Title: Agent Based Model Simulation Framework
Description: A high-performance, flexible and extensible framework to
develop continuous-time agent based models. Its high performance
allows it to simulate millions of agents efficiently. Agents are
defined by their states (arbitrary R lists). The events are handled in
chronological order. This avoids the multi-event interaction problem
in a time step of discrete-time simulations, and gives precise
outcomes. The states are modified by provided or user-defined events.
The framework provides a flexible and customizable implementation of
state transitions (either spontaneous or caused by agent
interactions), making the framework suitable to apply to epidemiology
and ecology, e.g., to model life history stages, competition and
cooperation, and disease and information spread. The agent
interactions are flexible and extensible. The framework provides
random mixing and network interactions, and supports multi-level
mixing patterns. It can be easily extended to other interactions such
as inter- and intra [...truncated...]
Author: Junling Ma [aut, cre]
Maintainer: Junling Ma <junlingm@uvic.ca>
Diff between ABM versions 0.4.2 dated 2025-01-14 and 0.4.3 dated 2025-01-25
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 5 +++++ R/Simulation.R | 8 +------- inst/include/RNG.h | 40 ++++++++++++++++++++++++++++++++++++++++ inst/include/Transition.h | 10 +++------- src/Agent.cpp | 5 ++--- src/Counter.cpp | 4 ++-- src/Population.cpp | 4 ++-- src/RNG.cpp | 9 +++++++++ src/Simulation.cpp | 7 ++++--- src/Transition.cpp | 5 ++--- 12 files changed, 85 insertions(+), 42 deletions(-)
Title: Detecting Influence Paths with Information Theory
Description: Traces information spread through interactions between features, utilising information theory measures and a higher-order generalisation of the concept of widest paths in graphs.
In particular, 'vistla' can be used to better understand the results of high-throughput biomedical experiments, by organising the effects of the investigated intervention in a tree-like hierarchy from direct to indirect ones, following the plausible information relay circuits.
Due to its higher-order nature, 'vistla' can handle multi-modality and assign multiple roles to a single feature.
Author: Miron B. Kursa [aut, cre]
Maintainer: Miron B. Kursa <m@mbq.me>
Diff between vistla versions 2.0.3 dated 2024-09-27 and 2.0.4 dated 2025-01-25
DESCRIPTION | 8 +++++--- MD5 | 15 ++++++++------- R/vistla.R | 1 + inst/CITATION |only inst/NEWS | 4 ++++ man/vistla.Rd | 2 ++ src/ensemble.h | 6 ++---- src/ingest.h | 5 +---- src/interface.h | 2 -- 9 files changed, 23 insertions(+), 20 deletions(-)
Title: Density-Based Spatial Clustering of Applications with Noise
(DBSCAN) and Related Algorithms
Description: A fast reimplementation of several density-based algorithms
of the DBSCAN family. Includes the clustering algorithms DBSCAN
(density-based spatial clustering of applications with noise) and
HDBSCAN (hierarchical DBSCAN), the ordering algorithm OPTICS (ordering
points to identify the clustering structure), shared nearest neighbor
clustering, and the outlier detection algorithms LOF (local outlier
factor) and GLOSH (global-local outlier score from hierarchies). The
implementations use the kd-tree data structure (from library ANN) for
faster k-nearest neighbor search. An R interface to fast kNN and
fixed-radius NN search is also provided. Hahsler, Piekenbrock and
Doran (2019) <doi:10.18637/jss.v091.i01>.
Author: Michael Hahsler [aut, cre, cph]
,
Matthew Piekenbrock [aut, cph],
Sunil Arya [ctb, cph],
David Mount [ctb, cph],
Claudia Malzer [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between dbscan versions 1.2.1 dated 2025-01-24 and 1.2.2 dated 2025-01-25
DESCRIPTION | 8 ++++---- MD5 | 38 +++++++++++++++++++------------------- NEWS.md | 5 +++++ R/RcppExports.R | 8 -------- inst/doc/dbscan.pdf |binary man/hdbscan.Rd | 11 ----------- src/JP.cpp | 1 + src/RcppExports.cpp | 25 ------------------------- src/UnionFind.h | 1 + src/connectedComps.cpp | 1 + src/dbcv.cpp | 15 +++++++++++++-- src/dendrogram.cpp | 2 +- src/hdbscan.cpp | 5 +++-- src/lof.cpp | 1 - src/mrd.cpp | 1 + src/mst.cpp | 1 - src/mst.h | 8 +++----- src/regionQuery.cpp | 1 - src/regionQuery.h | 1 + src/utilities.h | 7 ++++--- 20 files changed, 57 insertions(+), 83 deletions(-)
Title: Gene Locus Plot with Gene Annotations
Description: Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots <doi:10.1093/bioadv/vbaf006>.
