Global patterns and predictors of C:N:P in marine ecosystems

This repository contains code and data needed to reproduce the article:

Tanioka, T., Garcia, C.A., Larkin, A.A. et al. Global patterns and predictors of C:N:P in marine ecosystems. Commun Earth Environ 3, 271 (2022). https://doi.org/10.1038/s43247-022-00603-6

Instructions

All processing was done in R. This routine uses the drake R package to compile the output time table. First install drake:

install.packages("drake")

It also requires the package Orca installed. Follow instructions on https://github.com/plotly/orca on how to install.

Next you need to open an R session with working directory set to the root of the project.

This routine loads multiple packages which are found in R/packages.R, so make sure to successfully install and load them before running drake with the code below.

To reproduce particular targets outlined in R/plan.R, do e.g.:

drake::clean()
source("_drake.R")
drake::make(plan, targets = c("fig_1_pdf", "fig_2_pdf", "fig_3_highlat_pdf", "fig_3_lowlat_pdf", "fig_4_pdf", "fig_5_pdf","ed_fig_1_pdf","sp_table_2"), lock_envir = FALSE)

This example above will create Main Figures 1-4, Extended Data Figure 1, and Table 2 in Supplementary Information as presented in the manuscript along with all its dependencies.

All output will be automatically placed in a directory called output (it is going to be automatically created for you).

To reproduce all data analyses / figures / tables, and then make them available within an R session, do:

drake::clean()
source("_drake.R")
source("make.R")
drake::loadd()

This whole process should be completed in less than 5 minutes.

Main Figures 2a-c (created with ODV) are located in the separate pics folder. Supplementary Table 1 is a list of POM samples collected and is not reproduced here. Note that figures created here were subsequently cleaned using Adobe Illustrator for the manuscript.

This paper was produced using the following software and associated packages:

R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.6

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] Hmisc_4.6-0          Formula_1.2-4        cmocean_0.3-1        ocedata_0.1.8        oce_1.4-0           
 [6] testthat_3.1.0       sf_1.0-3             gsw_1.0-6            ncdf4_1.17           RColorBrewer_1.1-2  
[11] gratia_0.6.0         mgcv_1.8-38          nlme_3.1-153         matrixStats_0.61.0   mosaic_1.8.3        
[16] ggridges_0.5.3       mosaicData_0.20.2    ggformula_0.10.1     ggstance_0.3.5       lattice_0.20-45     
[21] scales_1.1.1         plotly_4.10.0        Matrix_1.3-4         multcomp_1.4-17      TH.data_1.1-0       
[26] survival_3.2-13      mvtnorm_1.1-3        MASS_7.3-54          pals_1.7             corrplot_0.90       
[31] hrbrthemes_0.8.0     viridis_0.6.2        viridisLite_0.4.0    ggpubr_0.4.0         rstan_2.21.2        
[36] StanHeaders_2.21.0-7 data.table_1.14.2    forcats_0.5.1        stringr_1.4.0        purrr_0.3.4         
[41] readr_2.0.2          tidyr_1.1.4          tibble_3.1.5         ggplot2_3.3.5        tidyverse_1.3.1     
[46] naniar_0.6.1         dplyr_1.0.7          plyr_1.8.6           drake_7.13.3        

loaded via a namespace (and not attached):
  [1] utf8_1.2.2          R.utils_2.11.0      tidyselect_1.1.1    htmlwidgets_1.5.4   grid_4.1.0         
  [6] munsell_0.5.0       base64url_1.4       codetools_0.2-18    units_0.7-2         withr_2.4.2        
 [11] colorspace_2.0-2    filelock_1.0.2      knitr_1.36          rstudioapi_0.13     stats4_4.1.0       
 [16] ggsignif_0.6.3      Rttf2pt1_1.3.9      labeling_0.4.2      polyclip_1.10-0     farver_2.1.0       
 [21] txtq_0.2.4          vctrs_0.3.8         generics_0.1.1      xfun_0.27           R6_2.5.1           
 [26] assertthat_0.2.1    nnet_7.3-16         gtable_0.3.0        processx_3.5.2      sandwich_3.0-1     
 [31] rlang_0.4.12        systemfonts_1.0.3   splines_4.1.0       rstatix_0.7.0       extrafontdb_1.0    
 [36] lazyeval_0.2.2      dichromat_2.0-0     checkmate_2.0.0     broom_0.7.9         mosaicCore_0.9.0   
 [41] inline_0.3.19       yaml_2.2.1          reshape2_1.4.4      abind_1.4-5         modelr_0.1.8       
 [46] crosstalk_1.1.1     backports_1.3.0     extrafont_0.17      tools_4.1.0         ellipsis_0.3.2     
 [51] jquerylib_0.1.4     ggdendro_0.1.22     proxy_0.4-26        Rcpp_1.0.7          base64enc_0.1-3    
 [56] progress_1.2.2      classInt_0.4-3      ps_1.6.0            prettyunits_1.1.1   rpart_4.1-15       
 [61] zoo_1.8-9           cluster_2.1.2       haven_2.4.3         ggrepel_0.9.1       fs_1.5.0           
 [66] magrittr_2.0.1      openxlsx_4.2.4      reprex_2.0.1        mvnfast_0.2.7       storr_1.2.5        
 [71] hms_1.1.1           patchwork_1.1.1     evaluate_0.14       leaflet_2.0.4.1     jpeg_0.1-9         
 [76] rio_0.5.27          readxl_1.3.1        gridExtra_2.3       compiler_4.1.0      maps_3.4.0         
 [81] KernSmooth_2.23-20  V8_3.4.2            crayon_1.4.1        R.oo_1.24.0         htmltools_0.5.2    
 [86] tzdb_0.2.0          visdat_0.5.3        RcppParallel_5.1.4  lubridate_1.8.0     DBI_1.1.1          
 [91] tweenr_1.0.2        dbplyr_2.1.1        car_3.0-11          cli_3.1.0           R.methodsS3_1.8.1  
 [96] parallel_4.1.0      igraph_1.2.7        pkgconfig_2.0.3     foreign_0.8-81      xml2_1.3.2         
[101] bslib_0.3.1         rvest_1.0.2         callr_3.7.0         digest_0.6.28       rmarkdown_2.11     
[106] cellranger_1.1.0    htmlTable_2.3.0     gdtools_0.2.3       curl_4.3.2          lifecycle_1.0.1    
[111] jsonlite_1.7.2      carData_3.0-4       mapproj_1.2.7       fansi_0.5.0         labelled_2.8.0     
[116] pillar_1.6.4        loo_2.4.1           fastmap_1.1.0       httr_1.4.2          pkgbuild_1.2.0     
[121] glue_1.4.2          zip_2.2.0           png_0.1-7           ggforce_0.3.3       class_7.3-19       
[126] stringi_1.7.5       sass_0.4.0          latticeExtra_0.6-29 e1071_1.7-9     

License

This repository is provided by the authors under the MIT License (MIT).

How to download this project for people not familiar with GitHub:

• on the project main page on GitHub, click on the green button clone or download and then click on Download ZIP

Bug reporting

• Please report any issues or bugs to Tatsuro Tanioka (tatsurt[at]uci.edu).