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 1.7.0 dated 2018-08-13 and 1.8.1 dated 2019-02-16
DESCRIPTION | 22 + MD5 | 48 ++-- R/approx_method.R | 83 +++---- R/netmap.R | 10 R/netphenogeno.R | 412 +++++++++++++++++----------------- R/netsnp.R | 398 ++++++++++++++++----------------- R/selectnet.R | 483 +++++++++++++++++++++++------------------ man/R.approx.Rd | 2 man/R.gibbs.Rd | 2 man/bp.Rd | 66 ++--- man/buildMap.Rd | 126 +++++----- man/cutoffs.Rd | 4 man/lower.upper.Rd | 90 +++---- man/netgwas-package.Rd | 4 man/netmap.Rd | 2 man/netphenogeno.Rd | 21 + man/netsnp.Rd | 8 man/plot.netgwasmap.Rd | 82 +++--- man/plot.select.Rd | 126 ++++++---- man/selectnet.Rd | 2 man/simGeno.Rd | 2 man/tetraPotato.Rd | 74 +++--- tests/testthat.R | 2 tests/testthat/test_buildMap.R | 17 - tests/testthat/test_netmap.R | 58 ---- 25 files changed, 1106 insertions(+), 1038 deletions(-)
Title: Utilizes the Black-Scholes Option Pricing Model to Perform
Strategic Option Analysis and Plot Option Strategies
Description: Utilizes the Black-Scholes-Merton option pricing model to
calculate key option analytics and graphical analysis of various option strategies.
Provides functions to calculate the option premium and option
greeks of European-style options.
Author: John T. Buynak [aut, cre]
Maintainer: John T. Buynak <jbuynak94@gmail.com>
Diff between optionstrat versions 1.0.0 dated 2018-12-09 and 1.1.0 dated 2019-02-16
optionstrat-1.0.0/optionstrat/man/iv.est.Rd |only optionstrat-1.1.0/optionstrat/DESCRIPTION | 6 optionstrat-1.1.0/optionstrat/MD5 | 22 optionstrat-1.1.0/optionstrat/NAMESPACE | 2 optionstrat-1.1.0/optionstrat/R/hello.R | 272 +++++++++- optionstrat-1.1.0/optionstrat/inst/doc/optionstrat_vignette.Rmd | 35 - optionstrat-1.1.0/optionstrat/inst/doc/optionstrat_vignette.html | 38 - optionstrat-1.1.0/optionstrat/man/calleval.Rd | 2 optionstrat-1.1.0/optionstrat/man/iv.calc.Rd |only optionstrat-1.1.0/optionstrat/man/opteval.Rd | 2 optionstrat-1.1.0/optionstrat/man/plotvertical.Rd | 4 optionstrat-1.1.0/optionstrat/man/puteval.Rd | 2 optionstrat-1.1.0/optionstrat/vignettes/optionstrat_vignette.Rmd | 35 - 13 files changed, 339 insertions(+), 81 deletions(-)
Title: An Implementation of Matrix Mathematics
Description: An implementation of matrix mathematics wherein operations are performed "by name."
Author: Matthew Heun [aut, cre] (<https://orcid.org/0000-0002-7438-214X>)
Maintainer: Matthew Heun <matthew.heun@me.com>
Diff between matsbyname versions 0.4.9 dated 2019-01-25 and 0.4.10 dated 2019-02-16
DESCRIPTION | 8 MD5 | 29 - NEWS.md | 11 R/Unary.R | 5 R/Utilities.R | 30 - README.md | 24 inst/CITATION |only inst/doc/applybyname-vignette.html | 354 +++++++++++--- inst/doc/matsbyname.html | 748 +++++++++++++++++++------------ man/fractionize_byname.Rd | 5 man/organize_args.Rd | 2 tests/testthat.R | 3 tests/testthat/test_Binary.R | 65 +- tests/testthat/test_CompletingMatrices.R | 15 tests/testthat/test_S3.R | 2 tests/testthat/test_Unary.R | 60 +- 16 files changed, 912 insertions(+), 449 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-12-09 0.1.0
Title: Import Various Data File Types as a Rectangular Form Using a
File Picker Dialogue Box
Description: Easy data importing for the most frequently used file formats in a 'tibble' form.
