Title: Similarity Regression
Description: Similarity regression,
evaluating the probability of association between sets of ontological terms
and binary response vector. A no-association model is compared with one in which
the log odds of a true response is linked to the semantic similarity
between terms and a latent characteristic ontological profile - 'Phenotype Similarity Regression for Identifying the Genetic Determinants of Rare Diseases', Greene et al 2016 <doi:10.1016/j.ajhg.2016.01.008>.
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between SimReg versions 3.3 dated 2021-02-15 and 3.4 dated 2024-02-20
DESCRIPTION | 11 MD5 | 38 +- NAMESPACE | 1 R/RcppExports.R | 46 +- R/inference.R | 13 R/ml.R | 1 R/prediction.R | 3 build/vignette.rds |binary inst/doc/SimReg-Introduction.R | 82 ++-- inst/doc/SimReg-Introduction.Rmd | 6 inst/doc/SimReg-Introduction.html | 693 ++++++++++++++++++++++++++------------ inst/doc/SimReg-Priors.R | 107 +++-- inst/doc/SimReg-Priors.Rmd | 11 inst/doc/SimReg-Priors.html | 678 +++++++++++++++++++++++++------------ man/SimReg-package.Rd | 6 man/posterior_prediction.Rd | 2 man/sim_reg.Rd | 14 src/RcppExports.cpp | 5 vignettes/SimReg-Introduction.Rmd | 6 vignettes/SimReg-Priors.Rmd | 11 20 files changed, 1135 insertions(+), 599 deletions(-)
Title: Graphical VAR for Experience Sampling Data
Description: Estimates within and between time point interactions in experience sampling data, using the Graphical vector autoregression model in combination with regularization. See also Epskamp, Waldorp, Mottus & Borsboom (2018) <doi:10.1080/00273171.2018.1454823>.
Author: Sacha Epskamp [aut, cre],
Eren Asena [ctb]
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between graphicalVAR versions 0.3.3 dated 2023-10-18 and 0.3.4 dated 2024-02-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 3 +++ man/graphicalVAR.Rd | 4 +++- 4 files changed, 12 insertions(+), 7 deletions(-)
Title: Working Examples for Reproducible Research Documents
Description: Templates, guides, and scripts for
writing documents in 'LaTeX' and 'R markdown' to produce
guides, slides, and reports. Special care is taken to
illustrate use of templates and customization opportunities.
Challenges and opportunities of 'HTML' output from 'R markdown'
receive special attention. Includes several vignettes
to assist new users of literate programming.
Author: Paul Johnson [aut, cre],
Brent Kaplan [ctb],
Meghan Sullivan [ctb],
Charles Redmon [ctb],
Zack Roman [ctb],
Chong Xing [ctb],
Longcan 'Emma' Huang [ctb],
Garrett Mills [ctb]
Maintainer: Paul Johnson <pauljohn@ku.edu>
Diff between stationery versions 1.0 dated 2021-10-08 and 1.1 dated 2024-02-20
stationery |only 1 file changed
Title: Explore Temporal and Other Phylogenetic Signals
Description: Sequences sampled at different time points can be used to infer molecular phylogenies on natural time scales, but if the sequences records inaccurate sampling times, that are not the actual sampling times, then it will affect the molecular phylogenetic analysis. This shiny application helps exploring temporal characteristics of the evolutionary trees through linear regression analysis and with the ability to identify and remove incorrect labels. The method was extended to support exploring other phylogenetic signals under strict and relaxed models.
Author: Guangchuang Yu [aut, cre, cph]
,
Xiao Luo [ctb],
Li Zhan [ctb],
Xuanan Zhu [ctb],
Jianfeng Lin [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between shinyTempSignal versions 0.0.6 dated 2024-01-22 and 0.0.7 dated 2024-02-20
DESCRIPTION | 20 + MD5 | 28 +- NAMESPACE | 21 +- NEWS.md | 12 + R/app_config.R | 1 R/app_server.R | 411 +++++++++++++++++++++++++---------------- R/app_ui.R | 91 +++++---- R/shinyTempSignal-package.R |only inst/doc/shinyTempSignal.Rmd | 6 inst/doc/shinyTempSignal.html | 53 +++-- man/app_server.Rd |only man/app_ui.Rd |only man/shinyTempSignal-package.Rd |only vignettes/figures/Figure1.png |binary vignettes/figures/Figure3.png |binary vignettes/figures/Figure4.png |binary vignettes/shinyTempSignal.Rmd | 6 17 files changed, 402 insertions(+), 247 deletions(-)
More information about shinyTempSignal at CRAN
Permanent link
Title: Assign Treatments, Power Calculations, Balances, Impact
Evaluation of Experiments
Description: Assists in the whole process of designing and evaluating Randomized Control Trials.
Robust treatment assignment by strata/blocks, that handles misfits;
Power calculations of the minimum detectable treatment effect or minimum populations;
Balance tables of T-test of covariates;
Balance Regression: (treatment ~ all x variables) with F-test of null model;
Impact_evaluation: Impact evaluation regressions. This function
gives you the option to include control_vars, fixed effect variables,
cluster variables (for robust SE), multiple endogenous variables and
multiple heterogeneous variables (to test treatment effect heterogeneity)
summary_statistics: Function that creates a summary statistics table with statistics
rank observations in n groups: Creates a factor variable with n groups. Each group has
a min and max label attach to each category.
Athey, Susan, and Guido W. Imbens (2017) <arXiv:1607.00698>.
Author: Isidoro Garcia-Urquieta [aut, cre]
Maintainer: Isidoro Garcia-Urquieta <isidoro.gu@gmail.com>
Diff between RCT versions 1.1.2 dated 2022-05-13 and 1.2 dated 2024-02-20
DESCRIPTION | 15 +- MD5 | 22 ++-- NEWS.md | 5 R/impact_eval.R | 196 +++++++++++++++++++------------------- README.md | 2 build/vignette.rds |binary inst/CITATION | 17 +-- inst/doc/my-vignette.R | 2 inst/doc/my-vignette.html | 15 +- man/RCT.Rd | 1 man/impact_eval.Rd | 12 +- tests/testthat/test_impact_eval.R | 46 ++++---- 12 files changed, 169 insertions(+), 164 deletions(-)
Title: Sweave Drivers with Extra Tricks Up their Sleeve
Description: Weave and tangle drivers for Sweave extending the
standard drivers. RweaveExtraLatex and RtangleExtra provide options
to completely ignore code chunks on weaving, tangling, or both.
Chunks ignored on weaving are not parsed, yet are written out
verbatim on tangling. Chunks ignored on tangling may be evaluated as
usual on weaving, but are completely left out of the tangled
scripts. The driver RtangleExtra also provides an option to specify
the extension of the file name (or remove it entirely) when
splitting is selected on tangling.
Author: Vincent Goulet [cre, aut],
R Core Team [aut]
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>
Diff between RweaveExtra versions 1.0-0 dated 2021-05-28 and 1.1-0 dated 2024-02-20
RweaveExtra-1.0-0/RweaveExtra/inst/examples/auto |only RweaveExtra-1.1-0/RweaveExtra/DESCRIPTION | 33 ++- RweaveExtra-1.1-0/RweaveExtra/MD5 | 20 +- RweaveExtra-1.1-0/RweaveExtra/NAMESPACE | 2 RweaveExtra-1.1-0/RweaveExtra/R/RweaveExtra.R | 93 +++++++++- RweaveExtra-1.1-0/RweaveExtra/build/partial.rdb |binary RweaveExtra-1.1-0/RweaveExtra/inst/NEWS.Rd |only RweaveExtra-1.1-0/RweaveExtra/inst/examples/example-extra.Rnw | 16 - RweaveExtra-1.1-0/RweaveExtra/man/RtangleExtra.Rd | 45 ++-- RweaveExtra-1.1-0/RweaveExtra/man/RweaveExtra-package.Rd | 23 +- RweaveExtra-1.1-0/RweaveExtra/man/RweaveExtraLatex.Rd | 2 RweaveExtra-1.1-0/RweaveExtra/man/RweaveExtraUtils.Rd | 9 12 files changed, 170 insertions(+), 73 deletions(-)
Title: Estimates and Plots Single-Level and Multilevel Latent Class
Models
Description: Efficiently estimates single- and multilevel latent class models with covariates, allowing for output visualization in all specifications. For more technical details, see Lyrvall et al (2023) <arXiv:2305.07276>.
Author: Roberto Di Mari [aut, cre],
Johan Lyrvall [aut],
Zsuzsa Bakk [ctb],
Jennifer Oser [ctb],
Jouni Kuha [ctb]
Maintainer: Roberto Di Mari <roberto.dimari@unict.it>
Diff between multilevLCA versions 1.4 dated 2023-12-04 and 1.5 dated 2024-02-20
multilevLCA-1.4/multilevLCA/src/rcpparma_hello_world.cpp |only multilevLCA-1.5/multilevLCA/DESCRIPTION | 8 multilevLCA-1.5/multilevLCA/MD5 | 17 multilevLCA-1.5/multilevLCA/R/MLCAfunctions.R | 112 +++--- multilevLCA-1.5/multilevLCA/R/RcppExports.R | 20 - multilevLCA-1.5/multilevLCA/build/partial.rdb |binary multilevLCA-1.5/multilevLCA/man/multiLCA.Rd | 10 multilevLCA-1.5/multilevLCA/src/LCAfit.cpp | 265 ++++----------- multilevLCA-1.5/multilevLCA/src/RcppExports.cpp | 65 --- multilevLCA-1.5/multilevLCA/src/multilevLC_EM.cpp | 105 ++++- 10 files changed, 225 insertions(+), 377 deletions(-)
Title: Probability Models and Statistical Analysis of Random
Multigraphs
Description: Methods and models for analysing multigraphs as introduced by Shafie (2015) <doi:10.21307/joss-2019-011>, including methods to study local and global properties <doi:10.1080/0022250X.2016.1219732> and goodness of fit tests.
Author: Termeh Shafie [aut, cre],
David Schoch [ctb]
Maintainer: Termeh Shafie <termeh.shafie@uni-konstanz.de>
Diff between multigraphr versions 0.1.0 dated 2021-09-16 and 0.2.0 dated 2024-02-20
DESCRIPTION | 22 MD5 | 42 - NEWS.md | 4 R/get_degree_seq.R | 4 R/get_edge_assignment_probs.R | 70 +- R/get_edge_multip_seq.R | 172 ++--- R/gof_test.R | 6 R/iea_model.R | 9 R/rsm_model.R | 363 +++++------ README.md | 66 +- build/vignette.rds |binary inst/doc/multigraphr.R | 2 inst/doc/multigraphr.Rmd | 10 inst/doc/multigraphr.html | 783 ++++++++++++++++++------ man/get_degree_seq.Rd | 4 man/get_edge_assignment_probs.Rd | 8 man/get_edge_multip_seq.Rd | 13 man/gof_test.Rd | 6 man/iea_model.Rd | 7 man/rsm_model.Rd | 12 tests/testthat/test-get_edge_assignment_probs.R | 27 vignettes/multigraphr.Rmd | 10 22 files changed, 1024 insertions(+), 616 deletions(-)
Title: Group Elastic Net Regularized GLMs and GAMs
Description: Efficient algorithms for fitting generalized linear and additive models with group elastic net penalties. Implements group lasso, group MCP, and group SCAD with an optional group ridge penalty. Computes the regularization path for linear regression (gaussian), logistic regression (binomial), multinomial logistic regression (multinomial), log-linear count regression (poisson and negative.binomial), and log-linear continuous regression (gamma and inverse gaussian). Supports default and formula methods for model specification, k-fold cross-validation for tuning the regularization parameters, and nonparametric regression via tensor product reproducing kernel (smoothing spline) basis function expansion.
Author: Nathaniel E. Helwig [aut, cre]
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
Diff between grpnet versions 0.2 dated 2023-09-08 and 0.3 dated 2024-02-20
ChangeLog | 37 ++++++++++++++++++++++++++- DESCRIPTION | 12 ++++---- MD5 | 50 ++++++++++++++++++------------------- NAMESPACE | 2 - R/grpnet.R | 6 ++-- R/grpnet.default.R | 63 ++++++++++++++++++++++++++++++++++++++++++++++- R/grpnet.formula.R | 4 ++ R/predict.cv.grpnet.R | 7 ++--- R/predict.grpnet.R | 21 +++++++++------ R/rk.R | 3 +- build/partial.rdb |binary man/coef.Rd | 4 +- man/cv.grpnet.Rd | 4 +- man/grpnet.Rd | 15 +++++++---- man/plot.grpnet.Rd | 4 +- man/predict.cv.grpnet.Rd | 7 ++--- man/predict.grpnet.Rd | 7 ++--- man/rk.Rd | 4 ++ man/rk.model.matrix.Rd | 2 + src/grpnet_binomial.f90 | 6 ++-- src/grpnet_gamma.f90 | 6 ++-- src/grpnet_gaussian.f90 | 5 ++- src/grpnet_invgaus.f90 | 6 ++-- src/grpnet_multinom.f90 | 6 ++-- src/grpnet_negbin.f90 | 6 ++-- src/grpnet_poisson.f90 | 6 ++-- 26 files changed, 205 insertions(+), 88 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Models for
Multiple or Multilayer Networks
Description: A set of extensions for the 'ergm' package to fit multilayer/multiplex/multirelational networks and samples of multiple networks. 'ergm.multi' is a part of the Statnet suite of packages for network analysis. See Krivitsky, Koehly, and Marcum (2020) <doi:10.1007/s11336-020-09720-7> and Krivitsky, Coletti, and Hens (2023) <doi:10.1080/01621459.2023.2242627>.
