Title: Generalized UniFrac Distances, Distance-Based Multivariate
Methods and Feature-Based Univariate Methods for Microbiome
Data Analysis
Description: A suite of methods for powerful and robust microbiome data analysis including data normalization, data simulation, community-level association testing and differential abundance analysis. It implements generalized UniFrac distances, Geometric Mean of Pairwise Ratios (GMPR) normalization, semiparametric data simulator, distance-based statistical methods, and feature-based statistical methods. The distance-based statistical methods include three extensions of PERMANOVA: (1) PERMANOVA using the Freedman-Lane permutation scheme, (2) PERMANOVA omnibus test using multiple matrices, and (3) analytical approach to approximating PERMANOVA p-value. Feature-based statistical methods include linear model-based methods for differential abundance analysis of zero-inflated high-dimensional compositional data.
Author: Jun Chen, Xianyang Zhang, Lu Yang
Maintainer: Jun Chen <chen.jun2@mayo.edu>
Diff between GUniFrac versions 1.5 dated 2022-04-05 and 1.6 dated 2022-05-17
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++++---- NAMESPACE | 3 +++ R/dICC.R |only inst/doc/ZicoSeq.html | 10 +++++----- man/adonis3.Rd | 13 ++++++------- man/dICC.Rd |only man/dICC.SE.asympt.Rd |only man/dICC.SE.bt.Rd |only 9 files changed, 26 insertions(+), 20 deletions(-)
Title: Flexible Randomization-Based Inference
Description: Allows the user to conduct randomization-based inference for a wide variety of experimental scenarios. The package leverages a potential outcomes framework to output randomization-based p-values and null intervals for test statistics geared toward any estimands of interest, according to the specified null and alternative hypotheses. Users can define custom randomization schemes so that the randomization distributions are accurate for their experimental settings. The package also creates visualizations of randomization distributions and can test multiple test statistics simultaneously.
Author: Joseph J. Lee and Tirthankar Dasgupta
Maintainer: Joseph J. Lee <joseph.j.lee@post.harvard.edu>
Diff between randomizationInference versions 1.0.3 dated 2015-01-09 and 1.0.4 dated 2022-05-17
DESCRIPTION | 10 - MD5 | 54 ++++---- NAMESPACE | 4 R/anovaF.R | 36 ++--- R/blockRand.R | 28 ++-- R/completeRand.R | 19 +- R/constEffect.R | 25 ++- R/diffMeans.R | 37 ++--- R/diffMeansVector.R | 29 ++-- R/latinRand.R | 36 ++--- R/randInterval.R | 44 +++--- R/randPlot.R | 50 +++---- R/randTest.R | 178 +++++++++++++++------------ R/withinBlockEffects.R | 39 +++-- R/zeroEffect.R | 6 man/anovaF.Rd | 19 +- man/blockRand.Rd | 8 - man/completeRand.Rd | 7 - man/constEffect.Rd | 38 ++--- man/diffMeans.Rd | 29 ++-- man/diffMeansVector.Rd | 22 ++- man/latinRand.Rd | 9 - man/randInterval.Rd | 43 ++++-- man/randPlot.Rd | 54 +++++--- man/randTest.Rd | 219 ++++++++++++++++++++++----------- man/randomizationInference-package.Rd | 222 +++++++++++++++++++++------------- man/withinBlockEffects.Rd | 25 ++- man/zeroEffect.Rd | 15 +- 28 files changed, 760 insertions(+), 545 deletions(-)
More information about randomizationInference at CRAN
Permanent link
Title: Infrastructure for Partially Observable Markov Decision
Processes (POMDP)
Description: Provides the infrastructure to define and analyze the solutions of Partially Observable Markov Decision Process (POMDP) models. Interfaces for various exact and approximate solution algorithms are available including value iteration, point-based value iteration and SARSOP. Smallwood and Sondik (1973) <doi:10.1287/opre.21.5.1071>.
Author: Michael Hahsler [aut, cph, cre],
Hossein Kamalzadeh [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between pomdp versions 1.0.1 dated 2022-03-27 and 1.0.2 dated 2022-05-17
pomdp-1.0.1/pomdp/man/plot_policy_graph.Rd |only pomdp-1.0.2/pomdp/DESCRIPTION | 19 pomdp-1.0.2/pomdp/MD5 | 97 ++-- pomdp-1.0.2/pomdp/NAMESPACE | 6 pomdp-1.0.2/pomdp/NEWS.md | 14 pomdp-1.0.2/pomdp/R/MDP.R | 60 ++- pomdp-1.0.2/pomdp/R/Maze.R | 2 pomdp-1.0.2/pomdp/R/POMDP.R | 265 +++++++------ pomdp-1.0.2/pomdp/R/optimal_action.R | 8 pomdp-1.0.2/pomdp/R/plot_belief_space.R | 68 +-- pomdp-1.0.2/pomdp/R/plot_policy_graph.R | 374 +++++++++++++------ pomdp-1.0.2/pomdp/R/plot_value_function.R | 5 pomdp-1.0.2/pomdp/R/policy.R | 6 pomdp-1.0.2/pomdp/R/read_write_POMDP.R | 20 - pomdp-1.0.2/pomdp/R/read_write_pomdp_solve.R | 7 pomdp-1.0.2/pomdp/R/reward.R | 42 +- pomdp-1.0.2/pomdp/R/round_stochchastic.R | 8 pomdp-1.0.2/pomdp/R/sample_belief_space.R | 68 ++- pomdp-1.0.2/pomdp/R/simulate_MDP.R |only pomdp-1.0.2/pomdp/R/simulate_POMDP.R |only pomdp-1.0.2/pomdp/R/solve_MDP.R | 3 pomdp-1.0.2/pomdp/R/solve_POMDP.R | 32 + pomdp-1.0.2/pomdp/R/solve_SARSOP.R | 6 pomdp-1.0.2/pomdp/R/transition_matrix.R | 149 +++---- pomdp-1.0.2/pomdp/R/update_belief.R | 242 ------------ pomdp-1.0.2/pomdp/R/visNetwork.R | 18 pomdp-1.0.2/pomdp/README.md | 2 pomdp-1.0.2/pomdp/build/vignette.rds |binary pomdp-1.0.2/pomdp/data/Maze.rda |binary pomdp-1.0.2/pomdp/data/Three_doors.rda |binary pomdp-1.0.2/pomdp/data/Tiger.rda |binary pomdp-1.0.2/pomdp/inst/doc/POMDP.Rmd | 8 pomdp-1.0.2/pomdp/inst/doc/POMDP.html | 12 pomdp-1.0.2/pomdp/man/MDP.Rd | 6 pomdp-1.0.2/pomdp/man/Maze.Rd | 2 pomdp-1.0.2/pomdp/man/POMDP.Rd | 26 - pomdp-1.0.2/pomdp/man/optimal_action.Rd | 7 pomdp-1.0.2/pomdp/man/plot_belief_space.Rd | 23 - pomdp-1.0.2/pomdp/man/plot_value_function.Rd | 3 pomdp-1.0.2/pomdp/man/policy.Rd | 2 pomdp-1.0.2/pomdp/man/policy_graph.Rd |only pomdp-1.0.2/pomdp/man/reward.Rd | 42 +- pomdp-1.0.2/pomdp/man/sample_belief_space.Rd | 24 - pomdp-1.0.2/pomdp/man/simulate_MDP.Rd |only pomdp-1.0.2/pomdp/man/simulate_POMDP.Rd | 30 - pomdp-1.0.2/pomdp/man/solve_MDP.Rd | 4 pomdp-1.0.2/pomdp/man/solve_POMDP.Rd | 9 pomdp-1.0.2/pomdp/man/solve_SARSOP.Rd | 2 pomdp-1.0.2/pomdp/man/transition_matrix.Rd | 32 + pomdp-1.0.2/pomdp/tests/testthat/test-solve_POMDP.R | 8 pomdp-1.0.2/pomdp/tests/testthat/test-solve_SARSOP.R | 3 pomdp-1.0.2/pomdp/vignettes/POMDP.Rmd | 8 52 files changed, 963 insertions(+), 809 deletions(-)
Title: Recursive Partitioning for Longitudinal Data and Right Censored
Data Using Baseline Covariates
Description: Constructs tree for continuous longitudinal data and survival data using baseline covariates as partitioning variables according to the 'LongCART' and 'SurvCART' algorithm, respectively. Later also included functions to calculate conditional power and predictive power of success based on interim results and probability of success for a prospective trial.
