NEWS

---

clinfun 1.1.5 (2023-10-19)

• clarified one-sided vs two-sided futility boundary for gsdesign functions

clinfun 1.1.4 (2023-10-12)

• added check for n; since it is for stopping early at least two values should be given
• addressed the warning in the example for calogrank; status had both death and transplant

clinfun 1.1.3 (2023-07-13)

• fixed the bug in ph2simon/twostage.admissible when minimax is also optimal
• ph2simon and toxbdry help have been made more clear

clinfun 1.1.2 (2023-06-19)

• changed all dfloat in fortran to dble
• print method for ph2simon now lists admissible designs

New Functionality

• plot and lines method for roc.curve includes the option for precision-recall curve
• roc.curve returns PPV and NPV which are needed for precision-recall curve

clinfun 1.1.1 (2023-03-07)

• changed class check to use inherits instead of comparing strings

New Functionality

• Added out.ties option to coxphCPE for discrete risk score case

clinfun 1.1.0 (2022-02-22)

New Functionality

• Added added admissible two stage design function
• Added added futilbdry function for sequential futility stopping
• added 1:r sample allocation in gsdesign functions
• Fixed the warnings messages from deltaAUC.f

New Documentation

• Added a NEWS.md file to track changes to the package.
• deposited development version on GitHub
• created {pkgdown} website and github actions for building site

clinfun 1.0.15 (2018-04-13)

• Added new function deltaAUC to test for difference in the area under the ROC curves from nested binary regression models.
• power.ladesign does exact null if number of combinations is small
• Added to help of fedesign, ph2simon and ph2single functions

clinfun 1.0.14 (2017-04-25)

• added init.c to register native routines

clinfun 1.0.13 (2016-11-30)

• permlogrank bug fix - strata option gave an error. Names of elements in survfit.object changed. (strata instead of ntimes.strata and n a vector).

clinfun 1.0.12 (2016-10-17)

• added aucVardiTest to compare growth curves

clinfun 1.0.11 (2015-08-12)

• check for misssing values in jonckheere.test

clinfun 1.0.10 (2015-05-18)

• bug fix for pselect; nlen > 3 should have been nlen > 2

clinfun 1.0.9 (2015-02-24)

• use requireNamespace to remove NOTES on functions using survival pkg

clinfun 1.0.8

• fix name swap in the result of mdrr in v1.0.7

clinfun 1.0.7

• new function mdrr added to calculate minimum detectable difference in response rates for given average response rate and class proportion

clinfun 1.0.6 (2014-07-22)

• On rare occasions jonckheere.test gave a p-value bigger than 1. Sometimes 2min(iPVAL, dPVAL, 1) can be larger than 1. Replace with 2min(iPVAL, dPVAL, 0.5) (Thanks to Drs. Shterev and Owzar of Duke).

clinfun 1.0.5 (2013-04-16)

• Fixed the bound checks

clinfun 1.0.4 (2013-01-23)

• Added the option to calculate continuity corrected sample size in the function gsdesign.binomial.

clinfun 1.0.3 (2012-10-15)

• Fixed two-sided p-value > 1 bug when statistic is exactly its mean.
• Fixed Rd file to address LaTeX warnings.

clinfun 1.0.2 (2012-09-26)

• integer overflow in djonck for the Jonckheere-Terpstra statistic. replace with pdf calculation using Mark van de Wiel convolution.
• Create seperate help for functions permlogrank and jonckheere.test

clinfun 1.0.1 (2012-08-14)

• Fix integer overflow because of n0n1 == 0 in roc.curve and nnnd == 0 in roc.area.test
• In coxphQuantile eliminate times for which survival probability is 0 or 1 from quantile computation.

clinfun 1.0.0 (2012-03-13)

• clinfun number changed to 1.0.0 in preparation for R 2.15.

• toxbdry now does the entire Pocock to O'Brien-Fleming range of boundaries. Added references for the method.
• Fixed linebreak in the help for coxphERR.

clinfun 0.9.9 (2012-01-18)

• Added coxphERR to calculate Heller's explained relative risk.
• Fixed NaN bug in toxbdry when priority="alt" is used.

clinfun 0.9.8 (2011-09-14)

• fixed bug in print.gsdesign for binomial case (p1,p2 instead of pC,pE)
• ROC functions now check that there are at least one each of status=0,1

clinfun 0.9.7 (2011-04-27)

• fixed fortran code to address gfortran-4.6 warnings
• added ktau a faster implementation of cor(x, y, method="k"). not in NAMESPACE. Should be called using clinfun:::ktau

• bug fix: roc.area.test integer overflow for large nn*nd.
• use sort function to speed up roc curve and area estimation.

clinfun 0.9.6 (2011-03-24)

• bug fix: roc.area.test gave NaN as the statistic and p-value when the markers are identical. Changed it to 0.

clinfun 0.9.5 (2011-03-09)

• bug fix: gsdesign funtions not returning the sample size / # events.

clinfun 0.9.4 (2011-02-25)

• twostage.inference for umvue, p-value and CI for 2 stage design.

clinfun 0.9.3 (2010-12-07)

• ph2simon was testing whether dim is null for feasible solution. Replaced with nrow == 0 since it is now possible to have 0 rows.

clinfun 0.9.2 (2010-11-10)

• Added functions to compute and plot the empirical ROC curve.

clinfun 0.9.1 (2010-11-05)

• Added functions for the area and permutation tests to compare ROC.
• Checks that min.diff is greater than 0 in pselect.

clinfun 0.9.0 (2010-11-03)

• Added a non-binding futility boundary to gsdesign

clinfun 0.8.10 (2010-04-16)

• variable names for returned data.frame in coxphQuantile
• examples in coxphQuantile & coxphCPE use status==2

clinfun 0.8.9 (2010-04-10)

• check R# clinfun so that coxphCPE works for any # clinfun (see 0.8.9)

clinfun 0.8.8 (2010-04-08)

• Change coxphCPE to reflect the fact that model.matrix.coxph doesn't have an intercept term.

• Added the function or2pcase

clinfun 0.8.7 (2009-11-22)

• Fixed the 0/0 bug in the revised pselect

clinfun 0.8.6 (2009-11-19)

• Changed Venkat's affiliation to MSKCC.
• Fixed pselect to calculate the selection probability correctly when only one treatment exceeds the min.resp threshold.

clinfun 0.8.5 (2009-07-18)

• Changed the Jonckheere-Terpstra statistic such that large value is indicative of increasing group locations and small for decreasing. Function warns that p-value is based on approximation for tied data.

clinfun 0.8.4 (2008-12-02)

• Added functionality to pselect. It can do unequal sample size for the case of two treatments. min.diff can be specified as a rate instead of number of responses. Output element names changed to be more descriptive.

clinfun 0.8.3 (2008-11-18)

• Fixed the bug CPS.ssize. call inside used fixed alpha, power & r.
• Fixed the bug in the approximate one-sided p-value of Jonckheere test. wrong tail was used.

clinfun 0.8.2 (2008-07-01)

• toxbdry allows the error threshold to prioritize when the sample size is too small to have both satisfied.

clinfun 0.8.1 (2008-06-17)

• Fixed gsdesign to allow for fixed sample designs. Help file fixed.

clinfun 0.8.0 (2008-05-23)

• New # clinfun with one new function power.lehmann.design