Title: Intentional release of native species undermines ecological stability
Authors: Akira Terui, Hirokazu Urabe, Masayuki Senzaki, Bungo Nishizawa
Two-species simulation – simulation with cdyns::cdynsim() (see R
package https://github.com/aterui/cdyns). Run
run_simulation_analytical.R. Simulation results are saved in
output/result_ricker_2sp.rds.
Whole community simulation – simulation with cdyns::cdynsim() (see
R package https://github.com/aterui/cdyns). Run run_simulation.R.
Simulation results are saved in output/result_ricker.rds.
State-space AR model – run run_jags_model_ssm_ar.R. Data sourced
from data_fmt_XXX.R files. Model code is model_ssm_ar.R
Regression – run run_jags_model_reg.R. Data sourced from
data_fmt_XXX.R files. Model code is model_reg.R
State-space Ricker model – run
run_jags_model_multi_ricker_sparse.R. Data sourced from
data_fmt_XXX.R files. Model code is model_multi_ricker_sparse.R
| dir | class | name | description |
|---|---|---|---|
| code | analysis | run_analysis_lmcheck.R | confirm Bayesian results with glmmTMB() |
| code | figure | figure_layout.R | layout empirical and theoretical patterns |
| code | figure | figure_obs_coef.R | figure codes for map (_map), coefficients (_coef), stock effect (_stock), or raw plot (_rawplot) |
| code | figure | figure_obs_map.R | figure codes for map (_map), coefficients (_coef), stock effect (_stock), or raw plot (_rawplot) |
| code | figure | figure_obs_rawplot.R | figure codes for map (_map), coefficients (_coef), stock effect (_stock), or raw plot (_rawplot) |
| code | figure | figure_obs_stock.R | figure codes for map (_map), coefficients (_coef), stock effect (_stock), or raw plot (_rawplot) |
| code | figure | figure_species_int.R | NA |
| code | figure | figure_theory.R | theoretical predictions for stocking & community dynamics in species-rich (no postfix) or 2-species scenarios (_2sp) |
| code | figure | si_figure_co.R | supporting figure codes for correlations in environmental variables (_cor), histograms for environmental data (_env), observed community dynamics (_obs_dyns), pairwise species interactions (_species_int), and scenario simulations in a species-rich community (_theory) |
| code | figure | si_figure_cor.R | supporting figure codes for correlations in environmental variables (_cor), histograms for environmental data (_env), observed community dynamics (_obs_dyns), pairwise species interactions (_species_int), and scenario simulations in a species-rich community (_theory) |
| code | figure | si_figure_env.R | supporting figure codes for correlations in environmental variables (_cor), histograms for environmental data (_env), observed community dynamics (_obs_dyns), pairwise species interactions (_species_int), and scenario simulations in a species-rich community (_theory) |
| code | figure | si_figure_obs_dyns.R | supporting figure codes for correlations in environmental variables (_cor), histograms for environmental data (_env), observed community dynamics (_obs_dyns), pairwise species interactions (_species_int), and scenario simulations in a species-rich community (_theory) |
| code | figure | si_figure_species_int.R | supporting figure codes for correlations in environmental variables (_cor), histograms for environmental data (_env), observed community dynamics (_obs_dyns), pairwise species interactions (_species_int), and scenario simulations in a species-rich community (_theory) |
| code | figure | si_figure_theory.R | theoretical predictions for stocking & community dynamics in species-rich (no postfix) or 2-species scenarios (_2sp) |
