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Changelog

clinfun 1.1.6 (08/11/2026)

  • Issue in dwilcox call in jtpdf.f due to wilcox_free(); fortran code rewritten
  • Rd files for some functions updated
  • version on GitHub (12/06/2023) - moved twostage.admissible call from print method to ph2simon; added reference

clinfun 1.1.5 (10/19/2023)

CRAN release: 2023-10-19

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

clinfun 1.1.4 (10/12/2023)

CRAN release: 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 (07/11/2023)

CRAN release: 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 (06/19/2023)

CRAN release: 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 (03/06/2023)

CRAN release: 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 (02/22/2022)

CRAN release: 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 (04/13/2018)

CRAN release: 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 (04/25/2017)

CRAN release: 2017-04-25

  • added init.c to register native routines

clinfun 1.0.13 (11/29/2016)

CRAN release: 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 (08/03/2016)

CRAN release: 2016-10-17

  • added aucVardiTest to compare growth curves

clinfun 1.0.11 (08/11/2015)

CRAN release: 2015-08-12

  • check for misssing values in jonckheere.test

clinfun 1.0.10 (05/18/2015)

CRAN release: 2015-05-18

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

clinfun 1.0.9 (02/24/2015)

CRAN release: 2015-02-24

  • use requireNamespace to remove NOTES on functions using survival pkg

clinfun 1.0.8 (02/19/2015)

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

clinfun 1.0.7 (02/19/2015)

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

clinfun 1.0.6 (06/10/2014)

CRAN release: 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 (04/16/2013)

CRAN release: 2013-04-16

  • Fixed the bound checks

clinfun 1.0.4 (01/22/2013)

CRAN release: 2013-01-23

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

clinfun 1.0.3 (10/15/2012)

CRAN release: 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 (09/25/2012)

CRAN release: 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 (08/14/2012)

CRAN release: 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 (03/13/2012)

CRAN release: 2012-03-13

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

    CRAN release: 2012-03-13

  • 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 (01/18/2012)

CRAN release: 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 (09/13/2011)

CRAN release: 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 (04/27/2011)

CRAN release: 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

clinfun 0.9.7 (04/25/2011)

CRAN release: 2011-04-27

  • 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 (03/24/2011)

CRAN release: 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 (03/09/2011)

CRAN release: 2011-03-09

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

clinfun 0.9.4 (02/24/2011)

CRAN release: 2011-02-25

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

clinfun 0.9.3 (12/06/2010)

CRAN release: 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 (11/05/2010)

CRAN release: 2010-11-10

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

clinfun 0.9.1 (11/03/2010)

CRAN release: 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 (11/01/2010)

CRAN release: 2010-11-03

  • Added a non-binding futility boundary to gsdesign

clinfun 0.8.10 (04/16/2010)

CRAN release: 2010-04-16

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

clinfun 0.8.9 (04/09/2010)

CRAN release: 2010-04-10

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

clinfun 0.8.8 (04/07/2010)

CRAN release: 2010-04-08

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

clinfun 0.8.8 (02/25/2010)

CRAN release: 2010-04-08

  • Added the function or2pcase

clinfun 0.8.7 (11/20/2009)

CRAN release: 2009-11-22

  • Fixed the 0/0 bug in the revised pselect

clinfun 0.8.6 (11/17/2009)

CRAN release: 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 (07/10/2009)

CRAN release: 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 (12/02/2008)

CRAN release: 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 (11/18/2008 & 09/18/2008)

CRAN release: 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 (06/20/2008)

CRAN release: 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 (06/17/2008)

CRAN release: 2008-06-17

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

clinfun 0.8.0 (05/23/2008)

CRAN release: 2008-05-23

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