Title: Monotone Multi-Layer Perceptron Neural Network
Description: Train and make predictions from a multi-layer perceptron neural
network with optional partial monotonicity constraints.
Author: Alex J. Cannon
Maintainer: Alex J. Cannon <alex.cannon@canada.ca>
Diff between monmlp versions 1.1.3 dated 2015-07-23 and 1.1.4 dated 2017-03-23
monmlp-1.1.3/monmlp/man/monmlp.cost.Rd |only monmlp-1.1.3/monmlp/man/monmlp.initialize.Rd |only monmlp-1.1.3/monmlp/man/monmlp.nlm.Rd |only monmlp-1.1.3/monmlp/man/monmlp.reshape.Rd |only monmlp-1.1.4/monmlp/DESCRIPTION | 10 +++--- monmlp-1.1.4/monmlp/MD5 | 29 ++++++++---------- monmlp-1.1.4/monmlp/NAMESPACE | 12 ++++++- monmlp-1.1.4/monmlp/R/gam.style.R | 12 +++---- monmlp-1.1.4/monmlp/R/monmlp.cost.R | 39 +++---------------------- monmlp-1.1.4/monmlp/R/monmlp.fit.R | 19 ++++++------ monmlp-1.1.4/monmlp/R/monmlp.grad.R |only monmlp-1.1.4/monmlp/R/monmlp.initialize.R | 15 +++++++-- monmlp-1.1.4/monmlp/R/monmlp.nlm.R | 35 ++++++++++++---------- monmlp-1.1.4/monmlp/R/monmlp.predict.R | 2 - monmlp-1.1.4/monmlp/man/gam.style.Rd | 5 +-- monmlp-1.1.4/monmlp/man/monmlp-package.Rd | 15 +++------ monmlp-1.1.4/monmlp/man/monmlp.fit.Rd | 42 ++++++++++++++++----------- monmlp-1.1.4/monmlp/man/monmlp.predict.Rd | 8 +++-- 18 files changed, 122 insertions(+), 121 deletions(-)
Title: GEV Conditional Density Estimation Network
Description: Implements a flexible nonlinear modelling framework for nonstationary
generalized extreme value analysis in hydroclimatology.
Author: Alex J. Cannon
Maintainer: Alex J. Cannon <alex.cannon@canada.ca>
Diff between GEVcdn versions 1.1.4 dated 2015-07-23 and 1.1.5 dated 2017-03-23
DESCRIPTION | 7 ++++--- MD5 | 10 +++++----- R/gevcdn.bag.R | 2 +- R/gevcdn.bootstrap.R | 13 ++++++------- man/gevcdn.bag.Rd | 27 ++++++++++++++------------- man/gevcdn.fit.Rd | 4 ++-- 6 files changed, 32 insertions(+), 31 deletions(-)
Title: Conditional Density Estimation Network Construction and
Evaluation
Description: Parameters of a user-specified probability distribution are modelled by a multi-layer perceptron artificial neural network. This framework can be used to implement probabilistic nonlinear models including mixture density networks, heteroscedastic regression models, zero-inflated models, and the like.
Author: Alex J. Cannon
Maintainer: Alex J. Cannon <alex.cannon@canada.ca>
Diff between CaDENCE versions 1.2.3 dated 2015-07-23 and 1.2.4 dated 2017-03-23
DESCRIPTION | 7 ++++--- MD5 | 12 ++++++------ R/cadence.fit.R | 4 ++-- R/gam.style.R | 6 +++--- R/rbf.R | 2 +- R/rprop.R | 4 ++-- R/xval.buffer.R | 6 +++--- 7 files changed, 21 insertions(+), 20 deletions(-)
Title: Normalisation of Psychometric Tests
Description: Functions for normalizing psychometric test scores. The normalization aims at correcting the metrological properties of the psychometric tests such as the ceiling and floor effects and the curvilinearity (unequal interval scaling). Functions to compute and plot predictions in the natural scale of the psychometric test from the estimates of a linear mixed model estimated on the normalized scores are also provided.
Author: Cecile Proust-Lima, Viviane Philipps
Maintainer: Cecile Proust-Lima <cecile.proust-lima@inserm.fr>
Diff between NormPsy versions 1.0.4 dated 2016-12-13 and 1.0.5 dated 2017-03-23
DESCRIPTION | 8 ++++---- MD5 | 13 ++++++++----- NAMESPACE | 2 +- R/predictMMSE.R | 16 ++++++++-------- man/ForInternalUse.Rd |only src/Makevars.in | 7 +++++-- src/Makevars.win | 7 +++++-- src/init.c |only src/normpsy.h |only 9 files changed, 31 insertions(+), 22 deletions(-)
Title: Extended Mixed Models Using Latent Classes and Latent Processes
Description: Estimation of various extensions of the mixed models including latent class mixed models, joint latent latent class mixed models and mixed models for curvilinear univariate or multivariate longitudinal outcomes using a maximum likelihood estimation method.
Author: Cecile Proust-Lima, Viviane Philipps, Amadou Diakite and Benoit Liquet
Maintainer: Cecile Proust-Lima <cecile.proust-lima@inserm.fr>
Diff between lcmm versions 1.7.6 dated 2016-12-13 and 1.7.7 dated 2017-03-23
DESCRIPTION | 8 - MD5 | 58 ++++++------ NAMESPACE | 3 R/Contlcmm.R | 208 ++++++++++++++++++++++++++++++---------------- R/Jointlcmm.R | 177 +++++++++++++++++++++++++-------------- R/Ordlcmm.R | 113 ++++++++++++++++++------ R/dynpred.R | 120 +++++++++++++++++--------- R/epoce.R | 57 +++++++++--- R/hlme.R | 94 +++++++++++++++----- R/multlcmm.R | 172 +++++++++++++++++++++++++++++--------- R/plot.predictY.R | 4 R/predictY.Jointlcmm.R | 141 ++++++++++++++++--------------- R/predictY.hlme.R | 94 ++++++++++---------- R/predictY.lcmm.R | 141 ++++++++++++++++++++----------- R/predictY.multlcmm.R | 58 ++++++++++-- R/predictlink.Jointlcmm.R | 40 +++++++- R/predictlink.lcmm.R | 40 +++++++- R/predictlink.multlcmm.R | 40 +++++++- inst/CITATION | 2 man/ForInternalUse.Rd | 11 ++ src/Jointhet.f90 | 4 src/Makevars | 5 - src/calculusTransfo.f90 | 4 src/hetmixCont.f90 | 4 src/hetmixContMult.f90 | 4 src/hetmixOrd.f90 | 4 src/init.c |only src/lcmm.h |only src/postprob2.f90 | 4 src/predictCont.f90 | 4 src/predictMult.f90 | 4 31 files changed, 1103 insertions(+), 515 deletions(-)
Title: Random Forests Model Selection and Performance Evaluation
Description: Utilities for Random Forest model selection, class balance
correction, significance test, cross validation and partial dependency
plots.
Author: Jeffrey S. Evans [cre, aut],
Melanie A. Murphy [ctb]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>
Diff between rfUtilities versions 2.0-0 dated 2016-04-27 and 2.0-1 dated 2017-03-23
DESCRIPTION | 11 ++---- MD5 | 66 ++++++++++++++++++------------------ R/rf.classBalance.R | 57 +++++++++++++++++++------------ R/rf.crossValidation.R | 2 - R/rf.modelSel.R | 6 +-- inst/CITATION | 6 +-- inst/NEWS | 6 +++ man/accuracy.Rd | 7 +-- man/multi.collinear.Rd | 9 ++-- man/occurrence.threshold.Rd | 7 +-- man/plot.occurrence.threshold.Rd | 1 man/plot.rf.cv.Rd | 1 man/plot.rf.modelSel.Rd | 1 man/plot.significance.Rd | 1 man/print.accuracy.Rd | 1 man/print.occurrence.threshold.Rd | 1 man/print.rf.cv.Rd | 1 man/print.rf.modelSel.Rd | 1 man/print.significance.Rd | 1 man/rf.class.sensitivity.Rd | 7 +-- man/rf.classBalance.Rd | 31 +++++++++++----- man/rf.crossValidation.Rd | 7 +-- man/rf.imp.freq.Rd | 1 man/rf.modelSel.Rd | 9 ++-- man/rf.partial.ci.Rd | 1 man/rf.partial.prob.Rd | 7 +-- man/rf.regression.fit.Rd | 1 man/rf.significance.Rd | 7 +-- man/rfu.news.Rd | 1 man/summary.accuracy.Rd | 1 man/summary.occurrence.threshold.Rd | 1 man/summary.rf.cv.Rd | 1 man/summary.rf.modelSel.Rd | 1 man/summary.significance.Rd | 1 34 files changed, 133 insertions(+), 130 deletions(-)
Title: Diversity Measures for Complex Systems
Description: Computes the most common diversity measures used in social and other sciences, and includes new measures from interdisciplinary research.