Author: Pavel N. Krivitsky [aut, cre] ,
Mark S. Handcock [ctb],
David R. Hunter [ctb],
Chad Klumb [ctb],
Pietro Coletti [ctb],
Joyce Cheng [ctb]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>
Diff between ergm.multi versions 0.2.0 dated 2023-05-30 and 0.2.1 dated 2024-02-20
DESCRIPTION | 25 LICENSE | 2 MD5 | 127 ++- R/InitErgmConstraint.R | 2 R/InitErgmProposal.blockdiag.R | 19 R/InitErgmTerm.R | 2 R/InitErgmTerm.dgw_sp.R | 2 R/InitErgmTerm.multilayer.R | 4 R/InitErgmTerm.multinet.R | 2 R/InitErgmTerm.spcache.multilayer.R | 2 R/InitWtErgmTerm.multinet.R | 2 R/block_blacklist.R | 2 R/combine.networks.R | 4 R/data.R | 4 R/ergm.multi-package.R | 22 R/ergmlhs.R | 2 R/gofN.R | 2 R/marg_cond_sim.R | 19 R/print.combined_networks.R | 2 R/zzz.R | 2 build/ergm.multi.pdf |binary build/partial.rdb |binary build/stage23.rdb |binary build/vignette.rds |binary inst/CITATION | 4 inst/NEWS.Rd | 37 + inst/REFERENCES.bib | 14 inst/doc/Goeyvaerts_reproduction.R | 4 inst/doc/Goeyvaerts_reproduction.html | 318 +++++----- inst/include/ergm.multi_MHblockdiag.h | 2 inst/include/ergm.multi_changestat_multilayer.h | 2 inst/include/ergm.multi_changestat_multilayer_common.do_not_include_directly.h | 2 inst/include/ergm.multi_stubs.c | 2 man/Lazega.Rd | 2 man/ergm.multi-package.Rd | 30 man/marg_cond_sim.Rd | 3 man/subnetwork_templates.Rd | 2 src/MHproposals_block.c | 2 src/MHproposals_block.h | 2 src/changestats_dgw_sp_ML.c | 2 src/changestats_dgw_sp_ML.h | 2 src/changestats_multilayer.c | 2 src/changestats_multinet.c | 2 src/changestats_spcache_ML.c | 2 src/ergm.multi_changestat_multinet.h | 2 src/ergm.multi_changestat_multinet_common.do_not_include_directly.h | 2 src/ergm.multi_wtchangestat_multinet.h | 2 src/include_stubs.c | 2 src/init.c | 2 src/mean_var.c | 2 src/wtchangestats_multinet.c | 2 tests/testthat.R | 2 tests/testthat/test-blockdiag.R |only tests/testthat/test-multilayer-CMB.R | 2 tests/testthat/test-multilayer-MLE.R | 2 tests/testthat/test-multilayer-MPLE.R | 2 tests/testthat/test-multilayer-direction.R | 2 tests/testthat/test-multilayer-heterogeneous-directedness.R | 2 tests/testthat/test-multilayer-mutuality.R | 2 tests/testthat/test-multilayer-summary.R | 2 tests/testthat/test-multilayer-triadic.R | 2 tests/testthat/test-multilayer.R | 2 tests/testthat/test-multinet.R | 2 tests/testthat/test-subnetcache.R | 2 tests/testthat/test-term-dgwesp-ml.R | 2 65 files changed, 397 insertions(+), 327 deletions(-)
Title: Additive and Multiplicative Effects Models for Networks and
Relational Data
Description: Analysis of dyadic network and relational data using additive and
multiplicative effects (AME) models. The basic model includes
regression terms, the covariance structure of the social relations model
(Warner, Kenny and Stoto (1979) <DOI:10.1037/0022-3514.37.10.1742>,
Wong (1982) <DOI:10.2307/2287296>), and multiplicative factor
models (Hoff(2009) <DOI:10.1007/s10588-008-9040-4>).
Several different link functions accommodate different
relational data structures, including binary/network data, normal
relational data, zero-inflated positive outcomes using a tobit model, ordinal relational data and data from
fixed-rank nomination schemes. Several of these link functions are
discussed in Hoff, Fosdick, Volfovsky and Stovel (2013)
<DOI:10.1017/nws.2013.17>. Development of this
software was supported in part by NIH grant R01HD067509.
Author: Peter Hoff [aut, cre],
Bailey Fosdick [aut],
Alex Volfovsky [aut],
Yanjun He [ctb]
Maintainer: Peter Hoff <peter.hoff@duke.edu>
Diff between amen versions 1.4.4 dated 2020-12-16 and 1.4.5 dated 2024-02-20
amen-1.4.4/amen/NEWS.md |only amen-1.4.4/amen/README.md |only amen-1.4.4/amen/inst/tutorial |only amen-1.4.4/amen/vignettes/binary_demo_cache |only amen-1.4.4/amen/vignettes/diy_Poisson_demo_cache |only amen-1.4.4/amen/vignettes/diy_binary_demo_cache |only amen-1.4.5/amen/DESCRIPTION | 10 - amen-1.4.5/amen/MD5 | 62 ++++------- amen-1.4.5/amen/NAMESPACE | 4 amen-1.4.5/amen/R/amen-package.R | 8 - amen-1.4.5/amen/R/plot.ame.R | 3 amen-1.4.5/amen/R/summary.ame.R | 3 amen-1.4.5/amen/R/xnet.R | 3 amen-1.4.5/amen/build/vignette.rds |binary amen-1.4.5/amen/inst/doc/amen.R |only amen-1.4.5/amen/inst/doc/amen.pdf |only amen-1.4.5/amen/inst/doc/binary_demo.html | 129 +++++++++-------------- amen-1.4.5/amen/inst/doc/diy_Poisson_demo.html | 71 ++++-------- amen-1.4.5/amen/inst/doc/diy_binary_demo.html | 75 ++++--------- amen-1.4.5/amen/man/amen-package.Rd | 8 + amen-1.4.5/amen/man/coldwar.Rd | 2 amen-1.4.5/amen/man/comtrade.Rd | 2 amen-1.4.5/amen/man/xnet.Rd | 6 - amen-1.4.5/amen/vignettes/binary_demo_files |only amen-1.4.5/amen/vignettes/diy_Poisson_demo_files |only amen-1.4.5/amen/vignettes/diy_binary_demo_files |only 26 files changed, 157 insertions(+), 229 deletions(-)
Title: Exact Sequential Analysis for Poisson and Binomial Data
Description: Functions to calculate exact critical values, statistical power, expected time to signal, and required sample sizes for performing exact sequential analysis. All these calculations can be done for either Poisson or binomial data, for continuous or group sequential analyses, and for different types of rejection boundaries. In case of group sequential analyses, the group sizes do not have to be specified in advance and the alpha spending can be arbitrarily settled.
Author: Ivair Ramos Silva and Martin Kulldorff
Maintainer: Ivair Ramos Silva <ivair@ufop.edu.br>
Diff between Sequential versions 4.3.2 dated 2023-12-15 and 4.3.3 dated 2024-02-20
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/Sequential-package.Rd | 7 +++++-- 3 files changed, 11 insertions(+), 8 deletions(-)
Title: Matching Methods for Time-Varying Observational Studies
Description: Implements popular methods for matching in time-varying
observational studies. Matching is difficult in this scenario because
participants can be treated at different times which may have an
influence on the outcomes. The core methods include: "Balanced Risk
Set Matching" from Li, Propert, and Rosenbaum (2011)
<doi:10.1198/016214501753208573> and "Propensity Score Matching with
Time-Dependent Covariates" from Lu (2005)
<doi:10.1111/j.1541-0420.2005.00356.x>. Some functions use the
'Gurobi' optimization back-end to improve the optimization problem
speed; the 'gurobi' R package and associated software can be
downloaded from <https://www.gurobi.com> after obtaining a license.
Author: Sean Kent [aut, cre, cph] ,
Mitchell Paukner [aut, cph]
Maintainer: Sean Kent <skent259@gmail.com>
Diff between rsmatch versions 0.2.0 dated 2023-06-29 and 0.2.1 dated 2024-02-20
DESCRIPTION | 9 +- MD5 | 18 ++--- NEWS.md | 5 + R/brsmatch.R | 124 ++++++++++++++++++++++++++++----------- R/coxpsmatch.R | 15 ++++ README.md | 17 ++--- inst/CITATION | 6 - man/brsmatch.Rd | 6 - tests/testthat/test-brsmatch.R | 86 +++++++++++++++++++++++++++ tests/testthat/test-coxpsmatch.R | 41 ++++++++++++ 10 files changed, 267 insertions(+), 60 deletions(-)
Title: Visualising Sets of Ontological Terms
Description: Create R plots visualising ontological terms and the relationships between them with various graphical options - Greene et al. 2017 <doi:10.1093/bioinformatics/btw763>.
Author: Daniel Greene <dg333@cam.ac.uk>
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between ontologyPlot versions 1.6 dated 2021-02-10 and 1.7 dated 2024-02-20
DESCRIPTION | 11 MD5 | 84 +- build/vignette.rds |binary inst/doc/plotting-ontological-terms.R | 98 +-- inst/doc/plotting-ontological-terms.Rmd | 2 inst/doc/plotting-ontological-terms.html | 689 +++++++++++++++-------- inst/doc/plotting-term-grids.R | 32 - inst/doc/plotting-term-grids.Rmd | 2 inst/doc/plotting-term-grids.html | 555 +++++++++++++----- man/annotation_grid.Rd | 12 man/calibrate_sizes.Rd | 1 man/colour_by_frequency.Rd | 9 man/colour_by_population_frequency.Rd | 10 man/colour_by_term_set.Rd | 10 man/dot_string.Rd | 1 man/get_adjacency_matrix.Rd | 1 man/get_node_friendly_long_names.Rd | 1 man/get_ontology_plot.Rd | 9 man/get_pseudo_adjacency_matrix.Rd | 1 man/get_shortened_names.Rd | 1 man/grid_terms.Rd | 1 man/label_by_frequency.Rd | 1 man/label_by_term_set.Rd | 1 man/long_labels.Rd | 1 man/n_most_frequent_terms.Rd | 9 man/official_labels.Rd | 1 man/onto_plot.Rd | 19 man/ontologyPlot-package.Rd | 12 man/p_values_for_occurrence_of_term_in_group.Rd | 1 man/plot.ontology_plot.Rd | 1 man/plot_annotation_grid.Rd | 1 man/print.ontology_plot.Rd | 1 man/remove_links.Rd | 1 man/remove_terms_with_less_than_n_occurrences.Rd | 9 man/remove_uninformative_terms.Rd | 1 man/simple_cap.Rd | 1 man/simple_labels.Rd | 1 man/to_svg_string.Rd | 1 man/width_by_frequency.Rd | 1 man/width_by_significance.Rd | 1 man/write_dot.Rd | 1 vignettes/plotting-ontological-terms.Rmd | 2 vignettes/plotting-term-grids.Rmd | 2 43 files changed, 1052 insertions(+), 547 deletions(-)
Title: Operating on Integer-Bounded Intervals
Description: Manipulate integer-bounded intervals including finding overlaps, piling and merging.
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between IntervalSurgeon versions 1.2 dated 2023-04-15 and 1.3 dated 2024-02-20
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- build/partial.rdb |binary build/vignette.rds |binary inst/doc/intro.html | 17 ++++++++++++----- man/IntervalSurgeon-package.Rd | 9 --------- 6 files changed, 22 insertions(+), 24 deletions(-)
More information about IntervalSurgeon at CRAN
Permanent link
Title: Geostatistical Modelling with Likelihood and Bayes
Description: Geostatistical modelling facilities using 'SpatRaster' and 'SpatVector'
objects are provided. Non-Gaussian models are fit using 'INLA', and Gaussian
geostatistical models use Maximum Likelihood Estimation. For details see Brown (2015) <doi:10.18637/jss.v063.i12>. The 'RandomFields' package is available at <https://www.wim.uni-mannheim.de/schlather/publications/software>.