| code | figure | si_figure_theory_2sp.R | theoretical predictions for stocking & community dynamics in species-rich (no postfix) or 2-species scenarios (_2sp) |
| code | format | data_fmt_fishdata.R | format data for regression (_reg), fish count data (_fishdata), stock data (_stock), and trait data (_trait) |
| code | format | data_fmt_reg.R | format data for regression (_reg), fish count data (_fishdata), stock data (_stock), and trait data (_trait) |
| code | format | data_fmt_stock.R | format data for regression (_reg), fish count data (_fishdata), stock data (_stock), and trait data (_trait) |
| code | format | data_fmt_trait.R | format data for regression (_reg), fish count data (_fishdata), stock data (_stock), and trait data (_trait) |
| code | gis | gis_environment.R | extract layer data for environment |
| code | gis | gis_ocean.R | extract layer data for ocean |
| code | gis | gis_watershed.R | delineate watersheds |
| code | jags | model_multi_ricker_sparse.R | jags model for joint state-space (_joint), multi-species ricker (_multi_ricker_sparse), and regression (_reg) |
| code | jags | model_reg.R | jags model for joint state-space (_joint), multi-species ricker (_multi_ricker_sparse), and regression (_reg) |
| code | jags | model_ssm_ar.R | jags model for joint state-space (_joint), multi-species ricker (_multi_ricker_sparse), and regression (_reg) |
| code | jags | run_jags_model_multi_ricker_sparse.R | jags model for joint state-space (_joint), multi-species ricker (_multi_ricker_sparse), and regression (_reg) |
| code | jags | run_jags_model_reg.R | jags model for joint state-space (_joint), multi-species ricker (_multi_ricker_sparse), and regression (_reg) |
| code | jags | run_jags_model_ssm_ar.R | jags model for joint state-space (_joint), multi-species ricker (_multi_ricker_sparse), and regression (_reg) |
| code | set | set_crs.R | set defaults |
| code | set | set_figure_theme.R | set defaults |
| code | set | set_functions.R | set defaults |
| code | set | set_readme.R | set defaults |
| code | set | set_rmd.R | set defaults |
| code | simulation | run_simulation.R | run simulation model for species rich (no postfix) and 2-species community (_analytical) or sensitivity analysis (_stvy) |
| code | simulation | run_simulation_analytical.R | run simulation model for species rich (no postfix) and 2-species community (_analytical) or sensitivity analysis (_stvy) |
| code | table | table_param_set.R | tables for theoretical parameters (_param_set), priors (_prior), species list (_species_list), and estimated regression (_reg and _stvy_analysis) or state-space model parameters (_ssm) |
| code | table | table_prior.R | tables for theoretical parameters (_param_set), priors (_prior), species list (_species_list), and estimated regression (_reg and _stvy_analysis) or state-space model parameters (_ssm) |
| code | table | table_reg.R | tables for theoretical parameters (_param_set), priors (_prior), species list (_species_list), and estimated regression (_reg and _stvy_analysis) or state-space model parameters (_ssm) |
| code | table | table_ricker.R | tables for theoretical parameters (_param_set), priors (_prior), species list (_species_list), and estimated regression (_reg and _stvy_analysis) or state-space model parameters (_ssm) |
| code | table | table_species_list.R | tables for theoretical parameters (_param_set), priors (_prior), species list (_species_list), and estimated regression (_reg and _stvy_analysis) or state-space model parameters (_ssm) |
