brfitzpatrick

Job script:

#!/bin/bash

#SBATCH --job-name=rfee
#SBATCH --workdir=/home/user.name/rfee/
#SBATCH --output=r_foreach_example_console_output.txt
#SBATCH --mem-per-cpu=100 # specify RAM per CPU here in Mb
#SBATCH --time=0:02:00

brfitzpatrick

How to submit R code to a Portable Batch System (PBS) managed High Performance Computing (HPC) Facility (e.g. QUT's HPC Facility 'Lyra').

You will need:

1. An account with the relevant HPC facility (QUT staff and HDR students can request access to the QUT facility here),
2. the R Script (.R file) you want to run,
3. a Job Script (.sub file) that tells Lyra how to run your R script and,
4. a file containing any data your R Script needs to run.

Note: These instructions work on a system running Debian (GNU + Linux) with the Gnome Desktop Environment.

brfitzpatrick

(custom-set-variables
 ;; custom-set-variables was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 '(custom-enabled-themes (quote (manoj-dark)))
 '(package-selected-packages (quote (polymode)))
 '(show-paren-mode t))

(electric-indent-mode -1)

brfitzpatrick

# general demo

setwd('~/Documents/directory_of_csv_files/')

# create a collection of .csv files names following some system

X <- expand.grid(LETTERS,1:10)

for(i in 1:nrow(X)){
  Data.i <- data.frame(matrix(data = rnorm(1000), nrow = 10))

brfitzpatrick

Online Courses

• Coursera (free option available)
• Lynda (subscription required)
• Further courses indexed on the RStudio Site

Books:

• R for Data Science by Hadley Wickham & Garrett Grolemund (an actual book that you can also read for free online)

Reference Cards/Cheat Sheets

• From RStudio

brfitzpatrick

input.seq <- 1:10

for(i in 1:length(input.seq)){
  file.con <-file(paste0('script', input.seq[i], '.R'))
  writeLines(
    text = c("source('my.fun.R')",
             paste0('result', i, ' <- my.fun(x = ', i, ", y = 'character input')"),
             paste0("save(list = 'result", i, "', file = 'result", i, ".RData')")
           ),
    con = file.con

brfitzpatrick

library(sp)
library(spdep)
library(tidyverse)
library(sf)

data(meuse)

nb.boundary.radius <- 750

nb.obj <- dnearneigh(x = select(meuse, x, y) %>% as.matrix(), d1 = 0, d2 = nb.boundary.radius, row.names = NULL, longlat = NULL, bounds=c("GT", "LE"))

brfitzpatrick

Preparing Elevation Data for Visualisation with rayshader

library(magrittr)
library(viridis)
library(raster)
library(rayshader)

brfitzpatrick

Preparing Elevation Data for Visualisation with rayshader

library(magrittr)
library(viridis)
library(raster)
library(rayshader)

brfitzpatrick

Ray(s) of blocks

a function for interacting with a Minecraft world via ROpenSci's miner package

ray produces one or more rays of blocks of length rng from the fid player's position in the direction given by their view orientation (center the cross hairs on your target). Rays of lava are particularly effective for igniting enemies. Persistent rays (pst = TRUE) of some safe block type provide quick but messy staircases and bridges. If you accidentally ignite yourself, a ray of water starting adjacent to your position (disp = 1) can save you if you run into it but you'll need to type fast. Non-persistant rays replace all blocks in their path first with the block type specified by rid then with empty blocks (air type) and thus may be thought of as destroying all in their path. To ignite a pack of enemies in rapid succession set rpt to the nu