Title: Sample Size Calculation using Restricted Mean Survival Time
Description: Calculates the power and sample size based on the difference in Restricted Mean Survival Time.
Author: Miki Horiguchi, Hajime Uno
Maintainer: Miki Horiguchi <horiguchimiki@gmail.com>
Diff between SSRMST versions 0.1.0 dated 2015-08-24 and 0.1.1 dated 2017-05-18
DESCRIPTION | 16 + MD5 | 23 +- NAMESPACE | 3 NEWS.md |only R/ssrmst.R | 338 +++++++++++++++++++++++++++++------------- build/vignette.rds |binary inst/doc/vignette-ssrmst.R | 8 inst/doc/vignette-ssrmst.Rmd | 54 +++--- inst/doc/vignette-ssrmst.html | 132 +++++++++------- man/SSRMST-package.Rd | 54 +++--- man/print.ssrmst.Rd | 3 man/ssrmst.Rd | 47 +++-- vignettes/vignette-ssrmst.Rmd | 54 +++--- 13 files changed, 447 insertions(+), 285 deletions(-)
Title: Interaction Between R and REDCap
Description: Encapsulates functions to streamline calls from R to the REDCap
API. REDCap (Research Electronic Data CAPture) is a web application for
building and managing online surveys and databases developed at Vanderbilt
University. The Application Programming Interface (API) offers an avenue
to access and modify data programmatically, improving the capacity for
literate and reproducible programming.
Author: Will Beasley [aut, cre],
David Bard [ctb],
Thomas Wilson [ctb],
John J Aponte [ctb],
Rollie Parrish [ctb],
Benjamin Nutter [ctb],
Andrew Peters [ctb],
Hao Zhu [ctb]
Maintainer: Will Beasley <wibeasley@hotmail.com>
Diff between REDCapR versions 0.9.7 dated 2016-09-09 and 0.9.8 dated 2017-05-18
REDCapR-0.9.7/REDCapR/R/validate-for-write.R |only REDCapR-0.9.7/REDCapR/man/validate_for_write.Rd |only REDCapR-0.9.7/REDCapR/tests/testthat/test-validate-for-write.R |only REDCapR-0.9.8/REDCapR/DESCRIPTION | 17 REDCapR-0.9.8/REDCapR/MD5 | 187 - REDCapR-0.9.8/REDCapR/NAMESPACE | 47 REDCapR-0.9.8/REDCapR/NEWS | 237 - REDCapR-0.9.8/REDCapR/R/REDCapR-package.R | 88 REDCapR-0.9.8/REDCapR/R/create-batch-glossary.R | 129 REDCapR-0.9.8/REDCapR/R/metadata-utilities.R | 191 - REDCapR-0.9.8/REDCapR/R/project-simple.R | 208 - REDCapR-0.9.8/REDCapR/R/redcap-column-sanitize.R | 100 REDCapR-0.9.8/REDCapR/R/redcap-download-file-oneshot.R | 322 - REDCapR-0.9.8/REDCapR/R/redcap-metadata-read.R | 287 - REDCapR-0.9.8/REDCapR/R/redcap-project.R | 222 - REDCapR-0.9.8/REDCapR/R/redcap-read-oneshot-eav.R |only REDCapR-0.9.8/REDCapR/R/redcap-read-oneshot.R | 455 +- REDCapR-0.9.8/REDCapR/R/redcap-read.R | 445 +- REDCapR-0.9.8/REDCapR/R/redcap-upload-file-oneshot.R | 271 - REDCapR-0.9.8/REDCapR/R/redcap-variables.R |only REDCapR-0.9.8/REDCapR/R/redcap-version.R |only REDCapR-0.9.8/REDCapR/R/redcap-write-oneshot.R | 348 - REDCapR-0.9.8/REDCapR/R/redcap-write.R | 297 - REDCapR-0.9.8/REDCapR/R/retrieve-credential.R | 410 +- REDCapR-0.9.8/REDCapR/R/retrieve-token.R | 242 - REDCapR-0.9.8/REDCapR/R/sanitize-token.R |only REDCapR-0.9.8/REDCapR/R/utilities.R | 90 REDCapR-0.9.8/REDCapR/R/validate.R |only REDCapR-0.9.8/REDCapR/README.md | 220 - REDCapR-0.9.8/REDCapR/build/vignette.rds |binary REDCapR-0.9.8/REDCapR/inst/doc/BasicREDCapROperations.R | 242 - REDCapR-0.9.8/REDCapR/inst/doc/BasicREDCapROperations.Rmd | 356 +- REDCapR-0.9.8/REDCapR/inst/doc/BasicREDCapROperations.html | 1770 +++++++--- REDCapR-0.9.8/REDCapR/inst/doc/SecurityDatabase.Rmd | 658 +-- REDCapR-0.9.8/REDCapR/inst/doc/SecurityDatabase.html | 770 ++-- REDCapR-0.9.8/REDCapR/inst/doc/TroubleshootingApiCalls.Rmd | 788 ++-- REDCapR-0.9.8/REDCapR/inst/doc/TroubleshootingApiCalls.html | 766 ++-- REDCapR-0.9.8/REDCapR/inst/doc/advanced-redcapr-operations.R |only REDCapR-0.9.8/REDCapR/inst/doc/advanced-redcapr-operations.Rmd |only REDCapR-0.9.8/REDCapR/inst/doc/advanced-redcapr-operations.html |only REDCapR-0.9.8/REDCapR/inst/misc/bad.credentials | 16 REDCapR-0.9.8/REDCapR/inst/misc/conflicting-rows.credentials | 16 REDCapR-0.9.8/REDCapR/inst/misc/example.credentials | 20 REDCapR-0.9.8/REDCapR/inst/misc/out-of-order.credentials | 16 REDCapR-0.9.8/REDCapR/inst/misc/vignette.css | 72 REDCapR-0.9.8/REDCapR/inst/misc/zero-rows.credentials | 12 REDCapR-0.9.8/REDCapR/inst/test-data/project-color-boxes/Readme.md | 106 REDCapR-0.9.8/REDCapR/inst/test-data/project-color-boxes/color-boxes-data-dictionary.csv | 6 REDCapR-0.9.8/REDCapR/inst/test-data/project-color-boxes/color-boxes-data.csv | 8 REDCapR-0.9.8/REDCapR/inst/test-data/project-longitudinal/longitudinal-data-dictionary.csv | 192 - REDCapR-0.9.8/REDCapR/inst/test-data/project-longitudinal/longitudinal-data.csv | 38 REDCapR-0.9.8/REDCapR/inst/test-data/project-russian/russian-data.csv | 8 REDCapR-0.9.8/REDCapR/inst/test-data/project-simple/simple-data-dictionary.csv | 34 REDCapR-0.9.8/REDCapR/inst/test-data/project-simple/simple-data.csv | 32 REDCapR-0.9.8/REDCapR/inst/test-data/project-simple/simple-metadata.csv | 34 REDCapR-0.9.8/REDCapR/man/REDCapR-package.Rd | 89 REDCapR-0.9.8/REDCapR/man/create_batch_glossary.Rd | 105 REDCapR-0.9.8/REDCapR/man/metadata_utilities.Rd | 148 REDCapR-0.9.8/REDCapR/man/redcap_column_sanitize.Rd | 93 REDCapR-0.9.8/REDCapR/man/redcap_download_file_oneshot.Rd | 194 - REDCapR-0.9.8/REDCapR/man/redcap_metadata_read.Rd | 137 REDCapR-0.9.8/REDCapR/man/redcap_project.Rd | 115 REDCapR-0.9.8/REDCapR/man/redcap_read.Rd | 207 - REDCapR-0.9.8/REDCapR/man/redcap_read_oneshot.Rd | 222 - REDCapR-0.9.8/REDCapR/man/redcap_read_oneshot_eav.Rd |only REDCapR-0.9.8/REDCapR/man/redcap_upload_file_oneshot.Rd | 181 - REDCapR-0.9.8/REDCapR/man/redcap_variables.Rd |only REDCapR-0.9.8/REDCapR/man/redcap_version.Rd |only REDCapR-0.9.8/REDCapR/man/redcap_write.Rd | 199 - REDCapR-0.9.8/REDCapR/man/redcap_write_oneshot.Rd | 169 REDCapR-0.9.8/REDCapR/man/replace_nas_with_explicit.Rd | 73 REDCapR-0.9.8/REDCapR/man/retrieve_credential.Rd | 133 REDCapR-0.9.8/REDCapR/man/retrieve_token.Rd | 137 REDCapR-0.9.8/REDCapR/man/sanitize_token.Rd |only REDCapR-0.9.8/REDCapR/man/validate.Rd |only REDCapR-0.9.8/REDCapR/tests/manual/README.md | 8 REDCapR-0.9.8/REDCapR/tests/manual/test-could-not-connect-rate.R | 104 REDCapR-0.9.8/REDCapR/tests/manual/test-stress-test-serial.R | 224 - REDCapR-0.9.8/REDCapR/tests/test-all.R | 10 REDCapR-0.9.8/REDCapR/tests/testthat/test-column-sanitize.R | 73 REDCapR-0.9.8/REDCapR/tests/testthat/test-create-batch-glossary.R | 156 REDCapR-0.9.8/REDCapR/tests/testthat/test-file-oneshot.R | 426 +- REDCapR-0.9.8/REDCapR/tests/testthat/test-metadata-read.R | 546 +-- REDCapR-0.9.8/REDCapR/tests/testthat/test-metadata-utilities.R | 60 REDCapR-0.9.8/REDCapR/tests/testthat/test-project.R | 142 REDCapR-0.9.8/REDCapR/tests/testthat/test-read-batch-longitudinal.R | 332 - REDCapR-0.9.8/REDCapR/tests/testthat/test-read-batch-simple.R | 914 ++--- REDCapR-0.9.8/REDCapR/tests/testthat/test-read-errors.R | 174 REDCapR-0.9.8/REDCapR/tests/testthat/test-read-oneshot-eav.R |only REDCapR-0.9.8/REDCapR/tests/testthat/test-read-oneshot.R | 668 +-- REDCapR-0.9.8/REDCapR/tests/testthat/test-read-russian.R | 92 REDCapR-0.9.8/REDCapR/tests/testthat/test-retrieve-credential-local.R | 304 - REDCapR-0.9.8/REDCapR/tests/testthat/test-retrieve-credential-mssql.R | 312 - REDCapR-0.9.8/REDCapR/tests/testthat/test-retrieve-token.R | 230 - REDCapR-0.9.8/REDCapR/tests/testthat/test-sanitize.R |only REDCapR-0.9.8/REDCapR/tests/testthat/test-utilities.R | 140 REDCapR-0.9.8/REDCapR/tests/testthat/test-validate.R |only REDCapR-0.9.8/REDCapR/tests/testthat/test-variables.R |only REDCapR-0.9.8/REDCapR/tests/testthat/test-version.R |only REDCapR-0.9.8/REDCapR/tests/testthat/test-write-batch.R | 360 +- REDCapR-0.9.8/REDCapR/tests/testthat/test-write-oneshot.R | 360 +- REDCapR-0.9.8/REDCapR/vignettes/BasicREDCapROperations.Rmd | 356 +- REDCapR-0.9.8/REDCapR/vignettes/SecurityDatabase.Rmd | 658 +-- REDCapR-0.9.8/REDCapR/vignettes/TroubleshootingApiCalls.Rmd | 788 ++-- REDCapR-0.9.8/REDCapR/vignettes/advanced-redcapr-operations.Rmd |only REDCapR-0.9.8/REDCapR/vignettes/styles.css |only 106 files changed, 10751 insertions(+), 9661 deletions(-)
Title: Broadcasts, Transmissions and Receptions in an Opportunistic
Network
Description: Computes the expectation of the number of broadcasts, transmissions and receptions considering an Opportunistic transport model. It provides theoretical results and also estimated values based on Monte Carlo simulations.
