extras/PackageMaintenance.R

In ohdsi-studies/Covid19VaccineAesiIncidenceRate: COVID-19 Vaccine AESI Incidence Characterization

# Copyright 2021 Observational Health Data Sciences and Informatics
#
# This file is part of Covid19VaccineAesiIncidenceRate19VaccineAesiIncidenceCharacterization19VaccineAesiIncidenceCharacterization
#
# 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::updatePackageNameFolder(packageName = "Covid19VaccineAesiIncidenceRate",
                                     recursive = T)
OhdsiRTools::checkUsagePackage("Covid19VaccineAesiIncidenceRate")
OhdsiRTools::updateCopyrightYearFolder()
devtools::document()
Sys.setenv(JAVA_HOME = "")
devtools::check()

# Create manual -----------------------------------------------------------
unlink("extras/Covid19VaccineAesiIncidenceRate.pdf")
shell("R CMD Rd2pdf ./ --output=extras/Covid19VaccineAesiIncidenceRate.pdf")

pkgdown::build_site()

# Establish the analysis settings json 1: impact of population characteristics
analysis1 <- list(name = "impact of population characteristics",
                  targetIds = list(104, 105, 106, 107, 126),
                  subgroupIds = list(1,
                                     2,
                                     21,
                                     22,
                                     31,
                                     32,
                                     41,
                                     42,
                                     51,
                                     52,
                                     61,
                                     62,
                                     71,
                                     72,
                                     81,
                                     82,
                                     91,
                                     92),
                  timeAtRiskIds = list(5),
                  outcomeIds = list(312,
                                    303,
                                    323,
                                    307,
                                    332,
                                    321,
                                    301,
                                    302,
                                    308,
                                    305,
                                    324,
                                    326,
                                    314,
                                    319,
                                    310,
                                    316,
                                    318))

# 2: 'Impact of anchoring (and future severity of illness)'
analysis2 <- list(name = "Impact of anchoring (and future severity of illness)",
                  targetIds = list(108, 109, 110, 111, 112, 113, 114),
                  subgroupIds = list(21,
                                     22,
                                     31,
                                     32,
                                     41,
                                     42,
                                     51,
                                     52,
                                     61,
                                     62,
                                     71,
                                     72,
                                     81,
                                     82,
                                     91,
                                     92),
                  timeAtRiskIds = list(1, 2, 3, 4, 5),
                  outcomeIds = list(312,
                                    303,
                                    323,
                                    307,
                                    332,
                                    321,
                                    301,
                                    302,
                                    308,
                                    305,
                                    324,
                                    326,
                                    314,
                                    319,
                                    310,
                                    316,
                                    318))

# 3: 'Impact of seasonal trends and COVID'
analysis3 <- list(name = "Impact of seasonal trends and COVID",
                  targetIds = list(104, 115, 116, 117, 118, 119, 120, 121),
                  subgroupIds = list(21,
                                     22,
                                     31,
                                     32,
                                     41,
                                     42,
                                     51,
                                     52,
                                     61,
                                     62,
                                     71,
                                     72,
                                     81,
                                     82,
                                     91,
                                     92),
                  timeAtRiskIds = list(4),
                  outcomeIds = list(312,
                                    303,
                                    323,
                                    307,
                                    332,
                                    321,
                                    301,
                                    302,
                                    308,
                                    305,
                                    324,
                                    326,
                                    314,
                                    319,
                                    310,
                                    316,
                                    318))

# 4: Impact of secular trends
analysis4 <- list(name = "Impact of secular trends",
                  targetIds = list(122, 123, 124),
                  subgroupIds = list(21,
                                     22,
                                     31,
                                     32,
                                     41,
                                     42,
                                     51,
                                     52,
                                     61,
                                     62,
                                     71,
                                     72,
                                     81,
                                     82,
                                     91,
                                     92),
                  timeAtRiskIds = list(5),
                  outcomeIds = list(312,
                                    303,
                                    323,
                                    307,
                                    332,
                                    321,
                                    301,
                                    302,
                                    308,
                                    305,
                                    324,
                                    326,
                                    314,
                                    319,
                                    310,
                                    316,
                                    318))

# 5: Impact of prior observation period
analysis5 <- list(name = "Impact of prior observation period",
                  targetIds = list(125),
                  subgroupIds = list(21,
                                     22,
                                     31,
                                     32,
                                     41,
                                     42,
                                     51,
                                     52,
                                     61,
                                     62,
                                     71,
                                     72,
                                     81,
                                     82,
                                     91,
                                     92),
                  timeAtRiskIds = list(5),
                  outcomeIds = list(312,
                                    303,
                                    323,
                                    307,
                                    332,
                                    321,
                                    301,
                                    302,
                                    308,
                                    305,
                                    324,
                                    326,
                                    314,
                                    319,
                                    310,
                                    316,
                                    318))

