Title: Simulation Education
Description: Contains various functions to be used for simulation education,
including simple Monte Carlo simulation functions, queueing simulation
functions, variate generation functions capable of producing independent
streams and antithetic variates, functions for illustrating random variate
generation for various discrete and continuous distributions, and functions
to compute time-persistent statistics. Also contains two queueing data sets
(one fabricated, one real-world) to facilitate input modeling.
Author: Barry Lawson, Larry Leemis
Maintainer: Barry Lawson <blawson@richmond.edu>
Diff between simEd versions 1.0.2 dated 2017-07-08 and 1.0.3 dated 2017-11-26
DESCRIPTION | 19 +++++----- MD5 | 56 ++++++++++++++++--------------- NAMESPACE | 6 +-- NEWS.md | 14 ++++++- R/craps.R |only R/galileo.R |only R/ibinom.R | 62 +++++++++++++++++++++++----------- R/iexp.R | 60 ++++++++++++++++++++++----------- R/igamma.R | 60 ++++++++++++++++++++++----------- R/igeom.R | 62 +++++++++++++++++++++++----------- R/inorm.R | 60 ++++++++++++++++++++++----------- R/iunif.R | 60 ++++++++++++++++++++++----------- R/iweibull.R | 60 ++++++++++++++++++++++----------- R/msq.R | 14 ++++--- R/ssq.R | 14 ++++--- README.md | 21 +++++++---- build/partial.rdb |binary man/craps.Rd |only man/galileo.Rd |only man/ibinom.Rd | 86 ++++++++++++++++++++++++++++++++++++----------- man/iexp.Rd | 90 ++++++++++++++++++++++++++++++++++++++----------- man/igamma.Rd | 72 +++++++++++++++++++++++++++++++++------ man/igeom.Rd | 81 ++++++++++++++++++++++++++++++++++---------- man/inorm.Rd | 92 ++++++++++++++++++++++++++++++++++++++------------- man/iunif.Rd | 88 +++++++++++++++++++++++++++++++++++++----------- man/iweibull.Rd | 90 ++++++++++++++++++++++++++++++++++++++----------- man/simEd-package.Rd | 18 +++++++-- man/ssq.Rd | 40 +++++++++++++--------- man/vexp.Rd | 2 - man/vnorm.Rd | 4 +- man/vweibull.Rd | 2 - 31 files changed, 879 insertions(+), 354 deletions(-)
Title: Global Surface Summary of the Day (GSOD) Weather Data from R
Description: Provides automated downloading, parsing, cleaning, unit conversion
and formatting of Global Surface Summary of the Day (GSOD) weather data from
the from the USA National Centers for Environmental Information (NCEI) for
use in R. Units are converted from from United States Customary System
(USCS) units to International System of Units (SI). Stations may be
individually checked for number of missing days defined by the user, where
stations with too many missing observations are omitted. Only stations with
valid reported latitude and longitude values are permitted in the final
data. Additional useful elements, saturation vapour pressure (es), actual
vapour pressure (ea) and relative humidity are calculated from the original
data and included in the final data set. The resulting data include station
identification information, state, country, latitude, longitude, elevation,
weather observations and associated flags. Data may be automatically saved
to disk. File output may be returned as a comma-separated values (CSV) or
GeoPackage (GPKG) file. Additional data are included with this R package: a
list of elevation values for stations between -60 and 60 degrees latitude
derived from the Shuttle Radar Topography Measuring Mission (SRTM). For
information on the GSOD data from NCEI, please see the GSOD readme.txt file
available from, <http://www1.ncdc.noaa.gov/pub/data/gsod/readme.txt>.
Author: Adam Sparks [aut, cre] (https://orcid.org/0000-0002-0061-8359),
Tomislav Hengl [aut] (https://orcid.org/0000-0002-9921-5129),
Andrew Nelson [aut] (https://orcid.org/0000-0002-7249-3778),
Hugh Parsonage [cph, ctb] (https://orcid.org/0000-0003-4055-0835),
Bob Rudis [cph, ctb] (https://orcid.org/0000-0001-5670-2640)
Maintainer: Adam Sparks <adamhsparks@gmail.com>
Diff between GSODR versions 1.1.0 dated 2017-10-28 and 1.1.1 dated 2017-11-26
DESCRIPTION | 26 MD5 | 64 +- NEWS.md | 31 R/GSODR-package.R | 41 - R/get_GSOD.R | 53 - R/get_inventory.R | 2 R/nearest_stations.R | 10 R/process_gz.R | 4 R/reformat_GSOD.R | 49 - R/update_station_list.R | 15 R/zzz.R | 19 README.md | 255 +++++--- inst/doc/GSODR.R | 58 - inst/doc/GSODR.Rmd | 36 - inst/doc/GSODR.html | 563 +++++++++++------- inst/doc/Specified_stations_for_a_range_of_years.Rmd | 1 inst/doc/Specified_stations_for_a_range_of_years.html | 221 ++++++- inst/doc/Working_with_spatial_and_climate_data.Rmd | 3 inst/doc/Working_with_spatial_and_climate_data.html | 217 ++++++ inst/extdata/isd_history.rda |binary man/GSODR.Rd | 41 - man/get_GSOD.Rd | 43 - man/get_inventory.Rd | 2 man/nearest_stations.Rd | 10 man/reformat_GSOD.Rd | 48 - man/update_station_list.Rd | 15 tests/testthat/test-get_GSOD.R | 15 tests/testthat/test-process_gz.R | 203 +++--- tests/testthat/test-reformat_GSOD.R | 8 tests/testthat/test-update_station_list.R | 22 vignettes/GSODR.Rmd | 36 - vignettes/Specified_stations_for_a_range_of_years.Rmd | 1 vignettes/Working_with_spatial_and_climate_data.Rmd | 3 33 files changed, 1362 insertions(+), 753 deletions(-)
Title: Bayesian Spectral Analysis Models using Gaussian Process Priors
Description: Contains functions to perform Bayesian inference
using a spectral analysis of Gaussian process priors.