Author: Myles Lewis [aut, cre]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between locuszoomr versions 0.3.5 dated 2024-09-15 and 0.3.6 dated 2025-01-25
DESCRIPTION | 8 MD5 | 45 ++--- NEWS.md | 4 R/genetrack_ly.R | 7 R/genetracks.R | 26 +- R/genetracks_grob.R | 18 -- R/gg_genetracks.R | 3 R/locus_ggplot.R | 4 R/locus_plot.R | 5 R/locus_plotly.R | 6 README.md | 35 +++ build/vignette.rds |binary inst/CITATION |only inst/doc/locuszoomr.R | 412 +++++++++++++++++++++++------------------------ inst/doc/locuszoomr.Rmd | 23 ++ inst/doc/locuszoomr.html | 52 +++-- man/genetrack_ly.Rd | 3 man/genetracks.Rd | 3 man/genetracks_grob.Rd | 3 man/gg_genetracks.Rd | 3 man/locus_ggplot.Rd | 3 man/locus_plot.Rd | 3 man/locus_plotly.Rd | 3 vignettes/locuszoomr.Rmd | 23 ++ 24 files changed, 414 insertions(+), 278 deletions(-)
Title: Estimation of the Structural Topic and Sentiment-Discourse Model
for Text Analysis
Description: The Structural Topic and Sentiment-Discourse (STS) model allows researchers to estimate topic models with document-level metadata that determines both topic prevalence and sentiment-discourse. The sentiment-discourse is modeled as a document-level latent variable for each topic that modulates the word frequency within a topic. These latent topic sentiment-discourse variables are controlled by the document-level metadata. The STS model can be useful for regression analysis with text data in addition to topic modeling’s traditional use of descriptive analysis. The method was developed in Chen and Mankad (2024) <doi:10.1287/mnsc.2022.00261>.
Author: Shawn Mankad [aut, cre],
Li Chen [aut]
Maintainer: Shawn Mankad <smankad@ncsu.edu>
Diff between sts versions 1.3 dated 2025-01-17 and 1.4 dated 2025-01-25
sts-1.3/sts/R/findRepresentativeDocs.STS.R |only sts-1.3/sts/R/printTopWords.STS.R |only sts-1.3/sts/man/findRepresentativeDocs.STS.Rd |only sts-1.3/sts/man/printTopWords.STS.Rd |only sts-1.4/sts/DESCRIPTION | 8 ++++---- sts-1.4/sts/MD5 | 18 ++++++++---------- sts-1.4/sts/NAMESPACE | 2 -- sts-1.4/sts/R/findRepresentativeDocs.R |only sts-1.4/sts/R/printTopWords.R |only sts-1.4/sts/inst/doc/vignette.pdf |binary sts-1.4/sts/man/findRepresentativeDocs.Rd | 22 ++++++++++++++++------ sts-1.4/sts/man/printTopWords.Rd | 22 +++++++++++++++------- sts-1.4/sts/vignettes/usingSTS.pdf |binary 13 files changed, 43 insertions(+), 29 deletions(-)
Title: Read Markdown Tables into Tibbles
Description: Efficient reading of raw markdown tables into tibbles. Designed to
accept content from strings, files, and URLs with the ability to extract
and read multiple tables from markdown for analysis.
Author: Jordan Bradford [aut, cre, cph]
Maintainer: Jordan Bradford <jrdnbradford@gmail.com>
Diff between readMDTable versions 0.3.0 dated 2025-01-07 and 0.3.1 dated 2025-01-25
DESCRIPTION | 7 ++++--- MD5 | 26 +++++++++++++------------- NEWS.md | 7 +++++++ R/extract_md_tables.R | 29 ++++++++++++++++------------- R/match_md_tables.R | 8 +++++--- R/read_md_table.R | 2 +- R/read_md_table_content.R | 8 ++------ README.md | 5 +++-- inst/doc/rvest-benchmarks.R | 16 ++++++++-------- inst/doc/rvest-benchmarks.Rmd | 16 ++++++++-------- inst/doc/rvest-benchmarks.html | 16 ++++++++-------- man/extract_md_tables.Rd | 29 ++++++++++++++++------------- tests/testthat/_snaps/read_md_table.md | 4 ++-- vignettes/rvest-benchmarks.Rmd | 16 ++++++++-------- 14 files changed, 101 insertions(+), 88 deletions(-)
Title: Read, Write and Edit xlsx Files
Description: Simplifies the creation of Excel .xlsx files by providing a
high level interface to writing, styling and editing worksheets.
Through the use of 'Rcpp', read/write times are comparable to the
'xlsx' and 'XLConnect' packages with the added benefit of removing the
dependency on Java.
