Title: Score Test Based on Saddlepoint Approximation
Description: Performs score test using saddlepoint approximation to estimate the null distribution.
Author: Rounak Dey, Seunggeun Lee
Maintainer: Rounak Dey <deyrnk@umich.edu>
Diff between SPAtest versions 1.1.1 dated 2017-06-22 and 2.0.0 dated 2017-09-17
DESCRIPTION | 8 +- MD5 | 6 - R/SPA_functions.R | 169 +++++++++++++++++++++++++++++++++++++++++++++------ man/ScoreTest_SPA.Rd | 28 +++++++- 4 files changed, 182 insertions(+), 29 deletions(-)
Title: Neyman-Pearson (NP) Classification Algorithms and NP Receiver
Operating Characteristic (NP-ROC) Curves
Description: In many binary classification applications, such as disease
diagnosis and spam detection, practitioners commonly face the need to limit
type I error (i.e., the conditional probability of misclassifying a class 0
observation as class 1) so that it remains below a desired threshold. To address
this need, the Neyman-Pearson (NP) classification paradigm is a natural choice;
it minimizes type II error (i.e., the conditional probability of misclassifying
a class 1 observation as class 0) while enforcing an upper bound, alpha, on the
type I error. Although the NP paradigm has a century-long history in hypothesis
testing, it has not been well recognized and implemented in classification
schemes. Common practices that directly limit the empirical type I error to
no more than alpha do not satisfy the type I error control objective because
the resulting classifiers are still likely to have type I errors much larger
than alpha. As a result, the NP paradigm has not been properly implemented
for many classification scenarios in practice. In this work, we develop the
first umbrella algorithm that implements the NP paradigm for all scoring-type
classification methods, including popular methods such as logistic regression,
support vector machines and random forests. Powered by this umbrella algorithm,
we propose a novel graphical tool for NP classification methods: NP receiver
operating characteristic (NP-ROC) bands, motivated by the popular receiver
operating characteristic (ROC) curves. NP-ROC bands will help choose in a data
adaptive way and compare different NP classifiers. The paper is available at
<arXiv:1608.03109>.
Author: Yang Feng, Jingyi Jessica Li and Xin Tong
Maintainer: Yang Feng <yang.feng@columbia.edu>
Diff between nproc versions 2.0.8 dated 2017-09-01 and 2.0.9 dated 2017-09-17
ChangeLog | 3 + DESCRIPTION | 33 ++++++++++++-- MD5 | 46 ++++++++++---------- R/compare.R | 4 - R/lines.nproc.R | 2 R/npc.R | 10 ++-- R/npfuns.R | 102 +++++++++++++++++++++++----------------------- R/nproc.R | 12 +++-- R/plot.nproc.R | 4 - R/predict.npc.R | 19 ++++---- build/vignette.rds |binary inst/doc/nproc-demo.R | 4 - inst/doc/nproc-demo.Rmd | 11 +++- inst/doc/nproc-demo.pdf |binary inst/nproc |only man/compare.Rd | 1 man/lines.nproc.Rd | 3 - man/npc.Rd | 9 ++-- man/nproc.Rd | 1 man/plot.nproc.Rd | 3 - man/predict.npc.Rd | 1 man/rocCV.Rd | 1 vignettes/nproc-demo.Rmd | 11 +++- vignettes/nproc-demo.html | 58 +++++++++++++------------- 24 files changed, 195 insertions(+), 143 deletions(-)
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. 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>
Diff between mgcv versions 1.8-20 dated 2017-09-09 and 1.8-21 dated 2017-09-17
ChangeLog | 17 DESCRIPTION | 6 MD5 | 34 - NAMESPACE | 2 R/bam.r | 12 R/fast-REML.r | 2 R/gam.fit3.r | 212 +++----- R/gam.fit4.r | 22 R/mgcv.r | 8 man/smooth.construct.tp.smooth.spec.Rd | 18 src/gdi.c | 238 --------- src/init.c | 2 src/matrix.c | 822 --------------------------------- src/matrix.h | 13 src/mgcv.c | 16 src/mgcv.h | 2 src/qp.c | 43 - src/qp.h | 2 18 files changed, 210 insertions(+), 1261 deletions(-)
Title: Trust, but Verify
Description: Declarative template-based framework for verifying that objects
meet structural requirements, and auto-composing error messages when they do
not.
