Title: Meta-Analysis of Medians
Description: Implements several methods to meta-analyze studies that report the
sample median of the outcome. When the primary studies are one-group
studies, the methods of McGrath et al. (2019) <doi:10.1002/sim.8013> and
Ozturk and Balakrishnan (2020) <doi:10.1002/sim.8738> can be applied to
estimate the pooled median. In the two-group context, the
methods of McGrath et al. (2020a) <doi:10.1002/bimj.201900036> can be
applied to estimate the pooled difference of medians across groups.
Additionally, a number of methods (e.g., McGrath et al. (2020b)
<doi:10.1177/0962280219889080>, Cai et al. (2021)
<doi:10.1177/09622802211047348>, and McGrath et al. (2023)
<doi:10.1177/09622802221139233>) are implemented to estimate
study-specific (difference of) means and their standard errors in order to
estimate the pooled (difference of) means. See McGrath et al. (in press)
<doi:10.1002/jrsm.1686> for a detailed guide on using the package.
Author: Sean McGrath [aut, cre] ,
XiaoFei Zhao [aut],
Stephan Katzenschlager [aut],
Omer Ozturk [aut],
Russell Steele [aut],
Andrea Benedetti [aut]
Maintainer: Sean McGrath <sean.mcgrath@mail.mcgill.ca>
Diff between metamedian versions 1.1.0 dated 2023-09-16 and 1.1.1 dated 2023-12-13
DESCRIPTION | 11 ++++++----- MD5 | 20 ++++++++++---------- NEWS.md | 6 ++++++ R/describe_studies.R | 1 + R/metamean.R | 15 ++++++++++----- R/metamedian.R | 9 +++++---- README.md | 5 +++++ man/describe_studies.Rd | 2 ++ man/metamean.Rd | 18 ++++++++++-------- man/metamedian.Rd | 8 +++++--- tests/testthat/test-describe_studies.R | 2 +- 11 files changed, 61 insertions(+), 36 deletions(-)
Title: Tropical Geometry Tools for Machine Learning
Description: Suite of tropical geometric tools for use in machine learning applications. These methods may be summarized in the following references: Yoshida, et al. (2022) <arxiv:2209.15045>, Barnhill et al. (2023) <arxiv:2303.02539>, Barnhill and Yoshida (2023) <doi:10.3390/math11153433>, Aliatimis et al. (2023) <arXiv:2306.08796>, Yoshida et al. (2022) <arXiv:2206.04206>, and Yoshida et al. (2019) <doi:10.1007/s11538-018-0493-4>.
Author: David Barnhill [aut, cre] ,
Ruriko Yoshida [aut],
Georgios Aliatimis [aut],
Keiji Miura [aut]
Maintainer: David Barnhill <david.barnhill@nps.edu>
Diff between TML versions 1.1.0 dated 2023-09-03 and 1.2.0 dated 2023-12-13
DESCRIPTION | 6 ++--- MD5 | 14 +++++++------ NAMESPACE | 1 R/convert.to.tree.R |only R/draw.tpolytope.R | 24 ++++++++++++++--------- R/tropical.ball.verts.R | 50 ++++++++++++++++++++++++++++++++++++------------ man/convert.to.tree.Rd |only man/draw.tpolytope.Rd | 10 +++++---- man/trop_bal.vert.Rd | 11 ++++++---- 9 files changed, 78 insertions(+), 38 deletions(-)
Title: Build a Metric Subspaces Data Model for a Data Source
Description: Neural networks are applied to create a density value function which approximates density values for a data source. The trained neural network is analyzed for different levels. For each level metric subspaces with density values above a level are determined. The obtained set of metric subspaces and the trained neural network are assembled into a data model. A prerequisite is the definition of a data source, the generation of generative data and the calculation of density values. These tasks are executed using package 'ganGenerativeData' <https://cran.r-project.org/package=ganGenerativeData>.
Author: Werner Mueller
Maintainer: Werner Mueller <werner.mueller5@chello.at>
Diff between ganDataModel versions 1.1.4 dated 2023-05-07 and 1.1.5 dated 2023-12-13
DESCRIPTION | 8 +-- MD5 | 6 +- man/ganDataModel-package.Rd | 17 +++---- src/dmInt.cpp | 96 -------------------------------------------- 4 files changed, 15 insertions(+), 112 deletions(-)
Title: Extra Binary Relational and Logical Operators
Description: Speed up common tasks, particularly logical or
relational comparisons and routine follow up tasks such as finding the
indices and subsetting. Inspired by mathematics, where something like:
3 < x < 6 is a standard, elegant and clear way to assert that
x is both greater than 3 and less than 6
(see for example <https://en.wikipedia.org/wiki/Relational_operator>),
a chaining operator is implemented. The chaining operator, %c%,
allows multiple relational operations to be used in quotes on the right
hand side for the same object, on the left hand side.
The %e% operator allows something like set-builder notation
(see for example <https://en.wikipedia.org/wiki/Set-builder_notation>)
to be used on the right hand side.
All operators have built in prefixes defined for all, subset, and which
to reduce the amount of code needed for common tasks, such as return those
values that are true.
Author: Joshua F. Wiley [aut, cre]
Maintainer: Joshua F. Wiley <jwiley.psych@gmail.com>
Diff between extraoperators versions 0.1.1 dated 2019-11-04 and 0.3.0 dated 2023-12-13
DESCRIPTION | 15 MD5 | 44 - NAMESPACE | 8 NEWS.md | 10 R/logical_all.R | 52 + R/logicals.R | 34 + R/subsetting.R | 16 R/which.R | 15 README.md | 21 build/vignette.rds |binary inst/doc/logicals-vignette.R | 360 ++++++------ inst/doc/logicals-vignette.Rmd | 23 inst/doc/logicals-vignette.html | 1164 +++++++++++++++++++++------------------ man/logicalall.Rd | 13 man/logicals.Rd | 12 man/logicalwhich.Rd | 12 man/subsetting.Rd | 12 tests/testthat.R | 1 tests/testthat/test-all.R | 7 tests/testthat/test-indices.R | 26 tests/testthat/test-logicals.R | 56 + tests/testthat/test-subsetting.R | 25 vignettes/logicals-vignette.Rmd | 23 23 files changed, 1187 insertions(+), 762 deletions(-)
More information about extraoperators at CRAN
Permanent link
Title: Phylogeny-Guided OTU-Specific Association Test for Microbiome
Data
Description: Implements the Phylogeny-Guided Microbiome OTU-Specific Association
Test method, which boosts the testing power by adaptively borrowing
information from phylogenetically close OTUs (operational taxonomic units)
of the target OTU. This method
is built on a kernel machine regression framework and allows for flexible
modeling of complex microbiome effects, adjustments for covariates, and
can accommodate both continuous and binary outcomes.
Author: Caizhi Huang [aut],
Jung-Ying Tzeng [aut],
Shannon T. Holloway [aut, cre]
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
Diff between POSTm versions 1.2 dated 2022-06-06 and 1.3 dated 2023-12-13
DESCRIPTION | 10 - MD5 | 11 - NEWS |only R/p.adjust.POST.R | 348 ++++++++++++++++++++++---------------------- build/vignette.rds |binary inst/doc/POSTm_vignette.pdf |binary man/p.adjust.Rd | 134 ++++++++-------- 7 files changed, 252 insertions(+), 251 deletions(-)
Title: Durability of Vaccine Efficacy Against SARS-CoV-2 Infection
Description: Implements a nonparametric maximum likelihood method for assessing
potentially time-varying vaccine efficacy (VE) against SARS-CoV-2 infection
under staggered enrollment and time-varying community transmission, allowing
crossover of placebo volunteers to the vaccine arm.
Lin, D. Y., Gu, Y., Zeng, D., Janes, H. E., and Gilbert, P. B. (2021)
<doi:10.1093/cid/ciab630>.
Author: Yu Gu [aut],
Shannon T. Holloway [aut, cre],
Dan-Yu Lin [aut]
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
Diff between iDOVE versions 1.4 dated 2022-06-07 and 1.5 dated 2023-12-13
DESCRIPTION | 12 MD5 | 34 - NAMESPACE | 1 NEWS | 61 ++- R/RcppExports.R | 70 +-- R/idove.R | 474 +++++++++++++------------- R/plot.iDOVE.R | 93 ++--- R/print.iDOVE.R | 83 ++-- build/vignette.rds |binary inst/doc/iDOVE_vignette.R | 1 inst/doc/iDOVE_vignette.Rmd | 773 +++++++++++++++++++++---------------------- inst/doc/iDOVE_vignette.pdf |binary man/idove.Rd | 3 man/plot.Rd | 3 man/print.Rd | 3 src/Makevars | 2 src/Makevars.win | 2 vignettes/iDOVE_vignette.Rmd | 773 +++++++++++++++++++++---------------------- 18 files changed, 1213 insertions(+), 1175 deletions(-)
Title: Durability of Vaccine Efficacy
Description: Implements maximum likelihood methods for
evaluating the durability of vaccine efficacy in a randomized,
placebo-controlled clinical trial with staggered enrollment of participants
and potential crossover of placebo recipients before the end of the trial.
Lin, D. Y., Zeng, D., and Gilbert, P. B. (2021)
<doi:10.1093/cid/ciab226>
and
Lin, D. Y., Gu, Y., Zeng, D., Janes, H. E., and Gilbert, P. B. (2021)
<doi:10.1093/cid/ciab630>.
Author: Danyu Lin [aut],
Yu Gu [aut],
Donglin Zeng [aut],
Shannon T. Holloway [aut, cre]
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
Diff between DOVE versions 1.9 dated 2022-06-07 and 1.10 dated 2023-12-13
DESCRIPTION | 12 MD5 | 38 - NAMESPACE | 1 NEWS | 143 +++-- R/RcppExports.R | 46 - R/dove.R | 427 ++++++++--------- R/dove2.R | 493 +++++++++---------- R/plot.DOVE.R | 169 +++--- R/print.DOVE.R | 133 ++--- build/vignette.rds |binary inst/doc/dove-vignette.R | 5 inst/doc/dove-vignette.Rmd | 1093 ++++++++++++++++++++++---------------------- inst/doc/dove-vignette.pdf |binary man/dove.Rd | 4 man/dove2.Rd | 3 man/plot.Rd | 3 man/print.Rd | 3 src/Makevars | 2 src/Makevars.win | 2 vignettes/dove-vignette.Rmd | 1093 ++++++++++++++++++++++---------------------- 20 files changed, 1856 insertions(+), 1814 deletions(-)
Title: Proportional Odds Model with Censored, Time-Lagged Categorical
Outcome
Description: Implements a semiparametric estimator for the odds ratio model with
censored, time-lagged, ordered categorical outcome in a randomized clinical
trial that incorporates baseline and time-dependent information.
Tsiatis, A. A. and Davidian, M. (2021) <arXiv:2106.15559>.
Author: Marie Davidian [aut],
A. A. Tsiatis [aut],
Shannon T. Holloway [aut, cre]
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
Diff between tLagPropOdds versions 1.8 dated 2022-06-07 and 1.9 dated 2023-12-13
DESCRIPTION | 10 ++--- MD5 | 8 ++-- NEWS | 70 ++++++++++++++++++++++------------------ R/tLagData.R | 96 ++++++++++++++++++++++++++++---------------------------- man/tLagData.Rd | 2 - 5 files changed, 97 insertions(+), 89 deletions(-)
Title: Analysis of Proportional Hazards Model with Sparse Longitudinal
Covariates
Description: Provides kernel weighting methods for estimation of proportional
hazards models with intermittently observed longitudinal covariates.
Cao H., Churpek M. M., Zeng D., and Fine J. P. (2015)
<doi:10.1080/01621459.2014.957289>.
Author: Hongyuan Cao, Mathew M. Churpek, Donglin Zeng, Jason P. Fine, and
Shannon T. Holloway
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
Diff between SurvLong versions 1.3 dated 2023-09-30 and 1.4 dated 2023-12-13
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NEWS | 6 ++++++ R/fullKernel.R | 14 +++++++------- R/lastValue.R | 8 ++++---- man/fullKernel.Rd | 14 +++++++------- man/halfKernel.Rd | 14 +++++++------- man/lastValue.Rd | 8 ++++---- man/nearValue.Rd | 8 ++++---- 9 files changed, 52 insertions(+), 46 deletions(-)
Title: Computation of Graphlet Orbit Counts in Sparse Graphs
Description: Implements orbit counting using a fast combinatorial approach.
Counts orbits of nodes and edges from edge matrix or data frame, or a
graph object from the graph package.
Author: Tomaz Hocevar [aut, cre],
Janez Demsar [aut]
Maintainer: Tomaz Hocevar <tomaz.hocevar@fri.uni-lj.si>
Diff between orca versions 1.1-1 dated 2016-07-28 and 1.1-2 dated 2023-12-13
DESCRIPTION | 21 ++++++++++----------- MD5 | 6 +++--- NAMESPACE | 2 +- src/count.cpp | 27 +++++++++++++++++++++++---- 4 files changed, 37 insertions(+), 19 deletions(-)
Title: Bayesian Non-Parametric Latent-Class Capture-Recapture
Description: Bayesian population size estimation using non parametric latent-class models.
Author: Daniel Manrique-Vallier
Maintainer: Daniel Manrique-Vallier <dmanriqu@indiana.edu>
Diff between LCMCR versions 0.4.13 dated 2023-05-24 and 0.4.14 dated 2023-12-13
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ configure | 18 +++++++++--------- configure.ac | 2 +- man/LCMCR-package.Rd | 4 ++-- src/R_Interface/R_Lcm_CR.cpp | 2 +- src/daniel2/R_Environ_Simple.cpp | 8 ++++---- 7 files changed, 27 insertions(+), 27 deletions(-)
Title: Classification and Visualization
Description: Miscellaneous functions for classification and visualization,
e.g. regularized discriminant analysis, sknn() kernel-density naive Bayes,
an interface to 'svmlight' and stepclass() wrapper variable selection
for supervised classification, partimat() visualization of classification rules
and shardsplot() of cluster results as well as kmodes() clustering for categorical data,
corclust() variable clustering, variable extraction from different variable clustering models
and weight of evidence preprocessing.
Author: Christian Roever, Nils Raabe, Karsten Luebke, Uwe Ligges, Gero Szepannek, Marc Zentgraf, David Meyer
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>
Diff between klaR versions 1.7-2 dated 2023-03-17 and 1.7-3 dated 2023-12-13
DESCRIPTION | 8 +++--- MD5 | 14 ++++++------ NEWS | 4 +++ data/B3.RData |binary data/countries.RData |binary man/pvs.Rd | 8 +++--- tests/testsklaR.R | 9 ------- tests/testsklaR.Rout.save | 53 ---------------------------------------------- 8 files changed, 19 insertions(+), 77 deletions(-)
Title: Bayesian Global Vector Autoregressions
Description: Estimation of Bayesian Global Vector Autoregressions (BGVAR) with different prior setups and the possibility to introduce stochastic volatility. Built-in priors include the Minnesota, the stochastic search variable selection and Normal-Gamma (NG) prior. For a reference see also Crespo Cuaresma, J., Feldkircher, M. and F. Huber (2016) "Forecasting with Global Vector Autoregressive Models: a Bayesian Approach", Journal of Applied Econometrics, Vol. 31(7), pp. 1371-1391 <doi:10.1002/jae.2504>. Post-processing functions allow for doing predictions, structurally identify the model with short-run or sign-restrictions and compute impulse response functions, historical decompositions and forecast error variance decompositions. Plotting functions are also available. The package has a companion paper: Boeck, M., Feldkircher, M. and F. Huber (2022) "BGVAR: Bayesian Global Vector Autoregressions with Shrinkage Priors in R", Journal of Statistical Software, Vol. 104(9), pp. 1-28 <doi:10.18 [...truncated...]
Author: Maximilian Boeck [aut, cre] ,
Martin Feldkircher [aut] ,
Florian Huber [aut] ,
Darjus Hosszejni [ctb]
Maintainer: Maximilian Boeck <maximilian.boeck@unibocconi.it>
Diff between BGVAR versions 2.5.4 dated 2023-12-11 and 2.5.5 dated 2023-12-13
DESCRIPTION | 6 ++--- MD5 | 10 ++++---- NEWS | 3 -- R/fevd.R | 56 ++++++++++++++++++++++--------------------------- inst/doc/examples.html | 4 +-- man/fevd.Rd | 2 - 6 files changed, 38 insertions(+), 43 deletions(-)
Title: Vaccine Efficacy Over Time
Description: Implements methods for inference on potential waning of vaccine
efficacy and for estimation of vaccine efficacy at a user-specified time
after vaccination based on data from a randomized, double-blind,
placebo-controlled vaccine trial in which participants may be unblinded
and placebo subjects may be crossed over to the study vaccine. The
methods also allow adjustment for possible confounding via inverse
probability weighting through specification of models for the trial
entry process, unblinding mechanisms, and the probability an unblinded
placebo participant accepts study vaccine: Tsiatis, A. A. and Davidian,
M. (2021) <arXiv:2102.13103> .
Author: Marie Davidian [aut],
A.A. Tsiatis [aut],
Shannon T. Holloway [aut, cre]
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
Diff between VEwaning versions 1.2 dated 2022-06-07 and 1.3 dated 2023-12-13
DESCRIPTION | 10 MD5 | 13 NEWS |only R/plot.VEwaning.R | 176 ++++++------- R/print.VEwaning.R | 98 +++---- R/ve.R | 160 ++++++------ R/veWaning.R | 704 ++++++++++++++++++++++++++--------------------------- man/veWaning.Rd | 4 8 files changed, 583 insertions(+), 582 deletions(-)
Title: Robust Online Bayesian Monitoring
Description: An implementation of Bayesian online changepoint detection (Adams and MacKay (2007) <arXiv:0710.3742>) with an option for probability based outlier detection and removal (Wendelberger et. al. (2021) <arXiv:2112.12899>). Building on the independent multivariate constant mean model implemented in the 'R' package 'ocp', this package models multivariate data as multivariate normal about a linear trend, defined by user input covariates, with an unstructured error covariance. Changepoints are identified based on a probability threshold for windows of points.
