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USMortality / Commands

Created December 21, 2024 18:33

Alignment of read 6bde649c-c7a2-4872-ab6f-147510942a0e and MN908947.3

	# DL: https://osf.io/dfvbz
	$ zstd -dc VeroInf24h.all.fastq.zst\|seqkit seq --rna2dna>VeroInf24h.all.fastq
	$ minimap2 -aY --sam-hit-only -t7 MN908947.3.fa VeroInf24h.all.fastq >temp.sam
	[..]
	$ seqkit grep -p "6bde649c-c7a2-4872-ab6f-147510942a0e" VeroInf24h.all.fastq > single_read.fastq
	minimap2 -a MN908947.3.fa single_read.fastq \| samtools sort -@ 7 - >temp_longest.bam
	samtools index temp_longest.bam

	samtools fasta temp_longest.bam > temp_longest.fa
	cat MN908947.3.fa temp_longest.fa \| mafft --globalpair --clustalout -

USMortality / germany_vae.r

Last active December 10, 2024 08:05

PEI Impfnebenwirkungen [Germany]

	library(dplyr)
	library(readxl)

	url <- paste0(
	"https://www.pei.de/SharedDocs/Downloads/DE/newsroom/dossiers/rohdaten-",
	"sicherheitsberichte/download-xls-uaw-daten-2020-12-27-bis-2023-12-31",
	".xlsx?__blob=publicationFile&v=5"
	)
	tempfile_path <- tempfile(fileext = ".xlsx")
	download.file(url, tempfile_path, mode = "wb") # Use mode = "wb" for binary files

USMortality / compare_disaggreation.r

Last active December 6, 2024 10:08

Life Expectancy at Birth [USA, 2022]

	library(tidyverse)
	library(demography)
	library(scales)

	sf <- 2
	width <- 600 * sf
	height <- 335 * sf

	options(vsc.dev.args = list(width = width, height = height, res = 72 * sf))

USMortality / data_usa_deaths_single_years.csv

Last active November 30, 2024 04:28

USA 2019 Deaths by single years

USMortality / .chart_usa_sads.r

Created November 28, 2024 19:33

Sudden Adult Death Syndrome (SADS) Deaths by ICD-10 Code [USA]

	library(tidyverse)
	library(scales)
	library(tsibble)
	library(fable)

	sf <- 2
	width <- 600 * sf
	height <- 335 * sf
	options(vsc.dev.args = list(width = width, height = height, res = 72 * sf))

USMortality / data_usa_ucd_mcd_deaths_2017-2022.sh

Created November 28, 2024 19:33

USA UCD/MCD Deaths 2017-2022

	#!/bin/sh

	BASE_URL="https://ftp.cdc.gov/pub/Health_Statistics/NCHS/Datasets/DVS/mortality"
	OUTPUT_DIR="mortality_data"
	YEARS="2017 2018 2019 2020 2021 2022"
	OUTPUT_CSV="mcd.csv"
	mkdir -p "$OUTPUT_DIR"
	echo "id,year,month,age,ucd,mcd" > "$OUTPUT_CSV"
	for YEAR in $YEARS; do
	YY="${YEAR: -2}" # Extract last two digits of the year

USMortality / .chart_bergamo_pull_forward2.r

Last active November 27, 2024 19:09

Pull Forward Effect in Large Mortality Event [Bergamo, Italy] n=10

	library(tsibble)
	library(fable)
	library(ggplot2)
	library(tidyverse)
	library(data.table)

	sf <- 2
	width <- 600 * sf
	height <- 335 * sf
	options(vsc.dev.args = list(width = width, height = height, res = 72 * sf))

USMortality / chart_bergamo_pull_forward.r

Last active November 26, 2024 17:35

Pull Forward Effect in Large Mortality Event [Bergamo, Italy]

	library(tsibble)
	library(fable)
	library(ggplot2)
	library(tidyverse)

	sf <- 2
	width <- 600 * sf
	height <- 335 * sf
	options(vsc.dev.args = list(width = width, height = height, res = 72 * sf))

USMortality / pull_forward_sim.r

Created November 24, 2024 01:55

Pull Forward Effect Simulation

	# Load necessary libraries
	library(dplyr)
	library(ggplot2)

	sf <- 2
	width <- 600 * sf
	height <- 335 * sf

	options(vsc.dev.args = list(width = width, height = height, res = 72 * sf))

USMortality / .chart_usa_presidential_elections_swing_states.r

Last active January 13, 2025 00:17

Presidential Elections Popular Vote Swing States [USA]

	library(readr)
	library(dplyr)
	library(tidyr)
	library(ggplot2)
	library(scales)

	sf <- 2
	width <- 600 * sf
	height <- 335 * sf
	options(vsc.dev.args = list(width = width, height = height, res = 72 * sf))

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