Title: Efficiently Retrieve and Process Satellite Imagery
Description: Downloads spatial data from spatiotemporal asset catalogs
('STAC'), computes standard spectral indices from the Awesome Spectral
Indices project (Montero et al. (2023) <doi:10.1038/s41597-023-02096-0>)
against raster data, and glues the outputs together into predictor bricks.
Methods focus on interoperability with the broader spatial ecosystem;
function arguments and outputs use classes from 'sf' and 'terra', and data
downloading functions support complex 'CQL2' queries using 'rstac'.
Author: Michael Mahoney [aut, cre] ,
Felipe Carvalho [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/636>),
Michael Sumner [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/636>),
Permian Global [cph, f [...truncated...]
Maintainer: Michael Mahoney <mike.mahoney.218@gmail.com>
Diff between rsi versions 0.3.1 dated 2024-10-22 and 0.3.2 dated 2025-01-21
DESCRIPTION | 6 MD5 | 58 ++--- NEWS.md | 9 R/calculate_indices.R | 23 +- R/download.R | 30 ++ R/get_stac_data.R | 86 ++++---- R/mask_functions.R | 1 R/misc.R | 8 R/query_and_sign.R | 6 R/stack_rasters.R | 2 README.md | 40 +-- build/partial.rdb |binary build/vignette.rds |binary data/alos_palsar_band_mapping.rda |binary data/dem_band_mapping.rda |binary data/landsat_band_mapping.rda |binary data/sentinel1_band_mapping.rda |binary data/sentinel2_band_mapping.rda |binary inst/doc/rsi.R | 96 ++++----- inst/doc/rsi.html | 330 +++++++++++++++++-------------- man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/get_stac_data.Rd | 6 man/rsi_download_rasters.Rd | 1 tests/testthat/test-get_stac_data.R | 13 + tests/testthat/test-mask_functions.R | 4 tests/testthat/test-misc.R | 2 30 files changed, 413 insertions(+), 308 deletions(-)
Title: Linear Networks Functionality of the 'spatstat' Family
Description: Defines types of spatial data on a linear network
and provides functionality for geometrical operations,
data analysis and modelling of data on a linear network,
in the 'spatstat' family of packages.
Contains definitions and support for linear networks, including creation of networks, geometrical measurements, topological connectivity, geometrical operations such as inserting and deleting vertices, intersecting a network with another object, and interactive editing of networks.
Data types defined on a network include point patterns, pixel images, functions, and tessellations.
Exploratory methods include kernel estimation of intensity on a network, K-functions and pair correlation functions on a network, simulation envelopes, nearest neighbour distance and empty space distance, relative risk estimation with cross-validated bandwidth selection. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Mont [...truncated...]
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Greg McSwiggan [aut, cph],
Tilman Davies [ctb, cph],
Mehdi Moradi [ctb, cph],
Suman Rakshit [ctb, cph],
Ottmar Cronie [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.linnet versions 3.2-3 dated 2024-11-19 and 3.2-5 dated 2025-01-21
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- NEWS | 23 +++++++++++++++++++++++ inst/doc/packagesizes.txt | 3 +++ inst/info/packagesizes.txt | 3 +++ man/distfun.lpp.Rd | 12 ++++++++++++ man/distmap.lpp.Rd | 11 +++++++++++ man/nndist.lpp.Rd | 11 +++++++++++ man/pairdist.lpp.Rd | 11 +++++++++++ tests/testsL.R | 16 +++++++++++++--- 10 files changed, 102 insertions(+), 18 deletions(-)
More information about spatstat.linnet at CRAN
Permanent link
Title: Dedicated 'ggplot2' Methods for 'fixest' Objects
Description: Provides 'ggplot2' equivalents of fixest::coefplot() and fixest::iplot(),
for producing nice coefficient plots and interaction plots. Enables some
additional functionality and convenience features, including grouped
multi-'fixest' object faceting and programmatic updates to existing plots
(e.g., themes and aesthetics).
Author: Grant McDermott [aut, cre] ,
Laurent Berge [ctb],
Teun van den Brand [ctb]
Maintainer: Grant McDermott <gmcd@amazon.com>
Diff between ggfixest versions 0.1.0 dated 2023-12-14 and 0.2.0 dated 2025-01-21
DESCRIPTION | 49 - MD5 | 110 +-- NEWS.md | 25 R/aggr_es.R | 12 R/ggcoefplot.R | 2 R/ggiplot.R | 47 + README.md | 13 build/vignette.rds |binary inst/doc/ggiplot.R | 2 inst/doc/ggiplot.html | 285 ++++----- inst/tinytest/_tinysnapshot/ggcoefplot_did.svg | 106 +-- inst/tinytest/_tinysnapshot/ggcoefplot_did_iid.svg | 106 +-- inst/tinytest/_tinysnapshot/ggcoefplot_group_names_prefix.svg | 86 +- inst/tinytest/_tinysnapshot/ggcoefplot_group_nonames.svg | 86 +- inst/tinytest/_tinysnapshot/ggcoefplot_group_none.svg | 2 inst/tinytest/_tinysnapshot/ggcoefplot_groupnames.svg | 86 +- inst/tinytest/_tinysnapshot/ggcoefplot_interactions.svg | 78 +- inst/tinytest/_tinysnapshot/ggcoefplot_interactions_multici.svg | 118 +-- inst/tinytest/_tinysnapshot/ggcoefplot_multi.svg | 100 +-- inst/tinytest/_tinysnapshot/ggcoefplot_multi_facet.svg | 132 ++-- inst/tinytest/_tinysnapshot/ggcoefplot_simple.svg | 64 +- inst/tinytest/_tinysnapshot/ggiplot_list.svg | 2 inst/tinytest/_tinysnapshot/ggiplot_multi_complex.svg | 316 +++++----- inst/tinytest/_tinysnapshot/ggiplot_multi_complex_kitchen.svg | 2 inst/tinytest/_tinysnapshot/ggiplot_multi_complex_kitchen_iid.svg | 2 inst/tinytest/_tinysnapshot/ggiplot_multi_complex_mci.svg | 2 inst/tinytest/_tinysnapshot/ggiplot_multi_csw.svg | 2 inst/tinytest/_tinysnapshot/ggiplot_multi_csw_facet.svg | 2 inst/tinytest/_tinysnapshot/ggiplot_multi_facet.svg | 2 inst/tinytest/_tinysnapshot/ggiplot_multi_facet_ribbon.svg | 2 inst/tinytest/_tinysnapshot/ggiplot_multi_lhs.svg | 2 inst/tinytest/_tinysnapshot/ggiplot_multi_lhs_csw.svg | 2 inst/tinytest/_tinysnapshot/ggiplot_multi_lhs_csw_facet.svg | 2 inst/tinytest/_tinysnapshot/ggiplot_multi_lhs_facet.svg | 2 inst/tinytest/_tinysnapshot/ggiplot_multi_lhs_facet_ribbon.svg | 2 inst/tinytest/_tinysnapshot/ggiplot_multi_single.svg | 2 inst/tinytest/_tinysnapshot/ggiplot_multi_single_kitchen.svg | 2 inst/tinytest/_tinysnapshot/ggiplot_multi_single_kitchen_ribbon.svg | 2 inst/tinytest/_tinysnapshot/ggiplot_multi_single_ribbon.svg | 108 +-- inst/tinytest/_tinysnapshot/ggiplot_multi_single_unnamed.svg | 2 inst/tinytest/_tinysnapshot/ggiplot_multi_sw_pt_join1.svg |only inst/tinytest/_tinysnapshot/ggiplot_multi_sw_pt_join2.svg |only inst/tinytest/_tinysnapshot/ggiplot_simple.svg | 2 inst/tinytest/_tinysnapshot/ggiplot_simple_errorbar.svg | 2 inst/tinytest/_tinysnapshot/ggiplot_simple_mci.svg | 2 inst/tinytest/_tinysnapshot/ggiplot_simple_mci_ribbon.svg | 2 inst/tinytest/_tinysnapshot/ggiplot_simple_ribbon.svg | 2 inst/tinytest/_tinysnapshot/ggiplot_stagg_mci.svg | 2 inst/tinytest/_tinysnapshot/ggiplot_stagg_mci_ribbon.svg | 2 inst/tinytest/test_ggiplot.R | 14 man/aggr_es.Rd | 2 man/figures/README-coefplot1-1.png |binary man/figures/README-coefplot2-1.png |binary man/figures/README-es1-1.png |binary man/figures/README-es2-1.png |binary man/figures/README-es3-1.png |binary man/ggcoefplot.Rd | 1 57 files changed, 1030 insertions(+), 968 deletions(-)
Title: Date-Time Types and Tools
Description: Provides a comprehensive library for date-time manipulations
using a new family of orthogonal date-time classes (durations, time
points, zoned-times, and calendars) that partition responsibilities so
that the complexities of time zones are only considered when they are
really needed. Capabilities include: date-time parsing, formatting,
arithmetic, extraction and updating of components, and rounding.
Author: Davis Vaughan [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Davis Vaughan <davis@posit.co>
Diff between clock versions 0.7.1 dated 2024-07-18 and 0.7.2 dated 2025-01-21
DESCRIPTION | 8 MD5 | 126 +-- NAMESPACE | 7 NEWS.md | 11 R/arithmetic.R | 2 R/calendar.R | 210 ++++- R/check.R | 114 ++- R/clock-codes.R | 2 R/clock-labels.R | 19 R/clock-locale.R | 10 R/cpp11.R | 507 +++++++++++-- R/date.R | 274 ++++--- R/duration.R | 182 +++- R/gregorian-year-day.R | 211 ++++- R/gregorian-year-month-day.R | 336 ++++++--- R/gregorian-year-month-weekday.R | 289 +++++-- R/import-standalone-obj-type.R | 107 +- R/import-standalone-types-check.R | 290 ++++--- R/iso-year-week-day.R | 319 ++++++-- R/limits.R | 12 R/naive-time.R | 120 ++- R/posixt.R | 661 +++++++++++++----- R/precision.R | 19 R/quarterly-year-quarter-day.R | 261 +++++-- R/strict.R | 10 R/sys-time.R | 78 +- R/time-point.R | 177 +++- R/utils.R | 106 +- R/week-year-week-day.R | 256 +++++- R/weekday.R | 64 + R/zoned-time.R | 102 +- R/zzz.R | 54 + README.md | 7 build/vignette.rds |binary inst/doc/clock.R | 12 inst/doc/clock.html | 4 inst/doc/faq.R | 28 inst/doc/faq.html | 4 inst/doc/recipes.R | 16 inst/doc/recipes.html | 4 src/quarterly-shim.h | 33 src/week-shim.h | 33 tests/testthat/_snaps/date.md | 5 tests/testthat/_snaps/gregorian-year-day.md | 10 tests/testthat/_snaps/gregorian-year-month-day.md | 10 tests/testthat/_snaps/gregorian-year-month-weekday.md | 10 tests/testthat/_snaps/iso-year-week-day.md | 10 tests/testthat/_snaps/quarterly-year-quarter-day.md | 10 tests/testthat/_snaps/week-year-week-day.md | 10 tests/testthat/test-calendar.R | 51 + tests/testthat/test-date.R | 57 + tests/testthat/test-duration.R | 213 ++++- tests/testthat/test-gregorian-year-day.R | 208 ++++- tests/testthat/test-gregorian-year-month-day.R | 350 ++++++++- tests/testthat/test-gregorian-year-month-weekday.R | 402 +++++++++- tests/testthat/test-iso-year-week-day.R | 310 +++++++- tests/testthat/test-naive-time.R | 148 +++- tests/testthat/test-posixt.R | 456 ++++++++++-- tests/testthat/test-quarterly-year-quarter-day.R | 339 +++++++-- tests/testthat/test-sys-time.R | 24 tests/testthat/test-time-point.R | 145 +++ tests/testthat/test-week-year-week-day.R | 333 +++++++-- tests/testthat/test-weekday.R | 2 tests/testthat/test-zoned-time.R | 132 +++ 64 files changed, 6404 insertions(+), 1916 deletions(-)
Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rücker <DOI:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015):
- common effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- three-level meta-analysis model;
- generalised linear mixed model;
- logistic regression with penalised likelihood for rare events;
- Hartung-Knapp method for random effects model;
- Kenward-Roger method for random effects model;
- prediction interval;
- statistical tests for funnel plot asymmetry;
- trim-and-fill method to evaluate bias in meta-analysis;
- meta-regression;
- cumulative meta-analysis and leave-one-out meta-analysis;
- import data from 'RevMan 5';
- produce forest plot summarising several (subgroup) meta-analyses.
