File:SARS-CoV-2-DZ.svg
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Summary
[edit]DescriptionSARS-CoV-2-DZ.svg |
Français : Comptages officiels quotidiens de SARS-CoV-2, dont les 28 jours du moindre bruit, 2020, Algérie ; données et analyse dans https://zenodo.org/record/3951152. Les lignes continues montre le bandeau Poisson de 68% de confiance pour un modèle médian quatre-voisins construit des données. Les points bleus sont les comptages officiels.
English: Official SARS-CoV-2 daily infection counts, 28-day period of least noise, 2020, Algeria; data and analysis in https://zenodo.org/record/3951152. The solid lines show a Poisson error band for a four-neighbours median model built from the data. Blue dots show the official counts. |
Date | |
Source | Own work |
Author | Boud |
Licensing
[edit]I, the copyright holder of this work, hereby publish it under the following license:
This file is licensed under the Creative Commons Attribution-Share Alike 4.0 International license.
- You are free:
- to share – to copy, distribute and transmit the work
- to remix – to adapt the work
- Under the following conditions:
- attribution – You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
- share alike – If you remix, transform, or build upon the material, you must distribute your contributions under the same or compatible license as the original.
Source code
[edit]#!/bin/bash
# dz_sarscov2_phi_i - Algerian SARS-CoV-2 pandemic data with phi_i from ArXiv:2007.11779v1
# (C) Wikimedia Commons User:Boud, 2020 CC-BY-SA-4.0
# https://creativecommons.org/licenses/by-sa/4.0/
# https://creativecommons.org/2015/10/08/cc-by-sa-4-0-now-one-way-compatible-with-gplv3/
# Refs: see
# * https://arxiv.org/abs/arXiv:2007.11779
# * https://zenodo.org/record/3951152
## Download daily data
## files to download
TMPdays=/tmp/tmp.alldata.tmponly
TMP28=/tmp/tmp.phi.tmponly
## plotting files
TMP0=/tmp/tmp.dz.0
TMPplus=/tmp/tmp.dz.plus
TMPminus=/tmp/tmp.dz.minus
TMPlowest28_1=/tmp/tmp.dz.lowest1
TMPlowest28_2=/tmp/tmp.dz.lowest2
LANG=C
DEBUG=NO
#DEBUG=YES
if [ "x$1" = "xw" ]; then
wget -O ${TMPdays} https://zenodo.org/record/3951152/files/WP_C19CCTF_SARSCoV2.dat
wget -O ${TMP28} https://zenodo.org/record/3951152/files/phi_N_28days.dat
fi
## Extract DZ data
day_one=$(grep DZ, ${TMPdays} | awk -F , '{print $1}'|head -n1)
N_days=$(grep DZ, ${TMPdays} | wc |awk '{print $1}')
dz_daily=$(grep DZ, ${TMPdays} |awk -F , '{cnew=$3-cold; cold=$3; print cnew}')
if [ "x${DEBUG}" = "xYES" ]; then
printf "${dz_daily}" | tr '\n' ' ' ; printf "\n"
fi
## Extract DZ least noisy period
dz_lowest_28_day1=$(grep ^DZ ${TMP28} | awk '{print $NF}')
dz_lowest_28_date1=$(grep DZ, ${TMPdays} | grep -n "${dz_lowest_28_day1}" | \
sed -e 's/:/,/' | awk -F , '{print $1}')
dz_lowest_28_date2=$(echo ${dz_lowest_28_date1} |awk '{print $1+27}')
if [ "x${DEBUG}" = "xYES" ]; then
printf "dz_lowest_28_date1=${dz_lowest_28_date1}\n"
printf "dz_lowest_28_date2=${dz_lowest_28_date2}\n"
fi
## Create median model (see Methods section of ArXiv:2007.11779)
dz_median_0=$(echo ${dz_daily[@]} | tr ' ' '\n' | \
LANG=C awk '{i+=1; c[5]=c[4]; c[4]=c[3]; c[3]=c[2]; c[2]=c[1]; c[1]=$1; \
d[4]=c[5]; d[3]=c[4]; d[2]=c[2]; d[1]=c[1]; \
asort(d,e); median = (e[2]+e[3])*0.5; \
if(i>=5)print median}')
first=$(echo ${dz_median_0}|awk '{print $1}')
last=$(echo ${dz_median_0}|awk '{print $NF}')
dz_median="${first} ${first} ${dz_median_0} ${last} ${last}"
if [ "x${DEBUG}" = "xYES" ]; then
printf "${dz_median}\n"
fi
## print days and Poisson bounds
echo ${dz_median} | tr ' ' '\n' | awk '{print NR,$1-sqrt($1)}' > ${TMPminus}
echo ${dz_median} | tr ' ' '\n' | awk '{print NR,$1+sqrt($1)}' > ${TMPplus}
echo ${dz_daily} | tr ' ' '\n' | awk '{print NR,$1}' > ${TMP0}
FORMAT=svg
#FORMAT=ps
X1=0
X2=${N_days}
Y1=0
Y2=700
X_label="date starting ${day_one}"
Y_label="number of infections"
title="least noisy 28 days: starting ${dz_lowest_28_day1} "
X_label="date commencant le ${day_one}"
Y_label="nombre d'infections"
title="28 j. moindre bruit: debut=${dz_lowest_28_day1}"
printf "${dz_lowest_28_date1} ${Y1}\n${dz_lowest_28_date1} ${Y2}\n" > ${TMPlowest28_1}
printf "${dz_lowest_28_date2} ${Y1}\n${dz_lowest_28_date2} ${Y2}\n" > ${TMPlowest28_2}
graph -T${FORMAT} -w 0.75 -W0.001 -X "${X_label}" -Y "${Y_label}" \
-x ${X1} ${X2} -y ${Y1} ${Y2} ${TMPminus} \
--reposition 0.0 0.0 1.0 --blankout 0.0 \
-x ${X1} ${X2} -y ${Y1} ${Y2} ${TMPplus} \
--reposition 0.0 0.0 1.0 --blankout 0.0 \
-C --pen-colors "1=blue:2=green:3=red" -m0 -S 16 \
-x ${X1} ${X2} -y ${Y1} ${Y2} ${TMP0} \
--reposition 0.0 0.0 1.0 --blankout 0.0 \
-m3 -W0.001 \
--frame-color red -L "${title}" --grid-style 1 \
-x ${X1} ${X2} -y ${Y1} ${Y2} ${TMPlowest28_2} \
--reposition 0.0 0.0 1.0 --blankout 0.0 \
-m3 -W0.001 \
--frame-color black -L "" \
-x ${X1} ${X2} -y ${Y1} ${Y2} ${TMPlowest28_1} \
> SARS-CoV-2-DZ.${FORMAT}
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Date/Time | Thumbnail | Dimensions | User | Comment | |
---|---|---|---|---|---|
current | 17:08, 2 August 2020 | 720 × 720 (59 KB) | Boud (talk | contribs) | Uploaded own work with UploadWizard |
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Short title | SVG drawing |
---|---|
Image title | This was produced by version 4.4 of GNU libplot, a free library for exporting 2-D vector graphics. |
Width | 8in |
Height | 8in |