Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially
distributed animal population sampled with an array of passive detectors,
such as traps, or by searching polygons or transects. Models incorporating
distance-dependent detection are fitted by maximizing the likelihood.
Tools are included for data manipulation and model selection.
Author: Murray Efford [aut, cre] ,
Philipp Jund [ctb] ),
David Fletcher [ctb] )
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 4.6.7 dated 2024-06-05 and 4.6.9 dated 2024-06-28
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS | 19 ++++++++++++++++++- R/fastsecrloglik.R | 3 ++- R/generalsecrloglik.R | 3 ++- R/sim.popn.R | 23 ++++++++++++----------- R/utility.R | 2 +- inst/doc/secr-datainput.pdf |binary inst/doc/secr-overview.pdf |binary man/gridcells.Rd | 2 +- man/secr-package.Rd | 4 ++-- man/setNumThreads.Rd | 2 +- man/writeGPS.Rd | 2 +- 13 files changed, 56 insertions(+), 36 deletions(-)
Title: Draw Histograms and Restricted Cubic Splines (RCS)
Description: You can use this function to easily draw a combined histogram and restricted cubic spline.
The function draws the graph through 'ggplot2'. RCS fitting requires the use of the rcs() function of the 'rms' package.
Can fit cox regression, logistic regression. This method was described by Per Kragh (2003) <doi:10.1002/sim.1497>.
Author: Qiang LIU [aut, cre]
Maintainer: Qiang LIU <dege857@163.com>
Diff between ggrcs versions 0.3.8 dated 2024-01-29 and 0.4.0 dated 2024-06-28
DESCRIPTION | 6 - MD5 | 12 +- NEWS.md | 2 R/ggrcs.R | 34 ++++-- build/vignette.rds |binary inst/doc/ggrcs_vignette.R | 2 inst/doc/ggrcs_vignette.html | 231 +++++++++++++++++++++---------------------- 7 files changed, 153 insertions(+), 134 deletions(-)
Title: Measuring Association with Recursive Binning
Description: An iterative implementation of a recursive binary partitioning algorithm to measure pairwise dependence with a modular design that allows user specification of the splitting logic and stop criteria. Helper functions provide suggested versions of both and support visualization and the computation of summary statistics on final binnings. For a complete description of the functionality and algorithm, see Salahub and Oldford (2023) <doi:10.48550/arXiv.2311.08561>.
Author: Chris Salahub [aut, cre]
Maintainer: Chris Salahub <chris.salahub@uwaterloo.ca>
Diff between AssocBin versions 0.1-0 dated 2023-11-23 and 1.0-0 dated 2024-06-28
DESCRIPTION | 10 - MD5 | 66 ++++--- NAMESPACE | 17 + R/binner.R | 229 ++++++++++++++++++++++++- R/bins.R |only R/data.R | 46 ++++- R/dispatch.R |only R/plotBinning.R | 121 ++++++++++--- R/scoring.R | 83 +++------ R/splitters.R | 438 ++++++++++++++++++++++++++++++++++++++---------- R/stopper.R | 10 - build/vignette.rds |binary data/heart.rda |only data/sp500pseudo.rda |binary inst/doc/AssocBin.R | 7 inst/doc/AssocBin.Rmd | 14 + inst/doc/AssocBin.html | 374 +++++++++++++++++++++++++--------------- inst/doc/complex.R |only inst/doc/complex.Rmd |only inst/doc/complex.html |only man/binner.Rd | 12 - man/catBinner.Rd |only man/halfCutTie.Rd | 17 + man/halfSplit.Rd | 2 man/heart.Rd |only man/inDep.Rd |only man/makeBin.Rd |only man/maxScoreSplit.Rd | 28 +-- man/methods.Rd |only man/plotBinning.Rd | 28 ++- man/rIntSplit.Rd |only man/rUnifSplit.Rd |only man/sandboxMaxSplit.Rd |only man/scorings.Rd | 36 +-- man/shadings.Rd | 17 - man/singleBinner.Rd |only man/sp500pseudo.Rd | 6 man/stopper.Rd | 8 man/uniBinner.Rd |only man/uniMaxScoreSplit.Rd | 10 - man/uniRIntSplit.Rd |only vignettes/AssocBin.Rmd | 14 + vignettes/complex.Rmd |only 43 files changed, 1158 insertions(+), 435 deletions(-)
Title: Basic Functions to Statistical Methods Course
Description: Basic statistical methods with some modifications for the course Statistical Methods at Federal University of Bahia (Brazil). All methods in this packages are explained in the text book of Montgomery and Runger (2010) <ISBN: 978-1-119-74635-5>.
Author: Gilberto Sassi [aut, cre],
Carolina Costa Mota Paraiba [aut]
Maintainer: Gilberto Sassi <sassi.pereira.gilberto@gmail.com>
Diff between statBasics versions 0.2.0 dated 2022-08-17 and 0.2.2 dated 2024-06-28
DESCRIPTION | 8 - MD5 | 12 - R/ci_1pop_norm.R | 5 R/ht_2pop_mean.R | 345 ++++++++++++++++++++++++++--------------------------- R/ht_2pop_prop.R | 339 ++++++++++++++++++++++++++-------------------------- R/ht_2pop_var.R | 209 ++++++++++++++++---------------- man/ht_2pop_var.Rd | 2 7 files changed, 466 insertions(+), 454 deletions(-)
Title: Density-Based Spatial Clustering of Applications with Noise
(DBSCAN) and Related Algorithms
Description: A fast reimplementation of several density-based algorithms of
the DBSCAN family. Includes the clustering algorithms DBSCAN (density-based
spatial clustering of applications with noise) and HDBSCAN (hierarchical
DBSCAN), the ordering algorithm OPTICS (ordering points to identify the
clustering structure), shared nearest neighbor clustering, and the outlier
detection algorithms LOF (local outlier factor) and GLOSH (global-local
outlier score from hierarchies). The implementations use the kd-tree data
structure (from library ANN) for faster k-nearest neighbor search. An R
interface to fast kNN and fixed-radius NN search is also provided.
Hahsler, Piekenbrock and Doran (2019) <doi:10.18637/jss.v091.i01>.
Author: Michael Hahsler [aut, cre, cph]
,
Matthew Piekenbrock [aut, cph],
Sunil Arya [ctb, cph],
David Mount [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between dbscan versions 1.1-12 dated 2023-11-28 and 1.2-0 dated 2024-06-28
dbscan-1.1-12/dbscan/src/ANN.cpp |only dbscan-1.1-12/dbscan/src/R_JP.cpp |only dbscan-1.1-12/dbscan/src/R_buildHDBSCAN.cpp |only dbscan-1.1-12/dbscan/src/R_cleanup.cpp |only dbscan-1.1-12/dbscan/src/R_comps.cpp |only dbscan-1.1-12/dbscan/src/R_dbscan.cpp |only dbscan-1.1-12/dbscan/src/R_dendrogram.cpp |only dbscan-1.1-12/dbscan/src/R_density.cpp |only dbscan-1.1-12/dbscan/src/R_frNN.cpp |only dbscan-1.1-12/dbscan/src/R_kNN.cpp |only dbscan-1.1-12/dbscan/src/R_lof.cpp |only dbscan-1.1-12/dbscan/src/R_mrd.cpp |only dbscan-1.1-12/dbscan/src/R_optics.cpp |only dbscan-1.1-12/dbscan/src/R_prims_mst.cpp |only dbscan-1.1-12/dbscan/src/R_regionQuery.cpp |only dbscan-1.1-12/dbscan/src/R_regionQuery.h |only dbscan-1.1-12/dbscan/src/bd_fix_rad_search.cpp |only dbscan-1.1-12/dbscan/src/bd_pr_search.cpp |only dbscan-1.1-12/dbscan/src/bd_search.cpp |only dbscan-1.1-12/dbscan/src/bd_tree.cpp |only dbscan-1.1-12/dbscan/src/bd_tree.h |only dbscan-1.1-12/dbscan/src/brute.cpp |only dbscan-1.1-12/dbscan/src/kd_dump.cpp |only dbscan-1.1-12/dbscan/src/kd_fix_rad_search.cpp |only dbscan-1.1-12/dbscan/src/kd_fix_rad_search.h |only dbscan-1.1-12/dbscan/src/kd_pr_search.cpp |only dbscan-1.1-12/dbscan/src/kd_pr_search.h |only dbscan-1.1-12/dbscan/src/kd_search.cpp |only dbscan-1.1-12/dbscan/src/kd_search.h |only dbscan-1.1-12/dbscan/src/kd_split.cpp |only dbscan-1.1-12/dbscan/src/kd_split.h |only dbscan-1.1-12/dbscan/src/kd_tree.cpp |only dbscan-1.1-12/dbscan/src/kd_tree.h |only dbscan-1.1-12/dbscan/src/kd_util.cpp |only dbscan-1.1-12/dbscan/src/kd_util.h |only dbscan-1.1-12/dbscan/src/perf.cpp |only dbscan-1.1-12/dbscan/src/pr_queue.h |only dbscan-1.1-12/dbscan/src/pr_queue_k.h |only dbscan-1.2-0/dbscan/DESCRIPTION | 24 - dbscan-1.2-0/dbscan/MD5 | 183 +++++----- dbscan-1.2-0/dbscan/NAMESPACE | 22 + dbscan-1.2-0/dbscan/NEWS.md | 19 + dbscan-1.2-0/dbscan/R/AAA_dbscan-package.R | 13 dbscan-1.2-0/dbscan/R/LOF.R | 8 dbscan-1.2-0/dbscan/R/broom-dbscan-tidiers.R |only dbscan-1.2-0/dbscan/R/dbscan.R | 57 ++- dbscan-1.2-0/dbscan/R/extractFOSC.R | 11 dbscan-1.2-0/dbscan/R/frNN.R | 17 dbscan-1.2-0/dbscan/R/hdbscan.R | 10 dbscan-1.2-0/dbscan/R/jpclust.R | 23 - dbscan-1.2-0/dbscan/R/kNN.R | 15 dbscan-1.2-0/dbscan/R/kNNdist.R | 24 + dbscan-1.2-0/dbscan/R/nobs.R |only dbscan-1.2-0/dbscan/R/optics.R | 20 - dbscan-1.2-0/dbscan/R/pointdensity.R | 2 dbscan-1.2-0/dbscan/R/predict.R | 20 - dbscan-1.2-0/dbscan/R/reachability.R | 2 dbscan-1.2-0/dbscan/R/sNN.R | 49 +- dbscan-1.2-0/dbscan/R/sNNclust.R | 7 dbscan-1.2-0/dbscan/README.md | 221 ++++++++---- dbscan-1.2-0/dbscan/build/partial.rdb |binary dbscan-1.2-0/dbscan/build/vignette.rds |binary dbscan-1.2-0/dbscan/inst/README_files/dbscan-1.png |binary dbscan-1.2-0/dbscan/inst/README_files/tidyverse-1.png |only dbscan-1.2-0/dbscan/inst/README_files/tidyverse3-1.png |only dbscan-1.2-0/dbscan/inst/doc/dbscan.pdf |binary dbscan-1.2-0/dbscan/inst/doc/hdbscan.R | 14 dbscan-1.2-0/dbscan/inst/doc/hdbscan.Rmd | 14 dbscan-1.2-0/dbscan/inst/doc/hdbscan.html | 14 dbscan-1.2-0/dbscan/man/NN.Rd | 2 dbscan-1.2-0/dbscan/man/comps.Rd | 2 dbscan-1.2-0/dbscan/man/dbscan-package.Rd | 37 +- dbscan-1.2-0/dbscan/man/dbscan.Rd | 44 +- dbscan-1.2-0/dbscan/man/dbscan_tidiers.Rd |only dbscan-1.2-0/dbscan/man/frNN.Rd | 6 dbscan-1.2-0/dbscan/man/jpclust.Rd | 3 dbscan-1.2-0/dbscan/man/kNN.Rd | 1 dbscan-1.2-0/dbscan/man/kNNdist.Rd | 9 dbscan-1.2-0/dbscan/man/sNN.Rd | 42 +- dbscan-1.2-0/dbscan/man/sNNclust.Rd | 2 dbscan-1.2-0/dbscan/src/ANN/ANN.cpp |only dbscan-1.2-0/dbscan/src/ANN/bd_fix_rad_search.cpp |only dbscan-1.2-0/dbscan/src/ANN/bd_pr_search.cpp |only dbscan-1.2-0/dbscan/src/ANN/bd_search.cpp |only dbscan-1.2-0/dbscan/src/ANN/bd_tree.cpp |only dbscan-1.2-0/dbscan/src/ANN/bd_tree.h |only dbscan-1.2-0/dbscan/src/ANN/brute.cpp |only dbscan-1.2-0/dbscan/src/ANN/kd_dump.cpp |only dbscan-1.2-0/dbscan/src/ANN/kd_fix_rad_search.cpp |only dbscan-1.2-0/dbscan/src/ANN/kd_fix_rad_search.h |only dbscan-1.2-0/dbscan/src/ANN/kd_pr_search.cpp |only dbscan-1.2-0/dbscan/src/ANN/kd_pr_search.h |only dbscan-1.2-0/dbscan/src/ANN/kd_search.cpp |only dbscan-1.2-0/dbscan/src/ANN/kd_search.h |only dbscan-1.2-0/dbscan/src/ANN/kd_split.cpp |only dbscan-1.2-0/dbscan/src/ANN/kd_split.h |only dbscan-1.2-0/dbscan/src/ANN/kd_tree.cpp |only dbscan-1.2-0/dbscan/src/ANN/kd_tree.h |only dbscan-1.2-0/dbscan/src/ANN/kd_util.cpp |only dbscan-1.2-0/dbscan/src/ANN/kd_util.h |only dbscan-1.2-0/dbscan/src/ANN/perf.cpp |only dbscan-1.2-0/dbscan/src/ANN/pr_queue.h |only dbscan-1.2-0/dbscan/src/ANN/pr_queue_k.h |only dbscan-1.2-0/dbscan/src/JP.cpp |only dbscan-1.2-0/dbscan/src/Makevars | 12 dbscan-1.2-0/dbscan/src/buildHDBSCAN.cpp |only dbscan-1.2-0/dbscan/src/cleanup.cpp |only dbscan-1.2-0/dbscan/src/comps.cpp |only dbscan-1.2-0/dbscan/src/dbscan.cpp |only dbscan-1.2-0/dbscan/src/dendrogram.cpp |only dbscan-1.2-0/dbscan/src/density.cpp |only dbscan-1.2-0/dbscan/src/frNN.cpp |only dbscan-1.2-0/dbscan/src/kNN.cpp |only dbscan-1.2-0/dbscan/src/lof.cpp |only dbscan-1.2-0/dbscan/src/mrd.cpp |only dbscan-1.2-0/dbscan/src/optics.cpp |only dbscan-1.2-0/dbscan/src/prims_mst.cpp |only dbscan-1.2-0/dbscan/src/regionQuery.cpp |only dbscan-1.2-0/dbscan/src/regionQuery.h |only dbscan-1.2-0/dbscan/tests/testthat.R | 4 dbscan-1.2-0/dbscan/tests/testthat/test-dbscan.R | 136 +++---- dbscan-1.2-0/dbscan/tests/testthat/test-fosc.R | 142 +++---- dbscan-1.2-0/dbscan/tests/testthat/test-frNN.R | 203 +++++------ dbscan-1.2-0/dbscan/tests/testthat/test-hdbscan.R | 130 +++---- dbscan-1.2-0/dbscan/tests/testthat/test-kNN.R | 262 +++++++------- dbscan-1.2-0/dbscan/tests/testthat/test-kNNdist.R | 41 +- dbscan-1.2-0/dbscan/tests/testthat/test-lof.R | 302 ++++++++--------- dbscan-1.2-0/dbscan/tests/testthat/test-optics.R | 200 +++++------ dbscan-1.2-0/dbscan/tests/testthat/test-opticsXi.R | 27 - dbscan-1.2-0/dbscan/tests/testthat/test-predict.R | 124 +++--- dbscan-1.2-0/dbscan/tests/testthat/test-sNN.R | 171 ++++----- dbscan-1.2-0/dbscan/vignettes/dbscan.bib | 42 +- dbscan-1.2-0/dbscan/vignettes/hdbscan.Rmd | 14 133 files changed, 1480 insertions(+), 1267 deletions(-)
Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for
the complete machine learning life cycle, see <https://mlflow.org/>.