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer <guido.schwarzer@uniklinik-freiburg.de>
Diff between meta versions 8.0-1 dated 2024-10-31 and 8.0-2 dated 2025-01-21
DESCRIPTION | 13 +- MD5 | 122 ++++++++++++------------ NAMESPACE | 1 NEWS.md | 46 +++++++-- R/as.data.frame.meta.R | 2 R/barplot.rob.R | 5 R/blup.meta.R | 9 + R/bracket.pairwise.R |only R/catmeth.R | 9 - R/estimates.R | 21 ++-- R/forest.R | 16 ++- R/gm.R | 3 R/longarm.R | 16 +-- R/meta-aux.R | 44 ++++---- R/meta-package.R | 13 +- R/metabias.R | 141 +++++++++++++++------------- R/metabias.rm5.R | 2 R/metabin.R | 53 +++------- R/metagen.R | 3 R/metainc.R | 17 ++- R/metaprop.R | 25 ++-- R/metarate.R | 24 ++-- R/metareg.R | 2 R/nnt.R | 2 R/pairwise.R | 208 +++++++++++++++++++++-------------------- R/print.meta.R | 8 - R/print.rm5.R | 2 R/print.summary.meta.R | 2 R/settings.meta-internal.R | 2 R/settings.meta.R | 6 - R/subset.longarm.R | 7 - R/subset.pairwise.R | 26 ++--- R/summary.rm5.R | 2 R/traffic_light.R | 7 - R/trimfill.rm5.R | 2 R/update.meta.R | 2 build/vignette.rds |binary inst/doc/meta-tutorial.R | 128 ++++++++++++------------- inst/doc/meta-tutorial.pdf |binary inst/doc/meta-workflow.pdf |binary man/as.data.frame.meta.Rd | 2 man/barplot.rob.Rd | 5 man/blup.meta.Rd | 8 + man/estimates.Rd | 21 ++-- man/forest.meta.Rd | 4 man/longarm.Rd | 3 man/meta-package.Rd | 13 +- man/metabias.Rd | 4 man/metabias.rm5.Rd | 2 man/metabin.Rd | 35 +----- man/metainc.Rd | 2 man/metaprop.Rd | 5 man/metarate.Rd | 6 - man/nnt.Rd | 2 man/pairwise.Rd | 226 +++++++++++++++++++++++---------------------- man/print.meta.Rd | 6 - man/print.rm5.Rd | 2 man/settings.meta.Rd | 6 - man/sub-.pairwise.Rd |only man/subset.pairwise.Rd | 13 -- man/summary.rm5.Rd | 2 man/traffic_light.Rd | 5 man/trimfill.rm5.Rd | 2 63 files changed, 717 insertions(+), 648 deletions(-)
Title: An Interface for Content-Based Identifiers
Description: An interface for creating, registering, and resolving content-based
identifiers for data management. Content-based identifiers rely on
the 'cryptographic' hashes to refer to the files they identify, thus,
anyone possessing the file can compute the identifier using a
well-known standard algorithm, such as 'SHA256'. By registering
a URL at which the content is accessible to a public archive (such as
Hash Archive) or depositing data in a scientific repository such 'Zenodo',
'DataONE' or 'SoftwareHeritage', the content identifier can serve
many functions typically associated with A Digital Object Identifier
('DOI'). Unlike location-based identifiers like 'DOIs', content-based
identifiers permit the same content to be registered in many locations.
Author: Carl Boettiger [aut, cre] ,
Jorrit Poelen [aut] ,
NSF OAC 1839201 [fnd]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between contentid versions 0.0.18 dated 2023-10-23 and 0.0.19 dated 2025-01-21
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/format_identifiers.R | 27 ++++++++++++++++++++++++--- R/zenodo_registry.R | 22 ++++++++++++++-------- build/vignette.rds |binary inst/doc/intro.html | 3 ++- 7 files changed, 54 insertions(+), 21 deletions(-)
Title: Multidimensional Penalized Splines for (Excess) Hazard Models,
Relative Mortality Ratio Models and Marginal Intensity Models
Description: Fits (excess) hazard, relative mortality ratio or marginal intensity models with multidimensional penalized splines allowing for
time-dependent effects, non-linear effects and interactions between several continuous covariates. In survival and net survival analysis, in addition to modelling the effect of time (via the baseline hazard), one has often to deal with several continuous covariates and model their functional forms, their time-dependent effects, and their interactions. Model specification becomes therefore a complex problem and penalized regression splines represent an appealing solution to that problem as splines offer the required flexibility while penalization limits overfitting issues. Current implementations of penalized survival models can be slow or unstable and sometimes lack some key features like taking into account expected mortality to provide net survival and excess hazard estimates. In contrast, survPen provides an automated, fast, and stable implementation (than [...truncated...]
Author: Mathieu Fauvernier [aut, cre],
Laurent Roche [aut],
Laurent Remontet [aut],
Zoe Uhry [ctb],
Nadine Bossard [ctb],
Elsa Coz [ctb]
Maintainer: Mathieu Fauvernier <mathieu.fauvernier@gmail.com>
Diff between survPen versions 2.0.0 dated 2024-12-02 and 2.0.1 dated 2025-01-21
survPen-2.0.0/survPen/R/survPenV2_00.r |only survPen-2.0.1/survPen/DESCRIPTION | 6 survPen-2.0.1/survPen/MD5 | 74 +++++----- survPen-2.0.1/survPen/NEWS | 7 survPen-2.0.1/survPen/R/survPenV2_01.r |only survPen-2.0.1/survPen/inst/doc/survival_analysis_with_survPen.html | 4 survPen-2.0.1/survPen/man/HeartFailure.Rd | 2 survPen-2.0.1/survPen/man/NR.beta.Rd | 2 survPen-2.0.1/survPen/man/NR.rho.Rd | 2 survPen-2.0.1/survPen/man/constraint.Rd | 2 survPen-2.0.1/survPen/man/cor.var.Rd | 2 survPen-2.0.1/survPen/man/crs.FP.Rd | 2 survPen-2.0.1/survPen/man/crs.Rd | 2 survPen-2.0.1/survPen/man/datCancer.Rd | 2 survPen-2.0.1/survPen/man/design.matrix.Rd | 2 survPen-2.0.1/survPen/man/expected.table.Rd | 2 survPen-2.0.1/survPen/man/instr.Rd | 2 survPen-2.0.1/survPen/man/inv.repam.Rd | 2 survPen-2.0.1/survPen/man/list.wicss.Rd | 2 survPen-2.0.1/survPen/man/model.cons.Rd | 2 survPen-2.0.1/survPen/man/predSNS.Rd | 2 survPen-2.0.1/survPen/man/predict.survPen.Rd | 2 survPen-2.0.1/survPen/man/print.summary.survPen.Rd | 2 survPen-2.0.1/survPen/man/pwcst.Rd | 2 survPen-2.0.1/survPen/man/rd.Rd | 2 survPen-2.0.1/survPen/man/repam.Rd | 2 survPen-2.0.1/survPen/man/robust.var.Rd | 2 survPen-2.0.1/survPen/man/smf.Rd | 2 survPen-2.0.1/survPen/man/smooth.cons.Rd | 2 survPen-2.0.1/survPen/man/smooth.cons.integral.Rd | 2 survPen-2.0.1/survPen/man/smooth.spec.Rd | 2 survPen-2.0.1/survPen/man/splitmult.Rd | 2 survPen-2.0.1/survPen/man/summary.survPen.Rd | 2 survPen-2.0.1/survPen/man/survPen.Rd | 3 survPen-2.0.1/survPen/man/survPen.fit.Rd | 2 survPen-2.0.1/survPen/man/survPenObject.Rd | 2 survPen-2.0.1/survPen/man/tensor.in.Rd | 2 survPen-2.0.1/survPen/man/tensor.prod.S.Rd | 2 survPen-2.0.1/survPen/man/tensor.prod.X.Rd | 2 39 files changed, 83 insertions(+), 75 deletions(-)
Title: Interval Estimation of Linear Models with Heteroskedasticity
Description: Calculates the interval estimates for the parameters of linear models with heteroscedastic regression using bootstrap - (Wild Bootstrap) and double bootstrap-t (Wild Bootstrap). It is also possible to calculate confidence intervals using the percentile bootstrap and percentile bootstrap double. The package can calculate consistent estimates of the covariance matrix of the parameters of linear regression models with heteroscedasticity of unknown form. The package also provides a function to consistently calculate the covariance matrix of the parameters of linear models with heteroscedasticity of unknown form. The bootstrap methods exported by the package are based on the master's thesis of the first author, available at <https://raw.githubusercontent.com/prdm0/hcci/master/references/dissertacao_mestrado.pdf>. The hcci package in previous versions was cited in the book VINOD, Hrishikesh D. Hands-on Intermediate Econometrics Using R: Templates for Learning Quantitative Methods and R [...truncated...]
Author: Pedro Rafael Diniz Marinho [aut, cre],
Francisco Cribari Neto [aut, ctb]
Maintainer: Pedro Rafael Diniz Marinho <pedro.rafael.marinho@gmail.com>
Diff between hcci versions 1.1.0 dated 2024-04-01 and 1.2.0 dated 2025-01-21
DESCRIPTION | 7 +++---- MD5 | 7 ++++--- NAMESPACE | 1 + R/QT.R | 4 ++-- man/QT.Rd |only 5 files changed, 10 insertions(+), 9 deletions(-)
Title: ACE and AVAS for Selecting Multiple Regression Transformations
Description: Two nonparametric methods for multiple regression transform selection are provided.
The first, Alternative Conditional Expectations (ACE),
is an algorithm to find the fixed point of maximal
correlation, i.e. it finds a set of transformed response variables that maximizes R^2
using smoothing functions [see Breiman, L., and J.H. Friedman. 1985. "Estimating Optimal Transformations
for Multiple Regression and Correlation". Journal of the American Statistical Association.
80:580-598. <doi:10.1080/01621459.1985.10478157>].
Also included is the Additivity Variance Stabilization (AVAS) method which works better than ACE when
correlation is low [see Tibshirani, R.. 1986. "Estimating Transformations for Regression via Additivity
and Variance Stabilization". Journal of the American Statistical Association. 83:394-405.
<doi:10.1080/01621459.1988.10478610>]. A good introduction to these two methods is in chapter 16 of
Frank Harrel's "Regression Modeling Strategies" in the Springer Serie [...truncated...]
Author: Phil Spector [aut],
Jerome Friedman [aut],
Robert Tibshirani [aut],
Thomas Lumley [aut],
Shawn Garbett [cre, aut] ,
Jonathan Baron [aut]
Maintainer: Shawn Garbett <shawn.garbett@vumc.org>
Diff between acepack versions 1.4.2 dated 2023-08-22 and 1.5.0 dated 2025-01-21
acepack-1.4.2/acepack/NEWS |only acepack-1.4.2/acepack/R/acepack.R |only acepack-1.4.2/acepack/R/zzz.R |only acepack-1.4.2/acepack/inst |only acepack-1.4.2/acepack/src/ace.f |only acepack-1.4.2/acepack/src/avas.f |only acepack-1.4.2/acepack/src/rlsmo.f |only acepack-1.4.2/acepack/tests/testthat/test_transform.R |only acepack-1.5.0/acepack/DESCRIPTION | 37 ++++- acepack-1.5.0/acepack/LICENSE | 4 acepack-1.5.0/acepack/MD5 | 48 ++++--- acepack-1.5.0/acepack/NAMESPACE | 9 - acepack-1.5.0/acepack/NEWS.md |only acepack-1.5.0/acepack/R/ace.R |only acepack-1.5.0/acepack/R/avas.R |only acepack-1.5.0/acepack/R/set_control.R |only acepack-1.5.0/acepack/README.md |only acepack-1.5.0/acepack/man/ace.Rd | 115 ++++++++++-------- acepack-1.5.0/acepack/man/avas.Rd | 104 ++++++++++------ acepack-1.5.0/acepack/man/set_control.Rd |only acepack-1.5.0/acepack/src/acedata.f90 |only acepack-1.5.0/acepack/src/acemod.f90 |only acepack-1.5.0/acepack/src/bakfit.f90 |only acepack-1.5.0/acepack/src/calcmu.f90 |only acepack-1.5.0/acepack/src/ctsub.f90 |only acepack-1.5.0/acepack/src/favas.f90 |only acepack-1.5.0/acepack/src/init.c | 31 +++- acepack-1.5.0/acepack/src/mace.f90 |only acepack-1.5.0/acepack/src/model.f90 |only acepack-1.5.0/acepack/src/montne.f90 |only acepack-1.5.0/acepack/src/rlsmo.f90 |only acepack-1.5.0/acepack/src/scail.f90 |only acepack-1.5.0/acepack/src/smooth.f90 |only acepack-1.5.0/acepack/src/smothr.f90 |only acepack-1.5.0/acepack/src/sort.f90 |only acepack-1.5.0/acepack/src/supersmoother.f90 |only acepack-1.5.0/acepack/src/supsmu.f90 |only acepack-1.5.0/acepack/tests/testthat/test_ace.R |only acepack-1.5.0/acepack/tests/testthat/test_avas.R |only acepack-1.5.0/acepack/tests/testthat/test_bullseye.R |only 40 files changed, 224 insertions(+), 124 deletions(-)
Title: Create, Manipulate and Query Parameter Terms
Description: Creates, manipulates, queries and repairs vectors of
parameter terms. Parameter terms are the labels used to reference
values in vectors, matrices and arrays. They represent the names in
coefficient tables and the column names in 'mcmc' and 'mcmc.list'
objects.
