Title: USGS ScienceBase Tools
Description: Tools for interacting with U.S. Geological Survey ScienceBase
<https://www.sciencebase.gov> interfaces. ScienceBase is a data cataloging and
collaborative data management platform. Functions included for querying
ScienceBase, and creating and fetching datasets.
Author: Tim Kern [cre],
Luke Winslow [aut],
Scott Chamberlain [aut],
Alison Appling [aut],
Jordan Read [aut]
Maintainer: Tim Kern <kernt@usgs.gov>
Diff between sbtools versions 1.1.3 dated 2016-08-19 and 1.1.6 dated 2016-09-27
DESCRIPTION | 17 +++++---- MD5 | 9 ++--- R/sbtools-package.R | 5 +- README.md | 88 +++++++++++++++++++++++++++++++++++++++++++++++++ inst/CITATION |only man/sbtools-package.Rd | 3 + 6 files changed, 108 insertions(+), 14 deletions(-)
Title: Principal Component Gene Set Enrichment
Description: Contains logic for computing the statistical association of variable groups, i.e., gene sets, with respect to the principal components of genomic data.
Author: H. Robert Frost
Maintainer: H. Robert Frost <rob.frost@dartmouth.edu>
Diff between PCGSE versions 0.2 dated 2014-05-07 and 0.3 dated 2016-09-27
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 9 ++++++--- R/SGSE.R | 2 +- 4 files changed, 15 insertions(+), 12 deletions(-)
Title: Dynamic Nomograms for Linear, Generalized Linear and
Proportional Hazard Models
Description: Demonstrate the results of a statistical model object as a dynamic nomogram in an 'RStudio' panel or web browser. DynNom supports a variety of model objects; 'lm', 'glm', 'coxph' and also 'Ols', 'Glm', 'lrm', 'cph' models.
Author: Amirhossein Jalali, Davood Roshan, Alberto Alvarez-Iglesias, John Newell
Maintainer: Amirhossein Jalali <a.jalali2@nuigalway.ie>
Diff between DynNom versions 3.0 dated 2016-09-20 and 3.0.1 dated 2016-09-27
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- man/DynNom.rms.Glm.Rd | 2 +- man/DynNom.rms.cph.Rd | 8 ++++---- man/DynNom.rms.lrm.Rd | 2 +- man/DynNom.rms.ols.Rd | 7 +++---- 6 files changed, 19 insertions(+), 20 deletions(-)
Title: Bayesian Latent Variable Analysis
Description: Fit a variety of Bayesian latent variable models, including confirmatory
factor analysis, structural equation models, and latent growth curve models.
Author: Edgar Merkle [aut, cre],
Yves Rosseel [aut]
Maintainer: Edgar Merkle <merklee@missouri.edu>
Diff between blavaan versions 0.2-1 dated 2016-09-20 and 0.2-2 dated 2016-09-27
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NAMESPACE | 3 ++- R/blav_object_inspect.R | 45 +++++++++++---------------------------------- R/postpred.R | 2 +- man/blavInspect.Rd |only 6 files changed, 22 insertions(+), 43 deletions(-)
Title: Function Collection Related to Plotting and Hydrology
Description: Draw horizontal histograms, color scattered points by 3rd dimension,
enhance date- and log-axis plots, zoom in X11 graphics,
use the unit hydrograph in a linear storage cascade, convert lists to data.frames,
fit multiple functions by regression (power, reciprocal, exponential, logarithmic,
polynomial, rational).
Author: Berry Boessenkool
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between berryFunctions versions 1.12.2 dated 2016-09-21 and 1.12.3 dated 2016-09-27
DESCRIPTION | 8 ++++---- MD5 | 21 +++++++++++---------- NEWS | 7 +++++++ R/createDoc.R | 2 +- R/createFun.R | 3 ++- R/dataDWD.R | 21 +++++++++++++++++++++ R/traceCall.R | 11 ++++++++++- inst/extdata/RainfallStationsMap.pdf |only man/createDoc.Rd | 2 +- man/createFun.Rd | 3 ++- man/dataDWD.Rd | 21 +++++++++++++++++++++ man/traceCall.Rd | 2 ++ 12 files changed, 82 insertions(+), 19 deletions(-)
More information about berryFunctions at CRAN
Permanent link
Title: Cooperative Game Theory
Description: Implementation of a common set of punctual solutions for Cooperative Game Theory.
