Files in brouwern/DRmencia

Data and code to replicate analyses for Latta, Brouwer, et al. 2018. PeerJ.

.Rbuildignore

.gitignore

DESCRIPTION

DRmencia.Rproj

NAMESPACE

R/DRmencia-package.r R/back_transform_reals.R R/buidCIs_ANOVA_pois_comm.R R/build_CIs_regrxn_pois_comm.R R/focal_spp.R R/getmultcompstats.R R/hello.R R/load_libraries.R R/plot_ANOVA_pois_comm.R R/plot_regrxn_pois_comm.R R/run_mhat_loop.R

R/trait_dat.RData

README.Rmd

_trash/mencia_cleaned.csv

_trash/temp.Rmd

_trash/temp.csv

_trash/temp.doc

_trash/temp_sp_N.csv

_trash/temp_sp_P_vs_NP.csv

_trash/temp_spp_codes.csv

_trash/temp_tables_5_6.csv

_trash/temp_tables_5_6.xlsx

analyses/1_community_misc/_trash/_3_comm_analyses_div.Rmd analyses/1_community_misc/_trash/_4_comm_analyses_even.Rmd analyses/1_community_misc/standard_comm_analyses/1a_comm_analysis_jaccard_nmds.Rmd analyses/1_community_misc/standard_comm_analyses/1b_comm_analyses_richness.Rmd analyses/1_community_misc/standard_comm_analyses/1c_comm_analyses_diversity.Rmd analyses/1_community_misc/standard_comm_analyses/1d_comm_analyses_evenness.Rmd analyses/1_community_misc/standard_comm_analyses/1e_plot_community_analysies.Rmd analyses/1_community_misc/trait_composition_mig_endem_habitat_diet/1_migrants_vs_residents.Rmd analyses/1_community_misc/trait_composition_mig_endem_habitat_diet/2_diet_composition_analysis.Rmd analyses/1_community_misc/trait_composition_mig_endem_habitat_diet/3_habitat_composition_analysis.Rmd analyses/1_community_misc/trait_composition_mig_endem_habitat_diet/traits_by_spp_richness.Rmd analyses/1_community_misc/trait_composition_mig_endem_habitat_diet/trash/_diet_compositions_cuts.Rmd analyses/1_community_misc/trait_composition_mig_endem_habitat_diet/trash/_temp_diet_NMDS.Rmd analyses/2_total_caps_per_spp_poisson_glmm/1_total_captures_multi_spp_poisson_glmm.Rmd analyses/2_total_caps_per_spp_poisson_glmm/2_total_captures_spp_specific_ANOVA_trends.Rmd analyses/2_total_caps_per_spp_poisson_glmm/3_total_captures_spp_specific_regression_with_X2.Rmd analyses/2_total_caps_per_spp_poisson_glmm/_trash/_overall_trends_mig_vs_residents.Rmd analyses/3_age_ratio_logit_glmm/1a_age_ratio.Rmd analyses/3_age_ratio_logit_glmm/1b_ANOVA_age_ratio.Rmd analyses/3_age_ratio_logit_glmm/_trash/_1a_age_ratio_vs_sex.Rmd analyses/3_age_ratio_logit_glmm/_trash/_1b_age_ratio_aceitillar.Rmd analyses/4_sex_ratio_logit_glmm/_trash/b_sex_ratio_aceitillar.Rmd analyses/4_sex_ratio_logit_glmm/a_sex_ratio.Rmd analyses/4_sex_ratio_logit_glmm/c_ANOVA_sex_ratio.Rmd analyses/5_condition_normal_lmm_and_lm/1_condition_Mhat_multi_spp_lmm.Rmd analyses/5_condition_normal_lmm_and_lm/2_condition_Mhat_ANOVA.Rmd analyses/5_condition_normal_lmm_and_lm/_trash/5_condition.Rmd analyses/5_condition_normal_lmm_and_lm/_trash/_model_condition_in_all_spp_with_lmer.Rmd analyses/6_site_persist_logit_glmm/1_set_up_sp_mencia.Rmd analyses/6_site_persist_logit_glmm/2_temp_set_up_sp_aceit.Rmd analyses/6_site_persist_logit_glmm/3_model_site_persist.Rmd analyses/7_insects/1_leaf_litter_analysis.Rmd analyses/7_insects/2_flying_insect_analysis.Rmd analyses/7_insects/3_make_arthro_plot.Rmd analyses/7_insects/_temp_insect_NMDS.Rmd analyses/7_insects/_trash/1_leaf_litter_analysis_explore.Rmd analyses/7_insects/_trash/_litter_cuts.Rmd analyses/_trash/_old_table5.Rmd analyses/_trash/_temp_merge_for_table5.Rmd analyses/_trash/_temp_recreate_table5.Rmd analyses/_trash/regression_age_and_sex.Rmd analyses/_trash/temp_ANOVA_tot_caps_by_hab.Rmd analyses/_trash/temp_boostrap_blups.Rmd analyses/_trash/temp_model_site_persistence.Rmd analyses/_trash/temp_regress_tot_caps_by_habitat.Rmd data-raw/0a_merge_annual_data.Rmd data-raw/0b_merge_site_persist_data.Rmd data-raw/1_finalize_annual_data.Rmd data-raw/1_finalize_condition_data.Rmd

