Title: Parallel Nonparametric Kernel Smoothing Methods for Mixed Data
Types Using 'MPI'
Description: Nonparametric (and semiparametric) kernel methods that seamlessly
handle a mix of continuous, unordered, and ordered factor data types. This
package is a parallel implementation of the 'np' package based on the 'MPI'
specification that incorporates the 'Rmpi' package (Hao Yu
<hyu@stats.uwo.ca>) with minor modifications and we are extremely grateful
to Hao Yu for his contributions to the 'R' community. We would like to
gratefully acknowledge support from the Natural Sciences and Engineering
Research Council of Canada (NSERC, <https://www.nserc-crsng.gc.ca/>), the
Social Sciences and Humanities Research Council of Canada (SSHRC,
<https://www.sshrc-crsh.gc.ca/>), and the Shared Hierarchical Academic
Research Computing Network (SHARCNET, <https://sharcnet.ca/>). We would
also like to acknowledge the contributions of the 'GNU GSL' authors. In
particular, we adapt the 'GNU GSL' B-spline routine 'gsl_bspline.c' adding
automated support for quantile knots (in addition t [...truncated...]
Author: Jeffrey S. Racine [aut, cre],
Tristen Hayfield [aut],
Hao Yu [ctb, cph],
The GSL Team [cph],
Numerical Recipes Software [cph]
Maintainer: Jeffrey S. Racine <racinej@mcmaster.ca>
Diff between npRmpi versions 0.70-4 dated 2026-06-26 and 0.70-5 dated 2026-07-14
CHANGELOG | 185 + DESCRIPTION | 10 MD5 | 502 ++-- NAMESPACE | 1 NEWS.md | 182 + R/Rcoll.R | 54 R/condensity.R | 46 R/condistribution.R | 46 R/density.R | 10 R/distribution.R | 10 R/lsqregression.R | 82 R/np.autodispatch.R | 83 R/np.cdhat.helpers.R | 36 R/np.condensity.R | 138 - R/np.condensity.bw.R | 144 - R/np.condensity.proper.R | 105 R/np.condistribution.R | 140 - R/np.condistribution.bw.R | 84 R/np.conmode.R | 158 + R/np.copula.R | 200 - R/np.density.R | 48 R/np.density.bw.R | 66 R/np.distribution.R | 36 R/np.distribution.bw.R | 197 - R/np.kernel.R | 17 R/np.lp.degree.search.R | 91 R/np.lsqregression.R | 243 + R/np.plot.engine.conbandwidth.R | 16 R/np.plot.engine.condbandwidth.R | 19 R/np.plot.engine.plbandwidth.R | 13 R/np.plot.engine.rbandwidth.R | 45 R/np.plot.engine.scbandwidth.R | 21 R/np.plot.engine.sibandwidth.R | 31 R/np.plot.helpers.R | 898 +++++-- R/np.plot.methods.R | 152 + R/np.plregression.R | 167 - R/np.plregression.bw.R | 36 R/np.qregression.R | 131 - R/np.reghat.R | 506 ++-- R/np.regression.R | 167 + R/np.regression.bw.R | 60 R/np.semihat.R | 42 R/np.sigtest.R | 2 R/np.singleindex.R | 725 ++++- R/np.singleindex.bw.R | 1244 +++++----- R/np.smoothcoef.R | 24 R/np.smoothcoef.bw.R | 267 +- R/plregression.R | 35 R/protocol_tags.R |only R/regression.R | 46 R/session.R | 7 R/singleindex.R | 4 R/smoothbandwidth.R | 16 R/util.R | 313 ++ README.md | 114 build/partial.rdb |binary build/vignette.rds |binary data/cps71.rda |binary demo/tools/cleanup | 54 demo/tools/makefile | 118 demo/tools/monitor_demo_cpu.sh | 98 demo/tools/parse_demo_results.R | 382 --- demo/tools/runall | 174 - demo/tools/summarize_cpu_monitor.R | 70 demo/tools/timing | 16 demo/tools/validate_demo_matrix.R |only inst/MPI_SETUP.md | 93 inst/RUN_DEMO.md | 45 inst/cleanup |only inst/demo_matrices/npsdeptest-sentinel.csv | 2 inst/demo_matrices/npunitest-sentinel.csv | 2 inst/demo_tools |only inst/runall |only inst/timing |only man/gradients.Rd | 33 man/np.condensity.Rd | 18 man/np.condensity.bw.Rd | 19 man/np.condistribution.Rd | 24 man/np.condistribution.bw.Rd | 48 man/np.conmode.Rd | 19 man/np.copula.Rd | 33 man/np.density.Rd | 13 man/np.density.bw.Rd | 20 man/np.distribution.Rd | 19 man/np.distribution.bw.Rd | 49 man/np.kernels.Rd | 27 man/np.options.Rd | 26 man/np.plot.Rd | 6 man/np.plregression.Rd | 13 man/np.qregression.Rd | 23 man/np.regression.Rd | 18 man/np.regression.bw.Rd | 15 man/np.sigtest.Rd | 8 man/np.singleindex.Rd | 52 man/np.singleindex.bw.Rd | 94 man/np.smoothcoef.Rd | 8 man/np.smoothcoef.bw.Rd | 48 man/npRmpi.session.Rd | 8 man/nplsqreg.Rd | 43 man/nplsqregbw.Rd | 10 src/headers.h | 3 src/jksum.c | 782 +++++- src/kernelcv.c | 49 src/kernele.c | 72 src/mat_vec.c | 54 src/np.c | 784 ++++-- src/nr.c | 18 tests/testthat/fixtures |only tests/testthat/helper-progress-shadow.R | 5 tests/testthat/test-attach-close-protocol-contract.R | 21 tests/testthat/test-attach-gennn-exdat-contract.R | 3 tests/testthat/test-autodispatch-call-helpers.R | 36 tests/testthat/test-autodispatch-materialize.R | 2 tests/testthat/test-autodispatch-option-sync-contract.R | 1 tests/testthat/test-bandwidth-summary-labels.R | 8 tests/testthat/test-bounded-distribution-truncated-cdf-contract.R |only tests/testthat/test-bounded-kernel-centered-normalization-contract.R |only tests/testthat/test-bounded-kernel-cvls-contract.R | 13 tests/testthat/test-bw-dispatch-contract.R | 1 tests/testthat/test-bw-dispatch-extended-contract.R | 3 tests/testthat/test-bw-eval-helper-contract.R | 9 tests/testthat/test-bw-summary-contract.R | 122 tests/testthat/test-check-core-smoke-nomad-public-api-contract.R |only tests/testthat/test-conditional-scale-metadata-contract.R | 10 tests/testthat/test-cv-path-lock-contract.R | 18 tests/testthat/test-demo-profile-makefile-contract.R | 8 tests/testthat/test-demo-results-wide-contract.R |only tests/testthat/test-formula-data-reentry-contract.R |only tests/testthat/test-formula-dispatch-npindex-contract.R |only tests/testthat/test-glp-validator-contract.R | 52 tests/testthat/test-kernelweights-direct.R | 6 tests/testthat/test-largeh-option-contract.R | 57 tests/testthat/test-ll-lp-degree1-parity.R | 14 tests/testthat/test-local-linear-raw-basis-error-guidance.R | 2 tests/testthat/test-mixed-data-gradient-first-difference-contract.R |only tests/testthat/test-mpi-examples.R | 99 tests/testthat/test-native-nomad-callback-source-contract.R |only tests/testthat/test-native-nomad-option-cleanup-contract.R | 66 tests/testthat/test-nomad-degree-search-family-progress-contract.R | 17 tests/testthat/test-nomad-shortcut-subprocess-contract.R | 1 tests/testthat/test-npc-conditional-higher-order-gradients.R | 24 tests/testthat/test-npcdens-audit-repair-contract.R |only tests/testthat/test-npcdens-cvls-generalized-nn-phase1-contract.R | 6 tests/testthat/test-npcdens-cvls-public-contract.R | 122 tests/testthat/test-npcdens-cvml-generalized-nn-phase1-contract.R | 6 tests/testthat/test-npcdens-native-derivative-workspace-contract.R |only tests/testthat/test-npcdens-proper-contract.R | 8 tests/testthat/test-npcdens-proper-fitted-subprocess-contract.R | 8 tests/testthat/test-npcdensbw-cvls-quadrature-controls-contract.R | 8 tests/testthat/test-npcdensbw-degree-search-nomad-progress-contract.R | 6 tests/testthat/test-npcdensbw-degree-search-nomad-routing-contract.R | 37 tests/testthat/test-npcdenshat.R | 6 tests/testthat/test-npcdist-audit-repair-contract.R |only tests/testthat/test-npcdist-cvls-fixed-phase1-contract.R | 6 tests/testthat/test-npcdist-cvls-generalized-nn-phase1-contract.R | 158 - tests/testthat/test-npcdist-cvls-public-contract.R | 4 tests/testthat/test-npcdist-proper-fitted-subprocess-contract.R | 8 tests/testthat/test-npcdistbw-degree-search-contract.R | 49 tests/testthat/test-npcdistbw-degree-search-nomad-accounting-contract.R | 3 tests/testthat/test-npconmode-audit-contracts.R |only tests/testthat/test-npcopula-audit-contracts.R |only tests/testthat/test-npcopula.R | 12 tests/testthat/test-npdeptest.R | 8 tests/testthat/test-npindex-ichimura-lc-gradient-contract.R | 92 tests/testthat/test-npindex-nomad-search-alignment-contract.R | 1 tests/testthat/test-npindex-public-nomad-smoke-contract.R |only tests/testthat/test-npindex-service-hygiene-contract.R |only tests/testthat/test-npindex.R | 146 + tests/testthat/test-npindexbw-degree-search-contract.R | 19 tests/testthat/test-npindexbw-nomad-payload-contract.R | 7 tests/testthat/test-nplsqreg-audit-contracts.R |only tests/testthat/test-nplsqreg-option-contract.R | 5 tests/testthat/test-npplreg-audit-contracts.R |only tests/testthat/test-npplreg-lp-degree-metadata.R | 5 tests/testthat/test-npplregbw-degree-search-contract.R | 77 tests/testthat/test-npqreg-audit-contracts.R |only tests/testthat/test-npqreg.R | 7 tests/testthat/test-npreg-adaptive-lc-exdat-contract.R | 68 tests/testthat/test-npreg-arg-contract.R | 2 tests/testthat/test-npreg-audit-contracts.R |only tests/testthat/test-npreg-cvls-glp-fixed-contract.R | 49 tests/testthat/test-npreg-fastpath-composition-contract.R | 4 tests/testthat/test-npreg-glp-higher-order.R | 271 +- tests/testthat/test-npreg-nomad-fit-bws-metadata-contract.R | 3 tests/testthat/test-npreg-nomad-shadow-fast-contract.R | 9 tests/testthat/test-npreg-tree-predicate-contract.R |only tests/testthat/test-npreg.R | 9 tests/testthat/test-npregbw-degree-search-helper-contract.R | 6 tests/testthat/test-npregbw-degree-search-nomad-progress-contract.R | 3 tests/testthat/test-npregbw-degree-search-nomad-routing-contract.R | 40 tests/testthat/test-npreghat-generalized-lp-owner-contract.R | 170 + tests/testthat/test-npreghat-gennn-degree1-contract.R | 92 tests/testthat/test-npreghat-lc-derivative-owner-contract.R | 40 tests/testthat/test-npreghat-public-error-symmetry-contract.R |only tests/testthat/test-npreghat.R | 402 --- tests/testthat/test-npregiv-state-contract.R | 6 tests/testthat/test-npscoef-backfit-iterate-contract.R |only tests/testthat/test-npscoef-categorical-profile-contract.R | 4 tests/testthat/test-npscoef-service-hygiene-contract.R |only tests/testthat/test-npscoef.R | 57 tests/testthat/test-npsigtest-attach-local-regression-contract.R | 3 tests/testthat/test-npsigtest.R | 4 tests/testthat/test-npudens-audit-repair-contract.R |only tests/testthat/test-npudens-fast-summary-contract.R | 28 tests/testthat/test-npudist-audit-repair-contract.R |only tests/testthat/test-npudist-categorical-profile-bw-contract.R | 3 tests/testthat/test-npudist-fast-summary-contract.R | 41 tests/testthat/test-plot-bootstrap-inid-fastpath-regression-contract.R | 79 tests/testthat/test-plot-bootstrap-interval-summary.R | 4 tests/testthat/test-plot-bootstrap-locality-contract.R | 6 tests/testthat/test-plot-bootstrap-npplreg-frozen-contract.R | 2 tests/testthat/test-plot-coef-option-contract.R | 4 tests/testthat/test-plot-conditional-adaptive-exact-fanout-contract.R | 4 tests/testthat/test-plot-conditional-gradient-fanout-contract.R | 10 tests/testthat/test-plot-conditional-localpoly-fanout-contract.R | 2 tests/testthat/test-plot-gradient-axis-label-contract.R |only tests/testthat/test-plot-mpi-only-bootstrap-contract.R | 18 tests/testthat/test-plot-nn-active-support-exact.R | 12 tests/testthat/test-plot-nn-exact-mpi-binding-contract.R | 2 tests/testthat/test-plot-plbandwidth-bias-center-contract.R | 11 tests/testthat/test-plot-proper-projection-fanout-contract.R | 4 tests/testthat/test-plot-rbandwidth-categorical-gradient-bootstrap.R | 95 tests/testthat/test-plot-scbandwidth-bias-center-contract.R | 11 tests/testthat/test-plot-sibandwidth-fixed-gradient-bootstrap.R | 5 tests/testthat/test-plot-singleindex-wild-bounded-contract.R |only tests/testthat/test-plot-warning-interface-contract.R | 21 tests/testthat/test-post-release-gradient-contracts.R |only tests/testthat/test-powell-fixed-continuous-floor-contract.R | 4 tests/testthat/test-powell-nn-cache-option-contract.R | 5 tests/testthat/test-profile-direct-autodispatch-contract.R | 7 tests/testthat/test-profile-manual-broadcast-conditional-autodispatch-contract.R | 3 tests/testthat/test-profile-timing-contract.R | 11 tests/testthat/test-progress-bandwidth-common-contract.R | 6 tests/testthat/test-progress-bandwidth-selection-contract.R | 10 tests/testthat/test-progress-condensdist-fit-contract.R | 9 tests/testthat/test-progress-core.R | 3 tests/testthat/test-progress-npcmstest-contract.R | 5 tests/testthat/test-progress-npdeneqtest-contract.R | 5 tests/testthat/test-progress-npdeptest-contract.R | 5 tests/testthat/test-progress-npindex-fit-contract.R | 64 tests/testthat/test-progress-npindexbw-contract.R | 44 tests/testthat/test-progress-npplreg-fit-contract.R | 34 tests/testthat/test-progress-npplregbw-contract.R | 25 tests/testthat/test-progress-npqcmstest-contract.R | 22 tests/testthat/test-progress-npreg-fit-contract.R | 8 tests/testthat/test-progress-npregiv-contract.R | 5 tests/testthat/test-progress-npscoefbw-contract.R | 6 tests/testthat/test-progress-npsdeptest-contract.R | 5 tests/testthat/test-progress-npsigtest-contract.R | 5 tests/testthat/test-progress-npsymtest-contract.R | 6 tests/testthat/test-progress-npunitest-contract.R | 5 tests/testthat/test-progress-plot-helpers-contract.R | 34 tests/testthat/test-progress-plot-target-label-contract.R | 16 tests/testthat/test-progress-static-contract.R | 17 tests/testthat/test-protocol-tags-contract.R |only tests/testthat/test-regression-bwmethod-constants-contract.R |only tests/testthat/test-regression-categorical-profile-compression-contract.R | 5 tests/testthat/test-regression-formula-contract.R | 4 tests/testthat/test-regression-nn-min-k-contract.R | 4 tests/testthat/test-resident-degree-objective-cache-contract.R |only tests/testthat/test-rmpi-small-guard-contracts.R | 21 tests/testthat/test-rmpi-wrapper-contracts.R | 9 tests/testthat/test-semihat.R | 103 tests/testthat/test-session-routing-subprocess-contract.R | 64 tests/testthat/test-spmd-step-contract.R | 16 tests/testthat/test-statmods-sort-contract.R | 2 tests/testthat/test-timing-summary-contract.R | 1 tests/testthat/test-transform-bounds-start-contract.R |only 268 files changed, 10231 insertions(+), 4908 deletions(-)
Title: Nonparametric Kernel Smoothing Methods for Mixed Data Types
Description: Nonparametric (and semiparametric) kernel methods that seamlessly handle a mix of continuous, unordered, and ordered factor data types. We would like to gratefully acknowledge support from the Natural Sciences and Engineering Research Council of Canada (NSERC, <https://www.nserc-crsng.gc.ca/>), the Social Sciences and Humanities Research Council of Canada (SSHRC, <https://www.sshrc-crsh.gc.ca/>), and the Shared Hierarchical Academic Research Computing Network (SHARCNET, <https://sharcnet.ca/>). We would also like to acknowledge the contributions of the GNU GSL authors. In particular, we adapt the GNU GSL B-spline routine gsl_bspline.c adding automated support for quantile knots (in addition to uniform knots), providing missing functionality for derivatives, and for extending the splines beyond their endpoints.