Author: Patrick Brown [aut, cre, cph]
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Diff between geostatsp versions 2.0.3 dated 2023-12-05 and 2.0.6 dated 2024-02-20
DESCRIPTION | 8 +- MD5 | 43 +++++++------- R/0gm.R | 58 +++++++++++-------- R/RFsimulate.R | 27 ++++++--- R/glgm.R | 8 ++ R/krige.R | 153 +++++++++++++++++++++++++++++----------------------- R/lgm.R | 5 - R/squareRaster.R | 4 - R/stackRasterList.R | 4 - build/geostatsp.pdf |binary build/stage23.rdb |binary inst/doc/glgm.R | 42 +++++++------- inst/doc/glgm.Rnw | 46 ++++++++------- inst/doc/glgm.pdf |binary inst/doc/lgcp.pdf |binary inst/extR/murder.R |only man/RFsimulate.Rd | 24 ++++---- man/gambiaUTM.Rd | 9 +-- man/rongelapUTM.Rd | 5 - man/simLgcp.Rd | 6 +- man/variog.Rd | 43 ++++++++++++-- tests/lgm.R | 10 +-- vignettes/glgm.Rnw | 46 ++++++++------- 23 files changed, 313 insertions(+), 228 deletions(-)
Title: Snapshots for Unit Tests using the 'tinytest' Framework
Description: Snapshots for unit tests using the 'tinytest' framework for R. Includes expectations to test base R and 'ggplot2' plots as well as console output from print().
Author: Vincent Arel-Bundock [aut, cre, cph]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between tinysnapshot versions 0.0.3 dated 2023-04-10 and 0.0.4 dated 2024-02-20
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/expect_snapshot_print.R | 1 + build/partial.rdb |binary 5 files changed, 12 insertions(+), 7 deletions(-)
Title: Gene Set Enrichment Analysis in R
Description: R-interface to C++ implementation of the rank/score permutation based GSEA test (Subramanian et al 2005 <doi: 10.1073/pnas.0506580102>).
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between gsEasy versions 1.4 dated 2021-05-26 and 1.5 dated 2024-02-20
DESCRIPTION | 10 MD5 | 30 - R/RcppExports.R | 22 - build/vignette.rds |binary data/GO_gene_sets.RData |binary data/datalist | 2 inst/doc/gsEasy-guide.R | 70 +-- inst/doc/gsEasy-guide.Rmd | 2 inst/doc/gsEasy-guide.html | 741 ++++++++++++++++++++++++++------------- man/GO_gene_sets.Rd | 4 man/get_GO_gene_sets.Rd | 10 man/get_ontological_gene_sets.Rd | 3 man/gsEasy-package.Rd | 11 man/gset.Rd | 13 src/RcppExports.cpp | 5 vignettes/gsEasy-guide.Rmd | 2 16 files changed, 592 insertions(+), 333 deletions(-)
Title: Assess the Diagnostic Power of Genomic Marker Combinations
Description: Population genetics package for designing diagnostic panels.
Candidate markers, marker combinations, and different panel sizes are
assessed for how well they can predict the source population of known
samples. Requires a genotype file of candidate markers in STRUCTURE format.
Methods for population cross-validation are described in Jombart (2008)
<doi:10.1093/bioinformatics/btn129>.
Author: Kim Vertacnik [cre, aut] ,
Oksana Vernygora [aut] ,
Julian Dupuis [aut]
Maintainer: Kim Vertacnik <kim.vertacnik@mailbox.org>
Diff between snpAIMeR versions 2.1.0 dated 2023-12-17 and 2.1.1 dated 2024-02-20
snpAIMeR-2.1.0/snpAIMeR/R/snpAIMeR_v2.1.0.R |only snpAIMeR-2.1.1/snpAIMeR/DESCRIPTION | 8 +++---- snpAIMeR-2.1.1/snpAIMeR/MD5 | 10 ++++----- snpAIMeR-2.1.1/snpAIMeR/NEWS.md | 4 ++- snpAIMeR-2.1.1/snpAIMeR/R/snpAIMeR_v2.1.1.R |only snpAIMeR-2.1.1/snpAIMeR/README.md | 14 ++++++------- snpAIMeR-2.1.1/snpAIMeR/man/snpAIMeR.Rd | 29 +++++++++++++--------------- 7 files changed, 33 insertions(+), 32 deletions(-)
Title: Item Response Theory and Computerized Adaptive Testing Functions
Description: A collection of Item Response Theory (IRT) and Computerized
Adaptive Testing (CAT) functions that are used in psychometrics.
Author: Emre Gonulates [aut, cre]
Maintainer: Emre Gonulates <egonulates@gmail.com>
Diff between irt versions 0.2.7 dated 2022-11-09 and 0.2.9 dated 2024-02-20
irt-0.2.7/irt/R/irt.R |only irt-0.2.7/irt/man/irt.Rd |only irt-0.2.7/irt/man/print.Item.Rd |only irt-0.2.9/irt/DESCRIPTION | 31 irt-0.2.9/irt/MD5 | 127 - irt-0.2.9/irt/NAMESPACE | 4 irt-0.2.9/irt/NEWS.md | 10 irt-0.2.9/irt/R/ability_estimation.R | 141 - irt-0.2.9/irt/R/bilog.R | 815 ++++++--- irt-0.2.9/irt/R/cat_sim.R | 59 irt-0.2.9/irt/R/cat_sim_helper_functions.R | 2 irt-0.2.9/irt/R/classification.R | 239 ++ irt-0.2.9/irt/R/dif.R | 109 + irt-0.2.9/irt/R/equate_stuirt.R |only irt-0.2.9/irt/R/generate_objects.R | 2 irt-0.2.9/irt/R/ipd.R | 529 +++++- irt-0.2.9/irt/R/irtpro.R |only irt-0.2.9/irt/R/item-class-methods.R | 38 irt-0.2.9/irt/R/item_analysis.R | 4 irt-0.2.9/irt/R/itempool-class-methods.R | 1 irt-0.2.9/irt/R/kernel_smoothing.R | 4 irt-0.2.9/irt/R/misc.R | 25 irt-0.2.9/irt/R/package-irt.R |only irt-0.2.9/irt/R/plot_cat_output.R | 26 irt-0.2.9/irt/R/plot_distractor_icc.R | 14 irt-0.2.9/irt/R/plot_icc.R | 75 irt-0.2.9/irt/R/plot_info.R | 14 irt-0.2.9/irt/R/plot_item.R | 4 irt-0.2.9/irt/R/plot_itempool.R | 20 irt-0.2.9/irt/R/plot_ks.R | 12 irt-0.2.9/irt/R/plot_resp_loglik.R | 4 irt-0.2.9/irt/R/resp_lik.R | 5 irt-0.2.9/irt/R/response-class-methods.R | 6 irt-0.2.9/irt/R/response-class.R | 6 irt-0.2.9/irt/R/response_set-class-methods.R | 1 irt-0.2.9/irt/R/testlet-class-methods.R | 1 irt-0.2.9/irt/R/winsteps.R |only irt-0.2.9/irt/R/zzz.R | 5 irt-0.2.9/irt/build/vignette.rds |binary irt-0.2.9/irt/inst/doc/irt-itempool.R | 6 irt-0.2.9/irt/inst/doc/irt-itempool.html | 572 ++---- irt-0.2.9/irt/inst/doc/irt-models.R | 2 irt-0.2.9/irt/inst/doc/irt-models.html | 751 +++------ irt-0.2.9/irt/inst/doc/irt-quick-start.R | 2 irt-0.2.9/irt/inst/doc/irt-quick-start.html | 820 ++++------ irt-0.2.9/irt/man/Response-class.Rd | 6 irt-0.2.9/irt/man/create_cat_design.Rd | 26 irt-0.2.9/irt/man/dif.Rd | 2 irt-0.2.9/irt/man/equate_stuirt.Rd |only irt-0.2.9/irt/man/est_ability.Rd | 130 - irt-0.2.9/irt/man/est_bilog.Rd | 485 +++-- irt-0.2.9/irt/man/est_irtpro.Rd |only irt-0.2.9/irt/man/est_winsteps.Rd |only irt-0.2.9/irt/man/info.Rd | 8 irt-0.2.9/irt/man/ipd.Rd | 134 + irt-0.2.9/irt/man/irt-package.Rd |only irt-0.2.9/irt/man/kappa_coef.Rd |only irt-0.2.9/irt/man/ks.Rd | 4 irt-0.2.9/irt/man/mean.Item.Rd | 8 irt-0.2.9/irt/man/plot.cat_output.Rd | 2 irt-0.2.9/irt/man/print-Item-method.Rd |only irt-0.2.9/irt/man/print.cat_output.Rd | 4 irt-0.2.9/irt/man/prob.Rd | 8 irt-0.2.9/irt/man/response.Rd | 2 irt-0.2.9/irt/man/sub-subset-Itempool-numeric-missing-method.Rd | 2 irt-0.2.9/irt/man/sub-subset-Response_set-numeric-missing-method.Rd | 2 irt-0.2.9/irt/man/sub-subset-Testlet-numeric-missing-method.Rd | 2 irt-0.2.9/irt/man/var.Item.Rd | 8 irt-0.2.9/irt/src/Makevars | 1 irt-0.2.9/irt/src/Makevars.win | 1 irt-0.2.9/irt/src/cat_select_next_item.cpp | 108 - 71 files changed, 3141 insertions(+), 2288 deletions(-)
Title: Super Learner Prediction
Description: Implements the super learner prediction method and contains a
library of prediction algorithms to be used in the super learner.
Author: Eric Polley [aut, cre],
Erin LeDell [aut],
Chris Kennedy [aut],
Sam Lendle [ctb],
Mark van der Laan [aut, ths]
Maintainer: Eric Polley <epolley@uchicago.edu>
Diff between SuperLearner versions 2.0-28.1 dated 2023-07-18 and 2.0-29 dated 2024-02-20
SuperLearner-2.0-28.1/SuperLearner/R/SL.extraTrees.R |only SuperLearner-2.0-28.1/SuperLearner/man/SL.extraTrees.Rd |only SuperLearner-2.0-28.1/SuperLearner/man/predict.SL.extraTrees.Rd |only SuperLearner-2.0-28.1/SuperLearner/tests/testthat/test-extraTrees.R |only SuperLearner-2.0-29/SuperLearner/DESCRIPTION | 20 SuperLearner-2.0-29/SuperLearner/MD5 | 74 SuperLearner-2.0-29/SuperLearner/NAMESPACE | 3 SuperLearner-2.0-29/SuperLearner/R/SL.bartMachine.R | 2 SuperLearner-2.0-29/SuperLearner/R/SL.cforest.R | 2 SuperLearner-2.0-29/SuperLearner/R/SL.gam.R | 7 SuperLearner-2.0-29/SuperLearner/R/SL.gbm.R | 6 SuperLearner-2.0-29/SuperLearner/R/SL.loess.R | 2 SuperLearner-2.0-29/SuperLearner/R/create.Learner.R | 2 SuperLearner-2.0-29/SuperLearner/R/predict.SuperLearner.R | 2 SuperLearner-2.0-29/SuperLearner/build/vignette.rds |binary SuperLearner-2.0-29/SuperLearner/inst/NEWS | 12 SuperLearner-2.0-29/SuperLearner/inst/doc/Guide-to-SuperLearner.R | 122 SuperLearner-2.0-29/SuperLearner/inst/doc/Guide-to-SuperLearner.Rmd | 38 SuperLearner-2.0-29/SuperLearner/inst/doc/Guide-to-SuperLearner.html | 1468 ++++++---- SuperLearner-2.0-29/SuperLearner/man/CV.SuperLearner.Rd | 4 SuperLearner-2.0-29/SuperLearner/man/CVFolds.Rd | 2 SuperLearner-2.0-29/SuperLearner/man/SL.bartMachine.Rd | 2 SuperLearner-2.0-29/SuperLearner/man/SL.biglasso.Rd | 10 SuperLearner-2.0-29/SuperLearner/man/SL.cforest.Rd | 2 SuperLearner-2.0-29/SuperLearner/man/SL.glmnet.Rd | 2 SuperLearner-2.0-29/SuperLearner/man/SL.ksvm.Rd | 3 SuperLearner-2.0-29/SuperLearner/man/SampleSplitSuperLearner.Rd | 4 SuperLearner-2.0-29/SuperLearner/man/SuperLearner.Rd | 4 SuperLearner-2.0-29/SuperLearner/man/recombineCVSL.Rd | 2 SuperLearner-2.0-29/SuperLearner/man/recombineSL.Rd | 2 SuperLearner-2.0-29/SuperLearner/man/summary.CV.SuperLearner.Rd | 2 SuperLearner-2.0-29/SuperLearner/man/write.method.template.Rd | 2 SuperLearner-2.0-29/SuperLearner/man/write.screen.template.Rd | 2 SuperLearner-2.0-29/SuperLearner/tests/testthat/test-SuperLearner.R | 4 SuperLearner-2.0-29/SuperLearner/tests/testthat/test-XGBoost.R | 6 SuperLearner-2.0-29/SuperLearner/tests/testthat/test-bartMachine.R | 16 SuperLearner-2.0-29/SuperLearner/tests/testthat/test-cforest.R | 18 SuperLearner-2.0-29/SuperLearner/tests/testthat/test-randomForest.R | 84 SuperLearner-2.0-29/SuperLearner/tests/testthat/test-summaryCVSuperLearner.R | 10 SuperLearner-2.0-29/SuperLearner/vignettes/Guide-to-SuperLearner.Rmd | 38 40 files changed, 1140 insertions(+), 839 deletions(-)
Title: Log-Linear Poisson Graphical Model with Hot-Deck Multiple
Imputation
Description: Infer log-linear Poisson Graphical Model with an auxiliary data
set. Hot-deck multiple imputation method is used to improve the reliability
of the inference with an auxiliary dataset. Standard log-linear Poisson
graphical model can also be used for the inference and the Stability
Approach for Regularization Selection (StARS) is implemented to drive the
selection of the regularization parameter. The method is fully described in
<doi:10.1093/bioinformatics/btx819>.