data-raw/README_rawdata.txt

data-raw/_trash/_finalize_annual_captures.Rmd data-raw/data-raw-aceitillar_96-02/0_proofing_Aceitillar.Rmd data-raw/data-raw-aceitillar_96-02/1a_cleaning_Aceitillar_site_persist.Rmd data-raw/data-raw-aceitillar_96-02/1b_reshape_Aceitillar_to_ann_cap.Rmd

data-raw/data-raw-aceitillar_96-02/CSV_Aceitillar_96-02/Aceitillar_96-02_for_Mencia_all_caps_CSV.csv

data-raw/data-raw-aceitillar_96-02/XLSX_Aceitillar_96-02/Aceitillar 96-02 for Mencia.xls

data-raw/data-raw-aceitillar_96-02/XLSX_Aceitillar_96-02/Aceitillar 96-02 for Mencia_working.xls

data-raw/data-raw-aceitillar_96-02/XLSX_Aceitillar_96-02/Dry Forest Net Captures for NB net hours.xls

data-raw/data-raw-aceitillar_96-02/XLSX_Aceitillar_96-02/net_hours_aceitillar_and_others.xlsx

data-raw/data-raw-aceitillar_96-02/_orig_vs_aceit_annual.csv

data-raw/data-raw-aceitillar_96-02/_trash/_aceit_cleaned.csv

data-raw/data-raw-aceitillar_96-02/_trash/_temp_analysis.Rmd

data-raw/data-raw-aceitillar_96-02/aceit_annual.csv

data-raw/data-raw-aceitillar_96-02/aceit_annual_inc_resight.csv

data-raw/data-raw-aceitillar_96-02/aceit_site_persist_clean.csv

data-raw/data-raw-bodymass/1_clean_condition_data.Rmd

data-raw/data-raw-bodymass/CSV_body_condition_both_sites/body_condition_mencia_aceitillar_SP_inds_only_CSV.csv

data-raw/data-raw-bodymass/CSV_body_condition_both_sites/body_condition_mencia_aceitillar_SP_inds_only_CSV_2.csv

data-raw/data-raw-bodymass/XLSX_body_condition_both_sites/BANA_subset.xlsx

data-raw/data-raw-bodymass/XLSX_body_condition_both_sites/Mencia body cond site pers indivs workin.xls

data-raw/data-raw-bodymass/XLSX_body_condition_both_sites/Mencia body cond site pers indivs.xls

data-raw/data-raw-bodymass/XLSX_body_condition_both_sites/README_body_condity_XLS_file.txt

data-raw/data-raw-bodymass/condition.RData

data-raw/data-raw-insects/data-raw-leaf-litter/1_clean_leaf_litter.Rmd

data-raw/data-raw-insects/data-raw-leaf-litter/CSV_leaf_litter_both_sites/leaf_litter_insects_CSV.csv

data-raw/data-raw-insects/data-raw-leaf-litter/XLSX_leaf_litter_both_sites/Mencia Leaf Litter Samples_ORIGINAL.xls

data-raw/data-raw-insects/data-raw-leaf-litter/XLSX_leaf_litter_both_sites/Mencia Leaf Litter Samples_WORKING.xls

data-raw/data-raw-insects/data-raw-leaf-litter/XLSX_leaf_litter_both_sites/README_leaf_litter_XLS_file.txt