Author: Philipp Schauberger [aut],
Alexander Walker [aut],
Luca Braglia [ctb],
Joshua Sturm [ctb],
Jan Marvin Garbuszus [ctb, cre],
Jordan Mark Barbone [ctb] ,
David Zimmermann [ctb],
Reinhold Kainhofer [ctb]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx versions 4.2.7.1 dated 2024-09-20 and 4.2.8 dated 2025-01-25
DESCRIPTION | 8 LICENSE | 2 MD5 | 33 - NEWS.md | 15 R/helperFunctions.R | 2 R/wrappers.R | 71 +- README.md | 48 + build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/Formatting.R | 526 ++++++++-------- inst/doc/Formatting.html | 9 inst/doc/Introduction.R | 778 ++++++++++++------------- inst/doc/Introduction.html | 9 inst/extdata/silent_worksheet_entries.xlsx |only man/figures/logo.png |only man/getCreators.Rd | 3 man/setLastModifiedBy.Rd | 2 tests/testthat/test-silent_worksheet_entries.R |only tests/testthat/test-wrappers.R | 147 ++++ 19 files changed, 912 insertions(+), 742 deletions(-)
Title: Joint Modeling of Traditional and Environmental DNA Survey Data
in a Bayesian Framework
Description: Models integrate environmental DNA (eDNA) detection data and traditional survey data to jointly estimate species catch rate (see package vignette: <https://ednajoint.netlify.app/>). Models can be used with count data via traditional survey methods (i.e., trapping, electrofishing, visual) and replicated eDNA detection/nondetection data via polymerase chain reaction (i.e., PCR or qPCR) from multiple survey locations. Estimated parameters include probability of a false positive eDNA detection, a site-level covariates that scale the sensitivity of eDNA surveys relative to traditional surveys, and catchability coefficients for traditional gear types. Models are implemented with a Bayesian framework (Markov chain Monte Carlo) using the 'Stan' probabilistic programming language.
Author: Abigail G. Keller [aut, cre],
Ryan P. Kelly [ctb],
Chitra M. Saraswati [rev],
Saras M. Windecker [rev]
Maintainer: Abigail G. Keller <agkeller@berkeley.edu>
Diff between eDNAjoint versions 0.3 dated 2025-01-17 and 0.3.1 dated 2025-01-25
DESCRIPTION | 8 MD5 | 26 +- R/stanmodels.R | 17 - R/utils-joint.R | 9 data/goby_data.rda |binary inst/stan/joint_continuous.stan | 3 inst/stan/joint_count.stan | 4 inst/stan/traditional_continuous.stan | 3 inst/stan/traditional_count.stan | 3 src/stanExports_joint_continuous.h | 288 +++++++++++++++---------------- src/stanExports_joint_count.h | 286 +++++++++++++++--------------- src/stanExports_traditional_continuous.h | 184 +++++++++---------- src/stanExports_traditional_count.h | 186 ++++++++++---------- tests/testthat/test-joint_model.R | 9 14 files changed, 505 insertions(+), 521 deletions(-)
Title: General Bivariate Copula Theory and Many Utility Functions
Description: Extensive functions for bivariate copula (bicopula) computations and related operations
for bicopula theory. The lower, upper, product, and select other bicopula are implemented along
with operations including the diagonal, survival copula, dual of a copula, co-copula, and
numerical bicopula density. Level sets, horizontal and vertical sections are supported. Numerical
derivatives and inverses of a bicopula are provided through which simulation is implemented.
Bicopula composition, convex combination, asymmetry extension, and products also are provided.
Support extends to the Kendall Function as well as the Lmoments thereof. Kendall Tau,
Spearman Rho and Footrule, Gini Gamma, Blomqvist Beta, Hoeffding Phi, Schweizer-
Wolff Sigma, tail dependency, tail order, skewness, and bivariate Lmoments are implemented, and
positive/negative quadrant dependency, left (right) increasing (decreasing) are available.
Other features include Kullback-Leibler Divergence, Vuong Procedure, spectral measure, [...truncated...]
