Title: Tools for Case 2 Best-Worst Scaling
Description: Provides three basic functions that support an implementation of Case 2 (profile case) best-worst scaling. The first is to convert an orthogonal main-effect design into questions, the second is to create a dataset suitable for analysis, and the third is to calculate count-based scores. For details, see Aizaki and Fogarty (2019) <doi:10.1016/j.jocm.2019.100171>.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>
Diff between support.BWS2 versions 0.3-1 dated 2021-11-23 and 0.4-0 dated 2022-05-23
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 3 +++ R/bws2.dataset.marginal.R | 4 ++++ R/bws2.dataset.paired.R | 4 ++++ inst/CITATION | 8 ++++---- 6 files changed, 24 insertions(+), 13 deletions(-)
Title: Pre-Process DNA Copy Number (CN) Data for Detection of CN Events
Description: DNA copy number data evaluation using both their initial form
(copy number as a noisy function of genomic position) and their
approximation by a piecewise-constant function (segmentation),
for the purpose of identifying genomic regions where the copy number
differs from the norm.
Author: Alex Krasnitz, Guoli Sun
Maintainer: Guoli Sun <guolisun87@gmail.com>
Diff between CNprep versions 2.0 dated 2014-12-31 and 2.2 dated 2022-05-23
DESCRIPTION | 18 +++++++++++------- MD5 | 4 ++-- NAMESPACE | 5 +++-- 3 files changed, 16 insertions(+), 11 deletions(-)
Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for
the complete machine learning life cycle, see <https://mlflow.org/>.
This package supports installing 'MLflow', tracking experiments,
creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre],
Javier Luraschi [aut],
Kevin Kuo [aut] ,
RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>
Diff between mlflow versions 1.25.1 dated 2022-04-20 and 1.26.0 dated 2022-05-23
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/python.R | 7 ++++++- R/tracking-server.R | 9 +++++++-- README.md | 4 ++-- man/mlflow_server.Rd | 2 +- tests/testthat/test-keras-model.R | 2 +- 7 files changed, 26 insertions(+), 16 deletions(-)
Title: Cores of Recurrent Events
Description: Given a collection of intervals with integer start and end
positions, find recurrently targeted regions and estimate the significance
of finding. Randomization is implemented by parallel methods, either
using local host machines, or submitting grid engine jobs.
Author: Alex Krasnitz, Guoli Sun
Maintainer: Guoli Sun <guolisun87@gmail.com>
Diff between CORE versions 3.0 dated 2014-12-29 and 3.2 dated 2022-05-23
DESCRIPTION | 14 +-- MD5 | 6 - NAMESPACE | 5 - R/CORE.R | 276 ++++++++++++++++++++++++++++++------------------------------ 4 files changed, 153 insertions(+), 148 deletions(-)
Title: Circle Manhattan Plot
Description: Manhattan plot, a type of scatter plot, was widely used to display the association results. However, it is usually time-consuming and laborious for a non-specialist user to write scripts and adjust parameters of an elaborate plot. Moreover, the ever-growing traits measured have necessitated the integration of results from different Genome-wide association study researches. Circle Manhattan Plot is the first open R package that can lay out. Genome-wide association study P-value results in both traditional rectangular patterns, QQ-plot and novel circular ones. United in only one bull's eye style plot, association results from multiple traits can be compared interactively, thereby to reveal both similarities and differences between signals. Additional functions include: highlight signals, a group of SNPs, chromosome visualization and candidate genes around SNPs.
Author: LiLin-Yin
Maintainer: LiLin-Yin <ylilin@163.com>
Diff between CMplot versions 4.0.0 dated 2022-01-13 and 4.1.0 dated 2022-05-23
DESCRIPTION | 8 +- MD5 | 6 - R/CMplot.r | 182 ++++++++++++++++++++++++++------------------------ man/CMplot-package.Rd | 23 ++++-- 4 files changed, 118 insertions(+), 101 deletions(-)
Title: Non-Ordered Vectors
Description: Functionality for manipulating values of associative
maps. Ordinary R vectors are unsuitable for working with values of
associative maps because elements of an R vector may be accessed by
reference to their location in the vector, but associative maps are
stored in arbitrary order. However, when associating keys with
values one needs both parts to be in 1-1 correspondence, so one
cannot dispense with the order entirely. The 'disordR' package
includes a single S4 class, disord. This class allows one to
perform only those operations appropriate for manipulating values of
associative maps and prevents any other operation (such as accessing
an element at a particular location). A useful heuristic is that
one is only allowed to access or modify a disord object using a
python list comprehension. The idea is to prevent ill-defined
operations on values (or keys) of associative maps, whose order is
undefined or at best implementation-specific, while allowing and
facilitating sensible operations.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between disordR versions 0.0-9 dated 2021-12-09 and 0.0-9-1 dated 2022-05-23
disordR-0.0-9-1/disordR/DESCRIPTION | 13 disordR-0.0-9-1/disordR/MD5 | 37 - disordR-0.0-9-1/disordR/NAMESPACE | 2 disordR-0.0-9-1/disordR/NEWS.md | 5 disordR-0.0-9-1/disordR/R/disordR.R | 57 +- disordR-0.0-9-1/disordR/README.md | 35 + disordR-0.0-9-1/disordR/build/vignette.rds |binary disordR-0.0-9-1/disordR/inst/doc/disordR.R | 86 +++ disordR-0.0-9-1/disordR/inst/doc/disordR.Rmd | 292 ++++++++----- disordR-0.0-9-1/disordR/inst/doc/disordR.html | 491 +++++++++------------- disordR-0.0-9-1/disordR/man/arith.Rd | 8 disordR-0.0-9-1/disordR/man/disord-class.Rd | 2 disordR-0.0-9-1/disordR/man/disord.Rd | 30 - disordR-0.0-9-1/disordR/man/drop.Rd | 17 disordR-0.0-9-1/disordR/man/extract.Rd | 34 + disordR-0.0-9-1/disordR/man/misc.Rd | 9 disordR-0.0-9-1/disordR/man/rdis.Rd | 21 disordR-0.0-9-1/disordR/tests/testthat/test_aaa.R | 11 disordR-0.0-9-1/disordR/vignettes/disordR.Rmd | 292 ++++++++----- disordR-0.0-9/disordR/man/elements.Rd |only 20 files changed, 855 insertions(+), 587 deletions(-)
Title: Build Machine Learning Models Like Using Python's Scikit-Learn
Library in R
Description: The idea is to provide a standard interface
to users who use both R and Python for building machine learning models.
This package provides a scikit-learn's fit, predict interface to
train machine learning models in R.
Author: Manish Saraswat [aut, cre]
Maintainer: Manish Saraswat <manish06saraswat@gmail.com>
Diff between superml versions 0.5.4 dated 2022-05-12 and 0.5.5 dated 2022-05-23
DESCRIPTION | 6 MD5 | 16 NEWS.md | 4 inst/doc/Guide-to-CountVectorizer.html | 18 inst/doc/Guide-to-TfidfVectorizer.html | 32 - inst/doc/introduction.R | 78 +-- inst/doc/introduction.Rmd | 8 inst/doc/introduction.html | 767 +++++++-------------------------- vignettes/introduction.Rmd | 8 9 files changed, 259 insertions(+), 678 deletions(-)
Title: Short Asynchronous Time-Series Analysis
Description: A graphical and automated pipeline for the analysis
of short time-series in R ('santaR'). This approach is designed to accommodate asynchronous
time sampling (i.e. different time points for different individuals),
inter-individual variability, noisy measurements and large numbers of variables.
Based on a smoothing splines functional model, 'santaR' is able to detect variables
highlighting significantly different temporal trajectories between study groups.
Designed initially for metabolic phenotyping, 'santaR' is also suited for other Systems Biology
disciplines. Command line and graphical analysis (via a 'shiny' application) enable fast and
parallel automated analysis and reporting, intuitive visualisation and comprehensive plotting
options for non-specialist users.
Author: Arnaud Wolfer [aut, cre] ,
Timothy Ebbels [ctb],
Joe Cheng [ctb]
Maintainer: Arnaud Wolfer <adwolfer@gmail.com>
Diff between santaR versions 1.2.2 dated 2022-05-23 and 1.2.3 dated 2022-05-23
santaR-1.2.2/santaR/vignettes/file3eac108b893.html |only santaR-1.2.2/santaR/vignettes/file3eac2035654c.html |only santaR-1.2.2/santaR/vignettes/file3eac490a1211.html |only santaR-1.2.2/santaR/vignettes/file3eac50e54547.html |only santaR-1.2.2/santaR/vignettes/file3eac6eaa7a38.html |only santaR-1.2.2/santaR/vignettes/file3eac79a54222.html |only santaR-1.2.2/santaR/vignettes/file495459c86ac2.html |only santaR-1.2.2/santaR/vignettes/file49547f98451a.html |only santaR-1.2.2/santaR/vignettes/file54b03fa44385.html |only santaR-1.2.2/santaR/vignettes/file54b0425d69f8.html |only santaR-1.2.3/santaR/DESCRIPTION | 8 +- santaR-1.2.3/santaR/MD5 | 26 ++----- santaR-1.2.3/santaR/inst/doc/advanced-command-line-functions.html | 12 +-- santaR-1.2.3/santaR/inst/doc/plotting-options.html | 36 +++++----- santaR-1.2.3/santaR/inst/doc/theoretical-background.html | 2 santaR-1.2.3/santaR/tests/testthat/test_dfSearch-AIC_smooth_spline.R | 24 +++--- santaR-1.2.3/santaR/tests/testthat/test_dfSearch-AICc_smooth_spline.R | 24 +++--- santaR-1.2.3/santaR/tests/testthat/test_dfSearch-BIC_smooth_spline.R | 24 +++--- santaR-1.2.3/santaR/tests/testthat/test_dfSearch-get_param_evolution.R | 4 - 19 files changed, 75 insertions(+), 85 deletions(-)
Title: Toolbox for Pseudo and Quasi Random Number Generation and Random
Generator Tests
Description: Provides (1) pseudo random generators - general linear congruential generators,
multiple recursive generators and generalized feedback shift register (SF-Mersenne Twister
algorithm and WELL generators); (2) quasi random generators - the Torus algorithm, the
Sobol sequence, the Halton sequence (including the Van der Corput sequence) and (3) some
generator tests - the gap test, the serial test, the poker test.
See e.g. Gentle (2003) <doi:10.1007/b97336>. The package can be provided
without the rngWELL dependency on demand.
Take a look at the Distribution task view of types and tests of random number generators.
Package in Memoriam of Diethelm and Barbara Wuertz.
Author: R port by Yohan Chalabi, Christophe Dutang, Petr Savicky and Diethelm Wuertz with some underlying C codes of the SFMT algorithm from M. Matsumoto and M. Saito, the Knuth-TAOCP RNG from D. Knuth.
Maintainer: Christophe Dutang <dutangc@gmail.com>
Diff between randtoolbox versions 1.31.1 dated 2021-10-30 and 2.0.0 dated 2022-05-23
randtoolbox-1.31.1/randtoolbox/R/qmc.R |only randtoolbox-1.31.1/randtoolbox/src/LowDiscrepancy-sobol.c |only randtoolbox-1.31.1/randtoolbox/src/LowDiscrepancy-sobol.h |only randtoolbox-1.31.1/randtoolbox/src/LowDiscrepancy.f |only randtoolbox-1.31.1/randtoolbox/src/LowDiscrepancy.s |only randtoolbox-1.31.1/randtoolbox/tests/test-sobol-Ccode.R |only randtoolbox-1.31.1/randtoolbox/tests/testHalton.R |only randtoolbox-1.31.1/randtoolbox/tests/testSobol.R |only randtoolbox-1.31.1/randtoolbox/tests/testStirling.R |only randtoolbox-1.31.1/randtoolbox/tests/testTorus.R |only randtoolbox-1.31.1/randtoolbox/tests/testWELL.R |only randtoolbox-1.31.1/randtoolbox/tests/testenvir.R |only randtoolbox-2.0.0/randtoolbox/DESCRIPTION | 10 randtoolbox-2.0.0/randtoolbox/MD5 | 77 - randtoolbox-2.0.0/randtoolbox/NAMESPACE | 5 randtoolbox-2.0.0/randtoolbox/R/binary-operator.R |only randtoolbox-2.0.0/randtoolbox/R/quasiRNG.R | 264 ---- randtoolbox-2.0.0/randtoolbox/R/randtoolboxEnv.R | 4 randtoolbox-2.0.0/randtoolbox/R/sobol-basic.R | 341 ++++-- randtoolbox-2.0.0/randtoolbox/build/vignette.rds |binary randtoolbox-2.0.0/randtoolbox/configure | 18 randtoolbox-2.0.0/randtoolbox/configure.ac | 2 randtoolbox-2.0.0/randtoolbox/inst/NEWS | 10 randtoolbox-2.0.0/randtoolbox/inst/doc/fullpres.R | 34 randtoolbox-2.0.0/randtoolbox/inst/doc/fullpres.Rnw | 113 +- randtoolbox-2.0.0/randtoolbox/inst/doc/fullpres.pdf |binary randtoolbox-2.0.0/randtoolbox/inst/doc/shortintro.pdf |binary randtoolbox-2.0.0/randtoolbox/man/quasiRNG.Rd | 37 randtoolbox-2.0.0/randtoolbox/man/sobol-test-func.Rd | 32 randtoolbox-2.0.0/randtoolbox/src/LowDiscrepancy-halton.c | 93 - randtoolbox-2.0.0/randtoolbox/src/LowDiscrepancy-halton.h | 88 - randtoolbox-2.0.0/randtoolbox/src/LowDiscrepancy-sobol-orig1111.c |only randtoolbox-2.0.0/randtoolbox/src/LowDiscrepancy-sobol-orig1111.h |only randtoolbox-2.0.0/randtoolbox/src/SFMT.h | 34 randtoolbox-2.0.0/randtoolbox/src/config.h | 4 randtoolbox-2.0.0/randtoolbox/src/init.c | 16 randtoolbox-2.0.0/randtoolbox/src/randtoolbox.c | 78 + randtoolbox-2.0.0/randtoolbox/src/randtoolbox.h | 6 randtoolbox-2.0.0/randtoolbox/src/version.c | 2 randtoolbox-2.0.0/randtoolbox/tests/test-Halton.R |only randtoolbox-2.0.0/randtoolbox/tests/test-Sobol.R |only randtoolbox-2.0.0/randtoolbox/tests/test-Stirling.R |only randtoolbox-2.0.0/randtoolbox/tests/test-Torus.R |only randtoolbox-2.0.0/randtoolbox/tests/test-WELL.R |only randtoolbox-2.0.0/randtoolbox/tests/test-binary-op.R |only randtoolbox-2.0.0/randtoolbox/tests/test-envir.R |only randtoolbox-2.0.0/randtoolbox/tests/test-mjrec.R |only randtoolbox-2.0.0/randtoolbox/tests/test-sobol-basic.R | 40 randtoolbox-2.0.0/randtoolbox/tests/test-sobol.V.R |only randtoolbox-2.0.0/randtoolbox/tests/test-sobol.directions.R |only randtoolbox-2.0.0/randtoolbox/vignettes/fullpres.Rnw | 113 +- randtoolbox-2.0.0/randtoolbox/vignettes/randtoolbox.bib | 553 +++++----- 52 files changed, 993 insertions(+), 981 deletions(-)
Title: Optimal Subset Cardinality Regression (OSCAR) Models Using the
L0-Pseudonorm
Description: Optimal Subset Cardinality Regression (OSCAR) models offer
regularized linear regression using the L0-pseudonorm, conventionally
known as the number of non-zero coefficients. The package estimates an
optimal subset of features using the L0-penalization via
cross-validation, bootstrapping and visual diagnostics. Effective
Fortran implementations are offered along the package for finding
optima for the DC-decomposition, which is used for transforming the
discrete L0-regularized optimization problem into a continuous
non-convex optimization task. These optimization modules include DBDC
('Double Bundle method for nonsmooth DC optimization' as described in
Joki et al. (2018) <doi:10.1137/16M1115733>) and LMBM ('Limited
Memory Bundle Method for large-scale nonsmooth optimization' as
in Haarala et al. (2004) <doi:10.1080/10556780410001689225>).
Multiple regression model families are supported: Cox, logistic,
and Gaussian.
Author: Teemu Daniel Laajala [aut, cre]
,
Kaisa Joki [aut],
Anni Halkola [aut]
Maintainer: Teemu Daniel Laajala <teelaa@utu.fi>
Diff between oscar versions 1.0.3 dated 2022-05-20 and 1.0.4 dated 2022-05-23
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/example.html | 6 +++--- src/Makevars | 1 - src/dbdc.f90 | 30 +++++++++++++++++++++--------- 5 files changed, 32 insertions(+), 21 deletions(-)
Title: Immunoglobulin Somatic Hypermutation Analysis
Description: Provides a computational framework for analyzing mutations in
immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of
antigen-driven selection pressure, mutational load quantification, building of
somatic hypermutation (SHM) models, and model-dependent distance calculations.
Also includes empirically derived models of SHM for both mice and humans.
Citations:
Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>,
Yaari, et al (2012) <doi:10.1093/nar/gks457>,
Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>,
Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.
Author: Mohamed Uduman [aut],
Namita Gupta [aut],
Susanna Marquez [aut],
Julian Zhou [aut],
Nima Nouri [aut],
Ang Cui [ctb],
Jason Vander Heiden [aut, cre],
Gur Yaari [aut],
Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@gmail.com>
Diff between shazam versions 1.1.0 dated 2021-07-08 and 1.1.1 dated 2022-05-23
shazam-1.1.0/shazam/vignettes/Shmulate-Vignette.html |only shazam-1.1.1/shazam/DESCRIPTION | 25 - shazam-1.1.1/shazam/MD5 | 52 +- shazam-1.1.1/shazam/NAMESPACE | 6 shazam-1.1.1/shazam/NEWS.md | 27 + shazam-1.1.1/shazam/R/ConvertNumbering.R |only shazam-1.1.1/shazam/R/DistToNearest.R | 2 shazam-1.1.1/shazam/R/MutationDefinitions.R | 2 shazam-1.1.1/shazam/R/MutationProfiling.R | 308 +++++++++++---- shazam-1.1.1/shazam/R/RegionsExtend.R | 4 shazam-1.1.1/shazam/R/Shazam.R | 11 shazam-1.1.1/shazam/R/TargetingModels.R | 6 shazam-1.1.1/shazam/R/kedd.R |only shazam-1.1.1/shazam/R/sysdata.rda |binary shazam-1.1.1/shazam/build/vignette.rds |binary shazam-1.1.1/shazam/inst/doc/Baseline-Vignette.pdf |binary shazam-1.1.1/shazam/inst/doc/DistToNearest-Vignette.R | 2 shazam-1.1.1/shazam/inst/doc/DistToNearest-Vignette.Rmd | 2 shazam-1.1.1/shazam/inst/doc/DistToNearest-Vignette.pdf |binary shazam-1.1.1/shazam/inst/doc/Mutation-Vignette.pdf |binary shazam-1.1.1/shazam/inst/doc/Shmulate-Vignette.pdf |binary shazam-1.1.1/shazam/inst/doc/Targeting-Vignette.pdf |binary shazam-1.1.1/shazam/man/MUTATION_SCHEMES.Rd | 2 shazam-1.1.1/shazam/man/convertNumbering.Rd |only shazam-1.1.1/shazam/man/slideWindowDb.Rd | 11 shazam-1.1.1/shazam/man/slideWindowSeq.Rd | 2 shazam-1.1.1/shazam/man/slideWindowTune.Rd | 11 shazam-1.1.1/shazam/man/slideWindowTunePlot.Rd | 30 + shazam-1.1.1/shazam/vignettes/DistToNearest-Vignette.Rmd | 2 29 files changed, 371 insertions(+), 134 deletions(-)
Title: Parameter Estimation in Conditional GEE for Recurrent Event Gap
Times
Description: Solves for the mean parameters, the variance parameter, and their asymptotic variance in a conditional GEE for recurrent event gap times, as described by Clement and Strawderman (2009) in the journal Biostatistics. Makes a parametric assumption for the length of the censored gap time.
