# Copyright 2020 Observational Health Data Sciences and Informatics
#
# This file is part of CaseCrossover
#
# 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.
# Format and check code
OhdsiRTools::formatRFolder()
OhdsiRTools::checkUsagePackage("CaseCrossover")
OhdsiRTools::updateCopyrightYearFolder()
devtools::spell_check()
# Create manual and vignette
unlink("extras/CaseCrossover.pdf")
shell("R CMD Rd2pdf ./ --output=extras/CaseCrossover.pdf")
rmarkdown::render("vignettes/SingleStudies.Rmd",
output_file = "../inst/doc/SingleStudies.pdf",
rmarkdown::pdf_document(latex_engine = "pdflatex",
toc = TRUE,
number_sections = TRUE))
unlink("inst/doc/SingleStudies.tex")
rmarkdown::render("vignettes/MultipleAnalyses.Rmd",
output_file = "../inst/doc/MultipleAnalyses.pdf",
rmarkdown::pdf_document(latex_engine = "pdflatex",
toc = TRUE,
number_sections = TRUE))
unlink("inst/doc/MultipleAnalyses.tex")
pkgdown::build_site()
OhdsiRTools::fixHadesLogo()
# Create arg functions:
library(CaseCrossover)
rCode <- c("# This file has been autogenerated. Do not change by hand. ")
rCode <- ParallelLogger::createArgFunction("getDbCaseCrossoverData",
excludeArgs = c("connectionDetails",
"cdmDatabaseSchema",
"oracleTempSchema",
"outcomeDatabaseSchema",
"outcomeTable",
"outcomeIds",
"nestingCohortDatabaseSchema",
"nestingCohortTable",
"nestingCohortId",
"exposureDatabaseSchema",
"exposureTable",
"exposureIds"),
rCode = rCode)
rCode <- ParallelLogger::createArgFunction("selectSubjectsToInclude",
excludeArgs = c("caseCrossoverData", "outcomeId"),
rCode = rCode)
rCode <- ParallelLogger::createArgFunction("getExposureStatus",
excludeArgs = c("caseCrossoverData", "subjects", "exposureId"),
rCode = rCode)
writeLines(rCode, "r/CreateArgFunctions.R")
OhdsiRTools::formatRFile("r/CreateArgFunctions.R")
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