Author: Madan G Kundu
Maintainer: Madan G Kundu <madan_g.kundu@yahoo.com>
Diff between LongCART versions 3.1 dated 2021-05-31 and 3.2 dated 2022-05-17
LongCART-3.1/LongCART/R/LongCART_02_Nov_20.R |only LongCART-3.1/LongCART/R/PPoS_betabinom1.R |only LongCART-3.1/LongCART/R/PPoS_betabinom2.R |only LongCART-3.1/LongCART/R/SurvCART_30May2021.R |only LongCART-3.1/LongCART/man/KMPlot.SurvCART.Rd |only LongCART-3.1/LongCART/man/ProfilePlot.LongCART.Rd |only LongCART-3.1/LongCART/man/plot.SurvCART.Rd |only LongCART-3.1/LongCART/man/text.SurvCART.Rd |only LongCART-3.2/LongCART/DESCRIPTION | 8 +-- LongCART-3.2/LongCART/MD5 | 47 ++++++++++++--------- LongCART-3.2/LongCART/NAMESPACE | 22 +++++++-- LongCART-3.2/LongCART/R/KMPlot.R |only LongCART-3.2/LongCART/R/LongCART_08May2022.R |only LongCART-3.2/LongCART/R/LongCART_predict.R |only LongCART-3.2/LongCART/R/LongCART_subfunctions.R |only LongCART-3.2/LongCART/R/ProfilePlot_08May2022.R |only LongCART-3.2/LongCART/R/SurvCART_plot_text.R |only LongCART-3.2/LongCART/R/SurvCART_predict.R |only LongCART-3.2/LongCART/R/SurvCART_rev_05May2022.R |only LongCART-3.2/LongCART/R/succ_ia_betabinom_one.R |only LongCART-3.2/LongCART/R/succ_ia_betabinom_two.R |only LongCART-3.2/LongCART/man/KMPlot.Rd |only LongCART-3.2/LongCART/man/LongCART.Rd | 20 ++++---- LongCART-3.2/LongCART/man/PoS.Rd | 4 + LongCART-3.2/LongCART/man/ProfilePlot.Rd |only LongCART-3.2/LongCART/man/StabCat.Rd | 2 LongCART-3.2/LongCART/man/StabCat.surv.Rd | 4 - LongCART-3.2/LongCART/man/StabCont.Rd | 2 LongCART-3.2/LongCART/man/StabCont.surv.Rd | 4 - LongCART-3.2/LongCART/man/SurvCART.Rd | 22 ++++++--- LongCART-3.2/LongCART/man/plot.Rd |only LongCART-3.2/LongCART/man/predict.Rd |only LongCART-3.2/LongCART/man/succ_ia.Rd | 4 + LongCART-3.2/LongCART/man/succ_ia_betabinom_one.Rd | 8 ++- LongCART-3.2/LongCART/man/succ_ia_betabinom_two.Rd | 4 + LongCART-3.2/LongCART/man/text.Rd |only 36 files changed, 92 insertions(+), 59 deletions(-)
Title: Topographic and Geologic Mapping
Description: Set of routines for making map projections (forward and inverse), topographic maps, perspective plots, geological maps, geological map symbols, geological databases, interactive plotting and selection of focus regions.
Author: Jonathan M. Lees [aut, cre]
Maintainer: Jonathan M. Lees <jonathan.lees@unc.edu>
Diff between GEOmap versions 2.4-4 dated 2018-01-18 and 2.5-0 dated 2022-05-17
DESCRIPTION | 10 +++--- MD5 | 34 ++++++++++----------- R/GLOB.XY.R | 51 ++++++++++++++++++++++++------- R/XSECEQ.R | 44 +++++++++++++++++++++------ R/XY.GLOB.R | 44 +++++++++++++++++++++------ R/antipolygon.R | 2 - R/plotGEOmapXY.R | 10 ++++-- R/plotworldmap.R | 84 ++++++++++++++++++++++++++++------------------------ R/setPROJ.R | 54 ++++++++++++++++++++++++++------- man/DATUMinfo.Rd | 2 - man/GEOTOPO.Rd | 13 ++++++-- man/LandSeaCol.Rd | 14 ++++++++ man/XSECEQ.Rd | 4 +- man/antipolygon.Rd | 6 +++ man/getETOPO.Rd | 20 ++++++++---- man/perpen.Rd | 2 - man/plotworldmap.Rd | 10 ++++-- man/subsetTOPO.Rd | 13 ++++++-- 18 files changed, 292 insertions(+), 125 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut, cre] ,
Melissa Hallow [aut],
Wenping Wang [aut],
Zufar Mulyukov [ctb],
Alan Hindmarsh [ctb],
Awad H. Al-Mohy [ctb],
Matt Dowle [ctb],
Cleve Moler [ctb],
David Cooley [ctb],
Drew Schmidt [ctb],
Arun Srinivasan [ctb],
Ernst Hair [...truncated...]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2 versions 2.0.6 dated 2022-05-09 and 2.0.7 dated 2022-05-17
DESCRIPTION | 6 +- MD5 | 25 +++++------ NAMESPACE | 1 NEWS.md | 14 +++++- R/mu-cov-downgrade.R |only R/mu.R | 66 +++++++++++++++++++---------- R/rxUiGet.R | 13 ++++- R/rxode2_md5.R | 2 inst/doc/rxode2-syntax.html | 14 +++--- inst/tools/workaround.R | 7 +-- man/rxUiGet.Rd | 3 + src/ode.h | 4 - tests/testthat/test-mu.R | 95 +++++++++++++++++++++++++++++++++++++++++-- tests/testthat/test-random.R | 32 +++++++------- 14 files changed, 209 insertions(+), 73 deletions(-)
Title: Finding Recurrent DNA Copy Number Alterations and Differences
Description: In tumor tissue, underlying genomic instability can lead to DNA copy number alterations,
e.g., copy number gains or losses. Sporadic copy number alterations occur randomly throughout the
genome, whereas recurrent alterations are observed in the same genomic region across multiple
independent samples, perhaps because they provide a selective growth advantage. Here we use
cyclic shift permutations to identify recurrent copy number alterations in a single cohort or
recurrent copy number differences in two cohorts based on a common set of genomic markers.