Author: David Clement
Maintainer: David Clement <dyc24@cornell.edu>
Diff between condGEE versions 0.1-4 dated 2013-08-17 and 0.2.0 dated 2022-05-23
condGEE-0.1-4/condGEE/data/asthma.txt.gz |only condGEE-0.1-4/condGEE/demo |only condGEE-0.1-4/condGEE/man/condMoments.Rd |only condGEE-0.2.0/condGEE/DESCRIPTION | 17 - condGEE-0.2.0/condGEE/MD5 | 32 ++- condGEE-0.2.0/condGEE/NAMESPACE | 16 - condGEE-0.2.0/condGEE/NEWS.md |only condGEE-0.2.0/condGEE/R/condGEE.R | 320 +++++++++++++++++-------------- condGEE-0.2.0/condGEE/R/condMoments.R | 99 +++++++-- condGEE-0.2.0/condGEE/README.md |only condGEE-0.2.0/condGEE/build |only condGEE-0.2.0/condGEE/data/asthma.txt |only condGEE-0.2.0/condGEE/inst |only condGEE-0.2.0/condGEE/man/K1.exp.Rd |only condGEE-0.2.0/condGEE/man/K1.norm.Rd |only condGEE-0.2.0/condGEE/man/K1.t3.Rd |only condGEE-0.2.0/condGEE/man/K2.exp.Rd |only condGEE-0.2.0/condGEE/man/K2.norm.Rd |only condGEE-0.2.0/condGEE/man/K2.t3.Rd |only condGEE-0.2.0/condGEE/man/asthma.Rd | 23 +- condGEE-0.2.0/condGEE/man/condGEE.Rd | 163 +++++++++------ condGEE-0.2.0/condGEE/tests |only condGEE-0.2.0/condGEE/vignettes |only 23 files changed, 397 insertions(+), 273 deletions(-)
Title: Revealed Preference and Attention Analysis in Random Limited
Attention Models
Description: It is widely documented in psychology, economics and other disciplines that socio-economic agent may not pay full attention to all available alternatives, rendering standard revealed preference theory invalid. This package implements the estimation and inference procedures of Cattaneo, Ma, Masatlioglu and Suleymanov (2020) <arXiv:1712.03448> and Cattaneo, Cheung, Ma, and Masatlioglu (2022) <arXiv:2110.10650>, which utilizes standard choice data to partially identify and estimate a decision maker's preference and attention. For inference, several simulation-based critical values are provided.
Author: Matias D. Cattaneo, Paul Cheung, Xinwei Ma, Yusufcan Masatlioglu, Elchin Suleymanov
Maintainer: Xinwei Ma <x1ma@ucsd.edu>
Diff between ramchoice versions 2.0 dated 2021-10-22 and 2.1 dated 2022-05-23
DESCRIPTION | 8 +++---- MD5 | 34 +++++++++++++++++--------------- NAMESPACE | 3 ++ R/auxiliaryFunctions.R | 24 +++++++++++----------- R/ramchoice-package.R | 8 +++---- R/revealAtte.R | 6 ++--- R/revealPref.R | 30 ++++++++++++++-------------- R/revealPrefModel.R |only build/partial.rdb |binary man/genMat.Rd | 4 +-- man/logitAtte.Rd | 8 +++---- man/logitSimu.Rd | 8 +++---- man/print.ramchoiceRevealPrefModel.Rd |only man/rAtte.Rd | 12 +++++------ man/ramchoice-package.Rd | 8 +++---- man/revealAtte.Rd | 6 ++--- man/revealPref.Rd | 12 +++++------ man/revealPrefModel.Rd |only man/sumData.Rd | 4 +-- man/summary.ramchoiceRevealPrefModel.Rd |only 20 files changed, 91 insertions(+), 84 deletions(-)
Title: Combined miRNA- And mRNA-Testing
Description: Package for combined miRNA- and mRNA-testing.
Author: Stephan Artmann, Klaus Jung, Tim Beissbarth
Maintainer: Stephan Artmann <stephanartmann@gmx.net>
Diff between miRtest versions 1.8 dated 2014-11-26 and 2.0 dated 2022-05-23
DESCRIPTION | 16 ++++++++-------- MD5 | 16 ++++++++-------- NAMESPACE | 3 ++- R/miRtest.R | 31 +++++-------------------------- build/vignette.rds |binary inst/doc/miRtest.Rnw | 3 +-- inst/doc/miRtest.pdf |binary man/miRtest.Rd | 3 --- vignettes/miRtest.Rnw | 3 +-- 9 files changed, 25 insertions(+), 50 deletions(-)
Title: (Robust) Mediation Analysis
Description: Perform mediation analysis via a (fast and robust) bootstrap test.
Author: Andreas Alfons [aut, cre] ,
Nufer Y. Ates [ctb]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Diff between robmed versions 0.10.1 dated 2022-03-17 and 0.11.0 dated 2022-05-23
robmed-0.10.1/robmed/vignettes/static-figures |only robmed-0.11.0/robmed/DESCRIPTION | 10 robmed-0.11.0/robmed/MD5 | 127 - robmed-0.11.0/robmed/NAMESPACE | 8 robmed-0.11.0/robmed/NEWS | 17 robmed-0.11.0/robmed/R/BSG2014.R |only robmed-0.11.0/robmed/R/boot.R | 506 ++--- robmed-0.11.0/robmed/R/ci_plot.R | 451 ++-- robmed-0.11.0/robmed/R/coef.R | 232 +- robmed-0.11.0/robmed/R/confint.R | 544 ++--- robmed-0.11.0/robmed/R/control.R | 8 robmed-0.11.0/robmed/R/density_plot.R | 363 +-- robmed-0.11.0/robmed/R/ellipse_plot.R | 431 ++-- robmed-0.11.0/robmed/R/fit_mediation.R | 136 + robmed-0.11.0/robmed/R/formula.R | 299 +-- robmed-0.11.0/robmed/R/p_value.R | 588 +++--- robmed-0.11.0/robmed/R/plot.R | 10 robmed-0.11.0/robmed/R/retest.R | 374 +-- robmed-0.11.0/robmed/R/robmed-package.R |only robmed-0.11.0/robmed/R/setup_ci_plot.R | 506 ++--- robmed-0.11.0/robmed/R/setup_density_plot.R | 450 ++-- robmed-0.11.0/robmed/R/setup_ellipse_plot.R | 1248 ++++++------- robmed-0.11.0/robmed/R/setup_weight_plot.R | 4 robmed-0.11.0/robmed/R/sim_mediation.R |only robmed-0.11.0/robmed/R/skew_elliptical.R | 777 ++++---- robmed-0.11.0/robmed/R/summary.R | 64 robmed-0.11.0/robmed/R/test_mediation.R | 53 robmed-0.11.0/robmed/R/utils.R | 418 ++-- robmed-0.11.0/robmed/R/weight_plot.R | 6 robmed-0.11.0/robmed/build/partial.rdb |binary robmed-0.11.0/robmed/build/vignette.rds |binary robmed-0.11.0/robmed/data/BSG2014.RData |binary robmed-0.11.0/robmed/inst/doc/robmed-intro.R | 35 robmed-0.11.0/robmed/inst/doc/robmed-intro.Rnw | 831 ++++---- robmed-0.11.0/robmed/inst/doc/robmed-intro.pdf |binary robmed-0.11.0/robmed/man/BSG2014.Rd | 278 +- robmed-0.11.0/robmed/man/boot_samples.Rd | 12 robmed-0.11.0/robmed/man/ci_plot.Rd | 23 robmed-0.11.0/robmed/man/coef.test_mediation.Rd | 6 robmed-0.11.0/robmed/man/confint.test_mediation.Rd | 14 robmed-0.11.0/robmed/man/cov_control.Rd | 4 robmed-0.11.0/robmed/man/density_plot.Rd | 23 robmed-0.11.0/robmed/man/ellipse_plot.Rd | 21 robmed-0.11.0/robmed/man/fit_mediation.Rd | 137 + robmed-0.11.0/robmed/man/m.Rd | 4 robmed-0.11.0/robmed/man/p_value.Rd | 12 robmed-0.11.0/robmed/man/plot-methods.Rd | 10 robmed-0.11.0/robmed/man/reg_control.Rd | 4 robmed-0.11.0/robmed/man/retest.Rd | 6 robmed-0.11.0/robmed/man/robmed-package.Rd | 9 robmed-0.11.0/robmed/man/setup_ci_plot.Rd | 4 robmed-0.11.0/robmed/man/setup_density_plot.Rd | 4 robmed-0.11.0/robmed/man/setup_ellipse_plot.Rd | 4 robmed-0.11.0/robmed/man/setup_weight_plot.Rd | 4 robmed-0.11.0/robmed/man/sim_mediation.Rd |only robmed-0.11.0/robmed/man/summary.test_mediation.Rd | 60 robmed-0.11.0/robmed/man/test_mediation.Rd | 131 + robmed-0.11.0/robmed/man/weight_plot.Rd | 6 robmed-0.11.0/robmed/tests/testthat/test_boot_covariance.R | 924 ++++----- robmed-0.11.0/robmed/tests/testthat/test_simulate.R |only robmed-0.11.0/robmed/vignettes/figures |only robmed-0.11.0/robmed/vignettes/robmed-intro.Rnw | 831 ++++---- robmed-0.11.0/robmed/vignettes/robmed.bib | 157 + 63 files changed, 6039 insertions(+), 5145 deletions(-)
Title: Fast Extrapolation of Time Features using K-Nearest Neighbors
Description: Fast extrapolation of univariate and multivariate time features using K-Nearest Neighbors. The compact set of hyper-parameters is tuned via grid or random search.
Author: Giancarlo Vercellino
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>
Diff between jenga versions 1.1.0 dated 2022-04-16 and 1.2.0 dated 2022-05-23
jenga-1.1.0/jenga/R/engine.R |only jenga-1.1.0/jenga/R/hood.R |only jenga-1.1.0/jenga/man/engine.Rd |only jenga-1.1.0/jenga/man/hood.Rd |only jenga-1.2.0/jenga/DESCRIPTION | 14 - jenga-1.2.0/jenga/MD5 | 14 - jenga-1.2.0/jenga/NAMESPACE | 14 + jenga-1.2.0/jenga/NEWS.md | 6 jenga-1.2.0/jenga/R/main.R | 487 ++++++++++++++++++++++++++++++++++------ jenga-1.2.0/jenga/man/jenga.Rd | 12 10 files changed, 456 insertions(+), 91 deletions(-)
Title: R Tools for Text Matrices, Embeddings, and Networks
Description: This is a collection of functions optimized for working with
with various kinds of text matrices. Focusing on
the text matrix as the primary object - represented
either as a base R dense matrix or a 'Matrix' package sparse
matrix - allows for a consistent and intuitive interface
that stays close to the underlying mathematical foundation
of computational text analysis. In particular, the package
includes functions for working with word embeddings,
text networks, and document-term matrices. Methods developed in
Stoltz and Taylor (2019) <doi:10.1007/s42001-019-00048-6>,
Taylor and Stoltz (2020) <doi:10.1007/s42001-020-00075-8>,
Taylor and Stoltz (2020) <doi:10.15195/v7.a23>, and
Stoltz and Taylor (2021) <doi:10.1016/j.poetic.2021.101567>.
Author: Dustin Stoltz [aut, cre] ,
Marshall Taylor [aut]
Maintainer: Dustin Stoltz <maintainers@textmapping.com>
Diff between text2map versions 0.1.4 dated 2022-04-12 and 0.1.5 dated 2022-05-23
DESCRIPTION | 14 +- MD5 | 49 ++++----- NAMESPACE | 28 ++++- NEWS.md | 18 +++ R/data.R | 28 +++++ R/utils-dtm.R | 147 +++++++++++++++++++++++++-- R/utils-embedding.R | 37 ++---- R/utils-methods.R | 26 ++++ README.md | 4 build/partial.rdb |binary build/vignette.rds |binary data/meta_shakespeare.rda |only inst/REFERENCES.bib |only inst/doc/CMDist-concept-movers-distance.R | 20 +++ inst/doc/CMDist-concept-movers-distance.Rmd | 101 +++++++++--------- inst/doc/CMDist-concept-movers-distance.html | 101 +++++++++--------- inst/doc/concept-class-analysis.html | 4 man/Matrix.Rd | 2 man/dtm_builder.Rd | 5 man/dtm_stats.Rd | 9 + man/dtm_stopper.Rd | 6 + man/get_regions.Rd | 26 ---- man/meta_shakespeare.Rd |only man/seq_builder.Rd |only tests/testthat/test-utils-dtm.R | 134 ------------------------ tests/testthat/test-utils-embeddings.R | 2 tests/testthat/test-utils-stopper.R |only vignettes/CMDist-concept-movers-distance.Rmd | 101 +++++++++--------- 28 files changed, 484 insertions(+), 378 deletions(-)
Title: Subtests Using Algorithmic Rummaging Techniques
Description: Construct subtests from a pool of items by using ant-colony-optimization, genetic algorithms, brute force, or random sampling.
Schultze (2017) <doi:10.17169/refubium-622>.
Author: Martin Schultze [aut, cre],
Johanna Schueller [ctb]
Maintainer: Martin Schultze <schultze@psych.uni-frankfurt.de>
Diff between stuart versions 0.9.1 dated 2020-08-26 and 0.10.0 dated 2022-05-23
DESCRIPTION | 14 +++--- MD5 | 85 +++++++++++++++++++++++++---------------- NAMESPACE | 11 +++++ R/bf.cycle.R | 6 +- R/bruteforce.R | 6 +- R/combinations.R | 2 R/crossvalidate.Mplus.R | 44 ++++++++++++--------- R/crossvalidate.R | 6 +- R/crossvalidate.lavaan.R | 41 +++++++++++++------ R/data.documentation.R | 29 +++++++++++++ R/data.prep.R | 12 ++--- R/empiricalobjective.R |only R/extractobjective.R |only R/fitness.R | 16 +++---- R/fixedobjective.R |only R/gene.R | 8 ++- R/helpers.R |only R/heuristics.R | 2 R/holdout.R | 50 ++++++++++++++++++++++-- R/kfold.R |only R/manualobjective.R |only R/mmas.R | 36 ++--------------- R/objectivematrices.R |only R/print.objectives.R |only R/print.stuartKfold.R |only R/print.summary.stuartKfold.R |only R/print.summary.stuartOutput.R | 5 +- R/randomsamples.R | 6 +- R/run.Mplus.R | 2 R/run.lavaan.R | 14 +++--- R/sanitycheck.R | 24 ++++++----- R/stuart.R | 6 +- R/stuart.bruteforce.R | 42 ++++++++++++++++---- R/stuart.gene.R | 60 ++++++++++++++++++++++++++-- R/stuart.mmas.R | 65 +++++++++++++++++++++++++++---- R/stuart.randomsamples.R | 45 ++++++++++++++++++--- R/summary.stuartKfold.R |only R/summary.stuartOutput.R | 3 - data/sia.rda |only man/as.stuartFixedObjective.Rd |only man/bruteforce.Rd | 1 man/crossvalidate.Rd | 10 ++++ man/empiricalobjective.Rd |only man/extractobjective.Rd |only man/fixedobjective.Rd |only man/gene.Rd | 4 + man/holdout.Rd | 4 + man/kfold.Rd |only man/mmas.Rd | 32 +-------------- man/objectivematrices.Rd |only man/randomsamples.Rd | 1 man/sia.Rd |only man/stuart-package.Rd | 6 +- 53 files changed, 484 insertions(+), 214 deletions(-)
Title: Orthogonal B-Spline Basis Functions
Description: Represents the basis functions for B-splines in a simple matrix
formulation that facilitates, taking integrals, derivatives, and
making orthogonal the basis functions.
Author: Andrew Redd
Maintainer: Andrew Redd <andrew.redd@hsc.utah.edu>
Diff between orthogonalsplinebasis versions 0.1.6 dated 2015-03-31 and 0.1.7 dated 2022-05-23
DESCRIPTION | 10 ++- MD5 | 32 +++++----- NAMESPACE | 55 +++++++++--------- NEWS | 14 +++- inst |only man/Hankel.Rd | 1 man/MatrixPower.Rd | 7 +- man/OrthogonalizeBasis.Rd | 5 - man/OuterProdSecondDerivative.Rd | 7 +- man/SplineBasis-class.Rd | 115 +++++++++++++++++++-------------------- man/SplineBasis.Rd | 86 ++++++++++++++--------------- man/evaluate-methods.Rd | 2 man/expand.knots.Rd | 64 ++++++++++----------- man/fitLS.Rd | 7 +- man/integrate-methods.Rd | 2 man/orthogonalize-methods.Rd | 2 man/orthogonalsplinebasis.Rd | 28 ++++----- tests |only 18 files changed, 221 insertions(+), 216 deletions(-)
More information about orthogonalsplinebasis at CRAN
Permanent link
Title: Analysis of MHC Data in Non-Model Species
Description: Twelve tools for bioinformatical processing and analysis of major
histocompatibility complex (MHC) data. The functions are tailored for amplicon data
sets that have been filtered using the 'dada2' method (for more information on
'dada2', visit <https://benjjneb.github.io/dada2/> ), but even other types of data
sets can be analyzed.
The DistCalc() function calculates Grantham, Sandberg, or p-distances from pairwise
comparisons of all sequences in a data set, and mean distances of all pairwise
comparisons within each sample in a data set. The function additionally outputs five
tables with physico-chemical z-descriptor values (based on Sandberg et al. 1998) for
each amino acid position in all sequences in the data set. These tables may be useful
for further downstream analyses, such as estimation of MHC supertypes.
The BootKmeans() function is a wrapper for the kmeans() function of the 'stats'
package, which allows for bootstrapping. Bootstrapping k-estimates may be
desirable in data sets, where e.g. BIC- vs. k-values do not produce clear
inflection points ("elbows"). BootKmeans() performs multiple runs of kmeans() and
estimates optimal k-values based on a user-defined threshold of BIC reduction. The
method is an automated and bootstrapped version of visually inspecting elbow plots
of BIC- vs. k-values.
The ClusterMatch() function is a tool for evaluating whether different k-means()
clustering models identify similar clusters, and summarize bootstrap model stats as
means for different estimated values of k. It is designed to take files produced by
the BootKmeans() function as input, but other data can be analysed if the
descriptions of the required data formats are observed carefully.
