add README.R for high level script

Author: n8thangreen

README.R

@@ -0,0 +1,107 @@
+## ----set-options, echo=FALSE, cache=FALSE--------------------------------
+options(width = 1000)
+
+## ----eval=FALSE----------------------------------------------------------
+## library(devtools)
+## install_github("n8thangreen/treeSimR")
+
+## ----eval=FALSE----------------------------------------------------------
+## library("treeSimR")
+
+## ----load packages, echo=FALSE, warning=FALSE----------------------------
+library(yaml)
+library(data.tree)
+devtools::load_all(".")
+
+
+## ------------------------------------------------------------------------
+# osList <- yaml.load(yaml)
+osList <- yaml.load_file("raw data/LTBI_dtree-cost-distns.yaml")
+osNode <- as.Node(osList)
+osNode
+
+## ------------------------------------------------------------------------
+osNode <- treeSimR::costeffectiveness_tree(yaml_tree = "raw data/LTBI_dtree-cost-distns.yaml")
+print(osNode, "type", "p", "distn", "mean", "sd")
+
+## ----eval=FALSE----------------------------------------------------------
+## library(listviewer)
+## l <- ToListSimple(osNode)
+## jsonedit(l)
+
+## ------------------------------------------------------------------------
+rpayoff <- osNode$Get(sampleNode)
+osNode$Set(payoff = rpayoff)
+print(osNode, "type", "p", "distn", "mean", "sd", "payoff")
+
+## ------------------------------------------------------------------------
+osNode$Do(payoff, traversal = "post-order", filterFun = isNotLeaf)
+
+print(osNode, "type", "p", "distn", "mean", "sd", "payoff")
+
+## ------------------------------------------------------------------------
+osNode <- calc_expectedValues(osNode)
+print(osNode, "type", "p", "distn", "mean", "sd", "payoff")
+
+## ------------------------------------------------------------------------
+MonteCarlo_expectedValues(osNode, n=100)
+
+## ------------------------------------------------------------------------
+path_probs <- calc_pathway_probs(osNode)
+osNode$Set(path_probs = path_probs)
+
+terminal_states <- data.frame(pathname = osNode$Get('pathString', filterFun = isLeaf),
+                              path_probs = osNode$Get('path_probs', filterFun = isLeaf))
+terminal_states
+
+## ------------------------------------------------------------------------
+startstate_prob <- matrix(NA, nrow = 3, ncol = 2,
+                          dimnames = list(c("<40k","40-150k",">150k"), c("LTBI","nonLTBI")))
+
+startstate.LTBI <- grepl("/Complete Treatment", x = terminal_states$pathname) | grepl("non-LTBI", x = terminal_states$pathname)
+
+startstate_prob["<40k","nonLTBI"] <- sum(terminal_states$path_probs[grepl("under 40k cob incidence", x = terminal_states$pathname) &
+                                                                  startstate.LTBI])
+
+startstate_prob["<40k","LTBI"] <- sum(terminal_states$path_probs[grepl("under 40k cob incidence", x = terminal_states$pathname) &
+                                                               !startstate.LTBI])
+
+startstate_prob["40-150k","nonLTBI"] <- sum(terminal_states$path_probs[grepl("40-150k cob incidence", x = terminal_states$pathname) &
+                                                                     startstate.LTBI])
+
+startstate_prob["40-150k","LTBI"] <- sum(terminal_states$path_probs[grepl("40-150k cob incidence", x = terminal_states$pathname) &
+                                                                  !startstate.LTBI])
+
+startstate_prob[">150k","nonLTBI"] <- sum(terminal_states$path_probs[grepl("over 150k cob incidence", x = terminal_states$pathname) &
+                                                                   startstate.LTBI])
+
+startstate_prob[">150k","LTBI"] <- sum(terminal_states$path_probs[grepl("over 150k cob incidence", x = terminal_states$pathname) &
+                                                                  !startstate.LTBI])
+
+knitr::kable(startstate_prob/sum(startstate_prob))
+
+## ------------------------------------------------------------------------
+osNode <- calc_riskprofile(osNode)
+print(osNode, "type", "path_prob", "path_payoff")
+
+## ------------------------------------------------------------------------
+plot(data.frame(osNode$Get('path_payoff', filterFun = isLeaf),
+           osNode$Get('path_prob', filterFun = isLeaf)), type="h",
+     xlab="payoff", ylab="probability")
+
+## ----eval=FALSE----------------------------------------------------------
+## ##TODO##
+## osNode$Do(decision, filterFun = function(x) x$type == 'decision')
+## osNode$Get('decision')[1]
+
+## ----eval=FALSE----------------------------------------------------------
+## ##TODO##
+## ## probabilty of successfully & correctly treating LTBI
+## dummy <- rep(0, osNode$totalCount)
+## dummy[12] <- 1
+## osNode$Set(payoff = dummy)
+## print(osNode, "type", "p", "distn", "mean", "sd", "payoff")
+## osNode$Do(payoff, traversal = "post-order", filterFun = isNotLeaf)
+## print(osNode, "type", "p", "distn", "mean", "sd", "payoff")
+## osNode$Get('payoff')[1]
+