In R4IDSR/epichecks: Report templates and helper functions for WHO surveillance data

## set the chunks of code to not show up in output
knitr::opts_chunk$set(echo = FALSE)

## Installing required packages for this template
required_packages <- c("here",       # define pathways to files
                       "rmarkdown",  # for formatting documents
                       "markdown",   # for formatting documents
                       "knitr"       # for cleaner tables
                       )

for (pkg in required_packages) {
  ## install packages if not already present
  if (!pkg %in% rownames(installed.packages())) {
    install.packages(pkg)
  }

  ## load packages to this current session 
  library(pkg, character.only = TRUE)
  }

## load the WHO logo from the package directory
knitr::include_graphics(system.file("extdata", "WHO_logo.png", package = "epichecks"))

\raggedleft

\raggedright

To Whom it May Concern,

Regarding: r i IDSR data for week r current_epiweek

Dear Sir or Madam,

This is to acknowledge receipt of routine surveillance data for your country (r i) for week r current_epiweek and to thank you for your continuous contribution to the global health security in the African region.

In order to continuously improve the effectiveness of disease surveillance in the African region, we would like to draw your attention to missing data and possible surpassed thresholds for verification and action where required.

## subset to current country being looped over
y <- message_list[[i]]

## get counts of messages
num_messages <- nrow(y)

## get counts of diseases
num_messages_disease <- length(unique(y[["disease/maladie"]]))

## get counts of districts
num_messages_district <- length(unique(y$district))

## subset to current country being looped over 
y <- alert_list[[i]]

## get counts of messages
num_alerts <- nrow(y)

## get counts of diseases
num_alerts_disease <- length(unique(y[["disease/maladie"]]))

## get counts of districts
num_alerts_district <- length(unique(y$district))

There were r num_messages issues of missing data, relating to r num_messages_disease different diseases in r num_messages_district different districts. Please verify if the missing data correspond to zero cases or faults in reporting, and amend the report accordingly. Indeed, as per the IDSR strategy, districts that do not have any cases should still be reported as zero (0) and not left blank.

There were r num_alerts alert thresholds triggered, relating to r num_alerts_disease different diseases in r num_alerts_district different districts.

Kindly find in the attached Excel spreadsheet, details of the diseases and districts with missing data or surpassed thresholds that need to be addressed.

Please send your verification report and/or revised IDSR weekly report to: [e-mail].

Sincerely yours,

On behalf of the WHO AFRO

HIR Team

\pagebreak

knitr::include_graphics(system.file("extdata", "WHO_logo.png", package = "epichecks"))

A qui de droit,

Sujet: r i Donées de SIMR relatives à la semaine r current_epiweek

Cher Monsieur ou Madame,

Nouse accusons réception des donées de surveillance de routine de votre pays (r i) de la semaine r current_epiweek et vous remercions de votre inlassable contribution à la sécurité sanitaire mondiale dans la région africaine.

En vue de continuer à améliorer l'efficacité de la surveillance des maladies dans la région africaine, nouse aimerions attire votre attention sur les donées manquantes et les situations ou le seuil d'alerte a été atteint, dans une perspective de vérification et d'action si nécessaire.

Il y a eu r num_messages données manquantes concernant r num_messages_disease maladies différentes et r num_messages_district districts sanitaires différents. En effet, conformément à la stratégie SIMR, les districts qui n'ont pas observé de cas ou décès d'une maladie donée, devrait rapporte zéro (0) et non laisser les cellules vides.

Il y a eu r num_alerts situations ou le seuil d'alerte a été atteint, concernant nottamentr num_alerts_disease maladies différents dans r num_alerts_district districts différents.

Veuillez trouver ci-joint, un fichier Excel comporant des détails sur nos observations sur les donées manquantes et les seuils d'alerte pour votre action.

Veuillez soumettre votre rapport de vérification et/ou le rapport hebdomadaire de SIMR amende à l'addresse suivant: [e-mail].

Bien cordialement.

Pour OMS AFRO
L'équipe HIR

R4IDSR/epichecks documentation built on Sept. 18, 2021, 2:03 p.m.