Author: Brodie Gaslam [aut, cre],
Paxdiablo [cph] (Hash table implementation in src/pfhash.h),
R Core Team [cph] (Used/adapted several code snippets from R sources,
see src/misc-alike.c and src/valname.c)
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between vetr versions 0.1.0 dated 2017-07-08 and 0.2.0 dated 2017-09-17
DESCRIPTION | 8 MD5 | 148 ++- NAMESPACE | 1 NEWS.md | 55 + R/all-bw.R |only R/benchmark.R | 12 R/cstringr.R | 32 R/misc.R | 10 R/settings.R | 11 R/system.R | 5 R/type.R | 12 R/validate.R | 23 R/validators.R | 6 README.md | 139 ++- build/vignette.rds |binary inst/doc/alike.R | 2 inst/doc/alike.Rmd | 4 inst/doc/alike.html | 136 +-- inst/doc/vetr.R | 25 inst/doc/vetr.Rmd | 56 - inst/doc/vetr.html | 166 +--- man/all_bw.Rd |only man/bench_mark.Rd | 8 man/type_alike.Rd | 2 man/type_of.Rd | 2 man/vet.Rd | 23 man/vet_token.Rd | 2 man/vetr.Rd | 10 man/vetr_settings.Rd | 14 src/alike.c | 667 ++++++++--------- src/alike.h | 156 ++- src/all-bw.c |only src/all-bw.h |only src/assumptions.c |only src/attr.c | 978 ++++++++++++------------- src/cstringr.c | 192 +++- src/cstringr.h | 13 src/eval.c | 478 +++++++----- src/fun.c | 50 - src/init.c | 12 src/lang.c | 239 +++--- src/merge.c | 61 + src/misc-alike.c | 111 ++ src/misc.c | 19 src/parse.c | 92 +- src/recurse.c | 2 src/settings.c | 28 src/settings.h | 3 src/strsub.c |only src/type.c | 51 - src/validate.c | 152 ++- src/validate.h | 68 + src/valname.c | 24 tests/run.R | 1 tests/unitizer/_pre |only tests/unitizer/alike.R | 17 tests/unitizer/alike.unitizer/data.rds |binary tests/unitizer/all-bw.R |only tests/unitizer/all-bw.unitizer |only tests/unitizer/classes.unitizer/data.rds |binary tests/unitizer/cstringr.R | 280 ++++++- tests/unitizer/cstringr.unitizer/data.rds |binary tests/unitizer/eval.unitizer/data.rds |binary tests/unitizer/helper |only tests/unitizer/internal.R | 3 tests/unitizer/internal.unitizer/data.rds |binary tests/unitizer/tev.unitizer/data.rds |binary tests/unitizer/type.unitizer/data.rds |binary tests/unitizer/validate.R | 44 + tests/unitizer/validate.args.R | 12 tests/unitizer/validate.args.unitizer/data.rds |binary tests/unitizer/validate.unitizer/data.rds |binary tests/valgrind |only vignettes/alike.Rmd | 4 vignettes/rmdhunks/declarative-checks.Rmd | 23 vignettes/rmdhunks/related-packages.Rmd | 37 vignettes/rmdhunks/trust-but-verify.Rmd | 2 vignettes/rmdhunks/vetting-expressions.Rmd | 15 vignettes/styles.css | 4 vignettes/vetr.Rmd | 56 - 80 files changed, 2839 insertions(+), 1967 deletions(-)
More information about DescriptiveStats.OBeu at CRAN
Permanent link
Title: Optimized Kernel Regularized Least Squares
Description: Functions for Kernel-Regularized Least Squares optimized for speed and memory usage are provided along with visualization tools. For working papers, sample code, and recent presentations visit <https://sites.google.com/site/petemohanty/software/>. bigKRLS, as well its dependencies, require current versions of R and its compilers (and RStudio if used). For details, see <https://github.com/rdrr1990/bigKRLS/blob/master/INSTALL.md>.