Author: Laura Wendelberger [aut],
Josh Gray [aut],
Brian Reich [aut],
Alyson Wilson [aut],
Shannon T. Holloway [aut, cre]
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
Diff between roboBayes versions 1.1 dated 2022-08-16 and 1.2 dated 2023-12-13
DESCRIPTION | 12 MD5 | 11 NAMESPACE | 1 NEWS |only R/roboBayes.R | 918 +++++++++++++++++++++++++++---------------------------- man/roboBayes.Rd | 523 +++++++++++++++---------------- src/Makevars | 2 7 files changed, 738 insertions(+), 729 deletions(-)
Title: Preprocessing and Feature Engineering Steps for Modeling
Description: A recipe prepares your data for modeling. We provide an
extensible framework for pipeable sequences of feature engineering
steps provides preprocessing tools to be applied to data. Statistical
parameters for the steps can be estimated from an initial data set and
then applied to other data sets. The resulting processed output can
then be used as inputs for statistical or machine learning models.
Author: Max Kuhn [aut, cre],
Hadley Wickham [aut],
Emil Hvitfeldt [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between recipes versions 1.0.8 dated 2023-08-25 and 1.0.9 dated 2023-12-13
recipes-1.0.8/recipes/tests/testthat/_snaps/classdist-shrunken.md |only recipes-1.0.9/recipes/DESCRIPTION | 8 recipes-1.0.9/recipes/MD5 | 708 +++++----- recipes-1.0.9/recipes/NAMESPACE | 1 recipes-1.0.9/recipes/NEWS.md | 32 recipes-1.0.9/recipes/R/BoxCox.R | 32 recipes-1.0.9/recipes/R/YeoJohnson.R | 20 recipes-1.0.9/recipes/R/aaa.R | 2 recipes-1.0.9/recipes/R/arrange.R | 13 recipes-1.0.9/recipes/R/bin2factor.R | 31 recipes-1.0.9/recipes/R/bs.R | 13 recipes-1.0.9/recipes/R/case_weights.R | 35 recipes-1.0.9/recipes/R/center.R | 20 recipes-1.0.9/recipes/R/class.R | 30 recipes-1.0.9/recipes/R/classdist.R | 31 recipes-1.0.9/recipes/R/classdist_shrunken.R | 25 recipes-1.0.9/recipes/R/colcheck.R | 15 recipes-1.0.9/recipes/R/corr.R | 32 recipes-1.0.9/recipes/R/count.R | 40 recipes-1.0.9/recipes/R/cut.R | 54 recipes-1.0.9/recipes/R/date.R | 23 recipes-1.0.9/recipes/R/deprecated-terms_select.R | 2 recipes-1.0.9/recipes/R/depth.R | 18 recipes-1.0.9/recipes/R/discretize.R | 58 recipes-1.0.9/recipes/R/dummy.R | 136 - recipes-1.0.9/recipes/R/dummy_extract.R | 38 recipes-1.0.9/recipes/R/dummy_multi_choice.R | 32 recipes-1.0.9/recipes/R/extract_parameter.R | 4 recipes-1.0.9/recipes/R/factor2string.R | 24 recipes-1.0.9/recipes/R/filter.R | 14 recipes-1.0.9/recipes/R/filter_missing.R | 14 recipes-1.0.9/recipes/R/formula.R | 9 recipes-1.0.9/recipes/R/geodist.R | 69 recipes-1.0.9/recipes/R/harmonic.R | 50 recipes-1.0.9/recipes/R/holiday.R | 22 recipes-1.0.9/recipes/R/hyperbolic.R | 14 recipes-1.0.9/recipes/R/ica.R | 25 recipes-1.0.9/recipes/R/import-standalone-obj-type.R |only recipes-1.0.9/recipes/R/import-standalone-types-check.R |only recipes-1.0.9/recipes/R/impute_bag.R | 16 recipes-1.0.9/recipes/R/impute_knn.R | 22 recipes-1.0.9/recipes/R/impute_linear.R | 39 recipes-1.0.9/recipes/R/impute_lower.R | 27 recipes-1.0.9/recipes/R/impute_mean.R | 24 recipes-1.0.9/recipes/R/impute_median.R | 11 recipes-1.0.9/recipes/R/impute_mode.R | 27 recipes-1.0.9/recipes/R/impute_roll.R | 15 recipes-1.0.9/recipes/R/indicate_na.R | 12 recipes-1.0.9/recipes/R/integer.R | 11 recipes-1.0.9/recipes/R/interact.R | 43 recipes-1.0.9/recipes/R/intercept.R | 22 recipes-1.0.9/recipes/R/inverse.R | 11 recipes-1.0.9/recipes/R/invlogit.R | 13 recipes-1.0.9/recipes/R/isomap.R | 16 recipes-1.0.9/recipes/R/kpca.R | 19 recipes-1.0.9/recipes/R/kpca_poly.R | 17 recipes-1.0.9/recipes/R/kpca_rbf.R | 17 recipes-1.0.9/recipes/R/lag.R | 14 recipes-1.0.9/recipes/R/lincomb.R | 20 recipes-1.0.9/recipes/R/log.R | 14 recipes-1.0.9/recipes/R/logit.R | 13 recipes-1.0.9/recipes/R/misc.R | 158 +- recipes-1.0.9/recipes/R/missing.R | 10 recipes-1.0.9/recipes/R/mutate.R | 13 recipes-1.0.9/recipes/R/mutate_at.R | 9 recipes-1.0.9/recipes/R/naomit.R | 12 recipes-1.0.9/recipes/R/newvalues.R | 11 recipes-1.0.9/recipes/R/nnmf.R | 19 recipes-1.0.9/recipes/R/nnmf_sparse.R | 25 recipes-1.0.9/recipes/R/normalize.R | 43 recipes-1.0.9/recipes/R/novel.R | 26 recipes-1.0.9/recipes/R/ns.R | 13 recipes-1.0.9/recipes/R/num2factor.R | 21 recipes-1.0.9/recipes/R/nzv.R | 11 recipes-1.0.9/recipes/R/ordinalscore.R | 13 recipes-1.0.9/recipes/R/other.R | 32 recipes-1.0.9/recipes/R/pca.R | 33 recipes-1.0.9/recipes/R/percentile.R | 20 recipes-1.0.9/recipes/R/pls.R | 70 recipes-1.0.9/recipes/R/poly.R | 56 recipes-1.0.9/recipes/R/poly_bernstein.R | 11 recipes-1.0.9/recipes/R/printing.R | 5 recipes-1.0.9/recipes/R/profile.R | 75 - recipes-1.0.9/recipes/R/range.R | 31 recipes-1.0.9/recipes/R/range_check.R | 68 recipes-1.0.9/recipes/R/ratio.R | 24 recipes-1.0.9/recipes/R/recipe.R | 244 ++- recipes-1.0.9/recipes/R/recipes-package.R | 1 recipes-1.0.9/recipes/R/regex.R | 37 recipes-1.0.9/recipes/R/relevel.R | 37 recipes-1.0.9/recipes/R/relu.R | 48 recipes-1.0.9/recipes/R/rename.R | 13 recipes-1.0.9/recipes/R/rename_at.R | 9 recipes-1.0.9/recipes/R/rm.R | 11 recipes-1.0.9/recipes/R/roles.R | 145 +- recipes-1.0.9/recipes/R/sample.R | 22 recipes-1.0.9/recipes/R/scale.R | 20 recipes-1.0.9/recipes/R/select.R | 10 recipes-1.0.9/recipes/R/selections.R | 6 recipes-1.0.9/recipes/R/shuffle.R | 13 recipes-1.0.9/recipes/R/slice.R | 19 recipes-1.0.9/recipes/R/spatialsign.R | 11 recipes-1.0.9/recipes/R/spline_b.R | 14 recipes-1.0.9/recipes/R/spline_convex.R | 11 recipes-1.0.9/recipes/R/spline_helpers.R | 4 recipes-1.0.9/recipes/R/spline_monotone.R | 11 recipes-1.0.9/recipes/R/spline_natural.R | 13 recipes-1.0.9/recipes/R/spline_nonnegative.R | 11 recipes-1.0.9/recipes/R/sqrt.R | 11 recipes-1.0.9/recipes/R/steps_and_checks.R | 2 recipes-1.0.9/recipes/R/string2factor.R | 24 recipes-1.0.9/recipes/R/tidy.R | 46 recipes-1.0.9/recipes/R/time.R | 27 recipes-1.0.9/recipes/R/tunable.R | 3 recipes-1.0.9/recipes/R/tune_args.R | 18 recipes-1.0.9/recipes/R/unknown.R | 27 recipes-1.0.9/recipes/R/unorder.R | 11 recipes-1.0.9/recipes/R/update-role-requirements.R | 59 recipes-1.0.9/recipes/R/update.R | 18 recipes-1.0.9/recipes/R/window.R | 53 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Title: Vaccine Efficacy Over Time - Variant Aware
Description: Implements methods for inference on potential waning of vaccine efficacy and for estimation of vaccine efficacy at a user-specified time after vaccination based on data from a randomized, double-blind, placebo-controlled vaccine trial in which participants may be unblinded and placebo subjects may be crossed over to the study vaccine. The methods also for variant stratification and allow adjustment for possible confounding via inverse probability weighting through specification of models for the trial entry process, unblinding mechanisms, and the probability an unblinded placebo participant accepts study vaccine.
Author: Marie Davidian [aut],
A.A. Tsiatis [aut],
Shannon T. Holloway [aut, cre]
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
Diff between VEwaningVariant versions 1.3 dated 2022-06-07 and 1.4 dated 2023-12-13
DESCRIPTION | 12 MD5 | 28 - NAMESPACE | 1 NEWS | 36 + R/RcppExports.R | 22 - R/plot.VEwaningVariant.R | 347 +++++++++---------- R/print.VEwaningVariant.R | 97 ++--- R/ve.R | 244 ++++++------- R/veWaningVariant.R | 834 +++++++++++++++++++++++----------------------- man/plot.Rd | 3 man/print.Rd | 3 man/ve.Rd | 4 man/veWaningVariant.Rd | 5 src/Makevars | 2 src/Makevars.win | 2 15 files changed, 842 insertions(+), 798 deletions(-)
More information about VEwaningVariant at CRAN
Permanent link
Title: Gene by Environment Interaction and Conditional Gene Tests for
Nuclear Families
Description: Does family-based gene by environment interaction tests, joint gene, gene-environment interaction test, and a test of a set of genes conditional on another set of genes.
Author: Thomas Hoffmann <tjhoffm@gmail.com>
Maintainer: Thomas Hoffmann <tjhoffm@gmail.com>
Diff between fbati versions 1.0-7 dated 2023-02-03 and 1.0-8 dated 2023-12-13
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ src/cgFbat.cpp | 8 ++++---- src/datamatrix.cpp | 2 +- src/fbatge.cpp | 18 +++++++++--------- src/fbatmeev.cpp | 4 ++-- src/joint.cpp | 2 +- 7 files changed, 27 insertions(+), 27 deletions(-)
Title: Read and Write 'Matlab' Files
Description: Read and write 'Matlab' MAT files from R. The 'rmatio'
package supports reading MAT version 4, MAT version 5 and MAT
compressed version 5. The 'rmatio' package can write version 5 MAT
files and version 5 files with variable compression.
Author: Stefan Widgren [aut, cre] ,
Christopher Hulbert [aut]
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between rmatio versions 0.18.0 dated 2023-02-05 and 0.19.0 dated 2023-12-13
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 6 ++++++ src/matio/mat5.c | 25 ++++++++++++------------- src/matio/read_data.c | 3 +-- src/rmatio.c | 4 ++-- 6 files changed, 29 insertions(+), 25 deletions(-)
Title: R Access to Mass-Spec Data
Description: R-based access to mass-spectrometry (MS) data. While many packages
exist to process MS data, many of these make it difficult to
access the underlying mass-to-charge ratio (m/z), intensity, and
retention time of the files
themselves. This package is designed to format MS data in a tidy fashion and
allows the user perform the plotting and analysis.
Author: William Kumler [aut, cre, cph],
Ricardo Cunha [ctb],
Ethan Bass [ctb]
Maintainer: William Kumler <wkumler@uw.edu>
Diff between RaMS versions 1.3.1 dated 2022-12-14 and 1.3.4 dated 2023-12-13
DESCRIPTION | 11 MD5 | 78 ++-- NAMESPACE | 3 NEWS.md | 9 R/extraHelperFunctions.R |only R/grabMSdataCode.R | 172 +++++---- R/grabMzmlFunctions.R | 8 R/grabMzxmlFunctions.R | 1 README.md | 44 ++ build/vignette.rds |binary inst/doc/Intro-to-RaMS.R | 11 inst/doc/Intro-to-RaMS.Rmd | 4 inst/doc/Intro-to-RaMS.html | 580 ++++++++++++++++---------------- inst/doc/Intro-to-tmzML.R | 1 inst/doc/Intro-to-tmzML.Rmd | 3 inst/doc/Intro-to-tmzML.html | 138 +++---- inst/doc/Minifying-files-with-RaMS.R | 1 inst/doc/Minifying-files-with-RaMS.Rmd | 1 inst/doc/Minifying-files-with-RaMS.html | 140 +++---- inst/doc/RaMS-and-friends.R | 1 inst/doc/RaMS-and-friends.Rmd | 1 inst/doc/RaMS-and-friends.html | 183 +++++----- inst/doc/speed_size_comparison.R |only inst/doc/speed_size_comparison.Rmd |only inst/doc/speed_size_comparison.html |only man/figures/README-mzgroupqplot-1.png |only man/grabAccessionData.Rd | 1 man/grabMSdata.Rd | 1 man/grabMzmlData.Rd | 1 man/grabMzxmlData.Rd | 1 man/mz_group.Rd |only man/pmppm.Rd | 2 man/qplotMS1data.Rd |only man/trapz.Rd |only tests/testthat/setup-load.R | 1 tests/testthat/test_errors_n_messes.R | 12 tests/testthat/test_extras.R |only vignettes/Intro-to-RaMS.Rmd | 4 vignettes/Intro-to-tmzML.Rmd | 3 vignettes/Minifying-files-with-RaMS.Rmd | 1 vignettes/RaMS-and-friends.Rmd | 1 vignettes/figures/ssc_vignette_renders |only vignettes/speed_size_comparison.Rmd |only 43 files changed, 777 insertions(+), 641 deletions(-)
Title: Dynamic Mixed-Membership Network Regression Model
Description: Stochastic collapsed variational inference on mixed-membership stochastic blockmodel for networks,
incorporating node-level predictors of mixed-membership vectors, as well as
dyad-level predictors. For networks observed over time, the model defines a hidden
Markov process that allows the effects of node-level predictors to evolve in discrete,
historical periods. In addition, the package offers a variety of utilities for
exploring results of estimation, including tools for conducting posterior
predictive checks of goodness-of-fit and several plotting functions. The package
implements methods described in Olivella, Pratt and Imai (2019) 'Dynamic Stochastic
Blockmodel Regression for Social Networks: Application to International Conflicts',
available at <https://www.santiagoolivella.info/pdfs/socnet.pdf>.
Author: Santiago Olivella [aut, cre],
Adeline Lo [aut, cre],
Tyler Pratt [aut, cre],
Kosuke Imai [aut, cre]
Maintainer: Santiago Olivella <olivella@unc.edu>
Diff between NetMix versions 0.2.0.1 dated 2022-11-16 and 0.2.0.2 dated 2023-12-13
DESCRIPTION | 11 +++++------ MD5 | 10 +++++----- NEWS | 5 +++++ R/plot.mmsbm.R | 4 ++-- README.md | 2 +- src/mmsbm_fit.cpp | 2 +- 6 files changed, 19 insertions(+), 15 deletions(-)
Title: Access, Retrieve, and Work with CMHC Data
Description: Wrapper around the Canadian Mortgage and Housing Corporation (CMHC) web interface. It enables programmatic and reproducible access to a wide variety of housing data from CMHC.
Author: Jens von Bergmann
Maintainer: Jens von Bergmann <jens@mountainmath.ca>
Diff between cmhc versions 0.2.6 dated 2023-10-06 and 0.2.7 dated 2023-12-13
DESCRIPTION | 6 - MD5 | 14 ++- NEWS.md | 4 + R/cmhc_geography.R | 22 ++---- R/helpers.R | 9 ++ README.md | 4 - data/cmhc_csd_translation_data_2023.rda |only inst/doc/basic_usage.html | 116 +++++++++++++++----------------- man/cmhc_csd_translation_data_2023.Rd |only 9 files changed, 90 insertions(+), 85 deletions(-)
Title: General-Purpose Unconstrained Non-Linear Optimization
Description: An algorithm for general-purpose unconstrained non-linear optimization.
The algorithm is of quasi-Newton type with BFGS updating of the inverse
Hessian and soft line search with a trust region type monitoring of the
input to the line search algorithm. The interface of 'ucminf' is
designed for easy interchange with 'optim'.