Author: Miguel R. Guevara <miguel.guevara@upla.cl>, Dominik Hartmann
<d.hartmann@uni-hohenheim.de>, Marcelo Mendoza
<marcelo.mendoza@usm.cl>
Maintainer: Miguel R. Guevara <miguel.guevara@upla.cl>
Diff between diverse versions 0.1.4 dated 2016-12-09 and 0.1.5 dated 2017-03-23
DESCRIPTION | 10 ++++++---- MD5 | 3 ++- inst/CITATION |only 3 files changed, 8 insertions(+), 5 deletions(-)
Title: Perform Phylogenetic Path Analysis
Description: A comprehensive and easy to use R implementation of confirmatory
phylogenetic path analysis as described by Von Hardenberg and Gonzalez-Voyer
(2012) <doi:10.1111/j.1558-5646.2012.01790.x>.
Author: Wouter van der Bijl
Maintainer: Wouter van der Bijl <wouter.van.der.bijl@zoologi.su.se>
Diff between phylopath versions 0.2.2 dated 2017-01-04 and 0.2.3 dated 2017-03-23
DESCRIPTION | 8 +++--- MD5 | 39 +++++++++++++++-------------- NEWS.md | 22 +++++++++++++--- R/DAG.R | 6 ++++ R/internal.R | 6 +--- R/phylopath.R | 51 ++++++++++++++++++++++++++++++++------- build/vignette.rds |binary inst/CITATION |only inst/doc/intro_to_phylopath.Rmd | 18 +++++++++++++ inst/doc/intro_to_phylopath.html | 21 +++++++++++++--- man/DAG.Rd | 1 man/average.Rd | 1 man/average_DAGs.Rd | 1 man/best.Rd | 1 man/choice.Rd | 1 man/coef_plot.Rd | 1 man/est_DAG.Rd | 5 +-- man/phylo_path.Rd | 16 ++++++------ man/rhino.Rd | 1 man/rhino_tree.Rd | 1 vignettes/intro_to_phylopath.Rmd | 18 +++++++++++++ 21 files changed, 155 insertions(+), 63 deletions(-)
Title: Group Iterative Multiple Model Estimation
Description: Automated identification and estimation of group- and
individual-level relations in time series data from within a structural
equation modeling framework.
Author: Stephanie Lane [aut, cre, trl],
Kathleen Gates [aut],
Peter Molenaar [aut],
Michael Hallquist [ctb],
Hallie Pike [ctb]
Maintainer: Stephanie Lane <slane@unc.edu>
Diff between gimme versions 0.2-0 dated 2016-11-20 and 0.2-1 dated 2017-03-23
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/gimme.R | 29 +++++++++++++++++++++-------- man/aggSEM.Rd | 1 - man/gimme-package.Rd | 1 - man/gimmeInteractive.Rd | 3 +-- man/gimmeSEM.Rd | 9 ++++----- man/indSEM.Rd | 1 - man/simData.Rd | 1 - man/ts.Rd | 1 - 10 files changed, 40 insertions(+), 34 deletions(-)
Title: Estimating Absolute Protein Quantities from Label-Free LC-MS/MS
Proteomics Data
Description: Determination of absolute protein quantities is necessary for multiple applications, such as mechanistic modeling of biological systems. Quantitative liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics can measure relative protein abundance on a system-wide scale. To estimate absolute quantitative information using these relative abundance measurements requires additional information such as heavy-labeled references of known concentration. Multiple methods have been using different references and strategies; some are easily available whereas others require more effort on the users end. Hence, we believe the field might benefit from making some of these methods available under an automated framework, which also facilitates validation of the chosen strategy. We have implemented the most commonly used absolute label-free protein abundance estimation methods for LC-MS/MS modes quantifying on either MS1-, MS2-levels or spectral counts together with validation algorithms to enable automated data analysis and error estimation. Specifically, we used Monte-carlo cross-validation and bootstrapping for model selection and imputation of proteome-wide absolute protein quantity estimation. Our open-source software is written in the statistical programming language R and validated and demonstrated on a synthetic sample.
Author: George Rosenberger, Hannes Roest, Christina Ludwig, Ruedi Aebersold, Lars Malmstroem
Maintainer: George Rosenberger <rosenberger@imsb.biol.ethz.ch>
Diff between aLFQ versions 1.3.3 dated 2016-01-05 and 1.3.4 dated 2017-03-23
aLFQ-1.3.3/aLFQ/inst/tests |only aLFQ-1.3.3/aLFQ/tests/units.R |only aLFQ-1.3.4/aLFQ/DESCRIPTION | 8 ++++---- aLFQ-1.3.4/aLFQ/MD5 | 16 ++++++++-------- aLFQ-1.3.4/aLFQ/R/ProteinInference.R | 2 +- aLFQ-1.3.4/aLFQ/man/aLFQ.package.Rd | 4 ++-- aLFQ-1.3.4/aLFQ/tests/Examples/aLFQ-Ex.Rout.save | 8 ++++---- aLFQ-1.3.4/aLFQ/tests/testthat |only aLFQ-1.3.4/aLFQ/tests/testthat.R |only 9 files changed, 19 insertions(+), 19 deletions(-)
Title: Optimum Contribution Selection and Population Genetics
Description: A framework for the optimization of breeding programs via optimum contribution selection. An easy to use set of function for computation of optimum contributions of selection candidates, and of the population genetic parameters to be optimized. These parameters can be estimated using pedigree or genotype information, and include kinships, kinships at native haplotype segments, and breed composition of crossbred individuals. They are suitable for managing genetic diversity, removing introgressed genetic material, and accelerating genetic gain. Additionally, functions are provided for computing genetic contributions from ancestors, inbreeding coefficients, the native effective size, the native genome equivalent, pedigree completeness, and for preparing and plotting pedigrees.
Author: Robin Wellmann
Maintainer: Robin Wellmann <r.wellmann@uni-hohenheim.de>
Diff between optiSel versions 0.3 dated 2017-02-23 and 0.5 dated 2017-03-23
DESCRIPTION | 15 - MD5 | 102 +++++---- NAMESPACE | 4 R/RcppExports.R | 8 R/completeness.R | 58 ++--- R/conttac.R | 52 ++-- R/genecont.R | 51 ++-- R/genecontALT.R |only R/makeA.R |only R/onAttach.R |only R/opticomp.R | 4 R/opticont.R | 9 R/pedBreedComp.R | 70 +++--- R/pedIBD.R | 21 - R/pedIBDatN.R | 128 +++++++---- R/pedIBDorM.R | 22 +- R/prePed.R | 76 +++++-- R/summary.Pedig.R | 26 +- build/partial.rdb |binary build/vignette.rds |only data/Cattle.rda |binary data/ExamplePed.rda |binary data/Kin.rda |binary data/PedigWithErrors.rda |binary data/Phen.rda |binary data/map.rda |binary inst/doc |only inst/extdata/Chr1.phased | 200 ------------------ inst/extdata/Chr2.phased | 100 --------- man/Cattle.Rd | 6 man/genecont.Rd | 19 + man/haplofreq.Rd | 3 man/makeA.Rd |only man/opticont.Rd | 508 +++++++++++++++++++++++------------------------ man/opticont4mb.Rd | 36 +-- man/pedBreedComp.Rd | 2 man/pedIBD.Rd | 9 man/pedIBDatN.Rd | 8 man/segBreedComp.Rd | 4 man/segIBDandN.Rd | 4 man/segN.Rd | 6 man/summary.Pedig.Rd | 6 src/Makevars | 1 src/Makevars.win | 1 src/RcppExports.cpp | 30 ++ src/init.c | 1 src/rcpp_genecont.cpp |only src/rcpp_makeA.cpp |only vignettes |only 49 files changed, 730 insertions(+), 860 deletions(-)
Title: Perform Mokken Scale Analysis in R
Description: Contains functions for performing Mokken
scale analysis on test and questionnaire data. It includes an automated
item selection algorithm, and various checks of model assumptions.
Author: L. Andries van der Ark <L.A.vanderArk@uva.nl>
Maintainer: L. Andries van der Ark <L.A.vanderArk@uva.nl>
Diff between mokken versions 2.8.4 dated 2016-11-19 and 2.8.5 dated 2017-03-23
DESCRIPTION | 10 +++++----- MD5 | 15 ++++++++++----- NAMESPACE | 6 ++++-- R/MLcoefH.R |only data/autonomySupport.rda |only inst/doc/GettingStartedWithMokken.pdf |binary man/MLcoefH.Rd |only man/autonomySupport.Rd |only man/mokken-package.Rd | 19 +++++++++++++------ src/Init.c |only src/mokken.c | 3 --- 11 files changed, 32 insertions(+), 21 deletions(-)
Title: Utilities to Handle WKT Spatial Data
Description: Utilities to generate bounding boxes from 'WKT' (Well-Known Text) objects and R data types, validate
'WKT' objects and convert object types from the 'sp' package into 'WKT' representations.
