Title: Utilities for Sweave Together with TeX 'listings' Package
Description: Provides utilities for defining R / Rd as "language" for TeX-package "listings" and for including R / Rd source file
(snippets) copied from R-forge in its most recent version (or another URL) thereby avoiding inconsistencies between
vignette and documented source code.
Author: Peter Ruckdeschel [cre, cph, aut]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between SweaveListingUtils versions 0.7.5 dated 2016-04-25 and 0.7.7 dated 2017-04-22
SweaveListingUtils-0.7.5/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout.save |only SweaveListingUtils-0.7.7/SweaveListingUtils/DESCRIPTION | 28 ++++------ SweaveListingUtils-0.7.7/SweaveListingUtils/MD5 | 12 ++-- SweaveListingUtils-0.7.7/SweaveListingUtils/inst/doc/ExampleSweaveListingUtils.Rnw | 20 +++---- SweaveListingUtils-0.7.7/SweaveListingUtils/inst/doc/ExampleSweaveListingUtils.pdf |binary SweaveListingUtils-0.7.7/SweaveListingUtils/man/0SweaveListingUtils-package.Rd | 6 +- SweaveListingUtils-0.7.7/SweaveListingUtils/tests/Examples/SweaveListingUtils-Ex.Rout |only SweaveListingUtils-0.7.7/SweaveListingUtils/vignettes/ExampleSweaveListingUtils.Rnw | 20 +++---- 8 files changed, 44 insertions(+), 42 deletions(-)
More information about SweaveListingUtils at CRAN
Permanent link
Title: 3D Scatter Plot
Description: Plots a three dimensional (3D) point cloud.
Author: Uwe Ligges <ligges@statistik.tu-dortmund.de>, Martin Maechler, Sarah Schnackenberg
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>
Diff between scatterplot3d versions 0.3-39 dated 2017-03-30 and 0.3-40 dated 2017-04-22
CHANGES | 1 + DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/scatterplot3d.R | 11 ++++++----- inst/doc/s3d.pdf |binary man/scatterplot3d.Rd | 5 +++-- 6 files changed, 19 insertions(+), 16 deletions(-)
Title: Reads Mass Spectrometry Data in Bruker *flex Format
Description: Reads data files acquired by Bruker Daltonics' matrix-assisted
laser desorption/ionization-time-of-flight mass spectrometer of the *flex
series.
Author: Sebastian Gibb [aut, cre]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between readBrukerFlexData versions 1.8.3 dated 2016-11-30 and 1.8.5 dated 2017-04-22
DESCRIPTION | 10 ++++----- MD5 | 40 +++++++++++++++++++------------------- NEWS | 7 ++++++ R/package.R | 4 +-- R/readAcquFile-functions.R | 24 +++++++++++++++++++++- R/readBrukerFlexFile-functions.R | 14 +++++++++++++ man/changePrecision.Rd | 1 man/cpSpecHpcMzXml.Rd | 1 man/double2singlePrecision.Rd | 1 man/extractHPCConstants.Rd | 1 man/grepAcquDoubleValue.Rd | 1 man/grepAcquValue.Rd | 1 man/hpc.Rd | 1 man/readAcquFile.Rd | 1 man/readBrukerFlexData-defunct.Rd | 3 -- man/readBrukerFlexData-package.Rd | 11 ++++------ man/readBrukerFlexDir.Rd | 1 man/readBrukerFlexFile.Rd | 1 man/readFidFile.Rd | 1 man/sampleName.Rd | 1 man/tof2mass.Rd | 1 21 files changed, 77 insertions(+), 49 deletions(-)
More information about readBrukerFlexData at CRAN
Permanent link
Title: Local Randomization Methods for RD Designs
Description: The regression discontinuity (RD) design is a popular quasi-experimental design for causal inference and policy evaluation. Under the local randomization approach, RD designs can be interpreted as randomized experiments inside a window around the cutoff. This package provides tools to perform randomization inference for RD designs under local randomization: rdrandinf() to perform hypothesis testing using randomization inference, rdwinselect() to select a window around the cutoff in which randomization is likely to hold, rdsensitivity() to assess the sensitivity of the results to different window lengths and null hypotheses and rdrbounds() to construct Rosenbaum bounds for sensitivity to unobserved confounders.
