Title: Pedigree Inference from SNPs
Description: Fast multi-generational pedigree inference from incomplete data on
hundreds of SNPs, including parentage assignment and sibship clustering.
See citation('sequoia') for more information.
Author: Jisca Huisman [aut, cre]
Maintainer: Jisca Huisman <jisca.huisman@gmail.com>
Diff between sequoia versions 1.0.0 dated 2018-03-29 and 1.0.2 dated 2018-04-01
DESCRIPTION | 8 +++---- MD5 | 10 ++++---- R/Sequoia_F90wrappers.R | 25 ++++++++++++++++++---- inst/Fortran/sequoia.f90 | 53 +++++++++++++++++++++-------------------------- inst/doc/sequoia.pdf |binary src/sequoia.f90 | 53 +++++++++++++++++++++-------------------------- 6 files changed, 78 insertions(+), 71 deletions(-)
Title: Dirichlet Process Bayesian Clustering, Profile Regression
Description: Bayesian clustering using a Dirichlet process mixture model. This model is an alternative to regression models, non-parametrically linking a response vector to covariate data through cluster membership. The package allows Bernoulli, Binomial, Poisson, Normal, survival and categorical response, as well as Normal and discrete covariates. It also allows for fixed effects in the response model, where a spatial CAR (conditional autoregressive) term can be also included. Additionally, predictions may be made for the response, and missing values for the covariates are handled. Several samplers and label switching moves are implemented along with diagnostic tools to assess convergence. A number of R functions for post-processing of the output are also provided. In addition to fitting mixtures, it may additionally be of interest to determine which covariates actively drive the mixture components. This is implemented in the package as variable selection. The main reference for the package is Liverani, Hastie, Azizi, Papathomas and Richardson (2015) <doi:10.18637/jss.v064.i07>.
Author: David I. Hastie, Silvia Liverani <liveranis@gmail.com> and Sylvia Richardson with contributions from Aurore J. Lavigne, Lucy Leigh, Lamiae Azizi, Xi Liu, Ruizhu Huang
Maintainer: Silvia Liverani <liveranis@gmail.com>
Diff between PReMiuM versions 3.1.6 dated 2017-11-02 and 3.1.7 dated 2018-04-01
ChangeLog | 14 +++++++++++++- DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NAMESPACE | 1 + R/postProcess.R | 17 ++++++++++++++--- man/PReMiuM-package.Rd | 4 ++-- man/profRegr.Rd | 2 +- src/PReMiuM.cpp | 1 - src/include/MCMC/sampler.h | 1 - src/include/PReMiuMIO.h | 2 +- src/include/PReMiuMModel.h | 1 - src/include/PReMiuMOptions.h | 4 ++-- src/include/PReMiuMProposals.h | 4 ++-- 13 files changed, 52 insertions(+), 31 deletions(-)
Title: ICS via a Shiny Application
Description: Performs Invariant Coordinate Selection (ICS) (Tyler, Critchley, Duembgen and Oja (2009) <doi:10.1111/j.1467-9868.2009.00706.x>) and especially ICS for multivariate outlier detection with application to quality control (Archimbaud, Nordhausen, Ruiz-Gazen (2016) <arXiv:1612.06118>) using a shiny app.
Author: Aurore Archimbaud, Joris May, Klaus Nordhausen, Anne Ruiz-Gazen
Maintainer: Klaus Nordhausen <klaus.nordhausen@tuwien.ac.at>
Diff between ICSShiny versions 0.4 dated 2017-11-16 and 0.5 dated 2018-04-01
DESCRIPTION | 10 ++++---- MD5 | 14 ++++++------ R/ICSShiny.R | 6 ++++- inst/ChangeLog | 9 ++++++++ inst/ICSShiny/global.R | 6 +++++ inst/ICSShiny/server.R | 55 ++++++++++++++++++++++++++++++++++++------------- inst/ICSShiny/ui.R | 10 ++++---- man/ICSShiny.Rd | 13 +++++++++-- 8 files changed, 89 insertions(+), 34 deletions(-)
Title: Functional Linear Mixed Models for Densely Sampled Data
Description: Estimation of functional linear mixed models for densely sampled data based on functional principal component analysis.
Author: Sonja Greven, Jona Cederbaum
Maintainer: Jona Cederbaum <Jona.Cederbaum@gmail.com>
Diff between denseFLMM versions 0.1.0 dated 2017-03-17 and 0.1.1 dated 2018-04-01
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: "Finding Groups in Data": Cluster Analysis Extended Rousseeuw et
al.
