Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-11 0.1.1
2019-12-06 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-14 1.2.4
2019-09-03 1.2.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-11-19 0.4.0
2017-03-23 0.3.0
2017-01-21 0.2.0
Title: Computation of Variance-Based Sensitivity Indices
Description: It allows to rapidly compute, bootstrap and plot up to third-order Sobol'-based sensitivity indices using several state-of-the-art first and total-order estimators. Sobol' indices can be computed either for models that yield a scalar as a model output or for systems of differential equations. The package also provides a suit of benchmark tests functions and several options to obtain publication-ready figures of the model output uncertainty and sensitivity-related analysis.
Author: Arnald Puy [aut, cre] (<https://orcid.org/0000-0001-9469-2156>),
Bertrand Ioos [ctb] (Author of included 'sensitivity' fragments),
Gilles Pujol [ctb] (Author of included 'sensitivity' fragments),
RStudio [cph] (Copyright holder of included 'sensitivity' fragments)
Maintainer: Arnald Puy <arnald.puy@pm.me>
Diff between sensobol versions 0.2.2 dated 2020-02-25 and 1.0.0 dated 2021-01-26
sensobol-0.2.2/sensobol/R/group_ranking.R |only sensobol-0.2.2/sensobol/R/sobol_boot.R |only sensobol-0.2.2/sensobol/R/utils-pipe.R |only sensobol-0.2.2/sensobol/inst/doc/sensobol.R |only sensobol-0.2.2/sensobol/inst/doc/sensobol.Rmd |only sensobol-0.2.2/sensobol/inst/doc/sensobol.html |only sensobol-0.2.2/sensobol/man/ishigami_Mapply.Rd |only sensobol-0.2.2/sensobol/man/pipe.Rd |only sensobol-0.2.2/sensobol/man/sobol_ci.Rd |only sensobol-0.2.2/sensobol/man/sobol_ci_dummy.Rd |only sensobol-0.2.2/sensobol/man/sobol_replicas.Rd |only sensobol-0.2.2/sensobol/tests/testthat/test-sobol_indices.R |only sensobol-0.2.2/sensobol/tests/testthat/test-your_function.R |only sensobol-0.2.2/sensobol/vignettes/sensobol.Rmd |only sensobol-1.0.0/sensobol/DESCRIPTION | 41 sensobol-1.0.0/sensobol/MD5 | 83 - sensobol-1.0.0/sensobol/NAMESPACE | 18 sensobol-1.0.0/sensobol/NEWS.md | 21 sensobol-1.0.0/sensobol/R/RcppExports.R |only sensobol-1.0.0/sensobol/R/plot_sobol.R | 418 +++-- sensobol-1.0.0/sensobol/R/sensobol-package.R |only sensobol-1.0.0/sensobol/R/sobol_indices.R | 898 +++++------ sensobol-1.0.0/sensobol/R/sobol_matrices.R | 305 ++- sensobol-1.0.0/sensobol/R/sobol_ode.R |only sensobol-1.0.0/sensobol/R/test_functions.R | 251 ++- sensobol-1.0.0/sensobol/R/vars_matrices.R |only sensobol-1.0.0/sensobol/R/vars_to.R |only sensobol-1.0.0/sensobol/README.md | 35 sensobol-1.0.0/sensobol/build/partial.rdb |binary sensobol-1.0.0/sensobol/build/vignette.rds |binary sensobol-1.0.0/sensobol/inst/CITATION |only sensobol-1.0.0/sensobol/inst/REFERENCES.bib | 263 +++ sensobol-1.0.0/sensobol/inst/doc/sensobol.Rnw |only sensobol-1.0.0/sensobol/inst/doc/sensobol.pdf |only sensobol-1.0.0/sensobol/man/bratley1988_Fun.Rd | 21 sensobol-1.0.0/sensobol/man/bratley1992_Fun.Rd | 23 sensobol-1.0.0/sensobol/man/ishigami_Fun.Rd |only sensobol-1.0.0/sensobol/man/metafunction.Rd |only sensobol-1.0.0/sensobol/man/oakley_Fun.Rd | 24 sensobol-1.0.0/sensobol/man/plot_multiscatter.Rd |only sensobol-1.0.0/sensobol/man/plot_scatter.Rd | 44 sensobol-1.0.0/sensobol/man/plot_sobol.Rd | 53 sensobol-1.0.0/sensobol/man/plot_uncertainty.Rd | 30 sensobol-1.0.0/sensobol/man/sobol_Fun.Rd | 18 sensobol-1.0.0/sensobol/man/sobol_dummy.Rd | 58 sensobol-1.0.0/sensobol/man/sobol_indices.Rd | 117 + sensobol-1.0.0/sensobol/man/sobol_matrices.Rd | 102 - sensobol-1.0.0/sensobol/man/sobol_ode.Rd |only sensobol-1.0.0/sensobol/man/vars_matrices.Rd |only sensobol-1.0.0/sensobol/man/vars_to.Rd |only sensobol-1.0.0/sensobol/src |only sensobol-1.0.0/sensobol/tests/testthat.R | 2 sensobol-1.0.0/sensobol/tests/testthat/test-sobol_boot.R |only sensobol-1.0.0/sensobol/tests/testthat/test-sobol_matrices.R | 62 sensobol-1.0.0/sensobol/vignettes/REFERENCES.bib | 321 +++ sensobol-1.0.0/sensobol/vignettes/sensobol.Rnw |only sensobol-1.0.0/sensobol/vignettes/sensobol_vignette.pdf |only 57 files changed, 2205 insertions(+), 1003 deletions(-)
Title: Cubature over Polygonal Domains
Description: Numerical integration of continuously differentiable
functions f(x,y) over simple closed polygonal domains.
The following cubature methods are implemented:
product Gauss cubature (Sommariva and Vianello, 2007,
<doi:10.1007/s10543-007-0131-2>),
the simple two-dimensional midpoint rule
(wrapping 'spatstat.geom' functions),
adaptive cubature for radially symmetric functions via line
integrate() along the polygon boundary (Meyer and Held, 2014,
<doi:10.1214/14-AOAS743>, Supplement B),
and integration of the bivariate Gaussian density based on
polygon triangulation.
For simple integration along the axes, the 'cubature' package
is more appropriate.
Author: Sebastian Meyer [aut, cre, trl]
(<https://orcid.org/0000-0002-1791-9449>),
Leonhard Held [ths],
Michael Hoehle [ths]
Maintainer: Sebastian Meyer <seb.meyer@fau.de>
Diff between polyCub versions 0.7.1 dated 2019-02-07 and 0.8.0 dated 2021-01-26
polyCub-0.7.1/polyCub/tests/test-all.R |only polyCub-0.7.1/polyCub/tests/testthat |only polyCub-0.8.0/polyCub/DESCRIPTION | 14 - polyCub-0.8.0/polyCub/MD5 | 80 +++---- polyCub-0.8.0/polyCub/NAMESPACE | 10 polyCub-0.8.0/polyCub/NEWS.md | 20 + polyCub-0.8.0/polyCub/R/circleCub.R | 66 ++--- polyCub-0.8.0/polyCub/R/coerce-gpc-methods.R | 118 +++++----- polyCub-0.8.0/polyCub/R/coerce-sp-methods.R | 123 +++++------ polyCub-0.8.0/polyCub/R/plotpolyf.R | 85 +++---- polyCub-0.8.0/polyCub/R/polyCub.SV.R | 158 +++++++------- polyCub-0.8.0/polyCub/R/polyCub.exact.Gauss.R | 11 polyCub-0.8.0/polyCub/R/polyCub.iso.R | 57 ++--- polyCub-0.8.0/polyCub/R/polyCub.midpoint.R | 32 +- polyCub-0.8.0/polyCub/R/sfg2gpc.R |only polyCub-0.8.0/polyCub/R/tools.R | 73 +++--- polyCub-0.8.0/polyCub/R/xylist.R | 165 ++++++++------ polyCub-0.8.0/polyCub/R/zzz.R | 59 ++--- polyCub-0.8.0/polyCub/README.md | 15 - polyCub-0.8.0/polyCub/build/partial.rdb |only polyCub-0.8.0/polyCub/build/vignette.rds |binary polyCub-0.8.0/polyCub/inst/doc/polyCub.R | 28 +- polyCub-0.8.0/polyCub/inst/doc/polyCub.Rmd | 22 + polyCub-0.8.0/polyCub/inst/doc/polyCub.html | 257 +++++++++++++---------- polyCub-0.8.0/polyCub/man/circleCub.Gauss.Rd | 4 polyCub-0.8.0/polyCub/man/coerce-gpc-methods.Rd | 8 polyCub-0.8.0/polyCub/man/coerce-sp-methods.Rd | 23 +- polyCub-0.8.0/polyCub/man/plot_polyregion.Rd | 7 polyCub-0.8.0/polyCub/man/plotpolyf.Rd | 23 -- polyCub-0.8.0/polyCub/man/polyCub-package.Rd | 29 +- polyCub-0.8.0/polyCub/man/polyCub.Rd | 19 - polyCub-0.8.0/polyCub/man/polyCub.SV.Rd | 44 ++- polyCub-0.8.0/polyCub/man/polyCub.exact.Gauss.Rd | 16 - polyCub-0.8.0/polyCub/man/polyCub.iso.Rd | 25 +- polyCub-0.8.0/polyCub/man/polyCub.midpoint.Rd | 39 +-- polyCub-0.8.0/polyCub/man/polygauss.Rd | 4 polyCub-0.8.0/polyCub/man/sfg2gpc.Rd |only polyCub-0.8.0/polyCub/man/xylist.Rd | 53 ++-- polyCub-0.8.0/polyCub/tests/polyiso_powerlaw.c |only polyCub-0.8.0/polyCub/tests/test-NWGL.R |only polyCub-0.8.0/polyCub/tests/test-polyCub.R |only polyCub-0.8.0/polyCub/tests/test-polyiso.R |only polyCub-0.8.0/polyCub/tests/test-regression.R |only polyCub-0.8.0/polyCub/vignettes/polyCub.Rmd | 22 + 44 files changed, 908 insertions(+), 801 deletions(-)
Title: Build MultiClass Pair-Based Classifiers using TSPs or RF
Description: A toolbox to train a single sample classifier that uses in-sample feature relationships. The relationships are represented as feature1 < feature2 (e.g. gene1 < gene2). We provide two options to go with. First is based on 'switchBox' package which uses Top-score pairs algorithm. Second is a novel implementation based on random forest algorithm. For simple problems we recommend to use one-vs-rest using TSP option due to its simplicity and for being easy to interpret. For complex problems RF performs better. Both lines filter the features first then combine the filtered features to make the list of all the possible rules (i.e. rule1: feature1 < feature2, rule2: feature1 < feature3, etc...). Then the list of rules will be filtered and the most important and informative rules will be kept. The informative rules will be assembled in an one-vs-rest model or in an RF model. We provide a detailed description with each function in this package to explain the filtration and training methodology in each line.