Author: Joe Thorley [aut, cre] ,
Kirill Mueller [aut] ,
Ayla Pearson [ctb] ,
Evan Amies-Galonski [ctb] ,
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between term versions 0.3.5 dated 2022-09-29 and 0.3.6 dated 2025-01-21
DESCRIPTION | 14 +-- MD5 | 112 +++++++++++++++--------------- NAMESPACE | 9 ++ NEWS.md | 11 ++ R/as-term-rcrd.R | 2 R/as-term.R | 8 +- R/chk.R | 2 R/complete-terms.R | 6 + R/consistent-term.R | 2 R/deprecated.R | 7 + R/extras.R | 4 - R/internal.R | 4 - R/is-inconsistent-terms.R | 6 + R/new-term-rcrd.R | 2 R/npdims.R | 2 R/params.R | 19 +++-- R/pars-terms.R | 6 - R/pars.R | 14 +-- R/pdims.R | 3 R/repair-terms.R | 3 R/scalar-term.R | 2 R/subset.R | 19 +++-- R/valid-term.R | 2 R/vec-cast-term.R | 4 - R/vld.R | 6 - README.md | 58 +++++++++------ man/as_term.Rd | 2 man/as_term_rcrd.Rd | 2 man/complete_terms.Rd | 2 man/deprecated.Rd | 4 - man/is_incomplete_terms.Rd | 2 man/is_inconsistent_terms.Rd | 2 man/new_term_rcrd.Rd | 2 man/params.Rd | 14 ++- man/pars.character.Rd | 2 man/pars.default.Rd | 2 man/pars_terms.Rd | 6 - man/subset.term.Rd | 2 man/subset.term_rcrd.Rd | 2 man/tindex.Rd | 4 - man/vld_term.Rd | 1 tests/testthat/test-anyduplicated.R | 1 tests/testthat/test-as-data-frame.R | 13 ++- tests/testthat/test-as-term-rcrd.R | 15 ++-- tests/testthat/test-complete-terms.R | 10 +- tests/testthat/test-consistent-term.R | 2 tests/testthat/test-dims.R | 1 tests/testthat/test-internal.R | 7 + tests/testthat/test-is-incomplete-terms.R | 3 tests/testthat/test-new-term-rcrd.R | 24 ++++-- tests/testthat/test-pars.R | 14 ++- tests/testthat/test-pdims.R | 3 tests/testthat/test-repair-terms.R | 48 ++++++++---- tests/testthat/test-scalar-term.R | 24 ++++-- tests/testthat/test-set-pars.R | 23 ++++-- tests/testthat/test-subset.R | 8 +- tests/testthat/test-valid-term.R | 4 - 57 files changed, 342 insertions(+), 234 deletions(-)
Title: Named Capture to Data Tables
Description: User-friendly functions for extracting a data
table (row for each match, column for each group)
from non-tabular text data using regular expressions,
and for melting columns that match a regular expression.
Patterns are defined using a readable syntax
that makes it easy to build complex patterns
in terms of simpler, re-usable sub-patterns.
Named R arguments are translated to column names
in the output; capture groups without names are used
internally in order to provide a standard interface
to three regular expression 'C' libraries
('PCRE', 'RE2', 'ICU').
Output can also include numeric columns via
user-specified type conversion functions.
Author: Toby Hocking [aut, cre]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between nc versions 2024.9.20 dated 2024-09-20 and 2025.1.21 dated 2025-01-21
DESCRIPTION | 6 MD5 | 240 NAMESPACE | 35 NEWS | 464 - R/alternatives.R | 380 - R/apply_type_funs.R | 158 R/capture_all_str.R | 891 +- R/capture_first_df.R | 309 R/capture_first_glob.R | 234 R/capture_first_vec.R | 283 R/capture_longer_spec.R | 80 R/capture_melt_multiple.R | 310 R/capture_melt_single.R | 216 R/check_names.R | 154 R/field.R | 198 R/group.R | 118 R/measure.R | 338 R/only_captures.R | 28 R/quantifier.R | 128 R/stop_for.R | 100 R/try.R | 32 R/var_args_list.R | 265 build/vignette.rds |binary inst/doc/v0-overview.R | 118 inst/doc/v0-overview.Rmd | 280 inst/doc/v0-overview.html | 1008 +- inst/doc/v1-capture-first.R | 428 - inst/doc/v1-capture-first.Rmd | 850 +- inst/doc/v1-capture-first.html | 1936 ++--- inst/doc/v2-capture-all.R | 238 inst/doc/v2-capture-all.Rmd | 514 - inst/doc/v2-capture-all.html | 1518 ++-- inst/doc/v3-capture-melt.R | 300 inst/doc/v3-capture-melt.Rmd | 640 - inst/doc/v3-capture-melt.html | 1612 ++-- inst/doc/v4-comparisons.R | 1030 +- inst/doc/v4-comparisons.Rmd | 1370 +-- inst/doc/v4-comparisons.html | 2646 +++---- inst/doc/v5-helpers.R | 172 inst/doc/v5-helpers.Rmd | 350 inst/doc/v5-helpers.html | 1018 +- inst/doc/v6-engines.R | 40 inst/doc/v6-engines.Rmd | 264 inst/doc/v6-engines.html | 915 +- inst/doc/v7-capture-glob.R | 314 inst/doc/v7-capture-glob.Rmd | 580 - inst/doc/v7-capture-glob.html | 1556 ++-- inst/extdata/MEDLINE_Fields.html | 3586 +++++----- inst/extdata/PMC3045577.nbib | 136 inst/extdata/RD12-0002_PP16HS_5sec_GM_F_1P.csv | 74 inst/extdata/chip-seq-chunk-db.R | 22 inst/extdata/chip-seq-chunk-db/H3K36me3_AM_immune/9/counts/McGill0101.bedGraph.head | 22 inst/extdata/chip-seq-chunk-db/H3K36me3_TDH_other/1/counts/McGill0019.bedGraph.head | 22 inst/extdata/chip-seq-chunk-db/H3K4me3_TDH_immune/9/counts/McGill0024.bedGraph.head | 22 inst/extdata/chip-seq-chunk-db/H3K4me3_XJ_immune/2/counts/McGill0024.bedGraph.head | 22 inst/extdata/compress-sizes.out | 12 inst/extdata/compress-times.out | 50 inst/extdata/namedCapture-refs.bib | 392 - inst/extdata/pepseq.txt | 6 inst/extdata/vignette.Rmd | 460 - inst/extdata/vignette.Rnw | 794 +- inst/extdata/vignettes/v0-overview.Rmd | 204 inst/extdata/vignettes/v1-capture-first.Rmd | 842 +- inst/extdata/vignettes/v2-capture-all.Rmd | 506 - inst/extdata/vignettes/v3-capture-melt.Rmd | 630 - inst/extdata/vignettes/v4-comparisons.Rmd | 1360 +-- inst/extdata/vignettes/v5-helpers.Rmd | 354 inst/extdata/vignettes/v6-engines.Rmd | 256 inst/test_engines.R | 38 man/alternatives.Rd | 94 man/alternatives_with_shared_groups.Rd | 184 man/altlist.Rd | 102 man/apply_type_funs.Rd | 52 man/capture_all_str.Rd | 824 +- man/capture_first_df.Rd | 243 man/capture_first_glob.Rd | 234 man/capture_first_vec.Rd | 235 man/capture_longer_spec.Rd | 70 man/capture_melt_multiple.Rd | 312 man/capture_melt_single.Rd | 216 man/check_df_names.Rd | 36 man/check_names.Rd | 40 man/collapse_some.Rd | 46 man/field.Rd | 204 man/group.Rd | 128 man/measure.Rd | 62 man/measure_multiple.Rd | 48 man/measure_single.Rd | 48 man/melt_list.Rd | 42 man/only_captures.Rd | 40 man/quantifier.Rd | 124 man/stop_for_capture_same_as_id.Rd | 38 man/stop_for_engine.Rd | 34 man/stop_for_subject.Rd | 34 man/subject_var_args.Rd | 37 man/try_or_stop_print_pattern.Rd | 44 man/var_args_list.Rd | 91 tests/testthat.R | 5 tests/testthat/test-CRAN-all.R | 294 tests/testthat/test-CRAN-alternatives.R | 348 tests/testthat/test-CRAN-df.R | 726 +- tests/testthat/test-CRAN-dt.R | 46 tests/testthat/test-CRAN-errors.R | 288 tests/testthat/test-CRAN-field.R | 72 tests/testthat/test-CRAN-glob.R | 67 tests/testthat/test-CRAN-group.R | 56 tests/testthat/test-CRAN-longer.R | 48 tests/testthat/test-CRAN-measure.R | 73 tests/testthat/test-CRAN-melt.R | 260 tests/testthat/test-CRAN-multiple.R | 912 +- tests/testthat/test-CRAN-quantifier.R | 178 tests/testthat/test-CRAN-subject.R | 98 tests/testthat/test-CRAN-vec.R | 724 +- vignettes/v0-overview.Rmd | 280 vignettes/v1-capture-first.Rmd | 850 +- vignettes/v2-capture-all.Rmd | 514 - vignettes/v3-capture-melt.Rmd | 640 - vignettes/v4-comparisons.Rmd | 1370 +-- vignettes/v5-helpers.Rmd | 350 vignettes/v6-engines.Rmd | 264 vignettes/v7-capture-glob.Rmd | 580 - 121 files changed, 23643 insertions(+), 23536 deletions(-)
Title: Geometrically Designed Spline Regression
Description: Spline Regression, Generalized Additive Models, and Component-wise Gradient
Boosting, utilizing Geometrically Designed (GeD) Splines. GeDS regression is a
non-parametric method inspired by geometric principles, for fitting spline regression
models with variable knots in one or two independent variables. It efficiently estimates
the number of knots and their positions, as well as the spline order, assuming the
response variable follows a distribution from the exponential family. GeDS models
integrate the broader category of Generalized (Non-)Linear Models, offering a flexible
approach to modeling complex relationships. A description of the method can be found in
Kaishev et al. (2016) <doi:10.1007/s00180-015-0621-7> and Dimitrova et al. (2023)
<doi:10.1016/j.amc.2022.127493>. Further extending its capabilities, GeDS's implementation
includes Generalized Additive Models (GAM) and Functional Gradient Boosting (FGB),
enabling versatile multivariate predictor modeling, as discuss [...truncated...]
Author: Dimitrina S. Dimitrova [aut],
Vladimir K. Kaishev [aut],
Andrea Lattuada [aut],
Emilio L. Saenz Guillen [aut, cre],
Richard J. Verrall [aut]
Maintainer: Emilio L. Saenz Guillen <Emilio.Saenz-Guillen@bayes.city.ac.uk>
Diff between GeDS versions 0.2.4 dated 2024-09-12 and 0.2.5 dated 2025-01-21
DESCRIPTION | 26 +-- MD5 | 34 ++-- R/BivariateFitter.R | 45 ++++-- R/IntegrateDerive.R | 75 +++++++--- R/Knotnew_R.R |only R/NGeDS.R | 18 +- R/NGeDSboost.R | 4 R/S3methods.R | 42 +++-- R/SplineReg_biv.R | 8 - R/UnivariateFitter.R | 71 ++++++--- R/plot_GeDSMethod.R | 330 ++++++++++++++++++++++++++++++++++++++------- R/tensorProd_R.R |only R/unexported.R | 9 - build/partial.rdb |binary man/Integrate.Rd | 15 +- man/NGeDS.Rd | 12 + man/NGeDSboost.Rd | 2 man/UnivariateFitters.Rd | 9 - man/plot-GeDSgam-method.Rd | 10 + 19 files changed, 535 insertions(+), 175 deletions(-)
Title: Asymptotic Timing
Description: Computing and visualizing comparative
asymptotic timings of different algorithms and code versions.
Also includes functionality for comparing empirical timings with
expected references such as linear or quadratic,
<https://en.wikipedia.org/wiki/Asymptotic_computational_complexity>
Also includes functionality for measuring asymptotic memory and other
quantities.
Author: Toby Hocking [aut, cre]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between atime versions 2024.11.29 dated 2024-12-02 and 2025.1.21 dated 2025-01-21
DESCRIPTION | 6 MD5 | 94 +-- NAMESPACE | 44 - NEWS | 385 +++++++------ R/atime.R | 577 ++++++++++---------- R/predict.R | 236 ++++---- R/references.R | 370 ++++++------- R/test.R | 618 +++++++++++----------- R/versions.R | 380 ++++++------- build/vignette.rds |binary inst/doc/Custom_Plots.R | 144 ++--- inst/doc/Custom_Plots.Rmd | 200 +++---- inst/doc/Custom_Plots.html | 494 ++++++++--------- inst/doc/Custom_References.R | 134 ++-- inst/doc/Custom_References.Rmd | 284 +++++----- inst/doc/Custom_References.html | 621 +++++++++++----------- inst/doc/Custom_Units.R | 138 ++-- inst/doc/Custom_Units.Rmd | 320 +++++------ inst/doc/Custom_Units.html | 643 +++++++++++------------ inst/doc/cum_median.R | 62 +- inst/doc/cum_median.Rmd | 104 +-- inst/doc/cum_median.html | 408 +++++++------- inst/doc/regex.R | 128 ++-- inst/doc/regex.Rmd | 192 +++--- inst/doc/regex.html | 536 +++++++++---------- inst/doc/sparse.R | 400 +++++++------- inst/doc/sparse.Rmd | 696 ++++++++++++------------ inst/doc/sparse.html | 1115 ++++++++++++++++++++-------------------- inst/example_tests.R | 82 +- inst/global_edit.R | 82 +- man/atime.Rd | 128 ++-- man/atime_grid.Rd | 198 +++---- man/atime_pkg.Rd | 188 +++--- man/atime_test.Rd | 128 ++-- man/atime_test_list.Rd | 164 ++--- man/atime_versions.Rd | 178 +++--- man/atime_versions_exprs.Rd | 174 +++--- man/atime_versions_remove.Rd | 26 man/glob_find_replace.Rd | 38 - man/references_best.Rd | 104 +-- tests/testthat.R | 3 tests/testthat/test-CRAN.R | 1025 ++++++++++++++++++------------------ vignettes/Custom_Plots.Rmd | 200 +++---- vignettes/Custom_References.Rmd | 284 +++++----- vignettes/Custom_Units.Rmd | 320 +++++------ vignettes/cum_median.Rmd | 104 +-- vignettes/regex.Rmd | 192 +++--- vignettes/sparse.Rmd | 696 ++++++++++++------------ 48 files changed, 6852 insertions(+), 6791 deletions(-)
Title: Extend 'tinytest' with 'diffobj' and 'tinysnapshot'
Description: The 'tinytest' package offers a light-weight zero-dependency unit-testing
framework to which this package adds support via the 'diffobj' package for 'diff'-style
textual comparison of R objects, as well as via 'tinysnapshot' package for visual
differences in plots.