Gaussian processes are represented with a Fourier series
based on cosine basis functions. Currently the package
includes parametric linear models, partial linear additive
models with/without shape restrictions, generalized linear
additive models with/without shape restrictions, and
density estimation model. To maximize computational
efficiency, the actual Markov chain Monte Carlo sampling
for each model is done using codes written in FORTRAN 90.
This software has been developed using funding supported by
Basic Science Research Program through the National Research
Foundation of Korea (NRF) funded by the Ministry of Education
(no. NRF-2016R1D1A1B03932178 and no. NRF-2017R1D1A3B03035235).
Author: Seongil Jo [aut, cre],
Taeryon Choi [aut],
Beomjo Park [aut, cre],
Peter J. Lenk [ctb]
Maintainer: Beomjo Park <beomjo@korea.ac.kr>
Diff between bsamGP versions 1.1.0 dated 2017-10-22 and 1.1.1 dated 2017-11-26
DESCRIPTION | 8 MD5 | 35 R/predict.bsam.R | 511 ++++----- README.md | 11 src/Makevars | 5 src/bsamTools.f90 | 4 src/bsaqam.f90 | 1942 +++++++++++++++++----------------- src/bsaqamdpscale.f90 | 2196 +++++++++++++++++++-------------------- src/bsaram.f90 | 1890 ++++++++++++++++----------------- src/bsaramdplocationscale.f90 | 2350 +++++++++++++++++++++--------------------- src/bsaramdpscale.f90 | 2144 +++++++++++++++++++------------------- src/gbsarlogitKS.f90 | 1724 +++++++++++++++--------------- src/gbsarlogitMH.f90 | 1800 ++++++++++++++++---------------- src/gbsarnegbinMH.f90 | 1886 ++++++++++++++++----------------- src/gbsarpoisMH.f90 | 1814 ++++++++++++++++---------------- src/gbsarpoisgammMH.f90 | 1950 +++++++++++++++++----------------- src/gbsarprobitAC.f90 | 1704 +++++++++++++++--------------- src/predictbsam.f90 | 320 +++-- src/predictgbsam.f90 |only 19 files changed, 11190 insertions(+), 11104 deletions(-)
Title: Utilities for Japanese Mesh Code
Description: Helpful functions for using mesh code (80km to 125m) data in Japan. Visualize mesh code using 'ggplot2' and 'leaflet', etc.
Author: Shinya Uryu [aut, cre] (0000-0002-0493-6186)
Maintainer: Shinya Uryu <suika1127@gmail.com>
Diff between jpmesh versions 0.4.0 dated 2017-09-29 and 1.0.0 dated 2017-11-26
jpmesh-0.4.0/jpmesh/R/mesh_rectangle.R |only jpmesh-0.4.0/jpmesh/data/prefecture_mesh.rda |only jpmesh-0.4.0/jpmesh/man/bundle_mesh_vars.Rd |only jpmesh-0.4.0/jpmesh/man/detect_mesh.Rd |only jpmesh-0.4.0/jpmesh/man/latlong_to_meshcode.Rd |only jpmesh-0.4.0/jpmesh/man/latlong_to_sepate_mesh.Rd |only jpmesh-0.4.0/jpmesh/man/mesh_area.Rd |only jpmesh-0.4.0/jpmesh/man/mesh_rectangle.Rd |only jpmesh-0.4.0/jpmesh/man/meshcode_to_latlon.Rd |only jpmesh-0.4.0/jpmesh/man/prefecture_mesh.Rd |only jpmesh-0.4.0/jpmesh/tests/testthat/test-detect_mesh.R |only jpmesh-0.4.0/jpmesh/tests/testthat/test-mesh_area.R |only jpmesh-1.0.0/jpmesh/DESCRIPTION | 25 jpmesh-1.0.0/jpmesh/MD5 | 66 - jpmesh-1.0.0/jpmesh/NAMESPACE | 22 jpmesh-1.0.0/jpmesh/NEWS.md | 6 jpmesh-1.0.0/jpmesh/R/administration_mesh.R | 33 jpmesh-1.0.0/jpmesh/R/data.R | 23 jpmesh-1.0.0/jpmesh/R/export_mesh.R | 52 - jpmesh-1.0.0/jpmesh/R/fine_separate.R | 65 - jpmesh-1.0.0/jpmesh/R/latlon_to_mesh.R | 163 +--- jpmesh-1.0.0/jpmesh/R/mesh_to_latlon.R | 70 + jpmesh-1.0.0/jpmesh/R/mesh_viewer.R | 43 - jpmesh-1.0.0/jpmesh/R/sysdata.rda |binary jpmesh-1.0.0/jpmesh/R/util.R | 373 ---------- jpmesh-1.0.0/jpmesh/README.md | 121 ++- jpmesh-1.0.0/jpmesh/data/sf_jpmesh.rda |only jpmesh-1.0.0/jpmesh/man/coords_to_mesh.Rd |only jpmesh-1.0.0/jpmesh/man/eval_jp_boundary.Rd |only jpmesh-1.0.0/jpmesh/man/export_mesh.Rd | 24 