################
### Metadata ###
################
# DATE LAST MODIFIED:
# 19/09/2023
# METADATA:
if(FALSE) {
<- 'BY-COVID WP5.2 Baseline Use Case: SARS-CoV-2 vaccine effectiveness - analytical pipeline'
title <- list('Marjan Meurisse','Javier González-Galindo','Santiago Royo-Sierra','Francisco Estupiñán-Romero','Nina Van Goethem','Enrique Bernal-Delgado')
authors <- '1.0.2'
version <- 'Marjan Meurisse'
maintainer <- 'Marjan.Meurisse@sciensano.be'
email <- list('csv upload')
input <- list('1_DQA.html','2_validation.html','3_imputation.html','4_matching.html','5_descriptive.html','6_survival-analysis.html','results-survival-analysis-<country>.xlsx')
output
}
################
### Overview ###
################
# This analytical pipeline corresponds to BY-COVID WP5 T5.2 baseline use case on “SARS-CoV-2 Vaccine(s) effectiveness in preventing SARS-CoV-2 infection”
# 0. General settings and loading of data
# -> Script: 0_global.R
# 1. Data Quality Assessment (DQA)
# -> Script: 1_DQA.QMD
# -> Output: 1_DQA.html
# 2. Validation
# -> Script: 2_validation.QMD
# -> Output: 2_validation.html
# 3. Imputation of missing values
# -> Script: 3_imputation.QMD
# -> Output: 3_imputation.html
# 4. Matching cases to controls (1:1) and assessing covariate balance after matching
# -> Script: 4_matching.QMD
# -> Output: 4_matching.html
# 5. Descriptive analysis
# -> Script: 5_descriptives.R
# -> Output: 5_descriptive.html
# 6. Survival analysis
# -> Script: 6_survival-analysis.R
# -> Output: 6_survival-analysis.html
# 0. General settings and loading of data
<- Sys.time()
start_global_time
source("./0_global.R")
# Remove auxiliary database if it already exists
if (file.exists(auxiliary_database_path)) {
file.remove(auxiliary_database_path)
}
# Remove log file if it already exists
if (file.exists(log_file_path)) {
file.remove(log_file_path)
}
[1] TRUE
# Load data
tryCatch({
f_load_data(create_db_tables = TRUE,
load_data = TRUE)
error = function(err) {
}, print(paste("MY ERROR: ",err))
::knit_exit()
knitr })
Data Quality Assessment
# 1. Data Quality Assessment (DQA)
<- Sys.time()
start_DQA_time
# Remove the file (html report) if it already exists
if (file.exists("../output/1_DQA.html")) {
file.remove("../output/1_DQA.html")
}
[1] TRUE
# Render the quarto document
tryCatch({
::quarto_render("./1_DQA.QMD", output_file = "1_DQA.html")
quartoerror = function(err) {
}, print(paste("MY ERROR: ",err))
})
processing file: 1_DQA.QMD
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| output file: 1_DQA.knit.md
|......................................................................| 100%
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Warning message:
In do_once((if (is_R_CMD_check()) stop else warning)("The function xfun::isFALSE() will be deprecated in the future. Please ", :
The function xfun::isFALSE() will be deprecated in the future. Please consider using base::isFALSE(x) or identical(x, FALSE) instead.
