Sat, 09 Nov 2019

Package rayrender updated to version 0.4.2 with previous version 0.4.0 dated 2019-10-09

Title: Build and Raytrace 3D Scenes
Description: Render scenes using pathtracing. Build 3D scenes out of spheres, cubes, planes, disks, triangles, line segments, cylinders, ellipsoids, and 3D models in the 'Wavefront' OBJ file format. Supports several material types, textures, multicore rendering, and tone-mapping. Based on the "Ray Tracing in One Weekend" book series. Peter Shirley (2018) <https://raytracing.github.io>.
Author: Tyler Morgan-Wall [aut, cph, cre] (<https://orcid.org/0000-0002-3131-3814>), Syoyo Fujita [ctb, cph], Melissa O'Neill [ctb, cph]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>

Diff between rayrender versions 0.4.0 dated 2019-10-09 and 0.4.2 dated 2019-11-09

 DESCRIPTION               |    6 +-
 MD5                       |   78 ++++++++++++++-------------
 NAMESPACE                 |    1 
 R/RcppExports.R           |    4 -
 R/add_object.R            |    4 -
 R/generate_cornell.R      |   12 ++--
 R/generate_ground.R       |   14 ++--
 R/materials.R             |   77 +++++++++++++++++++++------
 R/objects.R               |  129 ++++++++++++++++++++++++----------------------
 R/pig.R                   |   36 ++++++------
 R/r_obj.R                 |    6 +-
 R/render_scene.R          |   24 +++++---
 R/utils-pipe.R            |    2 
 man/add_object.Rd         |    4 -
 man/cube.Rd               |    6 +-
 man/cylinder.Rd           |   12 ++--
 man/dielectric.Rd         |    6 +-
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 man/disk.Rd               |   14 ++--
 man/ellipsoid.Rd          |    8 +-
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 man/lambertian.Rd         |   75 ++------------------------
 man/metal.Rd              |    2 
 man/obj_model.Rd          |   18 +++---
 man/pipe.Rd               |    2 
 man/r_obj.Rd              |    6 +-
 man/render_scene.Rd       |   11 ++-
 man/segment.Rd            |    8 +-
 man/sphere.Rd             |    6 +-
 man/triangle.Rd           |   10 +--
 man/xy_rect.Rd            |   10 +--
 man/xz_rect.Rd            |   10 +--
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 src/RcppExports.cpp       |    9 +--
 src/buildscene.h          |   28 ++++++++-
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 src/material.h            |   50 +++++++++++++++++
 src/mathinline.h          |   84 +++++++++++++++++++++++++++--
 src/pdf.h                 |   32 +++++++++++
 src/render_scene_rcpp.cpp |   40 +++++++-------
 src/vec3.h                |    1 
 41 files changed, 526 insertions(+), 343 deletions(-)

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New package patternplot with initial version 0.3.1
Package: patternplot
Type: Package
Title: Versatile Pie Charts, Ring Charts, Bar Charts and Box Plots using Patterns, Colors and Images
Version: 0.3.1
Maintainer: Chunqiao Luo <chunqiaoluo@gmail.com>
Imports: Rcpp (>= 0.11.0), R6 (>= 2.1.2), ggplot2 (>= 2.1.0), jpeg (>= 0.1-8), png (>= 0.1-7), grDevices, utils, RcppParallel, dplyr, gtable, gridExtra
Depends: R (>= 3.0.2)
Suggests: knitr, Cairo, RCurl, rmarkdown
Date: 2019-10-28
Authors@R: c( person("Chunqiao", "Luo", email = "chunqiaoluo@gmail.com", role = c("aut", "cre")),person("Shasha", "Bai", role = c("aut")) )
License: GPL
Description: Creates aesthetically pleasing and informative pie charts, ring charts, bar charts and box plots with colors, patterns, and images.
LinkingTo: Rcpp, RcppParallel
SystemRequirements: GNU make
RoxygenNote: 6.1.1
NeedsCompilation: yes
VignetteBuilder: knitr
Author: Chunqiao Luo [aut, cre], Shasha Bai [aut]
Packaged: 2019-11-05 22:11:27 UTC; chunqial
Repository: CRAN
Date/Publication: 2019-11-09 23:40:06 UTC

