2024-10-18 Florian Pein, version 2.1-10 * In multiple .cpp and .h files: set R_NO_REMAP and added Rf_ before all functions (error in the new CRAN version) * In computeBounds.Rd, critVal.Rd, stepFit.Rd, stepR-package.Rd: added package anchors for Rd \links 2023-11-13 Florian Pein, version 2.1-9 * tests.R: replaced is.null(warnings()) by length(warnings()) == 0 (reported with suggestion by Martin Maechler) 2023-07-27 Florian Pein, version 2.1-8 * DESCRIPTION: added explanation of SMUCE and HSMUCE (CRAN request) * Rd files: replaced \dontrun by \donttest (CRAN request) * tests: replaced installed.packages by find.package (CRAN request, faster run time) * critVal.R, stepsel.R, MRC.R, bounds.R: stores MC simulations in package enviroment and not in the global enviroment (CRAN request) 2023-07-18 Florian Pein, version 2.1-7 * test-critVal.R: changed tolerance when identifying tests that reject; added more informative tests for failed test * made sure that no chache files remain when testing the package (CRAN request) 2023-05-16 Florian Pein, version 2.1-6 * test-critVal.R: added a tolerance (suggested by CRAN Team) 2023-05-16 Florian Pein, version 2.1-6 * test-critVal.R: ensured that alpha is an integer in l. 16 (CRAN error on M1mac) 2023-05-12 Florian Pein, version 2.1-5 * test-critVal.R: correct tolerance in l. 19 (CRAN error on M1mac) 2022-01-30 Florian Pein, version 2.1-4 * Step.cpp: replaced std::sprintf by std::snprintf (CRAN warning) 2022-05-05 Florian Pein, version 2.1-3 * added FCONE's in choleskyDecomposition.cpp, DataLR.cpp, DataJsmurfLR.cpp, DataHjsmurfLR.cpp to deal with USE_FC_LEN_T being set (required for R-4.2.0) * added skip_on_cran and dontrun for faster tests and examples * removed \code in first argument of \item in \value in MRC.Rd and stepfitClass.Rd (CRAN note) 2022-01-27 Florian Pein, version 2.1-2 * new maintainer email adress 2020-08-23 Florian Pein, version 2.1-1 * DataLR.cpp: replaced delete by delete [] (indictated by CRAN tests) * testComputeStat.R: expect_equal instead of expect_identical in line 1466 (indictated by CRAN tests on Mac OS) 2020-08-03 Florian Pein, version 2.1-0 * depends now on R-3.3.0 (digest requires it) * added import of package lowpassFilter * computeStat: added input checks for argument signal * removed Convolve.cpp (is not needed anymore because of import of lowpassFilter) * new exported function .testSmallScales: for developers only, users should look at the function improveSmallScales in the package clampSeg * new parametric families jsmurf, jsmurfPS, jsmurfLR, hjsmurf, hjsmurfSPS, hjsmurfLR, 2Param, LR: for developers only, users should look at the functions jsmurf and hilde in package clampSeg 2019-11-03 Florian Pein, version 2.0-4 * new maintainer email adress * splitted keywords in stepR-package.Rd 2019-01-18 Florian Pein, version 2.0-3 * added ties = mean to call of approxfun in thresh.smuceR to avoid warnings R-devel (reported with suggestion by Martin Maechler) * more informative error message when the length of weights is wrong in critVal.R * depends now on >= R-3.1.0 (imported packages have such a dependency) 2018-04-06 Florian Pein, version 2.0-2 * new maintainer * removed packages in StepR.Rnw that are not required * added length(seed) == 1 to avoid if case with condition of length > 1 in monteCarloSimulation.R, updated tests in