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## uses.md

      
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                My work setup. Inspired by uses.tech and usesthis.com.
              
          
    Hardware


Computer 💻: Apple MacBook Air (13"), iPad (10.2") + Apple Pencil
Noise cancelling earphones 🎧: Bose QuietComfort (> 4 years old, still work)
Cloud computing ☁️: GCP (Google Cloud Computing)
Analog sketching ✍️: Caran d'Ache 825 pen (blue) + plain white paper, no lines.

Operating system


MacOS (Laptop)
Ubuntu (Cloud)


## 1-user-2019.md

      
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              July 17, 2019 14:09
            
              
                Notes + examples from useR!2019
              
          
    Notes from useR!2019

ToC


Wednesday
Thursday
Friday

Slides + Material


Program + Slides: https://user2019.r-project.org/talk_schedule/


## eshg-2019.md

      
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              April 8, 2022 07:05
            
              
                ESHG Göteborg 2019 https://2019.eshg.org/
              
          
    Notes from ESHG Göteborg 2019


Programme here.
Live tweeting by Emily Perry
Live tweeting by Kaitlin Samocha
#ESHG tweets

Content


Saturday


## new-features.md

      
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              May 11, 2019 14:24
            
              
                overview of current rsnps functions
              
          
    NCBI vs OPENSNP


split ropensnp and ncbi functions? ¯_(ツ)_/¯
adding a opensnp or dbsnp suffix to function name? see also https://ropensci.github.io/dev_guide/building.html#function-and-argument-naming

Function design


what about searching for pos and chr?
some of the functions only work for 1 SNP. extend for a vector of SNPs (e.g. genotypes())
add progressbar


## phylo-pca.md

      
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              July 18, 2022 23:15
            
              
                Estimating phylogenetic PCs
              
          
    Phylogenetic principal component analysis (in R)

The following is a guide on how to perform a phylogenetic principal component analysis.
The phylogenetic principal component analysis, short pPCA, has been proposed by Revell in 2009 and Jombart et al. 2010.
Jombart also implemented pPCA in the adephylo R-package.

  
## awk-cheatsheet
## adding column N as last column to a file
FILE=~/gwas.txt
N=98
awk '$NF="98"' $FILE  > tmp-file
sed -e '1s/98/N/' tmp-file > tmp2-file

## satrday-paris.R
## /////////////////////////////////
##       satRday Paris notes
##            (untidy)
## /////////////////////////////////

## Lionel Henry: Programming in the tidyverse
## tidyverse (data analysis, data manipulation, data cleaning) <----> r-lib (production prgramming)
##                                       dplyr, ggplot2, tidyr <----> vctrs, rland, devtools
## reprocibillity by few users                                 <----> reusability by many users

## howto-future.R

## //////////////////
## FUTURE PACKAGE
## //////////////////


## here is a function that sums up really slow
## ---------------------------------------------
slow_sum <- function(vec) {
  SUM <- 0

## schur-complement-example.R
## Schur complement

## add-banner.R

## Add banner comments to R scripts using
## [bannerCommenter](https://cran.r-project.org/web/packages/bannerCommenter/vignettes/Banded_comment_maker.pdf).

## header -----------------------------
bannerCommenter::banner("G2G-EBV analysis using GASTON", emph = TRUE)

## section -----------------------------
bannerCommenter::banner("0. Setup", centre = TRUE, bandChar = "/")
	## adding column N as last column to a file
	FILE=~/gwas.txt
	N=98
	awk '$NF="98"' $FILE > tmp-file
	sed -e '1s/98/N/' tmp-file > tmp2-file
	## /////////////////////////////////
	## satRday Paris notes
	## (untidy)
	## /////////////////////////////////

	## Lionel Henry: Programming in the tidyverse
	## tidyverse (data analysis, data manipulation, data cleaning) <----> r-lib (production prgramming)
	## dplyr, ggplot2, tidyr <----> vctrs, rland, devtools
	## reprocibillity by few users <----> reusability by many users

	## //////////////////
	## FUTURE PACKAGE
	## //////////////////


	## here is a function that sums up really slow
	## ---------------------------------------------
	slow_sum <- function(vec) {
	SUM <- 0