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################
# Markov model #
################

## Model set-up ----

t_names <- c("without_drug", "with_drug")
n_treatments <- length(t_names)

s_names  <- c("Asymptomatic_disease", "Progressive_disease", "Dead")

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ce_res <- ce_markov(start_pop = c(0, 1),
                    p_matrix,
                    c_matrix,
                    q_matrix)

#
ce_markov <- function(start_pop,
                      p_matrix,
                      c_matrix,
                      q_matrix,

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R: Presenting outputs
========================================================
author: Dr N Green
date: March 2018
autosize: false
width: 2440
height: 1200
css: custom.css

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#' Decision Tree Expected Values
#'
#' \deqn{C_i = \sum p_{ij} (C_{ij} + C_j)}
#'
#' @param vals Values on each edge (array) e.g. costs or QALYs
#' @param p Transition probabilities (array)
#'
#' @return expected value at each node (list)
#' @export

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#' Branch Joint Probability
#'
#' @param probs Branch conditional probabilities (array)
#'
#' @return
#' @export
#'
#' @examples
#' branch_joint_probs(probs) * cost
#'

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library(Rfast)
library(utils)


prob_test_outcome_combination <- function(prob,
                                          n_choose) {
  
  p_comb <- combn(x = prob, m = n_choose)
  n_comb <- combn(x = 1 - prob, m = length(prob) - n_choose)
  

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two_test_parallel_AND <- function(sens, spec) {
  
  list(
    sensitivity = sens*sens,
    specificity = spec + spec - spec*spec)
}

three_test_parallel_AND_2 <- function(sens, spec) {
  
  list(

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## ----setup, include=FALSE------------------------------------------------
knitr::opts_chunk$set(echo = TRUE)

## ---- eval=T,echo=T------------------------------------------------------
a <- 1
b <- 2
c <- -1
d <- 2

# Check if two values are the same. Note the difference between 

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## ----setup, include=FALSE------------------------------------------------
knitr::opts_chunk$set(echo = TRUE)

## ---- echo=T, eval=T-----------------------------------------------------
2 + 2

## ---- echo=T, eval=T-----------------------------------------------------
a <- 2 + 2

## ---- echo=T,eval=T------------------------------------------------------

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#--run in the old version of R
setwd("C:/Temp/")
packages <- installed.packages()[,"Package"]
save(packages, file="Rpackages")
Followed by this in the new version:

#--run in the new version
setwd("C:/Temp/")
load("Rpackages")
for (p in setdiff(packages, installed.packages()[,"Package"]))