Author: William Asquith [aut, cre]
Maintainer: William Asquith <william.asquith@ttu.edu>
Diff between copBasic versions 2.2.6 dated 2024-10-08 and 2.2.7 dated 2025-01-25
DESCRIPTION | 8 +-- MD5 | 70 +++++++++++++++--------------- NAMESPACE | 4 + NEWS | 29 +++++++++++- R/FRcop.R |only R/ORDSUMcop.R | 3 - R/ORDSUWcop.R | 4 - R/RAYcop.R | 5 ++ R/composite1COP.R | 38 ++++++++++++++++ R/composite2COP.R | 17 ++++++- R/kfuncCOP.R | 17 +++---- inst/OtherTest.R | 1 man/AMHcop.Rd | 16 +++--- man/COP.Rd | 83 +++++++++++++++++++----------------- man/EuvCOP.Rd | 1 man/EvuCOP.Rd | 1 man/FRcop.Rd |only man/JOcopB5.Rd | 16 ++++-- man/LzCOPpermsym.Rd | 5 +- man/ORDSUWcop.Rd | 8 +-- man/PLACKETTsim.Rd | 2 man/RAYcop.Rd | 24 +++++----- man/RFcop.Rd | 23 +++++----- man/aicCOP.Rd | 24 ++++------ man/asCOP.Rd | 110 ++++++++++++++++++++++++------------------------ man/composite1COP.Rd | 73 ++++++++++++++++++++++--------- man/composite2COP.Rd | 63 ++++++++++++++------------- man/copBasic-package.Rd | 40 ++++++++++------- man/densityCOP.Rd | 54 +++++++++++------------ man/densityCOPplot.Rd | 90 +++++++++++++++++++-------------------- man/jointCOP.Rd | 19 +++----- man/kfuncCOP.Rd | 25 +++++----- man/rhoCOP.Rd | 99 ++++++++++++++++++++++--------------------- man/semicorCOP.Rd | 2 man/simCOPmicro.Rd | 3 - man/tEVcop.Rd | 102 ++++++++++++++++++++++---------------------- man/wolfCOP.Rd | 82 +++++++++++++++++------------------ 37 files changed, 658 insertions(+), 503 deletions(-)
Title: Download Air Quality and Meteorological Information of Chile
Description: Download air quality and meteorological information of Chile from the National Air Quality System (S.I.N.C.A.)<https://sinca.mma.gob.cl/> dependent on the Ministry of the Environment and the Meteorological Directorate of Chile (D.M.C.)<https://www.meteochile.gob.cl/> dependent on the Directorate General of Civil Aeronautics.
Author: Francisco Catalan Meyer [aut, cre]
,
Manuel Leiva [aut] ,
Richard Toro [aut]
Maintainer: Francisco Catalan Meyer <francisco.catalan@ug.uchile.cl>
Diff between AtmChile versions 1.0.2 dated 2024-12-09 and 1.0.3 dated 2025-01-25
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/ChileAirQuality.R | 2 +- README.md | 12 +++++------- 4 files changed, 12 insertions(+), 14 deletions(-)
Title: 'Rcpp' Bindings for the Boost Date_Time Library
Description: Access to Boost Date_Time functionality for dates,
durations (both for days and date time objects), time zones, and
posix time ('ptime') is provided by using 'Rcpp modules'. The
posix time implementation can support high-resolution of up to
nano-second precision by using 96 bits (instead of 64 with R)
to present a 'ptime' object (but this needs recompilation with
a #define set).
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppBDT versions 0.2.6 dated 2022-10-30 and 0.2.7 dated 2025-01-25
RcppBDT-0.2.6/RcppBDT/demo/toPOSIXctTiming.R |only RcppBDT-0.2.7/RcppBDT/ChangeLog | 39 +++++++++++++++++++++++++++ RcppBDT-0.2.7/RcppBDT/DESCRIPTION | 19 ++++++++----- RcppBDT-0.2.7/RcppBDT/MD5 | 22 +++++++-------- RcppBDT-0.2.7/RcppBDT/R/RcppExports.R | 2 - RcppBDT-0.2.7/RcppBDT/README.md | 1 RcppBDT-0.2.7/RcppBDT/demo/00Index | 1 RcppBDT-0.2.7/RcppBDT/inst/NEWS.Rd | 10 ++++++ RcppBDT-0.2.7/RcppBDT/inst/examples |only RcppBDT-0.2.7/RcppBDT/man/cToPOSIXct.Rd | 2 - RcppBDT-0.2.7/RcppBDT/src/Makevars | 1 RcppBDT-0.2.7/RcppBDT/src/Makevars.win | 1 RcppBDT-0.2.7/RcppBDT/src/toPOSIXct.cpp | 2 - 13 files changed, 76 insertions(+), 24 deletions(-)
Title: Creating and Working with Pedigrees and Marker Data
Description: A comprehensive collection of tools for creating,
manipulating and visualising pedigrees and genetic marker data.
Pedigrees can be read from text files or created on the fly with
built-in functions. A range of utilities enable modifications like
adding or removing individuals, breaking loops, and merging pedigrees.
An online tool for creating pedigrees interactively, based on
'pedtools', is available at <https://magnusdv.shinyapps.io/quickped>.
'pedtools' is the hub of the 'pedsuite', a collection of packages for
pedigree analysis. A detailed presentation of the 'pedsuite' is given
in the book 'Pedigree Analysis in R' (Vigeland, 2021,
ISBN:9780128244302).
