Title: Fast Robust Moments
Description: Fast, numerically robust computation of weighted moments via 'Rcpp'.
Supports computation on vectors and matrices, and Monoidal append of moments.
Moments and cumulants over running fixed length windows can be computed,
as well as over time-based windows.
Moment computations are via a generalization of Welford's method, as described
by Bennett et. (2009) <doi:10.1109/CLUSTR.2009.5289161>.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Diff between fromo versions 0.2.3 dated 2024-11-07 and 0.2.4 dated 2024-11-29
ChangeLog | 5 DESCRIPTION | 8 MD5 | 64 +++--- NAMESPACE | 14 + R/RcppExports.R | 217 +++++++++++++++++++++ R/fromo.r | 6 R/zzz_centsums.R | 11 - README.md | 325 +++++++++++++++++++------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/fromo.Rnw | 346 ++++++++++++++++++++++++++++++++++- inst/doc/fromo.pdf |binary man/NEWS.Rd | 8 man/as.centsums.Rd | 40 +++- man/firstmoments.Rd | 11 - man/two_runningmoments.Rd |only man/two_t_runningmoments.Rd |only src/RcppExports.cpp | 327 +++++++++++++++++++++++++++++++++ src/common.h | 7 src/fromo.cpp | 11 - src/moment_interp.h | 1 src/running.h | 23 -- src/t_running.h | 35 +-- src/two_moment_interp.h |only src/two_running.cpp |only src/two_running.h |only src/two_t_running.cpp |only src/two_t_running.h |only src/two_welford.h |only src/vec_welford.h |only tests/testthat/test-correctness.r | 84 ++++++++ tests/testthat/test-running.r | 125 ++++++++++++ tests/testthat/test-trunning.r | 162 ++++++++++++++++ tools/figure/toy_zscore-1.png |binary tools/figure/trun_corr_testing-1.png |only tools/figure/trun_testing-1.png |binary vignettes/fromo.Rnw | 346 ++++++++++++++++++++++++++++++++++- vignettes/fromo.bib | 14 + 38 files changed, 1958 insertions(+), 232 deletions(-)
Title: Self-Validated Ensemble Models with Elastic Net Regression
Description: Implements Self-Validated Ensemble Models (SVEM, Lemkus et al. (2021) <doi:10.1016/j.chemolab.2021.104439>) using Elastic Net regression via 'glmnet' (Friedman et al. <doi:10.18637/jss.v033.i01>). SVEM averages predictions from multiple models fitted to fractionally weighted bootstraps of the data, tuned with anti-correlated validation weights. Also implements the randomized permutation whole model test for SVEM (Karl (2024) <doi:10.1016/j.chemolab.2024.105122>). \\Code for the whole model test was taken from the supplementary material of Karl (2024). Development of this package was assisted by 'GPT o1-preview' for code structure and documentation.
Author: Andrew T. Karl [cre, aut]
Maintainer: Andrew T. Karl <akarl@asu.edu>
Diff between SVEMnet versions 1.0.3 dated 2024-11-20 and 1.1.1 dated 2024-11-29
DESCRIPTION | 12 ++++++---- MD5 | 40 +++++++++++++++++++++++++----------- NAMESPACE | 1 NEWS |only R/SVEMnet-package.R | 4 ++- R/SVEMnet.R | 29 +++++++++++++------------- R/plot.svemnet.R | 4 +-- R/predict.svem_lasso.R | 23 +++++++------------- R/print.R |only R/svem_significance_test.R | 33 +++++++++++++++-------------- build/vignette.rds |only inst/doc |only inst/scripts |only man/SVEMnet-package.Rd | 4 ++- man/SVEMnet.Rd | 25 +++++++++++++--------- man/plot.svem_model.Rd | 4 +-- man/predict.svem_model.Rd | 6 ++--- man/print.svem_significance_test.Rd |only man/svem_significance_test.Rd | 27 +++++++++++------------- vignettes |only 20 files changed, 117 insertions(+), 95 deletions(-)
Title: Marginal Modeling for Exposure Data with Values Below the LOD
Description: Functions of marginal mean and quantile regression models are used to analyze environmental exposure and biomonitoring data with repeated measurements and non-detects (i.e., values below the limit of detection (LOD)), as well as longitudinal exposure data that include non-detects and time-dependent covariates.
Author: I-Chen Chen [cre, aut] ,
Philip Westgate [ctb],
Liya Fu [ctb]
Maintainer: I-Chen Chen <okv0@cdc.gov>
Diff between marlod versions 0.1.1 dated 2024-08-27 and 0.1.2 dated 2024-11-29
DESCRIPTION | 8 +-- MD5 | 14 ++--- inst/doc/marlod.R | 10 +-- inst/doc/marlod.Rmd | 14 ++--- inst/doc/marlod.html | 136 +++++++++++++++++++++++++-------------------------- man/Simdata15.Rd | 4 - man/Simdata58.Rd | 2 vignettes/marlod.Rmd | 14 ++--- 8 files changed, 101 insertions(+), 101 deletions(-)
Title: Transformation Models with Mixed Effects
Description: Likelihood-based estimation of mixed-effects transformation models
using the Template Model Builder ('TMB', Kristensen et al., 2016)
<doi:10.18637/jss.v070.i05>. The technical details of transformation models
are given in Hothorn et al. (2018) <doi:10.1111/sjos.12291>. Likelihood
contributions of exact, randomly censored (left, right, interval) and
truncated observations are supported. The random effects are assumed to be
normally distributed on the scale of the transformation function, the
marginal likelihood is evaluated using the Laplace approximation, and the
gradients are calculated with automatic differentiation (Tamasi & Hothorn,
2021) <doi:10.32614/RJ-2021-075>. Penalized smooth shift terms can be
defined using 'mgcv'.
