# 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
#' @import checkmate
#' @import ggplot2
#' @import methods
#' @import tibble
#' @importFrom grid grid.draw
#' @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 dbeta dgamma
#' setNames
#' @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
#' @importFrom knitr knit_print
#' @importFrom kableExtra kbl add_header_above column_spec collapse_rows
#' kable_styling add_footnote kable
#'
#' @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",
"delta0",
"alpha1",
"delta1",
"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",
"comp",
"X",
"skel_probs",
"is_combo",
"results",
"k",
"value",
"Parameter",
"intervals",
"Group",
"Tox"
))
# nolint end
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