Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-25 0.2.1
2024-11-23 0.2.0
2024-09-10 0.1.0
Title: An Interface to 'SUNDIALS' Ordinary Differential Equation (ODE)
Solvers
Description: Provides a way to call the functions in 'SUNDIALS' C ODE solving library (<https://computing.llnl.gov/projects/sundials>). Currently the serial version of ODE solver, 'CVODE', sensitivity calculator 'CVODES' and differential algebraic solver 'IDA' from the 'SUNDIALS' library are implemented. The package requires ODE to be written as an 'R' or 'Rcpp' function and does not require the 'SUNDIALS' library to be installed on the local machine.
Author: Satyaprakash Nayak [aut, cre, cph]
,
Lawrence Livermore National Security [cph],
Southern Methodist University [cph]
Maintainer: Satyaprakash Nayak <satyaprakash.nayak@gmail.com>
Diff between sundialr versions 0.1.5 dated 2024-11-11 and 0.1.6 dated 2024-12-14
sundialr-0.1.5/sundialr/inst/include/nvector/nvector_openmp.h |only sundialr-0.1.5/sundialr/inst/include/nvector/nvector_openmpdev.h |only sundialr-0.1.5/sundialr/inst/include/nvector/nvector_parallel.h |only sundialr-0.1.5/sundialr/inst/include/sundials/priv/sundials_mpi_errors_impl.h |only sundialr-0.1.5/sundialr/inst/include/sundials/sundials_config.in |only sundialr-0.1.5/sundialr/inst/include/sundials/sundials_cuda_policies.hpp |only sundialr-0.1.5/sundialr/inst/include/sundials/sundials_hip_policies.hpp |only sundialr-0.1.5/sundialr/inst/include/sundials/sundials_mpi_errors.h |only sundialr-0.1.5/sundialr/inst/include/sundials/sundials_nvector_senswrapper.h |only sundialr-0.1.5/sundialr/inst/include/sundials/sundials_sycl_policies.hpp |only sundialr-0.1.5/sundialr/inst/include/sundials/sundials_xbraid.h |only sundialr-0.1.5/sundialr/inst/include/sunlinsol/sunlinsol_cusolversp_batchqr.h |only sundialr-0.1.5/sundialr/inst/include/sunlinsol/sunlinsol_ginkgo.hpp |only sundialr-0.1.5/sundialr/inst/include/sunlinsol/sunlinsol_klu.h |only sundialr-0.1.5/sundialr/inst/include/sunlinsol/sunlinsol_kokkosdense.hpp |only sundialr-0.1.5/sundialr/inst/include/sunlinsol/sunlinsol_lapackband.h |only sundialr-0.1.5/sundialr/inst/include/sunlinsol/sunlinsol_lapackdense.h |only sundialr-0.1.5/sundialr/inst/include/sunlinsol/sunlinsol_magmadense.h |only sundialr-0.1.5/sundialr/inst/include/sunlinsol/sunlinsol_onemkldense.h |only sundialr-0.1.5/sundialr/inst/include/sunlinsol/sunlinsol_superludist.h |only sundialr-0.1.5/sundialr/inst/include/sunlinsol/sunlinsol_superlumt.h |only sundialr-0.1.5/sundialr/inst/include/sunmatrix/sunmatrix_cusparse.h |only sundialr-0.1.5/sundialr/inst/include/sunmatrix/sunmatrix_ginkgo.hpp |only sundialr-0.1.5/sundialr/inst/include/sunmatrix/sunmatrix_kokkosdense.hpp |only sundialr-0.1.5/sundialr/inst/include/sunmatrix/sunmatrix_magmadense.h |only sundialr-0.1.5/sundialr/inst/include/sunmatrix/sunmatrix_onemkldense.h |only sundialr-0.1.5/sundialr/inst/include/sunmatrix/sunmatrix_slunrloc.h |only sundialr-0.1.5/sundialr/inst/include/sunnonlinsol/sunnonlinsol_petscsnes.h |only sundialr-0.1.5/sundialr/src/Makevars |only sundialr-0.1.5/sundialr/src/sortTimes.cpp |only sundialr-0.1.5/sundialr/src/sundials |only sundialr-0.1.6/sundialr/DESCRIPTION | 6 sundialr-0.1.6/sundialr/LICENSE | 3 sundialr-0.1.6/sundialr/MD5 | 224 +--- sundialr-0.1.6/sundialr/NEWS | 7 sundialr-0.1.6/sundialr/R/zzz.R | 8 sundialr-0.1.6/sundialr/README.md | 16 sundialr-0.1.6/sundialr/cleanup |only sundialr-0.1.6/sundialr/cleanup.win |only sundialr-0.1.6/sundialr/configure |only sundialr-0.1.6/sundialr/configure.ac |only sundialr-0.1.6/sundialr/configure.win |only sundialr-0.1.6/sundialr/inst/COPYRIGHTS | 4 sundialr-0.1.6/sundialr/inst/doc/my-vignette.html | 8 sundialr-0.1.6/sundialr/inst/include/arkode |only sundialr-0.1.6/sundialr/inst/include/cvode/cvode_bandpre.h | 2 sundialr-0.1.6/sundialr/inst/include/cvodes/cvodes_bandpre.h | 2 sundialr-0.1.6/sundialr/inst/include/nvector/nvector_manyvector.h |only sundialr-0.1.6/sundialr/inst/include/sunadaptcontroller |only sundialr-0.1.6/sundialr/inst/include/sundials/LICENSE |only sundialr-0.1.6/sundialr/inst/include/sundials/NOTICE |only sundialr-0.1.6/sundialr/inst/include/sundials/priv/sundials_errors_impl.h | 22 sundialr-0.1.6/sundialr/inst/include/sundials/sundials_adaptcontroller.h | 39 sundialr-0.1.6/sundialr/inst/include/sundials/sundials_base.hpp | 2 sundialr-0.1.6/sundialr/inst/include/sundials/sundials_config.h | 28 sundialr-0.1.6/sundialr/inst/include/sundials/sundials_convertibleto.hpp | 2 sundialr-0.1.6/sundialr/inst/include/sundials/sundials_errors.h | 2 sundialr-0.1.6/sundialr/inst/include/sundials/sundials_export.h | 6 sundialr-0.1.6/sundialr/inst/include/sundials/sundials_math.h | 40 sundialr-0.1.6/sundialr/inst/include/sundials/sundials_memory.h | 4 sundialr-0.1.6/sundialr/inst/include/sundials/sundials_nvector.h | 2 sundialr-0.1.6/sundialr/inst/include/sundials/sundials_stepper.h |only sundialr-0.1.6/sundialr/inst/include/sunmemory |only sundialr-0.1.6/sundialr/inst/include/sunnonlinsol/sunnonlinsol_fixedpoint.h | 2 sundialr-0.1.6/sundialr/src/Makevars.in |only sundialr-0.1.6/sundialr/src/cvode.cpp | 12 sundialr-0.1.6/sundialr/src/cvodes.cpp | 40 sundialr-0.1.6/sundialr/src/cvsolve.cpp | 491 ++++------ sundialr-0.1.6/sundialr/src/scripts |only sundialr-0.1.6/sundialr/src/utils |only sundialr-0.1.6/sundialr/tools |only 71 files changed, 471 insertions(+), 501 deletions(-)
Title: Log-Likelihood Functions for 'rxode2'
Description: Provides the log-likelihoods with gradients from 'stan'
(Carpenter et al (2015), <doi:10.48550/arXiv.1509.07164>) needed
for generalized log-likelihood estimation in 'nlmixr2'
(Fidler et al (2019) <doi:10.1002/psp4.12445>). This is
split of to reduce computational burden of recompiling 'rxode2'
(Wang, Hallow and James (2016) <doi:10.1002/psp4.12052>) which runs
the 'nlmixr2' models during estimation.
Author: Matthew L. Fidler [aut, cre]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2ll versions 2.0.12 dated 2024-11-21 and 2.0.13 dated 2024-12-14
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ src/Makevars.in | 4 +--- 4 files changed, 11 insertions(+), 9 deletions(-)
Title: Scale Mixture of Skew-Normal Linear Mixed Models
Description: It fits scale mixture of skew-normal linear mixed models using either an expectation–maximization (EM) type algorithm or its accelerated version (Damped Anderson Acceleration with Epsilon Monotonicity, DAAREM), including some possibilities for modeling the within-subject dependence. Details can be found in Schumacher, Lachos and Matos (2021) <doi:10.1002/sim.8870>.
Author: Fernanda L. Schumacher [aut, cre]
,
Larissa A. Matos [aut] ,
Victor H. Lachos [aut] ,
Katherine A. L. Valeriano [aut]
,
Nicholas Henderson [ctb],
Ravi Varadhan [ctb]
Maintainer: Fernanda L. Schumacher <fernandalschumacher@gmail.com>
Diff between skewlmm versions 1.1.0 dated 2023-06-30 and 1.1.2 dated 2024-12-14
DESCRIPTION | 18 +++--- MD5 | 51 ++++++++++++------- NAMESPACE | 66 ++++++++++++++++++------- NEWS.md | 13 ++++ R/mainfunctions-sim.R | 16 +++--- R/mainfunctions.R | 99 +++++++++++++++++++++++++++++++++----- R/residuals.R | 83 +++++++++++++++++++------------ R/smnCens_prin.R | 2 README.md | 15 ++++- data |only man/UTIdata.Rd |only man/coef.Rd |only man/confint.Rd |only man/figures/README-example1-1.png |binary man/figures/README-example2-1.png |binary man/figures/README-example2-3.png |binary man/figures/skewlmm_hex.png |only man/fixef.Rd |only man/formula.Rd |only man/healy.plot.Rd | 6 +- man/lmmControl.Rd | 2 man/logLik.Rd |only man/miceweight.Rd |only man/nobs.Rd |only man/plot.Rd | 5 + man/plot.SMNCens.Rd | 4 - man/plot.acfresid.Rd | 5 + man/plot.mahalDist.Rd | 4 - man/plot.mahalDist.SMNCens.Rd | 4 - man/ranef.Rd | 10 +++ man/sigma.Rd |only man/weight_plot.Rd |only 32 files changed, 289 insertions(+), 114 deletions(-)
Title: Multi Environment Trials Analysis
Description: Performs stability analysis of multi-environment trial data
using parametric and non-parametric methods. Parametric methods
includes Additive Main Effects and Multiplicative Interaction (AMMI)
analysis by Gauch (2013) <doi:10.2135/cropsci2013.04.0241>, Ecovalence
by Wricke (1965), Genotype plus Genotype-Environment (GGE) biplot
analysis by Yan & Kang (2003) <doi:10.1201/9781420040371>, geometric
adaptability index by Mohammadi & Amri (2008)
<doi:10.1007/s10681-007-9600-6>, joint regression analysis by Eberhart
& Russel (1966) <doi:10.2135/cropsci1966.0011183X000600010011x>,
genotypic confidence index by Annicchiarico (1992), Murakami & Cruz's
(2004) method, power law residuals (POLAR) statistics by Doring et al.
