From 398b22df08122041889500b36713feb299842568 Mon Sep 17 00:00:00 2001
From: John Waller <ftw712@ku.dk>
Date: Mon, 15 Jul 2024 12:00:50 +0200
Subject: [PATCH] fixing a few formatting errors

---
 .../R/table_20240715115029.R                  | 82 +++++++++++++++++++
 .../R/table_20240715115244.R                  | 82 +++++++++++++++++++
 .../R/table_20240715115424.R                  | 82 +++++++++++++++++++
 build-table-script/R/table.R                  |  3 +-
 4 files changed, 248 insertions(+), 1 deletion(-)
 create mode 100644 .history/build-table-script/R/table_20240715115029.R
 create mode 100644 .history/build-table-script/R/table_20240715115244.R
 create mode 100644 .history/build-table-script/R/table_20240715115424.R

diff --git a/.history/build-table-script/R/table_20240715115029.R b/.history/build-table-script/R/table_20240715115029.R
new file mode 100644
index 0000000..74bc31b
--- /dev/null
+++ b/.history/build-table-script/R/table_20240715115029.R
@@ -0,0 +1,82 @@
+
+library(dplyr)
+library(purrr)
+library(gbifmt) # my library
+# setwd("C:/Users/ftw712/Desktop/doc-private-sector-data-publishing/")
+
+# harvest publishers and datasets private sector publishers directly from machineTags
+
+# dataset machine tags
+ds_mt = get_mt("privateSector.gbif.org",type="dataset",limit=500) %>% 
+mutate(link = paste0("https://www.gbif.org/dataset/",uuid)) %>%
+mutate(pd = "dataset") %>%
+select(link, `Activity sector` = value, pd, key = uuid) %>%
+glimpse()
+
+# publisher machine tags
+pb_mt = get_mt("privateSector.gbif.org",type="organization",limit=500) %>% 
+mutate(link = paste0("https://www.gbif.org/publisher/",uuid)) %>%
+mutate(pd = "publisher") %>%
+select(link, `Activity sector` = value, pd, key = uuid) %>%
+glimpse()
+
+# combine 
+ss = list(ds_mt,pb_mt) %>% 
+bind_rows() %>% 
+glimpse()
+
+gbif_country = rgbif::enumeration_country() %>% select(Country=title,iso2) %>% glimpse()
+
+pp = ss %>%
+dplyr::filter(pd == "publisher") %>%
+select(key,`Activity sector`) %>%
+mutate(name = map_chr(key,~rgbif::organizations(uuid=.x,limit=1)$data$title)) %>%
+mutate(`Occurrence records` = map_dbl(key,~ rgbif::occ_search(publishingOrg = .x,occurrenceStatus=NULL,limit=0)$meta$count)) %>% 
+mutate(Datasets = map_dbl(key,~rgbif::dataset_search(publishingOrg= .x,limit=0)$meta$count)) %>% 
+mutate(`Data citations` = map_dbl(key,~rgbif::lit_count(publishingOrg = .x))) %>%
+mutate(Company = paste0("https://www.gbif.org/publisher/",key,"[",name,"]")) %>%
+mutate(iso2 = map_chr(key,~rgbif::dataset_search(publishingOrg=.x,limit=1)$data$publishingCountry)) %>%
+merge(gbif_country,by="iso2") %>%
+glimpse()
+
+dd = ss %>% 
+dplyr::filter(pd == "dataset") %>%
+select(key,`Activity sector`) %>% 
+mutate(name = map_chr(key,~rgbif::dataset_get(uuid=.x)$title)) %>%
+mutate(`Occurrence records` = map_dbl(key,~
+rgbif::occ_search(datasetKey = .x,occurrenceStatus=NULL,limit=0)$meta$count)) %>%
+mutate(Datasets = 1) %>% 
+mutate(`Data citations` = map_dbl(key,~rgbif::lit_count(datasetKey = .x))) %>%
+mutate(Company = paste0("(https://www.gbif.org/dataset/",key,")[",name,"]")) %>% 
+mutate(p_key = map_chr(key,~ rgbif::dataset_get(uuid=.x)$publishingOrganizationKey)) %>%
+mutate(iso2 = map_chr(p_key,~rgbif::dataset_search(publishingOrg=.x,limit=1)$data$publishingCountry)) %>%
+merge(gbif_country,by="iso2") %>%
+select(-p_key) %>%
+glimpse()
+
+# combine tables 
+tt = rbind(pp,dd) %>% 
+arrange(name) %>%
+select(Company, `Activity sector`,	Country = iso2, Datasets, `Occurrence records`, `Data citations`) 
+
+# save csv and clean up  
+tt %>%  