Description: Methods for Cluster analysis. Much extended the original from
Peter Rousseeuw, Anja Struyf and Mia Hubert,
based on Kaufman and Rousseeuw (1990) "Finding Groups in Data".
Author: Martin Maechler [aut, cre],
Peter Rousseeuw [aut] (Fortran original),
Anja Struyf [aut] (S original),
Mia Hubert [aut] (S original),
Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000)),
Matthias Studer [ctb],
Pierre Roudier [ctb],
Juan Gonzalez [ctb],
Kamil Kozlowski [ctb]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between cluster versions 2.0.6 dated 2017-03-16 and 2.0.7 dated 2018-04-01
DESCRIPTION | 23 ++-- MD5 | 66 ++++++------ NAMESPACE | 6 - R/0aaa.R | 19 ++- R/clara.q | 9 + R/clusGapGen.R |only R/daisy.q | 6 - R/pam.q | 10 + inst/NEWS.Rd | 21 +++ inst/test-tools.R |only man/clara.Rd | 27 +++-- man/clusGap.Rd | 2 man/mona.Rd | 9 - man/pam.Rd | 3 man/silhouette.Rd | 17 +-- man/xclara.Rd | 52 ++++++++- src/clara.c | 190 +++++++++++++++++++++-------------- src/cluster.h | 19 ++- src/daisy.f | 5 src/init.c | 4 src/pam.c | 8 - tests/agnes-ex.R | 14 -- tests/agnes-ex.Rout.save | 35 ++---- tests/clara-NAs.Rout.save | 198 ++++++++++++++++++------------------- tests/clara-ex.R | 39 ++++--- tests/clara.Rout.save | 8 - tests/clusplot-out.Rout.save | 10 + tests/daisy-ex.Rout.save | 22 ++-- tests/diana-ex.Rout.save | 20 +-- tests/ellipsoid-ex.Rout.save | 8 - tests/mona.R | 2 tests/mona.Rout.save | 23 +--- tests/pam.Rout.save | 44 ++++---- tests/silhouette-default.Rout.save | 8 - tests/withAutoprint.R | 25 +--- 35 files changed, 540 insertions(+), 412 deletions(-)
Title: Generalize Lambda Distribution and Generalized Bootstrapping
Description: A collection of algorithms and functions
for fitting data to a generalized lambda distribution
via moment matching methods, and generalized
bootstrapping.
Author: Bin Wang <bwang@southalabama.edu>.
Maintainer: Bin Wang <bwang@southalabama.edu>
Diff between gb versions 1.1.8-8 dated 2013-08-08 and 2.3.3 dated 2018-04-01
DESCRIPTION | 18 ++++++++++-------- MD5 | 14 +++++++++----- NAMESPACE | 19 ++++++++++++++++++- R/ARL.R |only R/gb.R | 4 ++-- man/ARL.Rd |only man/fkde.Rd |only src/ARL.c |only src/gbd.c | 6 ------ src/init.c | 13 +++++++++++++ 10 files changed, 52 insertions(+), 22 deletions(-)
Title: Tidy Temporal Data Frames and Tools
Description: Provides a 'tbl_ts' class (the 'tsibble') to store and manage
temporal-context data in a data-centric format, which is built on top of
the 'tibble'. The 'tsibble' aims at manipulating and analysing temporal data
in a tidy and modern manner, including easily interpolate missing values,
aggregate over calendar periods, performing rolling window calculations,
and etc.
