Add alpha version shiny app

.gitignore

@@ -136,4 +136,10 @@ dmypy.json
 
 # Rendered notebooks
 *.html
-*.pdf
+*.pdf
+
+# Shinyapps.io connection
+rsconnect/
+
+.Rproj.user
+.Rhistory

app/.Rprofile

@@ -0,0 +1,11 @@
+# ------------------------- Settings (Do not edit) -------------------------- #
+
+if (Sys.info()[['user']] == 'shiny'){
+  VIRTUALENV_NAME = 'residualrisk'
+
+  # Running on shinyapps.io
+  Sys.setenv(PYTHON_PATH = 'python3')
+  Sys.setenv(VIRTUALENV_NAME = VIRTUALENV_NAME) # Installs into default shiny virtualenvs dir
+  Sys.setenv(RETICULATE_PYTHON = paste0('/home/shiny/.virtualenvs/', VIRTUALENV_NAME, '/bin/python'))
+
+}

app/about.md

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+## About
+
+This application implements a model for the infectious window period (IWP) with 
+NAT screening for a viral transfusion-transmissible infection. The default 
+parameters are appropriate for HIV, but with appropriate parameters the logic is
+equally applicable to other infections like HBV and HCV. The infectious-but-
+undetectable window period depends on:
+* the probability of transfusion transmission as a function of viral 
+concentration in the transfused component
+* the probability of non-detection as a function of viral concentration in the
+screening sample (which depends on the sensitivity of the NAT screening assay,
+minipool size and the retesting procedure)
+* the viral growth rate (or doubling time) during early infection ("ramp-up
+viremia")
+
+The infectious window period is given by the area under the joint probability of
+transfusion-transmission and non-detection.
+
+The residual risk of transfusion transmission despite screening is given by the
+probability that a random donation will be infection-positive and very recently
+acquired -- i.e. incidence x infectious window period.
+
+The model incorporates a "dose-response" model for the probability of 
+transfusion-transmission:
+* Belov, AA et al. (2020) Transfusion. Submitted.
+
+and an adaptation of the Weusten model for infectious window period:
+* Weusten, J. et al. (2011) Transfusion.
+
+Written by Eduard Grebe <[email protected]>.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the [GNU Affero General Public License]
+(https://www.gnu.org/licenses/agpl-3.0.en.html) as published by the Free 
+Software Foundation, either version 3 of the License, or (at your option) any 
+later version.

app/residualriskapp.Rproj

@@ -0,0 +1,13 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX