Title: Genome Interval Arithmetic in R
Description: Read and manipulate genome intervals and signals. Provides
functionality similar to command-line tool suites within R,
enabling interactive analysis and visualization of genome-scale data.
Author: Jay Hesselberth [aut, cre] (<https://orcid.org/0000-0002-6299-179X>),
Kent Riemondy [aut] (<https://orcid.org/0000-0003-0750-1273>)
Maintainer: Jay Hesselberth <jay.hesselberth@gmail.com>
Diff between valr versions 0.4.1 dated 2018-06-08 and 0.4.2 dated 2018-11-17
DESCRIPTION | 9 MD5 | 86 ++++---- NAMESPACE | 1 NEWS.md | 6 R/tbls.r | 8 R/valr-package.r | 2 build/vignette.rds |binary inst/doc/valr.html | 468 ++++++++++++++++++++++----------------------- inst/include/tools/utils.h | 3 man/bed12_to_exons.Rd | 1 man/bed_absdist.Rd | 1 man/bed_closest.Rd | 1 man/bed_cluster.Rd | 1 man/bed_complement.Rd | 1 man/bed_coverage.Rd | 1 man/bed_fisher.Rd | 1 man/bed_flank.Rd | 5 man/bed_intersect.Rd | 1 man/bed_jaccard.Rd | 1 man/bed_makewindows.Rd | 1 man/bed_map.Rd | 1 man/bed_merge.Rd | 1 man/bed_partition.Rd | 1 man/bed_projection.Rd | 1 man/bed_random.Rd | 1 man/bed_reldist.Rd | 1 man/bed_shift.Rd | 1 man/bed_shuffle.Rd | 1 man/bed_slop.Rd | 5 man/bed_subtract.Rd | 1 man/bed_window.Rd | 1 man/bound_intervals.Rd | 1 man/create_introns.Rd | 1 man/create_tss.Rd | 1 man/create_utrs3.Rd | 1 man/create_utrs5.Rd | 1 man/flip_strands.Rd | 1 man/interval_spacing.Rd | 1 man/read_bed.Rd | 5 man/read_genome.Rd | 1 man/read_vcf.Rd | 1 man/tbl_genome.Rd | 2 man/tbl_interval.Rd | 2 man/valr.Rd | 1 44 files changed, 336 insertions(+), 296 deletions(-)
Title: R Interface to the Species+ Database
Description: A programmatic interface to the Species+ <https://speciesplus.net/> database via the Species+/CITES Checklist API <https://api.speciesplus.net/>.
Author: Jonas Geschke [aut] (<https://orcid.org/0000-0002-5654-9313>),
Kevin Cazelles [aut, cre] (<https://orcid.org/0000-0001-6619-9874>),
Ignasi Bartomeus [aut] (<https://orcid.org/0000-0001-7893-4389>),
Jonathan Goldenberg [ctb],
Marie-Bé Leduc [ctb],
Yasmine Verzelen [ctb],
Noam Ross [rev],
Margaret Siple [rev]
Maintainer: Kevin Cazelles <kevin.cazelles@gmail.com>
Diff between rcites versions 0.1.0 dated 2018-08-11 and 1.0.0 dated 2018-11-17
rcites-0.1.0/rcites/R/sppplus_login.R |only rcites-0.1.0/rcites/R/sppplus_simplify.R |only rcites-0.1.0/rcites/R/sppplus_taxonconcept.R |only rcites-0.1.0/rcites/R/taxon_cites_legislation.R |only rcites-0.1.0/rcites/R/taxon_distribution.R |only rcites-0.1.0/rcites/R/taxon_eu_legislation.R |only rcites-0.1.0/rcites/R/taxon_references.R |only rcites-0.1.0/rcites/inst/doc/citesr-vignette.R |only rcites-0.1.0/rcites/inst/doc/citesr-vignette.Rmd |only rcites-0.1.0/rcites/inst/doc/citesr-vignette.html |only rcites-0.1.0/rcites/inst/tmp |only rcites-0.1.0/rcites/man/sppplus_login.Rd |only rcites-0.1.0/rcites/man/sppplus_simplify.Rd |only rcites-0.1.0/rcites/man/sppplus_taxonconcept.Rd |only rcites-0.1.0/rcites/man/taxon_cites_legislation.Rd |only rcites-0.1.0/rcites/man/taxon_distribution.Rd |only