Author: Nour-al-dain Marzouka
Maintainer: Nour-al-dain Marzouka <Nour-al-dain.Marzouka@med.lu.se>
Diff between multiclassPairs versions 0.4.0 dated 2020-11-20 and 0.4.1 dated 2021-01-26
DESCRIPTION | 6 MD5 | 24 NEWS.md | 9 R/functions.R | 13 inst/doc/Tutorial.R | 77 + inst/doc/Tutorial.Rmd | 98 + inst/doc/Tutorial.html | 1887 +++--------------------------------- man/filter_genes_TSP.Rd | 2 man/sort_rules_RF.Rd | 4 man/train_RF.Rd | 4 man/train_one_vs_rest_TSP.Rd | 6 vignettes/Tutorial.Rmd | 98 + vignettes/images/Accuracy_final.png |only vignettes/images/Both_CPUs.png |only 14 files changed, 479 insertions(+), 1749 deletions(-)
More information about multiclassPairs at CRAN
Permanent link
Title: Dynamic Modeling and Parameter Estimation in ODE Models
Description: The framework provides functions to generate ODEs of reaction
networks, parameter transformations, observation functions, residual functions,
etc. The framework follows the paradigm that derivative information should be
used for optimization whenever possible. Therefore, all major functions produce
and can handle expressions for symbolic derivatives. The methods used in dMod
were published in Kaschek et al, 2019, <doi:10.18637/jss.v088.i10>.
Author: Daniel Kaschek
Maintainer: Daniel Kaschek <daniel.kaschek@gmail.com>
Diff between dMod versions 1.0.1 dated 2020-02-10 and 1.0.2 dated 2021-01-26
dMod-1.0.1/dMod/man/python_version_request.Rd |only dMod-1.0.1/dMod/man/python_version_rpython.Rd |only dMod-1.0.1/dMod/man/python_version_sys.Rd |only dMod-1.0.2/dMod/DESCRIPTION | 13 +- dMod-1.0.2/dMod/MD5 | 19 +--- dMod-1.0.2/dMod/NAMESPACE | 3 dMod-1.0.2/dMod/R/dMod.R | 2 dMod-1.0.2/dMod/R/parClass.R | 2 dMod-1.0.2/dMod/R/steadyStates.R | 116 +------------------------- dMod-1.0.2/dMod/R/symmetryDetection.R | 28 +++--- dMod-1.0.2/dMod/build/vignette.rds |binary dMod-1.0.2/dMod/inst/doc/dMod.html | 24 ++--- 12 files changed, 50 insertions(+), 157 deletions(-)
Title: Create Visuals for Publication
Description: A small set of functions to aid in the production of visuals in ggplot2. Includes minimalist themes with transparent backgrounds and a suite of tools for building survival curves with risk tables.
Author: Eric Finnesgard [aut, cre]
Maintainer: Eric Finnesgard <efinite@outlook.com>
Diff between utile.visuals versions 0.2.5 dated 2020-05-01 and 0.3.0 dated 2021-01-26
utile.visuals-0.2.5/utile.visuals/R/connect.R |only utile.visuals-0.2.5/utile.visuals/man/connect_origin.Rd |only utile.visuals-0.3.0/utile.visuals/DESCRIPTION | 10 utile.visuals-0.3.0/utile.visuals/MD5 | 20 - utile.visuals-0.3.0/utile.visuals/NAMESPACE | 1 utile.visuals-0.3.0/utile.visuals/NEWS.md | 3 utile.visuals-0.3.0/utile.visuals/R/geoms.R | 145 +++++++------- utile.visuals-0.3.0/utile.visuals/R/gg.R | 102 ++++----- utile.visuals-0.3.0/utile.visuals/R/utils.R | 30 +- utile.visuals-0.3.0/utile.visuals/README.md | 48 ++-- utile.visuals-0.3.0/utile.visuals/man/geom_stepconfint.Rd | 5 utile.visuals-0.3.0/utile.visuals/man/ggrisktable.Rd | 88 ++++---- 12 files changed, 225 insertions(+), 227 deletions(-)
Title: Gaussian Process for Functional Data Analysis
Description: Functionalities for modelling functional data with
multidimensional inputs, multivariate functional data, and non-separable
and/or non-stationary covariance structure of function-valued processes.
In addition, there are functionalities for functional regression models where
the mean function depends on scalar and/or functional covariates and
the covariance structure depends on functional covariates.
The development version of the package can be found on
<https://github.com/gpfda/GPFDA-dev>.
Author: Jian Qing Shi, Yafeng Cheng, Evandro Konzen
Maintainer: Evandro Konzen <gpfda.r@gmail.com>
Diff between GPFDA versions 3.0.0 dated 2021-01-11 and 3.1.0 dated 2021-01-26
DESCRIPTION | 16 MD5 | 95 ++--- R/dataExampleGPFR.R | 8 R/dataExampleMGPR.R |only R/gp.functions6.R | 118 +++--- R/gpfr.functions6.R | 800 +++++++++++++++++++++++++---------------------- R/mgp.functions.R | 117 +++--- R/nsgp.functions.R | 31 - data/dataExampleGPFR.rda |binary data/dataExampleMGPR.rda |only inst/doc/co2.R | 23 - inst/doc/co2.Rmd | 25 - inst/doc/co2.html | 21 - inst/doc/gpfr.R | 43 +- inst/doc/gpfr.Rmd | 51 +- inst/doc/gpfr.html | 63 +-- inst/doc/gpr_ex1.R | 11 inst/doc/gpr_ex1.Rmd | 15 inst/doc/gpr_ex1.html | 11 inst/doc/gpr_ex2.R | 7 inst/doc/gpr_ex2.Rmd | 8 inst/doc/gpr_ex2.html | 2 inst/doc/mgpr.R | 56 ++- inst/doc/mgpr.Rmd | 75 +++- inst/doc/mgpr.html | 76 ++-- inst/doc/nsgpr.R | 15 inst/doc/nsgpr.Rmd | 15 inst/doc/nsgpr.html | 10 man/covMat.Rd | 12 man/dataExampleGPFR.Rd | 8 man/dataExampleMGPR.Rd |only man/gpfr.Rd | 120 +++---- man/gpfrPredict.Rd | 56 +-- man/gpr.Rd | 12 man/gprPredict.Rd | 8 man/mat2fd.Rd | 24 - man/mgpr.Rd | 2 man/mgprPredict.Rd | 14 man/nsgpr.Rd | 21 - man/nsgprPredict.Rd | 8 man/plot.gpfr.Rd | 26 + man/plot.gpr.Rd | 4 man/plot.mgpr.Rd | 34 + man/plotmgpCovFun.Rd | 17 vignettes/co2.Rmd | 25 - vignettes/gpfr.Rmd | 51 +- vignettes/gpr_ex1.Rmd | 15 vignettes/gpr_ex2.Rmd | 8 vignettes/mgpr.Rmd | 75 +++- vignettes/nsgpr.Rmd | 15 50 files changed, 1306 insertions(+), 961 deletions(-)
Title: Quantile G-Computation
Description: G-computation for a set of time-fixed exposures
with quantile-based basis functions, possibly under linearity and
homogeneity assumptions. This approach estimates a regression line
corresponding to the expected change in the outcome (on the link
basis) given a simultaneous increase in the quantile-based category
for all exposures. Works with continuous, binary, and right-censored
time-to-event outcomes. Reference: Alexander P. Keil, Jessie P.
Buckley, Katie M. OBrien, Kelly K. Ferguson, Shanshan Zhao, and
Alexandra J. White (2019) A quantile-based g-computation approach to
addressing the effects of exposure mixtures; <doi:10.1289/EHP5838>.
Author: Alexander Keil [aut, cre]
Maintainer: Alexander Keil <akeil@unc.edu>
Diff between qgcomp versions 2.6.0 dated 2020-10-06 and 2.7.0 dated 2021-01-26
qgcomp-2.6.0/qgcomp/tests/test_boot_vs_noboot.R |only qgcomp-2.6.0/qgcomp/tests/test_cox_msmtest.R |only qgcomp-2.6.0/qgcomp/tests/test_utilities.R |only qgcomp-2.6.0/qgcomp/tests/test_zi.R |only qgcomp-2.6.0/qgcomp/tests/test_zzzplots.R |only qgcomp-2.7.0/qgcomp/DESCRIPTION | 10 qgcomp-2.7.0/qgcomp/MD5 | 48 +- qgcomp-2.7.0/qgcomp/NEWS.md | 12 qgcomp-2.7.0/qgcomp/R/base.R | 41 + qgcomp-2.7.0/qgcomp/R/base_bounds.R | 102 ++-- qgcomp-2.7.0/qgcomp/R/base_extensions.R | 37 + qgcomp-2.7.0/qgcomp/R/base_hurdle.R | 30 - qgcomp-2.7.0/qgcomp/R/base_plots.R | 24 - qgcomp-2.7.0/qgcomp/R/base_samplesplits.R | 8 qgcomp-2.7.0/qgcomp/R/base_surv.R | 24 - qgcomp-2.7.0/qgcomp/R/base_zi.R | 36 - qgcomp-2.7.0/qgcomp/README.md | 4 qgcomp-2.7.0/qgcomp/build/vignette.rds |binary qgcomp-2.7.0/qgcomp/inst/doc/qgcomp-vignette.R | 100 ++-- qgcomp-2.7.0/qgcomp/inst/doc/qgcomp-vignette.Rmd | 229 +++++++--- qgcomp-2.7.0/qgcomp/inst/doc/qgcomp-vignette.html | 373 +++++++++++------ qgcomp-2.7.0/qgcomp/inst/fig/fighex.png |only qgcomp-2.7.0/qgcomp/man/mice.impute.leftcenslognorm.Rd | 25 - qgcomp-2.7.0/qgcomp/man/pointwisebound.noboot.Rd | 14 qgcomp-2.7.0/qgcomp/man/qgcomp.boot.Rd | 2 qgcomp-2.7.0/qgcomp/tests/test_id.R | 8 qgcomp-2.7.0/qgcomp/tests/test_mice.R | 54 ++ qgcomp-2.7.0/qgcomp/vignettes/qgcomp-vignette.Rmd | 229 +++++++--- 28 files changed, 928 insertions(+), 482 deletions(-)
Title: Parallel Chain Tools for Bayesian Kernel Machine Regression
Description: Bayesian kernel machine regression (from the 'bkmr'
package) is a Bayesian semi-parametric generalized linear model
approach under identity and probit links. There are a number of
functions in this package that extend Bayesian kernel machine
regression fits to allow multiple-chain inference and diagnostics,
which leverage functions from the 'future', 'rstan', and 'coda'
packages. Reference: Bobb, J. F., Henn, B. C., Valeri, L., & Coull,
B. A. (2018). Statistical software for analyzing the health effects of
multiple concurrent exposures via Bayesian kernel machine regression.
