update roxygen to 4.0 and add pain_relief categorical datset

dpastoor · Jun 5, 2014 · d2974d5 · d2974d5
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diff --git a/NAMESPACE b/NAMESPACE
@@ -1,2 +1,4 @@
+# Generated by roxygen2 (4.0.1): do not edit by hand
+
 export(list_datasets)
 export(print_datasets)
diff --git a/PKPDdatasets.Rproj b/PKPDdatasets.Rproj
@@ -9,8 +9,9 @@ UseSpacesForTab: Yes
 NumSpacesForTab: 2
 Encoding: UTF-8
 
-RnwWeave: Sweave
+RnwWeave: knitr
 LaTeX: pdfLaTeX
 
 BuildType: Package
+PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
diff --git a/R/categorical_datasets.R b/R/categorical_datasets.R
@@ -0,0 +1,26 @@
+#' Simulated anti-inflammatory pain trial
+#' 
+#' CTM_Nopain is a novel anti-inflammatory agent under preliminary investigation.  
+#' A dose-ranging trial was conducted comparing placebo with 3 doses of CTM_Nopain (5mg, 20mg and 80 mg QD).  
+#' The maximum tolerated dose is 160 mg per day.  
+#' Plasma concentrations (mg/L) of the drug were measured at 0, 0.5, 1, 1.5, 2, 2.5, 3-8 hours. 
+#' Pain score (0=no pain, 1=mild, 2=moderate, 3=severe) were obtained at time points when plasma concentration was collected.  
+#' A pain score of 2 or more is considered as no pain relief. 
+#' The model used is a one-compartment PK model with allometric model of weight on CL (exp 0.75) and volume (exp 1) 
+#' with direct PD effect (Emax model). 
+#' 
+#' \itemize{
+#'   \item ARM Factor with 4 levels
+#'   \item ID. Numerical ID  (1-160)
+#'   \item TIME Time in hours 
+#'   \item CONC Concentration (mg/L)
+#'   \item PAINRELIEF 0 (no relief) or 1 (relief)
+#'   \item PAINSCORE categorical pain score
+#'   \item DOSE Dose Given
+#' }
+#' @docType data
+#' @keywords datasets
+#' @name pain_relief
+#' @usage data(pain_relief)
+#' @format A data frame with 1920 rows and 7 variables
+NULL
diff --git a/data/pain_relief.rda b/data/pain_relief.rda
diff --git a/data/pain_score.rda b/data/pain_score.rda
diff --git a/man/PKPDdatasets.Rd b/man/PKPDdatasets.Rd
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.1): do not edit by hand
 \docType{package}
 \name{PKPDdatasets}
 \alias{PKPDdatasets}

diff --git a/man/list_datasets.Rd b/man/list_datasets.Rd
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.1): do not edit by hand
 \name{list_datasets}
 \alias{list_datasets}
 \title{List datasets available in PKPDdatasets package}

diff --git a/man/pain_relief.Rd b/man/pain_relief.Rd
@@ -0,0 +1,32 @@
+% Generated by roxygen2 (4.0.1): do not edit by hand
+\docType{data}
+\name{pain_relief}
+\alias{pain_relief}
+\title{Simulated anti-inflammatory pain trial}
+\format{A data frame with 1920 rows and 7 variables}
+\usage{
+data(pain_relief)
+}
+\description{
+CTM_Nopain is a novel anti-inflammatory agent under preliminary investigation.
+A dose-ranging trial was conducted comparing placebo with 3 doses of CTM_Nopain (5mg, 20mg and 80 mg QD).
+The maximum tolerated dose is 160 mg per day.
+Plasma concentrations (mg/L) of the drug were measured at 0, 0.5, 1, 1.5, 2, 2.5, 3-8 hours.
+Pain score (0=no pain, 1=mild, 2=moderate, 3=severe) were obtained at time points when plasma concentration was collected.
+A pain score of 2 or more is considered as no pain relief.
+The model used is a one-compartment PK model with allometric model of weight on CL (exp 0.75) and volume (exp 1)
+with direct PD effect (Emax model).
+}
+\details{
+\itemize{
+  \item ARM Factor with 4 levels
+  \item ID. Numerical ID  (1-160)
+  \item TIME Time in hours
+  \item CONC Concentration (mg/L)
+  \item PAINRELIEF 0 (no relief) or 1 (relief)
+  \item PAINSCORE categorical pain score
+  \item DOSE Dose Given
+}
+}
+\keyword{datasets}
+
diff --git a/man/print_datasets.Rd b/man/print_datasets.Rd
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.1): do not edit by hand
 \name{print_datasets}
 \alias{print_datasets}
 \title{Print datasets available in PKPDdatasets package}