Author: Oliver Keyes [aut, cre]
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between wicket versions 0.2.0 dated 2017-01-21 and 0.3.0 dated 2017-03-23
DESCRIPTION | 10 ++++----- MD5 | 47 +++++++++++++++++++++---------------------- NAMESPACE | 2 - NEWS | 5 ++++ R/RcppExports.R | 33 ++++++++++++++++-------------- R/wicket.R | 2 - README.md | 2 + build/vignette.rds |binary inst/doc/Introduction.R | 14 ++++++------ inst/doc/Introduction.Rmd | 14 ++++++------ inst/doc/Introduction.html | 18 ++++++++-------- man/bounding_wkt.Rd | 1 man/sp_convert.Rd | 1 man/validate_wkt.Rd | 8 +++---- man/wicket.Rd | 2 - man/wkt_bounding.Rd | 1 man/wkt_centroid.Rd | 8 +++---- man/wkt_coords.Rd | 20 +++++++++--------- src/centroid.cpp | 11 +++++----- src/def.h | 4 ++- src/init.c |only src/validate.cpp | 7 +++--- src/wkt_coords.cpp | 37 +++++++++++++++++---------------- tests/testthat/test_coords.R | 6 ++--- vignettes/Introduction.Rmd | 14 ++++++------ 25 files changed, 140 insertions(+), 127 deletions(-)
Title: Bayesian Modelling of Extremal Dependence in Time Series
Description: Characterisation of the extremal dependence structure of time series, avoiding pre-processing and filtering as done typically with peaks-over-threshold methods. It uses the conditional approach of Heffernan and Tawn (2004) <DOI:10.1111/j.1467-9868.2004.02050.x> which is very flexible in terms of extremal and asymptotic dependence structures, and Bayesian methods improve efficiency and allow for deriving measures of uncertainty. For example, the extremal index, related to the size of clusters in time, can be estimated and samples from its posterior distribution obtained.
Author: Thomas Lugrin
Maintainer: Thomas Lugrin <thomas.lugrin@epfl.ch>
Diff between tsxtreme versions 0.3 dated 2017-03-14 and 0.3.1 dated 2017-03-23
DESCRIPTION | 9 ++++----- MD5 | 10 +++++----- NEWS.md | 5 +++++ build/partial.rdb |binary src/etfit.cpp | 10 +++++----- src/etfit_externC.cpp | 2 +- 6 files changed, 20 insertions(+), 16 deletions(-)
Title: Bayesian Spatial Survival Analysis with Parametric Proportional
Hazards Models
Description: Bayesian inference for parametric proportional hazards spatial
survival models; flexible spatial survival models.
Author: Benjamin M. Taylor and Barry S. Rowlingson
Additional contributions
Ziyu Zheng
Maintainer: Benjamin M. Taylor <b.taylor1@lancaster.ac.uk>
Diff between spatsurv versions 1.0 dated 2017-03-07 and 1.1 dated 2017-03-23
DESCRIPTION | 8 MD5 | 54 ++-- R/GMRF.R | 55 ++-- R/log_posteriors_and_derivatives.R | 289 +++++++++++----------- R/log_posteriors_and_derivatives_SPDE.R | 327 ++++++++++++-------------- R/log_posteriors_and_derivatives_gridded.R | 321 ++++++++++++------------- R/log_posteriors_and_derivatives_polygonal.R | 319 ++++++++++++------------- R/nonspatial_log_likelihood_and_derivatives.R | 4 R/spatsurv.R | 8 R/survspat.R | 2 R/survspatNS.R | 86 +++--- inst/CITATION | 36 +- man/GammaFromY_SPDE.Rd | 2 man/NonSpatialLogLikelihood_or_gradient.Rd | 2 man/SPDEprec.Rd | 2 man/YFromGamma_SPDE.Rd | 2 man/getgrd.Rd | 2 man/logPosterior.Rd | 2 man/logPosterior_SPDE.Rd | 2 man/logPosterior_gridded.Rd | 2 man/logPosterior_polygonal.Rd | 2 man/maxlikparamPHsurv.Rd | 2 man/neighLocs.Rd | 2 man/neighOrder.Rd | 2 man/setupPrecMatStruct.Rd | 2 man/spatsurv-package.Rd | 6 man/survspat.Rd | 2 man/survspatNS.Rd | 4 28 files changed, 770 insertions(+), 777 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>,
Rolf Turner <r.turner@auckland.ac.nz>
and Ege Rubak <rubak@math.aau.dk>,
with substantial contributions of code by
Kasper Klitgaard Berthelsen;
Ottmar Cronie;
Yongtao Guan;
Ute Hahn;
Abdollah Jalilian;
Marie-Colette van Lieshout;
Tuomas Rajala;
Suman Rakshit;
Dominic Schuhmacher;
Rasmus Waagepetersen;
and Hangsheng Wang.
Additional contributions
by M. Adepeju;
C. Anderson;
Q.W. Ang;
M. Austenfeld;
S. Azaele;
M. Baddeley;
C. Beale;
M. Bell;
R. Bernhardt;
T. Bendtsen;
A. Bevan;
B. Biggerstaff;
A. Bilgrau;
L. Bischof;
C. Biscio;
R. Bivand;
J.M. Blanco Moreno;
F. Bonneu;
J. Burgos;
S. Byers;
Y.M. Chang;
J.B. Chen;
I. Chernayavsky;
Y.C. Chin;
B. Christensen;
J.-F. Coeurjolly;
K. Colyvas;
R. Corria Ainslie;
R. Cotton;
M. de la Cruz;
P. Dalgaard;
M. D'Antuono;
S. Das;
T. Davies;
P.J. Diggle;
P. Donnelly;
I. Dryden;
S. Eglen;
A. El-Gabbas;
B. Fandohan;
O. Flores;
E.D. Ford;
P. Forbes;
S. Frank;
J. Franklin;
N. Funwi-Gabga;
O. Garcia;
A. Gault;
J. Geldmann;
M. Genton;
S. Ghalandarayeshi;
J. Gilbey;
J. Goldstick;
P. Grabarnik;
C. Graf;
U. Hahn;
A. Hardegen;
M.B. Hansen;
M. Hazelton;
J. Heikkinen;
M. Hering;
M. Herrmann;
P. Hewson;
K. Hingee;
K. Hornik;
P. Hunziker;
J. Hywood;
R. Ihaka;
C. Icos;
A. Jammalamadaka;
R. John-Chandran;
D. Johnson;
M. Khanmohammadi;
R. Klaver;
P. Kovesi;
M. Kuhn;
J. Laake;
F. Lavancier;
T. Lawrence;
R.A. Lamb;
J. Lee;
G.P. Leser;
H.T. Li;
G. Limitsios;
A. Lister;
B. Madin;
M. Maechler;
J. Marcus;
K. Marchikanti;
R. Mark;
J. Mateu;
P. McCullagh;
U. Mehlig;
F. Mestre;
S. Meyer;
X.C. Mi;
L. De Middeleer;
R.K. Milne;
E. Miranda;
J. Moller;
M. Moradi;
V. Morera Pujol;
E. Mudrak;
G.M. Nair;
N. Najari;
N. Nava;
L.S. Nielsen;
F. Nunes;
J.R. Nyengaard;
J. Oehlschlaegel;
T. Onkelinx;
S. O'Riordan;
E. Parilov;
J. Picka;
N. Picard;
M. Porter;
S. Protsiv;
A. Raftery;
S. Rakshit;
B. Ramage;
P. Ramon;
X. Raynaud,
M. Reiter;
I. Renner;
T.O. Richardson;
B.D. Ripley;
E. Rosenbaum;
B. Rowlingson;
J. Rudokas;
J. Rudge;
C. Ryan;
F. Safavimanesh;
A. Sarkka;
C. Schank;
K. Schladitz;
S. Schutte;
B.T. Scott;
O. Semboli;
F. Semecurbe;
V. Shcherbakov;
G.C. Shen;
P. Shi;
H.-J. Ship;
I.-M. Sintorn;
Y. Song;
M. Spiess;
M. Stevenson;
K. Stucki;
M. Sumner;
P. Surovy;
B. Taylor;
T. Thorarinsdottir;
B. Turlach;
T. Tvedebrink;
K. Ummer;
M. Uppala;
A. van Burgel;
T. Verbeke;
M. Vihtakari;
A. Villers;
F. Vinatier;
S. Voss;
S. Wagner;
H. Wang;
H. Wendrock;
J. Wild;
C. Witthoft;
S. Wong;
M. Woringer;
M.E. Zamboni
and
A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 1.49-0 dated 2017-02-08 and 1.50-0 dated 2017-03-23
