rm(list=ls())
library("shiny")
library("rhandsontable")
library("deSolve")
library("ggplot2")
if("ubiquity" %in% rownames(installed.packages())){require(ubiquity)} else
{source(file.path('library', 'r_general', 'ubiquity.R')) }
cfg = build_system(output_directory = file.path(".", "output"),
temporary_directory = file.path(".", "transient"))
Rmdfile = "system_report.Rmd"
# If you run the app, put in the values you want in terms of parameters and
# dosing then run the simulation it should save the following file with a
# snapshot of the values that will be sent into the report for generation:
load(file.path("transient", "app_base", "app_post_sim.RData"))
params = list()
params$cfg = values$cfg
params$som = values$som
params$parameters = values$parameters
# This is needed for debugging
cfg$options$misc$operating_environment = 'script'
rmarkdown::render(Rmdfile,
params = params,
output_format = "html_document")
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