The HpltFind() function infers putative haplotypes from families in the data
set.
The GetHpltTable() and GetHpltStats() functions evaluate the accuracy of
the haplotype inference.
The PapaDiv() function compares parent pairs in the data set and calculate their
joint MHC diversity, taking into account sequence variants that occur in both
parents.
The ReplMatch() function matches replicates in data sets in order to evaluate
genotyping success.
The GetReplTable() and GetReplStats() functions perform such an evaluation.
The CreateFas() function creates a fasta file with all the sequences in the data
set.
The CreateSamplesFas() function creates individual fasta files for each sample in
the data set.
Author: Jacob Roved [aut, cre]
Maintainer: Jacob Roved <jacob.roved@biol.lu.se>
Diff between MHCtools versions 1.4.1 dated 2021-10-11 and 1.4.2 dated 2022-05-23
DESCRIPTION | 6 ++-- MD5 | 54 ++++++++++++++++++------------------- NEWS.md | 10 ++++++ R/BootKmeans_func_20210910.R | 13 ++++---- R/ClusterMatch_func_20210910.R | 13 ++++---- R/CreateFas_func_20170924.R | 13 ++++---- R/CreateSamplesFas_func_20170924.R | 13 ++++---- R/DistCalc_func_20200902.R | 13 ++++---- R/GetHpltStats_func_20200915.R | 13 ++++---- R/GetHpltTable_func_20200915.R | 13 ++++---- R/GetReplStats_func_20200914.R | 13 ++++---- R/GetReplTable_func_20200914.R | 13 ++++---- R/HpltFind_func_20200915.R | 13 ++++---- R/PapaDiv_func_20200915.R | 13 ++++---- R/ReplMatch_func_20200914.R | 13 ++++---- README.md | 6 ++++ man/BootKmeans.Rd | 13 ++++---- man/ClusterMatch.Rd | 13 ++++---- man/CreateFas.Rd | 13 ++++---- man/CreateSamplesFas.Rd | 13 ++++---- man/DistCalc.Rd | 13 ++++---- man/GetHpltStats.Rd | 13 ++++---- man/GetHpltTable.Rd | 13 ++++---- man/GetReplStats.Rd | 13 ++++---- man/GetReplTable.Rd | 13 ++++---- man/HpltFind.Rd | 13 ++++---- man/PapaDiv.Rd | 13 ++++---- man/ReplMatch.Rd | 13 ++++---- 28 files changed, 214 insertions(+), 174 deletions(-)
Title: Forest Analysis with Airborne Laser Scanning (LiDAR) Data
Description: Provides functions for forest analysis using airborne laser scanning (LiDAR remote sensing) data: tree detection (method 1 in Eysn et al. (2015) <doi:10.3390/f6051721>) and segmentation; forest parameters estimation and mapping with the area-based approach. It includes complementary steps for forest mapping: co-registration of field plots with LiDAR data (Monnet and Mermin (2014) <doi:10.3390/f5092307>); extraction of both physical (gaps, edges, trees) and statistical features from LiDAR data useful for e.g. habitat suitability modeling (Glad et al. (2020) <doi:10.1002/rse2.117>); model calibration with ground reference, and maps export.
Author: Jean-Matthieu Monnet [aut, cre]
,
Pascal Obstetar [ctb]
Maintainer: Jean-Matthieu Monnet <jean-matthieu.monnet@inrae.fr>
Diff between lidaRtRee versions 3.1.2 dated 2021-12-09 and 4.0.1 dated 2022-05-23
lidaRtRee-3.1.2/lidaRtRee/man/pointList2SPDF.Rd |only lidaRtRee-3.1.2/lidaRtRee/tests |only lidaRtRee-4.0.1/lidaRtRee/DESCRIPTION | 19 lidaRtRee-4.0.1/lidaRtRee/MD5 | 135 ++-- lidaRtRee-4.0.1/lidaRtRee/NAMESPACE | 4 lidaRtRee-4.0.1/lidaRtRee/R/aba.R | 193 +++--- lidaRtRee-4.0.1/lidaRtRee/R/chm_chablais3-data.R | 6 lidaRtRee-4.0.1/lidaRtRee/R/common.R | 365 ++++++------ lidaRtRee-4.0.1/lidaRtRee/R/coregistration.R | 286 ++++----- lidaRtRee-4.0.1/lidaRtRee/R/extdata.R | 8 lidaRtRee-4.0.1/lidaRtRee/R/gap_detection.R | 44 - lidaRtRee-4.0.1/lidaRtRee/R/metrics.R | 44 - lidaRtRee-4.0.1/lidaRtRee/R/optical_metrics.R | 4 lidaRtRee-4.0.1/lidaRtRee/R/quatre_montagnes-data.R | 4 lidaRtRee-4.0.1/lidaRtRee/R/raster_metrics.R | 46 - lidaRtRee-4.0.1/lidaRtRee/R/tree_detection.R | 324 +++++----- lidaRtRee-4.0.1/lidaRtRee/R/tree_inventory_chablais3-data.R | 6 lidaRtRee-4.0.1/lidaRtRee/R/tree_match.R | 52 - lidaRtRee-4.0.1/lidaRtRee/build/partial.rdb |binary lidaRtRee-4.0.1/lidaRtRee/data/chm_chablais3.rda |binary lidaRtRee-4.0.1/lidaRtRee/data/quatre_montagnes.rda |binary lidaRtRee-4.0.1/lidaRtRee/man/aa_las_chablais3.Rd |only lidaRtRee-4.0.1/lidaRtRee/man/aba_combine_strata.Rd | 2 lidaRtRee-4.0.1/lidaRtRee/man/aba_metrics.Rd | 5 lidaRtRee-4.0.1/lidaRtRee/man/aba_plot.Rd | 2 lidaRtRee-4.0.1/lidaRtRee/man/aba_predict.Rd | 23 lidaRtRee-4.0.1/lidaRtRee/man/add_vegetation_indices.Rd | 4 lidaRtRee-4.0.1/lidaRtRee/man/boxcox_itr.Rd | 4 lidaRtRee-4.0.1/lidaRtRee/man/boxcox_itr_bias_cor.Rd | 6 lidaRtRee-4.0.1/lidaRtRee/man/boxcox_tr.Rd | 4 lidaRtRee-4.0.1/lidaRtRee/man/chm_chablais3.Rd | 6 lidaRtRee-4.0.1/lidaRtRee/man/cimg2Raster.Rd | 23 lidaRtRee-4.0.1/lidaRtRee/man/circle2Raster.Rd | 6 lidaRtRee-4.0.1/lidaRtRee/man/clean_raster.Rd | 23 lidaRtRee-4.0.1/lidaRtRee/man/clouds_metrics.Rd | 2 lidaRtRee-4.0.1/lidaRtRee/man/clouds_tree_metrics.Rd | 2 lidaRtRee-4.0.1/lidaRtRee/man/convert_raster.Rd |only lidaRtRee-4.0.1/lidaRtRee/man/coregistration.Rd | 22 lidaRtRee-4.0.1/lidaRtRee/man/dem_filtering.Rd | 13 lidaRtRee-4.0.1/lidaRtRee/man/edge_detection.Rd | 19 lidaRtRee-4.0.1/lidaRtRee/man/ellipses4Crown.Rd | 2 lidaRtRee-4.0.1/lidaRtRee/man/gap_detection.Rd | 15 lidaRtRee-4.0.1/lidaRtRee/man/las_chablais3.Rd | 5 lidaRtRee-4.0.1/lidaRtRee/man/maxima_detection.Rd | 13 lidaRtRee-4.0.1/lidaRtRee/man/maxima_selection.Rd | 21 lidaRtRee-4.0.1/lidaRtRee/man/plot_matched.Rd | 2 lidaRtRee-4.0.1/lidaRtRee/man/plot_tree_inventory.Rd | 3 lidaRtRee-4.0.1/lidaRtRee/man/pointList2poly.Rd |only lidaRtRee-4.0.1/lidaRtRee/man/points2DSM.Rd | 10 lidaRtRee-4.0.1/lidaRtRee/man/points2DTM.Rd | 11 lidaRtRee-4.0.1/lidaRtRee/man/quatre_montagnes.Rd | 4 lidaRtRee-4.0.1/lidaRtRee/man/raster2Cimg.Rd | 15 lidaRtRee-4.0.1/lidaRtRee/man/raster_chull_mask.Rd | 13 lidaRtRee-4.0.1/lidaRtRee/man/raster_local_max.Rd | 17 lidaRtRee-4.0.1/lidaRtRee/man/raster_metrics.Rd | 19 lidaRtRee-4.0.1/lidaRtRee/man/raster_xy_mask.Rd | 8 lidaRtRee-4.0.1/lidaRtRee/man/raster_zonal_stats.Rd | 13 lidaRtRee-4.0.1/lidaRtRee/man/rasters2Cor.Rd | 31 - lidaRtRee-4.0.1/lidaRtRee/man/rasters_moving_cor.Rd | 29 lidaRtRee-4.0.1/lidaRtRee/man/seg_adjust.Rd | 19 lidaRtRee-4.0.1/lidaRtRee/man/segmentation.Rd | 15 lidaRtRee-4.0.1/lidaRtRee/man/std_tree_metrics.Rd | 2 lidaRtRee-4.0.1/lidaRtRee/man/terrain_points_metrics.Rd | 10 lidaRtRee-4.0.1/lidaRtRee/man/tree_extraction.Rd | 19 lidaRtRee-4.0.1/lidaRtRee/man/tree_inventory_chablais3.Rd | 6 lidaRtRee-4.0.1/lidaRtRee/man/tree_segmentation.Rd | 15 66 files changed, 1045 insertions(+), 978 deletions(-)
Title: Download Data from Kobotoolbox to R
Description: Wrapper for 'Kobotoolbox' APIs ver 2 mentioned at <https://support.kobotoolbox.org/api.html>, to download data from 'Kobotoolbox' to R. Small and simple package that adds immense convenience for the data professionals using 'Kobotoolbox'.
Author: Asitav Sen [aut, cre, cph]
Maintainer: Asitav Sen <hello@asitavsen.com>
Diff between KoboconnectR versions 1.1.0 dated 2022-05-16 and 1.1.1 dated 2022-05-23
DESCRIPTION | 6 - MD5 | 18 ++-- NAMESPACE | 2 NEWS.md | 5 + R/Koboconnect.R | 68 +++++++++++------- R/other.R | 112 +++++++++++++++++++------------ man/kobo_export_create.Rd | 5 + tests/testthat/test-kobo_df_download.R | 9 +- tests/testthat/test-kobo_export_create.R | 52 ++++++++++---- tests/testthat/test-kobotools_kpi_data.R | 7 - 10 files changed, 183 insertions(+), 101 deletions(-)
Title: An Import Mechanism for R
Description: Alternative mechanism for importing objects from packages
and R modules. The syntax allows for importing multiple objects with a single
command in an expressive way. The import package bridges some of the gap
between using library (or require) and direct (single-object) imports.
Furthermore the imported objects are not placed in the current environment.
Author: Stefan Milton Bache [aut],
Magnus Thor Torfason [aut, cre]
Maintainer: Magnus Thor Torfason <m@zulutime.net>
Diff between import versions 1.2.0 dated 2020-09-24 and 1.3.0 dated 2022-05-23
DESCRIPTION | 10 MD5 | 54 +- NEWS.md | 36 + R/S3.R |only R/badge.R |only R/from.R | 106 ++-- R/here.R | 2 R/into.R | 2 R/make_import_call.R | 4 build/vignette.rds |binary inst/WORDLIST |only inst/doc/import.R | 35 + inst/doc/import.Rmd | 119 +++- inst/doc/import.html | 714 ++++++++++++++++++--------- man/figures |only man/importfunctions.Rd | 25 tests/test_import/cleanup_environment.R | 4 tests/test_import/module_S3.R |only tests/test_import/module_hidden_objects.R |only tests/test_import/packageToTest |only tests/test_import/packageToTest_0.1.0.tar.gz |only tests/test_import/test_S3.R |only tests/test_import/test_from.R | 87 +++ tests/test_import/test_hidden_objects.R |only tests/test_import/test_into_and_here.R | 9 tests/test_import/test_into_param.R |only vignettes/import.Rmd | 119 +++- vignettes/lifecycle-experimental.svg |only 28 files changed, 965 insertions(+), 361 deletions(-)
Title: Generalized Joint Attribute Modeling
Description: Analyzes joint attribute data (e.g., species abundance) that are combinations of continuous and discrete data with Gibbs sampling. Full model and computation details are described in Clark et al. (2018) <doi:10.1002/ecm.1241>.
Author: James S. Clark, Daniel Taylor-Rodriquez
Maintainer: James S. Clark <jimclark@duke.edu>
Diff between gjam versions 2.6 dated 2022-04-15 and 2.6.2 dated 2022-05-23
DESCRIPTION | 8 MD5 | 16 R/gjamHfunctions.R | 974 +++++++++++++++++++++------------------ inst/doc/gjamVignette.R | 8 inst/doc/gjamVignette.Rmd | 10 inst/doc/gjamVignette.html | 86 +-- man/gjam-package.Rd | 4 man/gjamConditionalParameters.Rd | 2 vignettes/gjamVignette.Rmd | 10 9 files changed, 603 insertions(+), 515 deletions(-)
Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors as described in Migueles and colleagues (JMPB 2019), and van Hees and colleagues (JApplPhysiol 2014; PLoSONE 2015). The package has been developed and tested for binary data from 'GENEActiv' <https://www.activinsights.com/> and GENEA devices (not for sale), .csv-export data from 'Actigraph' <https://actigraphcorp.com> devices, and .cwa and .wav-format data from 'Axivity' <https://axivity.com>. These devices are currently widely used in research on human daily physical activity. Further, the package can handle accelerometer data file from any other sensor brand providing that the data is stored in csv format and has either no header or a two column header. Also the package allows for external function embedding.
Author: Vincent T van Hees [aut, cre],
Jairo H Migueles [aut],
Severine Sabia [ctb],
Matthew R Patterson [ctb],
Zhou Fang [ctb],
Jing Hua Zhao [ctb],
Joe Heywood [ctb],
Evgeny Mirkes [ctb],
Joan Capdevila Pujol [ctb],
Dan Jackson [ctb],
Lena Kushleyeva [ctb] [...truncated...]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>
Diff between GGIR versions 2.6-0 dated 2022-02-02 and 2.7-0 dated 2022-05-23
DESCRIPTION | 36 MD5 | 196 - NAMESPACE | 11 R/GGIR.R |only R/check_params.R | 31 R/cosinorAnalyses.R |only R/createConfigFile.R | 30 R/create_test_sleeplog_csv.R | 11 R/datadir2fnames.R | 10 R/extract_params.R | 20 R/g.IVIS.R | 113 - R/g.analyse.R | 28 R/g.analyse.avday.R | 104 R/g.analyse.perday.R | 6 R/g.analyse.perfile.R | 255 +- R/g.binread.R | 846 +++---- R/g.calibrate.R | 18 R/g.conv.actlog.R | 2 R/g.convert.part2.long.R | 18 R/g.cwaread.R | 12 R/g.dotorcomma.R | 5 R/g.extractheadervars.R | 17 R/g.getidfromheaderobject.R | 2 R/g.getmeta.R | 8 R/g.getstarttime.R | 2 R/g.imputeTimegaps.R | 44 R/g.inspectfile.R | 137 - R/g.loadlog.R | 74 R/g.part1.R | 28 R/g.part2.R | 62 R/g.part3.R | 21 R/g.part4.R | 78 R/g.part4_extractid.R | 65 R/g.part5.R | 19 R/g.part5.addfirstwake.R | 1 R/g.readaccfile.R | 20 R/g.readtemp_movisens.R | 8 R/g.report.part2.R | 113 - R/g.report.part4.R | 28 R/g.report.part5.R | 22 R/g.shell.GGIR.R | 287 -- R/g.sib.det.R | 3 R/get_nw_clip_block_params.R | 8 R/load_params.R | 32 R/read.myacc.csv.R | 17 R/tidyup_df.R |only build/vignette.rds |binary inst/NEWS.Rd | 77 inst/doc/ExternalFunction.R | 6 inst/doc/ExternalFunction.Rmd | 14 inst/doc/ExternalFunction.pdf |binary inst/doc/GGIR.R | 10 inst/doc/GGIR.Rmd | 137 - inst/doc/GGIR.html | 3484 ++++++++++++++++++++++++++----- inst/doc/TutorialDaySegmentAnalyses.R | 4 inst/doc/TutorialDaySegmentAnalyses.Rmd | 14 inst/doc/TutorialDaySegmentAnalyses.html | 1467 ++++++++++++- inst/doc/readmyacccsv.R |only inst/doc/readmyacccsv.Rmd |only inst/doc/readmyacccsv.html |only man/GGIR-package.Rd | 6 man/GGIR.Rd |only man/applyExtFunction.Rd | 4 man/cosinorAnalyses.Rd |only man/createConfigFile.Rd | 12 man/extract_params.Rd | 9 man/g.IVIS.Rd | 38 man/g.analyse.Rd | 5 man/g.analyse.avday.Rd | 9 man/g.analyse.perday.Rd | 4 man/g.analyse.perfile.Rd | 9 man/g.calibrate.Rd | 4 man/g.cwaread.Rd | 2 man/g.getmeta.Rd | 5 man/g.imputeTimegaps.Rd | 11 man/g.loadlog.Rd | 2 man/g.part1.Rd | 285 -- man/g.part2.Rd | 198 - man/g.part3.Rd | 92 man/g.part4.Rd | 29 man/g.part4_extradctid.Rd | 17 man/g.part5.Rd | 35 man/g.plot5.Rd | 16 man/g.readtemp_movisens.Rd | 2 man/g.report.part2.Rd | 27 man/g.report.part4.Rd | 14 man/g.report.part5.Rd | 14 man/g.shell.GGIR.Rd | 196 - man/get_nw_clip_block_params.Rd | 2 man/read.myacc.csv.Rd | 28 man/tidyup_df.Rd |only tests/testthat/test_chainof5parts.R | 20 tests/testthat/test_cosinor.R |only tests/testthat/test_g.IVIS.R | 33 tests/testthat/test_gbinread.R | 21 tests/testthat/test_gloadlog.R | 50 tests/testthat/test_greadaccfile.R | 40 tests/testthat/test_imputeTimegaps.R | 17 tests/testthat/test_load_check_params.R | 4 tests/testthat/test_part3_1_night.R | 4 tests/testthat/test_tidyup_df.R |only vignettes/ExternalFunction.Rmd | 14 vignettes/GGIR.Rmd | 137 - vignettes/TutorialDaySegmentAnalyses.Rmd | 14 vignettes/readmyacccsv.Rmd |only 105 files changed, 6587 insertions(+), 2903 deletions(-)
Title: Number Names
Description: Converts numeric vectors to character vectors of English
number names. Provides conversion to cardinals, ordinals, numerators,
and denominators. Supports negative and non-integer numbers.