; <doi:10.1186/s12940-018-0413-y>.
Author: Alexander Keil [aut, cre]
Maintainer: Alexander Keil <akeil@unc.edu>
Diff between bkmrhat versions 1.0.0 dated 2020-10-12 and 1.0.1 dated 2021-01-26
DESCRIPTION | 10 MD5 | 14 NEWS.md | 12 R/continue_funs.R | 2 R/parallel_funs.R | 4 R/repacked_funs.R | 28 - build/vignette.rds |binary inst/doc/bkmrhat-vignette.html | 602 ++++++++++++++++++++--------------------- 8 files changed, 342 insertions(+), 330 deletions(-)
Title: Wraps 'CCM' with Utility Functions
Description: Provides a set of functions to perform queries against the 'CCM' API <https://mohcontacttracing.my.salesforce.com>.
Author: James Lane [aut, cre]
Maintainer: James Lane <lanejames35@gmail.com>
Diff between ccmReportR versions 0.0.2 dated 2021-01-19 and 0.0.3 dated 2021-01-26
DESCRIPTION | 11 +++++++---- LICENSE | 4 ++-- MD5 | 37 +++++++++++++++++++++++-------------- NAMESPACE | 4 ++++ NEWS.md |only R/getAttribute.R | 20 ++++++++++---------- R/getCaseAttribute.R | 12 ++++++------ R/getCases.R | 8 ++++---- R/getExposureAttribute.R |only R/getExposures.R |only R/getHealthUnitByName.R | 8 ++++---- R/getOutbreakAttribute.R |only R/getOutbreaks.R |only R/makeTimestamp.R | 6 +++--- README.md | 11 +++++++++-- man/getAttribute.Rd | 14 +++++++------- man/getCaseAttribute.Rd | 10 +++++----- man/getCases.Rd | 6 +++--- man/getExposureAttribute.Rd |only man/getExposures.Rd |only man/getHealthUnitByName.Rd | 6 +++--- man/getOutbreakAttribute.Rd |only man/getOutbreaks.Rd |only man/makeTimestamp.Rd | 6 +++--- 24 files changed, 93 insertions(+), 70 deletions(-)
Title: Create, Modify and Analyse Phylogenetic Trees
Description: Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of node support;
calculation of ancestor-descendant relationships;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <http://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.
Author: Martin R. Smith [aut, cre, cph]
(<https://orcid.org/0000-0001-5660-1727>),
Emmanuel Paradis [cph] (<https://orcid.org/0000-0003-3092-2199>)
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeTools versions 1.4.1 dated 2020-12-09 and 1.4.2 dated 2021-01-26
DESCRIPTION | 6 MD5 | 60 +++--- NEWS.md | 6 R/ArtificialExtinction.R | 3 R/Support.R | 2 R/parse_files.R | 14 - R/tree_rearrangement.R | 10 - R/zzz.R | 4 build/partial.rdb |binary inst/WORDLIST | 1 inst/doc/filesystem-navigation.html | 217 ++++++++++++++++++++---- inst/doc/load-data.html | 239 +++++++++++++++++++++++---- inst/doc/load-trees.html | 217 ++++++++++++++++++++---- inst/include/TreeTools/root_tree.h | 17 - man/CollapseNode.Rd | 4 man/LabelSplits.Rd | 11 + man/NSplits.Rd | 2 man/NTip.Rd | 2 man/SplitFrequency.Rd | 12 + man/SplitsInBinaryTree.Rd | 2 man/TipLabels.Rd | 2 man/TipsInSplits.Rd | 2 man/as.Splits.Rd | 2 man/match.Rd | 2 src/TreeTools-init.c | 28 +-- src/ape_reorder.h | 57 +++--- tests/testthat/test-Support.R | 1 tests/testthat/test-mst.R | 1 tests/testthat/test-root_tree.h.R | 14 + tests/testthat/test-tree_generation-random.R | 6 tests/testthat/test-tree_rearrange.R | 5 31 files changed, 748 insertions(+), 201 deletions(-)
Title: Soil Database Interface
Description: A collection of functions for reading data from USDA-NCSS soil databases.
Author: Dylan Beaudette [aut],
Jay Skovlin [aut],
Stephen Roecker [aut],
Andrew Brown [aut, cre]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>
Diff between soilDB versions 2.5.8 dated 2020-10-21 and 2.5.9 dated 2021-01-26
DESCRIPTION | 8 MD5 | 84 ++-- NAMESPACE | 12 NEWS.md | 8 R/AAAA.R | 14 R/ISSR800.R |only R/KSSL_VG_model.R | 62 +++ R/OSDquery.R | 74 ++++ R/ROSETTA.R |only R/SDA-spatial.R | 1 R/SDA_query.R | 4 R/WCS-utils.R |only R/fetchHenry.R | 36 -- R/fetchKSSL.R | 6 R/fetchNASIS_pedons.R | 508 ++++++++++++++---------------- R/fetchOSD.R | 8 R/fetchSDA_spatial.R | 251 +++++++++----- R/get_component_from_LIMS.R | 12 R/get_hz_data_from_NASIS_db.R | 2 R/mukey-WCS.R |only build |only data/gopheridge.rda |binary data/loafercreek.rda |binary data/mineralKing.rda |binary man/ISSR800.wcs.Rd |only man/KSSL_VG_model.Rd | 72 ++-- man/OSDquery.Rd | 125 ++++--- man/ROSETTA.Rd |only man/SDA_query.Rd | 2 man/WCS_details.Rd |only man/fetchHenry.Rd | 1 man/fetchNASISWebReport.Rd | 6 man/fetchOSD.Rd | 1 man/fetchSDA_spatial.Rd | 33 + man/mukey.wcs.Rd |only tests/testthat/test-ISSR800.R |only tests/testthat/test-OSDquery.R | 30 - tests/testthat/test-ROSETTA.R |only tests/testthat/test-SDA_query.R | 48 -- tests/testthat/test-fetchKSSL.R | 134 +++---- tests/testthat/test-fetchNASIS.R | 6 tests/testthat/test-fetchNASISWebReport.R | 74 +--- tests/testthat/test-fetchOSD.R | 104 ++---- tests/testthat/test-fetchSCAN.R | 30 - tests/testthat/test-fetchSDA_component.R | 44 -- tests/testthat/test-fetchSDA_spatial.R | 77 +++- tests/testthat/test-fetchSoilGrids.R | 34 -- tests/testthat/test-mukey-WCS.R |only tests/testthat/test-siblings.R | 34 -- 49 files changed, 1027 insertions(+), 918 deletions(-)
Title: Memoisation of Functions
Description: Cache the results of a function so that when you
call it again with the same arguments it returns the pre-computed
value.
Author: Hadley Wickham [aut],
Jim Hester [aut, cre],
Winston Chang [aut],
Kirill Müller [aut],
Daniel Cook [aut],
Mark Edmondson [ctb]
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between memoise versions 1.1.0 dated 2017-04-21 and 2.0.0 dated 2021-01-26
DESCRIPTION | 59 ++++++++--- MD5 | 39 ++++--- NAMESPACE | 4 NEWS.md | 20 +++ R/cache_filesystem.R | 15 ++ R/cache_gcs.R |only R/cache_memory.R | 6 + R/cache_s3.R | 16 ++- R/memoise.R | 196 +++++++++++++++++++++++++++------------ R/old_cache.R |only README.md | 186 +++++++++++++++++++++++++++---------- man/cache_filesystem.Rd | 5 man/cache_gcs.Rd |only man/cache_s3.Rd | 5 man/drop_cache.Rd |only man/has_cache.Rd | 8 - man/is.memoised.Rd | 4 man/memoise.Rd | 56 ++++++++--- tests/testthat/helper.R | 11 +- tests/testthat/test-filesystem.R | 3 tests/testthat/test-gcs.R |only tests/testthat/test-memoise.R | 119 +++++++++++++++++++++++ tests/testthat/test-s3.R | 5 23 files changed, 585 insertions(+), 172 deletions(-)
Title: Estimation Methods for Markets in Disequilibrium
Description: Provides estimation methods for markets in equilibrium and
disequilibrium. Specifically, it supports the estimation of an equilibrium and
four disequilibrium models with both correlated and independent shocks.
It also provides post-estimation analysis tools, such as aggregation and
marginal effects calculations. The estimation methods are based on full
information maximum likelihood techniques given in Maddala and Nelson (1974)
<doi:10.2307/1914215>. They are implemented using the analytic derivative
expressions calculated in Karapanagiotis (2020) <doi:10.2139/ssrn.3525622>.
The equilibrium estimation constitutes a special case of
a system of simultaneous equations. The disequilibrium models, instead, replace
the market clearing condition with a short side rule and
allow for different specifications of price dynamics.