Author: K Herve Dakpo [ctb, cre],
Hans Bruun Nielsen [aut],
Stig Bousgaard Mortensen [aut]
Maintainer: K Herve Dakpo <k-herve.dakpo@inrae.fr>
Diff between ucminf versions 1.2.0 dated 2023-05-28 and 1.2.1 dated 2023-12-13
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 6 ++++++ src/interface.c | 7 ++++--- 4 files changed, 16 insertions(+), 9 deletions(-)
Title: Classification with Mixture Modelling
Description: Interface of 'MIXMOD' software for supervised, unsupervised and
semi-supervised classification with mixture modelling <doi: 10.18637/jss.v067.i06>.
Author: Florent Langrognet [aut],
Remi Lebret [aut],
Christian Poli [aut],
Serge Iovleff [aut],
Benjamin Auder [aut],
Parmeet Bhatia [ctb],
Anwuli Echenim [ctb],
Christophe Biernacki [ctb],
Gilles Celeux [ctb],
Gerard Govaert [ctb],
Julien Schueller [ctb],
Q [...truncated...]
Maintainer: Quentin Grimonprez <quentingrim@yahoo.fr>
Diff between Rmixmod versions 2.1.9 dated 2023-09-25 and 2.1.10 dated 2023-12-13
DESCRIPTION | 12 MD5 | 460 +- R/GaussianModel.R | 1 R/Rmixmod.R | 8 man/Rmixmod-package.Rd | 8 src/ClusteringInputHandling.cpp | 468 +- src/ClusteringInputHandling.h | 121 src/ClusteringOutputHandling.cpp | 151 src/ClusteringOutputHandling.h | 36 src/Conversion.cpp | 515 +- src/Conversion.h | 179 src/InputHandling.cpp | 152 src/InputHandling.h | 55 src/LearnOutputHandling.cpp | 202 - src/LearnOutputHandling.h | 34 src/OutputHandling.cpp | 460 +- src/OutputHandling.h | 65 src/clusteringMain.cpp | 665 +-- src/learnMain.cpp | 541 +- src/mixmod/Clustering/ClusteringInput.cpp | 169 src/mixmod/Clustering/ClusteringInput.h | 48 src/mixmod/Clustering/ClusteringMain.cpp | 400 -- src/mixmod/Clustering/ClusteringMain.h | 37 src/mixmod/Clustering/ClusteringModelOutput.cpp | 42 src/mixmod/Clustering/ClusteringModelOutput.h | 30 src/mixmod/Clustering/ClusteringOutput.cpp | 653 +-- src/mixmod/Clustering/ClusteringOutput.h | 71 src/mixmod/Clustering/ClusteringStrategy.cpp | 511 +- src/mixmod/Clustering/ClusteringStrategy.h | 101 src/mixmod/Clustering/ClusteringStrategyInit.cpp | 408 +- src/mixmod/Clustering/ClusteringStrategyInit.h | 110 src/mixmod/DiscriminantAnalysis/Learn/LearnInput.cpp | 127 src/mixmod/DiscriminantAnalysis/Learn/LearnInput.h | 33 src/mixmod/DiscriminantAnalysis/Learn/LearnMain.cpp | 226 - src/mixmod/DiscriminantAnalysis/Learn/LearnMain.h | 37 src/mixmod/DiscriminantAnalysis/Learn/LearnModelOutput.cpp | 60 src/mixmod/DiscriminantAnalysis/Learn/LearnModelOutput.h | 43 src/mixmod/DiscriminantAnalysis/Learn/LearnOutput.cpp | 634 +-- src/mixmod/DiscriminantAnalysis/Learn/LearnOutput.h | 44 src/mixmod/DiscriminantAnalysis/Learn/LearnStrategy.cpp | 33 src/mixmod/DiscriminantAnalysis/Learn/LearnStrategy.h | 22 src/mixmod/DiscriminantAnalysis/Predict/PredictInput.cpp | 71 src/mixmod/DiscriminantAnalysis/Predict/PredictInput.h | 43 src/mixmod/DiscriminantAnalysis/Predict/PredictMain.cpp | 104 src/mixmod/DiscriminantAnalysis/Predict/PredictMain.h | 37 src/mixmod/DiscriminantAnalysis/Predict/PredictModelOutput.cpp | 44 src/mixmod/DiscriminantAnalysis/Predict/PredictModelOutput.h | 30 src/mixmod/DiscriminantAnalysis/Predict/PredictOutput.cpp | 571 +-- src/mixmod/DiscriminantAnalysis/Predict/PredictOutput.h | 43 src/mixmod/DiscriminantAnalysis/Predict/PredictStrategy.cpp | 35 src/mixmod/DiscriminantAnalysis/Predict/PredictStrategy.h | 32 src/mixmod/Kernel/Algo/Algo.cpp | 151 src/mixmod/Kernel/Algo/Algo.h | 57 src/mixmod/Kernel/Algo/CEMAlgo.cpp | 41 src/mixmod/Kernel/Algo/CEMAlgo.h | 21 src/mixmod/Kernel/Algo/EMAlgo.cpp | 41 src/mixmod/Kernel/Algo/EMAlgo.h | 21 src/mixmod/Kernel/Algo/MAPAlgo.cpp | 31 src/mixmod/Kernel/Algo/MAPAlgo.h | 31 src/mixmod/Kernel/Algo/MAlgo.cpp | 31 src/mixmod/Kernel/Algo/MAlgo.h | 29 src/mixmod/Kernel/Algo/SEMAlgo.cpp | 60 src/mixmod/Kernel/Algo/SEMAlgo.h | 29 src/mixmod/Kernel/Criterion/BICCriterion.cpp | 29 src/mixmod/Kernel/Criterion/BICCriterion.h | 17 src/mixmod/Kernel/Criterion/CVCriterion.cpp | 183 src/mixmod/Kernel/Criterion/CVCriterion.h | 30 src/mixmod/Kernel/Criterion/Criterion.cpp | 17 src/mixmod/Kernel/Criterion/Criterion.h | 22 src/mixmod/Kernel/Criterion/CriterionOutput.cpp | 86 src/mixmod/Kernel/Criterion/CriterionOutput.h | 62 src/mixmod/Kernel/Criterion/ICLCriterion.cpp | 32 src/mixmod/Kernel/Criterion/ICLCriterion.h | 17 src/mixmod/Kernel/Criterion/NECCriterion.cpp | 26 src/mixmod/Kernel/Criterion/NECCriterion.h | 15 src/mixmod/Kernel/IO/BinaryData.cpp | 213 - src/mixmod/Kernel/IO/BinaryData.h | 83 src/mixmod/Kernel/IO/BinarySample.cpp | 32 src/mixmod/Kernel/IO/BinarySample.h | 33 src/mixmod/Kernel/IO/ColumnDescription.cpp | 17 src/mixmod/Kernel/IO/ColumnDescription.h | 50 src/mixmod/Kernel/IO/CompositeData.cpp | 106 src/mixmod/Kernel/IO/CompositeData.h | 68 src/mixmod/Kernel/IO/CompositeSample.cpp | 28 src/mixmod/Kernel/IO/CompositeSample.h | 42 src/mixmod/Kernel/IO/Data.cpp | 46 src/mixmod/Kernel/IO/Data.h | 112 src/mixmod/Kernel/IO/DataDescription.cpp | 108 src/mixmod/Kernel/IO/DataDescription.h | 60 src/mixmod/Kernel/IO/Description.cpp | 42 src/mixmod/Kernel/IO/Description.h | 103 src/mixmod/Kernel/IO/GaussianData.cpp | 136 src/mixmod/Kernel/IO/GaussianData.h | 74 src/mixmod/Kernel/IO/GaussianSample.cpp | 32 src/mixmod/Kernel/IO/GaussianSample.h | 30 src/mixmod/Kernel/IO/IndividualColumnDescription.cpp | 39 src/mixmod/Kernel/IO/IndividualColumnDescription.h | 29 src/mixmod/Kernel/IO/Input.cpp | 231 - src/mixmod/Kernel/IO/Input.h | 176 src/mixmod/Kernel/IO/Label.cpp | 144 src/mixmod/Kernel/IO/Label.h | 56 src/mixmod/Kernel/IO/LabelDescription.cpp | 103 src/mixmod/Kernel/IO/LabelDescription.h | 59 src/mixmod/Kernel/IO/LikelihoodOutput.cpp | 29 src/mixmod/Kernel/IO/LikelihoodOutput.h | 28 src/mixmod/Kernel/IO/ModelOutput.cpp | 127 src/mixmod/Kernel/IO/ModelOutput.h | 152 src/mixmod/Kernel/IO/ParameterDescription.cpp | 294 - src/mixmod/Kernel/IO/ParameterDescription.h | 164 src/mixmod/Kernel/IO/Partition.cpp | 201 - src/mixmod/Kernel/IO/Partition.h | 88 src/mixmod/Kernel/IO/Proba.cpp | 79 src/mixmod/Kernel/IO/Proba.h | 51 src/mixmod/Kernel/IO/ProbaDescription.cpp | 68 src/mixmod/Kernel/IO/ProbaDescription.h | 49 src/mixmod/Kernel/IO/ProbaOutput.cpp | 102 src/mixmod/Kernel/IO/ProbaOutput.h | 74 src/mixmod/Kernel/IO/QualitativeColumnDescription.cpp | 30 src/mixmod/Kernel/IO/QualitativeColumnDescription.h | 35 src/mixmod/Kernel/IO/QuantitativeColumnDescription.cpp | 26 src/mixmod/Kernel/IO/QuantitativeColumnDescription.h | 19 src/mixmod/Kernel/IO/Sample.cpp | 22 src/mixmod/Kernel/IO/Sample.h | 34 src/mixmod/Kernel/IO/UnusedColumnDescription.cpp | 21 src/mixmod/Kernel/IO/UnusedColumnDescription.h | 13 src/mixmod/Kernel/IO/WeightColumnDescription.cpp | 26 src/mixmod/Kernel/IO/WeightColumnDescription.h | 19 src/mixmod/Kernel/Model/BinaryModel.cpp | 34 src/mixmod/Kernel/Model/BinaryModel.h | 25 src/mixmod/Kernel/Model/Model.cpp | 1060 ++--- src/mixmod/Kernel/Model/Model.h | 223 - src/mixmod/Kernel/Model/ModelType.cpp | 323 - src/mixmod/Kernel/Model/ModelType.h | 94 src/mixmod/Kernel/Parameter/BinaryEParameter.cpp | 170 src/mixmod/Kernel/Parameter/BinaryEParameter.h | 51 src/mixmod/Kernel/Parameter/BinaryEjParameter.cpp | 200 - src/mixmod/Kernel/Parameter/BinaryEjParameter.h | 53 src/mixmod/Kernel/Parameter/BinaryEkParameter.cpp | 182 src/mixmod/Kernel/Parameter/BinaryEkParameter.h | 53 src/mixmod/Kernel/Parameter/BinaryEkjParameter.cpp | 207 - src/mixmod/Kernel/Parameter/BinaryEkjParameter.h | 52 src/mixmod/Kernel/Parameter/BinaryEkjhParameter.cpp | 274 - src/mixmod/Kernel/Parameter/BinaryEkjhParameter.h | 66 src/mixmod/Kernel/Parameter/BinaryParameter.cpp | 284 - src/mixmod/Kernel/Parameter/BinaryParameter.h | 126 src/mixmod/Kernel/Parameter/CompositeParameter.cpp | 389 -- src/mixmod/Kernel/Parameter/CompositeParameter.h | 77 src/mixmod/Kernel/Parameter/GaussianDiagParameter.cpp | 182 src/mixmod/Kernel/Parameter/GaussianDiagParameter.h | 45 src/mixmod/Kernel/Parameter/GaussianEDDAParameter.cpp | 313 - src/mixmod/Kernel/Parameter/GaussianEDDAParameter.h | 83 src/mixmod/Kernel/Parameter/GaussianGeneralParameter.cpp | 414 +- src/mixmod/Kernel/Parameter/GaussianGeneralParameter.h | 81 src/mixmod/Kernel/Parameter/GaussianHDDAParameter.cpp | 962 ++--- src/mixmod/Kernel/Parameter/GaussianHDDAParameter.h | 133 src/mixmod/Kernel/Parameter/GaussianParameter.cpp | 269 - src/mixmod/Kernel/Parameter/GaussianParameter.h | 111 src/mixmod/Kernel/Parameter/GaussianSphericalParameter.cpp | 135 src/mixmod/Kernel/Parameter/GaussianSphericalParameter.h | 23 src/mixmod/Kernel/Parameter/Parameter.cpp | 71 src/mixmod/Kernel/Parameter/Parameter.h | 164 src/mixmod/Matrix/DiagMatrix.cpp | 204 - src/mixmod/Matrix/DiagMatrix.h | 122 src/mixmod/Matrix/GeneralMatrix.cpp | 201 - src/mixmod/Matrix/GeneralMatrix.h | 148 src/mixmod/Matrix/Matrix.cpp | 43 src/mixmod/Matrix/Matrix.h | 104 src/mixmod/Matrix/SphericalMatrix.cpp | 194 - src/mixmod/Matrix/SphericalMatrix.h | 112 src/mixmod/Matrix/SymmetricMatrix.cpp | 241 - src/mixmod/Matrix/SymmetricMatrix.h | 143 src/mixmod/Utilities/Error.cpp | 31 src/mixmod/Utilities/Error.h | 25 src/mixmod/Utilities/ExampleDataUtil.cpp | 159 src/mixmod/Utilities/ExampleDataUtil.h | 39 src/mixmod/Utilities/Random.cpp | 45 src/mixmod/Utilities/Random.h | 7 src/mixmod/Utilities/Util.cpp | 559 +- src/mixmod/Utilities/Util.h | 679 +-- src/mixmod/Utilities/exceptions/DCVException.cpp | 47 src/mixmod/Utilities/exceptions/DCVException.h | 52 src/mixmod/Utilities/exceptions/DCVonlyInGaussianCaseException.cpp | 47 src/mixmod/Utilities/exceptions/DCVonlyInGaussianCaseException.h | 36 src/mixmod/Utilities/exceptions/ErrorEnumerations.h | 9 src/mixmod/Utilities/exceptions/Exception.cpp | 34 src/mixmod/Utilities/exceptions/Exception.h | 46 src/mixmod/Utilities/exceptions/InputException.cpp | 40 src/mixmod/Utilities/exceptions/InputException.h | 65 src/mixmod/Utilities/exceptions/NumericException.cpp | 37 src/mixmod/Utilities/exceptions/NumericException.h | 40 src/mixmod/Utilities/exceptions/OtherException.cpp | 37 src/mixmod/Utilities/exceptions/OtherException.h | 40 src/mixmod/Utilities/maths/Armadillo.h | 511 +- src/mixmod/Utilities/maths/Eigen.h | 590 +-- src/mixmod/Utilities/maths/GSL.h | 531 +- src/mixmod/Utilities/maths/ITpp.h | 516 +- src/mixmod/Utilities/maths/SelectLibrary.h | 13 src/mixmod/Utilities/mixmod.h | 32 src/mixmod_iostream/DomData.cpp | 508 +- src/mixmod_iostream/DomData.h | 40 src/mixmod_iostream/DomLabel.cpp | 704 +-- src/mixmod_iostream/DomLabel.h | 38 src/mixmod_iostream/DomOpProject.cpp | 239 - src/mixmod_iostream/DomOpProject.h | 71 src/mixmod_iostream/DomParameter.cpp | 386 -- src/mixmod_iostream/DomParameter.h | 43 src/mixmod_iostream/DomProba.cpp | 303 - src/mixmod_iostream/DomProba.h | 60 src/mixmod_iostream/DomProject.cpp | 50 src/mixmod_iostream/DomProject.h | 60 src/mixmod_iostream/IOStreamUtil.cpp | 1136 ++---- src/mixmod_iostream/IOStreamUtil.h | 228 - src/mixmod_iostream/NodeInput.cpp | 177 src/mixmod_iostream/NodeInput.h | 80 src/mixmod_iostream/NodeOpInput.cpp | 1892 ++++------ src/mixmod_iostream/NodeOpInput.h | 125 src/mixmod_iostream/NodeOpOutput.cpp | 811 ++-- src/mixmod_iostream/NodeOpOutput.h | 91 src/mixmod_iostream/NodeOutput.cpp | 63 src/mixmod_iostream/NodeOutput.h | 73 src/mixmod_iostream/to_be_removed/DomClusteringProject.cpp | 126 src/mixmod_iostream/to_be_removed/DomClusteringProject.h | 39 src/mixmod_iostream/to_be_removed/DomDAProject.cpp | 50 src/mixmod_iostream/to_be_removed/DomDAProject.h | 25 src/mixmod_iostream/to_be_removed/NodeClusteringInput.cpp | 1346 +++---- src/mixmod_iostream/to_be_removed/NodeClusteringInput.h | 95 src/mixmod_iostream/to_be_removed/NodeClusteringOutput.cpp | 426 +- src/mixmod_iostream/to_be_removed/NodeClusteringOutput.h | 72 src/predictMain.cpp | 547 +- src/xMain.cpp | 59 tests/heterogeneousDAtest.R | 6 231 files changed, 17780 insertions(+), 18961 deletions(-)
More information about WeightedTreemaps at CRAN
Permanent link
Title: Advanced Tensor Arithmetic with Named Indices
Description: Provides convenience functions for advanced
linear algebra with tensors and computation with data sets of
tensors on a higher level abstraction. It includes Einstein and
Riemann summing conventions, dragging, co- and contravariate
indices, parallel computations on sequences of tensors.
