Move species table code to new script #121

output/manuscript/papilio-table.csv

@@ -1,4 +1,4 @@
-"species","n_filtered","n_hosts","n_hosts_suff","ew"
+"Species","# Records","# Host species","# Host SDMs","Location"
 "P. appalachiensis",131,1,1,"East"
 "P. brevicauda",196,9,8,"East"
 "P. canadensis",7200,20,19,"East"

src/manuscript/tables-1-species.R

@@ -0,0 +1,58 @@
+# Create table with species information for manuscript
+# Erin Zylstra & Jeff Oliver
+# [email protected] & [email protected]
+# 2024-12-05
+
+library(dplyr)
+require(stringr)
+
+# Load insect-host information and gbif data summaries
+ih <- read.csv("data/insect-host.csv")
+gbif <- read.csv("data/gbif-pa-summary.csv")
+
+# File with east/west designation information
+ew <- read.csv(file = "data/insect-eastwest.csv")
+
+# Base of output filenames
+output_basename <- "output/manuscript/"
+
+# Get number of filtered records for each swallowtail spp
+insects <- gbif %>%
+  filter(str_detect(species, "Papilio")) 
+
+# Retain only those that have a presence/absence CSV file
+insects <- insects %>%
+  filter(pa_csv == "yes") %>%
+  select(species, n_filtered)
+
+# Get number of host plant species (total or with 40+ filtered records)
+ih2 <- ih %>%
+  select(insect, host_accepted) %>%
+  left_join(select(gbif, species, pa_csv), 
+            join_by("host_accepted" == "species")) %>%
+  group_by(insect) %>%
+  summarize(n_hosts = length(host_accepted),
+            n_hosts_suff = sum(pa_csv == "yes")) %>%
+  data.frame()
+
+# Add host species counts to insects data
+insects <- left_join(insects, ih2, join_by("species" == "insect"))
+
+# Add in east/west indicator & shorten names
+insects <- insects %>%
+  left_join(ew, by = c("species" = "insect")) %>%
+  mutate(species = str_replace(species, "Papilio", "P."))
+
+# Update column names more appropriate for manuscript
+insects <- insects %>%
+  rename(Species = species,
+         `# Records` = n_filtered,
+         `# Host species` = n_hosts,
+         `# Host SDMs` = n_hosts_suff,
+         Location = ew)
+
+# Write to file
+papilio_table <- paste0(output_basename, "papilio-table.csv")
+write.csv(x = insects, 
+          file = papilio_table, 
+          row.names = FALSE)