Title: Computing Subscores in Classical Test Theory and Item Response
Theory
Description: Functions for computing subscores for a test using different
methods in both classical test theory (CTT) and item response theory (IRT). This
package enables three sets of subscoring methods within the framework of CTT
and IRT: Wainer's augmentation method, Haberman's three subscoring methods, and
Yen's objective performance index (OPI). The package also includes the function
to compute Proportional Reduction of Mean Squared Errors (PRMSEs) in Haberman's
methods which are used to examine whether test subscores are of added value.
Author: Shenghai Dai [aut, cre],
Xiaolin Wang [aut],
Dubravka Svetina [aut]
Maintainer: Shenghai Dai <s.dai@wsu.edu>
Diff between subscore versions 3.0 dated 2019-03-03 and 3.1 dated 2019-04-12
DESCRIPTION | 10 +++++--- MD5 | 34 +++++++++++++++------------- NAMESPACE | 3 ++ R/CTTsub.R | 56 +++++++++++++++++++++++++++-------------------- R/Yen.Q3.r |only R/data.prep.R | 2 - R/subscore.corr.r | 11 ++++----- R/subscore.s.r | 26 +++++++++------------ R/subscore.sx.R | 27 ++++++++++------------ R/subscore.x.R | 29 ++++++++++-------------- data/TIMSS11G8M.data.rda |only man/CTTsub.Rd | 14 +++++++---- man/TIMSS11G8M.data.Rd |only man/Yen.Q3.Rd |only man/scored.data.Rd | 6 +++-- man/subscore.corr.Rd | 2 - man/subscore.s.Rd | 4 +-- man/subscore.sx.Rd | 4 +-- man/subscore.x.Rd | 4 +-- man/test.data.Rd | 3 -- 20 files changed, 123 insertions(+), 112 deletions(-)
Title: Calculate Accurate Precision-Recall and ROC (Receiver Operator
Characteristics) Curves
Description: Accurate calculations and visualization of precision-recall and ROC (Receiver Operator Characteristics)
curves.
Author: Takaya Saito [aut, cre],
Marc Rehmsmeier [aut]
Maintainer: Takaya Saito <takaya.saito@outlook.com>
Diff between precrec versions 0.10 dated 2019-03-05 and 0.10.1 dated 2019-04-12
precrec-0.10.1/precrec/DESCRIPTION | 8 precrec-0.10.1/precrec/MD5 | 34 --- precrec-0.10.1/precrec/NEWS.md | 4 precrec-0.10.1/precrec/R/RcppExports.R | 44 +-- precrec-0.10.1/precrec/build/vignette.rds |binary precrec-0.10.1/precrec/inst/doc/introduction.html | 111 +++++---- precrec-0.10.1/precrec/src/RcppExports.cpp | 190 ++++++++--------- precrec-0.10.1/precrec/src/precrec_misc.cpp |only precrec-0.10.1/precrec/src/precrec_misc.h |only precrec-0.10.1/precrec/src/precrec_mmx.cpp |only precrec-0.10.1/precrec/src/precrec_plx.cpp |only precrec-0.10/precrec/src/Makevars |only precrec-0.10/precrec/src/calc_auc.cpp |only precrec-0.10/precrec/src/calc_avg_curve.cpp |only precrec-0.10/precrec/src/calc_avg_point.cpp |only precrec-0.10/precrec/src/calc_basic_measures.cpp |only precrec-0.10/precrec/src/calc_uauc.cpp |only precrec-0.10/precrec/src/calc_uauc_frank.cpp |only precrec-0.10/precrec/src/conv_vec.cpp |only precrec-0.10/precrec/src/conv_vec.h |only precrec-0.10/precrec/src/convert_curve_avg_df.cpp |only precrec-0.10/precrec/src/convert_curve_df.cpp |only precrec-0.10/precrec/src/create_confusion_matrices.cpp |only precrec-0.10/precrec/src/create_prc_curve.cpp |only precrec-0.10/precrec/src/create_roc_curve.cpp |only precrec-0.10/precrec/src/format_labels.cpp |only precrec-0.10/precrec/src/get_score_ranks.cpp |only precrec-0.10/precrec/src/sort_indices_by_scores.cpp |only precrec-0.10/precrec/src/sort_indices_by_scores.h |only 29 files changed, 192 insertions(+), 199 deletions(-)
Title: Response Probability Functions
Description: The purpose of this package is to factor out logic and math common
to Item Factor Analysis fitting, diagnostics, and analysis. It is
envisioned as core support code suitable for more specialized IRT packages
to build upon. Complete access to optimized C functions are made available
with R_RegisterCCallable().
Author: Joshua Pritikin [cre, aut],
Jonathan Weeks [ctb],
Li Cai [ctb],
Carrie Houts [ctb],
Phil Chalmers [ctb],
Michael D. Hunter [ctb],
Carl F. Falk [ctb]
Maintainer: Joshua Pritikin <jpritikin@pobox.com>
Diff between rpf versions 0.60 dated 2019-03-08 and 0.62 dated 2019-04-12
DESCRIPTION | 9 +++-- MD5 | 21 +++++++------ NAMESPACE | 1 R/diagnose.R | 6 +-- R/util.R | 23 ++++++++++++++- inst/doc/diagnostics.html | 42 +++++++++++++-------------- man/SitemFit.Rd | 2 - man/collapseCategoricalCells.Rd |only src/diagnose.cpp | 61 ++++++++++++++++++++++++++-------------- src/glue.cpp | 2 - src/rpf.h | 2 - tests/testthat/test-fit.R | 13 ++++---- 12 files changed, 113 insertions(+), 69 deletions(-)
Title: Nested Association Mapping
Description: Designed for association studies in nested association mapping (NAM) panels, experimental and random panels. The method is described by Xavier et al. (2015) <doi:10.1093/bioinformatics/btv448>. It includes tools for genome-wide associations of multiple populations, marker quality control, population genetics analysis, genome-wide prediction, solving mixed models and finding variance components through likelihood and Bayesian methods.
Author: Alencar Xavier, William Muir, Katy Rainey, Shizhong Xu.
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between NAM versions 1.7.1 dated 2019-03-11 and 1.7.2 dated 2019-04-12
DESCRIPTION | 8 MD5 | 22 +- R/RcppExports.R | 8 R/reml.R | 2 inst/add/wgrMIXED.R | 453 +++++++++++++++++++++++++++++++++++++------ inst/doc/gwa_description.pdf |binary inst/doc/vignette1.html | 4 inst/doc/vignette2.html | 4 man/Internals.Rd | 4 man/NAM-package.Rd | 4 src/Functions.cpp | 199 ++++++++++++++++++ src/RcppExports.cpp | 27 ++ 12 files changed, 650 insertions(+), 85 deletions(-)
Title: A Wrapper for Querying KISTERS 'WISKI' Databases via the 'KiWIS'
API
Description: A wrapper for querying 'WISKI' databases via the 'KiWIS' 'REST' API. 'WISKI' is an 'SQL' relational database
used for the collection and storage of water data developed by KISTERS and 'KiWIS' is a 'REST' service that provides
access to 'WISKI' databases via HTTP requests (<https://water.kisters.de/en/technology-trends/kisters-and-open-data/>).
Contains a list of default databases (called 'hubs') and also allows users to provide their own 'KiWIS' URL.
Supports the entire query process- from metadata to specific time series values. All data is returned as tidy tibbles.
Author: Ryan Whaley [aut, cre],
Sam Albers [ctb]
Maintainer: Ryan Whaley <rdgwhaley@gmail.com>
Diff between kiwisR versions 0.1.4 dated 2019-03-10 and 0.1.5 dated 2019-04-12
DESCRIPTION | 6 +-- MD5 | 20 +++++----- NEWS.md | 17 +++++++++ R/ki_station_list.R | 6 +-- R/utils.R | 21 ----------- README.md | 54 ++++++++++++++++------------- tests/testthat/test_ki_group_list.R | 4 ++ tests/testthat/test_ki_station_list.R | 4 ++ tests/testthat/test_ki_timeseries_list.R | 4 ++ tests/testthat/test_ki_timeseries_values.R | 4 ++ tests/testthat/test_utils.R | 4 -- 11 files changed, 80 insertions(+), 64 deletions(-)
Title: Generalized Mortality Estimator
Description: Command-line and 'shiny' GUI implementation of the GenEst models for estimating bird and bat mortality at wind and solar power facilities, following Dalthorp, et al. (2018) <doi:10.3133/tm7A2>.
