Merge pull request #2 from NiklasHohmann/dev

Dev

Author: NiklasHohmann

.gitignore

@@ -4,4 +4,5 @@
 .Ruserdata
 
 # don't track csv files
-*.csv
+*.csv
+*.pdf

README.md

@@ -2,7 +2,7 @@
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10782803.svg)](https://doi.org/10.5281/zenodo.10782803)
 
-Supplementary code for _"A revised marine fossil record of the Mediterranean before and after the Messinian Salinity Crisis"_. Generates summary statistics and maps.
+Supplementary code for _"A revised marine fossil record of the Mediterranean before and after the Messinian Salinity Crisis"_ (Agiadi et al 2024, [DOI: 10.5194/essd-2024-75](https://doi.org/10.5194/essd-2024-75)). Generates summary statistics, figures, and maps.
 
 Project webpage: [REMARE project](https://sites.google.com/view/kagiadi/projects/remare)
 
@@ -51,7 +51,7 @@ source("code/download_data.R")
 to download the latest version of the database from Zenodo. Then, run
 
 ```R
-source("code/make_table.R")
+source("code/make_table_and_plots.R")
 ```
 
 in the console to produce the summary statistics of the database (stored in the variable `table`). You can view the values by running
@@ -60,12 +60,12 @@ in the console to produce the summary statistics of the database (stored in the
 table
 ```
 
-in the console. Details on producing the map are given in the file `code/make_maps.R`.
+in the console, and inspect the figures in `figs/`. Details on producing the map are given in the file `code/make_maps.R`.
 
 ## Repository structure  
 
 * _code_ : folder with R code
-  * _make_table.R_ : script to generate table 1
+  * _make_table_and_plots.R_ : script to generate table 1 and figures
   * _make_maps.R_ : script to generate the maps
   * _download_data.R_ : script to download data from Zenodo
 * _data_ : folder for raw data. Initially empty, will be filled with downloaded data after the script in `code/download_data.R` is run.
@@ -77,6 +77,13 @@ in the console. Details on producing the map are given in the file `code/make_ma
 * _README_ : README file
 * _renv.lock_ : lock file for `renv` package
 
+## References
+
+This repository downloads and uses data from
+
+* Agiadi, K., Hohmann, N., Gliozzi, E., Thivaiou, D., Francesca, B., Taviani, M., Bianucci, G., Collareta, A., Londeix, L., Faranda, C., Bulian, F., Koskeridou, E., Lozar, F., Mancini, A. M., Dominici, S., Moissette, P., Bajo Campos, I., Borghi, E., Iliopoulos, G., … Garcia-Castellanos, D. (2024). Revised marine fossil record of the Mediterranean before and after the Messinian Salinity Crisis [Data set]. Zenodo. https://doi.org/10.5281/zenodo.13358435
+
+
 ## Funding
 
 This work was supported by the Austrian Science Fund (FWF) project “Late Miocene Mediterranean Marine Ecosystem Crisis” (2022–2026), Project no. V 986, [DOI 10.55776/V986](https://www.doi.org/10.55776/V986) (PI: K.Agiadi). 

code/download_data.R

@@ -2,6 +2,7 @@
 # download latest version of the database from Zenodo, https://doi.org/10.5281/zenodo.12698765
 
 cat("Downloading raw data\n")
-zen4R::download_zenodo("10.5281/zenodo.12698765", path = "data/")
+
+zen4R::download_zenodo("10.5281/zenodo.13358435", path = "data/")
 
 cat("Data successfully downloaded! \n")

code/make_table.R code/make_table_and_plots.Rcode/make_table.R renamed to code/make_table_and_plots.R

@@ -64,3 +64,40 @@ table["total", "families"] <- sum(table[group_names,"families"])
 table
 
 cat("Table successfully generated!\n")
+
+#### make plots ####
+library(ggplot2)
+cat("Creating plots\n")
+## plot occurrences
+make_occ_plot = function(file_name){
+  df = data.frame(group = rep(group_names, each = 3),
+                  regions = rep(regions, length(group_names)),
+                  nocc = rep(NA, length(regions) * length(group_names)))
+  for (i in seq_len(nrow(df))){
+    df[i, "nocc"] = length(unique(messinian_db$ID[messinian_db$group.name == df$group[i] & messinian_db$region.new == df$regions[i]]))
+  }
+  ggplot(df, aes(x = group, fill = regions, y = nocc)) +
+    geom_bar(stat = "identity", position = "dodge") +
+    theme_classic()
+  ggsave(file_name)
+}
+make_occ_plot("figs/occ.pdf")
+
+make_loc_plot = function(file_name){
+  df = data.frame(group = rep(group_names, each = 3),
+                  regions = rep(regions, length(group_names)),
+                  nloc = rep(NA, length(regions) * length(group_names)))
+  for (i in seq_len(nrow(df))){
+    df[i, "nloc"] = length(unique(messinian_db$Locality[messinian_db$group.name == df$group[i] & messinian_db$region.new == df$regions[i]]))
+  }
+  
+  ggplot(df, aes(x = group, y = nloc, fill = regions)) +
+    geom_bar(position = position_dodge(), stat = "identity") +
+    theme_classic()
+  ggsave(file_name)
+}
+make_loc_plot("figs/locs.pdf")
+
+
+
+cat("Plots are in figs/ \n")

renv.lock

@@ -1,6 +1,6 @@
 {
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+    "Version": "4.4.1",
     "Repositories": [
       {
         "Name": "CRAN",
@@ -22,7 +22,7 @@
     },
     "MASS": {
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+      "Version": "7.3-61",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -33,11 +33,11 @@
         "stats",
         "utils"
       ],
-      "Hash": "a56a6365b3fa73293ea8d084be0d9bb0"
+      "Hash": "0cafd6f0500e5deba33be22c46bf6055"
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     "Matrix": {
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-      "Version": "1.6-4",
+      "Version": "1.7-0",
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@@ -50,7 +50,7 @@
         "stats",
         "utils"
       ],
-      "Hash": "d9c655b30a2edc6bb2244c1d1e8d549d"
+      "Hash": "1920b2f11133b12350024297d8a4ff4a"
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@@ -74,14 +74,14 @@
     },
     "Rcpp": {
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+      "Version": "1.0.13",
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       "Repository": "CRAN",
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-      "Hash": "5ea2700d21e038ace58269ecdbeb9ec0"