Additional functionality is provided to perform downstream analyses, including the creation of
summary files and graphics. DiNAMIC.Duo builds upon the original DiNAMIC package of Walter et al.
(2011) <doi:10.1093/bioinformatics/btq717> and leverages the theory developed in Walter et al.
(2015) <doi:10.1093/biomet/asv046>. A manuscript based on DiNAMIC.Duo is currently under development.
Author: Vonn Walter [aut, cre] ,
Hyo Young Choi [aut] ,
Xiaobei Zhao [aut] ,
Yan Gao [aut] ,
David Neil Hayes [aut]
Maintainer: Vonn Walter <vwalter1@pennstatehealth.psu.edu>
Diff between DiNAMIC.Duo versions 1.0.0 dated 2021-09-29 and 1.0.1 dated 2022-05-17
DESCRIPTION | 8 +++--- MD5 | 58 +++++++++++++++++++++++------------------------ NEWS.md | 13 ++++++++++ R/cyclicNullR.R | 22 ++++++++++++----- R/cyclicShiftColR.R | 9 +++++++ R/dataPrep.R | 13 ++++++++-- R/genomeChrPlot.R | 28 ++++++++++++++++------ R/genomePlot.R | 20 ++++++++++++---- R/luadSubset.R | 16 ++++++++---- R/luscSubset.R | 16 ++++++++---- R/pD.R | 15 ++++++------ R/peelingOne.R | 10 +++++++- R/peelingOneIterate.R | 5 ++++ R/peelingTwo.R | 11 ++++++++ R/peelingTwoIterate.R | 6 ++++ R/resultsProcess.R | 10 ++++++++ build/vignette.rds |binary man/cyclicNullR.Rd | 22 ++++++++++++----- man/cyclicShiftColR.Rd | 9 +++++++ man/dataPrep.Rd | 13 ++++++++-- man/genomeChrPlot.Rd | 28 ++++++++++++++++------ man/genomePlot.Rd | 20 ++++++++++++---- man/luadSubset.Rd | 16 ++++++++---- man/luscSubset.Rd | 16 ++++++++---- man/pD.Rd | 16 +++++++----- man/peelingOne.Rd | 10 +++++++- man/peelingOneIterate.Rd | 5 ++++ man/peelingTwo.Rd | 11 ++++++++ man/peelingTwoIterate.Rd | 6 ++++ man/resultsProcess.Rd | 11 ++++++++ 30 files changed, 332 insertions(+), 111 deletions(-)
Title: Univariate and Multivariate Spatial-Temporal Modeling
Description: Fits univariate and multivariate spatio-temporal
random effects models for point-referenced data using Markov chain Monte Carlo (MCMC). Details are given in Finley, Banerjee, and Gelfand (2015) <doi:10.18637/jss.v063.i13> and Finley and Banerjee <doi:10.1016/j.envsoft.2019.104608>.
Author: Andrew Finley [aut, cre],
Sudipto Banerjee [aut]
Maintainer: Andrew Finley <finleya@msu.edu>
Diff between spBayes versions 0.4-5 dated 2021-09-22 and 0.4-6 dated 2022-05-17
DESCRIPTION | 12 ++-- MD5 | 100 ++++++++++++++++++++--------------------- R/bayesLMRef.R | 3 - R/bayesRegression.R | 10 ++-- R/spDiag.R | 44 +++++++++++------- R/spDynLM.R | 3 - R/spGLM.R | 5 +- R/spLM.R | 5 +- R/spMvGLM.R | 11 ++-- R/spMvLM.R | 10 ++-- R/spPredict.R | 37 +++++++++------ R/spRecover.R | 21 +++++--- R/spSVC.R | 3 - man/FBC07.dat.Rd | 50 -------------------- src/mkSpCov.cpp | 6 ++ src/nonSpGLM_AMCMC.cpp | 6 ++ src/spDynLM.cpp | 98 +++++++++++++++++++++------------------- src/spGLM.cpp | 12 +++- src/spGLM_AMCMC.cpp | 20 ++++---- src/spLM.cpp | 26 ++++++---- src/spLMPredict.cpp | 24 +++++---- src/spLMRecover.cpp | 64 ++++++++++++++------------ src/spMPPMvDIC.cpp | 20 ++++---- src/spMisalign.cpp | 30 +++++++----- src/spMisalignGLM.cpp | 28 ++++++----- src/spMisalignGLMPredict.cpp | 12 +++- src/spMisalignPredict.cpp | 14 +++-- src/spMisalignRecover.cpp | 44 +++++++++--------- src/spMvGLM.cpp | 16 ++++-- src/spMvGLMPredict.cpp | 22 +++++---- src/spMvGLM_AMCMC.cpp | 29 ++++++----- src/spMvLM.cpp | 36 ++++++++------ src/spMvLMPredict.cpp | 40 +++++++++------- src/spMvLMRecover.cpp | 72 +++++++++++++++-------------- src/spPPDynLM.cpp | 104 ++++++++++++++++++++++--------------------- src/spPPGLM.cpp | 14 +++-- src/spPPGLM_AMCMC.cpp | 26 ++++++---- src/spPPLM.cpp | 53 +++++++++++---------- src/spPPLMPredict.cpp | 24 +++++---- src/spPPLMRecover.cpp | 27 ++++++----- src/spPPMvGLM.cpp | 20 ++++---- src/spPPMvGLMPredict.cpp | 16 ++++-- src/spPPMvGLM_AMCMC.cpp | 36 ++++++++------ src/spPPMvLM.cpp | 84 ++++++++++++++++++---------------- src/spPPMvLMPredict.cpp | 56 ++++++++++++----------- src/spPPMvLMRecover.cpp | 40 +++++++++------- src/spSVC.cpp | 31 +++++++----- src/spSVCPredictJoint.cpp | 18 ++++--- src/spSVCPredictMarg.cpp | 20 ++++---- src/spSVCRecover.cpp | 48 ++++++++++--------- src/util.cpp | 24 +++++---- 51 files changed, 854 insertions(+), 720 deletions(-)
Title: Root Mean Square Curvature Calculation
Description: Calculates the RMS intrinsic and parameter-effects curvatures of a nonlinear regression model. The curvatures are global measures of assessing whether a model/data set combination is close-to-linear or not. See Bates and Watts (1980) <doi:10.1002/9780470316757> and Ratkowsky and Reddy (2017) <doi:10.1093/aesa/saw098> for details.
Author: Peijian Shi [aut, cre],
Peter M. Ridland [aut],
David A. Ratkowsky [aut],
Yang Li [aut]
Maintainer: Peijian Shi <pjshi@njfu.edu.cn>
Diff between IPEC versions 0.1.3 dated 2020-06-27 and 1.0.1 dated 2022-05-17
DESCRIPTION | 25 +++++++++++------- MD5 | 34 ++++++++++++------------ R/bootIPEC.R | 17 +++--------- R/fitIPEC.R | 11 ++------ build/partial.rdb |binary data/shoots.rda |binary man/IPEC.Rd | 58 +++++++++++++++++++++++++----------------- man/aic.Rd | 7 ++--- man/biasIPEC.Rd | 8 +++-- man/bic.Rd | 7 ++--- man/bootIPEC.Rd | 74 +++++++++++++++++++++++++++++++----------------------- man/curvIPEC.Rd | 27 ++++++++++--------- man/derivIPEC.Rd | 5 ++- man/fitIPEC.Rd | 43 ++++++++++++++++++------------- man/isom.Rd | 5 ++- man/leaves.Rd | 3 -- man/shoots.Rd | 35 ++++++++++++------------- man/skewIPEC.Rd | 7 ++--- 18 files changed, 201 insertions(+), 165 deletions(-)
More information about iscoCrosswalks at CRAN
Permanent link
Title: Textual Data Analysis Package Used by the TXM Software
Description: Statistical exploration of textual corpora using several methods
from French 'Textometrie' (new name of 'Lexicometrie') and French 'Data Analysis' schools.