Author: Pantelis Karapanagiotis [aut, cre]
(<https://orcid.org/0000-0001-9871-1908>)
Maintainer: Pantelis Karapanagiotis <pikappa.devel@gmail.com>
Diff between diseq versions 0.0.14 dated 2020-11-30 and 0.1.1 dated 2021-01-26
diseq-0.0.14/diseq/R/diseq_base.R |only diseq-0.0.14/diseq/R/eq_2sls.R |only diseq-0.0.14/diseq/R/eq_base.R |only diseq-0.0.14/diseq/R/eq_fiml.R |only diseq-0.0.14/diseq/R/model_base.R |only diseq-0.0.14/diseq/man/diseq_base-class.Rd |only diseq-0.0.14/diseq/man/eq_2sls-class.Rd |only diseq-0.0.14/diseq/man/eq_base-class.Rd |only diseq-0.0.14/diseq/man/eq_fiml-class.Rd |only diseq-0.0.14/diseq/man/initialize_model_base.Rd |only diseq-0.0.14/diseq/man/model_base-class.Rd |only diseq-0.0.14/diseq/tests/testthat/test-2sls.R |only diseq-0.0.14/diseq/tests/testthat/test-fiml.R |only diseq-0.1.1/diseq/DESCRIPTION | 32 diseq-0.1.1/diseq/LICENSE | 2 diseq-0.1.1/diseq/MD5 | 131 +-- diseq-0.1.1/diseq/NAMESPACE | 8 diseq-0.1.1/diseq/NEWS.md | 44 + diseq-0.1.1/diseq/R/diseq.R | 18 diseq-0.1.1/diseq/R/diseq_basic.R | 12 diseq-0.1.1/diseq/R/diseq_deterministic_adjustment.R | 12 diseq-0.1.1/diseq/R/diseq_directional.R | 12 diseq-0.1.1/diseq/R/diseq_stochastic_adjustment.R | 60 - diseq-0.1.1/diseq/R/disequilibrium_model.R |only diseq-0.1.1/diseq/R/equilibrium_model.R |only diseq-0.1.1/diseq/R/market_model.R |only diseq-0.1.1/diseq/R/model_simulation.R | 353 ++++----- diseq-0.1.1/diseq/README.md | 332 +++++--- diseq-0.1.1/diseq/build/partial.rdb |only diseq-0.1.1/diseq/build/vignette.rds |binary diseq-0.1.1/diseq/inst/WORDLIST | 4 diseq-0.1.1/diseq/inst/doc/basic_usage.R | 40 - diseq-0.1.1/diseq/inst/doc/basic_usage.Rmd | 49 - diseq-0.1.1/diseq/inst/doc/basic_usage.html | 381 ++++------ diseq-0.1.1/diseq/inst/doc/market_clearing_assessment.R | 50 - diseq-0.1.1/diseq/inst/doc/market_clearing_assessment.Rmd | 51 - diseq-0.1.1/diseq/inst/doc/market_clearing_assessment.html | 360 ++++----- diseq-0.1.1/diseq/man/diseq.Rd | 8 diseq-0.1.1/diseq/man/disequilibrium_model-class.Rd |only diseq-0.1.1/diseq/man/equilibrium_model-class.Rd |only diseq-0.1.1/diseq/man/estimate.Rd | 51 - diseq-0.1.1/diseq/man/figures/design.png |binary diseq-0.1.1/diseq/man/figures/diseq_basic_model.png |binary diseq-0.1.1/diseq/man/figures/diseq_deterministic_adjustment_model.png |binary diseq-0.1.1/diseq/man/figures/diseq_directional_model.png |binary diseq-0.1.1/diseq/man/figures/diseq_stochastic_adjustment_model.png |binary diseq-0.1.1/diseq/man/figures/equilibrium.png |binary diseq-0.1.1/diseq/man/figures/logo.png |binary diseq-0.1.1/diseq/man/get_aggregate_demand.Rd | 6 diseq-0.1.1/diseq/man/get_aggregate_supply.Rd | 6 diseq-0.1.1/diseq/man/get_demand_descriptives.Rd | 6 diseq-0.1.1/diseq/man/get_demanded_quantities.Rd | 6 diseq-0.1.1/diseq/man/get_marginal_effect_at_mean.Rd | 6 diseq-0.1.1/diseq/man/get_mean_marginal_effect.Rd | 6 diseq-0.1.1/diseq/man/get_model_description.Rd | 6 diseq-0.1.1/diseq/man/get_normalized_shortages.Rd | 6 diseq-0.1.1/diseq/man/get_number_of_observations.Rd | 6 diseq-0.1.1/diseq/man/get_relative_shortages.Rd | 6 diseq-0.1.1/diseq/man/get_shortage_probabilities.Rd | 6 diseq-0.1.1/diseq/man/get_supplied_quantities.Rd | 6 diseq-0.1.1/diseq/man/get_supply_descriptives.Rd | 6 diseq-0.1.1/diseq/man/has_shortage.Rd | 6 diseq-0.1.1/diseq/man/initialize_market_model.Rd |only diseq-0.1.1/diseq/man/market_model-class.Rd |only diseq-0.1.1/diseq/man/maximize_log_likelihood.Rd |only diseq-0.1.1/diseq/man/minus_log_likelihood.Rd | 12 diseq-0.1.1/diseq/man/scores.Rd | 8 diseq-0.1.1/diseq/man/simulate_model_data.Rd | 2 diseq-0.1.1/diseq/src |only diseq-0.1.1/diseq/tests/testthat/helper-common.R | 266 +++--- diseq-0.1.1/diseq/tests/testthat/test-basic.R | 26 diseq-0.1.1/diseq/tests/testthat/test-deterministic_adjustment.R | 34 diseq-0.1.1/diseq/tests/testthat/test-directional.R | 34 diseq-0.1.1/diseq/tests/testthat/test-equilibrium.R |only diseq-0.1.1/diseq/tests/testthat/test-stochastic_adjustment.R | 36 diseq-0.1.1/diseq/vignettes/basic_usage.Rmd | 49 - diseq-0.1.1/diseq/vignettes/market_clearing_assessment.Rmd | 51 - 77 files changed, 1316 insertions(+), 1296 deletions(-)
Title: Spatial Crop Water Demand for Brazil
Description: Estimation of crop water demand can be processed via this package. As example, the data from 'TerraClimate' dataset (<http://www.climatologylab.org/terraclimate.html>) calibrated with automatic weather stations of National Meteorological Institute of Brazil is available in a coarse spatial resolution to do the crop water demand. However, the user have also the option to download the variables directly from 'TerraClimate' repository with the download.terraclimate function and access the original 'TerraClimate' products. If the user believes that is necessary calibrate the variables, there is another function to do it. Lastly, the estimation of the crop water demand present in this package can be run for all the Brazilian territory with 'TerraClimate' dataset.
Author: Roberto Filgueiras [aut, cre] (<https://orcid.org/0000-0002-0186-8907>),
Luan P. Venancio [aut] (<https://orcid.org/0000-0002-5544-8588>),
Catariny C. Aleman [aut] (<https://orcid.org/0000-0002-3894-3077>),
Fernando F. da Cunha [aut] (<https://orcid.org/0000-0002-1671-1021>)
Maintainer: Roberto Filgueiras <betofilgueiras@gmail.com>
Diff between cropDemand versions 1.0.0 dated 2021-01-22 and 1.0.1 dated 2021-01-26
DESCRIPTION | 10 ++++---- MD5 | 41 ++++++++++++++++++----------------- NAMESPACE | 1 NEWS.md |only R/LoadROI.R | 1 R/WaterDemand.R | 50 +++++++++++++++++++++++++++---------------- R/calibration_ppt_etp.R | 15 ++++++------ R/download_terraclimate.R | 40 +++++++++++++++++----------------- R/monthly_stack.R | 1 R/plot_AWC.R | 2 - R/see_brazil_biomes.R | 3 +- R/see_brazil_states.R | 5 ++-- man/download_terraclimate.Rd | 11 ++++++--- man/eto_calibration.Rd | 11 +++++---- man/figures |only man/loadROI.Rd | 3 +- man/monthly_stack.Rd | 3 +- man/plot_AWC.Rd | 3 +- man/ppt_calibration.Rd | 3 +- man/see_brazil_biomes.Rd | 3 +- man/see_brazil_states.Rd | 5 ++-- man/waterDemand.Rd | 25 ++++++++++++++++----- 22 files changed, 141 insertions(+), 95 deletions(-)
Title: Understand and Describe Bayesian Models and Posterior
Distributions
Description: Provides utilities to describe posterior distributions and Bayesian models. It includes point-estimates such as Maximum A Posteriori (MAP), measures of dispersion (Highest Density Interval - HDI; Kruschke, 2015 <doi:10.1016/C2012-0-00477-2>) and indices used for null-hypothesis testing (such as ROPE percentage, pd and Bayes factors).
Author: Dominique Makowski [aut, cre] (<https://orcid.org/0000-0001-5375-9967>),
Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>),
Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>),
Michael D. Wilson [aut] (<https://orcid.org/0000-0003-4143-7308>),
Paul-Christian Bürkner [rev],
Tristan Mahr [rev] (<https://orcid.org/0000-0002-8890-5116>),
Henrik Singmann [ctb] (<https://orcid.org/0000-0002-4842-3657>),
Quentin F. Gronau [ctb] (<https://orcid.org/0000-0001-5510-6943>),
Sam Crawley [ctb] (<https://orcid.org/0000-0002-7847-0411>)
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between bayestestR versions 0.8.0 dated 2020-12-05 and 0.8.2 dated 2021-01-26
bayestestR-0.8.0/bayestestR/R/update.bayesfactor_models.R |only bayestestR-0.8.0/bayestestR/man/update.bayesfactor_models.Rd |only bayestestR-0.8.2/bayestestR/DESCRIPTION | 10 bayestestR-0.8.2/bayestestR/MD5 | 201 bayestestR-0.8.2/bayestestR/NAMESPACE | 24 bayestestR-0.8.2/bayestestR/NEWS.md | 23 bayestestR-0.8.2/bayestestR/R/backports.R |only bayestestR-0.8.2/bayestestR/R/bayesfactor.R | 27 bayestestR-0.8.2/bayestestR/R/bayesfactor_inclusion.R | 45 bayestestR-0.8.2/bayestestR/R/bayesfactor_models.R | 128 bayestestR-0.8.2/bayestestR/R/bayesfactor_parameters.R | 141 bayestestR-0.8.2/bayestestR/R/ci.R | 12 bayestestR-0.8.2/bayestestR/R/convert_bayesian_to_frequentist.R | 10 bayestestR-0.8.2/bayestestR/R/describe_posterior.R | 49 bayestestR-0.8.2/bayestestR/R/describe_prior.R | 4 bayestestR-0.8.2/bayestestR/R/diagnostic_posterior.R | 6 bayestestR-0.8.2/bayestestR/R/effective_sample.R | 4 bayestestR-0.8.2/bayestestR/R/equivalence_test.R | 14 bayestestR-0.8.2/bayestestR/R/estimate_density.R | 16 bayestestR-0.8.2/bayestestR/R/eti.R | 17 bayestestR-0.8.2/bayestestR/R/hdi.R | 22 bayestestR-0.8.2/bayestestR/R/map_estimate.R | 5 bayestestR-0.8.2/bayestestR/R/mcse.R | 5 bayestestR-0.8.2/bayestestR/R/mhdior.R | 15 bayestestR-0.8.2/bayestestR/R/p_direction.R | 12 bayestestR-0.8.2/bayestestR/R/p_map.R | 25 bayestestR-0.8.2/bayestestR/R/p_rope.R | 12 bayestestR-0.8.2/bayestestR/R/p_significance.R | 11 bayestestR-0.8.2/bayestestR/R/point_estimate.R | 30 bayestestR-0.8.2/bayestestR/R/print.bayesfactor_inclusion.R | 42 bayestestR-0.8.2/bayestestR/R/print.bayesfactor_models.R | 77 bayestestR-0.8.2/bayestestR/R/print.bayesfactor_parameters.R | 50 bayestestR-0.8.2/bayestestR/R/print.bayesfactor_restricted.R | 20 bayestestR-0.8.2/bayestestR/R/print.ci.R | 35 bayestestR-0.8.2/bayestestR/R/print.describe_posterior.R | 2 bayestestR-0.8.2/bayestestR/R/rope.R | 9 bayestestR-0.8.2/bayestestR/R/rope_range.R | 50 bayestestR-0.8.2/bayestestR/R/si.R | 2 bayestestR-0.8.2/bayestestR/R/simulate_priors.R | 5 bayestestR-0.8.2/bayestestR/R/utils_bayesfactor.R | 66 bayestestR-0.8.2/bayestestR/R/utils_hdi_ci.R | 8 bayestestR-0.8.2/bayestestR/R/weighted_posteriors.R | 1 bayestestR-0.8.2/bayestestR/R/zzz.R | 2 bayestestR-0.8.2/bayestestR/README.md | 109 bayestestR-0.8.2/bayestestR/build/partial.rdb |binary bayestestR-0.8.2/bayestestR/inst/doc/bayes_factors.R | 19 bayestestR-0.8.2/bayestestR/inst/doc/bayes_factors.Rmd | 54 bayestestR-0.8.2/bayestestR/inst/doc/bayes_factors.html | 993 bayestestR-0.8.2/bayestestR/inst/doc/bayestestR.html | 581 bayestestR-0.8.2/bayestestR/inst/doc/credible_interval.R | 44 bayestestR-0.8.2/bayestestR/inst/doc/credible_interval.Rmd | 52 bayestestR-0.8.2/bayestestR/inst/doc/credible_interval.html | 647 bayestestR-0.8.2/bayestestR/inst/doc/example1.html | 579 bayestestR-0.8.2/bayestestR/inst/doc/example2.html | 589 bayestestR-0.8.2/bayestestR/inst/doc/example3.html | 577 bayestestR-0.8.2/bayestestR/inst/doc/guidelines.html | 577 bayestestR-0.8.2/bayestestR/inst/doc/indicesEstimationComparison.html | 577 bayestestR-0.8.2/bayestestR/inst/doc/indicesExistenceComparison.html | 577 bayestestR-0.8.2/bayestestR/inst/doc/mediation.html |24683 +++++++++- bayestestR-0.8.2/bayestestR/inst/doc/probability_of_direction.html | 577 bayestestR-0.8.2/bayestestR/inst/doc/region_of_practical_equivalence.html | 577 bayestestR-0.8.2/bayestestR/man/bayesfactor.Rd | 37 bayestestR-0.8.2/bayestestR/man/bayesfactor_inclusion.Rd | 10 bayestestR-0.8.2/bayestestR/man/bayesfactor_models.Rd | 41 bayestestR-0.8.2/bayestestR/man/bayesfactor_parameters.Rd | 149 bayestestR-0.8.2/bayestestR/man/bayesfactor_restricted.Rd | 26 bayestestR-0.8.2/bayestestR/man/ci.Rd | 2 bayestestR-0.8.2/bayestestR/man/convert_bayesian_as_frequentist.Rd | 10 bayestestR-0.8.2/bayestestR/man/describe_posterior.Rd | 35 bayestestR-0.8.2/bayestestR/man/diagnostic_posterior.Rd | 17 bayestestR-0.8.2/bayestestR/man/effective_sample.Rd | 148 bayestestR-0.8.2/bayestestR/man/equivalence_test.Rd | 10 bayestestR-0.8.2/bayestestR/man/eti.Rd | 2 bayestestR-0.8.2/bayestestR/man/figures/unnamed-chunk-11-1.png |only bayestestR-0.8.2/bayestestR/man/figures/unnamed-chunk-13-1.png |only bayestestR-0.8.2/bayestestR/man/figures/unnamed-chunk-15-1.png |only bayestestR-0.8.2/bayestestR/man/figures/unnamed-chunk-17-1.png |only bayestestR-0.8.2/bayestestR/man/figures/unnamed-chunk-8-1.png |binary bayestestR-0.8.2/bayestestR/man/figures/unnamed-chunk-9-1.png |binary bayestestR-0.8.2/bayestestR/man/hdi.Rd | 2 bayestestR-0.8.2/bayestestR/man/map_estimate.Rd | 10 bayestestR-0.8.2/bayestestR/man/mcse.Rd | 105 bayestestR-0.8.2/bayestestR/man/mhdior.Rd | 10 bayestestR-0.8.2/bayestestR/man/p_direction.Rd | 10 bayestestR-0.8.2/bayestestR/man/p_map.Rd | 12 bayestestR-0.8.2/bayestestR/man/p_rope.Rd | 150 bayestestR-0.8.2/bayestestR/man/p_significance.Rd | 10 bayestestR-0.8.2/bayestestR/man/point_estimate.Rd | 15 bayestestR-0.8.2/bayestestR/man/rope.Rd | 10 bayestestR-0.8.2/bayestestR/man/si.Rd | 31 bayestestR-0.8.2/bayestestR/man/weighted_posteriors.Rd | 2 bayestestR-0.8.2/bayestestR/tests/testthat/test-BFBayesFactor.R | 9 bayestestR-0.8.2/bayestestR/tests/testthat/test-bayesfactor_models.R | 104 bayestestR-0.8.2/bayestestR/tests/testthat/test-bayesfactor_parameters.R | 40 bayestestR-0.8.2/bayestestR/tests/testthat/test-bayesfactor_restricted.R | 17 bayestestR-0.8.2/bayestestR/tests/testthat/test-brms.R | 65 bayestestR-0.8.2/bayestestR/tests/testthat/test-ci.R | 68 bayestestR-0.8.2/bayestestR/tests/testthat/test-describe_posterior.R | 69 bayestestR-0.8.2/bayestestR/tests/testthat/test-emmGrid.R | 103 bayestestR-0.8.2/bayestestR/tests/testthat/test-hdi.R | 26 bayestestR-0.8.2/bayestestR/tests/testthat/test-rstanarm.R | 68 bayestestR-0.8.2/bayestestR/tests/testthat/test-si.R | 30 bayestestR-0.8.2/bayestestR/tests/testthat/test-weighted_posteriors.R | 1 bayestestR-0.8.2/bayestestR/vignettes/bayes_factors.Rmd | 54 bayestestR-0.8.2/bayestestR/vignettes/credible_interval.Rmd | 52 105 files changed, 26146 insertions(+), 8463 deletions(-)
Title: Run Code 'With' Temporarily Modified Global State
Description: A set of functions to run code 'with' safely and
temporarily modified global state. Many of these functions were
originally a part of the 'devtools' package, this provides a simple
package with limited dependencies to provide access to these
functions.
Author: Jim Hester [aut, cre],
Kirill Müller [aut],
Kevin Ushey [aut],
Hadley Wickham [aut],
Winston Chang [aut],
Jennifer Bryan [ctb],
Richard Cotton [ctb],
RStudio [cph]
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between withr versions 2.4.0 dated 2021-01-15 and 2.4.1 dated 2021-01-26
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NEWS.md | 4 ++++ tests/testthat/test-devices.R | 19 ++++++++++++++----- 4 files changed, 26 insertions(+), 13 deletions(-)
Title: Online Retail Dataset
Description: Transactions occurring for a UK-based and registered, non-store online
retail between 01/12/2010 and 09/12/2011 (Chen et. al., 2012, <doi:10.1145/1835804.1835882>).
This dataset is included in this package with the donor's permission, Dr. Daqing Chen.
Author: Allan Quadros [aut, cre] (<https://orcid.org/0000-0003-3250-5380>)
Maintainer: Allan Quadros <allanvcq@gmail.com>
Diff between onlineretail versions 0.1.0 dated 2020-11-20 and 0.1.1 dated 2021-01-26
DESCRIPTION | 16 +++++++++------- MD5 | 4 ++-- README.md | 8 +++++--- 3 files changed, 16 insertions(+), 12 deletions(-)
Title: Estimation of the Generalised Beta Distribution of the Second
Kind from Grouped Data
Description: Estimation of the generalized beta distribution of the second
kind (GB2) and related models using grouped data in form of income shares.
The GB2 family is a general class of distributions that provides an accurate
fit to income data. 'GB2group' includes functions to estimate the GB2, the
Singh-Maddala, the Dagum, the Beta 2, the Lognormal and the Fisk distributions.
'GB2group' deploys two different econometric strategies to estimate these
parametric distributions, the equally weighted minimum distance (EWMD) estimator and the
optimally weighted minimum distance (OMD) estimator. Asymptotic standard errors are reported for the
OMD estimates. Standard errors of the EWMD estimates are obtained by Monte
Carlo simulation. See Jorda et al. (2018) <arXiv:1808.09831> for a detailed
description of the estimation procedure.
Author: Vanesa Jorda <jordav@unican.es>, Jose Maria Sarabia
<jose.sarabia@unican.es>, Markus Jäntti <markus.jantti@sofi.su.se>.
Maintainer: Vanesa Jorda <jordav@unican.es>
Diff between GB2group versions 0.2.0 dated 2019-02-21 and 0.3.0 dated 2021-01-26
DESCRIPTION | 14 ++++----- MD5 | 36 +++++++++++------------ R/fit.plot.R | 14 ++++----- R/fitgroup_b2.R | 60 ++++++++++++++++++--------------------- R/fitgroup_da.R | 60 ++++++++++++++++++--------------------- R/fitgroup_f.R | 60 ++++++++++++++++++--------------------- R/fitgroup_gb2.R | 78 ++++++++++++++++++++++++--------------------------- R/fitgroup_ln.R | 59 ++++++++++++++++++-------------------- R/fitgroup_sm.R | 60 ++++++++++++++++++--------------------- R/moments.R | 2 - R/simsd.R | 53 +++++++++++++++++----------------- R/weighting_matrix.R | 2 - man/fit.plot.Rd | 5 +-- man/fitgroup.b2.Rd | 66 ++++++++++++++++++++++++------------------- man/fitgroup.da.Rd | 66 ++++++++++++++++++++++++------------------- man/fitgroup.f.Rd | 66 ++++++++++++++++++++++++------------------- man/fitgroup.gb2.Rd | 66 ++++++++++++++++++++++++------------------- man/fitgroup.ln.Rd | 66 ++++++++++++++++++++++++------------------- man/fitgroup.sm.Rd | 66 ++++++++++++++++++++++++------------------- 19 files changed, 468 insertions(+), 431 deletions(-)
Title: Bayesian Test Reliability Estimation
Description: When samples contain missing data, are small, or are suspected of bias,
estimation of scale reliability may not be trustworthy. A recommended solution
for this common problem has been Bayesian model estimation. Bayesian methods
rely on user specified information from historical data or researcher intuition
to more accurately estimate the parameters. This package provides a user friendly
interface for estimating test reliability. Here, reliability is modeled as a beta
distributed random variable with shape parameters alpha=true score variance and
beta=error variance (Tanzer & Harlow, 2020) <doi:10.1080/00273171.2020.1854082>.
