Title: Fitting and Predicting Large-Scale Nonlinear Regression Problems
using Multi-Resolution Functional ANOVA (MRFA) Approach
Description: Performs the MRFA approach proposed by Sung et al. (2017+) <arXiv:1709.07064> to fit
and predict nonlinear regression problems, particularly for large-scale and
high-dimensional problems. The application includes deterministic or stochastic
computer experiments, spatial datasets, and so on.
Author: Chih-Li Sung
Maintainer: Chih-Li Sung <iamdfchile@gmail.com>
Diff between MRFA versions 0.1 dated 2017-07-14 and 0.2 dated 2017-09-21
MRFA-0.1/MRFA/R/coef.MRFA.R |only MRFA-0.1/MRFA/R/print.MRFA.R |only MRFA-0.2/MRFA/DESCRIPTION | 10 +- MRFA-0.2/MRFA/MD5 | 20 ++-- MRFA-0.2/MRFA/R/MRFA_fit.R | 24 ----- MRFA-0.2/MRFA/R/confidence.MRFA.R | 167 ++++++++++++++++++----------------- MRFA-0.2/MRFA/R/grplasso_forward.R | 3 MRFA-0.2/MRFA/R/is.anydupicate.R | 36 +++++-- MRFA-0.2/MRFA/R/post_sigma.R |only MRFA-0.2/MRFA/R/unique.matrix.R |only MRFA-0.2/MRFA/R/update_candidate.R | 25 +++-- MRFA-0.2/MRFA/man/MRFA_fit.Rd | 2 MRFA-0.2/MRFA/man/confidence.MRFA.Rd | 16 +++ 13 files changed, 163 insertions(+), 140 deletions(-)
Title: Support for Metrological Applications
Description: Provides classes and calculation and plotting functions
for metrology applications, including measurement uncertainty estimation
and inter-laboratory metrology comparison studies.
Author: Stephen L R Ellison <s.ellison@lgc.co.uk>.
Maintainer: Stephen L R Ellison <s.ellison@lgc.co.uk>
Diff between metRology versions 0.9-23-2 dated 2016-11-02 and 0.9-26-2 dated 2017-09-21
DESCRIPTION | 12 ++++++------ MD5 | 43 ++++++++++++++++++++++++------------------- NAMESPACE | 14 +++++++++++++- R/MSD-class.r |only R/bootMSD.R |only R/cplot.R | 10 +++++++--- R/msd.R | 7 +++++-- R/reml_loc.r | 2 +- R/yplot.r | 39 ++++++++++++++++++++++++++++++++------- build/partial.rdb |binary data/GUM.H.1.rda |binary data/Pb.rda |binary data/RMstudy.rda |binary data/apricot.rda |binary data/chromium.rda |binary data/potassium.rda |binary man/bootMSD.Rd |only man/bootMSD_class.Rd |only man/cov.dellipse.Rd | 12 +++++++++++- man/cplot.Rd | 3 ++- man/metRology-package.Rd | 32 +++++++++++++++++++++++++++++++- man/msd.Rd | 16 +++++++++++++--- man/msd_class.Rd |only man/plot.d.ellipse.Rd | 6 +++++- man/pmsd.Rd | 4 +++- 25 files changed, 153 insertions(+), 47 deletions(-)
Title: Multiplicative Competitive Interaction (MCI) Model
Description: Market area models are used to analyze and predict store choices and market areas concerning retail and service locations. This package implements two market area models (Huff Model, Multiplicative Competitive Interaction Model) into R, while the emphases lie on 1.) fitting these models based on empirical data via OLS regression and nonlinear techniques and 2.) data preparation and processing (esp. interaction matrices and data preparation for the MCI Model).
Author: Thomas Wieland
Maintainer: Thomas Wieland <thomas.wieland.geo@googlemail.com>
Diff between MCI versions 1.3.1 dated 2017-07-18 and 1.3.2 dated 2017-09-21
MCI-1.3.1/MCI/inst |only MCI-1.3.2/MCI/DESCRIPTION | 8 ++++---- MCI-1.3.2/MCI/MD5 | 35 ++++++++++++++++++++++------------- MCI-1.3.2/MCI/NAMESPACE | 2 +- MCI-1.3.2/MCI/R/huff.lambda.R |only MCI-1.3.2/MCI/R/lm.beta.R |only MCI-1.3.2/MCI/data/DIY1.rda |only MCI-1.3.2/MCI/data/DIY2.rda |only MCI-1.3.2/MCI/data/DIY3.rda |only MCI-1.3.2/MCI/data/Freiburg1.rda |binary MCI-1.3.2/MCI/data/Freiburg2.rda |binary MCI-1.3.2/MCI/data/Freiburg3.rda |binary MCI-1.3.2/MCI/data/grocery1.rda |binary MCI-1.3.2/MCI/data/grocery2.rda |binary MCI-1.3.2/MCI/data/shopping1.rda |binary MCI-1.3.2/MCI/data/shopping2.rda |binary MCI-1.3.2/MCI/data/shopping3.rda |binary MCI-1.3.2/MCI/data/shopping4.rda |binary MCI-1.3.2/MCI/man/DIY1.Rd |only MCI-1.3.2/MCI/man/DIY2.Rd |only MCI-1.3.2/MCI/man/DIY3.Rd |only MCI-1.3.2/MCI/man/huff.fit.Rd | 2 ++ MCI-1.3.2/MCI/man/huff.lambda.Rd |only MCI-1.3.2/MCI/man/lm.beta.Rd |only 24 files changed, 29 insertions(+), 18 deletions(-)
Title: R Client for the 'Civis data science API'
Description: A set of tools around common workflows and a convenient interface to make
requests directly to the 'Civis data science API' <https://www.civisanalytics.com/platform/>.
Author: Patrick Miller [cre, aut],
Keith Ingersoll [aut],
Bill Lattner [ctb],
Anh Le [ctb],
Michelangelo D'Agostino [ctb],
Sam Weiss [ctb],
Danning Chen [ctb]
Maintainer: Patrick Miller <pmiller@civisanalytics.com>
Diff between civis versions 1.0.1 dated 2017-09-19 and 1.0.2 dated 2017-09-21
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ NAMESPACE | 3 +++ R/generate_client.R | 33 +++++++++++++++++++++++++++++++-- R/utils.R | 2 ++ man/fetch_and_generate_client.Rd |only tests/testthat/test_logs.R | 17 ++++++----------- tools/run_generate_client.R | 12 +----------- 8 files changed, 54 insertions(+), 34 deletions(-)
Title: Histogram-Valued Data Analysis
Description: In the framework of Symbolic Data Analysis, a relatively new
approach to the statistical analysis of multi-valued data, we consider
histogram-valued data, i.e., data described by univariate histograms. The
methods and the basic statistics for histogram-valued data are mainly based
on the L2 Wasserstein metric between distributions, i.e., a Euclidean metric
between quantile functions. The package contains unsupervised classification
techniques, least square regression and tools for histogram-valued data and for
histogram time series.
