Files in diazrenata/scadsanalysis
What the Package Does (One Line, Title Case)

.Rbuildignore

.gitignore

.travis.yml

DESCRIPTION

NAMESPACE

R/add_singletons.R R/count_elements.R R/data_handling.R R/download_data.R R/metrics.R R/render_reports.R R/rov_sampling.R R/sample_fs.R R/self_similarity_metrics.R R/utils-pipe.R README.md analysis/bbs_pipeline.R analysis/bbs_pipeline_jk.R analysis/fia_pipeline.R analysis/fia_short_pipeline_jk.R analysis/fia_small_pipeline.R analysis/fia_small_pipeline_jk.R analysis/gentry_pipeline.R analysis/gentry_pipeline_jk.R analysis/helper_scripts/jackknife.Rmd analysis/helper_scripts/jackknife.md

analysis/helper_scripts/jackknife_files/figure-gfm/unnamed-chunk-4-1.png

analysis/helper_scripts/jackknife_files/figure-gfm/unnamed-chunk-4-2.png

analysis/helper_scripts/load_results_for_exploring.R analysis/helper_scripts/make_all_ct.R analysis/helper_scripts/make_all_ct_jk.R analysis/helper_scripts/make_all_di.R analysis/helper_scripts/make_all_di_demo.R analysis/helper_scripts/make_all_di_jk.R analysis/helper_scripts/make_p_mamm.R analysis/helper_scripts/make_p_wide.R analysis/helper_scripts/ptables_plan.R analysis/howto.Rmd

analysis/howto.html

analysis/howto.md analysis/manuscript/finaledit/Appendices/ELEDiazGraphicalAbstract.pdf

analysis/manuscript/finaledit/Appendices/ELEDiazSA1.docx

analysis/manuscript/finaledit/Appendices/ELEDiazSA10.docx

analysis/manuscript/finaledit/Appendices/ELEDiazSA2.docx

analysis/manuscript/finaledit/Appendices/ELEDiazSA3.docx

analysis/manuscript/finaledit/Appendices/ELEDiazSA7.docx

analysis/manuscript/finaledit/Appendices/ELEDiazSA8.docx

analysis/manuscript/finaledit/Appendices/ELEDiazSA9.docx

analysis/manuscript/finaledit/Appendices/ELEDiazSF4.docx

analysis/manuscript/finaledit/Appendices/ELEDiazSF6.docx

analysis/manuscript/finaledit/Appendices/ELEDiazST5.docx

analysis/manuscript/finaledit/FiguresAndTables/figure_1.pdf analysis/manuscript/finaledit/FiguresAndTables/figure_2.pdf analysis/manuscript/finaledit/FiguresAndTables/figure_2_copy.pdf analysis/manuscript/finaledit/FiguresAndTables/figure_3.pdf analysis/manuscript/finaledit/FiguresAndTables/figure_4.pdf analysis/manuscript/finaledit/FiguresAndTables/figure_5.pdf analysis/manuscript/finaledit/FiguresAndTables/figure_6.pdf

analysis/manuscript/finaledit/FiguresAndTables/table_1.docx

analysis/manuscript/finaledit/MainText_final_ele.docx

analysis/manuscript/finaledit/MainText_final_ele.pdf analysis/manuscript/revision1/Appendices/ELEDiazGraphicalAbstract.pdf

analysis/manuscript/revision1/Appendices/ELEDiazSA1.docx

analysis/manuscript/revision1/Appendices/ELEDiazSA10.docx

analysis/manuscript/revision1/Appendices/ELEDiazSA2.docx

analysis/manuscript/revision1/Appendices/ELEDiazSA3.docx

analysis/manuscript/revision1/Appendices/ELEDiazSA7.docx

analysis/manuscript/revision1/Appendices/ELEDiazSA8.docx

analysis/manuscript/revision1/Appendices/ELEDiazSA9.docx

analysis/manuscript/revision1/Appendices/ELEDiazSF4.docx

analysis/manuscript/revision1/Appendices/ELEDiazSF6.docx

analysis/manuscript/revision1/Appendices/ELEDiazST5.docx

analysis/manuscript/revision1/FiguresAndTables/FigureLegends.docx

analysis/manuscript/revision1/FiguresAndTables/figure_1.pdf analysis/manuscript/revision1/FiguresAndTables/figure_2.pdf analysis/manuscript/revision1/FiguresAndTables/figure_2_second_copy.pdf analysis/manuscript/revision1/FiguresAndTables/figure_3.pdf analysis/manuscript/revision1/FiguresAndTables/figure_4.pdf analysis/manuscript/revision1/FiguresAndTables/figure_5.pdf analysis/manuscript/revision1/FiguresAndTables/figure_6.pdf