Author: JooYoung Seo [aut, cre],
Soyoung Choi [aut],
hyun seung Lee [ctb],
Jonghoen Kim [ctb]
Maintainer: JooYoung Seo <jooyoung@psu.edu>
Diff between ezpickr versions 1.0.0 dated 2019-02-02 and 1.0.1 dated 2019-02-16
DESCRIPTION | 20 ++++++++++++-------- MD5 | 31 +++++++++++++++++-------------- NAMESPACE | 1 + NEWS.md | 12 ++++++++++++ R/pick.R | 24 +++++++++++++----------- R/picko.R |only R/view.R | 39 ++++++++++++++++----------------------- R/zzz.R |only README.md | 11 ++++++++--- inst/NEWS | 12 ++++++++++++ inst/doc/ezpickr_vignette.R | 8 ++++++-- inst/doc/ezpickr_vignette.Rmd | 10 +++++++--- inst/doc/ezpickr_vignette.html | 18 +++++++++++------- man/ezpickr-package.Rd | 6 ++++++ man/pick.Rd | 3 +++ man/picko.Rd |only man/view.Rd | 16 +++++++++------- vignettes/ezpickr_vignette.Rmd | 10 +++++++--- 18 files changed, 140 insertions(+), 81 deletions(-)
Title: Consistent Significance Controlled Variable Selection in Linear
Regression
Description: Provide consistent significance controlled variable selection procedure with different directions (forward, backward, stepwise) based on diverse criteria (Mallows' Cp, AIC, BIC, adjusted r-square, p-value). The algorithm selects a final model with only significant variables based on a correction choice of False Discovery Rate, Bonferroni, or no correction.
Author: Jongwook Kim, Adriano Zanin Zambom
Maintainer: Jongwook Kim <jongwook226@gmail.com>
Diff between SignifReg versions 1.0 dated 2017-02-01 and 1.1 dated 2019-02-16
DESCRIPTION | 13 MD5 | 9 NAMESPACE | 2 R/SignifReg-internal.R |only R/SignifReg.R | 875 +++++++++++++++++++++++++------------------------ man/SignifReg.Rd | 134 +++---- 6 files changed, 530 insertions(+), 503 deletions(-)
Title: 'NEOS' Plug-in for the 'R' Optimization Interface
Description: Enhances the 'R' Optimization Infrastructure ('ROI') package
with a connection to the 'neos' server. 'ROI' optimization
problems can be directly be sent to the 'neos' server
and solution obtained in the typical 'ROI' style.
Author: Ronald Hochreiter [aut],
Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between ROI.plugin.neos versions 0.3-0 dated 2018-06-19 and 0.3-1 dated 2019-02-16
DESCRIPTION | 9 ++- MD5 | 18 +++---- R/neos_client.R | 38 ++++++++++++++- R/plugin.R | 59 +++++++++++++++++++++++ build/vignette.rds |binary inst/doc/ROI.plugin.neos_Introduction.Rnw | 72 +++++++++++++++++++++++++++-- inst/doc/ROI.plugin.neos_Introduction.pdf |binary tests/test_ROI_plugin_neos.R | 3 - tests/test_ROI_plugin_neos.Rout | 9 +-- vignettes/ROI.plugin.neos_Introduction.Rnw | 72 +++++++++++++++++++++++++++-- 10 files changed, 250 insertions(+), 30 deletions(-)
More information about ROI.plugin.neos at CRAN
Permanent link
Title: Higher Order Likelihood Inference
Description: Performs likelihood-based inference for a wide range of regression models. Provides higher-order approximations for inference based on extensions of saddlepoint type arguments as discussed in the book Applied Asymptotics: Case Studies in Small-Sample Statistics by Brazzale, Davison, and Reid (2007).
