Richard Morey richarddmorey

## dice_rolling.R
library(dplyr)
library(memoise)

# Rolls
k = 3
# Sides
n = 5

sumDist = function(n,k,maxn = n){
  do.call(

## create_covers.R
#' Create cover images for talks from a folder of PDFs
#'
#' Requires imagemagick to be installed and in the path for the convert command
#' @param pdf_dir Directory containing PDF files of papers
#' @param img_dir Directory to output all the image files
#' @param crop_height How big to make the cropped images, relative to full page
#' @param fade_height How much of the image to fade to transparent at the bottom
#' @param density resolution for PNG images
#'
create_covers = function(pdf_dir, img_dir, crop_height = .5, fade_height = .25, density = 300){

## testing_ricv.Rmd
---
title: "Testing ricv"
author: "Richard D. Morey"
date: "3/25/2022"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
```

## example.R
library(dplyr)
library(ggplot2)

# Create data
tibble(
  g = rep(c('A','B'), each = 50),
  z = rnorm(length(g))
  ) |>
  group_by(g) |>
  mutate(

## Lichtenstein_etal_1978_Tab5.csv

          
            Cause
            Rate_outof_205000000
            MVA_geom_mean
            MVA_resid
            Elec_geom_mean
            Elec_resid

            
              Smallpox
              0.00
              88.00
              
              37.00

            
              Poisoning by vitamins
              1.00
              237.00
              1.27
              44.00
              1.16

            
              Botulism
              2.00
              379.00
              1.97
              88.00
              1.96

            
              Measles
              5.00
              331.00
              1.39
              85.00
              1.47

            
              Fireworks
              6.00
              331.00
              1.54
              77.00
              1.26

            
              Smallpox vaccination
              8.00
              38.00
              0.17
              14.00
              0.22

            
              Whooping cough
              15.00
              171.00
              0.69
              51.00
              0.62

            
              Polio
              17.00
              202.00
              0.80
              47.00
              0.55

            
              Venomous bite or sting
              48.00
              535.00
              1.67
              233.00
              1.85

## subway_hist.R
library(dplyr)
library(ggplot2)
library(ggdist)

url = 'https://osf.io/846cb/download'
httr::GET(url, httr::write_disk(tf <- tempfile(fileext = ".xlsx")))

readxl::read_xlsx(tf) %>%
  mutate(
    DIRECTION = factor(DIRECTION, levels = c("WEST","EAST"),

## test_surveyjs.Rmd
---
title: "Test SurveyJS and Rmarkdown"
output:
  html_document:
    css: "https://unpkg.com/survey-jquery/survey.min.css"
editor_options:
  chunk_output_type: console
---

A test javascript survey by building a JSON object for [SurveyJS](https://surveyjs.io/).

## Bailey_Geary_2009.csv

          
            No
            homo
            CC
            Latitude
            north
            lat_from_o
            tpar
            meantemp
            hitemp
            lotemp
            diftemp
            Isosd
            dpop_30

            
              1
              1
              595
              27
              0
              35
              1
              17.8
              30
              1
              29
              0.218223437
              13

            
              2
              1
              475
              27
              0
              35
              1
              17.8
              30
              1
              29
              0.218223437
              13

            
              3
              1
              507
              27
              0
              35
              1
              17.8
              30
              1
              29
              0.218223437
              13

            
              4
              1
              570
              27
              0
              35
              1
              17.8
              30
              1
              29
              0.218223437
              13

            
              6
              1
              776
              4
              1
              4
              7
              24.7
              26
              11
              15
              0.212807364
              13

            
              7
              1
              506.333
              4
              1
              4
              7
              24.7
              26
              11
              15
              0.212807364
              13

            
              8
              1
              622.5
              4
              1
              4
              7
              24.7
              26
              11
              15
              0.212807364
              13

            
              5
              1
              500
              7
              1
              1
              7
              22.2
              25
              6
              19
              0.212807364
              13

            
              15
              1
              775
              40
              1
              32
              4
              5.8
              31
              -1
              32
              0.25577606
              16

## app2.R
# Test answer to https://stackoverflow.com/questions/68473292/prevent-double-execution-of-shiny-reactive-with-two-dependency-pathways/68475515#68475515
library(shiny)
library(digest)

ui <- fluidPage(

  sidebarLayout(
    sidebarPanel(
      textInput("M", "M:", ""),
      uiOutput("S_UI"),

## sample_constraints.R
## Define MVTN parameters
mu = c(-1,0,1)
Sigma = matrix(
  c(1,  0,  0,
    0,  1, .5,
    0, .5,  1
  ), 3,3)
p = length(mu)

library(mvtnorm)
	library(dplyr)
	library(memoise)

	# Rolls
	k = 3
	# Sides
	n = 5

	sumDist = function(n,k,maxn = n){
	do.call(
	#' Create cover images for talks from a folder of PDFs
	#'
	#' Requires imagemagick to be installed and in the path for the convert command
	#' @param pdf_dir Directory containing PDF files of papers
	#' @param img_dir Directory to output all the image files
	#' @param crop_height How big to make the cropped images, relative to full page
	#' @param fade_height How much of the image to fade to transparent at the bottom
	#' @param density resolution for PNG images
	#'
	create_covers = function(pdf_dir, img_dir, crop_height = .5, fade_height = .25, density = 300){
	---
	title: "Testing ricv"
	author: "Richard D. Morey"
	date: "3/25/2022"
	output: html_document
	---