jpmesh-1.0.0/jpmesh/man/figures |only jpmesh-1.0.0/jpmesh/man/fine_separate.Rd | 12 jpmesh-1.0.0/jpmesh/man/mesh_to_coords.Rd |only jpmesh-1.0.0/jpmesh/man/sf_jpmesh.Rd |only jpmesh-1.0.0/jpmesh/tests/testthat/test-administration_mesh.R | 8 jpmesh-1.0.0/jpmesh/tests/testthat/test-data.R | 14 jpmesh-1.0.0/jpmesh/tests/testthat/test-export_mesh.R | 6 jpmesh-1.0.0/jpmesh/tests/testthat/test-fine_separate.R | 8 jpmesh-1.0.0/jpmesh/tests/testthat/test-internal.R | 9 jpmesh-1.0.0/jpmesh/tests/testthat/test-latlong_to_meshcode.R | 52 - jpmesh-1.0.0/jpmesh/tests/testthat/test-meshcode_to_latlon.R | 26 41 files changed, 455 insertions(+), 766 deletions(-)
Title: Covariate Balancing Propensity Score
Description: Implements the covariate balancing propensity score (CBPS) proposed
by Imai and Ratkovic (2014) <DOI:10.1111/rssb.12027>. The propensity score is
estimated such that it maximizes the resulting covariate balance as well as the
prediction of treatment assignment. The method, therefore, avoids an iteration
between model fitting and balance checking. The package also implements several
extensions of the CBPS beyond the cross-sectional, binary treatment setting.
The current version implements the CBPS for longitudinal settings so that it can
be used in conjunction with marginal structural models from Imai and Ratkovic
(2015) <DOI:10.1080/01621459.2014.956872>, treatments with three- and four-
valued treatment variables, continuous-valued treatments from Fong, Hazlett,
and Imai (2015) <http://imai.princeton.edu/research/files/CBGPS.pdf>, and the
situation with multiple distinct binary treatments administered simultaneously.
In the future it will be extended to other settings including the generalization
of experimental and instrumental variable estimates. Recently we have added the
optimal CBPS which chooses the optimal balancing function and results in doubly
robust and efficient estimator for the treatment effect as well as high dimensional
CBPS when a large number of covariates exist.
Author: Christian Fong [aut, cre],
Marc Ratkovic [aut],
Kosuke Imai [aut],
Chad Hazlett [ctb],
Xiaolin Yang [ctb],
Sida Peng [ctb]
Maintainer: Christian Fong <christianfong@stanford.edu>
Diff between CBPS versions 0.14 dated 2017-10-02 and 0.15 dated 2017-11-26
ChangeLog | 3 DESCRIPTION | 10 MD5 | 63 ++- NAMESPACE | 80 +++- R/CBIV.R | 65 +++ R/CBMSM.R | 205 ++++++++++++ R/CBPS-package.R |only R/CBPSBinary.R | 629 ++++++++++++++++++------------------- R/CBPSContinuous.r | 3 R/CBPSMain.R | 407 +++++++++++++++++++++++ R/CBPSMultiTreat.r | 6 R/analytic_vcov.R | 67 +++ R/hdCBPS.R | 35 +- R/npCBPS.R | 127 +++++++ man/Blackwell.Rd | 29 + man/CBIV.Rd | 95 +++-- man/CBMSM.Rd | 179 ++++++---- man/CBMSM.fit.Rd |only man/CBPS.Rd | 171 ++++++---- man/CBPS.fit.Rd |only man/LaLonde.Rd | 35 +- man/balance.CBPS.Rd |only man/balance.CBPSContinuous.Rd |only man/balance.Rd | 41 +- man/balance.npCBPS.Rd |only man/hdCBPS.Rd | 33 + man/npCBPS.Rd | 114 ++++-- man/npCBPS.fit.Rd |only man/plot.CBMSM.Rd | 56 ++- man/plot.CBPS.Rd | 64 ++- man/plot.CBPSContinuous.Rd |only man/plot.npCBPS.Rd |only man/print.CBPS.Rd |only man/summary.CBPS.Rd | 43 +- man/vcov.CBPS.Rd | 49 +- man/vcov_outcome.CBPSContinuous.Rd |only man/vcov_outcome.Rd | 54 ++- tests |only 38 files changed, 1934 insertions(+), 729 deletions(-)
Title: Image Registration Using the 'NiftyReg' Library
Description: Provides an 'R' interface to the 'NiftyReg' image registration tools
<http://sourceforge.net/projects/niftyreg/>. Linear and nonlinear registration
are supported, in two and three dimensions.