It includes methods for exploring irregularity of distribution of lexicon features across
text sets or parts of texts (Specificity analysis); multi-dimensional exploration (Factorial analysis), etc.
Those methods are used in the TXM software.
Author: Sylvain Loiseau, Lise Vaudor, Matthieu Decorde, Serge Heiden
Maintainer: Matthieu Decorde <matthieu.decorde@ens-lyon.fr>
Diff between textometry versions 0.1.5 dated 2022-05-13 and 0.1.6 dated 2022-05-17
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 2 +- R/progression.R | 4 ++-- R/specificities.R | 8 ++++---- data/bfm.rda |binary data/robespierre.rda |binary inst/CITATION | 8 ++++---- man/bfm.Rd | 4 ++-- man/specificities.Rd | 2 +- 10 files changed, 27 insertions(+), 27 deletions(-)
Title: The Official SolveBio API Client
Description: R language bindings for SolveBio's API.
SolveBio is a biomedical knowledge hub that enables life science
organizations to collect and harmonize the complex, disparate
"multi-omic" data essential for today's R&D and BI needs.
For more information, visit <https://www.solvebio.com>.
Author: David Caplan
Maintainer: David Caplan <dcaplan@solvebio.com>
Diff between solvebio versions 2.13.0 dated 2022-04-26 and 2.14.0 dated 2022-05-17
DESCRIPTION | 8 ++-- MD5 | 10 +++-- NAMESPACE | 2 + NEWS.md | 6 +++ R/global_search.R | 70 +++++++++++++++++++++++++++++++++++++ man/GlobalSearch.facets.Rd |only man/GlobalSearch.subjects_count.Rd |only 7 files changed, 88 insertions(+), 8 deletions(-)
Title: Pull Data from an 'ArcGIS REST' API
Description: Functions to efficiently query 'ArcGIS REST' APIs
<https://developers.arcgis.com/rest/>.
Both spatial and SQL queries can be used to retrieve data.
Simple Feature (sf) objects are utilized to perform spatial queries.
This package was neither produced nor is maintained by Esri.
Author: Paul Frater [aut, cre] ,
Zac Driscoll [aut]
Maintainer: Paul Frater <paul.frater@wisconsin.gov>
Diff between arcpullr versions 0.2.3 dated 2022-03-09 and 0.2.5 dated 2022-05-17
DESCRIPTION | 6 ++-- MD5 | 34 ++++++++++++++------------ NAMESPACE | 2 + R/plot_layers.R | 6 +--- R/retrieve_layers.R | 21 +++++++++++++--- R/retrieve_layers_by_geometry.R | 40 +++++++++++++++++++++---------- R/sysdata.rda |only R/utilities.R | 43 +++++++++++++++++++++++++++++++++ inst/doc/intro_to_arcpullr.html | 6 +++- inst/doc/raster_layers.html | 6 +++- inst/doc/spatial_queries.R | 4 +-- inst/doc/spatial_queries.Rmd | 8 +++--- inst/doc/spatial_queries.html | 28 ++++++++++++--------- man/get_layers_by_spatial.Rd | 20 ++++++--------- man/get_spatial_layer.Rd | 5 +++ man/sf_objects.Rd | 5 +++ man/sp_rel_xref.Rd |only tests/testthat/test_utilities.R | 51 ++++++++++++++++++++++++++++++++++++++++ vignettes/spatial_queries.Rmd | 8 +++--- 19 files changed, 218 insertions(+), 75 deletions(-)
Title: Easily Create Production-Ready Rich Text Format (RTF) Table and
Figure
Description: Create production-ready Rich Text Format (RTF) table and figure with flexible format.
Author: Yilong Zhang [aut, cre],
Siruo Wang [aut],
Simiao Ye [aut],
Fansen Kong [aut],
Nan Xiao [ctb],
Madhusudhan Ginnaram [ctb],
Ruchitbhai Patel [ctb],
Huei-Ling Chen [ctb],
Peikun Wu [ctb],
Uday Preetham Palukuru [ctb],
Daniel Woodie [ctb],
Sarad Nepal [ [...truncated...]
Maintainer: Yilong Zhang <elong0527@gmail.com>
Diff between r2rtf versions 0.3.4 dated 2022-04-08 and 0.3.5 dated 2022-05-17
DESCRIPTION | 6 - MD5 | 20 ++-- NEWS.md | 7 + R/content_create.R | 28 +++++- R/data.R | 9 -- R/rtf_text.R | 4 R/rtf_title.R | 13 +-- build/vignette.rds |binary inst/doc/r2rtf-cran.html | 200 ++++++++++++++++++++++++++++++++++++++++++++++- man/r2rtf_adae.Rd | 4 man/r2rtf_adsl.Rd | 4 11 files changed, 255 insertions(+), 40 deletions(-)
Title: Package for Sequence Analysis by Local Score
Description: Functionalities for calculating the local score and calculating statistical relevance (p-value) to find a local Score in a sequence of given distribution (S. Mercier and J.-J. Daudin (2001) <https://hal.archives-ouvertes.fr/hal-00714174>) ; S. Karlin and S. Altschul (1990) <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC53667/> ; S. Mercier, D. Cellier and F. Charlot (2003) <https://hal.archives-ouvertes.fr/hal-00937529v1> ; A. Lagnoux, S. Mercier and P. Valois (2017) <doi:10.1093/bioinformatics/btw699> ).
Author: Sebastian Simon [aut],
David Robelin [aut, cre],
Sabine Mercier [aut],
Sebastien Dejean [aut],
The authors of Eigen the library for the included version of Eigen
[cph]
Maintainer: David Robelin <david.robelin@inrae.fr>
Diff between localScore versions 1.0.6 dated 2021-02-24 and 1.0.8 dated 2022-05-17
localScore-1.0.6/localScore/inst/doc/localScorePackageDocumentation.html |only localScore-1.0.8/localScore/DESCRIPTION | 12 - localScore-1.0.8/localScore/MD5 | 14 - localScore-1.0.8/localScore/build/vignette.rds |binary localScore-1.0.8/localScore/inst/doc/localScorePackageDocumentation.pdf |only localScore-1.0.8/localScore/src/Eigen/src/Core/AssignEvaluator.h | 4 localScore-1.0.8/localScore/src/Eigen/src/Core/products/GeneralMatrixVector.h | 12 - localScore-1.0.8/localScore/src/Eigen/src/Core/util/StaticAssert.h | 118 +++++----- localScore-1.0.8/localScore/src/RcppExports.cpp | 5 9 files changed, 85 insertions(+), 80 deletions(-)
Title: History Matching and Emulation Package
Description: A set of objects and functions for Bayes Linear emulation and history matching.