Author: Daniel Dalthorp [aut, cre],
Juniper Simonis [aut],
Lisa Madsen [aut],
Manuela Huso [aut],
Paul Rabie [aut],
Jeffrey Mintz [aut],
Robert Wolpert [aut],
Jared Studyvin [aut],
Franzi Korner-Nievergelt [aut]
Maintainer: Daniel Dalthorp <ddalthorp@usgs.gov>
Diff between GenEst versions 1.2.3 dated 2019-03-08 and 1.2.4 dated 2019-04-12
DESCRIPTION | 8 - MD5 | 26 ++-- R/app_content.R | 14 +- R/app_ui.R | 51 ++------ R/app_widgets.R | 20 +-- R/mortality_figure_functions.R | 5 R/mortality_functions.R | 6 R/searcher_efficiency_functions.R | 4 R/splits_figure_functions.R | 9 - build/vignette.rds |binary inst/doc/GenEstGUI.html | 9 - inst/doc/command-line-example.html | 125 ++++++++++---------- inst/doc/solar-examples.html | 35 +++-- inst/doc/wind-examples.html | 223 ++++++++++++++++++------------------- 14 files changed, 265 insertions(+), 270 deletions(-)
Title: Extracts Features from Text
Description: A tool for extracting some generic features (e.g., number of
words, line breaks, characters per word, URLs, lower case, upper case,
commas, periods, exclamation points, etc.) from strings of text.
Author: Michael Wayne Kearney [aut, cre]
(<https://orcid.org/0000-0002-0730-4694>)
Maintainer: Michael Wayne Kearney <kearneymw@missouri.edu>
Diff between textfeatures versions 0.3.0 dated 2018-11-29 and 0.3.2 dated 2019-04-12
textfeatures-0.3.0/textfeatures/R/min_var.R |only textfeatures-0.3.0/textfeatures/man/min_var.Rd |only textfeatures-0.3.2/textfeatures/DESCRIPTION | 10 textfeatures-0.3.2/textfeatures/MD5 | 28 - textfeatures-0.3.2/textfeatures/NAMESPACE | 10 textfeatures-0.3.2/textfeatures/NEWS.md | 7 textfeatures-0.3.2/textfeatures/R/count.R | 104 +++-- textfeatures-0.3.2/textfeatures/R/features-word_dims.R |only textfeatures-0.3.2/textfeatures/R/newdata.R |only textfeatures-0.3.2/textfeatures/R/sent.R |only textfeatures-0.3.2/textfeatures/R/sysdata.rda |binary textfeatures-0.3.2/textfeatures/R/textfeatures.R | 245 ++++--------- textfeatures-0.3.2/textfeatures/R/tweet-features.R |only textfeatures-0.3.2/textfeatures/R/utils.R | 4 textfeatures-0.3.2/textfeatures/R/word2vec.R | 23 - textfeatures-0.3.2/textfeatures/README.md | 1 textfeatures-0.3.2/textfeatures/man/textfeatures.Rd | 14 textfeatures-0.3.2/textfeatures/tests/testthat/test-main.R | 5 18 files changed, 219 insertions(+), 232 deletions(-)
Title: Execute Native Scripts
Description: Run complex native scripts with a single command, similar to system commands.
Author: Sagie Gur-Ari [aut, cre]
Maintainer: Sagie Gur-Ari <sagiegurari@gmail.com>
Diff between scriptexec versions 0.3.0 dated 2018-10-30 and 0.3.1 dated 2019-04-12
DESCRIPTION | 15 +++---- MD5 | 24 ++++++------ NAMESPACE | 1 NEWS.md | 6 +++ R/scriptexec.R | 51 +++++++++++++++++++------- README.md | 4 +- build/vignette.rds |binary man/create_system_call_args.Rd |only man/get_platform_value.Rd | 5 ++ man/modify_script.Rd | 4 +- tests/testthat/test_create_system_call_args.R |only tests/testthat/test_get_platform_value.R | 10 ++++- tests/testthat/test_modify_script.R | 22 ++++++++++- tools/build.R | 31 +++++++++++---- 14 files changed, 125 insertions(+), 48 deletions(-)
Title: Psychometric Functions from the Waller Lab
Description: Computes fungible coefficients and Monte Carlo data. Underlying theory for these functions is described in the following publications:
Waller, N. (2008). Fungible Weights in Multiple Regression. Psychometrika, 73(4), 691-703, <DOI:10.1007/s11336-008-9066-z>.
Waller, N. & Jones, J. (2009). Locating the Extrema of Fungible Regression Weights.
Psychometrika, 74(4), 589-602, <DOI:10.1007/s11336-008-9087-7>.
Waller, N. G. (2016). Fungible Correlation Matrices:
A Method for Generating Nonsingular, Singular, and Improper Correlation Matrices for
Monte Carlo Research. Multivariate Behavioral Research, 51(4), 554-568, <DOI:10.1080/00273171.2016.1178566>.
Jones, J. A. & Waller, N. G. (2015). The normal-theory and asymptotic distribution-free (ADF)
covariance matrix of standardized regression coefficients: theoretical extensions
and finite sample behavior. Psychometrika, 80, 365-378, <DOI:10.1007/s11336-013-9380-y>.
Waller, N. G. (2018). Direct Schmid-Leiman transformations and rank-deficient loadings matrices. Psychometrika, 83, 858-870. <DOI:10.1007/s11336-017-9599-0>.
Author: Niels Waller [aut, cre],
Jeff Jones [ctb],
Casey Giordano [ctb]
Maintainer: Niels Waller <nwaller@umn.edu>
Diff between fungible versions 1.80 dated 2019-03-06 and 1.81 dated 2019-04-12
fungible-1.80/fungible/inst/doc |only fungible-1.81/fungible/DESCRIPTION | 8 fungible-1.81/fungible/MD5 | 57 ++++--- fungible-1.81/fungible/NAMESPACE | 2 fungible-1.81/fungible/R/AmzBoxes.R |only fungible-1.81/fungible/R/GenerateBoxData.R |only fungible-1.81/fungible/R/HW.R |only fungible-1.81/fungible/R/faMAP.R | 9 - fungible-1.81/fungible/R/faMain.R | 210 +++++++++++++++++--------- fungible-1.81/fungible/R/faX.R | 33 +++- fungible-1.81/fungible/R/fals.R | 4 fungible-1.81/fungible/R/fapa.R | 85 +++++----- fungible-1.81/fungible/R/fareg.R |only fungible-1.81/fungible/R/orderFactors.R | 9 + fungible-1.81/fungible/R/rmsd.R | 5 fungible-1.81/fungible/data/AmzBoxes.rda |only fungible-1.81/fungible/data/HW.rda |only fungible-1.81/fungible/inst/CITATION | 4 fungible-1.81/fungible/man/AmzBoxes.Rd |only fungible-1.81/fungible/man/BiFAD.Rd | 28 ++- fungible-1.81/fungible/man/GenerateBoxData.Rd |only fungible-1.81/fungible/man/HW.Rd |only fungible-1.81/fungible/man/SLi.Rd | 21 +- fungible-1.81/fungible/man/SchmidLeiman.Rd | 26 ++- fungible-1.81/fungible/man/faAlign.Rd | 9 - fungible-1.81/fungible/man/faMAP.Rd | 4 fungible-1.81/fungible/man/faMain.Rd | 56 ++++-- fungible-1.81/fungible/man/faSort.Rd | 9 - fungible-1.81/fungible/man/faStandardize.Rd | 9 - fungible-1.81/fungible/man/faX.Rd | 47 ++++- fungible-1.81/fungible/man/fals.Rd | 9 - fungible-1.81/fungible/man/fapa.Rd | 13 - fungible-1.81/fungible/man/fareg.Rd |only fungible-1.81/fungible/man/orderFactors.Rd | 11 - fungible-1.81/fungible/man/promaxQ.Rd | 28 ++- 35 files changed, 460 insertions(+), 236 deletions(-)
Title: Fast and Exact Computation of Gaussian Stochastic Process
Description: Implements fast and exact computation of Gaussian stochastic process with the Matern kernel using forward filtering and backward smoothing algorithm. It allows for the cases with or without a noise. See the reference: Mengyang Gu and Yanxun Xu (2017) <arXiv:1711.11501>.
