/Lolli-Test-NRW

Primary LanguageR

Lolli-Test-NRW

SARS-CoV-2 infection dynamics in schools

Input Data

  • "df_list_clean$tbl_pools":
    "poolsId" - unique identifier
    "clientId" - unique identifier for every school
    "datum" - date on which the PCR was performed
    "ergebnis" - PCR result (1 for positive and 2 for negative)

  • "df_list_clean$tbl_singles":
    "singleId" - unique identifier
    "clientId" - unique identifier for every school
    "datum" - date on which the PCR was performed
    "ergebnis" - PCR result (1 for positive and 2 for negative)

  • "inzidenz_nrw":
    downloaded from RKI https://survstat.rki.de/Content/Query/Create.aspx
    rows - districts
    columns - calendar weeks
    entries - 7-day-incidence for 4-10 year olds

  • "SSIperSchool":
    "clientId" - unique identifier for every school
    "Kreisname" - district
    "Sozialindexstufe" - school social deprivation index

  • "poolAufloesung":
    based on script "poolResolution.R"
    "poolId" - unique identifier for pool-PCRs
    "singleId" - unique identifier for corresponding single-PCRs
    "Begruendung" - description if a positive pool-PCR for a positive single-PCR was found

  • "pool_infos":
    based on script "poolResolution.R"
    "poolsId" - unique identifier for pool-PCRs
    "clientId" - unique identifier for every school
    "nPos" - number of positive single-PCRs for the corresponding positive pool-PCR
    "datum" - date on which the pool-PCR was performed

  • "Soll_daten":
    based on script "classSize.R"
    "clientId" - unique identifier for every school
    "avgPoolGroesseVorJuni" - pool size when alternate classes were held
    "avgPoolGroesseAbJuni" - pool size for full-time schooling

  • "districtPerSchool":
    "clientId" - unique identifier for every school
    "district" - district

Output Figures

Figure 4e,f and Extended Figure 8

Class Size

Input Data

  • "df_list_clean$tbl_pools":
    "poolsId" - unique identifier
    "clientId" - unique identifier for every school
    "datum" - date on which the PCR was performed
    "ergebnis" - PCR result (1 for positive and 2 for negative)

  • "df_list_clean$tbl_singles":
    "singleId" - unique identifier
    "clientId" - unique identifier for every school
    "datum" - date on which the PCR was performed
    "ergebnis" - PCR result (1 for positive and 2 for negative)

  • "df_list_clean$sys_clients"
    "clientId" - unique identifier for every school
    "clientName" - school name
    "street" - school address
    "zipcode" - zipcode where the school is located
    "city" - city where the school is located

  • "20210505_Pooltesting_Schulliste_vUpdate_small":
    "Schulen" - school name
    "Addresse der Schule" - school address
    "PLZ" - zipcode where the school is located
    "Stadt" - city where the school is located
    "Klassenname" - class name
    "Klassenstaerke" - class size

Output Data

  • Soll_daten
    poolSollVorJuni : "avgPoolGroesseVorJuni" - pool size when alternate classes were held
    poolSollAbJuni: "avgPoolGroesseAbJuni" - pool size for full-time schooling

Pool resolution

Input Data

  • "df_list_clean$tbl_pools":
    "poolsId" - unique identifier
    "clientId" - unique identifier for every school
    "datum" - date on which the PCR was performed
    "ergebnis" - PCR result (1 for positive and 2 for negative)
    "klasseLabor" - class name

  • "df_list_clean$tbl_singles":
    "singleId" - unique identifier
    "clientId" - unique identifier for every school
    "datum" - date on which the PCR was performed
    "ergebnis" - PCR result (1 for positive and 2 for negative)
    "klasseLabor" - class name

  • "df_list_clean$sys_clients"
    "clientId" - unique identifier for every school
    "clientName" - school name
    "street" - school address
    "zipcode" - zipcode where the school is located
    "city" - city where the school is located
    "description" - another unique identifier for every school

  • "df_list_clean$tbl_stammdaten"
    "clientId" - unique identifier for every school
    "avgClassSize" - average size of the classes in one school

  • "Altersstruktur 20210630_SuS_Schulen mit Primarstufe.xlsx"
    "SCHULNR"- unique identifier for every school
    "Schulform" - type of school
    "SuS insgesamt" - Number of pupils per grade

Output Data

  • "pool_infos"
    "poolsId" - unique identifier for pool-PCRs
    "clientId" - unique identifier for every school
    "nPos" - number of positive single-PCRs for the corresponding positive pool-PCR
    "datum" - date on which the pool-PCR was performed

  • "poolAufloesung"
    "poolId" - unique identifier for pool-PCRs
    "singleId" - unique identifier for corresponding single-PCRs
    "Begruendung" - description if a positive pool-PCR for a positive single-PCR was found

1. System requirements

The code runs on Linux operating systems (Fedora 27) and has not been tested on other versions.

The code was developed on R-version 3.5.4 including following packages:

reshape 0.8.8
ggplot2 3.3.5
ggplus 0.1
readxl 1.3.1
writexl 1.4.0
xlsx 0.6.5

The code requires only a standard computer.

2. Installation Guide

There is no installation process needed and run time is negligible.

3. Demo

Run the script "SARS-CoV-2_infection_dynamics_in_schools.R" in folder "scripts/" that loads the demo data in folder "demo_data". The output is the Figure 4e,f and Extended Figure 8. The run time is negligible.

4. Instructions for use

Scripts are available in folder scripts/.