OneArmPhaseTwoStudy: Planing, Monitoring and Evaluating Oncological Phase 2 Studies

Purpose of this package is it to plan, monitor and evaluate oncological phase II studies. In general this kind of studies are single-arm trials with planned interim analysis and binary endpoint. To meet the resulting requirements, the package provides functions to calculate and evaluate 'Simon's two-stage designs' and 'so-called' 'subset designs'. If you are unfamiliar with this package a good starting point is to take a closer look at the functions getSolutions() and getSolutionsSub1().The web-based tool (https://imbi.shinyapps.io/phaseII-app/) extends the functionality of our R package by means of a proper dealing with over- and underrunning. The R function binom.test of the 'stats' R package and the package 'binom' might be helpful to assess the performance of the corresponding one-stage design as a reference.

Author
Marius Wirths
Date of publication
2016-05-23 11:28:04
Maintainer
Marius Wirths <wirths@imbi.uni-heidelberg.de>
License
GPL (>= 2)
Version
0.1.6

View on CRAN

Man pages

getCE
Calculates the conditional error.
get_CI
Calculates the confidence interval.
get_conditionalPower
Calculates the conditional power.
get_confidence_set
Calculates the confidence set.
getCP
Calculates the conditional power.
getCP_simon
Returns the conditional power.
getD_distributeToOne
Get the conditional errors.
getD_equally
Get the conditional errors equally.
getD_none
Get the conditional errors.
getD_proportionally
Get the conditional errors proportionally.
getN2
Calculates the number of patients which should be enrolled in...
getP
Calculates the p-value (binomial test).
get_p_exact_subset
Calculates the exact p value.
get_p_KC
Calculates the p-value.
get_r2_flex
Calculates the number of responses needed for the second...
getSolutions
Returns designs for a given "simon"-object (see 'setupSimon')
getSolutionsSub1
Calculates designs for a given "sub1"-object.
get_UMVUE_GMS
Calculates the "uniformly minimal variance unbiased...
get_UMVUE_GMS_subset_second_only
Calculates the "uniformly minimal variance unbiased...
get_UMVUE_GMS_subset_second_total
Calculates the "uniformly minimal variance unbiased...
plot_confidence_set
Plots the "confidence set" according to the observed...
plot_simon_study_state
Plots the study state of a given Simon's two-stage design.
plot_sub1_study_state
Plots the study state of a given subset design.
setSimonParams
Sets the parameters for a given "simon"-object.
setSub1Params
Sets the parameters for a given "sub1"-object.
setupSimon
Creates a "simon"-object.
setupSub1Design
Creates a "sub1"-object.
simon_module
Functions and Objects created by Rcpp for the "Simon's...
sub1_module
Functions and Objects created by Rcpp for the "subset design"
toDataframe
Helper function for 'getSolutions' and 'getSolutionsSub1'.

Files in this package

OneArmPhaseTwoStudy
OneArmPhaseTwoStudy/src
OneArmPhaseTwoStudy/src/result.cpp
OneArmPhaseTwoStudy/src/Makevars
OneArmPhaseTwoStudy/src/simon.cpp
OneArmPhaseTwoStudy/src/result.h
OneArmPhaseTwoStudy/src/design.h
OneArmPhaseTwoStudy/src/resultsub1.cpp
OneArmPhaseTwoStudy/src/sub1.h
OneArmPhaseTwoStudy/src/sub1.cpp
OneArmPhaseTwoStudy/src/resultsub1.h
OneArmPhaseTwoStudy/src/simon.h
OneArmPhaseTwoStudy/src/simonModule.h
OneArmPhaseTwoStudy/src/design.cpp
OneArmPhaseTwoStudy/src/Makevars.win
OneArmPhaseTwoStudy/src/sub1Module.h
OneArmPhaseTwoStudy/NAMESPACE
OneArmPhaseTwoStudy/R
OneArmPhaseTwoStudy/R/zzz.R
OneArmPhaseTwoStudy/MD5
OneArmPhaseTwoStudy/DESCRIPTION
OneArmPhaseTwoStudy/man
OneArmPhaseTwoStudy/man/getSolutionsSub1.Rd
OneArmPhaseTwoStudy/man/getP.Rd
OneArmPhaseTwoStudy/man/simon_module.Rd
OneArmPhaseTwoStudy/man/get_p_exact_subset.Rd
OneArmPhaseTwoStudy/man/get_UMVUE_GMS_subset_second_only.Rd
OneArmPhaseTwoStudy/man/get_confidence_set.Rd
OneArmPhaseTwoStudy/man/plot_simon_study_state.Rd
OneArmPhaseTwoStudy/man/getD_none.Rd
OneArmPhaseTwoStudy/man/get_conditionalPower.Rd
OneArmPhaseTwoStudy/man/get_UMVUE_GMS.Rd
OneArmPhaseTwoStudy/man/sub1_module.Rd
OneArmPhaseTwoStudy/man/get_r2_flex.Rd
OneArmPhaseTwoStudy/man/getCP_simon.Rd
OneArmPhaseTwoStudy/man/getSolutions.Rd
OneArmPhaseTwoStudy/man/setupSimon.Rd
OneArmPhaseTwoStudy/man/plot_sub1_study_state.Rd
OneArmPhaseTwoStudy/man/getCE.Rd
OneArmPhaseTwoStudy/man/get_UMVUE_GMS_subset_second_total.Rd
OneArmPhaseTwoStudy/man/getN2.Rd
OneArmPhaseTwoStudy/man/get_p_KC.Rd
OneArmPhaseTwoStudy/man/getD_distributeToOne.Rd
OneArmPhaseTwoStudy/man/setSub1Params.Rd
OneArmPhaseTwoStudy/man/getD_equally.Rd
OneArmPhaseTwoStudy/man/getD_proportionally.Rd
OneArmPhaseTwoStudy/man/toDataframe.Rd
OneArmPhaseTwoStudy/man/setSimonParams.Rd
OneArmPhaseTwoStudy/man/setupSub1Design.Rd
OneArmPhaseTwoStudy/man/getCP.Rd
OneArmPhaseTwoStudy/man/plot_confidence_set.Rd
OneArmPhaseTwoStudy/man/get_CI.Rd