Author: Earo Wang [aut, cre],
Di Cook [aut, ths],
Rob Hyndman [aut, ths]
Maintainer: Earo Wang <earo.wang@gmail.com>
Diff between tsibble versions 0.1.3 dated 2018-02-20 and 0.1.5 dated 2018-04-01
tsibble-0.1.3/tsibble/man/col-verb.Rd |only tsibble-0.1.3/tsibble/man/row-verb.Rd |only tsibble-0.1.5/tsibble/DESCRIPTION | 16 - tsibble-0.1.5/tsibble/MD5 | 85 +++-- tsibble-0.1.5/tsibble/NAMESPACE | 15 - tsibble-0.1.5/tsibble/NEWS.md | 29 + tsibble-0.1.5/tsibble/R/RcppExports.R | 4 tsibble-0.1.5/tsibble/R/as-tsibble.R | 299 +++++++++----------- tsibble-0.1.5/tsibble/R/dplyr-join.R | 2 tsibble-0.1.5/tsibble/R/dplyr-verbs.R | 255 +++++++++++------ tsibble-0.1.5/tsibble/R/fill-na.R | 16 - tsibble-0.1.5/tsibble/R/interval.R | 8 tsibble-0.1.5/tsibble/R/parse-key.R | 216 ++++++++++++-- tsibble-0.1.5/tsibble/R/split-by.R |only tsibble-0.1.5/tsibble/R/subset.R | 46 +-- tsibble-0.1.5/tsibble/R/tidyr-verbs.R | 6 tsibble-0.1.5/tsibble/R/ts-tsibble.R | 28 + tsibble-0.1.5/tsibble/R/tsummarise.R | 10 tsibble-0.1.5/tsibble/R/utils.R | 9 tsibble-0.1.5/tsibble/R/window.R | 96 ++---- tsibble-0.1.5/tsibble/README.md | 38 +- tsibble-0.1.5/tsibble/build/vignette.rds |binary tsibble-0.1.5/tsibble/data/pedestrian.rda |binary tsibble-0.1.5/tsibble/data/tourism.rda |binary tsibble-0.1.5/tsibble/inst/doc/intro-tsibble.html | 70 ++-- tsibble-0.1.5/tsibble/man/arrange.Rd |only tsibble-0.1.5/tsibble/man/as-tsibble.Rd | 3 tsibble-0.1.5/tsibble/man/build_tsibble.Rd |only tsibble-0.1.5/tsibble/man/filter.tbl_ts.Rd |only tsibble-0.1.5/tsibble/man/key-size.Rd | 6 tsibble-0.1.5/tsibble/man/key.Rd | 19 - tsibble-0.1.5/tsibble/man/key_update.Rd |only tsibble-0.1.5/tsibble/man/measured-vars.Rd |only tsibble-0.1.5/tsibble/man/mutate.Rd |only tsibble-0.1.5/tsibble/man/regular.Rd | 10 tsibble-0.1.5/tsibble/man/select.Rd |only tsibble-0.1.5/tsibble/man/slice.tbl_ts.Rd |only tsibble-0.1.5/tsibble/man/slide.Rd | 27 - tsibble-0.1.5/tsibble/man/split-by.Rd |only tsibble-0.1.5/tsibble/man/stretch.Rd | 6 tsibble-0.1.5/tsibble/man/summarise.Rd |only tsibble-0.1.5/tsibble/man/tile.Rd | 8 tsibble-0.1.5/tsibble/man/tsibble-package.Rd | 2 tsibble-0.1.5/tsibble/man/tsibble.Rd | 4 tsibble-0.1.5/tsibble/src/RcppExports.cpp | 12 tsibble-0.1.5/tsibble/src/utils-cpp.cpp | 17 + tsibble-0.1.5/tsibble/tests/testthat/test-dplyr.R | 82 ++++- tsibble-0.1.5/tsibble/tests/testthat/test-key.R |only tsibble-0.1.5/tsibble/tests/testthat/test-split.R |only tsibble-0.1.5/tsibble/tests/testthat/test-tsibble.R | 28 + tsibble-0.1.5/tsibble/tests/testthat/test-window.R | 1 51 files changed, 930 insertions(+), 543 deletions(-)
Title: Groovy Language Integration
Description: Integrates the Groovy scripting language with the R Project for Statistical Computing.
Author: Thomas P. Fuller <thomas.fuller@coherentlogic.com>
Maintainer: Thomas P. Fuller <thomas.fuller@coherentlogic.com>
Diff between rGroovy versions 1.2 dated 2018-01-16 and 1.3 dated 2018-04-01
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 2 ++ R/rGroovy.R | 4 ++-- tests/testthat/test_rGroovy.R | 13 +++++++++++++ 5 files changed, 25 insertions(+), 10 deletions(-)
Title: Marginal Proportional Hazards Mixture Cure Models with
Generalized Estimating Equations
Description: Features the marginal parametric and semi-parametric proportional hazards mixture cure models for analyzing clustered survival data with a possible cure fraction. A reference is Yi Niu and Yingwei Peng (2014) <doi:10.1016/j.jmva.2013.09.003>.
