Title: Processing various types of data on GEO and TCGA
Description: Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA)
provide us with a wealth of data, such as RNA-seq, DNA Methylation,
and Copy number variation data. It's easy to download data from TCGA using the
gdc tool, but processing these data into a format suitable for bioinformatics
analysis requires more work. This R package was developed to handle these data.
Author: Erqiang Hu [aut, cre]
Maintainer: Erqiang Hu <13766876214@163.com>
Diff between GeoTcgaData versions 0.2.2 dated 2020-01-07 and 0.2.3 dated 2020-02-22
GeoTcgaData-0.2.2/GeoTcgaData/inst/extdata/metadata.cart.2018-11-09.json |only GeoTcgaData-0.2.3/GeoTcgaData/DESCRIPTION | 6 GeoTcgaData-0.2.3/GeoTcgaData/MD5 | 52 GeoTcgaData-0.2.3/GeoTcgaData/NAMESPACE | 1 GeoTcgaData-0.2.3/GeoTcgaData/R/data.R | 8 GeoTcgaData-0.2.3/GeoTcgaData/R/id_conversion_all.r | 59 GeoTcgaData-0.2.3/GeoTcgaData/R/zzz.R |only GeoTcgaData-0.2.3/GeoTcgaData/README.md | 286 +-- GeoTcgaData-0.2.3/GeoTcgaData/build/vignette.rds |binary GeoTcgaData-0.2.3/GeoTcgaData/data/datalist |only GeoTcgaData-0.2.3/GeoTcgaData/data/hgnc_file.rda |only GeoTcgaData-0.2.3/GeoTcgaData/inst/doc/GeoTcgaData.R | 2 GeoTcgaData-0.2.3/GeoTcgaData/inst/doc/GeoTcgaData.Rmd | 6 GeoTcgaData-0.2.3/GeoTcgaData/inst/doc/GeoTcgaData.html | 130 - GeoTcgaData-0.2.3/GeoTcgaData/inst/extdata/cnv/00de3/HONGS_p_TCGAb3_75_76_77_NSP_G.txt | 148 - GeoTcgaData-0.2.3/GeoTcgaData/inst/extdata/cnv/00e8/MICHE_p_TCGAb_428_429_NS.txt | 196 +- GeoTcgaData-0.2.3/GeoTcgaData/inst/extdata/cnv/00f9/MINAE_p_TCGA_200_202_203_S.txt | 938 +++++----- GeoTcgaData-0.2.3/GeoTcgaData/inst/extdata/cnv/0a01/KNELT_p_TCGA_b123_131_S.txt | 912 ++++----- GeoTcgaData-0.2.3/GeoTcgaData/inst/extdata/methy/0a0b4/jhu-usc.e.H.4.lvl-3.TCGA-13-1405-01A-01D-0460-05.g.txt | 28 GeoTcgaData-0.2.3/GeoTcgaData/inst/extdata/methy/0a0b4/logs/file1.parcel | 198 +- GeoTcgaData-0.2.3/GeoTcgaData/inst/extdata/methy/0a6b/jhu-usc.e.H.10.lvl-3.TCGA-30-1880-01A-01D-0652-05.g.txt | 28 GeoTcgaData-0.2.3/GeoTcgaData/inst/extdata/methy/0a6b/logs/file2.parcel | 198 +- GeoTcgaData-0.2.3/GeoTcgaData/inst/extdata/methy/0ae7/jhu-usc.H.8.l.I.TCGA-30-1714-01A-02D-0563-05.g.txt | 28 GeoTcgaData-0.2.3/GeoTcgaData/inst/extdata/methy/0ae7/logs/file3.parcel | 198 +- GeoTcgaData-0.2.3/GeoTcgaData/inst/extdata/methy/0b32/jhu-usc.e.H.5.l.TCGA-13-1510-01A-02D-0475-05.gdc_hg38.txt | 28 GeoTcgaData-0.2.3/GeoTcgaData/inst/extdata/methy/0b32/logs/file4.parcel | 198 +- GeoTcgaData-0.2.3/GeoTcgaData/man/hgnc_file.Rd |only GeoTcgaData-0.2.3/GeoTcgaData/man/id_ava.Rd |only GeoTcgaData-0.2.3/GeoTcgaData/man/id_conversion_vector.Rd | 4 GeoTcgaData-0.2.3/GeoTcgaData/vignettes/GeoTcgaData.Rmd | 6 30 files changed, 1851 insertions(+), 1807 deletions(-)
Title: Create Compact Hash Digests of R Objects
Description: Implementation of a function 'digest()' for the creation
of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256',
'crc32', 'xxhash', 'murmurhash' and 'spookyhash' algorithms) permitting easy
comparison of R language objects, as well as functions such as'hmac()' to
create hash-based message authentication code. Please note that this package
is not meant to be deployed for cryptographic purposes for which more
comprehensive (and widely tested) libraries such as 'OpenSSL' should be
used.
