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Updating scripts, added license, contributor guidelines, shifting TODO lines to github issues

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kidwellj 2020-03-08 12:18:21 +00:00
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mapping_draft-hpc_optimised.Rmd
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@ -36,48 +36,67 @@ output:
---
```{r setup, include=FALSE}
require(knitr)
require(kableExtra)
# Note, this script has been written largely with RStudio on MacOS, but is compiled on
# an hpc cluster which runs Linux, so some tweaks below ensure smooth execution
# in both environments. Also, as above, the script is meant to output to both PDF and
# html_document knitr formats.
require(knitr) # used to knit RMarkdown format script into working documents in various formats
require(kableExtra) # used for markdown table formatting compatible with knitr
# note: some features of the below line are specific to html/pdf format and will need to be adapted pre-compile until dual outputs are working (see https://github.com/kidwellj/mapping_environmental_action/issues/2)
knitr::opts_chunk$set(fig.path='figures/', warning=FALSE, echo=FALSE, message=FALSE, dpi=300, fig.width=7)
# TODO: consider implementing knitcitations - https://github.com/cboettig/knitcitations
# TODO: fix simultaneous output towards PDF, see here: https://stackoverflow.com/questions/23621012/display-and-save-the-plot-simultaneously-in-r-rstudio
```
```{r load_packages, message=FALSE, warning=FALSE, include=FALSE}
## Default repo
# setwd("/Users/jeremy/gits/mapping_environmental_action")
# setwd("/Users/kidwellj/OneDrive\ -\ bham.ac.uk/writing/201708_mapping_environmental_action")
# Set up working machine independent working directory and environment
require(here) # used to keep working directory organised and portable
require(renv) # used to set up environment
require(usethis) # integrates git support for rStudio
# Set repository to be new standard, e.g. cloud server.
# This will avoid a dialogue box if packages are to be installed for below on first run.
# For smooth execution on command-line knitr - this will avoid a dialogue box
# if packages are to be installed for below on first run
local({r <- getOption("repos")
r["CRAN"] <- "https://cloud.r-project.org"
options(repos=r)
})
# TODO: remove sp etc. once sf is fully implemented
# TODO: automatically test for packages below on given execution environment and run install.packages() as needed.
require(RCurl) # used for fetching reproducible datasets
require(sf) # new simplefeature data class, supercedes sp in many ways
require(sp) # needed for proj4string, deprecated by sf()
require(rgdal) # deprecated by sf()
require(GISTools) # deprecated by sf()
require(rgeos) # deprecated by sf()
require(maptools)
# See issue https://github.com/kidwellj/mapping_environmental_action/issues/3 for progress re: migration from sp()
# require(sp) # needed for proj4string, deprecated by sf()
# require(rgdal) # deprecated by sf()
# require(GISTools) # deprecated by sf()
# require(rgeos) # deprecated by sf()
# require(maptools)
require(ggplot2)
require(tmap) # using as an alternative to base r graphics and ggplot for geospatial plots
require(tmaptools) # for get_asp_ratio below
require(grid) # using for inset maps on tmap
require(broom) # required for tidying SPDF to data.frame for ggplot2
require(tidyr) # using for grouped bar plot
require(plyr)
require(dplyr)
# require(plyr) # already a dependency of knitr, remove?
# require(dplyr) # already a dependency of knitr, remove?
require(reshape2) # using for grouped bar plot
require(scales)
# require(sqldf) # using sqldf to filter before loading very large data sets
## Packages required for PostGIS database access
# Many thanks to Sébastien Rochette for documentation here: https://www.r-bloggers.com/interact-with-postgis-from-r/
library(DBI)
library(RPostgres)
library(sqlpetr) # useful for visual DB panels in RStudio, see https://smithjd.github.io/sqlpetr/
# library(rpostgis)
library(dbplyr)
## Packages required for knitr output
## Packages used for features or issues relating to html_document knitr output
require(plotly) # allows for export of plots to dynamic web pages
require(gtable) # more powerful package for multi-plot layouts, not necessary for knitr
require(showtext) # for loading in fonts
require(extrafont) # font support
## Packages used for features or issues relating to pdf_document knitr format
# Note: implementation of fonts (currently commented out) is specific to pdf_document output
# require(showtext) # for loading in fonts
# require(extrafont) # font support
# Set up local workspace:
if (dir.exists("data") == FALSE) {
@ -96,12 +115,15 @@ if (dir.exists("derivedData") == FALSE) {
# data-sets and papers.
# Working with EPSG codes for spatialfeature CRS given the usage of this approach with sf()
# for discussion related to this fix, see https://gis.stackexchange.com/q/313761/41474
# TODO: remove below as part of overall migration to sf()
# See issue https://github.com/kidwellj/mapping_environmental_action/issues/3 for progress re: migration from sp()
bng <- CRS("+init=epsg:27700")
wgs84 <- CRS("+init=epsg:4326")
# Configure fonts for plots below
## Configure fonts for plots below, commented out currently because of incompatibilities
## Loading Google fonts (http://www.google.com/fonts)
# Note: implementation of fonts (currently commented out) is specific to pdf_document output
# font_add_google("Merriweather", "merriweather")
# The following will load in system fonts (uncomment and run as needed on first execution)
# font_import(pattern="[A/a]rial", prompt=FALSE)
@ -116,12 +138,25 @@ Until recently, environmentalism has been treated by governments and environment
```{r load_ecs_data, message=FALSE, warning=FALSE}
# read in Eco-Congregation Scotland data and-------------------
# ...turn it into a SpatialPointsDataFrame---------------------
# TODO: upload ECS-GIS-Locations_3.0.csv to zenodo repository, i.e.
# TODO: update below to match new dataset once it has been uploaded to zenodo
# if (file.exists("data/ECS-GIS-Locations_3.0.csv") == FALSE) {
# download.file("https://____.zip",
# destfile = "data/____.zip")
# unzip("data/____.zip", exdir = "data")
# }
# TODO: remove below as part of overall migration to sf()
# See issue https://github.com/kidwellj/mapping_environmental_action/issues/3 for progress re: migration from sp()
ecs <- read.csv("data/ECS-GIS-Locations_3.0.csv", comment.char="#")
# unnecessary with advent of sf (above)
coordinates(ecs) <- c("X", "Y")
# Modified to use EPSG code directly 27 Feb 2019
proj4string(ecs) <- bng
# Note, use of paste0 here relates to fix noted above.
# for discussion related to this approach, see https://gis.stackexchange.com/q/313761/41474
# read in Eco-Congregation Scotland data and-------------------
# ...turn it into a SpatialPointsDataFrame---------------------
ecs_sf <- st_as_sf(ecs, coords = c("X", "Y"), crs=paste0("+init=epsg:",27700))
```
@ -357,7 +392,7 @@ Though there are too few eco-congregations and transition groups for a numerical
```{r 01_admin_ecs_choropleth, fig.width=4, fig.cap="Figure 1"}
# Note: for more information on EU administrative levels, see here: https://ec.europa.eu/eurostat/web/nuts/national-structures-eu
# TODO: clip choropleth polygons to buildings shapefile (possble superceded by pverlay on lev2)
# TODO: clip choropleth polygons to buildings shapefile (possibly superceded by pverlay on lev2)
# Draw initial choropleth map of ECS concentration (using tmap and sf below by default)
# Revising re: CRS inset maps complete to here