Author: Yi Niu [aut, cre],
Hui Song [ctb],
Xiaoguang Wang [ctb],
Yingwei Peng [aut, ctb]
Maintainer: Yi Niu <niuyi@dlut.edu.cn>
Diff between geecure versions 1.0-2 dated 2017-11-27 and 1.0-6 dated 2018-04-01
DESCRIPTION | 13 +++-- MD5 | 31 ++++++++----- NAMESPACE | 1 R/basesurv.R | 11 +++- R/emes.R |only R/es.R | 4 - R/geebt.R | 2 R/geecure.R | 106 +++++++++++++++++++++++++++++++++------------ R/geecure2.R |only R/initial_Lambda.R | 8 +-- R/varest.R | 12 ++--- R/varest2.R |only data/tonsil.rda |only data/tonsil_bootsample.rda |only man/emes.Rd |only man/geecure-package.Rd | 6 +- man/geecure.Rd | 33 +++++++++++--- man/geecure2.Rd |only man/print.geecure2.Rd |only man/tonsil.Rd |only man/tonsil_bootsample.Rd |only man/varest2.Rd |only 22 files changed, 162 insertions(+), 65 deletions(-)
Title: Functional Linear Mixed Models for Irregularly or Sparsely
Sampled Data
Description: Estimation of functional linear mixed models for irregularly or
sparsely sampled data based on functional principal component analysis.
Author: Jona Cederbaum
Maintainer: Jona Cederbaum <Jona.Cederbaum@gmail.com>
Diff between sparseFLMM versions 0.2.0 dated 2017-09-23 and 0.2.2 dated 2018-04-01
DESCRIPTION | 10 +- MD5 | 5 - NEWS.md |only R/fpc_estimation.R | 236 ++++++++++++++++++++++++++--------------------------- 4 files changed, 126 insertions(+), 125 deletions(-)
Title: Seamless Integration Between R and 'Julia'
Description: Provides an R interface to 'Julia',
which is a high-level, high-performance dynamic programming language
for numerical computing, see <https://julialang.org/> for more information.
It provides a high-level interface as well as a low-level interface.
Using the high level interface, you could call any 'Julia' function just like
any R function with automatic type conversion. Using the low level interface,
you could deal with C-level SEXP directly while enjoying the convenience of
using a high-level programming language like 'Julia'.
Author: Changcheng Li [aut, cre],
Randy Lai [ctb],
Dmitri Grominski [ctb],
Nagi Teramo [ctb]
Maintainer: Changcheng Li <cxl508@psu.edu>
Diff between JuliaCall versions 0.12.1 dated 2018-02-24 and 0.12.2 dated 2018-04-01
DESCRIPTION | 8 +++---- MD5 | 26 ++++++++++++------------ NEWS.md | 11 ++++++++++ R/RMarkdown.R | 3 +- R/interface.R | 11 +--------- R/zzz.R | 12 +++++++---- README.md | 18 +++++++++++++++- build/vignette.rds |binary inst/doc/JuliaCall_in_Jupyter_R_Notebook.html | 4 +-- inst/doc/Julia_in_RMarkdown.html | 28 +++++++++++++------------- inst/julia/JuliaObject.jl | 2 - inst/julia/install_dependency.jl | 1 inst/julia/setup.jl | 8 +------ man/julia_setup.Rd | 6 +++-- 14 files changed, 80 insertions(+), 58 deletions(-)
Title: Estimated Marginal Means, aka Least-Squares Means
Description: Obtain estimated marginal means (EMMs) for many linear, generalized
linear, and mixed models. Compute contrasts or linear functions of EMMs,
trends, and comparisons of slopes. Plots and compact letter displays.
Least-squares means are discussed, and the term "estimated marginal means"
is suggested, in Searle, Speed, and Milliken (1980) Population marginal means
in the linear model: An alternative to least squares means, The American
Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.
Author: Russell Lenth [aut, cre, cph],
Jonathon Love [ctb],
Maxime Herve [ctb]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>
Diff between emmeans versions 1.1.2 dated 2018-02-24 and 1.1.3 dated 2018-04-01
DESCRIPTION | 8 +-- MD5 | 72 ++++++++++++++++---------------- NEWS.md | 20 ++++++++- R/cld-emm.R | 4 - R/contrast.R | 4 - R/emm-contr.R | 47 ++++++++++++--------- R/emm-list.R | 2 R/emmGrid-methods.R | 2 R/emmeans.R | 37 +++++++++++++++- R/helpers.R | 8 +++ R/multinom-support.R | 3 - R/ref-grid.R | 24 ++++++++-- R/summary.R | 11 ++++ README.md | 75 ++++++++++++++++++++++++++++------ inst/doc/FAQs.R | 4 + inst/doc/FAQs.Rmd | 19 +++++++- inst/doc/FAQs.html | 14 +++++- inst/doc/basics.html | 4 - inst/doc/comparisons.html | 24 ++++++---- inst/doc/confidence-intervals.html | 4 - inst/doc/extending.pdf |binary inst/doc/interactions.html | 18 ++++---- inst/doc/messy-data.html | 6 -- inst/doc/models.html | 4 - inst/doc/sophisticated.R | 24 ++++++++++ inst/doc/sophisticated.Rmd | 61 ++++++++++++++++++++++++++- inst/doc/sophisticated.html | 50 +++++++++++++++++++++- inst/doc/transformations.html | 4 - inst/doc/transition-from-lsmeans.html | 4 - inst/doc/utilities.html | 22 ++++----- man/emmc-functions.Rd | 55 +++++++++++++----------- man/emmeans.Rd | 36 ++++++++++++++-- man/ref_grid.Rd | 14 +++++- man/summary.emmGrid.Rd | 6 ++ man/update.emmGrid.Rd | 2 vignettes/FAQs.Rmd | 19 +++++++- vignettes/sophisticated.Rmd | 61 ++++++++++++++++++++++++++- 37 files changed, 591 insertions(+), 181 deletions(-)
Title: Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
Description: Calculates the Delaunay triangulation and the Dirichlet
or Voronoi tessellation (with respect to the entire plane) of
a planar point set. Plots triangulations and tessellations in
various ways. Clips tessellations to sub-windows. Calculates
perimeters of tessellations. Summarises information about the
tiles of the tessellation.