(2015) <doi:10.1016/j.fcr.2015.08.005>, scale-adjusted coefficient of
variation by Doring & Reckling (2018) <doi:10.1016/j.eja.2018.06.007>,
stability variance by Shukla (1972) <doi:10.1038/hdy.1972.87>,
weighted ave [...truncated...]
Author: Tiago Olivoto [aut, cre, cph]
Maintainer: Tiago Olivoto <tiagoolivoto@gmail.com>
Diff between metan versions 1.18.0 dated 2023-03-05 and 1.19.0 dated 2024-12-14
metan-1.18.0/metan/R/ammi_indexes.R |only metan-1.18.0/metan/R/fai_blup.R |only metan-1.18.0/metan/R/mtsi.R |only metan-1.18.0/metan/R/waasb.R |only metan-1.18.0/metan/build/metan.pdf |only metan-1.18.0/metan/man/metan-package.Rd |only metan-1.18.0/metan/vignettes/ammi.RData |only metan-1.18.0/metan/vignettes/cvali.RData |only metan-1.18.0/metan/vignettes/indexes.RData |only metan-1.18.0/metan/vignettes/metan.RData |only metan-1.18.0/metan/vignettes/plots_corr.RData |only metan-1.18.0/metan/vignettes/wratio.RData |only metan-1.19.0/metan/DESCRIPTION | 16 metan-1.19.0/metan/MD5 | 475 +++++------ metan-1.19.0/metan/NAMESPACE | 3 metan-1.19.0/metan/NEWS.md | 7 metan-1.19.0/metan/R/AMMI_indexes.R |only metan-1.19.0/metan/R/FAI_BLUP.R |only metan-1.19.0/metan/R/MTSI.R |only metan-1.19.0/metan/R/WAASB.R |only metan-1.19.0/metan/R/acv.R | 2 metan-1.19.0/metan/R/anova_ind.R | 13 metan-1.19.0/metan/R/anova_joint.R | 41 - metan-1.19.0/metan/R/blup_indexes.R | 2 metan-1.19.0/metan/R/clustering.R | 3 metan-1.19.0/metan/R/coincidence_index.R | 6 metan-1.19.0/metan/R/colindiag.R | 108 +- metan-1.19.0/metan/R/corr_ci.R | 2 metan-1.19.0/metan/R/corr_ss.R | 2 metan-1.19.0/metan/R/cv_ammi.R | 2 metan-1.19.0/metan/R/cv_blup.R | 2 metan-1.19.0/metan/R/gamem_met.R | 2 metan-1.19.0/metan/R/ge_plot.R | 42 - metan-1.19.0/metan/R/ge_stats.R | 4 metan-1.19.0/metan/R/get_model_data.R | 35 metan-1.19.0/metan/R/metan-package.r | 3 metan-1.19.0/metan/R/mgidi.R | 276 ++++-- metan-1.19.0/metan/R/mps.R | 5 metan-1.19.0/metan/R/mtmps.R | 4 metan-1.19.0/metan/R/non_collinear_vars.R | 15 metan-1.19.0/metan/R/path_coeff.R | 6 metan-1.19.0/metan/R/plaisted_peterson.R |only metan-1.19.0/metan/R/plot_scores.R | 2 metan-1.19.0/metan/R/utilities.R | 30 metan-1.19.0/metan/R/utils-tidy-eval.R | 214 ++--- metan-1.19.0/metan/R/utils_as.R | 2 metan-1.19.0/metan/R/venn_plot.R | 51 - metan-1.19.0/metan/R/waas.R | 4 metan-1.19.0/metan/R/waas_means.R | 2 metan-1.19.0/metan/R/wsmp.R | 4 metan-1.19.0/metan/R/zzz.R | 4 metan-1.19.0/metan/build/stage23.rdb |only metan-1.19.0/metan/build/vignette.rds |binary metan-1.19.0/metan/inst/doc/metan_start.R | 6 metan-1.19.0/metan/inst/doc/metan_start.Rmd | 2 metan-1.19.0/metan/inst/doc/metan_start.html | 662 ++++++++-------- metan-1.19.0/metan/man/Annicchiarico.Rd | 140 +-- metan-1.19.0/metan/man/Fox.Rd | 116 +- metan-1.19.0/metan/man/Huehn.Rd | 120 +- metan-1.19.0/metan/man/Schmildt.Rd | 150 +-- metan-1.19.0/metan/man/Select_helper.Rd | 214 ++--- metan-1.19.0/metan/man/Shukla.Rd | 136 +-- metan-1.19.0/metan/man/Smith_Hazel.Rd | 194 ++-- metan-1.19.0/metan/man/Thennarasu.Rd | 98 +- metan-1.19.0/metan/man/acv.Rd | 140 +-- metan-1.19.0/metan/man/ammi_indexes.Rd | 5 metan-1.19.0/metan/man/anova_ind.Rd | 199 ++-- metan-1.19.0/metan/man/anova_joint.Rd | 168 ++-- metan-1.19.0/metan/man/arrange_ggplot.Rd | 192 ++-- metan-1.19.0/metan/man/as.lpcor.Rd | 72 - metan-1.19.0/metan/man/barplots.Rd | 516 ++++++------ metan-1.19.0/metan/man/bind_cv.Rd | 116 +- metan-1.19.0/metan/man/blup_indexes.Rd | 216 ++--- metan-1.19.0/metan/man/can_corr.Rd | 222 ++--- metan-1.19.0/metan/man/clustering.Rd | 282 +++--- metan-1.19.0/metan/man/coincidence_index.Rd | 102 +- metan-1.19.0/metan/man/colindiag.Rd | 173 ++-- metan-1.19.0/metan/man/comb_vars.Rd | 96 +- metan-1.19.0/metan/man/corr_ci.Rd | 166 ++-- metan-1.19.0/metan/man/corr_coef.Rd | 194 ++-- metan-1.19.0/metan/man/corr_focus.Rd | 52 - metan-1.19.0/metan/man/corr_plot.Rd | 460 +++++------ metan-1.19.0/metan/man/corr_ss.Rd | 94 +- metan-1.19.0/metan/man/corr_stab_ind.Rd | 138 +-- metan-1.19.0/metan/man/correlated_vars.Rd | 112 +- metan-1.19.0/metan/man/covcor_design.Rd | 168 ++-- metan-1.19.0/metan/man/cv_ammi.Rd | 236 ++--- metan-1.19.0/metan/man/cv_ammif.Rd | 220 ++--- metan-1.19.0/metan/man/cv_blup.Rd | 280 +++--- metan-1.19.0/metan/man/data_alpha.Rd | 64 - metan-1.19.0/metan/man/data_g.Rd | 82 +- metan-1.19.0/metan/man/data_ge.Rd | 62 - metan-1.19.0/metan/man/data_ge2.Rd | 88 +- metan-1.19.0/metan/man/data_simula.Rd | 234 ++--- metan-1.19.0/metan/man/desc_stat.Rd | 340 ++++---- metan-1.19.0/metan/man/doo.Rd | 100 +- metan-1.19.0/metan/man/ecovalence.Rd | 106 +- metan-1.19.0/metan/man/env_dissimilarity.Rd | 160 +-- metan-1.19.0/metan/man/env_stratification.Rd | 166 ++-- metan-1.19.0/metan/man/fai_blup.Rd | 172 ++-- metan-1.19.0/metan/man/find_outliers.Rd | 114 +- metan-1.19.0/metan/man/gafem.Rd | 268 +++--- metan-1.19.0/metan/man/gai.Rd | 126 +-- metan-1.19.0/metan/man/gamem.Rd | 340 ++++---- metan-1.19.0/metan/man/gamem_met.Rd | 392 ++++----- metan-1.19.0/metan/man/ge_acv.Rd | 112 +- metan-1.19.0/metan/man/ge_cluster.Rd | 192 ++-- metan-1.19.0/metan/man/ge_details.Rd | 94 +- metan-1.19.0/metan/man/ge_effects.Rd | 102 +- metan-1.19.0/metan/man/ge_factanal.Rd | 150 +-- metan-1.19.0/metan/man/ge_means.Rd | 108 +- metan-1.19.0/metan/man/ge_plot.Rd | 175 ++-- metan-1.19.0/metan/man/ge_reg.Rd | 140 +-- metan-1.19.0/metan/man/ge_stats.Rd | 362 ++++---- metan-1.19.0/metan/man/ge_winners.Rd | 124 +-- metan-1.19.0/metan/man/get_corvars.Rd | 90 +- metan-1.19.0/metan/man/get_covmat.Rd | 74 - metan-1.19.0/metan/man/get_dist.Rd | 74 - metan-1.19.0/metan/man/get_model_data.Rd | 855 ++++++++++----------- metan-1.19.0/metan/man/gge.Rd | 224 ++--- metan-1.19.0/metan/man/gtb.Rd | 168 ++-- metan-1.19.0/metan/man/gytb.Rd | 234 ++--- metan-1.19.0/metan/man/impute_missing_val.Rd | 242 ++--- metan-1.19.0/metan/man/inspect.Rd | 116 +- metan-1.19.0/metan/man/int.effects.Rd | 26 metan-1.19.0/metan/man/is.lpcor.Rd | 64 - metan-1.19.0/metan/man/is_balanced_trial.Rd | 78 - metan-1.19.0/metan/man/lineplots.Rd | 306 +++---- metan-1.19.0/metan/man/lpcor.Rd | 130 +-- metan-1.19.0/metan/man/mahala.Rd | 102 +- metan-1.19.0/metan/man/mahala_design.Rd | 154 +-- metan-1.19.0/metan/man/make_long.Rd | 94 +- metan-1.19.0/metan/man/make_mat.Rd | 98 +- metan-1.19.0/metan/man/mantel_test.Rd | 102 +- metan-1.19.0/metan/man/meansGxE.Rd | 30 metan-1.19.0/metan/man/metan.Rd |only metan-1.19.0/metan/man/mgidi.Rd | 53 - metan-1.19.0/metan/man/mps.Rd | 406 ++++----- metan-1.19.0/metan/man/mtmps.Rd | 236 ++--- metan-1.19.0/metan/man/mtsi.Rd | 276 +++--- metan-1.19.0/metan/man/network_plot.Rd | 186 ++-- metan-1.19.0/metan/man/non_collinear_vars.Rd | 104 +- metan-1.19.0/metan/man/pairs_mantel.Rd | 280 +++--- metan-1.19.0/metan/man/path_coeff.Rd | 412 ++++------ metan-1.19.0/metan/man/performs_ammi.Rd | 218 ++--- metan-1.19.0/metan/man/pipe.Rd | 24 metan-1.19.0/metan/man/plaisted_peterson.Rd |only metan-1.19.0/metan/man/plot.anova_joint.Rd | 74 - metan-1.19.0/metan/man/plot.can_cor.Rd | 246 +++--- metan-1.19.0/metan/man/plot.clustering.Rd | 80 - metan-1.19.0/metan/man/plot.corr_coef.Rd | 208 ++--- metan-1.19.0/metan/man/plot.correlated_vars.Rd | 54 - metan-1.19.0/metan/man/plot.cvalidation.Rd | 234 ++--- metan-1.19.0/metan/man/plot.env_dissimilarity.Rd | 62 - metan-1.19.0/metan/man/plot.env_stratification.Rd | 80 - metan-1.19.0/metan/man/plot.fai_blup.Rd | 160 +-- metan-1.19.0/metan/man/plot.gafem.Rd | 76 - metan-1.19.0/metan/man/plot.gamem.Rd | 266 +++--- metan-1.19.0/metan/man/plot.ge_cluster.Rd | 46 - metan-1.19.0/metan/man/plot.ge_effects.Rd | 120 +- metan-1.19.0/metan/man/plot.ge_factanal.Rd | 274 +++--- metan-1.19.0/metan/man/plot.ge_reg.Rd | 166 ++-- metan-1.19.0/metan/man/plot.gge.Rd | 318 +++---- metan-1.19.0/metan/man/plot.mgidi.Rd | 215 ++--- metan-1.19.0/metan/man/plot.mtmps.Rd | 232 ++--- metan-1.19.0/metan/man/plot.mtsi.Rd | 217 ++--- metan-1.19.0/metan/man/plot.path_coeff.Rd | 122 +- metan-1.19.0/metan/man/plot.performs_ammi.Rd | 74 - metan-1.19.0/metan/man/plot.resp_surf.Rd | 122 +- metan-1.19.0/metan/man/plot.sh.Rd | 132 +-- metan-1.19.0/metan/man/plot.waas.Rd | 74 - metan-1.19.0/metan/man/plot.waasb.Rd | 304 +++---- metan-1.19.0/metan/man/plot.wsmp.Rd | 126 +-- metan-1.19.0/metan/man/plot_blup.Rd | 278 +++--- metan-1.19.0/metan/man/plot_ci.Rd | 216 ++--- metan-1.19.0/metan/man/plot_eigen.Rd | 190 ++-- metan-1.19.0/metan/man/plot_scores.Rd | 568 ++++++------- metan-1.19.0/metan/man/plot_waasby.Rd | 214 ++--- metan-1.19.0/metan/man/predict.gamem.Rd | 66 - metan-1.19.0/metan/man/predict.gge.Rd | 106 +- metan-1.19.0/metan/man/predict.performs_ammi.Rd | 110 +- metan-1.19.0/metan/man/predict.waas.Rd | 116 +- metan-1.19.0/metan/man/predict.waasb.Rd | 68 - metan-1.19.0/metan/man/print.Annicchiarico.Rd | 82 +- metan-1.19.0/metan/man/print.Fox.Rd | 74 - metan-1.19.0/metan/man/print.Huehn.Rd | 72 - metan-1.19.0/metan/man/print.Schmildt.Rd | 80 - metan-1.19.0/metan/man/print.Shukla.Rd | 82 +- metan-1.19.0/metan/man/print.Thennarasu.Rd | 72 - metan-1.19.0/metan/man/print.ammi_indexes.Rd | 2 metan-1.19.0/metan/man/print.anova_ind.Rd | 72 - metan-1.19.0/metan/man/print.anova_joint.Rd | 72 - metan-1.19.0/metan/man/print.can_cor.Rd | 78 - metan-1.19.0/metan/man/print.coincidence.Rd | 74 - metan-1.19.0/metan/man/print.colindiag.Rd | 72 - metan-1.19.0/metan/man/print.corr_coef.Rd | 72 - metan-1.19.0/metan/man/print.ecovalence.Rd | 80 - metan-1.19.0/metan/man/print.env_dissimilarity.Rd | 70 - metan-1.19.0/metan/man/print.env_stratification.Rd | 76 - metan-1.19.0/metan/man/print.gamem.Rd | 82 +- metan-1.19.0/metan/man/print.ge_factanal.Rd | 78 - metan-1.19.0/metan/man/print.ge_reg.Rd | 74 - metan-1.19.0/metan/man/print.ge_stats.Rd | 82 +- metan-1.19.0/metan/man/print.lpcor.Rd | 84 +- metan-1.19.0/metan/man/print.mgidi.Rd | 84 +- metan-1.19.0/metan/man/print.mtmps.Rd | 82 +- metan-1.19.0/metan/man/print.mtsi.Rd | 86 +- metan-1.19.0/metan/man/print.path_coeff.Rd | 92 +- metan-1.19.0/metan/man/print.performs_ammi.Rd | 72 - metan-1.19.0/metan/man/print.plaisted_peterson.Rd |only metan-1.19.0/metan/man/print.sh.Rd | 78 - metan-1.19.0/metan/man/print.superiority.Rd | 72 - metan-1.19.0/metan/man/print.waas.Rd | 80 - metan-1.19.0/metan/man/print.waas_means.Rd | 78 - metan-1.19.0/metan/man/print.waasb.Rd | 84 +- metan-1.19.0/metan/man/reexports.Rd | 60 - metan-1.19.0/metan/man/reorder_cormat.Rd | 66 - metan-1.19.0/metan/man/resca.Rd | 176 ++-- metan-1.19.0/metan/man/residual_plots.Rd | 226 ++--- metan-1.19.0/metan/man/resp_surf.Rd | 126 +-- metan-1.19.0/metan/man/select_pred.Rd | 100 +- metan-1.19.0/metan/man/solve_svd.Rd | 66 - metan-1.19.0/metan/man/split_factors.Rd | 124 +-- metan-1.19.0/metan/man/stars_pval.Rd | 76 - metan-1.19.0/metan/man/superiority.Rd | 116 +- metan-1.19.0/metan/man/themes.Rd | 108 +- metan-1.19.0/metan/man/tidyeval.Rd | 196 ++-- metan-1.19.0/metan/man/transpose_df.Rd | 72 - metan-1.19.0/metan/man/tukey_hsd.Rd | 90 +- metan-1.19.0/metan/man/utils_as.Rd | 178 ++-- metan-1.19.0/metan/man/utils_bind.Rd | 106 +- metan-1.19.0/metan/man/utils_class.Rd | 106 +- metan-1.19.0/metan/man/utils_data.Rd | 88 +- metan-1.19.0/metan/man/utils_data_org.Rd | 168 ++-- metan-1.19.0/metan/man/utils_mat.Rd | 152 +-- metan-1.19.0/metan/man/utils_na_zero.Rd | 296 +++---- metan-1.19.0/metan/man/utils_num_str.Rd | 390 ++++----- metan-1.19.0/metan/man/utils_progress.Rd | 220 ++--- metan-1.19.0/metan/man/utils_rows_cols.Rd | 606 +++++++------- metan-1.19.0/metan/man/utils_samples.Rd | 108 +- metan-1.19.0/metan/man/utils_sets.Rd | 134 +-- metan-1.19.0/metan/man/utils_stats.Rd | 580 +++++++------- metan-1.19.0/metan/man/utils_wd.Rd | 94 +- metan-1.19.0/metan/man/venn_plot.Rd | 215 ++--- metan-1.19.0/metan/man/waas.Rd | 402 ++++----- metan-1.19.0/metan/man/waas_means.Rd | 252 +++--- metan-1.19.0/metan/man/waasb.Rd | 544 ++++++------- metan-1.19.0/metan/man/wsmp.Rd | 204 ++--- metan-1.19.0/metan/vignettes/metan_start.Rmd | 2 249 files changed, 16358 insertions(+), 16116 deletions(-)
Title: Extended HOF (Huisman-Olff-Fresco) Models
Description: Extended and enhanced hierarchical logistic regression models (called Huisman-Olff-Fresco in biology, see Huisman et al. 1993 Journal of Vegetation Science <doi:10.1111/jvs.12050>) models. Response curves along one-dimensional gradients including no response, monotone, plateau, unimodal and bimodal models.
Author: Florian Jansen [aut, cre],
Jari Oksanen [aut]
Maintainer: Florian Jansen <florian.jansen@uni-rostock.de>
Diff between eHOF versions 1.15 dated 2024-01-29 and 1.16 dated 2024-12-14
DESCRIPTION | 18 +++++++--- MD5 | 50 ++++++++++++++------------- NAMESPACE | 40 +++++++++++----------- R/HOF.fun.r | 2 - R/HOF.r | 4 +- R/Para.deriv.r | 7 +-- R/Para.opt.r | 12 +++++- R/betaresp.r | 26 ++++++-------- R/coef.HOF.r | 3 - R/eHOF-package.R | 12 +++--- R/pick.model.r | 93 +++++++++++++++++++++++++++------------------------- R/plot.HOF.list.r | 23 +++++++----- R/plot.HOF.r | 30 ++++++++++------ R/print.HOF.list.r | 13 +------ R/print.HOF.r | 1 R/svHOF.r | 5 +- build/partial.rdb |only build/vignette.rds |binary inst/ChangeLog | 4 ++ inst/doc/eHOF.R | 14 ++++--- inst/doc/eHOF.Rnw | 19 ++++++---- inst/doc/eHOF.pdf |binary man/HOF.Rd | 2 - man/eHOF-package.Rd | 12 ++---- man/eHOF.Rd |only man/plot.HOF.Rd | 12 +++++- vignettes/eHOF.Rnw | 19 ++++++---- 27 files changed, 232 insertions(+), 189 deletions(-)
Title: Interface to 'dgpsi' for Deep and Linked Gaussian Process
Emulations
Description: Interface to the 'python' package 'dgpsi' for Gaussian process, deep Gaussian process,
and linked deep Gaussian process emulations of computer models and networks using stochastic imputation (SI).
The implementations follow Ming & Guillas (2021) <doi:10.1137/20M1323771> and
Ming, Williamson, & Guillas (2023) <doi:10.1080/00401706.2022.2124311> and
Ming & Williamson (2023) <doi:10.48550/arXiv.2306.01212>. To get started with the package,
see <https://mingdeyu.github.io/dgpsi-R/>.