This package supports installing 'MLflow', tracking experiments,
creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre],
Javier Luraschi [aut],
Kevin Kuo [aut] ,
RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>
Diff between mlflow versions 2.13.1 dated 2024-05-30 and 2.14.1 dated 2024-06-28
DESCRIPTION | 6 +++--- MD5 | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-)
Title: Clustering and Prediction using Multi-Task Gaussian Processes
with Common Mean
Description: An implementation for the multi-task Gaussian processes with common
mean framework. Two main algorithms, called 'Magma' and 'MagmaClust',
are available to perform predictions for supervised learning problems, in
particular for time series or any functional/continuous data applications.
The corresponding articles has been respectively proposed by Arthur Leroy,
Pierre Latouche, Benjamin Guedj and Servane Gey (2022)
<doi:10.1007/s10994-022-06172-1>, and Arthur Leroy, Pierre Latouche,
Benjamin Guedj and Servane Gey (2023) <https://jmlr.org/papers/v24/20-1321.html>.
Theses approaches leverage the learning of cluster-specific mean processes,
which are common across similar tasks, to provide enhanced prediction
performances (even far from data) at a linear computational cost (in
the number of tasks). 'MagmaClust' is a generalisation of 'Magma'
where the tasks are simultaneously clustered into groups, each being
associated to a specific mean process. User-oriented functions in th [...truncated...]
Author: Arthur Leroy [aut, cre] ,
Pierre Latouche [aut],
Pierre Pathe [ctb],
Alexia Grenouillat [ctb],
Hugo Lelievre [ctb]
Maintainer: Arthur Leroy <arthur.leroy.pro@gmail.com>
Diff between MagmaClustR versions 1.2.0 dated 2024-03-21 and 1.2.1 dated 2024-06-28
DESCRIPTION | 6 MD5 | 39 NEWS.md | 15 R/initialisation.R | 596 ++-- R/kernel-to-matrices.R | 1125 ++++---- R/plot-functions.R | 2054 ++++++++-------- R/prediction.R | 86 R/sampling.R | 17 R/training.R | 39 README.md | 28 man/check_symmetric.Rd |only man/figures/README-gif_Magma-1.gif |binary man/figures/README-train_and_predict_Magma-1.png |binary man/figures/README-train_and_predict_Magma_in_2-D-1.png |binary man/pred_magmaclust.Rd | 2 man/regularize_data.Rd | 22 man/select_nb_cluster.Rd | 6 man/train_gp.Rd | 4 man/train_gp_clust.Rd | 6 man/train_magma.Rd | 7 man/train_magmaclust.Rd | 6 21 files changed, 2095 insertions(+), 1963 deletions(-)
Title: Causal Inference Test
Description: A likelihood-based hypothesis testing approach is implemented for
assessing causal mediation. Described in Millstein, Chen, and Breton (2016),
<DOI:10.1093/bioinformatics/btw135>, it could be used to test for mediation
of a known causal association between a DNA variant, the 'instrumental variable',
and a clinical outcome or phenotype by gene expression or DNA methylation, the
potential mediator. Another example would be testing mediation of the effect
of a drug on a clinical outcome by the molecular target. The hypothesis test
generates a p-value or permutation-based FDR value with confidence intervals
to quantify uncertainty in the causal inference. The outcome can be represented
by either a continuous or binary variable, the potential mediator is continuous,
and the instrumental variable can be continuous or binary and is not limited to
a single variable but may be a design matrix representing multiple variables.
Author: Joshua Millstein [aut, cre]
Maintainer: Joshua Millstein <joshua.millstein@usc.edu>
Diff between cit versions 2.3.1 dated 2021-05-25 and 2.3.2 dated 2024-06-28
cit-2.3.1/cit/build |only cit-2.3.2/cit/DESCRIPTION | 11 ++++++----- cit-2.3.2/cit/MD5 | 19 +++++++++---------- cit-2.3.2/cit/inst/CITATION | 4 ++-- cit-2.3.2/cit/man/cit-package.Rd | 5 +++-- cit-2.3.2/cit/src/Makevars | 2 +- cit-2.3.2/cit/src/Makevars.win | 2 +- cit-2.3.2/cit/src/citconlog2.cpp | 6 ++++-- cit-2.3.2/cit/src/citconlog2cvr.cpp | 6 ++++-- cit-2.3.2/cit/src/citconlog3_perm.cpp | 6 ++++-- cit-2.3.2/cit/src/citconlog3cvr_perm.cpp | 6 ++++-- 11 files changed, 38 insertions(+), 29 deletions(-)
Title: Dynamically Generates Documentation from a 'Swagger' Compliant
API
Description: A collection of 'HTML', 'JavaScript', and 'CSS' assets that
dynamically generate beautiful documentation from a 'Swagger' compliant API:
<https://swagger.io/specification/>.
Author: Barret Schloerke [aut] ,
Javier Luraschi [aut],
Bruno Tremblay [cre, ctb],
RStudio [cph],
SmartBear Software [aut, cph]
Maintainer: Bruno Tremblay <cran@neoxone.com>
Diff between swagger versions 5.17.14 dated 2024-06-11 and 5.17.14.1 dated 2024-06-28
DESCRIPTION | 6 - MD5 | 18 ++--- NEWS.md | 50 ++++++++------- inst/dist5/package.json | 36 +++++------ inst/dist5/swagger-ui-bundle.js | 2 inst/dist5/swagger-ui-standalone-preset.js | 2 inst/dist5/swagger-ui.css | 4 - inst/dist5/swagger-ui.js | 2 man/swagger-package.Rd | 86 +++++++++++++-------------- tests/testthat/test-md5sum.R | 92 ++++++++++++++--------------- 10 files changed, 151 insertions(+), 147 deletions(-)
Title: A Notifier for R Users by 'WeChat'
Description: This is a 'WeChat' Notifier for R users to notice when script run complete.
Author: Lei Cui Developer [aut, ctr, cph, cre],
An Qin Researcher [fnd, ths],
Feng Jiang Engineer [ctb]
Maintainer: Lei Cui Developer <cuilei798@qq.com>
Diff between easyWechat versions 0.1.0 dated 2024-06-21 and 0.2.0 dated 2024-06-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/wechat.R | 15 ++++++++------- man/WechatMsg.Rd | 8 ++++---- man/WechatRobot.Rd | 2 +- 5 files changed, 20 insertions(+), 19 deletions(-)
Title: Mixed Effect Excess Hazard Models
Description: Fit flexible (excess) hazard regression models with the possibility of including non-proportional effects of covariables and of adding a random effect at the cluster level (corresponding to a shared frailty). A detailed description of the package functionalities is provided in Charvat and Belot (2021) <doi: 10.18637/jss.v098.i14>.
Author: Hadrien Charvat, Aurelien Belot, Juste Goungounga
Maintainer: Hadrien Charvat <h.charvat.ef@juntendo.ac.jp>
Diff between mexhaz versions 2.5 dated 2024-03-20 and 2.6 dated 2024-06-28
DESCRIPTION | 10 MD5 | 20 - NEWS | 6 R/mexhaz.R | 4 R/mexhazAlpha.R |only R/mexhazAlphaStd.R |only R/mexhazEgh.R | 46 ++- R/mexhazStd.R | 1 R/predict.mexhaz.R | 653 -------------------------------------------------- R/predictRec.R |only R/predictStd.R |only man/mexhaz.Rd | 8 man/predict.mexhaz.Rd | 2 13 files changed, 73 insertions(+), 677 deletions(-)
Title: Robust Linear Quantile Regression
Description: It fits a robust linear quantile regression model using a new family of zero-quantile distributions for the error term. Missing values and censored observations can be handled as well. This family of distribution includes skewed versions of the Normal, Student's t, Laplace, Slash and Contaminated Normal distribution. It also performs logistic quantile regression for bounded responses as shown in Galarza et.al.(2020) <doi:10.1007/s13571-020-00231-0>. It provides estimates and full inference. It also provides envelopes plots for assessing the fit and confidences bands when several quantiles are provided simultaneously.
Author: Christian E. Galarza <chedgala@espol.edu.ec>, Luis Benites <lbenitess@pucp.edu.pe>, Marcelo Bourguignon <m.p.bourguignon@gmail.com>, Victor H. Lachos <hlachos@uconn.edu>
Maintainer: Christian E. Galarza <cgalarza88@gmail.com>
Diff between lqr versions 5.0 dated 2022-08-15 and 5.1 dated 2024-06-28
DESCRIPTION | 12 ++++++------ MD5 | 20 ++++++++++---------- NAMESPACE | 7 +++---- build/partial.rdb |binary man/SKD.Rd | 4 ++-- man/best.lqr.Rd | 2 +- man/cens.lqr.Rd | 2 +- man/logbestlqr.Rd | 4 ++-- man/loglqr.Rd | 2 +- man/lqr-package.Rd | 4 ++-- man/lqr.Rd | 2 +- 11 files changed, 29 insertions(+), 30 deletions(-)
Title: Metagenome Coverage Estimation and Projections for 'Nonpareil'
Description: Plot, process, and analyze NPO files produced by
'Nonpareil' <http://enve-omics.ce.gatech.edu/nonpareil/>.
Author: Luis M. Rodriguez-R [aut, cre]
Maintainer: Luis M. Rodriguez-R <lmrodriguezr@gmail.com>
Diff between Nonpareil versions 3.4.0 dated 2022-01-28 and 3.5.3 dated 2024-06-28
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- R/Nonpareil.R | 4 ++-- man/Nonpareil.Rd | 13 ++++++++++++- man/Nonpareil.curve.Rd | 24 ++++++++++++++++++++---- man/Nonpareil.curve.batch.Rd | 10 ++++++++-- man/Nonpareil.set.Rd | 30 ++++++++++++++++++++---------- man/cash-Nonpareil.Curve-method.Rd | 1 - man/cash-Nonpareil.Set-method.Rd | 1 - man/cash-set-Nonpareil.Curve-method.Rd | 1 - man/cash-set-Nonpareil.Set-method.Rd | 1 - man/plot.Nonpareil.Curve.Rd | 28 ++++++++++++++++++++++------ man/plot.Nonpareil.Set.Rd | 10 ++++++++-- man/plus-Nonpareil.Set-ANY-method.Rd | 1 - 14 files changed, 109 insertions(+), 49 deletions(-)
Title: Template Model Builder: A General Random Effect Tool Inspired by
'ADMB'
Description: With this tool, a user should be able to quickly implement
complex random effect models through simple C++ templates. The package combines
'CppAD' (C++ automatic differentiation), 'Eigen' (templated matrix-vector
library) and 'CHOLMOD' (sparse matrix routines available from R) to obtain
an efficient implementation of the applied Laplace approximation with exact
derivatives. Key features are: Automatic sparseness detection, parallelism
through 'BLAS' and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph],
Brad Bell [cph],
Hans Skaug [ctb],
Arni Magnusson [ctb],
Casper Berg [ctb],
Anders Nielsen [ctb],
Martin Maechler [ctb],
Theo Michelot [ctb],
Mollie Brooks [ctb],
Alex Forrence [ctb],
Christoffer Moesgaard Albertsen [...truncated...]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between TMB versions 1.9.12 dated 2024-06-19 and 1.9.13 dated 2024-06-28
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 6 ++++++ src/utils.c | 2 +- 4 files changed, 14 insertions(+), 8 deletions(-)
Title: Work with Data from High-Resolution Biologging Tags
Description: High-resolution movement-sensor tags typically include accelerometers
to measure body posture and sudden movements or changes in speed,
magnetometers to measure direction of travel, and pressure sensors
to measure dive depth in aquatic or marine animals. The sensors in these tags usually sample many times per second. Some tags include sensors for speed, turning rate (gyroscopes), and sound. This package provides software tools to facilitate calibration, processing, and analysis of such data. Tools are provided for: data import/export;
calibration (from raw data to calibrated data in scientific units);
visualization (for example, multi-panel time-series plots);
data processing (such as event detection, calculation of derived metrics like jerk and
dynamic acceleration, dive detection, and dive parameter calculation); and statistical analysis (for example, track reconstruction, a rotation test, and Mahalanobis distance analysis).