Author: Balint Tamasi [aut, cre] ,
Torsten Hothorn [ctb]
Maintainer: Balint Tamasi <balint.tamasi+tramME@gmail.com>
Diff between tramME versions 1.0.6 dated 2024-07-02 and 1.0.7 dated 2024-11-29
DESCRIPTION | 8 +- MD5 | 18 +++- NEWS.md | 6 + build/vignette.rds |binary inst/doc/RJ-2021-075.R | 44 ++++++------ inst/doc/RJ-2021-075.pdf |binary inst/doc/mixed-effects-additive-models.R | 106 ++++++++++++++--------------- inst/doc/mixed-effects-additive-models.pdf |binary inst/doc/tramME-JSS.Rnw |only inst/doc/tramME-JSS.pdf |only vignettes/tramME-JSS.Rnw |only vignettes/tramME-JSS_orig.pdf |only 12 files changed, 95 insertions(+), 87 deletions(-)
Title: 'Rcpp' Interface to the APT Package Manager
Description: The 'APT Package Management System' provides Debian and
Debian-derived Linux systems with a powerful system to resolve package
dependencies. This package offers access directly from R. This can
only work on a system with a suitable 'libapt-pkg-dev' installation
so functionality is curtailed if such a library is not found.
Author: Dirk Eddelbuettel [aut, cre]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppAPT versions 0.0.9 dated 2022-05-25 and 0.0.10 dated 2024-11-29
ChangeLog | 35 ++++ DESCRIPTION | 14 + MD5 | 16 +- README.md | 12 - build/vignette.rds |binary inst/NEWS.Rd | 8 + inst/doc/binnmuAfterR340.html | 309 ++++++++++++++++++++++++++---------------- src/Makevars.in | 5 src/Makevars.win | 5 9 files changed, 261 insertions(+), 143 deletions(-)
Title: Causal Analysis of Observational Time-to-Event Data
Description: Implements target trial emulation methods to apply randomized
clinical trial design and analysis in an observational setting. Using
marginal structural models, it can estimate intention-to-treat and
per-protocol effects in emulated trials using electronic health
records. A description and application of the method can be found in
Danaei et al (2013) <doi:10.1177/0962280211403603>.
Author: Isaac Gravestock [aut, cre] ,
Li Su [aut],
Roonak Rezvani [aut] ,
Julia Moesch [aut],
Medical Research Council [fnd],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Isaac Gravestock <isaac.gravestock@roche.com>
Diff between TrialEmulation versions 0.0.3.9 dated 2024-09-09 and 0.0.4.0 dated 2024-11-29
TrialEmulation-0.0.3.9/TrialEmulation/man/predict.TE_msm.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/DESCRIPTION | 36 TrialEmulation-0.0.4.0/TrialEmulation/MD5 | 147 ++- TrialEmulation-0.0.4.0/TrialEmulation/NAMESPACE | 39 TrialEmulation-0.0.4.0/TrialEmulation/NEWS.md | 19 TrialEmulation-0.0.4.0/TrialEmulation/R/calculate_weights.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/data.R | 23 TrialEmulation-0.0.4.0/TrialEmulation/R/data_preparation.R | 2 TrialEmulation-0.0.4.0/TrialEmulation/R/data_simulation.R | 2 TrialEmulation-0.0.4.0/TrialEmulation/R/expand_trials.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/generics.R | 437 +++++++++- TrialEmulation-0.0.4.0/TrialEmulation/R/initiators.R | 2 TrialEmulation-0.0.4.0/TrialEmulation/R/modelling.R | 39 TrialEmulation-0.0.4.0/TrialEmulation/R/package.R | 3 TrialEmulation-0.0.4.0/TrialEmulation/R/predict.R | 47 - TrialEmulation-0.0.4.0/TrialEmulation/R/sampling.R | 63 + TrialEmulation-0.0.4.0/TrialEmulation/R/te_data.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/te_datastore.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/te_datastore_csv.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/te_datastore_duckdb.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/te_expansion.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/te_model_fitter.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/te_outcome_model.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/te_parsnip.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/te_stats_glm_logit.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/te_weights.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/trial_sequence.R |only TrialEmulation-0.0.4.0/TrialEmulation/R/utils.R | 33 TrialEmulation-0.0.4.0/TrialEmulation/README.md | 3 TrialEmulation-0.0.4.0/TrialEmulation/build/vignette.rds |binary TrialEmulation-0.0.4.0/TrialEmulation/data/data_censored.rda |only TrialEmulation-0.0.4.0/TrialEmulation/inst/WORDLIST | 33 TrialEmulation-0.0.4.0/TrialEmulation/inst/doc/Extending-TrialEmulation.R |only TrialEmulation-0.0.4.0/TrialEmulation/inst/doc/Extending-TrialEmulation.Rmd |only TrialEmulation-0.0.4.0/TrialEmulation/inst/doc/Extending-TrialEmulation.html |only TrialEmulation-0.0.4.0/TrialEmulation/inst/doc/Getting-Started.html | 194 ++-- TrialEmulation-0.0.4.0/TrialEmulation/inst/doc/new-interface.R |only TrialEmulation-0.0.4.0/TrialEmulation/inst/doc/new-interface.Rmd |only TrialEmulation-0.0.4.0/TrialEmulation/inst/doc/new-interface.html |only TrialEmulation-0.0.4.0/TrialEmulation/man/TrialEmulation-package.Rd | 3 TrialEmulation-0.0.4.0/TrialEmulation/man/calculate_weights.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/case_control_sampling_trials.Rd | 3 TrialEmulation-0.0.4.0/TrialEmulation/man/data_censored.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/data_preparation.Rd | 6 TrialEmulation-0.0.4.0/TrialEmulation/man/expand_trials.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/figures |only TrialEmulation-0.0.4.0/TrialEmulation/man/fit_msm.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/fit_outcome_model.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/fit_weights_model.