spatstat-1.49-0/spatstat/R/formulae.R |only spatstat-1.49-0/spatstat/R/locator.R |only spatstat-1.49-0/spatstat/R/primefactors.R |only spatstat-1.49-0/spatstat/R/resolve.defaults.R |only spatstat-1.49-0/spatstat/R/tapplysum.R |only spatstat-1.49-0/spatstat/R/utilarg.R |only spatstat-1.49-0/spatstat/R/utilmatrix.R |only spatstat-1.49-0/spatstat/R/utilseq.R |only spatstat-1.49-0/spatstat/R/utiltext.R |only spatstat-1.49-0/spatstat/R/xycircle.R |only spatstat-1.49-0/spatstat/R/xypolygon.R |only spatstat-1.49-0/spatstat/R/xysegment.R |only spatstat-1.49-0/spatstat/src/circxseg.c |only spatstat-1.49-0/spatstat/src/distseg.c |only spatstat-1.49-0/spatstat/src/fastinterv.c |only spatstat-1.49-0/spatstat/src/inxyp.c |only spatstat-1.49-0/spatstat/src/matchpoints.c |only spatstat-1.49-0/spatstat/src/ply.c |only spatstat-1.49-0/spatstat/src/ply.h |only spatstat-1.49-0/spatstat/src/primefax.c |only spatstat-1.49-0/spatstat/src/revcum.c |only spatstat-1.50-0/spatstat/DESCRIPTION | 15 spatstat-1.50-0/spatstat/MD5 | 483 ++++++++++----------- spatstat-1.50-0/spatstat/NAMESPACE | 168 ------- spatstat-1.50-0/spatstat/NEWS | 97 ++++ spatstat-1.50-0/spatstat/R/FGmultiInhom.R | 3 spatstat-1.50-0/spatstat/R/Jinhom.R | 6 spatstat-1.50-0/spatstat/R/Kest.R | 27 - spatstat-1.50-0/spatstat/R/Kmeasure.R | 2 spatstat-1.50-0/spatstat/R/areadiff.R | 6 spatstat-1.50-0/spatstat/R/areainter.R | 6 spatstat-1.50-0/spatstat/R/boundingcircle.R | 6 spatstat-1.50-0/spatstat/R/bw.diggle.R | 3 spatstat-1.50-0/spatstat/R/bw.pcf.R |only spatstat-1.50-0/spatstat/R/clip.psp.R | 3 spatstat-1.50-0/spatstat/R/close3Dpairs.R | 12 spatstat-1.50-0/spatstat/R/closepairs.R | 36 + spatstat-1.50-0/spatstat/R/clusterinfo.R | 7 spatstat-1.50-0/spatstat/R/connected.R | 6 spatstat-1.50-0/spatstat/R/crossdistlpp.R | 3 spatstat-1.50-0/spatstat/R/deldir.R | 9 spatstat-1.50-0/spatstat/R/density.ppp.R | 45 + spatstat-1.50-0/spatstat/R/density.psp.R | 3 spatstat-1.50-0/spatstat/R/dg.R | 3 spatstat-1.50-0/spatstat/R/dgs.R | 3 spatstat-1.50-0/spatstat/R/discarea.R | 3 spatstat-1.50-0/spatstat/R/dist2dpath.R | 3 spatstat-1.50-0/spatstat/R/distan3D.R | 24 - spatstat-1.50-0/spatstat/R/distances.R | 12 spatstat-1.50-0/spatstat/R/distanxD.R | 12 spatstat-1.50-0/spatstat/R/distmap.R | 26 - spatstat-1.50-0/spatstat/R/edgeRipley.R | 6 spatstat-1.50-0/spatstat/R/edges2triangles.R | 18 spatstat-1.50-0/spatstat/R/exactPdt.R | 3 spatstat-1.50-0/spatstat/R/exactdt.R | 3 spatstat-1.50-0/spatstat/R/fardist.R | 6 spatstat-1.50-0/spatstat/R/fgk3.R | 21 spatstat-1.50-0/spatstat/R/fiksel.R | 3 spatstat-1.50-0/spatstat/R/geyer.R | 3 spatstat-1.50-0/spatstat/R/hasclose.R | 24 - spatstat-1.50-0/spatstat/R/idw.R | 6 spatstat-1.50-0/spatstat/R/images.R | 17 spatstat-1.50-0/spatstat/R/kppm.R | 133 ++++- spatstat-1.50-0/spatstat/R/linalg.R | 21 spatstat-1.50-0/spatstat/R/lineardisc.R | 3 spatstat-1.50-0/spatstat/R/linequad.R | 12 spatstat-1.50-0/spatstat/R/linnet.R | 7 spatstat-1.50-0/spatstat/R/lintess.R | 3 spatstat-1.50-0/spatstat/R/lixellate.R | 3 spatstat-1.50-0/spatstat/R/localpcf.R | 6 spatstat-1.50-0/spatstat/R/lpp.R | 14 spatstat-1.50-0/spatstat/R/minnndist.R | 12 spatstat-1.50-0/spatstat/R/nncross.R | 6 spatstat-1.50-0/spatstat/R/nncross3D.R | 6 spatstat-1.50-0/spatstat/R/nndist.R | 12 spatstat-1.50-0/spatstat/R/nndistlpp.R | 24 - spatstat-1.50-0/spatstat/R/nnmap.R | 6 spatstat-1.50-0/spatstat/R/otherpackages.R | 12 spatstat-1.50-0/spatstat/R/pairdistlpp.R | 3 spatstat-1.50-0/spatstat/R/pcf.R | 21 spatstat-1.50-0/spatstat/R/pcfinhom.R | 17 spatstat-1.50-0/spatstat/R/pixellate.R | 16 spatstat-1.50-0/spatstat/R/polygood.R | 6 spatstat-1.50-0/spatstat/R/pp3.R | 4 spatstat-1.50-0/spatstat/R/ppm.R | 13 spatstat-1.50-0/spatstat/R/ppp.R | 41 + spatstat-1.50-0/spatstat/R/pppmatch.R | 21 spatstat-1.50-0/spatstat/R/ppx.R | 74 +-- spatstat-1.50-0/spatstat/R/psp2pix.R | 9 spatstat-1.50-0/spatstat/R/pspcross.R | 26 - spatstat-1.50-0/spatstat/R/quasirandom.R | 3 spatstat-1.50-0/spatstat/R/rPerfect.R | 18 spatstat-1.50-0/spatstat/R/random.R | 29 - spatstat-1.50-0/spatstat/R/rmh.default.R | 7 spatstat-1.50-0/spatstat/R/rmhmodel.R | 3 spatstat-1.50-0/spatstat/R/rmhmodel.ppm.R | 51 +- spatstat-1.50-0/spatstat/R/scanstat.R | 3 spatstat-1.50-0/spatstat/R/setcov.R | 5 spatstat-1.50-0/spatstat/R/smooth.ppp.R | 30 - spatstat-1.50-0/spatstat/R/sparse3Darray.R | 54 +- spatstat-1.50-0/spatstat/R/sparsecommon.R | 10 spatstat-1.50-0/spatstat/R/sparselinalg.R | 6 spatstat-1.50-0/spatstat/R/strauss.R | 6 spatstat-1.50-0/spatstat/R/sysdata.rda |binary spatstat-1.50-0/spatstat/R/weightedStats.R | 3 spatstat-1.50-0/spatstat/R/window.R | 7 spatstat-1.50-0/spatstat/R/wingeom.R | 10 spatstat-1.50-0/spatstat/build/vignette.rds |binary spatstat-1.50-0/spatstat/data/Kovesi.rda |binary spatstat-1.50-0/spatstat/data/amacrine.rda |binary spatstat-1.50-0/spatstat/data/anemones.rda |binary spatstat-1.50-0/spatstat/data/ants.rda 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spatstat-1.50-0/spatstat/data/hamster.rda |binary spatstat-1.50-0/spatstat/data/heather.rda |binary spatstat-1.50-0/spatstat/data/humberside.rda |binary spatstat-1.50-0/spatstat/data/hyytiala.rda |binary spatstat-1.50-0/spatstat/data/japanesepines.rda |binary spatstat-1.50-0/spatstat/data/lansing.rda |binary spatstat-1.50-0/spatstat/data/letterR.rda |binary spatstat-1.50-0/spatstat/data/longleaf.rda |binary spatstat-1.50-0/spatstat/data/mucosa.rda |binary spatstat-1.50-0/spatstat/data/murchison.rda |binary spatstat-1.50-0/spatstat/data/nbfires.rda |binary spatstat-1.50-0/spatstat/data/nztrees.rda |binary spatstat-1.50-0/spatstat/data/osteo.rda |binary spatstat-1.50-0/spatstat/data/paracou.rda |binary spatstat-1.50-0/spatstat/data/ponderosa.rda |binary spatstat-1.50-0/spatstat/data/pyramidal.rda |binary spatstat-1.50-0/spatstat/data/redwood.rda |binary spatstat-1.50-0/spatstat/data/redwood3.rda |binary spatstat-1.50-0/spatstat/data/redwoodfull.rda |binary 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spatstat-1.50-0/spatstat/man/rounding.Rd | 2 spatstat-1.50-0/spatstat/man/rpoisppx.Rd | 12 spatstat-1.50-0/spatstat/man/rshift.ppp.Rd | 2 spatstat-1.50-0/spatstat/man/rshift.splitppp.Rd | 2 spatstat-1.50-0/spatstat/man/runifpointx.Rd | 12 spatstat-1.50-0/spatstat/man/scalardilate.Rd | 2 spatstat-1.50-0/spatstat/man/scaletointerval.Rd | 2 spatstat-1.50-0/spatstat/man/sharpen.Rd | 2 spatstat-1.50-0/spatstat/man/sidelengths.owin.Rd | 2 spatstat-1.50-0/spatstat/man/spatstat-internal.Rd | 317 ------------- spatstat-1.50-0/spatstat/man/spatstat-package.Rd | 6 spatstat-1.50-0/spatstat/man/superimpose.Rd | 2 spatstat-1.50-0/spatstat/man/unitname.Rd | 2 spatstat-1.50-0/spatstat/src/denspt.c | 1 spatstat-1.50-0/spatstat/src/hasclose.h | 3 spatstat-1.50-0/spatstat/src/init.c | 12 spatstat-1.50-0/spatstat/src/proto.h | 26 - spatstat-1.50-0/spatstat/src/segdens.c | 4 spatstat-1.50-0/spatstat/tests/testsAtoF.R | 8 spatstat-1.50-0/spatstat/tests/testsLtoM.R | 26 - spatstat-1.50-0/spatstat/tests/testsNtoP.R | 5 spatstat-1.50-0/spatstat/tests/testsStoZ.R | 31 - spatstat-1.50-0/spatstat/vignettes/updates.Rnw | 215 ++++++++- 254 files changed, 1760 insertions(+), 1348 deletions(-)
Title: Safe Implementation of Monte Carlo Tests
Description: Algorithms for the implementation and evaluation of Monte Carlo tests, as well as for their use in multiple testing procedures.
