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Remove Nigeria sero data
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romain-ragonnet committed Oct 2, 2023
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1 change: 0 additions & 1 deletion autumn/projects/sm_covid2/common_school/included_countries.yml
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Expand Up @@ -246,7 +246,6 @@ national_sero:
LTU: Lithuania
MEX: Mexico
MWI: Malawi
NGA: Nigeria
NOR: Norway
NPL: Nepal
OMN: Oman
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4 changes: 2 additions & 2 deletions data/inputs/school-closure/serodata_national.csv
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177 changes: 88 additions & 89 deletions docs/tex/tex_descriptions/projects/sm_covid/serodata.tex
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Expand Up @@ -37,95 +37,94 @@
\begin{tabular}{p{2cm} | p{1.6cm} | p{1.6cm} | p{0.8cm} | p{0.8cm} | p{1cm} | p{1.3cm} | p{1.2cm} | p{1.2cm}}
\hline
\textbf{country} & \textbf{sampling start date} & \textbf{sampling end date} & \textbf{age min} & \textbf{age max} & \textbf{denom. value} & \textbf{serum pos prevalence} & \textbf{estimate grade} & \textbf{overall risk of bias} \\
\hline
\href{https://dx.doi.org/10.5694/mja2.51542}{\textcolor{blue}{Australia}} & 2020-11-03 & 2021-03-12 & & 19 & 1685 & 0.0023 & National & High \\
\hline
\href{https://dx.doi.org/10.1007/s15010-021-01639-0}{\textcolor{blue}{Austria}} & 2020-06-05 & 2020-12-04 & 18 & 72 & 20228 & 0.025 & National & High \\
\hline
\href{https://dx.doi.org/10.2807/1560-7917.ES.2022.27.9.2100419}{\textcolor{blue}{Belgium}} & 2020-10-12 & 2020-10-17 & & 101 & 2966 & 0.0418 & National & Low \\
\hline
\href{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8225319/}{\textcolor{blue}{Brazil}} & 2020-05-14 & 2020-06-23 & & & 89362 & 0.023 & National & Moderate \\
\hline
\href{https://serotracker.com/en/Explore}{\textcolor{blue}{Canada}} & 2021-04-13 & 2021-04-30 & 17 & & 16931 & 0.2692 & National & Moderate \\
\hline
\href{https://dx.doi.org/10.1186/s12879-022-07045-7}{\textcolor{blue}{Chile}} & 2020-09-25 & 2020-11-25 & 7 & 94 & 2493 & 0.104 & National & Low \\
\hline
\href{https://dx.doi.org/10.1016/j.lana.2022.100195}{\textcolor{blue}{Colombia}} & 2020-09-21 & 2020-12-11 & 5 & 80 & 17863 & 0.3253 & National & Moderate \\
\hline
\href{https://dx.doi.org/10.3390/pathogens10060774}{\textcolor{blue}{Croatia}} & 2020-12-15 & 2021-02-15 & & & 1436 & 0.251 & National & High \\
\hline
\href{https://doi.org/10.1038/s43856-022-00080-0}{\textcolor{blue}{Czechia}} & 2021-02-01 & 2021-03-31 & 18 & & 19548 & 0.51 & National & High \\
\hline
\href{https://dx.doi.org/10.1007/s10654-021-00796-8}{\textcolor{blue}{Denmark}} & 2020-12-01 & 2020-12-31 & 12 & & 4044 & 0.043 & National & Low \\
\hline