Author: Alyssa Imbert [aut],
Nathalie Vialaneix [aut, cre]
Maintainer: Nathalie Vialaneix <nathalie.vialaneix@inrae.fr>
Diff between RNAseqNet versions 0.1.4 dated 2020-06-08 and 0.1.5 dated 2024-02-20
RNAseqNet-0.1.4/RNAseqNet/NEWS |only RNAseqNet-0.1.4/RNAseqNet/README.md |only RNAseqNet-0.1.5/RNAseqNet/DESCRIPTION | 10 RNAseqNet-0.1.5/RNAseqNet/MD5 | 35 +-- RNAseqNet-0.1.5/RNAseqNet/NEWS.md |only RNAseqNet-0.1.5/RNAseqNet/R/data.R | 18 - RNAseqNet-0.1.5/RNAseqNet/R/donors.R | 2 RNAseqNet-0.1.5/RNAseqNet/R/main.R | 2 RNAseqNet-0.1.5/RNAseqNet/R/poisson_net.R | 4 RNAseqNet-0.1.5/RNAseqNet/build/partial.rdb |binary RNAseqNet-0.1.5/RNAseqNet/build/vignette.rds |binary RNAseqNet-0.1.5/RNAseqNet/inst/CITATION | 38 +-- RNAseqNet-0.1.5/RNAseqNet/inst/doc/RNAseqNet.R | 6 RNAseqNet-0.1.5/RNAseqNet/inst/doc/RNAseqNet.html | 233 ++++++++++---------- RNAseqNet-0.1.5/RNAseqNet/man/GLMnetwork.Rd | 2 RNAseqNet-0.1.5/RNAseqNet/man/imputeHD.Rd | 2 RNAseqNet-0.1.5/RNAseqNet/man/imputedGLMnetwork.Rd | 2 RNAseqNet-0.1.5/RNAseqNet/man/lung.Rd | 8 RNAseqNet-0.1.5/RNAseqNet/man/stabilitySelection.Rd | 2 RNAseqNet-0.1.5/RNAseqNet/man/thyroid.Rd | 10 20 files changed, 174 insertions(+), 200 deletions(-)
Title: Create Quizzes in GIFT Format
Description: Implementation of some functions to create quizzes
in the GIFT format. This format is used by several Virtual Learning
Environments such as Moodle.
Author: Maria Jose Haro-Delicado, Virgilio Gomez-Rubio and Francisco
Parreno-Torres
Maintainer: Virgilio Gomez-Rubio <virgilio.gomez@uclm.es>
Diff between RGIFT versions 0.1-6 dated 2023-11-17 and 0.1-7 dated 2024-02-20
RGIFT-0.1-6/RGIFT/.Rinstignore |only RGIFT-0.1-7/RGIFT/DESCRIPTION | 8 ++++---- RGIFT-0.1-7/RGIFT/MD5 | 6 +++--- RGIFT-0.1-7/RGIFT/R/generic.R | 4 ++-- RGIFT-0.1-7/RGIFT/inst/doc/RGIFT.pdf |binary 5 files changed, 9 insertions(+), 9 deletions(-)
Title: Model BIC Posterior Probability
Description: Fits the neighboring models of a fitted
structural equation model and assesses the model
uncertainty of the fitted model based on BIC posterior
probabilities, using the method presented in
Wu, Cheung, and Leung (2020)
<doi:10.1080/00273171.2019.1574546>.
Author: Shu Fai Cheung [aut, cre] ,
Huiping Wu [aut],
Shing On Leung [aut] ,
Ivan Jacob Agaloos Pesigan [ctb]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between modelbpp versions 0.1.2 dated 2023-09-21 and 0.1.3 dated 2024-02-20
DESCRIPTION | 19 MD5 | 84 +- NAMESPACE | 8 NEWS.md | 121 ++++ R/c_partables.R |only R/fit_many.R | 182 +++++- R/get_add.R | 60 +- R/get_drop.R | 46 + R/helpers1.R | 15 R/helpers2_for_model_check.R | 75 ++ R/helpers3_for_model_graph.R | 408 ++++++++++++++ R/helpers4_for_model_graph.R |only R/model_graph.R | 212 ++++++- R/model_set.R | 131 +++- R/partables_helpers.R |only R/print.model_set.R | 134 ++++ R/print.partables.R | 2 R/print.sem_outs.R | 4 README.md | 12 build/partial.rdb |binary build/vignette.rds |binary inst/doc/modelbpp.R | 12 inst/doc/modelbpp.Rmd | 10 inst/doc/modelbpp.html | 806 +++++++++++++++------------- inst/figures |only inst/tinytest/test_check_equivalent.R |only inst/tinytest/test_fit_many.R | 17 inst/tinytest/test_model_graph_user.R |only inst/tinytest/test_model_graph_user2.R |only inst/tinytest/test_model_set.R | 103 --- inst/tinytest/test_model_set_models_mixed.R |only inst/tinytest/test_model_set_more_models.R |only inst/tinytest/test_model_set_target_bpp.R |only inst/tinytest/test_model_set_update_bpp.R |only inst/tinytest/test_model_set_user_models.R |only inst/tinytest/test_model_set_user_priors.R |only inst/tinytest/test_net.R |only inst/tinytest/test_no_convergence.R |only inst/tinytest/test_partables_combine.R |only inst/tinytest/test_partables_helpers.R |only inst/tinytest/test_plot_model_est.R | 9 inst/tinytest/test_post_check_failed.R |only man/figures |only man/fit_many.Rd | 13 man/get_add.Rd | 8 man/get_drop.Rd | 8 man/manipulate_partables.Rd |only man/model_graph.Rd | 161 +++++ man/model_set.Rd | 25 man/modelbpp-package.Rd | 7 man/partables_helpers.Rd |only man/print.model_set.Rd | 29 + vignettes/ExportedItems.bib |only vignettes/modelbpp.Rmd | 10 54 files changed, 2130 insertions(+), 601 deletions(-)
Title: ILO Open Data via Ilostat Bulk Download Facility
Description: Tools to download data from the ilostat database
<https://ilostat.ilo.org> together with search and
manipulation utilities.
Author: David Bescond [aut, cre] ,
Mabelin Villarreal-Fuentes [ctb]
,
ILO Department of Statistics [cph, fnd]
Maintainer: David Bescond <bescond@ilo.org>
Diff between Rilostat versions 1.2 dated 2024-02-16 and 2.0.0 dated 2024-02-20
DESCRIPTION | 23 +++++++++++------------ MD5 | 16 ++++++++-------- NAMESPACE | 2 ++ NEWS.md | 6 +++++- R/Rilostat.R | 10 ++++++++-- R/get_ilostat.R | 26 +++++++------------------- R/get_ilostat_dic.R | 6 +++--- R/get_ilostat_toc.R | 21 +++++---------------- R/sysdata.rda |binary 9 files changed, 49 insertions(+), 61 deletions(-)
Title: Tools for Bayesian Analyses
Description: Provides tools for conducting Bayesian analyses and Bayesian model averaging
(Kass and Raftery, 1995, <doi:10.1080/01621459.1995.10476572>,
Hoeting et al., 1999, <doi:10.1214/ss/1009212519>). The package contains
functions for creating a wide range of prior distribution objects, mixing posterior
samples from 'JAGS' and 'Stan' models, plotting posterior distributions, and etc...
The tools for working with prior distribution span from visualization, generating 'JAGS'
and 'bridgesampling' syntax to basic functions such as rng, quantile, and distribution functions.
Author: Frantisek Bartos [aut, cre]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between BayesTools versions 0.2.16 dated 2023-07-10 and 0.2.17 dated 2024-02-20
DESCRIPTION | 6 MD5 | 31 - NAMESPACE | 1 NEWS.md | 9 R/JAGS-fit.R | 12 R/JAGS-marglik.R | 22 R/priors-informed.R | 959 ++++++++++++++++++++++++++++++----- R/tools.R | 32 - build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 48 + inst/doc/ComparisonR.html | 6 inst/doc/SpikeAndSlab.html | 4 man/bridgesampling_object.Rd |only man/check_input.Rd | 15 man/prior_informed.Rd | 15 man/prior_informed_medicine_names.Rd | 2 17 files changed, 998 insertions(+), 164 deletions(-)
Title: Image Processing Library Based on 'CImg'
Description: Fast image processing for images in up to 4 dimensions (two spatial
dimensions, one time/depth dimension, one colour dimension). Provides most
traditional image processing tools (filtering, morphology, transformations,
etc.) as well as various functions for easily analysing image data using R. The
package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image
processing.
Author: Simon Barthelme [aut],
David Tschumperle [ctb],
Jan Wijffels [ctb],
Haz Edine Assemlal [ctb],
Shota Ochi [ctb],
Aaron Robotham [cre],
Rodrigo Tobar [ctb]
Maintainer: Aaron Robotham <aaron.robotham@uwa.edu.au>
Diff between imager versions 0.45.2 dated 2023-05-10 and 0.45.8 dated 2024-02-20
DESCRIPTION | 6 MD5 | 46 ++--- NAMESPACE | 1 R/RcppExports.R | 12 - R/cimg_class.R | 2 R/splitcombine.R | 13 + build/vignette.rds |binary inst/doc/gettingstarted.R | 2 inst/doc/gettingstarted.Rmd | 2 inst/doc/gettingstarted.html | 349 +++++++++++++++++-------------------------- inst/doc/pixsets.R | 2 inst/doc/pixsets.Rmd | 2 inst/doc/pixsets.html | 290 ++++++++++++++--------------------- inst/include/imager.h | 3 man/distance_transform.Rd | 2 man/imager.Rd | 28 +++ man/imager.combine.Rd | 9 - man/warp.Rd | 6 src/RcppExports.cpp | 10 - src/morphology.cpp | 2 src/reductions.cpp | 98 +++++++++--- src/transformations.cpp | 6 vignettes/gettingstarted.Rmd | 2 vignettes/pixsets.Rmd | 2 24 files changed, 441 insertions(+), 454 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible
outcome to evaluate the effectiveness of a new therapy (the true endpoint) is
difficult to measure. In such a situation, it can be an effective strategy to
replace the true endpoint by a (bio)marker that is easier to measure and that
allows for a prediction of the treatment effect on the true endpoint (a
surrogate endpoint). The package 'Surrogate' allows for an evaluation of the
appropriateness of a candidate surrogate endpoint based on the meta-analytic,
information-theoretic, and causal-inference frameworks. Part of this software
has been developed using funding provided from the European Union's Seventh
Framework Programme for research, technological development and demonstration
(Grant Agreement no 602552), the Special Research Fund (BOF) of Hasselt
University (BOF-number: BOF2OCPO3), GlaxoSmithKline Biologicals, Baekeland
Mandaat (HBC.2022.0145), and Johnson & Johnson Innovative Medicine.
