################
### Metadata ###
################
# DATE LAST MODIFIED:
# 20/04/2023
# 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 <- '1.0.0'
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')
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
source("./0_global.R")
f_load_data(create_db_tables = TRUE,
load_data = TRUE)
[1] 10000
Data Quality Assessment
# 1. Data Quality Assessment (DQA)
if (file.exists("../output/1_DQA.html")) {
file.remove("../output/1_DQA.html")
}tryCatch({
::quarto_render("./1_DQA.QMD", output_file = "1_DQA.html")
quartofile.copy(from = "./1_DQA.html",
to = "../output/1_DQA.html")
file.remove("./1_DQA.html")
error = function(err) {
}, print(paste("MY ERROR: ",err))
::knit_exit()
knitr })
[31m
processing file: 1_DQA.QMD
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[31moutput file: 1_DQA.knit.md
[39m[1mpandoc --output 1_DQA.html[22m
to: html
standalone: true
self-contained: true
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
[1mmetadata[22m
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
[1] TRUE
Validation
# 2. Validation
if (file.exists("../output/2_validation.html")) {
file.remove("../output/2_validation.html")
}
tryCatch({
::quarto_render("./2_validation.QMD",
quartooutput_file = "2_validation.html")
file.copy(from = "./2_validation.html",
to = "../output/2_validation.html")
file.remove("./2_validation.html")
error = function(err) {
}, print(paste("MY ERROR: ",err))
::knit_exit()
quarto })
[31m
processing file: 2_validation.QMD
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[31moutput file: 2_validation.knit.md
[39m[1mpandoc --output 2_validation.html[22m
to: html
standalone: true
self-contained: true
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
[1mmetadata[22m
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
[1] TRUE
Imputation of missing values
# 3. Imputation of missing values
if (file.exists("../output/3_imputation.html")) {
file.remove("../output/3_imputation.html")
}
tryCatch({
::quarto_render("./3_imputation.QMD",
quartooutput_file = "3_imputation.html")
file.copy(from = "./3_imputation.html",
to = "../output/3_imputation.html")
file.remove("./3_imputation.html")
error = function(err) {
}, print(paste("MY ERROR: ",err))
::knit_exit()
knitr })
[31m
processing file: 3_imputation.QMD
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[31moutput file: 3_imputation.knit.md
[39m[1mpandoc --output 3_imputation.html[22m
to: html
standalone: true
self-contained: true
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
[1mmetadata[22m
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
[1] TRUE
Matching
# 4. Matching cases to controls (1:1) and assessing covariate balance after matching
if (file.exists("../output/4_matching.html")) {
file.remove("../output/4_matching.html")
}
tryCatch({
::quarto_render("./4_matching.QMD",
quartooutput_file = "4_matching.html")
file.copy(from = "./4_matching.html",
to = "../output/4_matching.html")
file.remove("./4_matching.html")
error = function(err) {
}, print(paste("MY ERROR: ",err))
::knit_exit()
knitr })
[31m
processing file: 4_matching.QMD
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[31moutput file: 4_matching.knit.md
[39m[31mWarning messages:
[39m[31m1: In .Internal(gc(verbose, reset, full)) :
closing unused connection 8 (<-view-localhost:11244)
2: [39m[31mIn .Internal(gc(verbose, reset, full)) :
closing unused connection 7 (<-view-localhost:11244)
3: In .Internal(gc(verbose, reset, full)) :
closing unused connection 6 (<-view-localhost:11244)
4: In .Internal(gc(verbose, reset, full)) :
closing unused connection 5 (<-view-localhost:11244)
[39m[1mpandoc --output 4_matching.html[22m
to: html
standalone: true
self-contained: true
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
[1mmetadata[22m
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
[1] TRUE
Descriptive analyses
# 5. Descriptive analysis
if (file.exists("../output/5_descriptive.html")) {
file.remove("../output/5_descriptive.html")
}tryCatch({
::quarto_render("./5_descriptives.QMD",
quartooutput_file = "5_descriptive.html")
file.copy(from = "./5_descriptive.html",
to = "../output/5_descriptive.html")
file.remove("./5_descriptive.html")
error = function(err) {
}, print(paste("MY ERROR: ",err))
::knit_exit()
knitr })
[31m
processing file: 5_descriptives.QMD
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[31moutput file: 5_descriptives.knit.md
[39m[1mpandoc --output 5_descriptive.html[22m
to: html
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self-contained: true