Author: Mengyang Gu [aut, cre]
Maintainer: Mengyang Gu <mgu6@jhu.edu>
Diff between FastGaSP versions 0.5.0 dated 2019-01-08 and 0.5.1 dated 2019-04-12
CHANGELOG |only DESCRIPTION | 8 +-- MD5 | 29 +++++----- R/RcppExports.R | 32 ++++++++---- R/functions.R | 23 ++++---- R/structure.R | 5 + build/partial.rdb |binary inst/extdata/example.r | 2 man/FastGaSP-package.Rd | 2 man/Get_log_det_S2.Rd | 3 - man/Kalman_smoother.Rd | 6 +- man/fgasp-class.Rd | 2 man/fgasp.Rd | 2 man/predict.fgasp.Rd | 7 +- src/RcppExports.cpp | 89 ++++++++++++++++++++++++--------- src/functions.cpp | 127 ++++++++++++++++++++++++++++++++++++++---------- 16 files changed, 241 insertions(+), 96 deletions(-)
Title: Duration-Based Quantities of Interest for the Cox Proportional
Hazards Model
Description: Functions for generating, simulating, and visualizing expected
durations and marginal changes in duration from the Cox proportional hazards
model.
Author: Kropko, Jonathan [aut, cre],
Harden, Jeffrey J. [aut]
Maintainer: "Kropko, Jonathan" <jkropko@virginia.edu>
Diff between coxed versions 0.2.0 dated 2018-08-23 and 0.2.4 dated 2019-04-12
DESCRIPTION | 8 MD5 | 62 NEWS.md |only R/boxsteffensmeier.R | 1 R/coxed.gam.tvc.R | 29 R/coxed.npsf.tvc.R | 37 R/coxed.package.R | 1 R/generate.lm.R | 18 R/sim.survdata.R | 6 build/vignette.rds |binary inst/doc/coxed.R | 22 inst/doc/coxed.Rmd | 28 inst/doc/coxed.html | 622 +++++-- inst/doc/simulating_survival_data.R | 2 inst/doc/simulating_survival_data.Rmd | 4 inst/doc/simulating_survival_data.html | 790 ++++++---- man/bootcov2.Rd | 5 man/boxsteffensmeier.Rd | 1 man/coxed-package.Rd | 1 man/coxed.gam.tvc.Rd | 5 man/generate.lm.Rd | 4 man/sim.survdata.Rd | 8 vignettes/coxed.Rmd | 28 vignettes/coxed_files |only vignettes/simulating_survival_data.Rmd | 4 vignettes/simulating_survival_data_cache/html/simsurv10_1d13901b75a23b9fd48ba1cba7e3cc8b.RData |binary vignettes/simulating_survival_data_cache/html/simsurv10_1d13901b75a23b9fd48ba1cba7e3cc8b.rdb |binary vignettes/simulating_survival_data_cache/html/simsurv10_1d13901b75a23b9fd48ba1cba7e3cc8b.rdx |binary vignettes/simulating_survival_data_files |only 29 files changed, 1093 insertions(+), 593 deletions(-)
Title: Recursive Partitioning and Regression Trees
Description: Recursive partitioning for classification,
regression and survival trees. An implementation of most of the
functionality of the 1984 book by Breiman, Friedman, Olshen and Stone.
Author: Terry Therneau [aut],
Beth Atkinson [aut, cre],
Brian Ripley [trl] (producer of the initial R port, maintainer
1999-2017)
Maintainer: Beth Atkinson <atkinson@mayo.edu>
Diff between rpart versions 4.1-13 dated 2018-02-23 and 4.1-15 dated 2019-04-12
rpart-4.1-13/rpart/data/solder.tab.gz |only rpart-4.1-13/rpart/man/solder.Rd |only rpart-4.1-15/rpart/ChangeLog | 7 + rpart-4.1-15/rpart/DESCRIPTION | 11 +- rpart-4.1-15/rpart/MD5 | 84 ++++++++-------- rpart-4.1-15/rpart/README.md |only rpart-4.1-15/rpart/build/vignette.rds |binary rpart-4.1-15/rpart/data/solder.rda |only rpart-4.1-15/rpart/inst/NEWS.Rd | 14 ++ rpart-4.1-15/rpart/inst/doc/longintro.R | 22 ++-- rpart-4.1-15/rpart/inst/doc/longintro.Rnw | 21 +--- rpart-4.1-15/rpart/inst/doc/longintro.pdf |binary rpart-4.1-15/rpart/inst/doc/usercode.Rnw | 68 +++++++++++++ rpart-4.1-15/rpart/inst/doc/usercode.pdf |binary rpart-4.1-15/rpart/man/figures |only rpart-4.1-15/rpart/man/post.rpart.Rd | 3 rpart-4.1-15/rpart/man/residuals.rpart.Rd | 2 rpart-4.1-15/rpart/man/solder.balance.Rd |only rpart-4.1-15/rpart/tests/Examples/rpart-Ex.Rout.save | 96 +++++++++---------- rpart-4.1-15/rpart/tests/backticks.R | 1 rpart-4.1-15/rpart/tests/backticks.Rout.save | 10 - rpart-4.1-15/rpart/tests/cost.R | 1 rpart-4.1-15/rpart/tests/cost.Rout.save | 11 -- rpart-4.1-15/rpart/tests/cptest.R | 2 rpart-4.1-15/rpart/tests/cptest.Rout.save | 11 +- rpart-4.1-15/rpart/tests/priors.R | 1 rpart-4.1-15/rpart/tests/priors.Rout.save | 10 - rpart-4.1-15/rpart/tests/rescale.R | 1 rpart-4.1-15/rpart/tests/rescale.Rout.save | 11 -- rpart-4.1-15/rpart/tests/testall.R | 2 rpart-4.1-15/rpart/tests/testall.Rout.save | 12 -- rpart-4.1-15/rpart/tests/treble.R | 1 rpart-4.1-15/rpart/tests/treble.Rout.save | 10 - rpart-4.1-15/rpart/tests/treble2.R | 2 rpart-4.1-15/rpart/tests/treble2.Rout.save | 11 +- rpart-4.1-15/rpart/tests/treble3.R | 2 rpart-4.1-15/rpart/tests/treble3.Rout.save | 11 +- rpart-4.1-15/rpart/tests/treble4.R | 1 rpart-4.1-15/rpart/tests/treble4.Rout.save | 10 - rpart-4.1-15/rpart/tests/usersplits.Rout.save | 9 - rpart-4.1-15/rpart/tests/xpred1.R | 1 rpart-4.1-15/rpart/tests/xpred1.Rout.save | 10 - rpart-4.1-15/rpart/tests/xpred2.R | 1 rpart-4.1-15/rpart/tests/xpred2.Rout.save | 11 -- rpart-4.1-15/rpart/vignettes/longintro.Rnw | 21 +--- rpart-4.1-15/rpart/vignettes/usercode.Rnw | 68 +++++++++++++ 46 files changed, 373 insertions(+), 197 deletions(-)
Title: Nonparametric and Stochastic Efficiency and Productivity
Analysis
Description: Provides a variety of tools for nonparametric and parametric efficiency measurement.
