WIP combining CANSAR and DMTS to get species with not published statu…

…s report

scripts/combineCANSAR_DMTS.R

@@ -0,0 +1,61 @@
+# Combine SAR DMTS data with existing database
+
+# This will fix species missing because they have no status report on the web
+
+# Could additionally use this as a way to start adding new species
+
+
+library(dplyr)
+library(stringr)
+library(tidyr)
+# load the database
+dat_pth <- "data-raw"
+
+db <- readr::read_csv(here::here(dat_pth, "data-out/CAN-SAR_database.csv"))
+
+# exported from SAR DMTS listing search page filtered by SARA Schedule = Schedule 1
+dmts <- readr::read_csv(here::here(dat_pth, "data-raw/SAR_DMTS_FullExport-20240926-154900.csv"))
+
+# link to species ids in db first
+
+db_link <- db %>%
+  select(speciesID, common_name, species, sara_status, cosewic_status,
+         web_pub_date, year_published, doc_type, date_of_listing) %>%
+  mutate(common_name = common_name %>% str_replace("populations", "population") %>%
+           str_replace_all("�", "é") %>%
+           str_replace_all("tope shark", "tope"))
+
+
+dmts_link <- dmts %>%
+  select(`COSEWIC ID`, `Listing ID`, `COSEWIC English common name`,
+         `COSEWIC Population (E)`, `COSEWIC Scientific Name`, `COSEWIC WS status`,
+         `Listing Common Name (English)`, `Listing Scientific Name`,
+         `Listing Taxonomic group (E)`, `Listing Population (E)`,
+         `On Schedule 1 date`, Endemic, `Ranges (E)`, `Type of Report`) %>%
+  mutate(common_name = paste(`COSEWIC English common name`,
+                             ifelse(is.na(`COSEWIC Population (E)`), "",
+                                    `COSEWIC Population (E)`)) %>%
+           str_to_lower() %>% str_trim() %>%
+           str_replace("populations", "population") %>%
+           str_replace_all("common five", "five") %>%
+           str_replace_all("eastern false", "false") %>%
+           str_remove_all("\\(|\\)") %>%
+           str_replace_all("’", "'") %>%
+           str_replace_all(" \\-| \\- |\\- ", "-") %>%
+           str_replace_all(" \\-| \\- |\\- ", "-") %>%
+           str_replace_all(" – ", "-") %>%
+           str_replace_all(" \\/| \\/ |\\/ ", "/")%>%
+           str_replace_all(" \\/| \\/ |\\/ ", "/")) %>%
+  full_join(db_link, by = "common_name")
+
+# some confusion due to species on Schedule 1 under one DU but new DU exists and
+# has COSEWIC status but hasn't been added to schedule 1 yet. Looks like in
+# CANSAR the old SARA status was applied to all three of the new DUs although
+# probably that is incorrect since only two were included in the previous DU and
+# the third was previously not assessed by COSEWIC and isn't really on SARA
+# registry.
+# CANSAR includes all species that were ever on schedule 1 it seems eg Sonora skipper
+
+
+# TODO stopped while looking at species in DMTS but not CANSAR, should filter
+# DMTS so only shows those listed before CANSAR end date