Author: Jon Clayden [cre, aut],
Marc Modat [aut],
Benoit Presles [aut],
Thanasis Anthopoulos [aut],
Pankaj Daga [aut]
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNiftyReg versions 2.6.0 dated 2017-06-27 and 2.6.1 dated 2017-11-26
RNiftyReg-2.6.0/RNiftyReg/src/Makevars |only RNiftyReg-2.6.1/RNiftyReg/DESCRIPTION | 8 ++-- RNiftyReg-2.6.1/RNiftyReg/MD5 | 18 +++++---- RNiftyReg-2.6.1/RNiftyReg/NEWS | 8 ++++ RNiftyReg-2.6.1/RNiftyReg/R/transform.R | 6 +++ RNiftyReg-2.6.1/RNiftyReg/cleanup |only RNiftyReg-2.6.1/RNiftyReg/configure |only RNiftyReg-2.6.1/RNiftyReg/configure.ac |only RNiftyReg-2.6.1/RNiftyReg/man/composeTransforms.Rd | 8 ++++ RNiftyReg-2.6.1/RNiftyReg/src/Makevars.in |only RNiftyReg-2.6.1/RNiftyReg/src/Makevars.win |only RNiftyReg-2.6.1/RNiftyReg/src/main.cpp | 21 ++++++++++- RNiftyReg-2.6.1/RNiftyReg/tests/testthat/test-25-transform.R | 1 13 files changed, 58 insertions(+), 12 deletions(-)
Title: Factor Adjusted Robust Multiple Testing
Description: Performs robust multiple testing for means in the presence of known and unknown latent factors. It implements a robust procedure to estimate distribution parameters using the Huber's loss function and accounts for strong dependence among coordinates via an approximate factor model. This method is particularly suitable for high dimensional data when there are many variables but only a small number of observations available. Moreover, the method is tailored to cases when the underlying distribution deviates from Gaussian, which is commonly assumed in the literature. Besides the results of hypotheses testing, the estimated underlying factors and diagnostic plots are also output. Multiple comparison correction is done after estimating the proportion of true null hypotheses using the method in Storey (2015) <https://github.com/jdstorey/qvalue>. See the paper on the 'FarmTest' method, Zhou et al.(2017) <https://goo.gl/68SJpd>, for detailed description of methods and further references.
Author: Koushiki Bose [aut, cre],
Yuan Ke [aut],
Wen-xin Zhou [aut]
Maintainer: Koushiki Bose <bose@princeton.edu>
Diff between FarmTest versions 1.0.0 dated 2017-10-24 and 1.0.1 dated 2017-11-26
FarmTest-1.0.0/FarmTest/R/farmtest-package.r |only FarmTest-1.0.1/FarmTest/DESCRIPTION | 6 FarmTest-1.0.1/FarmTest/MD5 | 22 FarmTest-1.0.1/FarmTest/R/FarmTest-package.r |only FarmTest-1.0.1/FarmTest/R/RcppExports.R | 8 FarmTest-1.0.1/FarmTest/R/load.R | 88 ++ FarmTest-1.0.1/FarmTest/inst/doc/farmtest-vignette.html | 472 ++++++++++------ FarmTest-1.0.1/FarmTest/man/FarmTest.Rd | 2 FarmTest-1.0.1/FarmTest/man/farm.FDR.Rd | 2 FarmTest-1.0.1/FarmTest/man/farm.scree.Rd | 2 FarmTest-1.0.1/FarmTest/man/farm.test.Rd | 6 FarmTest-1.0.1/FarmTest/src/Cfunctions.cpp | 107 --- FarmTest-1.0.1/FarmTest/src/RcppExports.cpp | 33 - 13 files changed, 412 insertions(+), 336 deletions(-)
Title: Reads 'SPSS' and 'SAS' Files from ASCII Data Files (.txt) and
Setup Files (.sps or .sas)
Description: Lets you open an 'SPSS' or 'SAS' data file using a .txt file that has the data and a .sps or .sas file with setup instructions. This will only run in a txt-sps or txt-sas pair in which the setup file contains instructions to open that text file. It will NOT open other text files, .sav, .por, or 'SAS' files.