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between pedtools versions 2.7.1 dated 2024-09-08 and 2.8.0 dated 2025-01-25
DESCRIPTION | 8 - MD5 | 47 +++---- NAMESPACE | 4 NEWS.md | 26 ++++ R/marker_genomatrix.R | 42 ++++-- R/marker_locusattributes.R | 30 +++- R/marker_utils.R | 66 ++++++++++ R/ped_loops.R | 226 ++++++++++++++++++++++++++---------- R/ped_plot.R | 3 R/ped_subgroups.R | 188 ++++++++++++++++++++++------- R/plot_methods.R | 32 +++-- R/utils.R | 5 build/vignette.rds |binary inst/doc/pedtools.R | 4 inst/doc/pedtools.Rmd | 5 inst/doc/pedtools.html | 27 ++-- man/getGenotypes.Rd | 17 +- man/harmoniseMarkers.Rd |only man/inbreedingLoops.Rd | 60 ++++----- man/locusAttributes.Rd | 12 + man/ped_subgroups.Rd | 25 ++- man/plot.ped.Rd | 3 man/plotmethods.Rd | 7 - tests/testthat/test-ped-relatives.R | 6 vignettes/pedtools.Rmd | 5 25 files changed, 606 insertions(+), 242 deletions(-)
Title: Exploring and Testing the Toolchain and System Libraries
Description: Helper functions that interface with the system utilities to learn
about the local build environment. Lets you explore 'make' rules to test the
local configuration, or query 'pkg-config' to find compiler flags and libs
needed for building packages with external dependencies. Also contains tools
to analyze which libraries that a installed R package linked to by inspecting
output from 'ldd' in combination with information from your distribution
package manager, e.g. 'rpm' or 'dpkg'.
Author: Jeroen Ooms [aut, cre, cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between maketools versions 1.3.1 dated 2024-10-04 and 1.3.2 dated 2025-01-25
DESCRIPTION | 6 +++--- MD5 | 6 +++--- build/vignette.rds |binary tests/testthat/test-sysdeps.R | 13 +++++-------- 4 files changed, 11 insertions(+), 14 deletions(-)
Title: Generate Citation File Format ('cff') Metadata for R Packages
Description: The Citation File Format version 1.2.0
<doi:10.5281/zenodo.5171937> is a human and machine readable file
format which provides citation metadata for software. This package
provides core utilities to generate and validate this metadata.
Author: Diego Hernangomez [aut, cre, cph]
,
Joao Martins [rev] ,
Scott Chamberlain [rev]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between cffr versions 1.1.1 dated 2024-08-16 and 1.2.0 dated 2025-01-25
DESCRIPTION | 9 MD5 | 61 +- NEWS.md | 11 R/cff_write.R | 39 + R/utils-alerts.R | 2 R/utils-cff_read.R | 757 +++++++++++++++++----------------- README.md | 184 ++++---- build/partial.rdb |binary build/vignette.rds |binary data/cran_to_spdx.rda |binary inst/WORDLIST | 6 inst/doc/cffr.R | 10 inst/doc/cffr.html | 8 inst/doc/crosswalk.R | 28 - inst/doc/crosswalk.Rmd | 21 inst/doc/crosswalk.html | 742 ++++++++++++++------------------- inst/examples/DESCRIPTION_codeberg |only inst/schemaorg.json | 4 man/cff_class.Rd | 4 man/cff_write.Rd | 6 tests/testthat/_snaps/as_cff.md | 4 tests/testthat/_snaps/cff_create.md | 2 tests/testthat/_snaps/cff_read.md | 1 tests/testthat/_snaps/methods.md | 29 - tests/testthat/_snaps/mock-package.md | 40 + tests/testthat/_snaps/utils-create.md | 63 ++ tests/testthat/test-as_cff.R | 326 +++++++------- tests/testthat/test-cff_create.R | 5 tests/testthat/test-methods.R | 26 - tests/testthat/test-mock-package.R | 218 ++++++--- tests/testthat/test-utils-create.R | 76 +-- vignettes/crosswalk.Rmd | 21 32 files changed, 1404 insertions(+), 1299 deletions(-)
Title: Database for Developing Transitivity Methodology in Network
Meta-Analysis
Description: Functions to access the database of 217 data-frames with aggregate
study-level characteristics (that may act as effect modifiers) extracted
from published systematic reviews with network meta-analysis. The database shall
only be used for developing and appraising the methodology to assess
the transitivity assumption quantitatively.