Author: Stacy DeRuiter [aut, cre, cph]
,
Mark Johnson [aut, cph],
David Sweeney [aut],
Ye Joo McNamara-Oh [aut],
Samuel Fynewever [aut],
Racheal Tejevbo [aut],
Tiago Marques [aut],
Yuqian Wang [aut],
Su Ogedegbe [aut]
Maintainer: Stacy DeRuiter <stacy.deruiter@calvin.edu>
Diff between tagtools versions 0.1.0 dated 2023-07-18 and 0.2.0 dated 2024-06-28
tagtools-0.1.0/tagtools/R/col_line.R |only tagtools-0.1.0/tagtools/man/col_line.Rd |only tagtools-0.2.0/tagtools/DESCRIPTION | 20 - tagtools-0.2.0/tagtools/MD5 | 89 ++--- tagtools-0.2.0/tagtools/NAMESPACE | 2 tagtools-0.2.0/tagtools/NEWS.md | 24 + tagtools-0.2.0/tagtools/R/check_AM.R | 10 tagtools-0.2.0/tagtools/R/col_line3.R | 100 +++--- tagtools-0.2.0/tagtools/R/comp_filt.R | 2 tagtools-0.2.0/tagtools/R/crop_all.R | 2 tagtools-0.2.0/tagtools/R/crop_to.R | 2 tagtools-0.2.0/tagtools/R/data.R | 46 +- tagtools-0.2.0/tagtools/R/decz.R | 2 tagtools-0.2.0/tagtools/R/depth_rate.R | 2 tagtools-0.2.0/tagtools/R/dive_stats.R | 342 +++++++++++----------- tagtools-0.2.0/tagtools/R/fir_nodelay.R | 2 tagtools-0.2.0/tagtools/R/interp2length.R | 4 tagtools-0.2.0/tagtools/R/make_specgram.R | 6 tagtools-0.2.0/tagtools/R/ocdr.R | 2 tagtools-0.2.0/tagtools/R/odba.R | 4 tagtools-0.2.0/tagtools/R/plott.R | 186 +++++++---- tagtools-0.2.0/tagtools/R/plott_base.R |only tagtools-0.2.0/tagtools/R/plott_static_panel.R |only tagtools-0.2.0/tagtools/R/read_cats.R | 22 + tagtools-0.2.0/tagtools/R/read_cats_csv.R | 13 tagtools-0.2.0/tagtools/R/rotation_test.R | 24 - tagtools-0.2.0/tagtools/README.md | 71 +++- tagtools-0.2.0/tagtools/man/beaked_whale.Rd | 2 tagtools-0.2.0/tagtools/man/check_AM.Rd | 10 tagtools-0.2.0/tagtools/man/col_line3.Rd | 2 tagtools-0.2.0/tagtools/man/comp_filt.Rd | 2 tagtools-0.2.0/tagtools/man/crop_all.Rd | 2 tagtools-0.2.0/tagtools/man/crop_to.Rd | 2 tagtools-0.2.0/tagtools/man/decz.Rd | 2 tagtools-0.2.0/tagtools/man/depth_rate.Rd | 2 tagtools-0.2.0/tagtools/man/dive_stats.Rd | 28 - tagtools-0.2.0/tagtools/man/draw_axis.Rd | 2 tagtools-0.2.0/tagtools/man/fir_nodelay.Rd | 2 tagtools-0.2.0/tagtools/man/harbor_seal.Rd | 2 tagtools-0.2.0/tagtools/man/interp2length.Rd | 4 tagtools-0.2.0/tagtools/man/make_specgram.Rd | 6 tagtools-0.2.0/tagtools/man/ocdr.Rd | 2 tagtools-0.2.0/tagtools/man/odba.Rd | 4 tagtools-0.2.0/tagtools/man/plott.Rd | 21 - tagtools-0.2.0/tagtools/man/plott_base.Rd |only tagtools-0.2.0/tagtools/man/plott_static_panel.Rd |only tagtools-0.2.0/tagtools/man/read_cats.Rd | 9 tagtools-0.2.0/tagtools/man/rotation_test.Rd | 23 - tagtools-0.2.0/tagtools/tests/testthat/Rplots.pdf |only 49 files changed, 608 insertions(+), 496 deletions(-)
Title: Segregation Analysis for Variant Interpretation
Description: An implementation of the full-likelihood Bayes factor (FLB)
for evaluating segregation evidence in clinical medical genetics. The
method was introduced by Thompson et al. (2003) <doi:10.1086/378100>.
This implementation supports custom penetrance values and liability
classes, and allows visualisations and robustness analysis as
presented in Ratajska et al. (2023) <doi:10.1002/mgg3.2107>. See also the
online app 'shinyseg', <https://chrcarrizosa.shinyapps.io/shinyseg>, which
offers interactive segregation analysis with many additional features
(Carrizosa et al. (2024) <doi:10.1093/bioinformatics/btae201>).
Author: Magnus Dehli Vigeland [aut, cre]
,
Christian Carrizosa [aut]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between segregatr versions 0.3.0 dated 2023-06-26 and 0.4.0 dated 2024-06-28
segregatr-0.3.0/segregatr/man/segregatr.Rd |only segregatr-0.4.0/segregatr/DESCRIPTION | 41 +++---- segregatr-0.4.0/segregatr/MD5 | 29 ++--- segregatr-0.4.0/segregatr/NEWS.md | 20 ++- segregatr-0.4.0/segregatr/R/FLB.R | 53 +++++----- segregatr-0.4.0/segregatr/R/plotSegregation.R | 2 segregatr-0.4.0/segregatr/R/segregatr-package.R | 25 ---- segregatr-0.4.0/segregatr/R/startdata_causative.R | 40 +++---- segregatr-0.4.0/segregatr/README.md | 39 ++++++- segregatr-0.4.0/segregatr/build/partial.rdb |binary segregatr-0.4.0/segregatr/inst/CITATION |only segregatr-0.4.0/segregatr/man/FLB.Rd | 6 - segregatr-0.4.0/segregatr/man/figures/README-sibex-1.png |binary segregatr-0.4.0/segregatr/man/segregatr-package.Rd |only segregatr-0.4.0/segregatr/tests/testthat/Rplots.pdf |binary segregatr-0.4.0/segregatr/tests/testthat/test-intro-errors.R | 22 ++-- segregatr-0.4.0/segregatr/tests/testthat/test-other-examples.R | 12 ++ 17 files changed, 167 insertions(+), 122 deletions(-)
Title: Data Exchange Between R and 'LabKey' Server
Description: The 'LabKey' client library for R makes it easy for R users to
load live data from a 'LabKey' Server, <https://www.labkey.com/>,
into the R environment for analysis, provided users have permissions
to read the data. It also enables R users to insert, update, and
delete records stored on a 'LabKey' Server, provided they have appropriate
permissions to do so.
Author: Peter Hussey
Maintainer: Cory Nathe <cnathe@labkey.com>
Diff between Rlabkey versions 3.2.2 dated 2024-06-07 and 3.2.3 dated 2024-06-28
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 3 +++ R/labkey.experiment.R | 7 +------ man/Rlabkey-package.Rd | 4 ++-- man/labkey.experiment.createRun.Rd | 33 +-------------------------------- man/labkey.experiment.saveBatch.Rd | 30 ------------------------------ 7 files changed, 17 insertions(+), 80 deletions(-)
Title: Recommended Learners for 'mlr3'
Description: Recommended Learners for 'mlr3'. Extends 'mlr3' with
interfaces to essential machine learning packages on CRAN. This
includes, but is not limited to: (penalized) linear and logistic
regression, linear and quadratic discriminant analysis, k-nearest
neighbors, naive Bayes, support vector machines, and gradient
boosting.
Author: Michel Lang [aut] ,
Quay Au [aut] ,
Stefan Coors [aut] ,
Patrick Schratz [aut] ,
Marc Becker [cre, aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3learners versions 0.6.0 dated 2024-03-13 and 0.7.0 dated 2024-06-28
DESCRIPTION | 36 ++++--- MD5 | 64 ++++++------- NAMESPACE | 1 NEWS.md | 5 + R/LearnerClassifXgboost.R | 112 +++++++++++++++++------- R/LearnerRegrXgboost.R | 93 +++++++++++++++---- R/zzz.R | 4 inst/paramtest/test_paramtest_classif.xgboost.R | 12 +- inst/paramtest/test_paramtest_regr.xgboost.R | 12 +- man/mlr3learners-package.Rd | 3 man/mlr_learners_classif.cv_glmnet.Rd | 10 +- man/mlr_learners_classif.glmnet.Rd | 8 - man/mlr_learners_classif.kknn.Rd | 8 - man/mlr_learners_classif.lda.Rd | 6 - man/mlr_learners_classif.log_reg.Rd | 10 +- man/mlr_learners_classif.multinom.Rd | 6 - man/mlr_learners_classif.naive_bayes.Rd | 6 - man/mlr_learners_classif.nnet.Rd | 8 - man/mlr_learners_classif.qda.Rd | 6 - man/mlr_learners_classif.ranger.Rd | 10 +- man/mlr_learners_classif.svm.Rd | 8 - man/mlr_learners_classif.xgboost.Rd | 70 +++++++++------ man/mlr_learners_regr.cv_glmnet.Rd | 10 +- man/mlr_learners_regr.glmnet.Rd | 8 - man/mlr_learners_regr.kknn.Rd | 8 - man/mlr_learners_regr.km.Rd | 28 +++--- man/mlr_learners_regr.lm.Rd | 6 - man/mlr_learners_regr.nnet.Rd | 8 - man/mlr_learners_regr.ranger.Rd | 8 - man/mlr_learners_regr.svm.Rd | 6 - man/mlr_learners_regr.xgboost.Rd | 71 +++++++++------ tests/testthat/test_classif_xgboost.R | 62 +++++++++++-- tests/testthat/test_regr_xgboost.R | 62 +++++++++++-- 33 files changed, 513 insertions(+), 262 deletions(-)
Title: Species Distribution and Abundance Modelling at High
Spatio-Temporal Resolution
Description: A collection of novel tools for generating species distribution and abundance models (SDM) that are dynamic through both space and time. These highly flexible functions incorporate spatial and temporal aspects across key SDM stages; including when cleaning and filtering species occurrence data, generating pseudo-absence records, assessing and correcting sampling biases and autocorrelation, extracting explanatory variables and projecting distribution patterns. Throughout, functions utilise Google Earth Engine and Google Drive to minimise the computing power and storage demands associated with species distribution modelling at high spatio-temporal resolution.
Author: Rachel Dobson [aut, cre, ctb] ,
Andy J. Challinor [aut, ctb] ,
Robert A. Cheke [aut, ctb] ,
Stewart Jennings [aut, ctb] ,
Stephen G. Willis [aut, ctb] ,
Martin Dallimer [aut, ctb]
Maintainer: Rachel Dobson <eerdo@leeds.ac.uk>
Diff between dynamicSDM versions 1.3.3 dated 2023-10-18 and 1.3.4 dated 2024-06-28
DESCRIPTION | 6 MD5 | 32 - R/brt_fit.R | 8 R/spatiotemp_bias.R | 4 R/spatiotemp_check.R | 278 ++++++------- R/spatiotemp_thin.R | 36 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/vignette1_response_data.R | 2 inst/doc/vignette1_response_data.html | 638 ++++++++----------------------- inst/doc/vignette2_explanatory_data.R | 4 inst/doc/vignette2_explanatory_data.html | 399 +++---------------- inst/doc/vignette3_modelling.R | 2 inst/doc/vignette3_modelling.html | 371 +++--------------- inst/doc/vignette4_projecting.R | 2 inst/doc/vignette4_projecting.html | 390 +++--------------- man/spatiotemp_check.Rd | 2 17 files changed, 588 insertions(+), 1586 deletions(-)
Title: Estimation in Difference-in-Difference Designs with Multiple
Groups and Periods
Description: Estimation of event-study Difference-in-Difference (DID) estimators in designs with multiple groups and periods, and with a potentially non-binary treatment that may increase or decrease multiple times.
Author: Diego Ciccia [aut, cre],
Felix Knau [aut],
Melitine Malezieux [aut],
Doulo Sow [aut],
Clement de Chaisemartin [aut]
Maintainer: Diego Ciccia <diego.ciccia@sciencespo.fr>
Diff between DIDmultiplegtDYN versions 1.0.12 dated 2024-06-20 and 1.0.13 dated 2024-06-28
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/did_multiplegt_main.R | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
More information about DIDmultiplegtDYN at CRAN
Permanent link
Title: Black-Box Optimization Toolkit
Description: Features highly configurable search spaces via the 'paradox'
package and optimizes every user-defined objective function. The
package includes several optimization algorithms e.g. Random Search,
Iterated Racing, Bayesian Optimization (in 'mlr3mbo') and Hyperband
(in 'mlr3hyperband'). bbotk is the base package of 'mlr3tuning',
'mlr3fselect' and 'miesmuschel'.