Author: Matias D. Cattaneo, Rocio Titiunik, Gonzalo Vazquez-Bare
Maintainer: Gonzalo Vazquez-Bare <gvazquez@umich.edu>
Diff between rdlocrand versions 0.1 dated 2017-04-07 and 0.2 dated 2017-04-22
DESCRIPTION | 6 +-- MD5 | 24 ++++++------- R/rdlocrand_fun.R | 57 ++++++++++++++++++++++++++++++-- R/rdlocrand_package.R | 8 ++-- R/rdrandinf.R | 34 ++++++++++--------- R/rdrbounds.R | 10 ++--- R/rdsensitivity.R | 14 +++---- R/rdwinselect.R | 83 +++++++++++++++++++++++++++++++---------------- man/rdlocrand-package.Rd | 6 +-- man/rdrandinf.Rd | 22 ++++++------ man/rdrbounds.Rd | 8 ++-- man/rdsensitivity.Rd | 10 ++--- man/rdwinselect.Rd | 29 +++++++++------- 13 files changed, 198 insertions(+), 113 deletions(-)
Title: Daily Based Morgan-Morgan-Finney (DMMF) Soil Erosion Model
Description: Implements the daily based Morgan-Morgan-Finney (DMMF) soil erosion model (Choi et al., 2017 <doi:10.3390/w9040278>) for estimating surface runoff and sediment budgets from a field or a catchment on a daily basis.
Author: Kwanghun Choi [aut, cre], Sebastian Arnhold [dtc, ctb], Bjoern Reineking [ths, ctb]
Maintainer: Kwanghun Choi <kwanghun.choi@yahoo.com>
Diff between DMMF versions 0.2.8.0 dated 2017-03-12 and 0.3.2.0 dated 2017-04-22
DESCRIPTION | 12 ++--- MD5 | 35 +++++++------- NAMESPACE | 2 NEWS.md | 19 +++++++ R/Function_DMMF.r | 21 +++++++- R/Function_MapChecker.r |only R/Function_SinkFill.r | 41 ++++++++++------- man/DMMF-package.Rd | 6 +- man/DMMF.Rd | 5 +- man/DMMF_Simple.Rd | 2 man/MapChecker.Rd |only man/Potato.Concave.Rd | 6 +- man/Potato.Convex.Rd | 6 +- man/SinkFill.Rd | 14 +++-- src/1_1_MMFAlg_d.f95 | 19 +++++-- src/2_1_SinkFillAlg.f95 | 105 ++++++++++++++++++++++++++++++++++---------- src/2_2_BoundaryChecker.f95 | 30 +++++++----- src/2_3_MapChecker.f95 |only src/DMMF.h | 7 ++ src/R_init_DMMF.c | 5 +- 20 files changed, 229 insertions(+), 106 deletions(-)
Title: Bayesian Evaluation of Variant Involvement in Mendelian Disease
Description: A fast integrative genetic association test for rare diseases based on a model for disease status given allele counts at rare variant sites. Probability of association, mode of inheritance and probability of pathogenicity for individual variants are all inferred in a Bayesian framework.
Author: Daniel Greene, Sylvia Richardson and Ernest Turro
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between BeviMed versions 4.0 dated 2017-03-01 and 5.0 dated 2017-04-22
DESCRIPTION | 12 - MD5 | 45 +++--- NAMESPACE | 1 NEWS.md | 16 ++ R/convenience.R | 202 +++++++++++++++++++---------- R/functions.R | 41 +++-- R/generics.R | 57 ++++---- inst/doc/Guide.R | 11 - inst/doc/Guide.Rnw | 77 +++++------ inst/doc/Guide.pdf |binary inst/doc/Intro.html | 65 ++++----- inst/doc/vcf.html | 4 man/bevimed.Rd | 8 - man/bevimed_polytomous.Rd |only man/call_cpp.Rd | 8 - man/extract_conditional_prob_pathogenic.Rd | 2 man/extract_prob_association.Rd | 6 man/extract_prob_pathogenic.Rd | 8 - man/log_BF.Rd | 4 man/prob_association.Rd | 6 man/prob_pathogenic.Rd | 6 man/summary.BeviMed.Rd | 5 src/sampling.cpp | 24 +-- vignettes/Guide.Rnw | 77 +++++------ 24 files changed, 385 insertions(+), 300 deletions(-)
Title: Basic Functions for Supporting an Implementation of Best-Worst
Scaling
Description: Provides three basic functions that support an implementation of object case (Case 1) best-worst scaling: one for converting a two-level orthogonal main-effect design/balanced incomplete block design into questions; one for creating a data set suitable for analysis; and one for calculating count-based scores.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>
Diff between support.BWS versions 0.1-3 dated 2015-04-27 and 0.1-4 dated 2017-04-22
DESCRIPTION | 8 ++++---- MD5 | 10 ++++++---- NAMESPACE | 1 + NEWS | 4 ++++ data/ricebws1.rda |only man/ricebws1.Rd |only man/support.BWS-package.Rd | 7 ++++++- 7 files changed, 21 insertions(+), 9 deletions(-)
Title: Hydrologic Modelling System for R Users
Description: Hydrologic modelling system is an object oriented tool which enables R users to simulate and analyze hydrologic events. The package proposes functions and methods for construction, simulation, visualization, and calibration of hydrologic systems.
