ginolhac

Installing Arch Linux with Full Disk Encryption

If you're aiming for a seamless Arch Linux installation in UEFI mode, follow along as this guide will walk you through the process step by step. We'll be using LUKS (Linux Unified Key Setup) and LVM (Logical Volume Manager) partitions on LUKS to achieve full disk encryption.

Note: I have updated this doc for UEFI mode. For those with BIOS/MBR systems, you can refer to the previous version, but keep in mind that it might be outdated and no longer accurate.

If you're only interested in installing Linux and not setting up dual boot with Windows, feel free to skip the Windows-related sections.

ginolhac

#' Flatten copy
#'
#' @param from Source directory path.
#' @param to Destination directory path.
#'
#' @return Destination directory path.
#'
#' @details
#' Copy all `.Rmd`, `.qmd`, and `.md` files from source to destination,
#' rename the `.qmd` and `.md` files with an additional `.Rmd` extension,

ginolhac

library(gganimate)

# rds object comes from this tutorial
# https://ulhpc-tutorials.readthedocs.io/en/latest/maths/R/#parallel-computing-using-hpc
res_tib <- read_rds("tsne_future.rds")

res_tib %>%
  unnest(tsne) %>%
  select(-output) %>%
  group_by(perplexities) %>%

ginolhac

#include <Rcpp.h>
using namespace Rcpp;

// [[Rcpp::export]]
SEXP with_string(CharacterVector names) {
  int size = names.size();
  std::vector<String> tmp;
  String strtmp;
  CharacterVector out_vec(tmp.begin(), tmp.end());
  

ginolhac

#include <Rcpp.h>
  using namespace Rcpp;

int vector_sign(IntegerVector x) {
  bool pos = false, neg = false;

  int n = x.size();
  for (int i = 0; i < n; ++i) {
    if (x[i] < 0) neg = true;
    if (x[i] > 0) pos = true;

ginolhac

#testdata
v1<-c("color", "red", "red", "red", "red", "green", "green", "green", "green", "yellow", "yellow", "yellow", "yellow", "blue", "blue", "blue", "blue")
v2<-c("year", "2015", "2014", "2013", "2012", "2015", "2014", "2013", "2012", "2015", "2014", "2013", "2012", "2015", "2014", "2013", "2012")
v3<-c("UK", "23", "34", "34", "11", "45", "32", "11", "76", "90", "13", "24", "12", "34", "23", "43", "28")
v4<-c("GER", "95", "43", "21", "43", "57", "22", "52", "34", "52", "56", "76", "90", "23", "78", "4", "12")
v5<-c("POL", "56", "78", "32", "56", "1", "8", "55", "45", "87", "12", "99", "66", "11", "45", "32", "11")
v6<-c("US", "56", "76", "90", "13", "11", "45", "32", "11", "11", "45", "38", "16","54","4","71","67")
df<-as.data.frame(rbind(v1,v2,v3,v4,v5,v6))

ginolhac

To -> or not to ->

In the blog post "A Step to the Right in R Assignments", by @hrbrmstr, and in later twitter discussions (e.g. here), it is argued that <- (and %<>% for that matter) is "illogical" and feels awkward.

Although I can see where the temptation comes from, I consider -> to be

ginolhac

library("ggplot2")
library("dplyr", warn.conflicts = FALSE)
library("gridExtra")

plot_id <- function(df, df2, type) {
  df %>%
    filter(`2^-ddCt` > 2, id == type) %>%
    mutate(analysis = "HKgenorm:arith") %>%
    ggplot(aes(x = ID, y = log2(`2^-ddCt`), colour = analysis))+
    geom_pointrange(aes(ymin = log2(`2^-ddCt.min`), ymax = log2(`2^-ddCt.max`)),

ginolhac

library("dplyr")
library("readr")
library("stringi")

# load file with names absolute paths
file.list <- list.files("/Volumes/gaia/", pattern='*.txt', full.names = TRUE)
# read them all as a list
df.list <- lapply(file.list, read_tsv)
# name list with correct id extracted from filenames
names(df.list) <- stri_extract_first(basename(file.list), regex = "patient_\\d")