Author: Marc Becker [cre, aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Martin Binder [aut],
Olaf Mersmann [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between bbotk versions 0.8.0 dated 2024-02-29 and 1.0.0 dated 2024-06-28
bbotk-0.8.0/bbotk/R/ArchiveBest.R |only bbotk-0.8.0/bbotk/R/CallbackOptimization.R |only bbotk-0.8.0/bbotk/R/ContextOptimization.R |only bbotk-0.8.0/bbotk/R/OptimizerCmaes.R |only bbotk-0.8.0/bbotk/R/OptimizerDesignPoints.R |only bbotk-0.8.0/bbotk/R/OptimizerFocusSearch.R |only bbotk-0.8.0/bbotk/R/OptimizerGenSA.R |only bbotk-0.8.0/bbotk/R/OptimizerGridSearch.R |only bbotk-0.8.0/bbotk/R/OptimizerIrace.R |only bbotk-0.8.0/bbotk/R/OptimizerNLoptr.R |only bbotk-0.8.0/bbotk/R/OptimizerRandomSearch.R |only bbotk-0.8.0/bbotk/man/ArchiveBest.Rd |only bbotk-0.8.0/bbotk/man/CallbackOptimization.Rd |only bbotk-0.8.0/bbotk/man/ContextOptimization.Rd |only bbotk-0.8.0/bbotk/man/callback_optimization.Rd |only bbotk-0.8.0/bbotk/man/optimize_default.Rd |only bbotk-0.8.0/bbotk/tests/testthat/helper_rs.R |only bbotk-0.8.0/bbotk/tests/testthat/test_Archive.R |only bbotk-0.8.0/bbotk/tests/testthat/test_ArchiveBest.R |only bbotk-0.8.0/bbotk/tests/testthat/test_OptimInstanceMultiCrit.R |only bbotk-0.8.0/bbotk/tests/testthat/test_OptimInstanceSingleCrit.R |only bbotk-1.0.0/bbotk/DESCRIPTION | 97 - bbotk-1.0.0/bbotk/MD5 | 272 ++-- bbotk-1.0.0/bbotk/NAMESPACE | 64 - bbotk-1.0.0/bbotk/NEWS.md | 13 bbotk-1.0.0/bbotk/R/Archive.R | 197 --- bbotk-1.0.0/bbotk/R/ArchiveAsync.R |only bbotk-1.0.0/bbotk/R/ArchiveBatch.R |only bbotk-1.0.0/bbotk/R/CallbackAsync.R |only bbotk-1.0.0/bbotk/R/CallbackBatch.R |only bbotk-1.0.0/bbotk/R/Codomain.R | 6 bbotk-1.0.0/bbotk/R/ContextAsync.R |only bbotk-1.0.0/bbotk/R/ContextBatch.R |only bbotk-1.0.0/bbotk/R/Objective.R | 62 - bbotk-1.0.0/bbotk/R/ObjectiveRFun.R | 22 bbotk-1.0.0/bbotk/R/ObjectiveRFunDt.R | 22 bbotk-1.0.0/bbotk/R/ObjectiveRFunMany.R | 19 bbotk-1.0.0/bbotk/R/OptimInstance.R | 218 +-- bbotk-1.0.0/bbotk/R/OptimInstanceAsync.R |only bbotk-1.0.0/bbotk/R/OptimInstanceAsyncMultiCrit.R |only bbotk-1.0.0/bbotk/R/OptimInstanceAsyncSingleCrit.R |only bbotk-1.0.0/bbotk/R/OptimInstanceBatch.R |only bbotk-1.0.0/bbotk/R/OptimInstanceBatchMultiCrit.R |only bbotk-1.0.0/bbotk/R/OptimInstanceBatchSingleCrit.R |only bbotk-1.0.0/bbotk/R/OptimInstanceMultiCrit.R | 77 - bbotk-1.0.0/bbotk/R/OptimInstanceSingleCrit.R | 65 - bbotk-1.0.0/bbotk/R/Optimizer.R | 68 - bbotk-1.0.0/bbotk/R/OptimizerAsync.R |only bbotk-1.0.0/bbotk/R/OptimizerAsyncDesignPoints.R |only bbotk-1.0.0/bbotk/R/OptimizerAsyncGridSearch.R |only bbotk-1.0.0/bbotk/R/OptimizerAsyncRandomSearch.R |only bbotk-1.0.0/bbotk/R/OptimizerBatch.R |only bbotk-1.0.0/bbotk/R/OptimizerBatchCmaes.R |only bbotk-1.0.0/bbotk/R/OptimizerBatchDesignPoints.R |only bbotk-1.0.0/bbotk/R/OptimizerBatchFocusSearch.R |only bbotk-1.0.0/bbotk/R/OptimizerBatchGenSA.R |only bbotk-1.0.0/bbotk/R/OptimizerBatchGridSearch.R |only bbotk-1.0.0/bbotk/R/OptimizerBatchIrace.R |only bbotk-1.0.0/bbotk/R/OptimizerBatchNLoptr.R |only bbotk-1.0.0/bbotk/R/OptimizerBatchRandomSearch.R |only bbotk-1.0.0/bbotk/R/Terminator.R | 10 bbotk-1.0.0/bbotk/R/TerminatorClockTime.R | 2 bbotk-1.0.0/bbotk/R/TerminatorCombo.R | 2 bbotk-1.0.0/bbotk/R/TerminatorEvals.R | 2 bbotk-1.0.0/bbotk/R/TerminatorNone.R | 4 bbotk-1.0.0/bbotk/R/TerminatorPerfReached.R | 2 bbotk-1.0.0/bbotk/R/TerminatorRunTime.R | 2 bbotk-1.0.0/bbotk/R/TerminatorStagnation.R | 2 bbotk-1.0.0/bbotk/R/as_terminator.R |only bbotk-1.0.0/bbotk/R/assertions.R | 104 + bbotk-1.0.0/bbotk/R/bb_optimize.R | 4 bbotk-1.0.0/bbotk/R/helper.R | 83 - bbotk-1.0.0/bbotk/R/mlr_callbacks.R | 6 bbotk-1.0.0/bbotk/R/sugar.R | 65 + bbotk-1.0.0/bbotk/R/worker_loops.R |only bbotk-1.0.0/bbotk/R/zzz.R | 1 bbotk-1.0.0/bbotk/README.md | 22 bbotk-1.0.0/bbotk/inst/WORDLIST | 8 bbotk-1.0.0/bbotk/inst/doc/bbotk.R | 4 bbotk-1.0.0/bbotk/inst/doc/bbotk.Rmd | 4 bbotk-1.0.0/bbotk/inst/doc/bbotk.html | 591 +++++----- bbotk-1.0.0/bbotk/man/Archive.Rd | 158 -- bbotk-1.0.0/bbotk/man/ArchiveAsync.Rd |only bbotk-1.0.0/bbotk/man/ArchiveBatch.Rd |only bbotk-1.0.0/bbotk/man/CallbackAsync.Rd |only bbotk-1.0.0/bbotk/man/CallbackBatch.Rd |only bbotk-1.0.0/bbotk/man/Codomain.Rd | 18 bbotk-1.0.0/bbotk/man/ContextAsync.Rd |only bbotk-1.0.0/bbotk/man/ContextBatch.Rd |only bbotk-1.0.0/bbotk/man/Objective.Rd | 52 bbotk-1.0.0/bbotk/man/ObjectiveRFun.Rd | 4 bbotk-1.0.0/bbotk/man/ObjectiveRFunDt.Rd | 4 bbotk-1.0.0/bbotk/man/ObjectiveRFunMany.Rd | 4 bbotk-1.0.0/bbotk/man/OptimInstance.Rd | 133 -- bbotk-1.0.0/bbotk/man/OptimInstanceAsync.Rd |only bbotk-1.0.0/bbotk/man/OptimInstanceAsyncMultiCrit.Rd |only bbotk-1.0.0/bbotk/man/OptimInstanceAsyncSingleCrit.Rd |only bbotk-1.0.0/bbotk/man/OptimInstanceBatch.Rd |only bbotk-1.0.0/bbotk/man/OptimInstanceBatchMultiCrit.Rd |only bbotk-1.0.0/bbotk/man/OptimInstanceBatchSingleCrit.Rd |only bbotk-1.0.0/bbotk/man/OptimInstanceMultiCrit.Rd | 74 - bbotk-1.0.0/bbotk/man/OptimInstanceSingleCrit.Rd | 61 - bbotk-1.0.0/bbotk/man/Optimizer.Rd | 28 bbotk-1.0.0/bbotk/man/OptimizerAsync.Rd |only bbotk-1.0.0/bbotk/man/OptimizerBatch.Rd |only bbotk-1.0.0/bbotk/man/as_terminator.Rd |only bbotk-1.0.0/bbotk/man/assign_result_default.Rd | 4 bbotk-1.0.0/bbotk/man/bb_optimize.Rd | 2 bbotk-1.0.0/bbotk/man/bbotk.backup.Rd | 2 bbotk-1.0.0/bbotk/man/bbotk_assertions.Rd | 40 bbotk-1.0.0/bbotk/man/bbotk_worker_loop.Rd |only bbotk-1.0.0/bbotk/man/callback_async.Rd |only bbotk-1.0.0/bbotk/man/callback_batch.Rd |only bbotk-1.0.0/bbotk/man/evaluate_queue_default.Rd |only bbotk-1.0.0/bbotk/man/mlr_optimizers_async_design_points.Rd |only bbotk-1.0.0/bbotk/man/mlr_optimizers_async_grid_search.Rd |only bbotk-1.0.0/bbotk/man/mlr_optimizers_async_random_search.Rd |only bbotk-1.0.0/bbotk/man/mlr_optimizers_cmaes.Rd | 30 bbotk-1.0.0/bbotk/man/mlr_optimizers_design_points.Rd | 30 bbotk-1.0.0/bbotk/man/mlr_optimizers_focus_search.Rd | 30 bbotk-1.0.0/bbotk/man/mlr_optimizers_gensa.Rd | 30 bbotk-1.0.0/bbotk/man/mlr_optimizers_grid_search.Rd | 30 bbotk-1.0.0/bbotk/man/mlr_optimizers_irace.Rd | 36 bbotk-1.0.0/bbotk/man/mlr_optimizers_nloptr.Rd | 30 bbotk-1.0.0/bbotk/man/mlr_optimizers_random_search.Rd | 30 bbotk-1.0.0/bbotk/man/mlr_terminators_none.Rd | 2 bbotk-1.0.0/bbotk/man/oi.Rd |only bbotk-1.0.0/bbotk/man/oi_async.Rd |only bbotk-1.0.0/bbotk/man/optimize_async_default.Rd |only bbotk-1.0.0/bbotk/man/optimize_batch_default.Rd |only bbotk-1.0.0/bbotk/man/search_start.Rd | 2 bbotk-1.0.0/bbotk/man/shrink_ps.Rd | 2 bbotk-1.0.0/bbotk/man/terminated_error.Rd |only bbotk-1.0.0/bbotk/man/trafo_xs.Rd |only bbotk-1.0.0/bbotk/tests/testthat/_snaps |only bbotk-1.0.0/bbotk/tests/testthat/helper.R | 43 bbotk-1.0.0/bbotk/tests/testthat/setup.R | 10 bbotk-1.0.0/bbotk/tests/testthat/teardown.R | 3 bbotk-1.0.0/bbotk/tests/testthat/test_ArchiveAsync.R |only bbotk-1.0.0/bbotk/tests/testthat/test_ArchiveBatch.R |only bbotk-1.0.0/bbotk/tests/testthat/test_Callback.R | 29 bbotk-1.0.0/bbotk/tests/testthat/test_Objective.R | 8 bbotk-1.0.0/bbotk/tests/testthat/test_OptimInstanceAsyncSingleCrit.R |only bbotk-1.0.0/bbotk/tests/testthat/test_OptimInstanceBatchMultiCrit.R |only bbotk-1.0.0/bbotk/tests/testthat/test_OptimInstanceBatchSingleCrit.R |only bbotk-1.0.0/bbotk/tests/testthat/test_OptimizerAsynDesignPoints.R |only bbotk-1.0.0/bbotk/tests/testthat/test_OptimizerAsynGridSearch.R |only bbotk-1.0.0/bbotk/tests/testthat/test_OptimizerAsync.R |only bbotk-1.0.0/bbotk/tests/testthat/test_OptimizerAsyncRandomSearch.R |only bbotk-1.0.0/bbotk/tests/testthat/test_OptimizerCmaes.R | 8 bbotk-1.0.0/bbotk/tests/testthat/test_OptimizerDesignPoints.R | 10 bbotk-1.0.0/bbotk/tests/testthat/test_OptimizerFocusSearch.R | 10 bbotk-1.0.0/bbotk/tests/testthat/test_OptimizerGenSA.R | 6 bbotk-1.0.0/bbotk/tests/testthat/test_OptimizerGridSearch.R | 10 bbotk-1.0.0/bbotk/tests/testthat/test_OptimizerIrace.R | 22 bbotk-1.0.0/bbotk/tests/testthat/test_OptimizerNLoptr.R | 6 bbotk-1.0.0/bbotk/tests/testthat/test_OptimizerRandomSearch.R | 14 bbotk-1.0.0/bbotk/tests/testthat/test_TerminatorClockTime.R | 4 bbotk-1.0.0/bbotk/tests/testthat/test_TerminatorCombo.R | 2 bbotk-1.0.0/bbotk/tests/testthat/test_TerminatorEvals.R | 8 bbotk-1.0.0/bbotk/tests/testthat/test_TerminatorNone.R | 4 bbotk-1.0.0/bbotk/tests/testthat/test_TerminatorPerfReached.R | 6 bbotk-1.0.0/bbotk/tests/testthat/test_TerminatorRunTime.R | 6 bbotk-1.0.0/bbotk/tests/testthat/test_TerminatorStagnation.R | 6 bbotk-1.0.0/bbotk/tests/testthat/test_TerminatorStagnationBatch.R | 8 bbotk-1.0.0/bbotk/tests/testthat/test_bb_optimize.R | 16 bbotk-1.0.0/bbotk/tests/testthat/test_deprecated.R |only bbotk-1.0.0/bbotk/tests/testthat/test_mlr_callbacks.R | 41 bbotk-1.0.0/bbotk/tests/testthat/test_mlr_optimizers.R | 4 bbotk-1.0.0/bbotk/tests/testthat/test_nds_selection.R | 2 bbotk-1.0.0/bbotk/vignettes/bbotk.Rmd | 4 171 files changed, 1615 insertions(+), 1631 deletions(-)
Title: Perform Boolean Operations on Large Numbers
Description: A set of Boolean operators which accept integers of any size, in any base from 2 to 36, including 2's complement format, and perform actions like "AND," "OR", "NOT", "SHIFTR/L" etc. The output can be in any base specified. A direct base to base converter is included.
Author: Carl Witthoft [aut, cre]
Maintainer: Carl Witthoft <cellocgw@gmail.com>
Diff between bigBits versions 1.2 dated 2024-03-26 and 1.3 dated 2024-06-28
bigBits-1.2/bigBits/R/AbigBoolean.R |only bigBits-1.3/bigBits/ChangeLog | 3 +- bigBits-1.3/bigBits/DESCRIPTION | 10 +++--- bigBits-1.3/bigBits/MD5 | 16 +++++----- bigBits-1.3/bigBits/NAMESPACE | 2 - bigBits-1.3/bigBits/R/base2base.R | 16 +++++++++- bigBits-1.3/bigBits/R/bigBoolean.R |only bigBits-1.3/bigBits/R/fracB2B.R | 50 +++++++++++++++++++++++++++++----- bigBits-1.3/bigBits/build/partial.rdb |binary bigBits-1.3/bigBits/man/fracB2B.Rd | 2 - 10 files changed, 74 insertions(+), 25 deletions(-)
Title: Creating and Working with Pedigrees and Marker Data
Description: A comprehensive collection of tools for creating,
manipulating and visualising pedigrees and genetic marker data.
Pedigrees can be read from text files or created on the fly with
built-in functions. A range of utilities enable modifications like
adding or removing individuals, breaking loops, and merging pedigrees.
An online tool for creating pedigrees interactively, based on
'pedtools', is available at <https://magnusdv.shinyapps.io/quickped>.
'pedtools' is the hub of the 'pedsuite', a collection of packages for
pedigree analysis. A detailed presentation of the 'pedsuite' is given
in the book 'Pedigree Analysis in R' (Vigeland, 2021,
ISBN:9780128244302).