Author: Jeffrey S. Racine [aut, cre],
Tristen Hayfield [aut]
Maintainer: Jeffrey S. Racine <racinej@mcmaster.ca>
Diff between np versions 0.70-4 dated 2026-06-26 and 0.70-5 dated 2026-07-14
CHANGELOG | 152 ++ DESCRIPTION | 8 MD5 | 358 ++-- NAMESPACE | 1 NEWS.md | 148 + R/condensity.R | 46 R/condistribution.R | 46 R/density.R | 10 R/distribution.R | 10 R/lsqregression.R | 82 - R/np.cdhat.helpers.R | 36 R/np.condensity.R | 95 - R/np.condensity.bw.R | 142 + R/np.condensity.proper.R | 105 + R/np.condistribution.R | 95 - R/np.condistribution.bw.R | 87 - R/np.conmode.R | 156 +- R/np.copula.R | 190 +- R/np.density.R | 34 R/np.density.bw.R | 46 R/np.distribution.R | 22 R/np.distribution.bw.R | 178 +- R/np.kernel.R | 17 R/np.lp.degree.search.R | 91 + R/np.lsqregression.R | 237 ++- R/np.plot.engine.conbandwidth.R | 16 R/np.plot.engine.condbandwidth.R | 19 R/np.plot.engine.plbandwidth.R | 13 R/np.plot.engine.rbandwidth.R | 47 R/np.plot.engine.scbandwidth.R | 21 R/np.plot.engine.sibandwidth.R | 31 R/np.plot.helpers.R | 670 +++++++- R/np.plot.methods.R | 152 +- R/np.plregression.R | 167 +- R/np.plregression.bw.R | 32 R/np.qregression.R | 141 + R/np.reghat.R | 364 ++-- R/np.regression.R | 120 + R/np.regression.bw.R | 74 R/np.semihat.R | 43 R/np.sigtest.R | 2 R/np.singleindex.R | 225 ++ R/np.singleindex.bw.R | 566 +++---- R/np.smoothcoef.R | 24 R/np.smoothcoef.bw.R | 171 +- R/plregression.R | 35 R/regression.R | 46 R/singleindex.R | 4 R/smoothbandwidth.R | 16 R/util.R | 313 +++- build/partial.rdb |binary build/vignette.rds |binary data/cps71.rda |binary inst/doc/np_entropy_tests.html | 2 inst/doc/np_getting_started.html | 8 man/gradients.Rd | 33 man/np.condensity.Rd | 33 man/np.condensity.bw.Rd | 19 man/np.condistribution.Rd | 24 man/np.condistribution.bw.Rd | 48 man/np.conmode.Rd | 19 man/np.copula.Rd | 33 man/np.density.Rd | 13 man/np.density.bw.Rd | 20 man/np.distribution.Rd | 19 man/np.distribution.bw.Rd | 49 man/np.kernels.Rd | 27 man/np.options.Rd | 21 man/np.plot.Rd | 6 man/np.plregression.Rd | 13 man/np.qregression.Rd | 23 man/np.regression.Rd | 18 man/np.regression.bw.Rd | 15 man/np.sigtest.Rd | 8 man/np.singleindex.Rd | 52 man/np.singleindex.bw.Rd | 94 - man/np.smoothcoef.Rd | 8 man/np.smoothcoef.bw.Rd | 51 man/nplsqreg.Rd | 43 man/nplsqregbw.Rd | 10 src/headers.h | 4 src/jksum.c | 757 ++++++++-- src/kernelb.c | 5 src/kernelcv.c | 48 src/mat_vec.c | 54 src/np.c | 751 ++++++--- src/nr.c | 18 tests/testthat/helper-plot-runtime-prototype.R |only tests/testthat/test-bandwidth-summary-labels.R | 8 tests/testthat/test-bounded-distribution-truncated-cdf-contract.R |only tests/testthat/test-bounded-kernel-centered-normalization-contract.R |only tests/testthat/test-bw-dispatch-extended-contract.R | 3 tests/testthat/test-bw-summary-contract.R | 122 + tests/testthat/test-check-core-smoke-nomad-public-api-contract.R |only tests/testthat/test-cv-path-lock-contract.R | 18 tests/testthat/test-formula-data-reentry-contract.R |only tests/testthat/test-formula-dispatch-npindex-contract.R | 101 + tests/testthat/test-glp-validator-contract.R | 52 tests/testthat/test-largeh-option-contract.R | 50 tests/testthat/test-local-linear-raw-basis-error-guidance.R | 2 tests/testthat/test-mixed-data-gradient-first-difference-contract.R |only tests/testthat/test-native-nomad-callback-source-contract.R |only tests/testthat/test-nomad-degree-search-family-progress-contract.R | 18 tests/testthat/test-nomad-timing-contract.R | 24 tests/testthat/test-npc-conditional-higher-order-gradients.R | 24 tests/testthat/test-npc-cv-shadow-proof-contract.R | 6 tests/testthat/test-npcd-nomad-shortcut-contract.R | 2 tests/testthat/test-npcdens-audit-repair-contract.R |only tests/testthat/test-npcdens-cvls-fixed-phase1-contract.R | 4 tests/testthat/test-npcdens-cvls-generalized-nn-phase1-contract.R | 6 tests/testthat/test-npcdens-cvls-public-contract.R | 53 tests/testthat/test-npcdens-cvml-generalized-nn-phase1-contract.R | 6 tests/testthat/test-npcdens-native-derivative-workspace-contract.R |only tests/testthat/test-npcdens-proper-contract.R | 9 tests/testthat/test-npcdensbw-degree-search-nomad-progress-contract.R | 6 tests/testthat/test-npcdist-audit-repair-contract.R |only tests/testthat/test-npcdist-cvls-fixed-phase1-contract.R | 6 tests/testthat/test-npcdist-cvls-generalized-nn-phase1-contract.R | 8 tests/testthat/test-npcdist-cvls-public-contract.R | 4 tests/testthat/test-npcdistbw-degree-search-nomad-accounting-contract.R | 3 tests/testthat/test-npconmode-audit-contracts.R |only tests/testthat/test-npcopula-audit-contracts.R |only tests/testthat/test-npcopula.R | 12 tests/testthat/test-npdeptest.R | 6 tests/testthat/test-npindex-ichimura-lc-gradient-contract.R | 89 + tests/testthat/test-npindex-progress-inner-suppression-contract.R |only tests/testthat/test-npindex-public-nomad-smoke-contract.R |only tests/testthat/test-npindex-r-nn-cache-contract.R | 2 tests/testthat/test-npindex.R | 84 + tests/testthat/test-npindexbw-degree-search-contract.R | 2 tests/testthat/test-npindexbw-nomad-payload-contract.R | 7 tests/testthat/test-npindexbw-start-control-contract.R | 7 tests/testthat/test-nplsqreg-audit-contracts.R |only tests/testthat/test-npplreg-audit-contracts.R |only tests/testthat/test-npqreg-audit-contracts.R |only tests/testthat/test-npqreg.R | 7 tests/testthat/test-npreg-arg-contract.R | 2 tests/testthat/test-npreg-audit-contracts.R |only tests/testthat/test-npreg-cvls-glp-fixed-contract.R | 2 tests/testthat/test-npreg-glp-higher-order.R | 168 ++ tests/testthat/test-npreg-tree-predicate-contract.R |only tests/testthat/test-npreg.R | 9 tests/testthat/test-npregbw-degree-search-helper-contract.R | 6 tests/testthat/test-npregbw-degree-search-nomad-progress-contract.R | 3 tests/testthat/test-npreghat-generalized-lp-owner-contract.R | 193 ++ tests/testthat/test-npreghat-lc-derivative-owner-contract.R | 69 tests/testthat/test-npreghat.R | 19 tests/testthat/test-npregiv-state-contract.R | 6 tests/testthat/test-npscoef-backfit-iterate-contract.R |only tests/testthat/test-npscoef-r-nn-cache-contract.R | 3 tests/testthat/test-npscoef.R | 54 tests/testthat/test-npscoefbw-start-control-contract.R | 11 tests/testthat/test-npudens-audit-repair-contract.R |only tests/testthat/test-npudens-fast-summary-contract.R | 27 tests/testthat/test-npudist-audit-repair-contract.R |only tests/testthat/test-npudist-fast-summary-contract.R | 41 tests/testthat/test-plot-contract.R | 6 tests/testthat/test-plot-densdist-fixed-reuse.R | 24 tests/testthat/test-plot-gradient-axis-label-contract.R |only tests/testthat/test-plot-plbandwidth-bias-center-contract.R | 11 tests/testthat/test-plot-rbandwidth-categorical-gradient-bootstrap.R | 184 ++ tests/testthat/test-plot-runtime-prototype-npcdens-slice-contract.R | 46 tests/testthat/test-plot-runtime-prototype-npindex-slice-contract.R | 18 tests/testthat/test-plot-runtime-prototype-npplreg-slice-contract.R | 18 tests/testthat/test-plot-runtime-prototype-npqreg-slice-contract.R | 46 tests/testthat/test-plot-runtime-prototype-npreg-slice-contract.R | 22 tests/testthat/test-plot-runtime-prototype-npscoef-slice-contract.R | 18 tests/testthat/test-plot-runtime-prototype-npudens-slice-contract.R | 26 tests/testthat/test-plot-scbandwidth-bias-center-contract.R | 11 tests/testthat/test-plot-sibandwidth-helper-contract.R | 2 tests/testthat/test-plot-singleindex-wild-bounded-contract.R |only tests/testthat/test-plot-unconditional-engine-certification-contract.R | 54 tests/testthat/test-plot-warning-interface-contract.R | 21 tests/testthat/test-post-release-gradient-contracts.R |only tests/testthat/test-progress-condensdist-fit-contract.R | 4 tests/testthat/test-progress-core.R | 10 tests/testthat/test-progress-npcdens-plot-contract.R | 4 tests/testthat/test-progress-npindex-fit-contract.R | 28 tests/testthat/test-progress-npindex-plot-contract.R | 2 tests/testthat/test-progress-npplreg-fit-contract.R | 86 - tests/testthat/test-progress-npplreg-plot-contract.R | 3 tests/testthat/test-progress-npplregbw-contract.R | 14 tests/testthat/test-progress-npreg-fit-contract.R | 2 tests/testthat/test-progress-npreg-plot-contract.R | 4 tests/testthat/test-progress-npscoef-plot-contract.R | 2 tests/testthat/test-progress-plot-helpers-contract.R | 34 tests/testthat/test-progress-static-contract.R | 12 tests/testthat/test-regression-bwmethod-constants-contract.R |only tests/testthat/test-regression-categorical-profile-compression-contract.R | 6 tests/testthat/test-resident-degree-objective-cache-contract.R |only tests/testthat/test-semihat.R | 91 + tests/testthat/test-semiparam-formula-response-name-contract.R | 31 tests/testthat/test-statmods-sort-contract.R | 2 tests/testthat/test-transform-bounds-start-contract.R |only 194 files changed, 7796 insertions(+), 2460 deletions(-)
Title: Regularized Non-Negative Matrix Factorization
Description: A proof of concept implementation of regularized non-negative matrix factorization optimization.
A non-negative matrix factorization factors non-negative matrix Y approximately as L R, for non-negative
matrices L and R of reduced rank. This package supports such factorizations with weighted objective and
regularization penalties. Allowable regularization penalties include L1 and L2 penalties on L and R,
as well as non-orthogonality penalties. This package provides multiplicative update algorithms, which are
a modification of the algorithm of Lee and Seung (2001)
<http://papers.nips.cc/paper/1861-algorithms-for-non-negative-matrix-factorization.pdf>, as well
as an additive update derived from that multiplicative update. See also Pav (2024) <doi:10.48550/arXiv.2410.22698>.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Diff between rnnmf versions 0.3.0 dated 2024-11-04 and 0.3.1 dated 2026-07-14
ChangeLog | 4 ++++ DESCRIPTION | 15 ++++++++------- MD5 | 31 ++++++++++++++++--------------- R/rnnmf-package.r | 7 ++++++- README.md | 8 +++++++- build/partial.rdb |only build/vignette.rds |binary inst/doc/rnnmf.Rnw | 2 +- inst/doc/rnnmf.pdf |binary man/NEWS.Rd | 7 +++++++ man/aurnmf.Rd | 5 +++-- man/gaurnmf.Rd | 5 +++-- man/giqpm.Rd | 5 +++-- man/murnmf.Rd | 5 +++-- man/rnnmf.Rd | 4 ++-- vignettes/rnnmf.Rnw | 2 +- vignettes/rnnmf.bib | 4 ++-- 17 files changed, 66 insertions(+), 38 deletions(-)
Title: Procrustes Application to Cophylogenetic Analysis
Description: Procrustes analyses to infer co-phylogenetic
matching between pairs of phylogenetic trees.
Author: Juan Antonio Balbuena [aut, cre],
Timothee Poisot [aut],
Matthew Hutchinson [aut],
Fernando Cagua [aut]
Maintainer: Juan Antonio Balbuena <j.a.balbuena@uv.es>
This is a re-admission after prior archival of version 0.4.2 dated 2020-08-25
Diff between paco versions 0.4.2 dated 2020-08-25 and 0.5.0 dated 2026-07-14
DESCRIPTION | 51 ++++++++++++++++++++++++++++++++++++++------------ MD5 | 10 ++++++--- NEWS.md |only R/residuals_paco.r | 2 - man/residuals_paco.Rd | 2 - tests |only 6 files changed, 48 insertions(+), 17 deletions(-)
Title: Fishes of British Columbia
Description: Provides raw and curated data on the codes, classification
and conservation status of freshwater fishes in British Columbia.
Marine fishes will be added in a future release.
Author: Evan Amies-Galonski [aut] ,
Joe Thorley [aut] ,
Nadine Hussein [aut] ,
Sarah Lyons [cre] ,
Bronwen Lewis [ctb],
Jesse Patterson [ctb],
Gordon Oliphant [ctb],
Seb Dalgarno [ctb] ,
Simon Norris [ctb],
Allan Irvine [ctb],
Poisson Consulting [cph, fnd],
[...truncated...]
Maintainer: Sarah Lyons <sarah@poissonconsulting.ca>
Diff between fishbc versions 0.2.1 dated 2021-05-12 and 0.2.2 dated 2026-07-14
DESCRIPTION | 90 +++++++------------ MD5 | 44 +++++---- NEWS.md | 12 ++ R/ab.R | 2 R/cdc.R | 2 R/common-name.R | 4 R/sysdata.rda |binary README.md | 39 ++++---- data/ab.rda |binary data/cdc.rda |binary data/freshwaterfish.rda |binary inst/WORDLIST | 2 man/ab.Rd | 4 man/cdc.Rd | 4 man/fishbc-package.Rd | 11 +- man/freshwaterfish.Rd | 2 tests/spelling.R |only tests/testthat/_snaps |only tests/testthat/test-ab.R | 19 +++- tests/testthat/test-cdc.R | 10 +- tests/testthat/test-common-name.R | 6 - tests/testthat/test-freshwaterfish.R | 135 ++++++++++++++++++++--------- tests/testthat/test-whse_fish_species_cd.R | 41 +++++--- 23 files changed, 257 insertions(+), 170 deletions(-)
Title: S4 Tools for Reading and Organizing Genetic Data
Description: Provides an integrated suite of tools for handling single
nucleotide polymorphism (SNP) genotype data in large-scale genetic
studies. Supports importing and merging genotype files, performing
quality control on SNP markers and samples, and preparing data for
downstream analyses using popular software such as 'FImpute' and
'PLINK'. Offers S4 classes and methods to efficiently encapsulate SNP
data, along with utilities for generating genotype summary statistics
and visualization. Additional functionalities include anticlustering
approaches for batch effect control, automated script generation for
external software, and streamlined workflows for large datasets
commonly encountered in animal and plant breeding programs. Designed
to facilitate reproducible and scalable SNP data analyses in
quantitative and statistical genetics.
Author: Vinicius Junqueira [aut, cre],
Roberto Higa [aut],
Fernando Flores Cardoso [aut],
Marcos Jun Iti Yokoo [aut]
Maintainer: Vinicius Junqueira <junqueiravinicius@hotmail.com>
Diff between SNPkit versions 0.1.0 dated 2026-06-26 and 0.1.2 dated 2026-07-14
SNPkit-0.1.0/SNPkit/man/cbind_SnpMatrix.Rd |only SNPkit-0.1.0/SNPkit/man/figures |only SNPkit-0.1.0/SNPkit/man/rbindSnpFlexible.Rd |only SNPkit-0.1.0/SNPkit/man/rbind_SnpMatrix.Rd |only SNPkit-0.1.2/SNPkit/DESCRIPTION | 9 SNPkit-0.1.2/SNPkit/MD5 | 61 +- SNPkit-0.1.2/SNPkit/NAMESPACE | 4 SNPkit-0.1.2/SNPkit/NEWS.md |only SNPkit-0.1.2/SNPkit/R/admixture.R | 70 ++- SNPkit-0.1.2/SNPkit/R/classes.R | 6 SNPkit-0.1.2/SNPkit/R/combine.R | 40 - SNPkit-0.1.2/SNPkit/R/getGeno.R | 142 ++++-- SNPkit-0.1.2/SNPkit/R/mat2SnpMatrix.R | 12 SNPkit-0.1.2/SNPkit/R/qcSNPs.R | 67 --- SNPkit-0.1.2/SNPkit/R/save_plink.R | 9 SNPkit-0.1.2/SNPkit/R/utils_anticlustering.R | 263 ++++++++---- SNPkit-0.1.2/SNPkit/R/utils_fQC.R | 208 +++++---- SNPkit-0.1.2/SNPkit/R/utils_geno.R | 3 SNPkit-0.1.2/SNPkit/README.md | 47 +- SNPkit-0.1.2/SNPkit/inst/doc/Introduction.Rmd | 8 SNPkit-0.1.2/SNPkit/inst/doc/Introduction.html | 17 SNPkit-0.1.2/SNPkit/man/check.identical.samples.by.block.Rd | 13 SNPkit-0.1.2/SNPkit/man/check.snp.no.position.Rd | 9 SNPkit-0.1.2/SNPkit/man/check.snp.same.position.Rd | 11 SNPkit-0.1.2/SNPkit/man/doPCA.Rd | 12 SNPkit-0.1.2/SNPkit/man/getGeno.Rd | 19 SNPkit-0.1.2/SNPkit/man/qcSNPs.Rd | 8 SNPkit-0.1.2/SNPkit/man/runAnticlusteringPCA.Rd | 38 + SNPkit-0.1.2/SNPkit/man/runPCA.Rd |only SNPkit-0.1.2/SNPkit/man/savePlink.Rd | 8 SNPkit-0.1.2/SNPkit/tests |only SNPkit-0.1.2/SNPkit/vignettes/Introduction.Rmd | 8 32 files changed, 671 insertions(+), 421 deletions(-)
Title: Custom Formatted Console Messages with Timing Support
Description: A lightweight message system relying purely on base R. Comes with built-in and pre styled message types and provides an easy way to create custom messages. Supports individually styled and colored text as well as timing information. Designed to make console output more informative and visually organized.
Author: Tim Siebenmorgen [aut, cre, cph]
Maintainer: Tim Siebenmorgen <qol_package@proton.me>
Diff between printify versions 1.0.2 dated 2026-06-17 and 1.0.3 dated 2026-07-14
DESCRIPTION | 6 - MD5 | 8 +- NEWS.md | 119 +++++++++++++++++++----------------- R/messages.R | 195 ++++++++++++++++++++++++++++++++++++++++------------------- README.md | 2 5 files changed, 206 insertions(+), 124 deletions(-)
Title: Automatic Differentiation of Multivariate Operations
Description: An object that supports automatic differentiation
of matrix- and multidimensional-valued functions with
respect to multidimensional independent variables.
Automatic differentiation is via 'forward accumulation'.