analysis/manuscript/revision1/FiguresAndTables/table_1.docx

analysis/manuscript/revision1/MainTextR1.docx

analysis/manuscript/revision1/MainTextR1_biorxiv.docx

analysis/manuscript/revision1/MainTextR1_biorxiv.pdf

analysis/manuscript/revision1/MainTextR1_ele.docx

analysis/manuscript/revision1/MainTextR1_ele.pdf

analysis/manuscript/revision1/Response_to_reviewers.docx

analysis/manuscript/revision1/Response_to_reviewers.pdf

analysis/manuscript/revision1/~$inTextR1.docx

analysis/manuscript/submission1/CL_draft.docx

analysis/manuscript/submission1/CoverLetter.docx

analysis/manuscript/submission1/Figures_and_Tables/Figure_legends.docx

analysis/manuscript/submission1/Figures_and_Tables/figure_1.pdf analysis/manuscript/submission1/Figures_and_Tables/figure_2.pdf analysis/manuscript/submission1/Figures_and_Tables/figure_3.pdf analysis/manuscript/submission1/Figures_and_Tables/figure_4.pdf

analysis/manuscript/submission1/Figures_and_Tables/table_1.docx

analysis/manuscript/submission1/MainText.docx

analysis/manuscript/submission1/MainText_EL_012021.pdf

analysis/manuscript/submission1/MainText_with_figures.docx

analysis/manuscript/submission1/MainText_with_figures_biorxiv.docx

analysis/manuscript/submission1/MainText_with_figures_biorxiv.pdf

analysis/manuscript/submission1/Reviews/response_thoughts.docx

analysis/manuscript/submission1/Reviews/reviews.docx

analysis/manuscript/submission1/Supplementary_material/ELEDiazSA2.docx

analysis/manuscript/submission1/Supplementary_material/ELEDiazSA3.docx

analysis/manuscript/submission1/Supplementary_material/ELEDiazSA4.docx

analysis/manuscript/submission1/Supplementary_material/ELEDiazSF1.docx

analysis/manuscript/submission1/Supplementary_material/ELEDiazSF5.docx

analysis/manuscript/submission1/Supplementary_material/ELEDiazST6.docx

analysis/manuscript/submission1/Supplementary_material/figure_s1.pdf analysis/manuscript/submission1/Supplementary_material/figure_s5.pdf

analysis/manuscript/submission1/Supplementary_material_biorxiv/AppendixS2.docx

analysis/manuscript/submission1/Supplementary_material_biorxiv/AppendixS3.docx

analysis/manuscript/submission1/Supplementary_material_biorxiv/AppendixS4.docx

analysis/manuscript/submission1/Supplementary_material_biorxiv/FigureS1.docx

analysis/manuscript/submission1/Supplementary_material_biorxiv/FigureS5.docx

analysis/manuscript/submission1/Supplementary_material_biorxiv/TableS6.docx

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analysis/reports/submission1/accessory/less_than_equal.Rmd analysis/reports/submission1/accessory/less_than_equal.md

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analysis/reports/submission1/accessory/misc_abund_mixes.Rmd

analysis/reports/submission1/accessory/misc_abund_mixes.html

analysis/reports/submission1/accessory/misc_abund_mixes.md analysis/reports/submission1/accessory/old_reports/95_interval.Rmd analysis/reports/submission1/accessory/old_reports/95_interval.md

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analysis/reports/submission1/accessory/old_reports/95_interval_portal.Rmd analysis/reports/submission1/accessory/old_reports/95_interval_portal.md

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analysis/reports/submission1/accessory/old_reports/all_di_old.csv

analysis/reports/submission1/accessory/old_reports/bbs_report.html

analysis/reports/submission1/accessory/old_reports/bbs_report.md

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analysis/reports/submission1/accessory/old_reports/cross_dataset.Rmd

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analysis/reports/submission1/accessory/old_reports/cross_dataset.md

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analysis/reports/submission1/accessory/old_reports/fia_short_report.html

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analysis/reports/submission1/accessory/zenodo.R

analysis/reports/submission1/all_di.csv

analysis/reports/submission1/appendix1_filtering.Rmd

analysis/reports/submission1/appendix3_sampling.docx

analysis/reports/submission1/appendix3_selfsimilarity.Rmd

analysis/reports/submission1/appendix3_selfsimilarity.docx

analysis/reports/submission1/figure_1.pdf analysis/reports/submission1/figure_2.pdf analysis/reports/submission1/figure_3.pdf analysis/reports/submission1/figure_4.pdf analysis/reports/submission1/figure_s4.Rmd

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analysis/reports/submission1/table_1.Rmd

analysis/reports/submission1/table_1.docx

analysis/reports/submission1/table_s6.Rmd

analysis/reports/submission1/table_s6.docx

analysis/reports/submission2/all_ct.csv

analysis/reports/submission2/all_ct_jk.csv

analysis/reports/submission2/all_di.csv

analysis/reports/submission2/all_di_columns.csv

analysis/reports/submission2/all_di_columns.xlsx

analysis/reports/submission2/all_di_jk.csv

analysis/reports/submission2/appendices/appendix1_filtering.Rmd

analysis/reports/submission2/appendices/appendix1_filtering.docx

analysis/reports/submission2/appendices/graphical_abstract.Rmd analysis/reports/submission2/appendices/graphical_abstract.md analysis/reports/submission2/appendices/graphical_abstract.pdf