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/initiators.Rd | 3 TrialEmulation-0.0.4.0/TrialEmulation/man/internal-methods.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/ipw_data.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/load_expanded_data.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/outcome_data.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/parsnip_model.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/predict_marginal.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/print_TE.Rd | 2 TrialEmulation-0.0.4.0/TrialEmulation/man/read_expanded_data.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/sample_expanded_data.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/save_expanded_data.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/save_to_csv.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/save_to_datatable.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/save_to_duckdb.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/set_censor_weight_model.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/set_data.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/set_expansion_options.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/set_outcome_model.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/set_switch_weight_model.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/show_weight_models.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/stats_glm_logit.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/summary_TE.Rd | 1 TrialEmulation-0.0.4.0/TrialEmulation/man/te_data-class.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/te_datastore-class.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/te_datastore_csv-class.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/te_datastore_duckdb-class.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/te_model_fitter-class.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/te_outcome_data-class.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/te_outcome_fitted-class.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/te_outcome_model-class.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/te_parsnip_model-class.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/te_stats_glm_logit-class.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/trial_msm.Rd | 6 TrialEmulation-0.0.4.0/TrialEmulation/man/trial_sequence-class.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/trial_sequence.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/man/weight_model_data_indices.Rd |only TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/_snaps/generics.md | 34 TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/_snaps/modelling.md | 80 + TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/_snaps/predict.md | 252 +++++ TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/_snaps/te_weights.md |only TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/_snaps/trial_sequence.md |only TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/data/new_pre_weight_func.rds |only TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/test-modelling.R | 117 ++ TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/test-predict.R | 69 + TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/test-sampling.R | 90 ++ TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/test-te_data.R |only TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/test-te_datastore.R |only TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/test-te_datastore_csv.R |only TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/test-te_datastore_duckdb.R |only TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/test-te_model_fitter.R |only TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/test-te_parsnip.R |only TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/test-te_weights.R |only TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/test-trial_sequence.R |only TrialEmulation-0.0.4.0/TrialEmulation/tests/testthat/test-utils.R | 6 TrialEmulation-0.0.4.0/TrialEmulation/vignettes/Extending-TrialEmulation.Rmd |only TrialEmulation-0.0.4.0/TrialEmulation/vignettes/img |only TrialEmulation-0.0.4.0/TrialEmulation/vignettes/new-interface.Rmd |only 106 files changed, 1591 insertions(+), 203 deletions(-)
More information about TrialEmulation at CRAN
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Title: Toolkit for Reduced Form and Structural Smooth Transition Vector
Autoregressive Models
Description: Maximum likelihood estimation of smooth transition vector
autoregressive models with various types of transition weight functions,
conditional distributions, and identification methods. Constrained
estimation with various types of constraints is available. Residual based
model diagnostics, forecasting, simulations, and calculation of impulse
response functions, generalized impulse response functions, and generalized
forecast error variance decompositions. See
Heather Anderson, Farshid Vahid (1998) <doi:10.1016/S0304-4076(97)00076-6>,
Helmut Lütkepohl, Aleksei Netšunajev (2017) <doi:10.1016/j.jedc.2017.09.001>,
Markku Lanne, Savi Virolainen (2024) <doi:10.48550/arXiv.2403.14216>,
Savi Virolainen (2024) <doi:10.48550/arXiv.2404.19707>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between sstvars versions 1.0.1 dated 2024-05-29 and 1.1.0 dated 2024-11-29