+mutate(`Datasets` = trimws(format(`Datasets`, nsmall=0, big.mark="\u202F"),which ="left")) %>%
+mutate(`Occurrence records` = trimws(format(`Occurrence records`, nsmall=0, big.mark="\u202F"),which ="left")) %>%
+mutate(`Data citations` = trimws(format(`Data citations`, nsmall=0, big.mark="\u202F"),which ="left")) %>%
+mutate(`Activity sector` = paste0("{",`Activity sector`,"}")) %>%
+mutate(`Country` = gsub(" ","_",`Country`)) %>%
+mutate(`Country` = paste0("{",`Country`,"}")) %>%
+write.table(file = "250-private-sector-table.csv", row.names = FALSE, col.names = FALSE, sep = ",", quote = FALSE)
+
+# totals table 
+tt %>% 
+summarise(
+Datasets = sum(Datasets),
+`Occurrence records` = sum(`Occurrence records`), 
+`Data citations` = sum(`Data citations`)
+) %>%
+mutate(`Datasets` = trimws(format(`Datasets`, nsmall=0, big.mark="\u202F"),which ="left")) %>%
+mutate(`Occurrence records` = trimws(format(`Occurrence records`, nsmall=0, big.mark="\u202F"),which ="left")) %>%
+mutate(`Data citations` = trimws(format(`Data citations`, nsmall=0, big.mark="\u202F"),which ="left")) %>%
+write.table(file = "260-private-sector-totals.csv", row.names = FALSE, col.names = FALSE, sep = ",", quote = FALSE) 
diff --git a/.history/build-table-script/R/table_20240715115244.R b/.history/build-table-script/R/table_20240715115244.R
new file mode 100644
index 0000000..c6ef1c8
--- /dev/null
+++ b/.history/build-table-script/R/table_20240715115244.R
@@ -0,0 +1,82 @@
+
+library(dplyr)
+library(purrr)
+library(gbifmt) # my library
+# setwd("C:/Users/ftw712/Desktop/doc-private-sector-data-publishing/")
+
+# harvest publishers and datasets private sector publishers directly from machineTags
+
+# dataset machine tags
+ds_mt = get_mt("privateSector.gbif.org",type="dataset",limit=500) %>% 
+mutate(link = paste0("https://www.gbif.org/dataset/",uuid)) %>%
+mutate(pd = "dataset") %>%
+select(link, `Activity sector` = value, pd, key = uuid) %>%
+glimpse()
+
+# publisher machine tags
+pb_mt = get_mt("privateSector.gbif.org",type="organization",limit=500) %>% 
+mutate(link = paste0("https://www.gbif.org/publisher/",uuid)) %>%
+mutate(pd = "publisher") %>%
+select(link, `Activity sector` = value, pd, key = uuid) %>%
+glimpse()
+
+# combine 
+ss = list(ds_mt,pb_mt) %>% 
+bind_rows() %>% 
+glimpse()
+
+gbif_country = rgbif::enumeration_country() %>% select(Country=title,iso2) %>% glimpse()
+
+pp = ss %>%
+dplyr::filter(pd == "publisher") %>%
+select(key,`Activity sector`) %>%
+mutate(name = map_chr(key,~rgbif::organizations(uuid=.x,limit=1)$data$title)) %>%
+mutate(`Occurrence records` = map_dbl(key,~ rgbif::occ_search(publishingOrg = .x,occurrenceStatus=NULL,limit=0)$meta$count)) %>% 
+mutate(Datasets = map_dbl(key,~rgbif::dataset_search(publishingOrg= .x,limit=0)$meta$count)) %>% 
+mutate(`Data citations` = map_dbl(key,~rgbif::lit_count(publishingOrg = .x))) %>%
+mutate(Company = paste0("https://www.gbif.org/publisher/",key,"[",name,"]")) %>%
+mutate(iso2 = map_chr(key,~rgbif::dataset_search(publishingOrg=.x,limit=1)$data$publishingCountry)) %>%
+merge(gbif_country,by="iso2") %>%
+glimpse()
+
+dd = ss %>% 
+dplyr::filter(pd == "dataset") %>%
+select(key,`Activity sector`) %>% 
+mutate(name = map_chr(key,~rgbif::dataset_get(uuid=.x)$title)) %>%
+mutate(`Occurrence records` = map_dbl(key,~
+rgbif::occ_search(datasetKey = .x,occurrenceStatus=NULL,limit=0)$meta$count)) %>%
+mutate(Datasets = 1) %>% 
+mutate(`Data citations` = map_dbl(key,~rgbif::lit_count(datasetKey = .x))) %>%
+mutate(Company = paste0("(https://www.gbif.org/dataset/",key,")[",name,"]")) %>% 