Author: Rolf Turner
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>
Diff between deldir versions 0.1-14 dated 2017-04-22 and 0.1-15 dated 2018-04-01
ChangeLog | 31 ++++++++++----- DESCRIPTION | 8 +-- MD5 | 26 ++++++------ NAMESPACE | 1 R/acw.R | 4 - R/plot.deldir.R | 7 +-- R/tile.list.R | 105 +++++++++++++++++++++++++++------------------------- R/triang.list.R | 4 - data/seaweed.rda |binary inst/ratfor/intri.r | 7 +-- man/plot.deldir.Rd | 34 +++++++++------- man/triMat.Rd | 17 +++++--- src/init.c | 18 ++++---- src/intri.f | 9 ++-- 14 files changed, 153 insertions(+), 118 deletions(-)
Title: Amend, Augment and Aid Analysis of John Snow's Cholera Data
Description: Amends errors, augments data and aids analysis of John Snow's map
of the 1854 London cholera outbreak.
Author: Peter Li [aut, cre]
Maintainer: Peter Li <lindbrook@gmail.com>
Diff between cholera versions 0.3.0 dated 2018-01-26 and 0.4.0 dated 2018-04-01
cholera-0.3.0/cholera/R/nearestPath.R |only cholera-0.3.0/cholera/R/nodeData.R |only cholera-0.3.0/cholera/data/pump.case.RData |only cholera-0.3.0/cholera/man/figures/README-expected_area-1.png |only cholera-0.3.0/cholera/man/nearestPath.Rd |only cholera-0.3.0/cholera/man/nodeData.Rd |only cholera-0.3.0/cholera/man/pump.case.Rd |only cholera-0.4.0/cholera/DESCRIPTION | 12 cholera-0.4.0/cholera/MD5 | 132 cholera-0.4.0/cholera/NAMESPACE | 5 cholera-0.4.0/cholera/NEWS | 56 cholera-0.4.0/cholera/R/addIndexCase.R | 2 cholera-0.4.0/cholera/R/addKernelDensity.R | 147 - cholera-0.4.0/cholera/R/addLandmarks.R | 165 + cholera-0.4.0/cholera/R/addNeighborhood.R |only cholera-0.4.0/cholera/R/addPump.R |only cholera-0.4.0/cholera/R/addSnow.R | 37 cholera-0.4.0/cholera/R/cholera.R | 13 cholera-0.4.0/cholera/R/classifierAudit.R | 39 cholera-0.4.0/cholera/R/data.R | 20 cholera-0.4.0/cholera/R/nearestPump.R | 222 + cholera-0.4.0/cholera/R/neighborhoodData.R |only cholera-0.4.0/cholera/R/pumpData.R | 24 cholera-0.4.0/cholera/R/simulateFatalities.R | 25 cholera-0.4.0/cholera/R/snowMap.R | 9 cholera-0.4.0/cholera/R/snowNeighborhood.R | 8 cholera-0.4.0/cholera/R/streetNameLocator.R | 80 cholera-0.4.0/cholera/R/timeSeries.R | 15 cholera-0.4.0/cholera/R/unstack.R | 23 cholera-0.4.0/cholera/R/walking.R | 1359 +++++----- cholera-0.4.0/cholera/R/walkingDistance.R | 222 + cholera-0.4.0/cholera/README.md | 63 cholera-0.4.0/cholera/build/vignette.rds |binary cholera-0.4.0/cholera/data/ortho.proj.pump.RData |binary cholera-0.4.0/cholera/data/ortho.proj.pump.vestry.RData |binary cholera-0.4.0/cholera/data/road.segments.RData |binary cholera-0.4.0/cholera/data/roads.RData |binary cholera-0.4.0/cholera/inst/doc/duplicate.missing.cases.html | 4 cholera-0.4.0/cholera/inst/doc/kernel.density.R |only cholera-0.4.0/cholera/inst/doc/kernel.density.Rmd |only cholera-0.4.0/cholera/inst/doc/kernel.density.html |only cholera-0.4.0/cholera/inst/doc/pump.neighborhoods.R | 11 cholera-0.4.0/cholera/inst/doc/pump.neighborhoods.Rmd | 38 cholera-0.4.0/cholera/inst/doc/pump.neighborhoods.html | 46 cholera-0.4.0/cholera/inst/doc/roads.R | 9 cholera-0.4.0/cholera/inst/doc/roads.Rmd | 85 cholera-0.4.0/cholera/inst/doc/roads.html | 498 --- cholera-0.4.0/cholera/inst/doc/time.series.html | 4 cholera-0.4.0/cholera/inst/doc/unstacking.bars.html | 4 cholera-0.4.0/cholera/man/addKernelDensity.Rd | 28 cholera-0.4.0/cholera/man/addNeighborhood.Rd |only cholera-0.4.0/cholera/man/addPump.Rd |only cholera-0.4.0/cholera/man/addSnow.Rd | 4 cholera-0.4.0/cholera/man/cholera-package.Rd | 13 cholera-0.4.0/cholera/man/classifierAudit.Rd | 5 cholera-0.4.0/cholera/man/figures/README-expected-1.png |binary cholera-0.4.0/cholera/man/figures/README-expected_area_polygons-1.png |only cholera-0.4.0/cholera/man/figures/README-voronoi-1.png |binary cholera-0.4.0/cholera/man/figures/README-walk-1.png |binary cholera-0.4.0/cholera/man/figures/README-walk7-1.png |binary cholera-0.4.0/cholera/man/nearestPump.Rd | 17 cholera-0.4.0/cholera/man/neighborhoodData.Rd |only cholera-0.4.0/cholera/man/neighborhoodWalking.Rd | 4 cholera-0.4.0/cholera/man/ortho.proj.pump.Rd | 3 cholera-0.4.0/cholera/man/ortho.proj.pump.vestry.Rd | 3 cholera-0.4.0/cholera/man/plot.walking.Rd | 11 cholera-0.4.0/cholera/man/plot.walking_distance.Rd | 2 cholera-0.4.0/cholera/man/print.walking.Rd | 4 cholera-0.4.0/cholera/man/print.walking_distance.Rd | 4 cholera-0.4.0/cholera/man/snowMap.Rd | 5 cholera-0.4.0/cholera/man/streetNameLocator.Rd | 13 cholera-0.4.0/cholera/man/timeSeries.Rd | 5 cholera-0.4.0/cholera/man/walkingDistance.Rd | 10 cholera-0.4.0/cholera/vignettes/kernel.density.Rmd |only cholera-0.4.0/cholera/vignettes/pump.neighborhoods.Rmd | 38 cholera-0.4.0/cholera/vignettes/roads.Rmd | 85 76 files changed, 2050 insertions(+), 1581 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-08-07 2.0.1
2017-04-24 1.0.1
2016-09-18 0.1.11
2016-08-16 0.1.10
2016-07-27 0.1.8
2016-07-23 0.1.7
2016-07-20 0.1.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-12-09 1.6
2017-04-27 1.5.1
2016-06-16 1.5
2015-09-18 1.4.1
2015-09-15 1.4
2014-12-22 1.3
2014-10-14 1.2
2014-08-20 1.1
2014-08-19 1.0
Title: Omnibus Test for Genetic Association Analysis using the Rank
Normal Transformation
Description: Implementation of genetic association tests that utilize the rank based inverse normal transformation (INT). The primary contribution is an omnibus test, which synthesizes two complementary INT-based approaches. In simulations against phenotypes with skewed and heavy tailed residual distributions, the omnibus test provided valid inference in the absence of a genotypic effect, and provided power comparable to the more powerful of the component methods in the presence of a genotypic effect. Under these settings, standard linear regression often failed to control the type I error.