Author: Alexander Rossell Hayes [aut, cre, cph]
,
Eli Pousson [ctb]
Maintainer: Alexander Rossell Hayes <alexander@rossellhayes.com>
Diff between nombre versions 0.4.0 dated 2021-10-25 and 0.4.1 dated 2022-05-23
DESCRIPTION | 14 ++++---- MD5 | 37 ++++++++++----------- NEWS.md | 7 ++++ R/adverbial.R | 26 ++++++++++---- R/cardinal.R | 66 ++++++++++++++++++++++---------------- R/collective.R | 8 +++- R/convert_fraction.R | 12 +++++- R/denominator.R | 33 ++++++++++++------- R/numerator.R | 2 - R/ordinal.R | 55 ++++++++++++------------------- R/ratio.R | 7 ++-- R/uncardinal.R | 12 +++--- R/utils.R |only man/nombre-package.Rd | 4 +- tests/testthat/test-adverbial.R | 8 ++++ tests/testthat/test-cardinal.R | 8 ++++ tests/testthat/test-collective.R | 8 ++++ tests/testthat/test-denominator.R | 8 ++++ tests/testthat/test-ordinal.R | 8 ++++ tests/testthat/test-ratio.R | 10 +++++ 20 files changed, 212 insertions(+), 121 deletions(-)
Title: Perform and Display Google Trends Queries
Description: An interface for retrieving and displaying the information
returned online by Google Trends is provided. Trends (number of
hits) over the time as well as geographic representation of the
results can be displayed.
Author: Philippe Massicotte [aut, cre],
Dirk Eddelbuettel [aut]
Maintainer: Philippe Massicotte <pmassicotte@hotmail.com>
Diff between gtrendsR versions 1.5.0 dated 2021-10-24 and 1.5.1 dated 2022-05-23
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/countries.R | 2 +- R/related_queries.R | 1 + R/related_topics.R | 5 +++-- R/zzz.R | 3 +++ man/countries.Rd | 2 +- 8 files changed, 24 insertions(+), 15 deletions(-)
Title: Fast and Stable Fitting of Generalized Linear Models using
'RcppEigen'
Description: Fits generalized linear models efficiently using 'RcppEigen'. The iteratively reweighted least squares
implementation utilizes the step-halving approach of Marschner (2011) <doi:10.32614/RJ-2011-012> to help safeguard
against convergence issues.
Author: Jared Huling [aut, cre],
Douglas Bates [cph],
Dirk Eddelbuettel [cph],
Romain Francois [cph],
Yixuan Qiu [cph]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between fastglm versions 0.0.2 dated 2022-04-24 and 0.0.3 dated 2022-05-23
fastglm-0.0.2/fastglm/src/bigmemory.h |only fastglm-0.0.2/fastglm/src/glm.h |only fastglm-0.0.2/fastglm/src/glm_base.h |only fastglm-0.0.2/fastglm/src/glm_big.h |only fastglm-0.0.3/fastglm/DESCRIPTION | 6 +-- fastglm-0.0.3/fastglm/MD5 | 16 +++++----- fastglm-0.0.3/fastglm/inst/doc/quick-usage-guide-to-the-fastglm-package.html | 12 +++---- fastglm-0.0.3/fastglm/inst/include |only fastglm-0.0.3/fastglm/src/bigmemory.cpp | 2 - fastglm-0.0.3/fastglm/src/fit_glm_dense.cpp | 2 - 10 files changed, 19 insertions(+), 19 deletions(-)
Title: R Interface to 'Keras'
Description: Interface to 'Keras' <https://keras.io>, a high-level neural
networks 'API'. 'Keras' was developed with a focus on enabling fast experimentation,
supports both convolution based networks and recurrent networks (as well as
combinations of the two), and runs seamlessly on both 'CPU' and 'GPU' devices.
Author: Tomasz Kalinowski [ctb, cph, cre],
Daniel Falbel [ctb, cph],
JJ Allaire [aut, cph],
Francois Chollet [aut, cph],
RStudio [ctb, cph, fnd],
Google [ctb, cph, fnd],
Yuan Tang [ctb, cph] ,
Wouter Van Der Bijl [ctb, cph],
Martin Studer [ctb, cph],
Sigrid [...truncated...]
Maintainer: Tomasz Kalinowski <tomasz.kalinowski@rstudio.com>
Diff between keras versions 2.8.0 dated 2022-02-09 and 2.9.0 dated 2022-05-23
keras-2.8.0/keras/R/generics.R |only keras-2.9.0/keras/DESCRIPTION | 14 keras-2.9.0/keras/MD5 | 246 +- keras-2.9.0/keras/NAMESPACE | 69 keras-2.9.0/keras/NEWS.md | 104 + keras-2.9.0/keras/R/Layer.R | 27 keras-2.9.0/keras/R/backend.R | 56 keras-2.9.0/keras/R/freeze.R | 124 + keras-2.9.0/keras/R/history.R | 4 keras-2.9.0/keras/R/initializers.R | 4 keras-2.9.0/keras/R/install.R | 17 keras-2.9.0/keras/R/layer-custom.R | 44 keras-2.9.0/keras/R/layer-methods.R | 22 keras-2.9.0/keras/R/layers-convolutional.R | 6 keras-2.9.0/keras/R/layers-core.R | 16 keras-2.9.0/keras/R/layers-noise.R | 30 keras-2.9.0/keras/R/layers-normalization.R | 39 keras-2.9.0/keras/R/layers-preprocessing.R | 48 keras-2.9.0/keras/R/layers-recurrent-cells.R | 2 keras-2.9.0/keras/R/layers-recurrent.R | 2 keras-2.9.0/keras/R/learning_rate_schedules.R |only keras-2.9.0/keras/R/metrics.R | 32 keras-2.9.0/keras/R/model.R | 100 - keras-2.9.0/keras/R/new-py-types.R |only keras-2.9.0/keras/R/package.R | 11 keras-2.9.0/keras/R/preprocessing.R | 205 +- keras-2.9.0/keras/R/py-classes.R | 164 + keras-2.9.0/keras/R/reexports.R | 4 keras-2.9.0/keras/R/regularizers.R | 37 keras-2.9.0/keras/R/utils.R | 241 ++ keras-2.9.0/keras/build/vignette.rds |binary keras-2.9.0/keras/inst/doc/applications.html | 252 +-- keras-2.9.0/keras/inst/doc/custom_layers.html | 569 +++--- keras-2.9.0/keras/inst/doc/custom_models.html | 175 -- keras-2.9.0/keras/inst/doc/faq.html | 823 +++------- keras-2.9.0/keras/inst/doc/functional_api.html | 648 +++---- keras-2.9.0/keras/inst/doc/guide_keras.html | 661 +++----- keras-2.9.0/keras/inst/doc/index.html | 247 --- keras-2.9.0/keras/inst/doc/saving_serializing.html | 483 ++--- keras-2.9.0/keras/inst/doc/sequential_model.html | 759 ++++----- keras-2.9.0/keras/inst/doc/training_callbacks.html | 246 +- keras-2.9.0/keras/inst/doc/training_visualization.html | 284 +-- keras-2.9.0/keras/man/Layer.Rd | 11 keras-2.9.0/keras/man/Metric.Rd | 47 keras-2.9.0/keras/man/adapt.Rd | 8 keras-2.9.0/keras/man/backend.Rd | 2 keras-2.9.0/keras/man/constraints.Rd | 4 keras-2.9.0/keras/man/create_layer_wrapper.Rd | 8 keras-2.9.0/keras/man/evaluate.keras.engine.training.Model.Rd | 2 keras-2.9.0/keras/man/fit.keras.engine.training.Model.Rd | 2 keras-2.9.0/keras/man/fit_generator.Rd | 6 keras-2.9.0/keras/man/freeze_weights.Rd | 49 keras-2.9.0/keras/man/get_config.Rd | 6 keras-2.9.0/keras/man/get_layer.Rd | 3 keras-2.9.0/keras/man/get_weights.Rd | 9 keras-2.9.0/keras/man/grapes-py_class-grapes.Rd | 36 keras-2.9.0/keras/man/grapes-set-active-grapes.Rd | 1 keras-2.9.0/keras/man/image_dataset_from_directory.Rd | 94 - keras-2.9.0/keras/man/initializer_glorot_normal.Rd | 2 keras-2.9.0/keras/man/initializer_glorot_uniform.Rd | 2 keras-2.9.0/keras/man/install_keras.Rd | 8 keras-2.9.0/keras/man/k_clip.Rd | 2 keras-2.9.0/keras/man/k_squeeze.Rd | 2 keras-2.9.0/keras/man/k_unstack.Rd |only keras-2.9.0/keras/man/keras_model_sequential.Rd | 2 keras-2.9.0/keras/man/layer_alpha_dropout.Rd | 38 keras-2.9.0/keras/man/layer_category_encoding.Rd | 1 keras-2.9.0/keras/man/layer_center_crop.Rd | 1 keras-2.9.0/keras/man/layer_conv_1d_transpose.Rd | 6 keras-2.9.0/keras/man/layer_conv_lstm_1d.Rd | 2 keras-2.9.0/keras/man/layer_conv_lstm_2d.Rd | 2 keras-2.9.0/keras/man/layer_conv_lstm_3d.Rd | 2 keras-2.9.0/keras/man/layer_cudnn_lstm.Rd | 2 keras-2.9.0/keras/man/layer_discretization.Rd | 1 keras-2.9.0/keras/man/layer_gru_cell.Rd | 4 keras-2.9.0/keras/man/layer_hashing.Rd | 17 keras-2.9.0/keras/man/layer_integer_lookup.Rd | 1 keras-2.9.0/keras/man/layer_lstm.Rd | 2 keras-2.9.0/keras/man/layer_lstm_cell.Rd | 6 keras-2.9.0/keras/man/layer_normalization.Rd | 1 keras-2.9.0/keras/man/layer_random_brightness.Rd |only keras-2.9.0/keras/man/layer_random_contrast.Rd | 2 keras-2.9.0/keras/man/layer_random_crop.Rd | 2 keras-2.9.0/keras/man/layer_random_flip.Rd | 2 keras-2.9.0/keras/man/layer_random_height.Rd | 2 keras-2.9.0/keras/man/layer_random_rotation.Rd | 2 keras-2.9.0/keras/man/layer_random_translation.Rd | 2 keras-2.9.0/keras/man/layer_random_width.Rd | 2 keras-2.9.0/keras/man/layer_random_zoom.Rd | 2 keras-2.9.0/keras/man/layer_rescaling.Rd | 1 keras-2.9.0/keras/man/layer_resizing.Rd | 1 keras-2.9.0/keras/man/layer_string_lookup.Rd | 1 keras-2.9.0/keras/man/layer_text_vectorization.Rd | 1 keras-2.9.0/keras/man/layer_unit_normalization.Rd |only keras-2.9.0/keras/man/learning_rate_schedule_cosine_decay.Rd |only keras-2.9.0/keras/man/learning_rate_schedule_cosine_decay_restarts.Rd |only keras-2.9.0/keras/man/learning_rate_schedule_exponential_decay.Rd |only keras-2.9.0/keras/man/learning_rate_schedule_inverse_time_decay.Rd |only keras-2.9.0/keras/man/learning_rate_schedule_piecewise_constant_decay.Rd |only keras-2.9.0/keras/man/learning_rate_schedule_polynomial_decay.Rd |only keras-2.9.0/keras/man/loss-functions.Rd | 6 keras-2.9.0/keras/man/metric_categorical_crossentropy.Rd | 6 keras-2.9.0/keras/man/metric_cosine_similarity.Rd | 4 keras-2.9.0/keras/man/metric_hinge.Rd | 4 keras-2.9.0/keras/man/metric_kullback_leibler_divergence.Rd | 4 keras-2.9.0/keras/man/metric_mean.Rd | 12 keras-2.9.0/keras/man/metric_mean_iou.Rd | 6 keras-2.9.0/keras/man/metric_mean_relative_error.Rd | 12 keras-2.9.0/keras/man/metric_mean_wrapper.Rd | 4 keras-2.9.0/keras/man/multi_gpu_model.Rd | 4 keras-2.9.0/keras/man/new-classes.Rd |only keras-2.9.0/keras/man/new_learning_rate_schedule_class.Rd |only keras-2.9.0/keras/man/plot.keras.engine.training.Model.Rd |only keras-2.9.0/keras/man/predict.keras.engine.training.Model.Rd | 6 keras-2.9.0/keras/man/predict_proba.Rd | 12 keras-2.9.0/keras/man/reexports.Rd | 3 keras-2.9.0/keras/man/regularizer_orthogonal.Rd |only keras-2.9.0/keras/man/summary.keras.engine.training.Model.Rd | 13 keras-2.9.0/keras/man/text_dataset_from_directory.Rd | 6 keras-2.9.0/keras/man/time_distributed.Rd | 4 keras-2.9.0/keras/man/timeseries_dataset_from_array.Rd | 63 keras-2.9.0/keras/man/zip_lists.Rd |only keras-2.9.0/keras/tests/testthat/test-Layer.R | 22 keras-2.9.0/keras/tests/testthat/test-freeze.R | 44 keras-2.9.0/keras/tests/testthat/test-layers-normalization.R | 12 keras-2.9.0/keras/tests/testthat/test-layers-preprocessing.R | 7 keras-2.9.0/keras/tests/testthat/test-metrics.R | 3 keras-2.9.0/keras/tests/testthat/test-model-persistence.R | 58 keras-2.9.0/keras/tests/testthat/test-preprocessing.R | 10 keras-2.9.0/keras/tests/testthat/test-py-class.R | 55 keras-2.9.0/keras/tests/testthat/test-utils.R | 52 keras-2.9.0/keras/tools/make-layer-wrapper.R | 4 keras-2.9.0/keras/tools/make-wrapper.R |only 133 files changed, 4071 insertions(+), 3592 deletions(-)
Title: Harmonizing CN8 and PC8 Product Codes
Description: Several functions are provided to harmonize CN8 (Combined Nomenclature
8 digits) and PC8 (Production Communautaire 8 digits) product codes over
time and the classification systems HS6 and BEC. Harmonization of CN8
codes are possible by default from 1995 to 2022 and of PC8 from 2001 to
2021, respectively.
Author: Christoph Baumgartner [cre, aut]
,
Stjepan Srhoj [aut] ,
Janette Walde [aut]
Maintainer: Christoph Baumgartner <Christoph.Baumgartner@uibk.ac.at>
Diff between harmonizer versions 0.2.1 dated 2022-03-07 and 0.3.0 dated 2022-05-23
DESCRIPTION | 22 MD5 | 71 NAMESPACE | 3 NEWS.md | 10 R/cn8_to_bec.R | 56 R/harmonize_cn8.R | 97 R/harmonize_pc8.R | 101 R/history_matrix_cn8.R | 6 R/pc8_to_bec.R | 59 R/utilize_cn8.R | 58 R/utilize_pc8.R | 50 inst/doc/harmonizer.Rmd | 49 inst/doc/harmonizer.html | 671 + inst/extdata/CN8/CN8_2021.rds |only inst/extdata/CN8/CN8_2022.rds |only inst/extdata/CN8/CN8_concordances_1988_2022.csv |only inst/extdata/HS6toBEC/HS1996toBEC.csv |only inst/extdata/HS6toBEC/HS2012toBEC.csv |10411 +++++++++++------------ inst/extdata/HS6toBEC/HS2017toBEC.csv |10775 ++++++++++++------------ inst/extdata/PC8/PC8_2001.rds |only inst/extdata/PC8/PC8_2001_2002.rds |only inst/extdata/PC8/PC8_2002.rds |only inst/extdata/PC8/PC8_2002_2003.rds |only inst/extdata/PC8/PC8_2003.rds |only inst/extdata/PC8/PC8_2003_2004.rds |only inst/extdata/PC8/PC8_2004.rds |only inst/extdata/PC8/PC8_2004_2005.rds |only inst/extdata/PC8/PC8_2005.rds |only inst/extdata/PC8/PC8_2005_2006.rds |only inst/extdata/PC8/PC8_2006.rds |only inst/extdata/PC8/PC8_2006_2007.rds |only inst/extdata/PC8/PC8_2017_2018.rds |only inst/extdata/PC8/PC8_2018.rds |only inst/extdata/PC8/PC8_2018_2019.rds |only inst/extdata/PC8/PC8_2019.rds |only inst/extdata/PC8/PC8_2019_2020.rds |only inst/extdata/PC8/PC8_2020.rds |only inst/extdata/PC8/PC8_2020_2021.rds |only inst/extdata/PC8/PC8_2021.rds |only inst/extdata/PC8/PC8_CN8_2001.rds |only inst/extdata/PC8/PC8_CN8_2002.rds |only inst/extdata/PC8/PC8_CN8_2003.rds |only inst/extdata/PC8/PC8_CN8_2004.rds |only inst/extdata/PC8/PC8_CN8_2005.rds |only inst/extdata/PC8/PC8_CN8_2020.rds |only inst/extdata/PC8/PC8_CN8_2021.rds |only man/harmonize_cn8.Rd | 14 man/harmonize_pc8.Rd | 14 man/history_martix_cn8.Rd | 2 man/utilize_cn8.Rd | 18 man/utilize_pc8.Rd | 18 vignettes/harmonizer.Rmd | 49 52 files changed, 11686 insertions(+), 10868 deletions(-)
Title: Inference of Gene Regulatory Networks
Description: We present 'corto' (Correlation Tool), a simple package to infer
gene regulatory networks and visualize master regulators from gene expression
data using DPI (Data Processing Inequality) and bootstrapping to recover edges.
An initial step is performed to calculate all significant
edges between a list of source nodes (centroids) and target genes.
Then all triplets containing two centroids and one target are tested
in a DPI step which removes edges. A bootstrapping process then calculates
the robustness of the network, eventually re-adding edges previously removed by DPI.
The algorithm has been optimized to run outside a computing cluster, using a fast correlation
implementation. The package finally provides functions to calculate network enrichment
analysis from RNA-Seq and ATAC-Seq signatures as described in the article by
Giorgi lab (2020) <doi:10.1093/bioinformatics/btaa223>.
Author: Federico M. Giorgi [aut, cre],
Daniele Mercatelli [ctb],
Gonzalo Lopez-Garcia [ctb]
Maintainer: Federico M. Giorgi <federico.giorgi@gmail.com>
Diff between corto versions 1.1.10 dated 2021-10-22 and 1.1.11 dated 2022-05-23
DESCRIPTION | 12 ++++++------ MD5 | 13 +++++++------ NAMESPACE | 4 +++- R/functions.R | 28 +++++++++++++++++++++++++++- R/gsea.R | 2 +- build/vignette.rds |binary inst/doc/corto_vignette.html | 6 +++++- man/barplot2.Rd |only 8 files changed, 49 insertions(+), 16 deletions(-)
Title: Analysis of Check-All-that-Apply (CATA) Data
Description: Functions for analyzing check-all-that-apply (CATA) data from consumer and sensory tests. Cochran's Q test, McNemar's test, and Penalty-Lift analysis provided, as described in for CATA data analysis by Meyners, Castura & Carr (2013) <doi:10.1016/j.foodqual.2013.06.010>. Cluster analysis can be performed using b-cluster analysis. The quality of cluster analysis solutions can be evaluated using various measures. The methods related to b-cluster analysis are described in a manuscript by Castura, Meyners, Varela & Naes (2022) <doi:10.1016/j.foodqual.2022.104564>.