Core functionality includes automated training of emulators to data, diagnostic functions
to ensure suitability, and a variety of proposal methods for generating 'waves' of points.
For details on the mathematical background, there are many papers available on the topic
(see references attached to function help files); for details of the functions in this package,
consult the manual or help files.
Author: Andrew Iskauskas [aut, cre]
Maintainer: Andrew Iskauskas <andrew.iskauskas@durham.ac.uk>
Diff between hmer versions 1.0.0 dated 2022-04-14 and 1.0.1 dated 2022-05-17
DESCRIPTION | 12 MD5 | 210 + NAMESPACE | 196 - NEWS.md | 28 R/CorrelatorDocumentation.R | 204 - R/Emulator.R | 1604 +++++++-------- R/EmulatorDocumentation.R | 352 +-- R/HierarchicalEmulatorDocumentation.R | 112 - R/VarianceEmulator.R | 1082 +++++----- R/correlations.R | 602 ++--- R/data.R | 312 +- R/derivative_functions.R | 388 +-- R/diagnosticplots.R | 980 ++++----- R/diagnostics.R | 1860 ++++++++--------- R/fullwave.R | 472 ++-- R/genpoints.R | 1740 ++++++++-------- R/idemc.R | 704 +++--- R/implausibility.R | 409 +-- R/modelbuilding.R | 1991 +++++++++--------- R/multiwaveplot.R | 1238 +++++------ R/plotting.R | 1458 ++++++------- R/utils.R | 619 +++-- README.md | 176 - build/vignette.rds |binary data/SIREmulators.rda |binary data/SIRMultiWaveEmulators.rda |binary inst/doc/demonstrating-the-hmer-package.Rmd | 562 ++--- inst/doc/demonstrating-the-hmer-package.html | 1336 ++++++------ inst/doc/emulationhandbook.Rmd | 802 +++---- inst/doc/emulationhandbook.html | 2288 ++++++++++----------- inst/doc/low-dimensional-examples.Rmd | 1290 ++++++------ inst/doc/low-dimensional-examples.html | 2324 +++++++++++----------- inst/doc/stochasticandbimodalemulation.Rmd | 704 +++--- inst/doc/stochasticandbimodalemulation.html | 1716 ++++++++-------- man/BirthDeath.Rd | 60 man/Correlator.Rd | 218 +- man/Emulator.Rd | 362 +-- man/HierarchicalEmulator.Rd | 128 - man/SIREmulators.Rd | 46 man/SIRImplausibility.Rd | 70 man/SIRMultiWaveData.Rd | 50 man/SIRMultiWaveEmulators.Rd | 46 man/SIRSample.Rd | 74 man/SIR_stochastic.Rd | 66 man/analyze_diagnostic.Rd | 150 - man/behaviour_plot.Rd | 130 - man/bimodal_emulator_from_data.Rd | 130 - man/classification_diag.Rd | 106 - man/comparison_diag.Rd | 94 man/diagnostic_wrap.Rd | 162 - man/directional_deriv.Rd | 86 man/directional_proposal.Rd | 156 - man/effect_strength.Rd | 146 - man/emulator_from_data.Rd | 356 +-- man/emulator_plot.Rd | 192 - man/exp_sq.Rd | 62 man/figures |only man/full_wave.Rd | 168 - man/gamma_exp.Rd | 70 man/generate_new_runs.Rd | 268 +- man/get_diagnostic.Rd | 190 - man/idemc.Rd | 220 +- man/individual_errors.Rd | 156 - man/matern.Rd | 68 man/nth_implausible.Rd | 188 - man/orn_uhl.Rd | 74 man/output_plot.Rd | 100 man/plot_actives.Rd | 108 - man/plot_lattice.Rd | 148 - man/plot_wrap.Rd | 96 man/problem_data.Rd | 52 man/rat_quad.Rd | 72 man/residual_diag.Rd | 88 man/simulator_plot.Rd | 146 - man/space_removal.Rd | 96 man/space_removed.Rd | 164 - man/standard_errors.Rd | 100 man/subset_emulators.Rd | 60 man/summary_diag.Rd | 104 man/validation_diagnostics.Rd | 158 - man/validation_pairs.Rd | 136 - man/variance_emulator_from_data.Rd | 110 - man/wave_dependencies.Rd | 172 - man/wave_points.Rd | 136 - man/wave_values.Rd | 214 +- tests |only vignettes/demonstrating-the-hmer-package.Rmd | 562 ++--- vignettes/demonstrating-the-hmer-package.Rmd.orig | 324 +-- vignettes/emulationhandbook.Rmd | 802 +++---- vignettes/emulationhandbook.Rmd.orig | 672 +++--- vignettes/low-dimensional-examples.Rmd | 1290 ++++++------ vignettes/low-dimensional-examples.Rmd.orig | 854 ++++---- vignettes/precompile.R | 22 vignettes/stoch-bimodal-imp-1.png |binary vignettes/stoch-propose-bimodal-1.png |binary vignettes/stochasticandbimodalemulation.Rmd | 704 +++--- vignettes/stochasticandbimodalemulation.Rmd.orig | 592 ++--- 97 files changed, 20148 insertions(+), 19997 deletions(-)
Title: Simulation-Based Power Analysis for Factorial Designs
Description: Functions to perform simulations of ANOVA designs of up to three factors. Calculates the observed power and average observed effect size for all main effects and interactions in the ANOVA, and all simple comparisons between conditions. Includes functions for analytic power calculations and additional helper functions that compute effect sizes for ANOVA designs, observed error rates in the simulations, and functions to plot power curves. Please see Lakens, D., & Caldwell, A. R. (2021). "Simulation-Based Power Analysis for Factorial Analysis of Variance Designs". <doi:10.1177/2515245920951503>.
