Title: EWAS using Reference-Free DNA Methylation Mixture Deconvolution
Description:
Reference-free method for conducting EWAS while deconvoluting DNA methylation arising as mixtures of cell types.
The older method (Houseman et al., 2014,<doi:10.1093/bioinformatics/btu029>) is similar to surrogate variable analysis (SVA and ISVA), except that it makes additional use of a biological mixture assumption.
The newer method (Houseman et al., 2016, <doi:10.1186/s12859-016-1140-4>) is similar to non-negative matrix factorization, with additional constraints and additional utilities.
Author: E. Andres Houseman, Sc.D.
Maintainer: E. Andres Houseman <eahouseman@gmail.com>
Diff between RefFreeEWAS versions 2.0 dated 2016-01-29 and 2.1 dated 2017-02-25
DESCRIPTION | 14 +++++++------- MD5 | 2 +- 2 files changed, 8 insertions(+), 8 deletions(-)
Title: 3D Reconstruction of Archaeological Excavations
Description: A toolset for 3D reconstruction and analysis of excavations. It provides methods to reconstruct natural and artificial surfaces based on field measurements. This allows to spatially contextualize documented subunits and features. Intended to be part of a 3D visualization workflow.
Author: Clemens Schmid [cre, cph, aut],
Benjamin Serbe [aut]
Maintainer: Clemens Schmid <clemens@nevrome.de>
Diff between recexcavAAR versions 0.2.2 dated 2016-10-16 and 0.3.0 dated 2017-02-25
DESCRIPTION | 24 ++--- MD5 | 82 ++++++++++-------- NAMESPACE | 5 + NEWS.md | 9 ++ R/RcppExports.R | 143 +++++++++++++++++++++++++++++++- R/cootrans_func.R |only R/geo_functions.R | 2 README.md | 15 ++- build/vignette.rds |binary data/KT_spits.rda |binary data/KT_squarecorners.rda |binary data/KT_vessel.rda |binary inst/doc/recexcavAAR-vignette-1.R | 29 ++++-- inst/doc/recexcavAAR-vignette-1.Rmd | 39 ++++++-- inst/doc/recexcavAAR-vignette-1.html | 107 ++++++++++------------- inst/doc/recexcavAAR-vignette-2.R | 35 +++++-- inst/doc/recexcavAAR-vignette-2.Rmd | 50 ++++++++--- inst/doc/recexcavAAR-vignette-2.html | 139 +++++++++++++------------------ inst/doc/recexcavAAR-vignette-3.R |only inst/doc/recexcavAAR-vignette-3.Rmd |only inst/doc/recexcavAAR-vignette-3.html |only man/KT_spits.Rd | 1 man/KT_squarecorners.Rd | 1 man/KT_vessel.Rd | 1 man/cootrans.Rd |only man/draw_circle.Rd |only man/draw_sphere.Rd |only man/fillhexa.Rd | 1 man/kriglist.Rd | 3 man/pnp.Rd | 3 man/pnpmulti.Rd | 1 man/posdec.Rd | 1 man/posdeclist.Rd | 1 man/rescale.Rd |only man/rotate.Rd |only man/spatiallong.Rd | 1 man/spatialwide.Rd | 1 man/spitcenter.Rd | 1 man/spitcenternat.Rd | 1 man/spitcenternatlist.Rd | 1 src/RcppExports.cpp | 66 ++++++++++++++ src/drawing_functions.cpp |only src/init.c |only src/pointinpoly.cpp | 2 tests/testthat/test_cootrans.R |only tests/testthat/test_drawing_functions.R |only vignettes/recexcavAAR-vignette-1.Rmd | 39 ++++++-- vignettes/recexcavAAR-vignette-2.Rmd | 50 ++++++++--- vignettes/recexcavAAR-vignette-3.Rmd |only 49 files changed, 582 insertions(+), 272 deletions(-)
Title: Variance-Covariance Matrix for Multivariate Meta-Analysis
Description: Compute variance-covariance matrix for multivariate meta-analysis. Effect sizes include correlation (r), mean difference (MD), standardized mean difference (SMD), log odds ratio (logOR), log risk ratio (logRR), and risk difference (RD).
