This directory accompanies the pre-print "The importance of habitat type and historical fire regimes in arthropod community response following large-scale wildfires" by Anna J. Holmquist, R.J. Cody Markelz, Ciera C. Martinez, Rosemary G. Gillespie . doi: https://doi.org/10.1101/2023.07.17.548903 Available here
We describe two docker containers below to run the data processing, analysis and statistical tests code in this repository. The data processing using easy to build containers with few dependencies. The analysis and statistics portion uses a larger container with many packages and dependencies. The analysis container is available on Docker Hub here. The code to rebuild both containers (mostly installing R packages and dependencies) is also provided below.
docker pull codymarkelz/holmquist-etal-edna-fire-paperTo run the following scripts: dada2_bf3.Rmd dada2_mco.Rmd
Change the path to match your directory where the data is located. See how to make the "biocontainers_dada2_tidyverse" container below using the biocontainers dada2 base.
docker run -it -v /PATH/TO/DIRECTORY:/DATA/ biocontainers_dada2_tidyverse /bin/bashTo run the following scripts: fire_cleanup.Rmd fire_analysis.Rmd
Change the path to match your directory path for where the data is located. Use our pre-built container, or follow the instructions below to install all the dependencies.
docker run --rm -p 8787:8787 -e PASSWORD=YOURNEWPASSWORD -v /PATH/TO/DIRECTORY:/home/rstudio/DATA codymarkelz/holmquist-etal-edna-fire-paperBrowser: http://localhost:8787/
user: rstudio pass: YOURNEWPASSWORD
Once signed in. Tools -> Global Options -> Appearance -> Editor theme: Solarized Dark
directory small datasets go here
directory to save intermediary files and output
directory for figure drafts and final figures
Download base container.
docker pull quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h619a076_1
docker run -it quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h619a076_1 /bin/bashinstall.packages("tidyverse")
install.packages("stringr")
sessionInfo(package = NULL)