# 6: Impact of phenotype definition and outcome clean window
analysis6 <- list(name = "Impact of phenotype definition and outcome clean window",
                  targetIds = list(104),
                  subgroupIds = list(21,
                                     22,
                                     31,
                                     32,
                                     41,
                                     42,
                                     51,
                                     52,
                                     61,
                                     62,
                                     71,
                                     72,
                                     81,
                                     82,
                                     91,
                                     92),
                  timeAtRiskIds = list(5),
                  outcomeIds = list(313,
                                    327,
                                    345,
                                    328,
                                    346,
                                    363,
                                    322,
                                    329,
                                    347,
                                    330,
                                    348,
                                    315,
                                    331,
                                    333,
                                    349,
                                    320,
                                    334,
                                    350,
                                    351,
                                    352,
                                    335,
                                    337,
                                    353,
                                    309,
                                    338,
                                    354,
                                    304,
                                    306,
                                    355,
                                    325,
                                    339,
                                    356,
                                    340,
                                    357,
                                    341,
                                    358,
                                    359,
                                    311,
                                    364,
                                    342,
                                    360,
                                    343,
                                    344,
                                    361,
                                    317,
                                    362))

# 7: TwT analysis
analysis7 <- list(name = "Impact of phenotype definition and outcome clean window",
                  targetIds = list(104),
                  subgroupIds = list(21,
                                     22,
                                     31,
                                     32,
                                     41,
                                     42,
                                     51,
                                     52,
                                     61,
                                     62,
                                     71,
                                     72,
                                     81,
                                     82,
                                     91,
                                     92),
                  timeAtRiskIds = list(5),
                  outcomeIds = list(345,
                                    332,
                                    426,
                                    349,
                                    334,
                                    347,
                                    346,
                                    344,
                                    343,
                                    341,
                                    340,
                                    339,
                                    338,
                                    337,
                                    336,
                                    335,
                                    342,
                                    333,
                                    331,
                                    427,
                                    448,
                                    457,
                                    458,
                                    459,
                                    460,
                                    461,
                                    462,
                                    463,
                                    464,
                                    465,
                                    466,
                                    467,
                                    468,
                                    469,
                                    475,
                                    430,
                                    473,
                                    474,
                                    472,
                                    476,
                                    477,
                                    478,
                                    479,
                                    470,
                                    456,
                                    455,
                                    454,
                                    452,
                                    451,
                                    480,
                                    481,
                                    482,
                                    382,
                                    550,
                                    383,
                                    449,
                                    385,
                                    348,
                                    380,
                                    386,
                                    387,
                                    388,
                                    390,
                                    392,
                                    391,
                                    381,
                                    389,
                                    384,
                                    396,
                                    393,
                                    394,
                                    395,
                                    397,
                                    400,
                                    398,
                                    399,
                                    401,
                                    407,
                                    405,
                                    404,
                                    403,
                                    402,
                                    406,
                                    408,
                                    409,
                                    410,
                                    411,
                                    483,
                                    484,
                                    485,
                                    486,
                                    487,
                                    488,
                                    489,
                                    523,
                                    524,
                                    525,
                                    526,
                                    527,
                                    528,
                                    533,
                                    534,
                                    535,
                                    536,
                                    537,
                                    538,
                                    539,
                                    540,
                                    541,
                                    542,
                                    543,
                                    544,
                                    545,
                                    546,
                                    547,
                                    548,
                                    549,
                                    532,
                                    531,
                                    530,
                                    529,
                                    551,
                                    552,
                                    553,
                                    554))

# analysisList = list(analysisList = list(analysis1, analysis2, analysis3, analysis4, analysis5,
# analysis6))
analysisList <- list(analysisList = list(analysis7))
analysisListJson <- RJSONIO::toJSON(analysisList, pretty = T)
analysisListFile <- "D:/git/ohdsi-studies/Covid19VaccineAesiIncidenceRate/inst/settings/analysisSettings.json"
write(analysisListJson, file = analysisListFile)

