Rename Farrington example to oxford

Author: msuchard

DESCRIPTION

@@ -17,7 +17,7 @@ Depends:
     BH (>= 1.51.0),
     RcppEigen (>= 0.3.2),
     Matrix
-Imports: 
+Imports:
     ff,
     ffbase
 LinkingTo: Rcpp,

R/ExampleData.R

@@ -0,0 +1,17 @@
+#' Self-controlled case series example
+#'
+#' A dataset containing the MMR vaccination / meningitis in Oxford example from
+#' Farrington and Whitaker.  There are 10 patients comprising 38 unique exposure intervals.
+#'
+#' @format A data frame with 38 rows and 6 variables:
+#' \describe{
+#'   \item{indiv}{patient identifier}
+#'   \item{event}{number of events in interval}
+#'   \item{interval}{interval length in days}
+#'   \item{agegr}{age group}
+#'   \item{exgr}{exposure group}
+#'   \item{loginterval}{log interval length}
+#'   ...
+#' }
+#' @source \url{http://statistics.open.ac.uk/sccs/r.htm}
+"oxford"

data-raw/chopdat.R data-raw/oxford.R

@@ -65,4 +65,4 @@ constructOxfordDataFrame <- function() {
                loginterval = log(interval[interval!=0]))        
 }
 
-chopdat <- constructOxfordDataFrame()
+oxford <- constructOxfordDataFrame()

data/chopdat.rda

@@ -6,10 +6,10 @@ test_that("Check simple SCCS as conditional logistic regression", {
     source("helper-conditionalPoisson.R")
     tolerance <- 1E-6    
     gold.clogit <- clogit(event ~ exgr + agegr + strata(indiv) + offset(loginterval), 
-                          data = chopdat)
+                          data = oxford)
 
     dataPtr <- createCyclopsDataFrame(event ~ exgr + agegr + strata(indiv) + offset(loginterval),
-                                  data = chopdat,
+                                  data = oxford,
                                   modelType = "clr")        
     cyclopsFit <- fitCyclopsModel(dataPtr,
                           prior = createPrior("none"))
@@ -22,10 +22,10 @@ test_that("Check simple SCCS as conditional Poisson regression", {
     tolerance <- 1E-3    
     gold.cp <- gnm(event ~ exgr + agegr + offset(loginterval), 
                    family = poisson, eliminate = indiv, 
-                   data = chopdat)
+                   data = oxford)
 
     dataPtr <- createCyclopsDataFrame(event ~ exgr + agegr + strata(indiv) + offset(loginterval),
-                                  data = chopdat,
+                                  data = oxford,
                                   modelType = "cpr")        
     cyclopsFit <- fitCyclopsModel(dataPtr,
                           prior = createPrior("none"))
@@ -39,10 +39,10 @@ test_that("Check simple SCCS as SCCS", {
     source("helper-conditionalPoisson.R")
     tolerance <- 1E-6    
     gold.clogit <- clogit(event ~ exgr + agegr + strata(indiv) + offset(loginterval), 
-                          data = chopdat)
+                          data = oxford)
 
-    dataPtr <- createCyclopsDataFrame(event ~ exgr + agegr + strata(indiv), time = chopdat$interval,
-                                  data = chopdat,
+    dataPtr <- createCyclopsDataFrame(event ~ exgr + agegr + strata(indiv), time = oxford$interval,
+                                  data = oxford,
                                   modelType = "sccs")        
     cyclopsFit <- fitCyclopsModel(dataPtr,
                           prior = createPrior("none"))

