dchiu911

# make sure we have latest version of BiocManager
renv::install("BiocManager")

# read lockfile records
lockfile <- renv:::renv_lockfile_read("renv.lock")
records <- lockfile$Packages

# keep only packages from Bioconductor
bioc <- Filter(function(record) {
  record$Source == "Bioconductor"

dchiu911

# sensitivity >=0.9, specificity >= 0.8
# 80% power, 5% prevalence
library(MKmisc)
power.diagnostic.test(sens = 0.95, delta = 0.05, power = 0.8, prev = 0.05)
power.diagnostic.test(spec = 0.9, delta = 0.1, power = 0.8, prev = 0.05)

dchiu911

# 1a. Download R to shared directory
cd /share/data/apps/R
wget https://cran.r-project.org/src/base/R-3/R-3.5.0.tar.gz
tar -zxvf R-3.5.0.tar.gz

# 1b. Try to configure R, but fails due to outdated libraries
cd R-3.5.0
./configure F77=gfortran --enable-R-shlib --enable-memory-profiling

# 2. Download and compile zlib

dchiu911

# In current R version ----------------------------------------------------

# install.packages("sessioninfo")

# Save info of installed packages from current R version
ip <- rownames(installed.packages(priority = "NA"))

# Save full metadata for packages with all dependencies available
pkg_info <- sessioninfo::package_info(pkgs = ip)
pkg_info$repository <- vapply(strsplit(pkg_info$source, " \\("), `[`, character(1), 1)

dchiu911

# Load packages
library(tidyverse)
library(caret)
library(microbenchmark)
library(splendid)

# Setup data
data(hgsc)
data <- hgsc
class <- as.factor(attr(hgsc, "class.true"))

dchiu911

library(tidyverse)
library(measurements)
library(lubridate)

#' @param speed speed on treadmill
#' @param distance kilometres
get_racetime <- function(speed = 7.5, distance = 5) {
  real_speed <-
    as.numeric(as.period(
      period(minute = 8, second = 0) - (speed - 7.5) * 10 * seconds(7),