DESCRIPTION | 10 MD5 | 240 +++---- NAMESPACE | 3 NEWS.md | 33 R/GIRFandGFEVD.R | 20 R/MAINest.R | 639 +++++++++++++----- R/RcppExports.R | 22 R/STVARconstruction.R | 363 +++++++++- R/argumentChecks.R | 73 +- R/data.R | 8 R/diagTests.R | 4 R/diagnosticPlot.R | 129 ++- R/distributionFuns.R |only R/eigens.R | 21 R/generateParams.R | 264 +++++-- R/geneticAlgorithm.R | 227 +++++- R/hypoTests.R | 13 R/jointSpectralRadius.R | 2 R/linearIRF.R | 17 R/loglikelihood.R | 175 +++-- R/miscS3methods.R | 5 R/moreEst.R | 1085 ++++++++++++++++++++++++++++---- R/morePlots.R |only R/numericalDifferentiation.R | 38 - R/parameterReforms.R | 95 +- R/pickParams.R | 76 +- R/printMethods.R | 45 + R/profileLogliks.R | 57 + R/residuals.R | 30 R/simulate.R | 52 + R/standardErrors.R | 13 R/uncondMoments.R | 19 README.md | 70 +- build/vignette.rds |binary inst/doc/sstvars-vignette.Rnw | 293 +++++++- inst/doc/sstvars-vignette.pdf |binary man/GAfit.Rd | 91 ++ man/STVAR.Rd | 62 + man/Wald_test.Rd | 4 man/acidata.Rd | 2 man/alt_stvar.Rd | 15 man/bound_JSR.Rd | 2 man/bounding_const_M.Rd |only man/calc_gradient.Rd | 17 man/change_parametrization.Rd | 34 - man/change_regime.Rd | 42 - man/check_constraints.Rd | 12 man/check_params.Rd | 38 - man/check_weightfun_pars.Rd | 7 man/diagnostic_plot.Rd | 10 man/estim_LS.Rd |only man/estim_NLS.Rd |only man/filter_estimates.Rd |only man/fitSSTVAR.Rd | 80 +- man/fitSTVAR.Rd | 174 ++--- man/fitbsSSTVAR.Rd | 59 + man/form_boldA.Rd | 4 man/generate_skewed_t.Rd |only man/get_alpha_mt.Rd | 4 man/get_boldA_eigens_par.Rd | 34 - man/get_hetsked_sstvar.Rd | 2 man/get_omega_eigens_par.Rd | 34 - man/get_regime_autocovs.Rd | 36 - man/get_regime_means.Rd | 36 - man/get_residuals.Rd | 55 + man/in_paramspace.Rd | 26 man/ind_Student_densities_Cpp.Rd | 4 man/ind_skewed_t_densities_Cpp.Rd |only man/iterate_more.Rd | 37 + man/loglikelihood.Rd | 57 + man/n_params.Rd | 19 man/pick_Am.Rd | 38 - man/pick_Ami.Rd | 38 - man/pick_Omegas.Rd | 44 - man/pick_W.Rd | 15 man/pick_allA.Rd | 38 - man/pick_distpars.Rd | 51 + man/pick_lambdas.Rd | 17 man/pick_phi0.Rd | 40 - man/pick_regime.Rd | 45 - man/pick_weightpars.Rd | 45 - man/plot_struct_shocks.Rd |only man/predict.stvar.Rd | 4 man/print.stvarsum.Rd | 6 man/profile_logliks.Rd | 6 man/random_distpars.Rd | 9 man/random_ind.Rd | 43 - man/random_weightpars.Rd | 12 man/reform_constrained_pars.Rd | 34 - man/reform_data.Rd | 9 man/reorder_B_columns.Rd | 3 man/simulate.stvar.Rd | 4 man/simulate_from_regime.Rd | 4 man/skewed_t_dens.Rd |only man/smart_distpars.Rd | 2 man/smart_ind.Rd | 56 + man/smart_weightpars.Rd | 4 man/sort_impactmats.Rd | 51 - man/sort_regimes.Rd | 22 man/stab_conds_satisfied.Rd | 38 - man/stand_t_dens.Rd |only man/standard_errors.Rd | 49 + man/stvar_to_sstvars110.Rd |only man/swap_B_signs.Rd | 3 man/swap_parametrization.Rd | 3 man/usacpu.Rd | 8 man/warn_eigens.Rd | 5 src/RcppExports.cpp | 19 src/get_Bt_Cpp.cpp | 2 src/ind_Student_densities_Cpp.cpp | 12 src/ind_skewed_t_densities_Cpp.cpp |only tests/testthat/test_GIRFandGFEVD.R | 51 + tests/testthat/test_MAINest.R | 7 tests/testthat/test_STVARconstruction.R | 81 ++ tests/testthat/test_argumentChecks.R | 569 ++++++++++++++++ tests/testthat/test_distributionFuns.R |only tests/testthat/test_eigens.R | 44 + tests/testthat/test_loglikelihood.R | 364 ++++++++++ tests/testthat/test_moreEst.R | 174 ++++- tests/testthat/test_parameterReforms.R | 439 ++++++++++++ tests/testthat/test_pickParams.R | 193 +++++ tests/testthat/test_predict.R | 28 tests/testthat/test_residuals.R | 34 + tests/testthat/test_simulate.R | 33 tests/testthat/test_standardErrors.R | 30 tests/testthat/test_uncondMoments.R | 70 ++ vignettes/refs.bib | 18 vignettes/sstvars-vignette.Rnw | 293 +++++++- 128 files changed, 6627 insertions(+), 1718 deletions(-)
Title: Tidy and Geospatial Kernel Smoothing
Description: Extensions of the kernel smoothing functions from the 'ks' package for compatibility with the tidyverse and geospatial ecosystems <doi:10.1007/s00180-024-01543-9>.
Author: Tarn Duong [aut, cre]
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between eks versions 1.0.5 dated 2024-05-01 and 1.0.6 dated 2024-11-29
CHANGELOG | 3 DESCRIPTION | 11 - MD5 | 10 build/vignette.rds |binary inst/doc/tidysf_kde.html | 487 ++++++++++++++++++++++++++--------------------- man/eks-package.Rd | 2 6 files changed, 293 insertions(+), 220 deletions(-)
Title: Fertility Models
Description: Four fertility models are fitted using non-linear least squares. These are the Hadwiger, the Gamma, the Model1 and Model2, following the terminology of the following paper: Peristera P. and Kostaki A. (2007). "Modeling fertility in modern populations". Demographic Research, 16(6): 141--194. <doi:10.4054/DemRes.2007.16.6>. Model based averaging is also supported.
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between fertilmodel versions 1.1 dated 2023-01-07 and 1.4 dated 2024-11-29
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ R/Gama.R | 18 ++++++++++-------- R/Hadwiger.R | 4 ++-- man/comb.Rd | 4 ++-- man/fertil.plot.Rd | 2 +- man/fertilmodel-package.Rd | 4 ++-- 7 files changed, 28 insertions(+), 25 deletions(-)
Title: Spatiotemporal Resampling Methods for 'mlr3'
Description: Extends the mlr3 machine learning framework with
spatio-temporal resampling methods to account for the presence of
spatiotemporal autocorrelation (STAC) in predictor variables. STAC may
cause highly biased performance estimates in cross-validation if
ignored. A JSS article is available at <doi:10.18637/jss.v111.i07>.