pandoc --output 1_DQA.html
to: html
standalone: true
self-contained: true
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
metadata
document-css: false
link-citations: true
date-format: long
lang: en
title: 'BY-COVID - WP5 - Baseline Use Case: SARS-CoV-2 vaccine effectiveness'
subtitle: Data Quality Assessment (DQA)
editor: visual
always_allow_html: 'yes'
title-block-banner: '#27445C'
Output created: 1_DQA.html
# Copy the file (html report) the 'output' folder
# (exit the knit when the file is not successfully created)
if(file.copy(from = "./1_DQA.html",
to = "../output/1_DQA.html") == TRUE) {
file.remove("./1_DQA.html")
else {
} ::knit_exit()
knitr }
[1] TRUE
Validation
# 2. Validation
<- Sys.time()
start_validation_time
# Remove the file (html report) if it already exists
if (file.exists("../output/2_validation.html")) {
file.remove("../output/2_validation.html")
}
[1] TRUE
# Render the quarto document
tryCatch({
::quarto_render("./2_validation.QMD", output_file = "2_validation.html")
quartoerror = function(err) {
}, print(paste("MY ERROR: ",err))
})
processing file: 2_validation.QMD
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output file: 2_validation.knit.md
Warning message:
In do_once((if (is_R_CMD_check()) stop else warning)("The function xfun::isFALSE() will be deprecated in the future. Please ", :
The function xfun::isFALSE() will be deprecated in the future. Please consider using base::isFALSE(x) or identical(x, FALSE) instead.
pandoc --output 2_validation.html
to: html
standalone: true
self-contained: true
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
metadata
document-css: false
link-citations: true
date-format: long
lang: en
title: 'BY-COVID - WP5 - Baseline Use Case: SARS-CoV-2 vaccine effectiveness assessment'
subtitle: Validation
editor: visual
always_allow_html: 'yes'
title-block-banner: '#27445C'
Output created: 2_validation.html
# Copy the file (html report) the 'output' folder
# (exit the knit when the file is not successfully created)
if(file.copy(from = "./2_validation.html",
to = "../output/2_validation.html") == TRUE) {
file.remove("./2_validation.html")
else {
} ::knit_exit()
knitr }
[1] TRUE
Imputation of missing values
# 3. Imputation of missing values
<- Sys.time()
start_imputation_time
# Remove the file (html report) if it already exists
if (file.exists("../output/3_imputation.html")) {
file.remove("../output/3_imputation.html")
}
[1] TRUE
# Render the quarto document
tryCatch({
::quarto_render("./3_imputation.QMD", output_file = "3_imputation.html")
quartoerror = function(err) {
}, print(paste("MY ERROR: ",err))
})
processing file: 3_imputation.QMD
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output file: 3_imputation.knit.md
Warning message:
In do_once((if (is_R_CMD_check()) stop else warning)("The function xfun::isFALSE() will be deprecated in the future. Please ", :
The function xfun::isFALSE() will be deprecated in the future. Please consider using base::isFALSE(x) or identical(x, FALSE) instead.
pandoc --output 3_imputation.html
to: html
standalone: true
self-contained: true
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
metadata
document-css: false
link-citations: true
date-format: long
lang: en
title: 'BY-COVID - WP5 - Baseline Use Case: SARS-CoV-2 vaccine effectiveness assessment'
subtitle: Imputation of missing values
editor: visual
always_allow_html: 'yes'
title-block-banner: '#27445C'
Output created: 3_imputation.html
# Copy the file (html report) the 'output' folder
# (exit the knit when the file is not successfully created)
if(file.copy(from = "./3_imputation.html",
to = "../output/3_imputation.html") == TRUE) {
file.remove("./3_imputation.html")
else {
} ::knit_exit()
knitr }
[1] TRUE
Matching
# 4. Matching cases to controls (1:1) and assessing covariate balance after matching
<- Sys.time()
start_matching_time
# Remove the file (html report) if it already exists
if (file.exists("../output/4_matching.html")) {
file.remove("../output/4_matching.html")
}
[1] TRUE
# Render the quarto document
tryCatch({
::quarto_render("./4_matching.QMD", output_file = "4_matching.html")
quartoerror = function(err) {
}, print(paste("MY ERROR: ",err))
})
processing file: 4_matching.QMD
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output file: 4_matching.knit.md
Warning messages:
1: In do_once((if (is_R_CMD_check()) stop else warning)("The function xfun::isFALSE() will be deprecated in the future. Please ", :
The function xfun::isFALSE() will be deprecated in the future. Please consider using base::isFALSE(x) or identical(x, FALSE) instead.