Author: Jacob Kaplan [aut, cre]
Maintainer: Jacob Kaplan <jkkaplan6@gmail.com>
Diff between asciiSetupReader versions 1.1 dated 2017-10-11 and 1.2 dated 2017-11-26
asciiSetupReader-1.1/asciiSetupReader/R/hello.R |only asciiSetupReader-1.1/asciiSetupReader/inst/extdata/example_data.txt |only asciiSetupReader-1.2/asciiSetupReader/DESCRIPTION | 12 asciiSetupReader-1.2/asciiSetupReader/MD5 | 38 ++ asciiSetupReader-1.2/asciiSetupReader/NAMESPACE | 4 asciiSetupReader-1.2/asciiSetupReader/R/helper.R | 127 +++++----- asciiSetupReader-1.2/asciiSetupReader/R/sas.R | 78 ++---- asciiSetupReader-1.2/asciiSetupReader/R/spss.R |only asciiSetupReader-1.2/asciiSetupReader/inst/doc/Introduction_to_asciiReader.R | 2 asciiSetupReader-1.2/asciiSetupReader/inst/doc/Introduction_to_asciiReader.Rmd | 2 asciiSetupReader-1.2/asciiSetupReader/inst/doc/Introduction_to_asciiReader.html | 76 ++--- asciiSetupReader-1.2/asciiSetupReader/inst/extdata/example_data.zip |only asciiSetupReader-1.2/asciiSetupReader/inst/testdata |only asciiSetupReader-1.2/asciiSetupReader/man/sas_ascii_reader.Rd | 12 asciiSetupReader-1.2/asciiSetupReader/man/spss_ascii_reader.Rd | 10 asciiSetupReader-1.2/asciiSetupReader/tests |only asciiSetupReader-1.2/asciiSetupReader/vignettes/Introduction_to_asciiReader.Rmd | 2 17 files changed, 191 insertions(+), 172 deletions(-)
More information about asciiSetupReader at CRAN
Permanent link
Title: R Interface to 'FOAAS'
Description: R access to the 'FOAAS' (F... Off As A Service) web service is provided.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between rfoaas versions 1.1.0 dated 2016-08-27 and 1.1.1 dated 2017-11-26
ChangeLog | 25 +++++++++++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 14 ++++++++------ R/foaas.R | 20 +++++++++++++++----- README.md | 13 ++++++++++--- demo |only man/rfoaas-package.Rd | 18 ++++++++++++++++-- tests/runTestsAgainstFOAAS.R | 34 ++++++++++++++++++++++++++++------ 8 files changed, 106 insertions(+), 26 deletions(-)
More information about intrinsicDimension at CRAN
Permanent link
Title: Quantitative Support of Decision Making under Uncertainty
Description: Supporting the quantitative analysis of binary welfare based
decision making processes using Monte Carlo simulations. Decision support
is given on two levels: (i) The actual decision level is to choose between
two alternatives under probabilistic uncertainty. This package calculates
the optimal decision based on maximizing expected welfare. (ii) The meta
decision level is to allocate resources to reduce the uncertainty in the
underlying decision problem, i.e to increase the current information to
improve the actual decision making process. This problem is dealt with
using the Value of Information Analysis. The Expected Value of
Information for arbitrary prospective estimates can be calculated as
well as Individual Expected Value of Perfect Information.
The probabilistic calculations are done via Monte Carlo
simulations. This Monte Carlo functionality can be used on its own.
Author: Eike Luedeling [cre, aut] (ICRAF),
Lutz Goehring [aut] (ICRAF and Lutz Goehring Consulting)
Maintainer: Eike Luedeling <eike@eikeluedeling.com>
Diff between decisionSupport versions 1.102.2 dated 2017-11-13 and 1.103.2 dated 2017-11-26
DESCRIPTION | 16 ++++++++------- MD5 | 62 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++- build |only inst/doc |only vignettes |only 5 files changed, 70 insertions(+), 8 deletions(-)
More information about decisionSupport at CRAN
Permanent link
Title: Lightweight Biology Software Installer
Description: Can be used to install and download massive bioinformatics analysis softwares and databases, such as NGS reads mapping tools with its required databases.