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between pedtools versions 2.6.0 dated 2024-03-31 and 2.7.0 dated 2024-06-28
pedtools-2.6.0/pedtools/R/plot_internal.R |only pedtools-2.6.0/pedtools/man/internalplot.Rd |only pedtools-2.7.0/pedtools/DESCRIPTION | 6 pedtools-2.7.0/pedtools/MD5 | 52 +-- pedtools-2.7.0/pedtools/NEWS.md | 25 + pedtools-2.7.0/pedtools/R/ped.R | 26 + pedtools-2.7.0/pedtools/R/ped_basic.R | 26 + pedtools-2.7.0/pedtools/R/ped_convert.R | 69 +++- pedtools-2.7.0/pedtools/R/ped_internal.R | 69 ++-- pedtools-2.7.0/pedtools/R/ped_modify.R | 2 pedtools-2.7.0/pedtools/R/ped_plot.R | 17 - pedtools-2.7.0/pedtools/R/ped_sex.R | 8 pedtools-2.7.0/pedtools/R/ped_utils.R | 43 +- pedtools-2.7.0/pedtools/R/plot_methods.R |only pedtools-2.7.0/pedtools/R/readPed.R | 32 + pedtools-2.7.0/pedtools/README.md | 18 - pedtools-2.7.0/pedtools/build/vignette.rds |binary pedtools-2.7.0/pedtools/inst/doc/pedtools.html | 170 +++++----- pedtools-2.7.0/pedtools/man/as.ped.Rd | 26 + pedtools-2.7.0/pedtools/man/getComponent.Rd | 13 pedtools-2.7.0/pedtools/man/ped.Rd | 21 - pedtools-2.7.0/pedtools/man/ped_basic.Rd | 5 pedtools-2.7.0/pedtools/man/ped_internal.Rd | 30 + pedtools-2.7.0/pedtools/man/plot.ped.Rd | 9 pedtools-2.7.0/pedtools/man/plotmethods.Rd |only pedtools-2.7.0/pedtools/man/readPed.Rd | 33 + pedtools-2.7.0/pedtools/man/validatePed.Rd | 12 pedtools-2.7.0/pedtools/tests/testthat/test-ped-creation.R | 4 pedtools-2.7.0/pedtools/tests/testthat/test-ped-modifications.R | 4 29 files changed, 454 insertions(+), 266 deletions(-)
Title: Hamiltonian Monte Carlo and Other Gradient-Based MCMC Sampling
Algorithms for 'nimble'
Description: Provides gradient-based MCMC sampling algorithms for use with the MCMC engine provided by the 'nimble' package. This includes two versions of Hamiltonian Monte Carlo (HMC) No-U-Turn (NUTS) sampling, and (under development) Langevin samplers. The `NUTS_classic` sampler implements the original HMC-NUTS algorithm as described in Hoffman and Gelman (2014) <doi:10.48550/arXiv.1111.4246>. The `NUTS` sampler is a modern version of HMC-NUTS sampling matching the HMC sampler available in version 2.32.2 of Stan (Stan Development Team, 2023). In addition, convenience functions are provided for generating and modifying MCMC configuration objects which employ HMC sampling.
Author: Daniel Turek [aut, cre],
Perry de Valpine [aut],
Christopher Paciorek [aut]
Maintainer: Daniel Turek <danielturek@gmail.com>
Diff between nimbleHMC versions 0.2.1 dated 2024-02-08 and 0.2.2 dated 2024-06-28
DESCRIPTION | 10 ++-- MD5 | 20 ++++---- R/HMC_configuration.R | 21 +++++--- R/HMC_samplers.R | 102 +++++++++++++++++++++++++++++-------------- man/addHMC.Rd | 15 +++--- man/buildHMC.Rd | 2 man/configureHMC.Rd | 2 man/nimbleHMC.Rd | 2 man/sampler_NUTS.Rd | 9 ++- man/sampler_NUTS_classic.Rd | 9 ++- tests/testthat/test-tuning.R | 18 +++---- 11 files changed, 130 insertions(+), 80 deletions(-)
Title: Simulate Package Installation and Attach
Description: Simulates the process of installing a package and then
attaching it. This is a key part of the 'devtools' package as it
allows you to rapidly iterate while developing a package.
Author: Hadley Wickham [aut],
Winston Chang [aut],
Jim Hester [aut],
Lionel Henry [aut, cre],
Posit Software, PBC [cph, fnd],
R Core team [ctb]
Maintainer: Lionel Henry <lionel@posit.co>
Diff between pkgload versions 1.3.4 dated 2024-01-16 and 1.4.0 dated 2024-06-28
DESCRIPTION | 16 +++--- MD5 | 40 +++++++++------- NEWS.md | 33 +++++++++++++ R/compilation-db.R |only R/dev-help.R | 9 ++- R/import-standalone-obj-type.R |only R/import-standalone-types-check.R |only R/load.R | 90 ++++++++++++++++++++++---------------- R/package-deps.R | 2 R/run-loadhooks.R | 9 +++ R/source.R | 55 ++++++++++++++++++----- R/utils.R | 15 ++++++ inst/print-var.mk |only man/load_all.Rd | 13 ++--- tests/testthat/_snaps/source.md | 2 tests/testthat/helper-pkgload.R | 7 -- tests/testthat/test-dll.R | 26 +++++----- tests/testthat/test-help.R | 18 ++++++- tests/testthat/test-load-hooks.R | 15 ------ tests/testthat/test-load.R | 4 - tests/testthat/test-metadata.R | 2 tests/testthat/test-s4-unload.R | 20 ++++---- tests/testthat/test-shim.R | 2 23 files changed, 238 insertions(+), 140 deletions(-)
Title: Axis Invariant Scatter Pie Plots
Description: Extends 'ggplot2' to help replace points in a scatter plot with pie-chart glyphs showing the relative proportions of different categories. The pie glyphs are independent of the axes and plot dimensions, to prevent distortions when the plot dimensions are changed.
Author: Rishabh Vishwakarma [aut, cre]
,
Caroline Brophy [aut],
Catherine Hurley [aut]
Maintainer: Rishabh Vishwakarma <vishwakr@tcd.ie>
Diff between PieGlyph versions 0.1.0 dated 2023-02-09 and 1.0.0 dated 2024-06-28
DESCRIPTION | 20 MD5 | 90 + NAMESPACE | 17 NEWS.md |only R/geom_pie_glyph.R | 475 ++++---- R/geom_pie_interactive.R |only R/pie_grob.R |only README.md | 53 build/vignette.rds |binary inst/WORDLIST |only inst/doc/PieGlyph.R | 27 inst/doc/PieGlyph.Rmd | 54 inst/doc/PieGlyph.html | 1247 ++++++++++++++++++++--- inst/doc/interactive-pie-glyphs.R |only inst/doc/interactive-pie-glyphs.Rmd |only inst/doc/interactive-pie-glyphs.html |only inst/doc/multinomial-classification-example.R | 6 inst/doc/multinomial-classification-example.html | 265 ++-- inst/doc/pie-lollipop-example.R | 2 inst/doc/pie-lollipop-example.html | 324 ++--- inst/doc/spatial-example.R | 4 inst/doc/spatial-example.html | 256 ++-- inst/doc/time-series-example.R | 2 inst/doc/time-series-example.html | 236 ++-- inst/doc/unusual-situations.R | 37 inst/doc/unusual-situations.Rmd | 34 inst/doc/unusual-situations.html | 469 ++++---- man/PieGlyph-package.Rd | 1 man/figures/README-interactive-1.png |only man/figures/README-stacked-1.png |binary man/figures/interactive-pie-glyphs.png |only man/geom_pie_glyph.Rd | 160 +- man/geom_pie_interactive.Rd |only man/pieGrob.Rd | 76 - man/scale_radius_continuous.Rd | 25 tests |only vignettes/PieGlyph.Rmd | 54 vignettes/interactive-pie-glyphs.Rmd |only vignettes/unusual-situations.Rmd | 34 39 files changed, 2626 insertions(+), 1342 deletions(-)
Title: Read, Plot and Analyse Output from the DEPONS Model
Description: Methods for analyzing population dynamics and movement tracks simulated using the DEPONS model <https://www.depons.eu> (v.3.0), for manipulating input raster files, shipping routes and for analyzing sound propagated from ships.
Author: Jacob Nabe-Nielsen and Caitlin K. Frankish
Maintainer: Jacob Nabe-Nielsen <jnn@ecos.au.dk>
Diff between DEPONS2R versions 1.2.2 dated 2023-09-18 and 1.2.3 dated 2024-06-28
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/raster-methods.R | 2 +- R/ships_methods.R | 38 +++++++++++++++++++++++++------------- R/z-accessors.R | 9 ++++----- build/partial.rdb |binary man/DeponsRaster-class.Rd | 2 +- man/crs.Rd | 5 ++--- man/shipdata.Rd | 3 +-- 9 files changed, 46 insertions(+), 37 deletions(-)
Title: Utility Functions
Description: Base R sometimes requires verbose statements for simple,
often recurring tasks, such as printing text without trailing
space, ending with newline. This package aims at providing
shorthands for such tasks.
Author: Tobias Schmidt [aut, cre]
Maintainer: Tobias Schmidt <tobias.schmidt331@gmail.com>
Diff between toscutil versions 2.7.4 dated 2023-09-05 and 2.8.0 dated 2024-06-28
toscutil-2.7.4/toscutil/man/now_ms.Rd |only toscutil-2.8.0/toscutil/DESCRIPTION | 15 toscutil-2.8.0/toscutil/MD5 | 88 +- toscutil-2.8.0/toscutil/NAMESPACE | 10 toscutil-2.8.0/toscutil/R/base.R | 318 +++------ toscutil-2.8.0/toscutil/R/check.R | 45 - toscutil-2.8.0/toscutil/R/doc.R |only toscutil-2.8.0/toscutil/R/func.R | 316 +-------- toscutil-2.8.0/toscutil/R/imports.R |only toscutil-2.8.0/toscutil/R/live.R | 9 toscutil-2.8.0/toscutil/R/path.R | 349 ++++------ toscutil-2.8.0/toscutil/R/time.R | 56 - toscutil-2.8.0/toscutil/R/trace.R |only toscutil-2.8.0/toscutil/inst/WORDLIST | 9 toscutil-2.8.0/toscutil/man/DOCSTRING_TEMPLATE.Rd | 6 toscutil-2.8.0/toscutil/man/caller.Rd | 31 toscutil-2.8.0/toscutil/man/capture.output2.Rd | 16 toscutil-2.8.0/toscutil/man/cat2.Rd | 21 toscutil-2.8.0/toscutil/man/catf.Rd | 29 toscutil-2.8.0/toscutil/man/check_pkg_docs.Rd |only toscutil-2.8.0/toscutil/man/config_dir.Rd | 15 toscutil-2.8.0/toscutil/man/config_file.Rd | 15 toscutil-2.8.0/toscutil/man/data_dir.Rd | 8 toscutil-2.8.0/toscutil/man/dput2.Rd | 12 toscutil-2.8.0/toscutil/man/fg.Rd |only toscutil-2.8.0/toscutil/man/find_description_file.Rd |only toscutil-2.8.0/toscutil/man/function_locals.Rd | 10 toscutil-2.8.0/toscutil/man/get_docstring.Rd | 4 toscutil-2.8.0/toscutil/man/get_formals.Rd | 8 toscutil-2.8.0/toscutil/man/get_pkg_docs.Rd |only toscutil-2.8.0/toscutil/man/getfd.Rd | 7 toscutil-2.8.0/toscutil/man/getpd.Rd | 17 toscutil-2.8.0/toscutil/man/help2.Rd | 19 toscutil-2.8.0/toscutil/man/home.Rd | 9 toscutil-2.8.0/toscutil/man/ifthen.Rd | 6 toscutil-2.8.0/toscutil/man/locals.Rd | 13 toscutil-2.8.0/toscutil/man/logf.Rd |only toscutil-2.8.0/toscutil/man/named.Rd | 13 toscutil-2.8.0/toscutil/man/norm_path.Rd | 3 toscutil-2.8.0/toscutil/man/now.Rd | 29 toscutil-2.8.0/toscutil/man/op-null-default.Rd | 3 toscutil-2.8.0/toscutil/man/read_description_file.Rd |only toscutil-2.8.0/toscutil/man/split_docstring.Rd | 4 toscutil-2.8.0/toscutil/man/sys.exit.Rd | 23 toscutil-2.8.0/toscutil/man/trace_package.Rd |only toscutil-2.8.0/toscutil/man/untrace_package.Rd |only toscutil-2.8.0/toscutil/man/update_docstring.Rd | 4 toscutil-2.8.0/toscutil/tests/testthat/test-caller.R | 2 toscutil-2.8.0/toscutil/tests/testthat/test-cat2.R |only toscutil-2.8.0/toscutil/tests/testthat/test-check_pkg_docs.R |only toscutil-2.8.0/toscutil/tests/testthat/test-extract_help_section.R |only toscutil-2.8.0/toscutil/tests/testthat/test-get_pkg_docs.R |only toscutil-2.8.0/toscutil/tests/testthat/test-logf.R |only toscutil-2.8.0/toscutil/tests/testthat/test-trace_func.R |only 54 files changed, 618 insertions(+), 924 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-03 0.2.3
Title: Statistical Learning on Sparse Matrices
Description: Implements many algorithms for statistical learning on
sparse matrices - matrix factorizations, matrix completion,
elastic net regressions, factorization machines.
Also 'rsparse' enhances 'Matrix' package by providing methods for
multithreaded <sparse, dense> matrix products and native slicing of
the sparse matrices in Compressed Sparse Row (CSR) format.
List of the algorithms for regression problems:
1) Elastic Net regression via Follow The Proximally-Regularized Leader (FTRL)
Stochastic Gradient Descent (SGD), as per McMahan et al(, <doi:10.1145/2487575.2488200>)
2) Factorization Machines via SGD, as per Rendle (2010, <doi:10.1109/ICDM.2010.127>)
List of algorithms for matrix factorization and matrix completion:
1) Weighted Regularized Matrix Factorization (WRMF) via Alternating Least
Squares (ALS) - paper by Hu, Koren, Volinsky (2008, <doi:10.1109/ICDM.2008.22>)
2) Maximum-Margin Matrix Factorization via ALS, paper by Rennie, Srebro
(2005, <doi:10.1145/110 [...truncated...]