Author: Deyu Ming [aut, cre, cph],
Daniel Williamson [aut]
Maintainer: Deyu Ming <deyu.ming.16@ucl.ac.uk>
Diff between dgpsi versions 2.4.0 dated 2024-01-14 and 2.5.0 dated 2024-12-14
dgpsi-2.4.0/dgpsi/R/kernel.R |only dgpsi-2.4.0/dgpsi/R/likelihood.R |only dgpsi-2.4.0/dgpsi/R/pei.R |only dgpsi-2.4.0/dgpsi/inst/doc/linked_DGP.R |only dgpsi-2.4.0/dgpsi/inst/doc/linked_DGP.Rmd |only dgpsi-2.4.0/dgpsi/inst/doc/linked_DGP.html |only dgpsi-2.4.0/dgpsi/inst/doc/motorcycle.R |only dgpsi-2.4.0/dgpsi/inst/doc/motorcycle.Rmd |only dgpsi-2.4.0/dgpsi/inst/doc/motorcycle.html |only dgpsi-2.4.0/dgpsi/inst/doc/seq_design.R |only dgpsi-2.4.0/dgpsi/inst/doc/seq_design.Rmd |only dgpsi-2.4.0/dgpsi/inst/doc/seq_design.html |only dgpsi-2.4.0/dgpsi/inst/doc/seq_design_2.R |only dgpsi-2.4.0/dgpsi/inst/doc/seq_design_2.Rmd |only dgpsi-2.4.0/dgpsi/inst/doc/seq_design_2.html |only dgpsi-2.4.0/dgpsi/man/Hetero.Rd |only dgpsi-2.4.0/dgpsi/man/NegBin.Rd |only dgpsi-2.4.0/dgpsi/man/Poisson.Rd |only dgpsi-2.4.0/dgpsi/man/kernel.Rd |only dgpsi-2.4.0/dgpsi/man/pei.Rd |only dgpsi-2.4.0/dgpsi/vignettes/images |only dgpsi-2.4.0/dgpsi/vignettes/linked_DGP.Rmd |only dgpsi-2.4.0/dgpsi/vignettes/motorcycle.Rmd |only dgpsi-2.4.0/dgpsi/vignettes/seq_design.Rmd |only dgpsi-2.4.0/dgpsi/vignettes/seq_design_2.Rmd |only dgpsi-2.5.0/dgpsi/DESCRIPTION | 15 dgpsi-2.5.0/dgpsi/MD5 | 165 +-- dgpsi-2.5.0/dgpsi/NAMESPACE | 17 dgpsi-2.5.0/dgpsi/NEWS.md | 33 dgpsi-2.5.0/dgpsi/R/alm.R | 910 +++++++++++++---- dgpsi-2.5.0/dgpsi/R/design.R | 1442 +++++++++++++++++---------- dgpsi-2.5.0/dgpsi/R/dgp.R | 301 +++-- dgpsi-2.5.0/dgpsi/R/dgpsi-package.R |only dgpsi-2.5.0/dgpsi/R/draw.R | 275 +++-- dgpsi-2.5.0/dgpsi/R/gp.R | 178 ++- dgpsi-2.5.0/dgpsi/R/initi_py.R | 94 + dgpsi-2.5.0/dgpsi/R/lgp.R | 473 ++++++++ dgpsi-2.5.0/dgpsi/R/mice.R | 275 +++-- dgpsi-2.5.0/dgpsi/R/plot.R | 740 +++++++++---- dgpsi-2.5.0/dgpsi/R/prediction.R | 465 +++++++- dgpsi-2.5.0/dgpsi/R/serialization.R |only dgpsi-2.5.0/dgpsi/R/update.R | 86 + dgpsi-2.5.0/dgpsi/R/utils.R | 1410 ++++++++++++++++++++++++-- dgpsi-2.5.0/dgpsi/R/validation.R | 642 +++++++++--- dgpsi-2.5.0/dgpsi/R/vigf.R | 893 +++++++++++++--- dgpsi-2.5.0/dgpsi/README.md | 27 dgpsi-2.5.0/dgpsi/build/partial.rdb |only dgpsi-2.5.0/dgpsi/build/vignette.rds |binary dgpsi-2.5.0/dgpsi/inst/CITATION | 16 dgpsi-2.5.0/dgpsi/inst/WORDLIST | 14 dgpsi-2.5.0/dgpsi/inst/doc/dgpsi.R | 116 +- dgpsi-2.5.0/dgpsi/inst/doc/dgpsi.Rmd | 86 - dgpsi-2.5.0/dgpsi/inst/doc/dgpsi.html | 237 ++-- dgpsi-2.5.0/dgpsi/man/alm.Rd | 137 +- dgpsi-2.5.0/dgpsi/man/combine.Rd | 26 dgpsi-2.5.0/dgpsi/man/continue.Rd | 29 dgpsi-2.5.0/dgpsi/man/deserialize.Rd |only dgpsi-2.5.0/dgpsi/man/design.Rd | 282 +++-- dgpsi-2.5.0/dgpsi/man/dgp.Rd | 145 +- dgpsi-2.5.0/dgpsi/man/dgpsi-package.Rd |only dgpsi-2.5.0/dgpsi/man/draw.Rd | 27 dgpsi-2.5.0/dgpsi/man/figures |only dgpsi-2.5.0/dgpsi/man/get_thread_num.Rd |only dgpsi-2.5.0/dgpsi/man/gp.Rd | 85 - dgpsi-2.5.0/dgpsi/man/init_py.Rd | 2 dgpsi-2.5.0/dgpsi/man/lgp.Rd | 104 + dgpsi-2.5.0/dgpsi/man/mice.Rd | 117 +- dgpsi-2.5.0/dgpsi/man/nllik.Rd | 23 dgpsi-2.5.0/dgpsi/man/pack.Rd | 25 dgpsi-2.5.0/dgpsi/man/plot.Rd | 58 - dgpsi-2.5.0/dgpsi/man/predict.Rd | 117 +- dgpsi-2.5.0/dgpsi/man/prune.Rd | 18 dgpsi-2.5.0/dgpsi/man/serialize.Rd |only dgpsi-2.5.0/dgpsi/man/set_id.Rd |only dgpsi-2.5.0/dgpsi/man/set_imp.Rd | 6 dgpsi-2.5.0/dgpsi/man/set_linked_idx.Rd | 8 dgpsi-2.5.0/dgpsi/man/set_thread_num.Rd |only dgpsi-2.5.0/dgpsi/man/set_vecchia.Rd |only dgpsi-2.5.0/dgpsi/man/summary.Rd | 28 dgpsi-2.5.0/dgpsi/man/trace_plot.Rd | 4 dgpsi-2.5.0/dgpsi/man/unpack.Rd | 4 dgpsi-2.5.0/dgpsi/man/update.Rd | 36 dgpsi-2.5.0/dgpsi/man/validate.Rd | 122 +- dgpsi-2.5.0/dgpsi/man/vigf.Rd | 124 +- dgpsi-2.5.0/dgpsi/man/window.Rd | 18 dgpsi-2.5.0/dgpsi/man/write.Rd | 10 dgpsi-2.5.0/dgpsi/vignettes/dgpsi |only dgpsi-2.5.0/dgpsi/vignettes/dgpsi.Rmd | 86 - dgpsi-2.5.0/dgpsi/vignettes/references.bib | 17 89 files changed, 7755 insertions(+), 2813 deletions(-)
Title: Mining Association Rules and Frequent Itemsets
Description: Provides the infrastructure for representing, manipulating
and analyzing transaction data and patterns (frequent itemsets and
association rules). Also provides C implementations of the
association mining algorithms Apriori and Eclat. Hahsler, Gruen and
Hornik (2005) <doi:10.18637/jss.v014.i15>.
Author: Michael Hahsler [aut, cre, cph]
,
Christian Buchta [aut, cph],
Bettina Gruen [aut, cph],
Kurt Hornik [aut, cph] ,
Christian Borgelt [ctb, cph],
Ian Johnson [ctb],
Makhlouf Ledmi [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arules versions 1.7-8 dated 2024-08-22 and 1.7-9 dated 2024-12-14
arules-1.7-8/arules/src/Makevars |only arules-1.7-9/arules/DESCRIPTION | 8 arules-1.7-9/arules/MD5 | 271 ++--- arules-1.7-9/arules/NEWS.md | 8 arules-1.7-9/arules/R/AAADefs.R | 109 +- arules-1.7-9/arules/R/Adult.R | 97 +- arules-1.7-9/arules/R/DATAFRAME.R | 84 + arules-1.7-9/arules/R/Epub.R | 18 arules-1.7-9/arules/R/Groceries.R | 14 arules-1.7-9/arules/R/Income.R | 88 + arules-1.7-9/arules/R/LIST.R | 52 - arules-1.7-9/arules/R/Matrix.R | 25 arules-1.7-9/arules/R/Mushroom.R | 14 arules-1.7-9/arules/R/SunBai.R | 12 arules-1.7-9/arules/R/abbreviate.R | 101 +- arules-1.7-9/arules/R/addComplement.R | 60 - arules-1.7-9/arules/R/appearance.R | 134 +- arules-1.7-9/arules/R/apriori.R | 71 - arules-1.7-9/arules/R/associations.R | 210 ++-- arules-1.7-9/arules/R/c.R | 126 +- arules-1.7-9/arules/R/check_installed.R | 36 arules-1.7-9/arules/R/confint.R | 334 +++---- arules-1.7-9/arules/R/control.R | 131 +- arules-1.7-9/arules/R/coverage.R | 43 arules-1.7-9/arules/R/crossTable.R | 45 arules-1.7-9/arules/R/discretize.R | 249 +++-- arules-1.7-9/arules/R/dissimilarity.R | 345 ++++--- arules-1.7-9/arules/R/duplicated.R | 40 arules-1.7-9/arules/R/eclat.R | 51 - arules-1.7-9/arules/R/extract.R | 210 ++-- arules-1.7-9/arules/R/fim4r.R | 279 +++--- arules-1.7-9/arules/R/hierarchy.R | 101 +- arules-1.7-9/arules/R/image.R | 47 - arules-1.7-9/arules/R/inspect.R | 337 ++++--- arules-1.7-9/arules/R/interestMeasures.R | 604 +++++++------ arules-1.7-9/arules/R/is.closed.R | 47 - arules-1.7-9/arules/R/is.generator.R | 49 - arules-1.7-9/arules/R/is.maximal.R | 47 - arules-1.7-9/arules/R/is.redundant.R | 112 +- arules-1.7-9/arules/R/is.significant.R | 64 - arules-1.7-9/arules/R/is.superset.R | 179 ++- arules-1.7-9/arules/R/itemCoding.R | 323 ++++-- arules-1.7-9/arules/R/itemFrequency.R | 334 ++++--- arules-1.7-9/arules/R/itemMatrix.R | 455 ++++++--- arules-1.7-9/arules/R/itemsets.R | 190 ++-- arules-1.7-9/arules/R/match.R | 150 ++- arules-1.7-9/arules/R/merge.R | 35 arules-1.7-9/arules/R/parameter.R | 274 +++-- arules-1.7-9/arules/R/plot.R | 4 arules-1.7-9/arules/R/pmml.R | 78 - arules-1.7-9/arules/R/predict.R | 43 arules-1.7-9/arules/R/random.transactions.R | 349 ++++--- arules-1.7-9/arules/R/read_write.R | 184 ++- arules-1.7-9/arules/R/ruleInduction.R | 332 ++++--- arules-1.7-9/arules/R/rules.R | 312 ++++-- arules-1.7-9/arules/R/sample.R | 56 - arules-1.7-9/arules/R/sets.R | 93 +- arules-1.7-9/arules/R/setsItemwise.R | 70 - arules-1.7-9/arules/R/size.R | 29 arules-1.7-9/arules/R/sort.R | 49 - arules-1.7-9/arules/R/subset.R | 102 +- arules-1.7-9/arules/R/support.R | 178 ++- arules-1.7-9/arules/R/supportingTransactions.R | 45 arules-1.7-9/arules/R/tidLists.R | 314 ++++-- arules-1.7-9/arules/R/transactions.R | 380 ++++---- arules-1.7-9/arules/R/unique.R | 37 arules-1.7-9/arules/R/warm.R | 94 +- arules-1.7-9/arules/README.md | 30 arules-1.7-9/arules/build/partial.rdb |binary arules-1.7-9/arules/build/vignette.rds |binary arules-1.7-9/arules/inst/doc/arules.pdf |binary arules-1.7-9/arules/man/APappearance-class.Rd | 18 arules-1.7-9/arules/man/Adult.Rd | 33 arules-1.7-9/arules/man/DATAFRAME.Rd | 11 arules-1.7-9/arules/man/Epub.Rd | 1 arules-1.7-9/arules/man/Income.Rd | 34 arules-1.7-9/arules/man/apriori.Rd | 19 arules-1.7-9/arules/man/c.Rd | 2 arules-1.7-9/arules/man/confint.Rd | 11 arules-1.7-9/arules/man/discretize.Rd | 73 - arules-1.7-9/arules/man/dissimilarity.Rd | 6 arules-1.7-9/arules/man/eclat.Rd | 3 arules-1.7-9/arules/man/extract.Rd | 2 arules-1.7-9/arules/man/fim4r.Rd | 58 - arules-1.7-9/arules/man/hierarchy.Rd | 3 arules-1.7-9/arules/man/inspect.Rd | 6 arules-1.7-9/arules/man/interestMeasure.Rd | 12 arules-1.7-9/arules/man/is.generator.Rd | 12 arules-1.7-9/arules/man/is.redundant.Rd | 26 arules-1.7-9/arules/man/is.superset.Rd | 4 arules-1.7-9/arules/man/itemCoding.Rd | 56 - arules-1.7-9/arules/man/itemFrequencyPlot.Rd | 14 arules-1.7-9/arules/man/itemMatrix-class.Rd | 34 arules-1.7-9/arules/man/itemsets-class.Rd | 6 arules-1.7-9/arules/man/match.Rd | 2 arules-1.7-9/arules/man/merge.Rd | 2 arules-1.7-9/arules/man/predict.Rd | 2 arules-1.7-9/arules/man/random.transactions.Rd | 14 arules-1.7-9/arules/man/read.Rd | 17 arules-1.7-9/arules/man/ruleInduction.Rd | 2 arules-1.7-9/arules/man/rules-class.Rd | 9 arules-1.7-9/arules/man/subset.Rd | 10 arules-1.7-9/arules/man/supportingTransactions.Rd | 22 arules-1.7-9/arules/man/tidLists-class.Rd | 26 arules-1.7-9/arules/man/transactions-class.Rd | 39 arules-1.7-9/arules/man/weclat.Rd | 28 arules-1.7-9/arules/man/write.Rd | 4 arules-1.7-9/arules/src/bitmat.c | 83 - arules-1.7-9/arules/src/bitmat.h | 6 arules-1.7-9/arules/src/istree.c | 126 -- arules-1.7-9/arules/src/istree.h | 27 arules-1.7-9/arules/src/reclat.c | 4 arules-1.7-9/arules/src/symtab.c | 37 arules-1.7-9/arules/src/symtab.h | 10 arules-1.7-9/arules/src/tract.c | 81 - arules-1.7-9/arules/src/tract.h | 32 arules-1.7-9/arules/tests/testthat/test-apriori.R | 14 arules-1.7-9/arules/tests/testthat/test-associations.R | 71 - arules-1.7-9/arules/tests/testthat/test-concise.R | 20 arules-1.7-9/arules/tests/testthat/test-confint.R | 27 arules-1.7-9/arules/tests/testthat/test-crossTable.R | 23 arules-1.7-9/arules/tests/testthat/test-discretize.R | 38 arules-1.7-9/arules/tests/testthat/test-eclat.R | 25 arules-1.7-9/arules/tests/testthat/test-extract.R | 4 arules-1.7-9/arules/tests/testthat/test-fim4r.R | 14 arules-1.7-9/arules/tests/testthat/test-interestMeasures.R | 159 +-- arules-1.7-9/arules/tests/testthat/test-itemCoding.R | 10 arules-1.7-9/arules/tests/testthat/test-itemMatrix.R | 82 + arules-1.7-9/arules/tests/testthat/test-matrix.R | 53 - arules-1.7-9/arules/tests/testthat/test-mine_concise.R | 4 arules-1.7-9/arules/tests/testthat/test-missing.R | 1 arules-1.7-9/arules/tests/testthat/test-read_write.R | 51 - arules-1.7-9/arules/tests/testthat/test-ruleInduction.R | 110 +- arules-1.7-9/arules/tests/testthat/test-sets.R | 52 - arules-1.7-9/arules/tests/testthat/test-tidLists.R | 29 arules-1.7-9/arules/tests/testthat/test-transactions.R | 59 - arules-1.7-9/arules/tests/testthat/test-warm.R | 45 137 files changed, 6346 insertions(+), 4964 deletions(-)
Title: Soil and Water Conservation
Description: Includes four functions: RFactor_calc(), RFactor_est(), KFactor() and SoilLoss(). The rainfall erosivity factors can be calculated or estimated, and soil erodibility will be estimated by the equation extracted from the monograph. Soil loss will be estimated by the product of five factors (rainfall erosivity, soil erodibility, length and steepness slope, cover-management factor and support practice factor. In the future, additional functions can be included. This efforts to advance research in soil and water conservation, with fast and accurate results.
Author: Dione Pereira Cardoso [aut, cre]
,
Paulo Cesar Ossani [aut] ,
Junior Cesar Avanzi [aut]
Maintainer: Dione Pereira Cardoso <cardoso.dione@gmail.com>
Diff between SoilConservation versions 1.0.0 dated 2024-05-03 and 1.0.1 dated 2024-12-14
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/RFactor_est.R | 2 +- man/SoilConservation.Rd | 4 ++-- 4 files changed, 10 insertions(+), 10 deletions(-)
More information about SoilConservation at CRAN
Permanent link
Title: FDR Based Multiple Testing Procedures with Adaptation for
Discrete Tests
Description: Implementations of the multiple testing procedures for discrete
tests described in the paper Döhler, Durand and Roquain (2018) "New FDR
bounds for discrete and heterogeneous tests" <doi:10.1214/18-EJS1441>. The
main procedures of the paper (HSU and HSD), their adaptive counterparts
(AHSU and AHSD), and the HBR variant are available and are coded to take as
input the results of a test procedure from package 'DiscreteTests', or a set
of observed p-values and their discrete support under their nulls. A
shortcut function to obtain such p-values and supports is also provided,
along with a wrapper allowing to apply discrete procedures directly to data.
Author: Sebastian Doehler [aut, ctb] ,
Florian Junge [aut, ctb, cre] ,
Guillermo Durand [aut, ctb] ,
Etienne Roquain [ctb],
Christina Kihn [ctb]
Maintainer: Florian Junge <diso.fbmn@h-da.de>
Diff between DiscreteFDR versions 2.0.1 dated 2024-10-24 and 2.1.0 dated 2024-12-14
DESCRIPTION | 33 ++++---- MD5 | 89 +++++++++++------------ NAMESPACE | 3 NEWS.md | 110 +++++++++++++++++----------- R/ADBH_fun.R | 17 ++-- R/Aux_fun.R | 8 -- R/DBH_fun.R | 28 ++++--- R/DBR_fun.R | 37 +++++---- R/DBY_fun.R |only R/DiscreteFDR-package.R | 7 + R/RcppExports.R | 54 ++------------ R/discreteBH_fun.R | 59 +++++++++------ R/discreteFDR_fun.R | 162 +++++++++++++++++++++++++++++++----------- R/fast_appli.R | 26 +++++- R/plot_funs.R | 15 ++- R/print_fun.R | 24 ++++-- R/summary_funs.R | 38 +++++---- R/support.R | 35 +++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/DiscreteFDR.html | 36 ++++++--- inst/doc/furtheranalyses.html | 16 ++-- inst/doc/toyexample.html | 20 ++++- man/ADBH.Rd | 38 +++++---- man/DBH.Rd | 38 +++++---- man/DBR.Rd | 47 +++++------- man/DBY.Rd |only man/DiscreteFDR.Rd | 8 +- man/direct.discrete.BH.Rd | 10 +- man/discrete.BH.Rd | 61 ++++++++------- man/fast.Discrete.Rd | 21 +++-- man/fisher.pvalues.support.Rd | 18 ++-- man/generate.pvalues.Rd | 5 - man/hist.DiscreteFDR.Rd | 8 +- man/kernel.Rd | 54 +------------- man/match.pvals.Rd | 16 ---- man/print.DiscreteFDR.Rd | 7 + man/summary.DiscreteFDR.Rd | 3 src/RcppExports.cpp | 56 +++++++++++--- src/helper.cpp | 93 ------------------------ src/helper.h | 56 ++++++-------- src/kernel.h | 131 ++++++++++++++++++--------------- src/kernel_ADBH.cpp | 86 +++++++++++++++------- src/kernel_DBH.cpp | 72 ++++++++++++++---- src/kernel_DBR.cpp | 44 ++++++++--- src/kernel_DBY.cpp |only src/kernel_common.cpp | 60 ++++----------- 47 files changed, 953 insertions(+), 796 deletions(-)
Title: Shared, Joint (Generalized) Frailty Models; Surrogate Endpoints
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package:
1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied.
2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope).
3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects.
4) Joint frailty models in the context of the joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed.
5) Joint general frailty models in the context of the joint modelling for recurrent events with terminal event data with two independent frailty terms.
6) Joint Nested fra [...truncated...]
Author: Virginie Rondeau [aut, cre] ,
Juan R. Gonzalez [aut],
Yassin Mazroui [aut],
Audrey Mauguen [aut],
Amadou Diakite [aut],
Alexandre Laurent [aut],
Myriam Lopez [aut],
Agnieszka Krol [aut],
Casimir L. Sofeu [aut],
Julien Dumerc [aut],
Denis Rustand [aut [...truncated...]
Maintainer: Virginie Rondeau <virginie.rondeau@u-bordeaux.fr>
Diff between frailtypack versions 3.6.4 dated 2024-11-15 and 3.6.5 dated 2024-12-14
frailtypack-3.6.4/frailtypack/man/figures/rt.png |only frailtypack-3.6.5/frailtypack/DESCRIPTION | 8 frailtypack-3.6.5/frailtypack/MD5 | 24 - frailtypack-3.6.5/frailtypack/NEWS | 9 frailtypack-3.6.5/frailtypack/R/frailtypack-package.R | 2 frailtypack-3.6.5/frailtypack/R/jointSurroPenal.R | 256 ++++++------- frailtypack-3.6.5/frailtypack/R/plot.jointSurroMed.R | 200 +++++----- frailtypack-3.6.5/frailtypack/R/plot.longiPenal.R | 1 frailtypack-3.6.5/frailtypack/R/summary.jointSurroMed.R | 36 - frailtypack-3.6.5/frailtypack/man/figures/pte.png |only frailtypack-3.6.5/frailtypack/man/frailtypack-package.Rd | 2 frailtypack-3.6.5/frailtypack/man/jointSurroPenal.Rd | 68 +-- frailtypack-3.6.5/frailtypack/man/plot.jointSurroMed.Rd | 6 frailtypack-3.6.5/frailtypack/man/summary.jointSurroMed.Rd | 6 14 files changed, 314 insertions(+), 304 deletions(-)
Title: Visualize and Process Output from 'VirusHunterGatherer'
Description: A collection of tools for downstream analysis of
'VirusHunterGatherer' output. Processing of hittables
and plotting of results, enabling better interpretation,
is made easier with the provided functions.