Author: Wim Van Der Elst [cre, aut],
Florian Stijven [aut],
Fenny Ong [aut],
Paul Meyvisch [aut],
Alvaro Poveda [aut],
Ariel Alonso [aut],
Hannah Ensor [aut],
Christoper Weir [aut],
Geert Molenberghs [aut]
Maintainer: Wim Van Der Elst <wim.vanderelst@gmail.com>
Diff between Surrogate versions 3.2.1 dated 2023-09-25 and 3.2.2 dated 2024-02-20
Surrogate-3.2.1/Surrogate/man/marginal_gof_scr.Rd |only Surrogate-3.2.2/Surrogate/DESCRIPTION | 30 Surrogate-3.2.2/Surrogate/MD5 | 172 +- Surrogate-3.2.2/Surrogate/NAMESPACE | 357 ++--- Surrogate-3.2.2/Surrogate/NEWS | 3 Surrogate-3.2.2/Surrogate/NEWS.md | 6 Surrogate-3.2.2/Surrogate/R/CausalDiagramContCont.R | 55 Surrogate-3.2.2/Surrogate/R/FixedBinContIT.r | 258 +-- Surrogate-3.2.2/Surrogate/R/ICA.Cont.Cont.MultS.R | 144 +- Surrogate-3.2.2/Surrogate/R/ICA.Sample.ContCont.R | 97 - Surrogate-3.2.2/Surrogate/R/ICAContCont.R | 109 - Surrogate-3.2.2/Surrogate/R/ICA_BinCont_copula.R | 95 + Surrogate-3.2.2/Surrogate/R/ICA_SurvSurv_copula.R | 43 Surrogate-3.2.2/Surrogate/R/ITCI-Dvine-inference-utils.R |only Surrogate-3.2.2/Surrogate/R/MICA.Sample.ContCont.R | 90 - Surrogate-3.2.2/Surrogate/R/MICAContCont.R | 88 - Surrogate-3.2.2/Surrogate/R/MinSurrContCont.R | 37 Surrogate-3.2.2/Surrogate/R/MufixedContCont.MultS.R |only Surrogate-3.2.2/Surrogate/R/MumixedContCont.MultS.R |only Surrogate-3.2.2/Surrogate/R/Plot.FixedDiscrDiscrIT.R | 7 Surrogate-3.2.2/Surrogate/R/copula_utils.R | 40 Surrogate-3.2.2/Surrogate/R/fit_model_BinCont_copula.R | 27 Surrogate-3.2.2/Surrogate/R/fit_model_SurvSurv.R | 146 +- Surrogate-3.2.2/Surrogate/R/goodness_of_fit_SurvSurv.R | 641 +++++++-- Surrogate-3.2.2/Surrogate/R/likelihood_copula_models.R | 246 +-- Surrogate-3.2.2/Surrogate/R/log_likelihoods.R | 458 +++--- Surrogate-3.2.2/Surrogate/R/plot.BinContCombnIT.R | 32 Surrogate-3.2.2/Surrogate/R/plot.Fano.BinBin.R | 22 Surrogate-3.2.2/Surrogate/R/plot.InfoTheoretic.R | 20 Surrogate-3.2.2/Surrogate/R/plot.MaxEntContCont.R | 23 Surrogate-3.2.2/Surrogate/R/plot.MetaAnalyticMTS.R | 67 Surrogate-3.2.2/Surrogate/R/plot.MetaAnalyticSTS.R | 20 Surrogate-3.2.2/Surrogate/R/plot.SurvSurv.R | 36 Surrogate-3.2.2/Surrogate/R/plot.TrialLevelIT.R | 11 Surrogate-3.2.2/Surrogate/R/plot.TrialLevelMA.R | 15 Surrogate-3.2.2/Surrogate/R/plot.TwoStageSurvSurv.R | 19 Surrogate-3.2.2/Surrogate/R/plot_ICABinBin.R | 693 ++++------ Surrogate-3.2.2/Surrogate/R/plot_ICABinCont.R | 73 - Surrogate-3.2.2/Surrogate/R/sensitivity_analysis_BinCont_copula.R | 671 ++++----- Surrogate-3.2.2/Surrogate/R/sensitivity_analysis_SurvSurv.R | 290 ++-- Surrogate-3.2.2/Surrogate/R/sensitivity_intervals.R |only Surrogate-3.2.2/Surrogate/R/summary.MuContCont.MultS.R |only Surrogate-3.2.2/Surrogate/R/utils.R | 1 Surrogate-3.2.2/Surrogate/README.md | 8 Surrogate-3.2.2/Surrogate/data/PANSS.rda |only Surrogate-3.2.2/Surrogate/man/Dvine_ICA_confint.Rd |only Surrogate-3.2.2/Surrogate/man/ICA.BinBin.Grid.Sample.Rd | 154 +- Surrogate-3.2.2/Surrogate/man/ICA.BinBin.Grid.Sample.Uncert.Rd | 152 +- Surrogate-3.2.2/Surrogate/man/ICABinBin.Rd | 202 +- Surrogate-3.2.2/Surrogate/man/ICA_given_model_constructor.Rd |only Surrogate-3.2.2/Surrogate/man/MICA.Sample.ContCont.Rd | 203 +- Surrogate-3.2.2/Surrogate/man/MICAContCont.Rd | 209 +-- Surrogate-3.2.2/Surrogate/man/MixedContContIT.Rd | 2 Surrogate-3.2.2/Surrogate/man/MufixedContCont.MultS.Rd |only Surrogate-3.2.2/Surrogate/man/MumixedContCont.MultS.Rd |only Surrogate-3.2.2/Surrogate/man/PANSS.Rd |only Surrogate-3.2.2/Surrogate/man/binary_continuous_loglik.Rd | 3 Surrogate-3.2.2/Surrogate/man/compute_ICA_BinCont.Rd | 6 Surrogate-3.2.2/Surrogate/man/compute_ICA_SurvSurv.Rd | 32 Surrogate-3.2.2/Surrogate/man/delta_method_log_mutinfo.Rd |only Surrogate-3.2.2/Surrogate/man/fit_copula_model_BinCont.Rd | 31 Surrogate-3.2.2/Surrogate/man/fit_copula_submodel_BinCont.Rd | 3 Surrogate-3.2.2/Surrogate/man/fit_model_SurvSurv.Rd | 37 Surrogate-3.2.2/Surrogate/man/log_likelihood_copula_model.Rd | 3 Surrogate-3.2.2/Surrogate/man/loglik_copula_scale.Rd | 8 Surrogate-3.2.2/Surrogate/man/marginal_gof_plots_scr.Rd |only Surrogate-3.2.2/Surrogate/man/marginal_gof_scr_S_plot.Rd |only Surrogate-3.2.2/Surrogate/man/mean_S_before_T_plot_scr.Rd |only Surrogate-3.2.2/Surrogate/man/new_vine_copula_ss_fit.Rd | 8 Surrogate-3.2.2/Surrogate/man/plot.InformationTheoretic.Rd | 152 +- Surrogate-3.2.2/Surrogate/man/sample_copula_parameters.Rd | 5 Surrogate-3.2.2/Surrogate/man/sample_deltas_BinCont.Rd | 18 Surrogate-3.2.2/Surrogate/man/sample_dvine.Rd | 6 Surrogate-3.2.2/Surrogate/man/sensitivity_analysis_BinCont_copula.Rd | 85 + Surrogate-3.2.2/Surrogate/man/sensitivity_analysis_SurvSurv_copula.Rd | 222 ++- Surrogate-3.2.2/Surrogate/man/sensitivity_intervals_Dvine.Rd |only Surrogate-3.2.2/Surrogate/man/summary.gen.Rd | 6 Surrogate-3.2.2/Surrogate/man/summary_level_bootstrap_ICA.Rd |only Surrogate-3.2.2/Surrogate/man/twostep_BinCont.Rd | 3 Surrogate-3.2.2/Surrogate/man/twostep_SurvSurv.Rd | 8 Surrogate-3.2.2/Surrogate/tests/testthat.R | 4 Surrogate-3.2.2/Surrogate/tests/testthat/Rplots.pdf |only Surrogate-3.2.2/Surrogate/tests/testthat/_snaps |only Surrogate-3.2.2/Surrogate/tests/testthat/fixtures |only Surrogate-3.2.2/Surrogate/tests/testthat/test-ICA_BinCont_copula.R | 191 +- Surrogate-3.2.2/Surrogate/tests/testthat/test-ICA_SurvSurv_copula.R | 92 - Surrogate-3.2.2/Surrogate/tests/testthat/test-ITCI-Dvine-inference-utils.R |only Surrogate-3.2.2/Surrogate/tests/testthat/test-fit_model_SurvSurv.R | 64 Surrogate-3.2.2/Surrogate/tests/testthat/test-goodness_of_fit_SurvSurv.R |only Surrogate-3.2.2/Surrogate/tests/testthat/test-log_likelihoods.R |only Surrogate-3.2.2/Surrogate/tests/testthat/test-sensitivity_analysis_BinCont_copula.R | 105 - Surrogate-3.2.2/Surrogate/tests/testthat/test-sensitivity_analysis_SurvSurv.R | 171 +- Surrogate-3.2.2/Surrogate/tests/testthat/test-sensitivity_intervals.R |only 93 files changed, 4135 insertions(+), 3200 deletions(-)
Title: Spatial Dependence for Simple Features
Description: An interface to 'spdep' to integrate with 'sf' objects and the 'tidyverse'.
Author: Josiah Parry [aut] ,
Dexter Locke [aut, cre]
Maintainer: Dexter Locke <dexter.locke@gmail.com>
Diff between sfdep versions 0.2.3 dated 2023-01-11 and 0.2.4 dated 2024-02-20
sfdep-0.2.3/sfdep/build/vignette.rds |only sfdep-0.2.3/sfdep/inst/doc |only sfdep-0.2.3/sfdep/vignettes |only sfdep-0.2.4/sfdep/DESCRIPTION | 26 - sfdep-0.2.4/sfdep/MD5 | 131 ++++------ sfdep-0.2.4/sfdep/NAMESPACE | 2 sfdep-0.2.4/sfdep/R/apply.R | 4 sfdep-0.2.4/sfdep/R/emerging-hostpot-analysis.R | 2 sfdep-0.2.4/sfdep/R/global-measures.R | 2 sfdep-0.2.4/sfdep/R/joincount-bv-impl.R | 2 sfdep-0.2.4/sfdep/R/joincount-uni-impl.R | 5 sfdep-0.2.4/sfdep/R/lisa.R | 9 sfdep-0.2.4/sfdep/R/localC.R | 8 sfdep-0.2.4/sfdep/R/localG.R | 8 sfdep-0.2.4/sfdep/R/nb-match-test-impl.R | 3 sfdep-0.2.4/sfdep/R/neighbors.R | 5 sfdep-0.2.4/sfdep/R/point-pattern-centers.R | 3 sfdep-0.2.4/sfdep/R/sfn-node-get.R | 3 sfdep-0.2.4/sfdep/R/sfnetworks.R | 10 sfdep-0.2.4/sfdep/R/spacetime-cube-set-cols.R | 3 sfdep-0.2.4/sfdep/R/spacetime-cube-test.R | 3 sfdep-0.2.4/sfdep/R/spacetime-local-gistar-impl.R | 2 sfdep-0.2.4/sfdep/R/spacetime-methods.R | 41 +-- sfdep-0.2.4/sfdep/R/utils-kernels.R | 2 sfdep-0.2.4/sfdep/R/utils-set-operations.R | 2 sfdep-0.2.4/sfdep/R/utils.R | 9 sfdep-0.2.4/sfdep/R/weights-contiguity.R | 3 sfdep-0.2.4/sfdep/README.md | 1 sfdep-0.2.4/sfdep/build/partial.rdb |binary sfdep-0.2.4/sfdep/man/as_spacetime.Rd | 31 +- sfdep-0.2.4/sfdep/man/center_mean.Rd | 3 sfdep-0.2.4/sfdep/man/emerging_hotspot_analysis.Rd | 2 sfdep-0.2.4/sfdep/man/global_c_perm.Rd | 4 sfdep-0.2.4/sfdep/man/global_c_test.Rd | 4 sfdep-0.2.4/sfdep/man/global_moran_bv.Rd | 2 sfdep-0.2.4/sfdep/man/global_moran_perm.Rd | 4 sfdep-0.2.4/sfdep/man/global_moran_test.Rd | 2 sfdep-0.2.4/sfdep/man/is_spacetime_cube.Rd | 3 sfdep-0.2.4/sfdep/man/jc_clc_perm_impl.Rd | 4 sfdep-0.2.4/sfdep/man/kernels.Rd | 2 sfdep-0.2.4/sfdep/man/local_c.Rd | 8 sfdep-0.2.4/sfdep/man/local_g.Rd | 2 sfdep-0.2.4/sfdep/man/local_g_spt.Rd | 2 sfdep-0.2.4/sfdep/man/local_jc_uni.Rd | 5 sfdep-0.2.4/sfdep/man/local_moran.Rd | 9 sfdep-0.2.4/sfdep/man/local_moran_bv.Rd | 4 sfdep-0.2.4/sfdep/man/nb_match_test.Rd | 3 sfdep-0.2.4/sfdep/man/nb_union.Rd | 2 sfdep-0.2.4/sfdep/man/permute_listw.Rd | 2 sfdep-0.2.4/sfdep/man/set_col.Rd | 3 sfdep-0.2.4/sfdep/man/st_as_edges.Rd | 7 sfdep-0.2.4/sfdep/man/st_as_graph.Rd | 4 sfdep-0.2.4/sfdep/man/st_as_nodes.Rd | 2 sfdep-0.2.4/sfdep/man/st_cardinalties.Rd | 4 sfdep-0.2.4/sfdep/man/st_contiguity.Rd | 3 sfdep-0.2.4/sfdep/man/st_nb_apply.Rd | 2 sfdep-0.2.4/sfdep/man/st_nb_lag.Rd | 2 sfdep-0.2.4/sfdep/man/st_weights.Rd | 3 sfdep-0.2.4/sfdep/tests/testthat/_snaps |only sfdep-0.2.4/sfdep/tests/testthat/test-local_g_perm_snapshot_test.R |only sfdep-0.2.4/sfdep/tests/testthat/test-nb-graph.R | 9 sfdep-0.2.4/sfdep/tests/testthat/test-node_get.R | 5 62 files changed, 242 insertions(+), 189 deletions(-)
Title: Composable Preprocessing Operators and Pipelines for Machine
Learning
Description: Toolset that enriches 'mlr' with a diverse set of preprocessing
operators. Composable Preprocessing Operators ("CPO"s) are first-class
R objects that can be applied to data.frames and 'mlr' "Task"s to modify
data, can be attached to 'mlr' "Learner"s to add preprocessing to machine
learning algorithms, and can be composed to form preprocessing pipelines.