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Package leaflet.providers updated to version 1.9.0 with previous version 1.8.0 dated 2019-07-15

Title: Leaflet Providers
Description: Contains third-party map tile provider information from 'Leaflet.js', <https://github.com/leaflet-extras/leaflet-providers>, to be used with the 'leaflet' R package. Additionally, 'leaflet.providers' enables users to retrieve up-to-date provider information between package updates.
Author: Leslie Huang [aut], Barret Schloerke [ctb, cre] (<https://orcid.org/0000-0001-9986-114X>), Leaflet Providers contributors [ctb, cph] (Leaflet Providers plugin), RStudio [cph, fnd]
Maintainer: Barret Schloerke <barret@rstudio.com>

Diff between leaflet.providers versions 1.8.0 dated 2019-07-15 and 1.9.0 dated 2019-11-09

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 7 files changed, 62 insertions(+), 42 deletions(-)

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Package bda (with last version 13.4.13) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2019-11-09 13.4.13
2018-01-04 10.1.9
2015-07-29 5.1.6
2015-04-04 5.1.3
2014-05-07 3.2.0-3
2014-03-06 3.1.3-2
2013-08-08 2.2.8-8
2013-04-20 2.1.4-19
2013-02-11 2.1.2-10
2013-02-09 2.1.2-8
2012-12-17 2.0.12-17
2012-11-12 2.0.11-11
2012-11-04 2.0.11-4
2012-07-31 1.2.7-31
2012-01-06 1.1.1-7

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Package kernlab updated to version 0.9-28 with previous version 0.9-27 dated 2018-08-10

Title: Kernel-Based Machine Learning Lab
Description: Kernel-based machine learning methods for classification, regression, clustering, novelty detection, quantile regression and dimensionality reduction. Among other methods 'kernlab' includes Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes and a QP solver.
Author: Alexandros Karatzoglou [aut, cre], Alex Smola [aut], Kurt Hornik [aut], National ICT Australia (NICTA) [cph], Michael A. Maniscalco [ctb, cph], Choon Hui Teo [ctb]
Maintainer: Alexandros Karatzoglou <alexandros.karatzoglou@gmail.com>

Diff between kernlab versions 0.9-27 dated 2018-08-10 and 0.9-28 dated 2019-11-09

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 MD5                   |   32 ++++++++++++++++----------------
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 17 files changed, 43 insertions(+), 38 deletions(-)

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Package aaSEA updated to version 1.1.0 with previous version 1.0.0 dated 2019-08-01

Title: Amino Acid Substitution Effect Analyser
Description: Given a protein multiple sequence alignment, it is daunting task to assess the effects of substitutions along sequence length. 'aaSEA' package is intended to help researchers to rapidly analyse property changes caused by single, multiple and correlated amino acid substitutions in proteins. Methods for identification of co-evolving positions from multiple sequence alignment are as described in : Pelé et al., (2017) <doi:10.4172/2379-1764.1000250>.
Author: Raja Sekhara Reddy D.M
Maintainer: Raja Sekhara Reddy D.M <raja.duvvuru@gmail.com>

Diff between aaSEA versions 1.0.0 dated 2019-08-01 and 1.1.0 dated 2019-11-09

 DESCRIPTION                       |    8 +-
 MD5                               |   12 +--
 R/getCorSites.R                   |   26 +++----
 inst/doc/aaSEA_Documentation.R    |    2 
 inst/doc/aaSEA_Documentation.Rmd  |    2 
 inst/doc/aaSEA_Documentation.html |  129 ++++++++++++++++++++++++++++----------
 vignettes/aaSEA_Documentation.Rmd |    2 
 7 files changed, 124 insertions(+), 57 deletions(-)