Author: K. Gerald van den Boogaart <boogaart@uni-greifswald.de>
Maintainer: K. Gerald van den Boogaart <boogaart@math.tu-freiberg.de>
Diff between tensorA versions 0.36.2 dated 2020-11-19 and 0.36.2.1 dated 2023-12-13
DESCRIPTION | 9 ++++----- MD5 | 14 +++++++------- man/choltensor.Rd | 4 ++-- man/invtensor.Rd | 2 +- man/normtensor.Rd | 4 ++-- man/reptensor.Rd | 4 ++-- man/solvetensor.Rd | 2 +- man/svdtensor.Rd | 2 +- 8 files changed, 20 insertions(+), 21 deletions(-)
Title: Probabilistic and Possibilistic Cluster Analysis
Description: Partitioning clustering divides the objects in a data set into non-overlapping subsets or clusters by using the prototype-based probabilistic and possibilistic clustering algorithms. This package covers a set of the functions for Fuzzy C-Means (Bezdek, 1974) <doi:10.1080/01969727308546047>, Possibilistic C-Means (Krishnapuram & Keller, 1993) <doi:10.1109/91.227387>, Possibilistic Fuzzy C-Means (Pal et al, 2005) <doi:10.1109/TFUZZ.2004.840099>, Possibilistic Clustering Algorithm (Yang et al, 2006) <doi:10.1016/j.patcog.2005.07.005>, Possibilistic C-Means with Repulsion (Wachs et al, 2006) <doi:10.1007/3-540-31662-0_6> and the other variants of hard and soft clustering algorithms. The cluster prototypes and membership matrices required by these partitioning algorithms are initialized with different initialization techniques that are available in the package 'inaparc'. As the distance metrics, not only the Euclidean distance but also a set of the commonly [...truncated...]
Author: Zeynel Cebeci [aut, cre],
Figen Yildiz [aut],
Alper Tuna Kavlak [aut],
Cagatay Cebeci [aut],
Hasan Onder [aut]
Maintainer: Zeynel Cebeci <zcebeci@cukurova.edu.tr>
Diff between ppclust versions 1.1.0 dated 2020-02-09 and 1.1.0.1 dated 2023-12-13
DESCRIPTION | 8 MD5 | 23 build/partial.rdb |only build/vignette.rds |binary data/x12.rda |binary data/x16.rda |binary inst/doc/fcm.R | 220 - inst/doc/fcm.html | 6960 ++++++++++++++++++++++++------------------------ inst/doc/upfc.R | 256 - inst/doc/upfc.html | 7027 +++++++++++++++++++++++++------------------------ man/gg.Rd | 4 man/gk.Rd | 10 man/ppclust-package.Rd | 12 13 files changed, 7407 insertions(+), 7113 deletions(-)
Title: Calculate Indices and Theoretical Physicochemical Properties of
Protein Sequences
Description: Includes functions to calculate several physicochemical properties and indices for amino-acid sequences as well as to read and plot 'XVG' output files from the 'GROMACS' molecular dynamics package.
Author: Daniel Osorio [aut, cre] ,
Paola Rondon-Villarreal [aut, ths]
,
Rodrigo Torres [aut, ths] ,
J. Sebastian Paez [ctb] ,
Luis Pedro Coelho [ctb] ,
Richel J.C. Bilderbeek [ctb] ,
Florian C. Sigloch [ctb]
Maintainer: Daniel Osorio <daniecos@uio.no>
Diff between Peptides versions 2.4.5 dated 2023-05-10 and 2.4.6 dated 2023-12-13
Peptides-2.4.5/Peptides/R/aacomp.R |only Peptides-2.4.6/Peptides/DESCRIPTION | 8 Peptides-2.4.6/Peptides/MD5 | 192 Peptides-2.4.6/Peptides/NAMESPACE | 80 Peptides-2.4.6/Peptides/R/RcppExports.R | 30 Peptides-2.4.6/Peptides/R/aaCheck.R | 32 Peptides-2.4.6/Peptides/R/aaComp.R |only Peptides-2.4.6/Peptides/R/aaDescriptors.R | 102 Peptides-2.4.6/Peptides/R/aaList.R | 26 Peptides-2.4.6/Peptides/R/aindex.R | 66 Peptides-2.4.6/Peptides/R/autocorrelation.R | 102 Peptides-2.4.6/Peptides/R/autocovariance.R | 96 Peptides-2.4.6/Peptides/R/blosumIndices.R | 58 Peptides-2.4.6/Peptides/R/boman.R | 106 Peptides-2.4.6/Peptides/R/charge.R | 172 Peptides-2.4.6/Peptides/R/cppFunctions.R | 4 Peptides-2.4.6/Peptides/R/crosscovariance.R | 118 Peptides-2.4.6/Peptides/R/crucianiProperties.R | 46 Peptides-2.4.6/Peptides/R/data-AA.R | 294 Peptides-2.4.6/Peptides/R/data-pepdata.R | 62 Peptides-2.4.6/Peptides/R/fasgaiVectors.R | 52 Peptides-2.4.6/Peptides/R/hmoment.R | 96 Peptides-2.4.6/Peptides/R/hydrophobicity.R | 382 Peptides-2.4.6/Peptides/R/instaindex.R | 866 Peptides-2.4.6/Peptides/R/kideraFactors.R | 90 Peptides-2.4.6/Peptides/R/lengthpep.R | 34 Peptides-2.4.6/Peptides/R/massShift.R | 175 Peptides-2.4.6/Peptides/R/membpos.R | 134 Peptides-2.4.6/Peptides/R/mswhimScores.R | 50 Peptides-2.4.6/Peptides/R/mw.R | 246 Peptides-2.4.6/Peptides/R/mz.R | 84 Peptides-2.4.6/Peptides/R/pI.R | 96 Peptides-2.4.6/Peptides/R/plotXVG.R | 102 Peptides-2.4.6/Peptides/R/protFP.R | 48 Peptides-2.4.6/Peptides/R/readXVG.R | 140 Peptides-2.4.6/Peptides/R/smilesStrings.R | 120 Peptides-2.4.6/Peptides/R/stScales.R | 48 Peptides-2.4.6/Peptides/R/tScales.R | 48 Peptides-2.4.6/Peptides/R/vhseScales.R | 56 Peptides-2.4.6/Peptides/R/zScales.R | 62 Peptides-2.4.6/Peptides/README.md | 134 Peptides-2.4.6/Peptides/data/datalist | 2 Peptides-2.4.6/Peptides/inst/CITATION | 24 Peptides-2.4.6/Peptides/inst/xvg-files/POPC.xvg |33378 +++++------ Peptides-2.4.6/Peptides/inst/xvg-files/POPE.xvg |33378 +++++------ Peptides-2.4.6/Peptides/inst/xvg-files/POPG.xvg |33378 +++++------ Peptides-2.4.6/Peptides/inst/xvg-files/RDF.xvg | 980 Peptides-2.4.6/Peptides/inst/xvg-files/epot.xvg | 2402 Peptides-2.4.6/Peptides/man/AAdata.Rd | 314 Peptides-2.4.6/Peptides/man/aIndex.Rd | 64 Peptides-2.4.6/Peptides/man/aaComp.Rd | 140 Peptides-2.4.6/Peptides/man/aaDescriptors.Rd | 62 Peptides-2.4.6/Peptides/man/aaList.Rd | 40 Peptides-2.4.6/Peptides/man/aaSMILES.Rd | 56 Peptides-2.4.6/Peptides/man/autoCorrelation.Rd | 96 Peptides-2.4.6/Peptides/man/autoCovariance.Rd | 96 Peptides-2.4.6/Peptides/man/blosumIndices.Rd | 60 Peptides-2.4.6/Peptides/man/boman.Rd | 70 Peptides-2.4.6/Peptides/man/charge.Rd | 168 Peptides-2.4.6/Peptides/man/crossCovariance.Rd | 104 Peptides-2.4.6/Peptides/man/crucianiProperties.Rd | 50 Peptides-2.4.6/Peptides/man/fasgaiVectors.Rd | 52 Peptides-2.4.6/Peptides/man/hmoment.Rd | 90 Peptides-2.4.6/Peptides/man/hydrophobicity.Rd | 388 Peptides-2.4.6/Peptides/man/instaIndex.Rd | 60 Peptides-2.4.6/Peptides/man/kideraFactors.Rd | 80 Peptides-2.4.6/Peptides/man/lengthpep.Rd | 52 Peptides-2.4.6/Peptides/man/massShift.Rd | 91 Peptides-2.4.6/Peptides/man/membpos.Rd | 104 Peptides-2.4.6/Peptides/man/mswhimScores.Rd | 52 Peptides-2.4.6/Peptides/man/mw.Rd | 106 Peptides-2.4.6/Peptides/man/mz.Rd | 56 Peptides-2.4.6/Peptides/man/pI.Rd | 106 Peptides-2.4.6/Peptides/man/pepdata.Rd | 80 Peptides-2.4.6/Peptides/man/plotXVG.Rd | 66 Peptides-2.4.6/Peptides/man/protFP.Rd | 52 Peptides-2.4.6/Peptides/man/readXVG.Rd | 80 Peptides-2.4.6/Peptides/man/stScales.Rd | 52 Peptides-2.4.6/Peptides/man/tScales.Rd | 52 Peptides-2.4.6/Peptides/man/vhseScales.Rd | 62 Peptides-2.4.6/Peptides/man/zScales.Rd | 64 Peptides-2.4.6/Peptides/src/RcppExports.cpp | 4 Peptides-2.4.6/Peptides/tests/testthat.R | 8 Peptides-2.4.6/Peptides/tests/testthat/test-SMILES.R | 70 Peptides-2.4.6/Peptides/tests/testthat/test.aaList.R | 20 Peptides-2.4.6/Peptides/tests/testthat/test.aacheck.R | 18 Peptides-2.4.6/Peptides/tests/testthat/test.aacomp.R | 58 Peptides-2.4.6/Peptides/tests/testthat/test.aindex.R | 30 Peptides-2.4.6/Peptides/tests/testthat/test.boman.R | 26 Peptides-2.4.6/Peptides/tests/testthat/test.charge.R | 112 Peptides-2.4.6/Peptides/tests/testthat/test.hmoment.R | 40 Peptides-2.4.6/Peptides/tests/testthat/test.hydrophobicity.R | 28 Peptides-2.4.6/Peptides/tests/testthat/test.instaindex.R | 28 Peptides-2.4.6/Peptides/tests/testthat/test.lengthpep.R | 28 Peptides-2.4.6/Peptides/tests/testthat/test.massShift.R | 70 Peptides-2.4.6/Peptides/tests/testthat/test.mw.R | 38 Peptides-2.4.6/Peptides/tests/testthat/test.mz.R | 50 Peptides-2.4.6/Peptides/tests/testthat/test.pI.R | 28 98 files changed, 55960 insertions(+), 55960 deletions(-)
Title: Longitudinal Data
Description: Tools for longitudinal data and joint longitudinal data (used by packages kml and kml3d).
Author: Christophe Genolini [cre, aut],
Bruno Falissard [ctb],
Dai Fang [ctb],
Patrice Kiener [ctb],
Luke Tierney [ctb]
Maintainer: Christophe Genolini <christophe.genolini@u-paris10.fr>
Diff between longitudinalData versions 2.4.5 dated 2023-02-09 and 2.4.5.1 dated 2023-12-13
DESCRIPTION | 10 ++--- MD5 | 78 ++++++++++++++++++++-------------------- R/imputCopyMean.R | 24 ++++++------ R/imputLinearInterpol.R | 2 - R/imputation.r | 2 - R/listPartition.r | 4 +- R/longData.r | 8 ++-- R/longData3d.r | 8 ++-- R/newPlot.r | 40 ++++++++++---------- R/parLongData.r | 14 +++---- R/partition.r | 46 +++++++++++------------ man/ListPartition-class.Rd | 6 +-- man/LongData-class.Rd | 4 +- man/LongData3d-class.Rd | 4 +- man/ParLongData-class.Rd | 2 - man/ParWindows-class.Rd | 4 +- man/Partition-class.Rd | 4 +- man/distFrechet.Rd | 6 +-- man/expandParLongData.Rd | 4 +- man/imputation.Rd | 20 +++++----- man/initializePartition.Rd | 4 +- man/longData-internal.Rd | 4 +- man/longData.Rd | 4 +- man/longData3d.Rd | 4 +- man/longDataFrom3d.Rd | 4 +- man/longDataTo3d.Rd | 4 +- man/longitudinalData-package.Rd | 4 +- man/makeLatexFile.Rd | 4 +- man/ordered.Rd | 4 +- man/parLongData.Rd | 2 - man/parWindows.Rd | 4 +- man/partition.Rd | 4 +- man/plot3dPdf.Rd | 4 +- man/plotTrajMeans.Rd | 4 +- man/plotTrajMeans3d.Rd | 4 +- man/qualityCriterion.Rd | 10 ++--- man/regroup.Rd | 4 +- man/restoreRealData.Rd | 4 +- man/scale.Rd | 4 +- man/windowsCut.Rd | 4 +- 40 files changed, 187 insertions(+), 187 deletions(-)
More information about longitudinalData at CRAN
Permanent link
Title: K-Means for Joint Longitudinal Data
Description: An implementation of k-means specifically design
to cluster joint trajectories (longitudinal data on
several variable-trajectories).
Like 'kml', it provides facilities to deal with missing
value, compute several quality criterion (Calinski and Harabatz,
Ray and Turie, Davies and Bouldin, BIC,...) and propose a graphical
interface for choosing the 'best' number of clusters. In addition, the 3D graph
representing the mean joint-trajectories of each cluster can be exported through
LaTeX in a 3D dynamic rotating PDF graph.
Author: Christophe Genolini [cre, aut],
Bruno Falissard [ctb],
Patrice Kiener [ctb],
Jean-Baptiste Pingault [ctb]
Maintainer: Christophe Genolini <christophe.genolini@u-paris10.fr>
Diff between kml3d versions 2.4.6 dated 2023-02-12 and 2.4.6.1 dated 2023-12-13
DESCRIPTION | 14 +++++++------- MD5 | 12 ++++++------ R/clusterLongData3d.r | 6 +++--- R/kml3d.r | 10 +++++----- data/pregnandiol.rda |binary man/generateArtificialLongData3d.Rd | 4 ++-- man/pregnandiol.Rd | 4 ++-- 7 files changed, 25 insertions(+), 25 deletions(-)
Title: K-Means for Longitudinal Data
Description: An implementation of k-means specifically design
to cluster longitudinal data. It provides facilities to deal with missing
value, compute several quality criterion (Calinski and Harabatz,
Ray and Turie, Davies and Bouldin, BIC, ...) and propose a graphical
interface for choosing the 'best' number of clusters.
Author: Christophe Genolini [cre, aut],
Bruno Falissard [ctb],
Patrice Kiener [ctb]
Maintainer: Christophe Genolini <christophe.genolini@u-paris10.fr>
Diff between kml versions 2.4.6 dated 2023-02-13 and 2.4.6.1 dated 2023-12-13
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/clusterLongData.R | 14 +++++++------- R/kml.R | 16 ++++++++-------- man/clusterLongData.Rd | 4 ++-- man/epipageShort.Rd | 4 ++-- man/generateArtificialLongData.Rd | 4 ++-- 7 files changed, 32 insertions(+), 32 deletions(-)
Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors as described in Migueles and colleagues (JMPB 2019), and van Hees and colleagues (JApplPhysiol 2014; PLoSONE 2015). The package has been developed and tested for binary data from 'GENEActiv' <https://activinsights.com/> and GENEA devices (not for sale), .csv-export data from 'Actigraph' <https://theactigraph.com> devices, and .cwa and .wav-format data from 'Axivity' <https://axivity.com>. These devices are currently widely used in research on human daily physical activity. Further, the package can handle accelerometer data file from any other sensor brand providing that the data is stored in csv format and has either no header or a two column header. Also the package allows for external function embedding.