Author: Jianfeng Li [aut, cre]
Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>
Diff between BioInstaller versions 0.2.2 dated 2017-10-31 and 0.3.1 dated 2017-11-26
BioInstaller-0.2.2/BioInstaller/inst/extdata/databases |only BioInstaller-0.2.2/BioInstaller/inst/extdata/docker.toml |only BioInstaller-0.2.2/BioInstaller/inst/extdata/github.toml |only BioInstaller-0.2.2/BioInstaller/inst/extdata/github_meta.toml |only BioInstaller-0.2.2/BioInstaller/inst/extdata/nongithub.toml |only BioInstaller-0.2.2/BioInstaller/inst/extdata/nongithub_meta.toml |only BioInstaller-0.2.2/BioInstaller/inst/extdata/parse_version.R |only BioInstaller-0.2.2/BioInstaller/inst/extdata/softwares_db_demo.yaml |only BioInstaller-0.3.1/BioInstaller/ChangeLog | 62 BioInstaller-0.3.1/BioInstaller/DESCRIPTION | 8 BioInstaller-0.3.1/BioInstaller/MD5 | 90 BioInstaller-0.3.1/BioInstaller/NAMESPACE | 3 BioInstaller-0.3.1/BioInstaller/R/BioInstaller.R | 2 BioInstaller-0.3.1/BioInstaller/R/active.R | 2 BioInstaller-0.3.1/BioInstaller/R/crawl.R | 32 BioInstaller-0.3.1/BioInstaller/R/docker.R | 5 BioInstaller-0.3.1/BioInstaller/R/info.R | 8 BioInstaller-0.3.1/BioInstaller/R/install.R | 64 BioInstaller-0.3.1/BioInstaller/R/install_utils.R | 19 BioInstaller-0.3.1/BioInstaller/R/meta.R |only BioInstaller-0.3.1/BioInstaller/R/utils_function.R | 19 BioInstaller-0.3.1/BioInstaller/R/versions.R | 4 BioInstaller-0.3.1/BioInstaller/README.md | 43 BioInstaller-0.3.1/BioInstaller/inst/doc/BioInstaller.R | 60 BioInstaller-0.3.1/BioInstaller/inst/doc/BioInstaller.Rmd | 67 BioInstaller-0.3.1/BioInstaller/inst/doc/BioInstaller.html | 1681 ++++++---- BioInstaller-0.3.1/BioInstaller/inst/doc/write_configuration_file.R | 6 BioInstaller-0.3.1/BioInstaller/inst/doc/write_configuration_file.Rmd | 6 BioInstaller-0.3.1/BioInstaller/inst/doc/write_configuration_file.html | 648 +-- BioInstaller-0.3.1/BioInstaller/inst/extdata/config |only BioInstaller-0.3.1/BioInstaller/inst/extdata/demo |only BioInstaller-0.3.1/BioInstaller/inst/extdata/scripts/parse_version.R |only BioInstaller-0.3.1/BioInstaller/man/change.info.Rd | 4 BioInstaller-0.3.1/BioInstaller/man/craw.all.versions.Rd | 14 BioInstaller-0.3.1/BioInstaller/man/del.info.Rd | 4 BioInstaller-0.3.1/BioInstaller/man/docker.search.Rd | 7 BioInstaller-0.3.1/BioInstaller/man/get.info.Rd | 4 BioInstaller-0.3.1/BioInstaller/man/get.meta.Rd |only BioInstaller-0.3.1/BioInstaller/man/get.meta.files.Rd |only BioInstaller-0.3.1/BioInstaller/man/install.bioinfo.Rd | 31 BioInstaller-0.3.1/BioInstaller/man/install.github.Rd | 11 BioInstaller-0.3.1/BioInstaller/man/install.nongithub.Rd | 24 BioInstaller-0.3.1/BioInstaller/man/show.installed.Rd | 4 BioInstaller-0.3.1/BioInstaller/tests/testthat/test_install_uilts.R | 8 BioInstaller-0.3.1/BioInstaller/tests/testthat/test_meta.R |only BioInstaller-0.3.1/BioInstaller/vignettes/BioInstaller.Rmd | 67 BioInstaller-0.3.1/BioInstaller/vignettes/write_configuration_file.Rmd | 6 47 files changed, 1903 insertions(+), 1110 deletions(-)
Title: Omics Data Integration Project
Description: Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are defined as combinations of all variables. Those components are then used to produce useful graphical outputs that enable better understanding of the relationships and correlation structures between the different data sets that are integrated. mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data. A non exhaustive list of methods include variants of generalised Canonical Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: N-integration with variants of Generalised Canonical Correlation Analysis and P-integration with variants of multi-group Partial Least Squares.
Author: Kim-Anh Le Cao, Florian Rohart, Ignacio Gonzalez, Sebastien Dejean with key contributors Benoit Gautier, Francois Bartolo
and contributions from Pierre Monget, Jeff Coquery, FangZou Yao, Benoit Liquet.
Maintainer: Kim-Anh Le Cao <kimanh.lecao@unimelb.edu.au>
Diff between mixOmics versions 6.3.0 dated 2017-10-13 and 6.3.1 dated 2017-11-26