Author: Axel Gandy <a.gandy@imperial.ac.uk> with contributions from Patrick Rubin-Delanchy <patrick.rubin-delanchy@imperial.ac.uk>, Georg Hahn <g.hahn11@imperial.ac.uk>, Dong Ding <dong.ding10@imperial.ac.uk>
Maintainer: Axel Gandy <a.gandy@imperial.ac.uk>
Diff between simctest versions 2.4.1 dated 2015-03-04 and 2.5 dated 2017-03-23
DESCRIPTION | 12 +- MD5 | 26 +++-- NAMESPACE | 8 + R/multithresh.R |only build/vignette.rds |binary inst/NEWS.Rd |only inst/doc/simctest-intro.pdf |binary inst/doc/simctest-mctest-intro.R |only inst/doc/simctest-mctest-intro.Rnw |only inst/doc/simctest-mctest-intro.pdf |only inst/doc/simctest-mmctest-intro.R | 46 +++++----- inst/doc/simctest-mmctest-intro.Rnw | 3 inst/doc/simctest-mmctest-intro.pdf |binary man/mctest.Rd |only src/init.c |only vignettes/papers.bib | 157 +++++++++++++++++++---------------- vignettes/simctest-mctest-intro.Rnw |only vignettes/simctest-mmctest-intro.Rnw | 3 18 files changed, 142 insertions(+), 113 deletions(-)
Title: Oxycline Index from Matrix Echograms
Description: Tools for oxycline depth calculation from echogram matrices.
Author: Wencheng Lau-Medrano [aut, cre],
Ricardo Oliveros-Ramos [ctb]
Maintainer: Wencheng Lau-Medrano <luis.laum@gmail.com>
Diff between oXim versions 1.1.2 dated 2016-12-16 and 1.2.1 dated 2017-03-23
DESCRIPTION | 8 +-- MD5 | 56 ++++++++++++------------ R/auxiliar.R | 17 +++++++ R/oXim-internal.R | 43 +++++++++++++++++++ R/oXim-main.R | 26 ++++++----- R/oxyclineData-internal.R | 83 ++++++++++++++++++++++--------------- build/vignette.rds |binary data/defaultFilterSettings.RData |binary demo/create_filter_configuration.R | 4 - inst/doc/vignette.Rmd | 6 +- inst/doc/vignette.html | 10 ++-- man/colPalette.Rd | 1 man/createFilterSetting.Rd | 11 ++-- man/defaultFilterSettings.Rd | 1 man/echogramPlot.Rd | 6 +- man/echogramPlot.echoData.Rd | 1 man/echogramPlot.oxyclineData.Rd | 1 man/getOxyrange.Rd | 6 +- man/oXim-package.Rd | 3 - man/plot.echoData.Rd | 1 man/plot.oxyclineData.Rd | 1 man/print.echoData.Rd | 1 man/print.oxyclineData.Rd | 1 man/print.summary.echoData.Rd | 1 man/print.summary.oxyclineData.Rd | 1 man/readEchograms.Rd | 1 man/summary.echoData.Rd | 1 man/summary.oxyclineData.Rd | 1 vignettes/vignette.Rmd | 6 +- 29 files changed, 182 insertions(+), 116 deletions(-)
Title: Read, Write and Edit XLSX Files
Description: Simplifies the creation of Excel .xlsx files by providing a high
level interface to writing, styling and editing worksheets. Through the use of
'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect' packages
with the added benefit of removing the dependency on Java.
Author: Alexander Walker [aut, cre],
Luca Braglia [ctb]
Maintainer: Alexander Walker <Alexander.Walker1989@gmail.com>
Diff between openxlsx versions 4.0.0 dated 2017-01-09 and 4.0.17 dated 2017-03-23
DESCRIPTION | 29 MD5 | 209 ++--- NAMESPACE | 4 NEWS | 45 + R/CommentClass.R | 4 R/RcppExports.R | 8 R/WorkbookClass.R | 199 ++++- R/baseXML.R | 14 R/conditional_formatting.R |only R/helperFunctions.R | 58 + R/loadWorkbook.R | 138 ++- R/openXL.R | 3 R/openxlsx.R | 11 R/readWorkbook.R | 15 R/sheet_data_class.R | 8 R/workbook_column_widths.R | 8 R/workbook_read_workbook.R | 22 R/workbook_write_data.R | 2 R/worksheet_class.R | 6 R/wrappers.R | 754 ++++++++------------ R/writeData.R | 53 - R/writeDataTable.R | 87 +- R/writexlsx.R | 6 README.md | 8 build/vignette.rds |binary inst/doc/Introduction.pdf |binary inst/doc/formatting.pdf |binary inst/doc/installation.pdf |binary inst/load_xlsx_testing.R | 13 inst/namedRegions.xlsx |only inst/readTest.xlsx |binary man/addFilter.Rd | 1 man/addStyle.Rd | 11 man/addWorksheet.Rd | 1 man/all.equal.Rd | 1 man/conditionalFormat.Rd | 7 man/conditionalFormatting.Rd | 53 + man/convertFromExcelRef.Rd | 1 man/convertToDate.Rd | 1 man/convertToDateTime.Rd | 1 man/copyWorkbook.Rd | 1 man/createComment.Rd | 1 man/createNamedRegion.Rd | 7 man/createStyle.Rd | 32 man/createWorkbook.Rd | 7 man/dataValidation.Rd | 21 man/deleteData.Rd | 1 man/figures |only man/freezePane.Rd | 1 man/getBaseFont.Rd | 1 man/getCellRefs.Rd | 1 man/getDateOrigin.Rd | 7 man/getNamedRegions.Rd | 3 man/getSheetNames.Rd | 1 man/getStyles.Rd | 1 man/getTables.Rd |only man/insertImage.Rd | 7 man/insertPlot.Rd | 7 man/int2col.Rd | 1 man/loadWorkbook.Rd | 7 man/makeHyperlinkString.Rd | 1 man/mergeCells.Rd | 7 man/modifyBaseFont.Rd | 1 man/names.Rd | 1 man/openXL.Rd | 3 man/openxlsx.Rd | 12 man/pageBreak.Rd | 1 man/pageSetup.Rd | 1 man/read.xlsx.Rd | 7 man/readWorkbook.Rd | 7 man/removeCellMerge.Rd | 7 man/removeColWidths.Rd | 7 man/removeComment.Rd | 1 man/removeFilter.Rd | 1 man/removeRowHeights.Rd | 7 man/removeTable.Rd |only man/removeWorksheet.Rd | 1 man/renameWorksheet.Rd | 1 man/replaceStyle.Rd | 7 man/saveWorkbook.Rd | 7 man/setColWidths.Rd | 14 man/setFooter.Rd | 1 man/setHeader.Rd | 1 man/setHeaderFooter.Rd | 7 man/setRowHeights.Rd | 7 man/sheetVisibility.Rd | 1 man/sheetVisible.Rd | 1 man/sheets.Rd | 7 man/showGridLines.Rd | 1 man/worksheetOrder.Rd | 1 man/write.xlsx.Rd | 7 man/writeComment.Rd | 1 man/writeData.Rd | 7 man/writeDataTable.Rd | 45 - man/writeFormula.Rd | 7 src/RcppExports.cpp | 15 src/load_workbook.cpp | 31 src/openxlsx_init.c |only src/read_workbook.cpp | 45 - src/write_file.cpp | 3 src/write_file_2.cpp | 2 tests/testthat/test-deleting_tables.R |only tests/testthat/test-encoding.R | 2 tests/testthat/test-load_read_file_read_equality3.R | 2 tests/testthat/test-loading_workbook.R | 6 tests/testthat/test-loading_workbook_tables.R |only tests/testthat/test-named_regions.R | 57 + tests/testthat/test-read_from_loaded_workbook.R | 126 +++ tests/testthat/test-skip_empty_rows.R |only tests/testthat/test-table_overlaps.R |only 110 files changed, 1390 insertions(+), 975 deletions(-)
Title: Imaging Engine, Tools for Application of Image Filters to Data
Matrices
Description: Provides fast application of image filters to data matrices,
using R and C++ algorithms.
