R/crmPack-package.R

In 0liver0815/onc-crmpack-test: Object-Oriented Implementation of CRM Designs

# nolint start

#####################################################################################
## Author: Daniel Sabanes Bove [sabanesd *a*t* roche *.* com]
## Project: Object-oriented implementation of CRM designs
##
## Time-stamp: <[crmPack-package.R] by DSB Mon 11/05/2015 17:47>
##
## Description:
## Package description.
##
## History:
## 29/01/2014   file creation
#####################################################################################

#' Object-oriented implementation of CRM designs
#'
#' @name crmPack-package
#' @aliases crmPack
#' @docType package
#' @title Object-oriented implementation of CRM designs
#' @author Daniel Sabanes Bove \email{daniel.sabanesbove@@gmx.net}, W
#' Wai Yin Yeung \email{winnie.yeung@@roche.com}
#' Giuseppe Palermo \email{giuseppe.palermo@@roche.com},
#' Thomas Jaki \email{jaki.thomas@@gmail.com}
# @useDynLib crmPack
#  cpp_glmBayesMfp cpp_bfgs cpp_optimize cpp_sampleGlm cpp_evalZdensity
#  cpp_coxfit
#' @import checkmate
#' @import ggplot2
#' @import methods
#' @importFrom gridExtra arrangeGrob
#' @importFrom graphics plot hist legend lines matlines matplot
#' @importFrom stats binomial coef cov2cor gaussian glm lm median model.matrix
#' optim pgamma plogis pnorm qgamma qlogis qnorm quantile rbinom rgamma approxfun
#' rnorm runif uniroot var vcov step mad pbeta
#' @importFrom utils data head tail capture.output
#' @importFrom lifecycle badge
#' @importFrom rjags jags.model jags.samples
#' @importFrom futile.logger flog.threshold flog.logger flog.trace TRACE FATAL
#' @keywords package
#' @references Sabanes Bove D, Yeung WY, Palermo G, Jaki T (2019).
#' "Model-Based Dose Escalation Designs in R with crmPack."
#' Journal of Statistical Software, 89(10), 1-22.
#' doi:10.18637/jss.v089.i10 (URL: http://doi.org/10.18637/jss.v089.i10).
{}

##' @keywords internal
.onAttach <- function(libname, pkgname)
{
    packageStartupMessage(
        "Type crmPackHelp() to open help browser\n",
        "Type crmPackExample() to open example\n")
}

## need to declare global variable / function
## names in order to avoid R CMD check notes:
globalVariables(c("log.betaZ",
                  "precW",
                  "pow",
                  "nObs",
                  "betaZ",
                  "x",
                  "betaW",
                  "xLevel",
                  "precW",
                  "z",
                  "nGrid",
                  "doseGrid",
                  "betaWintercept",
                  "delta",
                  "deltaStart",
                  "delta2",
                  "Effsamples",
                  "logit<-",
                  "rho0",
                  "alpha0",
                  "alpha1",
                  "inverse",
                  "priorCov",
                  "theta",
                  "comp0",
                  "w",
                  "DLTs",
                  "y",
                  "group",
                  "annotate",
                  "probSamples",
                  "prec",
                  "nu",
                  "samples",
                  "Type",
                  "patient",
                  "toxicity",
                  "ID",
                  "biomarker",
                  "traj",
                  "Statistic",
                  "perc",
                  "..density..",
                  "middle",
                  "lower",
                  "upper",
                  "middleBiomarker",
                  "lowerBiomarker",
                  "upperBiomarker",
                  "nObsshare",
                  "xshare",
                  "yshare",
                  "thisProb.PL",
                  "thisMeanEff.PL",
                  "thisSize.PL",
                  "probit<-",
                  "refDose",
                  "Tmax",
                  "u",
                  "eps",
                  "h",
                  "lambda",
                  "cadj",
                  "A",
                  "lambda_p",
                  "cond",
                  "t0",
                  "tend",
                  "t0_case",
                  "tend_case",
                  "yhat",
                  "ref_dose"))

# nolint end