Author: Aaron Caldwell [aut, cre],
Daniel Lakens [aut],
Lisa DeBruine [ctb],
Jonathon Love [ctb],
Frederik Aust [ctb]
Maintainer: Aaron Caldwell <arcaldwell49@gmail.com>
Diff between Superpower versions 0.1.2 dated 2021-05-25 and 0.2.0 dated 2022-05-17
Superpower-0.1.2/Superpower/tests/testthat/Rplots.pdf |only Superpower-0.2.0/Superpower/DESCRIPTION | 13 Superpower-0.2.0/Superpower/MD5 | 88 - Superpower-0.2.0/Superpower/NAMESPACE | 15 Superpower-0.2.0/Superpower/NEWS.md | 17 Superpower-0.2.0/Superpower/R/ANCOVA_analytic.R |only Superpower-0.2.0/Superpower/R/ANCOVA_contrast.R |only Superpower-0.2.0/Superpower/R/ANCOVA_factorial_power.R |only Superpower-0.2.0/Superpower/R/ANOVA_design.R | 22 Superpower-0.2.0/Superpower/R/ANOVA_exact.R | 5 Superpower-0.2.0/Superpower/R/alpha_standardized.R | 2 Superpower-0.2.0/Superpower/R/ancova_helper_functions.R |only Superpower-0.2.0/Superpower/R/generate_cor_matrix.R | 4 Superpower-0.2.0/Superpower/R/globals.R | 2 Superpower-0.2.0/Superpower/R/methods.ancova_power.R |only Superpower-0.2.0/Superpower/R/misc_functions.R | 14 Superpower-0.2.0/Superpower/R/oneway_ancova.R |only Superpower-0.2.0/Superpower/R/p_standardized.R | 2 Superpower-0.2.0/Superpower/README.md | 181 +- Superpower-0.2.0/Superpower/build/vignette.rds |binary Superpower-0.2.0/Superpower/inst/WORDLIST |only Superpower-0.2.0/Superpower/inst/doc/ANCOVAs.R |only Superpower-0.2.0/Superpower/inst/doc/ANCOVAs.Rmd |only Superpower-0.2.0/Superpower/inst/doc/ANCOVAs.html |only Superpower-0.2.0/Superpower/inst/doc/compromise_power.html | 459 +++++- Superpower-0.2.0/Superpower/inst/doc/emmeans_power.R | 3 Superpower-0.2.0/Superpower/inst/doc/emmeans_power.Rmd | 3 Superpower-0.2.0/Superpower/inst/doc/emmeans_power.html | 423 +++++ Superpower-0.2.0/Superpower/inst/doc/intro_to_superpower.R | 15 Superpower-0.2.0/Superpower/inst/doc/intro_to_superpower.Rmd | 27 Superpower-0.2.0/Superpower/inst/doc/intro_to_superpower.html | 735 ++++++++-- Superpower-0.2.0/Superpower/inst/doc/more_anova_designs.R | 62 Superpower-0.2.0/Superpower/inst/doc/more_anova_designs.Rmd | 62 Superpower-0.2.0/Superpower/inst/doc/more_anova_designs.html | 668 +++++++-- Superpower-0.2.0/Superpower/man/ANCOVA_analytic.Rd |only Superpower-0.2.0/Superpower/man/ANCOVA_contrast.Rd |only Superpower-0.2.0/Superpower/man/ANOVA_design.Rd | 8 Superpower-0.2.0/Superpower/man/alpha_standardized.Rd | 2 Superpower-0.2.0/Superpower/man/ancova_power-methods.Rd |only Superpower-0.2.0/Superpower/man/figures |only Superpower-0.2.0/Superpower/man/p_standardized.Rd | 2 Superpower-0.2.0/Superpower/man/power_oneway_ancova.Rd |only Superpower-0.2.0/Superpower/tests/spelling.R |only Superpower-0.2.0/Superpower/tests/testthat/test-ANOVA_compromise.R | 9 Superpower-0.2.0/Superpower/tests/testthat/test-ancova_analytic.R |only Superpower-0.2.0/Superpower/tests/testthat/test-anova_design.R | 2 Superpower-0.2.0/Superpower/tests/testthat/test-anova_exact.R | 4 Superpower-0.2.0/Superpower/tests/testthat/test-anova_power.R | 13 Superpower-0.2.0/Superpower/tests/testthat/test-morey.R | 3 Superpower-0.2.0/Superpower/tests/testthat/test-power_oneway_ancova.R |only Superpower-0.2.0/Superpower/vignettes/ANCOVAs.Rmd |only Superpower-0.2.0/Superpower/vignettes/emmeans_power.Rmd | 3 Superpower-0.2.0/Superpower/vignettes/intro_to_superpower.Rmd | 27 Superpower-0.2.0/Superpower/vignettes/more_anova_designs.Rmd | 62 Superpower-0.2.0/Superpower/vignettes/refs.json |only 55 files changed, 2374 insertions(+), 583 deletions(-)
Title: Disease-Drived Differential Proteins Co-Expression Network
Analysis
Description: Functions designed to connect disease-related differential proteins and
co-expression network. It provides the basic statics analysis included t test, ANOVA analysis.
The network construction is not offered by the package, you can used 'WGCNA' package which you
can learn in Peter et al. (2008) <doi:10.1186/1471-2105-9-559>. It also provides module analysis
included PCA analysis, two enrichment analysis, Planner maximally filtered graph extraction and
hub analysis.
Author: Kefu Liu [aut, cre]
Maintainer: Kefu Liu <liukefu19@163.com>
Diff between DDPNA versions 0.3.0 dated 2021-07-29 and 0.3.1 dated 2022-05-17
DESCRIPTION | 8 ++-- MD5 | 16 ++++---- R/MaxquantDataconvert.R | 84 +++++++++++++++++++++++++++-------------------- R/Moduleconstruction.R | 68 ++++++++++++++++++++------------------ R/missing_value_impute.R | 83 ++++++++++++++++++++++++++++++++++++++++------ R/network.R | 8 ++-- man/DDPNA-package.Rd | 7 +-- man/P.G.extract.Rd | 12 ++++++ man/wgcnatest.Rd | 45 +++++++++++++++---------- 9 files changed, 215 insertions(+), 116 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-17 0.15.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-05 0.7-6
2020-02-06 0.7-5
2017-09-27 0.7-4
2015-05-11 0.7-3
2014-02-03 0.7-2
2013-03-29 0.6-8
2012-12-03 0.6-6
2012-11-16 0.6-5
2012-05-16 0.6-4
2012-04-04 0.6-2
2012-01-04 0.6-0
2011-08-09 0.5-6
2011-06-30 0.5-4
Title: Estimation of the Rasch Model for Multistage Tests
Description: Provides conditional maximum likelihood (CML) item parameter estimation of sequential as well as cumulative deterministic multistage designs (Zwitser & Maris, 2015, <doi:10.1007/s11336-013-9369-6>) as well as probabilistic sequential and cumulative multistage designs (Steinfeld & Robitzsch, 2021, <doi:10.31234/osf.io/ew27f>). Supports CML item parameter estimation of conventional linear designs and additional functions for the likelihood ratio test (Andersen, 1973, <doi:10.1007/BF02291180>) as well as functions for the simulation of several kinds of multistage designs.
Author: Jan Steinfeld [cre, aut] ,
Alexander Robitzsch [aut]
Maintainer: Jan Steinfeld <jan.d.steinfeld@gmail.com>
Diff between tmt versions 0.3.0-20 dated 2022-01-20 and 0.3.1-2 dated 2022-05-17
DESCRIPTION | 10 +- MD5 | 27 +++-- NEWS.md | 4 R/helper_functions.R | 4 R/tmt_sim.R | 2 README.md | 24 +++-- build/partial.rdb |only inst/NEWS | 7 + inst/doc/introduction_to_tmt.Rmd | 3 inst/doc/introduction_to_tmt.html | 174 +++++++++++++++++++++++++++++++------- man/tmt-package.Rd | 4 src/esf_mst_sum_vector.cpp | 18 +-- src/esf_mst_sum_vector_s2.h | 8 - src/esf_nmst_sum_matrix.cpp | 6 - vignettes/introduction_to_tmt.Rmd | 3 15 files changed, 216 insertions(+), 78 deletions(-)
Title: Tools for Handling Indices and Proportions in Small Area
Estimation
Description: It allows for mapping proportions and indicators defined on the unit interval. It implements Beta-based small area methods comprising the classical Beta regression models, the Flexible Beta model and Zero and/or One Inflated extensions (Janicki 2020 <doi:10.1080/03610926.2019.1570266>). Such methods, developed within a Bayesian framework through Stan <https://mc-stan.org/>, come equipped with a set of diagnostics and complementary tools, visualizing and exporting functions. A Shiny application with a user-friendly interface can be launched to further simplify the process.