Author: Ruff Sergej [aut, cre] ,
Lauber Chris [ctb] ,
Chong Li Chuin [ctb]
Maintainer: Ruff Sergej <serijnh@gmail.com>
Diff between Virusparies versions 1.0.0 dated 2024-11-12 and 1.1.0 dated 2024-12-14
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/sysdata.rda |binary README.md | 17 +++++++++-------- 4 files changed, 16 insertions(+), 15 deletions(-)
Title: A Collection of Lovecraftian Tales and Texts
Description: A curated collection of Howard Phillips
Lovecraft's complete stories, collected for the purpose of text
analysis.
Author: Ruff Sergej [aut, cre]
Maintainer: Ruff Sergej <serijnh@gmail.com>
Diff between lovecraftr versions 1.0.0 dated 2024-11-14 and 1.2.0 dated 2024-12-14
DESCRIPTION | 7 - MD5 | 58 ++++++++- NAMESPACE | 12 +- R/fetch_lovecraft.R |only R/lovecraft_stories.R | 223 ++++++++++++++++++++++++++++++++++++++ R/lovecraftr-package.R | 21 +++ R/unearth_lovecraftian_tales.R | 86 +++++++++----- README.md |only data/alchemist.rda |only data/azathoth.rda |only data/beast_cave.rda |only data/book.rda |only data/cats.rda |only data/celephais.rda |only data/city.rda |only data/dagon.rda |only data/descendant.rda |only data/doom.rda |only data/erich_zann.rda |only data/hound.rda |only data/outsider.rda |only data/reanimator.rda |only data/shadow_time.rda |only data/temple.rda |only data/unknown_kadath.rda |only data/wall_sleep.rda |only data/witch_house.rda |only man/alchemist.Rd |only man/azathoth.Rd |only man/beast_cave.Rd |only man/book.Rd |only man/cats.Rd |only man/celephais.Rd |only man/city.Rd |only man/dagon.Rd |only man/descendant.Rd |only man/doom.Rd |only man/erich_zann.Rd |only man/fetch_lovecraft.Rd |only man/figures |only man/hound.Rd |only man/lovecraftr.Rd | 21 +++ man/outsider.Rd |only man/reanimator.Rd |only man/shadow_time.Rd |only man/temple.Rd |only man/unearth_lovecraftian_tales.Rd | 16 +- man/unknown_kadath.Rd |only man/wall_sleep.Rd |only man/witch_house.Rd |only tools |only 51 files changed, 390 insertions(+), 54 deletions(-)
Title: Extended Legends and Axes for 'ggplot2'
Description: A 'ggplot2' extension that focusses on expanding the
plotter's arsenal of guides. Guides in 'ggplot2' include axes and
legends. 'legendry' offers new axes and annotation options, as well as
new legends and colour displays.
Author: Teun van den Brand [aut, cre, cph]
Maintainer: Teun van den Brand <tahvdbrand@gmail.com>
Diff between legendry versions 0.1.0 dated 2024-11-01 and 0.2.0 dated 2024-12-14
legendry-0.1.0/legendry/R/guide_axis_base.R |only legendry-0.1.0/legendry/R/guide_axis_nested.R |only legendry-0.1.0/legendry/R/guide_colbar.R |only legendry-0.1.0/legendry/R/guide_colring.R |only legendry-0.1.0/legendry/R/guide_colsteps.R |only legendry-0.1.0/legendry/R/shapes_brackets.R |only legendry-0.1.0/legendry/R/shapes_caps.R |only legendry-0.1.0/legendry/tests/testthat/_snaps/compose_sandwich |only legendry-0.1.0/legendry/tests/testthat/_snaps/guide_axis_custom |only legendry-0.1.0/legendry/tests/testthat/_snaps/guide_axis_nested |only legendry-0.1.0/legendry/tests/testthat/_snaps/guide_colour_ring |only legendry-0.1.0/legendry/tests/testthat/_snaps/guide_colourbar_custom |only legendry-0.1.0/legendry/tests/testthat/_snaps/guide_coloursteps_custom |only legendry-0.1.0/legendry/tests/testthat/_snaps/guide_legend_base |only legendry-0.1.0/legendry/tests/testthat/test-compose_sandwich.R |only legendry-0.1.0/legendry/tests/testthat/test-guide_axis_custom.R |only legendry-0.1.0/legendry/tests/testthat/test-guide_axis_nested.R |only legendry-0.1.0/legendry/tests/testthat/test-guide_colour_ring.R |only legendry-0.1.0/legendry/tests/testthat/test-guide_colourbar_custom.R |only legendry-0.1.0/legendry/tests/testthat/test-guide_coloursteps_custom.R |only legendry-0.1.0/legendry/tests/testthat/test-guide_legend_base.R |only legendry-0.1.0/legendry/tests/testthat/test-shapes_brackets.R |only legendry-0.1.0/legendry/tests/testthat/test-shapes_caps.R |only legendry-0.1.0/legendry/tests/testthat/test-theme_registry.R |only legendry-0.2.0/legendry/DESCRIPTION | 6 legendry-0.2.0/legendry/MD5 | 182 +- legendry-0.2.0/legendry/NAMESPACE | 9 legendry-0.2.0/legendry/NEWS.md | 17 legendry-0.2.0/legendry/R/compose-.R | 462 ++--- legendry-0.2.0/legendry/R/guide-axis-base.R |only legendry-0.2.0/legendry/R/guide-axis-dendro.R |only legendry-0.2.0/legendry/R/guide-axis-nested.R |only legendry-0.2.0/legendry/R/guide-circles.R |only legendry-0.2.0/legendry/R/guide-colbar.R |only legendry-0.2.0/legendry/R/guide-colring.R |only legendry-0.2.0/legendry/R/guide-colsteps.R |only legendry-0.2.0/legendry/R/key-.R | 16 legendry-0.2.0/legendry/R/key-range.R | 852 +++++----- legendry-0.2.0/legendry/R/key-segment.R |only legendry-0.2.0/legendry/R/primitive-.R | 10 legendry-0.2.0/legendry/R/primitive-segments.R |only legendry-0.2.0/legendry/R/scale-dendro.R |only legendry-0.2.0/legendry/R/shapes-brackets.R |only legendry-0.2.0/legendry/R/shapes-caps.R |only legendry-0.2.0/legendry/R/themes.R | 6 legendry-0.2.0/legendry/R/utils-checks.R | 6 legendry-0.2.0/legendry/R/utils-text.R | 21 legendry-0.2.0/legendry/R/utils.R | 22 legendry-0.2.0/legendry/README.md | 2 legendry-0.2.0/legendry/man/bracket_options.Rd | 2 legendry-0.2.0/legendry/man/cap_options.Rd | 2 legendry-0.2.0/legendry/man/guide_axis_base.Rd | 4 legendry-0.2.0/legendry/man/guide_axis_dendro.Rd |only legendry-0.2.0/legendry/man/guide_axis_nested.Rd | 15 legendry-0.2.0/legendry/man/guide_circles.Rd |only legendry-0.2.0/legendry/man/guide_colbar.Rd | 4 legendry-0.2.0/legendry/man/guide_colring.Rd | 4 legendry-0.2.0/legendry/man/guide_colsteps.Rd | 4 legendry-0.2.0/legendry/man/guide_legend_base.Rd | 2 legendry-0.2.0/legendry/man/guide_legend_cross.Rd | 2 legendry-0.2.0/legendry/man/guide_legend_group.Rd | 2 legendry-0.2.0/legendry/man/key_group.Rd | 1 legendry-0.2.0/legendry/man/key_range.Rd | 1 legendry-0.2.0/legendry/man/key_segments.Rd |only legendry-0.2.0/legendry/man/key_specialty.Rd | 1 legendry-0.2.0/legendry/man/key_standard.Rd | 1 legendry-0.2.0/legendry/man/legendry_extensions.Rd | 13 legendry-0.2.0/legendry/man/primitive_box.Rd | 1 legendry-0.2.0/legendry/man/primitive_bracket.Rd | 1 legendry-0.2.0/legendry/man/primitive_fence.Rd | 1 legendry-0.2.0/legendry/man/primitive_labels.Rd | 1 legendry-0.2.0/legendry/man/primitive_line.Rd | 1 legendry-0.2.0/legendry/man/primitive_segments.Rd |only 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legendry-0.2.0/legendry/tests/testthat/test-compose-sandwich.R |only legendry-0.2.0/legendry/tests/testthat/test-gizmo-density.R | 180 +- legendry-0.2.0/legendry/tests/testthat/test-gizmo-histogram.R | 132 - legendry-0.2.0/legendry/tests/testthat/test-guide-axis-custom.R |only legendry-0.2.0/legendry/tests/testthat/test-guide-axis-dendro.R |only legendry-0.2.0/legendry/tests/testthat/test-guide-axis-nested.R |only legendry-0.2.0/legendry/tests/testthat/test-guide-circles.R |only legendry-0.2.0/legendry/tests/testthat/test-guide-colbar.R |only legendry-0.2.0/legendry/tests/testthat/test-guide-colring.R |only legendry-0.2.0/legendry/tests/testthat/test-guide-colsteps.R |only legendry-0.2.0/legendry/tests/testthat/test-guide-legend-base.R |only legendry-0.2.0/legendry/tests/testthat/test-key-group.R | 144 - legendry-0.2.0/legendry/tests/testthat/test-key-segment.R |only legendry-0.2.0/legendry/tests/testthat/test-primitive-segments.R |only legendry-0.2.0/legendry/tests/testthat/test-scale-dendro.R |only legendry-0.2.0/legendry/tests/testthat/test-shapes-brackets.R |only legendry-0.2.0/legendry/tests/testthat/test-shapes-caps.R |only legendry-0.2.0/legendry/tests/testthat/test-theme-registry.R |only 107 files changed, 1121 insertions(+), 1016 deletions(-)
Title: Retrieve and Analyze Clinical Trials in Public Registers
Description: A system for querying, retrieving and analyzing
protocol- and results-related information on clinical trials from
four public registers, the 'European Union Clinical Trials Register'
('EUCTR', <https://www.clinicaltrialsregister.eu/>),
'ClinicalTrials.gov' (<https://clinicaltrials.gov/> and also
translating queries the retired classic interface), the
'ISRCTN' (<http://www.isrctn.com/>) and the
'European Union Clinical Trials Information System'
('CTIS', <https://euclinicaltrials.eu/>).
Trial information is downloaded, converted and stored in a database
('PostgreSQL', 'SQLite', 'DuckDB' or 'MongoDB'; via package 'nodbi').
Documents in registers associated with trials can also be downloaded.
Other functions identify deduplicated records,
easily find and extract variables (fields) of interest even
from complex nested data as used by the registers,
merge variables and update queries.
The package can be used for meta-analysis and trend-analysis of
the design and cond [...truncated...]
