padamson’s gists

padamson / PyQuante Testing.ipynb

Created July 8, 2021 00:53 — forked from rpmuller/PyQuante Testing.ipynb

Notes, timings, and additional tests for the development of pyquante2 by comparing to to PyQuante (1.6.??).

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padamson / acronymTable.R

Created December 28, 2016 13:13

Reactive acronym list with renderDataTable, timevis, and Shiny

	output$acronyms <- DT::renderDataTable({
	firstDate <- input$timelineGroups_window[1]
	lastDate <- input$timelineGroups_window[2]
	data <- input$timelineGroups_data %>%
	select(label,start,end) %>%
	filter((is.na(end) & (start > firstDate & start < lastDate)) \|
	(!is.na(end) & (start < lastDate & end > firstDate)))
	acronyms %>%
	filter(grepl(
	paste(unlist(str_split(data$label,pattern=" ")),collapse="\|"),

padamson / rwml-R_listing4_3.R

Created December 28, 2016 10:54

ROC curve calculation for Listing 4.3 of Real-World Machine Learning

	# Returns the false-positive and true-positive rates at nPoints thresholds for
	# the given true and predicted labels
	# trueLabels: 0=FALSE; 1=TRUE
	rocCurve <- function(trueLabels, predictedProbs, nPoints=100, posClass=1){
	# Allocates the threshold and ROC lists
	thr <- seq(0,1,length=nPoints)
	tpr <- numeric(nPoints)
	fpr <- numeric(nPoints)

	# Precalculates values for the positive and negative cases, used in the loop

padamson / rwml-R_figure4_20.R

Created October 23, 2016 07:19

ROC curves for each class of the MNIST 10-class classifier

	library(ROCR)
	library(dplyr)

	mnistResultsDF <- data.frame(actual = mnistTest$label,
	fit = mnist.kknn$fit,
	as.data.frame(mnist.kknn$prob))

	plotROCs <- function(df, digitList) {
	firstPlot <- TRUE
	legendList <- NULL

padamson / rwml-R_figure4_19.R

Created October 23, 2016 07:04

Plot the confusion matrix for a 10-class MNIST handwritten digit classification problem

	library(caret)
	library(kknn)
	library(RColorBrewer)
	library(cowplot)

	mnist <- read.csv("data/mnist_small.csv",
	colClasses = c(label = "factor"))

	trainIndex <- createDataPartition(mnist$label, p = .8,
	list = FALSE,

padamson / rwml-R_figure3_10.R

Created October 16, 2016 00:14

Display four random digits from MNIST database

	mnist <- read.csv("data/mnist_small.csv",
	colClasses = c(label = "factor"))
	displayMnistSamples <- function(x) {
	for(i in x){
	y = as.matrix(mnist[i, 2:785])
	dim(y) = c(28, 28)
	image( y[,nrow(y):1], axes = FALSE, col = gray(0:255 / 255))
	text( 0.2, 0, mnist[i,1], cex = 3, col = 2, pos = c(3,4))
	}
	}

padamson / rwml-R_figure2_12.R

Last active October 1, 2016 13:37

Create mosaic plot for Real-World Machine Learning Figure 2.12

	library(vcd)
	mosaic(
	~ Sex + Survived,
	data = titanic,
	main = "Mosaic plot for Titanic data: Gender vs. survival",
	shade = TRUE,
	split_vertical = TRUE,
	labeling_args = list(
	set_varnames = c(
	Survived = "Survived?")

padamson / installAllRPackages.bash

Last active March 22, 2021 15:54

Bash script to install all R packages required by an R program

	#!/bin/bash
	#Install any packages required by an R file that aren't already installed

	if [ $# -ne 1 ]; then
	echo $0: usage: installAllRPackages.bash file
	exit 1
	fi

	file=$1

padamson / multi_smooth_ggpairs.R

Created February 17, 2016 02:07

Add two regression lines to plots in ggpairs

	require(datasets)
	data("swiss")
	require(GGally)
	require(ggplot2)

	my_fn <- function(data, mapping, ...){
	p <- ggplot(data = data, mapping = mapping) +
	geom_point() +
	geom_smooth(method=loess, fill="red", color="red", ...) +
	geom_smooth(method=lm, fill="blue", color="blue", ...)

Paul Adamson padamson