Author: Dirk Eddelbuettel <edd@debian.org> with contributions
by Antoine Lucas, Jarek Tuszynski, Henrik Bengtsson, Simon Urbanek,
Mario Frasca, Bryan Lewis, Murray Stokely, Hannes Muehleisen,
Duncan Murdoch, Jim Hester, Wush Wu, Qiang Kou, Thierry Onkelinx,
Michel Lang, Viliam Simko, Kurt Hornik, Radford Neal, Kendon Bell,
Matthew de Queljoe, Ion Suruceanu, and Bill Denney.
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between digest versions 0.6.24 dated 2020-02-12 and 0.6.25 dated 2020-02-22
ChangeLog | 8 ++++++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/digest.R | 2 +- inst/doc/sha1.html | 4 ++-- 5 files changed, 19 insertions(+), 11 deletions(-)
Title: Fits Cubic Bezier Spline Functions to Intertemporal and Risky
Choice Data
Description: Uses monotonically constrained Cubic Bezier Splines (CBS) to approximate latent utility functions in intertemporal choice and risky choice data.
PsyArXiv preprint: Lee, Glaze, Bradlow, Kable, (2019) <doi:10.31234/osf.io/2ugwr>.
Author: Sangil Lee [aut, cre]
Maintainer: Sangil Lee <sangillee3rd@gmail.com>
Diff between CBSr versions 1.0.2 dated 2020-02-22 and 1.0.3 dated 2020-02-22
DESCRIPTION | 12 ++++------ MD5 | 24 ++++++++++----------- NEWS.md | 21 ++++++++++++------- R/CBS_ITC.R | 24 ++++++++++++++++++++- R/CBS_RC.R | 22 +++++++++++++++++++- R/utils.R | 2 - README.md | 58 ++++++++--------------------------------------------- build/vignette.rds |binary inst/doc/CBS.Rnw | 2 - inst/doc/CBS.pdf |binary man/CBS_ITC.Rd | 21 +++++++++++++++++++ man/CBS_RC.Rd | 23 ++++++++++++++++++++- vignettes/CBS.Rnw | 2 - 13 files changed, 129 insertions(+), 82 deletions(-)
Title: Simulating the Development of h-Index Values
Description: H-index and h-alpha are a bibliometric indicators. This package
provides functions to simulate how these indicators may develop over time for
a given set of researchers and to visualize the simulation data.
The implementation is based on the 'STATA' ado h-index and is described in
more detail in Bornmann et al. (2019) <arXiv:1905.11052>.
Author: Alexander Tekles [aut, cre],
Lutz Bornmann [ctb],
Christian Ganser [ctb]
Maintainer: Alexander Tekles <alexander.tekles@soziologie.uni-muenchen.de>
Diff between hindex versions 0.1.0 dated 2019-07-12 and 0.2.0 dated 2020-02-22
DESCRIPTION | 10 MD5 | 23 NEWS.md | 14 R/plot_hsim.R | 358 +++++++++++---- R/simulate_hindex.R | 789 +++++++++++++++++++++++++++------- README.md | 12 man/figures/README-example-1.png |binary man/figures/README-example-2.png |binary man/figures/README-example-3.png |binary man/figures/README-example-4.png |only man/plot_hsim.Rd | 33 + man/simulate_hindex.Rd | 70 ++- tests/testthat/test-simulate_hindex.R | 131 +++++ 13 files changed, 1169 insertions(+), 271 deletions(-)
Title: Modelling Functions that Work with the Pipe
Description: Functions for modelling that help you seamlessly
integrate modelling into a pipeline of data manipulation and
visualisation.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between modelr versions 0.1.5 dated 2019-08-08 and 0.1.6 dated 2020-02-22
DESCRIPTION | 10 +++++----- MD5 | 30 +++++++++++++++--------------- NEWS.md | 4 ++++ R/bootstrap.R | 3 ++- R/na-warn.R | 1 - R/partition.R | 2 +- R/permute.R | 2 +- R/resample.R | 2 +- man/add_predictions.Rd | 3 +-- man/bootstrap.Rd | 7 +++++++ man/modelr-package.Rd | 2 +- man/na.warn.Rd | 2 -- man/resample.Rd | 7 +++++++ man/resample_bootstrap.Rd | 7 +++++++ man/resample_partition.Rd | 7 +++++++ man/seq_range.Rd | 2 +- 16 files changed, 60 insertions(+), 31 deletions(-)
Title: Enhancements for 'broom' Package Family
Description: Collection of functions to assist 'broom' and
'broom.mixed' package-related data analysis workflows. In particular,
the generic functions tidy(), glance(), and augment() choose
appropriate S3 methods from these two packages depending on which
package exports the needed method. The 'grouped_' variants of the
generics provides a convenient way to execute functions across a
combination of grouping variable(s) in a dataframe. Additionally,
tidy-and glance-like methods from 'parameters' and 'performance' can
also be accessed.