Author: Christian E. Galarza, Jonathan M. Olate
Maintainer: Christian E. Galarza <cgalarza88@gmail.com>
Diff between Opportunistic versions 1.0 dated 2017-05-09 and 1.1 dated 2017-05-18
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- R/Expected.R | 3 --- R/MonteCarlo.R | 4 +--- 4 files changed, 10 insertions(+), 14 deletions(-)
Title: Solve Systems of Nonlinear Equations
Description: Solve a system of nonlinear equations using a Broyden or a Newton method
with a choice of global strategies such as line search and trust region.
There are options for using a numerical or user supplied Jacobian,
for specifying a banded numerical Jacobian and for allowing
a singular or ill-conditioned Jacobian.
Author: Berend Hasselman
Maintainer: Berend Hasselman <bhh@xs4all.nl>
Diff between nleqslv versions 3.2 dated 2017-03-04 and 3.3 dated 2017-05-18
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 7 +++++++ man/searchzeros.Rd | 8 ++++---- src/nleqslv.c | 11 +++++++---- src/nwclsh.f | 5 +++-- 6 files changed, 30 insertions(+), 19 deletions(-)
Title: Gene-Based Segregation Test
Description: Implements the gene-based segregation test(GESE) and the weighted GESE test for identifying genes with causal variants of large effects for family-based sequencing data. The methods are described in Qiao, D. Lange, C., Laird, N.M., Won, S., Hersh, C.P., et al. (2017). <DOI:10.1002/gepi.22037>. Gene-based segregation method for identifying rare variants for family-based sequencing studies. Genet Epidemiol 41(4):309-319. More details can be found at <http://scholar.harvard.edu/dqiao/gese>.
Author: Dandi Qiao, Michael H. Cho
Maintainer: Dandi Qiao <redaq@channing.harvard.edu>
Diff between GESE versions 2.0.0 dated 2016-11-16 and 2.0.1 dated 2017-05-18
DESCRIPTION | 10 +++++----- MD5 | 28 ++++++++++++++-------------- R/GESE.R | 11 ++++++++--- build/partial.rdb |binary data/database.rda |binary inst/doc/my-vignette.Rmd | 2 +- inst/doc/my-vignette.pdf |binary man/GESE-internal.Rd | 2 +- man/GESE-package.Rd | 3 ++- man/GESE.Rd | 4 ++-- man/condSegProbF.Rd | 3 ++- man/getSegInfo.Rd | 3 ++- man/trim_oneLineage.Rd | 3 +-- man/trim_unrelated.Rd | 2 +- vignettes/my-vignette.Rmd | 2 +- 15 files changed, 40 insertions(+), 33 deletions(-)
Title: Dendrochronology Program Library in R
Description: Perform tree-ring analyses such as detrending, chronology
building, and cross dating. Read and write standard file formats
used in dendrochronology.
Author: Andy Bunn [aut, cph, cre, trl], Mikko Korpela [aut, trl], Franco Biondi [aut, cph], Filipe Campelo [aut, cph], Pierre Mérian [aut, cph], Fares Qeadan [aut, cph], Christian Zang [aut, cph], Allan Buras [ctb], Jacob Cecile [ctb], Manfred Mudelsee [ctb], Michael Schulz [ctb]
Maintainer: Andy Bunn <andy.bunn@wwu.edu>
Diff between dplR versions 1.6.5 dated 2017-02-03 and 1.6.6 dated 2017-05-18
ChangeLog | 79 +++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 23 +++++------- MD5 | 60 +++++++++++++++++--------------- NAMESPACE | 13 ++----- R/exactmean.R | 2 - R/helpers.R | 16 ++++++++ R/latexify.R | 8 ++-- R/rasterPlot.R | 7 ++- R/rcs.R | 68 ++++++++++++++++++++----------------- R/read.tucson.R | 3 + R/redfit.R | 36 ++++++++++--------- build/vignette.rds |binary inst/doc/chron-dplR.pdf |binary inst/doc/intro-dplR.pdf |binary inst/doc/timeseries-dplR.pdf |binary inst/doc/xdate-dplR.pdf |binary man/detrend.series.Rd | 4 +- man/rcs.Rd | 9 +++- man/redfit.Rd | 11 +++-- src/Makevars |only src/dplR-win.def |only src/exactmean.c | 1 src/gini.c | 1 src/init.c |only src/rcompact.c | 1 src/readloop.c | 1 src/redfit.c | 16 +++----- src/registered.h |only src/sens.c | 1 src/tbrm.c | 1 tests/testthat.R | 5 +- tests/testthat/test-chron.R | 4 +- tests/testthat/test-dplR.R | 4 +- 33 files changed, 245 insertions(+), 129 deletions(-)
Title: Exponentiation Operations
Description: Computation of matrix and scalar exponentiation.
Author: Albert Dorador
Maintainer: Albert Dorador <albert.dorador@estudiant.upc.edu>
Diff between powerplus versions 3.0 dated 2016-08-18 and 3.1 dated 2017-05-18
powerplus-3.0/powerplus/R/MatpowV3.R |only powerplus-3.0/powerplus/R/explusV2.R |only powerplus-3.1/powerplus/DESCRIPTION | 14 +++++++------- powerplus-3.1/powerplus/MD5 | 10 +++++----- powerplus-3.1/powerplus/R/MatpowV4.R |only powerplus-3.1/powerplus/R/explusV3.R |only powerplus-3.1/powerplus/man/Matpow.Rd | 18 ++++++++---------- powerplus-3.1/powerplus/man/explus.Rd | 19 ++++++++++++------- 8 files changed, 32 insertions(+), 29 deletions(-)
More information about LZeroSpikeInference at CRAN
Permanent link
Title: Blind Source Separation Methods for Tensor-Valued Observations
Description: Contains several utility functions for manipulating tensor-valued data (centering, multiplication from a single mode etc.) and the implementations of the following blind source separation methods for tensor-valued data: 'tPCA', 'tFOBI', 'tJADE', 'tgFOBI', 'tgJADE', 'tSOBI', 'tNSS.SD', 'tNSS.JD' and 'tNSS.TD.JD'.
Author: Joni Virta, Bing Li, Klaus Nordhausen, Hannu Oja
Maintainer: Joni Virta <jomivi@utu.fi>
Diff between tensorBSS versions 0.2 dated 2016-08-25 and 0.3 dated 2017-05-18
tensorBSS-0.2/tensorBSS/R/eigenVectors.R |only tensorBSS-0.2/tensorBSS/R/mAutoCovMatrix.R |only tensorBSS-0.2/tensorBSS/R/mFOBIMatrix.R |only tensorBSS-0.2/tensorBSS/R/mJADEMatrix.R |only tensorBSS-0.2/tensorBSS/R/mTGFOBIMatrix.R |only tensorBSS-0.2/tensorBSS/R/mTGJADEMatrix.R |only tensorBSS-0.2/tensorBSS/R/matrixCovariance.R |only tensorBSS-0.2/tensorBSS/R/symmetricPower.R |only tensorBSS-0.2/tensorBSS/src/tBSS.cpp |only tensorBSS-0.2/tensorBSS/src/tBSS.h |only tensorBSS-0.3/tensorBSS/DESCRIPTION | 10 +++---- tensorBSS-0.3/tensorBSS/MD5 | 34 ++++++++++++++------------- tensorBSS-0.3/tensorBSS/NAMESPACE | 4 +-- tensorBSS-0.3/tensorBSS/R/RcppExports.R |only tensorBSS-0.3/tensorBSS/R/arraySelectLast.R |only tensorBSS-0.3/tensorBSS/R/tJADE.R | 2 - tensorBSS-0.3/tensorBSS/R/tJADERotate.R | 15 +++++++++-- tensorBSS-0.3/tensorBSS/R/tNSS.JD.R |only tensorBSS-0.3/tensorBSS/R/tNSS.SD.R |only tensorBSS-0.3/tensorBSS/R/tNSS.TD.JD.R |only tensorBSS-0.3/tensorBSS/inst/ChangeLog | 9 ++++++- tensorBSS-0.3/tensorBSS/man/tFOBI.Rd | 2 - tensorBSS-0.3/tensorBSS/man/tNSS.JD.Rd |only tensorBSS-0.3/tensorBSS/man/tNSS.SD.Rd |only tensorBSS-0.3/tensorBSS/man/tNSS.TD.JD.Rd |only tensorBSS-0.3/tensorBSS/src/RcppExports.cpp |only tensorBSS-0.3/tensorBSS/src/tensorBSS.cpp |only tensorBSS-0.3/tensorBSS/src/tensorBSS.h |only tensorBSS-0.3/tensorBSS/src/tensorBSS_init.c |only 29 files changed, 47 insertions(+), 29 deletions(-)
Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate
the visual interpretation of large datasets in sedimentary geology. Includes
functionality for adaptive kernel density estimation, multidimensional scaling,
generalised procrustes analysis and individual differences scaling using a
variety of dissimilarity measures. Univariate provenance proxies, such as
single-grain ages or (isotopic) compositions are compared with the Kolmogorov-
Smirnov, Kuiper or Sircombe-Hazelton L2 distances. Categorical provenance
proxies, such as mineralogical, petrographic or chemical compositions are
compared with the Aitchison and Bray-Curtis distances. Also included are tools
to plot compositional data on ternary diagrams, to calculate the sample size
required for specified levels of statistical precision, and to assess the
effects of hydraulic sorting on detrital compositions. Includes an intuitive
query-based user interface for users who are not proficient in R.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between provenance versions 1.6 dated 2017-05-03 and 1.7 dated 2017-05-18
DESCRIPTION | 13 MD5 | 96 +-- NAMESPACE | 1 R/gui.R | 30 - R/provenance.R | 980 ------------------------------------- R/toolbox.R |only man/CLR.Rd | 3 man/GPA.Rd | 3 man/KDE.Rd | 1 man/KDEs.Rd | 1 man/KS.diss.Rd | 3 man/Kuiper.diss.Rd |only man/MDS.Rd | 23 man/Namib.Rd | 7 man/PCA.Rd | 3 man/SH.diss.Rd | 7 man/amalgamate.Rd | 7 man/as.acomp.Rd | 3 man/as.compositional.Rd | 3 man/as.data.frame.compositional.Rd | 3 man/botev.Rd | 7 man/bray.diss.Rd | 3 man/combine.Rd | 3 man/densities.Rd | 7 man/diss.Rd | 11 man/endmembers.Rd | 7 man/get.f.Rd | 3 man/get.n.Rd | 3 man/get.p.Rd | 3 man/indscal.Rd | 7 man/minsorting.Rd | 7 man/plot.GPA.Rd | 1 man/plot.INDSCAL.Rd | 1 man/plot.KDE.Rd | 1 man/plot.MDS.Rd | 1 man/plot.PCA.Rd | 1 man/plot.compositional.Rd | 1 man/plot.distributional.Rd | 1 man/plot.minsorting.Rd | 1 man/plot.ternary.Rd | 1 man/procrustes.Rd | 9 man/provenance.Rd | 35 + man/read.compositional.Rd | 3 man/read.densities.Rd | 3 man/read.distributional.Rd | 6 man/restore.Rd | 7 man/subset.compositional.Rd | 3 man/subset.distributional.Rd | 3 man/summaryplot.Rd | 1 man/ternary.Rd | 3 50 files changed, 189 insertions(+), 1141 deletions(-)
Title: Conditional Formatting in Data Frames
Description: Apply and visualize conditional formatting to data frames in R.
