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TRIPOD_template.Rmd
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---
title: "[TRIPOD 1] Identify the study as developing and/or validating a multivariable prediction model, the target population, and the outcome to be predicted."
author: 'Author One ^1,✉^, Author Two ^1^'
css: "production.css"
abstract: |
| [TRIPOD 2] Provide a summary of objectives, study design, setting, participants, sample size, predictors, outcome, statistical analysis, results, and conclusions.
documentclass: article
description: 'Manuscript'
clean: false
bibliography: efi_paper.bib
csl: harvard-cite-them-right.csl
output:
bookdown::html_document2:
fig_caption: true
self_contained: true
number_sections: false
keep_md: true
clean: false
bookdown::word_document2:
reference_docx: efi_template.docx
fig_caption: true
self_contained: true
keep_md: true
number_sections: false
---
```{r load_deps, echo=FALSE, message=FALSE, warning=FALSE,results='hide'}
.projpackages <- c('GGally','pander','dplyr','ggplot2','data.table'
,'survival','broom','forcats','table1','english','bookdown');
.deps <- c( 'analysis.R' );
.debug <- 0;
message(paste0('\n\n working dir: ',getwd(),'\n\n'));
cat('\n\nAvailable Files:',list.files(),sep='\n','\n');
.junk<-capture.output(source(file.path('./scripts/global.R'),chdir=TRUE,echo=!1
,local=TRUE));
# Set some formatting options for this document
panderOptions('table.alignment.default','right');
panderOptions('table.alignment.rownames','right');
panderOptions('table.split.table',Inf);
panderOptions('p.wrap','');
panderOptions('p.copula',', and ');
panderOptions('graph.fontfamily','serif');
# theme_get() gives default theme
theme_set(theme_bw(base_family = 'serif',base_size=14) +
theme(strip.background = element_rect(fill=NA,color=NA)
,strip.text = element_text(size=15)));
knitr::opts_chunk$set(echo=.debug>0, warning=.debug>0, message=.debug>0);
# detect current output format
.outfmt <- knitr::opts_knit$get('rmarkdown.pandoc.to');
if(is.null(.outfmt)){
.outfmt <- if(knitr::is_html_output()) 'html' else {
if(knitr::is_latex_output()) 'latex' else {
if(interactive()) 'html' else {
'unknown';
}}}};
message('.outfmt = ',.outfmt);
.currentscript <- current_scriptname('efi_patientsafety.Rmd');
.outcomenames <- c('vi_c_psi','vi_c_hospinfect','vi_c_hosptrauma'
,'vi_c_cardiac');
snip_outcomes <- rname(.outcomenames);
# limit the data to items of interest
# snippets ----
```
# Introduction/Background
[TRIPOD 3.a] Explain the medical context (including whether diagnostic or prognostic) and rationale for developing or validating the multivariable prediction model, including references to existing models.
[TRIPOD 3.b] Specify the objectives, including whether the study describes the development or validation of the model or both.
# Methods
## Source of data
[TRIPOD 4.a] Describe the study design or source of data (e.g., randomized trial, cohort, or registry data), separately for the development and validation data sets, if applicable.
[TRIPOD 4.b] Specify the key study dates, including start of accrual; end of accrual; and, if applicable, end of follow-up.
## Participants
[TRIPOD 5.a] Specify key elements of the study setting (e.g., primary care, secondary care, general population) including number and location of centres.
[TRIPOD 5.b] Describe eligibility criteria for participants.
[TRIPOD 5.c] Give details of treatments received, if relevant.
## Outcome
[TRIPOD 6.a] Clearly define the outcome that is predicted by the prediction model, including how and when assessed.
[TRIPOD 6.b] Report any actions to blind assessment of the outcome to be predicted.
## Predictors
[TRIPOD 7.a] Clearly define all predictors used in developing or validating the multivariable prediction model, including how and when they were measured.
[TRIPOD 7.b] Report any actions to blind assessment of predictors for the outcome and other predictors.
## Sample size
[TRIPOD 8] Explain how the study size was arrived at.
## Missing data
[TRIPOD 9] Describe how missing data were handled (e.g., complete-case analysis, single imputation, multiple imputation) with details of any imputation method.
## Statistical analysis methods
[TRIPOD 10.a, development only] Describe how predictors were handled in the analyses.
[TRIPOD 10.b, development only] Specify type of model, all model-building procedures (including any predictor selection), and method for internal validation.
[TRIPOD 10.c, validation only] For validation, describe how the predictions were calculated.
[TRIPOD 10.d] Specify all measures used to assess model performance and, if relevant, to compare multiple models.
[TRIPOD 10.e, validation only] Describe any model updating (e.g., recalibration) arising from the validation, if done.
## Risk groups
[TRIPOD 11] Provide details on how risk groups were created, if done.
## Development vs. validation
[TRIPOD 12, validation only] For validation, identify any differences from the development data in setting, eligibility criteria, outcome, and predictors.
# Results
## Participants
[TRIPOD 13.a] Describe the flow of participants through the study, including the number of participants with and without the outcome and, if applicable, a summary of the follow-up time. A diagram may be helpful.
[TRIPOD 13.b] Describe the characteristics of the participants (basic demographics, clinical features, available predictors), including the number of participants with missing data for predictors and outcome.
[TRIPOD 13.c, validation only] For validation, show a comparison with the development data of the distribution of important variables (demographics, predictors and outcome).
## Model development
[TRIPOD 14.a, development only] Specify the number of participants and outcome events in each analysis.
[TRIPOD 14.b, development only] If done, report the unadjusted association between each candidate predictor and outcome.
## Model specification
[TRIPOD 15.a, development only] Present the full prediction model to allow predictions for individuals (i.e., all regression coefficients, and model intercept or baseline survival at a given time point).
[TRIPOD 15.b, development only] Explain how to the use the prediction model.
## Model performance
[TRIPOD 16] Report performance measures (with CIs) for the prediction model.
## Model-updating
[TRIPOD 17, validation only] If done, report the results from any model updating (i.e., model specification, model performance).
# Discussion
## Limitations
[TRIPOD 18] Discuss any limitations of the study (such as nonrepresentative sample, few events per predictor, missing data).
## Interpretation
[TRIPOD 19.a, validation only] For validation, discuss the results with reference to performance in the development data, and any other validation data.
[TRIPOD 19.b] Give an overall interpretation of the results, considering objectives, limitations, results from similar studies, and other relevant evidence.
## Implications
[TRIPOD 20] Discuss the potential clinical use of the model and implications for future research.
# Conclusions
## Supplementary information
[TRIPOD 21] Provide information about the availability of supplementary resources, such as study protocol, Web calculator, and data sets.
# Acknowledgments
[TRIPOD 22] Give the source of funding and the role of the funders for the present study.
# References
---
date: '2021-08-08'
---