Small updates to readme, reading .gz files, and restoring mistakenly …

…deleted output files
pinskylab · Aug 18, 2020 · 2e98d0d · 2e98d0d
1 parent d259de3
commit 2e98d0d
Show file tree

Hide file tree

Showing 7 changed files with 8 additions and 4 deletions.
diff --git a/README.md b/README.md
@@ -172,7 +172,8 @@ All figures and Table S1 are produced by [plot_figures.r](code/plot_figures.r).<
 			1. Kappa thresholds from Morley et al. 2018 PLOS ONE: see above
 1. [Table S1](tables/tableS1.csv)
 	1. output/prioritizr_runs/solution\_\*.csv and output/prioritizr_runs/spp\_\*.csv: see above
-
+1. Table S4
+	1. [output/fishery_spps.csv](output/fishery_spps.csv): see above
 
 ## InVEST runs
 These are the detailed program settings used when InVEST was run.

diff --git a/code/5.2_evalprioritizr.r b/code/5.2_evalprioritizr.r
@@ -330,7 +330,7 @@ write.csv(goalsmetbymod2, file = paste0('output/goalsmetbymod_', runname2out, '.
 
 
 # read back in if needed
-goalsbyzonebymod1 <- fread(paste0('gunzip -c output/goalsbyzonebymod_', runname1out, '.csv.gz'), drop = 1)
-goalsbyzonebymod2 <- fread(paste0('gunzip -c output/goalsbyzonebymod_', runname2out, '.csv.gz'), drop = 1)
+goalsbyzonebymod1 <- fread(paste0('output/goalsbyzonebymod_', runname1out, '.csv.gz'), drop = 1)
+goalsbyzonebymod2 <- fread(paste0('output/goalsbyzonebymod_', runname2out, '.csv.gz'), drop = 1)
 goalsmetbymod1 <- fread(paste0('output/goalsmetbymod_', runname1out, '.csv'), drop = 1)
 goalsmetbymod2 <- fread(paste0('output/goalsmetbymod_', runname2out, '.csv'), drop = 1)
diff --git a/code/plot_figures.r b/code/plot_figures.r
@@ -144,7 +144,10 @@ rcps <- sort(unique(goalsmetbymod1$rcp))
 # Statistics
 # goals met, mid-century or end-of-century (for text)
 goalsmetbymod[year_range == '2041-2060', .(mean = mean(pmetstrict), sd = sd(pmetstrict)), by = c('type')] # mean and se across models and goals
-goalsmetbymod[year_range == '2081-2100', .(mean = mean(pmetstrict), sd = sd(pmetstrict)), by = c('type')] # mean and se across models and goals
+
+goalsmetbymod[year_range == '2081-2100' & rcp == '26', .(mean = mean(pmetstrict), sd = sd(pmetstrict)), by = c('type')] # mean and se across models and goals
+goalsmetbymod[year_range == '2081-2100' & rcp == '85', .(mean = mean(pmetstrict), sd = sd(pmetstrict)), by = c('type')] # mean and se across models and goals
+
 
 # p(80% goals met), end-of-century (for text)
 goalsmetbymod[year_range == '2081-2100', .(prop = 1 - sum(pmetstrict > 0.7)/.N), by = c('type')]

diff --git a/output/goalsbyzonebyensemble_2per_all.csv.gz b/output/goalsbyzonebyensemble_2per_all.csv.gz
diff --git a/output/goalsbyzonebyensemble_hist_all.csv.gz b/output/goalsbyzonebyensemble_hist_all.csv.gz
diff --git a/output/goalsbyzonebymod_2per_all.csv.gz b/output/goalsbyzonebymod_2per_all.csv.gz
diff --git a/output/goalsbyzonebymod_hist_all.csv.gz b/output/goalsbyzonebymod_hist_all.csv.gz