rebuilding readme

R/check_trans_probs.R

@@ -229,11 +229,11 @@ check_array_names_complete <- function(a_P, stop_if_not = F){
 #'   diag(a_P[,,x]) <- 1 - rowSums(a_P[,,x])
 #' }
 #'
-#' check_trans_prob_array(a_P = a_P, confirm_ok = F)
+#' check_trans_prob_array(a_P = a_P, stop_if_not = F)
 #' # introduce error
 #' a_P["H", "S", 1:10] <- 0
 #'
-#' check_trans_prob_array(a_P = a_P, confirm_ok = F)
+#' check_trans_prob_array(a_P = a_P, stop_if_not = F)
 #'
 #' }
 #'

README.Rmd

@@ -2,12 +2,8 @@
 output: github_document
 ---
 
-<!-- README.md is generated from README.Rmd. Please edit that file -->
-
-<!-- 
-
+<!-- README.md is generated from README.Rmd. Please edit that file 
 You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date. `devtools::build_readme()` is handy for this. 
-
 -->
 
 ```{r, include = FALSE}
@@ -23,6 +19,7 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/dark-peak-analytics/assertHE/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/dark-peak-analytics/assertHE/actions/workflows/R-CMD-check.yaml)
+
 <!-- badges: end -->
 
 The goal of assertHE is to identify errors and bugs in health economic evaluation models early in the development process.
@@ -42,13 +39,64 @@ library(assertHE)
 
 This is a basic example which shows you how to solve a common problem:
 
-```{r example}
+```{r example, eval = FALSE}
 library(assertHE)
 
+# create a transition probability array
+n_t <- 1000 # number of cycles
+v_hs_names <- c("H", "S", "D") # health states
+n_hs <- length(v_hs_names)
 
-## basic example code
-
+# create array of transition probabilities
+a_P <- array(
+ data = 0,
+ dim = c(n_hs, n_hs, n_t),
+ dimnames = list(v_hs_names, v_hs_names, 1:n_t)
+)
 
+# fill in transition probabilities for main transitions.
+a_P["H", "S",] <- 0.3
+a_P["H", "D",] <- 0.01
+a_P["S", "D",] <- 0.1
+a_P["S", "H",] <- 0.5
+
+# Fill in the proportion remaining in health state in each slice.
+# This is the remainder after all other transitions are accounted for.
+for(x in 1:n_t){
+ diag(a_P[,,x]) <- 1 - rowSums(a_P[,,x])
+}
+
+# Use the function from the package.
+# This check should return no error, the array is symmetric, numeric, values 
+# are between 0 and 1 and all rows sum to 1.
+# Note: stop_if_not = F returns warnings, stop_if_not = T returns errors.
+check_trans_prob_array(a_P = a_P, 
+                       stop_if_not = T)
+
+# We can introduce an error to see the output
+# In this case, we set the first 10 cycles of transition from H to S to 0.
+# This means that the rows don't sum to 1 for the H row for 1:10 cycle.
+a_P["H", "S", 1:10] <- 0
+
+check_trans_prob_array(a_P = a_P, 
+                       stop_if_not = F)
+
+# The output looks like this:
+
+# Warning message:
+# In check_array_rows_balanced(a_P, stop_if_not = stop_if_not) :
+#   Not valid transition probabilities
+#    Transition probabilities not valid from Health States:
+# 1                                           H; at cycle 1
+# 2                                           H; at cycle 2
+# 3                                           H; at cycle 3
+# 4                                           H; at cycle 4
+# 5                                           H; at cycle 5
+# 6                                           H; at cycle 6
+# 7                                           H; at cycle 7
+# 8                                           H; at cycle 8
+# 9                                           H; at cycle 9
+# 10                                         H; at cycle 10
 
 ```
 

README.md

@@ -1,14 +1,14 @@
 
-<!-- README.md is generated from README.Rmd. Please edit that file -->
-<!-- 
-&#10;You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date. `devtools::build_readme()` is handy for this. 
-&#10;-->
+<!-- README.md is generated from README.Rmd. Please edit that file 
+You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date. `devtools::build_readme()` is handy for this. 
+-->
 
 # assertHE
 
 <!-- badges: start -->
 
 [![R-CMD-check](https://github.com/dark-peak-analytics/assertHE/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/dark-peak-analytics/assertHE/actions/workflows/R-CMD-check.yaml)
+
 <!-- badges: end -->
 
 The goal of assertHE is to identify errors and bugs in health economic
@@ -33,8 +33,61 @@ This is a basic example which shows you how to solve a common problem:
 ``` r
 library(assertHE)
 
-
-## basic example code
+# create a transition probability array
+n_t <- 1000 # number of cycles
+v_hs_names <- c("H", "S", "D") # health states
+n_hs <- length(v_hs_names)
+
+# create array of transition probabilities
+a_P <- array(
+ data = 0,
+ dim = c(n_hs, n_hs, n_t),
+ dimnames = list(v_hs_names, v_hs_names, 1:n_t)
+)
+
+# fill in transition probabilities for main transitions.
+a_P["H", "S",] <- 0.3
+a_P["H", "D",] <- 0.01
+a_P["S", "D",] <- 0.1
+a_P["S", "H",] <- 0.5
+
+# Fill in the proportion remaining in health state in each slice.
+# This is the remainder after all other transitions are accounted for.
+for(x in 1:n_t){
+ diag(a_P[,,x]) <- 1 - rowSums(a_P[,,x])
+}
+
+# Use the function from the package.
+# This check should return no error, the array is symmetric, numeric, values 
+# are between 0 and 1 and all rows sum to 1.
+# Note: stop_if_not = F returns warnings, stop_if_not = T returns errors.
+check_trans_prob_array(a_P = a_P, 
+                       stop_if_not = T)
+
+# We can introduce an error to see the output
+# In this case, we set the first 10 cycles of transition from H to S to 0.
+# This means that the rows don't sum to 1 for the H row for 1:10 cycle.
+a_P["H", "S", 1:10] <- 0
+
+check_trans_prob_array(a_P = a_P, 
+                       stop_if_not = F)
+
+# The output looks like this:
+
+# Warning message:
+# In check_array_rows_balanced(a_P, stop_if_not = stop_if_not) :
+#   Not valid transition probabilities
+#    Transition probabilities not valid from Health States:
+# 1                                           H; at cycle 1
+# 2                                           H; at cycle 2
+# 3                                           H; at cycle 3
+# 4                                           H; at cycle 4
+# 5                                           H; at cycle 5
+# 6                                           H; at cycle 6
+# 7                                           H; at cycle 7
+# 8                                           H; at cycle 8
+# 9                                           H; at cycle 9
+# 10                                         H; at cycle 10
 ```
 
 [Robert Smith](https://www.linkedin.com/in/robert-smith-53b28438) <sup>