Author: J.C. Castura [aut, cre, ctb]
Maintainer: J.C. Castura <jcastura@compusense.com>
Diff between cata versions 0.0.10.8 dated 2022-03-05 and 0.0.10.9 dated 2022-05-23
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/cata.R | 2 +- build/partial.rdb |binary 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Load Data from Facebook API Marketing
Description: Load data by campaigns, ads, ad sets and insights, ad account and business manager
from Facebook Marketing API into R. For more details see official documents by Facebook
Marketing API <https://developers.facebook.com/docs/marketing-apis/>.
Author: Alexey Seleznev [aut, cre]
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rfacebookstat versions 2.5.0 dated 2021-12-16 and 2.6.2 dated 2022-05-23
rfacebookstat-2.5.0/rfacebookstat/build/vignette.rds |only rfacebookstat-2.5.0/rfacebookstat/inst/doc |only rfacebookstat-2.5.0/rfacebookstat/vignettes |only rfacebookstat-2.6.2/rfacebookstat/DESCRIPTION | 12 rfacebookstat-2.6.2/rfacebookstat/MD5 | 72 +-- rfacebookstat-2.6.2/rfacebookstat/NEWS.md | 20 rfacebookstat-2.6.2/rfacebookstat/R/authorization.R | 18 rfacebookstat-2.6.2/rfacebookstat/R/fbActions.R | 235 +++++----- rfacebookstat-2.6.2/rfacebookstat/R/fbDeleteAdAccountUsers.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbGetAdAccountCustomAudiences.R | 4 rfacebookstat-2.6.2/rfacebookstat/R/fbGetAdAccountUsers.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbGetAdAccountUsersPermissions.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbGetAdAccounts.R | 6 rfacebookstat-2.6.2/rfacebookstat/R/fbGetAdAccountsConversions.R | 4 rfacebookstat-2.6.2/rfacebookstat/R/fbGetAdCreative.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbGetAdSets.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbGetAdVideos.R | 4 rfacebookstat-2.6.2/rfacebookstat/R/fbGetAds.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbGetApps.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbGetBusinessManagers.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbGetBusinessManagersUsers.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbGetBusinessUserAdAccounts.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbGetCampaigns.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbGetCatalogs.R | 4 rfacebookstat-2.6.2/rfacebookstat/R/fbGetLongTimeToken.R |only rfacebookstat-2.6.2/rfacebookstat/R/fbGetMarketingStat.R | 8 rfacebookstat-2.6.2/rfacebookstat/R/fbGetPages.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbGetUserAdAccounts.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/fbUpdateAdAccountUsers.R | 2 rfacebookstat-2.6.2/rfacebookstat/R/zzz.R | 2 rfacebookstat-2.6.2/rfacebookstat/README.md | 119 ----- rfacebookstat-2.6.2/rfacebookstat/build/partial.rdb |binary rfacebookstat-2.6.2/rfacebookstat/man/fbGetCostData.Rd | 5 rfacebookstat-2.6.2/rfacebookstat/man/fbGetToken.Rd | 58 +- 34 files changed, 269 insertions(+), 330 deletions(-)
Title: 'Rcmdr' Plug-in GUI for Biclustering
Description: A plug-in for R Commander ('Rcmdr'). The package is a Graphical
User Interface (GUI) in which several biclustering methods can be executed,
followed by diagnostics and plots of the results. Further, the GUI also has
the possibility to connect the methods to more general diagnostic packages for
biclustering. Biclustering methods from 'biclust', 'fabia', 's4vd', 'iBBiG',
'isa2', 'BiBitR', 'rqubic' and 'BicARE' are implemented. Additionally, 'superbiclust' and
'BcDiag' are also implemented to be able to further investigate results. The
GUI also provides a couple of extra utilities to export, save, search through
and plot the results. 'RcmdrPlugin.BiclustGUI' also provides a very specific
framework for biclustering in which new methods, diagnostics and plots can be
added. Scripts were prepared so that R-package developers can freely design
their own dialogs in the GUI which can then be added by the maintainer of
'RcmdrPlugin.BiclustGUI'. These scripts do not required any knowledge of 'tcltk'
and 'Rcmdr' and are easy to fill in. (Note: rqubic currently requires manual installation through BiocManager::install('rqubic').)
Author: De Troyer Ewoud, Otava Martin
Maintainer: De Troyer Ewoud <ewoud.detroyer@uhasselt.be>
Diff between RcmdrPlugin.BiclustGUI versions 1.1.3 dated 2020-07-13 and 1.1.3.1 dated 2022-05-23
DESCRIPTION | 6 +++--- MD5 | 4 ++-- inst/doc/GuideBiclustGUI.pdf |binary 3 files changed, 5 insertions(+), 5 deletions(-)
More information about RcmdrPlugin.BiclustGUI at CRAN
Permanent link
Title: Bayesian Reconstruction of Disease Outbreaks by Combining
Epidemiologic and Genomic Data
Description: Bayesian reconstruction of disease outbreaks using epidemiological
and genetic information. Jombart T, Cori A, Didelot X, Cauchemez S, Fraser
C and Ferguson N. 2014. <doi:10.1371/journal.pcbi.1003457>. Campbell, F,
Cori A, Ferguson N, Jombart T. 2019. <doi:10.1371/journal.pcbi.1006930>.
Author: Thibaut Jombart [aut],
Finlay Campbell [aut, cre],
Rich Fitzjohn [aut],
Gerry Tonkin-Hill [ctb],
Kristjan Eldjarn [ctb],
Alexis Robert [ctb]
Maintainer: Finlay Campbell <finlaycampbell93@gmail.com>
Diff between outbreaker2 versions 1.1.2 dated 2021-02-09 and 1.1.3 dated 2022-05-23
outbreaker2-1.1.2/outbreaker2/vignettes/customisation_cache/html/run_new_move_5726c9b3e30924d986e3e44ffd6e0036.RData |only outbreaker2-1.1.2/outbreaker2/vignettes/customisation_cache/html/run_new_move_5726c9b3e30924d986e3e44ffd6e0036.rdb |only outbreaker2-1.1.2/outbreaker2/vignettes/customisation_cache/html/run_new_move_5726c9b3e30924d986e3e44ffd6e0036.rdx |only outbreaker2-1.1.2/outbreaker2/vignettes/customisation_cache/html/run_null_model_d112d898e13cade05279d2d90d34e60f.RData |only outbreaker2-1.1.2/outbreaker2/vignettes/customisation_cache/html/run_null_model_d112d898e13cade05279d2d90d34e60f.rdb |only outbreaker2-1.1.2/outbreaker2/vignettes/customisation_cache/html/run_null_model_d112d898e13cade05279d2d90d34e60f.rdx |only outbreaker2-1.1.2/outbreaker2/vignettes/customisation_cache/html/run_wt_ffbe1bb0ebffddc18bb5d3ae3b1b3a5f.RData |only outbreaker2-1.1.2/outbreaker2/vignettes/customisation_cache/html/run_wt_ffbe1bb0ebffddc18bb5d3ae3b1b3a5f.rdb |only outbreaker2-1.1.2/outbreaker2/vignettes/customisation_cache/html/run_wt_ffbe1bb0ebffddc18bb5d3ae3b1b3a5f.rdx |only outbreaker2-1.1.2/outbreaker2/vignettes/introduction_cache/html/config2_e0d3ea2635745de041b80aae763904c7.RData |only outbreaker2-1.1.2/outbreaker2/vignettes/introduction_cache/html/config2_e0d3ea2635745de041b80aae763904c7.rdb |only outbreaker2-1.1.2/outbreaker2/vignettes/introduction_cache/html/config2_e0d3ea2635745de041b80aae763904c7.rdx |only outbreaker2-1.1.2/outbreaker2/vignettes/introduction_cache/html/first_run_931e937e4e7a0450deb5a082d5d9b15b.RData |only outbreaker2-1.1.2/outbreaker2/vignettes/introduction_cache/html/first_run_931e937e4e7a0450deb5a082d5d9b15b.rdb |only outbreaker2-1.1.2/outbreaker2/vignettes/introduction_cache/html/first_run_931e937e4e7a0450deb5a082d5d9b15b.rdx |only outbreaker2-1.1.3/outbreaker2/DESCRIPTION | 12 outbreaker2-1.1.3/outbreaker2/MD5 | 86 outbreaker2-1.1.3/outbreaker2/NEWS.md | 13 outbreaker2-1.1.3/outbreaker2/R/get_cpp_api.R | 204 - outbreaker2-1.1.3/outbreaker2/R/outbreaker_data.R | 3 outbreaker2-1.1.3/outbreaker2/R/package.R | 82 outbreaker2-1.1.3/outbreaker2/R/palettes.R | 6 outbreaker2-1.1.3/outbreaker2/R/ref_priors.R | 100 outbreaker2-1.1.3/outbreaker2/R/zzz.R | 20 outbreaker2-1.1.3/outbreaker2/build/vignette.rds |binary outbreaker2-1.1.3/outbreaker2/inst/doc/Rcpp_API.html | 18 outbreaker2-1.1.3/outbreaker2/inst/doc/customisation.Rmd | 1370 +++++----- outbreaker2-1.1.3/outbreaker2/inst/doc/customisation.html | 42 outbreaker2-1.1.3/outbreaker2/inst/doc/introduction.html | 592 ++-- outbreaker2-1.1.3/outbreaker2/inst/doc/overview.html | 14 outbreaker2-1.1.3/outbreaker2/man/custom_likelihoods.Rd | 194 - outbreaker2-1.1.3/outbreaker2/man/get_cpp_api.Rd | 184 - outbreaker2-1.1.3/outbreaker2/man/outbreaker_package.Rd | 82 outbreaker2-1.1.3/outbreaker2/man/palettes.Rd | 2 outbreaker2-1.1.3/outbreaker2/src/RcppExports.cpp | 5 outbreaker2-1.1.3/outbreaker2/tests/testthat/test_sim_ctd.R | 56 outbreaker2-1.1.3/outbreaker2/vignettes/customisation.Rmd | 1370 +++++----- outbreaker2-1.1.3/outbreaker2/vignettes/customisation_cache/html/__packages | 1 outbreaker2-1.1.3/outbreaker2/vignettes/customisation_cache/html/run_new_move_201bee2736c15bd01aff7d66538c46bd.RData |only outbreaker2-1.1.3/outbreaker2/vignettes/customisation_cache/html/run_new_move_201bee2736c15bd01aff7d66538c46bd.rdb |only outbreaker2-1.1.3/outbreaker2/vignettes/customisation_cache/html/run_new_move_201bee2736c15bd01aff7d66538c46bd.rdx |only outbreaker2-1.1.3/outbreaker2/vignettes/customisation_cache/html/run_null_model_8771832d87831190a82188fc37cef737.RData |only outbreaker2-1.1.3/outbreaker2/vignettes/customisation_cache/html/run_null_model_8771832d87831190a82188fc37cef737.rdb |only outbreaker2-1.1.3/outbreaker2/vignettes/customisation_cache/html/run_null_model_8771832d87831190a82188fc37cef737.rdx |only outbreaker2-1.1.3/outbreaker2/vignettes/customisation_cache/html/run_wt_770f6e5ae6cc9263e7c7c554c148a8b2.RData |only outbreaker2-1.1.3/outbreaker2/vignettes/customisation_cache/html/run_wt_770f6e5ae6cc9263e7c7c554c148a8b2.rdb |only outbreaker2-1.1.3/outbreaker2/vignettes/customisation_cache/html/run_wt_770f6e5ae6cc9263e7c7c554c148a8b2.rdx |only outbreaker2-1.1.3/outbreaker2/vignettes/figs-customisation/res_null_priors-1.png |binary outbreaker2-1.1.3/outbreaker2/vignettes/figs-customisation/traces_custom_priors-4.png |binary outbreaker2-1.1.3/outbreaker2/vignettes/figs-customisation/traces_custom_priors-5.png |binary outbreaker2-1.1.3/outbreaker2/vignettes/figs-introduction/many_plots-1.png |binary outbreaker2-1.1.3/outbreaker2/vignettes/figs-introduction/many_plots-2.png |binary outbreaker2-1.1.3/outbreaker2/vignettes/introduction_cache/html/__packages | 1 outbreaker2-1.1.3/outbreaker2/vignettes/introduction_cache/html/config2_a6e218c734814a74f6d109430a70e31f.RData |only outbreaker2-1.1.3/outbreaker2/vignettes/introduction_cache/html/config2_a6e218c734814a74f6d109430a70e31f.rdb |only outbreaker2-1.1.3/outbreaker2/vignettes/introduction_cache/html/config2_a6e218c734814a74f6d109430a70e31f.rdx |only outbreaker2-1.1.3/outbreaker2/vignettes/introduction_cache/html/first_run_262464f50c8d3b374ad1083b0ea73503.RData |only outbreaker2-1.1.3/outbreaker2/vignettes/introduction_cache/html/first_run_262464f50c8d3b374ad1083b0ea73503.rdb |only outbreaker2-1.1.3/outbreaker2/vignettes/introduction_cache/html/first_run_262464f50c8d3b374ad1083b0ea73503.rdx |only 59 files changed, 2320 insertions(+), 2137 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation
Routines
Description: Fit and compare nonlinear mixed-effects models in differential
equations with flexible dosing information commonly seen in pharmacokinetics
and pharmacodynamics (Almquist, Leander, and Jirstrand 2015
<doi:10.1007/s10928-015-9409-1>). Differential equation solving is
by compiled C code provided in the 'rxode2' package
(Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Yuan Xiong [aut],
Rik Schoemaker [aut] ,
Justin Wilkins [aut] ,
Wenping Wang [aut],
Robert Leary [ctb],
Mason McComb [ctb] ,
Vipul Mann [aut],
Mirjam Trame [ctb],
Mahmoud Abdelwahab [ctb],
Teun Post [ctb],
Richard Hooijmai [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2est versions 2.0.6 dated 2022-05-12 and 2.0.7 dated 2022-05-23
nlmixr2est-2.0.6/nlmixr2est/R/mu-cov-downgrade.R |only nlmixr2est-2.0.7/nlmixr2est/DESCRIPTION | 10 - nlmixr2est-2.0.7/nlmixr2est/MD5 | 48 +++--- nlmixr2est-2.0.7/nlmixr2est/NAMESPACE | 1 nlmixr2est-2.0.7/nlmixr2est/NEWS.md | 19 ++ nlmixr2est-2.0.7/nlmixr2est/R/augPred.R | 49 ++++-- nlmixr2est-2.0.7/nlmixr2est/R/nlme.R | 6 nlmixr2est-2.0.7/nlmixr2est/R/nlmeRxUiGet.R | 2 nlmixr2est-2.0.7/nlmixr2est/R/nlmixr2Est.R | 57 ++++--- nlmixr2est-2.0.7/nlmixr2est/R/nlmixr2_md5.R |only nlmixr2est-2.0.7/nlmixr2est/R/nmObjHandle.R | 1 nlmixr2est-2.0.7/nlmixr2est/R/preProcessModel.R | 9 - nlmixr2est-2.0.7/nlmixr2est/R/saem.R | 3 nlmixr2est-2.0.7/nlmixr2est/R/saemRxUiGetModel.R | 21 +- nlmixr2est-2.0.7/nlmixr2est/R/sharedControl.R | 2 nlmixr2est-2.0.7/nlmixr2est/R/validate.R | 1 nlmixr2est-2.0.7/nlmixr2est/R/vpc.R | 30 +++- nlmixr2est-2.0.7/nlmixr2est/man/dot-saemDropMuRefFromModel.Rd | 4 nlmixr2est-2.0.7/nlmixr2est/man/vpcSim.Rd | 13 + nlmixr2est-2.0.7/nlmixr2est/src/inner.cpp | 73 +++++----- nlmixr2est-2.0.7/nlmixr2est/tests/testthat.R | 8 - nlmixr2est-2.0.7/nlmixr2est/tests/testthat/test-augpred.R | 32 ++++ nlmixr2est-2.0.7/nlmixr2est/tests/testthat/test-focei-wang2007.R | 8 - nlmixr2est-2.0.7/nlmixr2est/tests/testthat/test-saem-translate.R | 6 nlmixr2est-2.0.7/nlmixr2est/tests/testthat/test-update-estimates.R | 62 ++++---- nlmixr2est-2.0.7/nlmixr2est/tests/testthat/test-vpcSim.R | 14 - 26 files changed, 300 insertions(+), 179 deletions(-)
Title: Tools for Plotting Skew-T Diagrams and Wind Profiles
Description: A
collection of programs for
plotting SKEW-T,log p diagrams and wind profiles for data
collected by radiosondes (the typical weather balloon-borne
instrument). The format of this plot with companion lines to
assess atmospheric stability are both standard in meteorology
and difficult to create from basic graphics functions. Hence
this package. One novel feature is being able add several
profiles to the same plot for comparison.
Use "help(ExampleSonde)" for an explanation of the variables
needed and how they should be named in a data frame. See
<https://github.com/dnychka/Radiosonde> for the package home page.
Author: Doug Nychka, Eric Gilleland, Liangying Zhang, Tim Hoar, Kate Young
Maintainer: Doug Nychka <nychka@mines.edu>
Diff between RadioSonde versions 1.4 dated 2014-09-17 and 4.2 dated 2022-05-23
RadioSonde-1.4/RadioSonde/R/PWV.R |only RadioSonde-1.4/RadioSonde/R/getsonde.R |only RadioSonde-1.4/RadioSonde/R/plotsonde.R |only RadioSonde-1.4/RadioSonde/R/plotwind.R |only RadioSonde-1.4/RadioSonde/R/skewt.axis.R |only RadioSonde-1.4/RadioSonde/R/skewt.data.R |only RadioSonde-1.4/RadioSonde/R/skewt.points.R |only RadioSonde-1.4/RadioSonde/R/td.to.q.R |only RadioSonde-1.4/RadioSonde/data/ExampleSonde.rda |only RadioSonde-1.4/RadioSonde/data/ExampleSondeText.rda |only RadioSonde-1.4/RadioSonde/man/PWV.Rd |only RadioSonde-1.4/RadioSonde/man/getsonde.Rd |only RadioSonde-1.4/RadioSonde/man/plotsonde.Rd |only RadioSonde-1.4/RadioSonde/man/plotwind.Rd |only RadioSonde-1.4/RadioSonde/man/skewt.axis.Rd |only RadioSonde-1.4/RadioSonde/man/skewt.points.Rd |only RadioSonde-4.2/RadioSonde/DESCRIPTION | 33 ++++-- RadioSonde-4.2/RadioSonde/MD5 | 41 +++----- RadioSonde-4.2/RadioSonde/NAMESPACE | 8 + RadioSonde-4.2/RadioSonde/R/plotWind.R |only RadioSonde-4.2/RadioSonde/R/setupSkewt.R |only RadioSonde-4.2/RadioSonde/R/skewtPlot.R |only RadioSonde-4.2/RadioSonde/R/skewtUtilities.R |only RadioSonde-4.2/RadioSonde/R/skewty.R | 2 RadioSonde-4.2/RadioSonde/R/station.symbol.R | 9 + RadioSonde-4.2/RadioSonde/data/sonde1.RData |only RadioSonde-4.2/RadioSonde/data/sonde2.RData |only RadioSonde-4.2/RadioSonde/inst |only RadioSonde-4.2/RadioSonde/man/Example.Rd | 90 +++++++++++-------- RadioSonde-4.2/RadioSonde/man/RadioSonde-internal.Rd | 38 ++++++-- RadioSonde-4.2/RadioSonde/man/plotWind.Rd |only RadioSonde-4.2/RadioSonde/man/skewt.lines.Rd | 19 ---- RadioSonde-4.2/RadioSonde/man/skewtPlot.Rd |only RadioSonde-4.2/RadioSonde/man/station.symbol.Rd | 18 ++- 34 files changed, 148 insertions(+), 110 deletions(-)
Title: Metabolomics-Based Models for Imputing Risk
Description: Provides an intuitive framework for ad-hoc statistical analysis of 1H-NMR metabolomics by Nightingale Health. It allows to easily explore new metabolomics measurements assayed by Nightingale Health, comparing the distributions with a large Consortium (BBMRI-nl); project previously published metabolic scores [<doi:10.1016/j.ebiom.2021.103764>, <doi:10.1161/CIRCGEN.119.002610>, <doi:10.1038/s41467-019-11311-9>, <doi:10.7554/eLife.63033>, <doi:10.1161/CIRCULATIONAHA.114.013116>, <doi:10.1007/s00125-019-05001-w>]; and calibrate the metabolic surrogate values to a desired dataset.