Author: Oleg Badunenko [aut, cre],
Yaryna Kolomiytseva [aut],
Pavlo Mozharovskyi [aut]
Maintainer: Oleg Badunenko <oleg.badunenko@port.ac.uk>
Diff between npsf versions 0.4.2 dated 2019-01-02 and 0.5.1 dated 2019-04-12
ChangeLog | 8 DESCRIPTION | 10 MD5 | 25 - NAMESPACE | 2 R/nobs.npsf.R | 7 R/npsf-internal.R | 383 +++++++++++++++++++++++++ R/print.summary.npsf.R | 192 ++++++++++++ R/sf.R | 724 +++++++++++++++++++++++++++++++++++++++---------- man/sf.Rd | 55 +++ src/Makevars | 2 src/Makevars.win | 2 src/fourcomp.c |only src/init.c | 6 src/radial.cpp | 2 14 files changed, 1236 insertions(+), 182 deletions(-)
Title: Network-Based Genome Wide Association Studies
Description: A multi-core R package that contains a set of tools based on undirected graphical
models for accomplishing three important and interrelated goals in genetics: (1)
linkage map construction, (2) reconstructing intra- and inter-chromosomal conditional
interactions (linkage disequilibrium) networks, and (3) exploring high-dimensional
genotype-phenotype network and genotype-phenotype-environment interactions network.
We use conditional independence relationships between variables.
The netgwas package can deal with biparental inbreeding and outbreeding species with
any ploidy level, namely diploid (2 sets of chromosomes), triploid (3 sets of chromosomes),
tetraploid (4 sets of chromosomes) and so on. We target on high-dimensional data where
number of variables p is larger than number of sample sizes (p >> n). The computations
is memory-optimized using the sparse matrix output. The package is implemented the recent
developments in Behrouzi and Wit (2017) <doi:10.1111/rssc.12287> and Behrouzi and Wit (2017)
<arXiv:1710.01063>.
NOTICE proper functionality of 'netgwas' requires that the 'RBGL' package is installed from 'bioconductor'; for installation instruction please refer to the 'RBGL' web page given below.
Author: Pariya Behrouzi <https://orcid.org/0000-0001-6762-5433> and Ernst C. Wit
Maintainer: Pariya Behrouzi <pariya.behrouzi@gmail.com>
Diff between netgwas versions 1.9 dated 2019-03-26 and 1.10 dated 2019-04-12
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/netmap.R | 3 ++- R/netsnp.R | 6 +++--- R/selectnet.R | 4 +++- 5 files changed, 16 insertions(+), 13 deletions(-)
Title: Psychometric Meta-Analysis Toolkit
Description: Tools for computing bare-bones and psychometric meta-analyses and for generating psychometric data for use in meta-analysis simulations. Supports bare-bones, individual-correction, and artifact-distribution methods for meta-analyzing correlations and d values. Includes tools for converting effect sizes, computing sporadic artifact corrections, reshaping meta-analytic databases, computing multivariate corrections for range variation, and more. Bugs can be reported to <https://github.com/psychmeta/psychmeta/issues> or <issues@psychmeta.com>.
Author: Jeffrey A. Dahlke [aut, cre],
Brenton M. Wiernik [aut],
Michael T. Brannick [ctb] (Testing),
Jack Kostal [ctb] (Code for reshape_mat2dat function),
Sean Potter [ctb] (Testing; Code for cumulative and leave1out plots),
John Sakaluk [ctb] (Code for funnel and forest plots),
Yuejia (Mandy) Teng [ctb] (Testing)
Maintainer: Jeffrey A. Dahlke <dahlk068@umn.edu>
Diff between psychmeta versions 2.3.2 dated 2019-02-26 and 2.3.3 dated 2019-04-12
DESCRIPTION | 10 +- MD5 | 21 ++-- NEWS | 13 +++ R/convert_ma.R | 13 +++ R/get_stuff.R | 75 +++++++++-------- R/heterogeneity.R | 185 ++++++++++++++++++++++++++++++++++++++++--- R/impute_artifacts_wrapper.R | 16 ++- R/ma_r.R | 2 R/output.R | 6 - R/sensitivity_cumulative.R | 4 R/simulate_r.R | 10 +- man/conf.limits.nc.chisq.Rd |only 12 files changed, 283 insertions(+), 72 deletions(-)
Title: A Tool to Associate FASTA Sequences and Features
Description: Provides user friendly methods for the identification of sequence patterns that are statistically significantly associated with a property of the sequence. For instance, SeqFeatR allows to identify viral immune escape mutations for hosts of given HLA types. The underlying statistical method is Fisher's exact test, with appropriate corrections for multiple testing, or Bayes. Patterns may be point mutations or n-tuple of mutations. SeqFeatR offers several ways to visualize the results of the statistical analyses, see Budeus (2016) <doi:10.1371/journal.pone.0146409>.
Author: Bettina Budeus
Maintainer: Bettina Budeus <bettina.budeus@stud.uni-due.de>
Diff between SeqFeatR versions 0.3 dated 2018-11-30 and 0.3.1 dated 2019-04-12
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 5 +++++ R/getfreqs.R | 13 +++++++------ R/orPlot.R | 3 ++- build/vignette.rds |binary inst/doc/SeqFeatR_tutorial.pdf |binary 7 files changed, 24 insertions(+), 17 deletions(-)
Title: Variance Stabilizing Transformations for Single Cell UMI Data
Description: A normalization method for single-cell UMI count data using a
variance stabilizing transformation. The transformation is based on a
negative binomial regression model with regularized parameters. As part of the
same regression framework, this package also provides functions for
batch correction, and data correction. See Hafemeister and Satija 2019
<doi:10.1101/576827> for more details.
Author: Christoph Hafemeister [aut, cre]
(<https://orcid.org/0000-0001-6365-8254>)
Maintainer: Christoph Hafemeister <chafemeister@nygenome.org>
Diff between sctransform versions 0.1.0 dated 2018-11-18 and 0.2.0 dated 2019-04-12
sctransform-0.1.0/sctransform/man/denoise.Rd |only sctransform-0.1.0/sctransform/man/get_deviance_residuals.Rd |only sctransform-0.2.0/sctransform/DESCRIPTION | 23 - sctransform-0.2.0/sctransform/MD5 | 42 + sctransform-0.2.0/sctransform/NAMESPACE | 24 - sctransform-0.2.0/sctransform/R/RcppExports.R |only sctransform-0.2.0/sctransform/R/data.R | 4 sctransform-0.2.0/sctransform/R/denoise.R | 151 +++++- sctransform-0.2.0/sctransform/R/differential_expression.R |only sctransform-0.2.0/sctransform/R/plotting.R |only sctransform-0.2.0/sctransform/R/utils.R | 139 +++++- sctransform-0.2.0/sctransform/R/vst.R | 230 ++++++---- sctransform-0.2.0/sctransform/README.md | 19 sctransform-0.2.0/sctransform/man/compare_expression.Rd |only sctransform-0.2.0/sctransform/man/correct.Rd |only sctransform-0.2.0/sctransform/man/correct_counts.Rd |only sctransform-0.2.0/sctransform/man/get_residual_var.Rd |only sctransform-0.2.0/sctransform/man/get_residuals.Rd |only sctransform-0.2.0/sctransform/man/pbmc.Rd | 4 sctransform-0.2.0/sctransform/man/plot_model.Rd |only sctransform-0.2.0/sctransform/man/plot_model_pars.Rd |only sctransform-0.2.0/sctransform/man/robust_scale_binned.Rd | 5 sctransform-0.2.0/sctransform/man/row_gmean.Rd |only sctransform-0.2.0/sctransform/man/row_var.Rd |only sctransform-0.2.0/sctransform/man/smooth_via_pca.Rd |only sctransform-0.2.0/sctransform/man/vst.Rd | 32 - sctransform-0.2.0/sctransform/src |only sctransform-0.2.0/sctransform/tests/testthat/test_denoising.R | 22 sctransform-0.2.0/sctransform/tests/testthat/test_differential_expression.R |only sctransform-0.2.0/sctransform/tests/testthat/test_vst.R | 4 30 files changed, 516 insertions(+), 183 deletions(-)
Title: XML Output Functions for Easy Creation of Moodle Questions
Description: Provides a set of basic functions for creating Moodle XML
output files suited for importing questions in Moodle (a learning
management system, see <https://moodle.org/> for more information).
Author: Emmanuel Curis [aut, cre]
Maintainer: Emmanuel Curis <emmanuel.curis@parisdescartes.fr>
Diff between SARP.moodle versions 0.3.9 dated 2019-03-28 and 0.3.10 dated 2019-04-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/conversion_csv.R | 2 +- man/libre.moodle.Rd | 17 +++++++++-------- 4 files changed, 17 insertions(+), 16 deletions(-)
Title: Systematic Conservation Prioritization in R
Description: Conservation prioritization using integer
programming techniques. To solve large-scale problems, users
should install the 'gurobi' optimizer
(available from <http://www.gurobi.com/>).