Author: Min Lu
Maintainer: Min Lu <m.lu6@umiami.edu>
Diff between metavcov versions 0.1 dated 2017-02-20 and 1.0 dated 2017-02-25
DESCRIPTION | 8 ++--- MD5 | 40 +++++++++++++------------- man/Craft2003.Rd | 72 ++++++++++++++++++++++++------------------------ man/lgOR.vcov.Rd | 6 ++-- man/lgRR.vcov.Rd | 6 ++-- man/lgor_lgrr.Rd | 6 ++-- man/lgor_rd.Rd | 6 ++-- man/lgrr_rd.Rd | 6 ++-- man/md.vcov.Rd | 6 ++-- man/md_lgor.Rd | 6 ++-- man/md_lgrr.Rd | 6 ++-- man/md_rd.Rd | 6 ++-- man/md_smd.Rd | 6 ++-- man/metavcov-package.Rd | 13 ++++---- man/mix.vcov.Rd | 6 ++-- man/r.vcov.Rd | 10 +++--- man/rd.vcov.Rd | 6 ++-- man/smd.vcov.Rd | 6 ++-- man/smd_lgor.Rd | 6 ++-- man/smd_lgrr.Rd | 6 ++-- man/smd_rd.Rd | 6 ++-- 21 files changed, 120 insertions(+), 119 deletions(-)
Title: Analyse Sentiment of English Sentences
Description: Analyses sentiment of a sentence in English and assigns score to it. It can classify sentences to the following categories of sentiments:- Positive, Negative, very Positive, very negative,
Neutral or Sarcasm. For a vector of sentences, it counts the number of sentences in each
category of sentiment.In calculating the score, negation and various degrees
of adjectives are taken into consideration. It deals only with English sentences.
Author: Subhasree Bose <subhasree10.7@gmail.com> with contributons from Saptarsi Goswami.
Maintainer: Subhasree Bose <subhasree10.7@gmail.com>
Diff between RSentiment versions 2.1 dated 2016-12-25 and 2.1.1 dated 2017-02-25
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/test.R | 1 - inst/doc/Introduction.html | 4 ++-- 4 files changed, 9 insertions(+), 10 deletions(-)
Title: DMR Detection by Non-Homogeneous Hidden Markov Model from
Methylation Array Data
Description: Perform differential analysis for
methylation array data. Detect differentially
methylated regions (DMRs) from array M-values.
The core is a Non-homogeneous Hidden Markov Model
for estimating spatial correlation and a novel Constrained
Gaussian Mixture Model for modeling the M-value pairs of each individual locus.
Author: Linghao SHEN <sl013@ie.cuhk.edu.hk>
Maintainer: Linghao SHEN <sl013@ie.cuhk.edu.hk>
Diff between DMRMark versions 1.0 dated 2016-09-04 and 1.1.0 dated 2017-02-25
DESCRIPTION | 8 MD5 | 20 R/DMRMark_utils.R | 54 - R/FullSampler.R | 1370 +++++++++++++++++++++++++------------------------ R/mvScatter.R | 10 R/reformData.R | 33 - man/DMRMark-package.Rd | 8 man/DMRMark.Rd | 10 man/DMRViterbi.Rd | 6 man/MakeGSoptions.Rd | 18 man/mvScatter.Rd | 12 11 files changed, 789 insertions(+), 760 deletions(-)
Title: General Bivariate Copula Theory and Many Utility Functions
Description: Extensive functions for bivariate copula (bicopula) computations and related
operations concerning oft cited bicopula theory described by Nelsen (2006), Joe (2014), and
other selected works. The lower, upper, product, and select other bicopula are implemented.
Arbitrary bicopula expressions include the diagonal, survival copula, the dual of a copula,
co-copula, numerical bicopula density, and maximum likelihood estimation. Level
curves (sets), horizontal and vertical sections also are supported. Numerical derivatives and
inverses of a bicopula are provided; simulation by the conditional distribution method thus is
supported. Bicopula composition, convex combination, and products are provided. Support
extends to Kendall Function as well as the Lmoments thereof, Kendall Tau, Spearman Rho and
Footrule, Gini Gamma, Blomqvist Beta, Hoeffding Phi, Schweizer-Wolff Sigma, tail dependency
(including pseudo-polar representation) and tail order, skewness, and bivariate Lmoments.
Evaluators of positively/negatively quadrant dependency, left increasing and right
decreasing are available. Kullback-Leibler divergence, Vuong's procedure, Spectral Measure,
and Lcomoments for copula inference are available. Quantile and median regressions for
V with respect to U and U with respect to V are available. Empirical copulas (EC) are supported.