It renders a data frame with cells formatted according to
criteria defined by rules, using a syntax similar to 'ggplot2'. The table is
printed either opening a web browser or within the 'RStudio' viewer if
available. The conditional formatting rules allow to highlight cells
matching a condition or add a gradient background to a given column. This
package supports both 'HTML' and 'LaTeX' outputs in 'knitr' reports, and
exporting to an 'xlsx' file.
Author: Sergio Oller Moreno [aut, cph, cre]
Maintainer: Sergio Oller Moreno <sergioller@gmail.com>
Diff between condformat versions 0.5.0 dated 2017-01-23 and 0.6.0 dated 2017-05-18
DESCRIPTION | 14 +++--- MD5 | 64 ++++++++++++++-------------- NAMESPACE | 1 NEWS | 10 ++++ R/condformat.R | 2 R/condformat_render.R | 82 ++++++++++++++++++++----------------- R/shiny.R | 35 +++++---------- build/vignette.rds |binary inst/doc/introduction.html | 8 +-- inst/shinyexample/server.R | 30 ++++++++++++- inst/shinyexample/ui.R | 28 ++++++++++-- man/condformat-shiny.Rd | 7 +-- man/condformat.Rd | 1 man/condformat2excel.Rd | 1 man/condformat2html.Rd | 1 man/condformat2latex.Rd | 1 man/condformat2widget.Rd | 5 +- man/get_css_field.Rd | 1 man/knit_print.condformat_tbl.Rd | 1 man/lock_cells.Rd | 1 man/plus-.condformat_tbl.Rd | 1 man/print.condformat_tbl.Rd | 5 +- man/reexports.Rd | 2 man/render_rules_condformat_tbl.Rd | 1 man/rule_fill_discrete.Rd | 1 man/rule_fill_discrete_.Rd | 1 man/rule_fill_gradient.Rd | 1 man/rule_fill_gradient2.Rd | 1 man/rule_fill_gradient2_.Rd | 1 man/rule_fill_gradient_.Rd | 1 man/show_columns.Rd | 1 man/show_rows.Rd | 2 man/theme_htmlTable.Rd | 1 33 files changed, 175 insertions(+), 137 deletions(-)
Title: Regularization Paths for Regression Models with Grouped
Covariates
Description: Efficient algorithms for fitting the regularization path of
linear or logistic regression models with grouped penalties. This
includes group selection methods such as group lasso, group MCP, and
group SCAD as well as bi-level selection methods such as the group
exponential lasso, the composite MCP, and the group bridge.
Author: Patrick Breheny [aut, cre], Yaohui Zeng [ctb]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between grpreg versions 3.0-2 dated 2016-07-11 and 3.1-0 dated 2017-05-18
grpreg-3.0-2/grpreg/src/grpreg.c |only grpreg-3.0-2/grpreg/tests |only grpreg-3.1-0/grpreg/DESCRIPTION | 12 grpreg-3.1-0/grpreg/MD5 | 89 +- grpreg-3.1-0/grpreg/NEWS | 293 +++---- grpreg-3.1-0/grpreg/R/cv.grpreg.R | 44 - grpreg-3.1-0/grpreg/R/cv.grpsurv.R | 6 grpreg-3.1-0/grpreg/R/gBridge.R | 143 +-- grpreg-3.1-0/grpreg/R/grpreg.R | 157 +-- grpreg-3.1-0/grpreg/R/grpsurv.R | 113 +- grpreg-3.1-0/grpreg/R/multi.R | 3 grpreg-3.1-0/grpreg/R/newS.R |only grpreg-3.1-0/grpreg/R/newXG.R |only grpreg-3.1-0/grpreg/R/newY.R |only grpreg-3.1-0/grpreg/R/reorderGroups.R | 4 grpreg-3.1-0/grpreg/R/setupLambda.R | 30 grpreg-3.1-0/grpreg/build/vignette.rds |binary grpreg-3.1-0/grpreg/inst/doc/penalties.Rnw | 10 grpreg-3.1-0/grpreg/inst/doc/penalties.pdf |binary grpreg-3.1-0/grpreg/inst/doc/quick-start.Rnw | 2 grpreg-3.1-0/grpreg/inst/doc/quick-start.pdf |binary grpreg-3.1-0/grpreg/inst/tests/agreement.R |only grpreg-3.1-0/grpreg/inst/tests/basic-functionality.R | 120 +- grpreg-3.1-0/grpreg/inst/tests/coerce.R | 16 grpreg-3.1-0/grpreg/inst/tests/cv.R |only grpreg-3.1-0/grpreg/inst/tests/extra-features.R | 43 - grpreg-3.1-0/grpreg/inst/tests/grpsurv.R | 2 grpreg-3.1-0/grpreg/inst/tests/multitask.R | 3 grpreg-3.1-0/grpreg/inst/tests/standardization-orthogonalization.R | 1 grpreg-3.1-0/grpreg/man/Lung.Rd | 2 grpreg-3.1-0/grpreg/man/gBridge.Rd | 4 grpreg-3.1-0/grpreg/man/grpreg-internal.Rd | 2 grpreg-3.1-0/grpreg/man/grpreg.Rd | 50 - grpreg-3.1-0/grpreg/man/grpsurv.Rd | 14 grpreg-3.1-0/grpreg/src/gdfit_binomial.c | 49 - grpreg-3.1-0/grpreg/src/gdfit_cox.c | 57 - grpreg-3.1-0/grpreg/src/gdfit_gaussian.c | 417 ++++++++-- grpreg-3.1-0/grpreg/src/gdfit_poisson.c | 52 - grpreg-3.1-0/grpreg/src/grpreg_init.c |only grpreg-3.1-0/grpreg/src/lcdfit_binomial.c | 56 - grpreg-3.1-0/grpreg/src/lcdfit_cox.c | 60 - grpreg-3.1-0/grpreg/src/lcdfit_gaussian.c | 60 - grpreg-3.1-0/grpreg/src/lcdfit_poisson.c | 54 - grpreg-3.1-0/grpreg/src/maxprod.c | 8 grpreg-3.1-0/grpreg/src/standardize.c | 4 grpreg-3.1-0/grpreg/vignettes/penalties.Rnw | 10 grpreg-3.1-0/grpreg/vignettes/quick-start.Rnw | 2 47 files changed, 1130 insertions(+), 862 deletions(-)
Title: Ensemble Forecast Verification for Large Data Sets
Description: Set of tools to simplify application of atomic forecast
verification metrics for (comparative) verification of ensemble forecasts
to large data sets. The forecast metrics are imported from the
'SpecsVerification' package, and additional forecast metrics are provided
with this package. Alternatively, new user-defined forecast scores can be
implemented using the example scores provided and applied using the
functionality of this package.
Author: MeteoSwiss [aut, cph],
Jonas Bhend [cre],
Jacopo Ripoldi [ctb],
Claudia Mignani [ctb],
Irina Mahlstein [ctb],
Rebecca Hiller [ctb],
Christoph Spirig [ctb],
Mark Liniger [ctb],
Andreas Weigel [ctb],
Joaqu'in Bedia Jimenez [ctb],
Matteo De Felice [ctb],
Stefan Siegert [ctb]
Maintainer: Jonas Bhend <jonas.bhend@meteoswiss.ch>
Diff between easyVerification versions 0.4.1 dated 2017-03-13 and 0.4.2 dated 2017-05-18
DESCRIPTION | 12 ++++----- MD5 | 52 ++++++++++++++++++++-------------------- NEWS | 5 +++ R/convert2prob.R | 20 ++++++++++----- R/veriApply.R | 2 + R/veriUnwrap.R | 2 + build/vignette.rds |binary man/Ens2AFC.Rd | 1 man/EnsCorr.Rd | 1 man/EnsError.Rd | 3 -- man/EnsErrorss.Rd | 1 man/EnsIgn.Rd | 2 - man/EnsRoca.Rd | 5 ++- man/EnsSprErr.Rd | 1 man/FairSprErr.Rd | 1 man/changearg.Rd | 1 man/climFairRpss.Rd | 1 man/convert2prob.Rd | 4 +-- man/count2prob.Rd | 2 - man/easyVerification.Rd | 1 man/generateRef.Rd | 3 +- man/size.Rd | 1 man/toymodel.Rd | 4 +-- man/veriApply.Rd | 2 - man/veriUnwrap.Rd | 1 man/weisheimer.Rd | 1 tests/testthat/test_veriApply.R | 7 ++++- 27 files changed, 73 insertions(+), 63 deletions(-)
More information about easyVerification at CRAN
Permanent link
Title: Methods for Statistical Disclosure Control in Tabular Data
Description: Methods for statistical disclosure control in
tabular data such as primary and secondary cell suppression are covered in
this package.
Author: Bernhard Meindl
Maintainer: Bernhard Meindl <bernhard.meindl@statistik.gv.at>
Diff between sdcTable versions 0.22.4 dated 2017-04-07 and 0.22.6 dated 2017-05-18
DESCRIPTION | 8 - MD5 | 18 ++-- R/classes_tauBatch.r | 4 R/createArgusInput.R |only R/export_functions.r | 193 ----------------------------------------------- R/runArgusBatchFile.R |only R/tauBatch_helpers.R | 141 ++++++++++++++++++++-------------- build/vignette.rds |binary inst/doc/sdcTable.pdf |binary man/createArgusInput.Rd | 4 man/runArgusBatchFile.Rd | 13 +-- 11 files changed, 109 insertions(+), 272 deletions(-)
Title: Analyzes Clickstreams Based on Markov Chains
Description: A set of tools to read, analyze and write lists of click sequences
on websites (i.e., clickstream). A click can be represented by a number,
character or string. Clickstreams can be modeled as zero- (only computes
occurrence probabilities), first- or higher-order Markov chains.
Author: Michael Scholz
Maintainer: Michael Scholz <michael.scholz@uni-passau.de>
Diff between clickstream versions 1.2.0 dated 2017-04-10 and 1.2.1 dated 2017-05-18
DESCRIPTION | 10 +++++----- MD5 | 17 +++++++++-------- NAMESPACE | 2 ++ NEWS | 6 ++++++ R/Clickstream.r | 30 ++++++++++++++++++++++++++++++ R/MarkovChain.r | 13 +++++++++++-- R/clickstream-package.R | 4 ++-- man/as.ClickClust.Rd |only man/clickstream-package.Rd | 2 +- man/hmPlot-methods.Rd | 4 +++- 10 files changed, 69 insertions(+), 19 deletions(-)
Title: Process and Visualise Output from Atlantis Models
Description: Atlantis is an end-to-end marine ecosystem modelling framework. It was originally developed in Australia by E.A. Fulton, A.D.M. Smith and D.C. Smith (2007) and has since been adopted in many marine ecosystems around the world (<http://atlantis.cmar.csiro.au/www/en/atlantis.html>). The output of an Atlantis simulation is stored in various file formats like .netcdf and .txt and different output structures are used for the output variables like e.g. productivity or biomass. This package is used to convert the different output types to a unified format according to the "tidy-data" approach by H. Wickham (2014) <DOI:10.18637/jss.v059.i10>. Additionally, ecological metrics like for example spatial overlap of predator and prey or consumption can be calculated and visualised with this package. Due to the unified data structure it is very easy to share model output with each other and perform model comparisons.