Author: Jeffrey O Hanson [aut],
Richard Schuster [aut, cre],
Nina Morrell [aut],
Matthew Strimas-Mackey [aut],
Matthew E Watts [aut],
Peter Arcese [aut],
Joeseph Bennett [aut],
Hugh P Possingham [aut]
Maintainer: Richard Schuster <richard.schuster@glel.carleton.ca>
Diff between prioritizr versions 4.0.3 dated 2019-04-08 and 4.0.4 dated 2019-04-12
DESCRIPTION | 10 MD5 | 610 +- NAMESPACE | 346 - R/ArrayParameter-proto.R | 288 - R/Collection-proto.R | 334 - R/ConservationModifier-proto.R | 362 - R/ConservationProblem-proto.R | 1206 ++--- R/Constraint-proto.R | 48 R/Decision-proto.R | 50 R/Id.R | 114 R/MiscParameter-proto.R | 208 R/Objective-proto.R | 44 R/OptimizationProblem-methods.R | 622 +- R/OptimizationProblem-proto.R | 402 - R/Parameter-proto.R | 152 R/Parameters-proto.R | 330 - R/Penalty-proto.R | 50 R/Portfolio-proto.R | 188 R/RcppExports.R | 342 - R/ScalarParameter-proto.R | 258 - R/Solver-proto.R | 186 R/Target-proto.R | 48 R/add_absolute_targets.R | 432 - R/add_binary_decisions.R | 160 R/add_boundary_penalties.R | 658 +-- R/add_connectivity_penalties.R | 1066 ++-- R/add_contiguity_constraints.R | 610 +- R/add_cuts_portfolio.R | 254 - R/add_default_decisions.R | 34 R/add_default_objective.R | 18 R/add_default_portfolio.R | 32 R/add_default_solver.R | 78 R/add_default_targets.R | 18 R/add_feature_contiguity_constraints.R | 748 +-- R/add_feature_weights.R | 562 +- R/add_gurobi_solver.R | 334 - R/add_locked_in_constraints.R | 670 +-- R/add_locked_out_constraints.R | 568 +- R/add_loglinear_targets.R | 306 - R/add_lpsymphony_solver.R | 246 - R/add_mandatory_allocation_constraints.R | 204 R/add_manual_locked_constraints.R | 492 +- R/add_manual_targets.R | 634 +- R/add_max_cover_objective.R | 368 - R/add_max_features_objective.R | 314 - R/add_max_phylo_objective.R | 534 +- R/add_max_utility_objective.R | 294 - R/add_min_set_objective.R | 216 R/add_neighbor_contraints.R | 698 +-- R/add_pool_portfolio.R | 314 - R/add_proportion_decisions.R | 144 R/add_relative_targets.R | 332 - R/add_rsymphony_solver.R | 262 - R/add_semicontinuous_decisions.R | 168 R/add_shuffle_portfolio.R | 308 - R/binary_stack.R | 100 R/boundary_matrix.R | 350 - R/branch_matrix.R | 112 R/category_layer.R | 102 R/category_vector.R | 122 R/compile.R | 274 - R/connected_matrix.R | 360 - R/connectivity_matrix.R | 318 - R/constraints.R | 188 R/data.R | 386 - R/decisions.R | 160 R/deprecated.R | 72 R/fast_extract.R | 332 - R/feature_abundances.R | 324 - R/feature_names.R | 134 R/feature_representation.R | 818 +-- R/internal.R | 626 +- R/intersecting_units.R | 340 - R/loglinear_interpolation.R | 112 R/magrittr-operators.R | 152 R/marxan_boundary_data_to_matrix.R | 312 - R/marxan_problem.R | 722 +-- R/misc.R | 84 R/new_optimization_problem.R | 42 R/number_of_features.R | 152 R/number_of_planning_units.R | 116 R/number_of_total_units.R | 128 R/number_of_zones.R | 154 R/objectives.R | 160 R/package.R | 168 R/parallel.R | 368 - R/parameters.R | 996 ++-- R/penalties.R | 140 R/portfolios.R | 144 R/pproto.R | 150 R/predefined_optimization_problem.R | 198 R/print.R | 216 R/problem.R | 1658 +++---- R/rij_matrix.R | 262 - R/run_calculations.R | 164 R/show.R | 144 R/simulate.R | 264 - R/solve.R | 636 +- R/solvers.R | 212 R/targets.R | 150 R/tbl_df.R | 148 R/waiver.R | 62 R/zone_names.R | 140 R/zones.R | 382 - R/zzz.R | 12 README.md | 704 +-- build/vignette.rds |binary data/sim_features.rda |binary data/sim_features_zones.rda |binary data/sim_locked_in_raster.rda |binary data/sim_locked_out_raster.rda |binary data/sim_phylogeny.rda |binary data/sim_pu_lines.rda |binary data/sim_pu_points.rda |binary data/sim_pu_polygons.rda |binary data/sim_pu_raster.rda |binary data/sim_pu_zones_polygons.rda |binary data/sim_pu_zones_stack.rda |binary inst/doc/gurobi_installation.Rmd | 382 - inst/doc/gurobi_installation.html | 816 ++- inst/doc/prioritizr.Rmd | 1430 +++--- inst/doc/prioritizr.html | 2818 ++++++------- inst/doc/publication_record.Rmd | 62 inst/doc/publication_record.html | 346 + inst/doc/saltspring.Rmd | 400 - inst/doc/saltspring.html | 818 ++- inst/doc/tasmania.Rmd | 454 +- inst/doc/tasmania.html | 1134 +++-- inst/doc/zones.Rmd | 646 +- inst/doc/zones.html | 1900 ++++---- inst/extdata/input.dat | 110 inst/extdata/simulate_data.R | 320 - man/ArrayParameter-class.Rd | 200 man/Collection-class.Rd | 194 man/ConservationModifier-class.Rd | 256 - man/ConservationProblem-class.Rd | 594 +- man/Constraint-class.Rd | 32 man/Decision-class.Rd | 34 man/MiscParameter-class.Rd | 166 man/Objective-class.Rd | 26 man/OptimizationProblem-class.Rd | 248 - man/OptimizationProblem-methods.Rd | 288 - man/Parameter-class.Rd | 118 man/Parameters-class.Rd | 180 man/Penalty-class.Rd | 34 man/Portfolio-class.Rd | 132 man/ScalarParameter-class.Rd | 182 man/Solver-class.Rd | 134 man/Target-class.Rd | 32 man/add_absolute_targets.Rd | 308 - man/add_binary_decisions.Rd | 140 man/add_boundary_penalties.Rd | 486 +- man/add_connectivity_penalties.Rd | 820 +-- man/add_contiguity_constraints.Rd | 412 - man/add_cuts_portfolio.Rd | 170 man/add_default_decisions.Rd | 38 man/add_default_solver.Rd | 50 man/add_feature_contiguity_constraints.Rd | 446 +- man/add_feature_weights.Rd | 424 - man/add_gurobi_solver.Rd | 172 man/add_locked_in_constraints.Rd | 438 +- man/add_locked_out_constraints.Rd | 334 - man/add_loglinear_targets.Rd | 222 - man/add_lsymphony_solver.Rd | 166 man/add_mandatory_allocation_constraints.Rd | 148 man/add_manual_locked_constraints.Rd | 272 - man/add_manual_targets.Rd | 406 - man/add_max_cover_objective.Rd | 314 - man/add_max_features_objective.Rd | 254 - man/add_max_phylo_objective.Rd | 434 +- man/add_max_utility_objective.Rd | 240 - man/add_min_set_objective.Rd | 194 man/add_neighbor_constraints.Rd | 384 - man/add_pool_portfolio.Rd | 228 - man/add_proportion_decisions.Rd | 144 man/add_relative_targets.Rd | 302 - man/add_rsymphony_solver.Rd | 154 man/add_semicontinuous_decisions.Rd | 160 man/add_shuffle_portfolio.Rd | 164 man/array_parameters.Rd | 254 - man/as.Rd | 58 man/as.list.Rd | 38 man/binary_stack.Rd | 82 man/boundary_matrix.Rd | 194 man/branch_matrix.Rd | 90 man/category_layer.Rd | 88 man/category_vector.Rd | 94 man/compile.Rd | 118 man/connected_matrix.Rd | 226 - man/connectivity_matrix.Rd | 192 man/constraints.Rd | 192 man/decisions.Rd | 164 man/distribute_load.Rd | 142 man/fast_extract.Rd | 158 man/feature_abundances.Rd | 