data-raw/data-raw-insects/data-raw-sticky-traps/1_clean_sticky_traps.Rmd

data-raw/data-raw-insects/data-raw-sticky-traps/CSV_sticky_traps_both_sites/CSV_stick_traps_both_sites.csv

data-raw/data-raw-insects/data-raw-sticky-traps/CSV_sticky_traps_both_sites/CSV_stick_traps_both_sites.xlsx

data-raw/data-raw-insects/data-raw-sticky-traps/XLSX_sticky_traps_both_sites/Mencia Sticky Traps_ORIGINAL.xls

data-raw/data-raw-insects/data-raw-sticky-traps/XLSX_sticky_traps_both_sites/Mencia Sticky Traps_WORKING.xls

data-raw/data-raw-insects/data-raw-sticky-traps/XLSX_sticky_traps_both_sites/README_data_setup_notes.pptx

data-raw/data-raw-insects/data-raw-sticky-traps/XLSX_sticky_traps_both_sites/README_sticky_trap_XLS_file.txt

data-raw/data-raw-mencia/All Capture Table_complete for NB with net hours.xls

data-raw/data-raw-mencia/mencia_all_captures_by_year/0_proofing_merging_mencia_annual_caps.Rmd data-raw/data-raw-mencia/mencia_all_captures_by_year/1_clean_mencia_annual_cap.Rmd

data-raw/data-raw-mencia/mencia_all_captures_by_year/CSV_mencia_all_captures_by_yr/2003-04_All_Captures_CSV_skip5.csv

data-raw/data-raw-mencia/mencia_all_captures_by_year/CSV_mencia_all_captures_by_yr/2004-05_All_Captures_CSV_skip5.csv

data-raw/data-raw-mencia/mencia_all_captures_by_year/CSV_mencia_all_captures_by_yr/2005-06_All_Captures_CSV_skip5.csv

data-raw/data-raw-mencia/mencia_all_captures_by_year/CSV_mencia_all_captures_by_yr/2006-07_All_Captures_CSV_skip5.csv

data-raw/data-raw-mencia/mencia_all_captures_by_year/CSV_mencia_all_captures_by_yr/2007-08_All_Captures_CSV_skip5.csv

data-raw/data-raw-mencia/mencia_all_captures_by_year/XLSX_mencia_all_captures_by_yr/2003-04 All Captures.xls

data-raw/data-raw-mencia/mencia_all_captures_by_year/XLSX_mencia_all_captures_by_yr/2004-05 All Captures.xls

data-raw/data-raw-mencia/mencia_all_captures_by_year/XLSX_mencia_all_captures_by_yr/2005-06 All Captures.xls

data-raw/data-raw-mencia/mencia_all_captures_by_year/XLSX_mencia_all_captures_by_yr/2006-07 All Captures.xls

data-raw/data-raw-mencia/mencia_all_captures_by_year/XLSX_mencia_all_captures_by_yr/2007-08 All Captures.xls

data-raw/data-raw-mencia/mencia_all_captures_by_year/_3_finalize_mencia_captures_16.Rmd

data-raw/data-raw-mencia/mencia_all_captures_by_year/mencia_all_years.csv

data-raw/data-raw-mencia/mencia_all_captures_by_year/mencia_cleaned.csv

data-raw/data-raw-mencia/mencia_site_persistence/0_proofing_merging_mencia_site_persist.Rmd data-raw/data-raw-mencia/mencia_site_persistence/1_clean_mencia_site_persist.Rmd

data-raw/data-raw-mencia/mencia_site_persistence/CSV_mencia_site_persistence/mencia_all_b.csv

data-raw/data-raw-mencia/mencia_site_persistence/XLSX_mencia_site_persistence/All Mencia B.xls

data-raw/data-raw-mencia/mencia_site_persistence/XLSX_mencia_site_persistence/All Mencia B_Working.xls

data-raw/data-raw-mencia/mencia_site_persistence/_trash/_1b_reshape_mencia_site_persist.Rmd data-raw/data-raw-mencia/mencia_site_persistence/_trash/_finalize_mencia_site_persist.Rmd

data-raw/data-raw-mencia/mencia_site_persistence/_trash/_mencia_site_persist_cleaned.csv

