323 research outputs found
Data from: Intentional release of native species undermines ecological stability
No full textREADME Article Information
Title: Intentional release of native species undermines ecological stability
Authors: Akira Terui, Hirokazu Urabe, Masayuki Senzaki, Bungo Nishizawa
Analysis flow Theory
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.
Empirical
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.
aterui/mcbrnet: mcbrnet 1.2.3
No full textmcbrnet
Overview
mcbrnet is a collection of functions to perform metacommunity simulation in branching networks. Main functions include:
brnet() generates a random branching network with the specified number of patches and probability of branching. The function returns
adjacency and distance matrices, hypothetical environmental/disturbance values at each patch, and the number of patches upstream (akin to the watershed area in river networks). The output may be used in function mcsim() to simulate metacommunity dynamics in a branching network.
mcsim() simulates metacommunity dynamics. By default, it produces a square-shaped landscape with randomly distributed habitat patches (x- and y-coordinates are drawn from a uniform distribution). If a distance matrix is given, the function simulates metacommunity
dynamics in the specified landscape. Function mcsim() follows a general framework proposed by Thompson et al. (2020). However, it has several unique features that are detailed in Terui et al (2021).
igpsim() simulates three-species meta-food web dynamics with intraguild predation. This function shares many features with mcsim(). Currently under development.
ggbrnet() is a wrapper of ggraph functions for easy visualization of a network produced by brnet() .
adjtodist() converts an adjacency matrix to a distance matrix.
See Articles for instruction.
Citation
Current best citation for this package is:
Terui A, Kim S, Dolph CL, Kadoya T, Miyazaki Y. (2021) Emergent dual scaling of riverine biodiversity. Proceedings of the National Academy
of Sciences 118: e2105574118
Installation
The mcbrnet package can be installed with the following script:
#install.packages("remotes")
remotes::install_github("aterui/mcbrnet")
library(mcbrnet)
Change-log
v.1.2.3 (04/13/22)
fix a bug in fun_disp_mat()
add ggbrnet()
add disturbance arguments to mcsim() (p_disturb & m_disturb)
v.1.2.2 (03/24/22)
fix a bug in fun_igp()
v.1.2.1 (03/09/22)
implement internal functions to mcsim() and brnet()
remove argument weighted_distance_matrix from mcsim() and
brnet()
add argument dispersal_matrix to mcsim()
v.1.2.0 (03/09/22)
add a major function igpsim()
simplified brnet() and mcsim() by introducing internal
sub-functions
v.1.1.1 (12/07/21)
add a local noise parameter for disturbance values to brnet()
(argument sd_disturb_lon)
v.1.1.0 (08/02/21)
add disturbance arguments to brnet() added function adjtodist()
v.1.0.0 (05/03/21)
initial release
Funding
This material is based upon work supported by the National Science Foundation through the Division of Environmental Biology (DEB 2015634)
1変数代数方程式の微小根の上界を用いた近接根の計算 (Computer Algebra : Algorithms, Implementations and Applications)
No full textCode for: Emergent dual scaling of riverine biodiversity
No full textREADME
Article information
File descriptions
License
Session information
Article information
Title: Emergent dual scaling of riverine biodiversity
Author: Akira Terui, Seoghyun Kim, Christine L. Dolph, Taku Kadoya, Yusuke Miyazaki
File descriptions
See metadata.html (to view metadata.html, clone the repository and open metadata.html from your local computer). Note that the raw empirical data are not available in this repository due to licensing issues.
License
Code - MIT License
GIS layers adapted from the following materials are licensed under:
Copernicus Global Land Service: Creative Commons Attribution 4.0 International
WorldClim 1.4: Creative Commons Attribution-ShareAlike 4.0 International License
MERIT Hydro: Attribution-NonCommercial 4.0 International
Session information
## R version 4.1.0 (2021-05-18)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19042)
##
## Matrix products: default
##
## locale:
## [1] LC_COLLATE=English_United States.1252
## [2] LC_CTYPE=English_United States.1252
## [3] LC_MONETARY=English_United States.1252
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United States.1252
##
## attached base packages:
## [1] parallel stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] igraph_1.2.6 ggraph_2.0.5 iNEXT_2.0.20 avpc_0.0.1
## [5] kableExtra_1.3.4 knitr_1.33 doSNOW_1.0.19 snow_0.4-3
## [9] doParallel_1.0.16 iterators_1.0.13 mcbrnet_1.1.0 foreach_1.5.1
## [13] here_1.0.1 broom_0.7.9 sf_0.9-7 patchwork_1.1.1
## [17] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.6 purrr_0.3.4
## [21] readr_2.0.0 tidyr_1.1.3 tibble_3.1.2 ggplot2_3.3.5
## [25] tidyverse_1.3.1
##
## loaded via a namespace (and not attached):
## [1] fs_1.5.0 lubridate_1.7.10 webshot_0.5.2 httr_1.4.2
## [5] rprojroot_2.0.2 tools_4.1.0 backports_1.2.1 utf8_1.2.1
## [9] R6_2.5.0 KernSmooth_2.23-20 DBI_1.1.1 colorspace_2.0-1
## [13] withr_2.4.2 gridExtra_2.3 tidyselect_1.1.1 compiler_4.1.0
## [17] cli_3.0.1 rvest_1.0.1 pacman_0.5.1 xml2_1.3.2
## [21] scales_1.1.1 classInt_0.4-3 proxy_0.4-26 systemfonts_1.0.2
## [25] digest_0.6.27 rmarkdown_2.9 svglite_2.0.0 pkgconfig_2.0.3
## [29] htmltools_0.5.1.1 dbplyr_2.1.1 rlang_0.4.11 readxl_1.3.1
## [33] rstudioapi_0.13 farver_2.1.0 generics_0.1.0 jsonlite_1.7.2
## [37] magrittr_2.0.1 Rcpp_1.0.7 munsell_0.5.0 fansi_0.5.0
## [41] viridis_0.6.1 lifecycle_1.0.0 stringi_1.6.1 yaml_2.2.1
## [45] MASS_7.3-54 plyr_1.8.6 grid_4.1.0 ggrepel_0.9.1
## [49] crayon_1.4.1 graphlayouts_0.7.1 haven_2.4.1 hms_1.1.0
## [53] pillar_1.6.2 reshape2_1.4.4 codetools_0.2-18 reprex_2.0.0
## [57] glue_1.4.2 evaluate_0.14 modelr_0.1.8 tweenr_1.0.2
## [61] vctrs_0.3.8 tzdb_0.1.2 cellranger_1.1.0 polyclip_1.10-0
## [65] gtable_0.3.0 assertthat_0.2.1 xfun_0.23 ggforce_0.3.3
## [69] tidygraph_1.2.0 e1071_1.7-7 class_7.3-19 viridisLite_0.4.0
## [73] units_0.7-2 ellipsis_0.3.
キンジ GCD サンポウ GPGCD ノ フクソ ケイスウ タコウシキ エノ カクチョウ COMPUTER ALGEBRA DESIGN OF ALGORITHMS IMPLEMENTATIONS AND APPLICATIONS
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1ヘンスウ タコウシキ ノ サイキテキ ナ タコウシキ ジョウヨレツ ト イレコ ブブン シュウケツシキ COMPUTER ALGEBRA DESIGN OF ALGORITHMS IMPLEMENTATIONS AND APPLICATIONS
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