Author: Indrajeet Patil [aut, cre, ctb]
(<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between broomExtra versions 1.0.1 dated 2020-01-07 and 2.0.0 dated 2020-02-22
DESCRIPTION | 24 +-- MD5 | 39 +++-- NAMESPACE | 15 +- NEWS.md | 9 + R/easystats_to_tidy_names.R |only R/generics.R | 9 - R/generics_easystats.R |only R/reexports.R | 8 - README.md | 188 ++++++++++++++++++++++++-- build/broomExtra.pdf |binary inst/WORDLIST | 9 + inst/doc/available_methods.html | 48 ++---- inst/doc/tests_and_coverage.Rmd | 40 +++-- inst/doc/tests_and_coverage.html | 134 +++++++++++------- man/easystats_to_tidy_names.Rd |only man/glance_performance.Rd |only man/reexports.Rd | 51 +++---- man/tidy_parameters.Rd |only tests/README.md | 42 +++-- tests/spelling.R | 3 tests/testthat/test-easystats_to_tidy_names.R |only tests/testthat/test-generics.R | 17 -- tests/testthat/test-hybrid_generics.R |only vignettes/tests_and_coverage.Rmd | 40 +++-- 24 files changed, 443 insertions(+), 233 deletions(-)
Title: Set Operation
Description: More easy to get intersection, union or complementary set and combinations.
Author: Zhi Jin, Jing Zhang
Maintainer: Zhi Jin <nalanchongxuan@163.com>
Diff between set versions 1.0 dated 2019-09-20 and 1.1 dated 2020-02-22
set-1.0/set/R/COMMON.R |only set-1.0/set/R/and.R |only set-1.0/set/R/comp.R |only set-1.0/set/R/grapes_equals_grapes.R |only set-1.0/set/R/grepes_comp.R |only set-1.0/set/R/grepes_sub.R |only set-1.0/set/R/not.R |only set-1.0/set/R/or.R |only set-1.0/set/man/comp.Rd |only set-1.0/set/man/grapes-and-grapes.Rd |only set-1.0/set/man/grapes-comp-grapes.Rd |only set-1.0/set/man/grapes-not-grapes.Rd |only set-1.0/set/man/grapes-or-grapes.Rd |only set-1.0/set/man/grapes-sub-grapes.Rd |only set-1.1/set/DESCRIPTION | 6 ++-- set-1.1/set/MD5 | 43 +++++++++++++++------------------- set-1.1/set/NAMESPACE | 14 ++++++++--- set-1.1/set/R/a_and.R |only set-1.1/set/R/a_not.R |only set-1.1/set/R/a_or.R |only set-1.1/set/R/combination.R | 2 - set-1.1/set/R/grepes_and.R | 27 ++++++++++++++++++--- set-1.1/set/R/grepes_not.R | 26 ++++++++++++++++++-- set-1.1/set/R/grepes_or.R | 24 +++++++++++++++++- set-1.1/set/R/is.sub.R |only set-1.1/set/R/toVector.R | 35 ++++++++++++++++++--------- set-1.1/set/man/and.Rd | 6 ++-- set-1.1/set/man/and2.Rd |only set-1.1/set/man/is.sub.Rd |only set-1.1/set/man/not.Rd | 8 ++---- set-1.1/set/man/not2.Rd |only set-1.1/set/man/or.Rd | 4 +-- set-1.1/set/man/or2.Rd |only set-1.1/set/man/toVector.Rd |only 34 files changed, 134 insertions(+), 61 deletions(-)
Title: Hierarchical Climate Regionalization
Description: A tool for Hierarchical Climate Regionalization applicable to any correlation-based clustering.