Author: William Asquith
Maintainer: William Asquith <william.asquith@ttu.edu>
Diff between copBasic versions 2.0.4 dated 2016-06-03 and 2.0.5 dated 2017-02-25
copBasic-2.0.4/copBasic/R/StableTailDepFN.R |only copBasic-2.0.4/copBasic/man/StableTailDepFN.Rd |only copBasic-2.0.5/copBasic/ChangeLog | 34 ++++ copBasic-2.0.5/copBasic/DESCRIPTION | 24 ++- copBasic-2.0.5/copBasic/MD5 | 172 ++++++++++++------------ copBasic-2.0.5/copBasic/NAMESPACE | 6 copBasic-2.0.5/copBasic/R/PLACKETTcop.R | 8 - copBasic-2.0.5/copBasic/R/PLACKETTpar.R | 9 - copBasic-2.0.5/copBasic/R/kfuncCOP.R | 15 +- copBasic-2.0.5/copBasic/R/kfuncCOPlmoms.R | 2 copBasic-2.0.5/copBasic/R/sectionCOP.R | 6 copBasic-2.0.5/copBasic/R/stabtaildepf.R |only copBasic-2.0.5/copBasic/man/COP.Rd | 10 - copBasic-2.0.5/copBasic/man/COPinv.Rd | 4 copBasic-2.0.5/copBasic/man/COPinv2.Rd | 2 copBasic-2.0.5/copBasic/man/EMPIRcop.Rd | 17 +- copBasic-2.0.5/copBasic/man/EMPIRgrid.Rd | 10 - copBasic-2.0.5/copBasic/man/EMPIRgridder.Rd | 3 copBasic-2.0.5/copBasic/man/EMPIRgridderinv.Rd | 6 copBasic-2.0.5/copBasic/man/EMPIRqua.regress.Rd | 14 + copBasic-2.0.5/copBasic/man/EMPIRsim.Rd | 11 - copBasic-2.0.5/copBasic/man/FRECHETcop.Rd | 10 - copBasic-2.0.5/copBasic/man/GHcop.Rd | 34 ++-- copBasic-2.0.5/copBasic/man/HRcop.Rd | 2 copBasic-2.0.5/copBasic/man/N4212cop.Rd | 8 - copBasic-2.0.5/copBasic/man/PARETOcop.Rd | 2 copBasic-2.0.5/copBasic/man/PLACKETTcop.Rd | 6 copBasic-2.0.5/copBasic/man/PLACKETTpar.Rd | 44 ++---- copBasic-2.0.5/copBasic/man/PSP.Rd | 4 copBasic-2.0.5/copBasic/man/asCOP.Rd | 10 - copBasic-2.0.5/copBasic/man/bilmoms.Rd | 22 +-- copBasic-2.0.5/copBasic/man/blomCOP.Rd | 44 +++--- copBasic-2.0.5/copBasic/man/coCOP.Rd | 4 copBasic-2.0.5/copBasic/man/composite1COP.Rd | 8 - copBasic-2.0.5/copBasic/man/composite2COP.Rd | 21 +- copBasic-2.0.5/copBasic/man/composite3COP.Rd | 30 +--- copBasic-2.0.5/copBasic/man/convex2COP.Rd | 26 +-- copBasic-2.0.5/copBasic/man/copBasic-package.Rd | 46 +++--- copBasic-2.0.5/copBasic/man/copBasic.fitpara.Rd | 12 - copBasic-2.0.5/copBasic/man/densityCOP.Rd | 7 copBasic-2.0.5/copBasic/man/densityCOPplot.Rd | 15 -- copBasic-2.0.5/copBasic/man/derCOP.Rd | 10 - copBasic-2.0.5/copBasic/man/derCOP2.Rd | 15 +- copBasic-2.0.5/copBasic/man/derCOPinv.Rd | 6 copBasic-2.0.5/copBasic/man/derCOPinv2.Rd | 2 copBasic-2.0.5/copBasic/man/diagCOP.Rd | 2 copBasic-2.0.5/copBasic/man/diagCOPatf.Rd | 12 - copBasic-2.0.5/copBasic/man/duCOP.Rd | 10 - copBasic-2.0.5/copBasic/man/giniCOP.Rd | 12 - copBasic-2.0.5/copBasic/man/gridCOP.Rd | 2 copBasic-2.0.5/copBasic/man/hoefCOP.Rd | 6 copBasic-2.0.5/copBasic/man/isCOP.PQD.Rd | 18 +- copBasic-2.0.5/copBasic/man/isCOP.RTI.Rd | 18 -- copBasic-2.0.5/copBasic/man/isfuncCOP.Rd | 4 copBasic-2.0.5/copBasic/man/joeskewCOP.Rd | 25 +-- copBasic-2.0.5/copBasic/man/joint.curvesCOP.Rd | 16 +- copBasic-2.0.5/copBasic/man/joint.curvesCOP2.Rd | 20 +- copBasic-2.0.5/copBasic/man/jointCOP.Rd | 46 +++--- copBasic-2.0.5/copBasic/man/kfuncCOP.Rd | 64 ++++---- copBasic-2.0.5/copBasic/man/kfuncCOPinv.Rd | 8 - copBasic-2.0.5/copBasic/man/kfuncCOPlmoms.Rd | 50 +++++- copBasic-2.0.5/copBasic/man/kullCOP.Rd | 4 copBasic-2.0.5/copBasic/man/level.curvesCOP.Rd | 4 copBasic-2.0.5/copBasic/man/level.curvesCOP2.Rd | 4 copBasic-2.0.5/copBasic/man/level.setCOP.Rd | 2 copBasic-2.0.5/copBasic/man/level.setCOP2.Rd | 11 - copBasic-2.0.5/copBasic/man/med.regressCOP.Rd | 35 ++-- copBasic-2.0.5/copBasic/man/med.regressCOP2.Rd | 7 copBasic-2.0.5/copBasic/man/mleCOP.Rd | 18 +- copBasic-2.0.5/copBasic/man/prod2COP.Rd | 12 - copBasic-2.0.5/copBasic/man/psepolar.Rd | 2 copBasic-2.0.5/copBasic/man/qua.regressCOP.Rd | 3 copBasic-2.0.5/copBasic/man/rhoCOP.Rd | 8 - copBasic-2.0.5/copBasic/man/rhobevCOP.Rd | 8 - copBasic-2.0.5/copBasic/man/sectionCOP.Rd | 2 copBasic-2.0.5/copBasic/man/semicorCOP.Rd | 6 copBasic-2.0.5/copBasic/man/simCOP.Rd | 2 copBasic-2.0.5/copBasic/man/simCOPmicro.Rd | 4 copBasic-2.0.5/copBasic/man/simcomposite3COP.Rd | 6 copBasic-2.0.5/copBasic/man/spectralmeas.Rd | 20 +- copBasic-2.0.5/copBasic/man/stabtaildepf.Rd |only copBasic-2.0.5/copBasic/man/statTn.Rd | 11 - copBasic-2.0.5/copBasic/man/surCOP.Rd | 4 copBasic-2.0.5/copBasic/man/surfuncCOP.Rd | 2 copBasic-2.0.5/copBasic/man/taildepCOP.Rd | 4 copBasic-2.0.5/copBasic/man/tailordCOP.Rd | 8 - copBasic-2.0.5/copBasic/man/tauCOP.Rd | 5 copBasic-2.0.5/copBasic/man/vuongCOP.Rd | 4 copBasic-2.0.5/copBasic/man/wolfCOP.Rd | 2 89 files changed, 657 insertions(+), 595 deletions(-)
Title: Process Biogas Data and Predict Biogas Production
Description: High- and low-level functions for processing biogas data and predicting biogas production. Molar mass and calculated oxygen demand (COD') can be determined from a chemical formula. Measured gas volume can be corrected for water vapor and to (possibly user-defined) standard temperature and pressure. Gas composition, cumulative production, or other variables can be interpolated to a specified time. Cumulative biogas and methane production (and rates) can be calculated using volumetric, manometric, or gravimetric methods for any number of reactors. With cumulative methane production data and data on reactor contents, biochemical methane potential (BMP) can be calculated and summarized, including subtraction of the inoculum contribution and normalization by substrate mass. Cumulative production and production rates can be summarized in several different ways (e.g., omitting normalization) using the same function. Lastly, biogas quantity and composition can be predicted from substrate composition and additional, optional data.