rcites-0.1.0/rcites/man/taxon_eu_legislation.Rd |only rcites-0.1.0/rcites/man/taxon_references.Rd |only rcites-0.1.0/rcites/tests/testthat/test-distribution.R |only rcites-0.1.0/rcites/tests/testthat/test-wrongtype.R |only rcites-0.1.0/rcites/tests/testthat/test_pkghelpers.R |only rcites-0.1.0/rcites/vignettes/citesr-vignette.Rmd |only rcites-1.0.0/rcites/DESCRIPTION | 27 - rcites-1.0.0/rcites/MD5 | 80 +-- rcites-1.0.0/rcites/NAMESPACE | 29 - rcites-1.0.0/rcites/R/print.spp.R |only rcites-1.0.0/rcites/R/set_token.R |only rcites-1.0.0/rcites/R/spp_cites_legislation.R |only rcites-1.0.0/rcites/R/spp_distributions.R |only rcites-1.0.0/rcites/R/spp_eu_legislation.R |only rcites-1.0.0/rcites/R/spp_references.R |only rcites-1.0.0/rcites/R/spp_taxonconcept.R |only rcites-1.0.0/rcites/R/zzz.R | 370 +++++++++++++++- rcites-1.0.0/rcites/README.md | 103 +++- rcites-1.0.0/rcites/build/vignette.rds |binary rcites-1.0.0/rcites/inst/CITATION | 12 rcites-1.0.0/rcites/inst/doc/bulk_analysis.R |only rcites-1.0.0/rcites/inst/doc/bulk_analysis.Rmd |only rcites-1.0.0/rcites/inst/doc/bulk_analysis.html |only rcites-1.0.0/rcites/inst/doc/elephant.R |only rcites-1.0.0/rcites/inst/doc/elephant.Rmd |only rcites-1.0.0/rcites/inst/doc/elephant.html |only rcites-1.0.0/rcites/inst/doc/get_started.R |only rcites-1.0.0/rcites/inst/doc/get_started.Rmd |only rcites-1.0.0/rcites/inst/doc/get_started.html |only rcites-1.0.0/rcites/man/figures/rcites_logo.png |binary rcites-1.0.0/rcites/man/print.spp.Rd |only rcites-1.0.0/rcites/man/rcites.Rd | 39 + rcites-1.0.0/rcites/man/set_token.Rd |only rcites-1.0.0/rcites/man/spp_cites_legislation.Rd |only rcites-1.0.0/rcites/man/spp_distributions.Rd |only rcites-1.0.0/rcites/man/spp_eu_legislation.Rd |only rcites-1.0.0/rcites/man/spp_references.Rd |only rcites-1.0.0/rcites/man/spp_taxonconcept.Rd |only rcites-1.0.0/rcites/tests/test-all.R | 3 rcites-1.0.0/rcites/tests/testthat/helper-citesr.R | 9 rcites-1.0.0/rcites/tests/testthat/test-distributions.R |only rcites-1.0.0/rcites/tests/testthat/test-legislations.R | 136 +++-- rcites-1.0.0/rcites/tests/testthat/test-pkghelpers.R |only rcites-1.0.0/rcites/tests/testthat/test-references.R | 44 + rcites-1.0.0/rcites/tests/testthat/test-taxonconcept.R | 66 +- rcites-1.0.0/rcites/tests/testthat/test-wrongtoken.R | 21 rcites-1.0.0/rcites/vignettes/bulk_analysis.Rmd |only rcites-1.0.0/rcites/vignettes/elephant.Rmd |only rcites-1.0.0/rcites/vignettes/get_started.Rmd |only 65 files changed, 723 insertions(+), 216 deletions(-)
Title: Functions and C++ Header Files for Computation on Manifolds
Description: We provide a number of algorithms to estimate fundamental statistics including Fréchet mean and geometric median for manifold-valued data. Also, C++ header files are contained that implement elementary operations on manifolds such as Sphere, Grassmann, and others. See Bhattacharya and Bhattacharya (2012) <doi:10.1017/CBO9781139094764> if you are interested in statistics on manifolds, and Absil et al (2007) <isbn:978-0-691-13298-3> on computational aspects of optimization on matrix manifolds.