Author: Alexander Keth [aut, cre]
Maintainer: Alexander Keth <alexander.keth@uni-hamburg.de>
Diff between atlantistools versions 0.4.1 dated 2017-05-09 and 0.4.2 dated 2017-05-18
atlantistools-0.4.1/atlantistools/tests/figs/plot-species/line-plot.svg |only atlantistools-0.4.2/atlantistools/DESCRIPTION | 14 atlantistools-0.4.2/atlantistools/MD5 | 187 +++++----- atlantistools-0.4.2/atlantistools/R/agg-data.R | 2 atlantistools-0.4.2/atlantistools/R/calculate-biomass-spatial.R | 6 atlantistools-0.4.2/atlantistools/R/calculate-consumed-biomass.R | 2 atlantistools-0.4.2/atlantistools/R/change-avail.R | 2 atlantistools-0.4.2/atlantistools/R/change-prm-cohort.R | 2 atlantistools-0.4.2/atlantistools/R/change-prm.R | 5 atlantistools-0.4.2/atlantistools/R/combine-groups.R | 4 atlantistools-0.4.2/atlantistools/R/data.R | 32 - atlantistools-0.4.2/atlantistools/R/flip-layers.R | 10 atlantistools-0.4.2/atlantistools/R/get-boundary.R | 3 atlantistools-0.4.2/atlantistools/R/get-colpal.R | 2 atlantistools-0.4.2/atlantistools/R/get-groups.R | 12 atlantistools-0.4.2/atlantistools/R/get-growth-fishbase.R | 4 atlantistools-0.4.2/atlantistools/R/get-ids-fishbase.R | 2 atlantistools-0.4.2/atlantistools/R/load-dietcheck.R | 4 atlantistools-0.4.2/atlantistools/R/load-init-age.R | 4 atlantistools-0.4.2/atlantistools/R/load-nc-physics.R | 4 atlantistools-0.4.2/atlantistools/R/pipe.R | 2 atlantistools-0.4.2/atlantistools/R/plot-bar.R | 2 atlantistools-0.4.2/atlantistools/R/plot-consumed-biomass.R | 4 atlantistools-0.4.2/atlantistools/R/plot-diet-bec-dev.R | 4 atlantistools-0.4.2/atlantistools/R/plot-diet.R | 2 atlantistools-0.4.2/atlantistools/R/plot-spatial-box.R | 6 atlantistools-0.4.2/atlantistools/R/plot-spatial-ts.R | 4 atlantistools-0.4.2/atlantistools/R/plot-species.R | 4 atlantistools-0.4.2/atlantistools/R/preprocess-txt.R | 4 atlantistools-0.4.2/atlantistools/R/sc-init.R | 6 atlantistools-0.4.2/atlantistools/R/str-split-twice.R | 2 atlantistools-0.4.2/atlantistools/R/theme-atlantis.R | 4 atlantistools-0.4.2/atlantistools/R/utils.R | 13 atlantistools-0.4.2/atlantistools/README.md | 10 atlantistools-0.4.2/atlantistools/build/vignette.rds |binary atlantistools-0.4.2/atlantistools/inst/doc/model-calibration-species.Rmd | 2 atlantistools-0.4.2/atlantistools/inst/doc/model-calibration-species.pdf |binary atlantistools-0.4.2/atlantistools/inst/doc/model-calibration.Rmd | 2 atlantistools-0.4.2/atlantistools/inst/doc/model-calibration.pdf |binary atlantistools-0.4.2/atlantistools/inst/doc/model-comparison.Rmd | 2 atlantistools-0.4.2/atlantistools/inst/doc/model-comparison.pdf |binary atlantistools-0.4.2/atlantistools/inst/doc/model-preprocess.Rmd | 2 atlantistools-0.4.2/atlantistools/inst/doc/model-preprocess.html | 6 atlantistools-0.4.2/atlantistools/inst/doc/package-demo.Rmd | 2 atlantistools-0.4.2/atlantistools/inst/doc/package-demo.html | 6 atlantistools-0.4.2/atlantistools/man/agg_data.Rd | 2 atlantistools-0.4.2/atlantistools/man/calculate_biomass_spatial.Rd | 6 atlantistools-0.4.2/atlantistools/man/calculate_consumed_biomass.Rd | 2 atlantistools-0.4.2/atlantistools/man/change_avail.Rd | 2 atlantistools-0.4.2/atlantistools/man/change_prm.Rd | 4 atlantistools-0.4.2/atlantistools/man/change_prm_cohort.Rd | 2 atlantistools-0.4.2/atlantistools/man/combine_groups.Rd | 2 atlantistools-0.4.2/atlantistools/man/fishbase_data.Rd | 2 atlantistools-0.4.2/atlantistools/man/flip_layers.Rd | 10 atlantistools-0.4.2/atlantistools/man/get_colpal.Rd | 2 atlantistools-0.4.2/atlantistools/man/get_groups.Rd | 12 atlantistools-0.4.2/atlantistools/man/get_growth_fishbase.Rd | 4 atlantistools-0.4.2/atlantistools/man/get_ids_fishbase.Rd | 2 atlantistools-0.4.2/atlantistools/man/load_dietcheck.Rd | 2 atlantistools-0.4.2/atlantistools/man/load_init_age.Rd | 4 atlantistools-0.4.2/atlantistools/man/load_nc_physics.Rd | 2 atlantistools-0.4.2/atlantistools/man/plot_bar.Rd | 2 atlantistools-0.4.2/atlantistools/man/plot_consumed_biomass.Rd | 6 atlantistools-0.4.2/atlantistools/man/plot_diet.Rd | 2 atlantistools-0.4.2/atlantistools/man/plot_diet_bec_dev.Rd | 4 atlantistools-0.4.2/atlantistools/man/plot_spatial_box.Rd | 8 atlantistools-0.4.2/atlantistools/man/plot_spatial_ts.Rd | 6 atlantistools-0.4.2/atlantistools/man/plot_species.Rd | 4 atlantistools-0.4.2/atlantistools/man/preprocess_txt.Rd | 4 atlantistools-0.4.2/atlantistools/man/ref_bio_cons.Rd | 2 atlantistools-0.4.2/atlantistools/man/ref_bio_sp.Rd | 6 atlantistools-0.4.2/atlantistools/man/ref_dietmatrix.Rd | 2 atlantistools-0.4.2/atlantistools/man/ref_dm.Rd | 2 atlantistools-0.4.2/atlantistools/man/ref_eat.Rd | 2 atlantistools-0.4.2/atlantistools/man/ref_grazing.Rd | 2 atlantistools-0.4.2/atlantistools/man/ref_growth.Rd | 2 atlantistools-0.4.2/atlantistools/man/ref_n.Rd | 2 atlantistools-0.4.2/atlantistools/man/ref_nums.Rd | 2 atlantistools-0.4.2/atlantistools/man/ref_physics.Rd | 2 atlantistools-0.4.2/atlantistools/man/ref_resn.Rd | 2 atlantistools-0.4.2/atlantistools/man/ref_structn.Rd | 2 atlantistools-0.4.2/atlantistools/man/ref_vol.Rd | 2 atlantistools-0.4.2/atlantistools/man/ref_vol_dz.Rd | 2 atlantistools-0.4.2/atlantistools/man/sc_init.Rd | 2 atlantistools-0.4.2/atlantistools/man/str_split_twice.Rd | 2 atlantistools-0.4.2/atlantistools/man/theme_atlantis.Rd | 4 atlantistools-0.4.2/atlantistools/tests/figs/plot-species/line-plot-preprocess-biomass.svg |only atlantistools-0.4.2/atlantistools/tests/testthat/helper-fontconfig.R |only atlantistools-0.4.2/atlantistools/tests/testthat/test-conv-mg-n-bio-t.R | 8 atlantistools-0.4.2/atlantistools/tests/testthat/test-load-dietmatrix.R | 2 atlantistools-0.4.2/atlantistools/tests/testthat/test-plot-species.R | 6 atlantistools-0.4.2/atlantistools/vignettes/model-calibration-species.Rmd | 2 atlantistools-0.4.2/atlantistools/vignettes/model-calibration.Rmd | 2 atlantistools-0.4.2/atlantistools/vignettes/model-comparison.Rmd | 2 atlantistools-0.4.2/atlantistools/vignettes/model-preprocess.Rmd | 2 atlantistools-0.4.2/atlantistools/vignettes/package-demo.Rmd | 2 96 files changed, 290 insertions(+), 262 deletions(-)
Title: Numeric Routines for Optically Stimulated Luminescence Dating
Description: Package for optimizing regular numeric problems in optically stimulated luminescence
dating, such as: equivalent dose calculation, dose rate determination, growth curve fitting,
decay curve decomposition, statistical age model optimization, and statistical plot visualization.
Author: Jun Peng [aut, cre], Bo Li [aut], Jorge More [ctb], Burton Garbow [ctb], Kenneth Hillstrom [ctb], John Burkardt [ctb], Paul Gilbert [ctb], Ravi Varadhan [ctb]
Maintainer: Jun Peng <pengjun10@mails.ucas.ac.cn>
Diff between numOSL versions 2.2 dated 2017-04-04 and 2.3 dated 2017-05-18
DESCRIPTION | 8 MD5 | 48 +-- R/analyseBINdata.R | 55 +++ R/as_analyseBIN.R | 43 +- R/calED.R | 310 +++++++++++-------- R/calSARED.R | 418 +++++++++++++++----------- R/calSGCED.R | 782 ++++++++++++++++++++++++++++++++++++++------------ R/fastED.R | 18 - R/fitGrowth.R | 151 ++++++++- R/lsNORM.R | 218 +++++++++---- R/pickSARdata.R | 382 +++++++++++++++--------- R/scaleSGCN.R | 393 +++++++++++++++++++++---- man/analyseBINdata.Rd | 23 + man/as_analyseBIN.Rd | 13 man/calED.Rd | 35 +- man/calSARED.Rd | 21 - man/calSGCED.Rd | 79 +++-- man/decomp.Rd | 4 man/fitGrowth.Rd | 50 ++- man/loadBINdata.Rd | 2 man/lsNORM.Rd | 3 man/numOSL-package.Rd | 4 man/pickBINdata.Rd | 4 man/pickSARdata.Rd | 4 man/scaleSGCN.Rd | 45 ++ 25 files changed, 2184 insertions(+), 929 deletions(-)
Title: HTML Output Formats and Templates for 'rmarkdown' Documents
Description: HTML formats and templates for 'rmarkdown' documents, with some extra
features such as automatic table of contents, lightboxed figures, dynamic
crosstab helper.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>
Diff between rmdformats versions 0.3.2 dated 2017-03-21 and 0.3.3 dated 2017-05-18
DESCRIPTION | 10 ++++---- MD5 | 36 ++++++++++++++--------------- NEWS | 9 +++++++ R/html_dependencies.R | 2 - build/vignette.rds |binary inst/doc/introduction.html | 6 ++-- inst/templates/html_clean/clean.css | 15 ++++++++++++ inst/templates/html_docco/docco.css | 13 ++++++++++ inst/templates/material/material.css | 33 ++++++++++++++++++++++++++ inst/templates/material/material.js | 9 +++++-- inst/templates/readthedown/readthedown.css | 13 ++++++++++ man/create.doc.Rd | 1 man/html_clean.Rd | 1 man/html_docco.Rd | 1 man/knit_print.pilltabs.Rd | 1 man/material.Rd | 1 man/pilltabs.Rd | 1 man/print.pilltabs.Rd | 1 man/readthedown.Rd | 1 19 files changed, 117 insertions(+), 37 deletions(-)
Title: A General-Purpose Package for Dynamic Report Generation in R
Description: Provides a general-purpose tool for dynamic report generation in R
using Literate Programming techniques.
