mskyttner

server_config <- list(
  max_occurrence_records = 500000,
  server_max_url_length = 8150,
  brand = "ALA4R",
  notify = "Please use https://github.com/AtlasOfLivingAustralia/ALA4R/issues/ or email to support@ala.org.au",
  support_email = "support@ala.org.au",
  reasons_function = "ala_reasons",
  fields_function = "ala_fields",
  occurrences_function = "occurrences",
  config_function = "ala_config",

mskyttner

Filling out PDF files using staplr

Markus Skyttner 2019-06-10

# to render this into GitHub markdown:
# rmarkdown::render("name_of_this_file.R")

library(staplr)

mskyttner

library(vikingr)
library(dplyr)
library(purrr)
library(stringr)

log <- read_ais_log(vikingr_example("vikingr-visby-2019-ais-2"))

log_tail <- 
  log$message %>%
  str_replace("(.*?,){5}(.*?)", "\\2")

mskyttner

FROM rocker/r-ver:3.6.1

# this is the trestletech/plumber layers, now on a versioned R base

RUN apt-get update -qq && apt-get install -y --no-install-recommends \
  git-core \
  libssl-dev \
  libcurl4-gnutls-dev \
  curl \
  libsodium-dev \

mskyttner

library(dplyr)
library(duckdb)
library(vroom)

duckdb_version <- function() {
  con <- duckdb::dbConnect(duckdb::duckdb())
  on.exit(duckdb::dbDisconnect(con, shutdown = TRUE))
  res <- DBI::dbGetQuery(con, "PRAGMA version;")
  parse_semver <- function(x) {
    re <- "(\\d)+\\.(\\d+)\\.(\\d+).*$"

mskyttner

#!/bin/bash

# usage: ./duckdb-load.sh data.tsv duckdb tablename
# for example:
# ./duckdb-load.sh ark/hcaf_species_native.tsv duckdb_database hcaf_species_native

# TODO set pragma journal_mode=off or equiv settings
# if using .import and .sep '\t', an error appears:
# Error: multi-character column separators not allowed for import

mskyttner

#!/usr/bin/env Rscript

# usage for example:
# cat data/mydatafile.tsv | head -n 1000 | ./duckstream.R --sql "select mycolumn from stdin;"

library(optparse)
library(readr)
suppressPackageStartupMessages(library(duckdb))

option_list <- list(

mskyttner

# from SO post at https://stackoverflow.com/questions/72922418/create-rows-from-part-of-column-names/72939299

library(readr)
library(tidyr)
library(dplyr)
library(knitr)

so_blurb <- 
  "id|Date (05/19/2020)|Type (05/19/2020)|Date (06/03/2020)|Type (06/03/2020)|Type (10/23/2020|Date (10/23/2020)|Type (10/23/2020)
10629465|null|null|06/01/2020|E

mskyttner

# start a proxy server for a duckdb in-memory db, using the postgres wire format
docker run -it --rm -p 8080:5433 -e BUENAVISTA_HOST=0.0.0.0 -e BUENAVISTA_PORT=5433 ghcr.io/jwills/buenavista

# somewhere else (or here on the same host), start psql to issue a query against the proxy server
docker run --network host -it --rm postgres:latest psql -h $(hostname) -p 8080 -c "select 42"

mskyttner

---
title: "Quarto Dashboard Layout"
format: dashboard
---

## Row {height=50%}

### Column {.tabset}

```{r}