Author: Antonio Irpino [aut, cre]
Maintainer: Antonio Irpino <antonio.irpino@unicampania.it>
Diff between HistDAWass versions 0.1.6 dated 2017-02-13 and 0.1.7 dated 2017-09-21
DESCRIPTION | 14 MD5 | 194 +++++----- NAMESPACE | 3 R/All_classes.R | 22 - R/Met_MatH.R | 146 +++---- R/Met_distributionH.R | 90 ++-- R/Plotting_with_ggplot.R | 12 R/Utility.R | 27 + R/principal_components.R | 533 +++++++++++++++++++++++++--- R/regression.R | 3 R/unsuperv_classification.R | 11 man/Age_Pyramids_2014.Rd | 1 man/Agronomique.Rd | 1 man/BLOOD.Rd | 1 man/BloodBRITO.Rd | 1 man/Center.cell.MatH-methods.Rd | 1 man/China_Month.Rd | 1 man/China_Seas.Rd | 1 man/DouglasPeucker.Rd | 1 man/HTS-class.Rd | 3 man/HTS.exponential.smoothing.Rd | 2 man/HTS.moving.averages.Rd | 2 man/HTS.predict.knn.Rd | 1 man/HistDAWass-package.Rd | 9 man/MatH-class.Rd | 14 man/OzoneFull.Rd | 1 man/OzoneH.Rd | 1 man/RetHTS.Rd | 1 man/ShortestDistance.Rd | 1 man/TMatH-class.Rd | 3 man/TdistributionH-class.Rd | 3 man/WH.1d.PCA.Rd | 9 man/WH.MultiplePCA.Rd | 14 man/WH.SSQ-methods.Rd | 1 man/WH.SSQ2-methods.Rd | 1 man/WH.bind-methods.Rd | 1 man/WH.bind.col-methods.Rd | 1 man/WH.bind.row-methods.Rd | 1 man/WH.correlation-methods.Rd | 1 man/WH.correlation2-methods.Rd | 1 man/WH.mat.prod-methods.Rd | 1 man/WH.mat.sum-methods.Rd | 1 man/WH.plot_multiple_Spanish.funs.Rd |only man/WH.plot_multiple_indivs.Rd |only man/WH.regression.GOF.Rd | 1 man/WH.regression.two.components.Rd | 1 man/WH.regression.two.components.predict.Rd | 1 man/WH.var.covar-methods.Rd | 1 man/WH.var.covar2-methods.Rd | 1 man/WH.vec.mean-methods.Rd | 1 man/WH.vec.sum-methods.Rd | 1 man/WH_2d_Adaptive_Kohonen_maps.Rd | 2 man/WH_2d_Kohonen_maps.Rd | 2 man/WH_adaptive.kmeans.Rd | 2 man/WH_adaptive_fcmeans.Rd | 1 man/WH_fcmeans.Rd | 2 man/WH_hclust.Rd | 1 man/WH_kmeans.Rd | 2 man/WassSqDistH-methods.Rd | 1 man/checkEmptyBins-methods.Rd | 1 man/compP-methods.Rd | 1 man/compQ-methods.Rd | 1 man/crwtransform-methods.Rd | 7 man/data2hist.Rd | 1 man/distributionH-class.Rd | 11 man/dotpW-methods.Rd | 11 man/extract-methods.Rd | 1 man/get.MatH.ncols-methods.Rd | 1 man/get.MatH.nrows-methods.Rd | 1 man/get.MatH.rownames-methods.Rd | 1 man/get.MatH.stats-methods.Rd | 2 man/get.MatH.varnames-methods.Rd | 1 man/get.cell.MatH-methods.Rd | 1 man/get.distr-methods.Rd | 1 man/get.histo-methods.Rd | 1 man/get.m-methods.Rd | 1 man/get.s-methods.Rd | 1 man/is.registeredMH-methods.Rd | 7 man/kurtH-methods.Rd | 1 man/meanH-methods.Rd | 1 man/minus.Rd | 5 man/plot-HTS.Rd | 3 man/plot-MatH.Rd | 8 man/plot-TdistributionH.Rd | 3 man/plot-distributionH.Rd | 3 man/plotPredVsObs.Rd | 1 man/plot_errors.Rd | 1 man/plus-methods.Rd | 5 man/rQQ-methods.Rd | 7 man/register-methods.Rd | 7 man/registerMH-methods.Rd | 7 man/set.cell.MatH-methods.Rd | 3 man/show-MatH-methods.Rd | 3 man/show-distributionH-methods.Rd | 1 man/skewH-methods.Rd | 1 man/stations_coordinates.Rd | 1 man/stdH-methods.Rd | 1 man/subsetHTS-methods.Rd | 1 man/times-methods.Rd | 5 99 files changed, 922 insertions(+), 354 deletions(-)
Title: File Conversion for 'Gem Infrasound Logger'
Description: Reads data files from the 'Gem infrasound logger' for analysis and converts to segy format (which is convenient for reading with traditional seismic analysis software). The Gem infrasound logger is an in-development low-cost, lightweight, low-power instrument for recording infrasound in field campaigns; email the maintainer for more information.
Author: Jake Anderson
Maintainer: Jake Anderson <ajakef@gmail.com>
Diff between gemlog versions 0.22 dated 2017-09-09 and 0.24 dated 2017-09-21
DESCRIPTION | 6 - MD5 | 10 +- R/Convert.R | 205 ++++++++++++++++++++++++++++-------------------------- R/ReadGem.R | 45 ++++++++++- build/partial.rdb |binary man/ReadGem.Rd | 27 +++---- 6 files changed, 168 insertions(+), 125 deletions(-)
Title: Bayesian Additive Regression Trees
Description: Bayesian Additive Regression Trees (BART) provide flexible nonparametric modeling of covariates for continuous, binary and time-to-event outcomes. For more information on BART, see Chipman, George and McCulloch (2010) <doi:10.1214/09-AOAS285> and Sparapani, Logan, McCulloch and Laud (2016) <doi:10.1002/sim.6893>.
Author: Robert McCulloch [aut],
Rodney Sparapani [aut, cre],
Robert Gramacy [aut],
Matthew Pratola [aut],
Jean-Sebastien Roy [ctb],
Makoto Matsumoto [ctb],
Takuji Nishimura [ctb]
Maintainer: Rodney Sparapani <rsparapa@mcw.edu>
Diff between BART versions 1.2 dated 2017-04-30 and 1.3 dated 2017-09-21
BART-1.2/BART/src/BROWSE |only BART-1.2/BART/src/TAGS |only BART-1.3/BART/.Rinstignore |only BART-1.3/BART/DESCRIPTION | 29 +++-- BART-1.3/BART/MD5 | 177 ++++++++++++++++++++++++--------- BART-1.3/BART/NAMESPACE | 21 ++- BART-1.3/BART/NEWS |only BART-1.3/BART/R/crisk.bart.R | 26 ++-- BART-1.3/BART/R/crisk.pre.bart.R | 13 +- BART-1.3/BART/R/gewekediag.R |only BART-1.3/BART/R/lbart.R |only BART-1.3/BART/R/mbart.R |only BART-1.3/BART/R/mc.cores.openmp.R |only BART-1.3/BART/R/mc.crisk.bart.R | 67 ++++++------ BART-1.3/BART/R/mc.crisk.pwbart.R | 27 ++--- BART-1.3/BART/R/mc.pbart.R | 37 +++--- BART-1.3/BART/R/mc.pwbart.R | 24 ++-- BART-1.3/BART/R/mc.recur.bart.R | 69 +++++++----- BART-1.3/BART/R/mc.recur.pwbart.R | 24 ++-- BART-1.3/BART/R/mc.surv.bart.R | 64 ++++++----- BART-1.3/BART/R/mc.surv.pwbart.R | 22 ++-- BART-1.3/BART/R/mc.wbart.R | 37 ++---- BART-1.3/BART/R/pbart.R | 28 ++--- BART-1.3/BART/R/predict.criskbart.R |only BART-1.3/BART/R/predict.lbart.R |only BART-1.3/BART/R/predict.pbart.R |only BART-1.3/BART/R/predict.recurbart.R |only BART-1.3/BART/R/predict.survbart.R |only BART-1.3/BART/R/predict.wbart.R |only BART-1.3/BART/R/recur.bart.R | 63 +++++------ BART-1.3/BART/R/recur.pwbart.R |only BART-1.3/BART/R/spectrum0ar.R |only BART-1.3/BART/R/surv.bart.R | 46 ++++---- BART-1.3/BART/R/surv.pwbart.R |only BART-1.3/BART/R/wbart.R | 28 ++--- BART-1.3/BART/cleanup |only BART-1.3/BART/cleanup.win |only BART-1.3/BART/data/ACTG175.rda |binary BART-1.3/BART/data/arq.rda |only BART-1.3/BART/data/bladder.rda |binary BART-1.3/BART/data/datalist | 1 BART-1.3/BART/data/lung.rda |binary BART-1.3/BART/data/transplant.rda |binary BART-1.3/BART/data/xdm20.test.rda |binary BART-1.3/BART/data/xdm20.train.rda |binary BART-1.3/BART/data/ydm20.test.rda |binary BART-1.3/BART/data/ydm20.train.rda |binary BART-1.3/BART/demo |only BART-1.3/BART/inst |only BART-1.3/BART/man/arq.Rd |only BART-1.3/BART/man/crisk.bart.Rd | 62 ++++++----- BART-1.3/BART/man/gewekediag.Rd |only BART-1.3/BART/man/lbart.Rd |only BART-1.3/BART/man/mbart.Rd |only BART-1.3/BART/man/mc.cores.openmp.Rd |only BART-1.3/BART/man/mc.crisk.pwbart.Rd | 52 +++++---- BART-1.3/BART/man/mc.pbart.Rd | 17 ++- BART-1.3/BART/man/mc.surv.pwbart.Rd | 63 ++++++----- BART-1.3/BART/man/mc.wbart.Rd | 43 ++++---- BART-1.3/BART/man/pbart.Rd | 53 +++++---- BART-1.3/BART/man/predict.criskbart.Rd |only BART-1.3/BART/man/predict.recurbart.Rd |only BART-1.3/BART/man/predict.survbart.Rd |only BART-1.3/BART/man/predict.wbart.Rd |only BART-1.3/BART/man/pwbart.Rd | 49 --------- BART-1.3/BART/man/recur.bart.Rd | 99 +++++++++--------- BART-1.3/BART/man/recur.pre.bart.Rd | 2 BART-1.3/BART/man/spectrum0ar.Rd |only BART-1.3/BART/man/surv.bart.Rd | 43 ++++---- BART-1.3/BART/man/transplant.Rd | 4 BART-1.3/BART/man/wbart.Rd | 25 ++-- BART-1.3/BART/src/clbart.cpp |only BART-1.3/BART/src/cmbart.cpp |only BART-1.3/BART/src/common.h | 6 - BART-1.3/BART/src/cpbart.cpp | 65 +++++------- BART-1.3/BART/src/cwbart.cpp | 36 ++---- BART-1.3/BART/src/init.c | 6 + BART-1.3/BART/src/latent.cpp |only BART-1.3/BART/src/latent.h |only BART-1.3/BART/src/mc_cores_openmp.cpp |only BART-1.3/BART/src/rand_draws.cpp |only BART-1.3/BART/src/rand_draws.h |only BART-1.3/BART/src/randomkit.cpp |only BART-1.3/BART/src/randomkit.h |only BART-1.3/BART/src/rn.h | 29 ++--- BART-1.3/BART/src/rtnorm.cpp |only BART-1.3/BART/src/rtnorm.h | 32 ----- 87 files changed, 807 insertions(+), 682 deletions(-)
Title: Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column- and row- wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions.