Author: Yihui Xie [aut, cre],
Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Andre Simon [ctb] (the CSS files under inst/themes/ were derived from
the Highlight package http://www.andre-simon.de),
Aron Atkins [ctb],
Aaron Wolen [ctb],
Ashley Manton [ctb],
Ben Baumer [ctb],
Brian Diggs [ctb],
Cassio Pereira [ctb],
David Robinson [ctb],
Donald Arseneau [ctb, cph] (the framed package at inst/misc/framed.sty),
Doug Hemken [ctb],
Duncan Murdoch [ctb],
Fabian Hirschmann [ctb],
Fitch Simeon [ctb],
Forest Fang [ctb],
Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty),
Gregoire Detrez [ctb],
Hadley Wickham [ctb],
Heewon Jeon [ctb],
Henrik Bengtsson [ctb],
Hiroaki Yutani [ctb],
Ian Lyttle [ctb],
Hodges Daniel [ctb],
Jake Burkhead [ctb],
James Manton [ctb],
Jared Lander [ctb],
Jason Punyon [ctb],
Javier Luraschi [ctb],
Jeff Arnold [ctb],
Jeremy Ashkenas [ctb, cph] (the CSS file at
inst/misc/docco-classic.css),
Jeremy Stephens [ctb],
Jim Hester [ctb],
Joe Cheng [ctb],
Johannes Ranke [ctb],
John Honaker [ctb],
John Muschelli [ctb],
Jonathan Keane [ctb],
JJ Allaire [ctb],
Johan Toloe [ctb],
Joseph Larmarange [ctb],
Julien Barnier [ctb],
Kaiyin Zhong [ctb],
Kamil Slowikowski [ctb],
Karl Forner [ctb],
Kevin K. Smith [ctb],
Kirill Mueller [ctb],
Kohske Takahashi [ctb],
Michael Friendly [ctb],
Michal Bojanowski [ctb],
Michel Kuhlmann [ctb],
Nacho Caballero [ctb],
Nick Salkowski [ctb],
Noam Ross [ctb],
Qiang Li [ctb],
Ramnath Vaidyanathan [ctb],
Richard Cotton [ctb],
Robert Krzyzanowski [ctb],
Romain Francois [ctb],
Scott Kostyshak [ctb],
Sebastian Meyer [ctb],
Sietse Brouwer [ctb],
Simon de Bernard [ctb],
Sylvain Rousseau [ctb],
Taiyun Wei [ctb],
Thibaut Assus [ctb],
Thibaut Lamadon [ctb],
Thomas Leeper [ctb],
Tom Torsney-Weir [ctb],
Trevor Davis [ctb],
Viktoras Veitas [ctb],
Weicheng Zhu [ctb],
Wush Wu [ctb],
Zachary Foster [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between knitr versions 1.15.1 dated 2016-11-22 and 1.16 dated 2017-05-18
DESCRIPTION | 28 +++-- MD5 | 213 +++++++++++++++++++++--------------------- NAMESPACE | 3 R/block.R | 29 ++++- R/cache.R | 6 - R/citation.R | 2 R/defaults.R | 8 - R/engine.R | 65 +++++++++++- R/hooks-extra.R | 4 R/hooks-html.R | 19 ++- R/hooks-latex.R | 6 - R/hooks-md.R | 27 ++++- R/hooks.R | 6 - R/output.R | 15 +- R/package.R | 4 R/pandoc.R | 2 R/parser.R | 10 + R/pattern.R | 8 - R/plot.R | 11 +- R/spin.R | 2 R/table.R | 31 ++++-- R/utils-conversion.R | 28 +++++ R/utils-rd2html.R | 2 R/utils-sweave.R | 2 R/utils-upload.R | 2 R/utils-vignettes.R | 4 R/utils.R | 50 +++++++++ build/knitr.pdf |binary build/vignette.rds |binary inst/doc/docco-classic.html | 6 - inst/doc/docco-linear.html | 5 inst/doc/knit_expand.html | 4 inst/doc/knit_print.html | 8 - inst/doc/knitr-intro.html | 14 +- inst/doc/knitr-markdown.html | 4 inst/doc/knitr-refcard.pdf |binary inst/misc/docco-classic.html | 4 inst/misc/docco-template.html | 3 man/Sweave2knitr.Rd | 3 man/all_labels.Rd | 1 man/all_patterns.Rd | 3 man/asis_output.Rd | 1 man/chunk_hook.Rd | 9 - man/clean_cache.Rd | 1 man/combine_words.Rd | 1 man/current_input.Rd | 1 man/dep_auto.Rd | 3 man/dep_prev.Rd | 3 man/engine_output.Rd | 1 man/fig_chunk.Rd | 1 man/fig_path.Rd | 1 man/hook_animation.Rd | 3 man/hook_document.Rd | 3 man/hook_plot.Rd | 10 + man/image_uri.Rd | 7 - man/imgur_upload.Rd | 9 - man/include_graphics.Rd | 1 man/include_url.Rd | 3 man/inline_expr.Rd | 1 man/kable.Rd | 8 - man/knit.Rd | 11 +- man/knit2html.Rd | 1 man/knit2pandoc.Rd |only man/knit2pdf.Rd | 7 - man/knit2wp.Rd | 7 - man/knit_child.Rd | 3 man/knit_engines.Rd | 5 man/knit_exit.Rd | 1 man/knit_expand.Rd | 1 man/knit_filter.Rd | 1 man/knit_global.Rd | 1 man/knit_hooks.Rd | 5 man/knit_meta.Rd | 1 man/knit_params.Rd | 1 man/knit_params_yaml.Rd | 1 man/knit_patterns.Rd | 5 man/knit_print.Rd | 1 man/knit_rd.Rd | 1 man/knit_theme.Rd | 7 - man/knit_watch.Rd | 1 man/knitr-package.Rd | 11 +- man/load_cache.Rd | 1 man/opts_chunk.Rd | 5 man/opts_hooks.Rd | 3 man/opts_knit.Rd | 5 man/opts_template.Rd | 1 man/output_hooks.Rd | 12 +- man/pandoc.Rd | 3 man/pat_fun.Rd | 7 - man/plot_crop.Rd | 1 man/rand_seed.Rd | 3 man/raw_output.Rd | 3 man/read_chunk.Rd | 7 - man/read_rforge.Rd | 1 man/rocco.Rd | 7 - man/rst2pdf.Rd | 7 - man/set_alias.Rd | 1 man/set_header.Rd | 1 man/set_parent.Rd | 3 man/spin.Rd | 11 +- man/spin_child.Rd | 1 man/stitch.Rd | 1 man/vignette_engines.Rd | 3 man/wrap_rmd.Rd | 1 man/write_bib.Rd | 1 tests/testit/test-hooks.R | 3 tests/testit/test-plot.R | 3 tests/testit/test-utils.R | 7 + 108 files changed, 582 insertions(+), 301 deletions(-)
Title: Simply Create LaTeX and HTML Tables
Description: Creates HTML and LaTeX tables. Provides similar
functionality to 'xtable', but does more, with a simpler interface.
Author: David Hugh-Jones
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between huxtable versions 0.2.2 dated 2017-04-27 and 0.3.0 dated 2017-05-18
DESCRIPTION | 9 - MD5 | 56 +++---- NAMESPACE | 2 NEWS.md | 9 + R/HTML.R | 5 R/LaTeX.R | 6 R/attributes.R | 69 ++++++++ R/dplyr.R | 2 R/huxreg.R | 4 R/huxtable.R | 4 R/screen.R | 2 README.md | 6 inst/doc/design-principles.R | 2 inst/doc/design-principles.Rmd | 2 inst/doc/design-principles.html | 11 - inst/doc/huxreg.html | 304 +++++++++++++++++++-------------------- inst/doc/huxtable.R | 11 + inst/doc/huxtable.Rmd | 14 + inst/doc/huxtable.html | 245 ++++++++++++++++--------------- man/caption_pos.Rd | 8 - man/dplyr-verbs.Rd | 2 man/get_default_properties.Rd |only man/huxreg.Rd | 8 - man/left_border.Rd | 4 man/position.Rd | 4 man/set_default_properties.Rd |only tests/testthat/test-attributes.R | 11 + tests/testthat/test-huxreg.R | 14 + vignettes/design-principles.Rmd | 2 vignettes/huxtable.Rmd | 14 + 30 files changed, 489 insertions(+), 341 deletions(-)
Title: Group Sequential Enrichment Design
Description: Provides function to apply "Group sequential enrichment design incorporating subgroup selection" (GSED) method proposed by Magnusson and Turnbull (2013) <doi:10.1002/sim.5738>.
Author: Marie-Karelle Riviere
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between GSED versions 1.4 dated 2017-05-04 and 1.5 dated 2017-05-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/GSED.R | 8 +++++--- man/GSED-package.Rd | 4 ++-- 4 files changed, 14 insertions(+), 12 deletions(-)
More information about GeneralizedUmatrix at CRAN
Permanent link
Title: ROI Plug-in GLPK
Description: Enhances the R Optimization Infrastructure ('ROI') package by registering
the free 'GLPK' solver. It allows for solving mixed integer linear programming (MILP)
problems as well as all variants/combinations of LP, IP.
Author: Stefan Theussl [aut, cre]
Maintainer: Stefan Theussl <Stefan.Theussl@R-Project.org>
Diff between ROI.plugin.glpk versions 0.2-1 dated 2016-06-19 and 0.2-5 dated 2017-05-18
DESCRIPTION | 14 +++---- MD5 | 11 +++--- NAMESPACE | 4 +- R/plugin.R | 95 ++++++++++++++++++++++++++++++++++++++++++++---------- R/zzz.R | 19 +++++++--- man |only tests/test_glpk.R | 2 + 7 files changed, 109 insertions(+), 36 deletions(-)
More information about ROI.plugin.glpk at CRAN
Permanent link
Title: R/GNU Linear Programming Kit Interface
Description: R interface to the GNU Linear Programming Kit.
'GLPK' is open source software for solving large-scale linear programming (LP),
mixed integer linear programming ('MILP') and other related problems.
Author: Stefan Theussl [aut, cre],
Kurt Hornik [aut],
Christian Buchta [ctb],
Florian Schwendinger [ctb],
Heinrich Schuchardt [ctb]
Maintainer: Stefan Theussl <Stefan.Theussl@R-project.org>
Diff between Rglpk versions 0.6-2 dated 2016-06-14 and 0.6-3 dated 2017-05-18
DESCRIPTION | 13 ++++++----- MD5 | 22 ++++++++++-------- NAMESPACE | 2 - R/Rglpk_solve.R | 58 ++++++++++++++++++++++++++++++++++++-------------- R/Rglpk_write_file.R |only R/bounds.R | 2 - R/filereader.R | 6 ++--- R/zzz.R | 4 +-- inst/CHANGELOG | 6 +++++ man/Rglpk_solve.Rd | 11 ++++++--- src/Rglpk_read_file.c | 26 +++++++++++++++++++--- src/Rglpk_solve.c | 20 ++++++++++++++++- src/init.c |only 13 files changed, 123 insertions(+), 47 deletions(-)
Title: Flexible Relative Survival Analysis
Description: Package for parametric relative survival analyses. It allows to model non-linear and
non-proportional effects using splines (B-spline and truncated power basis). It also includes
both non proportional and non linear effects of
Remontet, L. et al. (2007) <DOI:10.1002/sim.2656> and
Mahboubi, A. et al. (2011) <DOI:10.1002/sim.4208>.