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
[1mmetadata[22m
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'
Output created: 5_descriptive.html
[1] TRUE
Survival analysis
# 6. Survival analysis
if (file.exists("../output/6_survival-analysis.html")) {
file.remove("../output/6_survival-analysis.html")
}tryCatch({
::quarto_render("./6_survival-analysis.QMD",
quartooutput_file = "6_survival-analysis.html")
file.copy(from = "./6_survival-analysis.html",
to = "../output/6_survival-analysis.html")
file.remove("./6_survival-analysis.html")
error = function(err) {
}, print(paste("MY ERROR: ",err))
::knit_exit()
knitr })
[31m
processing file: 6_survival-analysis.QMD
[39m
|
| | 0%
|
|.. | 3%
ordinary text without R code
|
|..... | 7%
label: metadata (with options)
List of 4
$ results: chr "hide"
$ message: logi FALSE
$ warning: logi FALSE
$ error : logi FALSE
|
|....... | 10%
ordinary text without R code
|
|.......... | 14%
label: general settings (with options)
List of 4
$ results: chr "hide"
$ message: logi FALSE
$ warning: logi FALSE
$ error : logi FALSE
|
|............ | 17%
ordinary text without R code
|
|.............. | 21%
label: load data (with options)
List of 4
$ results: chr "hide"
$ message: logi FALSE
$ warning: logi FALSE
$ error : logi FALSE
|
|................. | 24%
ordinary text without R code
|
|................... | 28%
label: survival (with options)
List of 4
$ results: chr "hide"
$ message: logi FALSE
$ warning: logi FALSE
$ error : logi FALSE
|
|...................... | 31%
ordinary text without R code
|
|........................ | 34%
label: survival plot (with options)
List of 4
$ results: chr "hide"
$ message: logi FALSE
$ warning: logi FALSE
$ error : logi FALSE
|
|........................... | 38%
ordinary text without R code
|
|............................. | 41%
label: survival plot cumulative events (with options)
List of 4
$ results: chr "hide"
$ message: logi FALSE
$ warning: logi FALSE
$ error : logi FALSE
|
|............................... | 45%
ordinary text without R code
|
|.................................. | 48%
label: x-time survival (with options)
List of 3
$ message: logi FALSE
$ warning: logi FALSE
$ error : logi FALSE
|
|.................................... | 52%
ordinary text without R code
|
|....................................... | 55%
label: median survival time (with options)
List of 3
$ message: logi FALSE
$ warning: logi FALSE
$ error : logi FALSE
|
|......................................... | 59%
ordinary text without R code
|
|........................................... | 62%
label: coxph HR (with options)
List of 4
$ results: chr "hide"
$ message: logi FALSE
$ warning: logi FALSE
$ error : logi FALSE
|
|.............................................. | 66%
ordinary text without R code
|
|................................................ | 69%
label: hazard ratio (with options)
List of 3
$ message: logi FALSE
$ warning: logi FALSE
$ error : logi FALSE
|
|................................................... | 72%
ordinary text without R code
|
|..................................................... | 76%
label: coxph model fit (with options)
List of 3
$ message: logi FALSE
$ warning: logi FALSE
$ error : logi FALSE
|
|........................................................ | 79%
ordinary text without R code
|
|.......................................................... | 83%
label: rmst2 (with options)
List of 3
$ message: logi FALSE
$ warning: logi FALSE
$ error : logi FALSE
|
|............................................................ | 86%
ordinary text without R code
|
|............................................................... | 90%
label: RMST and RMTL (with options)
List of 3
$ message: logi FALSE
$ warning: logi FALSE
$ error : logi FALSE
|
|................................................................. | 93%
ordinary text without R code
|
|.................................................................... | 97%
label: average treatment effect (with options)
List of 3
$ message: logi FALSE
$ warning: logi FALSE
$ error : logi FALSE
|
|......................................................................| 100%
ordinary text without R code
[31moutput file: 6_survival-analysis.knit.md
[39m[1mpandoc --output 6_survival-analysis.html[22m
to: html
standalone: true
self-contained: true
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
[1mmetadata[22m
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
[1] TRUE
if (file.exists(auxilary_database_path)) {
file.remove(auxilary_database_path)
}
[1] TRUE