Konrad Rudolph klmr

Vim Notes

Setup

The Vim on the server is horribly outdated. Many of the things below won’t work, or will require extensive setup. In order to ease the pain, I suggest using the version installed and maintained by Micha via the [EBI-predoc config][config].

Bugfixes

cmdescape fixes the use of parameters which contain special characters of the terminal (or spaces)
Regression: the updated version does not work with custom specified arguments. If this is desired, there should be an optional list parameter for this purpose.

Style fixes & Improvements

Single expressions do not need (and should not have) parentheses. This goes universally (and in particular, since R is a functional programming language, for functions).
There’s no need to forward %sed% to sed (and same for %grep%), it can be declared as an alias. In fact, the original function is somewhat redundant since operators can be called as functions.
Use `…` instead of '…' to specify unusual names: the former is syntactically a name while the latter is a string! It only “happens to work” because R has special lookup rules for functions when encountering a string. The same won’t work for other (non-function) objects though.

	capitalize <-
	p(fapply, toupper %.% p(substring, 1, 1), p(substring, 2)) %\|>%
	p(lapply, p(paste, collapse = '')) %\|>% unlist

	# versus

	capitalize <- function (str) paste(toupper(substring(str, 1, 1)),
	substring(str, 2), sep = '')

	# Usage (in both cases):

	#!/usr/bin/env bash

	maxwidth=800

	resize () {
	convert "$1" -resize $maxwidth "$2"
	}

	for image in large/*; do
	width=$(identify -format '%w' "$image")

	xsource(rcane.functional) # for `%\|%`

	# !!! IMPORTANT !!!
	# The Ensembl Biomart archive server is extremely slow. Therefore this code is
	# FOR EXPOSITION ONLY. Use the transcripts file shipped with the data for this
	# code instead.
	downloadTranscripts <- function (target) {
	require(biomaRt)
	ensMart <- useMart('ENSEMBL_MART_ENSEMBL',
	'mmusculus_gene_ensembl',

	#' Print relevant digits of a p-value.
	#'
	#' The idea is, under the assumption that H0 holds, to print as many digits of
	#' p as are strictly necessary to demonstrate H0. Turning this around, if we
	#' need to print many digits this probably means that we can reject H0.
	#'
	#' @param pvalue a single p-value
	#' @param max_precision limit the maximum number of leading zeros to display
	#' @param p typographic representation of the variable “p”
	pretty_p <- function (pvalue, max_precision = 5, p = bquote(italic(p))) {

	> library(microbenchmark)
	> m <- data.frame(a = sample.int(10, 100000, replace=T),
	b = sample.int(10, 100000, replace=T))
	> microbenchmark(m[-which(m[, 1] == 4 & m[, 2] == 5), ], m[! (m[, 1] == 4 & m[, 2] == 5), ])
	Unit: milliseconds
	expr min lq median uq max neval
	m[-which(m[, 1] == 4 & m[, 2] == 5), ] 27.59480 29.64628 30.09091 30.69976 42.04620 100
	m[!(m[, 1] == 4 & m[, 2] == 5), ] 29.00876 29.70103 30.41829 33.10700 42.29671 100
	> m <- as.matrix(m)
	microbenchmark(m[-which(m[, 1] == 4 & m[, 2] == 5), ], m[! (m[, 1] == 4 & m[, 2] == 5), ])

	$ ninja examples
	[4/7] AR
	FAILED: ar rcs bin/libnonius.a
	ar: no archive members specified
	usage: ar -d [-TLsv] archive file ...
	ar -m [-TLsv] archive file ...
	ar -m [-abiTLsv] position archive file ...
	ar -p [-TLsv] archive [file ...]
	ar -q [-cTLsv] archive file ...
	ar -r [-cuTLsv] archive file ...

	$ ninja examples
	[5/6] LINK obj/examples/example1.o
	FAILED: g++ -Wall -Wextra -pedantic -Werror -std=c++11 -g -flto obj/examples/example1.o -o bin/examples/example1 -lboost_system
	Undefined symbols for architecture x86_64:
	"__istype(int, unsigned long)", referenced from:
	std::ctype<char>::is(unsigned long, char) const in example1.o
	ld: symbol(s) not found for architecture x86_64
	collect2: error: ld returned 1 exit status
	[5/6] LINK obj/examples/example2.o
	FAILED: g++ -Wall -Wextra -pedantic -Werror -std=c++11 -g -flto obj/examples/example2.o -o bin/examples/example2 -lboost_system

	HOMEBREW_VERSION: 0.9.5
	ORIGIN: https://github.com/Homebrew/homebrew.git
	HEAD: 8d8763699f3b7d35b27e571e856984f49392b741
	HOMEBREW_PREFIX: /usr/local
	HOMEBREW_CELLAR: /usr/local/Cellar
	CPU: quad-core 64-bit sandybridge
	OS X: 10.9.1-x86_64
	Xcode: 5.0.2
	CLT: 5.0.1.0.1.1382131676
	Clang: 5.0 build 500