Author: Rezgar Arabzadeh ; Shahab Araghinejad
Maintainer: Rezgar Arabzadeh <rezgararabzadeh@ut.ac.ir>
Diff between RHMS versions 1.0 dated 2017-04-21 and 1.1 dated 2017-04-22
DESCRIPTION | 8 ++-- MD5 | 74 ++++++++++++++++++++--------------------- R/createSubbasin.R | 2 - R/createSubbasin.base.R | 4 +- R/createSubbasin.default.R | 10 ++++- R/sim.base.R | 13 +++---- R/transform.R | 57 +++++++++++++++++++++++++++++++ man/RHMS-package.Rd | 57 +++++++++++++++++++++---------- man/Zaab.Rd | 4 +- man/addObjectToBasin.Rd | 10 ++--- man/createBasin.Rd | 6 +-- man/createBasin.base.Rd | 8 ++-- man/createBasin.default.Rd | 8 ++-- man/createDiversion.Rd | 14 +++---- man/createDiversion.base.Rd | 14 +++---- man/createDiversion.default.Rd | 14 +++---- man/createJunction.Rd | 8 ++-- man/createJunction.base.Rd | 10 ++--- man/createJunction.default.Rd | 12 +++--- man/createReach.Rd | 18 ++++----- man/createReach.base.Rd | 20 +++++------ man/createReach.default.Rd | 20 +++++------ man/createReservoir.Rd | 12 +++--- man/createReservoir.base.Rd | 14 +++---- man/createReservoir.default.Rd | 14 +++---- man/createSubbasin.Rd | 29 +++++++++------- man/createSubbasin.base.Rd | 31 +++++++++-------- man/createSubbasin.default.Rd | 33 +++++++++--------- man/loss.Rd | 14 +++---- man/plot.sim.Rd | 8 ++-- man/reachRouting.Rd | 15 +++----- man/reservoirRouting.Rd | 10 ++--- man/sim.Rd | 6 +-- man/sim.base.Rd | 6 +-- man/sim.default.Rd | 6 +-- man/summary.sim.Rd | 8 ++-- man/transform.Rd | 28 +++++++++------ man/tune.Rd | 23 ++++++------ 38 files changed, 374 insertions(+), 274 deletions(-)
Title: Object Oriented Implementation of Distributions
Description: S4-classes and methods for distributions.