Author: Pete Mohanty [aut, cre], Robert Shaffer [aut]
Maintainer: Pete Mohanty <pete.mohanty@gmail.com>
Diff between bigKRLS versions 2.0.0 dated 2017-09-11 and 2.0.1 dated 2017-09-17
DESCRIPTION | 20 - MD5 | 22 - R/bigKRLS.R | 513 +++++++++++++++++++++++++------------------ inst/doc/bigKRLS_basics.html | 2 man/bigKRLS.Rd | 36 ++- man/crossvalidate.bigKRLS.Rd | 19 + man/load.bigKRLS.Rd | 4 man/predict.bigKRLS.Rd | 18 + man/save.bigKRLS.Rd | 13 - man/shiny.bigKRLS.Rd | 11 man/summary.bigKRLS.Rd | 15 + man/summary.bigKRLS_CV.Rd | 14 + 12 files changed, 442 insertions(+), 245 deletions(-)
Title: Implementation of SparseDC Algorithm
Description: Implements the algorithm described in
Barron, M., Zhang, S. and Li, J. "A sparse differential
clustering algorithm for tracing cell type changes via single-cell
RNA-sequencing data" (Unpublished). This algorithm clusters samples from two different
populations, links the clusters across the conditions and identifies
marker genes for these changes. The package was designed for scRNA-Seq
data but is also applicable to many other data types, just replace cells
with samples and genes with variables. The package also contains functions
for estimating the parameters for SparseDC as outlined in the paper.
Author: Jun Li [aut, cre],
Martin Barron [aut]
Maintainer: Jun Li <jun.li@nd.edu>
Diff between SparseDC versions 0.1.5 dated 2017-05-02 and 0.1.12 dated 2017-09-17
DESCRIPTION | 6 ++-- MD5 | 25 +++++++++++------- R/sim_data.R |only R/sparsedc_cluster.R | 3 -- R/sparsedc_gap.r |only R/update_mu.R | 2 - build/vignette.rds |binary inst/doc/SparseDC.R | 10 +++++++ inst/doc/SparseDC.Rmd | 53 ++++++++++++++++++++++++++++++++++++++- inst/doc/SparseDC.html | 64 ++++++++++++++++++++++++++++++------------------ man/generate_uni_dat.Rd |only man/sim_data.Rd |only man/sparsedc_cluster.Rd | 2 - man/sparsedc_gap.Rd |only man/update_mu.Rd | 2 - vignettes/SparseDC.Rmd | 53 ++++++++++++++++++++++++++++++++++++++- 16 files changed, 174 insertions(+), 46 deletions(-)
More information about SampleSize4ClinicalTrials at CRAN
Permanent link
Title: Fuzzy Clustering of Vegetation Data
Description: A set of functions to perform fuzzy clustering of vegetation data [De Cáceres et al. (2010) <doi:10.1111/j.1654-1103.2010.01211.x>] and to assess ecological community ressemblance on the basis of structure and composition [De Cáceres et al. (2013): <doi:10.1111/2041-210X.12116>].
Author: Miquel De Cáceres [aut, cre]
Maintainer: Miquel De Cáceres <miquelcaceres@gmail.com>
Diff between vegclust versions 1.6.5 dated 2016-12-21 and 1.7.1 dated 2017-09-17
DESCRIPTION | 26 + MD5 | 25 + NAMESPACE | 30 +- NEWS |only R/RcppExports.R |only R/trajectoryClustering.R |only R/trajectoryDistances.R |only build/vignette.rds |binary inst/doc/MedRegExample.Rnw | 458 +++++++++++++++++----------------- inst/doc/MedRegExample.pdf |binary inst/doc/TrajectoryAnalysis.R |only inst/doc/TrajectoryAnalysis.Rnw |only inst/doc/TrajectoryAnalysis.pdf |only inst/doc/VegetationClassification.pdf |binary man/trajectories.Rd |only src |only vignettes/MedRegExample.Rnw | 458 +++++++++++++++++----------------- vignettes/TrajectoryAnalysis.Rnw |only 18 files changed, 508 insertions(+), 489 deletions(-)
Title: Modelling Spatial Extremes
Description: Tools for the statistical modelling of spatial extremes using max-stable processes, copula or Bayesian hierarchical models. More precisely, this package allows (conditional) simulations from various parametric max-stable models, analysis of the extremal spatial dependence, the fitting of such processes using composite likelihoods or least square (simple max-stable processes only), model checking and selection and prediction. Other approaches (although not completely in agreement with the extreme value theory) are available such as the use of (spatial) copula and Bayesian hierarchical models assuming the so-called conditional assumptions. The latter approaches is handled through an (efficient) Gibbs sampler. Some key references: Davison et al. (2012) <doi:10.1214/11-STS376>, Padoan et al. (2010) <doi:10.1198/jasa.2009.tm08577>, Dombry et al. (2013) <doi:10.1093/biomet/ass067>.