Author: Sasha D. Hafner [aut, cre], Charlotte Rennuit [aut], Jin Mi Triolo [ctb], Ali Heidarzadeh Vazifehkhoran [ctb]
Maintainer: Sasha D. Hafner <saha@kbm.sdu.dk>
Diff between biogas versions 1.6.0 dated 2016-12-16 and 1.7.0 dated 2017-02-25
ChangeLog | 119 +++++++++++++++++++++++++++++++++++++++- DESCRIPTION | 8 +- MD5 | 21 +++---- NEWS | 43 ++++++++++++++ R/checkArgClassValue.R | 14 ++++ R/cumBg.R | 106 ++++++++++++++++++++++++++++++----- R/predBg.R | 2 R/startup.R |only R/summBg.R | 26 ++++++-- inst/doc/biogas_quick_start.pdf |binary inst/doc/predBg_function.pdf |binary man/cumBg.Rd | 55 +++++++++++++++++- 12 files changed, 350 insertions(+), 44 deletions(-)
Title: Analysis of the 'Elements of Metacommunity Structure'
Description: Functions to analyze coherence, boundary clumping, and turnover
following the pattern-based metacommunity analysis of Leibold and Mikkelson
2002. The package also includes functions to visualize ecological networks, and
to calculate modularity as a replacement to boundary clumping.
Author: Tad Dallas
Maintainer: Tad Dallas <tdallas@uga.edu>
Diff between metacom versions 1.4.4 dated 2016-04-13 and 1.4.5 dated 2017-02-25
metacom-1.4.4/metacom/R/IdentifyStructure.R |only metacom-1.4.4/metacom/man/IdentifyStructure.Rd |only metacom-1.4.5/metacom/DESCRIPTION | 10 metacom-1.4.5/metacom/MD5 | 32 -- metacom-1.4.5/metacom/NAMESPACE | 1 metacom-1.4.5/metacom/R/BoundaryClump.R | 179 +++++------ metacom-1.4.5/metacom/R/Coherence.R | 241 +++++++-------- metacom-1.4.5/metacom/R/Imagine.R | 160 +++++----- metacom-1.4.5/metacom/R/Metacommunity.R | 329 ++++++++++----------- metacom-1.4.5/metacom/R/Modularity.R | 389 ++++++++++++------------- metacom-1.4.5/metacom/R/NullMaker.R | 205 ++++++------- metacom-1.4.5/metacom/R/Turnover.R | 181 ++++++----- metacom-1.4.5/metacom/man/BoundaryClump.Rd | 9 metacom-1.4.5/metacom/man/Coherence.Rd | 11 metacom-1.4.5/metacom/man/Metacommunity.Rd | 5 metacom-1.4.5/metacom/man/Modularity.Rd | 4 metacom-1.4.5/metacom/man/NullMaker.Rd | 6 metacom-1.4.5/metacom/man/Turnover.Rd | 7 18 files changed, 903 insertions(+), 866 deletions(-)
Title: Embedding Interactive Charts Generated with ECharts Library into
Shiny Applications
Description: Embed interactive charts to their Shiny applications. These charts will be generated by ECharts library developed by Baidu (<http://echarts.baidu.com/>). Current version supports line chart, bar chart, pie chart, scatter plot, gauge, word cloud, radar chart, tree map, and heat map.
Author: Xiaodong Deng [aut, cre],
Hao Zhu [ctr],
Yiheng Li [ctr]
Maintainer: Xiaodong Deng <xd_deng@hotmail.com>
Diff between ECharts2Shiny versions 0.2.5 dated 2016-11-02 and 0.2.8 dated 2017-02-25
DESCRIPTION | 14 +- MD5 | 22 ++-- NEWS | 139 +++++++++++++------------- R/bar_chart.R | 32 +++++- R/pie_chart.R | 259 ++++++++++++++++++++++++++++--------------------- R/word_cloud.R | 215 +++++++++++++++++++++++++--------------- inst/doc/intro.Rmd | 234 ++++++++++++++++++++++---------------------- inst/doc/intro.html | 7 - man/renderBarChart.Rd | 7 + man/renderPieChart.Rd | 7 + man/renderWordcloud.Rd | 6 + vignettes/intro.Rmd | 234 ++++++++++++++++++++++---------------------- 12 files changed, 666 insertions(+), 510 deletions(-)