Author: Florian Camphausen [ctb] (contributed as student in the initial phase
--2005),
Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
Thomas Stabla [ctb] (contributed as student in the initial phase
--2005),
R Core Team [ctb, cph] (for source file ks.c/ routines 'pKS2' and
'pKolmogorov2x')
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distr versions 2.6 dated 2016-04-23 and 2.6.2 dated 2017-04-22
distr-2.6.2/distr/DESCRIPTION | 28 +++++++---------- distr-2.6.2/distr/MD5 | 31 +++++++++---------- distr-2.6.2/distr/NAMESPACE | 2 - distr-2.6.2/distr/R/Convpow.R | 9 +---- distr-2.6.2/distr/R/flat.R | 4 +- distr-2.6.2/distr/R/internals-qqplot.R | 9 +++-- distr-2.6.2/distr/demo/nFoldConvolution.R | 10 +----- distr-2.6.2/distr/inst/NEWS | 7 ++++ distr-2.6.2/distr/inst/doc/newDistributions.Rnw | 18 ++++++----- distr-2.6.2/distr/inst/doc/newDistributions.pdf |binary distr-2.6.2/distr/man/0distr-package.Rd | 10 +++--- distr-2.6.2/distr/man/sqrt-methods.Rd | 4 +- distr-2.6.2/distr/src/distr.h |only distr-2.6.2/distr/src/init.c |only distr-2.6.2/distr/src/ks.c | 7 ++-- distr-2.6.2/distr/vignettes/newDistributions.Rnw | 18 ++++++----- distr-2.6/distr/tests/Examples |only distr-2.6/distr/vignettes/newDistributions-exam1.pdf |only 18 files changed, 80 insertions(+), 77 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 0.1-12 dated 2016-03-06 and 0.1-14 dated 2017-04-22
ChangeLog | 60 +++++++++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 13 ++++++---- MD5 | 44 ++++++++++++++++++++++------------- NAMESPACE | 2 - R/binsrt.R | 2 - R/deldir.R | 26 +++++++++++++++++++-- R/dumpts.R | 2 - R/mnnd.R | 2 - R/plot.tile.list.R | 27 +++++++++++++++++----- R/prelimtlist.R |only R/print.tileInfo.R |only R/tile.list.R | 6 +++- R/tileInfo.R |only R/triMat.R | 30 ++++-------------------- R/triang.list.R | 2 - R/which.tile.R |only data |only man/deldir-internal.Rd | 10 ++++---- man/deldir.Rd | 12 +++++++-- man/plot.tile.list.Rd | 49 ++++++++++++++++++++++++++++++++-------- man/print.tileInfo.Rd |only man/seaweed.Rd |only man/tile.list.Rd | 5 ++++ man/tileInfo.Rd |only man/triMat.Rd | 13 ++++++++++ man/triang.list.Rd | 6 +++- man/which.tile.Rd |only src/init.c |only 28 files changed, 233 insertions(+), 78 deletions(-)
Title: Sensitivity Analysis for Causal Inference
Description: Utilities to investigate sensitivity to unmeasured confounding in
parametric models with either binary or continuous treatment.
Author: Nicole Bohme Carnegie [aut, cre],
Masataka Harada [aut],
Vincent Dorie [aut],
Jennifer Hill [ctb]
Maintainer: Nicole Bohme Carnegie <carnegin@uwm.edu>
Diff between treatSens versions 2.1.1 dated 2017-04-20 and 2.1.2 dated 2017-04-22
treatSens-2.1.1/treatSens/src/config.hpp |only treatSens-2.1.1/treatSens/src/external/config.h |only treatSens-2.1.2/treatSens/DESCRIPTION | 8 treatSens-2.1.2/treatSens/MD5 | 102 treatSens-2.1.2/treatSens/NAMESPACE | 76 treatSens-2.1.2/treatSens/R/X_partials.R | 122 treatSens-2.1.2/treatSens/R/calc_range.R | 396 - treatSens-2.1.2/treatSens/R/cibart.R | 128 treatSens-2.1.2/treatSens/R/cibart_treatmentModel.R | 122 treatSens-2.1.2/treatSens/R/cont_binary_mlm_stan.R | 180 treatSens-2.1.2/treatSens/R/genU_contY.R | 478 - treatSens-2.1.2/treatSens/R/grid_range.R | 300 treatSens-2.1.2/treatSens/R/guessNumCores.R | 42 treatSens-2.1.2/treatSens/R/hooks.R | 12 treatSens-2.1.2/treatSens/R/housekeeping.R | 190 treatSens-2.1.2/treatSens/R/multipleAssignment.R | 234 treatSens-2.1.2/treatSens/R/object_def.R | 502 - treatSens-2.1.2/treatSens/R/pweight.R | 104 treatSens-2.1.2/treatSens/R/sensPlot.R | 812 +- treatSens-2.1.2/treatSens/R/stanmodels.R | 80 treatSens-2.1.2/treatSens/R/treatSens.R | 1060 +- treatSens-2.1.2/treatSens/R/treatSensBART.R | 684 - treatSens-2.1.2/treatSens/R/utility.R | 96 treatSens-2.1.2/treatSens/R/warnings.R | 530 - treatSens-2.1.2/treatSens/R/zzz.R | 10 treatSens-2.1.2/treatSens/cleanup | 39 treatSens-2.1.2/treatSens/configure.ac | 158 treatSens-2.1.2/treatSens/configure.win | 6 treatSens-2.1.2/treatSens/exec/cont_binary_mlm.stan | 202 treatSens-2.1.2/treatSens/inst/CITATION | 60 treatSens-2.1.2/treatSens/man/sensPlot.Rd | 124 treatSens-2.1.2/treatSens/man/summary.Rd | 82 treatSens-2.1.2/treatSens/man/treatSens-package.Rd | 68 treatSens-2.1.2/treatSens/src/bartTreatmentModel.hpp | 62 treatSens-2.1.2/treatSens/src/config.hpp.in | 104 treatSens-2.1.2/treatSens/src/config.hpp.win | 28 treatSens-2.1.2/treatSens/src/external/config.h.in | 124 treatSens-2.1.2/treatSens/src/guessNumCores.cpp | 2 treatSens-2.1.2/treatSens/src/guessNumCores.hpp | 20 treatSens-2.1.2/treatSens/src/probitEMTreatmentModel.hpp | 32 treatSens-2.1.2/treatSens/src/probitTreatmentModel.hpp | 74 treatSens-2.1.2/treatSens/src/sensitivityAnalysis.hpp | 92 treatSens-2.1.2/treatSens/src/treatmentModel.hpp | 58 treatSens-2.1.2/treatSens/tests/testthat.R | 14 treatSens-2.1.2/treatSens/tests/testthat/test-01-glmFit.R | 46 treatSens-2.1.2/treatSens/tests/testthat/test-02-cibartTreatmentModel.R | 122 treatSens-2.1.2/treatSens/tests/testthat/test-03-continuous.R | 240 treatSens-2.1.2/treatSens/tests/testthat/test-04-binary.R | 156 treatSens-2.1.2/treatSens/tools/build-aux/config.guess | 3104 ++++---- treatSens-2.1.2/treatSens/tools/build-aux/config.sub | 3576 +++++----- treatSens-2.1.2/treatSens/tools/m4/ax_func_posix_memalign.m4 | 104 treatSens-2.1.2/treatSens/tools/m4/m4_ax_pthread.m4 | 664 - treatSens-2.1.2/treatSens/tools/make_cpp.R | 94 53 files changed, 7856 insertions(+), 7867 deletions(-)
Title: Statistical Tests and Graphics for Hardy-Weinberg Equilibrium
Description: Contains tools for exploring Hardy-Weinberg equilibrium for
diallelic genetic marker data. All classical tests (chi-square, exact,
likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium
are included in the package, as well as functions for power computation and
for the simulation of marker data under equilibrium and disequilibrium.
Routines for dealing with markers on the X-chromosome are included.
Functions for testing equilibrium in the presence of missing data by
using multiple imputation are also provided. Implements several graphics
for exploring the equilibrium status of a large set of diallelic markers:
ternary plots with acceptance regions, log-ratio plots and Q-Q plots.
Author: Jan Graffelman <jan.graffelman@upc.edu>
Maintainer: Jan Graffelman <jan.graffelman@upc.edu>
Diff between HardyWeinberg versions 1.5.6 dated 2016-03-29 and 1.5.7 dated 2017-04-22
DESCRIPTION | 14 ++++++++------ MD5 | 43 ++++++++++++++++++++++++++++--------------- NAMESPACE | 10 ++++++++-- R/HWABO.R |only R/HWExact.R | 8 ++++---- R/HWExactStats.R | 22 ++++++++++++++-------- R/HWTernaryPlot.R | 7 ++++--- R/MakeCounts.R | 4 ++++ R/RcppExports.R |only R/combineC.R |only R/genlabels.R |only build/vignette.rds |binary inst/doc/HardyWeinberg.R | 18 +++++++++--------- inst/doc/HardyWeinberg.Rnw | 9 +++++---- inst/doc/HardyWeinberg.pdf |binary man/HWABO.Rd |only man/HWChisq.Rd | 9 ++++++++- man/HWExact.Rd | 14 ++++++++++++-- man/HWExactStats.Rd | 10 +++++++++- man/ThetatoF.Rd |only man/genlabels.Rd |only src |only vignettes/HWGeno1.pdf |only vignettes/HWGeno2.pdf |only vignettes/HardyWeinberg.Rnw | 9 +++++---- vignettes/HardyWeinberg.bib | 9 +++++++++ vignettes/MourantQQPlot.pdf |only vignettes/workd.bat |only 28 files changed, 127 insertions(+), 59 deletions(-)