290 - man/feature_names.Rd | 78 man/feature_representation.Rd | 430 - man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-13-1.png |binary man/figures/README-unnamed-chunk-14-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/intersecting_units.Rd | 150 man/is.Rd | 42 man/is.parallel.Rd | 72 man/loglinear_interpolation.Rd | 92 man/marxan_boundary_data_to_matrix.Rd | 112 man/marxan_problem.Rd | 378 - man/matrix_parameters.Rd | 128 man/misc_parameter.Rd | 122 man/new_id.Rd | 70 man/new_optimization_problem.Rd | 48 man/new_waiver.Rd | 64 man/number_of_features.Rd | 86 man/number_of_planning_units.Rd | 74 man/number_of_total_units.Rd | 98 man/number_of_zones.Rd | 90 man/objectives.Rd | 164 man/parallel.Rd | 98 man/parameters.Rd | 66 man/penalties.Rd | 144 man/pipe.Rd | 62 man/portfolios.Rd | 148 man/pproto.Rd | 88 man/predefined_optimization_problem.Rd | 142 man/print.Rd | 108 man/prioritizr-deprecated.Rd | 64 man/prioritizr.Rd | 158 man/problem.Rd | 850 +-- man/rij_matrix.Rd | 144 man/run_calculations.Rd | 154 man/scalar_parameters.Rd | 230 - man/show.Rd | 76 man/sim_data.Rd | 336 - man/simulate_cost.Rd | 98 man/simulate_data.Rd | 94 man/simulate_species.Rd | 94 man/solve.Rd | 372 - man/solvers.Rd | 214 man/targets.Rd | 140 man/tee.Rd | 74 man/tibble-methods.Rd | 104 man/zone_names.Rd | 84 man/zones.Rd | 224 - src/Makevars | 6 tests/testthat.R | 28 tests/testthat/test_Id.R | 26 tests/testthat/test_OptimizationProblem.R | 246 - tests/testthat/test_Waiver.R | 22 tests/testthat/test_add_absolute_targets.R | 452 +- tests/testthat/test_add_boundary_penalties.R | 784 +-- tests/testthat/test_add_connectivity_penalties.R | 592 +- tests/testthat/test_add_contiguity_constraints.R | 492 +- tests/testthat/test_add_cuts_portfolio.R | 414 - tests/testthat/test_add_feature_contiguity_constraints.R | 878 ++-- tests/testthat/test_add_feature_weights.R | 726 +-- tests/testthat/test_add_locked_in_constraints.R | 1116 ++--- tests/testthat/test_add_locked_out_constraints.R | 1108 ++--- tests/testthat/test_add_loglinear_targets.R | 196 tests/testthat/test_add_mandatory_allocation_constraints.R | 370 - tests/testthat/test_add_manual_locked_constraints.R | 340 - tests/testthat/test_add_manual_targets.R | 360 - tests/testthat/test_add_max_cover_objective.R | 1048 ++-- tests/testthat/test_add_max_features_objective.R | 1210 ++--- tests/testthat/test_add_max_phylo_objective.R | 1530 +++---- tests/testthat/test_add_max_utility_objective.R | 1068 ++-- tests/testthat/test_add_min_set_objective.R | 626 +- tests/testthat/test_add_neighbor_constraints.R | 488 +- tests/testthat/test_add_pool_portfolio.R | 548 +- tests/testthat/test_add_relative_targets.R | 408 - tests/testthat/test_add_shuffle_portfolio.R | 538 +- tests/testthat/test_binary_stack.R | 66 tests/testthat/test_boundary_matrix.R | 360 - tests/testthat/test_branch_matrix.R | 68 tests/testthat/test_category_layer.R | 78 tests/testthat/test_category_vector.R | 58 tests/testthat/test_compile.R | 206 tests/testthat/test_connected_matrix.R | 200 tests/testthat/test_connectivity_matrix.R | 218 - tests/testthat/test_decisions.R | 446 +- tests/testthat/test_feature_abundances.R | 370 - tests/testthat/test_feature_representation.R | 702 +-- tests/testthat/test_internal.R | 82 tests/testthat/test_intersecting_units.R | 102 tests/testthat/test_marxan_problem.R | 506 +- tests/testthat/test_parallel.R | 80 tests/testthat/test_parameters.R | 864 +-- tests/testthat/test_pproto.R | 200 tests/testthat/test_problem.R | 1816 ++++---- tests/testthat/test_problem_negative.R | 1378 +++--- tests/testthat/test_rij_matrix.R | 230 - tests/testthat/test_simulate.R | 80 tests/testthat/test_solve.R | 560 +- tests/testthat/test_solvers.R | 210 tests/testthat/test_sp_to_polyset.R | 40 tests/testthat/test_zones.R | 78 vignettes/gurobi_installation.Rmd | 382 - vignettes/prioritizr.Rmd | 1430 +++--- vignettes/publication_record.Rmd | 62 vignettes/reference-style.csl | 402 - vignettes/references.bib | 634 +- vignettes/saltspring.Rmd | 400 - vignettes/tasmania.Rmd | 454 +- vignettes/zones.Rmd | 646 +- 306 files changed, 47506 insertions(+), 46320 deletions(-)
Title: Quantify the Robustness of Causal Inferences
Description: Statistical methods that quantify the conditions necessary to alter
inferences, also known as sensitivity analysis, are becoming increasingly
important to a variety of quantitative sciences. A series of recent works,
including Frank (2000) <doi:10.1177/0049124100029002001> and Frank et al.
(2013) <doi:10.3102/0162373713493129> extend previous sensitivity analyses
by considering the characteristics of omitted variables or unobserved cases
that would change an inference if such variables or cases were observed. These
analyses generate statements such as "an omitted variable would have to be
correlated at xx with the predictor of interest (e.g., treatment) and outcome
to invalidate an inference of a treatment effect". Or "one would have to replace
pp percent of the observed data with null hypothesis cases to invalidate the
inference". We implement these recent developments of sensitivity analysis and
provide modules to calculate these two robustness indices and generate such
statements in R. In particular, the functions konfound(), pkonfound() and
mkonfound() allow users to calculate the robustness of inferences for a user's
own model, a single published study and multiple studies respectively.
Author: Joshua M Rosenberg [aut, cre],
Ran Xu [ctb],
Kenneth A Frank [ctb]
Maintainer: Joshua M Rosenberg <jmichaelrosenberg@gmail.com>
Diff between konfound versions 0.1.1 dated 2019-01-21 and 0.1.2 dated 2019-04-12
DESCRIPTION | 9 ++-- MD5 | 23 +++++----- NEWS.md | 4 + R/konfound-glm.R | 2 R/konfound-lm.R | 2 R/konfound-lmer.R | 72 +++++++-------------------------- R/konfound.R | 5 +- R/mkonfound.R | 2 README.md | 40 +++++++++--------- build/vignette.rds |binary inst/doc/introduction-to-konfound.html | 10 +--- tests/testthat/test-mkonfound.r |only tests/testthat/test-pkonfound.R | 16 +++++++ 13 files changed, 84 insertions(+), 101 deletions(-)
Title: Generates a 3D Visualization of Volatility Skew and Stock Option
Parameters Plotted Over Time
Description: Generates a 3D graph which plots the volatility skew of a stock or a selected stock option parameter over time.
The default setting plots the net parameter position of a double vertical spread over time.