Author: Vincent T van Hees [aut, cre],
Jairo H Migueles [aut] ,
Severine Sabia [ctb],
Matthew R Patterson [ctb],
Zhou Fang [ctb],
Joe Heywood [ctb],
Joan Capdevila Pujol [ctb],
Lena Kushleyeva [ctb],
Mathilde Chen [ctb],
Manasa Yerramalla [ctb],
Patrick Bos [...truncated...]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>
Diff between GGIR versions 3.0-0 dated 2023-10-16 and 3.0-2 dated 2023-12-13
GGIR-3.0-0/GGIR/inst/doc/chapterInProgress.R |only GGIR-3.0-0/GGIR/inst/doc/chapterInProgress.Rmd |only GGIR-3.0-0/GGIR/inst/doc/chapterInProgress.html |only GGIR-3.0-0/GGIR/vignettes/chapterInProgress.Rmd |only GGIR-3.0-2/GGIR/DESCRIPTION | 16 GGIR-3.0-2/GGIR/MD5 | 135 ++-- GGIR-3.0-2/GGIR/NAMESPACE | 9 GGIR-3.0-2/GGIR/NEWS.md | 38 + GGIR-3.0-2/GGIR/R/GGIR.R | 87 +- GGIR-3.0-2/GGIR/R/check_log.R |only GGIR-3.0-2/GGIR/R/check_params.R | 95 ++ GGIR-3.0-2/GGIR/R/convertEpochData.R | 63 + GGIR-3.0-2/GGIR/R/createConfigFile.R | 4 GGIR-3.0-2/GGIR/R/datadir2fnames.R | 20 GGIR-3.0-2/GGIR/R/extract_params.R | 16 GGIR-3.0-2/GGIR/R/g.analyse.R | 97 +-- GGIR-3.0-2/GGIR/R/g.analyse.perfile.R | 48 - GGIR-3.0-2/GGIR/R/g.calibrate.R | 21 GGIR-3.0-2/GGIR/R/g.conv.actlog.R | 60 - GGIR-3.0-2/GGIR/R/g.getmeta.R | 29 GGIR-3.0-2/GGIR/R/g.impute.R | 153 ++++ GGIR-3.0-2/GGIR/R/g.imputeTimegaps.R | 17 GGIR-3.0-2/GGIR/R/g.part1.R | 9 GGIR-3.0-2/GGIR/R/g.part2.R | 22 GGIR-3.0-2/GGIR/R/g.part4.R | 15 GGIR-3.0-2/GGIR/R/g.part5.R | 16 GGIR-3.0-2/GGIR/R/g.part5.analyseRest.R | 14 GGIR-3.0-2/GGIR/R/g.part5.savetimeseries.R | 24 GGIR-3.0-2/GGIR/R/g.part6.R |only GGIR-3.0-2/GGIR/R/g.plot.R | 94 +- GGIR-3.0-2/GGIR/R/g.readaccfile.R | 4 GGIR-3.0-2/GGIR/R/g.report.part2.R | 2 GGIR-3.0-2/GGIR/R/g.report.part5.R | 4 GGIR-3.0-2/GGIR/R/g.report.part5_dictionary.R |only GGIR-3.0-2/GGIR/R/g.report.part6.R |only GGIR-3.0-2/GGIR/R/load_params.R | 36 - GGIR-3.0-2/GGIR/R/part6AlignIndividuals.R |only GGIR-3.0-2/GGIR/R/part6PairwiseAggregation.R |only GGIR-3.0-2/GGIR/R/read.myacc.csv.R | 1 GGIR-3.0-2/GGIR/R/sysdata.rda |only GGIR-3.0-2/GGIR/build/vignette.rds |binary GGIR-3.0-2/GGIR/data/data.metalong.RData |only GGIR-3.0-2/GGIR/data/data.ts.RData |only GGIR-3.0-2/GGIR/inst/doc/CutPoints.Rmd | 2 GGIR-3.0-2/GGIR/inst/doc/CutPoints.html | 10 GGIR-3.0-2/GGIR/inst/doc/ExternalFunction.pdf |binary GGIR-3.0-2/GGIR/inst/doc/GGIR.R | 2 GGIR-3.0-2/GGIR/inst/doc/GGIR.Rmd | 61 + GGIR-3.0-2/GGIR/inst/doc/GGIR.html | 514 ++++++++++------ GGIR-3.0-2/GGIR/inst/doc/GGIRParameters.Rmd | 3 GGIR-3.0-2/GGIR/inst/doc/GGIRParameters.html | 402 +++++++----- GGIR-3.0-2/GGIR/inst/doc/HouseHoldCoanalysis.R |only GGIR-3.0-2/GGIR/inst/doc/HouseHoldCoanalysis.Rmd |only GGIR-3.0-2/GGIR/inst/doc/HouseHoldCoanalysis.html |only GGIR-3.0-2/GGIR/man/GGIR-package.Rd | 6 GGIR-3.0-2/GGIR/man/GGIR.Rd | 211 ++++-- GGIR-3.0-2/GGIR/man/check_log.Rd |only GGIR-3.0-2/GGIR/man/data.metalong.Rd |only GGIR-3.0-2/GGIR/man/data.ts.Rd |only GGIR-3.0-2/GGIR/man/g.analyse.Rd | 9 GGIR-3.0-2/GGIR/man/g.impute.Rd | 5 GGIR-3.0-2/GGIR/man/g.imputeTimegaps.Rd | 5 GGIR-3.0-2/GGIR/man/g.part5.savetimeseries.Rd | 6 GGIR-3.0-2/GGIR/man/g.part6.Rd |only GGIR-3.0-2/GGIR/man/g.report.part5_dictionary.Rd |only GGIR-3.0-2/GGIR/man/g.report.part6.Rd |only GGIR-3.0-2/GGIR/man/load_params.Rd | 4 GGIR-3.0-2/GGIR/man/part6AlignIndividuals.Rd |only GGIR-3.0-2/GGIR/man/part6PairwiseAggregation.Rd |only GGIR-3.0-2/GGIR/tests/testthat/test_StudyDatesFile.R |only GGIR-3.0-2/GGIR/tests/testthat/test_chainof5parts.R | 25 GGIR-3.0-2/GGIR/tests/testthat/test_imputeTimegaps.R | 19 GGIR-3.0-2/GGIR/tests/testthat/test_lightPart5.R | 2 GGIR-3.0-2/GGIR/tests/testthat/test_load_check_params.R | 30 GGIR-3.0-2/GGIR/tests/testthat/test_part3_1_night.R | 5 GGIR-3.0-2/GGIR/tests/testthat/test_part3_no4am.R | 8 GGIR-3.0-2/GGIR/tests/testthat/test_part5_analyseRest.R | 17 GGIR-3.0-2/GGIR/tests/testthat/test_part6.R |only GGIR-3.0-2/GGIR/vignettes/CutPoints.Rmd | 2 GGIR-3.0-2/GGIR/vignettes/GGIR.Rmd | 61 + GGIR-3.0-2/GGIR/vignettes/GGIRParameters.Rmd | 3 GGIR-3.0-2/GGIR/vignettes/HouseHoldCoanalysis.Rmd |only 82 files changed, 1598 insertions(+), 963 deletions(-)
Title: Data and Code for Financial Accounting Research
Description: Handy functions and data to support a course book for accounting research.
Gow, Ian and Tongqing Ding (2022) 'Accounting Research: An Introductory Course' <https://iangow.github.io/far_book/>.
Author: Ian Gow [aut, cre]
Maintainer: Ian Gow <iandgow@gmail.com>
Diff between farr versions 0.2.30 dated 2023-01-28 and 0.2.39 dated 2023-12-13
DESCRIPTION | 15 +++-- MD5 | 114 ++++++++++++++++++++------------------- NAMESPACE | 2 NEWS.md | 28 +++++++++ R/data.R | 94 ++++++++++++++++++++++++++------ R/get_event_cum_rets.R | 3 - R/get_ff_ind.R | 4 - R/get_got_data.R | 2 R/get_idd_periods.R | 10 +-- R/get_me_breakpoints.R | 2 R/get_size_rets_monthly.R | 3 - R/get_test_scores.R | 12 ++-- R/get_trading_dates.R | 1 R/load_parquet.R |only R/pg_to_parquet.R |only R/roc.R | 14 ++-- R/rusboost.R | 3 - README.md | 4 - build/partial.rdb |binary data/cmsw_2018.rda |only data/fhk_firm_years.rda |binary data/fhk_pilot.rda |binary data/gvkey_ciks.rda |only data/sho_r3000.rda |binary data/sho_r3000_gvkeys.rda |binary data/sho_r3000_sample.rda |binary data/sho_tickers.rda |binary data/test_scores.rda |binary data/undisclosed_names.rda |binary man/aaer_dates.Rd | 3 - man/aaer_firm_year.Rd | 3 + man/apple_events.Rd | 1 man/auc.Rd | 2 man/bloomfield_2021.Rd | 5 + man/by_tag_year.Rd | 1 man/cmsw_2018.Rd |only man/comp.Rd | 1 man/confusion_stats.Rd | 4 - man/fhk_firm_years.Rd | 3 + man/fhk_pilot.Rd | 4 + man/get_event_cum_rets.Rd | 3 - man/get_got_data.Rd | 4 + man/get_size_rets_monthly.Rd | 4 - man/get_test_scores.Rd | 6 +- man/get_trading_dates.Rd | 1 man/gvkey_ciks.Rd |only man/iliev_2010.Rd | 7 +- man/llz_2018.Rd | 2 man/load_parquet.Rd |only man/michels_2017.Rd | 5 + man/ndcg.Rd | 6 +- man/pg_to_parquet.Rd |only man/roc.Rd | 2 man/rus.Rd | 5 - man/sho_r3000.Rd | 3 + man/sho_r3000_gvkeys.Rd | 2 man/sho_r3000_sample.Rd | 2 man/sho_tickers.Rd | 2 man/state_hq.Rd | 4 - man/test_scores.Rd | 2 man/undisclosed_names.Rd | 2 tests/testthat/test-get_ff_ind.R | 2 62 files changed, 254 insertions(+), 148 deletions(-)
Title: Bayesian Object Oriented Modeling
Description: A C++ library for Bayesian modeling, with an emphasis on Markov
chain Monte Carlo. Although boom contains a few R utilities (mainly plotting
functions), its primary purpose is to install the BOOM C++ library on your
system so that other packages can link against it.
Author: Steven L. Scott is the sole author and creator of the BOOM project.
Some code in the BOOM libraries has been modified from other open source
projects. These include Cephes , NEWUOA , and a
modified version of the R math libraries . Original
copyrig [...truncated...]
Maintainer: Steven L. Scott <steve.the.bayesian@gmail.com>
Diff between Boom versions 0.9.11 dated 2022-11-06 and 0.9.12 dated 2023-12-13
Boom-0.9.11/Boom/src/Models/Glm/IndependentRegressionModels.cpp |only Boom-0.9.12/Boom/DESCRIPTION | 10 Boom-0.9.12/Boom/MD5 | 203 +++--- Boom-0.9.12/Boom/R/sufstats.R | 4 Boom-0.9.12/Boom/inst/include/Eigen/src/SparseCore/TriangularSolver.h | 6 Boom-0.9.12/Boom/inst/include/LinAlg/Array.hpp | 2 Boom-0.9.12/Boom/inst/include/LinAlg/Eigen.hpp | 31 Boom-0.9.12/Boom/inst/include/LinAlg/Matrix.hpp | 13 Boom-0.9.12/Boom/inst/include/LinAlg/SpdMatrix.hpp | 23 Boom-0.9.12/Boom/inst/include/LinAlg/Vector.hpp | 5 Boom-0.9.12/Boom/inst/include/Models/ConstrainedVectorParams.hpp | 3 Boom-0.9.12/Boom/inst/include/Models/DataTypes.hpp | 2 Boom-0.9.12/Boom/inst/include/Models/FactorModels |only Boom-0.9.12/Boom/inst/include/Models/GP |only Boom-0.9.12/Boom/inst/include/Models/Glm/GlmCoefs.hpp | 3 Boom-0.9.12/Boom/inst/include/Models/Glm/IndependentRegressionModels.hpp | 56 + Boom-0.9.12/Boom/inst/include/Models/Glm/LoglinearModel.hpp | 4 Boom-0.9.12/Boom/inst/include/Models/Glm/PosteriorSamplers/BregVsSampler.hpp | 28 Boom-0.9.12/Boom/inst/include/Models/Glm/PosteriorSamplers/IndependentRegressionModelsPosteriorSampler.hpp | 17 Boom-0.9.12/Boom/inst/include/Models/Glm/PosteriorSamplers/RegressionConjSampler.hpp | 6 Boom-0.9.12/Boom/inst/include/Models/Glm/PosteriorSamplers/TRegressionSampler.hpp | 39 + Boom-0.9.12/Boom/inst/include/Models/Glm/RegressionModel.hpp | 24 Boom-0.9.12/Boom/inst/include/Models/Glm/TRegression.hpp | 108 +++ Boom-0.9.12/Boom/inst/include/Models/Glm/WeightedRegressionModel.hpp | 3 Boom-0.9.12/Boom/inst/include/Models/Hierarchical/HierarchicalZeroInflatedPoissonModel.hpp | 2 Boom-0.9.12/Boom/inst/include/Models/LowRankMvnModel.hpp |only Boom-0.9.12/Boom/inst/include/Models/MvnBase.hpp | 4 Boom-0.9.12/Boom/inst/include/Models/ParamTypes.hpp | 12 Boom-0.9.12/Boom/inst/include/Models/Policies/IID_DataPolicy.hpp | 2 Boom-0.9.12/Boom/inst/include/Models/Policies/ParamPolicy_3.hpp | 3 Boom-0.9.12/Boom/inst/include/Models/PositiveSemidefiniteData.hpp |only Boom-0.9.12/Boom/inst/include/Models/SpdParams.hpp | 8 Boom-0.9.12/Boom/inst/include/Models/StateSpace/DynamicInterceptRegression.hpp | 4 Boom-0.9.12/Boom/inst/include/Models/StateSpace/DynamicRegression.hpp | 2 Boom-0.9.12/Boom/inst/include/Models/StateSpace/Filters/KalmanFilterBase.hpp | 16 Boom-0.9.12/Boom/inst/include/Models/StateSpace/Multivariate/AdjustedDataWorkspace.hpp |only Boom-0.9.12/Boom/inst/include/Models/StateSpace/Multivariate/MultivariateStateSpaceModelBase.hpp | 39 - Boom-0.9.12/Boom/inst/include/Models/StateSpace/Multivariate/MultivariateStateSpaceRegressionDataPolicy.hpp |only Boom-0.9.12/Boom/inst/include/Models/StateSpace/Multivariate/MultivariateStateSpaceRegressionModel.hpp | 245 +------ Boom-0.9.12/Boom/inst/include/Models/StateSpace/Multivariate/PosteriorSamplers/MVSSRPS.hpp | 2 Boom-0.9.12/Boom/inst/include/Models/StateSpace/Multivariate/PosteriorSamplers/SLLPS.hpp | 9 Boom-0.9.12/Boom/inst/include/Models/StateSpace/Multivariate/PosteriorSamplers/StudentMvssPosteriorSampler.hpp |only Boom-0.9.12/Boom/inst/include/Models/StateSpace/Multivariate/ProxyScalarStateSpaceModel.hpp |only Boom-0.9.12/Boom/inst/include/Models/StateSpace/Multivariate/SharedStateModelManager.hpp |only Boom-0.9.12/Boom/inst/include/Models/StateSpace/Multivariate/StateModels/ScalarStateModelAdapter.hpp | 17 Boom-0.9.12/Boom/inst/include/Models/StateSpace/Multivariate/StudentMvssRegressionModel.hpp |only Boom-0.9.12/Boom/inst/include/Models/StateSpace/Multivariate/tests/mv_framework.hpp | 7 Boom-0.9.12/Boom/inst/include/Models/StateSpace/Multivariate/tests/student_regression_framework.hpp |only Boom-0.9.12/Boom/inst/include/Models/StateSpace/StateSpaceStudentRegressionModel.hpp | 3 Boom-0.9.12/Boom/inst/include/cpputil/Date.hpp | 2 Boom-0.9.12/Boom/inst/include/distributions.hpp | 14 Boom-0.9.12/Boom/inst/include/math/fft.hpp |only Boom-0.9.12/Boom/inst/include/math/kissfft |only Boom-0.9.12/Boom/inst/include/numopt/MarkovDecisionProcess.hpp | 2 Boom-0.9.12/Boom/inst/include/stats/IQagent.hpp | 23 Boom-0.9.12/Boom/inst/include/stats/acf.hpp |only Boom-0.9.12/Boom/inst/include/stats/quantile.hpp |only Boom-0.9.12/Boom/inst/include/uint.hpp | 2 Boom-0.9.12/Boom/man/Boom-package.Rd |only Boom-0.9.12/Boom/man/sufstat.Rd | 5 Boom-0.9.12/Boom/src/LinAlg/Array.cpp | 8 Boom-0.9.12/Boom/src/LinAlg/Eigen.cpp | 24 Boom-0.9.12/Boom/src/LinAlg/Matrix.cpp | 46 + Boom-0.9.12/Boom/src/LinAlg/SpdMatrix.cpp | 37 + Boom-0.9.12/Boom/src/LinAlg/Vector.cpp | 16 Boom-0.9.12/Boom/src/Makevars | 8 Boom-0.9.12/Boom/src/Models/ConstrainedVectorParams.cpp | 6 Boom-0.9.12/Boom/src/Models/FactorModels |only Boom-0.9.12/Boom/src/Models/GP |only Boom-0.9.12/Boom/src/Models/Glm/GlmCoefs.cpp | 5 Boom-0.9.12/Boom/src/Models/Glm/PosteriorSamplers/BregVsSampler.cpp | 50 + Boom-0.9.12/Boom/src/Models/Glm/PosteriorSamplers/PartRegSampler.cpp | 14 Boom-0.9.12/Boom/src/Models/Glm/PosteriorSamplers/RegressionConjSampler.cpp | 15 Boom-0.9.12/Boom/src/Models/Glm/PosteriorSamplers/TRegressionSampler.cpp | 90 ++ Boom-0.9.12/Boom/src/Models/Glm/RegressionModel.cpp | 39 + Boom-0.9.12/Boom/src/Models/Glm/TRegression.cpp | 21 Boom-0.9.12/Boom/src/Models/Glm/WeightedRegressionModel.cpp | 10 Boom-0.9.12/Boom/src/Models/LowRankMvnModel.cpp |only Boom-0.9.12/Boom/src/Models/ParamTypes.cpp | 18 Boom-0.9.12/Boom/src/Models/PositiveSemidefiniteData.cpp |only Boom-0.9.12/Boom/src/Models/SpdParams.cpp | 4 Boom-0.9.12/Boom/src/Models/StateSpace/Filters/ConditionallyIndependentKalmanFilter.cpp | 2 Boom-0.9.12/Boom/src/Models/StateSpace/Filters/KalmanFilterBase.cpp | 20 Boom-0.9.12/Boom/src/Models/StateSpace/Filters/MultivariateKalmanFilterBase.cpp | 119 ++- Boom-0.9.12/Boom/src/Models/StateSpace/Multivariate/MultivariateStateSpaceModelBase.cpp | 14 Boom-0.9.12/Boom/src/Models/StateSpace/Multivariate/MultivariateStateSpaceRegressionModel.cpp | 337 +--------- Boom-0.9.12/Boom/src/Models/StateSpace/Multivariate/PosteriorSamplers/MultivariateStateSpaceModelSampler.cpp | 2 Boom-0.9.12/Boom/src/Models/StateSpace/Multivariate/PosteriorSamplers/MvStateSpaceRegressionPosteriorSampler.cpp | 12 Boom-0.9.12/Boom/src/Models/StateSpace/Multivariate/PosteriorSamplers/SADSampler.cpp | 16 Boom-0.9.12/Boom/src/Models/StateSpace/Multivariate/PosteriorSamplers/SharedLocalLevelPosteriorSampler.cpp | 6 Boom-0.9.12/Boom/src/Models/StateSpace/Multivariate/PosteriorSamplers/StudentMvssPosteriorSampler.cpp |only Boom-0.9.12/Boom/src/Models/StateSpace/Multivariate/StateModels/ScalarStateModelAdapter.cpp | 18 Boom-0.9.12/Boom/src/Models/StateSpace/Multivariate/StudentMvssRegressionModel.cpp |only Boom-0.9.12/Boom/src/cpputil/LongString.cpp | 4 Boom-0.9.12/Boom/src/cpputil/lse.cpp | 10 Boom-0.9.12/Boom/src/distributions/gig.cpp | 2 Boom-0.9.12/Boom/src/distributions/mvn.cpp | 6 Boom-0.9.12/Boom/src/distributions/rmulti.cpp | 38 + Boom-0.9.12/Boom/src/distributions/student_fix.cpp | 6 Boom-0.9.12/Boom/src/extract_mixture_data.cpp | 52 - Boom-0.9.12/Boom/src/math/fft.cpp |only Boom-0.9.12/Boom/src/math/kissfft |only Boom-0.9.12/Boom/src/numopt/MarkovDecisionProcess.cpp | 11 Boom-0.9.12/Boom/src/print_R_timestamp.cpp | 2 Boom-0.9.12/Boom/src/stats/acf.cpp |only Boom-0.9.12/Boom/src/stats/quantile.cpp |only Boom-0.9.12/Boom/src/sufstats.cpp | 1 107 files changed, 1278 insertions(+), 824 deletions(-)
Title: Analysis of Overdispersed Data
Description: Provides a set of functions to analyse
overdispersed counts or proportions. Most of the methods are
already available elsewhere but are scattered in different
packages. The proposed functions should be considered as
complements to more sophisticated methods such as generalized
estimating equations (GEE) or generalized linear mixed effect
models (GLMM).