test-critVal.R, test-computeBounds.R, test-stepFit.R (reported by Tomas Kalibera) * updated references in stepR-package.Rd, comouteBounds.Rd, computeStat.Rd, critVal.Rd, monteCarloSimulation.Rd, parametricFamily.Rd, penalty.Rd, stepFit.Rd * added references to description * added \donttest to intervalSystem.Rd 2017-05-19 Florian Pein, version 2.0-1 * small changes in DESCRIPTION and stepR-package.Rd * added \donttest to stepR-package.Rd, computeBounds.Rd, critVal.Rs, monteCarloSimulation.Rd, stepFit.Rd because of long execution times 2017-05-15 Florian Pein, version 2.0-0 NEW * added functions stepFit, critVal, computeStat, computeBounds, monteCarloSimulation: NAMESPACE: added export(computeStat), export(computeBounds), export(stepFit), export(critVal), export(monteCarloSimulation) added files: in R: computeBounds.R, computeStat.R, critVal.R, intervalSystem.R, monteCarloSimulation.R, parametricFamily.R, stepFit.R in src: CallRoutines.cpp, ColMax.cpp, Compute.cpp, Compute.h, Convolve.cpp, CriticalValuesWeights.cpp, Data.cpp, Data.h, DataGauss.cpp, DataGauss.h, DataHsmuce.cpp, DataHsmuce.h, DataMDependentPS.cpp, DataMDependentPS.h, DynamicPrograms.cpp, DynamicPrograms.h, InOrdered.cpp, IntervalSystem.cpp, IntervalSystem.h, IntervalSystemAll.cpp, IntervalSystemAll.h, IntervalSystemAllLengths.cpp, IntervalSystemAllLengths.h, IntervalSystemDyaLen.cpp, IntervalSystemDyaLen.h, IntervalSystemDyaLenLengths.cpp, IntervalSystemDyaLenLengths.h, IntervalSystemDyaPar.cpp, IntervalSystemDyaPar.h, IntervalSystemDyaParLengths.cpp, IntervalSystemDyaParLengths.h, LocalOptimum.cpp, LocalOptimum.h, SingleBounds.cpp, SingleBounds.h in man: computeBounds.Rd, computeStat.Rd, critVal.Rd, family.Rd, intervalSystem.Rd, monteCarloSimultion.Rd, parametricFamily.Rd, penalty.Rd, stepFit.Rd in tests: testthat.R, folder testthat, therein: test-computeBounds.R, test-computeStat.R, test-critVal.R, test-monteCarloSimulation.R, test-stepFit.R folder inst/tests/comparisons, therein: indices.R, localCost.R, localEst.R, penalisation.R, singleBounds.R, singleStat.R * added imports of Rcpp (>= 0.12.3), R.cache (>= 0.10.0) and digest (>= 0.6.9), methods added linking to Rcpp added suggests of testthat (>= 1.0.0), knitr * NAMESPACE: added importFrom(methods, is) and importFrom(Rcpp, evalCpp) * added a vignette 'StepR': added folder vignettes, therein: StepR.Rnw, references.bib, added VignetteBuilder: knitr in DESCRIPTION CHANGES * changed author list, title and description of the package * changed dependency on R to R (>= 3.0.0) * NAMESPACE: replaced import(stats) by importFrom(stats, approxfun, AIC, BIC, convolve, dnorm, ecdf, fft, filter, fitted, mvfft, pnorm, qnorm, quantile, resid, rexp, rnorm, sd) * sdrobnorm: input is now checked, NAs will be removed with a warning, if the number of observations is too small for computing the result NA is returned with a warning instead of 0 or an error added arguments supressWarningNA = FALSE, supressWarningResultNA added test/testthat/test-sdrobnorm.R updated man sdrobnorm.Rd * stepfit: code of stepfit.R is moved to stepFit.R, documentation stepfit.Rd is renamed to stepfitClass.Rd * man: changed style of the references to suggested form * ChangeLog: added version numbers of the package DEPRECATED * added deprecation warning as a packageStartupMessage, added zzz.R * added deprecation warning to the documentation