---
title: "Constrained Predictors"
author: "Jenna Reps"
date: '`r Sys.Date()`'
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{Constrained Predictors}
%\VignetteEncoding{UTF-8}
%\VignetteEngine{knitr::rmarkdown}
---
## Constrained Predictors
### How to use the PhenotypeLibrary R package
Here we provide a set of phenotypes that can be used as predictors in prediction models or best practice research.
These phenotypes can be extracted from the PhenotypeLibrary R package. To install the R package run:
```{r, echo = TRUE, message = FALSE, warning = FALSE, tidy = FALSE, eval=FALSE}
remotes::install_github("ohdsi/PhenotypeLibrary")
```
To extract the cohort definition for Alcoholism with an id of 1165, just run:
```{r echo = TRUE, message = FALSE, warning = FALSE, tidy = FALSE, eval = FALSE}
PhenotypeLibrary::getPlCohortDefinitionSet(1165)
```
in general you can extract all the cohorts by running:
```{r echo = TRUE, message = FALSE, warning = FALSE, tidy = FALSE, eval = FALSE}
phenotypeDefinitions <- PhenotypeLibrary::getPlCohortDefinitionSet(1152:1215)
```
### The full set of predictor phenotypes
| Phenotype Name | Disorder classification | OHDSI Phenotype library ID |
|--------------------------------|--------------------|-------------------|
| Alcoholism | Behavioral | 1165 |
| Smoking | Behavioral | 1166 |
| Anemia | Blood | 1188 |
| Osteoarthritis | Bone | 1184 |
| Osteoporosis | Bone | 1185 |
| Cancer | Cancer | 1215 |
| Atrial fibrillation | Cardiovascular | 1160 |
| Congestive heart failure | Cardiovascular | 1154 |
| Coronary artery disease | Cardiovascular | 1162 |
| Heart valve disorder | Cardiovascular | 1172 |
| Hyperlipidemia | Cardiovascular | 1170 |
| Hypertension | Cardiovascular | 1198 |
| Angina | Cardiovascular | 1159 |
| Skin Ulcer | Debility | 1168 |
| Diabetes type 1 | Endocrine | 1193 |
| Diabetes type 2 | Endocrine | 1194 |
| Hypothyroidism | Endocrine | 1171 |
| Obesity | Endocrine | 1179 |
| Gastroesophageal reflux disease (GERD) | GI | 1178 |
| Gastrointestinal (GI) bleed | GI | 1197 |
| Inflammatory bowel disorder (IBD) | GI/Rheumatology | 1180 |
| Hormonal contraceptives | Gynecologic | 1190 |
| Antibiotics Aminoglycosides | Infection | 1201 |
| Antibiotics Carbapenems | Infection | 1202 |
| Antibiotics Cephalosporins | Infection | 1203 |
| Antibiotics Fluoroquinolones | Infection | 1204 |
| Antibiotics Glycopeptides and lipoglycopeptides | Infection | 1205 |
| Antibiotics Macrolides | Infection | 1206 |
| Antibiotics Monobactams | Infection | 1207 |
| Antibiotics Oxazolidinones | Infection | 1208 |
| Antibiotics Penicillins | Infection | 1209 |
| Antibiotics Polypeptides | Infection | 1210 |
| Antibiotics Rifamycins | Infection | 1211 |
| Antibiotics Sulfonamides | Infection | 1212 |
| Antibiotics Streptogramins | Infection | 1213 |
| Antibiotics Tetracyclines | Infection | 1214 |
| Pneumonia | Infection/Respiratory | 1199 |
| Sepsis | Infection | 1176 |
| Urinary tract infection (UTI) | Infection | 1186 |
| Hepatitis | Liver | 1169 |
| Anxiety | Mood | 1189 |
| Depression (MDD) | Mood | 1161 |
| Psychotic disorder | Mood | 1175 |
| Antiepileptics (pain) | Neurology/Pain | 1183 |
| Seizure | Neurology | 1153 |
| Hemorrhagic stroke | Neurology/Vascular | 1156 |
| Non-hemorrhagic stroke | Neurology/Vascular | 1155 |
| Acetaminophen prescription | Pain/Infection | 1187 |
| Low back pain | Pain | 1173 |
| Neuropathy | Pain/Neurology | 1174 |
| Opioids | Pain | 1182 |
| Acute kidney injury | Kidney | 1163 |
| Chronic kidney disease | Kidney | 1191 |
| Asthma | Respiratory | 1164 |
| Chronic obstructive pulmonary disorder (COPD) | Respiratory | 1192 |
| Dyspnea | Respiratory | 1195 |
| Respiratory failure | Respiratory | 1177 |
| Sleep apnea | Respiratory | 1167 |
| Rheumatoid arthritis | Rheumatology | 1200 |
| Steroids | Rheumatology/Pain/Pulmonary | 1181 |
| Peripheral vascular disease | Vascular | 1157 |
| Aspirin | Vascular | 1158 |
| Deep vein thrombosis (DVT) | Vascular | 1152 |
| Edema | Vascular | 1196 |