mixOmics-6.3.0/mixOmics/R/plotContrib.R |only mixOmics-6.3.0/mixOmics/man/plotContrib.Rd |only mixOmics-6.3.1/mixOmics/DESCRIPTION | 8 mixOmics-6.3.1/mixOmics/MD5 | 182 +++++++--------- mixOmics-6.3.1/mixOmics/NAMESPACE | 1 mixOmics-6.3.1/mixOmics/NEWS | 15 + mixOmics-6.3.1/mixOmics/R/LOGOCV.R | 2 mixOmics-6.3.1/mixOmics/R/MCV.block.splsda.R | 13 - mixOmics-6.3.1/mixOmics/R/MCV.splsda.R | 13 - mixOmics-6.3.1/mixOmics/R/block.spls.R | 2 mixOmics-6.3.1/mixOmics/R/block.splsda.R | 2 mixOmics-6.3.1/mixOmics/R/internal_mint.block.R | 24 +- mixOmics-6.3.1/mixOmics/R/internal_mint.block_helpers.R | 2 mixOmics-6.3.1/mixOmics/R/internal_wrapper.mint.R | 9 mixOmics-6.3.1/mixOmics/R/internal_wrapper.mint.block.R | 5 mixOmics-6.3.1/mixOmics/R/mint.block.spls.R | 2 mixOmics-6.3.1/mixOmics/R/mint.block.splsda.R | 2 mixOmics-6.3.1/mixOmics/R/mint.spls.R | 2 mixOmics-6.3.1/mixOmics/R/mint.splsda.R | 2 mixOmics-6.3.1/mixOmics/R/mixOmics.R | 6 mixOmics-6.3.1/mixOmics/R/nipals.R | 9 mixOmics-6.3.1/mixOmics/R/perf.R | 7 mixOmics-6.3.1/mixOmics/R/spls.R | 4 mixOmics-6.3.1/mixOmics/R/splsda.R | 2 mixOmics-6.3.1/mixOmics/R/t.test.process.R | 37 ++- mixOmics-6.3.1/mixOmics/R/tune.block.splsda.R | 6 mixOmics-6.3.1/mixOmics/R/tune.mint.splsda.R | 1 mixOmics-6.3.1/mixOmics/R/tune.splsda.R | 8 mixOmics-6.3.1/mixOmics/man/Koren.16S.Rd | 2 mixOmics-6.3.1/mixOmics/man/background.predict.Rd | 4 mixOmics-6.3.1/mixOmics/man/block.pls.Rd | 2 mixOmics-6.3.1/mixOmics/man/block.plsda.Rd | 10 mixOmics-6.3.1/mixOmics/man/block.spls.Rd | 15 - mixOmics-6.3.1/mixOmics/man/block.splsda.Rd | 20 - mixOmics-6.3.1/mixOmics/man/breast.TCGA.Rd | 2 mixOmics-6.3.1/mixOmics/man/cim.Rd | 16 - mixOmics-6.3.1/mixOmics/man/cimDiablo.Rd | 9 mixOmics-6.3.1/mixOmics/man/circosPlot.Rd | 13 - mixOmics-6.3.1/mixOmics/man/diverse.16S.Rd | 2 mixOmics-6.3.1/mixOmics/man/get.confusion_matrix.Rd | 5 mixOmics-6.3.1/mixOmics/man/image.tune.rcc.Rd | 2 mixOmics-6.3.1/mixOmics/man/imgCor.Rd | 2 mixOmics-6.3.1/mixOmics/man/ipca.Rd | 2 mixOmics-6.3.1/mixOmics/man/liver.toxicity.Rd | 2 mixOmics-6.3.1/mixOmics/man/logratio.transfo.Rd | 2 mixOmics-6.3.1/mixOmics/man/mat.rank.Rd | 2 mixOmics-6.3.1/mixOmics/man/mint.block.pls.Rd | 4 mixOmics-6.3.1/mixOmics/man/mint.block.plsda.Rd | 15 - mixOmics-6.3.1/mixOmics/man/mint.block.spls.Rd | 9 mixOmics-6.3.1/mixOmics/man/mint.block.splsda.Rd | 18 - mixOmics-6.3.1/mixOmics/man/mint.pca.Rd | 4 mixOmics-6.3.1/mixOmics/man/mint.pls.Rd | 4 mixOmics-6.3.1/mixOmics/man/mint.plsda.Rd | 9 mixOmics-6.3.1/mixOmics/man/mint.spls.Rd | 12 - mixOmics-6.3.1/mixOmics/man/mint.splsda.Rd | 14 - mixOmics-6.3.1/mixOmics/man/mixOmics.Rd | 25 +- mixOmics-6.3.1/mixOmics/man/network.Rd | 10 mixOmics-6.3.1/mixOmics/man/nipals.Rd | 4 mixOmics-6.3.1/mixOmics/man/nutrimouse.Rd | 2 mixOmics-6.3.1/mixOmics/man/pca.Rd | 6 mixOmics-6.3.1/mixOmics/man/perf.Rd | 21 + mixOmics-6.3.1/mixOmics/man/plot.perf.Rd | 9 mixOmics-6.3.1/mixOmics/man/plot.rcc.Rd | 2 mixOmics-6.3.1/mixOmics/man/plot.tune.Rd | 4 mixOmics-6.3.1/mixOmics/man/plotArrow.Rd | 6 mixOmics-6.3.1/mixOmics/man/plotDiablo.Rd | 2 mixOmics-6.3.1/mixOmics/man/plotIndiv.Rd | 2 mixOmics-6.3.1/mixOmics/man/plotLoadings.Rd | 8 mixOmics-6.3.1/mixOmics/man/plotVar.Rd | 4 mixOmics-6.3.1/mixOmics/man/pls.Rd | 11 mixOmics-6.3.1/mixOmics/man/plsda.Rd | 6 mixOmics-6.3.1/mixOmics/man/predict.Rd | 8 mixOmics-6.3.1/mixOmics/man/print.methods.Rd | 2 mixOmics-6.3.1/mixOmics/man/rcc.Rd | 6 mixOmics-6.3.1/mixOmics/man/selectVar.Rd | 2 mixOmics-6.3.1/mixOmics/man/sipca.Rd | 2 mixOmics-6.3.1/mixOmics/man/spca.Rd | 2 mixOmics-6.3.1/mixOmics/man/spls.Rd | 8 mixOmics-6.3.1/mixOmics/man/splsda.Rd | 8 mixOmics-6.3.1/mixOmics/man/stemcells.Rd | 2 mixOmics-6.3.1/mixOmics/man/summary.Rd | 2 mixOmics-6.3.1/mixOmics/man/tune.Rd | 21 + mixOmics-6.3.1/mixOmics/man/tune.block.splsda.Rd | 13 - mixOmics-6.3.1/mixOmics/man/tune.mint.splsda.Rd | 15 - mixOmics-6.3.1/mixOmics/man/tune.pca.Rd | 2 mixOmics-6.3.1/mixOmics/man/tune.rcc.Rd | 2 mixOmics-6.3.1/mixOmics/man/tune.splsda.Rd | 15 - mixOmics-6.3.1/mixOmics/man/tune.splslevel.Rd | 7 mixOmics-6.3.1/mixOmics/man/vac18.simulated.Rd | 2 mixOmics-6.3.1/mixOmics/man/vip.Rd | 2 mixOmics-6.3.1/mixOmics/man/withinVariation.Rd | 4 mixOmics-6.3.1/mixOmics/man/wrapper.rgcca.Rd | 4 mixOmics-6.3.1/mixOmics/man/wrapper.sgcca.Rd | 6 93 files changed, 448 insertions(+), 376 deletions(-)
Title: Error Propagation for R Vectors
Description: Support for painless automatic error propagation in numerical operations.