Author: Wencheng Lau-Medrano [aut, cre]
Maintainer: Wencheng Lau-Medrano <luis.laum@gmail.com>
Diff between imagine versions 1.1.0 dated 2016-12-01 and 1.1.1 dated 2017-03-23
DESCRIPTION | 10 +++++----- MD5 | 23 ++++++++++++----------- NAMESPACE | 2 +- R/RcppExports.R | 2 +- README.md | 10 ++++------ build/vignette.rds |binary inst/doc/vignette.html | 6 +++--- man/basic2DFilter.Rd | 3 +-- man/convolutions.Rd | 3 +-- man/image-package.Rd | 3 +-- man/wbImage.Rd | 1 - src/engines.cpp | 2 +- src/registerDynamicSymbols.c |only 13 files changed, 30 insertions(+), 35 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. Also, the generic DNbuilder() function in this package provides a simple and straightforward way to build and publish a dynamic nomogram on the web to use the app independent of R. 'DynNom' supports a variety of model objects; lm(), glm(), coxph() models and also ols(), Glm(), lrm(), cph() models in the 'rms' package.
Author: Amirhossein Jalali, Davood Roshan, Alberto Alvarez-Iglesias, John Newell
Maintainer: Amirhossein Jalali <a.jalali2@nuigalway.ie>
Diff between DynNom versions 4.0 dated 2016-12-14 and 4.1 dated 2017-03-23
DESCRIPTION | 12 - MD5 | 52 ++++---- NAMESPACE | 3 R/DNbuilder-coxph.R | 215 ++++++++++++++++------------------ R/DNbuilder-glm.R | 136 +++++++++++---------- R/DNbuilder-lm.R | 83 +++++++------ R/DNbuilder.R | 12 - R/DynNom.R | 22 +-- R/DynNom_coxph.R | 286 ++++++++++++++++++++++----------------------- R/DynNom_glm.R | 243 ++++++++++++++++++++------------------ R/DynNom_lm.R | 112 +++++++++-------- R/DynNom_rmsGlm.R | 307 +++++++++++++++++++++++++------------------------ R/DynNom_rmscph.R | 290 +++++++++++++++++++++++----------------------- R/DynNom_rmslrm.R | 160 +++++++++++++------------ R/DynNom_rmsols.R | 140 +++++++++++----------- man/DNbuilder.Rd | 8 - man/DNbuilder.coxph.Rd | 8 - man/DNbuilder.glm.Rd | 7 - man/DNbuilder.lm.Rd | 7 - man/DynNom.Rd | 16 +- man/DynNom.coxph.Rd | 8 - man/DynNom.glm.Rd | 9 - man/DynNom.lm.Rd | 7 - man/DynNom.rms.Glm.Rd | 7 - man/DynNom.rms.cph.Rd | 8 - man/DynNom.rms.lrm.Rd | 11 + man/DynNom.rms.ols.Rd | 9 - 27 files changed, 1141 insertions(+), 1037 deletions(-)
Title: Miscellaneous Tools for Chinese Text Mining and More
Description: Efforts are made to make Chinese text mining easier, faster, and robust to errors.
Document term matrix can be generated by only one line of code; detecting encoding,
segmenting and removing stop words are done automatically.
Some convenient tools are also supplied.
Author: Jiang Wu [aut, cre] (from Tsinghua University)
Maintainer: Jiang Wu <textidea@sina.com>
Diff between chinese.misc versions 0.1.3 dated 2017-03-13 and 0.1.4 dated 2017-03-23
DESCRIPTION | 11 ++++++----- MD5 | 18 +++++++++++------- NAMESPACE | 2 ++ NEWS | 8 ++++++++ R/aboutlocale.R | 20 +++++++++++++------- R/corp_or_dtm.R | 1 - R/create_ttm.R |only R/get_tmp_chi_locale.R |only R/zzz.r | 15 ++++++++++++++- man/corp_or_dtm.Rd | 1 - man/create_ttm.Rd |only man/get_tmp_chi_locale.Rd |only 12 files changed, 54 insertions(+), 22 deletions(-)
Title: Core Methods and Classes Used by 'aroma.*' Packages Part of the
Aroma Framework
Description: Core methods and classes used by higher-level aroma.* packages
part of the Aroma Project, e.g. aroma.affymetrix and aroma.cn.
Author: Henrik Bengtsson [aut, cre, cph],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.core versions 3.0.0 dated 2016-01-06 and 3.1.0 dated 2017-03-23
DESCRIPTION | 30 MD5 | 156 NAMESPACE | 5 NEWS | 3464 ++++++---- R/999.DEPRECATED.R | 43 R/AromaMicroarrayDataSetTuple.R | 1 R/AromaMicroarrayTabularBinaryFile.R | 17 R/AromaTabularBinaryFile.R | 16 R/AromaTransform.R | 6 R/AromaUnitFracBCnBinarySet.exportFracBDiffSet.R | 4 R/AromaUnitSignalBinarySet.writeDataFrame.R | 3 R/AromaUnitTotalCnBinaryFileList.R | 2 R/AromaUnitTotalCnBinarySet.exportTotalCnRatioSet.R | 2 R/ChromosomalModel.R | 1 R/ChromosomeExplorer.R | 2 R/CopyNumberChromosomalModel.R | 15 R/CopyNumberChromosomalModel.plotChromosomesLayers.R | 6 R/CopyNumberChromosomalModel.plotFitLayers.R | 4 R/CopyNumberChromosomalModel.plotSampleLayers.R | 2 R/CopyNumberOutliers.R | 2 R/CopyNumberRegions.EXT.R | 2 R/CopyNumberRegions.R | 2 R/CopyNumberSegmentationModel.R | 18 R/CopyNumberSegmentationModel.plot.R | 6 R/Explorer.R | 2 R/PairedPSCNData.PLOT.R | 31 R/ProbePositionEffects.R | 6 R/RichDataFrame.R | 3 R/norm2d.matrix.R | 2 R/shakyText.R | 4 R/smoothWRMA.matrix.R | 2 inst/testScripts/fileFormats/acf/test20090107,AromaUnitGenotypeCallSet.R | 2 inst/testScripts/system/CnSegmentation/test20100222,SEG,symmetry.Rex | 2 man/AromaCellTabularBinaryFile.Rd | 2 man/AromaGenomeTextFile.Rd | 2 man/AromaMicroarrayDataFile.Rd | 2 man/AromaMicroarrayDataSet.Rd | 2 man/AromaMicroarrayDataSetTuple.Rd | 2 man/AromaMicroarrayTabularBinaryFile.Rd | 2 man/AromaPlatform.Rd | 2 man/AromaRepository.Rd | 2 man/AromaTabularBinaryFile.Rd | 2 man/AromaTabularBinarySet.Rd | 2 man/AromaTransform.Rd | 2 man/AromaUnitCallFile.Rd | 2 man/AromaUnitCallSet.Rd | 2 man/AromaUnitFracBCnBinaryFile.Rd | 2 man/AromaUnitFracBCnBinarySet.Rd | 2 man/AromaUnitGenotypeCallFile.Rd | 2 man/AromaUnitGenotypeCallSet.Rd | 2 man/AromaUnitPscnBinaryFile.Rd | 2 man/AromaUnitPscnBinarySet.Rd | 2 man/AromaUnitSignalBinaryFile.Rd | 2 man/AromaUnitSignalBinarySet.Rd | 2 man/AromaUnitTabularBinaryFile.Rd | 2 man/AromaUnitTotalCnBinaryFile.Rd | 2 man/AromaUnitTotalCnBinarySet.Rd | 2 man/AromaUnitTypesFile.Rd | 2 man/BinnedScatter.Rd | 4 man/CbsModel.Rd | 2 man/ChromosomalModel.Rd | 2 man/ChromosomeExplorer.Rd | 2 man/CopyNumberChromosomalModel.Rd | 2 man/CopyNumberSegmentationModel.Rd | 2 man/Explorer.Rd | 2 man/GladModel.Rd | 2 man/HaarSegModel.Rd | 2 man/Non-documented_objects.Rd | 3 man/RawCopyNumberModel.Rd | 2 man/fit.CopyNumberSegmentationModel.Rd | 5 man/fitGenotypeCone.matrix.Rd | 2 man/fitGenotypeConeBySfit.matrix.Rd | 2 man/plotTracks.PairedPSCNData.Rd | 62 man/segmentByCBS.RawGenomicSignals.Rd | 2 man/segmentByMPCBS.RawGenomicSignals.Rd | 2 tests/RawGenomicSignals.SEG,MP.R | 2 tests/RawGenomicSignals.SEG.R | 2 tests/binScatter.R | 4 tests/fitGenotypeCone.R | 2 79 files changed, 2613 insertions(+), 1410 deletions(-)
More information about affluenceIndex at CRAN
Permanent link
Title: An S4 Lattice-Based Package for the Representation of
Multivariate Data
Description: Graphical functionalities for the representation of multivariate data. It is a complete re-implementation of the functions available in the 'ade4' package.