Author: Martin Binder [aut, cre],
Bernd Bischl [ctb],
Michel Lang [ctb],
Lars Kotthoff [ctb]
Maintainer: Martin Binder <developer.mb706@doublecaret.com>
Diff between mlrCPO versions 0.3.7-6 dated 2022-11-17 and 0.3.7-7 dated 2024-02-20
DESCRIPTION | 8 MD5 | 44 - NEWS | 3 R/CPOHelp.R | 2 README.md | 8 build/vignette.rds |binary inst/doc/a_1_getting_started.R | 8 inst/doc/a_1_getting_started.html | 826 +++++++++++++++++++---- inst/doc/a_2_mlrCPO_core.R | 12 inst/doc/a_2_mlrCPO_core.html | 675 +++++++++++++++--- inst/doc/a_3_all_CPOs.R | 14 inst/doc/a_3_all_CPOs.html | 405 +++++++++-- inst/doc/a_4_custom_CPOs.R | 16 inst/doc/a_4_custom_CPOs.html | 1139 +++++++++++++++++++++++++++----- inst/doc/z_1_getting_started_terse.R | 10 inst/doc/z_1_getting_started_terse.html | 826 +++++++++++++++++++---- inst/doc/z_2_mlrCPO_core_terse.R | 14 inst/doc/z_2_mlrCPO_core_terse.html | 675 +++++++++++++++--- inst/doc/z_3_all_CPOs_terse.R | 16 inst/doc/z_3_all_CPOs_terse.html | 405 +++++++++-- inst/doc/z_4_custom_CPOs_terse.R | 18 inst/doc/z_4_custom_CPOs_terse.html | 1123 ++++++++++++++++++++++++++----- man/cpoTemplate.Rd | 8 23 files changed, 5155 insertions(+), 1100 deletions(-)
Title: Circular Visualization
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here this package provides an implementation
of circular layout generation in R as well as an enhancement of available
software. The flexibility of the package is based on the usage of low-level
graphics functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
it gives users more convenience and freedom to design figures for
better understanding complex patterns behind multiple dimensional data.
The package is described in Gu et al. 2014 <doi:10.1093/bioinformatics/btu393>.
Author: Zuguang Gu [aut, cre]
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between circlize versions 0.4.15 dated 2022-05-10 and 0.4.16 dated 2024-02-20
DESCRIPTION | 10 +- LICENSE | 2 MD5 | 20 ++-- R/circos.arrow.R | 16 +-- R/low_level.R | 8 - R/utils.R | 2 build/vignette.rds |binary inst/CITATION | 11 -- inst/doc/circlize.Rmd | 13 ++- inst/doc/circlize.html | 201 +++++++++++-------------------------------------- vignettes/circlize.Rmd | 13 ++- 11 files changed, 96 insertions(+), 200 deletions(-)
Title: Visualize Proportions with Circles in a Plot
Description: Method for visualizing proportions between objects of different sizes.
The proportions are drawn as circles with different diameters, which makes them ideal
for visualizing proportions between planets.
Author: BenSt099 [aut, cre, cph]
Maintainer: BenSt099 <benst099@proton.me>
Diff between circlesplot versions 1.0.0 dated 2024-02-14 and 1.1.0 dated 2024-02-20
DESCRIPTION | 6 +- MD5 | 21 +++---- NAMESPACE | 1 NEWS.md |only R/circlesplot.R | 109 +++++++++++++++++++++++++++++++------- README.md | 23 +++++--- inst/doc/cp_vignette.Rmd | 42 +++++++++++--- inst/doc/cp_vignette.html | 56 +++++++++++++------ man/circlesplot.Rd | 14 +++- tests/testthat/test_circlesplot.R | 20 ++++++ vignettes/cp_vignette.Rmd | 42 +++++++++++--- vignettes/vign_1.png |binary 12 files changed, 258 insertions(+), 76 deletions(-)
Title: Classes for Storing and Manipulating Taxonomic Data
Description: Provides classes for storing and manipulating taxonomic data.
Most of the classes can be treated like base R vectors (e.g. can be used
in tables as columns and can be named). Vectorized classes can store taxon names
and authorities, taxon IDs from databases, taxon ranks, and other types of
information. More complex classes are provided to store taxonomic trees and
user-defined data associated with them.
Author: Scott Chamberlain [aut] ,
Zachary Foster [aut, cre]
Maintainer: Zachary Foster <zacharyfoster1989@gmail.com>
Diff between taxa versions 0.4.2 dated 2022-04-12 and 0.4.3 dated 2024-02-20
DESCRIPTION | 8 ++++---- MD5 | 27 ++++++++++++++------------- NEWS.md | 5 +++++ R/internal.R | 2 +- R/zzz.R | 5 ----- build/stage23.rdb |only build/taxa.pdf |binary man/classification.Rd | 4 ++-- man/default_db_ref.Rd | 9 --------- man/limited_print.Rd | 4 ++-- man/taxon_authority.Rd | 4 ++-- man/taxon_db.Rd | 4 ++-- man/taxon_id.Rd | 4 ++-- man/taxon_rank.Rd | 4 ++-- man/taxonomy.Rd | 4 ++-- 15 files changed, 38 insertions(+), 46 deletions(-)
Title: Bayesian Inference for Multinomial Models with Inequality
Constraints
Description: Implements Gibbs sampling and Bayes factors for multinomial models with
linear inequality constraints on the vector of probability parameters. As
special cases, the model class includes models that predict a linear order
of binomial probabilities (e.g., p[1] < p[2] < p[3] < .50) and mixture models
assuming that the parameter vector p must be inside the convex hull of a
finite number of predicted patterns (i.e., vertices). A formal definition of
inequality-constrained multinomial models and the implemented computational
methods is provided in: Heck, D.W., & Davis-Stober, C.P. (2019).
Multinomial models with linear inequality constraints: Overview and improvements
of computational methods for Bayesian inference. Journal of Mathematical
Psychology, 91, 70-87. <doi:10.1016/j.jmp.2019.03.004>.
Inequality-constrained multinomial models have applications in the area of
judgment and decision making to fit and test random utility models
(Regenwetter, M., Dana, J., & Davis [...truncated...]
Author: Daniel W. Heck [aut, cre]
Maintainer: Daniel W. Heck <daniel.heck@uni-marburg.de>
Diff between multinomineq versions 0.2.5 dated 2022-11-22 and 0.2.6 dated 2024-02-20
multinomineq-0.2.5/multinomineq/tests/testthat/Rplots.pdf |only multinomineq-0.2.6/multinomineq/DESCRIPTION | 10 multinomineq-0.2.6/multinomineq/MD5 | 31 multinomineq-0.2.6/multinomineq/R/data_hilbig2014_heck2017.R | 4 multinomineq-0.2.6/multinomineq/R/data_swop.R | 2 multinomineq-0.2.6/multinomineq/R/nirt.R | 2 multinomineq-0.2.6/multinomineq/R/strategy_multiattribute.R | 2 multinomineq-0.2.6/multinomineq/build/partial.rdb |binary multinomineq-0.2.6/multinomineq/build/vignette.rds |binary multinomineq-0.2.6/multinomineq/inst/doc/multinomineq_intro.R | 6 multinomineq-0.2.6/multinomineq/inst/doc/multinomineq_intro.html | 446 +++++----- multinomineq-0.2.6/multinomineq/man/heck2017.Rd | 2 multinomineq-0.2.6/multinomineq/man/hilbig2014.Rd | 2 multinomineq-0.2.6/multinomineq/man/nirt_to_Ab.Rd | 2 multinomineq-0.2.6/multinomineq/man/strategy_multiattribute.Rd | 2 multinomineq-0.2.6/multinomineq/man/swop5.Rd | 2 multinomineq-0.2.6/multinomineq/src/Makevars | 5 17 files changed, 257 insertions(+), 261 deletions(-)
Title: Tools for Parsing, Manipulating, and Graphing Taxonomic
Abundance Data
Description: A set of tools for parsing, manipulating, and graphing data
classified by a hierarchy (e.g. a taxonomy).
Author: Zachary Foster [aut, cre],
Niklaus Grunwald [ths],
Rob Gilmore [ctb]
Maintainer: Zachary Foster <zacharyfoster1989@gmail.com>
Diff between metacoder versions 0.3.6 dated 2023-04-03 and 0.3.7 dated 2024-02-20
metacoder-0.3.6/metacoder/man/taxa-package.Rd |only metacoder-0.3.7/metacoder/DESCRIPTION | 10 metacoder-0.3.7/metacoder/MD5 | 121 +- metacoder-0.3.7/metacoder/NAMESPACE | 2 metacoder-0.3.7/metacoder/NEWS.md | 4 metacoder-0.3.7/metacoder/R/heat_tree.R | 17 metacoder-0.3.7/metacoder/R/metacoder-package.R | 197 ++++ metacoder-0.3.7/metacoder/R/old_taxa--internal.R | 2 metacoder-0.3.7/metacoder/R/old_taxa--lazyhelpers.R | 1 metacoder-0.3.7/metacoder/R/old_taxa--package.R | 431 ++++------ metacoder-0.3.7/metacoder/R/old_taxa--taxmap--parsers.R | 16 metacoder-0.3.7/metacoder/R/old_taxa--taxonomy--internal.R | 5 metacoder-0.3.7/metacoder/build/vignette.rds |binary metacoder-0.3.7/metacoder/man/classifications.Rd | 8 metacoder-0.3.7/metacoder/man/extract_tax_data.Rd | 2 metacoder-0.3.7/metacoder/man/get_sort_var.Rd | 6 metacoder-0.3.7/metacoder/man/hierarchies.Rd | 4 metacoder-0.3.7/metacoder/man/hierarchy.Rd | 4 metacoder-0.3.7/metacoder/man/id_classifications.Rd | 8 metacoder-0.3.7/metacoder/man/is_branch.Rd | 8 metacoder-0.3.7/metacoder/man/is_internode.Rd | 8 metacoder-0.3.7/metacoder/man/is_leaf.Rd | 8 metacoder-0.3.7/metacoder/man/is_root.Rd | 8 metacoder-0.3.7/metacoder/man/is_stem.Rd | 8 metacoder-0.3.7/metacoder/man/limited_print.Rd | 4 metacoder-0.3.7/metacoder/man/lookup_tax_data.Rd | 8 metacoder-0.3.7/metacoder/man/map_data.Rd | 6 metacoder-0.3.7/metacoder/man/map_data_.Rd | 6 metacoder-0.3.7/metacoder/man/metacoder.Rd | 214 ++++ metacoder-0.3.7/metacoder/man/n_leaves.Rd | 6 metacoder-0.3.7/metacoder/man/n_leaves_1.Rd | 6 metacoder-0.3.7/metacoder/man/n_subtaxa.Rd | 6 metacoder-0.3.7/metacoder/man/n_subtaxa_1.Rd | 6 metacoder-0.3.7/metacoder/man/n_supertaxa.Rd | 6 metacoder-0.3.7/metacoder/man/n_supertaxa_1.Rd | 6 metacoder-0.3.7/metacoder/man/parse_dada2.Rd | 2 metacoder-0.3.7/metacoder/man/parse_edge_list.Rd | 4 metacoder-0.3.7/metacoder/man/parse_greengenes.Rd | 2 metacoder-0.3.7/metacoder/man/parse_heirarchies_to_taxonomy.Rd | 4 metacoder-0.3.7/metacoder/man/parse_mothur_tax_summary.Rd | 2 metacoder-0.3.7/metacoder/man/parse_mothur_taxonomy.Rd | 2 metacoder-0.3.7/metacoder/man/parse_newick.Rd | 2 metacoder-0.3.7/metacoder/man/parse_qiime_biom.Rd | 2 metacoder-0.3.7/metacoder/man/parse_raw_heirarchies_to_taxonomy.Rd | 5 metacoder-0.3.7/metacoder/man/parse_rdp.Rd | 2 metacoder-0.3.7/metacoder/man/parse_silva_fasta.Rd | 2 metacoder-0.3.7/metacoder/man/parse_tax_data.Rd | 6 metacoder-0.3.7/metacoder/man/parse_ubiome.Rd | 2 metacoder-0.3.7/metacoder/man/parse_unite_general.Rd | 2 metacoder-0.3.7/metacoder/man/taxa.Rd | 4 metacoder-0.3.7/metacoder/man/taxmap.Rd | 4 metacoder-0.3.7/metacoder/man/taxon_database.Rd | 4 metacoder-0.3.7/metacoder/man/taxon_id.Rd | 4 metacoder-0.3.7/metacoder/man/taxon_ids.Rd | 8 metacoder-0.3.7/metacoder/man/taxon_indexes.Rd | 8 metacoder-0.3.7/metacoder/man/taxon_name.Rd | 4 metacoder-0.3.7/metacoder/man/taxon_names.Rd | 8 metacoder-0.3.7/metacoder/man/taxon_rank.Rd | 4 metacoder-0.3.7/metacoder/man/taxon_ranks.Rd | 8 metacoder-0.3.7/metacoder/man/taxonomy.Rd | 4 metacoder-0.3.7/metacoder/tests/testthat/test--parsers_and_writers.R | 2 metacoder-0.3.7/metacoder/tests/testthat/test--taxmap_parsers.R | 6 62 files changed, 835 insertions(+), 424 deletions(-)
Title: A Traceability Focused Grammar of Clinical Data Summary
Description: A traceability focused tool created to simplify the data manipulation necessary to create clinical summaries.