Author: R port by Alessandra R. Brazzale <alessandra.brazzale@unipd.it>, following
earlier work by Douglas Bates. The function tem is based on work by Anthony Davison <Anthony.Davison@epfl.ch>
Maintainer: Alex-Antoine Fortin <alex@fortin.bio>
Diff between hoa versions 2.1.4 dated 2015-08-11 and 2.1.4.1 dated 2019-02-16
DESCRIPTION | 8 - MD5 | 60 ++++---- build/vignette.rds |binary data/C1.rda |binary data/C2.rda |binary data/C3.rda |binary data/C4.rda |binary data/M2.rda |binary data/M4.rda |binary data/aids.rda |binary data/airway.rda |binary data/babies.rda |binary data/chlorsulfuron.rda |binary data/daphnia.rda |binary data/darwin.rda |binary data/dormicum.rda |binary data/fraudulent.rda |binary data/fungal.rda |binary data/helicopter.rda |binary data/houses.rda |binary data/metsulfuron.rda |binary data/nuclear.rda |binary data/rabbits.rda |binary data/ria.rda |binary data/urine.rda |binary data/venice.rda |binary inst/CITATION | 6 inst/doc/Rnews-paper.R | 352 +++++++++++++++++++++++------------------------ inst/doc/Rnews-paper.Rnw | 2 inst/doc/Rnews-paper.pdf |binary man/profile.nlreg.Rd | 6 31 files changed, 217 insertions(+), 217 deletions(-)
Title: Inverse Probability of Censoring Weights to Deal with Treatment
Switch in Randomized Clinical Trials
Description: Contains functions for formatting clinical trials data and implementing inverse probability of censoring weights to handle treatment switches when estimating causal treatment effect in randomized clinical trials.
Author: Nathalie Graffeo [aut, cre],
Aurelien Latouche [aut],
Sylvie Chevret [aut]
Maintainer: Nathalie Graffeo <nathalie.graffeo@univ-amu.fr>
Diff between ipcwswitch versions 1.0.1 dated 2018-11-16 and 1.0.2 dated 2019-02-16
ipcwswitch-1.0.1/ipcwswitch/data/data.ipcw.rda |only ipcwswitch-1.0.1/ipcwswitch/man/data.ipcw.Rd |only ipcwswitch-1.0.2/ipcwswitch/DESCRIPTION | 8 +++--- ipcwswitch-1.0.2/ipcwswitch/MD5 | 29 +++++++++++------------ ipcwswitch-1.0.2/ipcwswitch/R/cens.ipw.R | 2 - ipcwswitch-1.0.2/ipcwswitch/R/ipcw.R | 4 +-- ipcwswitch-1.0.2/ipcwswitch/R/replicRows.R | 5 ++- ipcwswitch-1.0.2/ipcwswitch/R/timesToKeep.R | 2 - ipcwswitch-1.0.2/ipcwswitch/R/wideToLongTDC.R | 2 - ipcwswitch-1.0.2/ipcwswitch/data/SHIdat.rda |only ipcwswitch-1.0.2/ipcwswitch/inst |only ipcwswitch-1.0.2/ipcwswitch/man/SHIdat.Rd |only ipcwswitch-1.0.2/ipcwswitch/man/cens.ipw.Rd | 2 - ipcwswitch-1.0.2/ipcwswitch/man/ipcw.Rd | 4 +-- ipcwswitch-1.0.2/ipcwswitch/man/replicRows.Rd | 2 - ipcwswitch-1.0.2/ipcwswitch/man/timesTokeep.Rd | 2 - ipcwswitch-1.0.2/ipcwswitch/man/toydata.Rd | 6 ++-- ipcwswitch-1.0.2/ipcwswitch/man/wideToLongTDC.Rd | 2 - 18 files changed, 36 insertions(+), 34 deletions(-)
Title: Database Preferences and Skyline Computation
Description: Routines to select and visualize the maxima for a given strict
partial order. This especially includes the computation of the Pareto
frontier, also known as (Top-k) Skyline operator (see Börzsönyi, et al.
(2001) <doi:10.1109/ICDE.2001.914855>), and some generalizations
known as database preferences (see Kießling (2002)
<doi:10.1016/B978-155860869-6/50035-4>).