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Package Rmst updated to version 0.0.2 with previous version 0.0.1 dated 2019-11-01

Title: Computerized Adaptive Multistage Testing
Description: Assemble the panels of computerized adaptive multistage testing by the bottom-up and the top-down approach, and simulate the administration of the assembled panels. The full documentation and tutorials are at <https://github.com/xluo11/Rmst>. Reference: Luo and Kim (2018) <doi:10.1111/jedm.12174>.
Author: Xiao Luo [aut, cre]
Maintainer: Xiao Luo <xluo1986@gmail.com>

Diff between Rmst versions 0.0.1 dated 2019-11-01 and 0.0.2 dated 2019-11-09

 DESCRIPTION     |    6 +++---
 MD5             |   10 +++++-----
 R/assembly.R    |    1 +
 R/simulator.R   |    2 +-
 man/assembly.Rd |    1 +
 man/sim.Rd      |    2 +-
 6 files changed, 12 insertions(+), 10 deletions(-)

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Package LatticeKrig updated to version 8.4 with previous version 7.0 dated 2018-04-30

Title: Multi-Resolution Kriging Based on Markov Random Fields
Description: Methods for the interpolation of large spatial datasets. This package follows a "fixed rank Kriging" approach but provides a surface fitting method that can approximate standard spatial data models. Using a large number of basis functions allows for estimates that can come close to interpolating the observations (a spatial model with a small nugget variance.) Moreover, the covariance model for this method can approximate the Matern covariance family but also allows for a multi-resolution model and supports efficient computation of the profile likelihood for estimating covariance parameters. This is accomplished through compactly supported basis functions and a Markov random field model for the basis coefficients. These features lead to sparse matrices for the computations and this package makes of the R spam package for sparse linear algebra. An extension of this version over previous ones ( < 5.4 ) is the support for different geometries besides a rectangular domain. The Markov random field approach combined with a basis function representation makes the implementation of different geometries simple where only a few specific R functions need to be added with most of the computation and evaluation done by generic routines that have been tuned to be efficient. One benefit of this package's model/approach is the facility to do unconditional and conditional simulation of the field for large numbers of arbitrary points. There is also the flexibility for estimating non-stationary covariances and also the case when the observations are a linear combination (e.g. an integral) of the spatial process. Included are generic methods for prediction, standard errors for prediction, plotting of the estimated surface and conditional and unconditional simulation. See the 'LatticeKrig' GitHub repository for a vignette of this package. Development of this package was supported in part by the National Science Foundation Grant 1417857 and the National Center for Atmospheric Research.
Author: Douglas Nychka [aut, cre], Dorit Hammerling [aut], Stephan Sain [aut], Nathan Lenssen [aut], Colette Smirniotis [aut], Matthew Iverson [aut], University Corporation for Atmospheric Research [cph]
Maintainer: Douglas Nychka <nychka@ucar.edu>

Diff between LatticeKrig versions 7.0 dated 2018-04-30 and 8.4 dated 2019-11-09

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 54 files changed, 663 insertions(+), 440 deletions(-)

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Package benchmarkme updated to version 1.0.3 with previous version 1.0.2 dated 2019-08-19

Title: Crowd Sourced System Benchmarks
Description: Benchmark your CPU and compare against other CPUs. Also provides functions for obtaining system specifications, such as RAM, CPU type, and R version.
Author: Colin Gillespie [aut, cre] (<https://orcid.org/0000-0003-1787-0275>)
Maintainer: Colin Gillespie <csgillespie@gmail.com>

Diff between benchmarkme versions 1.0.2 dated 2019-08-19 and 1.0.3 dated 2019-11-09

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More information about benchmarkme at CRAN
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Package quantreg updated to version 5.52 with previous version 5.51 dated 2019-08-07

