Files in joshwlambert/DAISIEprepExtra
Scripts and documents to accompany and reproduce Lambert et al. application paper describing the DAISIEprep R package
.Rbuildignore
.Rprofile
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.gitignore
DAISIEprepExtra.Rproj
DESCRIPTION
LICENSE.md
NAMESPACE
NEWS.md
R/DAISIEprepExtra-package.R
R/data.R
README.md
data-raw/hawaii_asteraceae.R
data-raw/madagascar_mammals.R
data/hawaii_asters.rda
data/madagascar_mammals.rda
data/world_border.rda
inst/bash/install_DAISIEprepExtra.sh
inst/bash/run_multi_phylo_example.sh
inst/bash/run_performance.sh
inst/bash/run_performance_empirical.sh
inst/bash/run_performance_parallel.sh
inst/bash/run_posterior_phylo_example.sh
inst/bash/run_sensitivity.sh
inst/bash/run_sensitivity_parallel.sh
inst/bash/run_single_phylo_example.sh
inst/extdata/Hawaiian_Bidens_Knope_2020.tre
inst/extdata/Keeley_2021.tre
inst/extdata/Landis_2018_g4_mcc.tre
inst/extdata/Pacific_Bidens_Knope_2020.tre
inst/extdata/Upham_complete_mcc.tre
inst/extdata/Upham_complete_posterior_100.nex
inst/extdata/Upham_dna_mcc.tre
inst/extdata/Upham_dna_posterior_100.nex
inst/extdata/hawaii_asteraceae_checklist.csv
inst/extdata/madagascar_mammal_checklist.csv
inst/performance_data/performance_empirical.rds
inst/performance_data/performance_param_set_1.rds
inst/performance_data/performance_param_set_10.rds
inst/performance_data/performance_param_set_11.rds
inst/performance_data/performance_param_set_12.rds
inst/performance_data/performance_param_set_13.rds
inst/performance_data/performance_param_set_14.rds
inst/performance_data/performance_param_set_15.rds
inst/performance_data/performance_param_set_16.rds
inst/performance_data/performance_param_set_17.rds
inst/performance_data/performance_param_set_18.rds
inst/performance_data/performance_param_set_19.rds
inst/performance_data/performance_param_set_2.rds
inst/performance_data/performance_param_set_20.rds
inst/performance_data/performance_param_set_21.rds
inst/performance_data/performance_param_set_22.rds
inst/performance_data/performance_param_set_23.rds
inst/performance_data/performance_param_set_24.rds
inst/performance_data/performance_param_set_25.rds
inst/performance_data/performance_param_set_26.rds
inst/performance_data/performance_param_set_27.rds
inst/performance_data/performance_param_set_28.rds
inst/performance_data/performance_param_set_29.rds
inst/performance_data/performance_param_set_3.rds
inst/performance_data/performance_param_set_30.rds
inst/performance_data/performance_param_set_31.rds
inst/performance_data/performance_param_set_32.rds
inst/performance_data/performance_param_set_33.rds
inst/performance_data/performance_param_set_34.rds
inst/performance_data/performance_param_set_35.rds
inst/performance_data/performance_param_set_36.rds
inst/performance_data/performance_param_set_37.rds
inst/performance_data/performance_param_set_38.rds
inst/performance_data/performance_param_set_39.rds
inst/performance_data/performance_param_set_4.rds
inst/performance_data/performance_param_set_40.rds
inst/performance_data/performance_param_set_41.rds
inst/performance_data/performance_param_set_42.rds
inst/performance_data/performance_param_set_43.rds
inst/performance_data/performance_param_set_44.rds
inst/performance_data/performance_param_set_45.rds
inst/performance_data/performance_param_set_46.rds
inst/performance_data/performance_param_set_47.rds
inst/performance_data/performance_param_set_48.rds