Author: Steven E. Pav [aut, cre]
Maintainer: Steven E. Pav <shabbychef@gmail.com>
Diff between madness versions 0.2.8 dated 2023-08-21 and 0.2.9 dated 2026-07-14
ChangeLog | 4 +++ DESCRIPTION | 13 +++++----- MD5 | 45 +++++++++++++++++++------------------- R/data.r | 6 ++--- R/eigen.r | 4 +-- R/madness_pkg.r | 5 ++++ R/reshape.r | 3 +- README.md | 6 ----- build/partial.rdb |only build/vignette.rds |binary inst/doc/introducing_madness.Rnw | 11 +-------- inst/doc/introducing_madness.pdf |binary man/NEWS.Rd | 7 +++++ man/colsums.Rd | 2 - man/det.Rd | 4 --- man/eigen.Rd | 4 +-- man/extract-methods.Rd | 28 ++--------------------- man/madness-pkg.Rd | 1 man/max.Rd | 4 +-- man/norm.Rd | 5 ++-- man/reshapes.Rd | 3 +- man/stock_returns.Rd | 6 ++--- vignettes/common.bib | 34 +++++++++++++++++++--------- vignettes/introducing_madness.Rnw | 11 +-------- 24 files changed, 97 insertions(+), 109 deletions(-)
Title: Continuous Time Stochastic Modelling using Template Model
Builder
Description: Perform state and parameter inference, and forecasting, in
stochastic state-space systems using the 'ctsmTMB' R6 class. This
class provides a user-friendly interface for working with stochastic
state space models. Inference is based on maximum likelihood
estimation, with derivatives efficiently computed through automatic
differentiation enabled by the 'TMB'/'RTMB' packages (Kristensen et
al., 2016) <doi:10.18637/jss.v070.i05>. The available inference
methods include Kalman filters, in addition to a Laplace
approximation-based smoothing method. For further details of these
methods refer to the documentation of the 'CTSMR' package
<https://ctsm.info/ctsmr-reference.pdf> and Thygesen (2025)
<doi:10.48550/arXiv.2503.21358>. Forecasting capabilities include
moment predictions and stochastic path simulations implemented in
'C++' using 'Rcpp' (Eddelbuettel et al., 2018)
<doi:10.1080/00031305.2017.1375990> for computational efficiency.
Author: Phillip Vetter [aut, cre, cph],
Jan Moeller [ctb],
Uffe Thygesen [ctb],
Peder Bacher [ctb],
Henrik Madsen [ctb]
Maintainer: Phillip Vetter <pbrve@dtu.dk>
Diff between ctsmTMB versions 1.0.1 dated 2025-08-27 and 1.1.1 dated 2026-07-14
ctsmTMB-1.0.1/ctsmTMB/R/algo_returns.R |only ctsmTMB-1.0.1/ctsmTMB/R/algo_utilities_kalman_funs.R |only ctsmTMB-1.0.1/ctsmTMB/R/algo_utilities_misc_funs.R |only ctsmTMB-1.0.1/ctsmTMB/R/algo_utilities_strings.R |only ctsmTMB-1.0.1/ctsmTMB/src/ekf_filter.cpp |only ctsmTMB-1.0.1/ctsmTMB/src/ekf_predict.cpp |only ctsmTMB-1.0.1/ctsmTMB/src/ekf_simulate.cpp |only ctsmTMB-1.0.1/ctsmTMB/src/helper_funs2.h |only ctsmTMB-1.0.1/ctsmTMB/tests/testthat/test-first.R |only ctsmTMB-1.1.1/ctsmTMB/DESCRIPTION | 35 ctsmTMB-1.1.1/ctsmTMB/MD5 | 173 ctsmTMB-1.1.1/ctsmTMB/NAMESPACE | 21 ctsmTMB-1.1.1/ctsmTMB/NEWS.md | 29 ctsmTMB-1.1.1/ctsmTMB/R/RcppExports.R | 60 ctsmTMB-1.1.1/ctsmTMB/R/S3methods.R | 574 +- ctsmTMB-1.1.1/ctsmTMB/R/algo_estimate_RTMB.R | 789 ++- ctsmTMB-1.1.1/ctsmTMB/R/algo_estimate_TMB.R | 99 ctsmTMB-1.1.1/ctsmTMB/R/algo_filter.R | 133 ctsmTMB-1.1.1/ctsmTMB/R/algo_predict.R | 349 - ctsmTMB-1.1.1/ctsmTMB/R/algo_simulate.R | 207 ctsmTMB-1.1.1/ctsmTMB/R/algo_utils_kalman_funs.R |only ctsmTMB-1.1.1/ctsmTMB/R/algo_utils_misc_funs.R |only ctsmTMB-1.1.1/ctsmTMB/R/algo_utils_return_computations.R |only ctsmTMB-1.1.1/ctsmTMB/R/algo_utils_strings.R |only ctsmTMB-1.1.1/ctsmTMB/R/ctsmTMB.R | 2141 ++++------ ctsmTMB-1.1.1/ctsmTMB/R/method_estimate.R | 266 - ctsmTMB-1.1.1/ctsmTMB/R/method_filter.R | 357 - ctsmTMB-1.1.1/ctsmTMB/R/method_predict.R | 262 - ctsmTMB-1.1.1/ctsmTMB/R/method_simulate.R | 230 - ctsmTMB-1.1.1/ctsmTMB/R/method_smooth.R | 38 ctsmTMB-1.1.1/ctsmTMB/R/model_builders.R | 85 ctsmTMB-1.1.1/ctsmTMB/R/model_checkers.R | 246 - ctsmTMB-1.1.1/ctsmTMB/R/model_cpp_compilers.R | 161 ctsmTMB-1.1.1/ctsmTMB/R/model_cpp_writers.R | 246 - ctsmTMB-1.1.1/ctsmTMB/R/model_data_setters.R | 390 - ctsmTMB-1.1.1/ctsmTMB/R/model_drules_and_extrafuns.R | 45 ctsmTMB-1.1.1/ctsmTMB/R/model_flags.R | 68 ctsmTMB-1.1.1/ctsmTMB/R/model_rebuilders.R | 64 ctsmTMB-1.1.1/ctsmTMB/R/model_transformations.R | 203 ctsmTMB-1.1.1/ctsmTMB/R/model_utils.R | 86 ctsmTMB-1.1.1/ctsmTMB/R/utils.R |only ctsmTMB-1.1.1/ctsmTMB/R/zzz_data.R | 85 ctsmTMB-1.1.1/ctsmTMB/R/zzz_ggfortify_ggcpgram.R |only ctsmTMB-1.1.1/ctsmTMB/R/zzz_globalvariables.R | 29 ctsmTMB-1.1.1/ctsmTMB/R/zzz_imports.R | 5 ctsmTMB-1.1.1/ctsmTMB/R/zzz_predefined_models.R |only ctsmTMB-1.1.1/ctsmTMB/README.md | 448 +- ctsmTMB-1.1.1/ctsmTMB/build/vignette.rds |binary ctsmTMB-1.1.1/ctsmTMB/data/EstimateReferenceData.rda |only ctsmTMB-1.1.1/ctsmTMB/data/Ornstein.rda |binary ctsmTMB-1.1.1/ctsmTMB/data/Ornstein2D.rda |only ctsmTMB-1.1.1/ctsmTMB/data/OutputReferenceData.rda |only ctsmTMB-1.1.1/ctsmTMB/inst/doc/ctsmTMB.R | 58 ctsmTMB-1.1.1/ctsmTMB/inst/doc/ctsmTMB.Rmd | 116 ctsmTMB-1.1.1/ctsmTMB/inst/doc/ctsmTMB.html | 174 ctsmTMB-1.1.1/ctsmTMB/inst/doc/estimate.R | 17 ctsmTMB-1.1.1/ctsmTMB/inst/doc/estimate.Rmd | 290 + ctsmTMB-1.1.1/ctsmTMB/inst/doc/estimate.html | 448 +- ctsmTMB-1.1.1/ctsmTMB/inst/doc/observation_equations.R | 12 ctsmTMB-1.1.1/ctsmTMB/inst/doc/observation_equations.html | 8 ctsmTMB-1.1.1/ctsmTMB/inst/doc/predict.R | 224 - ctsmTMB-1.1.1/ctsmTMB/inst/doc/predict.Rmd | 544 +- ctsmTMB-1.1.1/ctsmTMB/inst/doc/predict.html | 807 ++- ctsmTMB-1.1.1/ctsmTMB/inst/doc/simulate.R | 205 ctsmTMB-1.1.1/ctsmTMB/inst/doc/simulate.Rmd | 554 +- ctsmTMB-1.1.1/ctsmTMB/inst/doc/simulate.html | 716 ++- ctsmTMB-1.1.1/ctsmTMB/inst/doc/using_another_optimizer.R | 26 ctsmTMB-1.1.1/ctsmTMB/inst/doc/using_another_optimizer.html | 109 ctsmTMB-1.1.1/ctsmTMB/inst/include/template_user_functions.h |only ctsmTMB-1.1.1/ctsmTMB/man/EstimateReferenceData.Rd |only ctsmTMB-1.1.1/ctsmTMB/man/Ornstein.Rd | 5 ctsmTMB-1.1.1/ctsmTMB/man/Ornstein2D.Rd |only ctsmTMB-1.1.1/ctsmTMB/man/OutputReferenceData.Rd |only ctsmTMB-1.1.1/ctsmTMB/man/create.Ornstein1D.model.Rd |only ctsmTMB-1.1.1/ctsmTMB/man/create.Ornstein2D.model.Rd |only ctsmTMB-1.1.1/ctsmTMB/man/ctsmTMB.Rd | 1253 ++--- ctsmTMB-1.1.1/ctsmTMB/man/newModel.Rd |only ctsmTMB-1.1.1/ctsmTMB/man/plot.ctsmTMB.fit.Rd | 50 ctsmTMB-1.1.1/ctsmTMB/man/plot.ctsmTMB.pred.Rd | 43 ctsmTMB-1.1.1/ctsmTMB/man/plot.ctsmTMB.profile.Rd | 32 ctsmTMB-1.1.1/ctsmTMB/man/print.ctsmTMB.Rd | 20 ctsmTMB-1.1.1/ctsmTMB/man/print.ctsmTMB.fit.Rd | 23 ctsmTMB-1.1.1/ctsmTMB/man/profile.ctsmTMB.fit.Rd | 30 ctsmTMB-1.1.1/ctsmTMB/man/summary.ctsmTMB.fit.Rd | 23 ctsmTMB-1.1.1/ctsmTMB/src/RcppExports.cpp | 334 + ctsmTMB-1.1.1/ctsmTMB/src/ekf_methods.cpp |only ctsmTMB-1.1.1/ctsmTMB/src/extra_utils.h |only ctsmTMB-1.1.1/ctsmTMB/src/filter_functions.cpp |only ctsmTMB-1.1.1/ctsmTMB/src/function_typedefs.h |only ctsmTMB-1.1.1/ctsmTMB/src/helpers_ukf.h |only ctsmTMB-1.1.1/ctsmTMB/src/lkf_methods.cpp |only ctsmTMB-1.1.1/ctsmTMB/src/misc_helpers.h |only ctsmTMB-1.1.1/ctsmTMB/src/ode_solvers.h |only ctsmTMB-1.1.1/ctsmTMB/src/pointer_helpers.cpp |only ctsmTMB-1.1.1/ctsmTMB/src/predict_functions.cpp |only ctsmTMB-1.1.1/ctsmTMB/src/sde_solvers.h |only ctsmTMB-1.1.1/ctsmTMB/src/simulate_functions.cpp |only ctsmTMB-1.1.1/ctsmTMB/src/ukf_methods.cpp |only ctsmTMB-1.1.1/ctsmTMB/src/ziggurat_seeder.h |only ctsmTMB-1.1.1/ctsmTMB/tests/testthat/test-estimate.R |only ctsmTMB-1.1.1/ctsmTMB/tests/testthat/test-filter.R |only ctsmTMB-1.1.1/ctsmTMB/tests/testthat/test-likelihood.R |only ctsmTMB-1.1.1/ctsmTMB/tests/testthat/test-parameters.R |only ctsmTMB-1.1.1/ctsmTMB/tests/testthat/test-predict.R |only ctsmTMB-1.1.1/ctsmTMB/tests/testthat/test-simulate.R |only ctsmTMB-1.1.1/ctsmTMB/tests/testthat/test-smooth.R |only ctsmTMB-1.1.1/ctsmTMB/tests/testthat/test_estimate_against_reference.R |only ctsmTMB-1.1.1/ctsmTMB/tests/testthat/test_filter_predict_simulate_against_reference.R |only ctsmTMB-1.1.1/ctsmTMB/vignettes/ctsmTMB.Rmd | 116 ctsmTMB-1.1.1/ctsmTMB/vignettes/estimate.Rmd | 290 + ctsmTMB-1.1.1/ctsmTMB/vignettes/predict.Rmd | 544 +- ctsmTMB-1.1.1/ctsmTMB/vignettes/simulate.Rmd | 554 +- 112 files changed, 9036 insertions(+), 6513 deletions(-)
Title: Missing Morphometric Data Simulation and Estimation
Description: Functions for simulating missing morphometric
data randomly, with taxonomic bias and with anatomical bias. LOST also
includes functions for estimating linear and geometric morphometric data.
Author: J. Arbour [aut, cre],
C. Brown [aut]
Maintainer: J. Arbour <jessica.arbour@mtsu.edu>
Diff between LOST versions 2.1.3 dated 2026-03-13 and 2.1.4 dated 2026-07-14
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/MissingGeoMorph.R | 47 ++++++++++++++++++++++++++--------------------- man/MissingGeoMorph.Rd | 7 +++++-- 4 files changed, 38 insertions(+), 30 deletions(-)
Title: Drawing Chinese National and Historical Flags with 'ggplot2'
Description: Provides programmatic implementations for drawing
Chinese national and historical flags using analytic geometry and
'ggplot2'-based vector graphics. Flag designs are constructed
entirely from geometric primitives such as polygons and rectangles,
without relying on external image files. The package is intended
for educational demonstration, reproducible visualization, and
procedural graphics in R.
Author: Zhaoshuo Liu [aut, cre]
Maintainer: Zhaoshuo Liu <liuzhaoshuo1997@outlook.com>
Diff between ggChinaFlag versions 0.2.0 dated 2026-07-04 and 0.3.0 dated 2026-07-14
DESCRIPTION | 7 - MD5 | 14 +- NAMESPACE | 2 NEWS.md |only R/flag_interface.R | 252 +++++++++++++++++++++++---------------------- R/plot_region_flag.R |only man/FlagStorage.Rd | 16 +- man/plotCNFlag.Rd | 9 + man/plot_HK_SAR_flag.Rd |only man/plot_Macao_SAR_flag.Rd |only 10 files changed, 159 insertions(+), 141 deletions(-)
Title: Sex- and Age-Standardized Metrics from the Centers for Disease
Control and Prevention (CDC) Growth Charts
Description: Calculation of sex- and age-standardized growth metrics
based on the 2000 CDC growth charts. Provides functions to generate
z-scores and percentiles for weight, height, and body mass index (BMI)
using the LMS method (lambda-mu-sigma). Includes extended BMI z-scores
for values above the 95th percentile to more accurately characterize
the sex- and age-standardized BMI of children with very high BMIs.
Author: David Freedman [aut, cre]
Maintainer: David Freedman <DavidSFreedman@gmail.com>
Diff between cdcanthro versions 0.2.0 dated 2026-05-22 and 0.2.1 dated 2026-07-14
cdcanthro-0.2.0/cdcanthro/NEWS.md |only cdcanthro-0.2.0/cdcanthro/data/cdc__ref__data.rda |only cdcanthro-0.2.0/cdcanthro/man/cdc__ref__data.Rd |only cdcanthro-0.2.1/cdcanthro/DESCRIPTION | 17 cdcanthro-0.2.1/cdcanthro/MD5 | 13 cdcanthro-0.2.1/cdcanthro/R/cdcanthro.R | 512 ++++++++++++---------- cdcanthro-0.2.1/cdcanthro/R/sysdata.rda |only cdcanthro-0.2.1/cdcanthro/R/zzz.R |only cdcanthro-0.2.1/cdcanthro/data/cdc_ref_data.rda |only cdcanthro-0.2.1/cdcanthro/man/cdc_ref_data.Rd |only cdcanthro-0.2.1/cdcanthro/man/cdcanthro.Rd | 17 11 files changed, 309 insertions(+), 250 deletions(-)
Title: Psychometric Analysis with Rasch Measurement Theory
Description: Streamlines reproducible Rasch measurement theory analyses
for ordinal item-response data, combining estimation routines from
'eRm', 'psychotools', 'mirt', 'iarm', and 'lavaan' with consistent
diagnostic, plotting, and reporting layers. Covers the four basic
psychometric criteria summarised by Christensen et al. (2021)
<doi:10.1111/sms.13908> -- unidimensionality, local independence,
ordered response category thresholds, and invariance across
subgroups -- together with item fit, targeting, reliability,
category functioning, and descriptive item-response plots. A
distinguishing feature is the use of simulation-based critical
values to replace rule-of-thumb cutoffs for conditional infit mean-square,
Yen's Q3 local-dependence statistic, the largest residual-PCA eigenvalue,
ordinal CFA fit indices, and partial-gamma DIF and local-dependence
coefficients, optionally augmented with multiplicity-corrected bootstrap
p-values. Outputs are knitr::kable() tables and
'ggplot2' figures suitab [...truncated...]