+mutate(p_key = map_chr(key,~ rgbif::dataset_get(uuid=.x)$publishingOrganizationKey)) %>%
+mutate(iso2 = map_chr(p_key,~rgbif::dataset_search(publishingOrg=.x,limit=1)$data$publishingCountry)) %>%
+merge(gbif_country,by="iso2") %>%
+select(-p_key) %>%
+glimpse()
+
+# combine tables 
+tt = rbind(pp,dd) %>% 
+arrange(name) %>%
+select(Company, `Activity sector`,	Country = iso2, Datasets, `Occurrence records`, `Data citations`) 
+
+# save csv and clean up  
+tt %>%  
+mutate(`Datasets` = trimws(format(`Datasets`, nsmall=0, big.mark="\u202F"),which ="left")) %>%
+mutate(`Occurrence records` = trimws(format(`Occurrence records`, nsmall=0, big.mark="\u202F"),which ="left")) %>%
+mutate(`Data citations` = trimws(format(`Data citations`, nsmall=0, big.mark="\u202F"),which ="left")) %>%
+mutate(`Activity sector` = gsub(" ","_",`Activity sector`)) %>%
+mutate(`Activity sector` = paste0("{",`Activity sector`,"}")) %>%
+mutate(`Country` = paste0("{",`Country`,"}")) %>%
+write.table(file = "250-private-sector-table.csv", row.names = FALSE, col.names = FALSE, sep = ",", quote = FALSE)
+
+# totals table 
+tt %>% 
+summarise(
+Datasets = sum(Datasets),
+`Occurrence records` = sum(`Occurrence records`), 
+`Data citations` = sum(`Data citations`)
+) %>%
+mutate(`Datasets` = trimws(format(`Datasets`, nsmall=0, big.mark="\u202F"),which ="left")) %>%
+mutate(`Occurrence records` = trimws(format(`Occurrence records`, nsmall=0, big.mark="\u202F"),which ="left")) %>%
+mutate(`Data citations` = trimws(format(`Data citations`, nsmall=0, big.mark="\u202F"),which ="left")) %>%
+write.table(file = "260-private-sector-totals.csv", row.names = FALSE, col.names = FALSE, sep = ",", quote = FALSE) 
diff --git a/.history/build-table-script/R/table_20240715115424.R b/.history/build-table-script/R/table_20240715115424.R
new file mode 100644
index 0000000..1f8344a
--- /dev/null
+++ b/.history/build-table-script/R/table_20240715115424.R
@@ -0,0 +1,82 @@
+
+library(dplyr)
+library(purrr)
+library(gbifmt) # my library
+# setwd("C:/Users/ftw712/Desktop/doc-private-sector-data-publishing/")
+
+# harvest publishers and datasets private sector publishers directly from machineTags
+
+# dataset machine tags
+ds_mt = get_mt("privateSector.gbif.org",type="dataset",limit=500) %>% 
+mutate(link = paste0("https://www.gbif.org/dataset/",uuid)) %>%
+mutate(pd = "dataset") %>%
+select(link, `Activity sector` = value, pd, key = uuid) %>%
+glimpse()
+
+# publisher machine tags
+pb_mt = get_mt("privateSector.gbif.org",type="organization",limit=500) %>% 
+mutate(link = paste0("https://www.gbif.org/publisher/",uuid)) %>%
+mutate(pd = "publisher") %>%
+select(link, `Activity sector` = value, pd, key = uuid) %>%
+glimpse()
+
+# combine 
+ss = list(ds_mt,pb_mt) %>% 
+bind_rows() %>% 
+glimpse()
+
+gbif_country = rgbif::enumeration_country() %>% select(Country=title,iso2) %>% glimpse()
+
+pp = ss %>%
+dplyr::filter(pd == "publisher") %>%
+select(key,`Activity sector`) %>%
+mutate(name = map_chr(key,~rgbif::organizations(uuid=.x,limit=1)$data$title)) %>%
+mutate(`Occurrence records` = map_dbl(key,~ rgbif::occ_search(publishingOrg = .x,occurrenceStatus=NULL,limit=0)$meta$count)) %>% 
+mutate(Datasets = map_dbl(key,~rgbif::dataset_search(publishingOrg= .x,limit=0)$meta$count)) %>% 
+mutate(`Data citations` = map_dbl(key,~rgbif::lit_count(publishingOrg = .x))) %>%
+mutate(Company = paste0("https://www.gbif.org/publisher/",key,"[",name,"]")) %>%
+mutate(iso2 = map_chr(key,~rgbif::dataset_search(publishingOrg=.x,limit=1)$data$publishingCountry)) %>%
+merge(gbif_country,by="iso2") %>%
+glimpse()
+
+dd = ss %>% 
+dplyr::filter(pd == "dataset") %>%
