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## Performance tuning `rbind.fill`

```{r setup, include=FALSE, cache=FALSE}
library(methods)
opts_chunk$set(cache=TRUE, dev="svg", tidy=FALSE,
               fig.width=5, fig.height=5, autodep=TRUE,
               fig.path='figure-')
with_dir <- function(dir, expr) {
  prev <- getwd()
  setwd(dir)

crowding

library(plyr)
library(ggplot2)
library(R.cache)
library(rstan)

#There is a sensor which either emits "yes" or "no." It adds up
#signals over some region of space (The "receptive field", which we
#model as having a Gaussian profile,) and emits a "yes" if the
#summed-up spatially weighted signals, plus unit additive noise, are
#over some threshold.

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library(ggplot2)
library(plyr)

theme_set(theme_bw())
theme_update(panel.border=element_blank())

# A reaction time experiment works as follows: On each trial, an
# observer is asked to view a stimulus and categorize it into one of
# multiple values. For instance, it may be a noisy motion stimulus,
# and the observer is asked to classify the motion as "leftward" or

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# User facing function
#
# to_math(x_1 + 1^{2 + 4} + 5 + sqrt(y) / 5 %/% 10)
# to_math(paste(x^2, y - 1, z_i))
# to_math(hat(tilde(ring(x))))
# to_math(pi*r^2)
# to_math(unknown_call(x, floor(sqrt(z))))
to_math <- function(x) {
  x <- substitute(x)
  env <- latex_env(x)

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#.bash_profile
TIMEOUT=10

function speak_if_long {
    last_command_time=$(HISTTIMEFORMAT="%s " history 1 | awk '{print $2}')
    if (( $(date -u +"%s") - $last_command_time > $TIMEOUT ))
    then
        say "I'm done"
    fi
}

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##

{ 
  ## let's go ahead and generate the possibilities. 

  x <- 2
  y <- pi
  z <- exp(1)
  `%^%` <- `^`
  `%/%` <- `/`

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;; R flymake support (if Flymake is available) This will call a script
;; "rflymake" with the path given; make sure it is on emac's exec-path
;; or give a full path.
(when (require 'flymake nil)
  (defun flymake-r-init ()
    (let* ((temp-file (flymake-init-create-temp-buffer-copy
                       'flymake-create-temp-inplace))
           (local-file (file-relative-name
                        temp-file
                        (file-name-directory buffer-file-name))))

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#negative numbers for "symbol" will be interpreted as Unicode values.
#But you must use a fint that supprots the symbols you want.

dataset <- chain(1:16, expand.grid(x=., y=.), mutate(shape=seq_along(x)))

print(ggplot(dataset) + aes(x=x, y=y, shape=factor(shape))
 + geom_point()
 + discrete_scale("shape", "manual", name="shape", palette=function(x) -seq(0x25A0L, length=x))
 + theme(legend.position="none")
 )

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#!/bin/bash
set -v verbose
trap exit ERR

#I want to extract a number of submodules from a larger project.
#Also to preserve untracked files (e.g. lengthy data build products)

CWD=`pwd`
REPO_DIR="direction_discrimination_analysis"
SUBMODULES="mothballed_writing previous_draft newer_draft"

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#put this in your ~/.bash_profile
#
#If a long-running command terminates, ring the bell and float the
#(OSX Terminal) window.
LONG_RUNNING=20 #how long is long? Enough for me to get bored and tab away.

function popup_if_long {
    last_command_time=$(HISTTIMEFORMAT="%s " history 1 | awk '{print $2}')
    if (( $(date -u +"%s") - $last_command_time > $LONG_RUNNING ))