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John Waller jhnwllr

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jhnwllr / zenodo_large_file_upload.r
Created February 18, 2022 14:47
# 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
@jhnwllr
jhnwllr / html_table_for_outlook.r
Created December 22, 2021 15:20
make an html table for pasting into outlook
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)) %>%
@jhnwllr
jhnwllr / tree_names.tsv
Created December 2, 2021 08:28
We can't make this file beautiful and searchable because it's too large.
scientificName
Abarema abbottii
Abarema acreana
Abarema adenophora
Abarema alexandri
Abarema asplenifolia
Abarema auriculata
Abarema barbouriana
Abarema barnebyana
Abarema brachystachya
@jhnwllr
jhnwllr / barplot_with_ggtext_caption
Created October 28, 2021 11:20
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)
@jhnwllr
jhnwllr / classic_bar_plot
Created October 25, 2021 10:49
Classic GBIF barplot used for everything
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("") +
@jhnwllr
jhnwllr / gbif_api_all_humming_bird_common_names.R
Created July 8, 2021 10:12
# 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() %>%
@jhnwllr
jhnwllr / citation.csv
Created July 6, 2021 11:42
We can't make this file beautiful and searchable because it's too large.
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
@jhnwllr
jhnwllr / upload_to_custom_downloads.sh
Created June 4, 2021 13:33
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/
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jhnwllr / zip_file_in_r.r
Created May 21, 2021 09:30
utils::zip(zipfile = dir, files = dir(dir, full.names = TRUE))
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jhnwllr / GBIF_azure_stats.scala
Last active April 29, 2021 13:53
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