Sean Davis seandavi

output: rmarkdown::html_document: highlight: pygments toc: true toc_depth: 3 fig_width: 5 bibliography: "r system.file(package='dummychapter1', 'vignettes', 'bibliography.bib')" vignette: > %\VignetteIndexEntry{dummychapter1}

	Name	Description
	task_id	Task ID.
	hash	Task hash code.
	native_id	Task ID given by the underlying execution system e.g. POSIX process PID when executed locally, job ID when executed by a grid engine, etc.
	process	Nextflow process name.
	tag	User provided identifier associated this task.
	name	Task name.
	status	Task status.
	exit	POSIX process exit status.
	module	Environment module used to run the task.

	#!/bin/bash
	# requires about 200G of disk space
	# downloads stuff
	# create disposable bucket
	# upload
	# bq load
	# remove bucket
	mkdir -p ss
	cd ss
	wget https://s3-us-west-2.amazonaws.com/ai2-s2-research-public/open-corpus/2022-01-01/manifest.txt

	#!/bin/bash
	CONTAINER=ghcr.io/seandavi/buildabiocworkshop
	ZONE=us-central1-a
	PASSWORD=rstudio
	INSTANCE=rs-2

	gcloud compute instances create-with-container $INSTANCE \
	--container-image $CONTAINER \
	--container-env PASSWORD=$PASSWORD \
	--tags rstudio

	#!/bin/bash
	gcloud compute instances create myinstance \
	--metadata-from-file=startup-script=startup.sh \
	--scopes=compute-rw

	start_date='2000-01-01'
	end_date = '2021-12-31'

	datefilter = function(date) {
	startdate = format(date,'%Y-%m-%d')
	return(sprintf("dt:release:from=%suntil=%s",startdate,startdate))
	}

	download_biosample = function(date) {
	require(httr)

	### Keybase proof

	I hereby claim:

	* I am seandavi on github.
	* I am seandavi (https://keybase.io/seandavi) on keybase.
	* I have a public key ASAQ8VtxEXZOXbXUmfgPSsE2L-mF4g5oHcMRkosW0EszDgo

	To claim this, I am signing this object:

	library(sars2pack)
	library(dplyr)
	library(zoo)
	library(cowplot)
	library(ggplot2)

	y = ecdc_data() %>% dplyr::group_by(iso3c) %>%
	add_incidence_column(count_column = 'confirmed') %>%
	align_to_baseline(confirmed>50,group_vars = 'iso3c') %>%
	dplyr::arrange(date) %>%

	browseURL('https://seandavi.github.io/ITR/r_intro_mechanics.html')
	1 + 1
	x = 10
	x
	y = 20
	y
	y + x

	browseURL('https://seandavi.github.io/ITR/vectors.html')
	# vectors