Author: Stéphane Dray <stephane.dray@univ-lyon1.fr> and Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>, with contributions from Jean Thioulouse. Based on earlier work by Alice Julien-Laferrière.
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between adegraphics versions 1.0-6 dated 2016-12-13 and 1.0-7 dated 2017-03-23
DESCRIPTION | 8 +++--- MD5 | 60 ++++++++++++++++++++++----------------------- R/ADEg.C1.R | 18 ++++++------- R/ADEg.S1.R | 2 + R/ADEg.S2.R | 4 ++- R/ADEg.T.R | 2 + R/ADEg.Tr.R | 6 +++- R/C1.barchart.R | 32 +++++++++++++++--------- R/C1.curve.R | 8 ++++-- R/C1.curves.R | 20 +++++++-------- R/C1.density.R | 4 +-- R/C1.dotplot.R | 10 ++++++- R/C1.gauss.R | 5 ++- R/C1.interval.R | 8 ++++-- R/ade4-plot.R | 8 +++--- R/multiplot.R | 32 ++++++++++++++++++------ build/vignette.rds |binary inst/doc/adegraphics.html | 25 ++++++++++-------- man/C1.barchart-class.Rd | 1 man/adeg.panel.Spatial.Rd | 2 - man/adeg.panel.hist.Rd | 2 - man/adeg.panel.join.Rd | 2 - man/adeg.panel.label.Rd | 4 +-- man/adeg.panel.nb.Rd | 8 +++--- man/adeg.panel.values.Rd | 4 +-- man/adegraphics-package.Rd | 6 ++-- man/changelatticetheme.Rd | 10 +++---- man/s.Spatial.Rd | 2 - man/s.image.Rd | 2 - man/s1d.barchart.Rd | 6 +++- vignettes/classes.png |binary 31 files changed, 177 insertions(+), 124 deletions(-)
Title: Analysis of Ecological Data : Exploratory and Euclidean Methods
in Environmental Sciences
Description: Multivariate data analysis and graphical display.
Author: Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between ade4 versions 1.7-5 dated 2016-12-13 and 1.7-6 dated 2017-03-23
ChangeLog | 144 DESCRIPTION | 12 MD5 | 249 - NAMESPACE | 7 R/RV.rtest.R | 4 R/RVdist.randtest.R | 4 R/between.R | 2 R/betwitdpcoa.R | 2 R/combine.4thcorner.R | 12 R/corkdist.R | 31 R/costatis.R | 4 R/dist.ktab.R | 6710 ++++++++++++++++++++++----------------------- R/fourthcorner.R | 12 R/fourthcorner.rlq.R | 10 R/fourthcorner2.R | 10 R/gearymoran.R | 4 R/krandtest.R | 47 R/mantel.randtest.R | 4 R/mantel.rtest.R | 6 R/multispati.randtest.R | 4 R/multispati.rtest.R | 4 R/niche.R | 4 R/orthogram.R | 16 R/plot.4thcorner.R | 2 R/procuste.R | 2 R/procuste.randtest.R | 4 R/procuste.rtest.R | 4 R/randtest.R | 42 R/randtest.amova.R | 4 R/randtest.between.R | 4 R/randtest.cca.R | 2 R/randtest.coinertia.R | 2 R/randtest.discrimin.R | 26 R/randtest.dpcoa.R | 3 R/randtest.pcaiv.R | 2 R/randtest.pcaivortho.R | 2 R/randtest.rlq.R | 10 R/rtest.R | 39 R/rtest.between.R | 2 R/rtest.discrimin.R | 2 R/statico.R | 10 R/testdim.R | 2 R/within.R | 4 man/RV.rtest.Rd | 3 man/RVdist.randtest.Rd | 3 man/acacia.Rd | 2 man/area.plot.Rd | 10 man/atlas.Rd | 6 man/atya.Rd | 14 man/avijons.Rd | 16 man/between.Rd | 8 man/buech.Rd | 2 man/butterfly.Rd | 7 man/bwca.dpcoa.Rd | 3 man/capitales.Rd | 15 man/casitas.Rd | 2 man/cca.Rd | 18 man/chats.Rd | 6 man/combine.4thcorner.Rd | 3 man/corkdist.Rd | 7 man/corvus.Rd | 4 man/costatis.randtest.Rd | 3 man/divc.Rd | 2 man/divcmax.Rd | 5 man/doubs.Rd | 18 man/dudi.fca.Rd | 10 man/elec88.Rd | 2 man/euro123.Rd | 8 man/fourthcorner.Rd | 10 man/gearymoran.Rd | 9 man/ggtortoises.Rd | 16 man/gridrowcol.Rd | 2 man/irishdata.Rd | 2 man/julliot.Rd | 20 man/jv73.Rd | 2 man/kcponds.Rd | 16 man/krandtest.Rd | 9 man/lascaux.Rd | 8 man/lizards.Rd | 4 man/mafragh.Rd | 21 man/mantel.randtest.Rd | 3 man/mantel.rtest.Rd | 3 man/maples.Rd | 31 man/mdpcoa.Rd | 5 man/meau.Rd | 3 man/multispati.Rd | 10 man/multispati.randtest.Rd | 9 man/multispati.rtest.Rd | 9 man/neig.Rd | 22 man/newick.eg.Rd | 4 man/nipals.Rd | 10 man/olympic.Rd | 12 man/oribatid.Rd | 16 man/orthobasis.Rd | 13 man/orthogram.Rd | 3 man/pcaivortho.Rd | 13 man/pcw.Rd | 2 man/phylog.Rd | 11 man/plot.between.Rd | 8 man/plot.within.Rd | 6 man/presid2002.Rd | 8 man/procuste.Rd | 20 man/procuste.randtest.Rd | 3 man/procuste.rtest.Rd | 3 man/randEH.Rd | 2 man/randboot.Rd | 2 man/randtest.Rd | 8 man/randxval.Rd | 2 man/rhizobium.Rd | 2 man/rpjdl.Rd | 4 man/rtest.Rd | 17 man/s.image.Rd | 6 man/s.kde2d.Rd | 2 man/s.logo.Rd | 2 man/santacatalina.Rd | 8 man/sarcelles.Rd | 2 man/scatter.coa.Rd | 6 man/statico.krandtest.Rd | 3 man/t3012.Rd | 4 man/tintoodiel.Rd | 8 man/trichometeo.Rd | 4 man/vegtf.Rd | 13 man/westafrica.Rd | 20 man/witwit.coa.Rd | 5 man/zealand.Rd | 8 src/init.c |only 126 files changed, 4125 insertions(+), 3996 deletions(-)
Title: Estimating Weight-Function Models for Publication Bias
Description: Estimates the Vevea and Hedges (1995) <doi:10.1007/BF02294384>
weight-function model. By specifying arguments, users can
also estimate the modified model described in Vevea and Woods (2005)
<doi:10.1037/1082-989X.10.4.428>, which may be more practical with small datasets. Users
can also specify moderators to estimate a linear model. The package functionality
allows users to easily extract the results of these analyses as R objects for
other uses. In addition, the package includes a function to launch both models as
a Shiny application. Although the Shiny application is also available online,
this function allows users to launch it locally if they choose.
Author: Kathleen M. Coburn [aut, cre],
Jack L. Vevea [aut]
Maintainer: Kathleen M. Coburn <kcoburn@ucmerced.edu>
Diff between weightr versions 1.1.0 dated 2017-03-12 and 1.1.1 dated 2017-03-23
DESCRIPTION | 6 +++--- MD5 | 4 ++-- NEWS | 24 ++---------------------- 3 files changed, 7 insertions(+), 27 deletions(-)
Title: Time Delay Estimation for Stochastic Time Series of
Gravitationally Lensed Quasars
Description: We provide a toolbox to estimate the time delay between the brightness time series of gravitationally lensed quasar images via Bayesian and profile likelihood approaches. The model is based on a state-space representation for irregularly observed time series data generated from a latent continuous-time Ornstein-Uhlenbeck process. Our Bayesian method adopts scientifically motivated hyper-prior distributions and a Metropolis-Hastings within Gibbs sampler, producing posterior samples of the model parameters that include the time delay. A profile likelihood of the time delay is a simple approximation to the marginal posterior distribution of the time delay. Both Bayesian and profile likelihood approaches complement each other, producing almost identical results; the Bayesian way is more principled but the profile likelihood is easier to implement.
Author: Hyungsuk Tak, Kaisey Mandel, David A. van Dyk, Vinay L. Kashyap, Xiao-Li Meng, and Aneta Siemiginowska
Maintainer: Hyungsuk Tak <hyungsuk.tak@gmail.com>
Diff between timedelay versions 1.0.5 dated 2016-12-13 and 1.0.6 dated 2017-03-23
DESCRIPTION | 8 +-- MD5 | 12 ++-- R/bayesian.R | 94 +++++++++++++++++++------------------- R/entirelogprofilelikelihood.R | 18 +++---- man/bayesian.Rd | 16 ++++-- man/entirelogprofilelikelihood.Rd | 8 +-- man/timedelay-package.Rd | 12 ++-- 7 files changed, 87 insertions(+), 81 deletions(-)
Title: R Bindings for ZeroMQ
Description: Interface to the 'ZeroMQ' lightweight messaging kernel (see <http://www.zeromq.org/> for more information).