Author: John T. Buynak
Maintainer: John T. Buynak <jbuynak94@gmail.com>
Diff between visualR versions 1.0.0 dated 2019-03-08 and 2.0.0 dated 2019-04-12
DESCRIPTION | 14 ++--- MD5 | 22 ++++---- NAMESPACE | 9 +++ R/available.R |only R/visual.R | 2 R/visualize.R | 136 ++++++++++++++++++++++++++++++++++++++------------ R/volskew.R |only inst/doc/visualr.Rmd | 7 ++ inst/doc/visualr.html | 11 +++- man/avoc.Rd |only man/visual.Rd | 2 man/visualize.Rd | 33 ++++++++---- man/volskew.Rd |only vignettes/visualr.Rmd | 7 ++ 14 files changed, 180 insertions(+), 63 deletions(-)
Title: Plot 'rpart' Models: An Enhanced Version of 'plot.rpart'
Description: Plot 'rpart' models. Extends plot.rpart() and text.rpart()
in the 'rpart' package.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between rpart.plot versions 3.0.6 dated 2018-11-24 and 3.0.7 dated 2019-04-12
DESCRIPTION | 10 - MD5 | 60 ++++----- NEWS | 10 + R/as.char.R | 40 +++--- R/check.index.R | 13 + R/lib.R | 196 ++++++++++++++++++++++-------- inst/doc/prp.pdf |binary inst/slowtests/header.R | 2 inst/slowtests/rpart.report.bat | 2 inst/slowtests/test.describe.col.bat | 2 inst/slowtests/test.imports.bat | 2 inst/slowtests/test.na.bat | 2 inst/slowtests/test.palette.R | 4 inst/slowtests/test.palette.Rout.save | 5 inst/slowtests/test.palette.bat | 2 inst/slowtests/test.prolog.R | 19 ++ inst/slowtests/test.prp.Rout.save | 25 +-- inst/slowtests/test.rpart.plot.R | 10 - inst/slowtests/test.rpart.plot.Rout.save | 25 +-- inst/slowtests/test.rpart.plot.bat | 2 inst/slowtests/test.rpart.rules.Rout.save | 5 inst/slowtests/test.rpart.rules.bat | 2 inst/slowtests/test.type5.R | 8 - inst/slowtests/test.type5.Rout.save | 16 +- inst/slowtests/test.type5.bat | 2 inst/slowtests/usersplits.bat | 2 inst/slowtests/vignette.R | 2 inst/slowtests/vignette.Rout.save | 3 inst/slowtests/vignette.bat | 2 inst/slowtests/webpage.figs.Rout.save | 1 inst/slowtests/webpage.figs.bat | 2 31 files changed, 307 insertions(+), 169 deletions(-)
Title: Model Based Clustering, Classification and Discriminant Analysis
Using the Mixture of Generalized Hyperbolic Distributions
Description: Carries out model-based clustering, classification and discriminant analysis using five different models. The models are all based on the generalized hyperbolic distribution. The first model 'MGHD' (Browne and McNicholas (2015) <doi:10.1002/cjs.11246>) is the classical mixture of generalized hyperbolic distributions. The 'MGHFA' (Tortora et al. (2016) <doi:10.1007/s11634-015-0204-z>) is the mixture of generalized hyperbolic factor analyzers for high dimensional data sets. The 'MSGHD'(Tortora et al. (2016) <arXiv:1403.2332v7>), mixture of multiple scaled generalized hyperbolic distributions. The 'cMSGHD' (Tortora et al. (2016) <arXiv:1403.2332v7>) is a 'MSGHD' with convex contour plots. The 'MCGHD' (Tortora et al. (2016) <arXiv:1403.2332v7>), mixture of coalesced generalized hyperbolic distributions is a new more flexible model.
Author: Cristina Tortora [aut, cre, cph], Aisha ElSherbiny [com], Ryan P. Browne [aut, cph], Brian C. Franczak [aut, cph], and Paul D. McNicholas [aut, cph], and Donald D. Amos [ctb].
Maintainer: Cristina Tortora <grikris1@gmail.com>
Diff between MixGHD versions 2.3.1 dated 2019-03-18 and 2.3.2 dated 2019-04-12
DESCRIPTION | 10 +++++----- MD5 | 30 +++++++++++++++--------------- man/DA.Rd | 9 +++++---- man/MCGHD.Rd | 4 ++-- man/MGHD.Rd | 4 ++-- man/MGHFA.Rd | 6 +++--- man/MSGHD.Rd | 4 ++-- man/MixGHD-class.Rd | 2 +- man/MixGHD.Rd | 2 +- man/cMSGHD.Rd | 4 ++-- man/dCGHD.Rd | 4 ++-- man/dGHD.Rd | 4 ++-- man/dMSGHD.Rd | 4 ++-- man/rCGHD.Rd | 4 ++-- man/rGHD.Rd | 4 ++-- man/rMSGHD.Rd | 4 ++-- 16 files changed, 50 insertions(+), 49 deletions(-)
Title: High-Dimensional Regression with Measurement Error
Description: Penalized regression for generalized linear models for
measurement error problems (aka. errors-in-variables). The package
contains a version of the lasso (L1-penalization) which corrects
for measurement error (Sorensen et al. (2015) <doi:10.5705/ss.2013.180>).
It also contains an implementation of the Generalized Matrix Uncertainty
Selector, which is a version the (Generalized) Dantzig Selector for the
case of measurement error (Sorensen et al. (2018) <doi:10.1080/10618600.2018.1425626>).
Author: Oystein Sorensen
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between hdme versions 0.2.2 dated 2019-03-07 and 0.2.3 dated 2019-04-12
hdme-0.2.2/hdme/R/gmu_lasso_binomial.R |only hdme-0.2.2/hdme/inst/doc/hdme-package.R |only hdme-0.2.2/hdme/inst/doc/hdme-package.Rmd |only hdme-0.2.2/hdme/inst/doc/hdme-package.html |only hdme-0.2.2/hdme/man/gmu_lasso_binomial.Rd |only hdme-0.2.2/hdme/vignettes/hdme-package.Rmd |only hdme-0.2.3/hdme/DESCRIPTION | 13 ++--- hdme-0.2.3/hdme/MD5 | 37 +++++++-------- hdme-0.2.3/hdme/NEWS.md | 6 ++ hdme-0.2.3/hdme/R/fit_mus.R | 2 hdme-0.2.3/hdme/R/mus_glm.R | 2 hdme-0.2.3/hdme/R/musalgorithm.R | 30 ++---------- hdme-0.2.3/hdme/README.md | 42 ++++-------------- hdme-0.2.3/hdme/build/partial.rdb |binary hdme-0.2.3/hdme/build/vignette.rds |binary hdme-0.2.3/hdme/inst/REFERENCES.bib | 19 ++++---- hdme-0.2.3/hdme/inst/doc/hdme.R |only hdme-0.2.3/hdme/inst/doc/hdme.Rmd |only hdme-0.2.3/hdme/inst/doc/hdme.html |only hdme-0.2.3/hdme/man/fit_mus.Rd | 2 hdme-0.2.3/hdme/man/mus_glm.Rd | 1 hdme-0.2.3/hdme/man/musalgorithm.Rd | 1 hdme-0.2.3/hdme/tests/testthat/test_corrected_lasso.R | 1 hdme-0.2.3/hdme/tests/testthat/test_gmus.R |only hdme-0.2.3/hdme/vignettes/hdme.Rmd |only 25 files changed, 63 insertions(+), 93 deletions(-)
Title: Robust Estimation in the Presence of Cellwise and Casewise
Contamination and Missing Data
Description: Robust Estimation of Multivariate Location and Scatter in the
Presence of Cellwise and Casewise Contamination and Missing Data.
