Update vignette plots. Add new data sets for JSS article

R/data.R

@@ -251,4 +251,25 @@
 #'   \item{death}{Factor indicating patient mortality (No,Yes)}
 #' }
 #' @source Simulated data - not from real patients.
-"PE"
+"PE"
+
+#' Example Conditional Probability Table Resulting from the \code{inputCPT} function.
+#'
+#' This is an example of the output generated by the \code{inputCPT} function as 
+#' illustrated in the article being submitted to JSS.  It is saved as an object 
+#' named \code{h} in the article.
+#' 
+#' @source No Source.  It's really just made up.
+"inputCPTExample"
+
+#' Conditional Probability Table for side effects as a function of emesis and drug.
+#'
+#' This is a conditional probability table used in the emesis example of the JSS article.
+#' 
+"SE.cpt"
+
+#' Conditional Probability Table for resolution of side effects as a function drugs and emesis.
+#'
+#' This is a conditional probability table used in the emesis example of the JSS article.
+#' 
+"Resolution.cpt"

man/Resolution.cpt.Rd

@@ -0,0 +1,31 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{Resolution.cpt}
+\alias{Resolution.cpt}
+\title{Conditional Probability Table for resolution of side effects as a function drugs and emesis.}
+\format{\preformatted{ cpt [1:2, 1:2, 1:2, 1:2, 1:3] 1 0 1 0 1 0 1 0 1 0 ...
+ - attr(*, "dimnames")=List of 5
+  ..$ SE        : chr [1:2] "No" "Yes"
+  ..$ TreatSE   : chr [1:2] "No" "Yes"
+  ..$ Emesis    : chr [1:2] "No" "Yes"
+  ..$ Drug      : chr [1:2] "Metoclopramide" "Ondansetron"
+  ..$ Resolution: chr [1:3] "NoSE" "Resolved" "Unresolved"
+ - attr(*, "model")='data.frame':	48 obs. of  7 variables:
+  ..$ SE        : Factor w/ 2 levels "No","Yes": 1 2 1 2 1 2 1 2 1 2 ...
+  ..$ TreatSE   : Factor w/ 2 levels "No","Yes": 1 1 2 2 1 1 2 2 1 1 ...
+  ..$ Emesis    : Factor w/ 2 levels "No","Yes": 1 1 1 1 2 2 2 2 1 1 ...
+  ..$ Drug      : Factor w/ 2 levels "Metoclopramide",..: 1 1 1 1 1 1 1 1 2 2 ...
+  ..$ Resolution: Factor w/ 3 levels "NoSE","Resolved",..: 1 1 1 1 1 1 1 1 1 1 ...
+  ..$ wt        : num [1:48] 1 0 1 0 1 0 1 0 1 0 ...
+  ..$ wt        : num [1:48] 1 0 1 0 1 0 1 0 1 0 ...
+ - attr(*, "class")= chr [1:2] "cpt" "array"
+}}
+\usage{
+Resolution.cpt
+}
+\description{
+This is a conditional probability table used in the emesis example of the JSS article.
+}
+\keyword{datasets}
+

man/SE.cpt.Rd

@@ -0,0 +1,27 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{SE.cpt}
+\alias{SE.cpt}
+\title{Conditional Probability Table for side effects as a function of emesis and drug.}
+\format{\preformatted{ cpt [1:2, 1:2, 1:2] 0.95 0.92 0.85 0.73 0.05 0.08 0.15 0.27
+ - attr(*, "dimnames")=List of 3
+  ..$ Emesis: chr [1:2] "No" "Yes"
+  ..$ Drug  : chr [1:2] "Metoclopramide" "Ondansetron"
+  ..$ SE    : chr [1:2] "No" "Yes"
+ - attr(*, "model")='data.frame':	8 obs. of  5 variables:
+  ..$ Emesis: Factor w/ 2 levels "No","Yes": 1 2 1 2 1 1 2 2
+  ..$ Drug  : Factor w/ 2 levels "Metoclopramide",..: 1 1 2 2 1 2 1 2
+  ..$ SE    : Factor w/ 2 levels "No","Yes": 2 2 2 2 1 1 1 1
+  ..$ wt    : num [1:8] 0.05 0.08 0.15 0.27 0.95 0.85 0.92 0.73
+  ..$ wt    : num [1:8] 0.05 0.08 0.15 0.27 0.95 0.85 0.92 0.73
+ - attr(*, "class")= chr [1:2] "cpt" "array"
+}}
+\usage{
+SE.cpt
+}
+\description{
+This is a conditional probability table used in the emesis example of the JSS article.
+}
+\keyword{datasets}
+

man/inputCPTExample.Rd

@@ -0,0 +1,30 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{inputCPTExample}
+\alias{inputCPTExample}
+\title{Example Conditional Probability Table Resulting from the \code{inputCPT} function.}
+\format{\preformatted{ cpt [1:2, 1:2] 0.77 0.15 0.23 0.85
+ - attr(*, "dimnames")=List of 2
+  ..$ disease: chr [1:2] "Healthy" "Diseased"
+  ..$ test   : chr [1:2] "---" "+++"
+ - attr(*, "model")='data.frame':	4 obs. of  4 variables:
+  ..$ disease: Factor w/ 2 levels "Healthy","Diseased": 1 2 1 2
+  ..$ test   : Factor w/ 2 levels "---","+++": 2 2 1 1
+  ..$ wt     : num [1:4] 0.23 0.85 0.77 0.15
+  ..$ wt     : num [1:4] 0.23 0.85 0.77 0.15
+ - attr(*, "class")= chr [1:2] "cpt" "array"
+}}
+\source{
+No Source.  It's really just made up.
+}
+\usage{
+inputCPTExample
+}
+\description{
+This is an example of the output generated by the \code{inputCPT} function as
+illustrated in the article being submitted to JSS.  It is saved as an object
+named \code{h} in the article.
+}
+\keyword{datasets}
+