Author: Daniele Bizzarri [aut, cre] ,
Marcel Reinders [aut, ths] ,
Marian Beekman [aut] ,
Pieternella Eline Slagboom [aut, ths]
,
Erik van den Akker [aut, ths]
Maintainer: Daniele Bizzarri <d.bizzarri@lumc.nl>
Diff between MiMIR versions 1.3 dated 2022-05-18 and 1.4 dated 2022-05-23
DESCRIPTION | 8 - MD5 | 60 +++++++------- R/datasets.R | 24 ++--- R/launchApp.R | 10 +- R/predictors_functions.R | 40 +++------ R/utils.R | 14 +-- inst/shinyApp/tabs/tab_surro_tables/server_surro_tables.R | 30 ++----- man/Ahola_Olli_betas.Rd | 2 man/BBMRI_hist_plot.Rd | 8 - man/BMI_LDL_eGFR.Rd | 6 - man/CVD_score_betas.Rd | 2 man/PARAM_metaboAge.Rd | 2 man/QCprep.Rd | 2 man/apply.fit.Rd | 2 man/apply.scale.Rd | 2 man/comp.CVD_score.Rd | 11 -- man/comp.T2D_Ahola_Olli.Rd | 2 man/comp.mort_score.Rd | 2 man/impute_miss.Rd | 2 man/metabolites_subsets.Rd | 8 - man/mort_betas.Rd | 2 man/plattCalibration.Rd | 2 man/prep_met_for_scores.Rd | 6 - man/report.dim.Rd | 2 man/startApp.Rd | 10 +- man/subset_metabolites_overlap.Rd | 2 man/subset_samples_miss.Rd | 2 man/subset_samples_sd.Rd | 2 man/subset_samples_zero.Rd | 2 man/synthetic_metabolic_dataset.Rd | 4 man/synthetic_phenotypic_dataset.Rd | 4 31 files changed, 125 insertions(+), 150 deletions(-)
Title: Computation of Generalized Nash Equilibria
Description: Provide functions to compute standard and generalized Nash Equilibria.
Optimization methods are available nonsmooth reformulation, fixed-point formulation,
minimization problem and constrained-equation reformulation.
See e.g. Kanzow and Facchinei (2010), <doi:10.1007/s10479-009-0653-x>.
Author: Christophe Dutang
Maintainer: Christophe Dutang <dutangc@gmail.com>
Diff between GNE versions 0.99-3.1 dated 2022-05-23 and 0.99-4 dated 2022-05-23
GNE-0.99-3.1/GNE/inst/TODOlist.txt |only GNE-0.99-3.1/GNE/vignettes/img |only GNE-0.99-4/GNE/DESCRIPTION | 10 +++++----- GNE-0.99-4/GNE/MD5 | 21 +++++++++------------ GNE-0.99-4/GNE/R/solv-eq.R | 2 +- GNE-0.99-4/GNE/R/solv-minpb.R | 4 ++-- GNE-0.99-4/GNE/R/util-minfindingFunc.R | 14 ++++++++------ GNE-0.99-4/GNE/build/vignette.rds |binary GNE-0.99-4/GNE/inst/NEWS | 5 +++++ GNE-0.99-4/GNE/inst/doc/GNE-howto.Rnw | 24 ++++++++++++------------ GNE-0.99-4/GNE/inst/doc/GNE-howto.pdf |binary GNE-0.99-4/GNE/vignettes/GNE-howto.Rnw | 24 ++++++++++++------------ 12 files changed, 54 insertions(+), 50 deletions(-)
Title: Tools for Nuclear Magnetic Resonance (NMR) Spectra Alignment,
Peak Based Processing, Quantitative Analysis and Visualizations
Description: Makes Nuclear Magnetic Resonance spectroscopy (NMR spectroscopy) data analysis as easy as possible by only requiring a small set of functions to perform an entire analysis. 'speaq' offers the possibility of raw spectra alignment and quantitation but also an analysis based on features whereby the spectra are converted to peaks which are then grouped and turned into features. These features can be processed with any number of statistical tools either included in 'speaq' or available elsewhere on CRAN. More details can be found in Vu et al. (2011) <doi:10.1186/1471-2105-12-405> and Beirnaert et al. (2018) <doi:10.1371/journal.pcbi.1006018>.
Author: Charlie Beirnaert, Trung Nghia Vu, Pieter Meysman, Kris Laukens and Dirk Valkenborg
Maintainer: Charlie Beirnaert <charlie_beirnaert@icloud.com>
Diff between speaq versions 2.6.1 dated 2019-12-10 and 2.7.0 dated 2022-05-23
speaq-2.6.1/speaq/data/datalist |only speaq-2.7.0/speaq/DESCRIPTION | 13 - speaq-2.7.0/speaq/MD5 | 21 +- speaq-2.7.0/speaq/NAMESPACE | 1 speaq-2.7.0/speaq/NEWS.md | 6 speaq-2.7.0/speaq/R/SCANT.R | 16 - speaq-2.7.0/speaq/R/Winedata.R | 2 speaq-2.7.0/speaq/build/vignette.rds |binary speaq-2.7.0/speaq/inst/doc/classic_speaq_vignette.html | 150 ++++++++++------- speaq-2.7.0/speaq/inst/doc/speaq2_illustrations.html | 69 ++++--- speaq-2.7.0/speaq/man/SCANT.Rd | 6 speaq-2.7.0/speaq/man/Winedata.Rd | 6 12 files changed, 170 insertions(+), 120 deletions(-)
Title: HTML Exportation for R Objects
Description: Includes HTML function and methods to write in an HTML
file. Thus, making HTML reports is easy. Includes a function
that allows redirection on the fly, which appears to be very
useful for teaching purpose, as the student can keep a copy of
the produced output to keep all that he did during the course.
Package comes with a vignette describing how to write HTML
reports for statistical analysis. Finally, a driver for 'Sweave'
allows to parse HTML flat files containing R code and to
automatically write the corresponding outputs (tables and
graphs).
Author: Eric Lecoutre [aut],
Milan Bouchet-Valat [cre, ctb],
Thomas Friedrichsmeier [ctb]
Maintainer: Milan Bouchet-Valat <nalimilan@club.fr>
Diff between R2HTML versions 2.3.2 dated 2016-06-23 and 2.3.3 dated 2022-05-23
DESCRIPTION | 8 MD5 | 86 NAMESPACE | 398 - NEWS | 336 - R/HTMLcore.R | 8198 +++++++++++++------------- R/HTMLlme.R | 458 - R/LaTeX.R | 84 R/grid.R | 594 - demo/00Index | 6 demo/dataframe.R | 10 demo/equations.R | 24 demo/grids.R | 28 inst/CITATION | 2 inst/doc/R2HTML.css | 72 inst/doc/dynamic.html | 6 inst/doc/dynamic_main.html | 44 inst/doc/dynamic_menu.html | 14 inst/doc/page1.html | 4 inst/doc/page2.html | 6 inst/doc/page3.html | 24 inst/doc/page4.html | 12 inst/output/Pastel.css | 164 inst/output/R2HTML.css | 490 - inst/output/SciViews.css | 160 inst/output/gridR2HTML.css | 14 inst/output/gridR2HTML.js | 558 - inst/output/runtime/lib/grid.js | 44 inst/output/runtime/styles/classic/Picasa.ini | 10 inst/output/runtime/styles/classic/grid.css | 44 inst/output/runtime/styles/flat/Picasa.ini | 10 inst/output/runtime/styles/flat/grid.css | 44 inst/output/runtime/styles/xp/Picasa.ini | 10 inst/output/runtime/styles/xp/grid.css | 64 inst/output/tablesort.htc | 412 - inst/samples/Pastel.css | 98 inst/samples/R2HTML.css | 118 inst/samples/example1.html | 82 inst/samples/example1.snw | 78 inst/samples/example2.html | 134 inst/samples/example2.snw | 104 inst/samples/example3.html | 158 inst/samples/example3.snw | 196 inst/samples/index.html | 130 man/HTMLInsertGraph.Rd | 2 44 files changed, 6773 insertions(+), 6765 deletions(-)
Title: Elitist Non-Dominated Sorting Genetic Algorithm
Description: Box-constrained multiobjective optimization using the
elitist non-dominated sorting genetic algorithm - NSGA-II.
Fast non-dominated sorting, crowding distance, tournament
selection, simulated binary crossover, and polynomial
mutation are called in the main program. The methods are
described in Deb et al. (2002) <doi:10.1109/4235.996017>.
Author: Ching-Shih Tsou <cstsou@mail.ntcb.edu.tw>
Maintainer: Ming-Chang (Alan) Lee <alan9956@ydu.edu.tw>
Diff between nsga2R versions 1.0 dated 2013-06-16 and 1.1 dated 2022-05-23
DESCRIPTION | 22 +++++++++++----------- MD5 | 4 ++-- NAMESPACE | 4 +++- 3 files changed, 16 insertions(+), 14 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-06-05 2.0.0
2015-12-29 1.0.5
2015-05-22 1.0.4
2015-04-10 1.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-05-28 1.0
2012-04-08 0.9
2009-06-24 0.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-06-26 2.0
2014-02-05 1.1
2014-01-27 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-01 1.2.3
2022-01-11 1.2.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-06-05 0.0.5
2014-06-03 0.0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-10-14 1.0.1
2010-06-30 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-07-02 1.2.0
2018-05-17 1.1.1
2018-04-11 1.1.0
2017-06-06 1.0.1
2016-12-09 1.0
2015-06-04 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-06-01 0.1-2
2006-12-20 0.1-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-04-20 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-06-17 0.5-0
2012-09-13 0.4-0
2010-12-07 0.3-1
2010-10-15 0.3-0
2010-05-22 0.2-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-18 1.4.6
2020-01-13 1.4.3
2019-05-18 1.4.1
Title: Implementation of the SVM-Maj Algorithm
Description: Implements the SVM-Maj algorithm to train data with support vector machine
as described in Groenen et al. (2008) <doi:10.1007/s11634-008-0020-9>.
This algorithm uses two efficient updates, one for linear kernel and one
for the nonlinear kernel.
Author: Hoksan Yip, Patrick J.F. Groenen, Georgi Nalbantov
Maintainer: Hok San Yip <hoksan@gmail.com>
Diff between SVMMaj versions 0.2.9 dated 2019-01-26 and 0.2.9.1 dated 2022-05-23
SVMMaj-0.2.9.1/SVMMaj/DESCRIPTION | 6 +++--- SVMMaj-0.2.9.1/SVMMaj/MD5 | 14 +++++++------- SVMMaj-0.2.9.1/SVMMaj/build/vignette.rds |binary SVMMaj-0.2.9.1/SVMMaj/data/AusCredit.rda |only SVMMaj-0.2.9.1/SVMMaj/data/diabetes.rda |only SVMMaj-0.2.9.1/SVMMaj/data/supermarket1996.RData |binary SVMMaj-0.2.9.1/SVMMaj/data/voting.rda |only SVMMaj-0.2.9.1/SVMMaj/inst/doc/paper.pdf |binary SVMMaj-0.2.9/SVMMaj/data/AusCredit.r |only SVMMaj-0.2.9/SVMMaj/data/diabetes.r |only SVMMaj-0.2.9/SVMMaj/data/voting.r |only 11 files changed, 10 insertions(+), 10 deletions(-)
Title: Breiman and Cutler's Random Forests for Classification and
Regression
Description: Classification and regression based on a forest of trees using random inputs, based on Breiman (2001) <DOI:10.1023/A:1010933404324>.
Author: Fortran original by Leo Breiman and Adele Cutler, R port by Andy Liaw and Matthew Wiener.
Maintainer: Andy Liaw <andy_liaw@merck.com>
Diff between randomForest versions 4.7-1 dated 2022-02-03 and 4.7-1.1 dated 2022-05-23
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- data/imports85.rda |binary man/combine.Rd | 2 +- man/getTree.Rd | 2 +- man/grow.Rd | 2 +- man/partialPlot.Rd | 2 +- man/predict.randomForest.Rd | 4 ++-- man/randomForest.Rd | 4 ++-- man/treesize.Rd | 2 +- man/varImpPlot.Rd | 2 +- 11 files changed, 23 insertions(+), 23 deletions(-)
Title: Convenient Tool for Solving the Prize-Collecting Steiner Tree
Problem
Description: The Prize-Collecting Steiner Tree problem asks to find a subgraph
connecting a given set of vertices with the most expensive nodes and least
expensive edges. Since it is proven to be NP-hard, exact and efficient algorithm
does not exist. This package provides convenient functionality for obtaining an
approximate solution to this problem using loopy belief propagation algorithm.
Author: Aleksei Krasikov <krasikov.as@phystech.edu>
Maintainer: Aleksei Krasikov <krasikov.as@phystech.edu>
Diff between pcSteiner versions 1.0.0 dated 2020-08-31 and 1.0.0.1 dated 2022-05-23
DESCRIPTION | 6 +++--- MD5 | 6 +++--- build/vignette.rds |binary inst/doc/tutorial.pdf |binary 4 files changed, 6 insertions(+), 6 deletions(-)
Title: Variational Autoencoder Models for IRT Parameter Estimation
Description: Based on the work of Curi, Converse, Hajewski, and Oliveira (2019) <doi:10.1109/IJCNN.2019.8852333>. This package provides easy-to-use functions which create a variational autoencoder (VAE) to be used for parameter estimation in Item Response Theory (IRT) - namely the Multidimensional Logistic 2-Parameter (ML2P) model. To use a neural network as such, nontrivial modifications to the architecture must be made, such as restricting the nonzero weights in the decoder according to some binary matrix Q. The functions in this package allow for straight-forward construction, training, and evaluation so that minimal knowledge of 'tensorflow' or 'keras' is required.
Author: Geoffrey Converse [aut, cre, cph],
Suely Oliveira [ctb, ths],
Mariana Curi [ctb]
Maintainer: Geoffrey Converse <converseg@gmail.com>
Diff between ML2Pvae versions 1.0.0 dated 2020-11-16 and 1.0.0.1 dated 2022-05-23
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- build/vignette.rds |binary data/correlation_matrix.rda |binary data/diff_true.rda |binary data/disc_true.rda |binary data/q_matrix.rda |binary data/responses.rda |binary data/theta_true.rda |binary inst/doc/ml2p_vae_vignette.pdf |binary 10 files changed, 12 insertions(+), 12 deletions(-)
Title: Limited-memory BFGS Optimization
Description: A wrapper built around the libLBFGS optimization library by Naoaki Okazaki. The lbfgs package implements both the Limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) and the Orthant-Wise Quasi-Newton Limited-Memory (OWL-QN) optimization algorithms. The L-BFGS algorithm solves the problem of minimizing an objective, given its gradient, by iteratively computing approximations of the inverse Hessian matrix. The OWL-QN algorithm finds the optimum of an objective plus the L1-norm of the problem's parameters. The package offers a fast and memory-efficient implementation of these optimization routines, which is particularly suited for high-dimensional problems.
Author: Antonio Coppola [aut, cre, cph],
Brandon Stewart [aut, cph],
Naoaki Okazaki [aut, cph],
David Ardia [ctb, cph],
Dirk Eddelbuettel [ctb, cph],
Katharine Mullen [ctb, cph],
Jorge Nocedal [ctb, cph]
Maintainer: Antonio Coppola <acoppola@college.harvard.edu>
Diff between lbfgs versions 1.2.1 dated 2014-08-31 and 1.2.1.1 dated 2022-05-23
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 3 ++- build/vignette.rds |binary data/Leukemia.RData |binary inst/doc/Vignette.pdf |binary 6 files changed, 11 insertions(+), 10 deletions(-)
Title: Various R Programming Tools
Description: Functions to assist in R programming, including:
- assist in developing, updating, and maintaining R and R packages ('ask', 'checkRVersion',
'getDependencies', 'keywords', 'scat'),
- calculate the logit and inverse logit transformations ('logit', 'inv.logit'),
- test if a value is missing, empty or contains only NA and NULL values ('invalid'),
- manipulate R's .Last function ('addLast'),
- define macros ('defmacro'),
- detect odd and even integers ('odd', 'even'),
- convert strings containing non-ASCII characters (like single quotes) to plain ASCII ('ASCIIfy'),
- perform a binary search ('binsearch'),
- sort strings containing both numeric and character components ('mixedsort'),
- create a factor variable from the quantiles of a continuous variable ('quantcut'),
- enumerate permutations and combinations ('combinations', 'permutation'),
- calculate and convert between fold-change and log-ratio ('foldchange',
'logratio2foldchange', 'foldchange2logratio'),
- calculate probabilities and generate random numbers from Dirichlet distributions
('rdirichlet', 'ddirichlet'),
- apply a function over adjacent subsets of a vector ('running'),
- modify the TCP\_NODELAY ('de-Nagle') flag for socket objects,
- efficient 'rbind' of data frames, even if the column names don't match ('smartbind'),
- generate significance stars from p-values ('stars.pval'),
- convert characters to/from ASCII codes ('asc', 'chr'),
- convert character vector to ASCII representation ('ASCIIfy'),
- apply title capitalization rules to a character vector ('capwords').
Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley
Maintainer: Gregory R. Warnes <greg@warnes.net>
Diff between gtools versions 3.9.2 dated 2021-06-06 and 3.9.2.1 dated 2022-05-23
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- data/ELISA.rda |binary data/badDend.rda |binary man/checkRVersion.Rd | 2 +- 5 files changed, 9 insertions(+), 9 deletions(-)
Title: Computation of Generalized Nash Equilibria
Description: Provide functions to compute standard and generalized Nash Equilibria.
Optimization methods are available nonsmooth reformulation, fixed-point formulation,
minimization problem and constrained-equation reformulation.