Author: Matthieu Lesnoff <matthieu.lesnoff@cirad.fr> and Renaud
Lancelot <renaud.lancelot@cirad.fr>
Maintainer: Renaud Lancelot <renaud.lancelot@cirad.fr>
Diff between aod versions 1.3.2 dated 2022-04-02 and 1.3.3 dated 2023-12-13
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++---------------- NAMESPACE | 2 +- NEWS | 2 +- R/show-glimML.R | 2 +- data/antibio.rda |binary data/cohorts.rda |binary data/dja.rda |binary data/lizards.rda |binary data/mice.rda |binary data/orob1.rda |binary data/orob2.rda |binary data/rabbits.rda |binary data/rats.rda |binary data/salmonella.rda |binary man/aic-class.Rd | 2 +- man/dja.Rd | 23 +++++++++++------------ 17 files changed, 35 insertions(+), 36 deletions(-)
Title: Time Series and Econometric Modeling
Description: Time series analysis, (dis)aggregation and manipulation, e.g. time series extension, merge, projection, lag, lead, delta, moving and cumulative average and product, selection by index, date and year-period, conversion to daily, monthly, quarterly, (semi)annually. Simultaneous equation models definition, estimation, simulation and forecasting with coefficient restrictions, error autocorrelation, exogenization, add-factors, impact and interim multipliers analysis, conditional equation evaluation, endogenous targeting and model renormalization, structural stability, stochastic simulation and forecast, optimal control.
Author: Andrea Luciani [aut, cre] ,
Roberto Stok [aut],
Bank of Italy [cph]
Maintainer: Andrea Luciani <andrea.luciani@bancaditalia.it>
Diff between bimets versions 3.0.1 dated 2023-05-15 and 3.0.2 dated 2023-12-13
DESCRIPTION | 8 MD5 | 92 +- NEWS.md | 13 R/bimets_model_functions.R | 1470 +++++++++++--------------------- R/bimets_ts_functions.R | 1414 +++++++++++------------------- README.md | 146 +-- build/vignette.rds |binary data/bimets_12F_YP2D__.RData |binary data/bimets_12L_YP2D__.RData |binary data/bimets_12_D2YP__.RData |binary data/bimets_1F_YP2D__.RData |binary data/bimets_1L_YP2D__.RData |binary data/bimets_1_D2YP__.RData |binary data/bimets_24F_YP2D__.RData |binary data/bimets_24L_YP2D__.RData |binary data/bimets_24_D2YP__.RData |binary data/bimets_2F_YP2D__.RData |binary data/bimets_2L_YP2D__.RData |binary data/bimets_2_D2YP__.RData |binary data/bimets_366_D2YP__.RData |binary data/bimets_366_YP2D__.RData |binary data/bimets_36F_YP2D__.RData |binary data/bimets_36L_YP2D__.RData |binary data/bimets_36_D2YP__.RData |binary data/bimets_3F_YP2D__.RData |binary data/bimets_3L_YP2D__.RData |binary data/bimets_3_D2YP__.RData |binary data/bimets_4F_YP2D__.RData |binary data/bimets_4L_YP2D__.RData |binary data/bimets_4_D2YP__.RData |binary data/bimets_53F_YP2D__.RData |binary data/bimets_53L_YP2D__.RData |binary data/bimets_53_D2YP__.RData |binary data/bimets_static_G90__.RData |binary data/bimets_static_TD90__.RData |binary data/bimets_static_startYear___.RData |binary data/bimets_static_totalLength___.RData |binary inst/doc/bimets.R | 163 ++- inst/doc/bimets.Rnw | 96 +- inst/doc/bimets.pdf |binary man/RENORM.Rd | 4 man/SIMULATE.Rd | 229 +++- man/STOCHSIMULATE.Rd | 4 man/TSLAG.Rd | 4 man/TSLEAD.Rd | 4 man/bimets-package.Rd | 1 vignettes/bimets.Rnw | 96 +- 47 files changed, 1708 insertions(+), 2036 deletions(-)
Title: Outlier Detection Using Invariant Coordinate Selection
Description: Multivariate outlier detection is performed using invariant coordinates where the package offers different methods to choose the appropriate components. ICS is a general multivariate technique with many applications in multivariate analysis. ICSOutlier offers a selection of functions for automated detection of outliers in the data based on a fitted ICS object or by specifying the dataset and the scatters of interest. The current implementation targets data sets with only a small percentage of outliers.
Author: Klaus Nordhausen [aut, cre] ,
Aurore Archimbaud [aut] ,
Anne Ruiz-Gazen [aut]
Maintainer: Klaus Nordhausen <klausnordhausenR@gmail.com>
Diff between ICSOutlier versions 0.3-1 dated 2023-09-18 and 0.4-0 dated 2023-12-13
ICSOutlier-0.3-1/ICSOutlier/inst/ChangeLog |only ICSOutlier-0.4-0/ICSOutlier/DESCRIPTION | 17 ICSOutlier-0.4-0/ICSOutlier/MD5 | 55 + ICSOutlier-0.4-0/ICSOutlier/NAMESPACE | 34 - ICSOutlier-0.4-0/ICSOutlier/NEWS |only ICSOutlier-0.4-0/ICSOutlier/R/ICSOutlier-package.R |only ICSOutlier-0.4-0/ICSOutlier/R/comp.norm.test.R | 84 ++ ICSOutlier-0.4-0/ICSOutlier/R/comp.simu.test.R | 321 +++++++-- ICSOutlier-0.4-0/ICSOutlier/R/datasets.R |only ICSOutlier-0.4-0/ICSOutlier/R/dist.simu.test.R | 373 +++++++++-- ICSOutlier-0.4-0/ICSOutlier/R/dist.simu.test.internal.R | 49 + ICSOutlier-0.4-0/ICSOutlier/R/ics.distances.R | 50 + ICSOutlier-0.4-0/ICSOutlier/R/ics.outlier.R | 539 ++++++++++++++-- ICSOutlier-0.4-0/ICSOutlier/build/partial.rdb |binary ICSOutlier-0.4-0/ICSOutlier/data/HTP2.rda |only ICSOutlier-0.4-0/ICSOutlier/data/HTP3.rda |only ICSOutlier-0.4-0/ICSOutlier/inst/CITATION | 18 ICSOutlier-0.4-0/ICSOutlier/man/HTP.Rd | 2 ICSOutlier-0.4-0/ICSOutlier/man/HTP2.Rd |only ICSOutlier-0.4-0/ICSOutlier/man/HTP3.Rd |only ICSOutlier-0.4-0/ICSOutlier/man/ICSOutlier-package.Rd | 64 - ICSOutlier-0.4-0/ICSOutlier/man/ICS_outlier.Rd |only ICSOutlier-0.4-0/ICSOutlier/man/comp.norm.test.Rd | 4 ICSOutlier-0.4-0/ICSOutlier/man/comp.simu.test.Rd | 4 ICSOutlier-0.4-0/ICSOutlier/man/comp_norm_test.Rd |only ICSOutlier-0.4-0/ICSOutlier/man/comp_simu_test.Rd |only ICSOutlier-0.4-0/ICSOutlier/man/dist.simu.test.Rd | 4 ICSOutlier-0.4-0/ICSOutlier/man/dist_simu_test.Rd |only ICSOutlier-0.4-0/ICSOutlier/man/ics.distances.Rd | 5 ICSOutlier-0.4-0/ICSOutlier/man/ics.outlier.Rd | 4 ICSOutlier-0.4-0/ICSOutlier/man/icsOut-class.Rd | 2 ICSOutlier-0.4-0/ICSOutlier/man/ics_distances.Rd |only ICSOutlier-0.4-0/ICSOutlier/man/plot.ICS_Out.Rd |only ICSOutlier-0.4-0/ICSOutlier/man/print.ICS_Out.Rd |only ICSOutlier-0.4-0/ICSOutlier/man/summary.ICS_Out.Rd |only ICSOutlier-0.4-0/ICSOutlier/tests |only 36 files changed, 1377 insertions(+), 252 deletions(-)
Title: Analyzes Real-World Treatment Patterns of a Study Population of
Interest
Description: Computes treatment patterns within a given cohort using the Observational
Medical Outcomes Partnership (OMOP) common data model (CDM). As described
in Markus, Verhamme, Kors, and Rijnbeek (2022) <doi:10.1016/j.cmpb.2022.107081>.
Author: Aniek Markus [aut] ,
Maarten van Kessel [cre]
Maintainer: Maarten van Kessel <m.l.vankessel@erasmusmc.nl>
Diff between TreatmentPatterns versions 2.6.1 dated 2023-12-11 and 2.6.2 dated 2023-12-13
TreatmentPatterns-2.6.1/TreatmentPatterns/inst/htmlTemplates |only TreatmentPatterns-2.6.1/TreatmentPatterns/man/createSankeyDiagram2.Rd |only TreatmentPatterns-2.6.1/TreatmentPatterns/man/createSunburstPlot2.Rd |only TreatmentPatterns-2.6.1/TreatmentPatterns/tests/testthat/test-createSankeyDiagram2.R |only TreatmentPatterns-2.6.1/TreatmentPatterns/tests/testthat/test-createSunburstPlot2.R |only TreatmentPatterns-2.6.2/TreatmentPatterns/DESCRIPTION | 6 TreatmentPatterns-2.6.2/TreatmentPatterns/MD5 | 57 - TreatmentPatterns-2.6.2/TreatmentPatterns/NAMESPACE | 2 TreatmentPatterns-2.6.2/TreatmentPatterns/NEWS.md | 16 TreatmentPatterns-2.6.2/TreatmentPatterns/R/InteractivePlots.R | 4 TreatmentPatterns-2.6.2/TreatmentPatterns/R/TreatmentPatterns-package.R | 11 TreatmentPatterns-2.6.2/TreatmentPatterns/R/computePathways.R | 68 - TreatmentPatterns-2.6.2/TreatmentPatterns/R/createSankeyDiagram.R | 155 ---- TreatmentPatterns-2.6.2/TreatmentPatterns/R/createSunburstPlot.R | 372 ---------- TreatmentPatterns-2.6.2/TreatmentPatterns/R/executeTreatmentPatterns.R | 67 - TreatmentPatterns-2.6.2/TreatmentPatterns/R/export.R | 110 +- TreatmentPatterns-2.6.2/TreatmentPatterns/inst/doc/DefiningCohorts.html | 16 TreatmentPatterns-2.6.2/TreatmentPatterns/inst/sql/selectData.sql | 2 TreatmentPatterns-2.6.2/TreatmentPatterns/man/computePathways.Rd | 72 - TreatmentPatterns-2.6.2/TreatmentPatterns/man/createSankeyDiagram.Rd | 36 TreatmentPatterns-2.6.2/TreatmentPatterns/man/createSunburstPlot.Rd | 30 TreatmentPatterns-2.6.2/TreatmentPatterns/man/executeTreatmentPatterns.Rd | 67 - TreatmentPatterns-2.6.2/TreatmentPatterns/man/export.Rd | 84 +- TreatmentPatterns-2.6.2/TreatmentPatterns/tests/testthat/test-computePathways.R | 18 TreatmentPatterns-2.6.2/TreatmentPatterns/tests/testthat/test-createSankeyDiagram.R | 182 +--- TreatmentPatterns-2.6.2/TreatmentPatterns/tests/testthat/test-createSunburstPlot.R | 49 - TreatmentPatterns-2.6.2/TreatmentPatterns/tests/testthat/test-executeTreatmentPatterns.R | 2 TreatmentPatterns-2.6.2/TreatmentPatterns/tests/testthat/test-export.R | 4 TreatmentPatterns-2.6.2/TreatmentPatterns/vignettes/articles/ComputingTreatmentPathways.Rmd | 12 29 files changed, 487 insertions(+), 955 deletions(-)
More information about TreatmentPatterns at CRAN
Permanent link
Title: Shiny App - Generate a Pdf Invoice with 'Rmarkdown'
Description: Generate an invoice containing a header with invoice number and businesses details. The invoice table contains
any of: salary, one-liner costs, grouped costs. Under the table signature and bank account details appear.
Pages are numbered when more than one. Source .json and .Rmd files are editable in the app. A .csv file with raw data can be downloaded.
This package includes functions for getting exchange rates between currencies based on
'quantmod' (Ryan and Ulrich, 2023 <https://CRAN.R-project.org/package=quantmod>).
Author: Fernando Roa [aut, cre]
Maintainer: Fernando Roa <froao@unal.edu.co>
Diff between shinyInvoice versions 0.0.2 dated 2023-12-01 and 0.0.3 dated 2023-12-13
DESCRIPTION | 15 MD5 | 38 - NEWS.md | 8 R/get_exchange_rates.R | 26 inst/shinyApps/invoice_app/app/json/grouped_costs.json | 46 + inst/shinyApps/invoice_app/app/json/oneliner_costs.json | 2 inst/shinyApps/invoice_app/app/json/salary.json | 2 inst/shinyApps/invoice_app/app/logic/list_to_df.R |only inst/shinyApps/invoice_app/app/logic/save_files.R | 22 inst/shinyApps/invoice_app/app/main.R | 11 inst/shinyApps/invoice_app/app/modules/currency_date.R | 9 inst/shinyApps/invoice_app/app/modules/grouped_costs.R | 12 inst/shinyApps/invoice_app/app/modules/salary.R | 8 inst/shinyApps/invoice_app/app/modules/spreadsheet.R |only inst/shinyApps/invoice_app/app/static/invoice_bank.svg | 322 +++++------ inst/shinyApps/invoice_app/app/static/invoice_grouped.svg | 326 +++++------ inst/shinyApps/invoice_app/app/static/invoice_header.svg | 348 ++++++------ inst/shinyApps/invoice_app/app/static/invoice_oneliners.svg | 322 +++++------ inst/shinyApps/invoice_app/app/static/invoice_salary.svg | 314 +++++----- man/GetExchangeRates.Rd | 22 man/shinyInvoice-package.Rd | 2 21 files changed, 961 insertions(+), 894 deletions(-)
Title: Fitting (Exponential/Diffusion) RT-MPT Models
Description: Fit (exponential or diffusion) response-time extended multinomial processing tree (RT-MPT) models
by Klauer and Kellen (2018) <doi:10.1016/j.jmp.2017.12.003> and Klauer, Hartmann, and Meyer-Grant (submitted).
The RT-MPT class not only incorporate frequencies like traditional multinomial processing tree (MPT) models,
but also latencies. This enables it to estimate process completion times and encoding plus motor execution times
next to the process probabilities of traditional MPTs. 'rtmpt' is a hierarchical Bayesian framework and posterior
samples are sampled using a Metropolis-within-Gibbs sampler (for exponential RT-MPTs) or Hamiltonian-within-Gibbs
sampler (for diffusion RT-MPTs).