+      "Hash": "f27411eb6d9c3dada5edd444b8416675"
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@@ -180,10 +180,10 @@
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+      "Version": "1.0-8",
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-      "Hash": "b7d8d8ee39869c18d8846a184dd8a1af"
+      "Hash": "da69e6b6f8feebec0827205aad3fdbd8"
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     "blob": {
       "Package": "blob",
@@ -226,7 +226,7 @@
     },
     "bslib": {
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+      "Version": "0.8.0",
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@@ -244,7 +244,7 @@
         "rlang",
         "sass"
       ],
-      "Hash": "8644cc53f43828f19133548195d7e59e"
+      "Hash": "b299c6741ca9746fb227debcb0f9fb6c"
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@@ -305,7 +305,7 @@
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+      "Version": "2.1-1",
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@@ -315,7 +315,7 @@
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         "stats"
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-      "Hash": "f20c47fd52fae58b4e377c37bb8c335b"
+      "Hash": "d954cb1c57e8d8b756165d7ba18aa55a"
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       "Package": "commonmark",
@@ -423,14 +423,14 @@
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+      "Version": "0.6.37",
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-      "Hash": "fd6824ad91ede64151e93af67df6376b"
+      "Hash": "33698c4b3127fc9f506654607fb73676"
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     "dplyr": {
       "Package": "dplyr",
@@ -1040,7 +1040,7 @@
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     "nlme": {
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+      "Version": "3.1-166",
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@@ -1050,17 +1050,17 @@
         "stats",
         "utils"
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-      "Hash": "2769a88be217841b1f33ed469675c3cc"
+      "Hash": "ccbb8846be320b627e6aa2b4616a2ded"
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     "openssl": {
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-      "Version": "2.2.0",
+      "Version": "2.2.1",
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         "askpass"
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-      "Hash": "2bcca3848e4734eb3b16103bc9aa4b8e"
+      "Hash": "c62edf62de70cadf40553e10c739049d"
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@@ -1233,7 +1233,7 @@
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+      "Version": "0.2.9",
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@@ -1245,7 +1245,7 @@
         "tidyr",
         "utils"
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-      "Hash": "7aabe63f0e0a33190643e25ba9dd3774"
+      "Hash": "7d812c4fa75df359492a135421fa0c12"
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     "readr": {
       "Package": "readr",
@@ -1317,9 +1317,12 @@
     "renv": {
       "Package": "renv",
       "Version": "1.0.7",
-      "OS_type": null,
-      "Repository": "CRAN",
-      "Source": "Repository"
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "utils"
+      ],
+      "Hash": "397b7b2a265bc5a7a06852524dabae20"
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     "reprex": {
       "Package": "reprex",
@@ -1356,7 +1359,7 @@
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-      "Version": "2.27",
+      "Version": "2.28",
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@@ -1375,7 +1378,7 @@
         "xfun",
         "yaml"
       ],
-      "Hash": "27f9502e1cdbfa195f94e03b0f517484"
+      "Hash": "062470668513dcda416927085ee9bdc7"
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@@ -1666,13 +1669,13 @@
     },
     "tinytex": {
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-      "Version": "0.51",
+      "Version": "0.52",
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       "Repository": "CRAN",
       "Requirements": [
         "xfun"
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-      "Hash": "d44e2fcd2e4e076f0aac540208559d1d"
+      "Hash": "cfbad971a71f0e27cec22e544a08bc3b"
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@@ -1697,13 +1700,13 @@
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         "R"
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-      "Hash": "303c19bfd970bece872f93a824e323d9"
+      "Hash": "34e965e62a41fcafb1ca60e9b142085b"
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@@ -1757,27 +1760,28 @@
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+      "Version": "3.0.1",
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       "Requirements": [
         "R",
         "grDevices",
         "graphics"
       ],
-      "Hash": "d31b6c62c10dcf11ec530ca6b0dd5d35"
+      "Hash": "07909200e8bbe90426fbfeb73e1e27aa"
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     "xfun": {
       "Package": "xfun",
-      "Version": "0.45",
+      "Version": "0.47",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
+        "R",
         "grDevices",
         "stats",
         "tools"
       ],
-      "Hash": "ca59c87fe305b16a9141a5874c3a7889"
+      "Hash": "36ab21660e2d095fef0d83f689e0477c"
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@@ -1794,10 +1798,10 @@
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     "yaml": {
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-      "Version": "2.3.9",
+      "Version": "2.3.10",
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-      "Hash": "9cb28d11799d93c953f852083d55ee9e"
+      "Hash": "51dab85c6c98e50a18d7551e9d49f76c"
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@@ -1825,7 +1829,7 @@
       "Package": "zip",
       "Version": "2.3.1",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
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   }