Author: Zachary McCaw [aut, cre]
Maintainer: Zachary McCaw <zmccaw@g.harvard.edu>
Diff between RNOmni versions 0.1.5 dated 2018-02-12 and 0.2.0 dated 2018-04-01
RNOmni-0.1.5/RNOmni/man/Omni.Rd |only RNOmni-0.1.5/RNOmni/man/PIINT.Rd |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/A02_e869ea9f66e2e3375eb1592b8b54b805.RData |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/A02_e869ea9f66e2e3375eb1592b8b54b805.rdb |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/A02_e869ea9f66e2e3375eb1592b8b54b805.rdx |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/A03_30f120fd6937c6e2e6ac673747e8dd76.RData |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/A03_30f120fd6937c6e2e6ac673747e8dd76.rdb |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/A03_30f120fd6937c6e2e6ac673747e8dd76.rdx |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/B01_81ddf28df43a030e130e4f3d652bb92c.RData |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/B01_81ddf28df43a030e130e4f3d652bb92c.rdb |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/B01_81ddf28df43a030e130e4f3d652bb92c.rdx |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/B02_4d74a2d7d8db7553f937efaae6e46085.RData |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/B02_4d74a2d7d8db7553f937efaae6e46085.rdb |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/B02_4d74a2d7d8db7553f937efaae6e46085.rdx |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/C01_0352f74e28cbc42dbbe955c2d7c878be.RData |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/C01_0352f74e28cbc42dbbe955c2d7c878be.rdb |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/C01_0352f74e28cbc42dbbe955c2d7c878be.rdx |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/C02_d1a70564e75da8c0cb6dab3cbd210b67.RData |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/C02_d1a70564e75da8c0cb6dab3cbd210b67.rdb |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/C02_d1a70564e75da8c0cb6dab3cbd210b67.rdx |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/C03_10038d4cc7be20b78210d632d940d5d5.RData |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/C03_10038d4cc7be20b78210d632d940d5d5.rdb |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/C03_10038d4cc7be20b78210d632d940d5d5.rdx |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/C04_d698d268675900b67ac7963af5aeb833.RData |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/C04_d698d268675900b67ac7963af5aeb833.rdb |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/C04_d698d268675900b67ac7963af5aeb833.rdx |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/C05_91a4a4ac35952a2f87c52f55b838cc09.RData |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/C05_91a4a4ac35952a2f87c52f55b838cc09.rdb |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_cache/html/C05_91a4a4ac35952a2f87c52f55b838cc09.rdx |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_files/figure-html/A03-1.png |only RNOmni-0.1.5/RNOmni/vignettes/RNOmni_files/figure-html/C05-1.png |only RNOmni-0.2.0/RNOmni/DESCRIPTION | 21 RNOmni-0.2.0/RNOmni/MD5 | 128 +- RNOmni-0.2.0/RNOmni/NAMESPACE | 19 RNOmni-0.2.0/RNOmni/R/DataDesc.R | 31 RNOmni-0.2.0/RNOmni/R/InputCheck.R |only RNOmni-0.2.0/RNOmni/R/RankNormal.R | 517 ++++------ RNOmni-0.2.0/RNOmni/R/RcppExports.R |only RNOmni-0.2.0/RNOmni/build/vignette.rds |binary RNOmni-0.2.0/RNOmni/data/G.rda |binary RNOmni-0.2.0/RNOmni/data/S.rda |binary RNOmni-0.2.0/RNOmni/data/X.rda |binary RNOmni-0.2.0/RNOmni/data/Y.rda |binary RNOmni-0.2.0/RNOmni/inst/doc/RNOmni.R | 159 --- RNOmni-0.2.0/RNOmni/inst/doc/RNOmni.Rmd | 181 --- RNOmni-0.2.0/RNOmni/inst/doc/RNOmni.html | 238 +--- RNOmni-0.2.0/RNOmni/man/AvgCorr.Rd | 8 RNOmni-0.2.0/RNOmni/man/BAT.Rd | 23 RNOmni-0.2.0/RNOmni/man/BootCorr.Rd | 5 RNOmni-0.2.0/RNOmni/man/DINT.Rd | 28 RNOmni-0.2.0/RNOmni/man/FIINT.Rd | 31 RNOmni-0.2.0/RNOmni/man/G.Rd | 11 RNOmni-0.2.0/RNOmni/man/IINT.Rd |only RNOmni-0.2.0/RNOmni/man/OmniP.Rd |only RNOmni-0.2.0/RNOmni/man/RNOmni.Rd | 67 - RNOmni-0.2.0/RNOmni/man/S.Rd | 8 RNOmni-0.2.0/RNOmni/man/X.Rd | 4 RNOmni-0.2.0/RNOmni/man/Y.Rd | 8 RNOmni-0.2.0/RNOmni/man/dotP.Rd |only RNOmni-0.2.0/RNOmni/man/eps.Rd |only RNOmni-0.2.0/RNOmni/man/errProj.Rd |only RNOmni-0.2.0/RNOmni/man/inCheck.Rd | 2 RNOmni-0.2.0/RNOmni/man/scaleParam.Rd |only RNOmni-0.2.0/RNOmni/man/scoreStat.Rd |only RNOmni-0.2.0/RNOmni/src |only RNOmni-0.2.0/RNOmni/vignettes/RNOmni.Rmd | 181 --- RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/A00_8304808dbc55cb12b87a8e4ff948e3f4.RData |binary RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/A00_8304808dbc55cb12b87a8e4ff948e3f4.rdb |binary RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/A00_8304808dbc55cb12b87a8e4ff948e3f4.rdx |binary RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/A01_f905d734149a88bc461d528c7d3733e2.RData |binary RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/A01_f905d734149a88bc461d528c7d3733e2.rdb |binary RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/A01_f905d734149a88bc461d528c7d3733e2.rdx |binary RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/A02_b984d39046bd38fa935cb2f419bbbcc9.RData |only RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/A02_b984d39046bd38fa935cb2f419bbbcc9.rdb |only RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/A02_b984d39046bd38fa935cb2f419bbbcc9.rdx |only RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/C01_23069a83de4afea5994a153337f6a0f2.RData |only RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/C01_23069a83de4afea5994a153337f6a0f2.rdb |only RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/C01_23069a83de4afea5994a153337f6a0f2.rdx |only RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/C02_2cf4a9ded8abcc557ca733d5edc8204d.RData |only RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/C02_2cf4a9ded8abcc557ca733d5edc8204d.rdb |only RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/C02_2cf4a9ded8abcc557ca733d5edc8204d.rdx |only RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/C03_38ceee70d0144867da577b43de8fe3c8.RData |only RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/C03_38ceee70d0144867da577b43de8fe3c8.rdb |only RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/C03_38ceee70d0144867da577b43de8fe3c8.rdx |only RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/unnamed-chunk-1_77da58766209fd057ff3ba87a03906ec.RData |only RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/unnamed-chunk-1_77da58766209fd057ff3ba87a03906ec.rdb |only RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/unnamed-chunk-1_77da58766209fd057ff3ba87a03906ec.rdx |only RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/unnamed-chunk-2_790d319e85ea3fdd0578cbf0e11660d5.RData |only RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/unnamed-chunk-2_790d319e85ea3fdd0578cbf0e11660d5.rdb |only RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/unnamed-chunk-2_790d319e85ea3fdd0578cbf0e11660d5.rdx |only RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/unnamed-chunk-3_62b20b5cbd6e5d427c6c82539046df00.RData |only RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/unnamed-chunk-3_62b20b5cbd6e5d427c6c82539046df00.rdb |only RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/unnamed-chunk-3_62b20b5cbd6e5d427c6c82539046df00.rdx |only RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/unnamed-chunk-4_5c14f926f372a06b4a931b8b8dde5eb5.RData |only RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/unnamed-chunk-4_5c14f926f372a06b4a931b8b8dde5eb5.rdb |only RNOmni-0.2.0/RNOmni/vignettes/RNOmni_cache/html/unnamed-chunk-4_5c14f926f372a06b4a931b8b8dde5eb5.rdx |only RNOmni-0.2.0/RNOmni/vignettes/RNOmni_files/figure-html/A01-1.png |binary 97 files changed, 675 insertions(+), 995 deletions(-)
Title: Robust Meta-Analysis and Meta-Regression
Description: Performs meta-analysis and meta-regression using standard and robust methods with confidence intervals based on the profile likelihood. Robust methods are based on alternative distributions for the random effect, either the t-distribution (Lee and Thompson, 2008 <doi:10.1002/sim.2897> or Baker and Jackson, 2008 <doi:10.1007/s10729-007-9041-8>) or mixtures of normals (Beath, 2014 <doi:10.1002/jrsm.1114>).
Author: Ken Beath [aut, cre],
Ben Bolker [aut],
R Development Core Team [aut]
Maintainer: Ken Beath <ken.beath@mq.edu.au>
Diff between metaplus versions 0.7-10 dated 2018-03-08 and 0.7-11 dated 2018-04-01
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/mymle.R | 1 + R/profilenorm.metaplus.R | 4 ++-- R/profilet.metaplus.R | 2 +- R/summary.metaplus.R | 2 +- build/vignette.rds |binary inst/NEWS | 4 ++++ 8 files changed, 20 insertions(+), 15 deletions(-)