Title: Quantile Regression
Description: Estimation and inference methods for models of conditional quantiles: Linear and nonlinear parametric and non-parametric (total variation penalized) models for conditional quantiles of a univariate response and several methods for handling censored survival data. Portfolio selection methods based on expected shortfall risk are also now included.
Author: Roger Koenker [cre, aut], Stephen Portnoy [ctb] (Contributions to Censored QR code), Pin Tian Ng [ctb] (Contributions to Sparse QR code), Achim Zeileis [ctb] (Contributions to dynrq code essentially identical to his dynlm code), Philip Grosjean [ctb] (Contributions to nlrq code), Cleve Moler [ctb] (author of several linpack routines), Brian D Ripley [trl, ctb] (Initial (2001) R port from S (to my everlasting shame -- how could I have been so slow to adopt R!) and for numerous other suggestions and useful advice)
Maintainer: Roger Koenker <rkoenker@illinois.edu>

Diff between quantreg versions 5.51 dated 2019-08-07 and 5.52 dated 2019-11-09

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Package shinyhelper updated to version 0.3.2 with previous version 0.3.1 dated 2018-10-28

Title: Easily Add Markdown Help Files to 'shiny' App Elements
Description: Creates a lightweight way to add markdown helpfiles to 'shiny' apps, using modal dialog boxes, with no need to observe each help button separately.
Author: Chris Mason-Thom [aut, cre]
Maintainer: Chris Mason-Thom <christopher.w.thom@outlook.com>

Diff between shinyhelper versions 0.3.1 dated 2018-10-28 and 0.3.2 dated 2019-11-09

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 shinyhelper-0.3.2/shinyhelper/NEWS.md                                                           |    4 ++
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 shinyhelper-0.3.2/shinyhelper/README.md                                                         |   15 ++++++-
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Package netCoin updated to version 1.1.23 with previous version 0.3.2 dated 2018-12-16

Title: Interactive Analytic Networks
Description: Create interactive analytic networks. It joins the data analysis power of R to obtain coincidences, co-occurrences and correlations, and the visualization libraries of 'JavaScript' in one package.
Author: Modesto Escobar <modesto@usal.es>, David Barrios <metal@usal.es>, Carlos Prieto <cprietos@usal.es>, Luis Martinez-Uribe <lmartinez@usal.es>.
Maintainer: Modesto Escobar <modesto@usal.es>

Diff between netCoin versions 0.3.2 dated 2018-12-16 and 1.1.23 dated 2019-11-09

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Package reReg (with last version 1.2.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2019-11-08 1.2.0
2018-10-22 1.1.6
2018-10-09 1.1.5
2018-05-30 1.1.4

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Package glmnet updated to version 3.0 with previous version 2.0-18 dated 2019-05-20

Title: Lasso and Elastic-Net Regularized Generalized Linear Models
Description: Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. Two recent additions are the multiple-response Gaussian, and the grouped multinomial regression. The algorithm uses cyclical coordinate descent in a path-wise fashion, as described in the papers listed in the URL below.
Author: Jerome Friedman [aut], Trevor Hastie [aut, cre], Rob Tibshirani [aut], Balasubramanian Narasimhan [aut], Noah Simon [aut], Junyang Qian [ctb]
Maintainer: Trevor Hastie <hastie@stanford.edu>

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Package earth updated to version 5.1.2 with previous version 5.1.1 dated 2019-04-12

Title: Multivariate Adaptive Regression Splines
Description: Build regression models using the techniques in Friedman's papers "Fast MARS" and "Multivariate Adaptive Regression Splines" <doi:10.1214/aos/1176347963>. (The term "MARS" is trademarked and thus not used in the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and Rob Tibshirani. Uses Alan Miller's Fortran utilities with Thomas Lumley's leaps wrapper.
Maintainer: Stephen Milborrow <milbo@sonic.net>

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Package data.tree updated to version 0.7.11 with previous version 0.7.8 dated 2018-09-24

