In nextpagesoft/hivEstimatesAccuracyReloaded: Improves Accuracy of HIV Estimates in EU/EEA Countries

IsEmptyString <- hivEstimatesAccuracyReloaded::IsEmptyString

knitr::opts_chunk$set(echo = FALSE, 
                      cache = FALSE,
                      results = "asis", 
                      message = FALSE, 
                      warning = FALSE, 
                      include = TRUE, 
                      fig.height = 4,
                      fig.width = 10)

---

Introduction

cat("Input data:", 
    "\n\n")
cat(sprintf("* File name: %s", params$Artifacts$FileName),
    "\n")
cat(sprintf("* %s", 
            ifelse(params$Artifacts$DiagYearRangeApply, 
                   sprintf("Filter on diagnosis year applied: [%s]", paste(params$Artifacts$DiagYearRange, collapse = ", ")),
                   "No filter on diagnosis year applied.")),
    "\n")


cat("\n", 
    "Adjustments:", 
    "\n\n")
for (adjustment in params$Artifacts$Adjustments) {
  cat(sprintf("* %s", adjustment$Name), "\n")
  for (parameter in adjustment$Parameters) {
    cat(sprintf("  * %s: %s", parameter$Label, as.character(parameter$Value)), "\n")
  }
}

cat("\n", "Report options:", "\n\n") 
cat(sprintf("* %s", 
            ifelse(params$ReportingDelay, 
                   "Correction of count of cases for reporting delay.",
                   "Original count of case.")),
    "\n")
cat(sprintf("* %s", 
            ifelse(params$Smoothing, 
                   "Smoothed version of calendar time.",
                   "Original calendar time.")),
    "\n")
cat(sprintf("* %s", 
            ifelse(params$CD4ConfInt, 
                   "CD4 plots with inter-quartile range.",
                   "CD4 plots without inter-quartile range.")),
    "\n")

if (!params$Artifacts$CD4Present) {
  cat("\n", "CD4 count is missing in both the unadjusted and the adjusted data. All CD4 related tables and figures are omitted in this report.", "\n")  
}

---

Comparison of data by Gender

Number of diagnoses per year

Data stratified by gender is shown only for unadjusted data since there were no missing data on gender after pre-processing, which takes place before adjustments.

Before and after adjustments

params$Artifacts$PlotOrigGenderCount
params$Artifacts$TblOrigGenderCount

Median CD4 cell count (cells/µL)

cat("### Before adjustments", "\n")
params$Artifacts$PlotOrigGenderCD4
params$Artifacts$TblOrigGenderCD4

cat("### After adjustments", " \n")
params$Artifacts$PlotMIGenderCD4
params$Artifacts$TblMIGenderCD4
if (!IsEmptyString(params$Artifacts$DataMIGenderCD4Message)) {
  cat(params$Artifacts$DataMIGenderCD4Message, "\n")
}

cat("CD4 cell count after adjustments is not available since no imputation adjustements have been run.", "\n")

cat("CD4 cell count results are not available due to full missingness of this attribute in the input data.", "\n")

---

Comparison of data by Transmission

Number of diagnoses per year

Before adjustments

params$Artifacts$PlotOrigTransCount
params$Artifacts$TblOrigTransCount

cat("### After adjustments", "\n")
params$Artifacts$PlotMITransCount
params$Artifacts$TblMITransCount
if (!IsEmptyString(params$Artifacts$dataMITransCountMessage)) {
  cat(params$Artifacts$dataMITransCountMessage, "\n")
}

Median CD4 cell count (cells/µL)

cat("### Before adjustments", "\n")
params$Artifacts$PlotOrigTransCD4
params$Artifacts$TblOrigTransCD4

cat("### After adjustments", "\n")
params$Artifacts$PlotMITransCD4
params$Artifacts$TblMITransCD4
if (!IsEmptyString(params$Artifacts$DataMITransCD4Message)) {
  cat(params$Artifacts$DataMITransCD4Message, "\n")
}

cat("CD4 cell count after adjustments is not available since no imputation adjustements have been run.", "\n")

cat("CD4 cell count results are not available due to full missingness of this attribute in the input data.", "\n")

---

Comparison of data by Migration

Number of diagnoses per year

Before adjustments

params$Artifacts$PlotOrigMigrCount
params$Artifacts$TblOrigMigrCount

cat("### After adjustments", "\n")
params$Artifacts$PlotMIMigrCount
params$Artifacts$TblMIMigrCount
if (!IsEmptyString(params$Artifacts$DataMIMigrCountMessage)) {
  cat(params$Artifacts$DataMIMigrCountMessage, "\n")
}

Median CD4 cell count (cells/µL)

cat("### Before adjustments", "\n")
params$Artifacts$PlotOrigMigrCD4
params$Artifacts$TblOrigMigrCD4

cat("### After adjustments", "\n")
params$Artifacts$PlotMIMigrCD4
params$Artifacts$TblMIMigrCD4
if (!IsEmptyString(params$Artifacts$DataMIMigrCD4Message)) {
  cat(params$Artifacts$DataMIMigrCD4Message, "\n")
}

cat("CD4 cell count after adjustments is not available since no imputation adjustements have been run.", "\n")

cat("CD4 cell count results are not available due to full missingness of this attribute in the input data.", "\n")

cat("-------------------------------------------------------------------", "\n")
cat("\n")
cat("# Comparison of the reported and estimated number of diagnoses per year", "\n")
params$Artifacts$TblRd

nextpagesoft/hivEstimatesAccuracyReloaded documentation built on March 14, 2020, 7:06 a.m.