Author: Joshua Ray Tanzer
Maintainer: Joshua Ray Tanzer <jtanzer@lifespan.org>
Diff between brxx versions 0.1.1 dated 2020-12-02 and 0.1.2 dated 2021-01-26
DESCRIPTION | 10 ++-- MD5 | 44 ++++++++++++-------- NAMESPACE | 18 ++++++-- NEWS.md | 3 + R/Scree.R |only R/Summarize.R |only R/bcor.R | 49 +++++++--------------- R/bcov.R | 31 ++++++-------- R/bomega.R | 12 +++-- R/bomega_general.R | 14 +++--- R/brxx_Cor.R | 22 ++++------ R/brxx_Cor_general.R | 14 ++++-- R/brxx_ICC.R | 11 +++-- R/brxx_ICC_general.R | 11 +++-- R/brxx_general.R | 17 +++++-- R/prep.R |only R/process.R |only R/standardize.R | 23 ++++++---- R/unpack.R |only README.md | 110 +++++++++++++++++++++++++++++++++++++++++++++++++-- man/bcor.Rd | 83 +++++++++++++++++++------------------- man/bcov.Rd | 85 +++++++++++++++++++-------------------- man/prep.Rd |only man/process.Rd |only man/scree.Rd |only man/standardize.Rd | 8 +++ man/summarize.Rd |only man/unpack.Rd |only 28 files changed, 355 insertions(+), 210 deletions(-)
Title: R Implementation of Leiden Clustering Algorithm
Description: Implements the 'Python leidenalg' module to be called in R.
Enables clustering using the leiden algorithm for partition a graph into communities.
See the 'Python' repository for more details: <https://github.com/vtraag/leidenalg>
Traag et al (2018) From Louvain to Leiden: guaranteeing well-connected communities. <arXiv:1810.08473>.
Author: S. Thomas Kelly [aut, cre, trl],
Vincent A. Traag [com]
Maintainer: S. Thomas Kelly <tom.kelly@riken.jp>
Diff between leiden versions 0.3.6 dated 2020-12-07 and 0.3.7 dated 2021-01-26
DESCRIPTION | 12 +-- MD5 | 42 ++++++------ NEWS.md | 6 + R/leiden.R | 19 +++-- inst/CITATION | 4 - inst/doc/benchmarking.html | 134 ++++++++++++++++++++-------------------- inst/doc/run_bipartite.R | 1 inst/doc/run_bipartite.Rmd | 1 inst/doc/run_bipartite.html | 16 ++-- inst/doc/run_igraph.html | 30 ++++---- inst/doc/run_leiden.html | 32 ++++----- inst/doc/run_multiplex.R | 41 +++++------- inst/doc/run_multiplex.Rmd | 41 +++++------- inst/doc/run_multiplex.html | 70 ++++++++++---------- tests/testthat/test_bipartite.R | 1 tests/testthat/test_igraph.R | 3 tests/testthat/test_leiden.R | 1 tests/testthat/test_methods.R | 1 tests/testthat/test_multiplex.R | 1 tests/testthat/test_weighted.R | 1 vignettes/run_bipartite.Rmd | 1 vignettes/run_multiplex.Rmd | 41 +++++------- 22 files changed, 255 insertions(+), 244 deletions(-)
Title: Systematic Screening of Study Data for Subgroup Effects
Description: Identifying outcome relevant subgroups has now become as simple as possible! The formerly lengthy and tedious search for the needle in a haystack will be replaced by a single, comprehensive and coherent presentation.
The central result of a subgroup screening is a diagram in which each single dot stands for a subgroup.
The diagram may show thousands of them. The position of the dot in the diagram is determined by the
sample size of the subgroup and the statistical measure of the treatment effect in that subgroup. The
sample size is shown on the horizontal axis while the treatment effect is displayed on the vertical axis. Furthermore,
the diagram shows the line of no effect and the overall study results. For small subgroups, which
are found on the left side of the plot, larger random deviations from the mean study effect are expected,
while for larger subgroups only small deviations from the study mean can be expected to be chance findings.
So for a study with no conspicuous subgroup effects, the dots in the figure are expected to form a
kind of funnel. Any deviations from this funnel shape hint to conspicuous subgroups.
This approach was presented in Muysers (2020) <doi:10.1007/s43441-019-00082-6> and referenced in Ballarini (2020) <doi:10.1002/pst.2012>.
New to version 3 is the Automatic Screening of one- or MUlti-factorial Subgroups (ASMUS) for documentation of the structured review of subgroup findings.
Author: Bodo Kirsch, Steffen Jeske, Susanne Lippert, Thomas Schmelter, Christoph Muysers, Hermann Kulmann
Maintainer: Bodo Kirsch <bodo.kirsch@bayer.com>
Diff between subscreen versions 3.0.2 dated 2020-12-03 and 3.0.3 dated 2021-01-26
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 10 ++++++++++ R/subscreencalc.R | 4 +--- inst/doc/subscreen.html | 4 ++-- inst/shiny-app/subscreen/app.R | 21 +++++++++++++-------- 6 files changed, 34 insertions(+), 21 deletions(-)
Title: An R Client-Side Interface to the 'OpenSky' API
Description: Provides functionalities and data structures to retrieve, analyze
and visualize aviation data. It includes a client interface to the 'OpenSky'
API <https://opensky-network.org>. It allows retrieval of flight information,
as well as aircraft state vectors.
Author: Rafael Ayala, Daniel Ayala, David Ruiz, Aleix Sellés, Lara Sellés Vidal
Maintainer: Rafael Ayala <r.ayala14@imperial.ac.uk>
Diff between openSkies versions 0.99.8 dated 2020-12-04 and 1.0.0 dated 2021-01-26
openSkies-0.99.8/openSkies/R/openSkies_queryFunctions.R |only openSkies-1.0.0/openSkies/DESCRIPTION | 24 openSkies-1.0.0/openSkies/MD5 | 60 openSkies-1.0.0/openSkies/NAMESPACE | 32 openSkies-1.0.0/openSkies/NEWS | 14 openSkies-1.0.0/openSkies/R/openSkies_checkInputFunctions.R | 20 openSkies-1.0.0/openSkies/R/openSkies_classDecoder.R |only openSkies-1.0.0/openSkies/R/openSkies_classDefinitions.R |only openSkies-1.0.0/openSkies/R/openSkies_clusteringFunctions.R |only openSkies-1.0.0/openSkies/R/openSkies_formatResponseFunctions.R |only openSkies-1.0.0/openSkies/R/openSkies_getFlightsFunctions.R |only openSkies-1.0.0/openSkies/R/openSkies_getMetadataFunctions.R |only openSkies-1.0.0/openSkies/R/openSkies_getStateVectorsFunctions.R |only openSkies-1.0.0/openSkies/R/openSkies_otherSupportFunctions.R | 136 openSkies-1.0.0/openSkies/R/openSkies_plottingFunctions.R |only openSkies-1.0.0/openSkies/R/openSkies_variableDefinitions.R | 2 openSkies-1.0.0/openSkies/build/vignette.rds |binary openSkies-1.0.0/openSkies/inst/doc/openSkies.Rmd | 9 openSkies-1.0.0/openSkies/inst/doc/openSkies.html | 2714 +--------- openSkies-1.0.0/openSkies/inst/images |only openSkies-1.0.0/openSkies/inst/unitTests/test_all.R | 8 openSkies-1.0.0/openSkies/man/ADSBDecoder.Rd |only openSkies-1.0.0/openSkies/man/clusterRoutesDBSCAN.Rd |only openSkies-1.0.0/openSkies/man/getAircraftFlights.Rd | 37 openSkies-1.0.0/openSkies/man/getAircraftMetadata.Rd |only openSkies-1.0.0/openSkies/man/getAircraftStateVectorsSeries.Rd | 55 openSkies-1.0.0/openSkies/man/getAirportArrivals.Rd | 27 openSkies-1.0.0/openSkies/man/getAirportDepartures.Rd | 27 openSkies-1.0.0/openSkies/man/getAirportMetadata.Rd |only openSkies-1.0.0/openSkies/man/getIntervalFlights.Rd | 31 openSkies-1.0.0/openSkies/man/getRouteMetadata.Rd |only openSkies-1.0.0/openSkies/man/getSingleTimeStateVectors.Rd | 61 openSkies-1.0.0/openSkies/man/getVectorSetFeatures.Rd |only openSkies-1.0.0/openSkies/man/getVectorSetListFeatures.Rd |only openSkies-1.0.0/openSkies/man/openSkiesAircraft.Rd |only openSkies-1.0.0/openSkies/man/openSkiesAirport.Rd |only openSkies-1.0.0/openSkies/man/openSkiesFlight.Rd |only openSkies-1.0.0/openSkies/man/openSkiesRoute.Rd |only openSkies-1.0.0/openSkies/man/openSkiesStateVector.Rd |only openSkies-1.0.0/openSkies/man/openSkiesStateVectorSet.Rd |only openSkies-1.0.0/openSkies/man/plotPlanes.Rd |only openSkies-1.0.0/openSkies/man/plotRoute.Rd |only openSkies-1.0.0/openSkies/man/plotRoutes.Rd |only openSkies-1.0.0/openSkies/vignettes/openSkies.Rmd | 9 44 files changed, 738 insertions(+), 2528 deletions(-)
More information about StratifiedSampling at CRAN
Permanent link
Title: A simple interface to the PROJ.4 cartographic projections
library
Description: A simple interface to lat/long projection and datum
transformation of the PROJ.4 cartographic projections library. It
allows transformation of geographic coordinates from one projection
and/or datum to another.
Author: Simon Urbanek <simon.urbanek@r-project.org>
Maintainer: Simon Urbanek <simon.urbanek@r-project.org>
Diff between proj4 versions 1.0-10 dated 2020-03-02 and 1.0-10.1 dated 2021-01-26
DESCRIPTION | 6 MD5 | 6 configure | 600 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++- configure.ac | 7 4 files changed, 603 insertions(+), 16 deletions(-)
Title: Synthetic Population Generator
Description: Generates high-entropy integer synthetic populations from marginal and (optionally) seed data using quasirandom sampling,
in arbitrary dimensionality (Smith, Lovelace and Birkin (2017) <doi:10.18564/jasss.3550>).
The package also provides an implementation of the Iterative Proportional Fitting (IPF) algorithm (Zaloznik (2011) <doi:10.13140/2.1.2480.9923>).