Author: Whit Armstrong [aut],
Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between rzmq versions 0.9.0 dated 2017-01-06 and 0.9.1 dated 2017-03-23
DESCRIPTION | 20 ++++++++++---------- MD5 | 7 ++++--- README.md | 4 ++-- configure | 9 ++------- src/register.c |only 5 files changed, 18 insertions(+), 22 deletions(-)
Title: Spectral Analysis Tools using Multitaper Method
Description: Implements multitaper spectral analysis using discrete prolate spheroidal sequences (Slepians) and sine tapers. It includes an adaptive weighted multitaper spectral estimate, a coherence estimate, Thomson's Harmonic F-test, and complex demodulation. The Slepians sequences are generated efficiently using a tridiagonal matrix solution, and jackknifed confidence intervals are available for most estimates.
Author: Karim Rahim <karim.rahim@queensu.ca>, Wesley S. Burr <wesley.burr@gmail.com>
Maintainer: Karim Rahim <karim.rahim@queensu.ca>
Diff between multitaper versions 1.0-12 dated 2016-04-26 and 1.0-13 dated 2017-03-23
DESCRIPTION | 12 ++--- MD5 | 17 ++++--- NAMESPACE | 5 +- R/dpss.R | 2 R/multitaper.R | 29 +++++++++++- inst/CITATION | 2 src/djt.f | 2 src/dpss.f90 | 112 ++++++++++++++++++++++++-------------------------- src/multitaper_init.c |only src/sine.f | 14 +++--- 10 files changed, 109 insertions(+), 86 deletions(-)
Title: Epidemiology Tools
Description: Tools for training and practicing epidemiologists including methods for two-way and multi-way contingency tables.
Author: Tomas J. Aragon [aut], Michael P. Fay
[ctb], Daniel Wollschlaeger [ctb], Adam Omidpanah [cre, ctb]
Maintainer: Adam Omidpanah <adam.omidpanah@wsu.edu>
Diff between epitools versions 0.5-7 dated 2012-09-30 and 0.5-8 dated 2017-03-23
DESCRIPTION | 30 ++++++++++++++++-------------- MD5 | 10 +++++----- NAMESPACE | 6 ++++++ R/riskratio.boot.R | 4 ++-- man/expand.table.Rd | 2 -- man/oswego.Rd | 2 +- 6 files changed, 30 insertions(+), 24 deletions(-)
Title: Crunch.io Data Tools
Description: The Crunch.io service <http://crunch.io/> provides a cloud-based
data store and analytic engine, as well as an intuitive web interface.
Using this package, analysts can interact with and manipulate Crunch
datasets from within R. Importantly, this allows technical researchers to
collaborate naturally with team members, managers, and clients who prefer a
point-and-click interface.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson <neal@crunch.io>
Diff between crunch versions 1.15.0 dated 2017-02-23 and 1.15.2 dated 2017-03-23
DESCRIPTION | 8 - MD5 | 62 ++++++------- NAMESPACE | 2 R/add-variable.R | 22 ++-- R/combine-categories.R | 8 - R/copy.R | 2 R/dataset.R | 2 R/export-dataset.R | 38 +++++++- R/expressions.R | 2 R/make-array.R | 2 R/share.R | 8 + R/tab-book.R | 23 ++--- R/univariate.R | 23 +++-- R/variable-type.R | 7 + R/weight.R | 2 man/crunch-is.Rd | 3 man/crunch-uni.Rd | 6 - man/exportDataset.Rd | 21 ++++ man/settings.Rd | 2 man/share.Rd | 5 - tests/testthat/api/datasets/2/variables-d118fa.json | 2 tests/testthat/api/datasets/2/variables.json | 2 tests/testthat/test-add-variable.R | 8 + tests/testthat/test-combine-categories.R | 2 tests/testthat/test-combine-responses.R | 2 tests/testthat/test-copy-variable.R | 2 tests/testthat/test-dataset-entity.R | 6 - tests/testthat/test-export-dataset.R | 51 ++++++++++- tests/testthat/test-share.R | 11 ++ tests/testthat/test-update-array.R | 90 ++++++++++++-------- tests/testthat/test-variables.R | 7 + tests/testthat/test-weighting.R | 1 32 files changed, 301 insertions(+), 131 deletions(-)
Title: Assertive Programming for R Analysis Pipelines
Description: Provides functionality to assert conditions
that have to be met so that errors in data used in
analysis pipelines can fail quickly. Similar to
'stopifnot()' but more powerful, friendly, and easier
for use in pipelines.
Author: Tony Fischetti [aut, cre]
Maintainer: Tony Fischetti <tony.fischetti@gmail.com>
Diff between assertr versions 2.0.0 dated 2017-03-17 and 2.0.2 dated 2017-03-23
DESCRIPTION | 6 MD5 | 12 R/assertions.R | 60 +-- R/predicates.R | 1 inst/doc/assertr.html | 4 tests/testthat/test-assertions.R | 719 +++++++++++++++++++++++++++------------ tests/testthat/test-row-redux.R | 26 + 7 files changed, 574 insertions(+), 254 deletions(-)
Title: Immunoglobulin Clonal Lineage and Diversity Analysis
Description: Provides immunoglobulin (Ig) sequence lineage reconstruction,
diversity profiling, and amino acid property analysis.
Author: Jason Vander Heiden [aut, cre],
Namita Gupta [aut],
Susanna Marquez [ctb],
Daniel Gadala-Maria [ctb],
Roy Jiang [ctb],
Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@yale.edu>
Diff between alakazam versions 0.2.5 dated 2016-08-05 and 0.2.6 dated 2017-03-23
DESCRIPTION | 21 ++--- MD5 | 143 +++++++++++++++++++-------------------- NAMESPACE | 10 ++ NEWS.md | 11 +++ R/Alakazam.R | 11 +-- R/Core.R | 69 ++++++++++-------- R/RcppExports.R | 2 inst/doc/AminoAcids-Vignette.pdf |binary inst/doc/Diversity-Vignette.pdf |binary inst/doc/Lineage-Vignette.pdf |binary inst/doc/Topology-Vignette.pdf |binary man/ABBREV_AA.Rd | 1 man/ChangeoClone-class.Rd | 4 - man/DEFAULT_COLORS.Rd | 1 man/DiversityCurve-class.Rd | 5 - man/DiversityTest-class.Rd | 4 - man/EdgeTest-class.Rd | 5 - man/ExampleDb.Rd | 1 man/ExampleTrees.Rd | 1 man/IMGT_REGIONS.Rd | 1 man/IUPAC_CODES.Rd | 3 man/MRCATest-class.Rd | 5 - man/alakazam.Rd | 2 man/aliphatic.Rd | 1 man/aminoAcidProperties.Rd | 1 man/buildPhylipLineage.Rd | 1 man/bulk.Rd | 1 man/calcCoverage.Rd | 1 man/calcDiversity.Rd | 1 man/charge.Rd | 1 man/collapseDuplicates.Rd | 1 man/countClones.Rd | 1 man/countGenes.Rd | 1 man/countPatterns.Rd | 1 man/estimateAbundance.Rd | 1 man/extractVRegion.Rd | 1 man/getAAMatrix.Rd | 1 man/getDNAMatrix.Rd | 1 man/getMRCA.Rd | 1 man/getPathLengths.Rd | 1 man/getSegment.Rd | 5 - man/gravy.Rd | 1 man/gridPlot.Rd | 1 man/isValidAASeq.Rd | 1 man/makeChangeoClone.Rd | 1 man/makeTempDir.Rd | 1 man/maskSeqEnds.Rd | 1 man/maskSeqGaps.Rd | 1 man/pairwiseDist.Rd | 1 man/pairwiseEqual.Rd | 1 man/permuteLabels.Rd | 1 man/plotAbundance.Rd | 1 man/plotDiversityCurve.Rd | 1 man/plotEdgeTest.Rd | 1 man/plotMRCATest.Rd | 1 man/plotSubtrees.Rd | 1 man/polar.Rd | 1 man/rarefyDiversity.Rd | 1 man/readChangeoDb.Rd | 3 man/seqDist.Rd | 1 man/seqEqual.Rd | 1 man/sortGenes.Rd | 1 man/stoufferMeta.Rd | 1 man/summarizeSubtrees.Rd | 1 man/tableEdges.Rd | 1 man/testDiversity.Rd | 1 man/testEdges.Rd | 1 man/testMRCA.Rd | 1 man/translateDNA.Rd | 1 man/translateStrings.Rd | 1 man/writeChangeoDb.Rd | 5 - src/Init.c |only src/RcppExports.cpp | 34 ++++----- 73 files changed, 183 insertions(+), 209 deletions(-)