Author: Patrick Roocks <mail@p-roocks.de>
Maintainer: Patrick Roocks <mail@p-roocks.de>
Diff between rPref versions 1.2 dated 2016-12-18 and 1.3 dated 2019-02-16
rPref-1.2/rPref/inst/test/test-algorithms.R |only rPref-1.2/rPref/inst/test/test-hasse.R |only rPref-1.2/rPref/inst/test/test-psel.R |only rPref-1.2/rPref/inst/test/test-strings.R |only rPref-1.3/rPref/DESCRIPTION | 25 rPref-1.3/rPref/MD5 | 83 - rPref-1.3/rPref/NAMESPACE | 114 +- rPref-1.3/rPref/NEWS | 16 rPref-1.3/rPref/R/RcppExports.R | 46 rPref-1.3/rPref/R/base-pref-macros.r | 188 +-- rPref-1.3/rPref/R/base-pref.r | 396 +++---- rPref-1.3/rPref/R/complex-pref.r | 478 ++++----- rPref-1.3/rPref/R/general-pref.r | 248 ++-- rPref-1.3/rPref/R/pred-succ.r | 432 ++++---- rPref-1.3/rPref/R/pref-classes.r | 1464 ++++++++++++++-------------- rPref-1.3/rPref/R/pref-eval.r | 653 ++++++------ rPref-1.3/rPref/R/rPref.r | 134 +- rPref-1.3/rPref/R/show-pref.r | 496 ++++----- rPref-1.3/rPref/R/visualize.r | 914 ++++++++--------- rPref-1.3/rPref/build/vignette.rds |binary rPref-1.3/rPref/inst/CITATION |only rPref-1.3/rPref/inst/doc/introduction.R | 84 - rPref-1.3/rPref/inst/doc/introduction.Rmd | 202 +-- rPref-1.3/rPref/inst/doc/introduction.html | 1068 ++++++++++---------- rPref-1.3/rPref/inst/doc/visualization.R | 106 +- rPref-1.3/rPref/inst/doc/visualization.Rmd | 240 ++-- rPref-1.3/rPref/inst/doc/visualization.html | 488 ++++----- rPref-1.3/rPref/inst/test/test-algorithms.r |only rPref-1.3/rPref/inst/test/test-hasse.r |only rPref-1.3/rPref/inst/test/test-pref.r | 246 ++-- rPref-1.3/rPref/inst/test/test-psel.r |only rPref-1.3/rPref/inst/test/test-strings.r |only rPref-1.3/rPref/man/base_pref.Rd | 8 rPref-1.3/rPref/man/base_pref_macros.Rd | 6 rPref-1.3/rPref/man/complex_pref.Rd | 310 ++--- rPref-1.3/rPref/man/general_pref.Rd | 175 +-- rPref-1.3/rPref/man/get_hasse_diag.Rd | 1 rPref-1.3/rPref/man/plot_btg.Rd | 4 rPref-1.3/rPref/man/plot_front.Rd | 1 rPref-1.3/rPref/man/pred_succ.Rd | 9 rPref-1.3/rPref/man/psel.Rd | 4 rPref-1.3/rPref/man/rPref.Rd | 2 rPref-1.3/rPref/man/show.pref.Rd | 162 +-- rPref-1.3/rPref/man/show.query.Rd | 103 - rPref-1.3/rPref/src/RcppExports.cpp | 24 rPref-1.3/rPref/vignettes/introduction.Rmd | 202 +-- rPref-1.3/rPref/vignettes/visualization.Rmd | 240 ++-- 47 files changed, 4715 insertions(+), 4657 deletions(-)
Title: Water Resources System Simulator
Description: Water resources system simulator is a tool for simulation and analysis of large-scale water resources systems. 'WRSS' proposes functions and methods for construction, simulation and analysis of primary storage and hydropower water resources features (e.g. reservoirs, aquifers, and etc.) based on Standard Operating Policy (SOP).
Author: Rezgar Arabzadeh; Parisa Aberi; Kaveh Panaghi; Shahab Araghinejad; Majid Montaseri
Maintainer: Rezgar Arabzadeh <rezgararabzadeh@ut.ac.ir>
Diff between WRSS versions 2.1 dated 2019-01-21 and 2.2 dated 2019-02-16
DESCRIPTION | 8 +- MD5 | 12 ++-- R/addObjectToArea.R | 65 ++++++++++++----------- R/risk.R | 11 ++- data |only man/WRSS-package.Rd | 138 +++++++++++++++++++++++++++++++++++++++++++++++++- man/figures/Thumbs.db |binary man/zarrineh.Rd |only 8 files changed, 189 insertions(+), 45 deletions(-)
Title: Plot Stacked Areas and Confidence Bands as Filled Polygons
Description: Plot stacked areas and confidence bands as filled polygons, or add
polygons to existing plots. A variety of input formats are supported,
including vectors, matrices, data frames, formulas, etc.
Author: Arni Magnusson [aut, cre]
Maintainer: Arni Magnusson <arni.magnusson@ices.dk>
Diff between areaplot versions 1.2-0 dated 2017-10-18 and 1.2-1 dated 2019-02-16
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++------- NAMESPACE | 1 + NEWS | 14 +++++++++++--- R/areaplot.R | 23 +++++++++++++---------- R/confplot.R | 9 +++++---- man/areaplot.Rd | 1 + man/confplot.Rd | 3 ++- 8 files changed, 46 insertions(+), 30 deletions(-)