Author: Loukia Spineli [aut, cre]
Maintainer: Loukia Spineli <Spineli.Loukia@mh-hannover.de>
Diff between tracenma versions 0.1.0 dated 2024-03-29 and 0.1.1 dated 2025-01-25
DESCRIPTION | 12 +- MD5 | 190 ++++++++++++++++++++-------------------- NEWS.md | 5 + R/dataset.R | 35 +++---- R/get.dataset.index_function.R | 20 +--- R/get.dataset_function.R | 20 ---- R/globals.R | 2 R/tracenma.R | 26 ++--- data/index.RData |binary inst/extdata/17018227_Chars.rds |binary inst/extdata/17651658_Chars.rds |binary inst/extdata/18482285.rds |binary inst/extdata/18482285_Chars.rds |binary inst/extdata/19144173.rds |binary inst/extdata/19144173_Chars.rds |binary inst/extdata/19604457_Chars.rds |binary inst/extdata/19637942.rds |binary inst/extdata/19637942_Chars.rds |binary inst/extdata/20825624_Chars.rds |binary inst/extdata/20847017_Chars.rds |binary inst/extdata/21123111.rds |binary inst/extdata/21182357.rds |binary inst/extdata/21182357_Chars.rds |binary inst/extdata/21697997.rds |binary inst/extdata/21697997_Chars.rds |binary inst/extdata/21831256.rds |binary inst/extdata/21831256_Chars.rds |binary inst/extdata/21943363_Chars.rds |binary inst/extdata/22044854.rds |binary inst/extdata/22044854_Chars.rds |binary inst/extdata/22142554_Chars.rds |binary inst/extdata/22151924_Chars.rds |binary inst/extdata/22340890_Chars.rds |binary inst/extdata/22418856.rds |binary inst/extdata/22443154.rds |binary inst/extdata/22462530_Chars.rds |binary inst/extdata/22486990_Chars.rds |binary inst/extdata/22592688.rds |binary inst/extdata/22700784_Chars.rds |binary inst/extdata/22732017.rds |binary inst/extdata/22732017_Chars.rds |binary inst/extdata/22776828_Chars.rds |binary inst/extdata/23042705.rds |binary inst/extdata/23042705_Chars.rds |binary inst/extdata/23057701_Chars.rds |binary inst/extdata/23150473.rds |binary inst/extdata/23150473_Chars.rds |binary inst/extdata/23205332.rds |binary inst/extdata/23351090_Chars.rds |binary inst/extdata/23442134.rds |binary inst/extdata/23442134_Chars.rds |binary inst/extdata/23538193_Chars.rds |binary inst/extdata/23550994.rds |binary inst/extdata/23550994_Chars.rds |binary inst/extdata/23686477.rds |binary inst/extdata/23686477_Chars.rds |binary inst/extdata/23870607.rds |binary inst/extdata/23870607_Chars.rds |binary inst/extdata/23919914_Chars.rds |binary inst/extdata/23971722.rds |binary inst/extdata/23971722_Chars.rds |binary inst/extdata/23975736.rds |binary inst/extdata/23975736_Chars.rds |binary inst/extdata/24009224.rds |binary inst/extdata/24009224_Chars.rds |binary inst/extdata/24131260.rds |binary inst/extdata/24166666.rds |binary inst/extdata/24176098.rds |binary inst/extdata/24176098_Chars.rds |binary inst/extdata/24671923_Chars.rds |binary inst/extdata/24749763.rds |binary inst/extdata/24749763_Chars.rds |binary inst/extdata/24969003_Chars.rds |binary inst/extdata/24989022.rds |binary inst/extdata/24989022_Chars.rds |binary inst/extdata/25114521_Chars.rds |binary inst/extdata/25184309_Chars.rds |binary inst/extdata/25226478_Chars.rds |binary inst/extdata/25249164.rds |binary inst/extdata/25249164_Chars.rds |binary inst/extdata/25286060_Chars.rds |binary inst/extdata/25361361.rds |binary inst/extdata/25361361_Chars.rds |binary inst/extdata/25375397.rds |binary inst/extdata/25375397_Chars.rds |binary inst/extdata/25555272_Chars.rds |binary inst/extdata/25583895.rds |binary inst/extdata/25583895_Chars.rds |binary inst/extdata/25760991.rds |binary inst/extdata/25760991_Chars.rds |binary inst/extdata/25793900.rds |binary inst/extdata/25793900_Chars.rds |binary man/get.dataset.Rd | 120 ++++++++++--------------- man/get.dataset.index.Rd | 21 +--- man/index.Rd | 36 +++---- man/tracenma-package.Rd | 26 ++--- 96 files changed, 232 insertions(+), 281 deletions(-)
Title: 3D Prioritization Algorithm
Description: Three-dimensional systematic conservation planning, conducting
nested prioritization analyses across multiple depth levels and
ensuring efficient resource allocation throughout the water column.
It provides a structured workflow designed to address biodiversity
conservation and management challenges in the 3 dimensions, while
facilitating users’ choices and parameterization (Doxa et al. 2025
<doi:10.1016/j.ecolmodel.2024.110919>).
