Last updated: 2025-05-25
Checks: 7 0
Knit directory: SaniVult/
This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(666) was run prior to running the
code in the R Markdown file. Setting a seed ensures that any results
that rely on randomness, e.g. subsampling or permutations, are
reproducible.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
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Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version b94bdec. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for
the analysis have been committed to Git prior to generating the results
(you can use wflow_publish or
wflow_git_commit). workflowr only checks the R Markdown
file, but you know if there are other scripts or data files that it
depends on. Below is the status of the Git repository when the results
were generated:
Ignored files:
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: ms/Almaraz et al. 2022 Ecol. Appl.pdf
Ignored: pipeline.R
Unstaged changes:
Modified: analysis/_site.yml
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the repository in which changes were
made to the R Markdown (analysis/Reproduce.Rmd) and HTML
(docs/Reproduce.html) files. If you’ve configured a remote
Git repository (see ?wflow_git_remote), click on the
hyperlinks in the table below to view the files as they were in that
past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | b94bdec | Pablo Almaraz | 2025-05-25 | Build site. |
| html | 9611ea2 | Pablo Almaraz | 2025-05-25 | Build site. |
| html | d24607c | Pablo Almaraz | 2025-05-25 | Build site. |
| html | 01e2d83 | Pablo Almaraz | 2025-05-25 | Build site. |
| html | 9ea8b52 | Pablo Almaraz | 2025-05-25 | Build site. |
| html | 3a8bc70 | Pablo Almaraz | 2025-05-25 | Add favicon RELab |
| html | 2c5f3ab | Pablo Almaraz | 2025-05-25 | Build site. |
| html | d9a4b8e | Pablo Almaraz | 2025-05-25 | Build site. |
| html | 9c32eb5 | Pablo Almaraz | 2025-05-25 | Build site. |
| Rmd | a6c7740 | Pablo Almaraz | 2025-05-25 | Update my new project |
Please look the README file for further details on
reproducing the results of this project. Note that the following chunks
are supposed to run sequentially.
Check that the pacman
package is installed. Alternatively, note that you can use the checkpoint
package to build an environment identical to the date of completion of
the present project. Look at the Session information tab
below. After pacman is
installed, the p_load function will check that the selected
packages are installed. If they are, it will load them; if not, it will
first install them and then load them.
# if (!require(checkpoint)) install.packages('checkpoint')
# checkpoint::checkpoint("2021-11-18")
if (!require(pacman)) install.packages('pacman')Cargando paquete requerido: pacmanpacman::p_load(tidyverse,runjags,coda,ggmcmc,xtable,data.table,viridis,ggsci,patchwork,mvtnorm,truncnorm,grateful)source("code/utilities.R")This will run the analyses in an order temporal sequence.
# All periods ####
for(TimePeriod in c("PreBSE","BSE","PostBSE")){
# Loada data: ####
load_data(TimePeriod)
# Find the equilibrium population and the variance of state variables: ####
find_equilibrium_population(TimePeriod,
adapt = 10000,
burnin = 100000,
sample = 1000,
thin = 100)
# Fit the SSSSDDDM: ####
fit_S4D3M(TimePeriod,
n.chains = 3,
adapt = 10000,
burnin = 500000,
sample = 1000,
thin = 500,
mcmc_diagnostics_plots = TRUE,
PPC_simulations = TRUE,
N_PPC_Fits = 100,
burnin_ppc = 100000,
sample_ppc = 1000,
thin_ppc = 100)
}The call to this function will produce all the figures in the paper
Figures()Once the analyses are completed and the figures produced, this shell
call to the Makefile will compile and open the manuscript
and related supplementary material:
make compile
sessionInfo()R version 4.5.0 (2025-04-11)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=es_ES.UTF-8 LC_NUMERIC=C
[3] LC_TIME=es_ES.UTF-8 LC_COLLATE=es_ES.UTF-8
[5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=es_ES.UTF-8
[7] LC_PAPER=es_ES.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Madrid
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] grateful_0.2.12 truncnorm_1.0-9 mvtnorm_1.3-3 patchwork_1.3.0
[5] ggsci_3.2.0 viridis_0.6.5 viridisLite_0.4.2 data.table_1.17.2
[9] xtable_1.8-4 ggmcmc_1.5.1.1 coda_0.19-4.1 runjags_2.2.2-5
[13] lubridate_1.9.4 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4
[17] purrr_1.0.4 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1
[21] ggplot2_3.5.2 tidyverse_2.0.0 pacman_0.5.1 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] gtable_0.3.6 xfun_0.52 bslib_0.9.0 processx_3.8.6
[5] GGally_2.2.1 lattice_0.22-7 callr_3.7.6 tzdb_0.5.0
[9] vctrs_0.6.5 tools_4.5.0 ps_1.9.1 generics_0.1.4
[13] parallel_4.5.0 pkgconfig_2.0.3 RColorBrewer_1.1-3 lifecycle_1.0.4
[17] compiler_4.5.0 farver_2.1.2 git2r_0.36.2 getPass_0.2-4
[21] httpuv_1.6.16 htmltools_0.5.8.1 sass_0.4.10 yaml_2.3.10
[25] later_1.4.2 pillar_1.10.2 jquerylib_0.1.4 whisker_0.4.1
[29] cachem_1.1.0 ggstats_0.9.0 tidyselect_1.2.1 digest_0.6.37
[33] stringi_1.8.4 rprojroot_2.0.4 fastmap_1.2.0 grid_4.5.0
[37] cli_3.6.5 magrittr_2.0.3 dichromat_2.0-0.1 withr_3.0.2
[41] scales_1.4.0 promises_1.3.2 timechange_0.3.0 rmarkdown_2.29.1
[45] httr_1.4.7 gridExtra_2.3 hms_1.1.3 evaluate_1.0.3
[49] knitr_1.50 rlang_1.1.6 Rcpp_1.0.14 glue_1.8.0
[53] rstudioapi_0.17.1 jsonlite_2.0.0 R6_2.6.1 plyr_1.8.9
[57] fs_1.6.6