V0.1.0

.Rbuildignore

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

.gitignore

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 # Shiny token, see https://shiny.rstudio.com/articles/shinyapps.html
 rsconnect/
+.Rproj.user

DESCRIPTION

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+Package: ReDish
+Title: Create an interactive graphic for the Evaluation of Drug-Induced Serious Hepatotoxicity (eDISH).
+Version: 0.0.1
+Authors@R: c(
+	person("Becca", "Krouse", email = "rebecca_krouse@rhoworld.com", role = c("cre","aut")),
+	person("Jeremy", "Wildfire", role = "aut"),
+	person("Rho Inc.", role = "cph"))
+Description: Description: An R interface for the 'safety-eDISH' 'JavaScript' charting library, which provides an interactive framework for evaluating drug-induced serious hepatotoxicity.
+Depends: R (>= 3.4.0)
+License: MIT + File LICENSE
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 6.1.0

LICENSE

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-MIT License
-
-Copyright (c) 2018 ASA-DIA-InteractiveSafetyGraphics
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2018
+COPYRIGHT HOLDER: Rho Inc.

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(eDISH)
+export(eDISHOutput)
+export(renderEDISH)
+import(htmlwidgets)

R/eDISH.R

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+#' Create an eDISH widget
+#'
+#' This function creates an interactive graphic for the Evaluation of Drug-Induced Serious Hepatotoxicity (eDISH)
+#'
+#' @param data A data frame containing the labs data. Data must be structured as one record per study participant per time point per lab measure. 
+#' 
+#' @import htmlwidgets
+#'
+#' @export
+eDISH <- function(data) {
+
+  # forward options using x
+  rSettings = list(
+    data = data
+  )
+
+  # create widget
+  htmlwidgets::createWidget(
+    name = 'eDISH',
+    rSettings,
+   # width = width,
+   # height = height,
+    package = 'ReDish' #,
+   # sizingPolicy = htmlwidgets::sizingPolicy(viewer.fill=FALSE)
+  )
+}
+
+#' Shiny bindings for eDISH
+#'
+#' Output and render functions for using eDISH within Shiny
+#' applications and interactive Rmd documents.
+#'
+#' @param outputId output variable to read from
+#' @param width,height Must be a valid CSS unit (like \code{'100\%'},
+#'   \code{'400px'}, \code{'auto'}) or a number, which will be coerced to a
+#'   string and have \code{'px'} appended.
+#' @param expr An expression that generates a eDISH
+#' @param env The environment in which to evaluate \code{expr}.
+#' @param quoted Is \code{expr} a quoted expression (with \code{quote()})? This
+#'   is useful if you want to save an expression in a variable.
+#'
+#' @name eDISH-shiny
+#'
+#' @export
+eDISHOutput <- function(outputId, width = '100%', height = '400px'){
+  htmlwidgets::shinyWidgetOutput(outputId, 'eDISH', width, height, package = 'ReDish')
+}
+
+#' @rdname eDISH-shiny
+#' @export
+renderEDISH <- function(expr, env = parent.frame(), quoted = FALSE) {
+  if (!quoted) { expr <- substitute(expr) } # force quoted
+  htmlwidgets::shinyRenderWidget(expr, eDISHOutput, env, quoted = TRUE)
+}

ReDish.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

inst/htmlwidgets/eDISH.js

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+HTMLWidgets.widget({
+
+  name: 'eDISH',
+
+  type: 'output',
+
+  factory: function(el, width, height) {
+
+    // TODO: define shared variables for this instance
+
+    return {
+
+      renderValue: function(rSettings) {
+
+
+        el.innerHTML = "<div class='edish'></div>";
+
+        let settings = {
+            max_width: 600,
+            value_col: 'AVAL',
+            measure_col: 'PARAM',
+            visitn_col: 'VISITNUM',
+            studyday_col: 'ADY',
+            normal_col_low: 'A1LO',
+            normal_col_high: 'A1HI',
+            id_col: 'USUBJID',
+            group_cols: ['TRTA','RACE','AGEGR1'],
+            filters: [
+                {
+                    value_col: 'TRTA',
+                    label: 'Treatment'
+                },
+                {
+                    value_col: 'SEX',
+                    label: 'Sex'
+                },
+                {
+                    value_col: 'RACE',
+                    label: 'Race'
+                },
+                {
+                    value_col: 'AGEGR1',
+                    label: 'Age group'
+                },
+            ],
+            measure_values:{
+              'ALT':'Alanine Aminotransferase (U/L)',
+              'AST':'Aspartate Aminotransferase (U/L)',
+              'TB':'Bilirubin (umol/L)',
+              'ALP':'Alkaline Phosphatase (U/L)'
+            }
+        };
+
+         rSettings.data = HTMLWidgets.dataframeToD3(rSettings.data);
+
+
+         console.log(settings);
+         console.log(rSettings);
+
+        safetyedish('.edish', settings).init(rSettings.data);
+
+      },
+
+      resize: function(width, height) {
+
+        // TODO: code to re-render the widget with a new size
+
+      }
+
+    };
+  }
+});

inst/htmlwidgets/eDISH.yaml

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+dependencies:
+  - name: d3
+    version: 3.5.17
+    src: htmlwidgets/lib/d3-3.5.17
+    script: d3.v3.min.js
+  - name: webcharts
+    version: 1.10.0
+    src: htmlwidgets/lib/webcharts-1.10.0
+    script: webcharts.js
+    stylesheet: webcharts.css
+  - name: safety-eDish
+    version: 0.12.1
+    src: htmlwidgets/lib/safety-eDISH-0.12.1
+    script: safetyedish.js 
+

inst/htmlwidgets/lib/d3-3.5.17/LICENSE

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+Copyright (c) 2010-2016, Michael Bostock
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* The name Michael Bostock may not be used to endorse or promote products
+  derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL MICHAEL BOSTOCK BE LIABLE FOR ANY DIRECT,
+INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY
+OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.