# R version 4.1.2 (2021-11-01)
# Platform: x86_64-conda-linux-gnu (64-bit)
# Running under: Debian GNU/Linux 10 (buster)
#
# Matrix products: default
# BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.18.so
#
# locale:
# [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
# [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
# [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
# [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
#
# attached base packages:
# [1] stats graphics grDevices utils datasets methods base
#
# other attached packages:
# [1] forcats_0.5.2 stringr_1.4.1 dplyr_1.0.9 purrr_0.3.4
# [5] readr_2.1.2 tidyr_1.2.0 tibble_3.1.6 ggplot2_3.3.5
# [9] tidyverse_1.3.2
#
# loaded via a namespace (and not attached):
# [1] pillar_1.7.0 compiler_4.1.2 cellranger_1.1.0
# [4] dbplyr_2.2.1 tools_4.1.2 lubridate_1.8.0
# [7] jsonlite_1.8.0 googledrive_2.0.0 lifecycle_1.0.1
# [10] gargle_1.2.0 gtable_0.3.0 pkgconfig_2.0.3
# [13] rlang_1.0.4 reprex_2.0.2 DBI_1.1.3
# [16] cli_3.3.0 haven_2.5.1 xml2_1.3.3
# [19] withr_2.4.3 httr_1.4.4 generics_0.1.3
# [22] vctrs_0.4.1 fs_1.5.2 hms_1.1.2
# [25] googlesheets4_1.0.1 grid_4.1.2 tidyselect_1.1.2
# [28] glue_1.6.2 R6_2.5.1 fansi_1.0.2
# [31] readxl_1.4.1 tzdb_0.3.0 modelr_0.1.9
# [34] magrittr_2.0.2 backports_1.4.1 scales_1.1.1
# [37] ellipsis_0.3.2 rvest_1.0.3 assertthat_0.2.1
# [40] colorspace_2.0-3 utf8_1.2.2 stringi_1.7.6
# [43] munsell_0.5.0 broom_1.0.0 crayon_1.5.0Outside of container.
docker commit intelligent_feistel biocontainers_dada2_tidyverse
docker images biocontainers_dada2_tidyverse
# REPOSITORY TAG IMAGE ID CREATED SIZE
# biocontainers_dada2_tidyverse latest c1f8a711f890 6 minutes ago 1.18GBDownload base containers.
docker pull rocker/tidyverse
docker run -it rocker/tidyverse /bin/bash
docker run -it rocker/geospatial /bin/bashinstall.packages("BAT", dependencies = TRUE)
install.packages("ape")
install.packages("vegan")
install.packages("devtools")
devtools::install_github("tobiasgf/lulu")
install.packages("venn", dependencies = TRUE)
install.packages("coin")
install.packages("ggpubr")
# load the packages to make sure they are working
library(BAT)
library(ape)
library(vegan)
library(lulu)
library(venn)
library(coin)
library(tidyverse)
library(ggpubr)
sessionInfo(package = NULL)
# R version 4.1.1 (2021-08-10)
# Platform: x86_64-pc-linux-gnu (64-bit)
# Running under: Ubuntu 20.04.3 LTS
# Matrix products: default
# BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
# locale:
# [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
# [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
# [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
# [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
# [9] LC_ADDRESS=C LC_TELEPHONE=C
# [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
# attached base packages:
# [1] stats graphics grDevices utils datasets methods base
# other attached packages:
# [1] ggpubr_0.6.0 reshape2_1.4.4 forcats_0.5.1 stringr_1.5.0
# [5] dplyr_1.1.0 purrr_1.0.1 readr_2.0.1 tidyr_1.3.0
# [9] tibble_3.2.1 ggplot2_3.4.1 tidyverse_1.3.1 coin_1.4-2
# [13] survival_3.2-11 venn_1.11 lulu_0.1.0 vegan_2.6-4
# [17] lattice_0.20-44 permute_0.9-7 ape_5.7-1 BAT_2.9.2
# loaded via a namespace (and not attached):
# [1] readxl_1.3.1 backports_1.2.1 plyr_1.8.6
# [4] sp_1.4-5 splines_4.1.1 listenv_0.8.0
# [7] usethis_2.0.1 TH.data_1.1-1 digest_0.6.27
# [10] htmltools_0.5.2 foreach_1.5.2 fansi_0.5.0
# [13] memoise_2.0.0 magrittr_2.0.1 cluster_2.1.2
# [16] doParallel_1.0.17 ks_1.14.0 remotes_2.4.0
# [19] tzdb_0.3.0 recipes_1.0.5 globals_0.16.2
# [22] fastcluster_1.2.3 modelr_0.1.8 gower_1.0.1
# [25] matrixStats_0.63.0 sandwich_3.0-2 hardhat_1.2.0
# [28] timechange_0.2.0 pdist_1.2.1 prettyunits_1.1.1
# [31] colorspace_2.0-2 rvest_1.0.1 haven_2.4.3
# [34] xfun_0.25 callr_3.7.0 crayon_1.4.1
# [37] jsonlite_1.7.2 libcoin_1.0-9 zoo_1.8-9
# [40] iterators_1.0.14 glue_1.6.2 gtable_0.3.0
# [43] ipred_0.9-14 pkgbuild_1.2.0 car_3.1-1
# [46] future.apply_1.10.0 maps_3.3.0 abind_1.4-5
# [49] scales_1.2.1 mvtnorm_1.1-3 DBI_1.1.1
# [52] rstatix_0.7.2 Rcpp_1.0.7 progress_1.2.2
# [55] palmerpenguins_0.1.1 magic_1.5-9 proxy_0.4-26
# [58] mclust_6.0.0 stats4_4.1.1 lava_1.7.2.1
# [61] prodlim_2019.11.13 httr_1.4.2 ellipsis_0.3.2
# [64] modeltools_0.2-23 farver_2.1.0 pkgconfig_2.0.3
# [67] nnet_7.3-16 dbplyr_2.1.1 utf8_1.2.2
# [70] caret_6.0-94 tidyselect_1.2.0 labeling_0.4.2
# [73] rlang_1.1.0 cachem_1.0.6 munsell_0.5.0
# [76] cellranger_1.1.0 tools_4.1.1 cli_3.6.0
# [79] generics_0.1.3 devtools_2.4.2 broom_0.7.9
# [82] fastmap_1.1.0 evaluate_0.14 geometry_0.4.5
# [85] yaml_2.2.1 processx_3.5.2 ModelMetrics_1.2.2.2
# [88] knitr_1.33 fs_1.5.0 admisc_0.31
# [91] future_1.32.0 nlme_3.1-152 pracma_2.4.2
# [94] xml2_1.3.2 compiler_4.1.1 rstudioapi_0.13
# [97] testthat_3.0.4 e1071_1.7-8 ggsignif_0.6.4
# [100] reprex_2.0.1 stringi_1.7.4 ps_1.6.0
# [103] desc_1.3.0 rgeos_0.5-5 Matrix_1.5-3
# [106] vctrs_0.6.0 pillar_1.8.1 lifecycle_1.0.3
# [109] BiocManager_1.30.16 cowplot_1.1.1 data.table_1.14.0
# [112] raster_3.4-13 R6_2.5.1 gridExtra_2.3
# [115] KernSmooth_2.23-20 parallelly_1.34.0 sessioninfo_1.1.1
# [118] codetools_0.2-18 ggpolypath_0.2.0 pkgload_1.2.1
# [121] MASS_7.3-54 assertthat_0.2.1 proto_1.0.0
# [124] rprojroot_2.0.2 withr_2.5.0 multcomp_1.4-23
# [127] mgcv_1.8-36 parallel_4.1.1 hms_1.1.0
# [130] terra_1.3-22 grid_4.1.1 rpart_4.1-15
# [133] timeDate_4022.108 class_7.3-19 rmarkdown_2.10
# [136] nls2_0.3-3 hypervolume_3.1.0 carData_3.0-5
# [139] pROC_1.18.0 lubridate_1.9.2
citation("BAT")
citation("lulu")
citation("ape")
citation("vegan")
citation("tidyverse")
citation("venn")
citation("coin")
citation("devtools")
citation("ggpubr")Outside of container.
# docker container ID with the newly installed packages
docker ps
docker commit -m "rocker_geospatial_fire_edna" 51b493fcf9c8 rocker_geospatial_fire_edna
docker image ls
docker tag 1a9b7c7945d1 codymarkelz/holmquist-etal-edna-fire-paper:pre-print
docker push codymarkelz/holmquist-etal-edna-fire-paper:pre-print