See e.g. Kanzow and Facchinei (2010), <doi:10.1007/s10479-009-0653-x>.
Author: Christophe Dutang
Maintainer: Christophe Dutang <christophe.dutang@ensimag.fr>
Diff between GNE versions 0.99-3 dated 2020-01-08 and 0.99-3.1 dated 2022-05-23
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/GNE-howto.R | 1 - inst/doc/GNE-howto.pdf |binary 5 files changed, 7 insertions(+), 8 deletions(-)
Title: Fast Nearest Neighbor Search Algorithms and Applications
Description: Cover-tree and kd-tree fast k-nearest neighbor search algorithms and related applications
including KNN classification, regression and information measures are implemented.
Author: Alina Beygelzimer, Sham Kakadet and John Langford ,
Sunil Arya and David Mount , Shengqiao Li
Maintainer: Shengqiao Li <lishengqiao@yahoo.com>
Diff between FNN versions 1.1.3 dated 2019-02-15 and 1.1.3.1 dated 2022-05-23
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++-------------- man/KL.dist.Rd | 2 +- man/KL.divergence.Rd | 2 +- man/crossentropy.Rd | 2 +- man/entropy.Rd | 2 +- man/get.knn.Rd | 2 +- man/knn.Rd | 2 +- man/knn.cv.Rd | 2 +- man/knn.dist.Rd | 2 +- man/knn.index.Rd | 2 +- man/knn.reg.Rd | 2 +- man/mutual_information.Rd | 2 +- man/ownn.rd | 2 +- man/print.knnRegCV.Rd | 2 +- 15 files changed, 30 insertions(+), 30 deletions(-)
Title: Family of Lasso Regression
Description: Provide the implementation of a family of Lasso variants including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating high dimensional sparse linear model. We adopt the alternating direction method of multipliers and convert the original optimization problem into a sequential L1 penalized least square minimization problem, which can be efficiently solved by linearization algorithm. A multi-stage screening approach is adopted for further acceleration. Besides the sparse linear model estimation, we also provide the extension of these Lasso variants to sparse Gaussian graphical model estimation including TIGER and CLIME using either L1 or adaptive penalty. Missing values can be tolerated for Dantzig selector and CLIME. The computation is memory-optimized using the sparse matrix output. For more information, please refer to <https://www.jmlr.org/papers/volume16/li15a/li15a.pdf>.
Author: Xingguo Li, Tuo Zhao, Lie Wang, Xiaoming Yuan, and Han Liu
Maintainer: Xingguo Li <xingguo.leo@gmail.com>
Diff between flare versions 1.7.0 dated 2020-11-30 and 1.7.0.1 dated 2022-05-23
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- build/vignette.rds |binary data/eyedata.rda |binary inst/doc/vignette.pdf |binary 5 files changed, 7 insertions(+), 7 deletions(-)
Title: Broadly Useful Convenient and Efficient R Functions
Description: Broadly useful convenient and efficient R functions
that bring users concise and elegant R data analyses.
This package includes easy-to-use functions for
(1) basic R programming
(e.g., set working directory to the path of currently opened file;
import/export data from/to files in any format;
print tables to Microsoft Word);
(2) multivariate computation
(e.g., compute scale sums/means/... with reverse scoring);
(3) reliability analyses and factor analyses;
(4) descriptive statistics and correlation analyses;
(5) t-test, multi-factor analysis of variance (ANOVA),
simple-effect analysis, and post-hoc multiple comparison;
(6) tidy report of statistical models
(to R Console and Microsoft Word);
(7) mediation and moderation analyses (PROCESS);
and (8) additional toolbox for statistics and graphics.
Author: Han-Wu-Shuang Bao [aut, cre]
Maintainer: Han-Wu-Shuang Bao <baohws@foxmail.com>
Diff between bruceR versions 0.8.6 dated 2022-04-13 and 0.8.7 dated 2022-05-23
bruceR-0.8.6/bruceR/R/bruceR_basic.R |only bruceR-0.8.6/bruceR/R/bruceR_stats_01_basic.R |only bruceR-0.8.6/bruceR/R/bruceR_stats_02_scale.R |only bruceR-0.8.6/bruceR/R/bruceR_stats_03_manova.R |only bruceR-0.8.6/bruceR/R/bruceR_stats_04_regress.R |only bruceR-0.8.6/bruceR/R/bruceR_stats_05_advance.R |only bruceR-0.8.6/bruceR/R/bruceR_stats_06_plot.R |only bruceR-0.8.6/bruceR/man/figures/logo.gif |only bruceR-0.8.7/bruceR/DESCRIPTION | 15 - bruceR-0.8.7/bruceR/MD5 | 136 +++++----- bruceR-0.8.7/bruceR/NAMESPACE | 16 + bruceR-0.8.7/bruceR/NEWS.md | 13 bruceR-0.8.7/bruceR/R/bruceR-stats_1_basic.R |only bruceR-0.8.7/bruceR/R/bruceR-stats_2_scale.R |only bruceR-0.8.7/bruceR/R/bruceR-stats_3_manova.R |only bruceR-0.8.7/bruceR/R/bruceR-stats_4_regress.R |only bruceR-0.8.7/bruceR/R/bruceR-stats_5_advance.R |only bruceR-0.8.7/bruceR/R/bruceR-stats_6_plot.R |only bruceR-0.8.7/bruceR/R/bruceR.R | 38 +- bruceR-0.8.7/bruceR/R/bruceR_utils.R |only bruceR-0.8.7/bruceR/README.md | 31 +- bruceR-0.8.7/bruceR/man/Alpha.Rd | 20 - bruceR-0.8.7/bruceR/man/CFA.Rd | 2 bruceR-0.8.7/bruceR/man/Corr.Rd | 20 - bruceR-0.8.7/bruceR/man/Describe.Rd | 20 - bruceR-0.8.7/bruceR/man/EFA.Rd | 2 bruceR-0.8.7/bruceR/man/EMMEANS.Rd | 15 - bruceR-0.8.7/bruceR/man/Freq.Rd | 2 bruceR-0.8.7/bruceR/man/GLM_summary.Rd | 2 bruceR-0.8.7/bruceR/man/HLM_ICC_rWG.Rd | 2 bruceR-0.8.7/bruceR/man/HLM_summary.Rd | 2 bruceR-0.8.7/bruceR/man/LOOKUP.Rd | 2 bruceR-0.8.7/bruceR/man/MANOVA.Rd | 19 + bruceR-0.8.7/bruceR/man/PROCESS.Rd | 2 bruceR-0.8.7/bruceR/man/Print.Rd | 2 bruceR-0.8.7/bruceR/man/RECODE.Rd | 6 bruceR-0.8.7/bruceR/man/RESCALE.Rd | 8 bruceR-0.8.7/bruceR/man/RGB.Rd | 2 bruceR-0.8.7/bruceR/man/Run.Rd | 2 bruceR-0.8.7/bruceR/man/TTEST.Rd | 2 bruceR-0.8.7/bruceR/man/add.Rd |only bruceR-0.8.7/bruceR/man/bruceR-demodata.Rd | 3 bruceR-0.8.7/bruceR/man/bruceR-package.Rd | 14 - bruceR-0.8.7/bruceR/man/cc.Rd | 11 bruceR-0.8.7/bruceR/man/ccf_plot.Rd | 2 bruceR-0.8.7/bruceR/man/cor_diff.Rd | 4 bruceR-0.8.7/bruceR/man/dtime.Rd | 2 bruceR-0.8.7/bruceR/man/export.Rd | 2 bruceR-0.8.7/bruceR/man/formatF.Rd | 2 bruceR-0.8.7/bruceR/man/formatN.Rd | 2 bruceR-0.8.7/bruceR/man/formula_expand.Rd | 2 bruceR-0.8.7/bruceR/man/formula_paste.Rd | 2 bruceR-0.8.7/bruceR/man/grand_mean_center.Rd | 2 bruceR-0.8.7/bruceR/man/granger_causality.Rd | 4 bruceR-0.8.7/bruceR/man/granger_test.Rd | 2 bruceR-0.8.7/bruceR/man/grapes-allin-grapes.Rd | 2 bruceR-0.8.7/bruceR/man/grapes-anyin-grapes.Rd | 2 bruceR-0.8.7/bruceR/man/grapes-grapes-COMPUTE-grapes-grapes.Rd | 72 ++++- bruceR-0.8.7/bruceR/man/grapes-nonein-grapes.Rd | 2 bruceR-0.8.7/bruceR/man/grapes-notin-grapes.Rd | 2 bruceR-0.8.7/bruceR/man/grapes-partin-grapes.Rd | 2 bruceR-0.8.7/bruceR/man/grapes-pow-grapes.Rd | 2 bruceR-0.8.7/bruceR/man/group_mean_center.Rd | 2 bruceR-0.8.7/bruceR/man/import.Rd | 2 bruceR-0.8.7/bruceR/man/lavaan_summary.Rd | 2 bruceR-0.8.7/bruceR/man/med_summary.Rd | 2 bruceR-0.8.7/bruceR/man/model_summary.Rd | 2 bruceR-0.8.7/bruceR/man/p.Rd | 2 bruceR-0.8.7/bruceR/man/pkg_depend.Rd | 4 bruceR-0.8.7/bruceR/man/pkg_install_suggested.Rd | 2 bruceR-0.8.7/bruceR/man/print_table.Rd | 2 bruceR-0.8.7/bruceR/man/regress.Rd | 2 bruceR-0.8.7/bruceR/man/rep_char.Rd | 2 bruceR-0.8.7/bruceR/man/scaler.Rd | 2 bruceR-0.8.7/bruceR/man/set.wd.Rd | 2 bruceR-0.8.7/bruceR/man/show_colors.Rd | 2 bruceR-0.8.7/bruceR/man/theme_bruce.Rd | 8 77 files changed, 332 insertions(+), 225 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-08 1.1-1
2012-10-18 1.0-1
2012-08-17 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-04-29 2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-22 1.1.0
2022-03-01 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-04-11 0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-19 2.3
2015-02-18 2.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-23 0.3.1
2021-05-01 0.3.0
2021-04-20 0.2.5
2020-08-06 0.2.2
2020-07-27 0.2.1
2020-07-26 0.2.0
2020-07-14 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-06-16 1.3-1
2011-10-17 1.1
2010-10-23 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-02-09 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-09-07 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-09-20 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-25 2.1.0
2019-09-23 2.0.0
2019-06-03 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-28 2.0.3
2021-05-28 1.9.9.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-02-19 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-12-01 0.3.5
2021-02-22 0.3.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-02-04 3.0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-02-24 0.03
2009-12-16 0.02
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-02 2.2
2019-05-01 2.1
2018-05-06 2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-11-18 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-12-10 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-09-07 1.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-05-27 2.4
2016-11-28 2.3
2015-12-17 2.2
2015-03-31 2.1
2015-02-19 2.0
2014-04-24 1.1
2014-04-23 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-11-08 0.3-7
2012-04-11 0.3-5
2009-09-29 0.3-4
2009-08-24 0.3-2
2009-01-01 0.2-2
2008-09-09 0.1-9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-10-25 1.16
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-03 2.0.0
2020-09-09 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-06-09 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-11-10 2.0
2020-09-15 1.9
2020-03-06 1.8
2020-01-09 1.7
2019-06-11 1.6
2019-01-30 1.5
2018-08-04 1.4
2017-04-11 1.3
2016-03-31 1.2
2015-09-14 1.1
2014-12-02 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-11-10 0.2.8
2021-04-09 0.1.2
2021-02-24 0.1.1
2021-02-22 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-02 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-07-04 1.3
2013-01-29 1.2
2012-12-24 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-06-03 1.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-11-11 1.2-60
2012-01-27 1.2-10
2010-04-16 1.1-10
2007-05-30 1.1-2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-31 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-11 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-20 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-03-08 3.0
2012-01-18 2.3
2011-02-25 2.2
2010-10-23 2.1
2010-10-19 2.0
2010-05-07 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-02-17 1.32
2010-01-09 1.30
2009-12-21 1.01
2009-12-18 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-18 0.1.4
2020-11-13 0.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-01-17 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-01-13 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-05 3.1.1
2012-05-23 3.1
2012-03-01 3.0
Title: Robust Quality Control Chart
Description: Constructs various robust quality control charts based on the median or Hodges-Lehmann estimator (location) and the median absolute deviation (MAD) or Shamos estimator (scale). The estimators used for the robust control charts are all unbiased with a sample of finite size. For more details, see Park, Kim and Wang (2022) <doi:10.1080/03610918.2019.1699114>. In addition, using this R package, the conventional quality control charts such as X-bar, S, R, p, np, u, c, g and h charts are also easily constructed. This work was partially supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (NRF-2017R1A2B4004169).
Author: Chanseok Park [aut, cre] ,
Min Wang [ctb]
Maintainer: Chanseok Park <statpnu@gmail.com>
Diff between rQCC versions 2.22.1 dated 2022-01-25 and 2.22.5 dated 2022-05-23
DESCRIPTION | 8 +- MD5 | 64 ++++++++++--------- NAMESPACE | 10 ++- R/racc.R |only build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 22 +++--- inst/NEWS.Rd | 10 ++- inst/doc/acc.Rnw | 21 +++--- inst/doc/acc.pdf |binary inst/doc/d3-calculations.pdf |only inst/doc/factors.cc.Rnw | 1 inst/doc/factors.cc.pdf |binary inst/doc/racc.Rnw |only inst/doc/racc.pdf |only inst/doc/rcc.Rnw | 5 - inst/doc/rcc.pdf |binary man/HL.Rd | 3 man/MAD.Rd | 3 man/RE.Rd | 3 man/Shamos.Rd | 3 man/acc.Rd | 21 +++--- man/evar.Rd | 3 man/finite.breakdown.Rd | 3 man/n.times.eBias.Rd | 3 man/n.times.eVar.Rd | 3 man/plot.Rd | 5 + man/pooledEstimator.Rd | 3 man/racc.Rd |only man/rcc.Rd | 3 man/unbiasing.factor.Rd | 3 vignettes/acc.Rnw | 21 +++--- vignettes/factors.cc.Rnw | 1 vignettes/rQCC.bib | 140 +++++++++++++++++++++++++++++-------------- vignettes/racc.Rnw |only vignettes/rcc.Rnw | 5 - 36 files changed, 234 insertions(+), 133 deletions(-)
Title: Visualization and Tools for Ichimoku Kinko Hyo Strategies
Description: An implementation of 'Ichimoku Kinko Hyo', also commonly known as
'cloud charts'. Static and interactive visualizations with tools for
creating, backtesting and development of quantitative 'ichimoku' strategies.
As described in Sasaki (1996, ISBN:4925152009), the technique is a refinement
on candlestick charting, originating from Japan and now in widespread use in
technical analysis worldwide. Translating as 'one-glance equilibrium chart',
it allows the price action and market structure of financial securities to
be determined 'at-a-glance'. Incorporates an interface with the OANDA
fxTrade API <https://developer.oanda.com/> for retrieving historical and
live streaming price data for major currencies, metals, commodities,
government bonds and stock indices.
Author: Charlie Gao [aut, cre]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between ichimoku versions 1.3.0 dated 2022-02-21 and 1.3.1 dated 2022-05-23
DESCRIPTION | 8 +- MD5 | 64 ++++++++-------- NEWS.md | 10 ++ R/ichimoku-package.R | 4 - R/iplot.R | 2 R/methods.R | 29 ++++--- R/mltools.R | 41 +++++----- R/oanda.R | 78 +++++++++++--------- R/plot.R | 18 +++- R/sysdata.rda |binary R/utils.R | 22 +++++ README.md | 2 build/vignette.rds |binary inst/doc/reference.R | 3 inst/doc/reference.Rmd | 9 ++ inst/doc/reference.html | 136 +++++++++++++++++++---------------- inst/doc/strategies.Rmd | 2 inst/doc/strategies.html | 103 +++++++++++++-------------- inst/doc/utilities.Rmd | 2 inst/doc/utilities.html | 14 +-- inst/doc/xoanda.Rmd | 4 - inst/doc/xoanda.html | 43 ++++++----- man/autoplot.ichimoku.Rd | 5 - man/figures/README-ichimoku-1.png |binary man/ichimoku-package.Rd | 2 man/oanda_chart.Rd | 5 - man/plot.ichimoku.Rd | 5 - src/shikokuchuo.c | 144 +++++++++++++++++--------------------- tests/testthat/test-plot.R | 5 - vignettes/reference.Rmd | 9 ++ vignettes/strategies.Rmd | 2 vignettes/utilities.Rmd | 2 vignettes/xoanda.Rmd | 4 - 33 files changed, 427 insertions(+), 350 deletions(-)
Title: Single-Species, Multi-Species, and Integrated Spatial Occupancy
Models
Description: Fits single-species, multi-species, and integrated non-spatial and spatial occupancy models using Markov Chain Monte Carlo (MCMC). Models are fit using Polya-Gamma data augmentation detailed in Polson, Scott, and Windle (2013) <doi:10.1080/01621459.2013.829001>. Spatial models are fit using either Gaussian processes or Nearest Neighbor Gaussian Processes (NNGP) for large spatial datasets. Details on NNGP models are given in Datta, Banerjee, Finley, and Gelfand (2016) <doi:10.1080/01621459.2015.1044091> and Finley, Datta, and Banerjee (2020) <arXiv:2001.09111>. Provides functionality for data integration of multiple single-species occupancy data sets using a joint likelihood framework. Details on data integration are given in Miller, Pacifici, Sanderlin, and Reich (2019) <doi:10.1111/2041-210X.13110>. Details on single-species and multi-species models are found in MacKenzie, Nichols, Lachman, Droege, Royle, and Langtimm (2002) <doi:10.1890/0012-9658(2002)083[2248:ESORWD]2.0.CO;2> and Dorazio and Royle <doi:10.1198/016214505000000015>, respectively.
Author: Jeffrey Doser [aut, cre],
Andrew Finley [aut]
Maintainer: Jeffrey Doser <doserjef@msu.edu>
Diff between spOccupancy versions 0.3.1 dated 2022-04-13 and 0.3.2 dated 2022-05-23
DESCRIPTION | 9 MD5 | 54 ++--- NAMESPACE | 1 NEWS.md | 8 R/generics.R | 31 +- R/mkSpCov.R |only R/spIntPGOcc.R | 111 ++++++++-- R/spMsPGOcc.R | 161 +++++++++++--- R/spPGOcc.R | 529 +++++++++++++++++++++++++++++++++---------------- R/waicOcc.R | 2 README.md | 47 ++-- build/partial.rdb |binary inst/CITATION | 16 - man/spIntPGOcc.Rd | 8 man/spMsPGOcc.Rd | 8 man/spPGOcc.Rd | 8 src/init.cpp | 12 - src/mkSpCov.cpp |only src/sfJSDMNNGP.cpp | 7 src/sfMsPGOccNNGP.cpp | 7 src/spIntPGOcc.cpp | 79 +++++-- src/spIntPGOccNNGP.cpp | 69 ++++-- src/spMsPGOcc.cpp | 68 ++++-- src/spMsPGOccNNGP.cpp | 67 ++++-- src/spOccupancy.h | 16 - src/spPGOcc.cpp | 80 +++++-- src/spPGOccNNGP.cpp | 328 +++++++++++++++++------------- src/util.cpp | 45 ++++ src/util.h | 2 29 files changed, 1214 insertions(+), 559 deletions(-)
Title: Short Asynchronous Time-Series Analysis
Description: A graphical and automated pipeline for the analysis
of short time-series in R ('santaR'). This approach is designed to accommodate asynchronous
time sampling (i.e. different time points for different individuals),
inter-individual variability, noisy measurements and large numbers of variables.