inst/performance_data/performance_param_set_49.rds
inst/performance_data/performance_param_set_5.rds
inst/performance_data/performance_param_set_50.rds
inst/performance_data/performance_param_set_51.rds
inst/performance_data/performance_param_set_52.rds
inst/performance_data/performance_param_set_53.rds
inst/performance_data/performance_param_set_54.rds
inst/performance_data/performance_param_set_55.rds
inst/performance_data/performance_param_set_56.rds
inst/performance_data/performance_param_set_57.rds
inst/performance_data/performance_param_set_58.rds
inst/performance_data/performance_param_set_59.rds
inst/performance_data/performance_param_set_6.rds
inst/performance_data/performance_param_set_60.rds
inst/performance_data/performance_param_set_7.rds
inst/performance_data/performance_param_set_8.rds
inst/performance_data/performance_param_set_9.rds
inst/plots/algo_plot.png
inst/plots/global_island.png
inst/plots/performance.png
inst/plots/performance_prob_endemic.png
inst/plots/performance_prob_on_island.png
inst/plots/pipeline_phylo.png
inst/plots/sensitivity.png
inst/plots/utility_plots.png
inst/scripts/algorithm_plot.R
inst/scripts/global_island.R
inst/scripts/missing_species.R
inst/scripts/multi_phylo_example.R
inst/scripts/performance.R
inst/scripts/performance_empirical.R
inst/scripts/performance_parallel.R
inst/scripts/pipeline_phylo.R
inst/scripts/plot_performance.R
inst/scripts/plot_sensitivity.R
inst/scripts/posterior_phylo_example.R
inst/scripts/sensitivity.R
inst/scripts/sensitivity_parallel.R
inst/scripts/single_phylo_example.R
inst/scripts/utility_plots.R
inst/sensitivity_data/sensitivity_tree_index_1.rds
inst/sensitivity_data/sensitivity_tree_index_10.rds
inst/sensitivity_data/sensitivity_tree_index_100.rds
inst/sensitivity_data/sensitivity_tree_index_11.rds
inst/sensitivity_data/sensitivity_tree_index_12.rds
inst/sensitivity_data/sensitivity_tree_index_13.rds
inst/sensitivity_data/sensitivity_tree_index_14.rds
inst/sensitivity_data/sensitivity_tree_index_15.rds
inst/sensitivity_data/sensitivity_tree_index_16.rds
inst/sensitivity_data/sensitivity_tree_index_17.rds
inst/sensitivity_data/sensitivity_tree_index_18.rds
inst/sensitivity_data/sensitivity_tree_index_19.rds
inst/sensitivity_data/sensitivity_tree_index_2.rds
inst/sensitivity_data/sensitivity_tree_index_20.rds
inst/sensitivity_data/sensitivity_tree_index_21.rds
inst/sensitivity_data/sensitivity_tree_index_22.rds
inst/sensitivity_data/sensitivity_tree_index_23.rds
inst/sensitivity_data/sensitivity_tree_index_24.rds
inst/sensitivity_data/sensitivity_tree_index_25.rds
inst/sensitivity_data/sensitivity_tree_index_26.rds
inst/sensitivity_data/sensitivity_tree_index_27.rds
inst/sensitivity_data/sensitivity_tree_index_28.rds
inst/sensitivity_data/sensitivity_tree_index_29.rds
inst/sensitivity_data/sensitivity_tree_index_3.rds
inst/sensitivity_data/sensitivity_tree_index_30.rds
inst/sensitivity_data/sensitivity_tree_index_31.rds
inst/sensitivity_data/sensitivity_tree_index_32.rds
inst/sensitivity_data/sensitivity_tree_index_33.rds
inst/sensitivity_data/sensitivity_tree_index_34.rds
inst/sensitivity_data/sensitivity_tree_index_35.rds
inst/sensitivity_data/sensitivity_tree_index_36.rds
inst/sensitivity_data/sensitivity_tree_index_37.rds
inst/sensitivity_data/sensitivity_tree_index_38.rds
inst/sensitivity_data/sensitivity_tree_index_39.rds
inst/sensitivity_data/sensitivity_tree_index_4.rds
inst/sensitivity_data/sensitivity_tree_index_40.rds
