diff --git a/NAMESPACE b/NAMESPACE index 05c5629..7d3bc60 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -7,13 +7,9 @@ export(fitDeepNNTorch) export(fitEstimator) export(fitTabNetTorch) export(gridCvDeep) -export(predictAndromeda) export(predictDeepEstimator) export(predictDeepNN) -export(predictPlp) -export(predictProbabilities) export(predictTabNetTorch) -export(predict_deepEstimator) export(setCIReNN) export(setCNNTorch) export(setCovNN) diff --git a/man/predictAndromeda.Rd b/man/predictAndromeda.Rd deleted file mode 100644 index 0903869..0000000 --- a/man/predictAndromeda.Rd +++ /dev/null @@ -1,36 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/Predict.R -\name{predictAndromeda} -\alias{predictAndromeda} -\title{Generated predictions from a regression model} -\usage{ -predictAndromeda( - coefficients, - population, - covariateData, - modelType = "logistic" -) -} -\arguments{ -\item{coefficients}{A names numeric vector where the names are the covariateIds, except for the -first value which is expected to be the intercept.} - -\item{population}{A data frame containing the population to do the prediction for} - -\item{covariateData}{An andromeda object containing the covariateData with predefined columns -(see below).} - -\item{modelType}{Current supported types are "logistic", "poisson", "cox" or "survival".} -} -\description{ -Generated predictions from a regression model -} -\details{ -These columns are expected in the outcome object: \tabular{lll}{ \verb{rowId} \tab(integer) \tab -Row ID is used to link multiple covariates (x) to a single outcome (y) \cr \verb{time} \tab(real) -\tab For models that use time (e.g. Poisson or Cox regression) this contains time \cr \tab -\tab(e.g. number of days) \cr } These columns are expected in the covariates object: \tabular{lll}{ -\verb{rowId} \tab(integer) \tab Row ID is used to link multiple covariates (x) to a single outcome -(y) \cr \verb{covariateId} \tab(integer) \tab A numeric identifier of a covariate \cr -\verb{covariateValue} \tab(real) \tab The value of the specified covariate \cr } -} diff --git a/man/predictPlp.Rd b/man/predictPlp.Rd deleted file mode 100644 index f1718a2..0000000 --- a/man/predictPlp.Rd +++ /dev/null @@ -1,27 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/Predict.R -\name{predictPlp} -\alias{predictPlp} -\title{predictPlp} -\usage{ -predictPlp(plpModel, population, plpData, index = NULL) -} -\arguments{ -\item{plpModel}{An object of type \code{plpModel} - a patient level prediction model} - -\item{population}{The population created using createStudyPopulation() who will have their risks predicted} - -\item{plpData}{An object of type \code{plpData} - the patient level prediction -data extracted from the CDM.} - -\item{index}{A data frame containing rowId: a vector of rowids and index: a vector of doubles the same length as the rowIds. If used, only the rowIds with a negative index value are used to calculate the prediction.} -} -\value{ -A dataframe containing the prediction for each person in the population with an attribute metaData containing prediction details. -} -\description{ -Predict the risk of the outcome using the input plpModel for the input plpData -} -\details{ -The function applied the trained model on the plpData to make predictions -} diff --git a/man/predictProbabilities.Rd b/man/predictProbabilities.Rd deleted file mode 100644 index affba63..0000000 --- a/man/predictProbabilities.Rd +++ /dev/null @@ -1,26 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/Predict.R -\name{predictProbabilities} -\alias{predictProbabilities} -\title{Create predictive probabilities} -\usage{ -predictProbabilities(predictiveModel, population, covariateData) -} -\arguments{ -\item{predictiveModel}{An object of type \code{predictiveModel} as generated using -\code{\link{fitPlp}}.} - -\item{population}{The population to calculate the prediction for} - -\item{covariateData}{The covariateData containing the covariates for the population} -} -\value{ -The value column in the result data.frame is: logistic: probabilities of the outcome, poisson: -Poisson rate (per day) of the outome, survival: hazard rate (per day) of the outcome. -} -\description{ -Create predictive probabilities -} -\details{ -Generates predictions for the population specified in plpData given the model. -}