Author: Aggeliki Doxa [aut] ,
Christos Adam [aut, cre] ,
Nikolaos Nagkoulis [aut] ,
Antonios D. Mazaris [aut] ,
Stelios Katsanevakis [aut]
Maintainer: Christos Adam <econp266@econ.soc.uoc.gr>
Diff between prior3D versions 0.1.3 dated 2024-11-15 and 0.1.5 dated 2025-01-25
DESCRIPTION | 15 ++++++++------- MD5 | 14 +++++++------- NEWS.md | 16 ++++++++++++++++ README.md | 16 ++++++++-------- inst/CITATION | 2 +- inst/doc/Introduction.Rmd | 10 +++++----- inst/doc/Introduction.html | 10 +++++----- vignettes/Introduction.Rmd | 10 +++++----- 8 files changed, 55 insertions(+), 38 deletions(-)
More information about serocalculator at CRAN
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Title: Likelihood-Based Confidence Interval in Structural Equation
Models
Description: Forms likelihood-based confidence intervals
(LBCIs) for parameters in structural equation modeling,
introduced in Cheung and Pesigan (2023)
<doi:10.1080/10705511.2023.2183860>. Currently
implements the algorithm illustrated by Pek and Wu
(2018) <doi:10.1037/met0000163>, and supports the robust
LBCI proposed by Falk (2018)
<doi:10.1080/10705511.2017.1367254>.
Author: Shu Fai Cheung [aut, cre] ,
Ivan Jacob Agaloos Pesigan [ctb]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between semlbci versions 0.11.2 dated 2024-06-06 and 0.11.3 dated 2025-01-25
DESCRIPTION | 8 MD5 | 27 - NAMESPACE | 5 NEWS.md | 19 + R/loglike_at.R | 11 R/loglike_at_user.R | 452 +++++++++++++++++++++++- README.md | 2 build/partial.rdb |binary build/vignette.rds |binary man/ci_bound_ur.Rd | 2 man/ci_bound_ur_i.Rd | 2 man/ci_bound_wn_i.Rd | 2 man/loglikelihood.Rd | 97 +++++ tests/testthat/test-ci_bound_wn_i_mg_ustd_sem.R | 4 tests/testthat/test-plot_likelihood_ur.R |only 15 files changed, 604 insertions(+), 27 deletions(-)
Title: Mediation, Moderation and Moderated-Mediation After Model
Fitting
Description: Computes indirect effects, conditional effects, and conditional
indirect effects in a structural equation model or path model after model
fitting, with no need to define any user parameters or label any paths in
the model syntax, using the approach presented in Cheung and Cheung
(2024) <doi:10.3758/s13428-023-02224-z>. Can also form bootstrap
confidence intervals by doing bootstrapping only once and reusing the
bootstrap estimates in all subsequent computations. Supports bootstrap
confidence intervals for standardized (partially or completely) indirect
effects, conditional effects, and conditional indirect effects as described
in Cheung (2009) <doi:10.3758/BRM.41.2.425> and Cheung, Cheung, Lau, Hui,
and Vong (2022) <doi:10.1037/hea0001188>. Model fitting can be done by
structural equation modeling using lavaan() or regression using lm().
Author: Shu Fai Cheung [aut, cre] ,
Sing-Hang Cheung [aut]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between manymome versions 0.2.5 dated 2024-12-08 and 0.2.7 dated 2025-01-25
DESCRIPTION | 8 MD5 | 108 ++-- NAMESPACE | 5 NEWS.md | 35 + R/print_indirect_list.R | 9 R/pseudo_jn.r | 2 R/q_functions_helpers.R |only R/q_mediation.R |only R/summary_lm_list.R | 266 +++++++++- README.md | 18 inst/CITATION | 6 inst/doc/do_boot.Rmd | 19 inst/doc/do_boot.html | 10 inst/doc/do_mc.Rmd | 18 inst/doc/do_mc.html | 10 inst/doc/do_mc_lavaan_mi.Rmd | 19 inst/doc/do_mc_lavaan_mi.html | 10 inst/doc/manymome.Rmd | 19 inst/doc/manymome.html | 10 inst/doc/med_lav.Rmd | 18 inst/doc/med_lav.html | 10 inst/doc/med_lm.Rmd | 18 inst/doc/med_lm.html | 10 inst/doc/mod_levels.Rmd | 18 inst/doc/mod_levels.html | 10 inst/doc/mome_lm.Rmd | 18 inst/doc/mome_lm.html | 10 man/manymome-package.Rd | 2 man/pseudo_johnson_neyman.Rd | 2 man/q_mediation.Rd |only man/summary.lm_list.Rd | 31 + tests/testthat/test_q_fct_mediation.R |only tests/testthat/test_q_fct_mediation_helpers.R |only tests/testthat/test_summary_lm_list.R | 47 + vignettes/articles/get_prod.Rmd | 18 vignettes/articles/manymome_cond_indirect_and_friends_workflow.Rmd | 18 vignettes/articles/manymome_do_boot_workflow.Rmd | 18 