\href{https://dx.doi.org/10.3389/fmed.2022.933260}{\textcolor{blue}{Ecuador}} & 2020-10-12 & 2020-10-19 & & & 1250 & 0.1168 & National & Moderate \\
\hline
\href{https://dx.doi.org/10.1186/s41182-022-00448-x}{\textcolor{blue}{Egypt}} & 2021-01-15 & 2021-06-15 & & & 2360 & 0.463 & National & Moderate \\
\hline
\href{https://dx.doi.org/10.1038/s41467-021-23233-6}{\textcolor{blue}{France}} & 2020-05-11 & 2020-05-17 & & & 3592 & 0.0493 & National & Low \\
\hline
\href{https://www.ifo.de/en/publikationen/2020/monograph-authorship/die-deutschen-und-corona}{\textcolor{blue}{Germany}} & 2020-10-26 & 2020-11-18 & 18 & & 9929 & 0.011 & National & Moderate \\
\hline
\href{https://revistas.ucr.ac.cr/index.php/psm/article/view/43261/46175}{\textcolor{blue}{Honduras}} & 2020-06-16 & 2020-06-23 & 5 & & 792 & 0.062 & National & Moderate \\
\hline
\href{https://dx.doi.org/10.1007/s11357-020-00226-9}{\textcolor{blue}{Hungary}} & 2020-05-01 & 2020-05-16 & 14 & & 10474 & 0.0068 & National & Low \\
\hline
\href{http://dx.doi.org/10.1016/j.ijid.2021.05.040}{\textcolor{blue}{India}} & 2020-12-18 & 2021-01-06 & 10 & & 28598 & 0.241 & National & Low \\
\hline
\href{https://dx.doi.org/10.1186/s12889-022-13464-7}{\textcolor{blue}{Iran}} & 2021-01-15 & 2021-03-15 & 10 & 90 & 7411 & 0.342 & National & Low \\
\hline
\href{https://dx.doi.org/10.1007/s10654-021-00749-1}{\textcolor{blue}{Israel}} & 2020-06-28 & 2020-09-14 & & & 54357 & 0.046 & National & Moderate \\
\hline
\href{https://www.istat.it/it/files//2020/08/ReportPrimiRisultatiIndagineSiero.pdf}{\textcolor{blue}{Italy}} & 2020-05-25 & 2020-07-15 & & & 64660 & 0.025 & National & Moderate \\
\hline
\href{https://dx.doi.org/10.3201/eid2702.204088}{\textcolor{blue}{Japan}} & 2020-06-01 & 2020-06-07 & 20 & & 7950 & 0.001 & National & Moderate \\
\hline
\href{http://dx.doi.org/10.1016/j.onehlt.2021.100292}{\textcolor{blue}{Jordan}} & 2020-12-27 & 2021-01-06 & & & 5044 & 0.342 & National & Moderate \\
\hline
\href{https://dx.doi.org/10.3390/ijerph19042263}{\textcolor{blue}{Kazakhstan}} & 2020-07-16 & 2021-07-07 & & & 85346 & 0.63 & National & High \\
\hline
\href{https://dx.doi.org/10.1001/jama.2021.15265}{\textcolor{blue}{Kenya}} & 2021-01-03 & 2021-03-15 & 16 & 64 & 3018 & 0.485 & National & Moderate \\
\hline
\href{https://dx.doi.org/10.1186/s12879-022-07031-z}{\textcolor{blue}{Lebanon}} & 2020-12-07 & 2021-01-15 & & & 2058 & 0.185 & National & Low \\
\hline
\href{https://www.journals.vu.lt/AML/article/view/22344}{\textcolor{blue}{Lithuania}} & 2020-08-10 & 2020-09-10 & 18 & 92 & 3089 & 0.014 & National & Moderate \\
\hline
\href{https://dx.doi.org/10.3201/eid2813.212348}{\textcolor{blue}{Malawi}} & 2020-10-14 & 2020-12-08 & & & 4261 & 0.078 & National & Low \\
\hline
\href{https://saludpublica.mx/index.php/spm/article/view/12847}{\textcolor{blue}{Mexico}} & 2020-08-15 & 2020-11-15 & 3 & 12 & 944 & 0.187 & National & Low \\
\hline