Author: Silvia De Nicolò [aut, cre] ,
Aldo Gardini [aut]
Maintainer: Silvia De Nicolò <silvia.denicolo@phd.unipd.it>
Diff between tipsae versions 0.0.4 dated 2022-02-10 and 0.0.6 dated 2022-05-17
DESCRIPTION | 6 MD5 | 64 +++-- R/benchmark.R | 2 R/check_fit.R | 4 R/density_summary.R | 2 R/export.R | 15 - R/extract.R | 26 +- R/map.R | 15 - R/plot_summary.R | 2 R/smoothing.R | 7 R/summary_fitsae.R | 4 R/util_fit.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/shiny_tipsae_vignette.pdf |only inst/doc/shiny_tipsae_vignette.pdf.asis |only inst/extdata/emilia_cs.rds |only inst/shiny_tipsae/server_files/data_load_server.R | 4 inst/shiny_tipsae/ui_files/data_smoothing.R | 2 inst/shiny_tipsae/ui_files/main_home.R | 7 inst/stan/include/transf_par_reff.stan | 2 man/density.summary_fitsae.Rd | 84 +++---- man/emilia.Rd | 72 +++--- man/emilia_cs.Rd | 76 +++--- man/emilia_shp.Rd | 58 ++--- man/export.Rd | 100 ++++---- man/extract.Rd | 82 +++---- man/fit_sae.Rd | 248 +++++++++++----------- man/plot.summary_fitsae.Rd | 118 +++++----- man/runShiny_tipsae.Rd | 52 ++-- man/smoothing.Rd | 146 ++++++------ man/summary.fitsae.Rd | 154 ++++++------- man/tipsae-package.Rd | 72 +++--- src/stanExports_global.h | 8 vignettes/shiny_tipsae_vignette.pdf.asis |only 35 files changed, 715 insertions(+), 719 deletions(-)
Title: Microbial Community Ecology Data Analysis
Description: A series of statistical and plotting approaches in microbial community ecology based on the R6 class. The classes are designed for data preprocessing, taxa abundance plotting, alpha diversity analysis, beta diversity analysis, differential abundance test, null model analysis, network analysis, machine learning, environmental data analysis and functional analysis.
Author: Chi Liu [aut, cre],
Felipe R. P. Mansoldo [ctb],
Umer Zeeshan Ijaz [ctb],
Chenhao Li [ctb],
Yang Cao [ctb],
Minjie Yao [ctb],
Xiangzhen Li [ctb]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between microeco versions 0.8.0 dated 2022-05-03 and 0.9.0 dated 2022-05-17
DESCRIPTION | 6 - MD5 | 30 ++--- R/trans_abund.R | 95 ++++++++++++---- R/trans_alpha.R | 19 ++- R/trans_beta.R | 2 R/trans_diff.R | 290 ++++++++++++++++++++++++++++++++++++++------------- R/trans_env.R | 2 R/trans_func.R | 20 ++- R/trans_network.R | 96 ++++++++++------ R/utility.R | 2 man/trans_abund.Rd | 89 ++++++++++++++- man/trans_alpha.Rd | 9 - man/trans_beta.Rd | 4 man/trans_diff.Rd | 46 +++++++- man/trans_env.Rd | 2 man/trans_network.Rd | 13 +- 16 files changed, 535 insertions(+), 190 deletions(-)
More information about marginaleffects at CRAN
Permanent link
Title: Fitting Single and Mixture of Generalised Lambda Distributions
Description: The fitting algorithms considered in this package have two major objectives. One is to provide a smoothing device to fit distributions to data using the weight and unweighted discretised approach based on the bin width of the histogram. The other is to provide a definitive fit to the data set using the maximum likelihood and quantile matching estimation. Other methods such as moment matching, starship method, L moment matching are also provided. Diagnostics on goodness of fit can be done via qqplots, KS-resample tests and comparing mean, variance, skewness and kurtosis of the data with the fitted distribution. References include the following: Karvanen and Nuutinen (2008) "Characterizing the generalized lambda distribution by L-moments" <doi:10.1016/j.csda.2007.06.021>, King and MacGillivray (1999) "A starship method for fitting the generalised lambda distributions" <doi:10.1111/1467-842X.00089>, Su (2005) "A Discretized Approach to Flexibly Fit Generalized Lambda Distributions to Data" <doi:10.22237/jmasm/1130803560>, Su (2007) "Nmerical Maximum Log Likelihood Estimation for Generalized Lambda Distributions" <doi:10.1016/j.csda.2006.06.008>, Su (2007) "Fitting Single and Mixture of Generalized Lambda Distributions to Data via Discretized and Maximum Likelihood Methods: GLDEX in R" <doi:10.18637/jss.v021.i09>, Su (2009) "Confidence Intervals for Quantiles Using Generalized Lambda Distributions" <doi:10.1016/j.csda.2009.02.014>, Su (2010) "Chapter 14: Fitting GLDs and Mixture of GLDs to Data using Quantile Matching Method" <doi:10.1201/b10159>, Su (2010) "Chapter 15: Fitting GLD to data using GLDEX 1.0.4 in R" <doi:10.1201/b10159>, Su (2015) "Flexible Parametric Quantile Regression Model" <doi:10.1007/s11222-014-9457-1>, Su (2021) "Flexible parametric accelerated failure time model"<doi:10.1080/10543406.2021.1934854>.
Author: Steve Su [aut, cre, cph] ,
Martin Maechler [aut],
Juha Karvanen [aut],
Robert King [aut],
Benjamin Dean [ctb],
R Core Team [aut]
Maintainer: Steve Su <allegro.su@gmail.com>
Diff between GLDEX versions 2.0.0.8 dated 2022-05-12 and 2.0.0.9 dated 2022-05-17
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- man/GLDEX.package.Rd | 4 ++-- src/GLDEX.c | 32 ++++++++++++++++---------------- 4 files changed, 26 insertions(+), 26 deletions(-)
Title: Bayesian Multinomial Logistic Normal Regression
Description: Provides methods for fitting and inspection of Bayesian Multinomial Logistic Normal Models using MAP estimation
and Laplace Approximation as developed in Silverman et. Al. (2022) <https://www.jmlr.org/papers/v23/19-882.html>. Key functionality is implemented in C++ for
scalability. 'fido' replaces the previous package 'stray'.
Author: Justin Silverman [aut],
Kim Roche [ctb],
Michelle Nixon [ctb, cre]
Maintainer: Michelle Nixon
<pistner@psu.edu>
Diff between fido versions 1.0.0 dated 2022-02-16 and 1.0.1 dated 2022-05-17
DESCRIPTION | 12 MD5 | 53 NEWS.md | 8 R/fidofit_methods.R | 6 R/mallard-data.R | 2 R/mallard_family-data.R | 4 configure | 2019 ++++++++++++++++++++++++++----------- configure.ac | 211 +++ data/mallard.RData |binary data/mallard_family.RData |binary inst/doc/introduction-to-fido.html | 516 ++++++++- inst/doc/mitigating-pcrbias.html | 318 +++++ inst/doc/non-linear-models.R | 30 inst/doc/non-linear-models.Rmd | 30 inst/doc/non-linear-models.html | 338 +++++- inst/doc/orthus.Rmd | 24 inst/doc/orthus.html | 403 ++++++- inst/doc/picking_priors.html | 234 ++++ inst/include/fido.h | 21 inst/include/fidoGenerated.h.in |only man/mallard.Rd | 2 man/mallard_family.Rd | 2 man/sample_prior.pibblefit.Rd | 6 src/Makevars.in | 3 tests/testthat/test-ilr.R | 3 vignettes/non-linear-models.Rmd | 30 vignettes/orthus.Rmd | 24 vignettes/orthus.Rmd.orig | 6 28 files changed, 3429 insertions(+), 876 deletions(-)
More information about dimensionalAnalysis at CRAN
Permanent link
Title: Cell-Typing using Variance Adjusted Mahalanobis Distances with
Multi-Labeling
Description: Creates multi-label cell-types for single-cell RNA-sequencing data based on weighted VAM scoring of cell-type specific gene sets. Schiebout, Frost (2022) <https://psb.stanford.edu/psb-online/proceedings/psb22/schiebout.pdf>.