Author: Magnus Johansson [aut, cre] ,
Nicklas Korsell [ctb] ,
Mirka Henninger [ctb] ,
Jan Radek [ctb]
Maintainer: Magnus Johansson <pgmj@pm.me>
Diff between easyRasch2 versions 1.0.0 dated 2026-07-05 and 1.1.0 dated 2026-07-14
easyRasch2-1.0.0/easyRasch2/vignettes/figures/rasch-cicc-plot-1.png |only easyRasch2-1.1.0/easyRasch2/DESCRIPTION | 8 easyRasch2-1.1.0/easyRasch2/MD5 | 115 ++--- easyRasch2-1.1.0/easyRasch2/NEWS.md | 115 +++++ easyRasch2-1.1.0/easyRasch2/R/bootstrap_restscore.R | 25 + easyRasch2-1.1.0/easyRasch2/R/cfa_cutoff.R | 31 - easyRasch2-1.1.0/easyRasch2/R/cicc_plot.R | 193 ++++++++-- easyRasch2-1.1.0/easyRasch2/R/conditional_infit.R | 31 + easyRasch2-1.1.0/easyRasch2/R/conditional_infit_mi.R | 17 easyRasch2-1.1.0/easyRasch2/R/dif_lr.R | 28 - easyRasch2-1.1.0/easyRasch2/R/dif_partgam.R | 22 - easyRasch2-1.1.0/easyRasch2/R/dif_tree.R | 35 + easyRasch2-1.1.0/easyRasch2/R/infitcutoff_plot.R | 4 easyRasch2-1.1.0/easyRasch2/R/item_parameters.R | 4 easyRasch2-1.1.0/easyRasch2/R/item_restscore.R | 27 + easyRasch2-1.1.0/easyRasch2/R/ld_partgam.R | 37 + easyRasch2-1.1.0/easyRasch2/R/local_dependence.R | 43 +- easyRasch2-1.1.0/easyRasch2/R/locdep_q3_plot.R | 5 easyRasch2-1.1.0/easyRasch2/R/martin_lof.R | 71 ++- easyRasch2-1.1.0/easyRasch2/R/person_fit.R | 29 - easyRasch2-1.1.0/easyRasch2/R/person_parameters.R | 4 easyRasch2-1.1.0/easyRasch2/R/reliability.R | 28 + easyRasch2-1.1.0/easyRasch2/R/residual_pca.R | 11 easyRasch2-1.1.0/easyRasch2/R/targeting_plot.R | 14 easyRasch2-1.1.0/easyRasch2/R/tile_plot.R | 56 ++ easyRasch2-1.1.0/easyRasch2/R/utils-validation.R | 19 easyRasch2-1.1.0/easyRasch2/README.md | 2 easyRasch2-1.1.0/easyRasch2/build/partial.rdb |binary easyRasch2-1.1.0/easyRasch2/build/vignette.rds |binary easyRasch2-1.1.0/easyRasch2/inst/doc/easyRasch2.Rmd | 60 +-- easyRasch2-1.1.0/easyRasch2/inst/doc/easyRasch2.html | 92 ++-- easyRasch2-1.1.0/easyRasch2/man/RMdifTree.Rd | 12 easyRasch2-1.1.0/easyRasch2/man/RMdimMartinLof.Rd | 15 easyRasch2-1.1.0/easyRasch2/man/RMitemICCPlot.Rd | 108 ++++- easyRasch2-1.1.0/easyRasch2/man/RMlocdepGamma.Rd | 5 easyRasch2-1.1.0/easyRasch2/man/RMlocdepQ3Cutoff.Rd | 9 easyRasch2-1.1.0/easyRasch2/man/RMpersonFit.Rd | 15 easyRasch2-1.1.0/easyRasch2/man/RMplotTile.Rd | 11 easyRasch2-1.1.0/easyRasch2/man/RMtargeting.Rd | 2 easyRasch2-1.1.0/easyRasch2/man/easyRasch2-package.Rd | 5 easyRasch2-1.1.0/easyRasch2/tests/testthat/test-bootstrap_restscore.R | 16 easyRasch2-1.1.0/easyRasch2/tests/testthat/test-cicc_plot.R | 42 ++ easyRasch2-1.1.0/easyRasch2/tests/testthat/test-conditional_infit.R | 24 + easyRasch2-1.1.0/easyRasch2/tests/testthat/test-dif_lr.R | 12 easyRasch2-1.1.0/easyRasch2/tests/testthat/test-dif_tree.R | 17 easyRasch2-1.1.0/easyRasch2/tests/testthat/test-infit_cutoff_plot.R | 17 easyRasch2-1.1.0/easyRasch2/tests/testthat/test-item_person_parameters.R | 21 + easyRasch2-1.1.0/easyRasch2/tests/testthat/test-item_restscore.R | 18 easyRasch2-1.1.0/easyRasch2/tests/testthat/test-local_dependence.R | 41 ++ easyRasch2-1.1.0/easyRasch2/tests/testthat/test-martin_lof.R | 81 ++++ easyRasch2-1.1.0/easyRasch2/tests/testthat/test-partgam_ld.R | 3 easyRasch2-1.1.0/easyRasch2/tests/testthat/test-person_fit.R | 21 + easyRasch2-1.1.0/easyRasch2/tests/testthat/test-reliability.R | 28 + easyRasch2-1.1.0/easyRasch2/tests/testthat/test-tile_plot.R | 20 + easyRasch2-1.1.0/easyRasch2/vignettes/easyRasch2.Rmd | 60 +-- easyRasch2-1.1.0/easyRasch2/vignettes/easyRasch2.Rmd.orig | 5 easyRasch2-1.1.0/easyRasch2/vignettes/figures/rasch-dif-cicc-1.png |binary easyRasch2-1.1.0/easyRasch2/vignettes/figures/rasch-pca-plot-1.png |binary easyRasch2-1.1.0/easyRasch2/vignettes/figures/rasch-tile-plot-1.png |binary 59 files changed, 1347 insertions(+), 387 deletions(-)
Title: Graphic Presentation of Complex Genomic and Network Data
Analysis
Description: Implements various simple function utilities and flexible pipelines to generate circular images for visualizing complex genomic and network data analysis features.
Author: Minghui Wang [aut, cre],
Bin Zhang [aut]
Maintainer: Minghui Wang <m.h.wang@live.com>
Diff between NetWeaver versions 0.0.6 dated 2019-02-26 and 1.0.0 dated 2026-07-14
NetWeaver-0.0.6/NetWeaver/R/rc.plot.sunburst.R |only NetWeaver-1.0.0/NetWeaver/DESCRIPTION | 20 NetWeaver-1.0.0/NetWeaver/MD5 | 35 - NetWeaver-1.0.0/NetWeaver/R/rc.get.coordinates.R | 19 NetWeaver-1.0.0/NetWeaver/R/rc.get.params.R | 6 NetWeaver-1.0.0/NetWeaver/R/rc.initialize.R | 18 NetWeaver-1.0.0/NetWeaver/R/rc.plot.grColLegend.R | 2 NetWeaver-1.0.0/NetWeaver/R/rc.plot.heatmap.R | 3 NetWeaver-1.0.0/NetWeaver/R/rc.plot.ideogram.R | 2 NetWeaver-1.0.0/NetWeaver/R/rc.plot.link.R | 18 NetWeaver-1.0.0/NetWeaver/build/vignette.rds |binary NetWeaver-1.0.0/NetWeaver/inst/doc/netweaver.R | 146 ++--- NetWeaver-1.0.0/NetWeaver/inst/doc/netweaver.Rmd | 396 +++++++------- NetWeaver-1.0.0/NetWeaver/inst/doc/netweaver.html | 540 +++++++++++++++----- NetWeaver-1.0.0/NetWeaver/man/rc.get.coordinates.Rd | 4 NetWeaver-1.0.0/NetWeaver/man/rc.initialize.Rd | 7 NetWeaver-1.0.0/NetWeaver/man/rc.plot.heatmap.Rd | 2 NetWeaver-1.0.0/NetWeaver/man/rc.plot.ideogram.Rd | 2 NetWeaver-1.0.0/NetWeaver/vignettes/netweaver.Rmd | 396 +++++++------- 19 files changed, 978 insertions(+), 638 deletions(-)
Title: Import, Inspect, Analyse, and Report Gazepoint GP3 Exports
Description: Tools for importing, inspecting, cleaning, summarising,
modelling, and reporting Gazepoint GP3 and Gazepoint Analysis CSV
exports. The package supports offline workflows for all-gaze,
fixation, pupil, area-of-interest, transition, time-course, quality-audit, and
manuscript-reporting analyses.
The package methodology is described in the peer-reviewed
software paper <doi:10.3390/jemr19040076>.
Author: Stefanos Balaskas [aut, cre]
Maintainer: Stefanos Balaskas <s.balaskas@ac.upatras.gr>
Diff between gp3tools versions 1.0.2 dated 2026-06-30 and 2.0.1 dated 2026-07-14
DESCRIPTION | 43 MD5 | 248 + NAMESPACE | 101 NEWS.md | 27 R/aoi_entropy.R |only R/aoi_sequence_helpers.R |only R/aoi_sequence_metrics.R |only R/as_gazepoint_master.R | 10 R/audit_gazepoint_master.R | 9 R/baseline_correct_gazepoint_pupil.R | 3 R/bayesian_planning_helpers.R |only R/binocular_trackloss_simulation_extensions.R |only R/cluster_permutation_extensions.R |only R/diagnose_gazepoint_glmm.R | 29 R/estimate_gazepoint_divergence_point.R | 30 R/experimental_bayesian_bridges.R |only R/export_gazepoint_master_audit.R | 52 R/face_export_import.R |only R/face_quality_audit.R |only R/face_reporting.R |only R/face_sync.R |only R/face_window_summaries.R |only R/final_statistical_extensions.R |only R/fixation_reliability.R |only R/flag_gazepoint_pupil.R | 3 R/flag_gazepoint_pupil_artifacts.R | 3 R/heatmap_spatial_visualisation.R |only R/interpolate_gazepoint_pupil.R | 3 R/markov_semimarkov_summaries.R |only R/missingness_coverage_extensions.R |only R/model_reporting_extensions.R |only R/multimodal_modelling.R |only R/package-globals.R |only R/phase_segmentation_extensions.R |only R/plot_aoi_timeline.R |only R/qc_reporting_bundle.R |only R/saccade_scanpath.R |only R/scanpath_qc_plot_extensions.R |only R/scanpath_similarity.R |only R/screen_coordinate_qc_extensions.R |only R/sequence_anomalies.R |only R/sequence_complexity.R |only R/sequence_distance.R |only R/simulation_bids_brms.R |only R/smooth_gazepoint_pupil.R | 17 R/statistical_extension_helpers.R |only R/stimulus_layout_qc_extensions.R |only R/summarise_gazepoint_pupil.R | 5 R/summarise_gazepoint_pupil_windows.R | 17 R/summarise_gazepoint_workflow.R | 6 R/timecourse_bootstrap.R |only R/validate_gazepoint_master.R | 5 README.md | 66 build/vignette.rds |binary inst/CITATION | 21 inst/doc/aoi_workflow.R | 8 inst/doc/aoi_workflow.Rmd | 19 inst/doc/aoi_workflow.html | 1372 ++++------ inst/doc/pupil_workflow.R | 8 inst/doc/pupil_workflow.Rmd | 19 inst/doc/pupil_workflow.html | 1259 ++++----- man/as_gazepoint_master.Rd | 158 - man/audit_gazepoint_aoi_screen_coverage.Rd |only man/audit_gazepoint_face_quality.Rd |only man/audit_gazepoint_face_sync.Rd |only man/audit_gazepoint_fixation_reliability.Rd |only man/audit_gazepoint_master.Rd | 103 man/audit_gazepoint_screen_bounds.Rd |only man/audit_gazepoint_timecourse_grid.Rd |only man/baseline_correct_gazepoint_pupil.Rd | 159 - man/bootstrap_gazepoint_timecourse.Rd |only man/check_gazepoint_bayesian_readiness.Rd |only man/classify_gazepoint_events_hmm.Rd |only man/clean_gazepoint_by_trackloss.Rd |only man/collect_gazepoint_qc_summaries.Rd |only man/combine_gazepoint_eyes.Rd |only man/compute_gazepoint_aoi_entropy.Rd |only man/compute_gazepoint_aoi_sequence_metrics.Rd |only man/compute_gazepoint_saccade_metrics.Rd |only man/compute_gazepoint_scanpath_geometry.Rd |only man/compute_gazepoint_scanpath_similarity.Rd |only man/compute_gazepoint_sequence_complexity.Rd |only man/compute_gazepoint_sequence_distance.Rd |only man/compute_gazepoint_sequence_recurrence.Rd |only man/compute_gazepoint_transition_network_metrics.Rd |only man/create_gazepoint_bayesian_sap.Rd |only man/create_gazepoint_brms_template.Rd |only man/create_gazepoint_face_reporting_checklist.Rd |only man/create_gazepoint_hddm_fit_script.Rd |only man/detect_gazepoint_fixations_ivt.Rd |only man/diagnose_gazepoint_cluster_design.Rd |only man/estimate_gazepoint_cluster_offset.Rd |only man/estimate_gazepoint_cluster_onset.Rd |only man/export_gazepoint_cluster_results.Rd |only man/export_gazepoint_heatmap_png.Rd |only man/export_gazepoint_master_audit.Rd | 159 - man/export_gazepoint_mne_cluster_input.Rd |only man/export_gazepoint_permuco_cluster_input.Rd |only man/export_gazepoint_permutes_cluster_input.Rd |only man/export_gazepoint_to_bids.Rd |only man/figures |only man/filter_gazepoint_cnn_uncertainty.Rd |only man/fit_gazepoint_aoi_brms.Rd |only man/fit_gazepoint_brms_model.Rd |only man/fit_gazepoint_face_window_lmm.Rd |only man/fit_gazepoint_multimodal_response_model.Rd |only man/flag_gazepoint_pupil.Rd | 133 man/flag_gazepoint_pupil_artifacts.Rd | 247 - man/flag_gazepoint_sequence_anomalies.Rd |only man/harmonize_gazepoint_screen_coordinates.Rd |only man/impute_gazepoint_pupil_gp.Rd |only man/interpolate_gazepoint_pupil.Rd | 139 - man/launch_gazepoint_qc_dashboard.Rd |only man/plot_gazepoint_aoi_timeline.Rd |only man/plot_gazepoint_cluster_null_distribution.Rd |only man/plot_gazepoint_cluster_permutation.Rd |only man/plot_gazepoint_face_quality.Rd |only man/plot_gazepoint_heatmap.Rd |only man/plot_gazepoint_heatmap_overlay.Rd |only man/plot_gazepoint_missingness_profile.Rd |only man/plot_gazepoint_model_residuals.Rd |only man/plot_gazepoint_phase_timeline.Rd |only man/plot_gazepoint_qc_overview.Rd |only man/plot_gazepoint_scanpath.Rd |only man/plot_gazepoint_scanpaths.Rd |only man/plot_gazepoint_stimulus_layout_qc.Rd |only man/plot_gazepoint_time_series.Rd |only man/plot_gazepoint_time_varying_effect.Rd |only man/prepare_gazepoint_hddm_export.Rd |only man/prepare_gazepoint_heatmap_data.Rd |only man/prepare_gazepoint_multimodal_data.Rd |only man/prepare_gazepoint_timecourse_test_data.Rd |only man/prepare_gazepoint_traminer_data.Rd |only man/read_gazepoint_face_export.Rd |only man/recommend_gazepoint_model_family.Rd |only man/report_gazepoint_cluster_permutation.Rd |only man/report_gazepoint_face_qc.Rd |only man/report_gazepoint_missingness.Rd |only man/report_gazepoint_multiverse.Rd |only man/report_gazepoint_phase_coverage.Rd |only man/report_gazepoint_qc_overview.Rd |only man/run_gazepoint_cluster_permutation_anova.Rd |only man/run_gazepoint_cluster_permutation_covariate_adjusted.Rd |only man/run_gazepoint_cluster_permutation_lmer.Rd |only man/run_gazepoint_cluster_permutation_parallel.Rd |only man/run_gazepoint_cluster_threshold_sensitivity.Rd |only man/run_gazepoint_multidimensional_cluster_permutation.Rd |only man/run_gazepoint_tfce.Rd |only man/segment_gazepoint_task_phases.Rd |only man/select_gazepoint_adaptive_trial.Rd |only man/simulate_gazepoint_cluster_timecourse_data.Rd |only man/simulate_gazepoint_data.Rd |only man/simulate_gazepoint_pupil_data.Rd |only man/smooth_gazepoint_pupil.Rd | 151 - man/standardize_gazepoint_face_columns.Rd |only man/summarise_gazepoint_markovchain.Rd |only man/summarise_gazepoint_pupil.Rd | 135 man/summarise_gazepoint_pupil_windows.Rd | 151 - man/summarise_gazepoint_semimarkov.Rd |only man/summarise_gazepoint_workflow.Rd | 68 man/summarize_gazepoint_coordinate_coverage.Rd |only man/summarize_gazepoint_face_quality.Rd |only man/summarize_gazepoint_face_reactivity.Rd |only man/summarize_gazepoint_face_windows.Rd |only man/summarize_gazepoint_missingness.Rd |only man/summarize_gazepoint_phase_coverage.Rd |only man/summarize_gazepoint_pupil_response_features.Rd |only man/summarize_gazepoint_qc_status.Rd |only man/summarize_gazepoint_time_clusters.Rd |only man/sync_gazepoint_face_data.Rd |only man/validate_gazepoint_master.Rd | 147 - tests/testthat/test-aoi_entropy.R |only tests/testthat/test-aoi_sequence_metrics.R |only tests/testthat/test-bayesian_planning_helpers.R |only tests/testthat/test-binocular_trackloss_simulation_extensions.R |only tests/testthat/test-cluster_permutation_batch_b.R |only tests/testthat/test-cluster_permutation_extensions.R |only tests/testthat/test-cluster_permutation_external_exports.R |only tests/testthat/test-cluster_permutation_guardrails.R |only tests/testthat/test-experimental_bayesian_bridges.R |only tests/testthat/test-export_gazepoint_master_audit.R | 66 tests/testthat/test-face_export_import.R |only tests/testthat/test-face_quality_audit.R |only tests/testthat/test-face_reporting.R |only tests/testthat/test-face_sync.R |only tests/testthat/test-face_window_summaries.R |only tests/testthat/test-final_statistical_extensions.R |only tests/testthat/test-fixation_reliability.R |only tests/testthat/test-heatmap_spatial_visualisation.R |only tests/testthat/test-markov_semimarkov_summaries.R |only tests/testthat/test-missingness_coverage_extensions.R |only tests/testthat/test-model_reporting_extensions.R |only tests/testthat/test-multimodal_modelling.R |only tests/testthat/test-phase_segmentation_extensions.R |only tests/testthat/test-plot_aoi_timeline.R |only tests/testthat/test-qc_reporting_bundle.R |only tests/testthat/test-saccade_scanpath.R |only tests/testthat/test-scanpath_qc_plot_extensions.R |only tests/testthat/test-scanpath_similarity.R |only tests/testthat/test-screen_coordinate_qc_extensions.R |only tests/testthat/test-sequence_anomalies.R |only tests/testthat/test-sequence_complexity.R |only tests/testthat/test-sequence_distance.R |only tests/testthat/test-simulation_bids_brms.R |only tests/testthat/test-stimulus_layout_qc_extensions.R |only tests/testthat/test-timecourse_bootstrap.R |only vignettes/aoi_workflow.Rmd | 19 vignettes/pupil_workflow.Rmd | 19 208 files changed, 2682 insertions(+), 2555 deletions(-)
Title: Automated Mendelian Randomization Pipelines and Visualizations
Description: Provides tools to summarize, analyze, and visualize results
from Mendelian randomization studies using summarized genetic
association data. The package includes functions for generating forest
plots and scatter plots at the single-nucleotide polymorphism
and Mendelian randomization method levels, and for fitting multiple
estimators in a unified pipeline, including inverse-variance weighted
estimation, Mendelian randomization Egger regression,
the weighted median estimator, the robust adjusted
profile score, Mendelian randomization pleiotropy residual sum
and outlier, Mendelian randomization with the genotype
recoding invariance property, and a Bayesian horseshoe
method. Related methods are described by Burgess (2013)
<doi:10.1002/gepi.21758>, Bowden (2015) <doi:10.1093/ije/dyv080>,
Bowden (2016) <doi:10.1002/gepi.21965>, Zhao (2020)
<doi:10.1214/19-AOS1866>, Verbanck (2018)
<doi:10.1038/s41588-018-0099-7>, Dudbridge (2025)
<doi:10.1371/journal.pgen.1011 [...truncated...]