Author: Iñaki Ucar [aut, cph, cre]
Maintainer: Iñaki Ucar <i.ucar86@gmail.com>
Diff between errors versions 0.1.0 dated 2017-09-26 and 0.2.0 dated 2017-11-26
errors-0.1.0/errors/man/matmult.Rd |only errors-0.2.0/errors/DESCRIPTION | 10 - errors-0.2.0/errors/MD5 | 47 +++-- errors-0.2.0/errors/NAMESPACE | 2 errors-0.2.0/errors/NEWS.md | 12 + errors-0.2.0/errors/R/errors.R | 36 ++-- errors-0.2.0/errors/R/math.R | 34 +++- errors-0.2.0/errors/R/misc.R | 182 ++++++++++++++++++++-- errors-0.2.0/errors/R/ops.R | 31 +++ errors-0.2.0/errors/R/plot.R | 19 +- errors-0.2.0/errors/R/print.R | 58 ++++--- errors-0.2.0/errors/R/summary.R | 31 ++- errors-0.2.0/errors/README.md | 83 +++------- errors-0.2.0/errors/man/Extract.errors.Rd |only errors-0.2.0/errors/man/as.data.frame.errors.Rd |only errors-0.2.0/errors/man/as.matrix.errors.Rd |only errors-0.2.0/errors/man/c.errors.Rd |only errors-0.2.0/errors/man/cbind.errors.Rd |only errors-0.2.0/errors/man/diff.errors.Rd |only errors-0.2.0/errors/man/errors.Rd | 43 +++-- errors-0.2.0/errors/man/format.errors.Rd | 12 + errors-0.2.0/errors/man/groupGeneric.errors.Rd |only errors-0.2.0/errors/man/matmult.errors.Rd |only errors-0.2.0/errors/man/plot.errors.Rd |only errors-0.2.0/errors/man/print.errors.Rd |only errors-0.2.0/errors/man/rep.errors.Rd |only errors-0.2.0/errors/man/t.errors.Rd |only errors-0.2.0/errors/man/type_sum.errors.Rd | 4 errors-0.2.0/errors/tests/testthat/test-misc.R | 69 ++++++++ errors-0.2.0/errors/tests/testthat/test-ops.R | 23 +- errors-0.2.0/errors/tests/testthat/test-summary.R | 4 31 files changed, 520 insertions(+), 180 deletions(-)
Title: WordNet Interface
Description: An interface to WordNet using the Jawbone Java API to WordNet.
WordNet (<http://wordnet.princeton.edu/>) is a large lexical database of
English. Nouns, verbs, adjectives and adverbs are grouped into sets of
cognitive synonyms (synsets), each expressing a distinct concept. Synsets
are interlinked by means of conceptual-semantic and lexical relations.
Please note that WordNet(R) is a registered tradename. Princeton
University makes WordNet available to research and commercial users
free of charge provided the terms of their license
(<http://wordnet.princeton.edu/wordnet/license/>) are followed, and
proper reference is made to the project using an appropriate
citation (<http://wordnet.princeton.edu/wordnet/citing-wordnet/>).
Author: Ingo Feinerer [aut],
Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>),
Mike Wallace [ctb, cph] (Jawbone Java WordNet API library)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between wordnet versions 0.1-13 dated 2017-11-12 and 0.1-14 dated 2017-11-26
wordnet-0.1-13/wordnet/R/onload.R |only wordnet-0.1-14/wordnet/DESCRIPTION | 6 +++--- wordnet-0.1-14/wordnet/MD5 | 8 ++++---- wordnet-0.1-14/wordnet/R/init.R |only wordnet-0.1-14/wordnet/R/synsets.R | 1 + wordnet-0.1-14/wordnet/inst/doc/wordnet.pdf |binary 6 files changed, 8 insertions(+), 7 deletions(-)