\href{https://mohp.gov.np/attachments/article/708/First%20Sero-prevalence\_final\_report\_04-04-2021.pdf}{\textcolor{blue}{Nepal}} & 2020-10-09 & 2020-10-22 & & & 3040 & 0.144 & National & Low \\
\hline
\href{https://dx.doi.org/10.1001/jamanetworkopen.2022.36053}{\textcolor{blue}{Nigeria}} & 2021-06-29 & 2021-08-21 & & & 4904 & 0.789 & National & Moderate \\
\hline
\href{https://dx.doi.org/10.1111/irv.12932}{\textcolor{blue}{Norway}} & 2020-12-27 & 2021-02-13 & & & 1912 & 0.032 & National & Moderate \\
\hline
\href{https://dx.doi.org/10.1016/j.ijid.2021.09.062}{\textcolor{blue}{Oman}} & 2020-11-08 & 2020-11-19 & 5 & & 4064 & 0.22 & National & Moderate \\
\hline
\href{https://bmjopen.bmj.com/content/12/4/e055381.abstract}{\textcolor{blue}{Pakistan}} & 2020-10-21 & 2020-11-08 & & & 4998 & 0.0702 & National & Moderate \\
\hline
\href{https://wwwnc.cdc.gov/eid/article/27/11/21-0636\_article}{\textcolor{blue}{Portugal}} & 2020-09-08 & 2020-10-14 & & & 13398 & 0.022 & National & Moderate \\
\hline
\href{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8702669/}{\textcolor{blue}{Senegal}} & 2020-06-15 & 2020-10-15 & & & 3231 & 0.204 & National & High \\
\hline
\href{https://papers.ssrn.com/sol3/papers.cfm?abstract\_id=3826194}{\textcolor{blue}{Singapore}} & 2020-11-15 & 2020-12-15 & 23 & 83 & 937 & 0.0016 & National & High \\
\hline
\href{https://dx.doi.org/10.1016/j.cmi.2021.03.009}{\textcolor{blue}{Slovenia}} & 2020-10-17 & 2020-11-10 & & 99 & 1211 & 0.0429 & National & Low \\
\hline
\href{https://assets.researchsquare.com/files/rs-690372/v2\_covered.pdf?c=1627923426}{\textcolor{blue}{South Africa}} & 2021-01-15 & 2021-05-15 & 15 & 69 & 16762 & 0.474 & National & Moderate \\
\hline
\href{https://bmjopen.bmj.com/content/11/4/e049837.abstract}{\textcolor{blue}{Rep. of Korea}} & 2020-09-24 & 2020-12-09 & 18 & 86 & 4085 & 0.0039 & National & Moderate \\
\hline
\href{https://www.mscbs.gob.es/ciudadanos/ene-covid/docs/ESTUDIO\_ENE-COVID19\_INFORME\_FINAL.pdf}{\textcolor{blue}{Spain}} & 2020-06-08 & 2020-06-22 & & & 62167 & 0.052 & National & Low \\
\hline
\href{https://www.folkhalsomyndigheten.se/contentassets/376f9021a4c84da08de18ac597284f0c/pavisning-antikroppar-genomgangen-covid-19-blodgivare-delrapport-2.pdf}{\textcolor{blue}{Sweden}} & 2020-11-23 & 2020-12-04 & & & 3183 & 0.07 & National & Moderate \\
\hline
\href{https://dx.doi.org/10.1093/cid/ciab626}{\textcolor{blue}{USA}} & 2020-08-09 & 2020-12-08 & 18 & & 4654 & 0.0471 & National & Low \\
\hline
\href{https://www.gov.uk/government/publications/national-covid-19-surveillance-reports}{\textcolor{blue}{UK}} & 2020-08-24 & 2020-09-18 & 17 & & 8230 & 0.061 & National & Low \\
\hline
\href{https://www.thelancet.com/journals/langlo/article/PIIS2214-109X(21)00053-X/fulltext}{\textcolor{blue}{Zambia}} & 2020-07-04 & 2020-07-27 & & & 2704 & 0.021 & National & Low \\