Author: Patrick Schratz [aut, cre] ,
Marc Becker [aut] ,
Jannes Muenchow [ctb] ,
Michel Lang [ctb]
Maintainer: Patrick Schratz <patrick.schratz@gmail.com>
Diff between mlr3spatiotempcv versions 2.3.1 dated 2024-04-17 and 2.3.2 dated 2024-11-29
DESCRIPTION | 17 - MD5 | 167 +++++----- NEWS.md | 5 R/ResamplingRepeatedSpCVBlock.R | 2 R/ResamplingRepeatedSpCVCoords.R | 2 R/ResamplingRepeatedSpCVDisc.R | 2 R/ResamplingRepeatedSpCVEnv.R | 2 R/ResamplingRepeatedSpCVTiles.R | 2 R/ResamplingRepeatedSpCVknndm.R | 2 R/ResamplingRepeatedSptCVCstf.R | 2 R/ResamplingSpCVBlock.R | 2 R/ResamplingSpCVBuffer.R | 2 R/ResamplingSpCVCoords.R | 2 R/ResamplingSpCVDisc.R | 2 R/ResamplingSpCVEnv.R | 2 R/ResamplingSpCVKnndm.R | 2 R/ResamplingSpCVTiles.R | 2 R/ResamplingSptCVCstf.R | 2 R/TaskClassifST.R | 2 R/TaskRegrST.R | 2 R/Task_classif_diplodia.R | 2 R/Task_classif_ecuador.R | 2 R/Task_regr_cookfarm_profiles.R | 2 R/as_task_classif_st.R | 4 R/as_task_regr_st.R | 4 R/autoplot.R | 14 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION |only inst/doc/mlr3spatiotempcv.html | 7 inst/doc/spatiotemp-viz.html | 8 man/TaskClassifST.Rd | 13 man/TaskRegrST.Rd | 13 man/as_task_classif_st.Rd | 4 man/as_task_regr_st.Rd | 4 man/autoplot.ResamplingCV.Rd | 8 man/autoplot.ResamplingCustomCV.Rd | 4 man/autoplot.ResamplingSpCVBlock.Rd | 2 man/mlr3spatiotempcv-package.Rd | 2 man/mlr_resamplings_repeated_spcv_block.Rd | 2 man/mlr_resamplings_repeated_spcv_coords.Rd | 2 man/mlr_resamplings_repeated_spcv_disc.Rd | 2 man/mlr_resamplings_repeated_spcv_env.Rd | 2 man/mlr_resamplings_repeated_spcv_knndm.Rd | 2 man/mlr_resamplings_repeated_spcv_tiles.Rd | 2 man/mlr_resamplings_repeated_sptcv_cstf.Rd | 2 man/mlr_resamplings_spcv_block.Rd | 2 man/mlr_resamplings_spcv_buffer.Rd | 2 man/mlr_resamplings_spcv_coords.Rd | 2 man/mlr_resamplings_spcv_disc.Rd | 2 man/mlr_resamplings_spcv_env.Rd | 2 man/mlr_resamplings_spcv_knndm.Rd | 2 man/mlr_resamplings_spcv_tiles.Rd | 2 man/mlr_resamplings_sptcv_cstf.Rd | 2 man/mlr_tasks_cookfarm_mlr3.Rd | 6 man/mlr_tasks_diplodia.Rd | 6 man/mlr_tasks_ecuador.Rd | 6 tests/testthat/_snaps/1-autoplot/custom-cv-fold-1-2-sample-fold-n.svg | 61 --- tests/testthat/_snaps/1-autoplot/custom-cv-fold-1-2.svg | 61 --- tests/testthat/_snaps/1-autoplot/cv-fold-1-2-groups-col-role.svg | 61 --- tests/testthat/_snaps/1-autoplot/cv-fold-1-2-sample-fold-n.svg | 61 --- tests/testthat/_snaps/1-autoplot/cv-fold-1-2.svg | 61 --- tests/testthat/_snaps/1-autoplot/repcv-fold-1-2-rep-1.svg | 61 --- tests/testthat/_snaps/1-autoplot/repspcvblock-fold-1-2-rep-1.svg | 61 --- tests/testthat/_snaps/1-autoplot/repspcvcoords-fold-1-2-rep-1.svg | 61 --- tests/testthat/_snaps/1-autoplot/repspcvcoords-fold-1-2-sample-fold-n.svg | 61 --- tests/testthat/_snaps/1-autoplot/repspcvenv-fold-1-2-rep-1.svg | 61 --- tests/testthat/_snaps/1-autoplot/spcvblock-fold-1-2-sample-fold-n.svg | 61 --- tests/testthat/_snaps/1-autoplot/spcvblock-fold-1-2.svg | 61 --- tests/testthat/_snaps/1-autoplot/spcvcoords-fold-1-2.svg | 61 --- tests/testthat/_snaps/1-autoplot/spcvenv-fold-1-2-sample-fold-n.svg | 61 --- tests/testthat/_snaps/1-autoplot/spcvenv-fold-1-2.svg | 61 --- tests/testthat/_snaps/2-autoplot/repspcvdisc-fold-1-2-sample-fold-n.svg | 61 --- tests/testthat/_snaps/2-autoplot/repspcvknndm-fold-1-2-sample-fold-n.svg | 61 --- tests/testthat/_snaps/2-autoplot/repspcvtiles-fold-1-2-rep-2.svg | 61 --- tests/testthat/_snaps/2-autoplot/repspcvtiles-fold-1-2-sample-fold-n.svg | 61 --- tests/testthat/_snaps/2-autoplot/repspcvtiles-fold-1-2.svg | 61 --- tests/testthat/_snaps/2-autoplot/spcvdisc-fold-1-2.svg | 61 --- tests/testthat/_snaps/2-autoplot/spcvknndm-fold-1-2.svg | 61 --- tests/testthat/_snaps/2-autoplot/sptcvcstf-2d-space-var-fold-1-2.svg | 61 --- tests/testthat/_snaps/2-autoplot/sptcvcstf-2d-time-var-fold-1-2-sample-fold-n.svg | 61 --- tests/testthat/_snaps/2-autoplot/sptcvcstf-2d-time-var-fold-1-2.svg | 61 --- tests/testthat/_snaps/autoplot_buffer/spcvbuffer-fold-1-2.svg | 61 --- tests/testthat/test-TaskClassifST.R | 2 85 files changed, 449 insertions(+), 1505 deletions(-)
More information about mlr3spatiotempcv at CRAN
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Title: Draw Network with Data
Description: Extends the 'ggplot2' plotting system to support network visualization. Inspired by 'ggtree', 'ggtangle' is designed to work with network associated data.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggtangle versions 0.0.4 dated 2024-10-30 and 0.0.5 dated 2024-11-29