Author: Isabelle Clerc-Urmès [aut], Michel Grzebyk [aut, cre], Guy Hédelin [ctb], CENSUR working survival group [ctb]
Maintainer: Michel Grzebyk <michel.grzebyk@inrs.fr>
Diff between flexrsurv versions 1.3.3 dated 2016-04-26 and 1.4.1 dated 2017-05-18
DESCRIPTION | 25 - MD5 | 153 ++++++---- NAMESPACE | 6 NEWS |only R/AllClass.R | 20 + R/NLL.NPH.func.R | 6 R/ReadDesignFlexrsurv.R | 4 R/SplineParam.R | 433 +++++++++++++++++++++++++++--- R/computeCumulativeHazard.R | 410 +++++++++++++++++++++++++++- R/computeLinearPredictor.R | 50 ++- R/computeStdErrorCumulativeHazard.R |only R/computeStdErrorLinearPredictor.R | 139 +++------ R/converged.R | 2 R/cutT.R | 4 R/default_bands.R | 3 R/flexrsurv.glm.fit.R | 2 R/flexrsurv.glmiterative.fit.R | 8 R/flexrsurv.ll.R | 1 R/flexrsurv.ll.fit.R | 57 ++- R/flexrsurv.ll.fromto.fit.R | 94 +++--- R/get_list_var.R | 6 R/gr_cumhaz_flexrsurv_GA0B0AB.R |only R/gr_cumhaz_flexrsurv_GA0B0AB_bh.R |only R/gr_cumhaz_flexrsurv_fromto_GA0B0AB.R |only R/gr_cumhaz_flexrsurv_fromto_GA0B0AB_bh.R |only R/gr_linkrate_flexrsurv_GA0B0AB.R |only R/gr_linkrate_flexrsurv_fromto_GA0B0AB.R |only R/gr_ll_flexrsurv_GA0B0AB.R | 50 +-- R/gr_ll_flexrsurv_GA0B0AB_bh.R | 91 +++--- R/gr_ll_flexrsurv_fromto_GA0B0AB.R | 50 ++- R/gr_ll_flexrsurv_fromto_GA0B0AB_bh.R | 57 ++- R/intTDfromto_base.R | 19 - R/ll_flexrsurv_GA0B0AB.R | 41 +- R/ll_flexrsurv_GA0B0AB_bh.R | 40 +- R/ll_flexrsurv_alpha0alpha.R | 32 +- R/ll_flexrsurv_alpha0alpha_bh.R | 38 +- R/ll_flexrsurv_beta0beta.R | 35 +- R/ll_flexrsurv_beta0beta_bh.R | 41 +- R/ll_flexrsurv_fromto_GA0B0AB.R | 24 + R/ll_flexrsurv_fromto_GA0B0AB_bh.R | 33 +- R/ll_flexrsurv_fromto_alpha0alpha.R | 32 +- R/ll_flexrsurv_fromto_alpha0alpha_bh.R | 32 +- R/ll_flexrsurv_fromto_beta0beta.R | 36 +- R/ll_flexrsurv_fromto_beta0beta_bh.R | 36 +- R/ll_flexrsurv_fromto_gamma0.R | 36 +- R/ll_flexrsurv_fromto_gamma0_bh.R | 40 +- R/ll_flexrsurv_gamma0.R | 28 + R/ll_flexrsurv_gamma0_bh.R | 41 +- R/make.formulastep.formula.R | 8 R/make.formulastep.terms.R | 10 R/make.glm.formula.R | 4 R/nl.td.func.R | 20 - R/opg_flexrsurv_G0A0B0AB.R | 51 ++- R/opg_flexrsurv_G0A0B0AB_bh.R | 57 ++- R/opg_flexrsurv_fromto_G0A0B0AB.R | 45 ++- R/opg_flexrsurv_fromto_G0A0B0AB_bh.R | 62 ++-- R/predict.flexrsurv.R |only R/predictCumulativeHazard.flexrsurv.R |only R/predictHazard.flexrsurv.R |only R/rateTD.R | 44 ++- R/rateTD_bh.R | 41 +- R/zzz.R | 6 build/partial.rdb |binary inst |only man/Flexrsurv.Rd | 43 ++ man/Flexrsurvpackage.Rd | 21 - man/NLLbetaNPHalpha.Rd | 4 man/NPH.Rd | 4 man/NPHNLL.Rd | 4 man/flexrsurv-internal.Rd | 11 man/predict.flexrsurv.Rd |only man/summary.flexrsurv.Rd | 8 src/EvaluateCLLinExSplineBasis.c |only src/EvaluateCLSplineBasis.c | 77 ++++- src/EvaluateESplineBasis.c |only src/EvaluateLinExSplineBasis.c |only src/EvaluateSplineBasis.c | 146 ++++------ src/EvaluateTPSplineBasis.c | 106 ------- src/GradientWeightedCumulativeExposure.c |only src/PredictESplineBasis.c |only src/PredictLinExSplineBasis.c |only src/PredictSplineBasis.c | 192 +++++++------ src/PredictTPSplineBasis.c | 41 -- src/SplineParam.h |only src/WeightedCumulativeExposure.c | 398 +++++++++++++++++---------- src/flexrsurv.h | 47 ++- src/init.c |only src/slowPredictLinExSplineBasis.c |only src/slowPredictSplineBasis.c |only 89 files changed, 2457 insertions(+), 1248 deletions(-)
Title: Functions of Complex or Real Variable
Description: Extension of several functions to the complex domain, including the matrix exponential and logarithm, and the determinant.
Author: Albert Dorador and Uffe Høgsbro Thygesen
Maintainer: Albert Dorador <albert.dorador@estudiant.upc.edu>
Diff between complexplus versions 2.0 dated 2016-11-23 and 2.1 dated 2017-05-18
complexplus-2.0/complexplus/R/matlog.R |only complexplus-2.1/complexplus/DESCRIPTION | 12 ++++++------ complexplus-2.1/complexplus/MD5 | 20 ++++++++++---------- complexplus-2.1/complexplus/R/DetV2.R | 2 +- complexplus-2.1/complexplus/R/Imzap.R | 4 ++-- complexplus-2.1/complexplus/R/matexp.R | 2 +- complexplus-2.1/complexplus/R/matlogV2.R |only complexplus-2.1/complexplus/man/Det.Rd | 1 - complexplus-2.1/complexplus/man/Imzap.Rd | 3 +-- complexplus-2.1/complexplus/man/matclass.Rd | 1 - complexplus-2.1/complexplus/man/matexp.Rd | 7 +++---- complexplus-2.1/complexplus/man/matlog.Rd | 9 ++++----- 12 files changed, 28 insertions(+), 33 deletions(-)
Title: Meta-Analysis using Structural Equation Modeling
Description: A collection of functions for conducting meta-analysis using a
structural equation modeling (SEM) approach via the 'OpenMx' package.
It also implements the two-stage SEM approach to conduct meta-analytic
structural equation modeling on correlation and covariance matrices.
Author: Mike W.-L. Cheung <mikewlcheung@nus.edu.sg>
Maintainer: Mike W.-L. Cheung <mikewlcheung@nus.edu.sg>
Diff between metaSEM versions 0.9.12 dated 2017-01-23 and 0.9.14 dated 2017-05-18
DESCRIPTION | 12 - MD5 | 95 ++++----- NAMESPACE | 6 NEWS | 9 R/genCor.R |only R/impliedR.R | 80 +++++++ R/meta.R | 3 R/smd.R |only R/summary.R | 3 R/tssem.R | 6 R/uniR.R | 8 build/vignette.rds |binary data/Aloe14.rda |binary data/BCG.rda |binary data/Becker09.rda |binary data/Becker83.rda |binary data/Becker92.rda |binary data/Becker94.rda |binary data/Berkey98.rda |binary data/Boer16.rda |binary data/Bornmann07.rda |binary data/Cheung00.rda |binary data/Cheung09.rda |binary data/Cooke16.rda |binary data/Cooper03.rda |binary data/Digman97.rda |binary data/HedgesOlkin85.rda |binary data/Hox02.rda |binary data/Hunter83.rda |binary data/Jaramillo05.rda |binary data/Mak09.rda |binary data/Nohe15A1.rda |binary data/Nohe15A2.rda |binary data/Norton13.rda |binary data/Roorda11.rda |binary data/issp05.rda |binary data/issp89.rda |binary data/wvs94a.rda |binary data/wvs94b.rda |binary inst/CITATION | 4 inst/doc/Examples.html | 491 +++++++++++++++++++++++++------------------------ inst/doc/metaSEM.pdf |binary man/Becker09.Rd | 4 man/impliedR.Rd | 17 + man/metaSEM-package.Rd | 4 man/rCorSam.Rd |only man/smdMES.Rd |only man/smdMTS.Rd |only man/summary.Rd | 14 - man/uniR1.Rd | 4 man/uniR2.Rd | 2 51 files changed, 456 insertions(+), 306 deletions(-)
Title: Estimating and Mapping Disaggregated Indicators
Description: Functions that support estimating, assessing and mapping regional
disaggregated indicators. So far, estimation methods comprise direct estimation
and the model-based approach Empirical Best Prediction (see "Small area
estimation of poverty indicators" by Molina and Rao (2010) <doi:10.1002/cjs.10051>),
as well as their precision estimates. The assessment of the used model
is supported by a summary and diagnostic plots. For a suitable presentation of
estimates, map plots can be easily created. Furthermore, results can easily be
exported to excel.
