├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ └── R-CMD-check.yaml ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── R ├── Configuration.R ├── Disk_window.R ├── Im_window.R ├── RcppExports.R ├── Rectangle_window.R ├── Rectangle_window_union.R ├── box_plot.R ├── catch-routine-registration.R ├── chord_diagram.R ├── compute_A1.R ├── compute_A2_plus_A3.R ├── compute_G2.R ├── compute_S.R ├── compute_papangelou.R ├── execute_until_time_limit.R ├── format_coefficient_vector.R ├── gibbsm.R ├── heat_map.R ├── model_parameters.R ├── plot_papangelou_intensity.R ├── potentials.R ├── print.gibbsm.R ├── rbinomialpp.R ├── rbirth.R ├── rgibbs.R ├── rppp.R ├── rstratpp.R ├── spatstat_generics.R ├── summary.gibbsm.R ├── trace_plot.R ├── vcov.gibbsm.R └── x_range.R ├── README.md ├── benchmarks ├── gibbsm.R ├── gibbsm_large.R ├── gibbsm_with_covariate.R ├── rHardcore.R ├── rStrauss.R ├── rbinomialpp.R ├── rppp.R └── rstratpp.R ├── man ├── Configuration.Rd ├── Disk_window.Rd ├── Im_window.Rd ├── Rectangle_window.Rd ├── Rectangle_window_union.Rd ├── access_coefficient.Rd ├── area.Disk_window.Rd ├── area.Im_window.Rd ├── area.Rd ├── area.Rectangle_window.Rd ├── area.Rectangle_window_union.Rd ├── as.Configuration.Rd ├── as.Window.Rd ├── as.data.frame.Configuration.Rd ├── as.owin.Disk_window.Rd ├── as.owin.Im_window.Rd ├── as.owin.Rd ├── as.owin.Rectangle_window.Rd ├── as.owin.Rectangle_window_union.Rd ├── as.ppp.Configuration.Rd ├── box_plot.Rd ├── chord_diagram_plot.Rd ├── compute_A1.Rd ├── compute_A2_plus_A3.Rd ├── compute_G2.Rd ├── compute_S.Rd ├── compute_papangelou.Rd ├── compute_papangelou.default.Rd ├── compute_papangelou.gibbsm.Rd ├── construct_if_missing.Rd ├── convert_names.Rd ├── create_list_of_fits.Rd ├── execute_until_time_limit.Rd ├── format_coefficient_vector.Rd ├── get_number_types_and_check_conformance.Rd ├── gibbsm.Rd ├── has_duplicates.Rd ├── heat_map.Rd ├── length.Configuration.Rd ├── make_summary_df.Rd ├── marks.Configuration.Rd ├── marks.Rd ├── model_parameters.Rd ├── plot.Window.Rd ├── plot.gibbsm.Rd ├── plot_papangelou.Rd ├── plot_papangelou.default.Rd ├── plot_papangelou.gibbsm.Rd ├── potentials.Rd ├── ppjsdm-package.Rd ├── print.summary_gibbsm.Rd ├── rbinomialpp.Rd ├── rbirth.Rd ├── rgibbs.Rd ├── rgibbs.default.Rd ├── rgibbs.gibbsm.Rd ├── rppp.Rd ├── rstratpp.Rd ├── show_medium_range_models.Rd ├── show_short_range_models.Rd ├── sub-.Configuration.Rd ├── summary.gibbsm.Rd ├── trace_plot.Rd ├── types.Rd ├── vcov.gibbsm.Rd ├── volume.Disk_window.Rd ├── volume.Im_window.Rd ├── volume.Rd ├── volume.Rectangle_window.Rd ├── volume.Rectangle_window_union.Rd ├── x_coordinates.Rd ├── x_range.Rd ├── y_coordinates.Rd └── y_range.Rd ├── ppjsdm.Rproj ├── scripts ├── conditional_simulation.R ├── covariate_influence_experiment.R ├── covariate_influence_experiment2.R ├── covariate_influence_experiment3.R ├── coverage_probabilities.R ├── coverage_probabilities_by_species.R ├── coverage_probabilities_more_species.R ├── coverage_probabilities_spatstat.R ├── find_radius.R ├── find_radius_single.R ├── inference_tests.R ├── more_inference_checks.R ├── plot_tests.R ├── sanity_checks.R ├── single_species_experiment.R ├── unknown_radius.R ├── unknown_radius2.R └── unknown_saturation.R ├── src ├── Makevars ├── Makevars.win ├── RcppExports.cpp ├── compute_papangelou.cpp ├── compute_vcov.cpp ├── configuration │ ├── configuration_manipulation.hpp │ ├── configuration_wrapper.hpp │ ├── get_number_points.hpp │ └── make_R_configuration.hpp ├── has_duplicates.cpp ├── make_types.cpp ├── point │ ├── point_manipulation.hpp │ └── square_distance.hpp ├── ppjsdm.dll ├── prepare_gibbsm_data.cpp ├── rbinomialpp.cpp ├── rbirth.cpp ├── rgibbs.cpp ├── rppp.cpp ├── rstratpp.cpp ├── saturated_model │ ├── compute_dispersion.hpp │ ├── compute_dispersion_fitting.hpp │ ├── compute_dispersion_implementation.hpp │ ├── compute_dispersion_vcov.hpp │ ├── exponential_family_model.hpp │ ├── potentials │ │ ├── medium_range_potentials.hpp │ │ ├── potential.hpp │ │ └── short_range_potentials.hpp │ ├── regression_vector.hpp │ └── saturated_model.hpp ├── show_models.cpp ├── simulation │ ├── birth_death.hpp │ ├── coupling_from_the_past.hpp │ ├── inhomogeneous_ppp.hpp │ ├── metropolis_hastings.hpp │ ├── rbinomialpp_single.hpp │ ├── rppp_single.hpp │ └── rstrat_single.hpp ├── test-dispersion.cpp ├── test-heap.cpp ├── test-runner.cpp └── utility │ ├── algebra.hpp │ ├── approximate_draw.hpp │ ├── array_size.hpp │ ├── backwards_markov_chain.hpp │ ├── call_on_list_or_vector.hpp │ ├── construct_if_missing.hpp │ ├── find_in_containers.hpp │ ├── flatten_strict_upper_triangular.hpp │ ├── for_each_container.hpp │ ├── get_list_or_first_element.hpp │ ├── get_number_types.hpp │ ├── gibbsm_helper_functions.hpp │ ├── heap.hpp │ ├── im_wrapper.hpp │ ├── is_symmetric_matrix.hpp │ ├── lightweight_matrix.hpp │ ├── make_default_types.hpp │ ├── subset_to_nonNA.hpp │ ├── sum.hpp │ ├── timer.hpp │ ├── window.hpp │ └── window_concrete.hpp ├── tests ├── testthat.R └── testthat │ ├── test-Configuration.R │ ├── test-Disk_window.R │ ├── test-Rectangle_window.R │ ├── test-compute_A1.R │ ├── test-compute_G2.R │ ├── test-compute_S.R │ ├── test-compute_papangelou.R │ ├── test-cpp.R │ ├── test-execute_until_time_limit.R │ ├── test-gibbsm.R │ ├── test-model_parameters.R │ ├── test-rbinomialpp.R │ └── test-rppp.R └── vignettes ├── .gitignore ├── isec2020_presentation_handout.pdf ├── isec2020_presentation_handout.pdf.asis └── model.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iflint1/ppjsdm/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.github/.gitignore: -------------------------------------------------------------------------------- 1 | *.html 2 | -------------------------------------------------------------------------------- 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