Author: Raphael Hartmann [aut, cre],
Karl C. Klauer [cph, aut, ctb, ths],
Constantin G. Meyer-Grant [aut, ctb],
Henrik Singmann [ctb, aut],
Jean Marie Linhart [ctb],
Frederick Novomestky [ctb]
Maintainer: Raphael Hartmann <raphael.hartmann@protonmail.com>
Diff between rtmpt versions 1.0-1 dated 2023-11-30 and 2.0-0 dated 2023-12-13
rtmpt-1.0-1/rtmpt/R/print_RTMPT.R |only rtmpt-1.0-1/rtmpt/man/fit_rtmpt.Rd |only rtmpt-1.0-1/rtmpt/man/fit_rtmpt_SBC.Rd |only rtmpt-1.0-1/rtmpt/man/set_params.Rd |only rtmpt-1.0-1/rtmpt/man/sim_rtmpt_data.Rd |only rtmpt-1.0-1/rtmpt/man/sim_rtmpt_data_SBC.Rd |only rtmpt-1.0-1/rtmpt/man/to_rtmpt_data.Rd |only rtmpt-1.0-1/rtmpt/man/to_rtmpt_model.Rd |only rtmpt-1.0-1/rtmpt/src/main.h |only rtmpt-2.0-0/rtmpt/DESCRIPTION | 34 rtmpt-2.0-0/rtmpt/MD5 | 122 rtmpt-2.0-0/rtmpt/NAMESPACE | 42 rtmpt-2.0-0/rtmpt/R/SBC_fit_rtmpt.R | 30 rtmpt-2.0-0/rtmpt/R/SimData.R | 10 rtmpt-2.0-0/rtmpt/R/call_rtmpt.R | 615 ++- rtmpt-2.0-0/rtmpt/R/get_diagnostics.R | 152 rtmpt-2.0-0/rtmpt/R/get_indices.R | 56 rtmpt-2.0-0/rtmpt/R/get_membership.R | 140 rtmpt-2.0-0/rtmpt/R/get_model.R | 324 + rtmpt-2.0-0/rtmpt/R/get_params.R | 182 - rtmpt-2.0-0/rtmpt/R/get_transformed_data.R | 301 + rtmpt-2.0-0/rtmpt/R/make_mcmc.R | 287 + rtmpt-2.0-0/rtmpt/R/print_rtmpt.R |only rtmpt-2.0-0/rtmpt/R/set_params.R | 755 +++- rtmpt-2.0-0/rtmpt/R/set_resps.R | 34 rtmpt-2.0-0/rtmpt/R/simulate_rtmpt.R | 20 rtmpt-2.0-0/rtmpt/R/simulate_rtmpt_SBC.R | 18 rtmpt-2.0-0/rtmpt/build/vignette.rds |binary rtmpt-2.0-0/rtmpt/inst/doc/rtmpt_guideline.R | 108 rtmpt-2.0-0/rtmpt/inst/doc/rtmpt_guideline.Rmd | 242 + rtmpt-2.0-0/rtmpt/inst/doc/rtmpt_guideline.html | 977 ++++- rtmpt-2.0-0/rtmpt/man/SimData.Rd | 10 rtmpt-2.0-0/rtmpt/man/a2a.Rd |only rtmpt-2.0-0/rtmpt/man/a2const.Rd |only rtmpt-2.0-0/rtmpt/man/delta2delta.Rd | 15 rtmpt-2.0-0/rtmpt/man/fit_drtmpt.Rd |only rtmpt-2.0-0/rtmpt/man/fit_ertmpt.Rd |only rtmpt-2.0-0/rtmpt/man/fit_ertmpt_SBC.Rd |only rtmpt-2.0-0/rtmpt/man/nu2const.Rd |only rtmpt-2.0-0/rtmpt/man/nu2nu.Rd |only rtmpt-2.0-0/rtmpt/man/omega2const.Rd |only rtmpt-2.0-0/rtmpt/man/omega2omega.Rd |only rtmpt-2.0-0/rtmpt/man/set_resps.Rd | 19 rtmpt-2.0-0/rtmpt/man/sim_ertmpt_data.Rd |only rtmpt-2.0-0/rtmpt/man/sim_ertmpt_data_SBC.Rd |only rtmpt-2.0-0/rtmpt/man/tau2tau.Rd | 23 rtmpt-2.0-0/rtmpt/man/tau2zero.Rd | 6 rtmpt-2.0-0/rtmpt/man/theta2const.Rd | 6 rtmpt-2.0-0/rtmpt/man/theta2theta.Rd | 6 rtmpt-2.0-0/rtmpt/man/to_drtmpt_data.Rd |only rtmpt-2.0-0/rtmpt/man/to_drtmpt_model.Rd |only rtmpt-2.0-0/rtmpt/man/to_ertmpt_data.Rd |only rtmpt-2.0-0/rtmpt/man/to_ertmpt_model.Rd |only rtmpt-2.0-0/rtmpt/src/Quelle.cpp |only rtmpt-2.0-0/rtmpt/src/adaptive_rejection_sampling.cpp | 23 rtmpt-2.0-0/rtmpt/src/additions.cpp | 1136 +++--- rtmpt-2.0-0/rtmpt/src/derivatives.cpp |only rtmpt-2.0-0/rtmpt/src/diagnosis.cpp | 2394 +++++++++---- rtmpt-2.0-0/rtmpt/src/diffusion.cpp |only rtmpt-2.0-0/rtmpt/src/gauss.h |only rtmpt-2.0-0/rtmpt/src/gibbs.cpp |only rtmpt-2.0-0/rtmpt/src/hamiltonian.cpp |only rtmpt-2.0-0/rtmpt/src/hcubature.cpp |only rtmpt-2.0-0/rtmpt/src/invtri.c | 41 rtmpt-2.0-0/rtmpt/src/joint.cpp |only rtmpt-2.0-0/rtmpt/src/lkj.cpp |only rtmpt-2.0-0/rtmpt/src/lnnorm.cpp | 216 - rtmpt-2.0-0/rtmpt/src/main.cpp | 1359 +++++-- rtmpt-2.0-0/rtmpt/src/mvtimes.cpp | 3220 ++++++++++-------- rtmpt-2.0-0/rtmpt/src/onetimes.cpp | 1246 ++++-- rtmpt-2.0-0/rtmpt/src/r_wrapper.cpp | 289 + rtmpt-2.0-0/rtmpt/src/rtimes.cpp | 26 rtmpt-2.0-0/rtmpt/src/rtmpt_init.c | 8 rtmpt-2.0-0/rtmpt/src/rts.h | 1012 ++++- rtmpt-2.0-0/rtmpt/src/rwiener.cpp |only rtmpt-2.0-0/rtmpt/src/specifics.cpp | 276 - rtmpt-2.0-0/rtmpt/src/times.cpp | 387 +- rtmpt-2.0-0/rtmpt/src/tools.cpp |only rtmpt-2.0-0/rtmpt/src/trait.cpp | 491 +- rtmpt-2.0-0/rtmpt/vignettes/rtmpt_guideline.Rmd | 242 + 80 files changed, 11284 insertions(+), 5616 deletions(-)
Title: Fitting Hidden Markov Models to Financial Data
Description: Fitting (hierarchical) hidden Markov models to financial data
via maximum likelihood estimation. See Oelschläger, L. and Adam, T.
"Detecting bearish and bullish markets in financial time series using
hierarchical hidden Markov models" (2021, Statistical Modelling)
<doi:10.1177/1471082X211034048> for a reference.
Author: Lennart Oelschlaeger [aut, cre]
,
Timo Adam [aut] ,
Rouven Michels [aut]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between fHMM versions 1.1.1 dated 2023-10-12 and 1.2.0 dated 2023-12-13
fHMM-1.1.1/fHMM/R/simulate_data.R |only fHMM-1.1.1/fHMM/R/utils.R |only fHMM-1.1.1/fHMM/man/Gamma2delta.Rd |only fHMM-1.1.1/fHMM/man/Gamma2gammasCon.Rd |only fHMM-1.1.1/fHMM/man/Gamma2gammasUncon.Rd |only fHMM-1.1.1/fHMM/man/check_date.Rd |only fHMM-1.1.1/fHMM/man/coef.fHMM_model.Rd |only fHMM-1.1.1/fHMM/man/dfCon2dfUncon.Rd |only fHMM-1.1.1/fHMM/man/dfUncon2dfCon.Rd |only fHMM-1.1.1/fHMM/man/find_closest_year.Rd |only fHMM-1.1.1/fHMM/man/gammasCon2Gamma.Rd |only fHMM-1.1.1/fHMM/man/gammasCon2gammasUncon.Rd |only fHMM-1.1.1/fHMM/man/gammasUncon2Gamma.Rd |only fHMM-1.1.1/fHMM/man/gammasUncon2gammasCon.Rd |only fHMM-1.1.1/fHMM/man/is_number.Rd |only fHMM-1.1.1/fHMM/man/is_tpm.Rd |only fHMM-1.1.1/fHMM/man/match_all.Rd |only fHMM-1.1.1/fHMM/man/muCon2muUncon.Rd |only fHMM-1.1.1/fHMM/man/muUncon2muCon.Rd |only fHMM-1.1.1/fHMM/man/npar.Rd |only fHMM-1.1.1/fHMM/man/par2parCon.Rd |only fHMM-1.1.1/fHMM/man/par2parUncon.Rd |only fHMM-1.1.1/fHMM/man/parCon2par.Rd |only fHMM-1.1.1/fHMM/man/parCon2parUncon.Rd |only fHMM-1.1.1/fHMM/man/parUncon2par.Rd |only fHMM-1.1.1/fHMM/man/parUncon2parCon.Rd |only fHMM-1.1.1/fHMM/man/predict.fHMM_model.Rd |only fHMM-1.1.1/fHMM/man/residuals.fHMM_model.Rd |only fHMM-1.1.1/fHMM/man/sample_tpm.Rd |only fHMM-1.1.1/fHMM/man/sigmaCon2sigmaUncon.Rd |only fHMM-1.1.1/fHMM/man/sigmaUncon2sigmaCon.Rd |only fHMM-1.1.1/fHMM/man/simulate_data.Rd |only fHMM-1.1.1/fHMM/man/simulate_markov_chain.Rd |only fHMM-1.1.1/fHMM/tests/testthat/test-simulate_data.R |only fHMM-1.1.1/fHMM/tests/testthat/test-utils.R |only fHMM-1.2.0/fHMM/DESCRIPTION | 13 fHMM-1.2.0/fHMM/MD5 | 181 - fHMM-1.2.0/fHMM/NAMESPACE | 34 fHMM-1.2.0/fHMM/NEWS.md | 74 fHMM-1.2.0/fHMM/R/compute_T_star.R | 10 fHMM-1.2.0/fHMM/R/compute_ci.R | 7 fHMM-1.2.0/fHMM/R/compute_residuals.R | 52 fHMM-1.2.0/fHMM/R/data_and_models.R | 27 fHMM-1.2.0/fHMM/R/decode_states.R | 157 - fHMM-1.2.0/fHMM/R/download_data.R | 145 - fHMM-1.2.0/fHMM/R/fHMM-package.R | 73 fHMM-1.2.0/fHMM/R/fHMM_colors.R | 5 fHMM-1.2.0/fHMM/R/fHMM_controls.R | 1185 +++++---- fHMM-1.2.0/fHMM/R/fHMM_data.R | 2 fHMM-1.2.0/fHMM/R/fHMM_events.R | 2 fHMM-1.2.0/fHMM/R/fHMM_likelihood.R |only fHMM-1.2.0/fHMM/R/fHMM_model.R | 336 -- fHMM-1.2.0/fHMM/R/fHMM_parameters.R | 1305 ++++++---- fHMM-1.2.0/fHMM/R/fHMM_sdds.R | 114 fHMM-1.2.0/fHMM/R/parameter_labels.R | 29 fHMM-1.2.0/fHMM/R/plot.R | 71 fHMM-1.2.0/fHMM/R/read_data.R | 2 fHMM-1.2.0/fHMM/R/reorder_states.R | 24 fHMM-1.2.0/fHMM/R/simulate_hmm.R |only fHMM-1.2.0/fHMM/README.md | 178 + fHMM-1.2.0/fHMM/data/dax_model_2n.rda |binary fHMM-1.2.0/fHMM/data/sim_model_2gamma.rda |binary fHMM-1.2.0/fHMM/data/sim_model_4lnorm.rda |binary fHMM-1.2.0/fHMM/inst/doc/fHMM.Rmd | 6 fHMM-1.2.0/fHMM/inst/doc/fHMM.html | 21 fHMM-1.2.0/fHMM/inst/doc/v01_model_definition.html | 4 fHMM-1.2.0/fHMM/inst/doc/v02_controls.R | 5 fHMM-1.2.0/fHMM/inst/doc/v02_controls.Rmd | 7 fHMM-1.2.0/fHMM/inst/doc/v02_controls.html | 22 fHMM-1.2.0/fHMM/inst/doc/v03_data_management.html | 2 fHMM-1.2.0/fHMM/inst/doc/v04_model_estimation.html | 4 fHMM-1.2.0/fHMM/inst/doc/v05_state_decoding_and_prediction.html | 2 fHMM-1.2.0/fHMM/inst/doc/v06_model_checking.html | 2 fHMM-1.2.0/fHMM/inst/doc/v07_model_selection.html | 2 fHMM-1.2.0/fHMM/man/compute_T_star.Rd | 9 fHMM-1.2.0/fHMM/man/compute_ci.Rd | 6 fHMM-1.2.0/fHMM/man/compute_residuals.Rd | 4 fHMM-1.2.0/fHMM/man/dax_model_2n.Rd | 5 fHMM-1.2.0/fHMM/man/dax_model_3t.Rd | 3 fHMM-1.2.0/fHMM/man/dax_vw_model.Rd | 3 fHMM-1.2.0/fHMM/man/decode_states.Rd | 40 fHMM-1.2.0/fHMM/man/download_data.Rd | 50 fHMM-1.2.0/fHMM/man/fHMM_model.Rd | 45 fHMM-1.2.0/fHMM/man/fHMM_parameters.Rd | 162 - fHMM-1.2.0/fHMM/man/fHMM_sdds.Rd | 51 fHMM-1.2.0/fHMM/man/figures/README-simulate-hmm-data-1.png |only fHMM-1.2.0/fHMM/man/fit_model.Rd | 7 fHMM-1.2.0/fHMM/man/ll_hmm.Rd |only fHMM-1.2.0/fHMM/man/nLL_hhmm.Rd | 2 fHMM-1.2.0/fHMM/man/nLL_hmm.Rd | 2 fHMM-1.2.0/fHMM/man/parameter_labels.Rd | 10 fHMM-1.2.0/fHMM/man/parameter_transformations.Rd |only fHMM-1.2.0/fHMM/man/set_controls.Rd | 414 ++- fHMM-1.2.0/fHMM/man/sim_model_2gamma.Rd | 8 fHMM-1.2.0/fHMM/man/sim_model_4lnorm.Rd | 5 fHMM-1.2.0/fHMM/man/simulate_hmm.Rd |only fHMM-1.2.0/fHMM/man/simulate_observations.Rd | 20 fHMM-1.2.0/fHMM/man/unemp_spx_model_3_2.Rd | 3 fHMM-1.2.0/fHMM/tests/testthat/_snaps/fHMM_controls.md | 22 fHMM-1.2.0/fHMM/tests/testthat/_snaps/fHMM_parameters.md |only fHMM-1.2.0/fHMM/tests/testthat/test-compare_models.R | 5 fHMM-1.2.0/fHMM/tests/testthat/test-download_data.R | 89 fHMM-1.2.0/fHMM/tests/testthat/test-fHMM_controls.R | 46 fHMM-1.2.0/fHMM/tests/testthat/test-fHMM_likelihood.R |only fHMM-1.2.0/fHMM/tests/testthat/test-fHMM_model.R | 75 fHMM-1.2.0/fHMM/tests/testthat/test-fHMM_parameters.R | 125 fHMM-1.2.0/fHMM/tests/testthat/test-fHMM_sdds.R | 86 fHMM-1.2.0/fHMM/tests/testthat/test-parameter_labels.R | 13 fHMM-1.2.0/fHMM/tests/testthat/test-reorder_states.R | 5 fHMM-1.2.0/fHMM/tests/testthat/test-simulate_hmm.R |only fHMM-1.2.0/fHMM/vignettes/dax.csv |only fHMM-1.2.0/fHMM/vignettes/fHMM.Rmd | 6 fHMM-1.2.0/fHMM/vignettes/ref.bib | 3 fHMM-1.2.0/fHMM/vignettes/v02_controls.Rmd | 7 114 files changed, 3297 insertions(+), 2137 deletions(-)
Title: R Interface to the 'Protocol Buffers' 'API' (Version 2 or 3)
Description: Protocol Buffers are a way of encoding structured data in an
efficient yet extensible format. Google uses Protocol Buffers for almost all
of its internal 'RPC' protocols and file formats. Additional documentation
is available in two included vignettes one of which corresponds to our 'JSS'
paper (2016, <doi:10.18637/jss.v071.i02>. A sufficiently recent version of
'Protocol Buffers' library is required; currently version 3.3.0 from 2017
is the stated minimum.
