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@padamson
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
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$label,pattern=" ")),collapse="|"),
@padamson
padamson / rwml-R_listing4_3.R
Created December 28, 2016 10:54
ROC curve calculation for Listing 4.3 of Real-World Machine Learning
# Returns the false-positive and true-positive rates at nPoints thresholds for
# the given true and predicted labels
# trueLabels: 0=FALSE; 1=TRUE
rocCurve <- function(trueLabels, predictedProbs, nPoints=100, posClass=1){
# Allocates the threshold and ROC lists
thr <- seq(0,1,length=nPoints)
tpr <- numeric(nPoints)
fpr <- numeric(nPoints)
# Precalculates values for the positive and negative cases, used in the loop
@padamson
padamson / rwml-R_figure4_20.R
Created October 23, 2016 07:19
ROC curves for each class of the MNIST 10-class classifier
library(ROCR)
library(dplyr)
mnistResultsDF <- data.frame(actual = mnistTest$label,
fit = mnist.kknn$fit,
as.data.frame(mnist.kknn$prob))
plotROCs <- function(df, digitList) {
firstPlot <- TRUE
legendList <- NULL
@padamson
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
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
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
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
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", ...)