It adds several features and a new clustering method (called, 'regional' linkage) to hierarchical
clustering in R ('hclust' function in 'stats' library): data regridding, coarsening spatial resolution,
geographic masking, contiguity-constrained clustering, data filtering by mean and/or variance
thresholds, data preprocessing (detrending, standardization, and PCA), faster correlation function
with preliminary big data support, different clustering methods, hybrid hierarchical clustering,
multivariate clustering (MVC), cluster validation, visualization of regionalization results, and
exporting region map and mean timeseries into NetCDF-4 file.
Author: Hamada S. Badr [aut, cre], Benjamin F. Zaitchik [aut], Amin K. Dezfuli [aut]
Maintainer: Hamada S. Badr <badr@jhu.edu>
Diff between HiClimR versions 2.1.5 dated 2019-12-10 and 2.1.6 dated 2020-02-22
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- R/HiClimR.R | 15 ++++++++------- R/HiClimR2nc.R | 7 ++++--- R/coarseR.R | 7 ++++--- R/fastCor.R | 7 ++++--- R/geogMask.R | 7 ++++--- R/grid2D.R | 7 ++++--- R/minSigCor.R | 7 ++++--- R/validClimR.R | 7 ++++--- README.md | 21 ++++++++++++++------- src/HiClimR.f90 | 5 +++-- 12 files changed, 67 insertions(+), 51 deletions(-)
Title: Fitting Linear Quantile Regression Mixed Models
Description: Fit a quantile regression mixed model using a sparse implementation of the
Frisch-Newton interior-point algorithm as described in
Portnoy and Koenker (1977, Statistical Science) <https://www.jstor.org/stable/2246217>.
Author: Sayyed Reza Alavian[aut,cre]
Majid Sarmad[ths]
Mehdi Jabbari Nooghabi[ths]
Hani Rezaee[ctb]
Saeed Zerehdaran[ctb]
Ferdowsi University Of Mashhad [cph]
Maintainer: Sayyed Reza Alavian <s.rezaalavian@mail.um.ac.ir>
Diff between LRQMM versions 1.2.0 dated 2020-01-07 and 1.2.1 dated 2020-02-22
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/lrqmm.R | 12 ++++++++---- man/lrqmm.Rd | 15 +++++++++++---- 4 files changed, 25 insertions(+), 14 deletions(-)
Title: Gianmarco Alberti Miscellaneous
Description: Contains many functions useful for univariate outlier detection, permutation-based t-test, permutation-based chi-square test, visualization of residuals, and bootstrap Cramer's V, plotting of the results of the Mann-Whitney and Kruskall-Wallis test, calculation of Brainerd-Robinson similarity coefficient and subsequent clustering, validation of logistic regression models, optimism-corrected AUC, robust Bland-Altman plot, calculation of posterior probability for different chronological relationships between two Bayesian radiocarbon phases, point pattern analysis, landform classification, clustering of spatial features.
Author: Gianmarco Alberti [aut, cre]
Maintainer: Gianmarco Alberti <gianmarcoalberti@gmail.com>
Diff between GmAMisc versions 1.0.0 dated 2018-08-14 and 1.1.0 dated 2020-02-22
DESCRIPTION | 12 ++--- MD5 | 27 +++++++------ NAMESPACE | 3 - NEWS.md |only R/NNa.R | 6 +- R/distDiffTest.R |only R/distRandSign.R | 99 ++++++++++++++++++++++++++++++++++++------------ R/perm_t_test.r | 56 +++++++++++++++++---------- R/pointsCovarCum.R | 2 R/pointsCovarDistr.R |only README.md | 43 +++++++++++++++++++- man/NNa.Rd | 4 - man/distDiffTest.Rd |only man/distRandSign.Rd | 19 ++++++++- man/perm.t.test.Rd | 25 +++++++----- man/pointsCovarCum.Rd | 2 man/pointsCovarDistr.Rd |only 17 files changed, 215 insertions(+), 83 deletions(-)
Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 4.1.0 dated 2019-12-17 and 4.2.0 dated 2020-02-22
secr-4.1.0/secr/src/apdot.cpp |only secr-4.2.0/secr/DESCRIPTION | 8 secr-4.2.0/secr/MD5 | 138 ++++++++--------- secr-4.2.0/secr/NAMESPACE | 2 secr-4.2.0/secr/NEWS | 24 ++ secr-4.2.0/secr/R/CV.R | 4 secr-4.2.0/secr/R/Fewstervarn.R | 119 ++++++++++---- secr-4.2.0/secr/R/RcppExports.R | 24 +- secr-4.2.0/secr/R/circular.R | 4 secr-4.2.0/secr/R/derivedMS.R | 23 +- secr-4.2.0/secr/R/esa.R | 41 +---- secr-4.2.0/secr/R/fastsecrloglik.R | 2 secr-4.2.0/secr/R/fxi.R | 209 +++++++++++++++----------- secr-4.2.0/secr/R/generalsecrloglik.R | 3 secr-4.2.0/secr/R/make.grid.R | 20 +- secr-4.2.0/secr/R/methods.R | 5 secr-4.2.0/secr/R/onLoad.R |only secr-4.2.0/secr/R/pdot.R | 42 ++--- secr-4.2.0/secr/R/preparedata.R | 36 +--- secr-4.2.0/secr/R/regionN.R | 5 secr-4.2.0/secr/R/reparameterize.R | 2 secr-4.2.0/secr/R/secr.design.MS.R | 2 secr-4.2.0/secr/R/secr.fit.R | 14 - secr-4.2.0/secr/R/sim.capthist.R | 1 secr-4.2.0/secr/R/suggest.buffer.R | 18 +- secr-4.2.0/secr/R/trap.builder.R | 156 +++++++++++++++++-- secr-4.2.0/secr/R/utility.R | 89 +++++++---- secr-4.2.0/secr/data/ovenbird.RData |binary secr-4.2.0/secr/data/ovensong.RData |binary secr-4.2.0/secr/data/possum.RData |binary secr-4.2.0/secr/data/secrdemo.RData |binary secr-4.2.0/secr/data/stoatDNA.RData |binary secr-4.2.0/secr/inst/doc/secr-datainput.pdf |binary secr-4.2.0/secr/inst/doc/secr-overview.Rmd | 32 ++- secr-4.2.0/secr/inst/doc/secr-overview.pdf |binary secr-4.2.0/secr/man/LLsurface.Rd | 6 secr-4.2.0/secr/man/OVpossum.Rd | 14 + secr-4.2.0/secr/man/PG.Rd | 2 secr-4.2.0/secr/man/Parallel.Rd | 112 ++++++++----- secr-4.2.0/secr/man/autoini.Rd | 7 secr-4.2.0/secr/man/confint.secr.Rd | 5 secr-4.2.0/secr/man/derivedMS.Rd | 5 secr-4.2.0/secr/man/details.Rd | 2 secr-4.2.0/secr/man/distancetotrap.Rd | 15 - secr-4.2.0/secr/man/empirical.Rd | 6 secr-4.2.0/secr/man/expected.n.Rd | 7 secr-4.2.0/secr/man/fx.total.Rd | 5 secr-4.2.0/secr/man/fxi.Rd | 19 -- secr-4.2.0/secr/man/make.lacework.Rd |only secr-4.2.0/secr/man/make.systematic.Rd | 23 ++ secr-4.2.0/secr/man/make.traps.Rd | 8 secr-4.2.0/secr/man/par.secr.fit.Rd | 8 secr-4.2.0/secr/man/pdot.Rd | 6 secr-4.2.0/secr/man/region.N.Rd | 11 - secr-4.2.0/secr/man/score.test.Rd | 7 secr-4.2.0/secr/man/secr-package.Rd | 4 secr-4.2.0/secr/man/secr.fit.Rd | 10 - secr-4.2.0/secr/man/secr.test.Rd | 5 secr-4.2.0/secr/man/setNumThreads.Rd |only secr-4.2.0/secr/man/sim.secr.Rd | 7 secr-4.2.0/secr/man/speed.Rd | 11 - secr-4.2.0/secr/man/suggest.buffer.Rd | 15 + secr-4.2.0/secr/man/trim.Rd | 4 secr-4.2.0/secr/src/RcppExports.cpp | 127 +++++++++------ secr-4.2.0/secr/src/detectfn.cpp | 225 ++++++++++++++-------------- secr-4.2.0/secr/src/pdot.cpp |only secr-4.2.0/secr/src/prwipolygonfxi.cpp |only secr-4.2.0/secr/src/prwisimple.cpp | 7 secr-4.2.0/secr/src/prwisimplefxi.cpp | 26 +-- secr-4.2.0/secr/src/secr.h | 22 +- secr-4.2.0/secr/src/trapping.cpp | 60 +++---- secr-4.2.0/secr/src/utils.cpp | 6 secr-4.2.0/secr/vignettes/secr-overview.Rmd | 32 ++- 73 files changed, 1113 insertions(+), 739 deletions(-)
Title: Multiple Imputation by Chained Equations with Random Forests
Description: Multiple Imputation has been shown to
be a flexible method to impute missing values by
Van Buuren (2007) <doi:10.1177/0962280206074463>.