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kyou@nd.edu>
Diff between RiemBase versions 0.1.0 dated 2018-11-04 and 0.2.0 dated 2018-11-17
RiemBase-0.1.0/RiemBase/R/mean.R |only RiemBase-0.1.0/RiemBase/R/median.R |only RiemBase-0.1.0/RiemBase/R/pdist.R |only RiemBase-0.1.0/RiemBase/R/pdist2.R |only RiemBase-0.1.0/RiemBase/R/rmean.R |only RiemBase-0.1.0/RiemBase/inst/include/riemfactory.h |only RiemBase-0.1.0/RiemBase/man/mean.Rd |only RiemBase-0.1.0/RiemBase/man/median.Rd |only RiemBase-0.1.0/RiemBase/man/pdist.Rd |only RiemBase-0.1.0/RiemBase/man/pdist2.Rd |only RiemBase-0.1.0/RiemBase/man/rmean.Rd |only RiemBase-0.2.0/RiemBase/DESCRIPTION | 12 + RiemBase-0.2.0/RiemBase/MD5 | 53 ++++---- RiemBase-0.2.0/RiemBase/NAMESPACE | 10 - RiemBase-0.2.0/RiemBase/R/rbase.mean.R |only RiemBase-0.2.0/RiemBase/R/rbase.median.R |only RiemBase-0.2.0/RiemBase/R/rbase.pdist.R |only RiemBase-0.2.0/RiemBase/R/rbase.pdist2.R |only RiemBase-0.2.0/RiemBase/R/rbase.robust.R |only RiemBase-0.2.0/RiemBase/build/partial.rdb |binary RiemBase-0.2.0/RiemBase/inst/include/manifolds/riem_01euclidean.h | 58 +++++--- RiemBase-0.2.0/RiemBase/inst/include/manifolds/riem_02sphere.h | 58 ++++++-- RiemBase-0.2.0/RiemBase/inst/include/manifolds/riem_03spd.h | 66 +++++++--- RiemBase-0.2.0/RiemBase/inst/include/manifolds/riem_04stiefel.h | 57 ++++++-- RiemBase-0.2.0/RiemBase/inst/include/manifolds/riem_05grassmann.h | 59 ++++++-- RiemBase-0.2.0/RiemBase/inst/include/procedures/riemfunc_dist.h | 8 - RiemBase-0.2.0/RiemBase/inst/include/procedures/riemfunc_equiv.h |only RiemBase-0.2.0/RiemBase/inst/include/procedures/riemfunc_exp.h | 8 - RiemBase-0.2.0/RiemBase/inst/include/procedures/riemfunc_extdist.h |only RiemBase-0.2.0/RiemBase/inst/include/procedures/riemfunc_invequiv.h |only RiemBase-0.2.0/RiemBase/inst/include/procedures/riemfunc_log.h | 8 - RiemBase-0.2.0/RiemBase/inst/include/procedures/riemfunc_nearest.h | 8 - RiemBase-0.2.0/RiemBase/inst/include/procedures/riemfunc_norm.h | 8 - RiemBase-0.2.0/RiemBase/inst/include/riemfactory.hpp |only RiemBase-0.2.0/RiemBase/man/rbase.mean.Rd |only RiemBase-0.2.0/RiemBase/man/rbase.median.Rd |only RiemBase-0.2.0/RiemBase/man/rbase.pdist.Rd |only RiemBase-0.2.0/RiemBase/man/rbase.pdist2.Rd |only RiemBase-0.2.0/RiemBase/man/rbase.robust.Rd |only RiemBase-0.2.0/RiemBase/src/engines.cpp | 2 40 files changed, 276 insertions(+), 139 deletions(-)
Title: Pacific Decadal Oscillation Index Data
Description: Monthly Pacific Decadal Oscillation (PDO) index
values from January 1900 to present.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>),
Nathan Mantua [aut, dtc],
Steven R. Hare [aut, dtc]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between rpdo versions 0.2.4 dated 2018-08-15 and 0.2.5 dated 2018-11-17
DESCRIPTION | 15 +++++++-------- MD5 | 14 +++++++------- NAMESPACE | 1 + NEWS.md | 4 ++++ R/namespace.R | 2 +- R/pdo-download.R | 8 ++++---- README.md | 55 +++++++++---------------------------------------------- data/pdo.rda |binary 8 files changed, 33 insertions(+), 66 deletions(-)
Title: Unified Algorithm for Non-convex Penalized Estimation for
Generalized Linear Models
Description: An efficient unified nonconvex penalized estimation algorithm for
Gaussian (linear), binomial Logit (logistic), Poisson, multinomial Logit,
and Cox proportional hazard regression models.
