Added initial version of drug utilization in children study code.

Author: schuemie

DrugsInPeds/.Rbuildignore

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+^\.travis\.yml$
+^.*\.Rproj$
+^\.Rproj\.user$
+documents

DrugsInPeds/.gitignore

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+# History files
+.Rhistory
+
+# Example code in package build process
+*-Ex.R
+
+# R data files from past sessions
+.Rdata
+.Rproj.user
+
+R/TC
+statement_*.sql
+errorReport.txt
+
+#C++ objects
+src/*.o
+src/*.so
+src/*.dll
+/Debug
+standalone/build/*

DrugsInPeds/DESCRIPTION

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+Package: DrugsInPeds
+Title: Exploration of drug utilization in children
+Version: 0.1
+Author: Martijn J. Schuemie [aut, cre]
+Maintainer: Martijn J. Schuemie <[email protected]>
+Description: What the study does (paragraph)
+Depends:
+    R (>= 3.1),
+    DatabaseConnector (>= 1.2.1)
+Imports:
+    SqlRender,
+    DBI,
+    mailR,
+    OhdsiSharing
+Suggests:
+    testthat
+License: Apache License 2.0
+LazyData: true

DrugsInPeds/DrugsInPeds.Rproj

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+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: No
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 4
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,namespace

DrugsInPeds/NAMESPACE

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+# Generated by roxygen2 (4.1.1): do not edit by hand
+
+export(email)
+export(execute)
+export(getDefaultStudyEmailSubject)
+export(getDefaultStudyFileName)
+export(getDefaultStudyFolder)
+export(getDestinationAddress)

DrugsInPeds/R/FigureMockups.R

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+# Copyright 2015 Observational Health Data Sciences and Informatics
+#
+# This file is part of DrugsInPeds
+#
+# 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.
+
+createMockupsForProtocol <- function(){
+    library(ggplot2)
+
+    #data <- expand.grid(c("CDARS","JMDC","NHIRD", "AUSOM","CCAE"), c("<2","2-11","12-18"), c("A","B","C","D","G","H","J","L","M","N","P"))
+    data <- expand.grid(c("CDARS","JMDC","NHIRD", "AUSOM","CCAE"), c("<2","2-11","12-18"), c("Alimentary","Blood","Cardiovascular","Dermatological","Genitourinary","Hormonal","Anti-infectives","Antineoplastic","Muscoskeletal","Nervous system","Antiparasitic drugs"))
+    colnames(data) <- c("Database","Age","Class")
+    data$Prevalence <- runif(nrow(data),0,100)
+
+    ggplot(data, aes(x = Age, y = Prevalence, group = Database, fill = Database)) +
+        geom_bar(stat = "identity") +
+        facet_grid(.~ Class) +
+        theme(axis.text.x = element_text(angle=-90),
+              strip.text.x = element_text(angle=-90))
+
+    ggsave("documents/mockup1.png", width = 9, height = 5, dpi= 200)
+
+    data <- expand.grid(c("CDARS","JMDC","NHIRD", "AUSOM","CCAE"), c("Male","Female"), c("Alimentary","Blood","Cardiovascular","Dermatological","Genitourinary","Hormonal","Anti-infectives","Antineoplastic","Muscoskeletal","Nervous system","Antiparasitic drugs"))
+    colnames(data) <- c("Database","Gender","Class")
+    data$Prevalence <- runif(nrow(data),0,100)
+
+    ggplot(data, aes(x = Gender, y = Prevalence, group = Database, fill = Database)) +
+        geom_bar(stat = "identity") +
+        facet_grid(.~ Class) +
+        theme(axis.text.x = element_text(angle=-90),
+              strip.text.x = element_text(angle=-90))
+
+    ggsave("documents/mockup2.png", width = 9, height = 5, dpi= 200)
+
+
+    data <- expand.grid(c("CDARS","JMDC","NHIRD", "AUSOM","CCAE"), c("<2","2-11","12-18"), c("Alimentary","Blood","Cardiovascular","Dermatological","Genitourinary","Hormonal","Anti-infectives","Antineoplastic","Muscoskeletal","Nervous system","Antiparasitic drugs"), 2008:2014)
+    colnames(data) <- c("Database","Age","Class", "Year")
+    data$Prevalence <- runif(nrow(data),0,100)
+
+    ggplot(data, aes(x = Year, y = Prevalence, group = Database, color = Database)) +
+        geom_line() +
+        facet_grid(Class ~ Age) +
+        theme(axis.text.x = element_text(angle=-90),
+              strip.text.y = element_text(angle=0))
+
+    ggsave("documents/mockup3.png", width = 7, height = 8, dpi= 200)
+}

DrugsInPeds/R/StudyInvariant.R

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+# Copyright 2015 Observational Health Data Sciences and Informatics
+#
+# This file is part of DrugsInPeds
+#
+# 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.
+
+#' @title Email results
+#'
+#' @details
+#' This function emails the result CSV files to the study coordinator.
+#'
+#' @return
+#' A list of files that were emailed.
+#'
+#' @param from     Return email address
+#' @param to			(Optional) Delivery email address (must be a gmail.com acccount)
+#' @param subject  (Optional) Subject line of email
+#' @param dataDescription A short description of the database
+#' @param file	(Optional) Name of local file with results; makee sure to use forward slashes (/)
+#'
+#' @export
+email <- function(from,
+                  to,
+                  subject,
+                  dataDescription,
+                  file) {
+
+    if (missing(from)) stop("Must provide return address")
+    if (missing(dataDescription)) stop("Must provide a data description")
+
+    if (missing(to)) to <- getDestinationAddress()
+    if (missing(subject)) subject <- getDefaultStudyEmailSubject()
+    if (missing(file)) file <- getDefaultStudyFileName()
+
+    if(!file.exists(file)) stop(paste(c("No results file named '",file,"' exists"),sep = ""))
+
+    tryCatch({
+        result <- mailR::send.mail(from = from,
+                                   to = to,
+                                   subject = subject,
+                                   body = paste("\n", dataDescription, "\n",
+                                                sep = ""),
+                                   smtp = list(host.name = "aspmx.l.google.com",
+                                               port = 25),
+                                   attach.files = file,
+                                   authenticate = FALSE,
+                                   send = TRUE)
+        if (result$isSendPartial()) {
+            stop("Unknown error in sending email")
+        } else {
+            writeLines(c(
+                "Sucessfully emailed the following file:",
+                paste("\t", file, sep = ""),
+                paste("to:", to)
+            ))
+        }
+    }, error = function(e) {
+        writeLines(c(
+            "Error in automatically emailing results, most likely due to security settings.",
+            "Please manually email the following file:",
+            paste("\t", file, sep = ""),
+            paste("to:", to)
+        ))
+    })
+}