Author: Andrew Smith [aut, cre],
Steven Johnson [ctb] (Sobol sequence generator implementation),
Massachusetts Institute of Technology [cph] (Sobol sequence generator
implementation),
John Burkhardt [ctb, cph] (C++ implementation of incomplete gamma
function),
G Bhattacharjee [ctb] (Original FORTRAN implementation of incomplete
gamma function)
Maintainer: Andrew Smith <andrew@friarswood.net>
Diff between humanleague versions 2.1.2 dated 2020-02-14 and 2.1.8 dated 2021-01-26
humanleague-2.1.2/humanleague/README.md |only humanleague-2.1.2/humanleague/tests/__pycache__ |only humanleague-2.1.2/humanleague/tests/test_all.py |only humanleague-2.1.8/humanleague/DESCRIPTION | 10 ++--- humanleague-2.1.8/humanleague/MD5 | 20 +++++------ humanleague-2.1.8/humanleague/src/IPF.h | 35 ++++++++++---------- humanleague-2.1.8/humanleague/src/Makevars | 2 - humanleague-2.1.8/humanleague/src/Microsynthesis.h | 6 +-- humanleague-2.1.8/humanleague/src/NDArrayUtils.h | 3 + humanleague-2.1.8/humanleague/src/TestStatFuncs.cpp | 1 humanleague-2.1.8/humanleague/src/UnitTester.cpp | 2 - humanleague-2.1.8/humanleague/src/UnitTester.h | 2 - humanleague-2.1.8/humanleague/src/module.cpp |only 13 files changed, 41 insertions(+), 40 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-06-28 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-20 0.2.0
2017-11-13 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-16 0.6.7
2019-10-14 0.6.6
2019-04-05 0.6.5
2019-03-11 0.6.4
2019-01-11 0.6.3
2019-01-10 0.6.2
2018-10-22 0.6.1
2018-10-09 0.6.0
2018-07-01 0.5.3
2018-06-25 0.5.2
2017-11-25 0.5.1
2017-11-22 0.5.0
2017-09-16 0.4.0
2017-07-15 0.3.5
2017-06-26 0.3.4
2017-06-18 0.3.3
2017-06-09 0.3.2
2017-06-08 0.3.1
2017-06-07 0.3.0
2017-01-20 0.2.0
2016-12-28 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-24 0.4.2
Title: Utilities for Working with NEON Data
Description: NEON data packages can be accessed through the NEON Data Portal <https://data.neonscience.org/home>
or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from
the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files
can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting
data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and
converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.
Author: Claire Lunch [aut, cre, ctb],
Christine Laney [aut, ctb],
Nathan Mietkiewicz [aut, ctb],
Eric Sokol [aut, ctb],
Kaelin Cawley [aut, ctb],
NEON (National Ecological Observatory Network) [aut]
Maintainer: Claire Lunch <clunch@battelleecology.org>
Diff between neonUtilities versions 1.3.9 dated 2021-01-12 and 2.0.0 dated 2021-01-26
neonUtilities-1.3.9/neonUtilities/tests/testthat/test_getDatatable.R |only neonUtilities-2.0.0/neonUtilities/DESCRIPTION | 12 neonUtilities-2.0.0/neonUtilities/MD5 | 57 +-- neonUtilities-2.0.0/neonUtilities/NAMESPACE | 5 neonUtilities-2.0.0/neonUtilities/R/byTileAOP.R | 12 neonUtilities-2.0.0/neonUtilities/R/findTablesByFormat.R | 2 neonUtilities-2.0.0/neonUtilities/R/getAPIHeaders.R |only neonUtilities-2.0.0/neonUtilities/R/getDatatable.R | 147 -------- neonUtilities-2.0.0/neonUtilities/R/getReadmePublicationDate.R | 23 - neonUtilities-2.0.0/neonUtilities/R/getZipUrls.R | 183 +++++++--- neonUtilities-2.0.0/neonUtilities/R/listFilesInZip.R | 2 neonUtilities-2.0.0/neonUtilities/R/listZipfiles.R | 2 neonUtilities-2.0.0/neonUtilities/R/loadByProduct.R | 7 neonUtilities-2.0.0/neonUtilities/R/makePosColumns.R | 11 neonUtilities-2.0.0/neonUtilities/R/stackByTable.R | 30 + neonUtilities-2.0.0/neonUtilities/R/stackDataFilesParallel.R | 67 ++- neonUtilities-2.0.0/neonUtilities/R/stackEddy.R | 6 neonUtilities-2.0.0/neonUtilities/R/stackFromStore.R | 56 ++- neonUtilities-2.0.0/neonUtilities/R/sysdata.rda |binary neonUtilities-2.0.0/neonUtilities/R/zipsByProduct.R | 41 +- neonUtilities-2.0.0/neonUtilities/README.md | 18 neonUtilities-2.0.0/neonUtilities/data/chem_bundles.rda |binary neonUtilities-2.0.0/neonUtilities/data/shared_aquatic.rda |binary neonUtilities-2.0.0/neonUtilities/data/shared_flights.rda |binary neonUtilities-2.0.0/neonUtilities/data/table_types.rda |binary neonUtilities-2.0.0/neonUtilities/man/getAPIHeaders.Rd |only neonUtilities-2.0.0/neonUtilities/man/getDatatable.Rd | 10 neonUtilities-2.0.0/neonUtilities/man/getZipUrls.Rd | 12 neonUtilities-2.0.0/neonUtilities/man/loadByProduct.Rd | 5 neonUtilities-2.0.0/neonUtilities/man/stackFromStore.Rd | 9 neonUtilities-2.0.0/neonUtilities/man/zipsByProduct.Rd | 5 31 files changed, 395 insertions(+), 327 deletions(-)
Title: Multi-Group Sparse Discriminant Analysis
Description: Implements Multi-Group Sparse Discriminant Analysis proposal of I.Gaynanova, J.Booth and M.Wells (2016), Simultaneous sparse estimation of canonical vectors in the p>>N setting, JASA <doi:10.1080/01621459.2015.1034318>.
Author: Irina Gaynanova
Maintainer: Irina Gaynanova <irinag@stat.tamu.edu>
Diff between MGSDA versions 1.4 dated 2016-06-13 and 1.5 dated 2021-01-26
DESCRIPTION | 10 +++++----- MD5 | 14 ++++++++------ NAMESPACE | 6 ++++-- README.md |only man/MGSDA-package.Rd | 8 ++++---- man/classifyV.Rd | 2 +- man/cv.dLDA.Rd | 2 +- man/dLDA.Rd | 2 +- src/MGSDA_init.c |only 9 files changed, 24 insertions(+), 20 deletions(-)
Title: Case-Wise and Cluster-Wise Derivatives for Mixed Effects Models
Description: Compute case-wise and cluster-wise derivative for mixed effects models with respect to fixed effects parameter, random effect (co)variances, and residual variance. This material is partially based on work supported by the National Science Foundation under Grant Number 1460719.
Author: Ting Wang [aut, cre],
Edgar Merkle [aut] (<https://orcid.org/0000-0001-7158-0653>),
Yves Rosseel [ctb]
Maintainer: Ting Wang <twb8d@mail.missouri.edu>
Diff between merDeriv versions 0.2-2 dated 2020-10-22 and 0.2-3 dated 2021-01-26
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 3 +++ R/estfun.lmerMod.R | 2 +- R/vcov.lmerMod.R | 2 +- build/partial.rdb |binary inst/tinytest/test_merDeriv.R | 12 ++++++++++++ 7 files changed, 27 insertions(+), 12 deletions(-)
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>
Diff between aqp versions 1.25 dated 2020-10-19 and 1.27 dated 2021-01-26
aqp-1.25/aqp/R/SPC-find_horizons.R |only aqp-1.25/aqp/R/psimplify.R |only aqp-1.25/aqp/R/sketch.R |only aqp-1.25/aqp/man/SPC-slab-methods.Rd |only aqp-1.25/aqp/man/SPC-slice-methods.Rd |only aqp-1.25/aqp/man/dot-parseHSD_formula.Rd |only aqp-1.25/aqp/man/fixOverlap.Rd |only aqp-1.25/aqp/man/profile_compare-methods.Rd |only aqp-1.25/aqp/man/subsetProfiles-methods.Rd |only aqp-1.25/aqp/man/texcl_to_ssc.Rd |only aqp-1.27/aqp/DESCRIPTION | 16 aqp-1.27/aqp/MD5 | 433 +- aqp-1.27/aqp/NAMESPACE | 6 aqp-1.27/aqp/NEWS.md | 43 aqp-1.27/aqp/R/Class-SoilProfileCollection.R | 195 - aqp-1.27/aqp/R/L1_profiles.R |only aqp-1.27/aqp/R/SoilProfileCollection-integrity.R | 4 aqp-1.27/aqp/R/SoilProfileCollection-iterators.R | 2 aqp-1.27/aqp/R/SoilProfileCollection-methods.R | 69 aqp-1.27/aqp/R/SoilProfileCollection-operators.R | 4 aqp-1.27/aqp/R/SoilProfileCollection-setters.R | 45 aqp-1.27/aqp/R/SoilProfileCollection-slice-methods.R | 560 +- aqp-1.27/aqp/R/accuracy_uncertainty.R | 217 - aqp-1.27/aqp/R/addBracket.R | 241 + aqp-1.27/aqp/R/addVolumeFraction.R | 24 aqp-1.27/aqp/R/aggregateColor.R | 181 aqp-1.27/aqp/R/aggregateSoilDepth.R | 131 aqp-1.27/aqp/R/allocate.R |only aqp-1.27/aqp/R/aqp-package.R |only aqp-1.27/aqp/R/bootstrapSoilTexture.R | 2 aqp-1.27/aqp/R/checkHzDepthLogic.R | 161 aqp-1.27/aqp/R/checkSPC.R | 13 aqp-1.27/aqp/R/colorContrast.R | 64 aqp-1.27/aqp/R/colorContrastPlot.R | 186 aqp-1.27/aqp/R/colorQuantiles.R | 242 + aqp-1.27/aqp/R/combine.R | 5 aqp-1.27/aqp/R/contrastChart.R | 107 aqp-1.27/aqp/R/contrastClass.R | 203 - aqp-1.27/aqp/R/data-documentation.R | 1937 +++++++++- aqp-1.27/aqp/R/denormalize.R | 120 aqp-1.27/aqp/R/depthOf.R | 4 aqp-1.27/aqp/R/duplicate.R | 4 aqp-1.27/aqp/R/estimatePSCS.R | 54 aqp-1.27/aqp/R/estimateSoilDepth.R | 2 aqp-1.27/aqp/R/evalGenHz.R | 80 aqp-1.27/aqp/R/evalMissingData.R | 197 - aqp-1.27/aqp/R/explainPlotSPC.R | 196 - aqp-1.27/aqp/R/f.noise.R | 241 - aqp-1.27/aqp/R/factor-level-setters.R | 1 aqp-1.27/aqp/R/findOverlap-fixOverlap.R |only aqp-1.27/aqp/R/generalize.hz.R | 147 aqp-1.27/aqp/R/get.increase.matrix.R | 124 aqp-1.27/aqp/R/get.ml.hz.R | 227 - aqp-1.27/aqp/R/getArgillicBounds.R | 85 aqp-1.27/aqp/R/getCambicBounds.R | 2 aqp-1.27/aqp/R/getClosestMunsellChip.R |only