The unified algorithm is implemented based on the convex concave procedure and
the algorithm can be applied to most of the existing nonconvex penalties.
The algorithm also supports convex penalty:
least absolute shrinkage and selection operator (LASSO).
Supported nonconvex penalties include
smoothly clipped absolute deviation (SCAD),
minimax concave penalty (MCP), truncated LASSO penalty (TLP),
clipped LASSO (CLASSO), sparse ridge (SRIDGE),
modified bridge (MBRIDGE) and modified log (MLOG).
For high-dimensional data (data set with many variables),
the algorithm selects relevant variables producing a parsimonious regression model.
Kim, D., Lee, S. and Kwon, S. (2018) <arXiv:1811.05061>,
Lee, S., Kwon, S. and Kim, Y. (2016) <doi:10.1016/j.csda.2015.08.019>,
Kwon, S., Lee, S. and Kim, Y. (2015) <doi:10.1016/j.csda.2015.07.001>.
(This research is funded by Julian Virtue Professorship from Center for Applied Research at Pepperdine
Graziadio Business School and the National Research Foundation of Korea.)
Author: Dongshin Kim [aut, cre, cph],
Sunghoon Kwon [aut, cph],
Sangin Lee [aut, cph]
Maintainer: Dongshin Kim <dongshin.kim@live.com>
Diff between ncpen versions 0.2.0 dated 2018-02-21 and 1.0.0 dated 2018-11-17
ncpen-0.2.0/ncpen/inst |only ncpen-0.2.0/ncpen/man/sam.gen.fun.Rd |only ncpen-1.0.0/ncpen/DESCRIPTION | 32 ncpen-1.0.0/ncpen/MD5 | 72 ncpen-1.0.0/ncpen/NAMESPACE | 12 ncpen-1.0.0/ncpen/NEWS.md | 12 ncpen-1.0.0/ncpen/R/RcppExports.R | 141 + ncpen-1.0.0/ncpen/R/ncpen_const.R |only ncpen-1.0.0/ncpen/R/ncpen_cpp_wrap.R | 1638 ++++++++++++---------- ncpen-1.0.0/ncpen/R/ncpen_package.R | 17 ncpen-1.0.0/ncpen/R/ncpen_util.R | 159 ++ ncpen-1.0.0/ncpen/R/ncpen_ux.R |only ncpen-1.0.0/ncpen/README.md | 16 ncpen-1.0.0/ncpen/man/coef.cv.ncpen.Rd | 48 ncpen-1.0.0/ncpen/man/coef.ncpen.Rd | 32 ncpen-1.0.0/ncpen/man/control.ncpen.Rd |only ncpen-1.0.0/ncpen/man/cv.ncpen.Rd | 169 +- ncpen-1.0.0/ncpen/man/cv.ncpen.reg.Rd |only ncpen-1.0.0/ncpen/man/fold.cv.ncpen.Rd |only ncpen-1.0.0/ncpen/man/gic.ncpen.Rd | 69 ncpen-1.0.0/ncpen/man/make.ncpen.data.Rd |only ncpen-1.0.0/ncpen/man/native_cpp_ncpen_fun_.Rd | 33 ncpen-1.0.0/ncpen/man/native_cpp_nr_fun_.Rd |only ncpen-1.0.0/ncpen/man/native_cpp_obj_fun_.Rd | 4 ncpen-1.0.0/ncpen/man/native_cpp_obj_grad_fun_.Rd | 4 ncpen-1.0.0/ncpen/man/native_cpp_obj_hess_fun_.Rd |only ncpen-1.0.0/ncpen/man/native_cpp_p_ncpen_fun_.Rd | 15 ncpen-1.0.0/ncpen/man/native_cpp_pen_fun_.Rd |only ncpen-1.0.0/ncpen/man/native_cpp_pen_grad_fun_.Rd |only ncpen-1.0.0/ncpen/man/native_cpp_qlasso_fun_.Rd | 10 ncpen-1.0.0/ncpen/man/native_cpp_set_dev_mode_.Rd |only ncpen-1.0.0/ncpen/man/ncpen-package.Rd | 17 ncpen-1.0.0/ncpen/man/ncpen.Rd | 224 +-- ncpen-1.0.0/ncpen/man/ncpen.reg.Rd |only ncpen-1.0.0/ncpen/man/plot.cv.ncpen.Rd | 33 ncpen-1.0.0/ncpen/man/plot.ncpen.Rd | 37 ncpen-1.0.0/ncpen/man/predict.ncpen.Rd | 85 - ncpen-1.0.0/ncpen/man/sam.gen.ncpen.Rd |only ncpen-1.0.0/ncpen/man/to.indicators.Rd | 2 ncpen-1.0.0/ncpen/man/to.ncpen.x.mat.Rd |only ncpen-1.0.0/ncpen/src/RcppExports.cpp | 126 + ncpen-1.0.0/ncpen/src/ncpen.cpp | 1315 +++++++++++------ ncpen-1.0.0/ncpen/src/ncpen.h | 44 ncpen-1.0.0/ncpen/src/ncpen_R.cpp | 193 ++ ncpen-1.0.0/ncpen/src/ncpen_init.c | 30 45 files changed, 2948 insertions(+), 1641 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-01-12 0.1.3
2017-06-16 0.1.1
Title: Data-Driven Identification of SVAR Models
Description: Implements data-driven identification methods for structural vector autoregressive (SVAR) models.
Based on an existing VAR model object (provided by e.g. VAR() from the 'vars' package), the structural
impact matrix is obtained via data-driven identification techniques (i.e. changes in volatility (Rigobon, R. (2003) <doi:10.1162/003465303772815727>),
least dependent innovations (Herwartz, H., Ploedt, M., (2016) <doi:10.1016/j.jimonfin.2015.11.001>) or non-Gaussian maximum likelihood (Lanne, M., Meitz, M., Saikkonen, P. (2017) <doi:10.1016/j.jeconom.2016.06.002>).
Author: Alexander Lange [aut, cre],
Bernhard Dalheimer [aut],
Helmut Herwartz [aut],
Simone Maxand [aut],
Hannes Riebl [ctb]
Maintainer: Alexander Lange <alexander.lange@uni-goettingen.de>
Diff between svars versions 1.2.1 dated 2018-08-08 and 1.2.2 dated 2018-11-17
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/bootstrap_mb.R | 12 ++---------- R/bootstrap_wild.R | 4 ++-- R/chow.test.R | 4 ++-- R/get_var_objects.R | 3 +++ R/id.st.R | 4 ++-- R/id_ngml_boot.R | 4 ++-- R/id_st_boot.R | 4 ++-- R/identifyNGML.R | 4 ++-- R/identifyVolatility.R | 4 ++-- R/identifyVolatility_boot.R | 4 ++-- R/summary.chow.R | 3 ++- 13 files changed, 39 insertions(+), 43 deletions(-)
Title: Computing Weighted Topological Overlaps (wTO) & Consensus wTO
Network
Description: Computes the Weighted Topological Overlap with positive and negative signs (wTO) networks given a data frame containing the mRNA count/ expression/ abundance per sample, and a vector containing the interested nodes of interaction (a subset of the elements of the full data frame). It also computes the cut-off threshold or p-value based on the individuals bootstrap or the values reshuffle per individual. It also allows the construction of a consensus network, based on multiple wTO networks. The package includes a visualization tool for the networks. More about the methodology can be found at <arXiv:1711.04702>.