Author: Ralf Herold [aut, cre]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between ctrdata versions 1.19.5 dated 2024-11-10 and 1.20.0 dated 2024-12-14
ctrdata-1.19.5/ctrdata/man/figures/README-ctrdata_json_postgresql.jpg |only ctrdata-1.20.0/ctrdata/DESCRIPTION | 14 ctrdata-1.20.0/ctrdata/MD5 | 148 +++--- ctrdata-1.20.0/ctrdata/NAMESPACE | 6 ctrdata-1.20.0/ctrdata/NEWS.md | 11 ctrdata-1.20.0/ctrdata/R/ctrGetQueryUrl.R | 56 ++ ctrdata-1.20.0/ctrdata/R/ctrLoadQueryIntoDb.R | 4 ctrdata-1.20.0/ctrdata/R/ctrOpenSearchPagesInBrowser.R | 42 - ctrdata-1.20.0/ctrdata/R/ctrShowOneTrial.R |only ctrdata-1.20.0/ctrdata/R/ctrdata-package.R | 25 - ctrdata-1.20.0/ctrdata/R/ctrdata-registers.R | 18 ctrdata-1.20.0/ctrdata/R/dbFindFields.R | 6 ctrdata-1.20.0/ctrdata/R/dbFindIdsUniqueTrials.R | 6 ctrdata-1.20.0/ctrdata/R/dbGetFieldsIntoDf.R | 23 - ctrdata-1.20.0/ctrdata/R/dbQueryHistory.R | 9 ctrdata-1.20.0/ctrdata/R/dfMergeVariablesRelevel.R | 5 ctrdata-1.20.0/ctrdata/R/dfName2Value.R | 10 ctrdata-1.20.0/ctrdata/R/dfTrials2Long.R | 215 +++++----- ctrdata-1.20.0/ctrdata/R/util_functions.R | 111 +++-- ctrdata-1.20.0/ctrdata/README.md | 18 ctrdata-1.20.0/ctrdata/inst/doc/ctrdata_install.pdf |binary ctrdata-1.20.0/ctrdata/inst/doc/ctrdata_retrieve.pdf |binary ctrdata-1.20.0/ctrdata/inst/doc/ctrdata_summarise.pdf |binary ctrdata-1.20.0/ctrdata/inst/htmlwidgets |only ctrdata-1.20.0/ctrdata/inst/tinytest/more_test_ctrdata_duckdb_ctis.R | 20 ctrdata-1.20.0/ctrdata/inst/tinytest/more_test_ctrdata_duckdb_euctr.R | 21 ctrdata-1.20.0/ctrdata/inst/tinytest/more_test_ctrdata_duckdb_isrctn.R | 18 ctrdata-1.20.0/ctrdata/inst/tinytest/more_test_ctrdata_mongo_local_ctgov2.R | 14 ctrdata-1.20.0/ctrdata/inst/tinytest/more_test_ctrdata_mongo_local_ctis.R | 21 ctrdata-1.20.0/ctrdata/inst/tinytest/more_test_ctrdata_mongo_local_euctr.R | 23 - ctrdata-1.20.0/ctrdata/inst/tinytest/more_test_ctrdata_mongo_local_isrctn.R | 19 ctrdata-1.20.0/ctrdata/inst/tinytest/more_test_ctrdata_mongo_remote_rw_ctgov.R | 15 ctrdata-1.20.0/ctrdata/inst/tinytest/more_test_ctrdata_mongo_remote_rw_ctis.R | 30 - ctrdata-1.20.0/ctrdata/inst/tinytest/more_test_ctrdata_mongo_remote_rw_euctr.R | 23 - ctrdata-1.20.0/ctrdata/inst/tinytest/more_test_ctrdata_param_checks.R | 7 ctrdata-1.20.0/ctrdata/inst/tinytest/more_test_ctrdata_postgres_ctis.R | 20 ctrdata-1.20.0/ctrdata/inst/tinytest/more_test_ctrdata_postgres_euctr.R | 19 ctrdata-1.20.0/ctrdata/inst/tinytest/more_test_ctrdata_postgres_isrctn.R | 18 ctrdata-1.20.0/ctrdata/inst/tinytest/test_ctrdata_duckdb_ctgov2.R | 14 ctrdata-1.20.0/ctrdata/inst/tinytest/test_ctrdata_other_functions.R | 13 ctrdata-1.20.0/ctrdata/inst/tinytest/test_ctrdata_postgres_ctgov2.R | 14 ctrdata-1.20.0/ctrdata/inst/tinytest/test_ctrdata_sqlite_ctgov.R | 14 ctrdata-1.20.0/ctrdata/inst/tinytest/test_ctrdata_sqlite_ctgov2.R | 14 ctrdata-1.20.0/ctrdata/inst/tinytest/test_ctrdata_sqlite_ctis.R | 20 ctrdata-1.20.0/ctrdata/inst/tinytest/test_ctrdata_sqlite_euctr.R | 21 ctrdata-1.20.0/ctrdata/inst/tinytest/test_ctrdata_sqlite_isrctn.R | 18 ctrdata-1.20.0/ctrdata/man/ctrDb.Rd | 5 ctrdata-1.20.0/ctrdata/man/ctrGetQueryUrl.Rd | 12 ctrdata-1.20.0/ctrdata/man/ctrLoadQueryIntoDb.Rd | 8 ctrdata-1.20.0/ctrdata/man/ctrOpenSearchPagesInBrowser.Rd | 8 ctrdata-1.20.0/ctrdata/man/ctrShowOneTrial.Rd |only ctrdata-1.20.0/ctrdata/man/ctrdata-registers.Rd | 18 ctrdata-1.20.0/ctrdata/man/ctrdata.Rd | 26 - ctrdata-1.20.0/ctrdata/man/dbFindFields.Rd | 10 ctrdata-1.20.0/ctrdata/man/dbFindIdsUniqueTrials.Rd | 11 ctrdata-1.20.0/ctrdata/man/dbGetFieldsIntoDf.Rd | 11 ctrdata-1.20.0/ctrdata/man/dbQueryHistory.Rd | 9 ctrdata-1.20.0/ctrdata/man/dfMergeVariablesRelevel.Rd | 4 ctrdata-1.20.0/ctrdata/man/dfName2Value.Rd | 4 ctrdata-1.20.0/ctrdata/man/dfTrials2Long.Rd | 3 ctrdata-1.20.0/ctrdata/man/figures/ctrdata_ctrShowOneTrial.jpg |only ctrdata-1.20.0/ctrdata/vignettes/boxpep.png |binary ctrdata-1.20.0/ctrdata/vignettes/ctrdata_summarise.Rmd | 149 +++--- ctrdata-1.20.0/ctrdata/vignettes/nb1.png |binary ctrdata-1.20.0/ctrdata/vignettes/nb2.png |binary ctrdata-1.20.0/ctrdata/vignettes/nbtrials.png |binary ctrdata-1.20.0/ctrdata/vignettes/phase23_paed_p_values.png |binary ctrdata-1.20.0/ctrdata/vignettes/phase23_paed_p_values_participants.png |binary ctrdata-1.20.0/ctrdata/vignettes/samplesizechanges.png |binary 69 files changed, 801 insertions(+), 600 deletions(-)
Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to safely and efficiently organize and execute
Monte Carlo simulation experiments in R.
The package controls the structure and back-end of Monte Carlo simulation experiments
by utilizing a generate-analyse-summarise workflow. The workflow safeguards against
common simulation coding issues, such as automatically re-simulating non-convergent results,
prevents inadvertently overwriting simulation files, catches error and warning messages
during execution, implicitly supports parallel processing with high-quality random number
generation, and provides tools for managing high-performance computing (HPC) array jobs
submitted to schedulers such as SLURM. For a pedagogical introduction to the package see
Sigal and Chalmers (2016) <doi:10.1080/10691898.2016.1246953>. For a more in-depth overview of
the package and its design philosophy see Chalmers and Adkins (2020) <doi:10.20982/tqmp.16.4.p248>.
Author: Phil Chalmers [aut, cre] ,
Matthew Sigal [ctb],
Ogreden Oguzhan [ctb],
Mikko Ronkko [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between SimDesign versions 2.17.1 dated 2024-08-17 and 2.18 dated 2024-12-14
DESCRIPTION | 8 +- MD5 | 68 ++++++++--------- NAMESPACE | 3 NEWS.md | 18 ++++ R/Design.R | 32 ++++++++ R/PBA.R | 27 +++++-- R/RobbinsMonro.R | 1 R/SimCollect.R | 56 ++++++++++++-- R/SimExtract.R | 3 R/SimFunctions.R | 2 R/SimResults.R | 17 +++- R/SimSolve.R | 148 +++++++++++++++++++++------------------ R/runArraySimulation.R | 36 +++++++-- R/runSimulation.R | 15 +++ R/util.R | 21 +++-- inst/doc/Catch_errors.Rmd | 2 inst/doc/Catch_errors.html | 18 ++-- inst/doc/Fixed_obj_fun.html | 10 +- inst/doc/HPC-computing.html | 4 - inst/doc/MultipleAnalyses.html | 4 - inst/doc/Parallel-computing.html | 4 - inst/doc/Saving-results.html | 83 ++++----------------- inst/doc/SimDesign-intro.html | 20 ++--- man/SimCollect.Rd | 17 +++- man/SimFunctions.Rd | 2 man/SimSolve.Rd | 135 ++++++++++++++++++----------------- man/createDesign.Rd | 14 +++ man/quiet.Rd | 4 - man/runArraySimulation.Rd | 14 ++- man/runSimulation.Rd | 15 +++ man/timeFormater.Rd | 4 + tests/tests/test-01-core.R | 19 +++++ tests/tests/test-02-aggregate.R | 8 +- tests/tests/test-03-array.R | 62 +++++++++++++++- vignettes/Catch_errors.Rmd | 2 35 files changed, 567 insertions(+), 329 deletions(-)
Title: Analysis of Spatial Stratified Heterogeneity
Description: Analyzing spatial factors and exploring spatial associations based on the concept of spatial stratified heterogeneity, while also taking into account local spatial dependencies, spatial interpretability, complex spatial interactions, and robust spatial stratification. Additionally, it supports the spatial stratified heterogeneity family established in academic literature.
