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John Waller
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Jul 15, 2024
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library(dplyr) | ||
library(purrr) | ||
library(gbifmt) # my library | ||
# setwd("C:/Users/ftw712/Desktop/doc-private-sector-data-publishing/") | ||
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# harvest publishers and datasets private sector publishers directly from machineTags | ||
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# 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() | ||
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# 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() | ||
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# combine | ||
ss = list(ds_mt,pb_mt) %>% | ||
bind_rows() %>% | ||
glimpse() | ||
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gbif_country = rgbif::enumeration_country() %>% select(Country=title,iso2) %>% glimpse() | ||
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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() | ||
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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() | ||
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# combine tables | ||
tt = rbind(pp,dd) %>% | ||
arrange(name) %>% | ||
select(Company, `Activity sector`, Country = iso2, Datasets, `Occurrence records`, `Data citations`) | ||
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# 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) | ||
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# 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) |
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Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,82 @@ | ||
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||
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() | ||
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||
# combine | ||
ss = list(ds_mt,pb_mt) %>% | ||
bind_rows() %>% | ||
glimpse() | ||
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||
gbif_country = rgbif::enumeration_country() %>% select(Country=title,iso2) %>% glimpse() | ||
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||
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() | ||
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||
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() | ||
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# combine tables | ||
tt = rbind(pp,dd) %>% | ||
arrange(name) %>% | ||
select(Company, `Activity sector`, Country = iso2, Datasets, `Occurrence records`, `Data citations`) | ||
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||
# 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) | ||
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||
# 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) |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -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() | ||
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||
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) |
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