Author: Dmitriy Selivanov [aut, cre, cph]
,
David Cortes [ctb],
Drew Schmidt [ctb] ,
Wei-Chen Chen [ctb]
Maintainer: Dmitriy Selivanov <selivanov.dmitriy@gmail.com>
Diff between rsparse versions 0.5.1 dated 2022-09-11 and 0.5.2 dated 2024-06-28
DESCRIPTION | 18 +++---- MD5 | 24 +++++----- NEWS.md | 4 + R/SoftALS.R | 2 R/model_ScaleNormalize.R | 2 R/model_WRMF.R | 93 ++++++++++++++++++++++++----------------- README.md | 30 +++---------- inst/include/wrmf_implicit.hpp | 40 ++++++++++------- man/ScaleNormalize.Rd | 2 man/soft_impute.Rd | 2 src/Makevars.in | 2 src/Makevars.win | 2 src/utils.cpp | 13 +++-- 13 files changed, 121 insertions(+), 113 deletions(-)
More information about mgi.report.reader at CRAN
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More information about LogisticCopula at CRAN
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Title: Tabular Data Suppression using Gaussian Elimination
Description: A statistical disclosure control tool to protect tables by suppression
using the Gaussian elimination secondary suppression algorithm. A suggestion is
to start by working with functions SuppressSmallCounts() and
SuppressDominantCells(). These functions use primary suppression functions for
the minimum frequency rule and the dominance rule, respectively. Novel
functionality for suppression of disclosive cells is also included. General
primary suppression functions can be supplied as input to the general working
horse function, GaussSuppressionFromData(). Suppressed frequencies can be
replaced by synthetic decimal numbers as described in
Langsrud (2019) <doi:10.1007/s11222-018-9848-9>.
Author: Oeyvind Langsrud [aut, cre] ,
Daniel Lupp [aut] ,
Hege Boevelstad [ctb],
Vidar Norstein Klungre [rev],
Statistics Norway [cph]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between GaussSuppression versions 0.8.5 dated 2024-05-22 and 0.8.8 dated 2024-06-28
DESCRIPTION | 18 ++++++----- MD5 | 62 +++++++++++++++++++------------------- NEWS.md | 5 +++ R/Candidates.R | 2 - R/GaussSuppressDec.R | 14 ++++---- R/GaussSuppressionFromData.R | 24 +++++++------- R/GaussSuppressionTwoWay.R | 14 ++++---- R/MaxContribution.R | 2 - R/NContributorsRule.R | 5 ++- R/Ncontributors.R | 2 - R/Primary.R | 2 - R/PrimaryFromSuppressedData.R | 2 - R/PrimaryRemoveWg.R | 4 +- R/Singleton.R | 4 +- R/SuppressKDisclosure.R | 2 - R/SuppressionFromDecimals.R | 6 +-- man/CandidatesDefault.Rd | 2 - man/GaussSuppressDec.Rd | 12 +++---- man/GaussSuppressionFromData.Rd | 24 +++++++------- man/GaussSuppressionTwoWay.Rd | 14 ++++---- man/MaxContribution.Rd | 2 - man/Ncontributors.Rd | 2 - man/PrimaryDefault.Rd | 2 - man/PrimaryFromSuppressedData.Rd | 2 - man/PrimaryRemoveWg.Rd | 4 +- man/SingletonDefault.Rd | 2 - man/SingletonUniqueContributor.Rd | 2 - man/SuppressDominantCells.Rd | 4 +- man/SuppressFewContributors.Rd | 4 +- man/SuppressKDisclosure.Rd | 2 - man/SuppressSmallCounts.Rd | 4 +- man/SuppressionFromDecimals.Rd | 4 +- 32 files changed, 132 insertions(+), 122 deletions(-)
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More information about fullRankMatrix at CRAN
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Title: In-Line Documentation for R
Description: Generate your Rd documentation, 'NAMESPACE' file, and
collation field using specially formatted comments. Writing
documentation in-line with code makes it easier to keep your
documentation up-to-date as your requirements change. 'roxygen2' is
inspired by the 'Doxygen' system for C++.
Author: Hadley Wickham [aut, cre, cph]
,
Peter Danenberg [aut, cph],
Gabor Csardi [aut],
Manuel Eugster [aut, cph],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between roxygen2 versions 7.3.1 dated 2024-01-22 and 7.3.2 dated 2024-06-28
DESCRIPTION | 8 +++--- MD5 | 40 ++++++++++++++++---------------- NEWS.md | 5 ++++ R/block.R | 2 - R/rd-eval.R | 1 R/rd.R | 6 ++-- R/utils.R | 8 ++++-- build/vignette.rds |binary inst/doc/extending.html | 2 - inst/doc/index-crossref.html | 2 - inst/doc/namespace.html | 2 - inst/doc/rd-formatting.html | 2 - inst/doc/rd-other.html | 2 - inst/doc/rd.html | 2 - inst/doc/reuse.html | 2 - inst/doc/roxygen2.html | 2 - man/roxy_block.Rd | 2 - tests/testthat/_snaps/rd-include-rmd.md | 4 ++- tests/testthat/_snaps/utils.md | 9 +++++++ tests/testthat/test-rd-include-rmd.R | 6 ++++ tests/testthat/test-utils.R | 10 ++++++++ 21 files changed, 75 insertions(+), 42 deletions(-)
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Title: Machine Learning in R - Next Generation
Description: Efficient, object-oriented programming on the
building blocks of machine learning. Provides 'R6' objects for tasks,
learners, resamplings, and measures. The package is geared towards
scalability and larger datasets by supporting parallelization and
out-of-memory data-backends like databases. While 'mlr3' focuses on
the core computational operations, add-on packages provide additional
functionality.
Author: Michel Lang [aut] ,
Bernd Bischl [aut] ,
Jakob Richter [aut] ,
Patrick Schratz [aut] ,
Giuseppe Casalicchio [ctb] ,
Stefan Coors [ctb] ,
Quay Au [ctb] ,
Martin Binder [aut],
Florian Pfisterer [aut] ,
Raphael Sonabend [aut] ,
Lennart Schneider [ctb] , [...truncated...]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3 versions 0.19.0 dated 2024-04-24 and 0.20.0 dated 2024-06-28
DESCRIPTION | 27 +- MD5 | 126 ++++++------ NAMESPACE | 4 NEWS.md | 4 R/HotstartStack.R | 4 R/Learner.R | 85 +++++++- R/LearnerClassifDebug.R | 103 +++++++++- R/MeasureInternalValidScore.R |only R/ResultData.R | 8 R/Task.R | 129 ++++++++++--- R/as_task.R | 2 R/as_task_classif.R | 10 - R/as_task_regr.R | 10 - R/as_task_unsupervised.R | 4 R/assertions.R | 7 R/benchmark.R | 3 R/helper.R | 19 + R/helper_hashes.R | 28 ++ R/marshal.R | 23 -- R/mlr_reflections.R | 8 R/resample.R | 8 R/set_validate.R |only R/worker.R | 228 +++++++++++++++++------ inst/testthat/helper_expectations.R | 33 ++- man/BenchmarkResult.Rd | 2 man/Learner.Rd | 77 +++++++ man/LearnerClassif.Rd | 2 man/LearnerRegr.Rd | 2 man/Measure.Rd | 8 man/MeasureClassif.Rd | 3 man/MeasureRegr.Rd | 3 man/MeasureSimilarity.Rd | 3 man/ResultData.Rd | 26 +- man/Task.Rd | 49 ++++ man/TaskClassif.Rd | 1 man/TaskRegr.Rd | 1 man/TaskSupervised.Rd | 1 man/TaskUnsupervised.Rd | 1 man/as_prediction.Rd | 2 man/as_task_classif.Rd | 10 - man/as_task_regr.Rd | 10 - man/as_task_unsupervised.Rd | 4 man/benchmark.Rd | 5 man/marshaling.Rd | 11 - man/mlr3-package.Rd | 6 man/mlr_assertions.Rd | 10 - man/mlr_learners_classif.debug.Rd | 14 + man/mlr_measures.Rd | 1 man/mlr_measures_aic.Rd | 1 man/mlr_measures_bic.Rd | 1 man/mlr_measures_classif.costs.Rd | 1 man/mlr_measures_debug_classif.Rd | 1 man/mlr_measures_elapsed_time.Rd | 1 man/mlr_measures_internal_valid_score.Rd |only man/mlr_measures_oob_error.Rd | 1 man/mlr_measures_selected_features.Rd | 1 man/mlr_sugar.Rd | 26 ++ man/resample.Rd | 5 tests/testthat/test_Learner.R | 192 +++++++++++++++++++ tests/testthat/test_MeasureInternalValidScore.R |only tests/testthat/test_Resampling.R | 14 - tests/testthat/test_Task.R | 121 +++++++++++- tests/testthat/test_benchmark.R | 33 +++ tests/testthat/test_marshal.R | 3 tests/testthat/test_mlr_learners_classif_debug.R | 28 +- tests/testthat/test_resample.R | 161 ++++++++++++++++ 66 files changed, 1381 insertions(+), 334 deletions(-)
Title: Causal Modeling with Coincidence Analysis
Description: Provides comprehensive functionalities for causal modeling with Coincidence Analysis (CNA), which is a configurational comparative method of causal data analysis that was first introduced in Baumgartner (2009) <doi:10.1177/0049124109339369>, and generalized in Baumgartner & Ambuehl (2018) <doi:10.1017/psrm.2018.45>. CNA is designed to recover INUS-causation from data, which is particularly relevant for analyzing processes featuring conjunctural causation (component causation) and equifinality (alternative causation). CNA is currently the only method for INUS-discovery that allows for multiple effects (outcomes/endogenous factors), meaning it can analyze common-cause and causal chain structures.
Author: Mathias Ambuehl [aut, cre, cph],
Michael Baumgartner [aut, cph],
Ruedi Epple [ctb],
Veli-Pekka Parkkinen [ctb],
Alrik Thiem [ctb]
Maintainer: Mathias Ambuehl <mathias.ambuehl@consultag.ch>
Diff between cna versions 3.6.0 dated 2024-06-07 and 3.6.1 dated 2024-06-28
DESCRIPTION | 8 MD5 | 18 R/cna.r | 27 + R/cna_accel.r | 29 - R/cna_aux.r | 105 +++++ R/hfunctions.R | 2 inst/NEWS | 3 inst/doc/cna.pdf |binary man/cna-package.Rd | 2 man/cna.Rd | 1029 ++++++++++++++++++++++++++--------------------------- 10 files changed, 677 insertions(+), 546 deletions(-)
Title: Monthly Climate Data for Germany, Usable for Heating and Cooling
Calculations
Description: This data package contains monthly climate data in Germany, it can be used for heating and
cooling calculations (external temperature, heating / cooling days, solar radiation).
Author: Tobias Loga [aut] ,
Guillaume Behem [aut],
Jens Calisti [cre]
Maintainer: Jens Calisti <jens@tangled.de>
Diff between clidamonger versions 1.1.0 dated 2024-02-14 and 1.2.0 dated 2024-06-28
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 6 +++++- README.md | 4 +++- data/data.sol.rda |binary data/data.ta.hd.rda |binary data/list.station.ta.rda |binary man/data.ta.hd.Rd | 2 +- man/list.station.ta.Rd | 2 +- 9 files changed, 22 insertions(+), 16 deletions(-)
Title: Structure Optimized Proximity Scaling
Description: Methods that use flexible variants of multidimensional scaling (MDS) which incorporate parametric nonlinear distance transformations and trade-off the goodness-of-fit fit with structure considerations to find optimal hyperparameters, also known as structure optimized proximity scaling (STOPS) (Rusch, Mair & Hornik, 2023,<doi:10.1007/s11222-022-10197-w>). The package contains various functions, wrappers, methods and classes for fitting, plotting and displaying different 1-way MDS models with ratio, interval, ordinal optimal scaling in a STOPS framework. These cover essentially the functionality of the package smacofx, including Torgerson (classical) scaling with power transformations of dissimilarities, SMACOF MDS with powers of dissimilarities, Sammon mapping with powers of dissimilarities, elastic scaling with powers of dissimilarities, spherical SMACOF with powers of dissimilarities, (ALSCAL) s-stress MDS with powers of dissimilarities, r-stress MDS, MDS with powers of diss [...truncated...]
