John Waller jhnwllr
jhnwllr
/ zenodo_large_file_upload.r
Created
February 18, 2022 14:47
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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
/ html_table_for_outlook.r
Created
December 22, 2021 15:20
make an html table for pasting into outlook
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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
/ tree_names.tsv
Created
December 2, 2021 08:28
We can't make this file beautiful and searchable because it's too large.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| scientificName | |
| Abarema abbottii | |
| Abarema acreana | |
| Abarema adenophora | |
| Abarema alexandri | |
| Abarema asplenifolia | |
| Abarema auriculata | |
| Abarema barbouriana | |
| Abarema barnebyana | |
| Abarema brachystachya |
jhnwllr
/ barplot_with_ggtext_caption
Created
October 28, 2021 11:20
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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
/ gbif_api_all_humming_bird_common_names.R
Created
July 8, 2021 10:12
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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
/ citation.csv
Created
July 6, 2021 11:42
We can't make this file beautiful and searchable because it's too large.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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
/ upload_to_custom_downloads.sh
Created
June 4, 2021 13:33
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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/ |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| utils::zip(zipfile = dir, files = dir(dir, full.names = TRUE)) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |
NewerOlder