Author: Sebastian Cano-Berlanga
Maintainer: Sebastian Cano-Berlanga <cano.berlanga@gmail.com>
Diff between GameTheory versions 2.0 dated 2015-08-10 and 2.4 dated 2016-09-27
DESCRIPTION | 8 - MD5 | 14 +- R/DefineGame.R | 86 +++++++++------- R/Nucleolus.R | 245 +++++++++++++++++++++++------------------------ R/NucleolusCapita.R | 161 ++++++++++++------------------ R/summary.Game.R | 7 - R/summary.ShapleyValue.R | 2 build/vignette.rds |binary 8 files changed, 253 insertions(+), 270 deletions(-)
Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data
visualization. Results of various statistical analyses (that are commonly used
in social sciences) can be visualized using this package, including simple and
cross tabulated frequencies, histograms, box plots, (generalized) linear models,
mixed effects models, PCA and correlation matrices, cluster analyses, scatter
plots, Likert scales, effects plots of regression models (including interaction
terms) and much more. This package supports labelled data.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjPlot versions 2.0.2 dated 2016-07-31 and 2.1.0 dated 2016-09-27
DESCRIPTION | 17 MD5 | 92 NAMESPACE | 415 +-- NEWS | 651 +++--- NEWS.md | 38 R/helpfunctions.R | 1724 ++++++++-------- R/plot_grid.R |only R/set_theme.R |only R/sjPlotAncovaLSMeans.R | 720 +++--- R/sjPlotClusterAnalysis.R | 2 R/sjPlotCorr.R | 10 R/sjPlotFrequencies.R | 143 - R/sjPlotGLME.R | 4834 ++++++++++++++++++++++----------------------- R/sjPlotGroupFrequencies.R | 25 R/sjPlotGroupPropTable.R | 3 R/sjPlotInteractions.R | 2 R/sjPlotLinreg.R | 101 R/sjPlotLinregMultiple.R | 76 R/sjPlotOdds.R | 16 R/sjPlotResiduals.R |only R/sjPlotSetTheme.R | 1614 ++++++--------- R/sjTabLinReg.R | 406 +-- R/sjTabOdds.R | 23 R/sjTabSPSS.R | 826 +++---- R/table_functions.R | 18 README.md | 88 build/partial.rdb |binary man/plot_grid.Rd |only man/save_plot.Rd | 116 - man/set_theme.Rd |only man/sjPlot-package.Rd | 106 man/sjc.kgap.Rd | 134 - man/sjc.qclus.Rd | 5 man/sjp.corr.Rd | 270 +- man/sjp.glm.Rd | 5 man/sjp.glmer.Rd | 5 man/sjp.glmm.Rd | 5 man/sjp.grpfrq.Rd | 5 man/sjp.int.Rd | 5 man/sjp.lm.Rd | 5 man/sjp.lmer.Rd | 5 man/sjp.lmm.Rd | 5 man/sjp.resid.Rd |only man/sjp.scatter.Rd | 5 man/sjp.setTheme.Rd | 536 ++-- man/sjt.glm.Rd | 33 man/sjt.glmer.Rd | 32 man/sjt.lm.Rd | 28 man/sjt.lmer.Rd | 62 man/view_df.Rd | 4 50 files changed, 6551 insertions(+), 6664 deletions(-)
Title: Subgroup Identification Based on Differential Effect Search
Description: Provides function to apply "Subgroup Identification based on Differential Effect Search" (SIDES) method proposed by Lipkovich et al. (2011) <doi:10.1002/sim.4289>.
Author: Marie-Karelle Riviere
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between SIDES versions 1.5 dated 2016-09-15 and 1.6 dated 2016-09-27
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/SIDES_MAIN.R | 4 ++-- man/SIDES-package.Rd | 4 ++-- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Quick Wraps 2
Description: A collection of (wrapper) functions the creator found useful
for quickly placing data summaries and formatted regression results into
'.Rnw' or '.Rmd' files. Functions for generating commonly used graphics,
such as receiver operating curves or Bland-Altman plots, are also provided
by 'qwraps2'. 'qwraps2' is a updated version of a package 'qwraps'. The
original version 'qwraps' was never submitted to CRAN but can be found at
<https://github.com/dewittpe/qwraps/>. The implementation and limited scope
of the functions within 'qwraps2' <https://github.com/dewittpe/qwraps2/> is
fundamentally different from 'qwraps'.