aqp-1.27/aqp/R/getSoilDepthClass.R | 59 aqp-1.27/aqp/R/glomApply.R | 2 aqp-1.27/aqp/R/group_by.R | 100 aqp-1.27/aqp/R/groupedProfilePlot.R | 251 - aqp-1.27/aqp/R/guessGenHzLevels.R | 79 aqp-1.27/aqp/R/harmonize.R | 12 aqp-1.27/aqp/R/huePosition.R | 77 aqp-1.27/aqp/R/hzBoundary.R | 278 - aqp-1.27/aqp/R/hzTransitionProbabilities.R | 256 - aqp-1.27/aqp/R/missingDataGrid.R | 86 aqp-1.27/aqp/R/mixMunsell.R | 204 - aqp-1.27/aqp/R/munsell2rgb.R | 439 +- aqp-1.27/aqp/R/mutate_profile.R | 141 aqp-1.27/aqp/R/panel.depth_function.R | 380 + aqp-1.27/aqp/R/permute_profile.R | 34 aqp-1.27/aqp/R/plotMultipleSPC.R | 222 - aqp-1.27/aqp/R/plotSPC.R | 540 +- aqp-1.27/aqp/R/plot_distance_graph.R | 127 aqp-1.27/aqp/R/previewColors.R | 58 aqp-1.27/aqp/R/profile_compare.R | 200 + aqp-1.27/aqp/R/random_profile.R | 393 +- aqp-1.27/aqp/R/rebuildSPC.R | 25 aqp-1.27/aqp/R/resample.twotheta.R | 80 aqp-1.27/aqp/R/segment.R | 146 aqp-1.27/aqp/R/sim.R | 235 - aqp-1.27/aqp/R/similarMunsellChips.R |only aqp-1.27/aqp/R/sketch-utils.R | 340 - aqp-1.27/aqp/R/slab.R | 491 ++ aqp-1.27/aqp/R/slicedHSD.R | 11 aqp-1.27/aqp/R/soilColorIndices.R | 136 aqp-1.27/aqp/R/soilColorSignature.R | 516 +- aqp-1.27/aqp/R/soiltexture.R |only aqp-1.27/aqp/R/spc2mpspline.R | 2 aqp-1.27/aqp/R/split.R | 2 aqp-1.27/aqp/R/splitLogicErrors.R |only aqp-1.27/aqp/R/tauW.R | 98 aqp-1.27/aqp/R/test_hz_logic.R | 88 aqp-1.27/aqp/R/texture.R | 327 + aqp-1.27/aqp/R/textureTriangleSummary.R | 2 aqp-1.27/aqp/R/unroll.R | 152 aqp-1.27/aqp/build |only aqp-1.27/aqp/data/datalist | 1 aqp-1.27/aqp/data/equivalent_munsell.rda |only aqp-1.27/aqp/demo/aqp.R | 317 - 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Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-15 0.21.01
2020-06-12 0.20.06
2020-03-02 0.20.03
2020-01-27 0.20.01
2019-10-07 0.19.10
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-10-24 1.1.2
2019-01-19 1.1.1
2019-01-07 1.1
2016-11-29 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-15 2.8
2020-09-04 2.7
2020-09-02 2.6
2020-03-20 2.5
2019-03-15 2.4
2018-07-26 2.3
2017-02-27 2.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-25 0.2.7
2020-12-07 0.2.6
2020-03-18 0.2.5
2019-04-15 0.2.4
2019-03-21 0.2.3
2019-01-21 0.2.2
2018-05-09 0.2.1
2017-07-10 0.1.3
2016-04-06 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-20 1.5.2
2020-09-12 1.5.1
2020-04-29 1.4.6
2019-01-03 1.4.5
2017-12-16 1.4.4
2017-03-06 1.4.3
2017-02-23 1.4.2
2016-02-06 1.4.1
2015-08-23 1.4.0
2014-02-20 1.3.9
2013-06-20 1.3.7
2013-03-28 1.3.6
2012-08-16 1.3.5
2012-05-08 1.3.4
2012-04-05 1.3.3
2012-03-28 1.3.2
2012-03-12 1.3.1
2012-02-06 1.2.9
2011-10-06 1.2.7
2011-05-27 1.2.6
2011-04-04 1.2.5
2011-03-01 1.2.4
2010-11-29 1.2.3
2010-10-07 1.2.2
2010-10-06 1.2.1
2010-09-15 1.2
2010-08-05 1.1
2010-06-13 1.0
2010-06-08 0.9.9
2010-04-25 0.9.8
2010-02-05 0.9.7
2009-10-21 0.9.6
2009-02-15 0.9.5
2008-11-04 0.9.4
2008-10-24 0.9.3
2008-10-23 0.9.2
2008-06-13 0.9.1
2008-01-29 0.9.0
2008-01-28 0.8.9
2008-01-13 0.8.7
2008-01-08 0.8.6
2007-11-09 0.8.4
2007-11-09 0.8.5
2007-10-19 0.8.3
2007-07-13 0.8.2
2007-07-09 0.8.1
2007-07-08 0.8.0
2007-02-17 0.7-8
Title: Downloading, Reading and Analysing PNADC Microdata
Description: Provides tools for downloading, reading and analysing the PNADC,
a household survey from Brazilian Institute of Geography and Statistics - IBGE.
The data must be downloaded from the official website <https://www.ibge.gov.br/>.
Further analysis must be made using package 'survey'.
Author: Douglas Braga [aut],
Gabriel Assuncao [aut, cre],
Luna Hidalgo [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>
Diff between PNADcIBGE versions 0.6.1 dated 2020-12-11 and 0.6.2 dated 2021-01-26
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- R/get_pnadc.R | 2 +- R/pnadc_deflator.R | 4 ++-- R/pnadc_labeller.R | 2 +- R/read_pnadc.R | 6 +++--- man/get_pnadc.Rd | 2 +- man/pnadc_deflator.Rd | 4 ++-- man/pnadc_labeller.Rd | 2 +- man/read_pnadc.Rd | 6 +++--- 10 files changed, 29 insertions(+), 29 deletions(-)
Title: Downloading, Reading and Analysing PNAD COVID19 Microdata
Description: Provides tools for downloading, reading and analysing the PNAD COVID19,
a household survey from Brazilian Institute of Geography and Statistics - IBGE.
The data must be downloaded from the official website <https://www.ibge.gov.br/>.
Further analysis must be made using package 'survey'.
Author: Gabriel Assuncao [aut, cre],
Luna Hidalgo [aut],
Douglas Braga [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>
Diff between COVIDIBGE versions 0.1.0 dated 2020-12-16 and 0.1.1 dated 2021-01-26
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- R/covid_deflator.R | 4 ++-- R/covid_labeller.R | 2 +- R/get_covid.R | 2 +- R/read_covid.R | 4 ++-- man/covid_deflator.Rd | 4 ++-- man/covid_labeller.Rd | 2 +- man/get_covid.Rd | 2 +- man/read_covid.Rd | 4 ++-- 10 files changed, 27 insertions(+), 27 deletions(-)
Title: Unbiased Single-Cell Transcriptomic Data Cell Type
Identification
Description: Assignment of cell type labels to single-cell RNA sequencing (scRNA-seq) clusters is often a time-consuming process that involves manual inspection of the cluster marker genes complemented with a detailed literature search. This is especially challenging when unexpected or poorly described populations are present. The clustermole R package provides methods to query thousands of human and mouse cell identity markers sourced from a variety of databases.
Author: Igor Dolgalev [aut, cre]
Maintainer: Igor Dolgalev <igor.dolgalev@nyumc.org>
Diff between clustermole versions 1.0.1 dated 2020-01-27 and 1.1.0 dated 2021-01-26
clustermole-1.0.1/clustermole/R/functions.R |only clustermole-1.0.1/clustermole/tests/testthat/test-functions.R |only clustermole-1.1.0/clustermole/DESCRIPTION | 17 clustermole-1.1.0/clustermole/MD5 | 39 clustermole-1.1.0/clustermole/NAMESPACE | 5 clustermole-1.1.0/clustermole/NEWS.md | 6 clustermole-1.1.0/clustermole/R/enrichment.R |only clustermole-1.1.0/clustermole/R/markers.R |only clustermole-1.1.0/clustermole/R/overlaps.R |only clustermole-1.1.0/clustermole/R/sysdata.rda |binary clustermole-1.1.0/clustermole/R/utils.R |only clustermole-1.1.0/clustermole/README.md | 55 - clustermole-1.1.0/clustermole/build/partial.rdb |only clustermole-1.1.0/clustermole/build/vignette.rds |binary clustermole-1.1.0/clustermole/inst/doc/clustermole-intro.R | 37 clustermole-1.1.0/clustermole/inst/doc/clustermole-intro.Rmd | 103 -- clustermole-1.1.0/clustermole/inst/doc/clustermole-intro.html | 443 ++++++---- clustermole-1.1.0/clustermole/man/clustermole_enrichment.Rd | 21 clustermole-1.1.0/clustermole/man/clustermole_markers.Rd | 12 clustermole-1.1.0/clustermole/man/clustermole_overlaps.Rd | 8 clustermole-1.1.0/clustermole/man/read_gmt.Rd | 2 clustermole-1.1.0/clustermole/tests/testthat/test-enrichment.R |only clustermole-1.1.0/clustermole/tests/testthat/test-markers.R |only clustermole-1.1.0/clustermole/tests/testthat/test-overlaps.R |only clustermole-1.1.0/clustermole/tests/testthat/test-utils.R |only clustermole-1.1.0/clustermole/vignettes/clustermole-intro.Rmd | 103 -- 26 files changed, 435 insertions(+), 416 deletions(-)
Title: Bayesian Modeling and Analysis of Spatially Correlated Survival
Data
Description: Provides several Bayesian survival models for spatial/non-spatial survival data: proportional hazards (PH), accelerated failure time (AFT), proportional odds (PO), and accelerated hazards (AH), a super model that includes PH, AFT, PO and AH as special cases, Bayesian nonparametric nonproportional hazards (LDDPM), generalized accelerated failure time (GAFT), and spatially smoothed Polya tree density estimation. The spatial dependence is modeled via frailties under PH, AFT, PO, AH and GAFT, and via copulas under LDDPM and PH. Model choice is carried out via the logarithm of the pseudo marginal likelihood (LPML), the deviance information criterion (DIC), and the Watanabe-Akaike information criterion (WAIC). See Zhou, Hanson and Zhang (2020) <doi:10.18637/jss.v092.i09>.
Author: Haiming Zhou <zhouh@niu.edu> and Timothy Hanson <hansont@stat.sc.edu>
Maintainer: Haiming Zhou <zhouh@niu.edu>
Diff between spBayesSurv versions 1.1.4 dated 2020-02-23 and 1.1.5 dated 2021-01-26
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- src/spSurv_SpatDens.cpp | 14 ++++++-------- src/spSurv_common.cpp | 6 ------ src/spSurv_common.h | 4 ---- 5 files changed, 14 insertions(+), 26 deletions(-)