Author: Dirk Eddelbuettel [aut, cre] ,
Alton Barbehenn [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between ttdo versions 0.0.9 dated 2023-02-22 and 0.0.10 dated 2025-01-21
ChangeLog | 41 ++++++++++++++++++++++++++++++++++ DESCRIPTION | 29 ++++++++++++++---------- MD5 | 22 +++++++++--------- NAMESPACE | 10 +++++--- R/expectations.R | 28 +++++++++++++++-------- R/expectations_xl.R | 4 +-- R/visual.R |only README.md | 2 - inst/NEWS.Rd | 15 ++++++++++++ man/expect_equal_with_diff.Rd | 5 ++-- man/expect_equal_xl.Rd | 2 - man/expect_visual_equal_with_diff.Rd |only man/ttdo_boolean_and_message_tests.Rd | 2 - 13 files changed, 120 insertions(+), 40 deletions(-)
More information about setariaviridis at CRAN
Permanent link
Title: Analysis of Basketball Data
Description: Collection of tools to work with European basketball data. Functions available are related to friendly
web scraping, data management and visualization. Data were obtained from <https://www.euroleaguebasketball.net/euroleague/>,
<https://www.euroleaguebasketball.net/eurocup/> and <https://www.acb.com/>, following the instructions
of their respectives robots.txt files, when available. Box score data are available for the three leagues.
Play-by-play data are also available for the Spanish league. Methods for analysis include a population pyramid,
2D plots, circular plots of players' percentiles, plots of players' monthly/yearly stats, team heatmaps,
team shooting plots, team four factors plots, cross-tables with the results of regular season games,
maps of nationalities, combinations of lineups, possessions-related variables, timeouts,
performance by periods, personal fouls and offensive rebounds.
Please see Vinue (2020) <doi:10.1089/big.2018.0124> and Vinue (2024) [...truncated...]
Author: Guillermo Vinue [aut, cre]
Maintainer: Guillermo Vinue <guillermo.vinue@uv.es>
Diff between BAwiR versions 1.3.2 dated 2024-01-09 and 1.3.3 dated 2025-01-21
DESCRIPTION | 17 - MD5 | 18 - NEWS | 4 R/do_stats_per_period.R | 5 build/vignette.rds |binary inst/doc/BAwiR.R | 214 +++++++++--------- inst/doc/BAwiR.html | 568 +++++++++++++++++++++++++++++++++--------------- inst/doc/BAwiR_pbp.R | 128 +++++----- inst/doc/BAwiR_pbp.html | 482 ++++++++++++++++++++++++++++++---------- man/BAwiR-package.Rd | 10 10 files changed, 955 insertions(+), 491 deletions(-)
Title: Snapshots for Unit Tests using the 'tinytest' Framework
Description: Snapshots for unit tests using the 'tinytest' framework for R. Includes expectations to test base R and 'ggplot2' plots as well as console output from print().
Author: Vincent Arel-Bundock [aut, cre, cph]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinysnapshot versions 0.0.7 dated 2025-01-13 and 0.0.8 dated 2025-01-21
DESCRIPTION | 6 +-- MD5 | 14 ++++----- NEWS.md | 4 ++ R/expect_snapshot_plot.R | 62 +++++++++++++++++++++++----------------- build/partial.rdb |binary inst/tinytest/test-png.R | 26 ++++++++++++++++ man/expect_equivalent_images.Rd | 3 + man/expect_snapshot_plot.Rd | 3 + 8 files changed, 81 insertions(+), 37 deletions(-)
Title: Manipulate 'JDemetra+' Workspaces
Description: Set of tools to manipulate the 'JDemetra+' workspaces.
Based on the 'RJDemetra' package (which interfaces with version 2 of the 'JDemetra+' (<https://github.com/jdemetra/jdemetra-app>), the seasonal adjustment software officially
recommended to the members of the European Statistical System (ESS) and the European System of Central Banks).
This package provides access to additional workspace manipulation functions such as metadata manipulation, raw paths and wrangling of several workspaces simultaneously.
These additional functionalities are useful as part of a CVS data production chain.
Author: Tanguy Barthelemy [aut, cre, art],
Alain Quartier-la-Tente [aut] ,
Institut national de la statistique et des etudes economiques [cph]
,
Anna Smyk [aut]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between rjdworkspace versions 1.1.8 dated 2025-01-09 and 1.1.9 dated 2025-01-21
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 8 +++++++- R/update_path.R | 23 +++++++++++++++++------ 4 files changed, 30 insertions(+), 13 deletions(-)
Title: High-Dimensional Analysis of Variance
Description: Functions and datasets to support Smilde, Marini, Westerhuis and Liland (2025, ISBN: 978-1-394-21121-0)
"Analysis of Variance for High-Dimensional Data - Applications in Life, Food and Chemical Sciences".
This implements and imports a collection of methods for HD-ANOVA data analysis with common interfaces, result- and plotting
functions, multiple real data sets and four vignettes covering a range different applications.
Author: Kristian Hovde Liland [aut, cre]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between HDANOVA versions 0.8.1 dated 2024-10-16 and 0.8.2 dated 2025-01-21
DESCRIPTION | 13 - MD5 | 52 +++--- NAMESPACE | 3 NEWS | 11 + R/apca.R | 11 + R/asca.R | 9 - R/asca_fit.R | 155 +++++++++++++------- R/asca_plots.R | 140 ++++++++++-------- R/limmpca.R | 6 R/model.frame.asca.R |only R/msca.R | 5 R/pcanova.R | 5 build/vignette.rds |binary inst/doc/vignette_B_ANOVA.R | 3 inst/doc/vignette_B_ANOVA.Rmd | 5 inst/doc/vignette_B_ANOVA.html | 317 ++++++++++++++++++++--------------------- inst/doc/vignette_C_ASCA.R | 5 inst/doc/vignette_C_ASCA.Rmd | 5 inst/doc/vignette_C_ASCA.html | 91 ++++++----- man/apca.Rd | 10 + man/asca.Rd | 8 - man/asca_fit.Rd | 12 + man/limmpca.Rd | 3 man/model.frame.asca.Rd |only man/msca.Rd | 4 man/pcanova.Rd | 4 vignettes/vignette_B_ANOVA.Rmd | 5 vignettes/vignette_C_ASCA.Rmd | 5 28 files changed, 516 insertions(+), 371 deletions(-)
Title: Visualising Multiple Pairwise Variable Correlations and Other
Scores
Description: We provide a tidy data structure and visualisations for multiple or grouped variable correlations,
general association measures scagnostics and other pairwise scores suitable for numerical, ordinal and nominal variables.
Supported measures include distance correlation, maximal information, ace correlation, Kendall's tau, and polychoric correlation.
Author: Amit Chinwan [aut],
Catherine Hurley [aut, cre]
Maintainer: Catherine Hurley <catherine.hurley@mu.ie>
Diff between bullseye versions 0.1.0 dated 2024-08-28 and 0.1.1 dated 2025-01-21
DESCRIPTION | 6 ++--- MD5 | 30 +++++++++++++-------------- NEWS.md | 6 +++++ R/pair_methods.R | 8 +++---- R/pair_scagnostics.R | 2 - R/pairwise.R | 3 +- build/vignette.rds |binary inst/doc/calc_pairwise.html | 2 - inst/doc/integrating.html | 14 ++++++------ inst/doc/vis_pairwise.R | 4 +-- inst/doc/vis_pairwise.html | 40 ++++++++++++++++++------------------- man/bullseye-package.Rd | 2 - man/pair_ace.Rd | 2 - man/pair_nmi.Rd | 4 ++- man/pair_scagnostics.Rd | 2 - tests/testthat/test-pair_methods.R | 12 +++++------ 16 files changed, 73 insertions(+), 64 deletions(-)
Title: Animated Interactive Grammar of Graphics
Description: Functions are provided for defining animated,
interactive data visualizations in R code, and rendering
on a web page. The 2018 Journal of Computational and
Graphical Statistics paper,
<doi:10.1080/10618600.2018.1513367>
describes the concepts implemented.
Author: Toby Hocking [aut, cre] ,
Biplab Sutradhar [ctb] ,
Hadley Wickham [aut] ,
Winston Chang [aut] ,
RStudio [cph] ,
Nicholas Lewin-Koh [aut] ,
Martin Maechler [aut] ,
Randall Prium [aut] ,
Susan VanderPlas [aut] ,
Carson Sievert [aut] ,
Kevin Ferris [aut [...truncated...]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between animint2 versions 2024.11.2 dated 2024-11-05 and 2025.1.21 dated 2025-01-21
DESCRIPTION | 6 MD5 | 1033 - NAMESPACE | 1061 - NEWS.md | 356 R/aaa-.r | 26 R/aes-calculated.r | 100 R/aes-colour-fill-alpha.r | 112 R/aes-group-order.r | 160 R/aes-linetype-size-shape.r | 128 R/aes-position.r | 78 R/aes.r | 472 R/annotation-custom.r | 194 R/annotation-logticks.r | 488 R/annotation-map.r | 144 R/annotation-raster.r | 180 R/annotation.r | 134 R/autoplot.r | 42 R/bench.r | 44 R/bin.R | 342 R/coord-.r | 162 R/coord-cartesian-.r | 206 R/coord-fixed.r | 94 R/coord-flip.r | 126 R/coord-map.r | 498 R/coord-munch.r | 394 R/coord-polar.r | 608 R/coord-quickmap.R | 72 R/coord-transform.r | 344 R/data.R | 378 R/facet-.r | 124 R/facet-grid-.r | 830 R/facet-labels.r | 1150 - R/facet-layout.r | 350 R/facet-locate.r | 168 R/facet-null.r | 152 R/facet-viewports.r | 100 R/facet-wrap.r | 926 R/fortify-lm.r | 172 R/fortify-map.r | 222 R/fortify-spatial.r | 182 R/fortify.r | 54 R/geom-.r | 1328 - R/geom-abline.r | 318 R/geom-bar.r | 268 R/geom-bin2d.r | 146 R/geom-blank.r | 76 R/geom-contour.r | 152 R/geom-count.r | 126 R/geom-crossbar.r | 190 R/geom-curve.r | 122 R/geom-defaults.r | 82 R/geom-density.r | 172 R/geom-density2d.r | 164 R/geom-dotplot.r | 570 R/geom-errorbar.r | 116 R/geom-errorbarh.r | 162 R/geom-freqpoly.r | 74 R/geom-hex.r | 266 R/geom-histogram.r | 190 R/geom-hline.r | 108 R/geom-jitter.r | 120 R/geom-label.R | 294 R/geom-linerange.r | 176 R/geom-map.r | 246 R/geom-path.r | 640 R/geom-point.r | 306 R/geom-pointrange.r | 98 R/geom-polygon.r | 228 R/geom-raster.r | 206 R/geom-rect.r | 162 R/geom-ribbon.r | 310 R/geom-rug.r | 190 R/geom-segment.r | 234 R/geom-smooth.r | 270 R/geom-spoke.r | 130 R/geom-text.r | 486 R/geom-tile.r | 218 R/geom-violin.r | 378 R/geom-vline.r | 108 R/gganimintproto.r | 570 R/ggplot2.r | 8 R/grob-absolute.r | 94 R/grob-dotstack.r | 94 R/grob-null.r | 48 R/grouping.r | 78 R/guide-colorbar.r | 876 R/guide-legend.r | 1038 - R/guides-.r | 586 R/guides-axis.r | 230 R/guides-grid.r | 60 R/hexbin.R | 76 R/labels.r | 188 R/layer.r | 640 R/legend-draw.r | 368 R/limits.r | 264 R/margins.R | 340 R/panel.r | 374 R/plot-build.r | 596 R/plot-construction.r | 238 R/plot-last.r | 38 R/plot.r | 332 R/position-.r | 184 R/position-collide.r | 220 R/position-dodge.r | 116 R/position-fill.r | 48 R/position-identity.r | 34 R/position-jitter.r | 104 R/position-jitterdodge.R | 118 R/position-nudge.R | 92 R/position-stack.r | 148 R/quick-plot.r | 314 R/range.r | 66 R/save.r | 270 R/scale-.r | 1266 - R/scale-alpha.r | 70 R/scale-brewer.r | 190 R/scale-continuous.r | 336 R/scale-date.r | 324 R/scale-discrete-.r | 282 R/scale-gradient.r | 226 R/scale-grey.r | 78 R/scale-hue.r | 116 R/scale-identity.r | 308 R/scale-linetype.r | 58 R/scale-manual.r | 172 R/scale-shape.r | 82 R/scale-size.r | 188 R/scale-type.R | 132 R/scales-.r | 258 R/stat-.r | 276 R/stat-bin.r | 280 R/stat-bin2d.r | 290 R/stat-bindot.r | 344 R/stat-binhex.r | 104 R/stat-contour.r | 226 R/stat-count.r | 142 R/stat-density-2d.r | 148 R/stat-density.r | 204 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inst/htmljs/index.html | 54 inst/htmljs/scripts.html | 18 inst/htmljs/vendor/d3.v3.js |15630 ++++++++-------- inst/htmljs/vendor/jquery-1.11.3.min.js | 10 inst/htmljs/vendor/selectize.css | 634 inst/htmljs/vendor/selectize.min.js | 4 inst/shiny/shinyAnimint.js | 34 man/FluView.Rd | 28 man/UStornadoes.Rd | 104 man/WorldBank.Rd | 68 man/absoluteGrob.Rd | 44 man/addSSandCSasAesthetics.Rd | 48 man/addShowSelectedForLegend.Rd | 42 man/add_theme.Rd | 38 man/aes.Rd | 98 man/aes_.Rd | 114 man/aes_all.Rd | 38 man/aes_auto.Rd | 34 man/aes_colour_fill_alpha.Rd | 122 man/aes_linetype_size_shape.Rd | 138 man/aes_position.Rd | 98 man/animint.Rd | 168 man/animint2-gganimintproto.Rd | 642 man/animint2dir.Rd | 220 man/animint2pages.Rd | 122 man/animintOutput.Rd | 34 man/annotate.Rd | 120 man/annotation_custom.Rd | 106 man/annotation_logticks.Rd | 218 man/annotation_map.Rd | 72 man/annotation_raster.Rd | 98 man/as.list.gganimintproto.Rd | 38 man/as_labeller.Rd | 90 man/autoplot.Rd | 48 man/benchplot.Rd 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Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-29 2.1.11
2023-09-20 2.1.10
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-19 0.0.1
Title: Bayesian partial least squares regression
Description: Fits the Bayesian partial least squares regression model
introduced in Urbas et al. (2024) <doi:10.1214/24-AOAS1947>. Suitable
for univariate and multivariate regression with high-dimensional data.
