SimonGoring

Getting From There to Here

This webinar is set up as a "storytelling" session, about how I work through my projects that are intended for publication. In practice this is now how I manage most of my projects that involve some element of data exploration and collaboration. I will be live-coding during the presentation and intend to do so in a way that will allow people to follow along to some degree.

The webinar will be recorded and so people should not feel obligated to code along, or to keep up. If you would like to follow along, or revisit the webinar at a later date, these are the programs and R packages that you will need.

Important Links

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#!/bin/bash
# This scrips is described in more detail at http://www.goring.org/resources/regex_bash_libraries.html

rinstall=0

while getopts "i" OPTION
do
	case $OPTION in
		i)
			echo Running installLib with the option to install packages.

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""" Import libraries and create the connection.  If the connection fails check the JSON file. """

import json
import csv
import re
import psycopg2

# Set to True if we want to delete the whole database as it runs:
dropall = True

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{
   "host": "localhost",
   "port": 5432,
   "database": "yourdatabase",
   "user": "postgres",
   "password": "postgres"
}

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# Use the newer Neotoma API to pull sites with Fagus into a map from a JSON response.
# Used as part of the Data Demo Derby (hosted by EarthRates)

small_occ <- httr::GET('http://api-dev.neotomadb.org/v2.0/data/occurrence/?taxonname=Fagus&limit=5000')

small_content <- httr::content(small_occ)

library(dplyr)

site_table <- small_content$data %>% 

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#  This needs to run in the directory in which you have Bacon installed.
#  If you do not currently have the `neotoma` package installed then uncomment
#  and run the following code. Right now you will need to install the package from GitHub
#  because our latest bug fixes haven't been pushed up into CRAN.
#
#  install.packages('devtools')
#  library(devtools)
#  install_github('ropensci/neotoma')
#
#  The Neotoma package is described more fully here:

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#  This script starts from scratch:

library(rgdal)
library(neotoma)
library(dplyr)
library(purrr)
library(sp)
library(datasets)
library(sf)

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RStudio Version: 1.0.136

> print(sessionInfo())
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

locale:
 [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8