data/oxford.rda

@@ -149,10 +149,10 @@ test_that("Check multitype SCCS", {
 #     source("helper-conditionalPoisson.R")
 #     tolerance <- 1E-6    
 #     gold.clogit <- clogit(event ~ exgr + agegr + strata(indiv) + offset(loginterval), 
-#                           data = chopdat)
+#                           data = oxford)
 #     
-#     dataPtr <- createCyclopsDataFrame(event ~ exgr + agegr + strata(indiv), time = chopdat$interval,
-#                                       data = chopdat,
+#     dataPtr <- createCyclopsDataFrame(event ~ exgr + agegr + strata(indiv), time = oxford$interval,
+#                                       data = oxford,
 #                                       modelType = "sccs")        
 #     cyclopsFit <- fitCyclopsModel(dataPtr,
 #                                   prior = createPrior("none"))

inst/tests/test-conditionalPoisson.R

@@ -1,12 +1,12 @@
 #' @return
 #'
-#' Returns an \code{\link{environment}} of class inheriting from \code{"ccdData"} that
+#' Returns an \code{\link{environment}} of class inheriting from \code{"cyclopsData"} that
 #' contains at least the following objects:
 #' \tabular{ll}{
-#'      \code{  ccdDataPtr} \tab    An Rcpp \code{externalptr} to the C++ object that holds the data.
+#'      \code{  cyclopsDataPtr} \tab    An Rcpp \code{externalptr} to the C++ object that holds the data.
 #'                                  The object contents does not get written to \code{.Rdata}, so
 #'                                  \code{ccdData} are not reusable across restarts of \code{R}. \cr
-#'      \code{  ccdInterfacePtr} \tab   An Rcpp \code{externalptr} to the C++ object that fits the data.
+#'      \code{  cyclopsInterfacePtr} \tab   An Rcpp \code{externalptr} to the C++ object that fits the data.
 #'                                      Again, this is not reusable across \code{R} invokations. \cr
 #'      \code{  timeLoad} \tab Amount of time (in seconds) taken to load the data. \cr
 #'  }

inst/tests/test-multitypePoisson.R

@@ -0,0 +1,27 @@
+% Generated by roxygen2 (4.0.1): do not edit by hand
+\docType{data}
+\name{oxford}
+\alias{oxford}
+\title{Self-controlled case series example}
+\format{A data frame with 38 rows and 6 variables:
+\describe{
+  \item{indiv}{patient identifier}
+  \item{event}{number of events in interval}
+  \item{interval}{interval length in days}
+  \item{agegr}{age group}
+  \item{exgr}{exposure group}
+  \item{loginterval}{log interval length}
+  ...
+}}
+\source{
+\url{http://statistics.open.ac.uk/sccs/r.htm}
+}
+\usage{
+oxford
+}
+\description{
+A dataset containing the MMR vaccination / meningitis in Oxford example from
+Farrington and Whitaker.  There are 10 patients comprising 38 unique exposure intervals.
+}
+\keyword{datasets}
+

man-roxygen/cyclopsData.R

@@ -12,13 +12,13 @@ readCyclopsData(fileName, modelType)
                                                  the name is relative to the current working directory, \code{\link{getwd}}.}
 }
 \value{
-Returns an \code{\link{environment}} of class inheriting from \code{"ccdData"} that
+Returns an \code{\link{environment}} of class inheriting from \code{"cyclopsData"} that
 contains at least the following objects:
 \tabular{ll}{
-     \code{  ccdDataPtr} \tab    An Rcpp \code{externalptr} to the C++ object that holds the data.
+     \code{  cyclopsDataPtr} \tab    An Rcpp \code{externalptr} to the C++ object that holds the data.
                                  The object contents does not get written to \code{.Rdata}, so
                                  \code{ccdData} are not reusable across restarts of \code{R}. \cr
-     \code{  ccdInterfacePtr} \tab   An Rcpp \code{externalptr} to the C++ object that fits the data.
+     \code{  cyclopsInterfacePtr} \tab   An Rcpp \code{externalptr} to the C++ object that fits the data.
                                      Again, this is not reusable across \code{R} invokations. \cr
      \code{  timeLoad} \tab Amount of time (in seconds) taken to load the data. \cr
  }