From 5dcc42d6bcbd89be6cbcf267088696d6610ff908 Mon Sep 17 00:00:00 2001 From: schuemie Date: Tue, 15 Jan 2019 10:27:05 -0500 Subject: [PATCH] New install dependency instructions --- extras/InstallDependencies.R | 6 +++--- extras/PostHocAnalyses.R | 15 +++++++++++---- 2 files changed, 14 insertions(+), 7 deletions(-) diff --git a/extras/InstallDependencies.R b/extras/InstallDependencies.R index d32d120..33bc399 100644 --- a/extras/InstallDependencies.R +++ b/extras/InstallDependencies.R @@ -24,10 +24,10 @@ install.packages(c("assertthat", "crayon", "bit", "cli", "devtools", "colorspace # assignInNamespace("version_info", c(devtools:::version_info, list("3.5" = list(version_min = "3.3.0", version_max = "99.99.99", path = "bin"))), "devtools") # find_rtools() +install.packages("Cyclops") devtools::install_github("ohdsi/SqlRender", dep = FALSE) -devtools::install_github("ohdsi/DatabaseConnectorJars", ref = "v1.0.0", dep = FALSE) -devtools::install_github("ohdsi/DatabaseConnector", ref = "v2.2.0", dep = FALSE) -devtools::install_github("ohdsi/Cyclops", ref = "v2.0.0", dep = FALSE) +devtools::install_github("ohdsi/DatabaseConnectorJars", dep = FALSE) +devtools::install_github("ohdsi/DatabaseConnector", dep = FALSE) devtools::install_github("ohdsi/FeatureExtraction", ref = "v2.1.5", dep = FALSE) devtools::install_github("ohdsi/ParallelLogger",ref = "develop",dep = FALSE) devtools::install_github("ohdsi/CohortMethod", dep = FALSE) diff --git a/extras/PostHocAnalyses.R b/extras/PostHocAnalyses.R index 8251922..1e26b04 100644 --- a/extras/PostHocAnalyses.R +++ b/extras/PostHocAnalyses.R @@ -22,8 +22,8 @@ outcomeModelReference <- readRDS(file.path(indicationFolder, "cmOutput", "outcomeModelReference1.rds")) targetId <- 4 -# comparatorId <- 15 # THZ -comparatorId <- 10 # dCCB +comparatorId <- 15 # THZ +# comparatorId <- 10 # dCCB outcomeId <- 32 censorId <- 1 analysisId <- 1 @@ -32,8 +32,13 @@ analysisId <- 1 pairedCohortTable <- paste(tablePrefix, tolower(indicationId), "pair_cohort", sep = "_") pathToCsv <- system.file("settings", "ExposuresOfInterest.csv", package = "Legend") exposuresOfInterest <- read.csv(pathToCsv) -censorDescendantIds <- exposuresOfInterest$includedConceptIds[exposuresOfInterest$cohortId == censorId] -censorDescendantIds <- as.numeric(strsplit(as.character(censorDescendantIds), ";")[[1]]) +exposuresOfInterest <- exposuresOfInterest[exposuresOfInterest$indicationId == indicationId, ] +# exposuresOfInterest <- exposuresOfInterest[exposuresOfInterest$cohortId == censorId, ] +censorDescendantIds <- exposuresOfInterest$includedConceptIds +censorDescendantIds <- as.numeric(unlist(strsplit(as.character(censorDescendantIds), ";"))) +censorDescendantIds <- c(censorDescendantIds, + exposuresOfInterest$conceptId[exposuresOfInterest$includedConceptIds == ""]) +censorDescendantIds <- unique(censorDescendantIds) sql <- "SELECT DATEDIFF(DAY, cohort_start_date, MIN(drug_era_start_date)) AS days_to_censor, cohort_start_date, subject_id @@ -85,3 +90,5 @@ stratPop$outcomeCount[idx] <- 0 om <- CohortMethod::fitOutcomeModel(population = stratPop, modelType = "cox", stratified = TRUE) om summary(om) +stratPop$stratumId <- NULL +CohortMethod::plotKaplanMeier(stratPop)