inst/sensitivity_data/sensitivity_tree_index_41.rds
inst/sensitivity_data/sensitivity_tree_index_42.rds
inst/sensitivity_data/sensitivity_tree_index_43.rds
inst/sensitivity_data/sensitivity_tree_index_44.rds
inst/sensitivity_data/sensitivity_tree_index_45.rds
inst/sensitivity_data/sensitivity_tree_index_46.rds
inst/sensitivity_data/sensitivity_tree_index_47.rds
inst/sensitivity_data/sensitivity_tree_index_48.rds
inst/sensitivity_data/sensitivity_tree_index_49.rds
inst/sensitivity_data/sensitivity_tree_index_5.rds
inst/sensitivity_data/sensitivity_tree_index_50.rds
inst/sensitivity_data/sensitivity_tree_index_51.rds
inst/sensitivity_data/sensitivity_tree_index_52.rds
inst/sensitivity_data/sensitivity_tree_index_53.rds
inst/sensitivity_data/sensitivity_tree_index_54.rds
inst/sensitivity_data/sensitivity_tree_index_55.rds
inst/sensitivity_data/sensitivity_tree_index_56.rds
inst/sensitivity_data/sensitivity_tree_index_57.rds
inst/sensitivity_data/sensitivity_tree_index_58.rds
inst/sensitivity_data/sensitivity_tree_index_59.rds
inst/sensitivity_data/sensitivity_tree_index_6.rds
inst/sensitivity_data/sensitivity_tree_index_60.rds
inst/sensitivity_data/sensitivity_tree_index_61.rds
inst/sensitivity_data/sensitivity_tree_index_62.rds
inst/sensitivity_data/sensitivity_tree_index_63.rds
inst/sensitivity_data/sensitivity_tree_index_64.rds
inst/sensitivity_data/sensitivity_tree_index_65.rds
inst/sensitivity_data/sensitivity_tree_index_66.rds
inst/sensitivity_data/sensitivity_tree_index_67.rds
inst/sensitivity_data/sensitivity_tree_index_68.rds
inst/sensitivity_data/sensitivity_tree_index_69.rds
inst/sensitivity_data/sensitivity_tree_index_7.rds
inst/sensitivity_data/sensitivity_tree_index_70.rds
inst/sensitivity_data/sensitivity_tree_index_71.rds
inst/sensitivity_data/sensitivity_tree_index_72.rds
inst/sensitivity_data/sensitivity_tree_index_73.rds
inst/sensitivity_data/sensitivity_tree_index_74.rds
inst/sensitivity_data/sensitivity_tree_index_75.rds
inst/sensitivity_data/sensitivity_tree_index_76.rds
inst/sensitivity_data/sensitivity_tree_index_77.rds
inst/sensitivity_data/sensitivity_tree_index_78.rds
inst/sensitivity_data/sensitivity_tree_index_79.rds
inst/sensitivity_data/sensitivity_tree_index_8.rds
inst/sensitivity_data/sensitivity_tree_index_80.rds
inst/sensitivity_data/sensitivity_tree_index_81.rds
inst/sensitivity_data/sensitivity_tree_index_82.rds
inst/sensitivity_data/sensitivity_tree_index_83.rds
inst/sensitivity_data/sensitivity_tree_index_84.rds
inst/sensitivity_data/sensitivity_tree_index_85.rds
inst/sensitivity_data/sensitivity_tree_index_86.rds
inst/sensitivity_data/sensitivity_tree_index_87.rds
inst/sensitivity_data/sensitivity_tree_index_88.rds
inst/sensitivity_data/sensitivity_tree_index_89.rds
inst/sensitivity_data/sensitivity_tree_index_9.rds
inst/sensitivity_data/sensitivity_tree_index_90.rds
inst/sensitivity_data/sensitivity_tree_index_91.rds
inst/sensitivity_data/sensitivity_tree_index_92.rds
inst/sensitivity_data/sensitivity_tree_index_93.rds
inst/sensitivity_data/sensitivity_tree_index_94.rds
inst/sensitivity_data/sensitivity_tree_index_95.rds
inst/sensitivity_data/sensitivity_tree_index_96.rds
inst/sensitivity_data/sensitivity_tree_index_97.rds
inst/sensitivity_data/sensitivity_tree_index_98.rds
inst/sensitivity_data/sensitivity_tree_index_99.rds
man/DAISIEprepExtra-package.Rd
man/hawaii_asters.Rd
man/madagascar_mammals.Rd
man/world_border.Rd
renv.lock
renv/.gitignore
renv/activate.R
renv/settings.dcf