Author: Mathieu Ribatet [aut, cre],
Richard Singleton [ctb],
R Core team [ctb]
Maintainer: Mathieu Ribatet <mathieu.ribatet@umontpellier.fr>
Diff between SpatialExtremes versions 2.0-4 dated 2017-08-24 and 2.0-5 dated 2017-09-17
DESCRIPTION | 8 MD5 | 12 NEWS | 7 R/modelChecking.R | 637 +++++++++++++++++++++----------------- R/simmaxstab.R | 3 inst/doc/SpatialExtremesGuide.pdf |binary src/condsimMaxStab.c | 10 7 files changed, 380 insertions(+), 297 deletions(-)
More information about SpatialExtremes at CRAN
Permanent link
Title: Deprecated 'classic' Rcpp API
Description: The RcppClassic package provides a deprecated C++ library which
facilitates the integration of R and C++. New projects should use the new Rcpp
API in the Rcpp package.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by David Reiss,
and based on code written during 2005 and 2006 by Dominick Samperi
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppClassic versions 0.9.6 dated 2015-01-10 and 0.9.7 dated 2017-09-17
RcppClassic-0.9.6/RcppClassic/inst/doc/RcppClassic-intro.Rnw |only RcppClassic-0.9.6/RcppClassic/vignettes/RcppClassic-intro.Rnw |only RcppClassic-0.9.7/RcppClassic/ChangeLog | 21 ++ RcppClassic-0.9.7/RcppClassic/DESCRIPTION | 19 - RcppClassic-0.9.7/RcppClassic/MD5 | 32 +-- RcppClassic-0.9.7/RcppClassic/NAMESPACE | 2 RcppClassic-0.9.7/RcppClassic/build/vignette.rds |binary RcppClassic-0.9.7/RcppClassic/cleanup | 3 RcppClassic-0.9.7/RcppClassic/inst/doc/RcppClassic-intro.R | 20 - RcppClassic-0.9.7/RcppClassic/inst/doc/RcppClassic-intro.Rmd |only RcppClassic-0.9.7/RcppClassic/inst/doc/RcppClassic-intro.pdf |binary RcppClassic-0.9.7/RcppClassic/inst/doc/RcppClassic-unitTests.pdf |binary RcppClassic-0.9.7/RcppClassic/inst/include/classic/RcppResultSet__backward.h | 29 +- RcppClassic-0.9.7/RcppClassic/src/Makevars | 4 RcppClassic-0.9.7/RcppClassic/src/Makevars.win | 74 +++---- RcppClassic-0.9.7/RcppClassic/src/RcppFunction.cpp | 40 +-- RcppClassic-0.9.7/RcppClassic/src/RcppResultSet.cpp | 103 +++++----- RcppClassic-0.9.7/RcppClassic/src/init.c |only RcppClassic-0.9.7/RcppClassic/vignettes/RcppClassic-intro.Rmd |only RcppClassic-0.9.7/RcppClassic/vignettes/pinp.cls |only 20 files changed, 179 insertions(+), 168 deletions(-)
Title: Miscellaneous Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics
paradigm. Provides new statistics to locate and tag peaks and valleys in 2D
plots, a statistics to add a label with the equation of a polynomial fitted
with lm(), or R^2 or adjusted R^2 or information criteria for any model
fitted with function lm(). Additional statistics give access to functions
in package 'broom'. Provides a function for flexibly converting time
series to data frames suitable for plotting with ggplot(). In addition
provides statistics and ggplot geometries useful for diagnosing what data
are passed to compute_group() and compute_panel() functions and to
geometries.