	```{r setup, include=FALSE}
	knitr::opts_chunk$set(echo = FALSE)
	```
	library(dplyr)
	library(ggplot2)

	# Create data
	tibble(
	g = rep(c('A','B'), each = 50),
	z = rnorm(length(g))
	) \|>
	group_by(g) \|>
	mutate(
Cause	Rate_outof_205000000	MVA_geom_mean	MVA_resid	Elec_geom_mean	Elec_resid
Smallpox	0.00	88.00		37.00
Poisoning by vitamins	1.00	237.00	1.27	44.00	1.16
Botulism	2.00	379.00	1.97	88.00	1.96
Measles	5.00	331.00	1.39	85.00	1.47
Fireworks	6.00	331.00	1.54	77.00	1.26
Smallpox vaccination	8.00	38.00	0.17	14.00	0.22
Whooping cough	15.00	171.00	0.69	51.00	0.62
Polio	17.00	202.00	0.80	47.00	0.55
Venomous bite or sting	48.00	535.00	1.67	233.00	1.85
	library(dplyr)
	library(ggplot2)
	library(ggdist)

	url = 'https://osf.io/846cb/download'
	httr::GET(url, httr::write_disk(tf <- tempfile(fileext = ".xlsx")))

	readxl::read_xlsx(tf) %>%
	mutate(
	DIRECTION = factor(DIRECTION, levels = c("WEST","EAST"),
	---
	title: "Test SurveyJS and Rmarkdown"
	output:
	html_document:
	css: "https://unpkg.com/survey-jquery/survey.min.css"
	editor_options:
	chunk_output_type: console
	---

	A test javascript survey by building a JSON object for [SurveyJS](https://surveyjs.io/).
No	homo	CC	Latitude	north	lat_from_o	tpar	meantemp	hitemp	lotemp	diftemp	Isosd	dpop_30
1	1	595	27	0	35	1	17.8	30	1	29	0.218223437	13
2	1	475	27	0	35	1	17.8	30	1	29	0.218223437	13
3	1	507	27	0	35	1	17.8	30	1	29	0.218223437	13
4	1	570	27	0	35	1	17.8	30	1	29	0.218223437	13
6	1	776	4	1	4	7	24.7	26	11	15	0.212807364	13
7	1	506.333	4	1	4	7	24.7	26	11	15	0.212807364	13
8	1	622.5	4	1	4	7	24.7	26	11	15	0.212807364	13
5	1	500	7	1	1	7	22.2	25	6	19	0.212807364	13
15	1	775	40	1	32	4	5.8	31	-1	32	0.25577606	16
	# Test answer to https://stackoverflow.com/questions/68473292/prevent-double-execution-of-shiny-reactive-with-two-dependency-pathways/68475515#68475515
	library(shiny)
	library(digest)

	ui <- fluidPage(

	sidebarLayout(
	sidebarPanel(
	textInput("M", "M:", ""),
	uiOutput("S_UI"),
	## Define MVTN parameters
	mu = c(-1,0,1)
	Sigma = matrix(
	c(1, 0, 0,
	0, 1, .5,
	0, .5, 1
	), 3,3)
	p = length(mu)

	library(mvtnorm)