Author: Szymon Urbas [aut, cre],
Pierre Lovera [ctb],
Robert Daly [ctb],
Alan O'Riordan [ctb],
Donagh Berry [ctb],
Isobel Claire Gormley [ctb]
Maintainer: Szymon Urbas <szymon.urbas@mu.ie>
Diff between bplsr versions 1.0.2 dated 2025-01-13 and 1.0.3 dated 2025-01-21
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/BPLSR.R | 8 ++++++-- README.md | 24 ++++++++++++------------ 4 files changed, 24 insertions(+), 20 deletions(-)
Title: Spatial Network Analysis
Description: Interface package for 'sala', the spatial network analysis library
from the 'depthmapX' software application. The R parts of the code are based
on the 'rdepthmap' package. Allows for the analysis of urban and
building-scale networks and provides metrics and methods usually found
within the Space Syntax domain. Methods in this package are described by K.
Al-Sayed, A. Turner, B. Hillier, S. Iida and A. Penn (2014) "Space Syntax
methodology", and also by A. Turner (2004)
<https://discovery.ucl.ac.uk/id/eprint/2651> "Depthmap 4: a researcher's
handbook".
Author: Petros Koutsolampros [cre, aut]
,
Fani Kostourou [ctb] ,
Kimon Krenz [ctb] ,
Alasdair Turner [ctb] ,
Tasos Varoudis [ctb] ,
Christian Sailer [ctb] ,
Eva Friedrich [ctb] ,
University College London [fnd, cph] ,
Spacelab UK [fnd]
Maintainer: Petros Koutsolampros <r-devel@pklampros.net>
Diff between alcyon versions 0.6.0 dated 2024-12-22 and 0.7.0 dated 2025-01-21
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 5 ++++- configure | 18 +++++++++--------- configure.ac | 2 +- src/libs/salalib/CMakeLists.txt | 4 ++++ src/libs/salalib/genlib/p2dpoly.cpp | 32 ++++++++++++++++++++++++-------- src/libs/salalib/genlib/p2dpoly.h | 18 +++++++++++++++--- src/libs/salalib/importutils.cpp | 4 ++-- src/libs/salalib/salashape.cpp | 10 +++++++--- src/libs/salalib/salashape.h | 2 +- src/process_isovist.cpp | 7 ++++++- tests/testthat.R | 6 +++++- 13 files changed, 94 insertions(+), 46 deletions(-)
Title: Reproducible Data Science Environments with 'Nix'
Description: Simplifies the creation of reproducible data science environments
using the 'Nix' package manager, as described in
Dolstra (2006) <ISBN 90-393-4130-3>. The included `rix()`
function generates a complete description of the environment as a
`default.nix` file, which can then be built using 'Nix'. This results in
project specific software environments with pinned versions of R, packages,
linked system dependencies, and other tools. Additional helpers make it easy
to run R code in 'Nix' software environments for testing and production.
Author: Bruno Rodrigues [aut, cre] ,
Philipp Baumann [aut] ,
David Watkins [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/625>),
Jacob Wujiciak-Jens [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/62 [...truncated...]
Maintainer: Bruno Rodrigues <bruno@brodrigues.co>
Diff between rix versions 0.14.3 dated 2025-01-10 and 0.14.4 dated 2025-01-21
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/renv_helpers.R | 32 +++++++++++++++++++++++++------- inst/extdata/available_df.csv | 2 ++ tests/testthat/test-renv_helpers.R | 2 +- 6 files changed, 40 insertions(+), 16 deletions(-)
Title: Read Human Mortality Database and Human Fertility Database Data
from the Web
Description: Utilities for reading data from the Human Mortality Database (<https://www.mortality.org>), Human Fertility Database (<https://www.humanfertility.org>), and similar databases from the web or locally into an R session as data.frame objects. These are the two most widely used sources of demographic data to study basic demographic change, trends, and develop new demographic methods. Other supported databases at this time include the Human Fertility Collection (<https://www.fertilitydata.org>), The Japanese Mortality Database (<https://www.ipss.go.jp/p-toukei/JMD/index-en.html>), and the Canadian Human Mortality Database (<http://www.bdlc.umontreal.ca/chmd/>). Arguments and data are standardized.
Author: Tim Riffe [aut, cre],
Carl Boe [aut],
Jason Hilton [aut],
Josh Goldstein [ctb],
Stephen Holzman [ctb],
Sam Hyun Yoo [ctb]
Maintainer: Tim Riffe <tim.riffe@gmail.com>
Diff between HMDHFDplus versions 2.0.3 dated 2023-06-20 and 2.0.6 dated 2025-01-21
DESCRIPTION | 23 ++++++++++++----------- MD5 | 14 +++++++------- NAMESPACE | 2 ++ NEWS.md | 14 ++++++++++++++ R/HFDutils.R | 47 ++++++++++++++++++++++++++++------------------- R/readHFD.R | 7 ++++--- man/HFDparse.Rd | 4 +++- man/readHFD.Rd | 4 +++- 8 files changed, 73 insertions(+), 42 deletions(-)
Title: Standardized Git Repository Data
Description: Obtain standardized data from multiple 'Git' services, including 'GitHub' and 'GitLab'.
Designed to be 'Git' service-agnostic, this package assists teams with activities spread across various
'Git' platforms by providing a unified way to access repository data.
Author: Maciej Banas [aut, cre],
Kamil Koziej [aut],
Karolina Marcinkowska [aut],
Matt Secrest [aut]
Maintainer: Maciej Banas <banasmaciek@gmail.com>
Diff between GitStats versions 2.2.0 dated 2025-01-14 and 2.2.1 dated 2025-01-21
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NEWS.md | 4 ++++ R/EngineRestGitHub.R | 5 ++--- R/EngineRestGitLab.R | 8 +++++--- inst/roche/roche_get_package_usage.R |only 6 files changed, 19 insertions(+), 13 deletions(-)
Title: High Performance Algorithms for Vine Copula Modeling
Description: Provides an interface to 'vinecopulib', a C++ library for vine
copula modeling. The 'rvinecopulib' package implements the core features of the
popular 'VineCopula' package, in particular inference algorithms for both vine
copula and bivariate copula models. Advantages over 'VineCopula' are a sleeker
and more modern API, improved performances, especially in high dimensions,
nonparametric and multi-parameter families, and the ability to model discrete
variables. The 'rvinecopulib' package includes 'vinecopulib' as header-only
C++ library (currently version 0.7.1). Thus users do not need to install
'vinecopulib' itself in order to use 'rvinecopulib'. Since their initial
releases, 'vinecopulib' is licensed under the MIT License, and 'rvinecopulib'
is licensed under the GNU GPL version 3.
Author: Thomas Nagler [aut, cre],
Thibault Vatter [aut]
Maintainer: Thomas Nagler <info@vinecopulib.org>
Diff between rvinecopulib versions 0.6.3.1.1 dated 2023-02-23 and 0.7.1.1.0 dated 2025-01-21
DESCRIPTION | 16 MD5 | 230 +-- NAMESPACE | 1 NEWS.md | 23 R/RcppExports.R | 28 R/bicop.R | 53 R/bicop_methods.R | 10 R/bicop_plot.R | 6 R/family_sets.R | 14 R/pairs_copula_data.R | 4 R/rosenblatt.R | 56 R/rvinecopulib.R | 2 R/tools.R | 87 - R/vine.R | 29 R/vine_methods.R | 9 R/vinecop.R | 104 + R/vinecop_methods.R | 7 README.md | 10 inst/include/vinecopulib-wrappers.hpp | 22 inst/include/vinecopulib.hpp | 24 inst/include/vinecopulib/bicop/abstract.hpp | 3 inst/include/vinecopulib/bicop/archimedean.hpp | 2 inst/include/vinecopulib/bicop/bb1.hpp | 2 inst/include/vinecopulib/bicop/bb6.hpp | 2 inst/include/vinecopulib/bicop/bb7.hpp | 2 inst/include/vinecopulib/bicop/bb8.hpp | 2 inst/include/vinecopulib/bicop/class.hpp | 29 inst/include/vinecopulib/bicop/clayton.hpp | 2 inst/include/vinecopulib/bicop/elliptical.hpp | 2 inst/include/vinecopulib/bicop/extreme_value.hpp |only inst/include/vinecopulib/bicop/family.hpp | 30 inst/include/vinecopulib/bicop/fit_controls.hpp | 13 inst/include/vinecopulib/bicop/frank.hpp | 2 inst/include/vinecopulib/bicop/gaussian.hpp | 2 inst/include/vinecopulib/bicop/gumbel.hpp | 4 inst/include/vinecopulib/bicop/implementation/abstract.ipp | 100 + inst/include/vinecopulib/bicop/implementation/archimedean.ipp | 2 inst/include/vinecopulib/bicop/implementation/bb1.ipp | 2 inst/include/vinecopulib/bicop/implementation/bb6.ipp | 2 inst/include/vinecopulib/bicop/implementation/bb7.ipp | 17 inst/include/vinecopulib/bicop/implementation/bb8.ipp | 2 inst/include/vinecopulib/bicop/implementation/class.ipp | 216 ++- inst/include/vinecopulib/bicop/implementation/clayton.ipp | 5 inst/include/vinecopulib/bicop/implementation/elliptical.ipp | 2 inst/include/vinecopulib/bicop/implementation/extreme_value.ipp |only inst/include/vinecopulib/bicop/implementation/family.ipp | 37 inst/include/vinecopulib/bicop/implementation/fit_controls.ipp | 95 + inst/include/vinecopulib/bicop/implementation/frank.ipp | 12 inst/include/vinecopulib/bicop/implementation/gaussian.ipp | 2 inst/include/vinecopulib/bicop/implementation/gumbel.ipp | 46 inst/include/vinecopulib/bicop/implementation/indep.ipp | 2 inst/include/vinecopulib/bicop/implementation/joe.ipp | 60 inst/include/vinecopulib/bicop/implementation/kernel.ipp | 2 inst/include/vinecopulib/bicop/implementation/parametric.ipp | 10 inst/include/vinecopulib/bicop/implementation/student.ipp | 2 inst/include/vinecopulib/bicop/implementation/tawn.ipp |only inst/include/vinecopulib/bicop/implementation/tll.ipp | 14 inst/include/vinecopulib/bicop/implementation/tools_select.ipp | 22 inst/include/vinecopulib/bicop/indep.hpp | 2 inst/include/vinecopulib/bicop/joe.hpp | 4 inst/include/vinecopulib/bicop/kernel.hpp | 2 inst/include/vinecopulib/bicop/parametric.hpp | 2 inst/include/vinecopulib/bicop/student.hpp | 2 inst/include/vinecopulib/bicop/tawn.hpp |only inst/include/vinecopulib/bicop/tll.hpp | 2 inst/include/vinecopulib/bicop/tools_select.hpp | 2 inst/include/vinecopulib/misc/fit_controls.hpp |only inst/include/vinecopulib/misc/implementation/tools_eigen.ipp | 7 