Author: Deisy Morselli Gysi, Andre Voigt, Tiago Miranda Fragoso, Eivind Almaas and Katja Nowick.
Maintainer: Deisy Morselli Gysi <deisy@bioinf.uni-leipzig.de>
Diff between wTO versions 1.6.2 dated 2018-10-14 and 1.6.3 dated 2018-11-17
DESCRIPTION | 8 MD5 | 22 - R/wTO.Complete2.R | 30 +- R/wTO.aux.each.R | 51 ++-- R/wTOfast.R | 76 ++++-- build/vignette.rds |binary inst/CITATION | 11 inst/doc/wTOvignette.html | 544 ++++++++++++++++++++++++++++------------------ man/NetVis.Rd | 9 man/wTO.Complete.Rd | 19 + man/wTO.aux.each.Rd | 2 man/wTO.fast.Rd | 19 + 12 files changed, 501 insertions(+), 290 deletions(-)
Title: Gaussian Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimation
Description: Gaussian finite mixture models fitted via EM algorithm for model-based clustering, classification, and density estimation, including Bayesian regularization, dimension reduction for visualisation, and resampling-based inference.
Author: Chris Fraley [aut],
Adrian E. Raftery [aut],
Luca Scrucca [aut, cre] (<https://orcid.org/0000-0003-3826-0484>),
Thomas Brendan Murphy [ctb] (<https://orcid.org/0000-0002-5668-7046>),
Michael Fop [ctb] (<https://orcid.org/0000-0003-3936-2757>)
Maintainer: Luca Scrucca <luca.scrucca@unipg.it>
Diff between mclust versions 5.4.1 dated 2018-06-27 and 5.4.2 dated 2018-11-17
DESCRIPTION | 23 MD5 | 76 +- NAMESPACE | 9 R/bootstrap.R | 7 R/densityMclust.R | 2 R/icl.R | 2 R/init.R | 28 R/mclust.R | 221 ++++++- R/mclustdr.R | 2 R/options.R | 10 R/toremove.R | 6 build/vignette.rds |binary data/Baudry_etal_2010_JCGS_examples.rda |binary data/GvHD.rda |binary data/acidity.rda |binary data/chevron.rda |binary data/cross.rda |binary data/diabetes.rda |binary data/thyroid.rda |binary data/wreath.rda |binary inst/CITATION | 6 inst/NEWS | 12 inst/doc/mclust.R | 35 + inst/doc/mclust.Rmd | 44 + inst/doc/mclust.html | 902 +++++++++++++++++--------------- man/GvHD.Rd | 15 man/Mclust.Rd | 25 man/MclustBootstrap.Rd | 2 man/clustCombi.Rd | 3 man/densityMclust.Rd | 6 man/hc.Rd | 33 - man/mclust.options.Rd | 50 - man/mclustBIC.Rd | 19 man/mclustBICupdate.Rd |only man/mclustLoglik.Rd |only man/plot.Mclust.Rd | 4 man/plot.MclustBoostrap.Rd | 4 man/plot.clustCombi.Rd | 6 man/plot.densityMclust.Rd | 2 vignettes/mclust.Rmd | 44 + 40 files changed, 998 insertions(+), 600 deletions(-)
Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from
Model Outputs
Description: Compute marginal effects from statistical models and returns the
result as tidy data frames. These data frames are ready to use with the
'ggplot2'-package. Marginal effects can be calculated for many different
models. Interaction terms, splines and polynomial terms are also supported.