Based on a smoothing splines functional model, 'santaR' is able to detect variables
highlighting significantly different temporal trajectories between study groups.
Designed initially for metabolic phenotyping, 'santaR' is also suited for other Systems Biology
disciplines. Command line and graphical analysis (via a 'shiny' application) enable fast and
parallel automated analysis and reporting, intuitive visualisation and comprehensive plotting
options for non-specialist users.
Author: Arnaud Wolfer [aut, cre] ,
Timothy Ebbels [ctb],
Joe Cheng [ctb]
Maintainer: Arnaud Wolfer <adwolfer@gmail.com>
Diff between santaR versions 1.2.0 dated 2022-04-09 and 1.2.2 dated 2022-05-23
DESCRIPTION | 12 ++-- MD5 | 55 +++++++++++++++------- NAMESPACE | 2 R/santaR.R | 2 R/santaR_pvalue_dist.R | 4 - R/santaR_pvalue_fit.R | 4 - R/santaR_start_GUI.R | 2 README.md | 2 inst/NEWS | 3 + inst/doc/advanced-command-line-functions.html | 12 ++-- inst/doc/plotting-options.html | 36 +++++++------- inst/doc/theoretical-background.html | 2 inst/shiny-GUI/SANTA-App/data/chooser.R | 4 - inst/shiny-GUI/SANTA-App/server.R | 7 +- inst/shiny-GUI/SANTA-App/server/server_analysis.R | 12 ++-- inst/shiny-GUI/SANTA-App/server/server_dfSearch.R | 2 inst/shiny-GUI/SANTA-App/ui.R | 13 ++--- inst/testdata |only tests |only vignettes/file495459c86ac2.html |only vignettes/file49547f98451a.html |only vignettes/file54b03fa44385.html |only vignettes/file54b0425d69f8.html |only 23 files changed, 102 insertions(+), 72 deletions(-)
Title: Pedigree Models
Description: Provides functions to estimate mixed probit models using, for
instance, pedigree data like in <doi:10.1002/sim.1603>. The models are also
commonly called liability threshold models. The approximation is
based on direct log marginal likelihood approximations like the randomized
Quasi-Monte Carlo suggested by <doi:10.1198/106186002394> with a similar
procedure to approximate the derivatives. The minimax tilting method
suggested by <doi:10.1111/rssb.12162> is also supported. Graph-based methods
are also provided that can be used to simplify pedigrees.
Author: Benjamin Christoffersen [cre, aut]
,
Alan Genz [cph],
Frank Bretz [cph],
Bjoern Bornkamp [cph],
Torsten Hothorn [cph],
Christophe Dutang [cph],
Diethelm Wuertz [cph],
R-core [cph],
Leo Belzile [cph],
Zdravko Botev [cph]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>
Diff between pedmod versions 0.2.0 dated 2022-04-28 and 0.2.1 dated 2022-05-23
pedmod-0.2.0/pedmod/man/figures |only pedmod-0.2.1/pedmod/DESCRIPTION | 8 pedmod-0.2.1/pedmod/MD5 | 137 - pedmod-0.2.1/pedmod/NAMESPACE | 3 pedmod-0.2.1/pedmod/NEWS.md | 18 pedmod-0.2.1/pedmod/R/RcppExports.R | 4 pedmod-0.2.1/pedmod/R/eval_wrappers.R | 92 + pedmod-0.2.1/pedmod/R/opt.R | 402 ++++ pedmod-0.2.1/pedmod/build/partial.rdb |binary pedmod-0.2.1/pedmod/inst/doc/pedigree_partitioning.html | 100 - pedmod-0.2.1/pedmod/inst/doc/pedmod.html | 794 +++++++-- pedmod-0.2.1/pedmod/man/eval_pedigree.Rd | 54 pedmod-0.2.1/pedmod/man/pedmod_profile.Rd | 6 pedmod-0.2.1/pedmod/man/pedmod_profile_nleq.Rd |only pedmod-0.2.1/pedmod/man/pedmod_profile_prop.Rd | 4 pedmod-0.2.1/pedmod/src/RcppExports.cpp | 25 pedmod-0.2.1/pedmod/src/cdfaprx.cpp | 807 +++++++++- pedmod-0.2.1/pedmod/src/cdfaprx.h | 562 +----- pedmod-0.2.1/pedmod/src/graph-partitioning.cpp | 2 pedmod-0.2.1/pedmod/src/norm-cdf-approx.h | 5 pedmod-0.2.1/pedmod/src/pedigree-ll.cpp | 387 ++++ pedmod-0.2.1/pedmod/src/pedigree-ll.h | 316 --- pedmod-0.2.1/pedmod/src/pnorm.h | 2 pedmod-0.2.1/pedmod/src/r-api.cpp | 151 + pedmod-0.2.1/pedmod/src/test-cdfaprx.cpp | 371 ++++ pedmod-0.2.1/pedmod/tests/testthat/test-eval-x.R | 29 pedmod-0.2.1/pedmod/tests/testthat/test-man-pages.R | 56 pedmod-0.2.1/pedmod/vignettes/figures/partitioning-also_reduce_cost-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-connected_start_pedigree_unconnected-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-find_partition_simulate_small_graph-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-find_partition_simulate_small_graph-2.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-larger_ex-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-more_clear_only_balanced-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-only_balanced-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-partion_w_cut_simulate_small_graph-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-partion_w_cut_simulate_small_graph-2.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-pedigree_example-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-pedigree_unconnected-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-pedigree_unconnected-2.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-pedigree_unconnected-3.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-show_family_as_graph-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-simulate_small_graph-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-unconnected_larger_ex-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-unconnected_larger_ex-2.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-unconnected_larger_ex-3.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-use_edge_weights_too-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-use_edge_weights_too-2.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-use_weights-1.png |binary pedmod-0.2.1/pedmod/vignettes/figures/partitioning-use_weights-2.png |binary 49 files changed, 3171 insertions(+), 1164 deletions(-)
Title: Fetch Economic and Financial Time Series Data from Public
Sources
Description: Download economic and financial time series from public sources,
including the St Louis Fed's FRED system, Yahoo Finance, the US Bureau of Labor Statistics,
the US Energy Information Administration, the World Bank, Eurostat, the European Central Bank,
the Bank of England, the UK's Office of National Statistics, Deutsche Bundesbank, and INSEE.
Author: Abiel Reinhart <abielr@gmail.com>
Maintainer: Abiel Reinhart <abielr@gmail.com>
Diff between pdfetch versions 0.2.6 dated 2022-02-25 and 0.2.7 dated 2022-05-23
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 4 ++++ R/pdfetch.R | 24 +++++++++++------------- 4 files changed, 22 insertions(+), 20 deletions(-)
Title: Structural Handling of Finnish Personal Identity Codes
Description: Structural handling of Finnish identity codes (natural persons and
organizations); extract information, check ID validity and diagnostics.
Author: Pyry Kantanen [aut, cre] ,
Mans Magnusson [aut],
Jussi Paananen [aut],
Juho Kopra [ctb],
Oskari Luomala [ctb],
Tuomo Nieminen [ctb],
Leo Lahti [aut]
Maintainer: Pyry Kantanen <pyry.kantanen@gmail.com>
Diff between hetu versions 1.0.1 dated 2020-10-24 and 1.0.7 dated 2022-05-23
DESCRIPTION | 66 +- MD5 | 67 +- NAMESPACE | 14 NEWS.md | 38 + R/hetu-deprecated.R | 2 R/hetu.R | 272 +++++---- R/hetu_control_char.R |only R/hetu_diagnostic.R | 58 - R/pin_age.R | 54 + R/pin_ctrl.R | 109 ++- R/pin_date.R | 8 R/pin_sex.R | 22 R/pin_to_date.R | 4 R/quickdf.R |only R/rpin.R | 242 ++++---- README.md | 138 +++- build/vignette.rds |binary inst/CITATION | 41 - inst/doc/hetu.R | 4 inst/doc/hetu.Rmd | 18 inst/doc/hetu.html | 1323 +++++++++++++++++++++++++++------------------ man/bid_ctrl.Rd | 6 man/figures |only man/hetu.Rd | 59 +- man/hetu_control_char.Rd |only man/hetu_diagnostic.Rd | 36 - man/pin_age.Rd | 19 man/pin_ctrl.Rd | 21 man/pin_date.Rd | 12 man/pin_sex.Rd | 17 man/quickdf.Rd |only man/rbid.Rd | 5 man/rpin.Rd | 55 + man/satu_control_char.Rd |only man/satu_ctrl.Rd |only tests/testthat.R | 1 tests/testthat/test_hetu.R | 80 +- vignettes/hetu.Rmd | 18 38 files changed, 1688 insertions(+), 1121 deletions(-)
Title: Automated Cleaning of Fossil Occurrence Data
Description: Functions to automate the detection and resolution of taxonomic and stratigraphic errors in fossil occurrence datasets. Functions were developed using data from the Paleobiology Database.
Author: Joe Flannery-Sutherland [aut, cre]
,
Nussaïbah Raja-Schoob [aut, ctb],
Ádam Kocsis [aut, ctb],
Wolfgang Kiessling [aut]
Maintainer: Joe Flannery-Sutherland <jf15558@bristol.ac.uk>
Diff between fossilbrush versions 1.0.1 dated 2022-05-19 and 1.0.2 dated 2022-05-23
fossilbrush-1.0.1/fossilbrush/R/GTS2020_scale.R |only fossilbrush-1.0.1/fossilbrush/man/GTS2020_scale.Rd |only fossilbrush-1.0.2/fossilbrush/DESCRIPTION | 6 fossilbrush-1.0.2/fossilbrush/MD5 | 24 fossilbrush-1.0.2/fossilbrush/NAMESPACE | 3 fossilbrush-1.0.2/fossilbrush/R/chrono_scale.R |only fossilbrush-1.0.2/fossilbrush/R/flag_ranges.R | 572 ++-- fossilbrush-1.0.2/fossilbrush/R/get_pbdb.R | 1159 ++++------ fossilbrush-1.0.2/fossilbrush/inst/doc/fossilbrush_vignette.R | 7 fossilbrush-1.0.2/fossilbrush/inst/doc/fossilbrush_vignette.Rmd | 373 +-- fossilbrush-1.0.2/fossilbrush/inst/doc/fossilbrush_vignette.pdf |binary fossilbrush-1.0.2/fossilbrush/man/chrono_scale.Rd |only fossilbrush-1.0.2/fossilbrush/man/flag_ranges.Rd | 6 fossilbrush-1.0.2/fossilbrush/man/get_pbdb.Rd | 2 fossilbrush-1.0.2/fossilbrush/vignettes/fossilbrush_vignette.Rmd | 373 +-- 15 files changed, 1260 insertions(+), 1265 deletions(-)
Title: Robust and Sparse Methods for High Dimensional Linear and Binary
and Multinomial Regression
Description: Fully robust versions of the elastic net estimator are introduced for linear and binary and multinomial regression, in particular high dimensional data. The algorithm searches for outlier free subsets on which the classical elastic net estimators can be applied. A reweighting step is added to improve the statistical efficiency of the proposed estimators. Selecting appropriate tuning parameters for elastic net penalties are done via cross-validation.
Author: Fatma Sevinc Kurnaz and Irene Hoffmann and Peter Filzmoser
Maintainer: Fatma Sevinc Kurnaz <fatmasevinckurnaz@gmail.com>
Diff between enetLTS versions 0.1.0 dated 2018-01-22 and 1.1.0 dated 2022-05-23
enetLTS-0.1.0/enetLTS/R/InitialSubsets.R |only enetLTS-0.1.0/enetLTS/R/enetLTS-internal.R |only enetLTS-0.1.0/enetLTS/R/enetLTS.R |only enetLTS-1.1.0/enetLTS/DESCRIPTION | 20 enetLTS-1.1.0/enetLTS/MD5 | 76 +-- enetLTS-1.1.0/enetLTS/NAMESPACE | 25 - enetLTS-1.1.0/enetLTS/R/Csteps.R | 212 +++++---- enetLTS-1.1.0/enetLTS/R/coef.enetLTS.R | 31 - enetLTS-1.1.0/enetLTS/R/cv.binomial.enetLTS.R |only enetLTS-1.1.0/enetLTS/R/cv.enetLTS.R | 220 ++------- enetLTS-1.1.0/enetLTS/R/cv.gaussian.enetLTS.R |only enetLTS-1.1.0/enetLTS/R/cv.multinomial.enetLTS.R |only enetLTS-1.1.0/enetLTS/R/enetLTS.binom.R |only enetLTS-1.1.0/enetLTS/R/enetLTS.gaus.R |only enetLTS-1.1.0/enetLTS/R/enetLTS.main.R |only enetLTS-1.1.0/enetLTS/R/enetLTS.multinom.R |only enetLTS-1.1.0/enetLTS/R/fitted.enetLTS.R | 164 ++++--- enetLTS-1.1.0/enetLTS/R/initialSubsets.R |only enetLTS-1.1.0/enetLTS/R/lambda00.R | 3 enetLTS-1.1.0/enetLTS/R/nonzeroCoef.enetLTS.R | 38 + enetLTS-1.1.0/enetLTS/R/objectiveFunc.R | 54 +- enetLTS-1.1.0/enetLTS/R/plotCoef.enetLTS.R | 154 ++++-- enetLTS-1.1.0/enetLTS/R/plotDiagnostic.enetLTS.R | 222 ++++++---- enetLTS-1.1.0/enetLTS/R/plotResid.enetLTS.R | 441 +++++++++++--------- enetLTS-1.1.0/enetLTS/R/predict.enetLTS.R | 320 ++++++-------- enetLTS-1.1.0/enetLTS/R/print.enetLTS.R | 17 enetLTS-1.1.0/enetLTS/R/residuals.enetLTS.R | 92 ++-- enetLTS-1.1.0/enetLTS/R/standardizeXY.R |only enetLTS-1.1.0/enetLTS/R/startCstep500.R |only enetLTS-1.1.0/enetLTS/R/utilities.R | 109 ---- enetLTS-1.1.0/enetLTS/R/warmCsteps.R | 223 ++++++---- enetLTS-1.1.0/enetLTS/R/weights.enetLTS.R | 1 enetLTS-1.1.0/enetLTS/R/weightsFuncs.R |only enetLTS-1.1.0/enetLTS/man/coef.enetLTS.Rd | 56 +- enetLTS-1.1.0/enetLTS/man/cv.enetLTS.Rd | 31 - enetLTS-1.1.0/enetLTS/man/enetLTS-package.Rd | 211 +++++---- enetLTS-1.1.0/enetLTS/man/fitted.enetLTS.Rd | 64 +- enetLTS-1.1.0/enetLTS/man/nonzeroCoef.enetLTS.Rd | 70 ++- enetLTS-1.1.0/enetLTS/man/plot.enetLTS.Rd | 44 + enetLTS-1.1.0/enetLTS/man/plotCoef.enetLTS.Rd | 53 +- enetLTS-1.1.0/enetLTS/man/plotDiagnostic.enetLTS.Rd | 52 +- enetLTS-1.1.0/enetLTS/man/plotResid.enetLTS.Rd | 56 +- enetLTS-1.1.0/enetLTS/man/predict.enetLTS.Rd | 74 +-- enetLTS-1.1.0/enetLTS/man/print.enetLTS.Rd | 55 +- enetLTS-1.1.0/enetLTS/man/residuals.enetLTS.Rd | 52 +- enetLTS-1.1.0/enetLTS/man/weights.enetLTS.Rd | 52 +- 46 files changed, 1837 insertions(+), 1455 deletions(-)
Title: Constrained Regression for Survey Data
Description: Domain mean estimation with monotonicity or block monotone constraints. See Xu X, Meyer MC and Opsomer JD (2021)<doi:10.1016/j.jspi.2021.02.004> for more details.
Author: Xiyue Liao
Maintainer: Xiyue Liao <xiyue.liao@csulb.edu>
Diff between csurvey versions 1.2 dated 2021-08-12 and 1.3 dated 2022-05-23
csurvey-1.2/csurvey/man/csvy.fit.Rd |only csurvey-1.2/csurvey/man/decr.Rd |only csurvey-1.2/csurvey/man/fitted.csvy.Rd |only csurvey-1.2/csurvey/man/incr.Rd |only csurvey-1.2/csurvey/man/plotpersp.Rd |only csurvey-1.2/csurvey/man/plotpersp.csvy.Rd |only csurvey-1.2/csurvey/man/print.csvy.Rd |only csurvey-1.3/csurvey/ChangeLog |only csurvey-1.3/csurvey/DESCRIPTION | 16 csurvey-1.3/csurvey/MD5 | 16 csurvey-1.3/csurvey/NAMESPACE | 26 csurvey-1.3/csurvey/R/csurvey.R | 1399 ++++++++++++++++++++---------- csurvey-1.3/csurvey/man/csvy.Rd | 232 +++- 13 files changed, 1153 insertions(+), 536 deletions(-)
Title: Bayesian Group Sequential Design for Ordinal Data
Description: The proposed group-sequential trial design is based on Bayesian methods for ordinal endpoints,
including three methods, the proportional-odds-model (PO)-based, non-proportional-odds-model (NPO)-based,
and PO/NPO switch-model-based designs, which makes our proposed methods generic to be able to deal with
various scenarios.
Richard J. Barker, William A. Link (2013) <doi:10.1080/00031305.2013.791644>.
Thomas A. Murray, Ying Yuan, Peter F. Thall, Joan H. Elizondo, Wayne L.Hofstetter (2018) <doi:10.1111/biom.12842>.
Chengxue Zhong, Haitao Pan, Hongyu Miao (2021) <arXiv:2108.06568>.
Author: Chengxue Zhong [aut, cre],
Haitao Pan [aut],
Hongyu Miao [aut]
Maintainer: Chengxue Zhong <chengxue.zhong@uth.tmc.edu>
Diff between BayesOrdDesign versions 0.1.0 dated 2021-09-21 and 0.1.1 dated 2022-05-23
DESCRIPTION | 9 +- MD5 | 26 +++---- R/Bayes_Ord_Design_NPO.R | 26 +++---- R/Bayes_Ord_Design_PO.R | 19 ++--- R/Bayes_Ord_Design_Switch.R | 37 ++++++---- R/OC_func_NPO.R | 21 +++-- R/OC_func_PO.R | 19 +++-- R/OC_func_Switch.R | 60 ++++++++-------- R/funcs.R | 157 +++++++++++++++++++++++++++++++++++++++----- R/rjmcmc_internal.R | 8 +- man/get_oc_NPO.Rd | 4 - man/get_oc_Switch.Rd | 20 ++--- man/ss_npo.Rd | 5 - man/ss_switch.Rd | 6 - 14 files changed, 281 insertions(+), 136 deletions(-)
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