inst/include/vinecopulib/misc/implementation/tools_interpolation.ipp | 41 inst/include/vinecopulib/misc/implementation/tools_optimization.ipp | 12 inst/include/vinecopulib/misc/implementation/tools_stats.ipp | 236 ++- inst/include/vinecopulib/misc/tools_batch.hpp | 2 inst/include/vinecopulib/misc/tools_bobyqa.hpp | 2 inst/include/vinecopulib/misc/tools_constants.hpp | 2 inst/include/vinecopulib/misc/tools_eigen.hpp | 7 inst/include/vinecopulib/misc/tools_integration.hpp | 2 inst/include/vinecopulib/misc/tools_interface.hpp | 2 inst/include/vinecopulib/misc/tools_interpolation.hpp | 3 inst/include/vinecopulib/misc/tools_optimization.hpp | 12 inst/include/vinecopulib/misc/tools_optional.hpp |only inst/include/vinecopulib/misc/tools_serialization.hpp | 2 inst/include/vinecopulib/misc/tools_stats.hpp | 64 - inst/include/vinecopulib/misc/tools_stats_ghalton.hpp | 2 inst/include/vinecopulib/misc/tools_stats_sobol.hpp | 2 inst/include/vinecopulib/misc/tools_stl.hpp | 33 inst/include/vinecopulib/misc/tools_thread.hpp | 2 inst/include/vinecopulib/misc/triangular_array.hpp | 6 inst/include/vinecopulib/version.hpp | 6 inst/include/vinecopulib/vinecop/class.hpp | 19 inst/include/vinecopulib/vinecop/fit_controls.hpp | 24 inst/include/vinecopulib/vinecop/implementation/class.ipp | 627 +++++++--- inst/include/vinecopulib/vinecop/implementation/fit_controls.ipp | 143 +- inst/include/vinecopulib/vinecop/implementation/rvine_structure.ipp | 54 inst/include/vinecopulib/vinecop/implementation/tools_select.ipp | 40 inst/include/vinecopulib/vinecop/rvine_structure.hpp | 72 - inst/include/vinecopulib/vinecop/tools_select.hpp | 2 man/as.bicop.Rd |only man/bicop.Rd | 10 man/bicop_dist.Rd | 3 man/bicop_methods.Rd | 8 man/emp_cdf.Rd | 2 man/mBICV.Rd | 2 man/pairs_copula_data.Rd | 4 man/plot.bicop_dist.Rd | 6 man/predict_bicop.Rd | 2 man/rosenblatt.Rd | 27 man/rvinecopulib.Rd | 9 man/vine.Rd | 4 man/vinecop.Rd | 15 src/RcppExports.cpp | 100 - src/vinecopulib-interface.cpp | 139 +- tests/testthat/Rplots.pdf | 547 ++++---- tests/testthat/test_bicop.R | 9 tests/testthat/test_bicop_dist.R | 7 tests/testthat/test_rosenblatt.R | 26 tests/testthat/test_rvine_structure.R | 27 tests/testthat/test_vine.R | 12 tests/testthat/test_vine_dist.R | 30 tests/testthat/test_vinecop.R | 25 tests/testthat/testthat-problems.rds |only 120 files changed, 2596 insertions(+), 1344 deletions(-)
Title: R Bayesian Evidence Synthesis Tools
Description: Tool-set to support Bayesian evidence synthesis. This
includes meta-analysis, (robust) prior derivation from historical
data, operating characteristics and analysis (1 and 2 sample
cases). Please refer to Weber et al. (2021) <doi:10.18637/jss.v100.i19>
for details on applying this package while Neuenschwander et al. (2010)
<doi:10.1177/1740774509356002> and Schmidli et al. (2014)
<doi:10.1111/biom.12242> explain details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Beat Neuenschwander [ctb],
Heinz Schmidli [ctb],
Baldur Magnusson [ctb],
Yue Li [ctb],
Satrajit Roychoudhury [ctb],
Lukas A. Widmer [ctb] ,
Trustees of Columbia University [cph]
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between RBesT versions 1.8-0 dated 2025-01-08 and 1.8-1 dated 2025-01-21
DESCRIPTION | 12 +++++++----- MD5 | 16 ++++++++-------- NEWS.md | 7 +++++++ R/mixess.R | 8 ++++++-- R/sysdata.rda |binary inst/doc/RBesT.pdf |binary inst/doc/introduction.html | 6 +++--- man/RBesT-package.Rd | 1 + tests/testthat/test-utils.R | 7 +++++++ 9 files changed, 39 insertions(+), 18 deletions(-)
Title: Colors for NEST Graphs
Description: Clinical reporting figures require to use consistent colors
and configurations. As a part of the Roche open-source clinical
reporting project, namely the NEST project, the 'nestcolor' package
specifies the color code and default theme with specifying 'ggplot2'
theme parameters. Users can easily customize color and theme settings
before using the reset of NEST packages to ensure consistent settings
in both static and interactive output at the downstream.
Author: Joe Zhu [aut, cre] ,
Emily de la Rua [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between nestcolor versions 0.1.2 dated 2023-06-09 and 0.1.3 dated 2025-01-21
DESCRIPTION | 40 ++++++++++++++----------- MD5 | 16 +++++----- NEWS.md | 5 ++- R/color_palette.R | 16 +++++----- build/vignette.rds |binary inst/WORDLIST | 4 +- inst/doc/nestcolor.R | 8 ++--- inst/doc/nestcolor.html | 74 ++++++++++++++++++++++-------------------------- man/color_palette.Rd | 16 +++++----- 9 files changed, 90 insertions(+), 89 deletions(-)
Title: Multi-Scale Geomorphometric Terrain Attributes
Description: Calculates multi-scale geomorphometric terrain attributes from regularly gridded digital terrain models using a variable focal windows size (Ilich et al. (2023) <doi:10.1111/tgis.13067>).
Author: Alexander Ilich [aut, cre] ,
Vincent Lecours [aut],
Benjamin Misiuk [aut],
Steven Murawski [aut]
Maintainer: Alexander Ilich <ailich@usf.edu>
Diff between MultiscaleDTM versions 0.9 dated 2025-01-17 and 0.9.1 dated 2025-01-21
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/SlpAsp.R | 19 ++++++++++++------- inst/doc/README.html | 4 ++-- man/SlpAsp.Rd | 9 ++++++--- 5 files changed, 27 insertions(+), 19 deletions(-)
Title: Joint and Individual Regression
Description: An R package that implements the JICO algorithm [Wang, P., Wang, H., Li, Q., Shen, D., & Liu, Y. (2024). <Journal of Computational and Graphical Statistics, 33(3), 763-773>].
It aims at solving the multi-group regression problem. The algorithm decomposes the responses from multiple groups into shared and group-specific
components, which are driven by low-rank approximations of joint and individual structures from the covariates respectively.
Author: Peiyao Wang [aut, cre]
Maintainer: Peiyao Wang <peiyaow76@gmail.com>
Diff between JICO versions 0.0 dated 2023-05-08 and 0.1 dated 2025-01-21
DESCRIPTION | 14 +++++++------- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++-- R/continuum.R | 20 ++++++++++---------- R/utils.R | 2 +- README.md | 30 +++++++++++++++++++++++------- man/DIAG.Rd | 2 +- man/continuum.Rd | 4 ++-- man/continuum.multigroup.iter.Rd | 6 +++--- man/cv.continnum.iter.Rd | 4 ++-- tests/testthat/test-continuum.R | 16 ++++++++-------- 11 files changed, 69 insertions(+), 53 deletions(-)
Title: Package for Community Ecology and Suitability Analysis
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt [cre, aut]
Maintainer: Roeland Kindt <RoelandCEKindt@gmail.com>
Diff between BiodiversityR versions 2.17-1 dated 2025-01-10 and 2.17-1.1 dated 2025-01-21
DESCRIPTION | 8 +- MD5 | 6 - R/caprescale.R | 173 +++++++++++++++++++++++++++++---------------------------- inst/ChangeLog | 27 +++++--- 4 files changed, 114 insertions(+), 100 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Models for
Networks
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGMs). 'ergm' is a part of the Statnet suite of packages for network analysis. See Hunter, Handcock, Butts, Goodreau, and Morris (2008) <doi:10.18637/jss.v024.i03> and Krivitsky, Hunter, Morris, and Klumb (2023) <doi:10.18637/jss.v105.i06>.
Author: Mark S. Handcock [aut],
David R. Hunter [aut],
Carter T. Butts [aut],
Steven M. Goodreau [aut],
Pavel N. Krivitsky [aut, cre] ,
Martina Morris [aut],
Li Wang [ctb],
Kirk Li [ctb],
Skye Bender-deMoll [ctb],
Chad Klumb [ctb],
Michal Bojanowski [ctb] ,
[...truncated...]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>
Diff between ergm versions 4.7.5 dated 2024-11-06 and 4.8.1 dated 2025-01-21
ergm-4.7.5/ergm/tests/testthat/test-Sum.R |only ergm-4.8.1/ergm/DESCRIPTION | 52 ergm-4.8.1/ergm/LICENSE | 2 ergm-4.8.1/ergm/MD5 | 725 +++--- ergm-4.8.1/ergm/NAMESPACE | 2 ergm-4.8.1/ergm/R/InitErgmConstraint.R | 92 ergm-4.8.1/ergm/R/InitErgmConstraint.blockdiag.R | 2 ergm-4.8.1/ergm/R/InitErgmConstraint.hints.R | 2 ergm-4.8.1/ergm/R/InitErgmConstraint.operator.R |only ergm-4.8.1/ergm/R/InitErgmProposal.R | 2 ergm-4.8.1/ergm/R/InitErgmProposal.dyadnoise.R | 2 ergm-4.8.1/ergm/R/InitErgmReference.R | 2 ergm-4.8.1/ergm/R/InitErgmTerm.R | 168 - ergm-4.8.1/ergm/R/InitErgmTerm.auxnet.R | 2 ergm-4.8.1/ergm/R/InitErgmTerm.bipartite.R | 2 ergm-4.8.1/ergm/R/InitErgmTerm.bipartite.degree.R | 2 ergm-4.8.1/ergm/R/InitErgmTerm.blockop.R | 2 ergm-4.8.1/ergm/R/InitErgmTerm.coincidence.R | 2 ergm-4.8.1/ergm/R/InitErgmTerm.dgw_sp.R | 2 ergm-4.8.1/ergm/R/InitErgmTerm.diversity.R |only ergm-4.8.1/ergm/R/InitErgmTerm.extra.R | 2 ergm-4.8.1/ergm/R/InitErgmTerm.indices.R | 2 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ergm-4.8.1/ergm/R/ergm-defunct.R | 18 ergm-4.8.1/ergm/R/ergm-deprecated.R | 4 ergm-4.8.1/ergm/R/ergm-internal.R | 2 ergm-4.8.1/ergm/R/ergm-options.R | 16 ergm-4.8.1/ergm/R/ergm-package.R | 2 ergm-4.8.1/ergm/R/ergm-terms-index.R | 14 ergm-4.8.1/ergm/R/ergm.CD.fixed.R | 2 ergm-4.8.1/ergm/R/ergm.Cprepare.R | 2 ergm-4.8.1/ergm/R/ergm.MCMCse.R | 2 ergm-4.8.1/ergm/R/ergm.MCMLE.R | 2 ergm-4.8.1/ergm/R/ergm.R | 4 ergm-4.8.1/ergm/R/ergm.allstats.R | 2 ergm-4.8.1/ergm/R/ergm.auxstorage.R | 14 ergm-4.8.1/ergm/R/ergm.bounddeg.R | 2 ergm-4.8.1/ergm/R/ergm.bridge.R | 2 ergm-4.8.1/ergm/R/ergm.design.R | 2 ergm-4.8.1/ergm/R/ergm.errors.R | 2 ergm-4.8.1/ergm/R/ergm.estimate.R | 2 ergm-4.8.1/ergm/R/ergm.eta.R | 2 ergm-4.8.1/ergm/R/ergm.etagrad.R | 2 ergm-4.8.1/ergm/R/ergm.etagradmult.R | 2 ergm-4.8.1/ergm/R/ergm.etamap.R | 2 ergm-4.8.1/ergm/R/ergm.geodistn.R | 2 ergm-4.8.1/ergm/R/ergm.getCDsample.R | 2 ergm-4.8.1/ergm/R/ergm.getMCMCsample.R | 2 ergm-4.8.1/ergm/R/ergm.getnetwork.R | 2 ergm-4.8.1/ergm/R/ergm.initialfit.R | 2 ergm-4.8.1/ergm/R/ergm.llik.R | 2 ergm-4.8.1/ergm/R/ergm.llik.obs.R | 2 ergm-4.8.1/ergm/R/ergm.logitreg.R | 2 ergm-4.8.1/ergm/R/ergm.mple.R | 2 ergm-4.8.1/ergm/R/ergm.pen.glm.R | 2 ergm-4.8.1/ergm/R/ergm.phase12.R | 2 ergm-4.8.1/ergm/R/ergm.pl.R | 12 ergm-4.8.1/ergm/R/ergm.san.R | 2 ergm-4.8.1/ergm/R/ergm.stepping.R | 2 ergm-4.8.1/ergm/R/ergm.stocapprox.R | 4 ergm-4.8.1/ergm/R/ergm.utility.R | 74 ergm-4.8.1/ergm/R/ergmMPLE.R | 2 ergm-4.8.1/ergm/R/ergm_estfun.R | 2 ergm-4.8.1/ergm/R/ergm_keyword.R | 2 ergm-4.8.1/ergm/R/ergm_model.R | 5 ergm-4.8.1/ergm/R/ergm_model.utils.R | 2 ergm-4.8.1/ergm/R/ergm_mplecov.R | 2 ergm-4.8.1/ergm/R/ergm_proposal.R | 13 ergm-4.8.1/ergm/R/ergm_response.R | 2 ergm-4.8.1/ergm/R/ergm_state.R | 2 ergm-4.8.1/ergm/R/ergmlhs.R | 2 ergm-4.8.1/ergm/R/formula.utils.R | 12 ergm-4.8.1/ergm/R/get.node.attr.R | 2 ergm-4.8.1/ergm/R/godfather.R | 2 ergm-4.8.1/ergm/R/gof.ergm.R | 2 ergm-4.8.1/ergm/R/is.curved.R | 2 ergm-4.8.1/ergm/R/is.dyad.independent.R | 2 ergm-4.8.1/ergm/R/is.inCH.R | 2 ergm-4.8.1/ergm/R/is.na.ergm.R | 2 ergm-4.8.1/ergm/R/is.valued.R | 2 ergm-4.8.1/ergm/R/logLik.ergm.R | 7 ergm-4.8.1/ergm/R/mcmc.diagnostics.ergm.R | 2 ergm-4.8.1/ergm/R/network.list.R | 2 ergm-4.8.1/ergm/R/network.update.R | 2 ergm-4.8.1/ergm/R/nonidentifiability.R | 2 ergm-4.8.1/ergm/R/nparam.R | 2 ergm-4.8.1/ergm/R/obs.constraints.R | 2 ergm-4.8.1/ergm/R/parallel.utils.R | 2 ergm-4.8.1/ergm/R/param_names.R | 2 ergm-4.8.1/ergm/R/predict.ergm.R | 2 ergm-4.8.1/ergm/R/print.ergm.R | 2 ergm-4.8.1/ergm/R/print.network.list.R | 2 ergm-4.8.1/ergm/R/print.summary.ergm.R | 2 ergm-4.8.1/ergm/R/rank_test.ergm.R | 2 ergm-4.8.1/ergm/R/rlebdm.R | 17 ergm-4.8.1/ergm/R/simulate.ergm.R | 2 ergm-4.8.1/ergm/R/simulate.formula.R | 2 ergm-4.8.1/ergm/R/summary.ergm.R | 2 ergm-4.8.1/ergm/R/summary.ergm_model.R | 2 ergm-4.8.1/ergm/R/summary.network.list.R | 2 ergm-4.8.1/ergm/R/summary.statistics.network.R | 2 ergm-4.8.1/ergm/R/to_ergm_Cdouble.R | 2 ergm-4.8.1/ergm/R/vcov.ergm.R | 2 ergm-4.8.1/ergm/R/wtd.median.R | 2 ergm-4.8.1/ergm/R/zzz.R | 2 ergm-4.8.1/ergm/build/partial.rdb |binary ergm-4.8.1/ergm/build/stage23.rdb |binary ergm-4.8.1/ergm/inst/CITATION | 4 ergm-4.8.1/ergm/inst/NEWS.Rd | 148 + ergm-4.8.1/ergm/inst/REFERENCES.bib | 14 ergm-4.8.1/ergm/inst/doc/ergm-term-crossRef.html | 1138 +++++++--- ergm-4.8.1/ergm/inst/doc/ergm.R | 42 ergm-4.8.1/ergm/inst/doc/ergm.html | 32 ergm-4.8.1/ergm/inst/doc/nodal_attributes.html | 4 ergm-4.8.1/ergm/inst/include/MHproposal.h | 2 ergm-4.8.1/ergm/inst/include/changestat.h | 2 ergm-4.8.1/ergm/inst/include/edgelist.h | 2 ergm-4.8.1/ergm/inst/include/edgetree.h | 2 ergm-4.8.1/ergm/inst/include/ergm_BDNodeLists.h | 2 ergm-4.8.1/ergm/inst/include/ergm_BDStratBlocks.h | 2 ergm-4.8.1/ergm/inst/include/ergm_BDStrat_proposals.h | 2 ergm-4.8.1/ergm/inst/include/ergm_MHproposal.h | 11 ergm-4.8.1/ergm/inst/include/ergm_MHproposal_bd.h | 2 ergm-4.8.1/ergm/inst/include/ergm_MHproposals_degree.h |only ergm-4.8.1/ergm/inst/include/ergm_MHstorage.h | 2 ergm-4.8.1/ergm/inst/include/ergm_Rutil.h | 2 ergm-4.8.1/ergm/inst/include/ergm_block.h | 2 ergm-4.8.1/ergm/inst/include/ergm_changestat.h | 2 ergm-4.8.1/ergm/inst/include/ergm_changestat_auxnet.h | 2 ergm-4.8.1/ergm/inst/include/ergm_changestat_common.do_not_include_directly.h | 2 ergm-4.8.1/ergm/inst/include/ergm_changestat_operator.h | 2 ergm-4.8.1/ergm/inst/include/ergm_changestats_auxnet.h | 2 ergm-4.8.1/ergm/inst/include/ergm_changestats_operator.h | 2 ergm-4.8.1/ergm/inst/include/ergm_constants.h | 18 ergm-4.8.1/ergm/inst/include/ergm_dyad_hashmap.h | 2 ergm-4.8.1/ergm/inst/include/ergm_dyad_hashmap_utils.h | 2 ergm-4.8.1/ergm/inst/include/ergm_dyadgen.h | 13 ergm-4.8.1/ergm/inst/include/ergm_edgelist.h | 2 ergm-4.8.1/ergm/inst/include/ergm_edgetree.h | 2 ergm-4.8.1/ergm/inst/include/ergm_edgetree_common.do_not_include_directly.h | 2 ergm-4.8.1/ergm/inst/include/ergm_edgetree_inline.do_not_include_directly.h | 2 ergm-4.8.1/ergm/inst/include/ergm_edgetree_types.h | 2 ergm-4.8.1/ergm/inst/include/ergm_etamap.h | 2 ergm-4.8.1/ergm/inst/include/ergm_hash_edgelist.h | 2 ergm-4.8.1/ergm/inst/include/ergm_khash.h | 10 ergm-4.8.1/ergm/inst/include/ergm_kvec.h | 2 ergm-4.8.1/ergm/inst/include/ergm_model.h | 2 ergm-4.8.1/ergm/inst/include/ergm_nodelist.h | 2 ergm-4.8.1/ergm/inst/include/ergm_rlebdm.h | 2 ergm-4.8.1/ergm/inst/include/ergm_state.h | 2 ergm-4.8.1/ergm/inst/include/ergm_storage.h | 2 ergm-4.8.1/ergm/inst/include/ergm_stubs.c | 58 ergm-4.8.1/ergm/inst/include/ergm_unsorted_edgelist.h | 2 ergm-4.8.1/ergm/inst/include/ergm_util.h | 2 ergm-4.8.1/ergm/inst/include/ergm_weighted_population.h | 2 ergm-4.8.1/ergm/inst/include/ergm_wtMHproposal.h | 11 ergm-4.8.1/ergm/inst/include/ergm_wtchangestat.h | 2 ergm-4.8.1/ergm/inst/include/ergm_wtchangestat_operator.h | 2 ergm-4.8.1/ergm/inst/include/ergm_wtchangestats_operator.h | 2 ergm-4.8.1/ergm/inst/include/ergm_wtedgetree.h | 2 ergm-4.8.1/ergm/inst/include/ergm_wtedgetree_inline.do_not_include_directly.h | 2 ergm-4.8.1/ergm/inst/include/ergm_wtmodel.h | 2 ergm-4.8.1/ergm/inst/include/ergm_wtstate.h | 2 ergm-4.8.1/ergm/inst/include/model.h | 2 ergm-4.8.1/ergm/inst/include/wtMHproposal.h | 2 ergm-4.8.1/ergm/inst/include/wtchangestat.h | 2 ergm-4.8.1/ergm/inst/include/wtedgetree.h | 2 ergm-4.8.1/ergm/inst/include/wtmodel.h | 2 ergm-4.8.1/ergm/man/Dyads-ergmConstraint-3aee3115.Rd | 2 ergm-4.8.1/ergm/man/Project-ergmTerm-36962a06.Rd |only ergm-4.8.1/ergm/man/b1covrange-ergmTerm-24a903d2.Rd |only ergm-4.8.1/ergm/man/b1factordistinct-ergmTerm-f897b95c.Rd |only ergm-4.8.1/ergm/man/b2covrange-ergmTerm-5e2bcc86.Rd |only ergm-4.8.1/ergm/man/b2factordistinct-ergmTerm-076e6026.Rd |only ergm-4.8.1/ergm/man/ergm-defunct.Rd | 22 ergm-4.8.1/ergm/man/ergm-deprecated.Rd | 32 ergm-4.8.1/ergm/man/ergm-options.Rd | 14 ergm-4.8.1/ergm/man/ergm.mple.Rd | 4 ergm-4.8.1/ergm/man/fixallbut-ergmConstraint-ea96b2e0.Rd | 2 ergm-4.8.1/ergm/man/macros/ergm-spec.Rd | 2 ergm-4.8.1/ergm/man/macros/ergmCSS.Rd | 2 ergm-4.8.1/ergm/man/macros/ergmTerm.Rd | 2 ergm-4.8.1/ergm/man/macros/uid-algo.Rd | 2 ergm-4.8.1/ergm/man/nodecovrange-ergmTerm-7ae91499.Rd |only ergm-4.8.1/ergm/man/nodefactordistinct-ergmTerm-3445048c.Rd |only ergm-4.8.1/ergm/man/nodeicovrange-ergmTerm-29a8edd7.Rd |only ergm-4.8.1/ergm/man/nodeifactordistinct-ergmTerm-25cbd312.Rd |only ergm-4.8.1/ergm/man/nodeocovrange-ergmTerm-382e45c5.Rd |only ergm-4.8.1/ergm/man/nodeofactordistinct-ergmTerm-f159e5dc.Rd |only ergm-4.8.1/ergm/man/rlebdm.Rd | 6 ergm-4.8.1/ergm/man/samplk.Rd | 2 ergm-4.8.1/ergm/man/sampson.Rd | 2 ergm-4.8.1/ergm/src/CD.c | 2 ergm-4.8.1/ergm/src/CD.c.template.do_not_include_directly.h | 2 ergm-4.8.1/ergm/src/CD.h | 2 ergm-4.8.1/ergm/src/CD.h.template.do_not_include_directly.h | 2 ergm-4.8.1/ergm/src/MCMC.c | 2 ergm-4.8.1/ergm/src/MCMC.c.template.do_not_include_directly.h | 2 ergm-4.8.1/ergm/src/MCMC.h | 2 ergm-4.8.1/ergm/src/MCMC.h.template.do_not_include_directly.h | 2 ergm-4.8.1/ergm/src/MHproposal.c | 9 ergm-4.8.1/ergm/src/MHproposal_bd.c | 2 ergm-4.8.1/ergm/src/MHproposals.c | 2 ergm-4.8.1/ergm/src/MHproposals.h | 2 ergm-4.8.1/ergm/src/MHproposals_bipartite.c | 2 ergm-4.8.1/ergm/src/MHproposals_degree.c | 5 ergm-4.8.1/ergm/src/MHproposals_dyadnoise.c | 2 ergm-4.8.1/ergm/src/MHproposals_triadic.c | 14 ergm-4.8.1/ergm/src/MPLE.c | 2 ergm-4.8.1/ergm/src/MPLE.h | 2 ergm-4.8.1/ergm/src/SAN.c | 2 ergm-4.8.1/ergm/src/SAN.c.template.do_not_include_directly.h | 2 ergm-4.8.1/ergm/src/SAN.h | 2 ergm-4.8.1/ergm/src/SAN.h.template.do_not_include_directly.h | 2 ergm-4.8.1/ergm/src/allstatistics.c | 2 ergm-4.8.1/ergm/src/changestat.c | 2 ergm-4.8.1/ergm/src/changestats.c | 65 ergm-4.8.1/ergm/src/changestats.h | 2 ergm-4.8.1/ergm/src/changestats_auxnet.c | 2 ergm-4.8.1/ergm/src/changestats_auxnetalike.c | 2 ergm-4.8.1/ergm/src/changestats_coincidence.c | 2 ergm-4.8.1/ergm/src/changestats_concurrentties.c | 2 ergm-4.8.1/ergm/src/changestats_dgw_sp.c | 80 ergm-4.8.1/ergm/src/changestats_dgw_sp.h | 116 - ergm-4.8.1/ergm/src/changestats_diversity.c |only ergm-4.8.1/ergm/src/changestats_experimental.c | 44 ergm-4.8.1/ergm/src/changestats_experimental.h | 2 ergm-4.8.1/ergm/src/changestats_homoproportion.c | 2 ergm-4.8.1/ergm/src/changestats_indices.c | 2 ergm-4.8.1/ergm/src/changestats_interaction.c | 2 ergm-4.8.1/ergm/src/changestats_internal.c | 2 ergm-4.8.1/ergm/src/changestats_operator.c | 36 ergm-4.8.1/ergm/src/changestats_projection.c |only ergm-4.8.1/ergm/src/changestats_spcache.c | 2 ergm-4.8.1/ergm/src/changestats_test.c | 2 ergm-4.8.1/ergm/src/edgetree.c | 2 ergm-4.8.1/ergm/src/edgetree_inline.do_not_include_directly.h | 2 ergm-4.8.1/ergm/src/ergm_Rutil.c |only ergm-4.8.1/ergm/src/ergm_dyad_hashmap_utils.c | 2 ergm-4.8.1/ergm/src/ergm_dyadgen.c | 56 ergm-4.8.1/ergm/src/ergm_omp.c | 2 ergm-4.8.1/ergm/src/ergm_omp.h | 2 ergm-4.8.1/ergm/src/ergm_rlebdm.c | 2 ergm-4.8.1/ergm/src/ergm_state.c | 2 ergm-4.8.1/ergm/src/ergm_type_defs_common.h | 2 ergm-4.8.1/ergm/src/ergm_wtstate.c | 2 ergm-4.8.1/ergm/src/ergm_wttype_defs_common.h | 2 ergm-4.8.1/ergm/src/etamap.c | 31 ergm-4.8.1/ergm/src/geodist.c | 2 ergm-4.8.1/ergm/src/godfather.c | 2 ergm-4.8.1/ergm/src/init.c | 4 ergm-4.8.1/ergm/src/model.c | 25 ergm-4.8.1/ergm/src/netstats.c | 2 ergm-4.8.1/ergm/src/test_weighted_population.c | 2 