Author: Peter DeWitt [aut, cre],
Tell Bennett [ctb]
Maintainer: Peter DeWitt <dewittpe@gmail.com>
Diff between qwraps2 versions 0.2.1 dated 2016-05-30 and 0.2.2 dated 2016-09-27
DESCRIPTION | 9 +-- MD5 | 38 ++++++++++---- NAMESPACE | 10 +++ R/RcppExports.R | 2 R/confusion_matrix.R | 9 +-- R/mean_ci.R | 20 +++++-- R/qable.R | 135 +++++++++++++++++---------------------------------- R/summary_table.R |only README.md | 49 ++++++++++++------ build |only inst |only man/mean_ci.Rd | 16 ++++-- man/qable.Rd | 101 ++++++++------------------------------ man/summary_table.Rd |only src/RcppExports.cpp | 18 +++--- tests |only vignettes |only 17 files changed, 182 insertions(+), 225 deletions(-)
Title: Detecting Isotope, Adduct and Homologue Relations in LC-MS Data
Description: Screening a HRMS data set for peaks related by (1) isotope patterns, (2) different adducts of the same molecule and/or (3) homologue series. The resulting isotopic pattern and adduct groups can then be combined to so-called components, with homologue series information attached. Also allows plotting and filtering HRMS data for mass defects, frequent m/z distances and components vs. non-components.
Author: Martin Loos
Maintainer: Martin Loos <mloos@looscomputing.ch>
Diff between nontarget versions 1.8 dated 2016-03-14 and 1.9 dated 2016-09-27
DESCRIPTION | 12 +- MD5 | 30 ++--- NEWS | 5 R/combine.R | 142 +++++++++++--------------- R/deter.iso.R | 2 R/homol.search.R | 252 +++++++++++++++++++++++++++++++++-------------- R/ms.filter.R | 8 - R/nontarget.R | 2 R/pattern.search.R | 28 +---- R/plotcomp.R | 2 R/rm.sat.R | 2 man/combine.Rd | 12 +- man/homol.search.Rd | 9 - man/nontarget-package.Rd | 6 - man/pattern.search.Rd | 4 src/massCpp.cpp | 2 16 files changed, 304 insertions(+), 214 deletions(-)
Title: Functional Rarity Indices Computation
Description: Computes functional rarity indices as proposed by Violle et al (accepted).
Various indices can be computed using both regional and local information.
Functional Rarity combines both the functional aspect of rarity as well as
the extent aspect of rarity.
Author: Matthias Grenié [aut, cre],
Pierre Denelle [aut],
Caroline Tucker [aut]
Maintainer: Matthias Grenié <matthias.grenie@gmail.com>
Diff between funrar versions 1.0.0 dated 2016-07-15 and 1.0.1 dated 2016-09-27
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/stack_matrix.R | 25 ++++++++++++++++++++----- README.md | 16 ++++++++++++---- build/vignette.rds |binary inst/doc/rarity_indices.Rmd | 4 ++-- inst/doc/rarity_indices.html | 9 ++++----- inst/doc/sparse_matrices.html | 30 +++++++++++++++--------------- man/matrix_to_stack.Rd | 4 +++- man/stack_to_matrix.Rd | 1 + tests/testthat/test-tidy_matrix.R | 27 ++++++++++++++++++++++++++- vignettes/rarity_indices.Rmd | 4 ++-- 12 files changed, 100 insertions(+), 50 deletions(-)
Title: Neyman-Pearson Receiver Operating Characteristics
Description: Given a sample of class 0 and class 1 and a classification method, the package generates the corresponding Neyman-Pearson classifier with a pre-specified type-I error control and Neyman-Pearson Receiver Operating Characteristics.