of BesselPolynomial, contMC, dfilter, jsmurf, transit, MRC, MRC.1000, MRC.asymptotic, MRC.asymptotic.dyadic, bounds, family, smuceR 2017-04-18 Florian Pein, version 1.0-7 * registration of functions: added src/init.c, library is registered by useDynLib(stepR, .registration = TRUE), replaced exportPattern by export (CRAN Note), changed .NAME arguments in .Call statements in steppath.R, stepcand.R, stepbound.R * Step.cpp: added missing PROTECT()s (reported by Tomas Kalibera, https://github.com/kalibera/rchk) 2016-10-10 Florian Pein, version 1.0-6 * BinTree.h, Bounds.cpp, Jump.h, Step.h: define NO_C_HEADERS only for R versions older than 3.3.0 added #include and using std::size_t if macro is defined (CRAN notes and feedback from Brian Ripley) * Step.cpp: added #include * StepGaussVar.cpp, StepPoisson.cpp, StepBinom.cpp: added #include 2016-09-29 Florian Pein, version 1.0-5 * BinTree.h, Bounds.cpp, Jump.h, Step.h: added #define NO_C_HEADERS true to disable C headers; replaced them by C++ headers cstdlib, cstdio, climits, cmath; changed order of headers (R headers should be the last ones) * Step.cpp, StepPoisson.cpp, StepGaussVar.cpp, StepBinom.cpp: added std:: in front of sprintf, log (reported by http://www.stats.ox.ac.uk/pub/bdr/C++Solaris) * BinTree.h: changed Stack__H into BINTREE__H * Jump.cpp: removed R headers (they are included by Jump.h) * CITATION: changed url to canonical format (https://CRAN.R-project.org/package=stepR) 2016-03-24 Florian Pein, version 1.0-4 * NAMESPACE: added importFrom("graphics", "lines", "par", "plot", "points") (CRAN notes) * DESCRIPTION: added graphics as a dependency 2015-06-05 Thomas Hotz * jumpint.R, jumpint.Rd: plotting of confidence bands for binomial is now possible for expected values (dataspace = TRUE) as in lines.stepfit. 2015-06-04 Thomas Hotz, version 1.0-3 * stepR-package.Rd: added references Boysen et al., Yao * stepbound.Rd: updated reference Frick et al. * stepbound.Rd: updated reference Hotz, Schütte et al. * stepR-package.Rd, compare.Rd, smuceR.Rd: updated reference Futschik et al. * stepR-package.Rd, compare.Rd, MRC.Rd, smuceR.Rd, stepbound.Rd, stepsel.Rd: inserted "line breaks" into references * bounds.Rd, MRC.Rd: no longer mention vignette (reported by Theresa Schüler) * DESCRIPTION: Timo Aspelmeier is new maintainer (and presumably another new author) * ChangeLog: corrected dates of last two changes (reported by Timo Aspelmeier) 2015-04-29 Thomas Hotz, version 1.0-2 * family.Rd: corrected explanation of param for family Gauss (reported by Florian Pein) * steppath.R, tests.R: accordingly corrected calculation of logLik if that param had been specified and added test for its calculation * sdrobnorm.Rd: explained reference (reported by Florian Pein) * DESCRIPTION: added Florian Pein as contributor, removed inaccurate date * bug-fix release 2015-04-21 Thomas Hotz * jumpint.R: corrected plotting of confidence bands (reported and solution suggested by by Florian Pein) * stebound.R: corrected R to C style indices for bounds.rev$start (also by Florian Pein) * smuceR.R: corrected computation of alpha when MRC.1000 is used (also by Florian Pein) 2015-03-04 Thomas Hotz, version 1.0-1 * StepPoisson.cpp, StepBinom.cpp: added explicit casting in log() to ensure compilation under solaris 2015-02-16 Thomas Hotz, version 1.0-0 * first version (1.0) on CRAN