Author: Romain Francois, Dirk Eddelbuettel, Murray Stokely and Jeroen Ooms
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RProtoBuf versions 0.4.20 dated 2022-11-03 and 0.4.21 dated 2023-12-13
ChangeLog | 56 +++++++++++++++++ DESCRIPTION | 8 +- MD5 | 122 +++++++++++++++++++------------------- R/00classes.R | 71 ++++++++++------------ R/add.R | 7 -- R/aslist.R | 14 ++-- R/clear.R | 11 +-- R/clone.R | 3 R/completion.R | 54 ++++++++-------- R/containing_type.R | 8 +- R/debug_string.R | 25 +++---- R/descriptor.R | 15 ++-- R/extensions.R | 5 - R/field_count.R | 42 ++++++------- R/has.R | 6 - R/identical.R | 10 +-- R/initialized.R | 3 R/internals.R | 6 - R/lookup.R | 3 R/merge.R | 9 +- R/read.R | 20 ++---- R/serialize.R | 4 - R/set.R | 25 +++---- R/size.R | 16 ++-- R/swap.R | 5 - R/text_format.R | 2 R/with.R | 7 -- R/wrapper_CodedInputStream.R | 18 ++--- R/wrapper_CodedOutputStream.R | 43 ++++--------- R/wrapper_EnumDescriptor.R | 21 +++--- R/wrapper_EnumValueDescriptor.R | 4 - R/wrapper_FieldDescriptor.R | 24 +++---- R/wrapper_MethodDescriptor.R | 5 - R/wrapper_ServiceDescriptor.R | 18 ++--- R/wrapper_ZeroCopyInputStream.R | 54 ++++++++-------- R/zzz.R | 2 README.md | 6 - build/vignette.rds |binary configure | 34 +++++----- configure.ac | 2 inst/NEWS.Rd | 13 +++- inst/doc/RProtoBuf-intro.pdf |binary inst/doc/RProtoBuf-paper.pdf |binary inst/doc/RProtoBuf-quickref.pdf |binary inst/tinytest/data/encoding.proto | 3 inst/tinytest/test_serialize.R | 3 man/ArrayInputStream-class.Rd | 5 - man/ArrayOutputStream-class.Rd | 5 - man/Descriptor-class.Rd | 51 +++++++-------- man/EnumValueDescriptor-class.Rd | 8 -- man/FileDescriptor-class.Rd | 3 man/FileInputStream-class.Rd | 13 +--- man/FileOutputStream-class.Rd | 13 +--- man/Message-class.Rd | 57 ++++++++--------- man/ZeroCopyInputStream-class.Rd | 9 -- man/ZeroCopyOutputStream-class.Rd | 12 --- man/swap.Rd | 8 -- src/Makevars.ucrt | 4 - src/RSourceTree.cpp | 29 +++++++++ src/RSourceTree.h | 6 + src/wrapper_Descriptor.cpp | 13 +++- src/wrapper_Message.cpp | 6 + 62 files changed, 542 insertions(+), 507 deletions(-)
Title: Optimal Distribution Preserving Down-Sampling of Bio-Medical
Data
Description: An optimized method for distribution-preserving class-proportional down-sampling of bio-medical data.
Author: Jorn Lotsch [aut,cre] ,
Sebastian Malkusch [aut] ,
Alfred Ultsch [aut]
Maintainer: Jorn Lotsch <j.lotsch@em.uni-frankfurt.de>
Diff between opdisDownsampling versions 0.8.2 dated 2022-05-24 and 0.8.3 dated 2023-12-13
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/CompDistrib.R | 3 ++- inst/CITATION | 29 +++++++++++++---------------- 4 files changed, 21 insertions(+), 23 deletions(-)
More information about opdisDownsampling at CRAN
Permanent link
Title: Functions for Community Data and Ordinations
Description: A collection of functions useful in (vegetation) community analyses and ordinations. Includes automatic species selection for ordination diagrams, NMDS stress/scree plots, species response curves, merging of taxa as well as calculation and sorting of synoptic tables.
Author: Friedemann von Lampe [aut, cre],
Jenny Schellenberg [aut]
Maintainer: Friedemann von Lampe <fvonlampe@uni-goettingen.de>
Diff between goeveg versions 0.6.5 dated 2023-06-13 and 0.7.1 dated 2023-12-13
goeveg-0.6.5/goeveg/R/data_schedenenv.r |only goeveg-0.6.5/goeveg/R/data_schedenveg.r |only goeveg-0.6.5/goeveg/R/dimcheckMDS.R |only goeveg-0.6.5/goeveg/man/dimcheckMDS.Rd |only goeveg-0.7.1/goeveg/DESCRIPTION | 13 goeveg-0.7.1/goeveg/MD5 | 49 +- goeveg-0.7.1/goeveg/NAMESPACE | 6 goeveg-0.7.1/goeveg/NEWS.md | 10 goeveg-0.7.1/goeveg/R/cov2per.R |only goeveg-0.7.1/goeveg/R/cv.r | 5 goeveg-0.7.1/goeveg/R/main.r | 2 goeveg-0.7.1/goeveg/R/merge_taxa.R |only goeveg-0.7.1/goeveg/R/ordiselect.r | 57 ++ goeveg-0.7.1/goeveg/R/racurve.r | 3 goeveg-0.7.1/goeveg/R/scale_tabs.r |only goeveg-0.7.1/goeveg/R/schedenenv.r |only goeveg-0.7.1/goeveg/R/schedenveg.r |only goeveg-0.7.1/goeveg/R/screeplot_NMDS.R |only goeveg-0.7.1/goeveg/R/synsort.R | 266 +++++++------ goeveg-0.7.1/goeveg/R/syntable.R | 585 ++++++++++++++++-------------- goeveg-0.7.1/goeveg/README.md | 17 goeveg-0.7.1/goeveg/build/partial.rdb |binary goeveg-0.7.1/goeveg/data/scale_tabs.rda |only goeveg-0.7.1/goeveg/man/cov2per.Rd |only goeveg-0.7.1/goeveg/man/cv.Rd | 5 goeveg-0.7.1/goeveg/man/merge_taxa.Rd |only goeveg-0.7.1/goeveg/man/ordiselect.Rd | 2 goeveg-0.7.1/goeveg/man/scale_tabs.Rd |only goeveg-0.7.1/goeveg/man/schedenenv.Rd | 26 - goeveg-0.7.1/goeveg/man/schedenveg.Rd | 4 goeveg-0.7.1/goeveg/man/screeplot_NMDS.Rd |only goeveg-0.7.1/goeveg/man/synsort.Rd | 329 ++++++++-------- goeveg-0.7.1/goeveg/man/syntable.Rd | 226 ++++++----- 33 files changed, 887 insertions(+), 718 deletions(-)
Title: Rounded Mixture Package
Description: Performs univariate probability mass function estimation via Bayesian nonparametric mixtures of rounded kernels as in Canale and Dunson (2011) <doi:10.1198/jasa.2011.tm10552>.
Author: Antonio Canale [aut, cre],
Nicola Lunardon [ctb]
Maintainer: Antonio Canale <antonio.canale@unipd.it>
Diff between rmp versions 2.1 dated 2023-08-25 and 2.2 dated 2023-12-13
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/npmpois.c | 4 ++-- src/rmg.c | 6 +++--- 4 files changed, 12 insertions(+), 12 deletions(-)
Title: Population and Evolutionary Genetics Analysis System
Description: Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.
Author: Emmanuel Paradis [aut, cre, cph]
,
Thibaut Jombart [aut, cph] ,
Zhian N. Kamvar [aut, cph] ,
Brian Knaus [aut, cph] ,
Klaus Schliep [aut, cph] ,
Alastair Potts [aut, cph] ,
David Winter [aut, cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between pegas versions 1.2 dated 2023-02-23 and 1.3 dated 2023-12-13
DESCRIPTION | 10 +- MD5 | 35 ++++---- NEWS | 31 +++++++ R/haplotype.R | 161 ++++++++++++++++++++++++----------------- R/tajima.test.R | 6 - R/zzz.R | 5 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/PlotHaploNet.pdf |binary inst/doc/ReadingFiles.Rnw | 14 +-- inst/doc/ReadingFiles.pdf |binary man/MMD.Rd | 16 ++-- man/haploNet.Rd | 6 + man/options_themes_haploNet.Rd | 74 ++++++++++-------- man/pegas-package.Rd | 2 man/read.loci.Rd | 2 src/mst.c |only src/pegas.c | 6 + vignettes/ReadingFiles.Rnw | 14 +-- 19 files changed, 230 insertions(+), 152 deletions(-)
Title: Processing and Analysing Animal Trajectories
Description: Tools to handle, manipulate and explore trajectory data, with an emphasis on data from tracked animals. The package is designed to support large studies with several million location records and keep track of units where possible. Data import directly from 'movebank' <https://www.movebank.org/cms/movebank-main> and files is facilitated.
Author: Bart Kranstauber [aut, cre] ,
Kamran Safi [aut] ,
Anne K. Scharf [aut]
Maintainer: Bart Kranstauber <b.kranstauber@uva.nl>
Diff between move2 versions 0.2.6 dated 2023-11-05 and 0.2.7 dated 2023-12-13
move2-0.2.6/move2/tests/testthat/Rplots.pdf |only move2-0.2.6/move2/tests/testthat/test-interpolate.R |only move2-0.2.7/move2/DESCRIPTION | 6 move2-0.2.7/move2/MD5 | 73 - move2-0.2.7/move2/NEWS.md | 8 move2-0.2.7/move2/R/movebank_api.R | 11 move2-0.2.7/move2/R/movebank_constants.R | 4 move2-0.2.7/move2/R/movebank_get_vocabulary.R | 9 move2-0.2.7/move2/R/mt_aeqd_crs.R | 1 move2-0.2.7/move2/R/mt_azimuth.R | 4 move2-0.2.7/move2/R/mt_distance.R | 1 move2-0.2.7/move2/R/mt_filter_movebank_visible.R | 2 move2-0.2.7/move2/R/mt_filter_unique.R | 31 move2-0.2.7/move2/R/mt_interpolate.R | 25 move2-0.2.7/move2/R/mt_read.R | 10 move2-0.2.7/move2/R/mt_stack.R | 1 move2-0.2.7/move2/R/mt_time.R | 2 move2-0.2.7/move2/build/vignette.rds |binary move2-0.2.7/move2/inst/WORDLIST | 1 move2-0.2.7/move2/inst/doc/convert.html | 232 +-- move2-0.2.7/move2/inst/doc/filtering_tracks.html | 1095 +++++++-------- move2-0.2.7/move2/inst/doc/movebank.R | 29 move2-0.2.7/move2/inst/doc/movebank.Rmd | 32 move2-0.2.7/move2/inst/doc/movebank.html | 977 +++++++------ move2-0.2.7/move2/inst/doc/programming_move2_object.html | 404 +++-- move2-0.2.7/move2/inst/doc/trajectory_analysis.html | 537 +++---- move2-0.2.7/move2/man/movebank_download_study.Rd | 7 move2-0.2.7/move2/man/mt_aeqd_crs.Rd | 2 move2-0.2.7/move2/man/mt_azimuth.Rd | 5 move2-0.2.7/move2/man/mt_distance.Rd | 3 move2-0.2.7/move2/man/mt_filter_movebank_visible.Rd | 2 move2-0.2.7/move2/man/mt_filter_unique.Rd | 34 move2-0.2.7/move2/man/mt_interpolate.Rd | 2 move2-0.2.7/move2/man/mt_read.Rd | 11 move2-0.2.7/move2/man/mt_stack.Rd | 2 move2-0.2.7/move2/man/mt_time.Rd | 2 move2-0.2.7/move2/tests/testthat/test-mt_as_move2.R | 2 move2-0.2.7/move2/tests/testthat/test-mt_interpolate.R |only move2-0.2.7/move2/vignettes/movebank.Rmd | 32 39 files changed, 1928 insertions(+), 1671 deletions(-)
More information about crew.aws.batch at CRAN
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Title: Nonparametric Estimation of Time-Dependent ROC, Brier Score, and
Survival Difference from Right Censored Time-to-Event Data with
or without Competing Risks
Description: The tdROC package facilitates the estimation of time-dependent ROC
(Receiver Operating Characteristic) curves and the Area Under the time-dependent
ROC Curve (AUC) in the context of survival data, accommodating scenarios with
right censored data and the option to account for competing risks. In addition
to the ROC/AUC estimation, the package also estimates time-dependent Brier score and
survival difference. Confidence intervals of various estimated quantities can be
obtained from bootstrap. The package also offers plotting functions for visualizing
time-dependent ROC curves.
Author: Xiaoyang Li [aut, cre],
Zhe Yin [aut],
Liang Li [aut, ths]
Maintainer: Xiaoyang Li <xli35@mdanderson.org>
Diff between tdROC versions 1.0 dated 2016-03-29 and 2.0 dated 2023-12-13
tdROC-1.0/tdROC/R/calc.AUC.R |only tdROC-1.0/tdROC/R/is.monotone.R |only tdROC-1.0/tdROC/man/calc.AUC.Rd |only tdROC-1.0/tdROC/man/is.monotone.Rd |only tdROC-1.0/tdROC/man/plot.tdROC.Rd |only tdROC-2.0/tdROC/DESCRIPTION | 48 +- tdROC-2.0/tdROC/LICENSE |only tdROC-2.0/tdROC/MD5 | 49 ++ tdROC-2.0/tdROC/NAMESPACE | 21 - tdROC-2.0/tdROC/R/AUC.cr.R |only tdROC-2.0/tdROC/R/AUC_calc_integral.R |only tdROC-2.0/tdROC/R/Melano.R |only tdROC-2.0/tdROC/R/RcppExports.R |only tdROC-2.0/tdROC/R/calc.kw.R | 52 +-- tdROC-2.0/tdROC/R/forRcpp.R |only tdROC-2.0/tdROC/R/mayo.R | 31 + tdROC-2.0/tdROC/R/plot.tdROC.R | 124 ++++--- tdROC-2.0/tdROC/R/plot.tdROC.cr.R |only tdROC-2.0/tdROC/R/td.kw.cr.R |only tdROC-2.0/tdROC/R/tdBrier.R |only tdROC-2.0/tdROC/R/tdROC.R | 518 +++++++++++++++++++------------ tdROC-2.0/tdROC/R/tdROC.cr.R |only tdROC-2.0/tdROC/R/tdSurvDiff.R |only tdROC-2.0/tdROC/R/utils-pipe.R |only tdROC-2.0/tdROC/data/Melano.rda |only tdROC-2.0/tdROC/man/AUC.cr.Rd |only tdROC-2.0/tdROC/man/AUC_calc_integral.Rd |only tdROC-2.0/tdROC/man/Melano.Rd |only tdROC-2.0/tdROC/man/calc.kw.Rd | 3 tdROC-2.0/tdROC/man/mayo.Rd | 26 + tdROC-2.0/tdROC/man/pipe.Rd |only tdROC-2.0/tdROC/man/plot_tdROC.Rd |only tdROC-2.0/tdROC/man/plot_tdROC_cr.Rd |only tdROC-2.0/tdROC/man/td.kw.cr.Rd |only tdROC-2.0/tdROC/man/tdBrier.Rd |only tdROC-2.0/tdROC/man/tdROC.Rd | 155 ++++++--- tdROC-2.0/tdROC/man/tdROC.cr.Rd |only tdROC-2.0/tdROC/man/tdSurvDiff.Rd |only tdROC-2.0/tdROC/src |only 39 files changed, 643 insertions(+), 384 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Melissa Hallow [aut],
Wenping Wang [aut],
Zufar Mulyukov [ctb],
Alan Hindmarsh [ctb],
Arun Srinivasan [ctb],
Awad H. Al-Mohy [ctb],
Cleve Moler [ctb],
Drew Schmidt [ctb],
Ernst Hairer [ctb],
Gerhard Wanner [ctb],
Gilber [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 2.1.0 dated 2023-12-11 and 2.1.1 dated 2023-12-13
DESCRIPTION | 6 +++--- MD5 | 32 ++++++++++++++++---------------- R/rxode2_md5.R | 2 +- inst/doc/rxode2-syntax.html | 30 +++++++++++++++--------------- inst/include/rxode2.h | 24 ++++++++++++------------ src/approx.c | 5 +---- src/call_dvode.c | 8 +------- src/cfode_static.c | 6 +++--- src/dop853.c | 20 ++++++++++---------- src/forder.cpp | 5 +---- src/handle_evid.c | 8 ++------ src/init.c | 5 +---- src/intdy.c | 7 ++++--- src/lsoda.c | 7 ++++--- src/par_solve.cpp | 10 +++------- src/solsy.c | 5 ++--- src/utilc.c | 16 ++++++---------- 17 files changed, 85 insertions(+), 111 deletions(-)
Title: Runs Monte Carlo Markov Chain - With Either 'JAGS', 'nimble' or
'greta' - While Adjusting Burn-in and Thinning Parameters
Description: The function runMCMC_btadjust() returns a mcmc.list object which is the output of a
Markov Chain Monte Carlo obtained - from either 'JAGS', 'nimble' or 'greta' - after adjusting burn-in and thinning parameters to meet
pre-specified criteria in terms of convergence & effective sample size.
Author: Frederic Gosselin [cre, aut] ,
Institut national de recherche pour l'agriculture, l'alimentation et
l'environnement [cph]
Maintainer: Frederic Gosselin <frederic.gosselin@inrae.fr>
Diff between runMCMCbtadjust versions 1.0.4 dated 2023-11-10 and 1.0.5 dated 2023-12-13
DESCRIPTION | 6 MD5 | 10 NEWS.md | 13 R/runMCMC_btadjust.r | 124 ++++-- inst/doc/runMCMCbtadjust_Presentation.html | 518 ++++++++++++++--------------- man/runMCMC_btadjust.Rd | 12 6 files changed, 372 insertions(+), 311 deletions(-)
More information about runMCMCbtadjust at CRAN
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Title: An R Port of the 'ImageJ' Plugin 'Auto Threshold'
Description: Algorithms for automatically finding appropriate thresholds
for numerical data, with special functions for thresholding images.
Provides the 'ImageJ' 'Auto Threshold' plugin functionality to R
users. See <https://imagej.net/plugins/auto-threshold> and Landini et
al. (2017) <DOI:10.1111/jmi.12474>.
Author: Rory Nolan [aut, cre, trl] ,
Luis Alvarez [ctb] ,
Sergi Padilla-Parra [ctb, ths]
,
Gabriel Landini [ctb, cph]
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between autothresholdr versions 1.4.1 dated 2023-01-28 and 1.4.2 dated 2023-12-13
DESCRIPTION | 10 - MD5 | 18 +- NEWS.md | 6 R/RcppExports.R | 2 build/vignette.rds |binary inst/CITATION | 6 inst/doc/finding-thresholds.html | 218 ++++++++++++++++---------------- inst/doc/thresholding-image-stacks.html | 68 ++++----- inst/doc/thresholding-images.html | 54 +++---- src/RcppExports.cpp | 8 - 10 files changed, 198 insertions(+), 192 deletions(-)
More information about autothresholdr at CRAN
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