vignettes/articles/manymome_do_mc_workflow.Rmd | 2 vignettes/articles/manymome_draw_q_parallel-1.png |only vignettes/articles/manymome_draw_q_serial-1.png |only vignettes/articles/manymome_draw_q_simple-1.png |only vignettes/articles/med_mg.Rmd | 5 vignettes/articles/med_mg.Rmd.original | 2 vignettes/articles/q_mediation.Rmd |only vignettes/articles/q_mediation.Rmd.original |only vignettes/do_boot.Rmd | 19 vignettes/do_boot.Rmd.original | 17 vignettes/do_mc.Rmd | 18 vignettes/do_mc.Rmd.original | 18 vignettes/do_mc_lavaan_mi.Rmd | 19 vignettes/do_mc_lavaan_mi.Rmd.original | 17 vignettes/manymome.Rmd | 19 vignettes/manymome.Rmd.original | 17 vignettes/med_lav.Rmd | 18 vignettes/med_lav.Rmd.original | 18 vignettes/med_lm.Rmd | 18 vignettes/med_lm.Rmd.original | 18 vignettes/mod_levels.Rmd | 18 vignettes/mome_lm.Rmd | 18 vignettes/mome_lm.Rmd.original | 18 60 files changed, 802 insertions(+), 297 deletions(-)
Title: Simple Presentation of Estimated Exponential Semi-Variograms
Description: User friendly interface based on the R package 'gstat' to fit
exponential parametric models to empirical semi-variograms in order to
model the spatial correlation structure of health data. Geo-located
health outcomes of survey participants may be used to model spatial
effects on health in an ego-centred approach. The package contains a
range of functions to help explore the spatial structure of the data
as well as visualize the fit of exponential models for various
metaparameter combinations with respect to the number of lag intervals
and maximal distance. Furthermore, the outcome of interest can be
adjusted for covariates by fitting a linear regression in a
preliminary step before the semi-variogram fitting process.
Author: Julia Dyck [aut, cre],
Odile Sauzet [aut],
Jan-Ole Koslik [aut]
Maintainer: Julia Dyck <j.dyck@uni-bielefeld.de>
Diff between EgoCor versions 1.3.0 dated 2025-01-20 and 1.3.2 dated 2025-01-25
DESCRIPTION | 6 - MD5 | 28 +++--- R/par.uncertainty.function.R | 12 +- R/sv.sep.R | 8 + R/vario.mod.function.gstat.R | 5 - build/partial.rdb |binary inst/doc/Intro_to_EgoCor.R | 11 +- inst/doc/Intro_to_EgoCor.Rmd | 11 +- inst/doc/Intro_to_EgoCor.html | 93 +++++++++++----------- man/par.uncertainty.Rd | 6 - tests/testthat/test-one_resample_analysis_check.R | 4 tests/testthat/test-par.uncertainty.function.R | 26 +++--- tests/testthat/test-sv.sep.R | 4 tests/testthat/test-vario.mod.function.gstat.R | 21 ++-- vignettes/Intro_to_EgoCor.Rmd | 11 +- 15 files changed, 140 insertions(+), 106 deletions(-)
Title: Comprehensive Batch Effect Diagnostics and Harmonization
Description: Provides a comprehensive framework for batch effect diagnostics, harmonization, and post-harmonization downstream analysis. Features include interactive visualization tools, robust statistical tests, and a range of harmonization techniques. Additionally, 'ComBatFamQC' enables the creation of life-span age trend plots with estimated age-adjusted centiles and facilitates the generation of covariate-corrected residuals for analytical purposes. Methods for harmonization are based on approaches described in Johnson et al., (2007) <doi:10.1093/biostatistics/kxj037>, Beer et al., (2020) <doi:10.1016/j.neuroimage.2020.117129>, Pomponio et al., (2020) <doi:10.1016/j.neuroimage.2019.116450>, and Chen et al., (2021) <doi:10.1002/hbm.25688>.
Author: Zheng Ren [aut, cre, cph] ,
Andrew Chen [aut, cph] ,
Elizabeth Horwath [ctb]
Maintainer: Zheng Ren <zren1422@gmail.com>
Diff between ComBatFamQC versions 1.0.2 dated 2025-01-20 and 1.0.4 dated 2025-01-25
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS.md | 12 ++++++++++++ R/Help_Func.R | 6 +++++- R/age_shiny.R | 11 ++++++++--- R/comfam_shiny.R | 2 +- man/age_list_gen.Rd | 8 +++++--- tests/testthat/test-age_shiny.R | 3 ++- tests/testthat/test-comfam_shiny.R | 3 ++- tests/testthat/test-help_function.R | 6 ++++-- 10 files changed, 53 insertions(+), 26 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-01-10 3.2.0
2022-11-25 3.0.0
2022-02-11 2.8.2