# Verify the analysis settings ---------------
targetRef <- system.file("settings/targetRef.csv",
                         package = "Covid19VaccineAesiIncidenceRate",
                         mustWork = TRUE)
subgroupRef <- system.file("settings/subgroupRef.csv",
                           package = "Covid19VaccineAesiIncidenceRate",
                           mustWork = TRUE)
outcomeRef <- system.file("settings/outcomeRef.csv",
                          package = "Covid19VaccineAesiIncidenceRate",
                          mustWork = TRUE)
tarRef <- system.file("settings/timeAtRisk.csv",
                      package = "Covid19VaccineAesiIncidenceRate",
                      mustWork = TRUE)

targetCohort <- readr::read_csv(targetRef, col_types = readr::cols())
subgroupCohorts <- readr::read_csv(subgroupRef, col_types = readr::cols())
outcomeCohorts <- readr::read_csv(outcomeRef, col_types = readr::cols())
tars <- readr::read_csv(tarRef, col_types = readr::cols())

targetIds <- targetCohort$cohortId
subgroupIds <- subgroupCohorts$cohortId
outcomeIds <- outcomeCohorts$outcomeId
tarIds <- tars$time_at_risk_id

analysisListJsonFromFile <- paste(readLines(analysisListFile), collapse = "\n")
analysisListFromFile <- RJSONIO::fromJSON(analysisListJsonFromFile)
compareLists <- function(x, y) {
  xCompareY <- x %in% y
  xInY <- which(xCompareY)
  return(length(x) == length(xInY))
}

for (i in 1:length(analysisListFromFile$analysisList)) {
  print(paste(i, analysisListFromFile$analysisList[[i]]$name))
  if (!(compareLists(analysisListFromFile$analysisList[[i]]$targetIds, targetIds))) {
    warning("Target ID mismatch from targetRef.csv file.")
  }
  # These are generated dynamically by runIncidenceAnalysis.sql so we can't check these at design time.
  # if (!(compareLists(analysisListFromFile$analysisList[[i]]$subgroupIds, subgroupIds))) {
  # warning('Subgroup ID mismatch from subgroupRef.csv file.') }
  if (!(compareLists(analysisListFromFile$analysisList[[i]]$outcomeIds, outcomeIds))) {
    warning("Outcome ID mismatch from outcomeRef.csv file.")
  }
  if (!(compareLists(analysisListFromFile$analysisList[[i]]$timeAtRiskIds, tarIds))) {
    warning("Time-at-risk ID mismatch from timeAtRisk.csv file.")
  }
}

# Check the warnings if any are generated to find configuration errors


# Store environment in which the study was executed -----------------------
OhdsiRTools::insertEnvironmentSnapshotInPackage("Covid19VaccineAesiIncidenceRate")
OhdsiRTools::createRenvLockFile(rootPackage = "Covid19VaccineAesiIncidenceRate")

# Check all files for UTF-8 Encoding and ensure there are no non-ASCII characters
OhdsiRTools::findNonAsciiStringsInFolder()

packageFiles <- list.files(path = ".", recursive = TRUE)
if (!all(utf8::utf8_valid(packageFiles))) {
  print("Found invalid UTF-8 encoded files")
}

# Create the Renv lock file
OhdsiRTools::createRenvLockFile("Covid19VaccineAesiIncidenceRate",
                                additionalRequiredPackages = c('keyring', "DatabaseConnector","dplyr","ROhdsiWebApi",
                                                               "stringr","SqlRender","tidyr", "plyr"))

# Validate cohort SQL file names ------------
targetCohorts <- Covid19VaccineAesiIncidenceRate::readCsv("settings/targetRef.csv")
targetCohorts$cohortFolder <- "target"
subgroupCohorts <- Covid19VaccineAesiIncidenceRate::readCsv("settings/subgroupRef.csv")
subgroupCohorts$cohortFolder <- "subgroup"
outcomeCohorts <- Covid19VaccineAesiIncidenceRate::readCsv("settings/outcomeRef.csv")
outcomeCohorts$cohortFolder <- "outcome"
# Reformat the outcomeCohorts dataframe to match target/subgroup
outcomeCohortsReformatted <- outcomeCohorts[, c("outcomeId",
                                                "outcomeName",
                                                "fileName",
                                                "cohortFolder")]
names(outcomeCohortsReformatted) <- c("cohortId", "cohortName", "fileName", "cohortFolder")
allCohorts <- rbind(targetCohorts, subgroupCohorts, outcomeCohortsReformatted)

# Obtain the list of SQL files in the list
packageSqlFiles <- list.files(system.file(file.path("sql/sql_server/"),
                                          package = "Covid19VaccineAesiIncidenceRate"), recursive = TRUE)

for (i in 1:nrow(allCohorts)) {
  # Verify that the path to the SQL file is correct and matches with case sensitivity
  sqlFileName <- file.path(allCohorts$cohortFolder[i], allCohorts$fileName[i])
  fileFound <- sqlFileName %in% packageSqlFiles
  if (!fileFound) {
    warning(paste(sqlFileName,
                  "not found in package. This is likely due to a difference in case sensitivity."))
  }
}