Author: Andy Leung, Mike Danilov, Victor Yohai, Ruben Zamar
Maintainer: Claudio Agostinelli <claudio.agostinelli@unitn.it>
Diff between GSE versions 4.1 dated 2016-12-30 and 4.2 dated 2019-04-12
ChangeLog | 12 +++++++++++- DESCRIPTION | 14 +++++++------- MD5 | 25 +++++++++++++------------ NAMESPACE | 14 +++++++++----- R/GSE-utils.R | 2 +- R/TSGS.R | 4 ++-- R/generic.R | 10 +++++----- man/SummaryCov-class.Rd | 12 ++++++------ man/TSGS.Rd | 4 ++-- man/get-methods.Rd | 10 ++++++---- man/wages.Rd | 4 ++-- src/gse.cpp | 4 ++-- src/gse.h | 2 +- src/init.c |only 14 files changed, 67 insertions(+), 50 deletions(-)
Title: Use and Explore 'CRU' 'CL' v. 2.0 Climatology Elements
Description: Provides functions that automate downloading and importing
University of East Anglia Climate Research Unit ('CRU') 'CL' v. 2.0
climatology data, facilitates the calculation of minimum temperature and
maximum temperature and formats the data into a tidy data frame as a
'tibble' or a list of 'raster' 'stack' objects for use. 'CRU' 'CL' v. 2.0
data are a gridded climatology of 1961-1990 monthly means released in 2002
and cover all land areas (excluding Antarctica) at 10 arcminutes
(0.1666667 degree) resolution. For more information see the description of
the data provided by the University of East Anglia Climate Research Unit,
<https://crudata.uea.ac.uk/cru/data/hrg/tmc/readme.txt>.
Author: Adam Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>)
Maintainer: Adam Sparks <adamhsparks@gmail.com>
Diff between getCRUCLdata versions 0.2.5 dated 2018-09-12 and 0.3.0 dated 2019-04-12
DESCRIPTION | 29 +-- MD5 | 50 ++--- NAMESPACE | 2 NEWS.md | 27 ++ R/create_CRU_df.R | 79 ++++---- R/create_CRU_stack.R | 131 +++++++------- R/getCRUCLdata.R | 23 +- R/get_CRU.R | 110 ----------- R/get_CRU_df.R | 62 +++--- R/get_CRU_stack.R | 64 +++--- R/internal_functions.R | 307 ++++++++++++++++++++++----------- README.md | 8 build/vignette.rds |binary inst/doc/getCRUCLdata.R | 7 inst/doc/getCRUCLdata.Rmd | 42 ++-- inst/doc/getCRUCLdata.html | 39 +--- man/create_CRU_df.Rd | 68 ++++--- man/create_CRU_stack.Rd | 101 ++++++---- man/getCRUCLdata.Rd | 23 +- man/get_CRU_df.Rd | 31 +-- man/get_CRU_stack.Rd | 24 +- tests/testthat/test-create_CRU_df.R | 4 tests/testthat/test-create_CRU_stack.R | 6 tests/testthat/test-create_stack.R | 4 tests/testthat/test_get_local.R | 5 vignettes/getCRUCLdata.Rmd | 42 ++-- 26 files changed, 679 insertions(+), 609 deletions(-)
Title: PD-Clustering and Factor PD-Clustering
Description: Probabilistic distance clustering (PD-clustering) is an iterative, distribution free, probabilistic clustering method. PD-clustering assigns units to a cluster according to their probability of membership, under the constraint that the product of the probability and the distance of each point to any cluster centre is a constant. PD-clustering is a flexible method that can be used with non-spherical clusters, outliers, or noisy data. PDQ is an extension of the algorithm for clusters of different size. Factor PD-clustering (FPDC) is a recently proposed factor clustering method that involves a linear transformation of variables and a cluster optimizing the PD-clustering criterion. It works on high dimensional datasets.
Author: Cristina Tortora [aut, cre, cph], Noe Vidales [aut], and Paul D. McNicholas [fnd]
Maintainer: Cristina Tortora <grikris1@gmail.com>
Diff between FPDclustering versions 1.2 dated 2017-08-23 and 1.3 dated 2019-04-12
DESCRIPTION | 15 ++++++++------- MD5 | 6 ++++-- NAMESPACE | 4 ++-- R/PDQ.R |only man/PDQ.Rd |only 5 files changed, 14 insertions(+), 11 deletions(-)
Title: Multivariate Adaptive Regression Splines
Description: Build regression models using the techniques in Friedman's
papers "Fast MARS" and "Multivariate Adaptive Regression
Splines" <doi:10.1214/aos/1176347963>.
(The term "MARS" is trademarked and thus not used in
the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and
Rob Tibshirani. Uses Alan Miller's Fortran utilities
with Thomas Lumley's leaps wrapper.
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between earth versions 5.1.0 dated 2019-04-03 and 5.1.1 dated 2019-04-12
DESCRIPTION | 10 +-- MD5 | 18 +++--- NEWS | 12 +++- R/lib.R | 96 ++++++++++++++++++++-------------- build/partial.rdb |binary inst/doc/earth-notes.pdf |binary inst/doc/earth-varmod.pdf |binary inst/slowtests/test.full.Rout.save | 4 - inst/slowtests/test.weights.R | 1 inst/slowtests/test.weights.Rout.save | 4 - 10 files changed, 83 insertions(+), 62 deletions(-)
Title: Web Application Framework for R
Description: Makes it incredibly easy to build interactive web
applications with R. Automatic "reactive" binding between inputs and
outputs and extensive prebuilt widgets make it possible to build
beautiful, responsive, and powerful applications with minimal effort.
Author: Winston Chang [aut, cre],
Joe Cheng [aut],
JJ Allaire [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
RStudio [cph],
jQuery Foundation [cph] (jQuery library and jQuery UI library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/www/shared/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/www/shared/jqueryui/AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Stefan Petre [ctb, cph] (Bootstrap-datepicker library),
Andrew Rowls [ctb, cph] (Bootstrap-datepicker library),
Dave Gandy [ctb, cph] (Font-Awesome font),
Brian Reavis [ctb, cph] (selectize.js library),
Kristopher Michael Kowal [ctb, cph] (es5-shim library),
es5-shim contributors [ctb, cph] (es5-shim library),
Denis Ineshin [ctb, cph] (ion.rangeSlider library),
Sami Samhuri [ctb, cph] (Javascript strftime library),
SpryMedia Limited [ctb, cph] (DataTables library),
John Fraser [ctb, cph] (showdown.js library),
John Gruber [ctb, cph] (showdown.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
R Core Team [ctb, cph] (tar implementation from R)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between shiny versions 1.3.0 dated 2019-04-07 and 1.3.1 dated 2019-04-12
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 20 +++++++++++++++++++- R/graph.R | 7 ++++++- inst/www/shared/shiny.js | 2 +- inst/www/shared/shiny.min.js | 4 ++-- 6 files changed, 36 insertions(+), 13 deletions(-)
Title: Interface to 'Python'
Description: Interface to 'Python' modules, classes, and functions. When calling
into 'Python', R data types are automatically converted to their equivalent 'Python'
types. When values are returned from 'Python' to R they are converted back to R
types. Compatible with all versions of 'Python' >= 2.7.
Author: Kevin Ushey [aut, cre],
JJ Allaire [aut],
RStudio [cph, fnd],
Yuan Tang [aut, cph] (<https://orcid.org/0000-0001-5243-233X>),
Dirk Eddelbuettel [ctb, cph],
Bryan Lewis [ctb, cph],
Marcus Geelnard [ctb, cph] (TinyThread library,
http://tinythreadpp.bitsnbites.eu/)
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between reticulate versions 1.11.1 dated 2019-03-06 and 1.12 dated 2019-04-12
DESCRIPTION | 16 +- MD5 | 54 ++++---- NEWS.md | 19 ++ R/conda.R | 122 ++++++++++++++++--- R/config.R | 60 ++++++++- R/conversion.R | 16 +- R/install.R | 7 - R/package.R | 54 ++------ R/use_python.R | 51 ++++--- R/utils.R | 37 +++++ R/virtualenv.R | 74 ++++++++--- build/vignette.rds |binary inst/python/rpytools/__pycache__ |only inst/python/rpytools/output.pyc |binary inst/python/rpytools/test.pyc |binary inst/python/rpytools/thread.pyc |binary man/conda-tools.Rd | 6 man/py_install.Rd | 4 man/use_python.Rd | 4 man/virtualenv-tools.Rd | 13 +- tests/testthat/resources/eng-reticulate-example.Rmd | 1 tests/testthat/resources/eng-reticulate-example.html | 19 +- tests/testthat/test-help-handlers.R | 9 - tests/testthat/test-python-datetime.R | 17 +- tests/testthat/test-python-knitr-engine.R | 1 tests/testthat/test-python-pandas.R | 9 + 26 files changed, 416 insertions(+), 177 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-02-02 0.1.1
2018-07-27 0.1.0