Author: Thomas Rusch [aut, cre] ,
Patrick Mair [aut] ,
Kurt Hornik [ctb]
Maintainer: Thomas Rusch <thomas.rusch@wu.ac.at>
Diff between stops versions 1.0-1 dated 2023-01-20 and 1.6-2 dated 2024-06-28
stops-1.0-1/stops/R/bcstress.R |only stops-1.0-1/stops/R/extras.R |only stops-1.0-1/stops/R/lmds.R |only stops-1.0-1/stops/R/optimizations.R |only stops-1.0-1/stops/R/powerstress.R |only stops-1.0-1/stops/man/apStressMin.Rd |only stops-1.0-1/stops/man/bcStressMin.Rd |only stops-1.0-1/stops/man/cmds.Rd |only stops-1.0-1/stops/man/cmdscale.Rd |only stops-1.0-1/stops/man/conf_adjust.Rd |only stops-1.0-1/stops/man/doubleCenter.Rd |only stops-1.0-1/stops/man/enorm.Rd |only stops-1.0-1/stops/man/lmds.Rd |only stops-1.0-1/stops/man/mkBmat.Rd |only stops-1.0-1/stops/man/mkPower.Rd |only stops-1.0-1/stops/man/mkPower2.Rd |only stops-1.0-1/stops/man/plot.cmdscaleE.Rd |only stops-1.0-1/stops/man/plot.smacofP.Rd |only stops-1.0-1/stops/man/plot3d.cmdscaleE.Rd |only stops-1.0-1/stops/man/plot3d.stops.Rd |only stops-1.0-1/stops/man/plot3dstatic.Rd |only stops-1.0-1/stops/man/plot3dstatic.cmdscaleE.Rd |only stops-1.0-1/stops/man/plot3dstatic.stops.Rd |only stops-1.0-1/stops/man/powerStressMin.Rd |only stops-1.0-1/stops/man/print.cmdscale.Rd |only stops-1.0-1/stops/man/print.sammon.Rd |only stops-1.0-1/stops/man/print.summary.smacofP.Rd |only stops-1.0-1/stops/man/procruster.Rd |only stops-1.0-1/stops/man/sammon.Rd |only stops-1.0-1/stops/man/secularEq.Rd |only stops-1.0-1/stops/man/sqdist.Rd |only stops-1.0-1/stops/man/stop_bcstress.Rd |only stops-1.0-1/stops/man/summary.cmdscale.Rd |only stops-1.0-1/stops/man/summary.sammon.Rd |only stops-1.0-1/stops/man/summary.smacofP.Rd |only stops-1.0-1/stops/man/torgerson.Rd |only stops-1.6-2/stops/DESCRIPTION | 31 stops-1.6-2/stops/MD5 | 172 +- stops-1.6-2/stops/NAMESPACE | 65 - stops-1.6-2/stops/NEWS | 66 + stops-1.6-2/stops/R/bootmds.stops.R |only stops-1.6-2/stops/R/coef.stops.R |only stops-1.6-2/stops/R/jackmds.stops.R |only stops-1.6-2/stops/R/ljoptim.R |only stops-1.6-2/stops/R/plot.stops.R |only stops-1.6-2/stops/R/print.stops.R |only stops-1.6-2/stops/R/residuals.stops.R |only stops-1.6-2/stops/R/spp.R |only stops-1.6-2/stops/R/stop_apstress.R |only stops-1.6-2/stops/R/stop_bcmds.R |only stops-1.6-2/stops/R/stop_clca.R |only stops-1.6-2/stops/R/stop_clda.R |only stops-1.6-2/stops/R/stop_cmdscale.R |only stops-1.6-2/stops/R/stop_elastic.R |only stops-1.6-2/stops/R/stop_isomap.R |only stops-1.6-2/stops/R/stop_lmds.R |only stops-1.6-2/stops/R/stop_powerelastic.R |only stops-1.6-2/stops/R/stop_powermds.R |only stops-1.6-2/stops/R/stop_powersammon.R |only stops-1.6-2/stops/R/stop_powerstress.R |only stops-1.6-2/stops/R/stop_rpowerstress.R |only stops-1.6-2/stops/R/stop_rstress.R |only stops-1.6-2/stops/R/stop_sammon.R |only stops-1.6-2/stops/R/stop_sammon2.R |only stops-1.6-2/stops/R/stop_smacofSphere.R |only stops-1.6-2/stops/R/stop_smacofSym.R |only stops-1.6-2/stops/R/stop_smdda.R |only stops-1.6-2/stops/R/stop_smds.R |only stops-1.6-2/stops/R/stop_spmdda.R |only stops-1.6-2/stops/R/stop_spmds.R |only stops-1.6-2/stops/R/stop_sstress.R |only stops-1.6-2/stops/R/stoploss.R |only stops-1.6-2/stops/R/stops-package.R | 305 ++++ stops-1.6-2/stops/R/stops.R | 1474 ------------------------ stops-1.6-2/stops/R/structurednessindices.R | 75 + stops-1.6-2/stops/R/summary.stops.R |only stops-1.6-2/stops/R/tgpoptim.R |only stops-1.6-2/stops/build/vignette.rds |binary stops-1.6-2/stops/inst/CITATION | 63 - stops-1.6-2/stops/man/bootmds.stops.Rd |only stops-1.6-2/stops/man/c_clumpiness.Rd | 2 stops-1.6-2/stops/man/c_clusteredness.Rd | 2 stops-1.6-2/stops/man/c_convexity.Rd | 2 stops-1.6-2/stops/man/c_hierarchy.Rd | 2 stops-1.6-2/stops/man/c_outlying.Rd | 2 stops-1.6-2/stops/man/c_shepardness.Rd |only stops-1.6-2/stops/man/c_skinniness.Rd | 2 stops-1.6-2/stops/man/c_sparsity.Rd | 2 stops-1.6-2/stops/man/c_striatedness.Rd | 2 stops-1.6-2/stops/man/c_stringiness.Rd | 2 stops-1.6-2/stops/man/coef.stops.Rd | 2 stops-1.6-2/stops/man/jackmds.stops.Rd |only stops-1.6-2/stops/man/ljoptim.Rd | 4 stops-1.6-2/stops/man/plot.stops.Rd | 14 stops-1.6-2/stops/man/print.stops.Rd | 2 stops-1.6-2/stops/man/print.summary.stops.Rd | 2 stops-1.6-2/stops/man/residuals.stops.Rd | 2 stops-1.6-2/stops/man/stop_apstress.Rd | 25 stops-1.6-2/stops/man/stop_bcmds.Rd |only stops-1.6-2/stops/man/stop_clca.Rd |only stops-1.6-2/stops/man/stop_cldae.Rd |only stops-1.6-2/stops/man/stop_cldak.Rd |only stops-1.6-2/stops/man/stop_cmdscale.Rd | 24 stops-1.6-2/stops/man/stop_elastic.Rd | 17 stops-1.6-2/stops/man/stop_isomap1.Rd | 15 stops-1.6-2/stops/man/stop_isomap2.Rd | 15 stops-1.6-2/stops/man/stop_lmds.Rd | 17 stops-1.6-2/stops/man/stop_powerelastic.Rd | 19 stops-1.6-2/stops/man/stop_powermds.Rd | 19 stops-1.6-2/stops/man/stop_powersammon.Rd | 13 stops-1.6-2/stops/man/stop_powerstress.Rd | 17 stops-1.6-2/stops/man/stop_rpowerstress.Rd | 15 stops-1.6-2/stops/man/stop_rstress.Rd | 21 stops-1.6-2/stops/man/stop_sammon.Rd | 19 stops-1.6-2/stops/man/stop_sammon2.Rd | 15 stops-1.6-2/stops/man/stop_smacofSphere.Rd | 15 stops-1.6-2/stops/man/stop_smacofSym.Rd | 17 stops-1.6-2/stops/man/stop_smddae.Rd |only stops-1.6-2/stops/man/stop_smddak.Rd |only stops-1.6-2/stops/man/stop_smds.Rd |only stops-1.6-2/stops/man/stop_spmddae.Rd |only stops-1.6-2/stops/man/stop_spmddak.Rd |only stops-1.6-2/stops/man/stop_spmds.Rd |only stops-1.6-2/stops/man/stop_sstress.Rd | 19 stops-1.6-2/stops/man/stoploss.Rd | 6 stops-1.6-2/stops/man/stops-package.Rd |only stops-1.6-2/stops/man/stops.Rd | 138 -- stops-1.6-2/stops/man/summary.stops.Rd | 2 stops-1.6-2/stops/man/tgpoptim.Rd | 4 129 files changed, 818 insertions(+), 1929 deletions(-)
Title: Managing and Building of Quarterly Life Tables
Description: Manages, builds and computes statistics and datasets for the
construction of quarterly (sub-annual) life tables by exploiting micro-data from
either a general or an insured population.
References:
Pavía and Lledó (2022) <doi:10.1111/rssa.12769>.
Pavía and Lledó (2023) <doi:10.1017/asb.2023.16>.
Acknowledgements:
The authors wish to thank Consellería de Educación, Universidades y Empleo, Generalitat Valenciana (grant AICO/2021/257), Ministerio de Ciencia e Innovación (grant PID2021-128228NB-I00) and Fundación Mapfre (grant 'Modelización espacial e intra-anual de la mortalidad en España. Una herramienta automática para el cálculo de productos de vida') for supporting this research.
Author: Jose M. Pavia [aut, cre] ,
Josep Lledo [aut]
Maintainer: Jose M. Pavia <jose.m.pavia@uv.es>
Diff between qlifetable versions 0.0.2-4 dated 2024-01-24 and 0.0.2-5 dated 2024-06-28
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NEWS.md | 8 +++++++- R/SAI_shortcut_1.R | 2 ++ R/annual2quarterly.R | 22 +++++++++------------- R/compute_SAI.R | 2 ++ R/crude_mx_sh2.R | 2 ++ R/crude_mx_sh3.R | 2 ++ R/plot.SAI.R | 26 +++++++++++++++----------- man/SAI_shortcut_1.Rd | 2 ++ man/annual2quarterly.Rd | 18 +++++++----------- man/compute_SAI.Rd | 2 ++ man/crude_mx_sh2.Rd | 2 ++ man/crude_mx_sh3.Rd | 2 ++ 14 files changed, 71 insertions(+), 53 deletions(-)
Title: Visualizing the Decision Rules Underlying Binary Classification
Description: Visualization of decision rules for binary classification and Receiver Operating Characteristic (ROC) curve estimation under different generalizations proposed in the literature:
- making the classification subsets flexible to cover those scenarios where both extremes of the
marker are associated with a higher risk of being positive, considering two thresholds
(gROC() function);
- transforming the marker by a proper function trying to improve the classification performance
(hROC() function);
- when dealing with multivariate markers, considering a proper transformation to univariate space
trying to maximize the resulting AUC of the TPR for each FPR (multiROC() function).
The classification regions behind each point of the ROC curve are displayed in both static
graphics (plot_buildROC(), plot_regions() or plot_funregions() function) or
videos (movieROC() function).
Author: Sonia Perez-Fernandez [aut, cre]
Maintainer: Sonia Perez-Fernandez <perezsonia@uniovi.es>
Diff between movieROC versions 0.1.0 dated 2024-02-05 and 0.1.1 dated 2024-06-28
movieROC-0.1.0/movieROC/R/biROC.R |only movieROC-0.1.0/movieROC/R/plot.buildROC.R |only movieROC-0.1.0/movieROC/R/plot.funregions.R |only movieROC-0.1.0/movieROC/R/plot.regions.R |only movieROC-0.1.0/movieROC/man/biROC.Rd |only movieROC-0.1.0/movieROC/man/multiROC.default.Rd |only movieROC-0.1.0/movieROC/man/plot.buildROC.Rd |only movieROC-0.1.0/movieROC/man/plot.funregions.Rd |only movieROC-0.1.0/movieROC/man/plot.regions.Rd |only movieROC-0.1.1/movieROC/DESCRIPTION | 31 ++-- movieROC-0.1.1/movieROC/MD5 | 56 ++++---- movieROC-0.1.1/movieROC/NAMESPACE | 31 +--- movieROC-0.1.1/movieROC/R/KangFunctions.R | 4 movieROC-0.1.1/movieROC/R/gROC.R | 4 movieROC-0.1.1/movieROC/R/hROC.R | 24 +++ movieROC-0.1.1/movieROC/R/movieROC.R | 114 ++++------------ movieROC-0.1.1/movieROC/R/multiROC.R | 142 +++++++++++++++------ movieROC-0.1.1/movieROC/R/plot.R | 4 movieROC-0.1.1/movieROC/R/plot_buildROC.R |only movieROC-0.1.1/movieROC/R/plot_funregions.R |only movieROC-0.1.1/movieROC/R/plot_regions.R |only movieROC-0.1.1/movieROC/R/print.R | 138 ++++---------------- movieROC-0.1.1/movieROC/build/vignette.rds |only movieROC-0.1.1/movieROC/inst |only movieROC-0.1.1/movieROC/man/gROC.Rd | 18 ++ movieROC-0.1.1/movieROC/man/gROC_param.Rd | 3 movieROC-0.1.1/movieROC/man/hROC.Rd | 49 ++++--- movieROC-0.1.1/movieROC/man/movieROC.Rd | 32 +--- movieROC-0.1.1/movieROC/man/movieROC2_densities.Rd | 12 + movieROC-0.1.1/movieROC/man/multiROC.Rd |only movieROC-0.1.1/movieROC/man/plot.Rd | 8 - movieROC-0.1.1/movieROC/man/plot_buildROC.Rd |only movieROC-0.1.1/movieROC/man/plot_densities.Rd | 2 movieROC-0.1.1/movieROC/man/plot_densityROC.Rd | 4 movieROC-0.1.1/movieROC/man/plot_funregions.Rd |only movieROC-0.1.1/movieROC/man/plot_regions.Rd |only movieROC-0.1.1/movieROC/man/print.Rd | 6 movieROC-0.1.1/movieROC/vignettes |only 38 files changed, 324 insertions(+), 358 deletions(-)
Title: Modeling Over Dispersed Binomial Outcome Data Using BMD and ABD
Description: Contains Probability Mass Functions, Cumulative Mass
Functions, Negative Log Likelihood value, parameter estimation and
modeling data using Binomial Mixture Distributions (BMD) (Manoj et al
(2013) <doi:10.5539/ijsp.v2n2p24>) and Alternate Binomial
Distributions (ABD) (Paul (1985) <doi:10.1080/03610928508828990>),
also Journal article to use the package(<doi:10.21105/joss.01505>).