Title: General Purpose Hierarchical Data Structure
Description: Create tree structures from hierarchical data, and traverse the tree in various orders. Aggregate, cumulate, print, plot, convert to and from data.frame and more. Useful for decision trees, machine learning, finance, conversion from and to JSON, and many other applications.
Author: Russ Hyde [ctb] (improve dependencies), Chris Hammill [ctb] (improve getting), Facundo Munoz [ctb] (improve list conversion), Markus Wamser [ctb] (fixed some typos), Pierre Formont [ctb] (additional features), Kent Russel [ctb] (documentation), Noam Ross [ctb] (fixes), Duncan Garmonsway [ctb] (fixes), Christoph Glur [aut, cre] (R interface)
Maintainer: Christoph Glur <christoph.glur@ipub.com>

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Package bda updated to version 13.4.13 with previous version 10.1.9 dated 2018-01-04

Title: Density Estimation for Grouped Data
Description: Functions for density estimation based on grouped data, and next-generation gene expression data.
Author: Bin Wang <bwang831@gmail.com>
Maintainer: Bin Wang <bwang831@gmail.com>

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Package QTLRel updated to version 1.4 with previous version 1.1 dated 2019-03-25

Title: Tools for Mapping of Quantitative Traits of Genetically Related Individuals and Calculating Identity Coefficients from Pedigrees
Description: This software provides tools for quantitative trait mapping in populations such as advanced intercross lines where relatedness among individuals should not be ignored. It can estimate background genetic variance components, impute missing genotypes, simulate genotypes, perform a genome scan for putative quantitative trait loci (QTL), and plot mapping results. It also has functions to calculate identity coefficients from pedigrees, especially suitable for pedigrees that consist of a large number of generations, or estimate identity coefficients from genotypic data in certain circumstances.
Author: Riyan Cheng [aut, cre]
Maintainer: Riyan Cheng <riyancheng@hotmail.com>

Diff between QTLRel versions 1.1 dated 2019-03-25 and 1.4 dated 2019-11-09

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Package gamRR updated to version 0.7.0 with previous version 0.6.0 dated 2019-03-20

Title: Calculate the RR for the GAM
Description: To calculate the relative risk (RR) for the generalized additive model.
Author: Zhicheng Du, Wangjian Zhang, Yuantao Hao
Maintainer: Zhicheng Du<dgdzc@hotmail.com>

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Package survival updated to version 3.1-7 with previous version 3.1-6 dated 2019-11-06

Title: Survival Analysis
Description: Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre], Thomas Lumley [ctb, trl] (original S->R port and R maintainer until 2009)
Maintainer: Terry M Therneau <therneau.terry@mayo.edu>

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Package mgcv updated to version 1.8-31 with previous version 1.8-30 dated 2019-10-24

Title: Mixed GAM Computation Vehicle with Automatic Smoothness Estimation
Description: Generalized additive (mixed) models, some of their extensions and other generalized ridge regression with multiple smoothing parameter estimation by (Restricted) Marginal Likelihood, Generalized Cross Validation and similar, or using iterated nested Laplace approximation for fully Bayesian inference. See Wood (2017) <doi:10.1201/9781315370279> for an overview. Includes a gam() function, a wide variety of smoothers, 'JAGS' support and distributions beyond the exponential family.
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>

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Package learnr updated to version 0.10.0 with previous version 0.9.2.1 dated 2018-06-29

Title: Interactive Tutorials for R
Description: Create interactive tutorials using R Markdown. Use a combination of narrative, figures, videos, exercises, and quizzes to create self-paced tutorials for learning about R and R packages.
Author: Barret Schloerke [aut, cre] (<https://orcid.org/0000-0001-9986-114X>), JJ Allaire [aut], Barbara Borges [aut], RStudio, Inc. [cph], Ajax.org B.V. [ctb, cph] (Ace library), Zeno Rocha [ctb, cph] (clipboard.js library), Nick Payne [ctb, cph] (Bootbox library), Jake Archibald [ctb, cph] (idb-keyval library)
Maintainer: Barret Schloerke <barret@rstudio.com>

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Package gender updated to version 0.5.3 with previous version 0.5.2 dated 2018-03-07