| code | table | table_ssm_ar.R | tables for theoretical parameters (_param_set), priors (_prior), species list (_species_list), and estimated regression (_reg and _stvy_analysis) or state-space model parameters (_ssm) |
| code | NA | library.R | NA |
| data_fmt | data | data_env_fmt.rds | formatted data for species trait (_trait), ocean data (_ocean), environment (_env), fish abundance (_hkd_prtwsd), and fish stocking (_hkd_prtwsd_stock) |
| data_fmt | data | data_hkd_prtwsd_fmt.csv | formatted data for species trait (_trait), ocean data (_ocean), environment (_env), fish abundance (_hkd_prtwsd), and fish stocking (_hkd_prtwsd_stock) |
| data_fmt | data | data_hkd_prtwsd_stock_fmt.csv | formatted data for species trait (_trait), ocean data (_ocean), environment (_env), fish abundance (_hkd_prtwsd), and fish stocking (_hkd_prtwsd_stock) |
| data_fmt | data | data_ocean_fmt.rds | formatted data for species trait (_trait), ocean data (_ocean), environment (_env), fish abundance (_hkd_prtwsd), and fish stocking (_hkd_prtwsd_stock) |
| data_fmt | data | data_trait.rds | formatted data for species trait (_trait), ocean data (_ocean), environment (_env), fish abundance (_hkd_prtwsd), and fish stocking (_hkd_prtwsd_stock) |
## R version 4.2.1 (2022-06-23 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19045)
##
## Matrix products: default
##
## locale:
## [1] LC_COLLATE=English_United States.utf8
## [2] LC_CTYPE=English_United States.utf8
## [3] LC_MONETARY=English_United States.utf8
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United States.utf8
##
## attached base packages:
## [1] parallel stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] whitebox_2.1.5 stars_0.5-6 abind_1.4-5
## [4] sf_1.0-8 exactextractr_0.9.0 raster_3.6-3
## [7] sp_1.5-0 terra_1.6-17 knitr_1.40.4
## [10] stargazer_5.2.3 msir_1.3.3 corrplot_0.92
## [13] here_1.0.1 scales_1.2.1 forecast_8.18
## [16] loo_2.5.1 runjags_2.2.1-7 doSNOW_1.0.20
## [19] snow_0.4-4 doParallel_1.0.17 iterators_1.0.14
## [22] foreach_1.5.2 cdyns_0.1.0 cowplot_1.1.1
## [25] ggspatial_1.1.6 ggridges_0.5.4 ggside_0.2.1
## [28] patchwork_1.1.2 forcats_0.5.2 stringr_1.4.1
## [31] dplyr_1.0.10 purrr_0.3.5 readr_2.1.3
## [34] tidyr_1.2.1 tibble_3.1.8 ggplot2_3.3.6
## [37] tidyverse_1.3.2
##
## loaded via a namespace (and not attached):
## [1] googledrive_2.0.0 colorspace_2.0-3 ellipsis_0.3.2
## [4] class_7.3-20 mclust_5.4.10 rprojroot_2.0.3
## [7] fs_1.5.2 rstudioapi_0.14 proxy_0.4-27
## [10] fansi_1.0.3 lubridate_1.8.0 xml2_1.3.3
## [13] codetools_0.2-18 jsonlite_1.8.3 broom_1.0.1
## [16] dbplyr_2.2.1 compiler_4.2.1 httr_1.4.4
## [19] backports_1.4.1 assertthat_0.2.1 fastmap_1.1.0
## [22] gargle_1.2.1 cli_3.4.1 htmltools_0.5.3
## [25] tools_4.2.1 coda_0.19-4 gtable_0.3.1
## [28] glue_1.6.2 Rcpp_1.0.9 cellranger_1.1.0
## [31] fracdiff_1.5-1 vctrs_0.5.1 urca_1.3-3
## [34] nlme_3.1-160 lmtest_0.9-40 lwgeom_0.2-9
## [37] timeDate_4021.106 xfun_0.34 rvest_1.0.3
## [40] lifecycle_1.0.3 pacman_0.5.1 googlesheets4_1.0.1
## [43] zoo_1.8-11 hms_1.1.2 yaml_2.3.6
## [46] quantmod_0.4.20 curl_4.3.3 stringi_1.7.8
## [49] highr_0.9 tseries_0.10-52 e1071_1.7-11
## [52] checkmate_2.1.0 TTR_0.24.3 rlang_1.0.6
## [55] pkgconfig_2.0.3 matrixStats_0.62.0 evaluate_0.17
## [58] lattice_0.20-45 tidyselect_1.2.0 magrittr_2.0.3
## [61] R6_2.5.1 generics_0.1.3 DBI_1.1.3
## [64] pillar_1.8.1 haven_2.5.1 withr_2.5.0
## [67] units_0.8-0 xts_0.12.2 nnet_7.3-18
## [70] modelr_0.1.9 crayon_1.5.2 KernSmooth_2.23-20
## [73] utf8_1.2.2 tzdb_0.3.0 rmarkdown_2.17
## [76] grid_4.2.1 readxl_1.4.1 reprex_2.0.2
## [79] digest_0.6.30 classInt_0.4-8 munsell_0.5.0
## [82] quadprog_1.5-8