DESCRIPTION | 10 +-- MD5 | 29 +++++----- NAMESPACE | 2 NEWS.md | 16 +++++ R/AllGenerics.r | 4 - R/cnet.r | 132 +++++++++++++++++++++++++++++++++++++++++------- R/ggtangle-package.R |only R/graph.r | 22 ++++---- R/utilities.r | 5 + build/vignette.rds |binary inst/doc/ggtangle.R | 43 +++++++++++++++ inst/doc/ggtangle.Rmd | 52 ++++++++++++++++++ inst/doc/ggtangle.html | 61 +++++++++++++++++++--- man/cnetplot.Rd | 4 - man/geom_cnet_label.Rd |only man/ggtangle-package.Rd |only vignettes/ggtangle.Rmd | 52 ++++++++++++++++++ 17 files changed, 375 insertions(+), 57 deletions(-)
Title: Sequence Symmetry Analysis Using the Observational Medical
Outcomes Partnership Common Data Model
Description: Calculating crude sequence ratio, adjusted sequence ratio and
confidence intervals using data mapped to the Observational Medical
Outcomes Partnership Common Data Model.
Author: Xihang Chen [aut, cre] ,
Tyman Stanford [aut] ,
Berta Raventos [aut] ,
Nicole Pratt [aut] ,
Ed Burn [aut] ,
Marti Catala [aut] ,
Danielle Newby [aut] ,
Nuria Mercade-Besora [aut] ,
Mike Du [aut] ,
Yuchen Guo [aut] ,
Kim Lopez [aut] ,
Marta Alcalde-He [...truncated...]
Maintainer: Xihang Chen <xihang.chen@ndorms.ox.ac.uk>
Diff between CohortSymmetry versions 0.1.4 dated 2024-11-15 and 0.2.0 dated 2024-11-29
CohortSymmetry-0.1.4/CohortSymmetry/R/displayTables.R |only CohortSymmetry-0.1.4/CohortSymmetry/R/inputValidation.R |only CohortSymmetry-0.1.4/CohortSymmetry/man/tableSequenceRatiosOptions.Rd |only CohortSymmetry-0.1.4/CohortSymmetry/tests/testthat/test-displayTable.R |only CohortSymmetry-0.1.4/CohortSymmetry/tests/testthat/test-test-dbs.R |only CohortSymmetry-0.2.0/CohortSymmetry/DESCRIPTION | 17 CohortSymmetry-0.2.0/CohortSymmetry/MD5 | 89 CohortSymmetry-0.2.0/CohortSymmetry/NAMESPACE | 2 CohortSymmetry-0.2.0/CohortSymmetry/R/generateSequenceCohortSet.R | 80 CohortSymmetry-0.2.0/CohortSymmetry/R/getConfidenceInterval.R | 82 CohortSymmetry-0.2.0/CohortSymmetry/R/helpers.R | 15 CohortSymmetry-0.2.0/CohortSymmetry/R/plotSequenceRatios.R | 250 - CohortSymmetry-0.2.0/CohortSymmetry/R/plotTemporalSymmetry.R | 168 CohortSymmetry-0.2.0/CohortSymmetry/R/summariseSequenceRatios.R | 17 CohortSymmetry-0.2.0/CohortSymmetry/R/summariseTemporalSymmetry.R | 247 - CohortSymmetry-0.2.0/CohortSymmetry/R/tableSequenceRatios.R |only CohortSymmetry-0.2.0/CohortSymmetry/R/tableTemporalSymmetry.R |only CohortSymmetry-0.2.0/CohortSymmetry/inst/WORDLIST | 133 CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a01_Introduction.R | 29 CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a01_Introduction.Rmd | 264 - CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a01_Introduction.html | 508 -- CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a02_Generate_a_sequence_cohort.html | 6 CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a03_Summarise_sequence_ratios.R | 16 CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a03_Summarise_sequence_ratios.Rmd | 206 - CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a03_Summarise_sequence_ratios.html | 91 CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a04_Visualise_sequence_ratios.R | 34 CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a04_Visualise_sequence_ratios.Rmd | 316 - CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a04_Visualise_sequence_ratios.html | 1812 ---------- CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a05_Summarise_temporal_symmetry.R | 5 CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a05_Summarise_temporal_symmetry.Rmd | 234 - CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a05_Summarise_temporal_symmetry.html | 42 CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a06_Visualise_temporal_symmetry.R | 20 CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a06_Visualise_temporal_symmetry.Rmd | 225 - CohortSymmetry-0.2.0/CohortSymmetry/inst/doc/a06_Visualise_temporal_symmetry.html | 50 CohortSymmetry-0.2.0/CohortSymmetry/man/plotSequenceRatios.Rd | 15 CohortSymmetry-0.2.0/CohortSymmetry/man/summariseTemporalSymmetry.Rd | 2 CohortSymmetry-0.2.0/CohortSymmetry/man/tableSequenceRatios.Rd | 33 CohortSymmetry-0.2.0/CohortSymmetry/man/tableTemporalSymmetry.Rd |only CohortSymmetry-0.2.0/CohortSymmetry/tests/testthat/test-dbs.R |only CohortSymmetry-0.2.0/CohortSymmetry/tests/testthat/test-generateSequenceCohortSet.R | 10 CohortSymmetry-0.2.0/CohortSymmetry/tests/testthat/test-plotSequenceRatio.R | 16 CohortSymmetry-0.2.0/CohortSymmetry/tests/testthat/test-plotTemporalSymmetry.R | 271 - CohortSymmetry-0.2.0/CohortSymmetry/tests/testthat/test-summariseSequenceRatios.R | 69 CohortSymmetry-0.2.0/CohortSymmetry/tests/testthat/test-summariseTemporalSymmetry.R | 321 - CohortSymmetry-0.2.0/CohortSymmetry/tests/testthat/test-tableSequenceRatios.R |only CohortSymmetry-0.2.0/CohortSymmetry/tests/testthat/test-tableTemporalSymmetry.R |only CohortSymmetry-0.2.0/CohortSymmetry/vignettes/a01_Introduction.Rmd | 264 - CohortSymmetry-0.2.0/CohortSymmetry/vignettes/a03_Summarise_sequence_ratios.Rmd | 206 - CohortSymmetry-0.2.0/CohortSymmetry/vignettes/a04_Visualise_sequence_ratios.Rmd | 316 - CohortSymmetry-0.2.0/CohortSymmetry/vignettes/a05_Summarise_temporal_symmetry.Rmd | 234 - CohortSymmetry-0.2.0/CohortSymmetry/vignettes/a06_Visualise_temporal_symmetry.Rmd | 225 - 51 files changed, 2123 insertions(+), 4817 deletions(-)
More information about CohortSymmetry at CRAN
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Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data
visualization. Results of various statistical analyses (that are commonly used
in social sciences) can be visualized using this package, including simple and
cross tabulated frequencies, histograms, box plots, (generalized) linear models,
mixed effects models, principal component analysis and correlation matrices,
cluster analyses, scatter plots, stacked scales, effects plots of regression
models (including interaction terms) and much more. This package supports
labelled data.
Author: Daniel Luedecke [aut, cre] ,
Alexander Bartel [ctb] ,
Carsten Schwemmer [ctb],
Chuck Powell [ctb] ,
Amir Djalovski [ctb],
Johannes Titz [ctb]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between sjPlot versions 2.8.16 dated 2024-05-13 and 2.8.17 dated 2024-11-29
DESCRIPTION | 14 ++++----- MD5 | 52 ++++++++++++++++++------------------ NEWS.md | 22 ++++++++++----- R/plot_frq.R | 2 - R/plot_grid.R | 20 ++++++------- R/plot_grpfrq.R | 2 - R/plot_type_eff.R | 12 ++++++-- R/plot_type_int.R | 7 ++++ build/vignette.rds |binary inst/doc/blackwhitefigures.html | 12 ++++---- inst/doc/custplot.R | 4 +- inst/doc/custplot.html | 32 +++++++++++----------- inst/doc/plot_interactions.html | 26 +++++++++--------- inst/doc/plot_likert_scales.html | 20 ++++++------- inst/doc/plot_marginal_effects.R | 2 - inst/doc/plot_marginal_effects.html | 26 +++++++++--------- inst/doc/plot_model_estimates.html | 34 +++++++++++------------ inst/doc/sjtitemanalysis.html | 6 ++-- inst/doc/tab_bayes.R | 46 +++++++++++++++---------------- inst/doc/tab_bayes.html | 30 ++++++++++---------- inst/doc/tab_mixed.R | 2 - inst/doc/tab_mixed.html | 12 ++++---- inst/doc/tab_model_estimates.html | 6 ++-- inst/doc/tab_model_robust.R | 2 - inst/doc/tab_model_robust.html | 2 - inst/doc/table_css.html | 6 ++-- man/plot_grid.Rd | 8 ++--- 27 files changed, 212 insertions(+), 195 deletions(-)
Title: Rendering Parameterized SQL and Translation to Dialects
Description: A rendering tool for parameterized SQL that also translates into
different SQL dialects. These dialects include 'Microsoft SQL Server', 'Oracle',
'PostgreSql', 'Amazon RedShift', 'Apache Impala', 'IBM Netezza', 'Google BigQuery', 'Microsoft PDW', 'Snowflake',
'Azure Synapse Analytics Dedicated', 'Apache Spark', 'SQLite', and 'InterSystems IRIS'.
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between SqlRender versions 1.19.0 dated 2024-10-09 and 1.19.1 dated 2024-11-29
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 8 ++++++++ inst/csv/replacementPatterns.csv | 10 +++++++++- inst/doc/UsingSqlRender.pdf |binary tests/testthat/test-translate-iris.R | 7 +++++++ 6 files changed, 33 insertions(+), 10 deletions(-)
More information about greta.censored at CRAN
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Title: Extreme Value Analysis
Description: General functions for performing extreme value analysis. In particular, allows for inclusion of covariates into the parameters of the extreme-value distributions, as well as estimation through MLE, L-moments, generalized (penalized) MLE (GMLE), as well as Bayes. Inference methods include parametric normal approximation, profile-likelihood, Bayes, and bootstrapping. Some bivariate functionality and dependence checking (e.g., auto-tail dependence function plot, extremal index estimation) is also included. For a tutorial, see Gilleland and Katz (2016) <doi: 10.18637/jss.v072.i08> and for bootstrapping, please see Gilleland (2020) <doi: 10.1175/JTECH-D-20-0070.1>.