Author: Manos Papadakis, Michail Tsagris, Marios Dimitriadis, Stefanos Fafalios, Ioannis Tsamardinos, Matteo Fasiolo, Giorgos Borboudakis, John Burkardt, Changliang Zou and Kleanthi Lakiotaki
Maintainer: Manos Papadakis <papadakm95@gmail.com>
Diff between Rfast versions 1.8.2 dated 2017-07-21 and 1.8.3 dated 2017-09-21
Rfast-1.8.2/Rfast/R/sort_index.R |only Rfast-1.8.2/Rfast/man/Order.Rd |only Rfast-1.8.2/Rfast/man/nth.Rd |only Rfast-1.8.2/Rfast/man/sort_cor_vectors.Rd |only Rfast-1.8.2/Rfast/src/Diag_fill.cpp |only Rfast-1.8.2/Rfast/src/Diag_matrix.cpp |only Rfast-1.8.2/Rfast/src/Digamma.cpp |only Rfast-1.8.2/Rfast/src/Lgamma.cpp |only Rfast-1.8.2/Rfast/src/Trigamma.cpp |only Rfast-1.8.2/Rfast/src/all__functions.cpp |only Rfast-1.8.2/Rfast/src/bhattacharyya_dist.cpp |only Rfast-1.8.2/Rfast/src/canberra1_dist.cpp |only Rfast-1.8.2/Rfast/src/canberra2_dist.cpp |only Rfast-1.8.2/Rfast/src/col_any.cpp |only Rfast-1.8.2/Rfast/src/col_false.cpp |only Rfast-1.8.2/Rfast/src/col_len_sort_un_int.cpp |only Rfast-1.8.2/Rfast/src/col_mads.cpp |only Rfast-1.8.2/Rfast/src/col_max.cpp |only Rfast-1.8.2/Rfast/src/col_means.cpp |only Rfast-1.8.2/Rfast/src/col_meds.cpp |only Rfast-1.8.2/Rfast/src/col_min.cpp |only Rfast-1.8.2/Rfast/src/col_min_max.cpp |only Rfast-1.8.2/Rfast/src/col_nth.cpp |only Rfast-1.8.2/Rfast/src/col_order.cpp |only Rfast-1.8.2/Rfast/src/col_prods.cpp |only Rfast-1.8.2/Rfast/src/col_shuffle.cpp |only Rfast-1.8.2/Rfast/src/col_sums.cpp |only Rfast-1.8.2/Rfast/src/col_tabulate.cpp |only Rfast-1.8.2/Rfast/src/col_true.cpp |only Rfast-1.8.2/Rfast/src/col_true_false.cpp |only Rfast-1.8.2/Rfast/src/comb_n.cpp |only Rfast-1.8.2/Rfast/src/design_matrix_big.cpp |only Rfast-1.8.2/Rfast/src/euclidean_dist.cpp |only Rfast-1.8.2/Rfast/src/hellinger_dist.cpp |only Rfast-1.8.2/Rfast/src/kullback_leibler_dist.cpp |only Rfast-1.8.2/Rfast/src/len_sort_unique_double.cpp |only Rfast-1.8.2/Rfast/src/len_sort_unique_int.cpp |only Rfast-1.8.2/Rfast/src/lgstc_pssn.cpp |only Rfast-1.8.2/Rfast/src/lgstc_pssn.h |only Rfast-1.8.2/Rfast/src/logistic_only_b.cpp |only Rfast-1.8.2/Rfast/src/manhattan_dist.cpp |only Rfast-1.8.2/Rfast/src/max_dist.cpp |only Rfast-1.8.2/Rfast/src/min_dist.cpp |only Rfast-1.8.2/Rfast/src/min_max_percent.cpp |only Rfast-1.8.2/Rfast/src/minkowski_dist.cpp |only Rfast-1.8.2/Rfast/src/permutation_next.cpp |only Rfast-1.8.2/Rfast/src/permutation_prev.cpp |only Rfast-1.8.2/Rfast/src/poisson_only_b.cpp |only Rfast-1.8.2/Rfast/src/rep_col.cpp |only Rfast-1.8.2/Rfast/src/row_any.cpp |only Rfast-1.8.2/Rfast/src/row_false.cpp |only Rfast-1.8.2/Rfast/src/row_len_sort_un_int.cpp |only Rfast-1.8.2/Rfast/src/row_mads.cpp |only Rfast-1.8.2/Rfast/src/row_max.cpp |only Rfast-1.8.2/Rfast/src/row_means.cpp |only Rfast-1.8.2/Rfast/src/row_meds.cpp |only Rfast-1.8.2/Rfast/src/row_min.cpp |only Rfast-1.8.2/Rfast/src/row_min_max.cpp |only Rfast-1.8.2/Rfast/src/row_nth.cpp |only Rfast-1.8.2/Rfast/src/row_order.cpp |only Rfast-1.8.2/Rfast/src/row_prods.cpp |only Rfast-1.8.2/Rfast/src/row_shuffle.cpp |only Rfast-1.8.2/Rfast/src/row_sums.cpp |only Rfast-1.8.2/Rfast/src/row_tabulate.cpp |only Rfast-1.8.2/Rfast/src/row_true.cpp |only Rfast-1.8.2/Rfast/src/row_true_false.cpp |only Rfast-1.8.2/Rfast/src/sort_cor_vecs.cpp |only Rfast-1.8.2/Rfast/src/sort_index.cpp |only Rfast-1.8.2/Rfast/src/sort_string.cpp |only Rfast-1.8.2/Rfast/src/sort_unique_double.cpp |only Rfast-1.8.2/Rfast/src/sort_unique_int.cpp |only Rfast-1.8.2/Rfast/src/total_dist.cpp |only Rfast-1.8.2/Rfast/src/total_variation_dist.cpp |only Rfast-1.8.2/Rfast/src/upper_triangle.cpp |only Rfast-1.8.2/Rfast/src/vec_comb_n.cpp |only Rfast-1.8.3/Rfast/DESCRIPTION | 10 Rfast-1.8.3/Rfast/MD5 | 585 +++++++++++++--------- Rfast-1.8.3/Rfast/NAMESPACE | 2 Rfast-1.8.3/Rfast/NEWS.md |only Rfast-1.8.3/Rfast/R/Diag.fill.R | 6 Rfast-1.8.3/Rfast/R/Diag.matrix.R | 6 Rfast-1.8.3/Rfast/R/Dist.R | 35 - Rfast-1.8.3/Rfast/R/Order.R | 7 Rfast-1.8.3/Rfast/R/Rnorm.R |only Rfast-1.8.3/Rfast/R/Sort.R | 11 Rfast-1.8.3/Rfast/R/allbetas.R | 16 Rfast-1.8.3/Rfast/R/ancovas.R | 6 Rfast-1.8.3/Rfast/R/anova_qpois.reg.R |only Rfast-1.8.3/Rfast/R/bcdcor.R |only Rfast-1.8.3/Rfast/R/bic.fs.reg.R |only Rfast-1.8.3/Rfast/R/bincomb.R |only Rfast-1.8.3/Rfast/R/checkAliases.R | 4 Rfast-1.8.3/Rfast/R/checkExamples.R | 15 Rfast-1.8.3/Rfast/R/circlin.cor.R |only Rfast-1.8.3/Rfast/R/colMaxs.R | 11 Rfast-1.8.3/Rfast/R/colMedians.R | 8 Rfast-1.8.3/Rfast/R/colMins.R | 11 Rfast-1.8.3/Rfast/R/colOrder.R | 4 Rfast-1.8.3/Rfast/R/colexp2.mle.R |only Rfast-1.8.3/Rfast/R/colexpmle.R |only Rfast-1.8.3/Rfast/R/colgammamle.R |only Rfast-1.8.3/Rfast/R/colgeom.mle.R | 4 Rfast-1.8.3/Rfast/R/colhameans.R | 2 Rfast-1.8.3/Rfast/R/colinvgauss.mle.R |only Rfast-1.8.3/Rfast/R/colkurtosis.R |only Rfast-1.8.3/Rfast/R/collaplace.mle.R |only Rfast-1.8.3/Rfast/R/collindley.mle.R |only Rfast-1.8.3/Rfast/R/colmaxboltz.mle.R |only Rfast-1.8.3/Rfast/R/colmeans.R | 8 Rfast-1.8.3/Rfast/R/colnormal.mle.R |only Rfast-1.8.3/Rfast/R/colnth.R | 8 Rfast-1.8.3/Rfast/R/colpareto.mle.R |only Rfast-1.8.3/Rfast/R/colpois.mle.R |only Rfast-1.8.3/Rfast/R/colrayleigh.mle.R |only Rfast-1.8.3/Rfast/R/colskewness.R |only Rfast-1.8.3/Rfast/R/colsums.R | 8 Rfast-1.8.3/Rfast/R/colvm.mle.R |only Rfast-1.8.3/Rfast/R/colwatsons.R |only Rfast-1.8.3/Rfast/R/comb_n.R | 27 - Rfast-1.8.3/Rfast/R/corpairs.R | 4 Rfast-1.8.3/Rfast/R/dcor.R |only Rfast-1.8.3/Rfast/R/dcor.ttest.R |only Rfast-1.8.3/Rfast/R/dcov.R |only Rfast-1.8.3/Rfast/R/diri.nr2.R | 85 +-- Rfast-1.8.3/Rfast/R/dista.R | 7 Rfast-1.8.3/Rfast/R/dvar.R |only Rfast-1.8.3/Rfast/R/eachrow.R |only Rfast-1.8.3/Rfast/R/edist.R | 30 - Rfast-1.8.3/Rfast/R/exp2.mle.R |only Rfast-1.8.3/Rfast/R/expregs.R |only Rfast-1.8.3/Rfast/R/fish.kent.R |only Rfast-1.8.3/Rfast/R/foldnorm.mle.R | 12 Rfast-1.8.3/Rfast/R/ftest.R | 2 Rfast-1.8.3/Rfast/R/ftests.R | 2 Rfast-1.8.3/Rfast/R/geom.nb.R |only Rfast-1.8.3/Rfast/R/geom.regs.R |only Rfast-1.8.3/Rfast/R/glm_logistic.R | 7 Rfast-1.8.3/Rfast/R/group.all.R |only Rfast-1.8.3/Rfast/R/group.any.R |only Rfast-1.8.3/Rfast/R/group.mad.R |only Rfast-1.8.3/Rfast/R/group.max.R |only Rfast-1.8.3/Rfast/R/group.mean.R |only Rfast-1.8.3/Rfast/R/group.med.R |only Rfast-1.8.3/Rfast/R/group.min.R |only Rfast-1.8.3/Rfast/R/group.min_max.R |only Rfast-1.8.3/Rfast/R/group.sum.R | 4 Rfast-1.8.3/Rfast/R/group.var.R |only Rfast-1.8.3/Rfast/R/hd.eigen.R | 29 - Rfast-1.8.3/Rfast/R/is_element.R | 9 Rfast-1.8.3/Rfast/R/james.R |only Rfast-1.8.3/Rfast/R/knn.cv.R |only Rfast-1.8.3/Rfast/R/kuiper.R |only Rfast-1.8.3/Rfast/R/kurt.R |only Rfast-1.8.3/Rfast/R/kurt.test2.R |only Rfast-1.8.3/Rfast/R/list.ftests.R |only Rfast-1.8.3/Rfast/R/lomax.mle.R | 6 Rfast-1.8.3/Rfast/R/lower_tri.R | 12 Rfast-1.8.3/Rfast/R/mad2.R |only Rfast-1.8.3/Rfast/R/matrnorm.R |only Rfast-1.8.3/Rfast/R/multinom.reg.R |only Rfast-1.8.3/Rfast/R/multinom.regs.R |only Rfast-1.8.3/Rfast/R/mv.eeltest1.R |only Rfast-1.8.3/Rfast/R/mv.eeltest2.R |only Rfast-1.8.3/Rfast/R/mvkurtosis.R |only Rfast-1.8.3/Rfast/R/negbin.mle.R | 2 Rfast-1.8.3/Rfast/R/normlog.mle.R | 2 Rfast-1.8.3/Rfast/R/normlog.reg.R |only Rfast-1.8.3/Rfast/R/normlog.regs.R |only Rfast-1.8.3/Rfast/R/percent.ttest.R |only Rfast-1.8.3/Rfast/R/percent.ttests.R |only Rfast-1.8.3/Rfast/R/poisson.nb.R | 13 Rfast-1.8.3/Rfast/R/prop.reg.R | 4 Rfast-1.8.3/Rfast/R/qpois.regs.R |only Rfast-1.8.3/Rfast/R/rayleigh.mle.R | 5 Rfast-1.8.3/Rfast/R/rel.risk.R |only Rfast-1.8.3/Rfast/R/rep_col.R | 4 Rfast-1.8.3/Rfast/R/rep_row.R |only Rfast-1.8.3/Rfast/R/rint.mle.R | 11 Rfast-1.8.3/Rfast/R/rint.reg.R | 50 - Rfast-1.8.3/Rfast/R/rint.regs.R |only Rfast-1.8.3/Rfast/R/rm.anova.R |only Rfast-1.8.3/Rfast/R/rmdp.R | 9 Rfast-1.8.3/Rfast/R/rowMaxs.R | 3 Rfast-1.8.3/Rfast/R/rowMins.R | 3 Rfast-1.8.3/Rfast/R/rowOrder.R | 4 Rfast-1.8.3/Rfast/R/rownth.R | 8 Rfast-1.8.3/Rfast/R/score.betaregs.R | 1 Rfast-1.8.3/Rfast/R/score.gammaregs.R | 2 Rfast-1.8.3/Rfast/R/score.geomregs.R | 2 Rfast-1.8.3/Rfast/R/score.glms.R | 6 Rfast-1.8.3/Rfast/R/score.multinomregs.R | 11 Rfast-1.8.3/Rfast/R/score.weibregs.R | 3 Rfast-1.8.3/Rfast/R/skew.R |only Rfast-1.8.3/Rfast/R/skew.test2.R |only Rfast-1.8.3/Rfast/R/sort_cor_vectors.R | 4 Rfast-1.8.3/Rfast/R/sort_mat.R | 21 Rfast-1.8.3/Rfast/R/sort_unique.length.R | 5 Rfast-1.8.3/Rfast/R/spdinv.R |only Rfast-1.8.3/Rfast/R/spml.mle.R | 12 Rfast-1.8.3/Rfast/R/spml.reg.R | 23 Rfast-1.8.3/Rfast/R/submatrix.R |only Rfast-1.8.3/Rfast/R/tobit.mle.R | 31 - Rfast-1.8.3/Rfast/R/total.dist.R | 12 Rfast-1.8.3/Rfast/R/total.dista.R | 4 Rfast-1.8.3/Rfast/R/ttests.R | 6 Rfast-1.8.3/Rfast/R/univglms.R | 7 Rfast-1.8.3/Rfast/R/upper_tri.R | 9 Rfast-1.8.3/Rfast/R/watson.R |only Rfast-1.8.3/Rfast/R/wigner.mle.R | 22 Rfast-1.8.3/Rfast/R/wrapcauchy.mle.R | 3 Rfast-1.8.3/Rfast/man/Diag.fill.Rd | 12 Rfast-1.8.3/Rfast/man/Dist.Rd | 12 Rfast-1.8.3/Rfast/man/Rfast-package.Rd | 12 Rfast-1.8.3/Rfast/man/Rnorm.Rd |only Rfast-1.8.3/Rfast/man/Sort.Rd | 37 - Rfast-1.8.3/Rfast/man/Table.Rd | 8 Rfast-1.8.3/Rfast/man/XopY.sum.Rd | 25 Rfast-1.8.3/Rfast/man/allttests.Rd | 10 Rfast-1.8.3/Rfast/man/ancova1.Rd | 4 Rfast-1.8.3/Rfast/man/ancovas.Rd | 4 Rfast-1.8.3/Rfast/man/anova_propreg.Rd | 14 Rfast-1.8.3/Rfast/man/beta.mle.Rd | 6 Rfast-1.8.3/Rfast/man/bic.fs.reg.Rd |only Rfast-1.8.3/Rfast/man/checkNamespace.Rd | 40 - Rfast-1.8.3/Rfast/man/cholesky.Rd | 4 Rfast-1.8.3/Rfast/man/circlin.cor.Rd |only Rfast-1.8.3/Rfast/man/colAny.Rd | 2 Rfast-1.8.3/Rfast/man/colMedians.Rd | 5 Rfast-1.8.3/Rfast/man/colMins.Rd | 7 Rfast-1.8.3/Rfast/man/colOrder.Rd | 30 - Rfast-1.8.3/Rfast/man/colTrue.Rd | 2 Rfast-1.8.3/Rfast/man/colkurtosis.Rd |only Rfast-1.8.3/Rfast/man/colmeans.Rd | 10 Rfast-1.8.3/Rfast/man/colnormal.mle.Rd |only Rfast-1.8.3/Rfast/man/colnth.Rd | 39 + Rfast-1.8.3/Rfast/man/colrow.zero.Rd | 4 Rfast-1.8.3/Rfast/man/colsums.Rd | 5 Rfast-1.8.3/Rfast/man/colwatsons.Rd |only Rfast-1.8.3/Rfast/man/comb_n.Rd | 8 Rfast-1.8.3/Rfast/man/cor.fsreg.Rd | 4 Rfast-1.8.3/Rfast/man/corpairs.Rd | 12 Rfast-1.8.3/Rfast/man/count_value.Rd | 4 Rfast-1.8.3/Rfast/man/cova.Rd | 9 Rfast-1.8.3/Rfast/man/dcor.Rd |only Rfast-1.8.3/Rfast/man/dcor.ttest.Rd |only Rfast-1.8.3/Rfast/man/dcov.Rd |only Rfast-1.8.3/Rfast/man/diri.nr2.Rd | 17 Rfast-1.8.3/Rfast/man/dista.Rd | 8 Rfast-1.8.3/Rfast/man/edist.Rd | 37 - Rfast-1.8.3/Rfast/man/eel.test2.Rd | 2 Rfast-1.8.3/Rfast/man/expregs.Rd |only Rfast-1.8.3/Rfast/man/fish.kent.Rd |only Rfast-1.8.3/Rfast/man/g2tests.Rd | 2 Rfast-1.8.3/Rfast/man/gammamle.Rd | 2 Rfast-1.8.3/Rfast/man/gaussian.nb.Rd | 24 Rfast-1.8.3/Rfast/man/geom.regs.Rd |only Rfast-1.8.3/Rfast/man/glm_logistic.Rd | 5 Rfast-1.8.3/Rfast/man/group.sum.Rd | 5 Rfast-1.8.3/Rfast/man/group.var.Rd |only Rfast-1.8.3/Rfast/man/is.symmetric.Rd | 2 Rfast-1.8.3/Rfast/man/james.Rd |only Rfast-1.8.3/Rfast/man/knn.Rd | 6 Rfast-1.8.3/Rfast/man/knn.cv.Rd |only Rfast-1.8.3/Rfast/man/kuiper.Rd |only Rfast-1.8.3/Rfast/man/list.ftests.Rd |only Rfast-1.8.3/Rfast/man/logistic.cat1.Rd | 2 Rfast-1.8.3/Rfast/man/lower_tri.Rd | 12 Rfast-1.8.3/Rfast/man/mad2.Rd |only Rfast-1.8.3/Rfast/man/matrix.sum.Rd | 2 Rfast-1.8.3/Rfast/man/matrnorm.Rd |only Rfast-1.8.3/Rfast/man/multinom.reg.Rd |only Rfast-1.8.3/Rfast/man/multinom.regs.Rd |only Rfast-1.8.3/Rfast/man/mv.eeltest1.Rd |only Rfast-1.8.3/Rfast/man/mv.eeltest2.Rd |only Rfast-1.8.3/Rfast/man/mvkurtosis.Rd |only Rfast-1.8.3/Rfast/man/normal.mle.Rd | 16 Rfast-1.8.3/Rfast/man/normlog.reg.Rd |only Rfast-1.8.3/Rfast/man/normlog.regs.Rd |only Rfast-1.8.3/Rfast/man/odds.ratio.Rd | 7 Rfast-1.8.3/Rfast/man/percent.ttest.Rd |only Rfast-1.8.3/Rfast/man/percent.ttests.Rd |only Rfast-1.8.3/Rfast/man/permutation.Rd | 8 Rfast-1.8.3/Rfast/man/prop.reg.Rd | 6 Rfast-1.8.3/Rfast/man/proptests.Rd | 12 Rfast-1.8.3/Rfast/man/qpois.reg.Rd | 33 - Rfast-1.8.3/Rfast/man/read.directory.Rd | 3 Rfast-1.8.3/Rfast/man/rep_col.Rd | 25 Rfast-1.8.3/Rfast/man/rint.regbx.Rd | 10 Rfast-1.8.3/Rfast/man/rint.regs.Rd |only Rfast-1.8.3/Rfast/man/rm.anova.Rd |only Rfast-1.8.3/Rfast/man/rowTrue.Rd | 2 Rfast-1.8.3/Rfast/man/score.betaregs.Rd | 1 Rfast-1.8.3/Rfast/man/score.glms.Rd | 2 Rfast-1.8.3/Rfast/man/sftests.Rd | 2 Rfast-1.8.3/Rfast/man/skew.Rd |only Rfast-1.8.3/Rfast/man/skew.test2.Rd |only Rfast-1.8.3/Rfast/man/sort_mat.Rd | 7 Rfast-1.8.3/Rfast/man/sort_unique.Rd | 2 Rfast-1.8.3/Rfast/man/sourceR.Rd | 6 Rfast-1.8.3/Rfast/man/spdinv.Rd |only Rfast-1.8.3/Rfast/man/spml.reg.Rd | 9 Rfast-1.8.3/Rfast/man/standardise.Rd | 2 Rfast-1.8.3/Rfast/man/submatrix.Rd |only Rfast-1.8.3/Rfast/man/total.dist.Rd | 15 Rfast-1.8.3/Rfast/man/vm.mle.Rd | 3 Rfast-1.8.3/Rfast/src/Diag.cpp |only Rfast-1.8.3/Rfast/src/Order.cpp | 37 - Rfast-1.8.3/Rfast/src/Sort.cpp | 33 - Rfast-1.8.3/Rfast/src/bcdcor.cpp |only Rfast-1.8.3/Rfast/src/bic_fs_reg.cpp |only Rfast-1.8.3/Rfast/src/bincomb.cpp |only Rfast-1.8.3/Rfast/src/calc_bic_fs_reg.cpp |only Rfast-1.8.3/Rfast/src/calc_bic_fs_reg.h |only Rfast-1.8.3/Rfast/src/calc_k_nn.cpp | 7 Rfast-1.8.3/Rfast/src/calc_k_nn.h | 5 Rfast-1.8.3/Rfast/src/calc_k_nn_cv.cpp |only Rfast-1.8.3/Rfast/src/calc_k_nn_cv.h |only Rfast-1.8.3/Rfast/src/calc_pc_skel.h | 1 Rfast-1.8.3/Rfast/src/calc_qpois_regs.cpp |only Rfast-1.8.3/Rfast/src/calc_qpois_regs.h |only Rfast-1.8.3/Rfast/src/check_aliases.cpp | 11 Rfast-1.8.3/Rfast/src/cholesky.cpp | 6 Rfast-1.8.3/Rfast/src/col_max_p.cpp |only Rfast-1.8.3/Rfast/src/col_mean_p.cpp |only Rfast-1.8.3/Rfast/src/col_meds_p.cpp |only Rfast-1.8.3/Rfast/src/col_min_p.cpp |only Rfast-1.8.3/Rfast/src/col_row_any.cpp |only Rfast-1.8.3/Rfast/src/col_row_false.cpp |only Rfast-1.8.3/Rfast/src/col_row_len_sort_un_int.cpp |only Rfast-1.8.3/Rfast/src/col_row_mads.cpp |only Rfast-1.8.3/Rfast/src/col_row_max.cpp |only Rfast-1.8.3/Rfast/src/col_row_means.cpp |only Rfast-1.8.3/Rfast/src/col_row_meds.cpp |only Rfast-1.8.3/Rfast/src/col_row_min.cpp |only Rfast-1.8.3/Rfast/src/col_row_min_max.cpp |only Rfast-1.8.3/Rfast/src/col_row_nth.cpp |only Rfast-1.8.3/Rfast/src/col_row_nth_p.cpp |only Rfast-1.8.3/Rfast/src/col_row_order.cpp |only Rfast-1.8.3/Rfast/src/col_row_prods.cpp |only Rfast-1.8.3/Rfast/src/col_row_shuffle.cpp |only Rfast-1.8.3/Rfast/src/col_row_sums.cpp |only Rfast-1.8.3/Rfast/src/col_row_tabulate.cpp |only Rfast-1.8.3/Rfast/src/col_row_true.cpp |only Rfast-1.8.3/Rfast/src/col_row_true_false.cpp |only Rfast-1.8.3/Rfast/src/col_sum_p.cpp |only Rfast-1.8.3/Rfast/src/combn.cpp |only Rfast-1.8.3/Rfast/src/dcor.cpp |only Rfast-1.8.3/Rfast/src/dcov.cpp |only Rfast-1.8.3/Rfast/src/design_matrix.cpp | 31 + Rfast-1.8.3/Rfast/src/diri_nr_type2.cpp | 2 Rfast-1.8.3/Rfast/src/dista.cpp | 22 Rfast-1.8.3/Rfast/src/dists.cpp |only Rfast-1.8.3/Rfast/src/dists_vec.cpp |only Rfast-1.8.3/Rfast/src/dvar.cpp |only Rfast-1.8.3/Rfast/src/eachrow.cpp |only Rfast-1.8.3/Rfast/src/edist.cpp | 2 Rfast-1.8.3/Rfast/src/fs_reg.cpp | 280 ---------- Rfast-1.8.3/Rfast/src/fs_reg_ext.cpp |only Rfast-1.8.3/Rfast/src/fs_reg_ext.h |only Rfast-1.8.3/Rfast/src/fs_reg_st.cpp |only Rfast-1.8.3/Rfast/src/fs_reg_st.h |only Rfast-1.8.3/Rfast/src/g2_helpers.cpp |only Rfast-1.8.3/Rfast/src/gamma.cpp |only Rfast-1.8.3/Rfast/src/geom_regs.cpp |only Rfast-1.8.3/Rfast/src/glm_logistic.cpp | 107 ++-- Rfast-1.8.3/Rfast/src/glm_poisson.cpp | 6 Rfast-1.8.3/Rfast/src/gold_rat2.cpp |only Rfast-1.8.3/Rfast/src/gold_rat3.cpp |only Rfast-1.8.3/Rfast/src/group_all.cpp |only Rfast-1.8.3/Rfast/src/group_any.cpp |only Rfast-1.8.3/Rfast/src/group_mad.cpp |only Rfast-1.8.3/Rfast/src/group_max.cpp |only Rfast-1.8.3/Rfast/src/group_mean.cpp |only Rfast-1.8.3/Rfast/src/group_med.cpp |only Rfast-1.8.3/Rfast/src/group_min.cpp |only Rfast-1.8.3/Rfast/src/group_min_max.cpp |only Rfast-1.8.3/Rfast/src/group_sum.cpp | 53 - Rfast-1.8.3/Rfast/src/group_var.cpp |only Rfast-1.8.3/Rfast/src/init.c | 536 +++++++++++--------- Rfast-1.8.3/Rfast/src/is_element.cpp | 20 Rfast-1.8.3/Rfast/src/k_nn.cpp | 12 Rfast-1.8.3/Rfast/src/k_nn_cv.cpp |only Rfast-1.8.3/Rfast/src/len_sort_unique.cpp |only Rfast-1.8.3/Rfast/src/logistic_only.cpp | 60 ++ Rfast-1.8.3/Rfast/src/lower_tri.cpp | 24 Rfast-1.8.3/Rfast/src/mad2.cpp |only Rfast-1.8.3/Rfast/src/min_max.cpp | 31 + Rfast-1.8.3/Rfast/src/mn.cpp | 186 ++---- Rfast-1.8.3/Rfast/src/mn.h | 43 - Rfast-1.8.3/Rfast/src/multinom_regs.cpp |only Rfast-1.8.3/Rfast/src/normlog_reg.cpp |only Rfast-1.8.3/Rfast/src/normlog_regs.cpp |only Rfast-1.8.3/Rfast/src/only_glm.cpp |only Rfast-1.8.3/Rfast/src/only_glm.h |only Rfast-1.8.3/Rfast/src/partial_sort.cpp | 8 Rfast-1.8.3/Rfast/src/permutation.cpp | 58 ++ Rfast-1.8.3/Rfast/src/poisson_only.cpp | 56 ++ Rfast-1.8.3/Rfast/src/prop_reg.cpp | 102 ++- Rfast-1.8.3/Rfast/src/prop_regs.cpp | 3 Rfast-1.8.3/Rfast/src/qpois_reg.cpp | 3 Rfast-1.8.3/Rfast/src/qpois_regs.cpp |only Rfast-1.8.3/Rfast/src/read_examples.cpp | 22 Rfast-1.8.3/Rfast/src/reg_lib.cpp |only Rfast-1.8.3/Rfast/src/reg_lib.h |only Rfast-1.8.3/Rfast/src/regression.cpp | 53 + Rfast-1.8.3/Rfast/src/rep.cpp |only Rfast-1.8.3/Rfast/src/rint_reg.cpp |only Rfast-1.8.3/Rfast/src/rint_regs.cpp |only Rfast-1.8.3/Rfast/src/sort_mat.cpp | 32 - Rfast-1.8.3/Rfast/src/sort_mat_p.cpp |only Rfast-1.8.3/Rfast/src/sort_mat_stable.cpp | 28 - Rfast-1.8.3/Rfast/src/sort_mat_stable_p.cpp |only Rfast-1.8.3/Rfast/src/sort_unique.cpp |only Rfast-1.8.3/Rfast/src/submatrix.cpp |only Rfast-1.8.3/Rfast/src/sum_eachrow.cpp |only Rfast-1.8.3/Rfast/src/system_files.cpp | 34 - Rfast-1.8.3/Rfast/src/system_files.h | 3 Rfast-1.8.3/Rfast/src/templates.h |only Rfast-1.8.3/Rfast/src/total_dista.cpp | 18 Rfast-1.8.3/Rfast/src/total_dists.cpp |only Rfast-1.8.3/Rfast/src/upper_tri.cpp |only Rfast-1.8.3/Rfast/src/varcomps_mle.cpp | 4 422 files changed, 2179 insertions(+), 1691 deletions(-)
Title: Programmatic Utilities for Manipulating Formulas, Expressions,
Calls, Assignments and Other R Objects
Description: These utilities facilitate the programmatic manipulations of
formulas, expressions, calls, assignments and other R language objects.