diff --git a/man/sd_iv_rich_pkpd.Rd b/man/sd_iv_rich_pkpd.Rd
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.1): do not edit by hand
 \docType{data}
 \name{sd_iv_rich_pkpd}
 \alias{sd_iv_rich_pkpd}
@@ -7,30 +8,36 @@
 data(sd_iv_rich_pkpd)
 }
 \description{
-A dataset containing simulated PKPD data. A single IV bolus
-dose was given and rich pharmacokinetic and pharmacodynamic
-measurements were taken. Demographic data of Age, Weight,
-Gender, and Race were collected.
+A dataset containing simulated PKPD data. A single IV bolus dose was given and rich pharmacokinetic
+and pharmacodynamic measurements were taken. Demographic data of Age, Weight, Gender, and Race were collected.
 }
 \details{
-The model used is a one-compartment PK model with
-allometric model of weight on CL (exp 0.75) and volume (exp
-1) with direct PD effect (Emax model).
+The model used is a one-compartment PK model with allometric model of weight on CL (exp 0.75) and volume (exp 1)
+with direct PD effect (Emax model).
 
-\itemize{ \item ID. Numerical ID (1-100) \item TIME Time in
-hours (0-12) \item COBS. Plasma concentration in \item
-EOBS.  \item WEIGHT. Weight in kg \item AGE. Age in years
-\item DOSE. Three dose levels: 1, 10, and 100 mg \item SEX.
-Male or Female gender identification \item RACE.
-AfricanAmerican, Caucasian, Others, and Asian races \item
-AMT. Amount of drug given, time dependent, in milligrams }
+\itemize{
+  \item ID. Numerical ID  (1-100)
+  \item TIME Time in hours (0-12)
+  \item COBS. Plasma concentration in
+  \item EOBS.
+  \item WEIGHT. Weight in kg
+  \item AGE. Age in years
+  \item DOSE. Three dose levels: 1, 10, and 100 mg
+  \item SEX. Male or Female gender identification
+  \item RACE. AfricanAmerican, Caucasian, Others, and Asian races
+  \item AMT. Amount of drug given, time dependent, in milligrams
+}
 
-Parameters used to simulate data: \tabular{lcr}{ Parameter
-\tab Mean \tab Variance (BSV)\cr CL (L/hr) \tab 1 \tab 0.16
-(40\%)\cr V (L) \tab 10 \tab 0.09 (30\%)\cr Residual error:
-Proportional \tab 0 \tab 10\%\cr Emax \tab 10 \tab sd = 1.4
-units\cr EC50 (mg/L) \tab 2 \tab 0.09 (30\%)\cr Residual
-Error on Effect \tab 0 \tab sd = 0.5 units }
+Parameters used to simulate data:
+  \tabular{lcr}{
+Parameter                    \tab Mean \tab Variance (BSV)\cr
+CL (L/hr)                    \tab 1    \tab 0.16 (40\%)\cr
+V (L)                        \tab 10   \tab 0.09 (30\%)\cr
+Residual error: Proportional \tab 0    \tab 10\%\cr
+Emax                         \tab 10   \tab sd = 1.4 units\cr
+EC50 (mg/L)                  \tab 2    \tab 0.09 (30\%)\cr
+Residual Error on Effect     \tab 0    \tab sd = 0.5 units
+}
 }
 \keyword{datasets}
 
diff --git a/man/sd_oral_richpk.Rd b/man/sd_oral_richpk.Rd
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.1): do not edit by hand
 \docType{data}
 \name{sd_oral_richpk}
 \alias{sd_oral_richpk}
@@ -7,17 +8,20 @@
 data(sd_oral_richpk)
 }
 \description{
-A dataset containing dose, plasma concentration and time
-data, as well as demographic data of Age, Weight, Gender,
-and Race for each individual
+A dataset containing dose, plasma concentration and time data, as well as
+ demographic data of Age, Weight, Gender, and Race for each individual
 }
 \details{
-\itemize{ \item ID. Numerical ID (1--50) \item Time. Time
-in hours (0--24) \item Amt. Amount of drug given, time
-dependent, in milligrams \item Conc. Plasma concentration
-in mg/L \item Age. Age in years \item Weight. Weight in kg
-\item Gender. Male or Female gender identification \item
-Dose. Dose given to each individual in milligrams }
+\itemize{
+  \item ID. Numerical ID  (1--50)
+  \item Time. Time in hours (0--24)
+  \item Amt. Amount of drug given, time dependent, in milligrams
+  \item Conc. Plasma concentration in mg/L
+  \item Age. Age in years
+  \item Weight. Weight in kg
+	 \item Gender. Male or Female gender identification
+  \item Dose. Dose given to each individual in milligrams
+}
 }
 \keyword{datasets}