Author: Eli Miller [aut] ,
Mike Stackhouse [aut, cre] ,
Ashley Tarasiewicz [aut],
Nathan Kosiba [ctb] ,
Sadchla Mascary [ctb],
Andrew Bates [ctb],
Shiyu Chen [ctb],
Oleksii Mikryukov [ctb],
Atorus Research LLC [cph]
Maintainer: Mike Stackhouse <mike.stackhouse@atorusresearch.com>
Diff between Tplyr versions 1.2.0 dated 2024-02-14 and 1.2.1 dated 2024-02-20
DESCRIPTION | 6 - MD5 | 45 +++++------ NAMESPACE | 1 NEWS.md | 3 R/count_bindings.R | 7 + R/meta-builders.R | 38 +++++++-- R/meta.R | 89 ++++++++++++++++++++++ R/meta_utils.R | 47 +++++++++--- inst/doc/Tplyr.html | 12 +-- inst/doc/custom-metadata.R | 10 ++ inst/doc/custom-metadata.Rmd | 15 +++ inst/doc/custom-metadata.html | 102 +++++++++++++++++--------- inst/doc/denom.html | 110 ++++++++++++++-------------- inst/doc/metadata.R | 27 ++++++ inst/doc/metadata.Rmd | 45 +++++++++++ inst/doc/metadata.html | 159 +++++++++++++++++++++++++++++++++++++++-- man/add_anti_join.Rd |only man/get_meta_subset.Rd | 4 + tests/testthat/_snaps/count.md | 6 + tests/testthat/_snaps/meta.md | 47 +++++++++++- tests/testthat/test-count.R | 19 ++-- tests/testthat/test-meta.R | 102 ++++++++++++++++++++++++++ vignettes/custom-metadata.Rmd | 15 +++ vignettes/metadata.Rmd | 45 +++++++++++ 24 files changed, 796 insertions(+), 158 deletions(-)
Title: 'REDCap' Data Management
Description: REDCap Data Management - REDCapDM is a comprehensive package that enables users to seamlessly handle data exported directly from REDCap or through API connections. This tool facilitates various functions, including data preprocessing, report generation for queries such as outliers or missing values, and tracking of identified queries. 'REDCap' (Research Electronic Data CAPture; <https://projectredcap.org>) is a web application developed at Vanderbilt University, designed for creating and managing online surveys and databases. The API connection provides users with the capability to programmatically access both data and project metadata, including the data dictionary, from the web.
Author: Joao Carmezim [aut, cre],
Pau Satorra [aut],
Judith Penafiel [aut],
Esther Garcia [aut],
Natalia Pallares [aut],
Cristian Tebe [aut]
Maintainer: Joao Carmezim <jcarmezim@igtp.cat>
Diff between REDCapDM versions 0.9.7 dated 2024-02-06 and 0.9.8 dated 2024-02-20
DESCRIPTION | 6 MD5 | 26 - NEWS.md | 10 R/rd_transform.R | 81 +++-- R/redcap_data.R | 52 ++- inst/doc/Data-reading-and-processing.Rmd | 5 inst/doc/Data-reading-and-processing.html | 18 - inst/doc/REDCapDM.R | 6 inst/doc/REDCapDM.Rmd | 24 + inst/doc/REDCapDM.html | 482 +++++++++++++++--------------- man/rd_transform.Rd | 7 man/redcap_data.Rd | 15 vignettes/Data-reading-and-processing.Rmd | 5 vignettes/REDCapDM.Rmd | 24 + 14 files changed, 448 insertions(+), 313 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre],
Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 10.5 dated 2024-01-10 and 10.6 dated 2024-02-20
DESCRIPTION | 8 MD5 | 50 ++--- R/Binary_ANOVA.R | 7 R/Copula.R | 2 R/Multivariate_Regression.R | 5 R/NNS_VAR.R | 5 R/Nowcast.R | 4 R/RcppExports.R | 4 README.md | 4 inst/doc/NNSvignette_Clustering_and_Regression.html | 76 ++++---- inst/doc/NNSvignette_Correlation_and_Dependence.R | 2 inst/doc/NNSvignette_Correlation_and_Dependence.Rmd | 2 inst/doc/NNSvignette_Correlation_and_Dependence.html | 4 inst/doc/NNSvignette_Forecasting.R | 2 inst/doc/NNSvignette_Forecasting.Rmd | 4 inst/doc/NNSvignette_Forecasting.html | 4 man/NNS.nowcast.Rd | 4 man/NNS_bin.Rd | 3 man/PM.matrix.Rd | 2 src/partial_moments.cpp | 164 ++++++------------- src/partial_moments_rcpp.cpp | 4 tests/testthat/Rplots.pdf |binary tests/testthat/test_Copula.R | 6 tests/testthat/test_Partial_Moments.R | 16 - vignettes/NNSvignette_Correlation_and_Dependence.Rmd | 2 vignettes/NNSvignette_Forecasting.Rmd | 4 26 files changed, 173 insertions(+), 215 deletions(-)
Title: A 'ggplot2' Implement of Venn Diagram
Description: Easy-to-use functions to generate 2-7 sets Venn or upset plot in publication quality.
'ggVennDiagram' plot Venn or upset using well-defined geometry dataset and 'ggplot2'. The shapes of 2-4 sets
Venn use circles and ellipses, while the shapes of 4-7 sets Venn use irregular polygons (4 has both forms), which
are developed and imported from another package 'venn', authored by Adrian Dusa. We provided internal functions to
integrate shape data with user provided sets data, and calculated the geometry of every regions/intersections
of them, then separately plot Venn in four components, set edges/labels, and region edges/labels.
From version 1.0, it is possible to customize these components as you demand in ordinary 'ggplot2' grammar.
From version 1.4.4, it supports unlimited number of sets, as it can draw a plain upset plot automatically when
number of sets is more than 7.
Author: Chun-Hui Gao [aut, cre] ,
Guangchuang Yu [ctb] ,
Adrian Dusa [aut, cph] ,
Turgut Yigit Akyol [ctb]
Maintainer: Chun-Hui Gao <gaospecial@gmail.com>
Diff between ggVennDiagram versions 1.5.0 dated 2024-01-13 and 1.5.2 dated 2024-02-20
DESCRIPTION | 9 +- MD5 | 38 ++++++----- NEWS.md | 13 +++ R/plot_shapes.R | 2 R/process_data.R | 18 +++-- R/regions.R | 5 - R/upset_plot.R | 102 +++++++++++++++++++++++------- README.md | 20 +++-- build/vignette.rds |binary inst/doc/VennCalculator.R |only inst/doc/VennCalculator.Rmd |only inst/doc/VennCalculator.html |only inst/doc/fully-customed.html | 2 inst/doc/using-ggVennDiagram.html | 4 - man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-13-1.png |binary man/figures/README-unnamed-chunk-14-1.png |binary man/plot_shapes.Rd | 10 +- man/process_upset_data.Rd | 12 ++- man/upset-plot.Rd | 27 +++++++ man/venn_data.Rd | 12 +++ vignettes/VennCalculator.Rmd |only 22 files changed, 206 insertions(+), 68 deletions(-)
Title: Fatty Acid Metabolic Analysis
Description: Fatty acid metabolic analysis aimed to the estimation of FA import (I), de novo synthesis (S), fractional contribution of the 13C-tracers (D0, D1, D2), elongation (E) and desaturation (Des) based on mass isotopologue data.
Author: Maribel Alcoriza-Balaguer [aut, cre],
Juan Carlos Garcia-Canaveras [ctb],
Agustin Lahoz [ths]
Maintainer: Maribel Alcoriza-Balaguer <maribel_alcoriza@iislafe.es>
Diff between FAMetA versions 0.1.5 dated 2023-01-11 and 0.1.6 dated 2024-02-20
FAMetA-0.1.5/FAMetA/inst/extdata |only FAMetA-0.1.6/FAMetA/DESCRIPTION | 10 FAMetA-0.1.6/FAMetA/MD5 | 29 FAMetA-0.1.6/FAMetA/R/FAMetA.R | 2 FAMetA-0.1.6/FAMetA/R/internal.R | 7 FAMetA-0.1.6/FAMetA/R/metabolicanalysis.R | 13 FAMetA-0.1.6/FAMetA/R/processing.R | 17 FAMetA-0.1.6/FAMetA/build/vignette.rds |binary FAMetA-0.1.6/FAMetA/data/desaturationsdb.rda |binary FAMetA-0.1.6/FAMetA/data/parameters.rda |binary FAMetA-0.1.6/FAMetA/inst/doc/vignette.R | 28 FAMetA-0.1.6/FAMetA/inst/doc/vignette.html | 804 +++++++++++++-------------- FAMetA-0.1.6/FAMetA/man/desaturationsdb.Rd | 2 FAMetA-0.1.6/FAMetA/man/parameters.Rd | 2 14 files changed, 461 insertions(+), 453 deletions(-)
Title: Ecological Inference by Linear Programming under Homogeneity
Description: Provides a bunch of algorithms based on linear programming for estimating, under
the homogeneity hypothesis, RxC ecological contingency tables (or vote transition matrices)
using mainly aggregate data (from voting units).
References:
Pavía and Romero (2022) <doi:10.1177/00491241221092725>.
Pavía (2023) <doi:10.1007/s43545-023-00658-y>.
Pavía and Romero (2024) <doi:10.1093/jrsssa/qnae013>.
Pavía (2024) A local convergent ecological inference algorithm for RxC tables.
Pavía and Penadés (2024). A bottom-up approach for ecological inference.
Romero, Pavía, Martín and Romero (2020) <doi:10.1080/02664763.2020.1804842>.
Acknowledgements:
The authors wish to thank Consellería de Educación, Universidades y Empleo, Generalitat Valenciana (grant AICO/2021/257) and Ministerio de Economía e Innovación (grant PID2021-128228NB-I00) for supporting this research.
