From 5a08d8a52328fb7838e2d1ccdd1ade80f1a560b6 Mon Sep 17 00:00:00 2001 From: jreps Date: Thu, 7 Sep 2023 18:12:56 -0400 Subject: [PATCH] adding pages to website - adding benchmark tasks and constrained predictors to website --- _pkgdown.yml | 8 + vignettes/BenchmarkTasks.Rmd | 306 ++++++++++++++++++++++++++++ vignettes/BestPractices.rmd | 18 +- vignettes/ConstrainedPredictors.Rmd | 86 ++++++++ 4 files changed, 415 insertions(+), 3 deletions(-) create mode 100644 vignettes/BenchmarkTasks.Rmd create mode 100644 vignettes/ConstrainedPredictors.Rmd diff --git a/_pkgdown.yml b/_pkgdown.yml index 2ad97fef6..d3f9ef550 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -20,6 +20,8 @@ navbar: - reference - articles - tutorial + - benchmarks + - predictors - bestpractice - news right: [hades, github] @@ -39,6 +41,12 @@ navbar: bestpractice: text: Best Practices href: articles/BestPractices.html + benchmarks: + text: Benchmarks + href: articles/BenchmarkTasks.html + predictors: + text: Predictors + href: articles/ConstrainedPredictors.html news: text: Changelog href: news/index.html diff --git a/vignettes/BenchmarkTasks.Rmd b/vignettes/BenchmarkTasks.Rmd new file mode 100644 index 000000000..13eb511ab --- /dev/null +++ b/vignettes/BenchmarkTasks.Rmd @@ -0,0 +1,306 @@ +--- +title: "Benchmark Tasks" +author: "Jenna Reps, Ross Williams, Peter R. Rijnbeek" +date: '`r Sys.Date()`' +header-includes: + - \usepackage{fancyhdr} + - \pagestyle{fancy} + - \fancyhead{} + - \fancyhead[CO,CE]{Installation Guide} + - \fancyfoot[CO,CE]{PatientLevelPrediction Package Version `r utils::packageVersion("PatientLevelPrediction")`} + - \fancyfoot[LE,RO]{\thepage} + - \renewcommand{\headrulewidth}{0.4pt} + - \renewcommand{\footrulewidth}{0.4pt} +output: + pdf_document: + includes: + in_header: preamble.tex + number_sections: yes + toc: yes + word_document: + toc: yes + html_document: + number_sections: yes + toc: yes +--- + + +## Benchmark Tasks For Large-Scale Empirical Analyses + +Here we provide a set of diverse prediction tasks that can be used when evaluating the impact of the model design choice when developing models using observational data. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Target Cohort (index) + +Outcome + +Time-at-risk + +Link +
+Patients with an outpatient visit in 2017 with no prior cancer (first visit in 2017) + +Lung cancer + +1 day - 3 years after index + +
+Patients newly diagnosed with major depressive disorder (date of first record) + +Bipolar + +1 day - 365 day after index + +
+Patients with an outpatient visit in 2019 + +Dementia + +1 day - 3 years after index + +
+Patients with an outpatient visit and a positive COVID test + +Hospitalization with pneumonia + +1 day - 30 days after index + +
+Patients with an outpatient visit and a positive COVID test + +Hospitalization with pneumonia that required intensive services (ventilation, intubation, tracheotomy, or extracorporeal membrane oxygenation) or death + +1 day - 30 days after index + +
+Patients with an outpatient visit and a positive COVID test + +Death + +1 day - 30 days after index + +
+Patients with T2DM who were treated with metformin and who became new adult users of one of sulfonylureas, thiazolidinediones, dipeptidyl peptidase-4 inhibitors, glucagon-like peptide-1 receptor agonists, or sodium-glucose co-transporter-2 inhibitors (date of secondary drug). Patients with HF or patients treated with insulin on or prior to the index date were excluded from the analysis. Patients were required to have been enrolled for at least 365 days before cohort entry. + +Heart Failure + +1 to 365 days + +
+Patients newly diagnosed with atrial fibrilation (date of initial afib record) + +Ischemic stroke + +1 to 365 days + +
+Patients undergoing elective major non-cardiac surgery (date of surgery). Patients were required to have been enrolled for at least 365 days before cohort entry. + +Earliest of AMI cardiac arrest or death (MACE) + +O to 30 days + +
+Patients starting intravitreal Anti-VEGF (date of administration) + +Kidney Failure + +1 to 365 days + +
+Pregnancy women (start of pregnancy) + +Preeclampsia + +During pregnancy + +
+Pregnancy women (start of pregnancy) + +Still birth + +During pregnancy + +
+Patients with COPD (first record) + +Cardiovascular event and death + +1-30 days and 1-90 days + +
+Patients starting menopause (first record) + +Depression + +1 day - 3-years + +
+Patients with anemia (date of first anemia record) + +Colorectal cancer + +1 day - 1-year + +
+Patients with quadriplegia (date of first quadriplegia record) + +Death + +1 day - 1-year + +
+Patient undergoing + + + + + +
+ + + + + + +
+ \ No newline at end of file diff --git a/vignettes/BestPractices.rmd b/vignettes/BestPractices.rmd index 9c27f3f7c..b59ba6c5e 100644 --- a/vignettes/BestPractices.rmd +++ b/vignettes/BestPractices.rmd @@ -101,7 +101,7 @@ Data Creation Impact of over/under-sampling -Study being developed +Paper under review @@ -125,7 +125,7 @@ Model development How much data do we need for prediction - Learning curves at scale -Preprint link +International Journal of Medical Informatics @@ -165,6 +165,18 @@ Study needs to be done + + +Model development + + +Can we use ensembles to combine different algorithm models within a database to improve models transportability? + + +Study Complete + + + Model development @@ -173,7 +185,7 @@ Model development Can we use ensembles to combine models developed using different databases to improve models transportability? - Paper under review at BMC + BMC Medical Informatics and Decision Making diff --git a/vignettes/ConstrainedPredictors.Rmd b/vignettes/ConstrainedPredictors.Rmd new file mode 100644 index 000000000..506830952 --- /dev/null +++ b/vignettes/ConstrainedPredictors.Rmd @@ -0,0 +1,86 @@ +--- +title: "Constrained predictors" +author: "Jenna Reps" +date: '`r Sys.Date()`' +header-includes: + - \usepackage{fancyhdr} + - \pagestyle{fancy} + - \fancyhead{} + - \fancyhead[CO,CE]{Installation Guide} + - \fancyfoot[CO,CE]{PatientLevelPrediction Package Version `r utils::packageVersion("PatientLevelPrediction")`} + - \fancyfoot[LE,RO]{\thepage} + - \renewcommand{\headrulewidth}{0.4pt} + - \renewcommand{\footrulewidth}{0.4pt} +output: + pdf_document: + includes: + in_header: preamble.tex + number_sections: yes + toc: yes + word_document: + toc: yes + html_document: + number_sections: yes + toc: yes +--- + + +## Constrained Predictors + +Here we provide a set of phenotypes that can be used as predictors in prediction models or best practice research. + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Phenotype Name + +Category + +ATLAS link +
+Acetaminophen prescirption + +Medication + +ATLAS link +
+Alcoholism + +Lifestyle + +ATLAS link +
+Anemia + + + +ATLAS link +
+ \ No newline at end of file