benjamin-chan

set STATATMP=E:\Share\Temp\chanb\StataMP
E:\Share\Applications\Stata14\StataMP-64.exe /UseRegistryStartin

benjamin-chan

loadPkg <- function (pkg) {
  # pkg should be an as.character() object
  repos <- "http://cloud.r-project.org"
  if (!require(pkg, character.only=TRUE)) {
    install.packages(pkg, dependencies=TRUE, repos=repos)
  }
  require(pkg, character.only=TRUE)
}
# loadPkg("data.table")
# loadPkg("xtable")

benjamin-chan

colorPalette <- function () {
  c(rgb(  1,  67, 134, maxColorValue=255),
    rgb(119, 120, 123, maxColorValue=255),
    rgb(139, 184, 234, maxColorValue=255),
    rgb(188, 190, 192, maxColorValue=255),
    rgb( 94, 122, 162, maxColorValue=255),
    rgb(223, 122,  28, maxColorValue=255))
}

benjamin-chan

year <- 13
url <- sprintf("https://www.cms.gov/Medicare/Coding/HCPCSReleaseCodeSets/Downloads/%02danweb.zip",
               year)
f <- tempfile()
download.file(url, f)
file.info(f)
unzip(f, list=TRUE)
unzip(f, exdir=tempdir())
list.files(tempdir())
f <- file.path(tempdir(), sprintf("HCPC20%02d_A-N.txt", year))

benjamin-chan

makeMetadata <- function(D, note=NULL) {
  if (is.data.frame(D)) {
    list(objectName = deparse(substitute(D)),
         timeStamp = sprintf("%s", Sys.time()),
         objectSize = format(object.size(D), units="auto"),
         note = note,
         rowCount = nrow(D),
         colCount = ncol(D),
         colNames = names(D),
         colClasses = sapply(D, class),

benjamin-chan

# Source: http://depts.washington.edu/uwruca/ruca-data.php
# Code definitions: http://depts.washington.edu/uwruca/ruca-codes.php
url <- "http://depts.washington.edu/uwruca/ruca_data/2006%20Complete%20Excel%20RUCA%20file.xls.zip"
path <- tempdir()
f <- tempfile()
download.file(url, f)
unzip(f, list=TRUE)
filenames <- unzip(f, list=TRUE)[, "Name"]
isValidFile <- grep("^[0-9a-z]", filenames, ignore.case=TRUE)
unzip(f, files=filenames[isValidFile], exdir=path)

benjamin-chan

flow <- function (x, switch=NULL) {
  # `x` is a character vector of items to diagram
  # switch is an optional vector (logical or integer)
  #   specifying if the element of `x` is run (TRUE or 1) or not (FALSE or 0)
  # Usage:
  # > flow(c("Part 1", "Part 2", "...", "Part N"),
  # +      c(TRUE, FALSE, ..., TRUE))
  require(DiagrammeR, quietly=TRUE)
  require(devtools, quietly=TRUE)
  if (packageVersion("devtools") >= "1.12.0") {

benjamin-chan

if (!require(devtools)) {install.packages("devtools")}
library(devtools)
source_gist("https://gist.github.com/benjamin-chan/3b59313e8347fffea425")
loadPkg("doParallel")
loadPkg("data.table")

J <- 30  # This is the number of models to fit
N <- 2E5  # This is the size of the dataset
i <- rep(1:N, each=J)
D <- data.table(i,  # id

benjamin-chan

library(data.table)
nBins <- 25
breaks <- seq(0, 1, length.out=nBins+1)
midpoints <- breaks[1:nBins] + (breaks[2:(nBins+1)] - breaks[1:nBins]) / 2
D <- data.table(x = runif(1e4))
D <- D[, xBinned := cut(x, breaks=breaks, labels=sprintf("%.2f", midpoints))]
D <- D[,
       .(.N,
         label=as.character(xBinned),
         min = min(x),

benjamin-chan

Parallel GLM tuning

Benjamin Chan
r Sys.time()

Clear the workspace environment and load packages.

rm(list=ls())
gc()