John Waller jhnwllr

## zenodo_large_file_upload.r
# zenodo large file upload

library(httr)
library(dplyr)
library(purrr)

# get your token here
# https://zenodo.org/account/settings/applications/
token = ""
deposit_id = 6137047 # fill in form

## html_table_for_outlook.r
library(dplyr)
library(purrr)
library(xtable)

d = readr::read_tsv("C:/Users/ftw712/Desktop/Legume/data/legume_unmatched.tsv")  %>%
arrange(-count) %>%
glimpse() %>%
head(30) %>%
mutate(n_suggestions =  map_int(v_scientificname,~nrow(rgbif::name_suggest(.x)$data))) %>%
mutate(n_suggestions = format(n_suggestions, nsmall = 0)) %>%

## tree_names.tsv
scientificName
Abarema abbottii
Abarema acreana
Abarema adenophora
Abarema alexandri
Abarema asplenifolia
Abarema auriculata
Abarema barbouriana
Abarema barnebyana
Abarema brachystachya

## barplot_with_ggtext_caption
library(ggplot2)
library(ggtext)
library(extrafont)
font_import()
loadfonts(device = "win")

windowsFonts()

breaks = scales::pretty_breaks(n = 7)(c(0,900e3))
labels = gbifapi::plot_label_maker(breaks,unit_MK = "K",unit_scale = 1e-3)

## classic_bar_plot
library(ggplot2)

breaks = scales::pretty_breaks(n = 5)(c(0,3e6))
labels = gbifapi::plot_label_maker(breaks,unit_MK = "K",unit_scale = 1e-3)

p = ggplot(pd,aes(class,n)) +
scale_y_continuous(breaks = breaks,label = labels) +
geom_col(stat="identity",fill="#4B9E46") +
coord_flip() +
xlab("") +

## gbif_api_all_humming_bird_common_names.R
# example showing usefulness of GBIF API when combined with purrr
library(dplyr)
library(httr)
library(purrr)
library(jsonlite)

"Trochilidae" %>% # sci name for humming birds
paste0("https://api.gbif.org/v1/species/match?name=",.) %>%
GET() %>%
content() %>%

## citation.csv
0f85c38c-92ad-407b-b21e-54932bdc6058	1
267cc444-4df8-4d9e-8a6b-6b13e3600a84	92
a0992ffa-00c1-4d7b-8366-e18c9ec1a168	5
7df0563f-2415-43c3-8865-f803f92ca5fe	16
08b92fdc-9bba-469a-8382-0d7f0fb89bb7	1
93806ea9-3fff-4376-8d8e-062e5ece35bf	2
fc802397-f995-4145-93d7-fee098887602	11
ae830ee1-1095-40a7-8384-95d7039acaa4	4
dc935b9b-2f74-4b50-8dd3-9c4a91dbfe44	5
5b0dfb7c-9e7e-4e3e-b438-5e25073759ba	1

## upload_to_custom_downloads.sh
FILE_NAME="Taxon.tsv"
COPY_DIR="/cygdrive/c/Users/ftw712/Desktop/"
scp -r $COPY_DIR$FILE_NAME jwaller@c5gateway-vh.gbif.org:/mnt/auto/misc/download.gbif.org/custom_download/jwaller/

## zip_file_in_r.r
utils::zip(zipfile = dir, files = dir(dir, full.names = TRUE))

## GBIF_azure_stats.scala
import org.apache.spark.sql.functions._
val wasbs_path = "wasbs://gbif@ai4edataeuwest.blob.core.windows.net/occurrence/20210413/occurrence.parquet/*"

val df = spark.read.parquet(wasbs_path)

// Number species total
df.select("specieskey").distinct().count()
// Number species by Kingdom
df.select("kingdom","specieskey").distinct().groupBy("kingdom").count().orderBy(desc("count")).show()
// Number records total
	# zenodo large file upload

	library(httr)
	library(dplyr)
	library(purrr)

	# get your token here
	# https://zenodo.org/account/settings/applications/
	token = ""
	deposit_id = 6137047 # fill in form
	library(dplyr)
	library(purrr)
	library(xtable)

	d = readr::read_tsv("C:/Users/ftw712/Desktop/Legume/data/legume_unmatched.tsv") %>%
	arrange(-count) %>%
	glimpse() %>%
	head(30) %>%
	mutate(n_suggestions = map_int(v_scientificname,~nrow(rgbif::name_suggest(.x)$data))) %>%
	mutate(n_suggestions = format(n_suggestions, nsmall = 0)) %>%
	scientificName
	Abarema abbottii
	Abarema acreana
	Abarema adenophora
	Abarema alexandri
	Abarema asplenifolia
	Abarema auriculata
	Abarema barbouriana
	Abarema barnebyana
	Abarema brachystachya
	library(ggplot2)
	library(ggtext)
	library(extrafont)
	font_import()
	loadfonts(device = "win")

	windowsFonts()

	breaks = scales::pretty_breaks(n = 7)(c(0,900e3))
	labels = gbifapi::plot_label_maker(breaks,unit_MK = "K",unit_scale = 1e-3)
	library(ggplot2)

	breaks = scales::pretty_breaks(n = 5)(c(0,3e6))
	labels = gbifapi::plot_label_maker(breaks,unit_MK = "K",unit_scale = 1e-3)

	p = ggplot(pd,aes(class,n)) +
	scale_y_continuous(breaks = breaks,label = labels) +
	geom_col(stat="identity",fill="#4B9E46") +
	coord_flip() +
	xlab("") +
	# example showing usefulness of GBIF API when combined with purrr
	library(dplyr)
	library(httr)
	library(purrr)
	library(jsonlite)

	"Trochilidae" %>% # sci name for humming birds
	paste0("https://api.gbif.org/v1/species/match?name=",.) %>%
	GET() %>%
	content() %>%
	0f85c38c-92ad-407b-b21e-54932bdc6058 1
	267cc444-4df8-4d9e-8a6b-6b13e3600a84 92
	a0992ffa-00c1-4d7b-8366-e18c9ec1a168 5
	7df0563f-2415-43c3-8865-f803f92ca5fe 16
	08b92fdc-9bba-469a-8382-0d7f0fb89bb7 1
	93806ea9-3fff-4376-8d8e-062e5ece35bf 2
	fc802397-f995-4145-93d7-fee098887602 11
	ae830ee1-1095-40a7-8384-95d7039acaa4 4
	dc935b9b-2f74-4b50-8dd3-9c4a91dbfe44 5
	5b0dfb7c-9e7e-4e3e-b438-5e25073759ba 1
	FILE_NAME="Taxon.tsv"
	COPY_DIR="/cygdrive/c/Users/ftw712/Desktop/"
	scp -r $COPY_DIR$FILE_NAME jwaller@c5gateway-vh.gbif.org:/mnt/auto/misc/download.gbif.org/custom_download/jwaller/
	import org.apache.spark.sql.functions._
	val wasbs_path = "wasbs://gbif@ai4edataeuwest.blob.core.windows.net/occurrence/20210413/occurrence.parquet/*"

	val df = spark.read.parquet(wasbs_path)

	// Number species total
	df.select("specieskey").distinct().count()
	// Number species by Kingdom
	df.select("kingdom","specieskey").distinct().groupBy("kingdom").count().orderBy(desc("count")).show()
	// Number records total