Title: Predict Gender from Names Using Historical Data
Description: Infers state-recorded gender categories from first names and dates of birth using historical datasets. By using these datasets instead of lists of male and female names, this package is able to more accurately infer the gender of a name, and it is able to report the probability that a name was male or female. GUIDELINES: This method must be used cautiously and responsibly. Please be sure to see the guidelines and warnings about usage in the 'README' or the package documentation.
Author: Lincoln Mullen [aut, cre] (<https://orcid.org/0000-0001-5103-6917>), Cameron Blevins [ctb], Ben Schmidt [ctb]
Maintainer: Lincoln Mullen <lincoln@lincolnmullen.com>

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Package aqp updated to version 1.18 with previous version 1.17 dated 2019-10-28

Title: Algorithms for Quantitative Pedology
Description: The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps/>. Components of the AQP project (aqp, soilDB, sharpshootR, soilReports packages) serve an important role in routine data analysis within the USDA-NRCS Soil Science Division. The AQP suite of R packages offer a convenient platform for bridging the gap between pedometric theory and practice.
Author: Dylan Beaudette [aut, cre], Pierre Roudier [aut, ctb], Andrew Brown [aut, ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>

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 aqp-1.18/aqp/man/colorQuantiles.Rd                   |    3 
 aqp-1.18/aqp/man/confusionIndex.Rd                   |   70 +--
 aqp-1.18/aqp/man/contrastChart.Rd                    |only
 aqp-1.18/aqp/man/contrastClass.Rd                    |only
 aqp-1.18/aqp/man/denormalize.Rd                      |only
 aqp-1.18/aqp/man/f.noise.Rd                          |  310 +++++++--------
 aqp-1.18/aqp/man/fixOverlap.Rd                       |only
 aqp-1.18/aqp/man/generalize.hz.Rd                    |   29 +
 aqp-1.18/aqp/man/glom.Rd                             |    2 
 aqp-1.18/aqp/man/huePosition.Rd                      |only
 aqp-1.18/aqp/man/jacobs2000.Rd                       |only
 aqp-1.18/aqp/man/munsell2rgb.Rd                      |   25 +
 aqp-1.18/aqp/man/plot_distance_graph.Rd              |   78 +--
 aqp-1.18/aqp/man/profile_compare-methods.Rd          |  372 +++++++++---------
 aqp-1.18/aqp/man/resample.twotheta.Rd                |   94 ++--
 aqp-1.18/aqp/man/rruff.sample.Rd                     |   74 +--
 aqp-1.18/aqp/man/shannonEntropy.Rd                   |   74 +--
 aqp-1.18/aqp/man/soilPalette.Rd                      |only
 aqp-1.18/aqp/man/soil_minerals.Rd                    |  140 +++---
 aqp-1.18/aqp/man/sp6.Rd                              |  114 ++---
 aqp-1.18/aqp/man/tauW.Rd                             |  216 +++++-----
 aqp-1.18/aqp/man/texture.triangle.low.rv.high.Rd     |  131 +++---
 aqp-1.18/aqp/man/union.Rd                            |    2 
 aqp-1.18/aqp/tests/testthat/test-SPC-objects.R       |   76 +++
 aqp-1.18/aqp/tests/testthat/test-SPC-union.R         |   31 +
 aqp-1.18/aqp/tests/testthat/test-aggregateColor.R    |only
 aqp-1.18/aqp/tests/testthat/test-color-conversion.R  |   39 +
 aqp-1.18/aqp/tests/testthat/test-colorContrast.R     |only
 aqp-1.18/aqp/tests/testthat/test-denormalize.R       |only
 aqp-1.18/aqp/tests/testthat/test-genhz.R             |only
 aqp-1.18/aqp/tests/testthat/test-overlap.R           |only
 aqp-1.18/aqp/tests/testthat/test-plotSPC.R           |only
 aqp-1.18/aqp/tests/testthat/test-profile_compare.R   |   16 
 aqp-1.18/aqp/tests/testthat/test-surface-thickness.R |    2 
 89 files changed, 2505 insertions(+), 1870 deletions(-)

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