Author: Kelin Zhong [aut, cre],
Chia-Ling Kuo [aut]
Maintainer: Kelin Zhong <kelinzhonguconn@gmail.com>
Diff between autoMR versions 1.2.0 dated 2026-06-12 and 1.2.1 dated 2026-07-14
autoMR-1.2.0/autoMR/R/mr_workflows.R |only autoMR-1.2.1/autoMR/DESCRIPTION | 10 +++++----- autoMR-1.2.1/autoMR/MD5 | 10 +++++----- autoMR-1.2.1/autoMR/R/mr_pipelines.R |only autoMR-1.2.1/autoMR/man/dot-draw_scatter_plot.Rd | 2 +- autoMR-1.2.1/autoMR/man/plot_mr_scatter.Rd | 2 +- autoMR-1.2.1/autoMR/man/run_mr_analysis.Rd | 2 +- 7 files changed, 13 insertions(+), 13 deletions(-)
Title: Data Sets for 'specmine'
Description: Provides the data sets used to exemplify 'specmine'. These data
sets were formerly distributed with 'specmine', but they exceed current
CRAN policy for package size.
Author: Christopher Costa [aut],
Marcelo Maraschin [aut],
Miguel Rocha [aut],
Pedro Fontao [aut, cre],
Sara Cardoso [aut],
Telma Afonso [aut],
C. Beleites [cph],
Jie Hao [cph],
Bruno Pereira [aut]
Maintainer: Pedro Fontao <pedrofontao812004@gmail.com>
This is a re-admission after prior archival of version 0.0.2 dated 2021-02-17
Diff between specmine.datasets versions 0.0.2 dated 2021-02-17 and 0.0.3 dated 2026-07-14
DESCRIPTION | 59 +++++++--- MD5 | 23 ++-- NAMESPACE | 4 NEWS.md |only R/data.R | 249 +++++++++++++++++++++++----------------------- README.md | 78 +++++++------- data/spinalCord.rda |binary man/cachexia.Rd | 52 ++++----- man/cassavaPPD.Rd | 50 ++++----- man/propolis.Rd | 79 +++++++------- man/propolisSampleList.Rd | 79 +++++++------- man/spectra_options.Rd | 31 ++--- man/spinalCord.Rd | 53 ++++----- 13 files changed, 388 insertions(+), 369 deletions(-)
More information about specmine.datasets at CRAN
Permanent link
Title: Non-Parametric Tests of Independence Between Random Vectors
Description: Non-parametric tests of independence (mutual or serial) between some quantitative random vectors, as described in Bilodeau M. and Lafaye de Micheaux P. (2009) <doi:10.1016/j.jspi.2008.11.006>, in Beran R., Bilodeau M. and Lafaye de Micheaux P. (2007) <doi:10.1016/j.jmva.2007.01.009> and in Fan Y., Lafaye de Micheaux P., Penev S. and Salopek D. (2017) <doi:10.1016/j.jmva.2016.09.014>.
Author: Pierre Lafaye De Micheaux [aut, cre] ,
Martin Bilodeau [aut],
Yanan Fan [aut],
Spiridon Penev [aut],
Donna Salopek [aut],
Cleve Moler [cph] ,
Jack Dongarra [cph] ,
Richard Hanson [cph] ,
Sven Hammarling [cph] ,
Jeremy Du Croz [cph]
Maintainer: Pierre Lafaye De Micheaux <lafaye@unsw.edu.au>
This is a re-admission after prior archival of version 0.5 dated 2020-12-18
Diff between IndependenceTests versions 0.5 dated 2020-12-18 and 0.7 dated 2026-07-14
DESCRIPTION | 34 ++++++------ MD5 | 66 ++++++++++++------------- NAMESPACE | 4 + R/A-dep-tests.R | 59 ++++++++++++++++------ R/mdcov-lambdas.R | 3 - TODO | 72 +++++++++++++++++++++++++++ inst/CITATION | 12 ++-- inst/HISTORY | 26 +++++++++ man/A-dep-tests.Rd | 4 - src/Makevars | 10 --- src/cubature1.cpp | 12 ++-- src/myzhpevx.cpp | 118 +++++++++++---------------------------------- src/othersfortran/dlanst.f | 2 src/othersfortran/dlascl.f | 2 src/othersfortran/dlasrt.f | 2 src/othersfortran/dstebz.f | 4 - src/othersfortran/ilaenv.f | 44 +++++++++++++--- src/othersfortran/ilazlc.f | 8 +-- src/othersfortran/ilazlr.f | 8 +-- src/othersfortran/xerbla.f | 6 +- src/othersfortran/zhptrd.f | 16 +++--- src/othersfortran/zladiv.f | 12 ++-- src/othersfortran/zlanhp.f | 10 +-- src/othersfortran/zlarf.f | 20 +++---- src/othersfortran/zlarfg.f | 16 +++--- src/othersfortran/zlaset.f | 16 +++--- src/othersfortran/zlasr.f | 14 ++--- src/othersfortran/zlassq.f | 6 +- src/othersfortran/zstein.f | 8 +-- src/othersfortran/zsteqr.f | 10 +-- src/othersfortran/zung2l.f | 12 ++-- src/othersfortran/zung2r.f | 12 ++-- src/othersfortran/zupgtr.f | 16 +++--- src/othersfortran/zupmtr.f | 22 ++++---- 34 files changed, 389 insertions(+), 297 deletions(-)
More information about IndependenceTests at CRAN
Permanent link
Title: Exact Date and Duration Arithmetic on an Annual Grid
Description: Standardised mapping of dates onto a discrete annual grid,
together with exact date and duration arithmetic. This matters when
the primary unit is years but the input data uses dates. Examples are
actuarial mortality experience analysis and valuation of life
assurance and annuities, for which mortality rates are defined per
year but experience and valuation data are typically defined using
dates.
Author: Tim Gordon [aut, cre]
Maintainer: Tim Gordon <tim.gordon@btinternet.com>
Diff between datey versions 0.1.0 dated 2026-07-07 and 0.1.1 dated 2026-07-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 6 ++++++ README.md | 19 +++++++++++++------ src/S_durationy.cpp | 21 ++++++++++++++------- 5 files changed, 40 insertions(+), 20 deletions(-)
Title: 'SAS' Linear Model
Description: This is a core implementation of 'SAS' procedures for linear models - GLM, REG, ANOVA, TTEST, FREQ, and UNIVARIATE. Some R packages provide Type II and Type III SS. However, the results of nested and complex designs are often different from those of 'SAS'. Different results do not necessarily mean incorrectness. However, many want the same results as 'SAS'. This package aims to achieve that.
Reference: Littell RC, Stroup WW, Freund RJ (2002, ISBN:0-471-22174-0).
Author: Kyun-Seop Bae [aut, cre]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between sasLM versions 1.0.0 dated 2026-06-15 and 1.0.1 dated 2026-07-14
sasLM-1.0.0/sasLM/inst/doc/Report-Different-Simplest2606121557.pdf |only sasLM-1.0.0/sasLM/inst/doc/Report-NOT-OKs2606121557.pdf |only sasLM-1.0.0/sasLM/inst/doc/Validation-Report-GLM-2606121701.pdf |only sasLM-1.0.0/sasLM/inst/doc/index.html |only sasLM-1.0.1/sasLM/DESCRIPTION | 11 +-- sasLM-1.0.1/sasLM/MD5 | 36 ++++++++-- sasLM-1.0.1/sasLM/NAMESPACE | 13 ++- sasLM-1.0.1/sasLM/R/IQLM.R |only sasLM-1.0.1/sasLM/R/OQLM.R |only sasLM-1.0.1/sasLM/R/QualReportLM.R |only sasLM-1.0.1/sasLM/R/addSigFieldLM.R |only sasLM-1.0.1/sasLM/R/signPDFLM.R |only sasLM-1.0.1/sasLM/R/writeMD5LM.R |only sasLM-1.0.1/sasLM/build |only sasLM-1.0.1/sasLM/inst/NEWS.Rd | 11 +++ sasLM-1.0.1/sasLM/inst/OQ |only sasLM-1.0.1/sasLM/inst/extdoc |only sasLM-1.0.1/sasLM/man/IQLM.Rd |only sasLM-1.0.1/sasLM/man/OQLM.Rd |only sasLM-1.0.1/sasLM/man/addSigFieldLM.Rd |only sasLM-1.0.1/sasLM/man/signPDFLM.Rd |only sasLM-1.0.1/sasLM/man/writeMD5LM.Rd |only sasLM-1.0.1/sasLM/vignettes |only 23 files changed, 54 insertions(+), 17 deletions(-)
Title: Identifies Package Differences
Description: Identifies differences between
versions of a package. Specifically, the functions help
determine if there are breaking changes from one package version
to the next. The package also includes a stability assessment,
to help you determine the overall stability of a package, or even
an entire repository.
Author: David Bosak [aut, cre],
Brian Varney [ctb],
Kevin Putschko [ctb]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between pkgdiff versions 1.0.3 dated 2026-05-10 and 1.0.4 dated 2026-07-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/utilities.R | 3 ++- tests/testthat/test-pkgrepo.R | 2 +- 5 files changed, 14 insertions(+), 9 deletions(-)
Title: Sampling Error Estimation for Complex Surveys
Description: Estimates sampling errors and produces indicator tables for
complex survey data. Supports weighted totals, proportions, standard
errors, confidence intervals, coefficients of variation, design effects,
unweighted frequencies, grouped estimates, domain estimates, optional
stratification and clustering variables, and customizable exports to
'.xlsx' files. Survey estimation is based on design-based inference using
Taylor series linearization implemented in the 'survey' package (Lumley,
2004, <doi:10.18637/jss.v009.i08>; Lumley, 2010,
ISBN:9780470284308). The package provides a reproducible workflow for
official statistics, household surveys, and applied survey research.
Author: Luis Burgos [aut, cre]
Maintainer: Luis Burgos <lburgoss1996@gmail.com>
Diff between svySE versions 0.1.0 dated 2026-07-10 and 0.2.0 dated 2026-07-14
DESCRIPTION | 28 MD5 | 41 - NAMESPACE | 2 NEWS.md | 25 R/calculo.R | 304 +++++--- R/exportar.R | 423 ++++++++++-- R/simple.R |only README.md | 659 ++++++++++++++++--- inst/CITATION | 4 inst/doc/svySE-basic-workflow.R | 287 +++++++- inst/doc/svySE-basic-workflow.Rmd | 547 +++++++++++++++ inst/doc/svySE-basic-workflow.html | 993 +++++++++++++++++++++++++---- man/print.svySE_simple_result.Rd |only man/svySE_calc.Rd | 22 man/svySE_simple.Rd |only man/svySE_xlsx.Rd | 77 +- tests/testthat/test-calculo-diseno.R |only tests/testthat/test-calculo-division.R |only tests/testthat/test-calculo-validaciones.R |only tests/testthat/test-calculo.R | 364 ++++++++++ tests/testthat/test-columnas.R | 179 ++++- tests/testthat/test-config.R | 205 +++++ tests/testthat/test-exportar.R | 507 +++++++++++++- tests/testthat/test-simple.R |only vignettes/svySE-basic-workflow.Rmd | 547 +++++++++++++++ 25 files changed, 4602 insertions(+), 612 deletions(-)
Title: Lining Up Two Sets of Measurements
Description: Tools for detecting and correcting sample mix-ups between two sets
of measurements, such as between gene expression data on two
tissues. This is a revised version of the 'lineup' package, to be
more general and not tied to the 'qtl' package.
Author: Karl W Broman [aut, cre]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between lineup2 versions 0.6 dated 2021-06-15 and 0.8 dated 2026-07-14
DESCRIPTION | 13 MD5 | 23 - NEWS.md | 8 R/cluster_util.R | 2 R/lineup2-package.R | 2 README.md | 30 +- build/vignette.rds |binary data/lineup2ex.RData |binary inst/doc/lineup2.Rmd | 12 inst/doc/lineup2.html | 676 +++++++++++++++++++++++++++++++++++++------------ man/figures |only man/lineup2-package.Rd | 19 + vignettes/lineup2.Rmd | 12 13 files changed, 602 insertions(+), 195 deletions(-)
Title: Automatic Toolkit for Construction, Optimization, Scoring and
Simulation of Forced-Choice Tests
Description: Forced-choice (FC) response has gained increasing popularity
and interest for its resistance to faking when well-designed (Cao &
Drasgow, 2019 <doi:10.1037/apl0000414>). To established well-designed
FC scales, typically each item within a block should measure different
trait and have similar level of social desirability (Zhang et al.,
2020 <doi:10.1177/1094428119836486>). Recent study also suggests the
importance of high inter-item agreement of social desirability between
items within a block (Pavlov et al., 2021
<doi:10.31234/osf.io/hmnrc>). In addition to this, FC developers may
also need to maximize factor loading differences (Brown &
Maydeu-Olivares, 2011 <doi:10.1177/0013164410375112>) or minimize item
location differences (Cao & Drasgow, 2019 <doi:10.1037/apl0000414>)
depending on scoring models. Decision of which items should be
assigned to the same block, also called as item pairing, is thus critical
to the quality of an FC test. Becau [...truncated...]
Author: Mengtong Li [cre, aut] ,
Tianjun Sun [aut] ,
Bo Zhang [aut]
Maintainer: Mengtong Li <mt_li@fudan.edu.cn>
Diff between autoFC versions 1.0.0.1001 dated 2026-06-10 and 1.0.0.1002 dated 2026-07-14
DESCRIPTION | 6 MD5 | 40 +- NAMESPACE | 4 NEWS.md | 5 R/convert_comp_to_log.R |only R/generate_cfc_lavaan_syntax.R |only R/generate_tirt_lavaan_syntax.R | 551 ++++++++++++++++++------------------- R/generate_tirt_mplus_syntax.R | 3 R/generate_tirt_stan_syntax.R | 455 +++++++++++++++--------------- R/get_simulation_matrices.R | 140 ++++----- R/prepare_tirt_stan_data.R | 3 R/score_cfc_lavaan.R |only R/score_tirt_ipsative.R | 193 ++++++------ R/simulate_fc_data.R |only inst/doc/intro-to-autoFC.html | 4 man/convert_comp_to_log.Rd |only man/generate_cfc_lavaan_syntax.Rd |only man/generate_tirt_lavaan_syntax.Rd | 3 man/generate_tirt_mplus_syntax.Rd | 3 man/generate_tirt_stan_syntax.Rd | 3 man/get_simulation_matrices.Rd | 13 man/prepare_tirt_stan_data.Rd | 3 man/score_cfc_lavaan.Rd |only man/score_tirt_ipsative.Rd | 3 man/simulate_fc_data.Rd |only 25 files changed, 717 insertions(+), 715 deletions(-)
Title: Windowed Cross Correlation
Description: Calculates Windowed Cross Correlation for pairs of time series.
Provides support for surrogate analysis for nonparametric test of significance.
Calculates aggregate statistics over a range of parameter values.
Plots the results as Windowed Cross Correlation plots and heat maps.
The software is described in Boker, S. M., Rotondo, J. L., Xu, M., & King, K. (2002). Windowed cross-correlation and peak picking for the analysis of variability in the association between behavioral time series. Psychological Methods, 7(3), 338.
Author: Steven Boker [aut, cre],
Minquan Xu [aut],
Sareena Chadha [aut],
Christopher Welker [aut],
Jingyun Wu [aut],
Pascal Deboeck [aut],
Aaron Peikert [aut],
Claude [aut]
Maintainer: Steven Boker <smb3u@virginia.edu>
Diff between wcc versions 0.3.1 dated 2026-04-21 and 0.4.0 dated 2026-07-14
DESCRIPTION | 24 +-- MD5 | 48 +++--- NEWS.md | 57 +++++++ R/wccAggregate.R | 33 +++- R/wccCalc.R | 128 +++++++++++++++- R/wccCalcBatch.R |only R/wccFindDyadParam.R | 65 +++++++- R/wccPeakPick.R | 336 +++++++++++++++----------------------------- R/wccPlot.R | 12 + R/wccSurrogateDyads.R | 12 + README.md |only demo/00Index | 1 demo/benchmarkWCC.R |only man/wcc-internal.Rd |only man/wcc-package.Rd | 6 man/wccAggregate.Rd | 84 +++++------ man/wccCalc.Rd | 26 +-- man/wccCalcBatch.Rd |only man/wccFindDyadParam.Rd | 140 +++++++++++++++--- man/wccHeatMap.Rd | 14 - man/wccPeakPick-internal.Rd |only man/wccPeakPick.Rd | 16 +- man/wccPlot.Rd | 38 ++-- man/wccSurrogateDyads.Rd | 36 ++-- src/Makevars |only src/init.c | 4 src/windcross.c | 6 src/windcrosscum.c |only tests |only 29 files changed, 690 insertions(+), 396 deletions(-)
Title: Non-Parametric Trend Tests and Change-Point Detection
Description: The analysis of environmental data often requires
the detection of trends and change-points.
This package includes tests for trend detection
(Cox-Stuart Trend Test, Mann-Kendall Trend Test,
(correlated) Hirsch-Slack Test,
partial Mann-Kendall Trend Test, multivariate (multisite)
Mann-Kendall Trend Test, (Seasonal) Sen's slope,
partial Pearson and Spearman correlation trend test),
change-point detection (Lanzante's test procedures,
Pettitt's test, Buishand Range Test,
Buishand U Test, Standard Normal Homogeinity Test),
detection of non-randomness (Wallis-Moore Phase Frequency Test,
Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test)
and the two sample Robust Rank-Order Distributional Test.
Author: Thorsten Pohlert [aut, cre]
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between trend versions 1.1.6 dated 2023-10-10 and 1.1.7 dated 2026-07-14
DESCRIPTION | 13 +++++++------ MD5 | 16 ++++++++-------- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 9 +++++++++ inst/doc/trend.R | 2 -- inst/doc/trend.Rnw | 2 +- inst/doc/trend.pdf |binary vignettes/trend.Rnw | 2 +- 9 files changed, 26 insertions(+), 18 deletions(-)
Title: Information Bottleneck Methods for Clustering Mixed-Type Data
Description: Implements multiple variants of the Information Bottleneck ('IB') method
for clustering datasets containing continuous, categorical (nominal/ordinal) and mixed-type variables.
The package provides deterministic, agglomerative, generalised,
sequential, and standard IB clustering algorithms that preserve relevant information while
forming interpretable clusters. The Deterministic Information Bottleneck is described in
Costa et al. (2026) <doi:10.1016/j.patcog.2026.113580>. The standard IB method
originates from Tishby et al. (2000) <doi:10.48550/arXiv.physics/0004057>,
the agglomerative variant from Slonim and Tishby (1999) <https://papers.nips.cc/paper/1651-agglomerative-information-bottleneck>,
the generalised IB from Strouse and Schwab (2017) <doi:10.1162/NECO_a_00961>,
and the sequential IB from Slonim et al. (2002) <doi:10.1145/564376.564401>.