Author: Wenbo Lv [aut, cre, cph] ,
Yangyang Lei [aut] ,
Fangmei Liu [aut] ,
Jianwu Yan [aut] ,
Yongze Song [aut] ,
Wufan Zhao [aut]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between gdverse versions 1.3 dated 2024-11-16 and 1.3-1 dated 2024-12-14
gdverse-1.3-1/gdverse/DESCRIPTION | 8 gdverse-1.3-1/gdverse/MD5 | 41 - gdverse-1.3-1/gdverse/NEWS.md | 156 ++-- gdverse-1.3-1/gdverse/R/gd.R | 180 ++-- gdverse-1.3-1/gdverse/R/gozh.R | 466 ++++++------ gdverse-1.3-1/gdverse/R/opgd.R | 268 +++---- gdverse-1.3-1/gdverse/R/spd_lesh.R | 250 +++--- gdverse-1.3-1/gdverse/R/srsgd.R | 196 ++--- gdverse-1.3-1/gdverse/README.md | 9 gdverse-1.3-1/gdverse/inst/doc/gd.Rmd | 860 +++++++++++------------ gdverse-1.3-1/gdverse/inst/doc/opgd.Rmd | 428 +++++------ gdverse-1.3-1/gdverse/inst/doc/opgd.html | 2 gdverse-1.3-1/gdverse/inst/doc/shegd.Rmd | 390 +++++----- gdverse-1.3-1/gdverse/man/plot.gd_result.Rd | 2 gdverse-1.3-1/gdverse/man/plot.gozh_result.Rd | 2 gdverse-1.3-1/gdverse/man/plot.opgd_result.Rd | 2 gdverse-1.3-1/gdverse/man/plot.srsgd_result.Rd | 2 gdverse-1.3-1/gdverse/man/spd_lesh.Rd | 12 gdverse-1.3-1/gdverse/vignettes/gd.Rmd | 860 +++++++++++------------ gdverse-1.3-1/gdverse/vignettes/opgd.Rmd | 428 +++++------ gdverse-1.3-1/gdverse/vignettes/shegd.Rmd | 390 +++++----- gdverse-1.3/gdverse/man/figures/gdverse_funs.png |only 22 files changed, 2473 insertions(+), 2479 deletions(-)
Title: Single-Species, Multi-Species, and Integrated Spatial Occupancy
Models
Description: Fits single-species, multi-species, and integrated non-spatial and spatial occupancy models using Markov Chain Monte Carlo (MCMC). Models are fit using Polya-Gamma data augmentation detailed in Polson, Scott, and Windle (2013) <doi:10.1080/01621459.2013.829001>. Spatial models are fit using either Gaussian processes or Nearest Neighbor Gaussian Processes (NNGP) for large spatial datasets. Details on NNGP models are given in Datta, Banerjee, Finley, and Gelfand (2016) <doi:10.1080/01621459.2015.1044091> and Finley, Datta, and Banerjee (2022) <doi:10.18637/jss.v103.i05>. Provides functionality for data integration of multiple single-species occupancy data sets using a joint likelihood framework. Details on data integration are given in Miller, Pacifici, Sanderlin, and Reich (2019) <doi:10.1111/2041-210X.13110>. Details on single-species and multi-species models are found in MacKenzie, Nichols, Lachman, Droege, Royle, and Langtimm (2002) <doi:10.1890/0012-9658(2 [...truncated...]
Author: Jeffrey Doser [aut, cre],
Andrew Finley [aut],
Marc Kery [ctb]
Maintainer: Jeffrey Doser <jwdoser@ncsu.edu>
Diff between spOccupancy versions 0.7.6 dated 2024-04-19 and 0.8.0 dated 2024-12-14
DESCRIPTION | 17 MD5 | 257 +++-- NAMESPACE | 25 NEWS.md | 32 R/PGOcc.R | 1833 ++++++++++++++++++++--------------------- R/generics.R | 836 +++++++++++++----- R/getSVCSamples.R | 6 R/intMsPGOcc.R | 318 +++---- R/intPGOcc.R | 788 ++++++++++++++--- R/lfJSDM.R | 60 - R/lfMsPGOcc.R | 59 - R/msPGOcc.R | 56 - R/plot-generics.R | 12 R/postHocLM.R | 4 R/ppcOcc.R | 132 ++ R/sfJSDM.R | 61 - R/sfMsPGOcc.R | 81 - R/simIntMsOcc.R | 339 ++++--- R/simIntOcc.R | 140 +++ R/simMsOcc.R | 4 R/simTIntOcc.R |only R/simTOcc.R | 6 R/spIntPGOcc.R | 1189 +++++++++++++++++++++----- R/spMsPGOcc.R | 103 +- R/spPGOcc.R | 46 - R/stIntPGOcc.R |only R/stMsPGOcc.R | 48 - R/stPGOcc.R | 51 - R/svcMsPGOcc.R | 58 - R/svcPGBinom.R | 33 R/svcPGOcc.R | 38 R/svcTIntPGOcc.R |only R/svcTMsPGOcc.R | 72 - R/svcTPGBinom.R | 132 +- R/svcTPGOcc.R | 48 - R/tIntPGOcc.R |only R/tMsPGOcc.R | 38 R/tPGOcc.R | 32 R/updateMCMC.R | 174 +++ R/waicOcc.R | 75 - README.md | 83 - inst/CITATION | 2 man/PGOcc.Rd | 7 man/fitted.stIntPGOcc.Rd |only man/fitted.svcTIntPGOcc.Rd |only man/fitted.tIntPGOcc.Rd |only man/intMsPGOcc.Rd | 23 man/intPGOcc.Rd | 43 man/lfJSDM.Rd | 5 man/lfMsPGOcc.Rd | 5 man/msPGOcc.Rd | 7 man/predict.PGOcc.Rd | 3 man/predict.intMsPGOcc.Rd | 60 - man/predict.intPGOcc.Rd | 8 man/predict.lfJSDM.Rd | 3 man/predict.lfMsPGOcc.Rd | 7 man/predict.msPGOcc.Rd | 3 man/predict.sfJSDM.Rd | 3 man/predict.sfMsPGOcc.Rd | 3 man/predict.spIntPGOcc.Rd | 10 man/predict.spMsPGOcc.Rd | 37 man/predict.spPGOcc.Rd | 3 man/predict.stIntPGOcc.Rd |only man/predict.stMsPGOcc.Rd | 19 man/predict.stPGOcc.Rd | 2 man/predict.svcMsPGOcc.Rd | 12 man/predict.svcPGBinom.Rd | 2 man/predict.svcPGOcc.Rd | 2 man/predict.svcTIntPGOcc.Rd |only man/predict.svcTMsPGOcc.Rd | 18 man/predict.svcTPGBinom.Rd | 2 man/predict.svcTPGOcc.Rd | 4 man/predict.tIntPGOcc.Rd |only man/predict.tMsPGOcc.Rd | 2 man/predict.tPGOcc.Rd | 2 man/residuals.PGOcc.Rd |only man/residuals.spPGOcc.Rd |only man/residuals.svcPGOcc.Rd |only man/sfJSDM.Rd | 10 man/sfMsPGOcc.Rd | 7 man/simIntMsOcc.Rd | 15 man/simIntOcc.Rd | 7 man/simTIntOcc.Rd |only man/simTOcc.Rd | 2 man/spIntPGOcc.Rd | 46 - man/spMsPGOcc.Rd | 4 man/spOccupancy-package.Rd | 2 man/spPGOcc.Rd | 11 man/stIntPGOcc.Rd |only man/stMsPGOcc.Rd | 4 man/stPGOcc.Rd | 6 man/summary.stIntPGOcc.Rd |only man/summary.svcTIntPGOcc.Rd |only man/summary.tIntPGOcc.Rd |only man/svcMsPGOcc.Rd | 27 man/svcPGBinom.Rd | 26 man/svcPGOcc.Rd | 26 man/svcTIntPGOcc.Rd |only man/svcTMsPGOcc.Rd | 26 man/svcTPGBinom.Rd | 26 man/svcTPGOcc.Rd | 37 man/tIntPGOcc.Rd |only man/tMsPGOcc.Rd | 5 man/tPGOcc.Rd | 10 man/updateMCMC.Rd | 16 src/PGOcc.cpp | 6 src/init.cpp | 12 src/intMsPGOcc.cpp | 2 src/intPGOcc.cpp | 370 +++++++- src/lfJSDM.cpp | 140 +-- src/msPGOcc.cpp | 2 src/postHocLM.cpp | 6 src/sfMsPGOccNNGPPredict.cpp | 14 src/spIntPGOcc.cpp | 382 +++++++- src/spIntPGOccNNGP.cpp | 393 +++++++- src/spMsPGOcc.cpp | 40 src/spMsPGOccNNGP.cpp | 42 src/spMsPGOccPredict.cpp | 12 src/spOccupancy.h | 1057 +++++++++++++---------- src/spPGOcc.cpp | 30 src/spPGOccNNGP.cpp | 38 src/spPGOccNNGPPredict.cpp | 14 src/spPGOccPredict.cpp | 10 src/stIntPGOccNNGP.cpp |only src/stMsPGOccNNGP.cpp | 42 src/stPGOccNNGP.cpp | 44 src/stPGOccNNGPPredict.cpp | 14 src/svcMsPGOccNNGP.cpp | 42 src/svcMsPGOccNNGPPredict.cpp | 14 src/svcPGBinomNNGP.cpp | 28 src/svcPGOccNNGP.cpp | 34 src/svcPGOccNNGPPredict.cpp | 16 src/svcTIntPGOccNNGP.cpp |only src/svcTMsPGOccNNGP.cpp | 42 src/svcTMsPGOccNNGPPredict.cpp | 16 src/svcTPGBinomNNGP.cpp | 30 src/svcTPGOccNNGP.cpp | 45 - src/svcTPGOccNNGPPredict.cpp | 18 src/tIntPGOcc.cpp |only src/tMsPGOcc.cpp | 36 src/tPGOcc.cpp | 32 141 files changed, 7118 insertions(+), 3801 deletions(-)
Title: Matrices for Repeat-Sales Price Indexes
Description: Calculate the matrices in
Shiller (1991, <doi:10.1016/S1051-1377(05)80028-2>) that serve as the
foundation for many repeat-sales price indexes.
Author: Steve Martin [aut, cre, cph]
Maintainer: Steve Martin <marberts@protonmail.com>
Diff between rsmatrix versions 0.2.8 dated 2023-11-19 and 0.2.9 dated 2024-12-14
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Title: Bayesian Quantile Regression for Ordinal Models
Description: Package provides functions for estimation and inference in Bayesian quantile regression with ordinal outcomes. An ordinal model with 3 or more outcomes (labeled OR1 model) is estimated by a combination of Gibbs sampling and Metropolis-Hastings (MH) algorithm. Whereas an ordinal model with exactly 3 outcomes (labeled OR2 model) is estimated using a Gibbs sampling algorithm. The summary output presents the posterior mean, posterior standard deviation, 95% credible intervals, and the inefficiency factors along with the two model comparison measures – logarithm of marginal likelihood and the deviance information criterion (DIC). The package also provides functions for computing the covariate effects and other functions that aids either the estimation or inference in quantile ordinal models.
Rahman, M. A. (2016).“Bayesian Quantile Regression for Ordinal Models.” Bayesian Analysis, 11(1): 1-24 <doi: 10.1214/15-BA939>.
Yu, K., and Moyeed, R. A. (2001). “Bayesian Quantile Regression.” St [...truncated...]
Author: Mohammad Arshad Rahman Developer [aut],
Prajual Maheshwari [cre]
Maintainer: Prajual Maheshwari <prajual1391@gmail.com>
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Title: Make, Update, and Query Binary Causal Models
Description: Users can declare causal models over binary nodes, update beliefs about causal types given data, and calculate arbitrary queries. Updating is implemented in 'stan'. See Humphreys and Jacobs, 2023, Integrated Inferences (<DOI: 10.1017/9781316718636>) and Pearl, 2009 Causality (<DOI:10.1017/CBO9780511803161>).
Author: Clara Bicalho [ctb],
Jasper Cooper [ctb],
Macartan Humphreys [aut] ,
Till Tietz [aut, cre] ,
Alan Jacobs [aut],
Merlin Heidemanns [ctb],
Lily Medina [aut] ,
Julio Solis [ctb],
Georgiy Syunyaev [aut]
Maintainer: Till Tietz <ttietz2014@gmail.com>
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