Author: H. Robert Frost [aut],
Courtney Schiebout [aut, cre]
Maintainer: Courtney Schiebout <courtney.t.schiebout.gr@dartmouth.edu>
Diff between CAMML versions 0.1.1 dated 2021-12-15 and 0.2.1 dated 2022-05-17
DESCRIPTION | 12 ++++++------ MD5 | 22 ++++++++++++++-------- NAMESPACE | 8 ++++++-- R/BuildGeneSets.R | 2 +- R/CAMML.R | 7 +++++-- R/ChIMP.R |only build/vignette.rds |binary inst/doc/CAMML_FigureVignette.pdf |binary inst/doc/CAMML_Quick_Vignette.pdf |binary inst/doc/CAMML_Vignette.pdf |binary inst/doc/ChIMPVignette.Rnw |only inst/doc/ChIMPVignette.pdf |only man/ChIMP.Rd |only vignettes/ChIMPVignette.Rnw |only vignettes/ChIMPVignette1.pdf |only 15 files changed, 32 insertions(+), 19 deletions(-)
Title: HTML Output Formats and Templates for 'rmarkdown' Documents
Description: HTML formats and templates for 'rmarkdown' documents, with some extra
features such as automatic table of contents, lightboxed figures, dynamic
crosstab helper.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@cnrs.fr>
Diff between rmdformats versions 1.0.3 dated 2021-10-06 and 1.0.4 dated 2022-05-17
DESCRIPTION | 10 +++---- MD5 | 24 ++++++++--------- NEWS.md | 10 +++++++ R/html_template.R | 21 +++++++-------- R/pilltabs.R | 37 ++++++++++----------------- inst/templates/downcute/downcute.css | 6 ++++ inst/templates/material/material.css | 2 - inst/templates/material/material.html | 16 +++++------ inst/templates/navigation-1.1/codefolding.js | 27 ++++++++++++++----- inst/templates/navigation-1.1/sourceembed.js | 11 +++++--- inst/templates/readthedown/readthedown.css | 36 +++++--------------------- inst/templates/robobook/robobook.css | 4 ++ man/pilltabs.Rd | 4 +- 13 files changed, 108 insertions(+), 100 deletions(-)
Title: Bayesian Exponential Smoothing Models with Trend Modifications
Description: An implementation of a number of Global Trend models for time series forecasting
that are Bayesian generalizations and extensions of some Exponential Smoothing models.
The main differences/additions include 1) nonlinear global trend, 2) Student-t error
distribution, and 3) a function for the error size, so heteroscedasticity. The methods
are particularly useful for short time series. When tested on the well-known M3 dataset,
they are able to outperform all classical time series algorithms. The models are fitted
with MCMC using the 'rstan' package.
Author: Slawek Smyl [aut],
Christoph Bergmeir [aut, cre],
Erwin Wibowo [aut],
To Wang Ng [aut],
Trustees of Columbia University [cph]
Maintainer: Christoph Bergmeir <christoph.bergmeir@monash.edu>
Diff between Rlgt versions 0.1-3 dated 2019-06-14 and 0.1-4 dated 2022-05-17
Rlgt-0.1-3/Rlgt/src/Makevars.win |only Rlgt-0.1-4/Rlgt/ChangeLog | 4 Rlgt-0.1-4/Rlgt/DESCRIPTION | 13 Rlgt-0.1-4/Rlgt/MD5 | 53 - Rlgt-0.1-4/Rlgt/R/Rlgt-package.R | 6 Rlgt-0.1-4/Rlgt/R/data.R | 2 Rlgt-0.1-4/Rlgt/build/vignette.rds |binary Rlgt-0.1-4/Rlgt/configure |only Rlgt-0.1-4/Rlgt/configure.win |only Rlgt-0.1-4/Rlgt/demo/basicDemos.R | 3 Rlgt-0.1-4/Rlgt/inst/doc/GT_models.R | 2 Rlgt-0.1-4/Rlgt/inst/doc/GT_models.html | 655 +++++++++++----------- Rlgt-0.1-4/Rlgt/inst/doc/gettingStarted.R | 2 Rlgt-0.1-4/Rlgt/inst/doc/gettingStarted.Rmd | 44 - Rlgt-0.1-4/Rlgt/inst/doc/gettingStarted.html | 569 +++++++++---------- Rlgt-0.1-4/Rlgt/man/Rlgt-package.Rd | 20 Rlgt-0.1-4/Rlgt/man/forecast.rlgtfit.Rd | 9 Rlgt-0.1-4/Rlgt/man/iclaims.example.Rd | 8 Rlgt-0.1-4/Rlgt/man/initModel.Rd | 10 Rlgt-0.1-4/Rlgt/man/posterior_interval.rlgtfit.Rd | 3 Rlgt-0.1-4/Rlgt/man/rlgt.Rd | 14 Rlgt-0.1-4/Rlgt/man/rlgt.control.Rd | 31 - Rlgt-0.1-4/Rlgt/man/rlgtfit.Rd | 17 Rlgt-0.1-4/Rlgt/man/umcsent.example.Rd | 6 Rlgt-0.1-4/Rlgt/src/Makevars | 8 Rlgt-0.1-4/Rlgt/src/stan_files/LGT.stan | 11 Rlgt-0.1-4/Rlgt/src/stan_files/S2GT.stan | 9 Rlgt-0.1-4/Rlgt/src/stan_files/SGT.stan | 9 Rlgt-0.1-4/Rlgt/vignettes/gettingStarted.Rmd | 44 - 29 files changed, 836 insertions(+), 716 deletions(-)
Title: Various R Programming Tools for Model Fitting
Description: Various R programming tools for model fitting.
Author: Gregory R. Warnes, Ben Bolker, Thomas Lumley, and Randall C
Johnson. Contributions from Randall C. Johnson are Copyright
SAIC-Frederick, Inc. Funded by the Intramural Research
Program, of the NIH, National Cancer Institute, Center for
Cancer Researc [...truncated...]
Maintainer: Gregory R. Warnes <greg@warnes.net>
Diff between gmodels versions 2.18.1 dated 2018-06-25 and 2.18.1.1 dated 2022-05-17
DESCRIPTION | 6 +++--- MD5 | 4 ++-- man/estimable.Rd | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-02 1.1-4
2020-05-15 1.0-9
2020-04-29 1.0-8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-03-01 1.31
2012-09-23 1.1
2012-07-31 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-17 3.2.4
2019-04-28 3.2.3
2019-02-28 3.2.2
2018-05-15 3.1.1
2018-04-07 3.1
2018-02-13 2.2
2018-01-03 2.1
2017-12-13 1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-08-19 1.0