\hline
\hline
\href{https://dx.doi.org/10.5694/mja2.51542}{\textcolor{blue}{Australia}} & 2020-11-03 & 2021-03-12 & & 19 & 1685 & 0.23\% & National & High \\
\hline
\href{https://dx.doi.org/10.1007/s15010-021-01639-0}{\textcolor{blue}{Austria}} & 2020-06-05 & 2020-12-04 & 18 & 72 & 20228 & 2.5\% & National & High \\
\hline
\href{https://dx.doi.org/10.2807/1560-7917.ES.2022.27.9.2100419}{\textcolor{blue}{Belgium}} & 2020-10-12 & 2020-10-17 & & 101 & 2966 & 4.18\% & National & Low \\
\hline
\href{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8225319/}{\textcolor{blue}{Brazil}} & 2020-05-14 & 2020-06-23 & & & 89362 & 2.3\% & National & Moderate \\
\hline
\href{https://serotracker.com/en/Explore}{\textcolor{blue}{Canada}} & 2021-04-13 & 2021-04-30 & 17 & & 16931 & 26.92\% & National & Moderate \\
\hline
\href{https://dx.doi.org/10.1186/s12879-022-07045-7}{\textcolor{blue}{Chile}} & 2020-09-25 & 2020-11-25 & 7 & 94 & 2493 & 10.4\% & National & Low \\
\hline
\href{https://dx.doi.org/10.1016/j.lana.2022.100195}{\textcolor{blue}{Colombia}} & 2020-09-21 & 2020-12-11 & 5 & 80 & 17863 & 32.53\% & National & Moderate \\
\hline
\href{https://dx.doi.org/10.3390/pathogens10060774}{\textcolor{blue}{Croatia}} & 2020-12-15 & 2021-02-15 & & & 1436 & 25.1\% & National & High \\
\hline
\href{https://doi.org/10.1038/s43856-022-00080-0}{\textcolor{blue}{Czechia}} & 2021-02-01 & 2021-03-31 & 18 & & 19548 & 51.0\% & National & High \\
\hline
\href{https://dx.doi.org/10.1007/s10654-021-00796-8}{\textcolor{blue}{Denmark}} & 2020-12-01 & 2020-12-31 & 12 & & 4044 & 4.3\% & National & Low \\
\hline
\href{https://dx.doi.org/10.3389/fmed.2022.933260}{\textcolor{blue}{Ecuador}} & 2020-10-12 & 2020-10-19 & & & 1250 & 11.68\% & National & Moderate \\
\hline
\href{https://dx.doi.org/10.1186/s41182-022-00448-x}{\textcolor{blue}{Egypt}} & 2021-01-15 & 2021-06-15 & & & 2360 & 46.3\% & National & Moderate \\
\hline
\href{https://dx.doi.org/10.1038/s41467-021-23233-6}{\textcolor{blue}{France}} & 2020-05-11 & 2020-05-17 & & & 3592 & 4.93\% & National & Low \\
\hline
\href{https://www.ifo.de/en/publikationen/2020/monograph-authorship/die-deutschen-und-corona}{\textcolor{blue}{Germany}} & 2020-10-26 & 2020-11-18 & 18 & & 9929 & 1.1\% & National & Moderate \\
\hline
\href{https://revistas.ucr.ac.cr/index.php/psm/article/view/43261/46175}{\textcolor{blue}{Honduras}} & 2020-06-16 & 2020-06-23 & 5 & & 792 & 6.2\% & National & Moderate \\
\hline
\href{https://dx.doi.org/10.1007/s11357-020-00226-9}{\textcolor{blue}{Hungary}} & 2020-05-01 & 2020-05-16 & 14 & & 10474 & 0.68\% & National & Low \\
\hline
\href{http://dx.doi.org/10.1016/j.ijid.2021.05.040}{\textcolor{blue}{India}} & 2020-12-18 & 2021-01-06 & 10 & & 28598 & 24.1\% & National & Low \\
\hline
\href{https://dx.doi.org/10.1186/s12889-022-13464-7}{\textcolor{blue}{Iran}} & 2021-01-15 & 2021-03-15 & 10 & 90 & 7411 & 34.2\% & National & Low \\