Author: Ann-Kristin Kreutzmann [aut],
Soeren Pannier [aut, cre],
Natalia Rojas-Perilla [aut],
Timo Schmid [aut],
Matthias Templ [aut],
Nikos Tzavidis [aut]
Maintainer: Soeren Pannier <soeren.pannier@fu-berlin.de>
Diff between emdi versions 1.0.0 dated 2016-11-08 and 1.1.0 dated 2017-05-18
emdi-1.0.0/emdi/R/framework.R |only emdi-1.0.0/emdi/R/indicator_functions.R |only emdi-1.0.0/emdi/tests/testthat/ebp_test.xlsx |only emdi-1.0.0/emdi/tests/testthat/excel_output_all.xlsx |only emdi-1.1.0/emdi/DESCRIPTION | 37 + emdi-1.1.0/emdi/MD5 | 119 +++-- emdi-1.1.0/emdi/NAMESPACE | 13 emdi-1.1.0/emdi/NEWS.md |only emdi-1.1.0/emdi/R/check_direct_arguments.R |only emdi-1.1.0/emdi/R/check_ebp_arguments.R | 15 emdi-1.1.0/emdi/R/direct_estimation.R |only emdi-1.1.0/emdi/R/direct_variance.R |only emdi-1.1.0/emdi/R/ebp.R | 99 ++-- emdi-1.1.0/emdi/R/emdi.R | 17 emdi-1.1.0/emdi/R/emdiObject.R | 43 + emdi-1.1.0/emdi/R/estimators.emdi.R | 130 +++++ emdi-1.1.0/emdi/R/eusilcA_pop.R | 8 emdi-1.1.0/emdi/R/eusilcA_smp.R | 9 emdi-1.1.0/emdi/R/framework_direct.R |only emdi-1.1.0/emdi/R/framework_ebp.R |only emdi-1.1.0/emdi/R/load_shape.R |only emdi-1.1.0/emdi/R/map_plot.R | 162 ++++--- emdi-1.1.0/emdi/R/mse_emdi.R | 46 -- emdi-1.1.0/emdi/R/mse_estimation.R | 245 +++++++--- emdi-1.1.0/emdi/R/optimal_parameter.R | 68 --- emdi-1.1.0/emdi/R/plot.emdi.R | 47 +- emdi-1.1.0/emdi/R/point_estimation.R | 81 --- emdi-1.1.0/emdi/R/point_estimation_direct.R |only emdi-1.1.0/emdi/R/print.emdi.R | 102 ++-- emdi-1.1.0/emdi/R/summary.emdi.R | 358 ++++++++-------- emdi-1.1.0/emdi/R/transformation_functions.R | 2 emdi-1.1.0/emdi/R/write.excel.emdi.R | 130 +++++ emdi-1.1.0/emdi/build |only emdi-1.1.0/emdi/data/eusilcA_pop.RData |only emdi-1.1.0/emdi/data/eusilcA_pop.rda |binary emdi-1.1.0/emdi/data/eusilcA_smp.RData |only emdi-1.1.0/emdi/data/eusilcA_smp.rda |binary emdi-1.1.0/emdi/inst/doc |only emdi-1.1.0/emdi/man/as.data.frame.estimators.emdi.Rd |only emdi-1.1.0/emdi/man/as.matrix.estimators.emdi.Rd |only emdi-1.1.0/emdi/man/data_transformation.Rd | 1 emdi-1.1.0/emdi/man/direct.Rd |only emdi-1.1.0/emdi/man/ebp.Rd | 73 +-- emdi-1.1.0/emdi/man/emdi.Rd | 18 emdi-1.1.0/emdi/man/emdiObject.Rd | 44 + emdi-1.1.0/emdi/man/estimators.Rd | 1 emdi-1.1.0/emdi/man/estimators.emdi.Rd | 24 - emdi-1.1.0/emdi/man/eusilcA_pop.Rd | 9 emdi-1.1.0/emdi/man/eusilcA_smp.Rd | 10 emdi-1.1.0/emdi/man/head.estimators.emdi.Rd | 28 + emdi-1.1.0/emdi/man/load_shapeaustria.Rd |only emdi-1.1.0/emdi/man/map_plot.Rd | 55 +- emdi-1.1.0/emdi/man/plot.emdi.Rd | 42 - emdi-1.1.0/emdi/man/print.emdi.Rd | 5 emdi-1.1.0/emdi/man/print.estimators.emdi.Rd | 1 emdi-1.1.0/emdi/man/print.summary.emdi.Rd | 1 emdi-1.1.0/emdi/man/subset.estimators.emdi.Rd |only emdi-1.1.0/emdi/man/summary.emdi.Rd | 73 +-- emdi-1.1.0/emdi/man/tail.estimators.emdi.Rd | 28 + emdi-1.1.0/emdi/man/write.excel.Rd | 50 +- emdi-1.1.0/emdi/tests/testthat/arpr_all.csv |only emdi-1.1.0/emdi/tests/testthat/arpr_all_cali.csv |only emdi-1.1.0/emdi/tests/testthat/arpr_all_naive.csv |only emdi-1.1.0/emdi/tests/testthat/eusilc.RData |only emdi-1.1.0/emdi/tests/testthat/eusilc.csv |only emdi-1.1.0/emdi/tests/testthat/gini_all.csv |only emdi-1.1.0/emdi/tests/testthat/gini_all_cali.csv |only emdi-1.1.0/emdi/tests/testthat/gini_all_naive.csv |only emdi-1.1.0/emdi/tests/testthat/qsr_all.csv |only emdi-1.1.0/emdi/tests/testthat/qsr_all_cali.csv |only emdi-1.1.0/emdi/tests/testthat/qsr_all_naive.csv |only emdi-1.1.0/emdi/tests/testthat/test_direct_estimation.R |only emdi-1.1.0/emdi/tests/testthat/test_ebp.R | 8 emdi-1.1.0/emdi/tests/testthat/test_mse_estimation.R | 3 emdi-1.1.0/emdi/tests/testthat/test_optimal_par.R | 2 emdi-1.1.0/emdi/tests/testthat/test_point_estimation.R | 2 emdi-1.1.0/emdi/vignettes |only 77 files changed, 1304 insertions(+), 905 deletions(-)
Title: Manipulate and Visualize VCF Data
Description: Facilitates easy manipulation of variant call format (VCF) data.
Functions are provided to rapidly read from and write to VCF files. Once
VCF data is read into R a parser function extracts matrices of data. This
information can then be used for quality control or other purposes. Additional
functions provide visualization of genomic data. Once processing is complete
data may be written to a VCF file (*.vcf.gz). It also may be converted into
other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between
VCF data and familiar R software.
Author: Brian J. Knaus [cre, aut],
Niklaus J. Grunwald [aut],
Eric C. Anderson [ctb],
David J. Winter [ctb],
Zhian N. Kamvar [ctb]
Maintainer: Brian J. Knaus <briank.lists@gmail.com>
Diff between vcfR versions 1.4.0 dated 2017-01-07 and 1.5.0 dated 2017-05-18
vcfR-1.4.0/vcfR/tests/testthat/test_windowing.R |only vcfR-1.5.0/vcfR/DESCRIPTION | 44 ++--- vcfR-1.5.0/vcfR/MD5 | 161 ++++++++++---------- vcfR-1.5.0/vcfR/NAMESPACE | 4 vcfR-1.5.0/vcfR/R/RcppExports.R | 4 vcfR-1.5.0/vcfR/R/chromR-method.R | 22 ++ vcfR-1.5.0/vcfR/R/chromR_functions.R | 28 ++- vcfR-1.5.0/vcfR/R/chromo_plot.R | 22 ++ vcfR-1.5.0/vcfR/R/create_chromR.R | 25 +++ vcfR-1.5.0/vcfR/R/genetic_diff.R |only vcfR-1.5.0/vcfR/R/queryMETA.R | 5 vcfR-1.5.0/vcfR/R/vcfR-method.R | 137 ++++++++--------- vcfR-1.5.0/vcfR/R/vcfR.R | 7 vcfR-1.5.0/vcfR/R/vcfR2DNAbin.R | 9 - vcfR-1.5.0/vcfR/R/vcfR_test.R | 2 vcfR-1.5.0/vcfR/README.md | 15 + vcfR-1.5.0/vcfR/build/vignette.rds |binary vcfR-1.5.0/vcfR/inst/CITATION | 7 vcfR-1.5.0/vcfR/inst/doc/converting_data.html | 31 ++- vcfR-1.5.0/vcfR/inst/doc/filtering_data.html | 20 +- vcfR-1.5.0/vcfR/inst/doc/intro_to_vcfR.html | 20 +- vcfR-1.5.0/vcfR/inst/doc/ranking_data.html | 18 +- vcfR-1.5.0/vcfR/inst/doc/sequence_coverage.html | 11 - vcfR-1.5.0/vcfR/inst/doc/vcf_data.html | 61 +++---- vcfR-1.5.0/vcfR/inst/doc/visualization_1.html | 20 +- vcfR-1.5.0/vcfR/inst/doc/visualization_2.html | 8 vcfR-1.5.0/vcfR/inst/doc/workflow.html | 8 vcfR-1.5.0/vcfR/man/AD_frequency.Rd | 1 vcfR-1.5.0/vcfR/man/INFO2df.Rd | 1 vcfR-1.5.0/vcfR/man/addID.Rd | 1 vcfR-1.5.0/vcfR/man/chromR-class.Rd | 1 vcfR-1.5.0/vcfR/man/chromR-method.Rd | 13 - vcfR-1.5.0/vcfR/man/chromR_functions.Rd | 6 vcfR-1.5.0/vcfR/man/chrom_to_vcfR.Rd | 1 vcfR-1.5.0/vcfR/man/chromo_plot.Rd | 7 vcfR-1.5.0/vcfR/man/create_chromR.Rd | 7 vcfR-1.5.0/vcfR/man/drplot.Rd | 3 vcfR-1.5.0/vcfR/man/extract_gt.Rd | 1 vcfR-1.5.0/vcfR/man/fasta_output.Rd | 1 vcfR-1.5.0/vcfR/man/freq_peak.Rd | 1 vcfR-1.5.0/vcfR/man/genetic_diff.Rd |only vcfR-1.5.0/vcfR/man/genotype_matrix.Rd | 1 vcfR-1.5.0/vcfR/man/getFIX.Rd | 31 +-- vcfR-1.5.0/vcfR/man/heatmap_bp.Rd | 1 vcfR-1.5.0/vcfR/man/io_vcfR.Rd | 1 vcfR-1.5.0/vcfR/man/is_het.Rd | 3 vcfR-1.5.0/vcfR/man/maf.Rd | 1 vcfR-1.5.0/vcfR/man/masplit.Rd | 1 vcfR-1.5.0/vcfR/man/ordisample.Rd | 1 vcfR-1.5.0/vcfR/man/pipe.Rd | 1 vcfR-1.5.0/vcfR/man/proc_chromR.Rd | 5 vcfR-1.5.0/vcfR/man/queryMETA.Rd | 1 vcfR-1.5.0/vcfR/man/query_gt.Rd | 5 vcfR-1.5.0/vcfR/man/ranking.Rd | 1 vcfR-1.5.0/vcfR/man/summary_tables.Rd | 1 vcfR-1.5.0/vcfR/man/vcfR-method.Rd | 50 +++--- vcfR-1.5.0/vcfR/man/vcfR.Rd | 5 vcfR-1.5.0/vcfR/man/vcfR2DNAbin.Rd | 3 vcfR-1.5.0/vcfR/man/vcfR_conversion.Rd | 3 vcfR-1.5.0/vcfR/man/vcfR_example.Rd | 3 vcfR-1.5.0/vcfR/man/vcfR_test.Rd | 3 vcfR-1.5.0/vcfR/man/vcfR_to_tidy_conversion.Rd | 11 - vcfR-1.5.0/vcfR/man/windowing.Rd | 5 vcfR-1.5.0/vcfR/src/Makevars | 8 vcfR-1.5.0/vcfR/src/RcppExports.cpp | 9 + vcfR-1.5.0/vcfR/src/extractGT2NM.cpp | 25 ++- vcfR-1.5.0/vcfR/src/gt_to_popsum.cpp | 25 ++- vcfR-1.5.0/vcfR/src/init.c |only vcfR-1.5.0/vcfR/src/is_het.cpp | 1 vcfR-1.5.0/vcfR/src/vcfRCommon.cpp | 10 + vcfR-1.5.0/vcfR/tests/testthat.R | 37 +++- vcfR-1.5.0/vcfR/tests/testthat/test_1_vcf.R | 2 vcfR-1.5.0/vcfR/tests/testthat/test_2_chromR.R | 22 ++ vcfR-1.5.0/vcfR/tests/testthat/test_3_extract_gt.R | 34 ++++ vcfR-1.5.0/vcfR/tests/testthat/test_chromR_method.R | 14 + vcfR-1.5.0/vcfR/tests/testthat/test_chromo_plot.R | 34 +++- vcfR-1.5.0/vcfR/tests/testthat/test_genetic_diff.R |only vcfR-1.5.0/vcfR/tests/testthat/test_get.R | 4 vcfR-1.5.0/vcfR/tests/testthat/test_io.R | 17 -- vcfR-1.5.0/vcfR/tests/testthat/test_is_het.R | 3 vcfR-1.5.0/vcfR/tests/testthat/test_proc_chromR.R |only vcfR-1.5.0/vcfR/tests/testthat/test_rank_variants.R | 25 +-- vcfR-1.5.0/vcfR/tests/testthat/test_var_window.R | 25 +-- vcfR-1.5.0/vcfR/tests/testthat/test_vcfR_methods.R | 31 +++ vcfR-1.5.0/vcfR/tools |only 85 files changed, 735 insertions(+), 461 deletions(-)
Title: Create Dashboards with 'Shiny'
Description: Create dashboards with 'Shiny'. This package provides
a theme on top of 'Shiny', making it easy to create attractive dashboards.