Author: Pedro J. Aphalo [aut, cre],
Kamil Slowikowski [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggpmisc versions 0.2.15 dated 2017-05-14 and 0.2.16 dated 2017-09-17
ggpmisc-0.2.15/ggpmisc/inst/doc/a-user-guide.R |only ggpmisc-0.2.15/ggpmisc/inst/doc/a-user-guide.Rmd |only ggpmisc-0.2.15/ggpmisc/inst/doc/a-user-guide.html |only ggpmisc-0.2.15/ggpmisc/inst/doc/b-examples-dens2d.R |only ggpmisc-0.2.15/ggpmisc/inst/doc/b-examples-dens2d.Rmd |only ggpmisc-0.2.15/ggpmisc/inst/doc/b-examples-dens2d.html |only ggpmisc-0.2.15/ggpmisc/inst/doc/c-debug.R |only ggpmisc-0.2.15/ggpmisc/inst/doc/c-debug.Rmd |only ggpmisc-0.2.15/ggpmisc/inst/doc/c-debug.html |only ggpmisc-0.2.15/ggpmisc/inst/staticdocs |only ggpmisc-0.2.15/ggpmisc/vignettes/a-user-guide.Rmd |only ggpmisc-0.2.15/ggpmisc/vignettes/b-examples-dens2d.Rmd |only ggpmisc-0.2.15/ggpmisc/vignettes/c-debug.Rmd |only ggpmisc-0.2.16/ggpmisc/DESCRIPTION | 21 +- ggpmisc-0.2.16/ggpmisc/MD5 | 64 ++++---- ggpmisc-0.2.16/ggpmisc/NAMESPACE | 9 + ggpmisc-0.2.16/ggpmisc/NEWS | 10 + ggpmisc-0.2.16/ggpmisc/R/geom-debug.R | 69 +++++---- ggpmisc-0.2.16/ggpmisc/R/ggpmisc.R | 20 ++ ggpmisc-0.2.16/ggpmisc/R/layer-manip.R |only ggpmisc-0.2.16/ggpmisc/R/stat-fit-broom.R | 129 +++++------------ ggpmisc-0.2.16/ggpmisc/R/stat-poly-eq.R | 3 ggpmisc-0.2.16/ggpmisc/README.md | 36 ++-- ggpmisc-0.2.16/ggpmisc/build/vignette.rds |binary ggpmisc-0.2.16/ggpmisc/inst/CITATION | 2 ggpmisc-0.2.16/ggpmisc/inst/doc/user-guide-1.R |only ggpmisc-0.2.16/ggpmisc/inst/doc/user-guide-1.Rmd |only ggpmisc-0.2.16/ggpmisc/inst/doc/user-guide-1.html |only ggpmisc-0.2.16/ggpmisc/inst/doc/user-guide-2.R |only ggpmisc-0.2.16/ggpmisc/inst/doc/user-guide-2.Rmd |only ggpmisc-0.2.16/ggpmisc/inst/doc/user-guide-2.html |only ggpmisc-0.2.16/ggpmisc/inst/doc/user-guide-3.R |only ggpmisc-0.2.16/ggpmisc/inst/doc/user-guide-3.Rmd |only ggpmisc-0.2.16/ggpmisc/inst/doc/user-guide-3.html |only ggpmisc-0.2.16/ggpmisc/inst/doc/user-guide-4.R |only ggpmisc-0.2.16/ggpmisc/inst/doc/user-guide-4.Rmd |only ggpmisc-0.2.16/ggpmisc/inst/doc/user-guide-4.html |only ggpmisc-0.2.16/ggpmisc/man/delete_layers.Rd |only ggpmisc-0.2.16/ggpmisc/man/edit_layers.Rd |only ggpmisc-0.2.16/ggpmisc/man/geom_debug.Rd | 10 + ggpmisc-0.2.16/ggpmisc/man/ggpmisc-package.Rd | 21 ++ ggpmisc-0.2.16/ggpmisc/man/stat_fit_augment.Rd | 29 +-- ggpmisc-0.2.16/ggpmisc/man/stat_fit_glance.Rd | 15 + ggpmisc-0.2.16/ggpmisc/man/stat_fit_tidy.Rd | 11 - ggpmisc-0.2.16/ggpmisc/man/stat_poly_eq.Rd | 4 ggpmisc-0.2.16/ggpmisc/vignettes/user-guide-1.Rmd |only ggpmisc-0.2.16/ggpmisc/vignettes/user-guide-2.Rmd |only ggpmisc-0.2.16/ggpmisc/vignettes/user-guide-3.Rmd |only ggpmisc-0.2.16/ggpmisc/vignettes/user-guide-4.Rmd |only 49 files changed, 253 insertions(+), 200 deletions(-)
Title: Pakistan Population Census 2017
Description: Provides data sets and functions for exploration of Pakistan Population Census 2017 (<http://www.pbscensus.gov.pk/>).
Author: Muhammad Yaseen [aut, cre]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between PakPC2017 versions 0.2.0 dated 2017-09-14 and 0.3.0 dated 2017-09-17
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 7 ++++++- data/PakPC2017City10.RData |binary inst/doc/PakPC2017-Intro.pdf |binary 5 files changed, 13 insertions(+), 8 deletions(-)