ergm-4.8.1/ergm/src/wtCD.c | 2 ergm-4.8.1/ergm/src/wtCD.h | 2 ergm-4.8.1/ergm/src/wtMCMC.c | 2 ergm-4.8.1/ergm/src/wtMCMC.h | 2 ergm-4.8.1/ergm/src/wtMHproposal.c | 9 ergm-4.8.1/ergm/src/wtMHproposals.c | 2 ergm-4.8.1/ergm/src/wtSAN.c | 2 ergm-4.8.1/ergm/src/wtSAN.h | 2 ergm-4.8.1/ergm/src/wtchangestats.c | 2 ergm-4.8.1/ergm/src/wtchangestats.h | 2 ergm-4.8.1/ergm/src/wtchangestats_operator.c | 6 ergm-4.8.1/ergm/src/wtchangestats_operator.h | 2 ergm-4.8.1/ergm/src/wtchangestats_test.c | 2 ergm-4.8.1/ergm/src/wtedgetree.c | 2 ergm-4.8.1/ergm/src/wtedgetree_inline.do_not_include_directly.h | 2 ergm-4.8.1/ergm/src/wtgodfather.c | 2 ergm-4.8.1/ergm/src/wtmodel.c | 28 ergm-4.8.1/ergm/src/wtnetstats.c | 2 ergm-4.8.1/ergm/tests/requireNamespaceTest.R | 2 ergm-4.8.1/ergm/tests/testthat.R | 2 ergm-4.8.1/ergm/tests/testthat/helper-edges-MLE.R | 2 ergm-4.8.1/ergm/tests/testthat/helper-expect-summary.R | 2 ergm-4.8.1/ergm/tests/testthat/setup.R |only ergm-4.8.1/ergm/tests/testthat/test-C-curved.R | 8 ergm-4.8.1/ergm/tests/testthat/test-as.network.numeric.R | 66 ergm-4.8.1/ergm/tests/testthat/test-basis.R | 2 ergm-4.8.1/ergm/tests/testthat/test-bd.R | 2 ergm-4.8.1/ergm/tests/testthat/test-bipartite-missing-data.R | 2 ergm-4.8.1/ergm/tests/testthat/test-bridge-target.stats.R | 2 ergm-4.8.1/ergm/tests/testthat/test-c-ergm_model.R | 2 ergm-4.8.1/ergm/tests/testthat/test-checkpointing.R | 2 ergm-4.8.1/ergm/tests/testthat/test-constrain-blockdiag.R | 6 ergm-4.8.1/ergm/tests/testthat/test-constrain-degrees-edges.R | 2 ergm-4.8.1/ergm/tests/testthat/test-constrain-dind.R | 2 ergm-4.8.1/ergm/tests/testthat/test-constrain-egocentric.R | 2 ergm-4.8.1/ergm/tests/testthat/test-constraints.R | 29 ergm-4.8.1/ergm/tests/testthat/test-drop.R | 2 ergm-4.8.1/ergm/tests/testthat/test-ergm-godfather.R | 2 ergm-4.8.1/ergm/tests/testthat/test-ergm-proposal-unload.R | 2 ergm-4.8.1/ergm/tests/testthat/test-ergm-san.R | 2 ergm-4.8.1/ergm/tests/testthat/test-ergm-term-doc.R | 6 ergm-4.8.1/ergm/tests/testthat/test-ergm.bridge.llr.R | 2 ergm-4.8.1/ergm/tests/testthat/test-ergmMPLE.R | 2 ergm-4.8.1/ergm/tests/testthat/test-fix.curved.R | 2 ergm-4.8.1/ergm/tests/testthat/test-geodistn.R | 2 ergm-4.8.1/ergm/tests/testthat/test-gflomiss.R | 2 ergm-4.8.1/ergm/tests/testthat/test-gmonkmiss.R | 2 ergm-4.8.1/ergm/tests/testthat/test-gof.R | 2 ergm-4.8.1/ergm/tests/testthat/test-level-select.R | 2 ergm-4.8.1/ergm/tests/testthat/test-metrics.R | 2 ergm-4.8.1/ergm/tests/testthat/test-miss-dep.R | 2 ergm-4.8.1/ergm/tests/testthat/test-miss.CD.R | 4 ergm-4.8.1/ergm/tests/testthat/test-miss.R | 4 ergm-4.8.1/ergm/tests/testthat/test-mple-cov.R | 2 ergm-4.8.1/ergm/tests/testthat/test-mple-largenetwork.R | 2 ergm-4.8.1/ergm/tests/testthat/test-mple-offset.R | 2 ergm-4.8.1/ergm/tests/testthat/test-mple-target.R | 2 ergm-4.8.1/ergm/tests/testthat/test-networkLite.R | 2 ergm-4.8.1/ergm/tests/testthat/test-nodemix.R | 2 ergm-4.8.1/ergm/tests/testthat/test-nodrop.R | 2 ergm-4.8.1/ergm/tests/testthat/test-nonident-test.R | 2 ergm-4.8.1/ergm/tests/testthat/test-nonunique-names.R | 2 ergm-4.8.1/ergm/tests/testthat/test-offsets.R | 2 ergm-4.8.1/ergm/tests/testthat/test-operators.R | 2 ergm-4.8.1/ergm/tests/testthat/test-parallel.R | 2 ergm-4.8.1/ergm/tests/testthat/test-predict.ergm.R | 2 ergm-4.8.1/ergm/tests/testthat/test-proposal-bdstrattnt.R | 2 ergm-4.8.1/ergm/tests/testthat/test-runtime-diags.R | 2 ergm-4.8.1/ergm/tests/testthat/test-scoping.R | 2 ergm-4.8.1/ergm/tests/testthat/test-shrink-into-CH.R | 2 ergm-4.8.1/ergm/tests/testthat/test-simple.R | 2 ergm-4.8.1/ergm/tests/testthat/test-simulate-batch.R | 2 ergm-4.8.1/ergm/tests/testthat/test-snctrl.R | 2 ergm-4.8.1/ergm/tests/testthat/test-stocapprox.R | 6 ergm-4.8.1/ergm/tests/testthat/test-target-offset.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-For.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-Offset.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-Sum.R |only ergm-4.8.1/ergm/tests/testthat/test-term-attrcov.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-b12factor.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-b12nodematch.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-bipartite.R | 42 ergm-4.8.1/ergm/tests/testthat/test-term-directed.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-diversity.R |only ergm-4.8.1/ergm/tests/testthat/test-term-edgecov.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-errors.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-flexible.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-gw-sp.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-hamming.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-mm.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-options.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-project.R |only ergm-4.8.1/ergm/tests/testthat/test-term-undirected.R | 2 ergm-4.8.1/ergm/tests/testthat/test-term-valued.R | 2 ergm-4.8.1/ergm/tests/testthat/test-u-function.R | 6 ergm-4.8.1/ergm/tests/testthat/test-update.network.R | 2 ergm-4.8.1/ergm/tests/testthat/test-valued-sim.R | 5 ergm-4.8.1/ergm/tests/testthat/test-valued-terms.R | 6 ergm-4.8.1/ergm/tests/testthat/test-weighted-population.R | 2 375 files changed, 2498 insertions(+), 1632 deletions(-)
Title: Detect Elevations and Gaps in Mapped Sequencing Read Coverage
Description: Automate the detection of gaps and elevations in mapped sequencing
read coverage using a 2D pattern-matching algorithm. 'ProActive' detects, characterizes
and visualizes read coverage patterns in both genomes and metagenomes. Optionally,
users may provide gene annotations associated with their genome or metagenome
in the form of a .gff file. In this case, 'ProActive' will generate an additional
output table containing the gene annotations found within the detected regions of gapped
and elevated read coverage. Additionally, users can search for gene
annotations of interest in the output read coverage plots.
Author: Jessie Maier [aut, cre, cph] ,
Manuel Kleiner [aut, ths]
Maintainer: Jessie Maier <jlmaier@ncsu.edu>
Diff between ProActive versions 0.0.2 dated 2025-01-14 and 0.1.0 dated 2025-01-21
ProActive-0.0.2/ProActive/R/ProActive.R |only ProActive-0.0.2/ProActive/man/ProActive.Rd |only ProActive-0.1.0/ProActive/DESCRIPTION | 13 ProActive-0.1.0/ProActive/MD5 | 50 ProActive-0.1.0/ProActive/NAMESPACE | 5 ProActive-0.1.0/ProActive/NEWS.md | 13 ProActive-0.1.0/ProActive/R/GPsInElevGaps.R | 16 ProActive-0.1.0/ProActive/R/ProActive-package.R | 21 ProActive-0.1.0/ProActive/R/ProActiveDetect.R |only ProActive-0.1.0/ProActive/R/bestMatchListFunctions.R | 19 ProActive-0.1.0/ProActive/R/chunkingFunctions.R | 2 ProActive-0.1.0/ProActive/R/geneAnnotationPlot.R |only ProActive-0.1.0/ProActive/R/geneAnnotationSearch.R |only ProActive-0.1.0/ProActive/R/patternMatcher.R | 7 ProActive-0.1.0/ProActive/R/plotProActiveResults.R | 5 ProActive-0.1.0/ProActive/R/sampleMetagenomeResults.R | 4 ProActive-0.1.0/ProActive/R/sysdata.rda |binary ProActive-0.1.0/ProActive/README.md | 119 + ProActive-0.1.0/ProActive/inst/doc/ProActiveVignette.R | 53 ProActive-0.1.0/ProActive/inst/doc/ProActiveVignette.Rmd | 347 +++-- ProActive-0.1.0/ProActive/inst/doc/ProActiveVignette.html | 678 ++++++---- ProActive-0.1.0/ProActive/man/GPsInElevGaps.Rd | 12 ProActive-0.1.0/ProActive/man/ProActive-package.Rd | 22 ProActive-0.1.0/ProActive/man/ProActiveDetect.Rd |only ProActive-0.1.0/ProActive/man/classifSumm.Rd | 5 ProActive-0.1.0/ProActive/man/geneAnnotationPlot.Rd |only ProActive-0.1.0/ProActive/man/geneAnnotationSearch.Rd |only ProActive-0.1.0/ProActive/man/sampleMetagenomeResults.Rd | 4 ProActive-0.1.0/ProActive/tests/testthat/test-testProActive.R | 4 ProActive-0.1.0/ProActive/vignettes/ProActiveVignette.Rmd | 347 +++-- 30 files changed, 1162 insertions(+), 584 deletions(-)
Title: R Toolkit for 'Databricks'
Description: Collection of utilities that improve using 'Databricks' from R.
Primarily functions that wrap specific 'Databricks' APIs
(<https://docs.databricks.com/api>), 'RStudio' connection pane support, quality
of life functions to make 'Databricks' simpler to use.
Author: Zac Davies [aut, cre],
Rafi Kurlansik [aut],
Databricks [cph, fnd]
Maintainer: Zac Davies <zac@databricks.com>
Diff between brickster versions 0.2.5 dated 2024-11-13 and 0.2.6 dated 2025-01-21
DESCRIPTION | 6 +-- MD5 | 56 +++++++++++++++---------------- NEWS.md | 4 ++ R/package-auth.R | 2 - R/request-helpers.R | 12 +++--- R/volume-fs.R | 2 - inst/doc/cluster-management.html | 4 +- inst/doc/managing-jobs.html | 4 +- inst/doc/remote-repl.html | 4 +- inst/doc/setup-auth.html | 4 +- tests/testthat/test-auth.R | 43 +++++++++++------------ tests/testthat/test-clusters.R | 4 -- tests/testthat/test-dbfs.R | 5 -- tests/testthat/test-execution-contexts.R | 2 - tests/testthat/test-experiments.R | 2 - tests/testthat/test-feature-store.R | 2 - tests/testthat/test-jobs.R | 5 +- tests/testthat/test-libraries.R | 3 - tests/testthat/test-misc-helpers.R | 2 - tests/testthat/test-mlflow-dbrx.R | 4 -- tests/testthat/test-repos.R | 2 - tests/testthat/test-secrets.R | 2 - tests/testthat/test-sql-connector.R | 2 - tests/testthat/test-sql-execution.R | 2 - tests/testthat/test-unity-catalog.R | 5 -- tests/testthat/test-vector-search.R | 4 -- tests/testthat/test-volumes.R | 5 -- tests/testthat/test-warehouses.R | 2 - tests/testthat/test-workspace-folder.R | 2 - 29 files changed, 92 insertions(+), 104 deletions(-)