These objects all share the same structure: a left-hand side, operator and
right-hand side. This packages provides methods for accessing and
modifying this structures as well as extracting and replacing names and
symbols from these objects.
Author: Christopher Brown [aut, cre],
Decision Patterns [cph]
Maintainer: Christopher Brown <chris.brown@decisionpatterns.com>
Diff between formula.tools versions 1.6.1 dated 2017-02-27 and 1.6.8 dated 2017-09-21
formula.tools-1.6.1/formula.tools/NEWS |only formula.tools-1.6.8/formula.tools/DESCRIPTION | 44 ++-- formula.tools-1.6.8/formula.tools/LICENSE |only formula.tools-1.6.8/formula.tools/MD5 | 43 ++-- formula.tools-1.6.8/formula.tools/NAMESPACE | 2 formula.tools-1.6.8/formula.tools/NEWS.md |only formula.tools-1.6.8/formula.tools/R/as.character.formula.R | 1 formula.tools-1.6.8/formula.tools/R/env.R |only formula.tools-1.6.8/formula.tools/R/is.one.sided.R | 95 +++++++--- formula.tools-1.6.8/formula.tools/R/is.two.sided.R | 46 +++- formula.tools-1.6.8/formula.tools/R/op.type.R | 10 - formula.tools-1.6.8/formula.tools/R/parts.R | 7 formula.tools-1.6.8/formula.tools/R/parts.lhs.get.R | 14 - formula.tools-1.6.8/formula.tools/R/parts.lhs.set.R | 29 ++- formula.tools-1.6.8/formula.tools/R/parts.op.get.R | 10 - formula.tools-1.6.8/formula.tools/R/parts.op.set.R | 18 + formula.tools-1.6.8/formula.tools/R/parts.rhs.get.R | 10 - formula.tools-1.6.8/formula.tools/R/parts.rhs.set.R | 12 + formula.tools-1.6.8/formula.tools/README.md | 31 +-- formula.tools-1.6.8/formula.tools/man/as.character.formula.Rd | 1 formula.tools-1.6.8/formula.tools/man/env.Rd |only formula.tools-1.6.8/formula.tools/man/formula.parts.Rd | 52 +++-- formula.tools-1.6.8/formula.tools/man/is.one.sided.Rd | 66 +++--- formula.tools-1.6.8/formula.tools/man/op.type.Rd | 3 formula.tools-1.6.8/formula.tools/tests/testthat/test-lhs.r | 14 + 25 files changed, 357 insertions(+), 151 deletions(-)
Title: Elastic Functional Data Analysis
Description: Performs alignment, PCA, and modeling of multidimensional and
unidimensional functions using the square-root velocity framework
(Srivastava et al., 2011 <arXiv:1103.3817> and
Tucker et al., 2014 <DOI:10.1016/j.csda.2012.12.001>). This framework
allows for elastic analysis of functional data through phase and
amplitude separation.
Author: J. Derek Tucker <jdtuck@sandia.gov>
Maintainer: J. Derek Tucker <jdtuck@sandia.gov>
Diff between fdasrvf versions 1.8.1 dated 2017-04-30 and 1.8.2 dated 2017-09-21
DESCRIPTION | 8 +- MD5 | 131 +++++++++++++++++++++----------------- NAMESPACE | 10 ++ NEWS | 13 ++- R/AmplitudeBoxplot.R | 112 ++++++++++---------------------- R/PhaseBoxplot.R | 92 ++++++++------------------ R/align_fPCA.R | 8 +- R/curve_geodesic.R | 2 R/elastic.distance.R | 27 ++++--- R/elastic_logistic.R | 6 - R/elastic_mlogistic.R | 6 - R/elastic_prediction.R | 6 - R/elastic_regression.R | 6 - R/f_to_srvf.R | 11 +-- R/fdasrvf-package.r | 23 ++++++ R/function_mean_bayes.R | 2 R/gauss_model.R | 24 ++++-- R/geometry.R | 9 -- R/gradient.R | 4 - R/horizFPCA.R | 26 ++----- R/image_funcs.R | 6 - R/invertGamma.R |only R/kmeans.R |only R/optimum.reparam.R | 2 R/outlier.detection.R | 2 R/pair_align_functions.R | 2 R/pair_align_functions_bayes.R | 35 +++++++--- R/pair_align_image.R | 15 ++-- R/plot.ampbox.R |only R/plot.fdakma.R |only R/plot.fdawarp.R |only R/plot.hfpca.R |only R/plot.phbox.R |only R/plot.vfpca.R |only R/reparam_curve.R | 4 - R/reparam_image.R | 4 - R/srsf_to_f.R | 4 - R/summary.fdawarp.R |only R/time_warping.R | 37 +++------- R/vertFPCA.R | 39 +++-------- README.md | 2 data/datalist | 2 data/growth_vel.RData |only data/image.RData |only data/simu_warp.RData |binary data/simu_warp_median.RData |binary man/AmplitudeBoxplot.Rd | 20 +---- man/PhaseBoxplot.Rd | 8 +- man/align_fPCA.Rd | 8 +- man/curve_geodesic.Rd | 2 man/elastic.distance.Rd | 2 man/elastic.logistic.Rd | 6 - man/elastic.mlogistic.Rd | 6 - man/elastic.prediction.Rd | 6 - man/elastic.regression.Rd | 6 - man/f_to_srvf.Rd | 2 man/function_mean_bayes.Rd | 2 man/gauss_model.Rd | 15 +--- man/gradient.Rd | 4 - man/growth_vel.Rd |only man/horizFPCA.Rd | 12 +-- man/im.Rd |only man/invertGamma.Rd |only man/kmeans_align.Rd |only man/optimum.reparam.Rd | 2 man/outlier.detection.Rd | 2 man/pair_align_functions.Rd | 2 man/pair_align_functions_bayes.Rd | 12 ++- man/pair_align_image.Rd | 8 ++ man/reparam_curve.Rd | 4 - man/time_warping.Rd | 6 - man/vertFPCA.Rd | 17 +--- src/Makevars.win | 3 src/fdasrsf/bayesian.cpp | 16 +++- 74 files changed, 409 insertions(+), 442 deletions(-)
Title: Searching for Optimal Clustering Procedure for a Data Set
Description: Distance measures (GDM1, GDM2, Sokal-Michener, Bray-Curtis, for symbolic interval-valued data), cluster quality indices (Calinski-Harabasz, Baker-Hubert, Hubert-Levine, Silhouette, Krzanowski-Lai, Hartigan, Gap, Davies-Bouldin), data normalization formulas, data generation (typical and non-typical data), HINoV method, replication analysis, linear ordering methods, spectral clustering, agreement indices between two partitions, plot functions (for categorical and symbolic interval-valued data).