Author: Amalan Mahendran [aut, cre] ,
Pushpakanthie Wijekoon [aut, ctb]
Maintainer: Amalan Mahendran <amalan0595@gmail.com>
Diff between fitODBOD versions 1.5.1 dated 2024-02-09 and 1.5.2 dated 2024-06-28
DESCRIPTION | 13 +- MD5 | 217 +++++++++++++++++------------------ NAMESPACE | 1 R/AddBin.R | 81 +++---------- R/Beta.R | 121 ++++--------------- R/BetaCorrBin.R | 29 ---- R/COMPBin.R | 35 ----- R/CorrBin.R | 81 +++---------- R/GHGbeta.R | 57 ++------- R/Gamma.R | 50 ++------ R/Gbeta1.R | 129 ++++---------------- R/Kumaraswamy.R | 58 +-------- R/LMultiBin.R | 21 --- R/MultiBin.R | 66 ++-------- R/SimulateBOD.R | 5 R/Triangle.R | 144 ++++------------------- R/Uniform.R | 42 +----- build/partial.rdb |binary inst/REFERENCES.bib |only man/EstMGFBetaBin.Rd | 16 -- man/EstMLEAddBin.Rd | 16 -- man/EstMLEBetaBin.Rd | 16 -- man/EstMLEBetaCorrBin.Rd | 5 man/EstMLECOMPBin.Rd | 6 man/EstMLECorrBin.Rd | 16 -- man/EstMLEGHGBB.Rd | 7 - man/EstMLEGammaBin.Rd | 4 man/EstMLEGrassiaIIBin.Rd | 4 man/EstMLEKumBin.Rd | 3 man/EstMLELMBin.Rd | 4 man/EstMLEMcGBB.Rd | 16 -- man/EstMLEMultiBin.Rd | 13 -- man/EstMLETriBin.Rd | 16 -- man/GenerateBOD.Rd | 4 man/NegLLAddBin.Rd | 16 -- man/NegLLBetaBin.Rd | 16 -- man/NegLLBetaCorrBin.Rd | 5 man/NegLLCOMPBin.Rd | 6 man/NegLLCorrBin.Rd | 16 -- man/NegLLGHGBB.Rd | 7 - man/NegLLGammaBin.Rd | 4 man/NegLLGrassiaIIBin.Rd | 4 man/NegLLKumBin.Rd | 3 man/NegLLLMBin.Rd | 4 man/NegLLMcGBB.Rd | 16 -- man/NegLLMultiBin.Rd | 13 -- man/NegLLTriBin.Rd | 16 -- man/dAddBin.Rd | 16 -- man/dBETA.Rd | 9 - man/dBetaBin.Rd | 14 -- man/dBetaCorrBin.Rd | 5 man/dCOMPBin.Rd | 8 - man/dCorrBin.Rd | 16 -- man/dGAMMA.Rd | 3 man/dGBeta1.Rd | 16 -- man/dGHGBB.Rd | 7 - man/dGHGBeta.Rd | 7 - man/dGammaBin.Rd | 4 man/dGrassiaIIBin.Rd | 4 man/dKUM.Rd | 14 -- man/dKumBin.Rd | 3 man/dLMBin.Rd | 4 man/dMcGBB.Rd | 16 -- man/dMultiBin.Rd | 13 -- man/dTRI.Rd | 20 --- man/dTriBin.Rd | 16 -- man/dUNI.Rd | 7 - man/dUniBin.Rd | 10 - man/fitAddBin.Rd | 16 -- man/fitBetaBin.Rd | 14 -- man/fitBetaCorrBin.Rd | 5 man/fitCOMPBin.Rd | 6 man/fitCorrBin.Rd | 16 -- man/fitGHGBB.Rd | 7 - man/fitGammaBin.Rd | 4 man/fitGrassiaIIBin.Rd | 4 man/fitKumBin.Rd | 3 man/fitLMBin.Rd | 4 man/fitMcGBB.Rd | 16 -- man/fitMultiBin.Rd | 13 -- man/fitTriBin.Rd | 16 -- man/mazBETA.Rd | 9 - man/mazGAMMA.Rd | 3 man/mazGBeta1.Rd | 16 -- man/mazGHGBeta.Rd | 7 - man/mazKUM.Rd | 14 -- man/mazTRI.Rd | 20 --- man/mazUNI.Rd | 7 - man/pAddBin.Rd | 16 -- man/pBETA.Rd | 9 - man/pBetaBin.Rd | 16 -- man/pBetaCorrBin.Rd | 5 man/pCOMPBin.Rd | 8 - man/pCorrBin.Rd | 16 -- man/pGAMMA.Rd | 3 man/pGBeta1.Rd | 16 -- man/pGHGBB.Rd | 7 - man/pGHGBeta.Rd | 7 - man/pGammaBin.Rd | 4 man/pGrassiaIIBin.Rd | 4 man/pKUM.Rd | 14 -- man/pKumBin.Rd | 3 man/pLMBin.Rd | 4 man/pMcGBB.Rd | 16 -- man/pMultiBin.Rd | 13 -- man/pTRI.Rd | 20 --- man/pTriBin.Rd | 16 -- man/pUNI.Rd | 7 - man/pUniBin.Rd | 10 - tests/testthat/test-Overdispersion.R | 4 110 files changed, 524 insertions(+), 1528 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-06-27 0.18.2
2024-06-26 0.18.1
2023-09-25 0.18.0
2022-11-18 0.17.1
2021-11-24 0.17
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-06-25 0.18.2
2021-11-06 0.18.1
2020-02-26 0.18.0
2018-12-10 0.17.0
2018-09-28 0.16.0
2018-06-01 0.15.3
2018-05-02 0.15.2
2018-03-27 0.15.1
2018-03-25 0.15
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-05-30 0.7.0
2024-05-24 0.6.4
2024-04-29 0.6.3
2024-04-19 0.6.2
2023-12-12 0.6.1
2023-10-03 0.6.0
2023-04-06 0.5.1
2023-03-10 0.5.0
2022-12-06 0.4.0
2021-11-08 0.3.0
2021-06-21 0.2.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-05-28 2.7.0
2024-04-22 2.6.1
2023-08-30 2.6.0
2023-04-06 2.5.1
2023-03-13 2.5.0
2023-02-14 2.4.2
2022-11-30 2.3.1
2022-10-10 2.3.0
2022-03-01 2.2.95
2021-11-06 2.2.9
2021-06-22 2.2.8
2021-06-08 2.2.7
2021-05-28 2.2.6
2020-03-18 2.2.5
2019-07-18 2.2.4
2019-02-13 2.2.3
2019-01-21 2.2.2
2018-10-18 2.2.1
2018-09-28 2.2.0
2018-06-04 2.1.2
2018-05-02 2.1.1
2018-02-23 2.1.0
Title: Generalized Linear Mixed Model Trees
Description: Recursive partitioning based on (generalized) linear mixed models
(GLMMs) combining lmer()/glmer() from 'lme4' and lmtree()/glmtree() from
'partykit'. The fitting algorithm is described in more detail in Fokkema,
Smits, Zeileis, Hothorn & Kelderman (2018; <DOI:10.3758/s13428-017-0971-x>).
Author: Marjolein Fokkema [aut, cre],
Achim Zeileis [aut]
Maintainer: Marjolein Fokkema <M.Fokkema@fsw.leidenuniv.nl>
Diff between glmertree versions 0.2-4 dated 2023-09-09 and 0.2-5 dated 2024-06-28
DESCRIPTION | 10 +++++----- MD5 | 24 +++++++++++++----------- NAMESPACE | 11 ++++++++--- R/betamertree.R | 7 ++----- R/cv.glmertree.R |only R/glmertree.R | 35 +++++++++++++++++++++++++---------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/glmertree.pdf |binary man/GrowthCurveDemo.Rd | 6 ++++++ man/MHserviceDemo.Rd | 6 ++++++ man/betamertree.Rd | 12 +++++++++--- man/cv.glmertree.Rd |only man/glmertree.Rd | 16 +++++++++++++--- 14 files changed, 87 insertions(+), 40 deletions(-)
Title: Generalized Boosted Regression Models
Description: An implementation of extensions to Freund and Schapire's AdaBoost
algorithm and Friedman's gradient boosting machine. Includes regression
methods for least squares, absolute loss, t-distribution loss, quantile
regression, logistic, multinomial logistic, Poisson, Cox proportional hazards
partial likelihood, AdaBoost exponential loss, Huberized hinge loss, and
Learning to Rank measures (LambdaMart). Originally developed by Greg Ridgeway.
Newer version available at github.com/gbm-developers/gbm3.
Author: Greg Ridgeway [aut, cre] ,
Daniel Edwards [ctb],
Brian Kriegler [ctb],
Stefan Schroedl [ctb],
Harry Southworth [ctb],
Brandon Greenwell [ctb] ,
Bradley Boehmke [ctb] ,
Jay Cunningham [ctb],
GBM Developers [aut]
Maintainer: Greg Ridgeway <gridge@upenn.edu>
Diff between gbm versions 2.1.9 dated 2024-01-10 and 2.2.2 dated 2024-06-28
DESCRIPTION | 34 +++++++++----------- MD5 | 76 +++++++++++++++++++++++----------------------- R/gbm-internals.R | 2 - R/gbm-package.R | 7 +--- R/gbm.fit.R | 38 +++++++++-------------- R/gbmCrossVal.R | 4 +- R/utils.R | 2 - build/vignette.rds |binary inst/doc/gbm.pdf |binary man/gbm-package.Rd | 10 +++++- src/adaboost.cpp | 2 - src/adaboost.h | 4 +- src/bernoulli.cpp | 2 - src/bernoulli.h | 4 +- src/buildinfo.h | 1 src/coxph.h | 10 +++--- src/gaussian.h | 6 +-- src/gbm.cpp | 1 src/gbm.h | 4 +- src/gbm_engine.h | 2 - src/gbmentry.cpp | 85 +++++++++++++++++++++++++++++----------------------- src/huberized.h | 4 +- src/laplace.cpp | 66 ++++++++++++++++++++-------------------- src/laplace.h | 7 +++- src/locationm.cpp | 8 +--- src/locationm.h | 2 - src/matrix.h | 16 ++++----- src/multinomial.cpp | 46 ++++++++++++++++++++-------- src/multinomial.h | 3 + src/node.h | 6 +-- src/node_factory.h | 8 +--- src/node_search.cpp | 2 - src/node_search.h | 2 - src/node_terminal.h | 4 -- src/pairwise.cpp | 26 +++++++-------- src/pairwise.h | 20 ++++++------ src/poisson.h | 8 ++-- src/quantile.cpp | 4 +- src/quantile.h | 2 - 39 files changed, 275 insertions(+), 253 deletions(-)
Title: Bayesian Estimation of Structural Vector Autoregressive Models
Description: Provides fast and efficient procedures for Bayesian analysis of Structural Vector Autoregressions. This package estimates a wide range of models, including homo-, heteroskedastic, and non-normal specifications. Structural models can be identified by adjustable exclusion restrictions, time-varying volatility, or non-normality. They all include a flexible three-level equation-specific local-global hierarchical prior distribution for the estimated level of shrinkage for autoregressive and structural parameters. Additionally, the package facilitates predictive and structural analyses such as impulse responses, forecast error variance and historical decompositions, forecasting, verification of heteroskedasticity, non-normality, and hypotheses on autoregressive parameters, as well as analyses of structural shocks, volatilities, and fitted values. Beautiful plots, informative summary functions, and extensive documentation complement all this. The implemented techniques align closely with thos [...truncated...]
Author: Tomasz Wozniak [aut, cre]
Maintainer: Tomasz Wozniak <wozniak.tom@pm.me>
Diff between bsvars versions 3.0 dated 2024-06-19 and 3.0.1 dated 2024-06-28
DESCRIPTION | 8 +- MD5 | 24 +++---- NEWS.md | 8 ++ R/compute_variance_decompositions.R | 9 +- R/forecast.R | 24 +++---- inst/include/bsvars_RcppExports.h | 29 +++++++- inst/tinytest/test_compute_variance_decomposition.R | 66 +++++++++++++++++++- src/RcppExports.cpp | 55 ++++++++++++++-- src/bsvarTOOLs.cpp | 15 +++- src/bsvarTOOLs.h | 5 - src/forecast.cpp | 51 ++++----------- src/verify.cpp | 59 ++++++++++++++--- src/verify.h | 14 +++- 13 files changed, 265 insertions(+), 102 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-06-13 0.10.2
2023-11-24 0.0.3
Title: Space-Time Point Pattern Simulation, Visualisation and Analysis
Description: Many of the models encountered in applications of point process methods to the study of spatio-temporal phenomena are covered in 'stpp'. This package provides statistical tools for analyzing the global and local second-order properties of spatio-temporal point processes, including estimators of the space-time inhomogeneous K-function and pair correlation function. It also includes tools to get static and dynamic display of spatio-temporal point patterns. See Gabriel et al (2013) <doi:10.18637/jss.v053.i02>.
Author: Edith Gabriel [aut, cre],
Peter J Diggle [aut],
Barry Rowlingson [aut],
Francisco J Rodriguez-Cortes [aut]
Maintainer: Edith Gabriel <edith.gabriel@inrae.fr>
Diff between stpp versions 2.0-7 dated 2022-11-30 and 2.0-8 dated 2024-06-28
stpp-2.0-7/stpp/README.md |only stpp-2.0-8/stpp/CHANGES | 6 ++++++ stpp-2.0-8/stpp/DESCRIPTION | 12 ++++++------ stpp-2.0-8/stpp/MD5 | 23 +++++++++++------------ stpp-2.0-8/stpp/NAMESPACE | 3 ++- stpp-2.0-8/stpp/R/kmmr.R | 8 ++++---- stpp-2.0-8/stpp/build/vignette.rds |binary stpp-2.0-8/stpp/data/fmd.rda |binary stpp-2.0-8/stpp/data/northcumbria.rda |binary stpp-2.0-8/stpp/inst/doc/docs.Rmd | 4 ++-- stpp-2.0-8/stpp/inst/doc/docs.html | 8 ++++---- stpp-2.0-8/stpp/src/kmmrcore.f | 2 +- stpp-2.0-8/stpp/vignettes/docs.Rmd | 4 ++-- 13 files changed, 38 insertions(+), 32 deletions(-)
Title: One-Dimensional Probability Distribution Support for the
'spatstat' Family
Description: Estimation of one-dimensional probability distributions
including kernel density estimation, weighted empirical cumulative
distribution functions, Kaplan-Meier and reduced-sample estimators
for right-censored data, heat kernels, kernel properties,
quantiles and integration.
Author: Adrian Baddeley [aut, cre, cph]
,
Tilman M. Davies [aut, ctb, cph]
,
Martin L. Hazelton [aut, ctb, cph]
,
Ege Rubak [aut, cph] ,
Rolf Turner [aut, cph] ,
Greg McSwiggan [ctb, cph]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.univar versions 2.0-3 dated 2024-04-29 and 3.0-0 dated 2024-06-28
DESCRIPTION | 10 ++++---- MD5 | 27 +++++++++++++++------- NAMESPACE | 19 +++++++++++++++ NEWS | 49 ++++++++++++++++++++++++++++++++++++++++ R/adaptive.R |only R/bw.abram.default.R |only R/quantiledensity.R | 1 R/rounding.R |only R/uniquemap.R |only R/weightedStats.R | 26 +++++++++++++-------- inst/doc/packagesizes.txt | 2 - inst/info |only man/bw.abram.Rd |only man/bw.abram.default.Rd |only man/densityAdaptiveKernel.Rd |only man/firstdigit.Rd |only man/rounding.Rd |only man/spatstat.univar-internal.Rd | 4 +++ man/spatstat.univar-package.Rd | 23 ++++++++++++++++++ man/uniquemap.default.Rd |only 20 files changed, 137 insertions(+), 24 deletions(-)
More information about spatstat.univar at CRAN
Permanent link
Title: Microbial Community Ecology Data Analysis
Description: A series of statistical and plotting approaches in microbial community ecology based on the R6 class. The classes are designed for data preprocessing, taxa abundance plotting, alpha diversity analysis, beta diversity analysis, differential abundance test, null model analysis, network analysis, machine learning, environmental data analysis and functional analysis.
Author: Chi Liu [aut, cre],
Felipe R. P. Mansoldo [ctb],
Minjie Yao [ctb],
Xiangzhen Li [ctb]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between microeco versions 1.7.1 dated 2024-05-23 and 1.8.0 dated 2024-06-28
DESCRIPTION | 6 MD5 | 50 +++--- R/microtable.R | 6 R/trans_abund.R | 4 R/trans_alpha.R | 147 +++++++++++------ R/trans_beta.R | 159 +++++++++++-------- R/trans_classifier.R | 339 ++++++++++++++++++++++++++++++----------- R/trans_diff.R | 69 +++++--- R/trans_env.R | 47 +++-- R/trans_func.R | 17 +- R/trans_network.R | 26 +-- R/trans_norm.R | 6 R/trans_nullmodel.R | 6 R/utility.R | 2 data/fungi_func_FUNGuild.RData |binary man/microtable.Rd | 6 man/trans_abund.Rd | 4 man/trans_alpha.Rd | 59 ++++--- man/trans_beta.Rd | 73 ++++---- man/trans_classifier.Rd | 205 +++++++++++++++++++----- man/trans_diff.Rd | 26 ++- man/trans_env.Rd | 6 man/trans_func.Rd | 6 man/trans_network.Rd | 22 +- man/trans_norm.Rd | 6 man/trans_nullmodel.Rd | 6 26 files changed, 893 insertions(+), 410 deletions(-)