\hline
\href{https://dx.doi.org/10.1007/s10654-021-00749-1}{\textcolor{blue}{Israel}} & 2020-06-28 & 2020-09-14 & & & 54357 & 4.6\% & National & Moderate \\
\hline
\href{https://www.istat.it/it/files//2020/08/ReportPrimiRisultatiIndagineSiero.pdf}{\textcolor{blue}{Italy}} & 2020-05-25 & 2020-07-15 & & & 64660 & 2.5\% & National & Moderate \\
\hline
\href{https://dx.doi.org/10.3201/eid2702.204088}{\textcolor{blue}{Japan}} & 2020-06-01 & 2020-06-07 & 20 & & 7950 & 0.1\% & National & Moderate \\
\hline
\href{http://dx.doi.org/10.1016/j.onehlt.2021.100292}{\textcolor{blue}{Jordan}} & 2020-12-27 & 2021-01-06 & & & 5044 & 34.2\% & National & Moderate \\
\hline
\href{https://dx.doi.org/10.3390/ijerph19042263}{\textcolor{blue}{Kazakhstan}} & 2020-07-16 & 2021-07-07 & & & 85346 & 63.0\% & National & High \\
\hline
\href{https://dx.doi.org/10.1001/jama.2021.15265}{\textcolor{blue}{Kenya}} & 2021-01-03 & 2021-03-15 & 16 & 64 & 3018 & 48.5\% & National & Moderate \\
\hline
\href{https://dx.doi.org/10.1186/s12879-022-07031-z}{\textcolor{blue}{Lebanon}} & 2020-12-07 & 2021-01-15 & & & 2058 & 18.5\% & National & Low \\
\hline
\href{https://www.journals.vu.lt/AML/article/view/22344}{\textcolor{blue}{Lithuania}} & 2020-08-10 & 2020-09-10 & 18 & 92 & 3089 & 1.4\% & National & Moderate \\
\hline
\href{https://dx.doi.org/10.3201/eid2813.212348}{\textcolor{blue}{Malawi}} & 2020-10-14 & 2020-12-08 & & & 4261 & 7.8\% & National & Low \\
\hline
\href{https://saludpublica.mx/index.php/spm/article/view/12847}{\textcolor{blue}{Mexico}} & 2020-08-15 & 2020-11-15 & 3 & 12 & 944 & 18.7\% & National & Low \\
\hline
\href{https://mohp.gov.np/attachments/article/708/First%20Sero-prevalence\_final\_report\_04-04-2021.pdf}{\textcolor{blue}{Nepal}} & 2020-10-09 & 2020-10-22 & & & 3040 & 14.4\% & National & Low \\
\hline
\href{https://dx.doi.org/10.1111/irv.12932}{\textcolor{blue}{Norway}} & 2020-12-27 & 2021-02-13 & & & 1912 & 3.2\% & National & Moderate \\
\hline
\href{https://dx.doi.org/10.1016/j.ijid.2021.09.062}{\textcolor{blue}{Oman}} & 2020-11-08 & 2020-11-19 & 5 & & 4064 & 22.0\% & National & Moderate \\
\hline
\href{https://bmjopen.bmj.com/content/12/4/e055381.abstract}{\textcolor{blue}{Pakistan}} & 2020-10-21 & 2020-11-08 & & & 4998 & 7.02\% & National & Moderate \\
\hline
\href{https://wwwnc.cdc.gov/eid/article/27/11/21-0636\_article}{\textcolor{blue}{Portugal}} & 2020-09-08 & 2020-10-14 & & & 13398 & 2.2\% & National & Moderate \\
\hline
\href{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8702669/}{\textcolor{blue}{Senegal}} & 2020-06-15 & 2020-10-15 & & & 3231 & 20.4\% & National & High \\
\hline
\href{https://papers.ssrn.com/sol3/papers.cfm?abstract\_id=3826194}{\textcolor{blue}{Singapore}} & 2020-11-15 & 2020-12-15 & 23 & 83 & 937 & 0.16\% & National & High \\
\hline