2: In .Internal(gc(verbose, reset, full)) :
closing unused connection 8 (<-kubernetes.docker.internal:11609)
3: In .Internal(gc(verbose, reset, full)) :
closing unused connection 7 (<-kubernetes.docker.internal:11609)
4: In .Internal(gc(verbose, reset, full)) :
closing unused connection 6 (<-kubernetes.docker.internal:11609)
5: In .Internal(gc(verbose, reset, full)) :
closing unused connection 5 (<-kubernetes.docker.internal:11609)
pandoc --output 4_matching.html
to: html
standalone: true
self-contained: true
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
metadata
document-css: false
link-citations: true
date-format: long
lang: en
title: 'BY-COVID - WP5 - Baseline Use Case: COVID-19 vaccine effectiveness assessment'
subtitle: 'Matching cases to controls (1:1) and assessing covariate balance after matching'
editor: visual
always_allow_html: 'yes'
title-block-banner: '#27445C'
Output created: 4_matching.html
# Copy the file (html report) the 'output' folder
# (exit the knit when the file is not successfully created)
if(file.copy(from = "./4_matching.html",
to = "../output/4_matching.html") == TRUE) {
file.remove("./4_matching.html")
else {
} ::knit_exit()
knitr }
[1] TRUE
Descriptive analyses
# 5. Descriptive analysis
<- Sys.time()
start_descriptive_time
# Remove the file (html report) if it already exists
if (file.exists("../output/5_descriptive.html")) {
file.remove("../output/5_descriptive.html")
}
[1] TRUE
# Render the quarto document
tryCatch({
::quarto_render("./5_descriptives.QMD", output_file = "5_descriptive.html")
quartoerror = function(err) {
}, print(paste("MY ERROR: ",err))
})
processing file: 5_descriptives.QMD
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output file: 5_descriptives.knit.md
Warning message:
In do_once((if (is_R_CMD_check()) stop else warning)("The function xfun::isFALSE() will be deprecated in the future. Please ", :
The function xfun::isFALSE() will be deprecated in the future. Please consider using base::isFALSE(x) or identical(x, FALSE) instead.
pandoc --output 5_descriptive.html
to: html
standalone: true
self-contained: true
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
metadata
document-css: false
link-citations: true
date-format: long
lang: en
title: 'BY-COVID - WP5 - Baseline Use Case: COVID-19 vaccine effectiveness assessment'
subtitle: Descriptive analyses
editor: visual
always_allow_html: 'yes'
title-block-banner: '#27445C'
[33mWARNING: Unable to parse table from raw html block: skipping.
[39m[33mWARNING: Unable to parse table from raw html block: skipping.
[39mOutput created: 5_descriptive.html
# Copy the file (html report) the 'output' folder
# (exit the knit when the file is not successfully created)
if(file.copy(from = "./5_descriptive.html",
to = "../output/5_descriptive.html") == TRUE) {
file.remove("./5_descriptive.html")
else {
} ::knit_exit()
knitr }
[1] TRUE
Survival analysis
# 6. Survival analysis
<- Sys.time()
start_survival_time
# Remove the file (html report) if it already exists
if (file.exists("../output/6_survival-analysis.html")) {
file.remove("../output/6_survival-analysis.html")
}
[1] TRUE
# Render the quarto document
tryCatch({
::quarto_render("./6_survival-analysis.QMD", output_file = "6_survival-analysis.html")
quartoerror = function(err) {
}, print(paste("MY ERROR: ",err))
})
processing file: 6_survival-analysis.QMD
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|
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|
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|
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|
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|
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|
|...................................................... | 77%
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|
|....................................................... | 79%
ordinary text without R code
|
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label: cumulative incidence by residence area 2 (with options)
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|
|......................................................... | 82%
ordinary text without R code
|
|.......................................................... | 83%
label: coxph HR by residence area (with options)
List of 4
$ results: chr "hide"
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|
|........................................................... | 84%
ordinary text without R code
|
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label: hazard ratio by residence area (with options)
List of 3
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|
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ordinary text without R code
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|.............................................................. | 88%
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|
|............................................................... | 90%
ordinary text without R code
|
|................................................................ | 91%
label: rmst2 by residence area (with options)
List of 3
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|
|................................................................. | 92%
ordinary text without R code
|
|................................................................. | 94%
label: RMST and RMTL by residence area (with options)
List of 3
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$ warning: logi FALSE
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|
|.................................................................. | 95%
ordinary text without R code
|
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label: average treatment effect by residence area (with options)
List of 3
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|
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|
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output file: 6_survival-analysis.knit.md
Warning message:
In do_once((if (is_R_CMD_check()) stop else warning)("The function xfun::isFALSE() will be deprecated in the future. Please ", :
The function xfun::isFALSE() will be deprecated in the future. Please consider using base::isFALSE(x) or identical(x, FALSE) instead.