Author: Yang Feng, Jessica Li and Xin Tong
Maintainer: Yang Feng <yang.feng@columbia.edu>
Diff between nproc versions 1.2 dated 2016-08-11 and 2.0.1 dated 2016-09-27
nproc-1.2/nproc/R/npc.core.R |only nproc-1.2/nproc/R/nproc.core.R |only nproc-1.2/nproc/vignettes/nproc-demo.html |only nproc-2.0.1/nproc/ChangeLog | 25 ++- nproc-2.0.1/nproc/DESCRIPTION | 8 - nproc-2.0.1/nproc/MD5 | 39 ++--- nproc-2.0.1/nproc/NAMESPACE | 5 nproc-2.0.1/nproc/R/compare.R |only nproc-2.0.1/nproc/R/lines.nproc.R |only nproc-2.0.1/nproc/R/npc.R | 147 ++++++++---------- nproc-2.0.1/nproc/R/npfuns.R | 225 ++++++++++++++++------------- nproc-2.0.1/nproc/R/nproc.R | 100 +++++++----- nproc-2.0.1/nproc/R/plot.nproc.R | 53 ------ nproc-2.0.1/nproc/R/predict.npc.R | 17 -- nproc-2.0.1/nproc/build/vignette.rds |binary nproc-2.0.1/nproc/inst/doc/nproc-demo.R | 13 + nproc-2.0.1/nproc/inst/doc/nproc-demo.Rmd | 17 +- nproc-2.0.1/nproc/inst/doc/nproc-demo.pdf |binary nproc-2.0.1/nproc/man/compare.Rd |only nproc-2.0.1/nproc/man/lines.nproc.Rd |only nproc-2.0.1/nproc/man/npc.Rd | 61 +++---- nproc-2.0.1/nproc/man/nproc.Rd | 45 ++--- nproc-2.0.1/nproc/man/plot.nproc.Rd | 11 - nproc-2.0.1/nproc/vignettes/nproc-demo.Rmd | 17 +- 24 files changed, 402 insertions(+), 381 deletions(-)
Title: Bayesian Non-Homogenous Markov and Mixture Models (Multiple Time
Series)
Description: Bayesian HMM and NHMM modeling for multiple time series. The emission distribution can be mixtures of Gammas, Poissons, Normals and zero inflation is possible.
Author: Tracy Holsclaw
Maintainer: Tracy Holsclaw <iamrandom@iamrandom.com>
Diff between NHMM versions 3.5 dated 2014-11-26 and 3.6 dated 2016-09-27
DESCRIPTION | 13 - MD5 | 10 NAMESPACE | 9 R/NHMMmain.R | 11 R/OBIC.R | 4 src/RcppExports.cpp | 660 ++++++++++++++++++++-------------------------------- 6 files changed, 295 insertions(+), 412 deletions(-)
Title: Non-Parametric Multiple Change-Point Analysis of Multivariate
Data
Description: Implements various procedures for finding
multiple change-points. Two methods make use of dynamic
programming and probabilistic pruning, with no distributional
assumptions other than the existence of certain absolute
moments in one method. Hierarchical and exact search methods
are included. All methods return the set of estimated change-
points as well as other summary information.
Author: Nicholas A. James, Wenyu Zhang and David S. Matteson
Maintainer: Nicholas A. James <nj89@cornell.edu>
Diff between ecp versions 2.0.0 dated 2015-05-20 and 3.0.0 dated 2016-09-27
DESCRIPTION | 24 +- MD5 | 21 +- NAMESPACE | 3 NEWS | 11 - R/cp3o.R | 31 +++ R/energyChangePoint.R | 3 build/vignette.rds |binary man/e.cp3o.Rd | 4 man/ks.cp3o.Rd |only src/Makevars | 2 src/Makevars.win | 2 src/efast.cpp | 512 ++++++++++++++++++++++++++++++++++++++++++++------ 12 files changed, 526 insertions(+), 87 deletions(-)
Title: Analysis of Binary Character Evolution
Description: Fits a hidden rates model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as hidden states in a Markov process and various other functions for evaluating models of binary character evolution.
Author: Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Jeffrey C. Oliver <jeffreycoliver@gmail.com>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>
Diff between corHMM versions 1.19 dated 2016-06-13 and 1.20 dated 2016-09-27
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/ancRECON.R | 2 +- R/rayDISC.R | 14 ++++++-------- 4 files changed, 14 insertions(+), 16 deletions(-)