Alan O'Callaghan alanocallaghan

## ace-mode-translations.json
{
    "c": "c_cpp",
    "c++": "c_cpp",
    "c#": "csharp",
    "f#": "fsharp",
    "fortran free form": "fortran",
    "gradle": "groovy",
    "json with comments": "json",
    "rmarkdown": "markdown",
    "shell": "bash",

## slab-problem.Rmd
library("ggplot2")
library("ggdist")
library("latex2exp")

set.seed(42)
means <- rnorm(4)
df_slabplot <- rbind(
    data.frame(
        method = "hmc",
        bj = rnorm(4000, mean = rep(means, each = 1000)),

## export-references.sh
## using natbib
## when finished adding refs, run
bibexport --nosave -o [LOCAL_BIB_FILE] main.aux
## then switch the \bibliography command from the central file to the local one, ie change
# % \bibliography{[CENTRAL_BIB_FILE]}
# % \bibliography{[LOCAL_BIB_FILE]}

# % with biblatex you would run something like
jabref -n --aux main.aux,[LOCAL_BIB_FILE] [CENTRAL_BIB_FILE]
## and again switch which bib file you're working with

## act-conda-sm-clust.sh
#!/usr/bin/env bash

set -eu
if [ -f ~/miniconda3/etc/profile.d/conda.sh ]; then
    [ -z "${CONDA_EXE}" ] && echo "Error, missing \$CONDA_EXE !" && exit 1
    CONDA_BASE=$(${CONDA_EXE} info --base)
    ADDR2LINE=""
    source $CONDA_BASE/etc/profile.d/conda.sh
    conda activate $1 || exit 1
fi

## setup-intro-stats-r.R
library(utils)
for (pkg in rownames(installed.packages(priority="base"))) library(pkg, character.only=TRUE)

pkgs <- c(
    "NHANES",
    "RNHANES",
    "ggplot2",
    "jtools",
    "interactions",
    "patchwork",

## pca-animation.R
# R port of Dmitry Kobak's excellent PCA animations.
# See https://gist.github.com/anonymous/7d888663c6ec679ea65428715b99bfdd
# for matlab/octave code
dir.create("gif", showWarnings = FALSE)
set.seed(42)

X <- matrix(rnorm(200), ncol = 2)
X <- X %*% chol(matrix(c(1, 0.6, 0.6, 0.6), ncol = 2, byrow = TRUE))
X <- apply(X, 2, function(col) col - mean(col))

## bugs.md

      
              1 file
            
          
              0 forks
            
          
              0 comments
            
          
              1 star
            
          
                alanocallaghan
                / bugs.md
            
            
              Last active
              July 29, 2022 14:13
            
              
                Bugs
              
          
    A catalogue of the bugs that have caused me not insignificant amounts of pain

R


Dropping attributes
matrix[, 1, drop=FALSE]


Autocompletion for thee but not for me


## scRNAseq-mixture-experiments.R
library("scRNAseq")
library("scater")
library("scran")
library("flexmix")
library("mixtools")
library("viridis")
library("annotables")
theme_set(theme_bw())

sce <- ZeiselBrainData()

## cats_and_dogs_log2.R
library("ggplot2")
library("usmap")
library("httr")
library("readxl")

# Read data
GET("https://query.data.world/s/pth2w34nwc6uhg7mmvr7n56257y2gw", write_disk(tf <- tempfile(fileext = ".xlsx")))
pets <- read_excel(tf)

pets <- pets[!colnames(pets) %in% "X"]

## .nanorc
############################################
#  Syntax highlighting for R               #
#  by Stephen Haptonstahl                  #
#  March 15, 2009                          #
#  http://srh.ucdavis.edu/drupal/node/20   #
#  edited by Mike Miller                   #
#  Placed on GitHub by Alan O'Callaghan    #
#  (could no longer find the original)      #
############################################
	{
	"c": "c_cpp",
	"c++": "c_cpp",
	"c#": "csharp",
	"f#": "fsharp",
	"fortran free form": "fortran",
	"gradle": "groovy",
	"json with comments": "json",
	"rmarkdown": "markdown",
	"shell": "bash",
	library("ggplot2")
	library("ggdist")
	library("latex2exp")

	set.seed(42)
	means <- rnorm(4)
	df_slabplot <- rbind(
	data.frame(
	method = "hmc",
	bj = rnorm(4000, mean = rep(means, each = 1000)),
	## using natbib
	## when finished adding refs, run
	bibexport --nosave -o [LOCAL_BIB_FILE] main.aux
	## then switch the \bibliography command from the central file to the local one, ie change
	# % \bibliography{[CENTRAL_BIB_FILE]}
	# % \bibliography{[LOCAL_BIB_FILE]}

	# % with biblatex you would run something like
	jabref -n --aux main.aux,[LOCAL_BIB_FILE] [CENTRAL_BIB_FILE]
	## and again switch which bib file you're working with
	#!/usr/bin/env bash

	set -eu
	if [ -f ~/miniconda3/etc/profile.d/conda.sh ]; then
	[ -z "${CONDA_EXE}" ] && echo "Error, missing \$CONDA_EXE !" && exit 1
	CONDA_BASE=$(${CONDA_EXE} info --base)
	ADDR2LINE=""
	source $CONDA_BASE/etc/profile.d/conda.sh
	conda activate $1 \|\| exit 1
	fi
	library(utils)
	for (pkg in rownames(installed.packages(priority="base"))) library(pkg, character.only=TRUE)

	pkgs <- c(
	"NHANES",
	"RNHANES",
	"ggplot2",
	"jtools",
	"interactions",
	"patchwork",
	# R port of Dmitry Kobak's excellent PCA animations.
	# See https://gist.github.com/anonymous/7d888663c6ec679ea65428715b99bfdd
	# for matlab/octave code
	dir.create("gif", showWarnings = FALSE)
	set.seed(42)

	X <- matrix(rnorm(200), ncol = 2)
	X <- X %*% chol(matrix(c(1, 0.6, 0.6, 0.6), ncol = 2, byrow = TRUE))
	X <- apply(X, 2, function(col) col - mean(col))
	library("scRNAseq")
	library("scater")
	library("scran")
	library("flexmix")
	library("mixtools")
	library("viridis")
	library("annotables")
	theme_set(theme_bw())

	sce <- ZeiselBrainData()
	library("ggplot2")
	library("usmap")
	library("httr")
	library("readxl")

	# Read data
	GET("https://query.data.world/s/pth2w34nwc6uhg7mmvr7n56257y2gw", write_disk(tf <- tempfile(fileext = ".xlsx")))
	pets <- read_excel(tf)

	pets <- pets[!colnames(pets) %in% "X"]
	############################################
	# Syntax highlighting for R #
	# by Stephen Haptonstahl #
	# March 15, 2009 #
	# http://srh.ucdavis.edu/drupal/node/20 #
	# edited by Mike Miller #
	# Placed on GitHub by Alan O'Callaghan #
	# (could no longer find the original) #
	############################################