The two main functions are ggpredict() and ggeffect(). There is a generic
plot()-method to plot the results using 'ggplot2'.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between ggeffects versions 0.6.0 dated 2018-10-11 and 0.7.0 dated 2018-11-17
DESCRIPTION | 15 MD5 | 71 +- NAMESPACE | 3 NEWS.md | 21 R/ggeffect.R | 4 R/ggpredict.R | 95 ++- R/plot.R | 18 R/predictions.R | 119 ++++ R/pretty_range.R | 17 R/print.R | 79 ++- R/select_helpers.R | 28 - R/utils.R | 61 ++ R/utils_expand_data_to_grid.R | 57 ++ R/utils_handle_labels.R | 12 R/utils_parse_vars_arguments.R | 16 README.md | 102 +++- build/vignette.rds |binary inst/doc/effectsatvalues.R | 50 ++ inst/doc/effectsatvalues.Rmd | 98 +++- inst/doc/effectsatvalues.html | 679 ++++++++++------------------ inst/doc/marginaleffects.R | 29 - inst/doc/marginaleffects.Rmd | 17 inst/doc/marginaleffects.html | 953 +++++++++++++++------------------------- inst/doc/plotmethod.R | 42 - inst/doc/plotmethod.Rmd | 6 inst/doc/plotmethod.html | 443 ++++-------------- inst/doc/stata.html | 512 ++++++--------------- man/emm.Rd | 24 - man/ggpredict.Rd | 41 + man/pretty_range.Rd | 14 tests/testthat/test-condition.R |only tests/testthat/test-glmmTMB.R | 29 - tests/testthat/test-lmer.R | 13 tests/testthat/test-negbin.R |only tests/testthat/test-print.R |only vignettes/effectsatvalues.Rmd | 98 +++- vignettes/marginaleffects.Rmd | 17 vignettes/plotmethod.Rmd | 6 38 files changed, 1838 insertions(+), 1951 deletions(-)
Title: Connect to the 'jamovi' Statistical Spreadsheet
Description: Methods to access data sets from the 'jamovi' statistical
spreadsheet (see <https://www.jamovi.org> for more information) from R.
Author: Jonathon Love [aut, cre]
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmvconnect versions 1.0.4 dated 2018-08-11 and 1.0.5 dated 2018-11-17
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- src/readdf.cpp | 23 +++++++++++++++++++++-- 3 files changed, 28 insertions(+), 9 deletions(-)
Title: Dynamic Slicing
Description: Dynamic slicing is a method designed for dependency detection between a categorical variable and a continuous variable. It could be applied for non-parametric hypothesis testing and gene set enrichment analysis.
Author: Chao Ye and Bo Jiang
Maintainer: Chao Ye <yechao1009@gmail.com>
Diff between dslice versions 1.1.5 dated 2015-11-16 and 1.2.0 dated 2018-11-17
DESCRIPTION | 8 ++-- MD5 | 35 +++++++++++++------- NAMESPACE | 2 - R/RcppExports.R | 20 +++++++++++ build/vignette.rds |binary data/gsa_exp.RData |binary data/gsa_label.RData |binary data/gsa_set.RData |binary inst/CITATION | 8 ++-- inst/doc/dslice.Rnw | 2 - inst/doc/dslice.pdf |binary man/bfslice_c.Rd |only man/bfslice_eqp_c.Rd |only man/bfslice_eqp_u.Rd |only man/bfslice_u.Rd |only src/RcppExports.cpp | 84 ++++++++++++++++++++++++++++++++++++++++++++++++++ src/bfslice_c.cpp |only src/bfslice_eqp_c.cpp |only src/bfslice_eqp_u.cpp |only src/bfslice_u.cpp |only src/dslice_init.cpp |only vignettes/dslice.Rnw | 2 - vignettes/dslice.bib | 10 +++++ 23 files changed, 147 insertions(+), 24 deletions(-)