Expanding on this, random forests have been shown
to be an accurate model by Stekhoven and Buhlmann
<arXiv:1105.0828> to impute missing values in datasets.
They have the added benefits of returning out of bag
error and variable importance estimates, as well as
being simple to run in parallel.
Author: Sam Wilson [aut, cre]
Maintainer: Sam Wilson <samwilson303@gmail.com>
Diff between miceRanger versions 1.3.1 dated 2020-02-14 and 1.3.4 dated 2020-02-22
miceRanger-1.3.1/miceRanger/R/fillMissing.R |only miceRanger-1.3.1/miceRanger/tests/testthat/test-miceRanger.R |only miceRanger-1.3.4/miceRanger/DESCRIPTION | 6 miceRanger-1.3.4/miceRanger/MD5 | 97 - miceRanger-1.3.4/miceRanger/NAMESPACE | 1 miceRanger-1.3.4/miceRanger/NEWS.md | 18 miceRanger-1.3.4/miceRanger/R/addDatasets.R | 15 miceRanger-1.3.4/miceRanger/R/addIterations.R | 15 miceRanger-1.3.4/miceRanger/R/amputeData.R | 4 miceRanger-1.3.4/miceRanger/R/completeData.R | 4 miceRanger-1.3.4/miceRanger/R/getCorrMetric.R | 2 miceRanger-1.3.4/miceRanger/R/getVarImps.R | 2 miceRanger-1.3.4/miceRanger/R/impute.R | 13 miceRanger-1.3.4/miceRanger/R/miceRanger.R | 131 +- miceRanger-1.3.4/miceRanger/R/plotDistributions.R | 2 miceRanger-1.3.4/miceRanger/R/plotImputationVariance.R | 9 miceRanger-1.3.4/miceRanger/R/plotModelError.R | 2 miceRanger-1.3.4/miceRanger/R/plotVarConvergence.R | 2 miceRanger-1.3.4/miceRanger/R/plotVarImportance.R | 7 miceRanger-1.3.4/miceRanger/R/runIterations.R | 20 miceRanger-1.3.4/miceRanger/R/sampleMiceDefs.R | 7 miceRanger-1.3.4/miceRanger/R/smallFuncs.R |only miceRanger-1.3.4/miceRanger/data/sampleMiceDefs.RData |binary miceRanger-1.3.4/miceRanger/inst/doc/diagnosticPlotting.R | 41 miceRanger-1.3.4/miceRanger/inst/doc/diagnosticPlotting.Rmd | 3 miceRanger-1.3.4/miceRanger/inst/doc/diagnosticPlotting.html | 598 ++++++--- miceRanger-1.3.4/miceRanger/inst/doc/miceAlgorithm.R | 64 - miceRanger-1.3.4/miceRanger/inst/doc/miceAlgorithm.Rmd | 2 miceRanger-1.3.4/miceRanger/inst/doc/miceAlgorithm.html | 608 ++++++--- miceRanger-1.3.4/miceRanger/inst/doc/usingMiceRanger.R | 195 +-- miceRanger-1.3.4/miceRanger/inst/doc/usingMiceRanger.Rmd | 13 miceRanger-1.3.4/miceRanger/inst/doc/usingMiceRanger.html | 637 ++++++---- miceRanger-1.3.4/miceRanger/man/addDatasets.Rd | 4 miceRanger-1.3.4/miceRanger/man/amputeData.Rd | 4 miceRanger-1.3.4/miceRanger/man/completeData.Rd | 2 miceRanger-1.3.4/miceRanger/man/getVarImps.Rd | 2 miceRanger-1.3.4/miceRanger/man/impute.Rd | 7 miceRanger-1.3.4/miceRanger/man/miceRanger.Rd | 64 - miceRanger-1.3.4/miceRanger/man/plotDistributions.Rd | 3 miceRanger-1.3.4/miceRanger/man/plotImputationVariance.Rd | 7 miceRanger-1.3.4/miceRanger/man/plotModelError.Rd | 2 miceRanger-1.3.4/miceRanger/man/plotVarConvergence.Rd | 2 miceRanger-1.3.4/miceRanger/man/plotVarImportance.Rd | 9 miceRanger-1.3.4/miceRanger/man/sampleMiceDefs.Rd | 7 miceRanger-1.3.4/miceRanger/tests/testthat/test-addingDatasets.R | 1 miceRanger-1.3.4/miceRanger/tests/testthat/test-addingIterations.R | 1 miceRanger-1.3.4/miceRanger/tests/testthat/test-comprehensive.R |only miceRanger-1.3.4/miceRanger/tests/testthat/test-plotting.R | 4 miceRanger-1.3.4/miceRanger/tests/testthat/test-setupFailures.R |only miceRanger-1.3.4/miceRanger/vignettes/diagnosticPlotting.Rmd | 3 miceRanger-1.3.4/miceRanger/vignettes/miceAlgorithm.Rmd | 2 miceRanger-1.3.4/miceRanger/vignettes/usingMiceRanger.Rmd | 13 52 files changed, 1690 insertions(+), 965 deletions(-)
Title: 'DataRobot' Predictive Modeling API
Description: For working with the 'DataRobot' predictive modeling platform's API <https://www.datarobot.com/>.
