update folder structure

MindTheGap-ERC · Sep 3, 2024 · 2599255 · 2599255
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diff --git a/README.md b/README.md
@@ -27,10 +27,10 @@ to install all dependencies required for the analyses.
 To reproduce the results, run
 
 ```R
-source("code/analyses.R)
+source("code/analyses.R")
 ```
 
-in the RStudio console. This will run both analyses (site 690 and Steinbruch Schmidt), generate all figues and save them in the `figs/` folder, and save the data under `data/site690_data.Rdata` and `data/sbs_data.Rdata`.
+in the RStudio console. This will run both analyses (site 690 and Steinbruch Schmidt), generate all figues and save them in the `figs/` folder, and save the data under `data/res/site690_data.Rdata` and `data/res/sbs_data.Rdata`.
 
 ## Repository structure
 
@@ -39,6 +39,7 @@ in the RStudio console. This will run both analyses (site 690 and Steinbruch Sch
   * _analysis_site690.R_ : code for the PETM example
   * _analyses.R_ : runs both examples
 * _data_ : folder for data
+  * _res_ : folder for resulst. Initially empty, filled once `code/analyses.R` is run
   * _raw_ : folder for raw data, read only!
     * _SbS_XRF_forfactor3.csv_ : data for Steinbruch Schmidt example, from da Silva (2020, 2024)
     * _Farley_and_Eltgroth_2003_supp_data_1_site690.csv_ : data for the PETM example, from Farley and Eltgroth (2003 a, b)

diff --git a/code/analyses.R b/code/analyses.R
@@ -3,4 +3,4 @@ source("code/analysis_site690.R")
 cat("Running analysis for Steinbruch Schmidt\n")
 source("code/analysis_steinbruch_schmidt.R")
 
-cat("done! Generated figures are in the folder figs/, data is in data/site690_data.Rdata and data/sbs_data.Rdata. \n")
+cat("done! Generated figures are in the folder figs/, data is in data/res/site690_data.Rdata and data/res/sbs_data.Rdata. \n")
diff --git a/code/analysis_site690.R b/code/analysis_site690.R
@@ -480,4 +480,4 @@ ggsave("figs/site690_joint_duration.png", plot = plt, width = fig_width_cm, heig
 
 
 
-save(my_adm_const, my_adm_dec, my_adm_inc, interval_cond_stats, sedr_stats, petm_main_stats, petm_recovery_stats, file = "data/site690_data.Rdata")
+save(my_adm_const, my_adm_dec, my_adm_inc, interval_cond_stats, sedr_stats, petm_main_stats, petm_recovery_stats, file = "data/res/site690_data.Rdata")
diff --git a/code/analysis_steinbruch_schmidt.R b/code/analysis_steinbruch_schmidt.R
@@ -490,4 +490,4 @@ plt = egg::ggarrange(r2_plot_secc, eTimeOpt_plot_secc,  ncol = 2, nrow = 1, labe
 ggsave("figs/r2_plot_secc_join.png", plot = plt, width = fig_width_cm, height = 8, unit = "cm", dpi = dpi)
 
 
-save(adm_prec_abs, adm_prec_float, adm_secc_abs, adm_secc_float, prec_ages, ff_mean_diff, ff_2sigma_diff, ff_2sigma_rat, ff_mean_diff_da_silva, ff_mean_diff_gradstein, uke_stats, time_ke_stats, file = "data/sbs_data.Rdata")
+save(adm_prec_abs, adm_prec_float, adm_secc_abs, adm_secc_float, prec_ages, ff_mean_diff, ff_2sigma_diff, ff_2sigma_rat, ff_mean_diff_da_silva, ff_mean_diff_gradstein, uke_stats, time_ke_stats, file = "data/res/sbs_data.Rdata")
diff --git a/data/res/.gitkeep.txt b/data/res/.gitkeep.txt
Original file line number	Diff line number	Diff line change
Expand Up		@@ -480,4 +480,4 @@ ggsave("figs/site690_joint_duration.png", plot = plt, width = fig_width_cm, heig



		save(my_adm_const, my_adm_dec, my_adm_inc, interval_cond_stats, sedr_stats, petm_main_stats, petm_recovery_stats, file = "data/site690_data.Rdata")
		save(my_adm_const, my_adm_dec, my_adm_inc, interval_cond_stats, sedr_stats, petm_main_stats, petm_recovery_stats, file = "data/res/site690_data.Rdata")
Original file line number	Diff line number	Diff line change
Expand Up		@@ -490,4 +490,4 @@ plt = egg::ggarrange(r2_plot_secc, eTimeOpt_plot_secc, ncol = 2, nrow = 1, labe
		ggsave("figs/r2_plot_secc_join.png", plot = plt, width = fig_width_cm, height = 8, unit = "cm", dpi = dpi)


		save(adm_prec_abs, adm_prec_float, adm_secc_abs, adm_secc_float, prec_ages, ff_mean_diff, ff_2sigma_diff, ff_2sigma_rat, ff_mean_diff_da_silva, ff_mean_diff_gradstein, uke_stats, time_ke_stats, file = "data/sbs_data.Rdata")
		save(adm_prec_abs, adm_prec_float, adm_secc_abs, adm_secc_float, prec_ages, ff_mean_diff, ff_2sigma_diff, ff_2sigma_rat, ff_mean_diff_da_silva, ff_mean_diff_gradstein, uke_stats, time_ke_stats, file = "data/res/sbs_data.Rdata")