Author: Angelos Markos [aut, cre],
Efthymios Costa [aut],
Ioanna Papatsouma [aut]
Maintainer: Angelos Markos <amarkos@gmail.com>
Diff between IBclust versions 1.3 dated 2026-05-11 and 1.4 dated 2026-07-14
DESCRIPTION | 15 - MD5 | 61 +++-- NAMESPACE | 31 +++ R/AIB.R | 47 +++- R/AIBmix.R | 117 +++-------- R/DIBmix.R | 148 +++----------- R/DIBmix_iterate.R | 2 R/GIBmix.R | 130 +++--------- R/IBclust-package.R | 137 ++++++++++++- R/IBmix.R | 130 +++--------- R/aibclust-class.R | 9 R/aibclust-methods.R | 215 +++++++++++++++++--- R/as_hclust.R |only R/coord_to_pxy_eval_R.R |only R/find_elbow.R |only R/gibclust-methods.R | 473 ++++++++++++++++++++++++++++++++++++++++++---- R/importance.R | 15 - R/info_metrics.R |only R/input_checks.R | 6 R/sIBmix.R |only R/sIBmix_iterate.R |only R/sibclust-class.R |only R/sibclust-methods.R |only build/partial.rdb |binary inst/CITATION | 2 inst/REFERENCES.bib | 7 man/AIBmix.Rd | 99 ++------- man/DIBmix.Rd | 137 ++----------- man/GIBmix.Rd | 121 ++--------- man/IBclust-package.Rd | 135 ++++++++++++- man/IBmix.Rd | 121 +++-------- man/aibclust-methods.Rd |only man/as.hclust.aibclust.Rd |only man/find_elbow.Rd |only man/gibclust-methods.Rd |only man/info_metrics.Rd |only man/predict.gibclust.Rd |only man/predict.sibclust.Rd |only man/sIBmix.Rd |only man/sibclust-methods.Rd |only 40 files changed, 1288 insertions(+), 870 deletions(-)
Title: Distribution Comparison Through Density Ratio Estimation
Description: Fast, flexible and user-friendly tools for distribution comparison
through direct density ratio estimation. The estimated density ratio can be
used for covariate shift adjustment, outlier-detection, change-point detection,
classification and evaluation of synthetic data quality. The package implements
multiple non-parametric estimation techniques (unconstrained least-squares
importance fitting, ulsif(), Kullback-Leibler importance estimation procedure,
kliep(), spectral density ratio estimation, spectral(), kernel mean matching,
kmm(), and least-squares hetero-distributional subspace search, lhss()).
with automatic tuning of hyperparameters. Helper functions are available for
two-sample testing and visualizing the density ratios. For an overview on
density ratio estimation, see Sugiyama et al. (2012) <doi:10.1017/CBO9781139035613>
for a general overview, and the help files for references on the specific
estimation techniques.
Author: Thom Volker [aut, cre] ,
Carlos Gonzalez Poses [ctb],
Erik-Jan van Kesteren [ctb]
Maintainer: Thom Volker <thombenjaminvolker@gmail.com>
Diff between densityratio versions 0.2.2 dated 2025-07-18 and 0.2.3 dated 2026-07-14
densityratio-0.2.2/densityratio/man/distance.Rd |only densityratio-0.2.2/densityratio/man/kernel_gaussian.Rd |only densityratio-0.2.3/densityratio/DESCRIPTION | 11 densityratio-0.2.3/densityratio/MD5 | 165 +++--- densityratio-0.2.3/densityratio/NEWS.md | 8 densityratio-0.2.3/densityratio/R/RcppExports.R | 28 - densityratio-0.2.3/densityratio/R/checks.R | 12 densityratio-0.2.3/densityratio/R/data.R | 23 densityratio-0.2.3/densityratio/R/kliep.R | 9 densityratio-0.2.3/densityratio/R/kmm.R | 8 densityratio-0.2.3/densityratio/R/lhss.R | 11 densityratio-0.2.3/densityratio/R/spectral.R | 1 densityratio-0.2.3/densityratio/R/ulsif.R | 19 densityratio-0.2.3/densityratio/README.md | 49 +- densityratio-0.2.3/densityratio/build/partial.rdb |binary densityratio-0.2.3/densityratio/build/vignette.rds |binary densityratio-0.2.3/densityratio/inst/doc/covariate-shift.Rmd | 35 - densityratio-0.2.3/densityratio/inst/doc/covariate-shift.html | 57 +- densityratio-0.2.3/densityratio/inst/doc/densityratio.Rmd | 64 +- densityratio-0.2.3/densityratio/inst/doc/densityratio.html | 85 +-- densityratio-0.2.3/densityratio/inst/doc/high-dim-testing.html | 5 densityratio-0.2.3/densityratio/inst/examples/kliep-example.R | 13 densityratio-0.2.3/densityratio/inst/examples/kmm-example.R | 14 densityratio-0.2.3/densityratio/inst/examples/lhss-example.R | 15 densityratio-0.2.3/densityratio/inst/examples/spectral-example.R | 13 densityratio-0.2.3/densityratio/inst/examples/ulsif-example.R | 13 densityratio-0.2.3/densityratio/man/colon.Rd | 43 - densityratio-0.2.3/densityratio/man/denominator_small.Rd | 38 - densityratio-0.2.3/densityratio/man/figures/README-densities-1.png |binary densityratio-0.2.3/densityratio/man/figures/README-plot-methods-1.png |binary densityratio-0.2.3/densityratio/man/figures/README-plot-univ-1.png |binary densityratio-0.2.3/densityratio/man/figures/logo.png |binary densityratio-0.2.3/densityratio/man/insurance.Rd | 50 +- densityratio-0.2.3/densityratio/man/kidiq.Rd | 54 +- densityratio-0.2.3/densityratio/man/kliep.Rd | 212 ++++---- densityratio-0.2.3/densityratio/man/kmm.Rd | 243 +++++----- densityratio-0.2.3/densityratio/man/lhss.Rd | 217 ++++---- densityratio-0.2.3/densityratio/man/numerator_small.Rd | 38 - densityratio-0.2.3/densityratio/man/permute.Rd | 142 ++--- densityratio-0.2.3/densityratio/man/plot_bivariate.Rd | 13 densityratio-0.2.3/densityratio/man/plot_univariate.Rd | 13 densityratio-0.2.3/densityratio/man/predict.kliep.Rd | 113 ++-- densityratio-0.2.3/densityratio/man/predict.kmm.Rd | 114 ++-- densityratio-0.2.3/densityratio/man/predict.lhss.Rd | 123 ++--- densityratio-0.2.3/densityratio/man/predict.ulsif.Rd | 125 ++--- densityratio-0.2.3/densityratio/man/print.kliep.Rd | 103 ++-- densityratio-0.2.3/densityratio/man/print.kmm.Rd | 104 ++-- densityratio-0.2.3/densityratio/man/print.lhss.Rd | 97 ++- densityratio-0.2.3/densityratio/man/print.spectral.Rd | 99 ++-- densityratio-0.2.3/densityratio/man/print.summary.kliep.Rd | 103 ++-- densityratio-0.2.3/densityratio/man/print.summary.kmm.Rd | 104 ++-- densityratio-0.2.3/densityratio/man/print.summary.lhss.Rd | 97 ++- densityratio-0.2.3/densityratio/man/print.summary.spectral.Rd | 99 ++-- densityratio-0.2.3/densityratio/man/print.summary.ulsif.Rd | 99 ++-- densityratio-0.2.3/densityratio/man/print.ulsif.Rd | 99 ++-- densityratio-0.2.3/densityratio/man/spectral.Rd | 223 ++++----- densityratio-0.2.3/densityratio/man/summary.kliep.Rd | 143 +++-- densityratio-0.2.3/densityratio/man/summary.kmm.Rd | 144 +++-- densityratio-0.2.3/densityratio/man/summary.lhss.Rd | 127 ++--- densityratio-0.2.3/densityratio/man/summary.spectral.Rd | 129 ++--- densityratio-0.2.3/densityratio/man/summary.ulsif.Rd | 129 ++--- densityratio-0.2.3/densityratio/man/ulsif.Rd | 223 ++++----- densityratio-0.2.3/densityratio/src/RcppExports.cpp | 27 - densityratio-0.2.3/densityratio/src/densityratio.h | 6 densityratio-0.2.3/densityratio/src/dist.cpp | 17 densityratio-0.2.3/densityratio/src/lhss.cpp | 27 - densityratio-0.2.3/densityratio/src/ulsif.cpp | 33 - densityratio-0.2.3/densityratio/tests/testthat.R | 10 densityratio-0.2.3/densityratio/tests/testthat/test-checks.R | 11 densityratio-0.2.3/densityratio/tests/testthat/test-kliep.R | 1 densityratio-0.2.3/densityratio/tests/testthat/test-lhss.R | 2 densityratio-0.2.3/densityratio/tests/testthat/test-ulsif.R | 1 densityratio-0.2.3/densityratio/vignettes/covariate-shift-plot-dr-bivariate-1.png |binary densityratio-0.2.3/densityratio/vignettes/covariate-shift-plot-dr-cs-1.png |binary densityratio-0.2.3/densityratio/vignettes/covariate-shift-plot-dr-rs-1.png |binary densityratio-0.2.3/densityratio/vignettes/covariate-shift-plot-dr-univariate-1.png |binary densityratio-0.2.3/densityratio/vignettes/covariate-shift.Rmd | 35 - densityratio-0.2.3/densityratio/vignettes/covariate-shift.Rmd.orig | 3 densityratio-0.2.3/densityratio/vignettes/densityratio-bandwidth-note-1.png |binary densityratio-0.2.3/densityratio/vignettes/densityratio-plot-bivariate-1.png |binary densityratio-0.2.3/densityratio/vignettes/densityratio-plot-dr-1.png |binary densityratio-0.2.3/densityratio/vignettes/densityratio-plot-univariate-1.png |binary densityratio-0.2.3/densityratio/vignettes/densityratio-regularization-note-1.png |binary densityratio-0.2.3/densityratio/vignettes/densityratio.Rmd | 64 +- densityratio-0.2.3/densityratio/vignettes/render.R |only 85 files changed, 2516 insertions(+), 2039 deletions(-)
Title: Support for Spatial Objects Within the 'mlr3' Ecosystem
Description: Extends the 'mlr3' ML framework with methods for spatial
objects. Data storage and prediction are supported for packages
'terra', 'raster' and 'stars'.
Author: Marc Becker [aut, cre] ,
Patrick Schratz [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3spatial versions 0.6.1 dated 2025-09-14 and 0.7.0 dated 2026-07-14
DESCRIPTION | 9 MD5 | 94 +++--- NEWS.md | 6 R/DataBackendRaster.R | 80 +++-- R/DataBackendVector.R | 10 R/LearnerClassifSpatial.R | 11 R/LearnerRegrSpatial.R | 5 R/TaskClassifST.R | 45 ++- R/TaskClassif_leipzig.R | 2 R/TaskRegrST.R | 35 +- R/as_task_classif_st.R | 79 +++++ R/as_task_regr_st.R | 72 ++++- R/data.R | 14 - R/helper.R | 14 - R/predict_spatial.R | 102 +++++-- R/zzz.R | 26 + build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/benchmark.Rmd | 2 inst/doc/benchmark.html | 7 man/DataBackendRaster.Rd | 256 +++++++++--------- man/DataBackendVector.Rd | 69 ++--- man/TaskClassifST.Rd | 218 +++++++--------- man/TaskRegrST.Rd | 215 +++++++-------- man/as_data_backend.Rd | 7 man/block_size.Rd | 2 man/figures/logo.png |binary man/generate_stack.Rd | 2 man/mask_stack.Rd | 4 man/mlr3spatial-package.Rd | 6 man/predict_spatial.Rd | 20 + man/sample_stack.Rd | 2 tests/testthat/helper_expectations.R | 7 tests/testthat/helper_learner.R | 4 tests/testthat/test_DataBackendRaster.R | 381 ++++++++++++++++++++++------ tests/testthat/test_DataBackendVector.R | 4 tests/testthat/test_LearnerClassifSpatial.R | 52 +++ tests/testthat/test_LearnerRegrSpatial.R | 11 tests/testthat/test_TaskClassifST.R | 11 tests/testthat/test_TaskRegrST.R | 11 tests/testthat/test_as_task_classif_st.R | 77 +++-- tests/testthat/test_as_task_regr_st.R | 78 +++-- tests/testthat/test_as_task_unsupervised.R | 47 ++- tests/testthat/test_bock_size.R | 72 +++-- tests/testthat/test_data.R | 9 tests/testthat/test_predict_spatial.R | 193 +++++++++++--- vignettes/benchmark.Rmd | 2 vignettes/benchmark.Rmd.orig | 2 48 files changed, 1570 insertions(+), 806 deletions(-)
Title: Bayesian Hierarchical Analysis of Cognitive Models of Choice
Description: Fit Bayesian (hierarchical) cognitive models
using a linear modeling language interface using particle Metropolis Markov
chain Monte Carlo sampling with Gibbs steps. The diffusion decision model (DDM),
linear ballistic accumulator model (LBA), racing diffusion model (RDM), and the lognormal
race model (LNR) are supported. Additionally, users can specify their own likelihood
function and/or choose for non-hierarchical
estimation, as well as for a diagonal, blocked or full multivariate normal
group-level distribution to test individual differences. Prior specification
is facilitated through methods that visualize the (implied) prior.
A wide range of plotting functions assist in assessing model convergence and
posterior inference. Models can be easily evaluated using functions
that plot posterior predictions or using relative model comparison metrics
such as information criteria or Bayes factors.
References: Stevenson et al. (2024) <doi:10.31234/osf.io/2e4dq>.
Author: Niek Stevenson [aut, cre] ,
Michelle Donzallaz [aut],
Andrew Heathcote [aut],
Steven Miletic [aut],
Luke Strickland [ctb],
Frank Hezemans [ctb],
Raphael Hartmann [ctb],
Karl C. Klauer [ctb],
Steven G. Johnson [ctb],
Jean M. Linhart [ctb],
Brian Gough [...truncated...]
Maintainer: Niek Stevenson <niek.stevenson@gmail.com>
Diff between EMC2 versions 3.4.1 dated 2026-01-12 and 3.5.0 dated 2026-07-14
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Title: R Bindings to the Calendaring Functionality of 'QuantLib'
Description: 'QuantLib' bindings are provided for R using 'Rcpp' via an evolved version
of the initial header-only 'Quantuccia' project offering an subset of 'QuantLib' (now
maintained separately just for the calendaring subset). See the included file 'AUTHORS'
for a full list of contributors to 'QuantLib' (and hence also 'Quantuccia').
Author: Dirk Eddelbuettel [aut, cre] ,
QuantLib Authors [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between qlcal versions 0.1.1 dated 2026-04-15 and 0.1.2 dated 2026-07-14
ChangeLog | 44 ++++++ DESCRIPTION | 8 - MD5 | 54 ++++--- R/calendars.R | 11 + build/partial.rdb |binary inst/NEWS.Rd | 12 + src/Makevars.in | 12 + src/Makevars.win.in | 8 + src/calendars.cpp | 32 +++- src/ql/optional.hpp | 3 src/ql/patterns/observable.hpp | 6 src/ql/shared_ptr.hpp | 2 src/ql/time/calendars/all.hpp | 8 + src/ql/time/calendars/croatia.cpp |only src/ql/time/calendars/croatia.hpp |only src/ql/time/calendars/india.cpp | 219 ++++++++++++++++-------------- src/ql/time/calendars/india.hpp | 2 src/ql/time/calendars/islamicholidays.cpp |only src/ql/time/calendars/islamicholidays.hpp |only src/ql/time/calendars/israel.cpp | 79 ++++++++++ src/ql/time/calendars/israel.hpp | 55 ++++++- src/ql/time/calendars/malta.cpp |only src/ql/time/calendars/malta.hpp |only src/ql/time/calendars/montenegro.cpp |only src/ql/time/calendars/montenegro.hpp |only src/ql/time/calendars/northmacedonia.cpp |only src/ql/time/calendars/northmacedonia.hpp |only src/ql/time/calendars/nullcalendar.hpp | 2 src/ql/time/calendars/serbia.cpp |only src/ql/time/calendars/serbia.hpp |only src/ql/time/calendars/slovenia.cpp |only src/ql/time/calendars/slovenia.hpp |only src/ql/time/calendars/southkorea.cpp | 1 src/ql/time/calendars/uzbekistan.cpp |only src/ql/time/calendars/uzbekistan.hpp |only src/ql/time/date.hpp | 2 36 files changed, 416 insertions(+), 144 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-10 0.7.0
2023-06-07 0.6.0
2023-03-06 0.5.0
2022-11-29 0.4.0
2022-09-01 0.3.0
2022-05-30 0.2.0
2022-02-15 0.1.2
Title: S3 Classes and Methods for Tidy Functional Data
Description: Provides S3 vector types for functional data represented on
grids, in spline bases, or via functional principal components.
Supports arithmetic and summary methods, plotting, derivation,
integration, smoothing, registration, and data import/export for these
functional vectors. Includes data-wrangling tools for re-evaluation,
subsetting, sub-assignment, zooming into sub-domains, and extracting
functional features such as minima, maxima, and their locations.
Enables joint analysis of functional and scalar variables by integrating
functional vectors into standard data frames.
Author: Fabian Scheipl [aut, cre, cph] ,
Jeff Goldsmith [aut],
Maximilian Muecke [aut] ,
Julia Wrobel [ctb] ,
Sebastian Fischer [ctb]
Maintainer: Fabian Scheipl <fabian.scheipl@googlemail.com>
Diff between tf versions 0.4.1 dated 2026-04-07 and 0.5.0 dated 2026-07-14
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Title: Pediatrics Extension Package for ADaM in 'R' Asset Library
Description: A toolbox for programming Clinical Data Standards Interchange
Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R.
ADaM datasets are a mandatory part of any New Drug or Biologics
License Application submitted to the United States Food and Drug
Administration (FDA). Analysis derivations are implemented in
accordance with the "Analysis Data Model Implementation Guide" (CDISC
Analysis Data Model Team, 2021,
<https://www.cdisc.org/standards/foundational/adam>). The package is
an extension package of the 'admiral' package for pediatric clinical
trials.
Author: Fanny Gautier [aut, cre] ,
Ross Farrugia [aut],
Zelos Zhu [aut],
Sukalpo Saha [aut],
Lina Patil [aut],
Samia Kabi [aut],
Laura Liao [ctb],
Remigiusz Kudlacz [ctb],
Pierre Wallet [ctb],
Amin Sherzad [ctb],
David Freedman [ctb],
Mahmoud Hamza [ctb],
Cy [...truncated...]