Author: Ron Pearson [aut], Zachary Deane-Mayer [aut], David Chudzicki [aut], Dallin Akagi [aut], Sergey Yurgenson [aut], Thakur Raj Anand [aut], Peter Hurford [aut]
Maintainer: Peter Hurford <api-maintainer@datarobot.com>
Diff between datarobot versions 2.16.0 dated 2020-01-07 and 2.17.0 dated 2020-02-22
datarobot-2.16.0/datarobot/R/TestUtilities.R |only datarobot-2.16.0/datarobot/R/TransferrableModels.R |only datarobot-2.16.0/datarobot/man/DeleteTransferrableModel.Rd |only datarobot-2.16.0/datarobot/man/DownloadTransferrableModel.Rd |only datarobot-2.16.0/datarobot/man/GetTransferrableModel.Rd |only datarobot-2.16.0/datarobot/man/ListTransferrableModels.Rd |only datarobot-2.16.0/datarobot/man/RequestTransferrableModel.Rd |only datarobot-2.16.0/datarobot/man/SetupProjectFromMySQL.Rd |only datarobot-2.16.0/datarobot/man/SetupProjectFromOracle.Rd |only datarobot-2.16.0/datarobot/man/SetupProjectFromPostgreSQL.Rd |only datarobot-2.16.0/datarobot/man/UpdateTransferrableModel.Rd |only datarobot-2.16.0/datarobot/man/UploadTransferrableModel.Rd |only datarobot-2.17.0/datarobot/DESCRIPTION | 6 datarobot-2.17.0/datarobot/MD5 | 132 +++-- datarobot-2.17.0/datarobot/NAMESPACE | 24 - datarobot-2.17.0/datarobot/NEWS | 32 + datarobot-2.17.0/datarobot/R/DataRobotRequests.R | 68 ++- datarobot-2.17.0/datarobot/R/Deployment.R |only datarobot-2.17.0/datarobot/R/Enums.R | 24 + datarobot-2.17.0/datarobot/R/FeatureAssociations.R |only datarobot-2.17.0/datarobot/R/FeatureLogs.R | 2 datarobot-2.17.0/datarobot/R/Featurelists.R | 3 datarobot-2.17.0/datarobot/R/Features.R | 168 +++++-- datarobot-2.17.0/datarobot/R/GetPredictions.R | 6 datarobot-2.17.0/datarobot/R/Partitions.R | 34 + datarobot-2.17.0/datarobot/R/PredictionDatasets.R | 24 - datarobot-2.17.0/datarobot/R/PredictionExplanations.R | 11 datarobot-2.17.0/datarobot/R/SetupProject.R | 222 ---------- datarobot-2.17.0/datarobot/R/StartAutopilot.R | 5 datarobot-2.17.0/datarobot/R/utils.R |only datarobot-2.17.0/datarobot/build/vignette.rds |binary datarobot-2.17.0/datarobot/inst/doc/AdvancedTuning.html | 4 datarobot-2.17.0/datarobot/inst/doc/AdvancedVignette.html | 6 datarobot-2.17.0/datarobot/inst/doc/Calendars.html | 4 datarobot-2.17.0/datarobot/inst/doc/ComparingSubsets.html | 4 datarobot-2.17.0/datarobot/inst/doc/ComplianceDocumentation.Rmd | 51 ++ datarobot-2.17.0/datarobot/inst/doc/ComplianceDocumentation.html | 52 ++ datarobot-2.17.0/datarobot/inst/doc/DatetimePartitionedProjects.html | 4 datarobot-2.17.0/datarobot/inst/doc/Deployment.R |only datarobot-2.17.0/datarobot/inst/doc/Deployment.Rmd |only datarobot-2.17.0/datarobot/inst/doc/Deployment.html |only datarobot-2.17.0/datarobot/inst/doc/IntroductionToDataRobot.Rmd | 2 datarobot-2.17.0/datarobot/inst/doc/IntroductionToDataRobot.html | 6 datarobot-2.17.0/datarobot/inst/doc/Multiclass.html | 4 datarobot-2.17.0/datarobot/inst/doc/PartialDependence.html | 4 datarobot-2.17.0/datarobot/inst/doc/PredictionExplanations.html | 4 datarobot-2.17.0/datarobot/inst/doc/RatingTables.html | 4 datarobot-2.17.0/datarobot/inst/doc/TimeSeries.R | 6 datarobot-2.17.0/datarobot/inst/doc/TimeSeries.Rmd | 14 datarobot-2.17.0/datarobot/inst/doc/TimeSeries.html | 14 datarobot-2.17.0/datarobot/inst/doc/TrainingPredictions.html | 4 datarobot-2.17.0/datarobot/inst/doc/VariableImportance.html | 4 datarobot-2.17.0/datarobot/man/BatchFeaturesTypeTransform.Rd |only datarobot-2.17.0/datarobot/man/CheckUrl.Rd |only datarobot-2.17.0/datarobot/man/CreateDatetimePartitionSpecification.Rd | 17 datarobot-2.17.0/datarobot/man/CreateDeployment.Rd |only datarobot-2.17.0/datarobot/man/DeleteDeployment.Rd |only datarobot-2.17.0/datarobot/man/ExpectHasKeys.Rd | 2 datarobot-2.17.0/datarobot/man/GenerateDatetimePartition.Rd | 16 datarobot-2.17.0/datarobot/man/GetDatetimePartition.Rd | 16 datarobot-2.17.0/datarobot/man/GetDeployment.Rd |only datarobot-2.17.0/datarobot/man/GetDeploymentDriftTrackingSettings.Rd |only datarobot-2.17.0/datarobot/man/GetFeatureAssociationMatrix.Rd |only datarobot-2.17.0/datarobot/man/GetFeatureAssociationMatrixDetails.Rd |only datarobot-2.17.0/datarobot/man/GetFeaturelist.Rd | 3 datarobot-2.17.0/datarobot/man/GetModelingFeaturelist.Rd | 3 datarobot-2.17.0/datarobot/man/GetTimeSeriesFeatureDerivationLog.Rd | 2 datarobot-2.17.0/datarobot/man/ListDeployments.Rd |only datarobot-2.17.0/datarobot/man/ListPredictionServers.Rd |only datarobot-2.17.0/datarobot/man/ListPredictions.Rd | 4 datarobot-2.17.0/datarobot/man/MakeDataRobotRequest.Rd | 6 datarobot-2.17.0/datarobot/man/ModelReplacementReason.Rd |only datarobot-2.17.0/datarobot/man/Predict.Rd | 10 datarobot-2.17.0/datarobot/man/ReplaceDeployedModel.Rd |only datarobot-2.17.0/datarobot/man/RequestPredictions.Rd | 11 datarobot-2.17.0/datarobot/man/UpdateDeploymentDriftTrackingSettings.Rd |only datarobot-2.17.0/datarobot/man/ValidateReplaceDeployedModel.Rd |only datarobot-2.17.0/datarobot/man/VariableTransformTypes.Rd |only datarobot-2.17.0/datarobot/tests/testthat/helper-fixtures.R | 9 datarobot-2.17.0/datarobot/tests/testthat/test-StartAutopilot.R | 19 datarobot-2.17.0/datarobot/vignettes/ComplianceDocumentation.Rmd | 51 ++ datarobot-2.17.0/datarobot/vignettes/Deployment.Rmd |only datarobot-2.17.0/datarobot/vignettes/IntroductionToDataRobot.Rmd | 2 datarobot-2.17.0/datarobot/vignettes/TimeSeries.Rmd | 14 84 files changed, 656 insertions(+), 481 deletions(-)