WARNING: Warning: diff of engine output timed out. No source lines will be available.
pandoc --output 6_survival-analysis.html
to: html
standalone: true
self-contained: true
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
metadata
document-css: false
link-citations: true
date-format: long
lang: en
title: 'BY-COVID - WP5 - Baseline Use Case: COVID-19 vaccine effectiveness assessment'
subtitle: Survival analysis
editor: visual
always_allow_html: 'yes'
title-block-banner: '#27445C'
Output created: 6_survival-analysis.html
# Copy the file (html report) the 'output' folder
# (exit the knit when the file is not successfully created)
if(file.copy(from = "./6_survival-analysis.html",
to = "../output/6_survival-analysis.html") == TRUE) {
file.remove("./6_survival-analysis.html")
# Copy the results for meta-analysis (xlsx file)
<- grep(".xlsx", list.files(path="./", full.names = TRUE, recursive = TRUE), value = TRUE)
file_xlsx file.copy(from = file_xlsx,
to = paste0("../output/",sub('.*./', '', file_xlsx)))
file.remove(file_xlsx)
# Copy the results for meta-analysis (rds file)
<- grep(".rds", list.files(path="./", full.names = TRUE, recursive = TRUE), value = TRUE)
file_rds file.copy(from = file_rds,
to = paste0("../output/",sub('.*./', '', file_rds)))
file.remove(file_rds)
else {
} ::knit_exit()
knitr }
logical(0)
# Assess the runtime
info(logger,
paste0("
========================================================================================
",
"Runtime","
",
"========================================================================================
"))
<- Sys.time()
end_time
info(logger_simple, paste0("Overall runtime: ", round(difftime(end_time,start_global_time)[[1]],2), " ", units(difftime(end_time,start_global_time))))
info(logger_simple, paste0("Runtime 0_global.R: ", round(difftime(start_DQA_time,start_global_time)[[1]],2), " ", units(difftime(start_DQA_time,start_global_time))))
info(logger_simple, paste0("Runtime 1_DQA.QMD: ", round(difftime(start_validation_time,start_DQA_time)[[1]],2), " ", units(difftime(start_validation_time,start_DQA_time))))
info(logger_simple, paste0("Runtime 2_validation.QMD: ", round(difftime(start_imputation_time,start_validation_time)[[1]],2), " ", units(difftime(start_imputation_time,start_validation_time))))
info(logger_simple, paste0("Runtime 3_imputation.QMD: ", round(difftime(start_matching_time,start_imputation_time)[[1]],2), " ", units(difftime(start_matching_time,start_imputation_time))))
info(logger_simple, paste0("Runtime 4_matching.QMD: ", round(difftime(start_descriptive_time,start_matching_time)[[1]],2), " ", units(difftime(start_descriptive_time,start_matching_time))))
info(logger_simple, paste0("Runtime 5_descriptives.QMD: ", round(difftime(start_survival_time,start_descriptive_time)[[1]],2), " ", units(difftime(start_survival_time,start_descriptive_time))))
info(logger_simple, paste0("Runtime 6_survival-analysis.QMD: ", round(difftime(end_time,start_survival_time)[[1]],2), " ", units(difftime(end_time,start_survival_time))))