Maintainer: Fanny Gautier <fanny.gautier@cytel.com>
Diff between admiralpeds versions 0.3.0 dated 2026-01-23 and 0.4.0 dated 2026-07-14
DESCRIPTION | 15 MD5 | 77 ++-- NAMESPACE | 1 NEWS.md | 29 + R/admiralpeds-package.R | 6 R/derive_params_growth_age.R | 67 +++- README.md | 7 inst/WORDLIST | 2 inst/doc/admiralpeds.Rmd | 2 inst/doc/admiralpeds.html | 2 inst/doc/advs.R | 80 ++++ inst/doc/advs.Rmd | 135 +++++++- inst/doc/advs.html | 412 +++++++++++++++++++------ man/admiralpeds-package.Rd | 9 man/cdc_bmiage.Rd | 4 man/cdc_htage.Rd | 4 man/cdc_wtage.Rd | 4 man/derive_interp_records.Rd | 2 man/derive_params_growth_age.Rd | 48 ++ man/derive_params_growth_height.Rd | 4 man/figures/atorus_logo.png |binary man/figures/pfizer_logo.png |binary man/figures/roche_logo.png |binary man/find_closest_bin.Rd | 6 man/get_bins.Rd | 6 man/set_bins.Rd | 6 man/who_bmi_for_age_boys.Rd | 4 man/who_bmi_for_age_girls.Rd | 4 man/who_hc_for_age_boys.Rd | 4 man/who_hc_for_age_girls.Rd | 4 man/who_lgth_ht_for_age_boys.Rd | 4 man/who_lgth_ht_for_age_girls.Rd | 4 man/who_wt_for_age_boys.Rd | 4 man/who_wt_for_age_girls.Rd | 4 man/who_wt_for_lgth_boys.Rd | 4 man/who_wt_for_lgth_girls.Rd | 4 tests/testthat/test-derive_params_growth_age.R | 145 ++++++++ vignettes/admiralpeds.Rmd | 2 vignettes/advs.Rmd | 135 +++++++- vignettes/articles |only 40 files changed, 1033 insertions(+), 217 deletions(-)
Title: Directly Adjusted Estimates
Description: Compute estimates and confidence intervals of weighted
averages quickly and easily. Weighted averages are computed using
data.table for speed. Confidence intervals are approximated using the
delta method with either using known formulae or via algorithmic or
numerical derivation.
Author: Joonas Miettinen [cre, aut]
Maintainer: Joonas Miettinen <joonas.miettinen@cancer.fi>
Diff between directadjusting versions 0.6.1 dated 2026-02-04 and 0.7.0 dated 2026-07-14
DESCRIPTION | 12 - MD5 | 22 +- NEWS.md | 16 + R/delta_method.R | 16 - R/direct_adjusting.R | 351 ++++++++++++++++++++++++------------- R/package_directadjusting.R | 8 R/utils.R | 12 - R/weights.R | 77 ++++---- README.md | 10 - man/confidence_intervals.Rd | 282 ++++++++++++++--------------- man/directadjusting-package.Rd | 320 ++++++++++++++++++--------------- man/directly_adjusted_estimates.Rd | 119 ++++++++++-- 12 files changed, 757 insertions(+), 488 deletions(-)
More information about directadjusting at CRAN
Permanent link
Title: Safe Formula-Based Regularized Generalized Linear Models
Description: A formula-based wrapper around 'glmnet' that brings the
'glm()'-compatible modeling workflow to regularized generalized
linear models. Training-time 'terms', 'xlevels', and 'contrasts'
are stored on the fit object and reused at predict time, so the
design matrix is reconstructed consistently across sessions.
Complete-case bookkeeping is exposed via 'nobs_info', and linearly
dependent columns are detected by a QR pivot and reported as 'NA'
in 'coef()' and 'summary()' (the 'stats::glm()' convention),
distinguishing "not identifiable" from "shrunk to zero by the
penalty". Novel factor levels at predict time raise the same error
'stats::predict.glm()' does by default, with
'on_new_levels = "na"' as a production-style opt-in. Accepts
character family strings ('gaussian', 'binomial', 'poisson',
'cox', 'multinomial', 'mgaussian') and any 'glm' family object the
underlying 'glmnet' itself accepts, including 'Gamma' and
fixed-theta negative binomial via 'MASS::negative.binomial'.
Author: Koki Tsuyuzaki [aut, cre]
Maintainer: Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>
Diff between fbrglm versions 0.0.1 dated 2026-06-22 and 0.1.0 dated 2026-07-14
DESCRIPTION | 8 - MD5 | 25 ++--- NAMESPACE | 6 + NEWS.md | 35 +++++++ R/fbrglm.R | 1 R/methods.R | 200 +++++++++++++++++++++++++++++++++++++++-- R/residuals.R |only README.md | 15 ++- inst/doc/fbrglm.Rmd | 2 inst/doc/fbrglm.html | 2 man/reexports.Rd |only tests/testthat/test-basic.R | 33 +++++- tests/testthat/test-broom.R |only tests/testthat/test-families.R | 55 +++++++++++ vignettes/fbrglm.Rmd | 2 15 files changed, 355 insertions(+), 29 deletions(-)
Title: Multivariate Spatio-Temporal Models using Structural Equations
Description: Fits a wide variety of multivariate spatio-temporal models
with simultaneous and lagged interactions among variables (including
vector autoregressive spatio-temporal ('VAST') dynamics)
for areal, continuous, or network spatial domains.
It includes time-variable, space-variable, and space-time-variable
interactions using dynamic structural equation models ('DSEM')
as expressive interface, and the 'mgcv' package to specify splines
via the formula interface. See Thorson et al. (2025)
<doi:10.1111/geb.70035> for more details.
Author: James T. Thorson [aut, cre] ,
Sean C. Anderson [aut]
Maintainer: James T. Thorson <James.Thorson@noaa.gov>
Diff between tinyVAST versions 1.6.1 dated 2026-06-30 and 1.6.2 dated 2026-07-14
tinyVAST-1.6.1/tinyVAST/tests/testthat/Rplots.pdf |only tinyVAST-1.6.2/tinyVAST/DESCRIPTION | 8 tinyVAST-1.6.2/tinyVAST/MD5 | 32 tinyVAST-1.6.2/tinyVAST/NEWS.md | 7 tinyVAST-1.6.2/tinyVAST/build/partial.rdb |binary tinyVAST-1.6.2/tinyVAST/build/vignette.rds |binary tinyVAST-1.6.2/tinyVAST/inst/doc/dsem.html | 61 tinyVAST-1.6.2/tinyVAST/inst/doc/mgcv.html | 6 tinyVAST-1.6.2/tinyVAST/inst/doc/model-description.html | 97 tinyVAST-1.6.2/tinyVAST/inst/doc/multiple_data.html | 8 tinyVAST-1.6.2/tinyVAST/inst/doc/spatial.html | 8 tinyVAST-1.6.2/tinyVAST/inst/doc/spatial_factor_analysis.html | 15 tinyVAST-1.6.2/tinyVAST/src/tinyVAST.cpp | 1078 ---------- tinyVAST-1.6.2/tinyVAST/src/utils.h |only tinyVAST-1.6.2/tinyVAST/tests/testthat/test-basic-fits.R | 48 tinyVAST-1.6.2/tinyVAST/tests/testthat/test-dsem.R | 1 tinyVAST-1.6.2/tinyVAST/tests/testthat/test-index-standardization.R | 6 tinyVAST-1.6.2/tinyVAST/tests/testthat/test-smooths.R | 4 18 files changed, 175 insertions(+), 1204 deletions(-)
Title: Tools for the IUCN Red List of Ecosystems and Species
Description: A toolbox created by members of the International Union for
Conservation of Nature (IUCN) Red List of Ecosystems Committee for
Scientific Standards. Primarily, it is a set of tools suitable for
calculating the metrics required for making assessments of species and
ecosystems against the IUCN Red List of Threatened Species and the
IUCN Red List of Ecosystems categories and criteria. See the IUCN
website for detailed guidelines, the criteria, publications and other
information.
Author: Calvin Lee [aut] ,
Nicholas Murray [aut] ,
Aniko Toth [cre, aut] ,
Jose R. Ferrer-Paris [aut]
Maintainer: Aniko Toth <anikobtoth@gmail.com>
Diff between redlistr versions 1.0.4 dated 2023-10-02 and 2.1.0 dated 2026-07-14
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Title: Analysis of Oceanographic Data
Description: Supports the analysis of Oceanographic data, including 'ADCP'
measurements, measurements made with 'argo' floats, 'CTD' measurements,
sectional data, sea-level time series, coastline and topographic data, etc.
Provides specialized functions for calculating seawater properties such as
potential temperature in either the 'UNESCO' or 'TEOS-10' equation of state.
Produces graphical displays that conform to the conventions of the
Oceanographic literature. This package is discussed extensively by
Kelley (2018) "Oceanographic Analysis with R" <doi:10.1007/978-1-4939-8844-0>.
Author: Dan Kelley [aut, cre] ,
Clark Richards [aut] ,
Chantelle Layton [ctb] coauthor),
British Geological Survey [ctb, cph]
Maintainer: Dan Kelley <Dan.Kelley@Dal.Ca>
Diff between oce versions 1.8-3 dated 2024-08-17 and 1.8-4 dated 2026-07-14
oce-1.8-3/oce/inst/extdata/ctd_aml.csv.gz |only oce-1.8-3/oce/man/ctd_aml.csv.gz.Rd |only oce-1.8-4/oce/DESCRIPTION | 26 oce-1.8-4/oce/MD5 | 628 +++--- oce-1.8-4/oce/NAMESPACE | 78 oce-1.8-4/oce/NEWS.md | 507 +++-- oce-1.8-4/oce/R/AllClass.R | 802 +------- oce-1.8-4/oce/R/AllClassFlags.R |only oce-1.8-4/oce/R/RcppExports.R | 4 oce-1.8-4/oce/R/accessors.R | 47 oce-1.8-4/oce/R/adp.R | 833 +++----- oce-1.8-4/oce/R/adp.nortek.ad2cp.R | 1777 +++++++++++++------ oce-1.8-4/oce/R/adp.nortek.ad2cp.bottom.track.R |only oce-1.8-4/oce/R/adp.rdi.R | 331 ++- oce-1.8-4/oce/R/adp.sontek.R | 34 oce-1.8-4/oce/R/adv.R | 12 oce-1.8-4/oce/R/adv.nortek.R | 2 oce-1.8-4/oce/R/amsr.R | 180 + oce-1.8-4/oce/R/argo.R | 62 oce-1.8-4/oce/R/argo2ctd.R |only oce-1.8-4/oce/R/as_ctd.R |only oce-1.8-4/oce/R/bin.R | 50 oce-1.8-4/oce/R/bodc.R |only oce-1.8-4/oce/R/coastline.R | 96 - oce-1.8-4/oce/R/colors.R | 542 +++++ oce-1.8-4/oce/R/ctd.R | 1093 +---------- oce-1.8-4/oce/R/ctd.aml.R | 211 +- oce-1.8-4/oce/R/ctd.saiv.R | 23 oce-1.8-4/oce/R/ctd.sbe.R | 1295 +++++++------ oce-1.8-4/oce/R/ctd.ssda.R | 2 oce-1.8-4/oce/R/ctd.woce.R | 5 oce-1.8-4/oce/R/echosounder.R | 10 oce-1.8-4/oce/R/extdata.R | 87 oce-1.8-4/oce/R/g1sst.R | 4 oce-1.8-4/oce/R/imagep.R | 27 oce-1.8-4/oce/R/ladp.R | 2 oce-1.8-4/oce/R/landsat.R | 6 oce-1.8-4/oce/R/lobo.R | 2 oce-1.8-4/oce/R/magfield.R |only oce-1.8-4/oce/R/magic.R |only oce-1.8-4/oce/R/map.R | 200 +- oce-1.8-4/oce/R/met.R | 128 - oce-1.8-4/oce/R/misc.R | 451 +--- oce-1.8-4/oce/R/netcdf.R | 477 ++++- oce-1.8-4/oce/R/oce.R | 954 +--------- oce-1.8-4/oce/R/odf.R | 2 oce-1.8-4/oce/R/rename.R |only oce-1.8-4/oce/R/rsk.R | 335 +-- oce-1.8-4/oce/R/rsk2ctd.R |only oce-1.8-4/oce/R/satellite.R | 2 oce-1.8-4/oce/R/sealevel.R | 53 oce-1.8-4/oce/R/sealevel_gc_2026.R |only oce-1.8-4/oce/R/section.R | 201 +- oce-1.8-4/oce/R/spectral.R | 254 +- oce-1.8-4/oce/R/sw.R | 161 + oce-1.8-4/oce/R/tides.R | 324 --- oce-1.8-4/oce/R/units.R | 235 ++ oce-1.8-4/oce/R/webtide.R |only oce-1.8-4/oce/R/windrose.R | 2 oce-1.8-4/oce/R/xbt.R | 396 +++- oce-1.8-4/oce/build/partial.rdb |binary oce-1.8-4/oce/build/vignette.rds |binary oce-1.8-4/oce/data/rsk.rda |binary oce-1.8-4/oce/inst/WORDLIST | 1005 +++++----- oce-1.8-4/oce/inst/doc/A_oce.R | 82 oce-1.8-4/oce/inst/doc/A_oce.Rmd | 60 oce-1.8-4/oce/inst/doc/A_oce.html | 215 -- oce-1.8-4/oce/inst/doc/B_ctd.R | 86 oce-1.8-4/oce/inst/doc/B_ctd.Rmd | 26 oce-1.8-4/oce/inst/doc/B_ctd.html | 82 oce-1.8-4/oce/inst/doc/C_adp.R | 40 oce-1.8-4/oce/inst/doc/C_adp.html | 28 oce-1.8-4/oce/inst/doc/D_map_projections.R | 2 oce-1.8-4/oce/inst/doc/D_map_projections.html | 29 oce-1.8-4/oce/inst/doc/E_flags.R | 42 oce-1.8-4/oce/inst/doc/E_flags.html | 13 oce-1.8-4/oce/inst/doc/F_subclassing.html | 53 oce-1.8-4/oce/inst/doc/G_altering_defaults.R | 2 oce-1.8-4/oce/inst/doc/G_altering_defaults.Rmd | 5 oce-1.8-4/oce/inst/doc/G_altering_defaults.html | 23 oce-1.8-4/oce/inst/doc/H_tides.R |only oce-1.8-4/oce/inst/doc/H_tides.Rmd |only oce-1.8-4/oce/inst/doc/H_tides.html |only oce-1.8-4/oce/inst/extdata/D4902337_219.nc |only oce-1.8-4/oce/inst/extdata/ctd_aml_type1.csv.gz |only oce-1.8-4/oce/inst/extdata/ctd_aml_type3.csv.gz |only oce-1.8-4/oce/inst/extdata/dictionary_codas.csv |only oce-1.8-4/oce/inst/extdata/dictionary_ioos.csv |only oce-1.8-4/oce/inst/extdata/dictionary_sbe.csv |only oce-1.8-4/oce/inst/extdata/xbt2.edf |only oce-1.8-4/oce/inst/extdata/xbt_noaa2 |only oce-1.8-4/oce/man/CTD_BCD2014666_008_1_DN.ODF.gz.Rd | 13 oce-1.8-4/oce/man/D4902337_219.nc.Rd |only oce-1.8-4/oce/man/ODFNames2oceNames.Rd | 7 oce-1.8-4/oce/man/ad2cpCodeToName.Rd | 4 oce-1.8-4/oce/man/ad2cpHeaderValue.Rd | 23 oce-1.8-4/oce/man/adpFlagPastBoundary.Rd | 24 oce-1.8-4/oce/man/adpRdiFileTrim.Rd | 34 oce-1.8-4/oce/man/adp_rdi.000.Rd | 9 oce-1.8-4/oce/man/argo-class.Rd | 2 oce-1.8-4/oce/man/argo.Rd | 4 oce-1.8-4/oce/man/argo2ctd.Rd |only oce-1.8-4/oce/man/argoGrid.Rd | 2 oce-1.8-4/oce/man/argoNames2oceNames.Rd | 9 oce-1.8-4/oce/man/as.argo.Rd | 2 oce-1.8-4/oce/man/as.ctd.Rd | 112 - oce-1.8-4/oce/man/as.sealevel.Rd | 1 oce-1.8-4/oce/man/as.unit.Rd | 35 oce-1.8-4/oce/man/as.xbt.Rd | 4 oce-1.8-4/oce/man/beamToXyzAdpAD2CP.Rd | 2 oce-1.8-4/oce/man/bodcNames2oceNames.Rd |only oce-1.8-4/oce/man/cnvName2oceName.Rd | 174 + oce-1.8-4/oce/man/colormap.Rd | 1 oce-1.8-4/oce/man/colormapGMT.Rd | 1 oce-1.8-4/oce/man/concatenate-adp-method.Rd | 7 oce-1.8-4/oce/man/concatenate-list-method.Rd | 18 oce-1.8-4/oce/man/concatenate-oce-method.Rd | 4 oce-1.8-4/oce/man/concatenate.Rd | 7 oce-1.8-4/oce/man/ctd-class.Rd | 4 oce-1.8-4/oce/man/ctd.Rd | 4 oce-1.8-4/oce/man/ctd.cnv.gz.Rd | 13 oce-1.8-4/oce/man/ctdDecimate.Rd | 6 oce-1.8-4/oce/man/ctdFindProfiles.Rd | 4 oce-1.8-4/oce/man/ctdFindProfilesRBR.Rd | 6 oce-1.8-4/oce/man/ctdRaw.Rd | 4 oce-1.8-4/oce/man/ctdRepair.Rd | 8 oce-1.8-4/oce/man/ctdTrim.Rd | 4 oce-1.8-4/oce/man/ctd_aml_type1.csv.gz.Rd |only oce-1.8-4/oce/man/ctd_aml_type3.csv.gz.Rd |only oce-1.8-4/oce/man/d200321-001.ctd.gz.Rd | 13 oce-1.8-4/oce/man/d201211_0011.cnv.gz.Rd | 13 oce-1.8-4/oce/man/defaultFlags.Rd | 2 oce-1.8-4/oce/man/download.amsr.Rd | 52 oce-1.8-4/oce/man/download.met.Rd | 4 oce-1.8-4/oce/man/handleFlags-argo-method.Rd | 2 oce-1.8-4/oce/man/handleFlags-ctd-method.Rd | 4 oce-1.8-4/oce/man/handleFlags-oce-method.Rd | 2 oce-1.8-4/oce/man/handleFlags-vector-method.Rd | 2 oce-1.8-4/oce/man/handleFlagsInternal.Rd | 2 oce-1.8-4/oce/man/imagep.Rd | 22 oce-1.8-4/oce/man/initialize-ctd-method.Rd | 4 oce-1.8-4/oce/man/initializeFlagScheme-ctd-method.Rd | 4 oce-1.8-4/oce/man/initializeFlagScheme-oce-method.Rd | 2 oce-1.8-4/oce/man/initializeFlagScheme.Rd | 2 oce-1.8-4/oce/man/initializeFlagSchemeInternal.Rd | 2 oce-1.8-4/oce/man/initializeFlags-oce-method.Rd | 2 oce-1.8-4/oce/man/initializeFlags.Rd | 2 oce-1.8-4/oce/man/initializeFlagsInternal.Rd | 2 oce-1.8-4/oce/man/interpBarnes.Rd | 8 oce-1.8-4/oce/man/locationForGsw.Rd | 6 oce-1.8-4/oce/man/lonlat2map.Rd | 9 oce-1.8-4/oce/man/magneticField.Rd | 102 - 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oce-1.8-4/oce/src/echosounder.cpp | 105 - oce-1.8-4/oce/src/fillgap1d.cpp | 2 oce-1.8-4/oce/src/gappy_index.cpp | 63 oce-1.8-4/oce/src/geod.cpp | 199 +- oce-1.8-4/oce/src/get_bit.cpp | 10 oce-1.8-4/oce/src/gradient.cpp | 26 oce-1.8-4/oce/src/igrf14.f |only oce-1.8-4/oce/src/interp_barnes.cpp | 178 - oce-1.8-4/oce/src/ldc_ad2cp_in_file.cpp | 444 ++-- oce-1.8-4/oce/src/ldc_rdi_in_file.cpp | 18 oce-1.8-4/oce/src/ldc_rdi_in_file_new.cpp | 18 oce-1.8-4/oce/src/locate_byte_sequences.cpp | 2 oce-1.8-4/oce/src/magdec.f | 8 oce-1.8-4/oce/src/map.cpp | 28 oce-1.8-4/oce/src/oce_approx.cpp | 213 +- oce-1.8-4/oce/src/oce_convolve.cpp | 93 oce-1.8-4/oce/src/run.cpp | 24 oce-1.8-4/oce/src/sontek_adp.cpp | 95 - oce-1.8-4/oce/src/sontek_adv.cpp | 6 oce-1.8-4/oce/src/trap.cpp | 24 oce-1.8-4/oce/src/trim.cpp | 6 oce-1.8-4/oce/tests/testthat/test_accessors.R | 11 oce-1.8-4/oce/tests/testthat/test_ad2cp_1.R |only oce-1.8-4/oce/tests/testthat/test_ad2cp_2.R | 34 oce-1.8-4/oce/tests/testthat/test_ad2cp_3.R | 16 oce-1.8-4/oce/tests/testthat/test_ad2cp_4.R | 79 oce-1.8-4/oce/tests/testthat/test_adp.R | 13 oce-1.8-4/oce/tests/testthat/test_amsr.R | 10 oce-1.8-4/oce/tests/testthat/test_argo.R | 34 oce-1.8-4/oce/tests/testthat/test_ctd.R | 101 - 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Title: Nested Cross-Validation with 'glmnet' and 'caret'
Description: Implements nested k*l-fold cross-validation for lasso and elastic-net regularised linear models via the 'glmnet' package and other machine learning models via the 'caret' package <doi:10.1093/bioadv/vbad048>. Cross-validation of 'glmnet' alpha mixing parameter and embedded fast filter functions for feature selection are provided. Described as double cross-validation by Stone (1977) <doi:10.1111/j.2517-6161.1977.tb01603.x>. Also implemented is a method using outer CV to measure unbiased model performance metrics when fitting Bayesian linear and logistic regression shrinkage models using the horseshoe prior over parameters to encourage a sparse model as described by Piironen & Vehtari (2017) <doi:10.1214/17-EJS1337SI>.
