initial BipolarMissclassificationValidation commit

added code to create cohorts, apply simple score model, evaluate it, calculate summary survival info, find relationship between predicted score and outcome over 10 years

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+*.html

BipolarMisclassificationValidation.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: ISO8859-1
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

DESCRIPTION

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+Package: BipolarMisclassificationValidation
+Type: Package
+Title: External Validation of Model Predicting Bipolar Misdiagnosed as MDD
+Version: 0.0.1
+Date: 2020-01-01
+Author: Jenna Reps
+Maintainer: Jenna Reps <youremail@address>
+Description: This study applies and evaluates a simple score model to OMOP CDM data that predicts which newly diagnosed MDD patients will be diagnosed with bipolar within the next 3 years 
+License: Apache License 2.0
+Depends:
+  R (>= 3.3.0), 
+  DatabaseConnector (>= 1.11.4),
+  survival
+Imports:
+  FeatureExtraction (>= 2.0.0),
+  SqlRender,
+  Cyclops (>= 1.2.2),
+  PatientLevelPrediction (>= 3.0.10),
+  ggplot2,
+  gridExtra,
+  ff,
+  ffbase (>= 0.12.1),
+  ParallelLogger,
+  OhdsiSharing
+Suggests:
+  testthat
+NeedsCompilation: no
+RoxygenNote: 6.0.1

HydraConfig.json

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+{
+"skeletonType": "PatientLevelPredictionValidationStudy",
+"skeletonVersion": "v0.0.1",
+"requiredHydraVersion": "v0.0.3",
+"actions":[{
+"type": "fileNameFindAndReplace",
+"input": "packageName",
+"find": "bipolarValidation"
+},{
+"type": "stringFindAndReplace",
+"input": "packageName",
+"find": "bipolarValidation"
+},{
+"type": "jsonArrayToCsv",
+"input": "cohortDefinitions",
+"mapping": [{"source": "id", "target": "cohortId"},
+{"source": "id", "target": "atlasId"},
+{"source": "name", "target": "name", "modifiers": ["convertToFileName"]}],
+"output": "inst/settings/CohortsToCreate.csv"
+},{
+"type": "jsonArrayToJson",
+"input": "cohortDefinitions",
+"fileName": "name",
+"payload": "expression",
+"output": "inst/cohorts"
+},{
+"type": "jsonArrayToSql",
+"input": "cohortDefinitions",
+"fileName": "name",
+"payload": "expression",
+"output": "inst/sql/sql_server"
+},
+{
+		"type": "jsonToJson",
+		"input": "",
+		"output": "inst/settings/plpAnalysisList.json"
+	}]
+}

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(checkInstall)
+export(createCohorts)
+export(execute)
+export(getTable1)
+export(packageResults)
+export(transportPlpModels)
+import(DatabaseConnector)

R/PackageResults.R

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+# Copyright 2018 Observational Health Data Sciences and Informatics
+#
+# This file is part of PredictionNetworkStudySkeleton
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+#' Package the results for sharing with OHDSI researchers
+#'
+#' @details
+#' This function packages the results.
+#'
+#' @param outputFolder        Name of local folder to place results; make sure to use forward slashes
+#'                            (/)
+#' @param minCellCount        The minimum number of subjects contributing to a count before it can be included in the results.
+#'
+#' @export
+packageResults <- function(outputFolder,
+                           minCellCount = 5) {
+  if(missing(outputFolder)){
+    stop('Missing outputFolder...')
+  }
+
+  # transport the results
+
+  #create export subfolder in workFolder
+  exportFolder <- file.path(outputFolder, "resultsToShare")
+
+  if (!file.exists(exportFolder)){
+    dir.create(exportFolder, recursive = T)
+  }
+
+  # loads analysis results
+  if(file.exists(file.path(outputFolder, 'validationResults.rds'))){
+    plpResult <- readRDS(file.path(outputFolder, 'validationResults.rds'))
+
+    if(minCellCount==0){
+      minCellCount <- NULL
+    }
+    result <- PatientLevelPrediction::transportPlp(plpResult, save = F,
+                                                   n=minCellCount,
+                                                   includeEvaluationStatistics=T,
+                                                   includeThresholdSummary=T,
+                                                   includeDemographicSummary=T,
+                                                   includeCalibrationSummary =T,
+                                                   includePredictionDistribution=T,
+                                                   includeCovariateSummary=T)
+    saveRDS(result, file.path(exportFolder, 'validationResults.rds'))
+
+  }
+
+
+
+  ### Add all to zip file ###
+  zipName <- paste0(outputFolder, '.zip')
+  OhdsiSharing::compressFolder(exportFolder, zipName)
+  # delete temp folder
+  unlink(exportFolder, recursive = T)
+
+  writeLines(paste("\nStudy results are compressed and ready for sharing at:", zipName))
+  return(zipName)
+}

R/SkeletonValidationPackage.R

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+# @file SkeletonValidationPackage.R
+#
+# Copyright 2018 Observational Health Data Sciences and Informatics
+#
+# This file is part of SkeletonValidationPackage
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+#' SkeletonValidationPackage
+#'
+#' @docType package
+#' @name SkeletonValidationPackage
+#' @import DatabaseConnector
+NULL