PatientLevelPrediction6.5.1 package

Calculate the average precision

brierScore

Calculate the calibration in large

calibrationLine

Compute the area under the ROC curve

Computes grid performance with a specified performance function

Sets up a python environment to use for PLP (can be conda or venv)

covariateSummary

Extracts covariates based on cohorts

Create a setting that holds the details about the cdmDatabase connecti...

Create the PatientLevelPrediction database result schema settings

Creates default list of settings specifying what parts of runPlp to ex...

Create the settings for defining how the plpData are split into test/v...

Creates list of settings specifying what parts of runPlp to execute

Create the settings for defining how the plpData are split into test/v...

Create the settings for defining any feature engineering that will be ...

createGlmModel

Create Iterative Imputer settings

createLearningCurve

Create the settings for logging the progression of the analysis

Specify settings for developing a single model

Create the settings for normalizing the data @param type The type of n...

Create the results tables to store PatientLevelPrediction models and r...

Create the settings for preprocessing the trainData.

Create the settings for random foreat based feature selection

Create the settings for removing rare features

createRestrictPlpDataSettings define extra restriction settings when c...

Create the settings for defining how the trainData from splitData ar...

Create Simple Imputer settings

Plug an existing scikit learn python model into the PLP framework

Create the settings for adding a spline for continuous variables

Create the settings for using stratified imputation.

Create a study population

create the study population settings

Create a temporary model location

Create the settings for defining any feature selection that will be do...

createValidationDesign - Define the validation design for external val...

createValidationSettings define optional settings for performing exter...

Run a list of predictions diagnoses

diagnostic - Investigates the prediction problem settings - use before...

evaluatePlp

externalValidateDbPlp - Validate a model on new databases

Exports all the results from a database into csv files

fitPlp

Get a sparse summary of the calibration

Extracts covariates based on cohorts

Get a demographic summary

Create a plpData object from the Eunomia database'

Extract the patient level prediction data from the server

Calculates the prediction distribution

Calculates the prediction distribution

Calculate all measures for sparse ROC

Calculate the Integrated Calibration Index from Austin and Steyerberg ...

Function to insert results into a database from csvs

Create sqlite database with the results

Imputation

join two lists

Cartesian product

Load the multiple prediction json settings from a file

Load the plpData from a folder

loads the plp model

Loads the evalaution dataframe

Loads the plp result saved as json/csv files for transparent sharing

Loads the prediction dataframe to json

Map covariate and row Ids so they start from 1

Migrate Data model

A function that normalizes continous features to have values between 0...

Calculate the model-based concordance, which is a calculation of the e...

Plot the outcome incidence over time

PatientLevelPrediction

Permutation Feature Importance

Plot the Observed vs. expected incidence, by age and gender

Plot the F1 measure efficiency frontier using the sparse thresholdSumm...

Plot the train/test generalizability diagnostic

plotLearningCurve

Plot the net benefit

Plot all the PatientLevelPrediction plots

Plot the precision-recall curve using the sparse thresholdSummary data...

Plot the Predicted probability density function, showing prediction ov...

Plot the side-by-side boxplots of prediction distribution, by class

Plot the preference score probability density function, showing predic...

Plot the smooth calibration as detailed in Calster et al. "A calibrati...

Plot the calibration

Plot the conventional calibration

Plot the ROC curve using the sparse thresholdSummary data frame

Plot the variable importance scatterplot

Predictive mean matching using lasso

Create predictive probabilities

predict using a logistic regression model

predictPlp

A function that wraps around FeatureExtraction::tidyCovariateData to n...

Print a plpData object

Print a summary.plpData object

recalibratePlp

recalibratePlpRefit

A function that removes rare features from the data

A function that normalizes continous by the interquartile range and op...

Run a list of predictions analyses

runPlp - Develop and internally evaluate a model using specified setti...

Save the modelDesignList to a json file

Save the plpData to folder

Saves the plp model

Saves the result from runPlp into the location directory

Save the plp result as json files and csv files for transparent sharin...

Saves the prediction dataframe to a json file

Create setting for AdaBoost with python DecisionTreeClassifier base es...

Create setting for lasso Cox model

Create setting for the scikit-learn DecisionTree with python

Create setting for gradient boosting machine model using gbm_xgboost i...

Create setting for Iterative Hard Thresholding model

Create modelSettings for lasso logistic regression

Create setting for gradient boosting machine model using lightGBM (htt...

Create setting for neural network model with python's scikit-learn. Fo...

Create setting for naive bayes model with python

Use the python environment created using configurePython()

Create setting for random forest model using sklearn

Create setting for the python sklearn SVM (SVC function)

Simple Imputation

Generate simulated data

Loads sklearn python model from json

Saves sklearn python model object to json in path

Split the plpData into test/train sets using a splitting settings of c...

Summarize a plpData object

Convert the plpData in COO format into a sparse R matrix

validateExternal - Validate model performance on new data

externally validate the multiple plp models across new datasets

open a local shiny app for viewing the result of a PLP analyses from a...

open a local shiny app for viewing the result of a multiple PLP analys...

viewPlp - Interactively view the performance and model settings