Package: EpiReport 1.0.1

Lore Merdrignac

EpiReport: Epidemiological Report

Drafting an epidemiological report in 'Microsoft Word' format for a given disease, similar to the Annual Epidemiological Reports published by the European Centre for Disease Prevention and Control. Through standalone functions, it is specifically designed to generate each disease specific output presented in these reports and includes: - Table with the distribution of cases by Member State over the last five years; - Seasonality plot with the distribution of cases at the European Union / European Economic Area level, by month, over the past five years; - Trend plot with the trend and number of cases at the European Union / European Economic Area level, by month, over the past five years; - Age and gender bar graph with the distribution of cases at the European Union / European Economic Area level. Two types of datasets can be used: - The default dataset of dengue 2015-2019 data; - Any dataset specified as described in the vignette.

Authors:Lore Merdrignac [aut, ctr, cre], Tommi Karki [aut, fnd], Esther Kissling [aut, ctr], Joana Gomes Dias [aut, fnd]

EpiReport_1.0.1.tar.gz
EpiReport_1.0.1.zip(r-4.5)EpiReport_1.0.1.zip(r-4.4)EpiReport_1.0.1.zip(r-4.3)
EpiReport_1.0.1.tgz(r-4.4-any)EpiReport_1.0.1.tgz(r-4.3-any)
EpiReport_1.0.1.tar.gz(r-4.5-noble)EpiReport_1.0.1.tar.gz(r-4.4-noble)
EpiReport_1.0.1.tgz(r-4.4-emscripten)EpiReport_1.0.1.tgz(r-4.3-emscripten)
EpiReport.pdf |EpiReport.html
EpiReport/json (API)
NEWS

# Install 'EpiReport' in R:
install.packages('EpiReport', repos = c('https://epiverse-connect.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/eu-ecdc/epireport/issues

Datasets:
  • AERparams - Dataset describing the parameters for the epidemiological report production
  • DENGUE2019 - Dataset including Dengue data for 2015-2019
  • MSCode - Dataset correspondence table between country names and country code
  • SALM2016 - Dataset including Salmonellosis data for 2012-2016

On CRAN:

4.80 score 10 stars 14 scripts 269 downloads 3 mentions 28 exports 76 dependencies

Last updated 4 years agofrom:05d2249ce1. Checks:OK: 3 NOTE: 4. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 09 2024
R-4.5-winNOTENov 09 2024
R-4.5-linuxNOTENov 09 2024
R-4.4-winNOTENov 09 2024
R-4.4-macNOTENov 09 2024
R-4.3-winOKNov 09 2024
R-4.3-macOKNov 09 2024

Exports:body_replace_gg_at_bkmcleanECDCTablecleanMeasureCodeEcdcColorsfilterDiseasegetAERgetAgeGendergetMapgetSeasongetTableByMSgetTemplategetTrendincludeMaporderQuasinumplotAgeplotAgeGenderplotBarplotBarGroupedplotBarGroupedHplotBarHplotPieplotSeasonalityplotTSplotTS12MAvgplotTSGroupedpreviewMapshapeECDCFlexTabletoCapTitle

Dependencies:askpassbase64encbslibcachemclicolorspacecpp11data.tabledigestdplyrevaluatefansifarverfastmapflextablefontawesomefontBitstreamVerafontLiberationfontquiverfsgdtoolsgenericsggplot2gluegtablehighrhtmltoolsisobandjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeofficeropensslpillarpkgconfigpngpurrrR6raggrappdirsRColorBrewerRcpprlangrmarkdownsassscalesstringistringrsyssystemfontstextshapingtibbletidyrtidyselecttinytexutf8uuidvctrsviridisLitewithrxfunxml2yamlzipzoo

The 'Epidemiological Report' Package

Rendered fromEpiReport_Vignette.Rmdusingknitr::rmarkdownon Nov 09 2024.

Last update: 2021-02-04
Started: 2018-10-19

Readme and manuals

Help Manual

Help pageTopics
Dataset describing the parameters for the epidemiological report productionAERparams
Replace a plot at a bookmark locationbody_replace_gg_at_bkm
Cleaning the final tablecleanECDCTable
Clean the MeasureCode variablecleanMeasureCode
Dataset including Dengue data for 2015-2019DENGUE2019
Colour palettes following the March 2018 ECDC guidelines for presentation of surveillance dataEcdcColors
Filter disease parametersfilterDisease
Get full disease-specific epidemiological reportgetAER
Get disease-specific age and gender bar graphgetAgeGender
Get disease-specific map: distribution of cases by Member StategetMap
Get disease-specific seasonality graph: distribution of cases by monthgetSeason
Get disease-specific table: distribution of cases by Member State (GeoCode)getTableByMS
Get epidemiological report (empty) templategetTemplate
Get disease-specific trend plot: trend and number of cases by monthgetTrend
Including PNG map in the 'Microsoft Word' templateincludeMap
Dataset correspondence table between country names and country codeMSCode
Order 'quasinumerical' categorical vectors (increasing order)orderQuasinum
Age bar graphplotAge
Age and Gender bar graphplotAgeGender
Bar graphplotBar
Grouped bar graphplotBarGrouped
Horizontal grouped bar graphplotBarGroupedH
Horizontal bar graphplotBarH
Pie chartplotPie
Seasonality line graphplotSeasonality
Time series plotplotTS
Time series with 12-month moving averageplotTS12MAvg
Multiple time series plotplotTSGrouped
Previewing the PNG mappreviewMap
Dataset including Salmonellosis data for 2012-2016SALM2016
Shaping the final table (layout, title, color, font)shapeECDCFlexTable
Capitalise first lettertoCapTitle