(MILLIGAN, G.W., COOPER, M.C. (1985) <doi:10.1007/BF02294245>,
HUBERT, L., ARABIE, P. (1985), <doi:10.1007%2FBF01908075>,
RAND, W.M. (1971) <doi:10.1080/01621459.1971.10482356>,
JAJUGA, K., WALESIAK, M. (2000) <doi:10.1007/978-3-642-57280-7_11>,
MILLIGAN, G.W., COOPER, M.C. (1988) <doi:10.1007/BF01897163>,
CORMACK, R.M. (1971) <doi:10.2307/2344237>,
JAJUGA, K., WALESIAK, M., BAK, A. (2003) <doi:10.1007/978-3-642-55721-7_12>,
CARMONE, F.J., KARA, A., MAXWELL, S. (1999) <doi:10.2307/3152003>,
DAVIES, D.L., BOULDIN, D.W. (1979) <doi:10.1109/TPAMI.1979.4766909>,
CALINSKI, T., HARABASZ, J. (1974) <doi:10.1080/03610927408827101>,
HUBERT, L. (1974) <doi:10.1080/01621459.1974.10480191>,
TIBSHIRANI, R., WALTHER, G., HASTIE, T. (2001) <doi:10.1111/1467-9868.00293>,
KRZANOWSKI, W.J., LAI, Y.T. (1988) <doi:10.2307/2531893>,
BRECKENRIDGE, J.N. (2000) <doi:10.1207/S15327906MBR3502_5>,
WALESIAK, M., DUDEK, A. (2008) <doi:10.1007/978-3-540-78246-9_11>).
Author: Marek Walesiak <marek.walesiak@ue.wroc.pl> Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Maintainer: Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Diff between clusterSim versions 0.46-1 dated 2017-09-11 and 0.46-2 dated 2017-09-21
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/data.Normalization.r | 12 ++++++------ 3 files changed, 12 insertions(+), 12 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 0.2.7 dated 2017-06-15 and 0.2.8 dated 2017-09-21
DESCRIPTION | 10 - MD5 | 36 +++--- NEWS.md | 23 +++- R/Lineage.R | 53 ++++++--- R/RcppExports.R | 8 - R/Sequence.R | 219 +++++++++++++++++++++++++++++---------- README.md | 7 + inst/doc/AminoAcids-Vignette.pdf |binary inst/doc/Diversity-Vignette.pdf |binary inst/doc/GeneUsage-Vignette.pdf |binary inst/doc/Lineage-Vignette.pdf |binary inst/doc/Topology-Vignette.pdf |binary man/buildPhylipLineage.Rd | 32 ++++- man/collapseDuplicates.Rd | 27 ++++ man/makeChangeoClone.Rd | 8 - man/maskSeqEnds.Rd | 10 + man/maskSeqGaps.Rd | 10 + man/pairwiseDist.Rd | 10 - src/RcppExports.cpp | 16 +- 19 files changed, 341 insertions(+), 128 deletions(-)
Title: R Tools for Inferring New Immunoglobulin Alleles from Rep-Seq
Data
Description: Infers the V genotype of an individual from immunoglobulin (Ig)
repertoire-sequencing (Rep-Seq) data, including detection of any novel
alleles. This information is then used to correct existing V allele calls
from among the sample sequences.
Author: Daniel Gadala-Maria [aut],
Jason Vander Heiden [ctb, cre],
Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@yale.edu>
Diff between tigger versions 0.2.10 dated 2017-07-03 and 0.2.11 dated 2017-09-21
DESCRIPTION | 8 - MD5 | 28 ++-- NAMESPACE | 13 +- NEWS.md | 6 R/functions.R | 259 +++++++++++++++++++++++++++--------------- R/tigger.R | 19 +-- README.md | 2 inst/doc/Tigger-Vignette.R | 6 inst/doc/Tigger-Vignette.Rmd | 4 inst/doc/Tigger-Vignette.pdf |binary man/findNovelAlleles.Rd | 11 + man/inferGenotype.Rd | 13 +- man/plotNovel.Rd | 5 man/reassignAlleles.Rd | 9 - vignettes/Tigger-Vignette.Rmd | 4 15 files changed, 247 insertions(+), 140 deletions(-)
Title: General Frailty Models: Shared, Joint and Nested Frailty Models
with Prediction
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package:
1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied.
2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope).
3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects.
4) Joint frailty models in the context of the joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed.
5) Joint general frailty models in the context of the joint modelling for recurrent events with terminal event data with two independent frailty terms.
6) Joint Nested frailty models in the context of the joint modelling for recurrent events with terminal event, for hierarchically clustered data (with two levels of clustering) by including two iid gamma random effects.
7) Multivariate joint frailty models for two types of recurrent events and a terminal event.
8) Joint models for longitudinal data and a terminal event.
9) Trivariate joint models for longitudinal data, recurrent events and a terminal event.
Prediction values are available (for a terminal event or for a new recurrent event). Left-truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata are allowed. In each model, the random effects have the gamma or normal distribution. Now, you can also consider time-varying covariates effects in Cox, shared and joint frailty models (1-5). The package includes concordance measures for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey
Mauguen, Agnieszka Krol, Amadou Diakite, Alexandre Laurent and Myriam Lopez
Maintainer: Virginie Rondeau <Virginie.Rondeau@inserm.fr>
Diff between frailtypack versions 2.12.4 dated 2017-09-01 and 2.12.5 dated 2017-09-21
DESCRIPTION | 8 +++++--- MD5 | 2 +- 2 files changed, 6 insertions(+), 4 deletions(-)
Title: Improved False Positive Control of Gene-Permuting GSEA with
Absolute Filtering
Description: Gene-set enrichment analysis (GSEA) is popularly used to assess the enrichment of differential signal in a pre-defined gene-set without using a cutoff threshold for differential expression. The significance of enrichment is evaluated through sample- or gene-permutation method. Although the sample-permutation approach is highly recommended due to its good false positive control, we must use gene-permuting method if the number of samples is small. However, such gene-permuting GSEA (or preranked GSEA) generates a lot of false positive gene-sets as the inter-gene correlation in each gene set increases. These false positives can be successfully reduced by filtering with the one-tailed absolute GSEA results. This package provides a function that performs gene-permuting GSEA calculation with or without the absolute filtering. Without filtering, users can perform (original) two-tailed or one-tailed absolute GSEA.
Author: Sora Yoon <yoonsora@unist.ac.kr>
Maintainer: Sora Yoon <yoonsora@unist.ac.kr>
Diff between AbsFilterGSEA versions 1.5 dated 2016-08-26 and 1.5.1 dated 2017-09-21
DESCRIPTION | 14 +++++------- MD5 | 16 ++++++------- NAMESPACE | 1 R/GenePermGSEA.R | 25 ++++++++++++--------- R/RcppExports.R | 6 ++--- data/example.rda |binary man/GenePermGSEA.Rd | 11 +++++---- man/example.Rd | 60 ++++++++++++++++++++++++++-------------------------- src/RcppExports.cpp | 38 +++++++++++++++++++++++--------- 9 files changed, 95 insertions(+), 76 deletions(-)
Title: Datasets for 'spatstat'
Description: Contains all the datasets for the 'spatstat' package.
Author: Adrian Baddeley [aut, cre],
Rolf Turner [aut],
Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.data versions 1.0-1 dated 2017-09-14 and 1.1-0 dated 2017-09-21
DESCRIPTION | 11 ++++++----- MD5 | 32 ++++++++++++++++++++++++-------- NAMESPACE | 8 ++++++-- R |only inst/doc/packagesizes.txt | 2 +- inst/rawdata |only man/betacells.Rd | 8 +++++--- man/copyExampleFiles.Rd |only man/ganglia.Rd | 6 +++--- man/redwood.Rd | 2 +- man/redwoodfull.Rd | 6 +++--- man/residualspaper.Rd | 2 +- 12 files changed, 50 insertions(+), 27 deletions(-)
Title: The Moving Epidemic Method Web Application
Description: Web application created in the Shiny framework for the 'mem' R package.
Author: Jose E. Lozano [aut, cre]
Maintainer: Jose E. Lozano <lozalojo@gmail.com>
Diff between memapp versions 2.4 dated 2017-09-01 and 2.5 dated 2017-09-21
DESCRIPTION | 10 ++--- MD5 | 8 ++-- inst/shinyapp/helpers.R | 92 ++++++++++++++++++++++++++++++++++++++++-------- inst/shinyapp/server.R | 67 +++++++++++++++++++++++++++------- inst/shinyapp/ui.R | 10 ++--- 5 files changed, 143 insertions(+), 44 deletions(-)