Dan Hicks dhicks

## pairs.R
library(foreach)
library(doSNOW)
library(dplyr)
library(httr)

google_books_count = function (search_terms) {
    require(httr)
    terms = str_c(search_terms, collapse = '+')
    query_url = str_c('https://www.googleapis.com/books/v1/volumes',
                      '?',

## PubMed grant extraction.R
library(rentrez)
library(magrittr)
library(xml2)

xml_raw = entrez_fetch(db="pubmed",
                       id=27019001,
                       rettype = 'xml')
xml_parsed = read_xml(xml_raw)

grant_id = xml_find_all(xml_parsed, '//Grant') %>%

## analysis.csv

          
            given
            family
            title
            pub_year

            
              A
              Avramides
              The Subject's Point of View * By KATALIN FARKAS
              2009

            
              A
              Woodfield
              Doing Without Concepts By Edouard Machery * By EDOUARD MACHERY
              2009

            
              A C
              Paseau
              How to type: reply to Halbach
              2009

            
              A C
              Paseau
              Why the subtraction argument does not add up
              2002

            
              A C
              Paseau
              An exact measure of paradox
              2012

            
              A C
              Paseau
              Did Frege commit a cardinal sin?
              2015

            
              A C
              Paseau
              The overgeneration argument(s): A succinct refutation
              2013

            
              A W
              Heathcote
              Gettier and the stopped clock
              2012

            
              A W
              Moore
              Not to be Taken at Face Value
              2009

## mwe.R
library(rstan)
## options(mc.cores = parallel::detectCores())

## Data should be here:  <https://drive.google.com/open?id=1BUV8mChrZ0UkyW2G4EHB5wc1taUpMZUM>
load('mwe.Rdata')
## dataf: The data; response is `w_use`
## W_3nn:  row-normalized spatial weights matrix, based on 3 nearest neighbors, in triplet sparse form
## W_dnn:  row-normalized spatial weights matrix, distance-based, in triplet sparse form

parsed = stanc(file = 'sdm.stan', verbose = TRUE)

## apqsync.sh
#!/bin/bash
## This script synchronizes AlpineQuest tracks using rsync, then converts them to gpx

RED='\033[0;31m'
NC='\033[0m'
echo -e "${RED}Make sure SSHDroid is running before using this script${NC}"
startfolder="$PWD"

## SSHDroid: <https://play.google.com/store/apps/details?id=berserker.android.apps.sshdroid&hl=en_US>
apqfolder="/Users/danhicks/Google Drive/hiking/GPS tracks/AlpineQuest conversion/AlpineQuest sync"

## cleveland.R
## Cleveland Dot Plots or Dumbell Plots
## This gist notes some approaches for drawing Cleveland dot plots or dumbell plots in `ggplot`

library(tidyverse)

n = 10
dataf = tibble(x = rep(1:n, 2),
               category = c(rep('A', n), rep('B', n)),
               value = x + 2*(category == 'B'))

## shading.R
## It took me three days to find this solution!

## <https://stackoverflow.com/questions/44688623/adding-custom-images-to-ggplot-facets/44897816#44897816>
annotation_custom2 <- function (grob, xmin = -Inf, xmax = Inf, ymin = -Inf, ymax = Inf, data)
    {
        layer(data = data, stat = StatIdentity, position = PositionIdentity,
              geom = ggplot2:::GeomCustomAnn,
              inherit.aes = FALSE, params = list(grob = grob,
                                                 xmin = xmin, xmax = xmax,
                                                 ymin = ymin, ymax = ymax))

## fixcalibre
#!/bin/bash
## Just a little Bash wrapper for a Ghostscript call
gs -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sOutputFile="$2" "$1"

## sample_size_sim.R
## If one group is much larger than the other, does this
## inflate type I error rates or bias estimates?
library(tidyverse)
library(broom)
library(tictoc)

set.seed(2020-03-16)

## Parameters ----
a_n = 300

## parse_and_allocate.R
## Parses a roster page saved from Canvas and allocates students to groups within discussion sections

## To use:
## 1. Navigate to the People page in a Canvas course using your browser
## 2. Right-click on the page and select "Save as"
## 3a. `Rscript parse.R path/to/roster.html`
## -OR-
## 3b. Save it to `data_folder` as `roster.html`. `Rscript parse.R` or run in RStudio.