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analysis/reports/submission2/appendices/portal_di.csv

analysis/reports/submission2/appendices/portal_samples.csv

analysis/reports/submission2/appendices/s10_very_small_results.Rmd

analysis/reports/submission2/appendices/s10_very_small_results.docx

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analysis/reports/submission2/appendices/s4_dissimilarity_fig.Rmd

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analysis/reports/submission2/appendices/s6_breadth_index_fig.Rmd

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analysis/reports/submission2/appendices/s7_complete_resampling_results.Rmd

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analysis/reports/submission2/style_reference.docx

analysis/reports/submission2/table1_extreme_values.Rmd

analysis/reports/submission2/table1_extreme_values.docx

analysis/reports/submission2/table1_extreme_values.md

analysis/reports/submission2/table1_extreme_values_formatting.docx

analysis/rev_prototyping/jacknifed_datasets/bbs_jk.csv

analysis/rev_prototyping/jacknifed_datasets/fia_jk.csv

analysis/rev_prototyping/jacknifed_datasets/fia_small_jk.csv

analysis/rev_prototyping/jacknifed_datasets/gentry_jk.csv

analysis/rev_prototyping/jacknifed_datasets/mcdb_jk.csv

analysis/rev_prototyping/jacknifed_datasets/misc_jk.csv

codecov.yml

inst/abund_data/bbs_spab.csv

inst/abund_data/fia_spab.csv

inst/abund_data/gentry_spab.csv

inst/abund_data/mcdb_spab.csv

inst/abund_data/misc_abund_spab.csv

inst/abund_data/portal_plants_spab.csv

inst/macdb_data/MACD_metadata.pdf

inst/macdb_data/community_analysis_data.csv

inst/macdb_data/experiments_analysis_data.csv

inst/macdb_data/orderedcomparisons.csv

inst/macdb_data/ref_analysis_data.csv

inst/macdb_data/sites_analysis_data.csv

inst/site_data/mammal_community_db_sites.csv

man/add_dis.Rd man/add_singletons.Rd man/add_singletons_dataset.Rd man/build_net.Rd man/compare_props_fs.Rd man/compare_props_off.Rd man/compare_props_off_full.Rd man/count_below.Rd man/count_elements.Rd man/download_data.Rd man/filter_fia.Rd man/filter_fia_small.Rd man/filter_miscabund.Rd man/fs_cd.Rd man/fs_diff_sampler.Rd man/fs_div.Rd man/fs_r2.Rd man/get_fs_diffs.Rd man/get_percentile.Rd man/get_percentiles.Rd man/get_statevars.Rd man/list_sites.Rd man/load_dataset.Rd man/pipe.Rd man/po_central_tendency.Rd man/proportion_off.Rd man/pull_di.Rd man/pull_di_net.Rd man/rep_diff_sampler.Rd man/sample_fs.Rd man/sample_fs_wrapper.Rd

scadsanalysis.Rproj

slurm_clustermq.tmpl

submit_bbs_jk_pipeline.sbatch

submit_bbs_pipeline.sbatch

submit_fia_jk_pipeline.sbatch

submit_fia_pipeline.sbatch

submit_fia_small_jk_pipeline.sbatch

submit_fia_small_pipeline.sbatch

submit_gentry_jk_pipeline.sbatch

submit_gentry_pipeline.sbatch

submit_mcdb_jk_pipeline.sbatch

submit_mcdb_pipeline.sbatch

submit_misc_jk_pipeline.sbatch

submit_misc_pipeline.sbatch

submit_net_pipeline.sbatch

submit_p_pipeline.sbatch

tests/testthat.R tests/testthat/test01_data_handling.R tests/testthat/test02_add_singletons.R tests/testthat/test03_statevars.R tests/testthat/test04_sample_fs.R tests/testthat/test05_diversity_indices.R tests/testthat/test07_count_elements.R tests/testthat/test08_build_net.R tests/testthat/test09_central_tendency.R tests/testthat/test10_self_sim.R

working-data/abund_data/bbs_spab.csv

working-data/abund_data/fia_short_spab.csv

working-data/abund_data/fia_small_spab.csv

working-data/abund_data/fia_spab.csv

working-data/abund_data/gentry_spab.csv

working-data/abund_data/macdb_spab.csv

working-data/abund_data/mcdb_spab.csv

working-data/abund_data/misc_abund_short_spab.csv

working-data/abund_data/misc_abund_spab.csv

working-data/abund_data/portal_plants_manip_spab.csv

working-data/abund_data/portal_plants_spab.csv

working-data/macdb_data/MACD_metadata.pdf

working-data/macdb_data/community_analysis_data.csv

working-data/macdb_data/experiments_analysis_data.csv

working-data/macdb_data/orderedcomparisons.csv

working-data/macdb_data/ref_analysis_data.csv

working-data/macdb_data/sites_analysis_data.csv

working-data/site_data/mammal_community_db_sites.csv

diazrenata/scadsanalysis documentation built on May 14, 2021, 6:59 p.m.

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