\href{https://dx.doi.org/10.1016/j.cmi.2021.03.009}{\textcolor{blue}{Slovenia}} & 2020-10-17 & 2020-11-10 & & 99 & 1211 & 4.29\% & National & Low \\
\hline
\href{https://assets.researchsquare.com/files/rs-690372/v2\_covered.pdf?c=1627923426}{\textcolor{blue}{South Africa}} & 2021-01-15 & 2021-05-15 & 15 & 69 & 16762 & 47.4\% & National & Moderate \\
\hline
\href{https://bmjopen.bmj.com/content/11/4/e049837.abstract}{\textcolor{blue}{Rep. of Korea}} & 2020-09-24 & 2020-12-09 & 18 & 86 & 4085 & 0.39\% & National & Moderate \\
\hline
\href{https://www.mscbs.gob.es/ciudadanos/ene-covid/docs/ESTUDIO\_ENE-COVID19\_INFORME\_FINAL.pdf}{\textcolor{blue}{Spain}} & 2020-06-08 & 2020-06-22 & & & 62167 & 5.2\% & National & Low \\
\hline
\href{https://www.folkhalsomyndigheten.se/contentassets/376f9021a4c84da08de18ac597284f0c/pavisning-antikroppar-genomgangen-covid-19-blodgivare-delrapport-2.pdf}{\textcolor{blue}{Sweden}} & 2020-11-23 & 2020-12-04 & & & 3183 & 7.0\% & National & Moderate \\
\hline
\href{https://dx.doi.org/10.1093/cid/ciab626}{\textcolor{blue}{USA}} & 2020-08-09 & 2020-12-08 & 18 & & 4654 & 4.71\% & National & Low \\
\hline
\href{https://www.gov.uk/government/publications/national-covid-19-surveillance-reports}{\textcolor{blue}{UK}} & 2020-08-24 & 2020-09-18 & 17 & & 8230 & 6.1\% & National & Low \\
\hline
\href{https://www.thelancet.com/journals/langlo/article/PIIS2214-109X(21)00053-X/fulltext}{\textcolor{blue}{Zambia}} & 2020-07-04 & 2020-07-27 & & & 2704 & 2.1\% & National & Low \\
\hline


\end{tabular}
\end{center}
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Binary file modified docs/tex/user/rragonnet/sm_covid.pdf
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24 changes: 10 additions & 14 deletions notebooks/user/rragonnet/project_specific/School_Closure/country_inclusion.ipynb
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Expand Up @@ -290,6 +290,7 @@
" \"220523_Bangladesh_icddrb\", # actually subnational\n",
" \"221212_USA_RTIInternational_Bangladesh\", # pregnant women\n",
" \"210727_Canada_CBS\", # cannot find reports of this study. Also, no URL in SeroTracker \n",
" \"221011_Nigeria_UniversityofIlorin\", \n",
"]\n",
"redflag_filter = ~sero_data[\"study_name\"].isin(red_flags)"
]
Expand Down Expand Up @@ -347,6 +348,15 @@
"filtered_sero_data_national = filtered_sero_data_national[filtered_sero_data_national[\"low_vaccination\"] == True]"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"filtered_sero_data_national[filtered_sero_data_national['country'] == \"Nigeria\"]"
]
},
{
"cell_type": "code",
"execution_count": null,
Expand Down Expand Up @@ -585,20 +595,6 @@
"with open(included_countries_path, 'w') as outfile:\n",
" yaml.dump(included_dict, outfile, default_flow_style=False)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
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