John Waller jhnwllr
jhnwllr
/ zenodo_large_file_upload.r
Created
February 18, 2022 14:47
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| # 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
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| 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
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| 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
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| 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) |
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| 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
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| # 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
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| 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
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| 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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| utils::zip(zipfile = dir, files = dir(dir, full.names = TRUE)) |
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| 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 |
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