_ability.R R/LV_competitive_ability.R R/LW_project_alpha_global_lambdacov_none_alphacov_none.R R/cxr_competitive_response.R R/LV_species_fitness.R R/cxr_er_model_template.R R/calculate_densities.R R/vital_rate.R R/glm_example_coefs.R R/cxr_get_model_bounds.R R/cxr_er_fit.R R/LW_pm_alpha_pairwise_lambdacov_global_alphacov_pairwise.R R/avg_fitness_diff.R R/LV_demographic_ratio.R R/get_densities.R R/cxr_check_input_data.R R/abundance_projection.R R/LW_project_alpha_pairwise_lambdacov_none_alphacov_none.R R/cxr_sort_params.R R/cxr_return_init_length.R R/cxr_demographic_ratio.R R/cxr_init_er_params.R R/LW_er_lambdacov_none_effectcov_none_responsecov_none.R R/LV_pm_alpha_pairwise_lambdacov_global_alphacov_pairwise.R R/RK_project_alpha_pairwise_lambdacov_global_alphacov_pairwise.R R/species_rates.R R/LV_project_alpha_global_lambdacov_none_alphacov_none.R R/spatial_sampling.R R/LW_pm_alpha_global_lambdacov_none_alphacov_none.R R/build_param.R R/BH_demographic_ratio.R R/metapopulation_example_param.R R/RK_er_lambdacov_global_effectcov_global_responsecov_global.R inst/doc/V6_Metapopulation_projections.Rmd inst/doc/V3_Coexistence_metrics.R inst/doc/V3_Coexistence_metrics.Rmd inst/doc/V2_Data_formats.R inst/doc/V1_Getting_started.R inst/doc/V6_Metapopulation_projections.R inst/doc/V5_Abundance_projections.R inst/doc/V1_Getting_started.Rmd inst/doc/V5_Abundance_projections.Rmd inst/doc/V2_Data_formats.Rmd inst/doc/V4_Models.R inst/doc/V4_Models.Rmd tests/test-all.R tests/testthat/test-functions.R tests/testthat/test-metapopulations.R tests/testthat/test-mct_functions.R tests/testthat/test-projections.R vignettes/V6_Metapopulation_projections.Rmd vignettes/V3_Coexistence_metrics.Rmd vignettes/V1_Getting_started.Rmd vignettes/V5_Abundance_projections.Rmd vignettes/V2_Data_formats.Rmd vignettes/V4_Models.Rmd man/LV_pm_alpha_global_lambdacov_none_alphacov_none.Rd man/LW_pm_alpha_pairwise_lambdacov_none_alphacov_none.Rd man/LW_pm_alpha_pairwise_lambdacov_global_alphacov_pairwise.Rd man/niche_overlap.Rd man/RK_project_alpha_none_lambdacov_none_alphacov_none.Rd man/cxr_generate_test_data.Rd man/LV_er_lambdacov_global_effectcov_global_responsecov_global.Rd man/RK_pm_alpha_pairwise_lambdacov_global_alphacov_global.Rd man/vital_rate.Rd man/RK_project_alpha_global_lambdacov_none_alphacov_none.Rd man/summary.cxr_pm_multifit.Rd man/cxr_pm_fit.Rd man/LV_pm_alpha_none_lambdacov_none_alphacov_none.Rd man/spatial_sampling.Rd man/generate_vital_rate_coefs.Rd man/LV_project_alpha_global_lambdacov_none_alphacov_none.Rd man/LW_project_alpha_pairwise_lambdacov_none_alphacov_none.Rd man/competitive_ability.Rd man/LW_project_alpha_pairwise_lambdacov_global_alphacov_global.Rd man/calculate_densities.Rd man/build_param.Rd man/avg_fitness_diff.Rd man/BH_project_alpha_none_lambdacov_none_alphacov_none.Rd man/vec_permutation_matrices.Rd man/RK_project_alpha_pairwise_lambdacov_none_alphacov_none.Rd man/LW_project_alpha_global_lambdacov_none_alphacov_none.Rd man/cxr_er_fit.Rd man/metapopulation_example_param.Rd man/RK_pm_alpha_pairwise_lambdacov_global_alphacov_pairwise.Rd man/BH_er_lambdacov_global_effectcov_global_responsecov_global.Rd man/RK_er_lambdacov_global_effectcov_global_responsecov_global.Rd man/LV_project_alpha_none_lambdacov_none_alphacov_none.Rd man/abundance_projection.Rd man/LW_pm_alpha_global_lambdacov_none_alphacov_none.Rd man/LW_project_alpha_pairwise_lambdacov_global_alphacov_pairwise.Rd man/species_rates.Rd man/cxr-package.Rd man/LW_pm_alpha_none_lambdacov_none_alphacov_none.Rd man/BH_pm_alpha_pairwise_lambdacov_none_alphacov_none.Rd man/cxr_er_bootstrap.Rd man/BH_project_alpha_global_lambdacov_none_alphacov_none.Rd man/BH_project_alpha_pairwise_lambdacov_none_alphacov_none.Rd man/LW_project_alpha_none_lambdacov_none_alphacov_none.Rd man/salinity_list.Rd man/LV_er_lambdacov_none_effectcov_none_responsecov_none.Rd man/RK_pm_alpha_global_lambdacov_none_alphacov_none.Rd man/cxr_pm_bootstrap.Rd man/fitness_ratio.Rd man/LV_pm_alpha_pairwise_lambdacov_global_alphacov_pairwise.Rd man/RK_pm_alpha_none_lambdacov_none_alphacov_none.Rd man/BH_er_lambdacov_none_effectcov_none_responsecov_none.Rd man/BH_pm_alpha_pairwise_lambdacov_global_alphacov_global.Rd man/BH_pm_alpha_global_lambdacov_none_alphacov_none.Rd man/species_fitness.Rd man/summary.cxr_pm_fit.Rd man/summary.cxr_er_fit.Rd man/BH_pm_alpha_pairwise_lambdacov_global_alphacov_pairwise.Rd man/neigh_list.Rd man/BH_project_alpha_pairwise_lambdacov_global_alphacov_global.Rd man/LV_project_alpha_pairwise_lambdacov_global_alphacov_global.Rd man/abundance.Rd man/LV_pm_alpha_pairwise_lambdacov_none_alphacov_none.Rd man/fill_demography_matrix.Rd man/LV_pm_alpha_pairwise_lambdacov_global_alphacov_global.Rd man/LW_pm_alpha_pairwise_lambdacov_global_alphacov_global.Rd man/LV_project_alpha_pairwise_lambdacov_global_alphacov_pairwise.Rd man/RK_project_alpha_pairwise_lambdacov_global_alphacov_global.Rd man/cxr_pm_multifit.Rd man/BH_pm_alpha_none_lambdacov_none_alphacov_none.Rd man/densities_to_df.Rd man/fill_dispersal_matrix.Rd man/LW_er_lambdacov_global_effectcov_global_responsecov_global.Rd man/RK_project_alpha_pairwise_lambdacov_global_alphacov_pairwise.Rd man/glm_example_coefs.Rd man/LV_project_alpha_pairwise_lambdacov_none_alphacov_none.Rd man/RK_er_lambdacov_none_effectcov_none_responsecov_none.Rd man/RK_pm_alpha_pairwise_lambdacov_none_alphacov_none.Rd man/LW_er_lambdacov_none_effectcov_none_responsecov_none.Rd man/BH_project_alpha_pairwise_lambdacov_global_alphacov_pairwise.Rd man/fill_transition_matrix.Rd