Author: Myles Lewis [aut, cre] ,
Athina Spiliopoulou [aut] ,
Cankut Cubuk [ctb] ,
David Rios Santini [ctb],
Katriona Goldmann [ctb] ,
Ryan C. Thompson [ctb]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
This is a re-admission after prior archival of version 0.8.2 dated 2026-04-10
Diff between nestedcv versions 0.8.2 dated 2026-04-10 and 0.9.0 dated 2026-07-14
DESCRIPTION | 17 ++- MD5 | 55 +++++------ NAMESPACE | 2 NEWS.md | 24 ++++ R/cva.glmnet.R | 18 ++- R/nestcv.train.R | 9 - R/nestcv_SuperLearner.R | 6 - R/nestedcv.R | 11 ++ R/outercv.R | 6 - R/plots.R | 3 R/shap.R | 216 ++++++++++++++++++++++++++++++++------------ R/utils.R | 8 + R/varImp.R | 17 +-- build/vignette.rds |binary inst/doc/nestedcv.html | 92 +++++++++--------- inst/doc/nestedcv_shap.R | 46 +++++---- inst/doc/nestedcv_shap.Rmd | 99 ++++++++++++-------- inst/doc/nestedcv_shap.html | 134 +++++++++++++++------------ man/coef.nestcv.glmnet.Rd | 2 man/glmnet_coefs.Rd | 4 man/lm_filter.Rd | 4 man/nestcv.explain.Rd |only man/plot_shap_bar.Rd | 3 man/plot_shap_beeswarm.Rd | 3 man/pls_filter.Rd | 2 man/predSummary.Rd | 2 man/pred_nestcv_glmnet.Rd | 65 ++++++------- man/ttest_filter.Rd | 6 - vignettes/nestedcv_shap.Rmd | 99 ++++++++++++-------- 29 files changed, 593 insertions(+), 360 deletions(-)
Title: Functional Multivariable Mendelian Randomization
Description: Implements Multivariable Functional Mendelian Randomization (MV-FMR) to estimate time-varying causal effects of multiple longitudinal exposures on health outcomes. Extends univariable functional Mendelian Randomisation (MR) (Tian et al., 2024 <doi:10.1002/sim.10222>) to the multivariable setting, enabling joint estimation of multiple time-varying exposures with pleiotropy and mediation scenarios. Key features include: (1) data-driven cross-validation for basis component selection, (2) handling of mediation pathways between exposures, (3) support for both continuous and binary outcomes using Generalized Method of Moments (GMM) and control function approaches, (4) one-sample and two-sample MR designs, (5) bootstrap inference and instrument diagnostics including Q-statistics for overidentification testing. Methods are described in Fontana et al. (2025) <doi:10.48550/arXiv.2512.19064>.
Author: Nicole Fontana [aut, cre],
Francesca Ieva [aut, ths],
Piercesare Secchi [aut, ths]
Maintainer: Nicole Fontana <nicole.fontana@polimi.it>
Diff between mvfmr versions 0.1.0 dated 2026-02-09 and 0.2.0 dated 2026-07-14
DESCRIPTION | 9 MD5 | 77 - R/all_functions.R | 86 - R/estimation_automatic.R | 1798 ++++++++++---------------- R/estimation_beta.R | 25 R/fmvmr_main.R | 595 ++++---- R/simulation.R | 615 ++++---- R/utilities.R | 48 README.md | 483 +++--- demo/tests_manuscript.R | 290 +--- inst/doc/multivariable-fmr.R | 156 +- inst/doc/multivariable-fmr.Rmd | 181 +- inst/doc/multivariable-fmr.html | 493 +++---- inst/doc/univariable-fmr.R | 71 - inst/doc/univariable-fmr.Rmd | 83 - inst/doc/univariable-fmr.html | 267 +-- inst/examples/test_MV-FMR.R | 163 +- inst/examples/test_U-FMR.R | 133 - man/AUTOMATIC_Multi_FMVMR_twosample_simple.Rd | 23 man/AUTOMATIC_Multi_MVFMR.Rd | 37 man/IS.Rd | 9 man/Separate_Multi_FMVMR_twosample_simple.Rd | 44 man/Separate_Multi_MVFMR.Rd | 42 man/block_idx.Rd |only man/cf_logit.Rd | 10 man/compute_offsets.Rd |only man/fmvmr_separate_twosample.Rd | 59 man/fmvmr_twosample.Rd | 37 man/getX_multi_exposure.Rd | 15 man/getX_multi_exposure_mediation.Rd | 26 man/getY_multi_exposure.Rd | 20 man/gmm_lm_onesample.Rd | 9 man/gmm_twosample_simple.Rd | 9 man/mvfmr.Rd | 42 man/mvfmr_separate.Rd | 48 man/recycle_arg.Rd |only tests |only vignettes/multivariable-fmr.Rmd | 181 +- vignettes/univariable-fmr.Rmd | 83 - 39 files changed, 3072 insertions(+), 3195 deletions(-)
Title: Hierarchical Neyman-Pearson Classification for Ordered Classes
Description: The Hierarchical Neyman-Pearson (H-NP) classification framework
extends the Neyman-Pearson classification paradigm to multi-class settings
where classes have a natural priority ordering. This is particularly useful
for classification in unbalanced dataset, for example, disease severity
classification, where under-classification errors (misclassifying patients
into less severe categories) are more consequential than other
misclassifications. The package implements H-NP umbrella algorithms that
controls under-classification errors under user specified control levels
with high probability. It supports the creation of H-NP classifiers using
scoring functions based on built-in classification methods (including
logistic regression, support vector machines, and random forests), as well
as user-trained scoring functions. The package exports `base_function()`
to train these built-in base learners directly for use in the H-NP
pipeline.
Author: Che Shen [aut, cre] ,
Lujia Yang [aut] ,
Lijia Wang [aut] ,
Shunan Yao [aut]
Maintainer: Che Shen <chshen3-c@my.cityu.edu.hk>
Diff between HNPclassifier versions 0.2.0 dated 2026-06-27 and 0.2.1 dated 2026-07-14
DESCRIPTION | 10 ++++++---- MD5 | 9 +++++---- NAMESPACE | 1 + NEWS.md | 48 ++++++------------------------------------------ R/hnp_package.r | 23 +++++++++++++++++++++++ man/base_function.Rd |only 6 files changed, 41 insertions(+), 50 deletions(-)
Title: Ultrahigh-Resolution Mass Spectrometry Data Evaluation for
Complex Organic Matter
Description: Provides tools for assigning molecular formulas from exact masses
obtained by ultrahigh-resolution mass spectrometry. The methodology follows
the workflow described in Leefmann et al. (2019) <doi:10.1002/rcm.8315>.
The package supports the inspection, filtering and visualization of
molecular formula data and includes utilities for calculating common
molecular parameters (e.g., double bond equivalents, DBE). A graphical
user interface is available via the 'shiny'-based 'ume' application.
Author: Boris Koch [aut, cre] ,
Stephan Frickenhaus [ctb] ,
Shuxian Gao [ctb] ,
Oliver Lechtenfeld [ctb] ,
Tim Leefmann [ctb] ,
Fabian Moye [ctb]
Maintainer: Boris Koch <boris.koch@awi.de>
Diff between ume versions 1.6.1 dated 2026-05-09 and 1.7.1 dated 2026-07-14
ume-1.6.1/ume/R/calc_number_assignments.R |only ume-1.6.1/ume/data/nice_labels_dt.rda |only ume-1.6.1/ume/data/tab_ume_labels.rda |only ume-1.6.1/ume/man/nice_labels_dt.Rd |only ume-1.6.1/ume/man/tab_ume_labels.Rd |only ume-1.6.1/ume/tests/testthat/test-calc_number_assignments.R |only ume-1.7.1/ume/DESCRIPTION | 22 ume-1.7.1/ume/LICENSE | 4 ume-1.7.1/ume/MD5 | 311 ++-- ume-1.7.1/ume/NAMESPACE | 8 ume-1.7.1/ume/NEWS.md | 649 +++++----- ume-1.7.1/ume/R/add_known_mf.R | 271 +++- ume-1.7.1/ume/R/as_mfd.R |only ume-1.7.1/ume/R/as_peaklist.R | 97 + ume-1.7.1/ume/R/as_ume_matrix.R |only ume-1.7.1/ume/R/assign_formulas.R | 13 ume-1.7.1/ume/R/calc_data_summary.R | 21 ume-1.7.1/ume/R/calc_isotope_pattern.R | 63 ume-1.7.1/ume/R/calc_logratio.R |only ume-1.7.1/ume/R/calc_neutral_mass.R | 1 ume-1.7.1/ume/R/calc_norm_int.R | 2 ume-1.7.1/ume/R/calc_number_assignment.R |only ume-1.7.1/ume/R/calc_number_occurrence.R | 3 ume-1.7.1/ume/R/calc_recalibrate_ms.R | 11 ume-1.7.1/ume/R/check_objects.R | 2 ume-1.7.1/ume/R/create_custom_formula_library.R | 4 ume-1.7.1/ume/R/create_time_flattened_mfd.R |only ume-1.7.1/ume/R/create_ume_formula_library.R | 2 ume-1.7.1/ume/R/data.R | 128 + ume-1.7.1/ume/R/download_library.R | 270 +++- ume-1.7.1/ume/R/eval_isotopes.R | 4 ume-1.7.1/ume/R/export_ume_results.R | 8 ume-1.7.1/ume/R/filter.R | 2 ume-1.7.1/ume/R/filter_multi_assignments.R |only ume-1.7.1/ume/R/find_kegg_pathways_by_formula.R |only ume-1.7.1/ume/R/get_isotope_info.R | 2 ume-1.7.1/ume/R/global.R | 20 ume-1.7.1/ume/R/main_docu.R | 4 ume-1.7.1/ume/R/tools.R | 195 ++- ume-1.7.1/ume/R/ume_utilities.R | 12 ume-1.7.1/ume/R/uplot_cluster.R | 227 ++- ume-1.7.1/ume/R/uplot_dbe_minus_o_freq.R | 5 ume-1.7.1/ume/R/uplot_diff_ms.R | 6 ume-1.7.1/ume/R/uplot_hc_vs_m.R | 123 - ume-1.7.1/ume/R/uplot_ma_vs_mz.R | 124 - ume-1.7.1/ume/R/uplot_ms.R | 8 ume-1.7.1/ume/R/uplot_pca.R | 126 + ume-1.7.1/ume/R/uplot_ratios.R | 48 ume-1.7.1/ume/R/uplot_reproducibility.R | 11 ume-1.7.1/ume/R/uplot_ri_vs_sample.R | 145 +- ume-1.7.1/ume/R/uplot_vk.R | 25 ume-1.7.1/ume/R/uplots_layout_internal.R | 135 +- ume-1.7.1/ume/R/ustats_outlier.R | 2 ume-1.7.1/ume/R/zero_filling.R |only ume-1.7.1/ume/README.md | 79 - ume-1.7.1/ume/data/known_mf.rda |binary ume-1.7.1/ume/data/ume_name_dictionary.rda |only ume-1.7.1/ume/inst/doc/ume.R | 36 ume-1.7.1/ume/inst/doc/ume.Rmd | 70 - ume-1.7.1/ume/inst/doc/ume.html | 354 ++--- ume-1.7.1/ume/man/add_known_mf.Rd | 151 +- ume-1.7.1/ume/man/add_missing_element_columns.Rd | 4 ume-1.7.1/ume/man/as_mfd.Rd |only ume-1.7.1/ume/man/as_peaklist.Rd | 7 ume-1.7.1/ume/man/as_ume_matrix.Rd |only ume-1.7.1/ume/man/assign_formulas.Rd | 16 ume-1.7.1/ume/man/build_isotope_map.Rd | 14 ume-1.7.1/ume/man/calc_data_summary.Rd | 45 ume-1.7.1/ume/man/calc_dbe.Rd | 24 ume-1.7.1/ume/man/calc_eval_params.Rd | 34 ume-1.7.1/ume/man/calc_exact_mass.Rd | 24 ume-1.7.1/ume/man/calc_ideg.Rd | 24 ume-1.7.1/ume/man/calc_isotope_pattern.Rd | 229 ++- ume-1.7.1/ume/man/calc_logratio.Rd |only ume-1.7.1/ume/man/calc_ma.Rd | 24 ume-1.7.1/ume/man/calc_neutral_mass.Rd | 27 ume-1.7.1/ume/man/calc_nm.Rd | 24 ume-1.7.1/ume/man/calc_norm_int.Rd | 24 ume-1.7.1/ume/man/calc_number_assignment.Rd | 26 ume-1.7.1/ume/man/calc_number_occurrence.Rd | 24 ume-1.7.1/ume/man/calc_recalibrate_ms.Rd | 29 ume-1.7.1/ume/man/calc_time_flattened_mfd.Rd |only ume-1.7.1/ume/man/check_formula_library.Rd | 17 ume-1.7.1/ume/man/check_mfd.Rd | 7 ume-1.7.1/ume/man/check_neutral_mf.Rd | 6 ume-1.7.1/ume/man/check_table_schema.Rd | 44 ume-1.7.1/ume/man/classify_files.Rd | 162 +- ume-1.7.1/ume/man/convert_data_table_to_molecular_formulas.Rd | 6 ume-1.7.1/ume/man/convert_molecular_formula_to_data_table.Rd | 6 ume-1.7.1/ume/man/create_custom_formula_library.Rd | 14 ume-1.7.1/ume/man/create_isotope_expanded_table.Rd | 8 ume-1.7.1/ume/man/dot-as_peaklist_from_numeric.Rd | 6 ume-1.7.1/ume/man/dot-extract_library_version.Rd | 36 ume-1.7.1/ume/man/dot-f_label.Rd | 96 - 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ume-1.7.1/ume/man/main_docu.Rd | 4 ume-1.7.1/ume/man/masses.Rd | 9 ume-1.7.1/ume/man/mf_data_demo.Rd | 18 ume-1.7.1/ume/man/order_columns.Rd | 4 ume-1.7.1/ume/man/peaklist_demo.Rd | 5 ume-1.7.1/ume/man/read_xml_peaklist.Rd | 14 ume-1.7.1/ume/man/remove_blanks.Rd | 14 ume-1.7.1/ume/man/remove_id_columns.Rd | 4 ume-1.7.1/ume/man/remove_unknown_columns.Rd | 4 ume-1.7.1/ume/man/revert_column_names.Rd | 36 ume-1.7.1/ume/man/search_mf_targets.Rd | 14 ume-1.7.1/ume/man/subset_known_mf.Rd | 14 ume-1.7.1/ume/man/ume_assign_formulas.Rd | 60 ume-1.7.1/ume/man/ume_filter_formulas.Rd | 20 ume-1.7.1/ume/man/ume_logo_raster.Rd | 38 ume-1.7.1/ume/man/ume_name_dictionary.Rd |only ume-1.7.1/ume/man/uplot_cluster.Rd | 119 + ume-1.7.1/ume/man/uplot_cvm.Rd | 48 ume-1.7.1/ume/man/uplot_dbe_minus_o_freq.Rd | 48 ume-1.7.1/ume/man/uplot_dbe_vs_c.Rd | 48 ume-1.7.1/ume/man/uplot_dbe_vs_ma.Rd | 48 ume-1.7.1/ume/man/uplot_dbe_vs_o.Rd | 48 ume-1.7.1/ume/man/uplot_freq_ma.Rd | 48 ume-1.7.1/ume/man/uplot_freq_vs_ppm.Rd | 42 ume-1.7.1/ume/man/uplot_hc_vs_m.Rd | 111 - 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ume-1.7.1/ume/vignettes/vignette_ume.pdf |binary 170 files changed, 4455 insertions(+), 2921 deletions(-)