## Setup ----
	library(foreach)
	library(doSNOW)
	library(dplyr)
	library(httr)

	google_books_count = function (search_terms) {
	require(httr)
	terms = str_c(search_terms, collapse = '+')
	query_url = str_c('https://www.googleapis.com/books/v1/volumes',
	'?',
	library(rentrez)
	library(magrittr)
	library(xml2)

	xml_raw = entrez_fetch(db="pubmed",
	id=27019001,
	rettype = 'xml')
	xml_parsed = read_xml(xml_raw)

	grant_id = xml_find_all(xml_parsed, '//Grant') %>%
given	family	title	pub_year
A	Avramides	The Subject's Point of View * By KATALIN FARKAS	2009
A	Woodfield	Doing Without Concepts By Edouard Machery * By EDOUARD MACHERY	2009
A C	Paseau	How to type: reply to Halbach	2009
A C	Paseau	Why the subtraction argument does not add up	2002
A C	Paseau	An exact measure of paradox	2012
A C	Paseau	Did Frege commit a cardinal sin?	2015
A C	Paseau	The overgeneration argument(s): A succinct refutation	2013
A W	Heathcote	Gettier and the stopped clock	2012
A W	Moore	Not to be Taken at Face Value	2009
	library(rstan)
	## options(mc.cores = parallel::detectCores())

	## Data should be here: <https://drive.google.com/open?id=1BUV8mChrZ0UkyW2G4EHB5wc1taUpMZUM>
	load('mwe.Rdata')
	## dataf: The data; response is `w_use`
	## W_3nn: row-normalized spatial weights matrix, based on 3 nearest neighbors, in triplet sparse form
	## W_dnn: row-normalized spatial weights matrix, distance-based, in triplet sparse form

	parsed = stanc(file = 'sdm.stan', verbose = TRUE)
	#!/bin/bash
	## This script synchronizes AlpineQuest tracks using rsync, then converts them to gpx

	RED='\033[0;31m'
	NC='\033[0m'
	echo -e "${RED}Make sure SSHDroid is running before using this script${NC}"
	startfolder="$PWD"

	## SSHDroid: <https://play.google.com/store/apps/details?id=berserker.android.apps.sshdroid&hl=en_US>
	apqfolder="/Users/danhicks/Google Drive/hiking/GPS tracks/AlpineQuest conversion/AlpineQuest sync"
	## Cleveland Dot Plots or Dumbell Plots
	## This gist notes some approaches for drawing Cleveland dot plots or dumbell plots in `ggplot`

	library(tidyverse)

	n = 10
	dataf = tibble(x = rep(1:n, 2),
	category = c(rep('A', n), rep('B', n)),
	value = x + 2*(category == 'B'))
	## It took me three days to find this solution!

	## <https://stackoverflow.com/questions/44688623/adding-custom-images-to-ggplot-facets/44897816#44897816>
	annotation_custom2 <- function (grob, xmin = -Inf, xmax = Inf, ymin = -Inf, ymax = Inf, data)
	{
	layer(data = data, stat = StatIdentity, position = PositionIdentity,
	geom = ggplot2:::GeomCustomAnn,
	inherit.aes = FALSE, params = list(grob = grob,
	xmin = xmin, xmax = xmax,
	ymin = ymin, ymax = ymax))
	#!/bin/bash
	## Just a little Bash wrapper for a Ghostscript call
	gs -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sOutputFile="$2" "$1"
	## If one group is much larger than the other, does this
	## inflate type I error rates or bias estimates?
	library(tidyverse)
	library(broom)
	library(tictoc)

	set.seed(2020-03-16)

	## Parameters ----
	a_n = 300
	## Parses a roster page saved from Canvas and allocates students to groups within discussion sections

	## To use:
	## 1. Navigate to the People page in a Canvas course using your browser
	## 2. Right-click on the page and select "Save as"
	## 3a. `Rscript parse.R path/to/roster.html`
	## -OR-
	## 3b. Save it to `data_folder` as `roster.html`. `Rscript parse.R` or run in RStudio.

	## Setup ----