data-raw/data-raw-mencia/mencia_site_persistence/_trash/_scrub_mencia_site_persist.Rmd

data-raw/data-raw-mencia/mencia_site_persistence/_trash/_site_persist_cleaned.csv

data-raw/data-raw-mencia/mencia_site_persistence/mencia_site_persist_clean.csv

data-raw/data-raw-mencia/temp_compare_ann_caps_and_site_persist_data.Rmd

data-raw/net_hours_all_sites/net_hours_all_sites.xlsx

data-raw/temp_reshape_for_mig_status.Rmd

data/01022018.RData

data/ann_caps.RData

data/ann_caps4age_ratio.RData

data/ann_caps4sex_ratio.RData

data/ann_counts

data/ann_counts.RData

data/annual_captures.RData

data/bb.RData

data/community_dat.RData

data/community_dat_pooled.RData

data/condition.RData

data/condition_Mhat.RData

data/flying.RData

data/litter.RData

data/net_hours.csv

data/site_persist.RData

data/sp_binomial.RData

data/sp_individual.RData

data/spp_list.csv

data/spp_matrix.RData

data/spp_matrix_pooled.RData

data/trait_dat.RData

man/hello.Rd

manuscript/original/Mencia MS_for Condor_original.docx

manuscript/original/Mencia decision.docx

manuscript/original/temp_spp_trait_table.pdf

manuscript/original/~$ncia MS_for Condor_original.docx

manuscript/revision_NLB/Mencia MS_for Condor_NLB_020817.docx

manuscript/revision_NLB/Mencia_methods_updates.docx

manuscript/revision_NLB/Mencia_stat_methods_ORIGINAL.docx

manuscript/revision_NLB/Mencia_stat_methods_REVISED.docx

manuscript/revision_NLB/Mencia_tables_and_plots.docx

manuscript/revision_NLB/NMDS_figure.docx

manuscript/revision_NLB/references.docx

manuscript/revision_NLB/references2.docx

models/WORKSPACE_age_ratio_regression.RData

models/WORKSPACE_leaf_litter_insect_analysis.RData

models/WRKSPC_age_rat_AOV_migVres_NOT_ind_spp.RData

models/WRKSPC_condition_ANOVA.RData

models/WRKSPC_condition_regression.RData

models/WRKSPC_diet_composition.RData

models/ind_spp_abund_trends.RData

notes/022018_capture_effort.pptx

notes/_013118_fixing_repeated_obs.pptx

notes/data_processing_staps.pptx

notes/sampling_occassion_by_year_and_month.xlsx

plots/anovaplot_even

plots/anovaplot_even.RData

plots/anovaplot_pois_div.RData

plots/anovaplot_pois_spprich

plots/anovaplot_pois_spprich.RData

plots/gg_flying_insects_anova.RData

plots/gg_flying_insects_regression.RData

plots/gg_litter_insects_anova.RData

plots/gg_litter_insects_regression.RData

plots/regrxnplot_even.RData

plots/regrxnplot_pois_div.RData

plots/regrxnplot_pois_spprich.RData

tables/Table_x_test_statistics.xlsx

tables/ind_spp_condition_trends_with_Aceitillar.csv

tables/ind_spp_condition_trends_with_Aceitillar.xlsx

tables/jaccard_sor.csv

tables/jaccard_sor.xlsx

tables/make_table_5_6_final.Rmd tables/make_tables5_6_age_etc.Rmd tables/make_tables5_6_site_persist.Rmd

tables/study_design_table.xlsx

tables/tables5_6.csv

tables/tables_total_captures_spp_specific_ANOVA_trends/ind_spp_trends_with_Aceitillar.csv

tables/tables_total_captures_spp_specific_ANOVA_trends/ind_spp_trends_with_Aceitillar.xlsx

tables/tables_total_captures_spp_specific_ANOVA_trends/ind_spp_trends_with_Aceitillar_update.csv

tables/tables_total_captures_spp_specific_ANOVA_trends/ind_spp_trends_with_Aceitillar_update.xlsx

tables/temp_tables_5_6_age_etc.csv

tables/temp_tables_5_6_site_persist.csv

tables/year_squared_test_stats.csv

tests/testthat.R

brouwern/DRmencia documentation built on May 6, 2019, 12:24 p.m.