+select(key,`Activity sector`) %>% 
+mutate(name = map_chr(key,~rgbif::dataset_get(uuid=.x)$title)) %>%
+mutate(`Occurrence records` = map_dbl(key,~
+rgbif::occ_search(datasetKey = .x,occurrenceStatus=NULL,limit=0)$meta$count)) %>%
+mutate(Datasets = 1) %>% 
+mutate(`Data citations` = map_dbl(key,~rgbif::lit_count(datasetKey = .x))) %>%
+mutate(Company = paste0("https://www.gbif.org/dataset/",key,"[",name,"]")) %>% 
+mutate(p_key = map_chr(key,~ rgbif::dataset_get(uuid=.x)$publishingOrganizationKey)) %>%
+mutate(iso2 = map_chr(p_key,~rgbif::dataset_search(publishingOrg=.x,limit=1)$data$publishingCountry)) %>%
+merge(gbif_country,by="iso2") %>%
+select(-p_key) %>%
+glimpse()
+
+# combine tables 
+tt = rbind(pp,dd) %>% 
+arrange(name) %>%
+select(Company, `Activity sector`,	Country = iso2, Datasets, `Occurrence records`, `Data citations`) 
+
+# save csv and clean up  
+tt %>%  
+mutate(`Datasets` = trimws(format(`Datasets`, nsmall=0, big.mark="\u202F"),which ="left")) %>%
+mutate(`Occurrence records` = trimws(format(`Occurrence records`, nsmall=0, big.mark="\u202F"),which ="left")) %>%
+mutate(`Data citations` = trimws(format(`Data citations`, nsmall=0, big.mark="\u202F"),which ="left")) %>%
+mutate(`Activity sector` = gsub(" ","_",`Activity sector`)) %>%
+mutate(`Activity sector` = paste0("{",`Activity sector`,"}")) %>%
+mutate(`Country` = paste0("{",`Country`,"}")) %>%
+write.table(file = "250-private-sector-table.csv", row.names = FALSE, col.names = FALSE, sep = ",", quote = FALSE)
+
+# totals table 
+tt %>% 
+summarise(
+Datasets = sum(Datasets),
+`Occurrence records` = sum(`Occurrence records`), 
+`Data citations` = sum(`Data citations`)
+) %>%
+mutate(`Datasets` = trimws(format(`Datasets`, nsmall=0, big.mark="\u202F"),which ="left")) %>%
+mutate(`Occurrence records` = trimws(format(`Occurrence records`, nsmall=0, big.mark="\u202F"),which ="left")) %>%
+mutate(`Data citations` = trimws(format(`Data citations`, nsmall=0, big.mark="\u202F"),which ="left")) %>%
+write.table(file = "260-private-sector-totals.csv", row.names = FALSE, col.names = FALSE, sep = ",", quote = FALSE) 
diff --git a/build-table-script/R/table.R b/build-table-script/R/table.R
index b55a036..1f8344a 100644
--- a/build-table-script/R/table.R
+++ b/build-table-script/R/table.R
@@ -47,7 +47,7 @@ mutate(`Occurrence records` = map_dbl(key,~
 rgbif::occ_search(datasetKey = .x,occurrenceStatus=NULL,limit=0)$meta$count)) %>%
 mutate(Datasets = 1) %>% 
 mutate(`Data citations` = map_dbl(key,~rgbif::lit_count(datasetKey = .x))) %>%
-mutate(Company = paste0("(https://www.gbif.org/dataset/",key,")[",name,"]")) %>% 
+mutate(Company = paste0("https://www.gbif.org/dataset/",key,"[",name,"]")) %>% 
 mutate(p_key = map_chr(key,~ rgbif::dataset_get(uuid=.x)$publishingOrganizationKey)) %>%
 mutate(iso2 = map_chr(p_key,~rgbif::dataset_search(publishingOrg=.x,limit=1)$data$publishingCountry)) %>%
 merge(gbif_country,by="iso2") %>%
@@ -64,6 +64,7 @@ tt %>%
 mutate(`Datasets` = trimws(format(`Datasets`, nsmall=0, big.mark="\u202F"),which ="left")) %>%
 mutate(`Occurrence records` = trimws(format(`Occurrence records`, nsmall=0, big.mark="\u202F"),which ="left")) %>%
 mutate(`Data citations` = trimws(format(`Data citations`, nsmall=0, big.mark="\u202F"),which ="left")) %>%
+mutate(`Activity sector` = gsub(" ","_",`Activity sector`)) %>%
 mutate(`Activity sector` = paste0("{",`Activity sector`,"}")) %>%
 mutate(`Country` = paste0("{",`Country`,"}")) %>%
 write.table(file = "250-private-sector-table.csv", row.names = FALSE, col.names = FALSE, sep = ",", quote = FALSE)