Author: Eric Gilleland [aut, cre]
Maintainer: Eric Gilleland <eric.gilleland@colostate.edu>
Diff between extRemes versions 2.1-4 dated 2024-02-02 and 2.2 dated 2024-11-29
DESCRIPTION | 18 +++++++++++------- MD5 | 26 +++++++++++++------------- build/partial.rdb |binary inst/CITATION | 2 +- man/Peak.Rd | 2 +- man/Potomac.Rd | 2 +- man/ci.fevd.Rd | 2 +- man/datagrabber.Rd | 2 +- man/decluster.Rd | 2 +- man/distill.fevd.Rd | 2 +- man/fevd.Rd | 4 ++-- man/findpars.Rd | 2 +- man/xbooter.Rd | 2 +- man/xtibber.Rd | 2 +- 14 files changed, 36 insertions(+), 32 deletions(-)
Title: Connect to an OMOP Common Data Model
Description: Provides tools for working with observational health data in the
Observational Medical Outcomes Partnership (OMOP) Common Data Model format with a pipe friendly syntax.
Common data model database table references are stored in a single compound object along with metadata.
Author: Adam Black [aut, cre] ,
Artem Gorbachev [aut],
Edward Burn [aut],
Marti Catala Sabate [aut]
Maintainer: Adam Black <black@ohdsi.org>
Diff between CDMConnector versions 1.6.0 dated 2024-11-13 and 1.6.1 dated 2024-11-29
DESCRIPTION | 6 - MD5 | 12 +- NEWS.md | 4 R/cohort_ddl.R | 2 inst/doc/a01_getting-started.html | 34 ++--- inst/doc/a02_cohorts.html | 188 +++++++++++++++++---------------- inst/doc/a06_using_cdm_attributes.html | 4 7 files changed, 130 insertions(+), 120 deletions(-)
Title: Discontinuous Hamiltonian Monte Carlo with Varying Trajectory
Length
Description: Hamiltonian Monte Carlo for both continuous and discontinuous
posterior distributions with customisable trajectory length
termination criterion. See Nishimura et al. (2020) <doi:10.1093/biomet/asz083> for
the original Discontinuous Hamiltonian Monte Carlo,
Hoffman et al. (2014) <doi:10.48550/arXiv.1111.4246> and Betancourt (2016)
<doi:10.48550/arXiv.1601.00225> for the definition of possible Hamiltonian
Monte Carlo termination criteria.
Author: Paolo Manildo [aut, cre]
Maintainer: Paolo Manildo <paolo.manildo@studenti.unipd.it>
Diff between XDNUTS versions 1.5 dated 2024-10-28 and 1.5.3 dated 2024-11-29
DESCRIPTION | 8 MD5 | 28 R/interface.R | 63 - build/partial.rdb |binary inst/doc/Tutorial_for_main_functions.R | 10 inst/doc/Tutorial_for_main_functions.Rmd | 16 inst/doc/Tutorial_for_main_functions.html | 246 +-- src/dnuts.cpp | 11 src/epsilon_adapt.cpp | 143 ++ src/epsilon_init.cpp | 1852 ++++++++++++++---------------- src/epsilon_init.h | 131 +- src/globals_functions.cpp | 29 src/single_nuts.cpp | 280 ++-- vignettes/REFERENCES.bib | 11 vignettes/Tutorial_for_main_functions.Rmd | 16 15 files changed, 1427 insertions(+), 1417 deletions(-)
Title: Predicted Means for Linear and Semiparametric Models
Description: Providing functions to diagnose and make inferences from various linear models,
such as those obtained from 'aov', 'lm', 'glm', 'gls', 'lme', 'lmer', 'glmmTMB' and 'semireg'.
Inferences include predicted means and standard errors, contrasts, multiple comparisons,
permutation tests, adjusted R-square and graphs.
Author: Dongwen Luo [aut, cre],
Siva Ganesh [ctb],
John Koolaard [ctb]
Maintainer: Dongwen Luo <dongwen.luo@agresearch.co.nz>
Diff between predictmeans versions 1.1.0 dated 2024-02-29 and 1.1.1 dated 2024-11-29
DESCRIPTION | 22 ++- MD5 | 60 ++++----- NAMESPACE | 10 - R/CookD.R | 2 R/Kmatrix.R | 96 +++++++------- R/PMplot.R | 2 R/R2_glmm.R | 41 +++--- R/contrastmeans.R | 6 R/covariatemeans.R | 23 +++ R/misc.R | 214 ++++++++++++++++++++------------- R/mymodelparm.R | 4 R/permanova.lmer.R | 2 R/permlmer.R | 2 R/predictmeans.R | 283 +++++++++++++++++++++++++++----------------- R/residplot.R | 4 R/rsplot.lme.R | 2 R/semipred.R | 28 +++- R/semireg_tmb.R | 24 +-- R/varcomp.R | 41 ++++-- man/CookD.Rd | 4 man/PMplot.Rd | 7 - man/covariatemeans.Rd | 15 +- man/permanova.lmer.Rd | 10 - man/permmodels.Rd | 42 +++--- man/predictmeans-package.Rd | 5 man/predictmeans.Rd | 35 ++--- man/residplot.Rd | 4 man/semipred.Rd | 56 ++++---- man/semireg.Rd | 24 +-- man/semireg_tmb.Rd | 40 +++--- man/varcomp.Rd | 2 31 files changed, 659 insertions(+), 451 deletions(-)