Author: Winston Chang [aut, cre],
Barbara Borges Ribeiro [aut],
RStudio [cph],
Almasaeed Studio [ctb, cph] (AdminLTE theme for Bootstrap),
Adobe Systems Incorporated [ctb, cph] (Source Sans Pro font)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between shinydashboard versions 0.5.3 dated 2016-09-20 and 0.6.0 dated 2017-05-18
shinydashboard-0.5.3/shinydashboard/inst/AdminLTE/README-shiny-mods.md |only shinydashboard-0.6.0/shinydashboard/DESCRIPTION | 10 shinydashboard-0.6.0/shinydashboard/LICENSE | 8 shinydashboard-0.6.0/shinydashboard/MD5 | 99 +- shinydashboard-0.6.0/shinydashboard/NEWS.md | 51 + shinydashboard-0.6.0/shinydashboard/R/dashboardHeader.R | 15 shinydashboard-0.6.0/shinydashboard/R/dashboardPage.R | 12 shinydashboard-0.6.0/shinydashboard/R/dashboardSidebar.R | 65 + shinydashboard-0.6.0/shinydashboard/R/deps.R | 4 shinydashboard-0.6.0/shinydashboard/R/utils.R | 21 shinydashboard-0.6.0/shinydashboard/inst/AdminLTE/AdminLTE.css | 73 + shinydashboard-0.6.0/shinydashboard/inst/AdminLTE/AdminLTE.min.css | 4 shinydashboard-0.6.0/shinydashboard/inst/AdminLTE/_all-skins.css | 103 -- shinydashboard-0.6.0/shinydashboard/inst/AdminLTE/_all-skins.min.css | 2 shinydashboard-0.6.0/shinydashboard/inst/AdminLTE/app.js | 165 ++-- shinydashboard-0.6.0/shinydashboard/inst/AdminLTE/app.js.map |only shinydashboard-0.6.0/shinydashboard/inst/AdminLTE/app.min.js | 2 shinydashboard-0.6.0/shinydashboard/inst/AdminLTE/app.min.js.map | 2 shinydashboard-0.6.0/shinydashboard/inst/shinydashboard.css | 28 shinydashboard-0.6.0/shinydashboard/inst/shinydashboard.js | 400 ++++++---- shinydashboard-0.6.0/shinydashboard/inst/shinydashboard.js.map |only shinydashboard-0.6.0/shinydashboard/inst/shinydashboard.min.js |only shinydashboard-0.6.0/shinydashboard/inst/shinydashboard.min.js.map |only shinydashboard-0.6.0/shinydashboard/man/box.Rd | 1 shinydashboard-0.6.0/shinydashboard/man/dashboardBody.Rd | 1 shinydashboard-0.6.0/shinydashboard/man/dashboardHeader.Rd | 1 shinydashboard-0.6.0/shinydashboard/man/dashboardPage.Rd | 1 shinydashboard-0.6.0/shinydashboard/man/dashboardSidebar.Rd | 5 shinydashboard-0.6.0/shinydashboard/man/dropdownMenu.Rd | 10 shinydashboard-0.6.0/shinydashboard/man/dropdownMenuOutput.Rd | 1 shinydashboard-0.6.0/shinydashboard/man/infoBox.Rd | 1 shinydashboard-0.6.0/shinydashboard/man/menuItemOutput.Rd | 1 shinydashboard-0.6.0/shinydashboard/man/menuOutput.Rd | 1 shinydashboard-0.6.0/shinydashboard/man/messageItem.Rd | 1 shinydashboard-0.6.0/shinydashboard/man/notificationItem.Rd | 1 shinydashboard-0.6.0/shinydashboard/man/renderDropdownMenu.Rd | 1 shinydashboard-0.6.0/shinydashboard/man/renderMenu.Rd | 1 shinydashboard-0.6.0/shinydashboard/man/renderValueBox.Rd | 3 shinydashboard-0.6.0/shinydashboard/man/shinydashboard.Rd | 1 shinydashboard-0.6.0/shinydashboard/man/sidebarMenu.Rd | 16 shinydashboard-0.6.0/shinydashboard/man/sidebarMenuOutput.Rd | 1 shinydashboard-0.6.0/shinydashboard/man/sidebarSearchForm.Rd | 1 shinydashboard-0.6.0/shinydashboard/man/sidebarUserPanel.Rd | 1 shinydashboard-0.6.0/shinydashboard/man/tabBox.Rd | 1 shinydashboard-0.6.0/shinydashboard/man/tabItem.Rd | 1 shinydashboard-0.6.0/shinydashboard/man/tabItems.Rd | 1 shinydashboard-0.6.0/shinydashboard/man/tagAssert.Rd | 1 shinydashboard-0.6.0/shinydashboard/man/taskItem.Rd | 1 shinydashboard-0.6.0/shinydashboard/man/updateTabItems.Rd | 1 shinydashboard-0.6.0/shinydashboard/man/validColors.Rd | 1 shinydashboard-0.6.0/shinydashboard/man/validStatuses.Rd | 1 shinydashboard-0.6.0/shinydashboard/man/valueBox.Rd | 1 shinydashboard-0.6.0/shinydashboard/man/valueBoxOutput.Rd | 3 53 files changed, 712 insertions(+), 414 deletions(-)
More information about shinydashboard at CRAN
Permanent link
Title: Functions for Base Types and Core R and 'Tidyverse' Features
Description: A toolbox for working with base types, core R features
like the condition system, and core 'Tidyverse' features like tidy
evaluation.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between rlang versions 0.1 dated 2017-05-06 and 0.1.1 dated 2017-05-18
rlang-0.1.1/rlang/DESCRIPTION | 8 rlang-0.1.1/rlang/MD5 | 86 ++-- rlang-0.1.1/rlang/NAMESPACE | 3 rlang-0.1.1/rlang/NEWS.md | 54 +++ rlang-0.1.1/rlang/R/attr.R | 5 rlang-0.1.1/rlang/R/cnd.R | 4 rlang-0.1.1/rlang/R/compat-lazyeval.R | 2 rlang-0.1.1/rlang/R/compat-oldrel.R | 2 rlang-0.1.1/rlang/R/compat-purrr.R | 2 rlang-0.1.1/rlang/R/dots.R | 16 rlang-0.1.1/rlang/R/env.R | 63 ++- rlang-0.1.1/rlang/R/eval-tidy.R | 19 - rlang-0.1.1/rlang/R/expr-lang.R | 29 + rlang-0.1.1/rlang/R/expr-node.R | 34 + rlang-0.1.1/rlang/R/operators.R | 2 rlang-0.1.1/rlang/R/stack.R | 3 rlang-0.1.1/rlang/R/vector-coercion.R | 12 rlang-0.1.1/rlang/README.md | 32 + rlang-0.1.1/rlang/build/vignette.rds |binary rlang-0.1.1/rlang/inst/doc/tidy-evaluation.R | 2 rlang-0.1.1/rlang/inst/doc/tidy-evaluation.Rmd | 70 +--- rlang-0.1.1/rlang/inst/doc/tidy-evaluation.html | 32 - rlang-0.1.1/rlang/man/dots_list.Rd | 16 rlang-0.1.1/rlang/man/env.Rd | 30 + rlang-0.1.1/rlang/man/env_unbind.Rd | 4 rlang-0.1.1/rlang/man/is_pairlist.Rd | 17 rlang-0.1.1/rlang/man/lang.Rd | 17 rlang-0.1.1/rlang/man/new_cnd.Rd | 4 rlang-0.1.1/rlang/man/pairlist.Rd | 4 rlang-0.1.1/rlang/man/set_attrs.Rd | 5 rlang-0.1.1/rlang/man/stack.Rd | 3 rlang-0.1.1/rlang/src/capture.c | 4 rlang-0.1.1/rlang/src/formula.c | 6 rlang-0.1.1/rlang/src/init.c | 86 ++-- rlang-0.1.1/rlang/src/lang.c |only rlang-0.1.1/rlang/src/replace-na.c | 2 rlang-0.1.1/rlang/src/unquote.c | 2 rlang-0.1.1/rlang/src/utils.h | 1 rlang-0.1.1/rlang/tests/testthat/test-env.R | 15 rlang-0.1.1/rlang/tests/testthat/test-quo-enquo.R | 18 + rlang-0.1.1/rlang/tests/testthat/test-tidy-eval.R | 9 rlang-0.1.1/rlang/tests/testthat/test-types-coercion.R | 5 rlang-0.1.1/rlang/vignettes/releases/rlang-0.1.Rmd | 293 +++++++---------- rlang-0.1.1/rlang/vignettes/tidy-evaluation.Rmd | 70 +--- rlang-0.1/rlang/src/symbol.h |only 45 files changed, 656 insertions(+), 435 deletions(-)
Title: SNP-Set (Sequence) Kernel Association Test
Description: Functions for kernel-regression-based association tests including Burden test, SKAT and SKAT-O. These methods aggregate individual SNP score statistics in a SNP set and efficiently compute SNP-set level p-values.
Author: Seunggeun (Shawn) Lee, with contributions from Larisa Miropolsky and Michael Wu
Maintainer: Seunggeun (Shawn) Lee <leeshawn@umich.edu>
Diff between SKAT versions 1.2.1 dated 2016-06-28 and 1.3.0 dated 2017-05-18
SKAT-1.2.1/SKAT/src/Binary_resampling.c |only SKAT-1.2.1/SKAT/src/interface.cpp |only SKAT-1.2.1/SKAT/src/kernel_func.c |only SKAT-1.3.0/SKAT/DESCRIPTION | 8 - SKAT-1.3.0/SKAT/MD5 | 57 +++---- SKAT-1.3.0/SKAT/NAMESPACE | 2 SKAT-1.3.0/SKAT/R/Binary_MAIN.R | 10 - SKAT-1.3.0/SKAT/R/Joint_CommonRare.R | 12 - SKAT-1.3.0/SKAT/R/MAIN.R | 43 ++++- SKAT-1.3.0/SKAT/R/Main_SSD.R | 10 - SKAT-1.3.0/SKAT/R/SKAT_EMMAX.R | 66 +++++++- SKAT-1.3.0/SKAT/R/SKAT_Linear.R | 11 + SKAT-1.3.0/SKAT/R/SKAT_Logistic.R | 9 - SKAT-1.3.0/SKAT/R/SKAT_Meta_Optimal.R |only SKAT-1.3.0/SKAT/build/vignette.rds |binary SKAT-1.3.0/SKAT/data/SKAT.example.ChrX.rda |binary SKAT-1.3.0/SKAT/data/SKAT.example.rda |binary SKAT-1.3.0/SKAT/data/SKAT.fam.example.rda |binary SKAT-1.3.0/SKAT/data/SKAT.haplotypes.rda |binary SKAT-1.3.0/SKAT/data/SKATBinary.example.rda |binary SKAT-1.3.0/SKAT/inst/doc/SKAT.R | 116 +++++++++++++-- SKAT-1.3.0/SKAT/inst/doc/SKAT.Rnw | 208 +++++++++++++++++++--------- SKAT-1.3.0/SKAT/inst/doc/SKAT.pdf |binary SKAT-1.3.0/SKAT/man/SKAT.rd | 7 SKAT-1.3.0/SKAT/man/SKAT_ChrX.rd | 6 SKAT-1.3.0/SKAT/man/SKAT_NULL_emmaX.rd | 4 SKAT-1.3.0/SKAT/src/Binary_global.cpp | 8 - SKAT-1.3.0/SKAT/src/Binary_global.h | 18 +- SKAT-1.3.0/SKAT/src/Binary_resampling.cpp |only SKAT-1.3.0/SKAT/src/interface_new.cpp |only SKAT-1.3.0/SKAT/src/kernel_func.cpp |only SKAT-1.3.0/SKAT/src/qfc.cpp | 6 SKAT-1.3.0/SKAT/vignettes/SKAT.Rnw | 208 +++++++++++++++++++--------- 33 files changed, 564 insertions(+), 245 deletions(-)