Author: Jose M. Pavia [aut, cre] ,
Rafael Romero [aut]
Maintainer: Jose M. Pavia <jose.m.pavia@uv.es>
Diff between lphom versions 0.3.1-1 dated 2022-03-21 and 0.3.5-4 dated 2024-02-20
DESCRIPTION | 25 MD5 | 81 +- NAMESPACE | 1 NEWS.md |only R/auxiliar.R | 516 ++++++++++++++++- R/auxiliar_lp_apriori.R | 64 +- R/confidence_intervals_pjk.R | 8 R/error_lphom.R | 3 R/lclphom.R | 402 ++++++++----- R/lp_apriori.R | 190 +++--- R/lphom.R | 1211 +++++++++++++++++++++++++++++----------- R/lphom_dual.R | 4 R/lphom_joint.R | 12 R/nslphom.R | 310 ++++++---- R/nslphom_dual.R | 16 R/nslphom_joint.R | 24 R/plot.R | 10 R/print.R | 4 R/rslphom.R |only R/summary.R | 4 R/tslphom.R | 300 ++++++--- R/tslphom_dual.R | 10 R/tslphom_joint.R | 16 build/partial.rdb |binary inst/CITATION | 87 +- man/confidence_intervals_pjk.Rd | 3 man/error_lphom.Rd | 3 man/lclphom.Rd | 293 ++++++--- man/lp_apriori.Rd | 148 ++-- man/lphom.Rd | 236 +++++-- man/lphom_dual.Rd | 5 man/lphom_joint.Rd | 6 man/nslphom.Rd | 285 ++++++--- man/nslphom_dual.Rd | 17 man/nslphom_joint.Rd | 18 man/plot.lphom.Rd | 10 man/print.lphom.Rd | 4 man/print.summary.lphom.Rd | 2 man/rslphom.Rd |only man/summary.lphom.Rd | 4 man/tslphom.Rd | 269 +++++--- man/tslphom_dual.Rd | 11 man/tslphom_joint.Rd | 12 43 files changed, 3184 insertions(+), 1440 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-12-18 1.0.11
2023-11-05 1.0.10
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-02-07 1.1.3
2022-12-12 1.1.2
2022-11-07 1.1.1
2022-10-06 1.1.0
2022-06-01 1.0.3
2022-05-24 1.0.2
2022-05-19 1.0.1
2022-05-17 1.0.0
Title: Joint Model of Heterogeneous Repeated Measures and Survival Data
Description: Maximum likelihood estimation for the semi-parametric joint modeling of competing risks and longitudinal data in the presence of heterogeneous within-subject variability, proposed by Li and colleagues (2023) <arXiv:2301.06584>.
The proposed method models the within-subject variability of the biomarker and associates it with the risk of the competing risks event. The time-to-event data is modeled using a (cause-specific) Cox proportional hazards regression model with time-fixed covariates.
The longitudinal outcome is modeled using a mixed-effects location and scale model. The association is captured by shared random effects. The model
is estimated using an Expectation Maximization algorithm.
Author: Shanpeng Li [aut, cre],
Jin Zhou [ctb],
Hua Zhou [ctb],
Gang Li [ctb]
Maintainer: Shanpeng Li <lishanpeng0913@ucla.edu>
Diff between JMH versions 1.0.2 dated 2023-06-15 and 1.0.3 dated 2024-02-20
DESCRIPTION | 10 - MD5 | 95 ++++++++++-------- NAMESPACE | 3 R/AUCJMMLSM.R |only R/Diff.R | 28 +++++ R/DiffSF.R | 22 ++++ R/GetESFad.R |only R/GetEad.R |only R/GetGHmatrix.R | 52 +++++++++ R/Getinit.R | 148 ++++++++++++++-------------- R/JMH.R | 1 R/JMMLSM.R | 112 ++++++++++++++------- R/MAEQJMMLSM.R | 27 ++++- R/PEJMMLSM.R | 4 R/RcppExports.R | 28 +++++ R/bootsfitMESA.R |only R/bootsfitRI.R | 52 +++++++-- R/bootsfitRISF.R | 18 ++- R/bootsfitRIhomo.R |only R/getLoglike.R | 52 ++++++++- R/getLoglikeSF.R | 44 +++++++- R/logLik.R | 16 +++ R/print.JMMLSM.R | 81 ++++++++------- R/print.survfitJMMLSM.R | 2 R/simJMMESA.R |only R/simJMdataRI.R | 4 R/simJMdataRIhomo.R |only R/simfitMESA.R |only R/simfitRI.R | 49 ++++++--- R/simfitRIhomo.R |only R/summary.AUCJMMLSM.R |only R/summary.JMMLSM.R | 6 - R/survfitJMMLSM.R | 54 +++++++--- README.md | 224 +++++++++++++++++++++++++++++++++++++++++- man/AUCJMMLSM.Rd |only man/JMMLSM.Rd | 24 +++- man/MAEQJMMLSM.Rd | 12 +- man/PEJMMLSM.Rd | 6 - man/figures |only man/summary.AUCJMMLSM.Rd |only src/RcppExports.cpp | 248 +++++++++++++++++++++++++++++++++++++++++++---- src/basics.cpp | 10 + src/basics.h | 2 src/getCov.cpp | 12 +- src/getCovSF.cpp | 13 +- src/getEC.cpp | 4 src/getECIF.cpp | 104 +++++++++++++++++++ src/getECSF.cpp | 2 src/getECSFad.cpp |only src/getECad.cpp |only src/getES.cpp | 87 ++++++++++++++++ src/getMC.cpp | 2 src/getMCSF.cpp | 2 src/getloglikeC.cpp | 2 src/getloglikeCSF.cpp | 2 src/getloglikeCSFad.cpp |only src/getloglikeCad.cpp |only 57 files changed, 1359 insertions(+), 305 deletions(-)
Title: Build and Raytrace 3D Scenes
Description: Render scenes using pathtracing. Build 3D scenes out of spheres, cubes, planes, disks, triangles, cones, curves, line segments, cylinders, ellipsoids, and 3D models in the 'Wavefront' OBJ file format or the PLY Polygon File Format. Supports several material types, textures, multicore rendering, and tone-mapping. Based on the "Ray Tracing in One Weekend" book series. Peter Shirley (2018) <https://raytracing.github.io>.
Author: Tyler Morgan-Wall [aut, cph, cre]
,
Syoyo Fujita [ctb, cph],
Melissa O'Neill [ctb, cph],
Vilya Harvey [ctb, cph]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between rayrender versions 0.31.2 dated 2023-12-10 and 0.32.2 dated 2024-02-20
rayrender-0.31.2/rayrender/src/cone.cpp |only rayrender-0.31.2/rayrender/src/cone.h |only rayrender-0.32.2/rayrender/DESCRIPTION | 18 rayrender-0.32.2/rayrender/MD5 | 81 rayrender-0.32.2/rayrender/NAMESPACE | 15 rayrender-0.32.2/rayrender/R/RcppExports.R | 8 rayrender-0.32.2/rayrender/R/animate_objects.R | 26 rayrender-0.32.2/rayrender/R/csg_construct.R | 38 rayrender-0.32.2/rayrender/R/group_objects.R | 17 rayrender-0.32.2/rayrender/R/materials.R | 193 +- rayrender-0.32.2/rayrender/R/objects.R | 830 ++++------ rayrender-0.32.2/rayrender/R/post_process_scene.R | 3 rayrender-0.32.2/rayrender/R/prepare_scene_list.R | 279 +-- rayrender-0.32.2/rayrender/R/ray_animated_transform.R |only rayrender-0.32.2/rayrender/R/ray_material.R |only rayrender-0.32.2/rayrender/R/ray_scene.R |only rayrender-0.32.2/rayrender/R/ray_shape_info.R |only rayrender-0.32.2/rayrender/R/ray_transform.R |only rayrender-0.32.2/rayrender/R/render_animation.R | 5 rayrender-0.32.2/rayrender/R/render_scene.R | 5 rayrender-0.32.2/rayrender/R/scene_row.R | 2 rayrender-0.32.2/rayrender/R/zzz.R | 47 rayrender-0.32.2/rayrender/man/cylinder.Rd | 4 rayrender-0.32.2/rayrender/man/diffuse.Rd | 2 rayrender-0.32.2/rayrender/man/extruded_path.Rd | 70 rayrender-0.32.2/rayrender/man/glossy.Rd | 12 rayrender-0.32.2/rayrender/man/is_rendering_in_knitr.Rd |only rayrender-0.32.2/rayrender/man/light.Rd | 2 rayrender-0.32.2/rayrender/man/metal.Rd | 2 rayrender-0.32.2/rayrender/man/microfacet.Rd | 12 rayrender-0.32.2/rayrender/man/ray_animated_transform.Rd |only rayrender-0.32.2/rayrender/man/ray_material.Rd |only rayrender-0.32.2/rayrender/man/ray_scene.Rd |only rayrender-0.32.2/rayrender/man/ray_shape_info.Rd |only rayrender-0.32.2/rayrender/man/ray_transform.Rd |only rayrender-0.32.2/rayrender/man/raymesh_model.Rd | 4 rayrender-0.32.2/rayrender/man/render_animation.Rd | 2 rayrender-0.32.2/rayrender/src/RcppExports.cpp | 18 rayrender-0.32.2/rayrender/src/buildscene.cpp | 1227 ++++++--------- rayrender-0.32.2/rayrender/src/buildscene.h | 49 rayrender-0.32.2/rayrender/src/curve.h | 6 rayrender-0.32.2/rayrender/src/material.cpp | 4 rayrender-0.32.2/rayrender/src/material.h | 5 rayrender-0.32.2/rayrender/src/mesh3d.cpp | 4 rayrender-0.32.2/rayrender/src/mesh3d.h | 4 rayrender-0.32.2/rayrender/src/render_animation_rcpp.cpp | 127 - rayrender-0.32.2/rayrender/src/render_scene_rcpp.cpp | 77 rayrender-0.32.2/rayrender/src/trianglemesh.cpp | 102 - 48 files changed, 1540 insertions(+), 1760 deletions(-)
Title: Geostatistical Analysis and Design of Optimal Spatial Sampling
Networks
Description: Estimation of the variogram through trimmed mean, radial basis
functions (optimization, prediction and cross-validation), summary
statistics from cross-validation, pocket plot, and design of
optimal sampling networks through sequential and simultaneous
points methods.
Author: Carlos Melo <cmelo@udistrital.edu.co>, Ali Santacruz, Oscar
Melo <oomelom@unal.edu.co>
Maintainer: Ali Santacruz <amsantac@unal.edu.co>
Diff between geospt versions 1.0-3 dated 2023-10-10 and 1.0-4 dated 2024-02-20
geospt-1.0-3/geospt/R/network.design.r |only geospt-1.0-4/geospt/DESCRIPTION | 10 - geospt-1.0-4/geospt/MD5 | 30 ++-- geospt-1.0-4/geospt/NAMESPACE | 6 geospt-1.0-4/geospt/R/criteria.cv.R |only geospt-1.0-4/geospt/R/graph.idw.R |only geospt-1.0-4/geospt/R/graph.rbf.R | 109 ++++++++------ geospt-1.0-4/geospt/R/idw.cv.R |only geospt-1.0-4/geospt/R/network.design.R |only geospt-1.0-4/geospt/R/pocket.plot.R | 219 ++++++++++++++---------------- geospt-1.0-4/geospt/data/ariari.rda |only geospt-1.0-4/geospt/data/ariprec.rda |only geospt-1.0-4/geospt/inst/CITATION | 4 geospt-1.0-4/geospt/man/ariari.Rd |only geospt-1.0-4/geospt/man/ariprec.Rd |only geospt-1.0-4/geospt/man/criteria.cv.Rd |only geospt-1.0-4/geospt/man/geospt-package.Rd | 4 geospt-1.0-4/geospt/man/graph.idw.Rd |only geospt-1.0-4/geospt/man/graph.rbf.Rd | 2 geospt-1.0-4/geospt/man/idw.cv.Rd |only geospt-1.0-4/geospt/man/network.design.Rd | 47 +++--- geospt-1.0-4/geospt/man/pocket.plot.Rd | 8 - 22 files changed, 233 insertions(+), 206 deletions(-)
Title: Tools for Assessing Estimability of Linear Predictions
Description: Provides tools for determining estimability of linear functions
of regression coefficients, and 'epredict' methods that handle
non-estimable cases correctly. Estimability theory is discussed in
many linear-models textbooks including Chapter 3 of Monahan, JF (2008),
"A Primer on Linear Models", Chapman and Hall (ISBN 978-1-4200-6201-4).
Author: Russell Lenth [aut, cre, cph]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>
Diff between estimability versions 1.4.1 dated 2022-08-05 and 1.5 dated 2024-02-20
DESCRIPTION | 12 +++++++----- MD5 | 21 +++++++++++++-------- NAMESPACE | 1 + R/epredict.lm.R | 7 ++++--- R/estimability.R | 23 +++++++++++++++++++---- README.md | 1 - build |only inst/NEWS | 9 +++++++++ inst/doc |only man/epredict.lm.Rd | 21 ++++++++++++++++++--- man/nonest.basis.Rd | 12 +++++++++++- vignettes |only 12 files changed, 82 insertions(+), 25 deletions(-)
Title: Tools for Autoregressive Conditional Duration Models
Description: Package for Autoregressive Conditional Duration (ACD, Engle and Russell, 1998) models. Creates trade, price or volume durations from transactions (tic) data, performs diurnal adjustments, fits various ACD models and tests them.
Author: Markus Belfrage
Maintainer: Markus Belfrage <markus.belfrage@gmail.com>
Diff between ACDm versions 1.0.4.2 dated 2022-11-16 and 1.0.4.3 dated 2024-02-20
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/testRmACD.Rd | 12 ++++++------ 3 files changed, 12 insertions(+), 12 deletions(-)