Title: A Framework for Data-Driven Stochastic Disease Spread
Simulations
Description: Provides an efficient and very flexible framework to
conduct data-driven epidemiological modeling in realistic large
scale disease spread simulations. The framework integrates
infection dynamics in subpopulations as continuous-time Markov
chains using the Gillespie stochastic simulation algorithm and
incorporates available data such as births, deaths and movements
as scheduled events at predefined time-points. Using C code for
the numerical solvers and 'OpenMP' (if available) to divide work
over multiple processors ensures high performance when simulating
a sample outcome. One of our design goals was to make the package
extendable and enable usage of the numerical solvers from other R
extension packages in order to facilitate complex epidemiological
research. The package contains template models and can be extended
with user-defined models. For more details see the paper by
Widgren, Bauer, Eriksson and Engblom (2019)
<doi:10.18637/jss.v091.i12>.
Author: Stefan Widgren [aut, cre] (<https://orcid.org/0000-0001-5745-2284>),
Robin Eriksson [aut] (<https://orcid.org/0000-0002-4291-712X>),
Stefan Engblom [aut] (<https://orcid.org/0000-0002-3614-1732>),
Pavol Bauer [aut] (<https://orcid.org/0000-0003-4328-7171>),
Attractive Chaos [cph] (Author of 'kvec.h', a generic dynamic array)
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between SimInf versions 6.3.0 dated 2019-05-26 and 6.4.0 dated 2019-11-11
SimInf-6.3.0/SimInf/NEWS |only SimInf-6.4.0/SimInf/DESCRIPTION | 10 SimInf-6.4.0/SimInf/MD5 | 20 - SimInf-6.4.0/SimInf/NEWS.md |only SimInf-6.4.0/SimInf/build/vignette.rds |binary SimInf-6.4.0/SimInf/inst/CITATION | 37 +- SimInf-6.4.0/SimInf/inst/doc/SimInf.R | 6 SimInf-6.4.0/SimInf/inst/doc/SimInf.Rnw | 518 ++++++++++++++++--------------- SimInf-6.4.0/SimInf/inst/doc/SimInf.pdf |binary SimInf-6.4.0/SimInf/tests/mparse.R | 4 SimInf-6.4.0/SimInf/vignettes/SimInf.Rnw | 518 ++++++++++++++++--------------- SimInf-6.4.0/SimInf/vignettes/SimInf.bib | 3 12 files changed, 602 insertions(+), 514 deletions(-)
Title: QTL Genome-Wide Composite Interval Mapping with Graphical User
Interface
Description: Conduct multiple quantitative trait loci (QTL) mapping under the framework of random-QTL-effect linear mixed model. First, each position on the genome is detected in order to obtain a negative logarithm P-value curve against genome position. Then, all the peaks on each effect (additive or dominant) curve are viewed as potential QTL, all the effects of the potential QTL are included in a multi-QTL model, their effects are estimated by empirical Bayes in doubled haploid population or by adaptive lasso in F2 population, and true QTL are identified by likelihood radio test. See Wen et al. (2018) <doi:10.1093/bib/bby058>.
Author: Zhang Ya-Wen, Wen Yang-Jun, Wang Shi-Bo, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Diff between QTL.gCIMapping.GUI versions 1.0 dated 2018-06-15 and 2.0 dated 2019-11-11
QTL.gCIMapping.GUI-1.0/QTL.gCIMapping.GUI/R/QTL.gCIMapping.R |only QTL.gCIMapping.GUI-1.0/QTL.gCIMapping.GUI/inst/extdata/GCIM_Cov.csv |only QTL.gCIMapping.GUI-1.0/QTL.gCIMapping.GUI/inst/extdata/GCIM_Cov.txt |only QTL.gCIMapping.GUI-2.0/QTL.gCIMapping.GUI/DESCRIPTION | 15 QTL.gCIMapping.GUI-2.0/QTL.gCIMapping.GUI/MD5 | 38 QTL.gCIMapping.GUI-2.0/QTL.gCIMapping.GUI/NAMESPACE | 5 QTL.gCIMapping.GUI-2.0/QTL.gCIMapping.GUI/R/QTL.gCIMapping.GUI.R |only QTL.gCIMapping.GUI-2.0/QTL.gCIMapping.GUI/R/WangF.R | 1060 ++++----- QTL.gCIMapping.GUI-2.0/QTL.gCIMapping.GUI/R/WenF.r | 1126 ++++------ QTL.gCIMapping.GUI-2.0/QTL.gCIMapping.GUI/data/gen.rda |binary QTL.gCIMapping.GUI-2.0/QTL.gCIMapping.GUI/data/genf2.rda |binary QTL.gCIMapping.GUI-2.0/QTL.gCIMapping.GUI/data/map.rda |binary QTL.gCIMapping.GUI-2.0/QTL.gCIMapping.GUI/data/mapf2.rda |binary QTL.gCIMapping.GUI-2.0/QTL.gCIMapping.GUI/data/phe.rda |binary QTL.gCIMapping.GUI-2.0/QTL.gCIMapping.GUI/data/phef2.rda |binary QTL.gCIMapping.GUI-2.0/QTL.gCIMapping.GUI/inst/doc/Instruction.pdf |binary QTL.gCIMapping.GUI-2.0/QTL.gCIMapping.GUI/inst/extdata/ICIM_Cov.csv |only QTL.gCIMapping.GUI-2.0/QTL.gCIMapping.GUI/inst/extdata/ICIM_Cov.txt |only QTL.gCIMapping.GUI-2.0/QTL.gCIMapping.GUI/man/QTL.gCIMapping.GUI.Rd | 16 QTL.gCIMapping.GUI-2.0/QTL.gCIMapping.GUI/man/WangF.Rd | 2 QTL.gCIMapping.GUI-2.0/QTL.gCIMapping.GUI/man/WangS.Rd | 11 QTL.gCIMapping.GUI-2.0/QTL.gCIMapping.GUI/man/WenF.Rd | 4 QTL.gCIMapping.GUI-2.0/QTL.gCIMapping.GUI/man/WenS.Rd | 12 23 files changed, 1071 insertions(+), 1218 deletions(-)
More information about QTL.gCIMapping.GUI at CRAN
Permanent link
Title: QTL Genome-Wide Composite Interval Mapping
Description: Conduct multiple quantitative trait loci (QTL) mapping under the framework of random-QTL-effect linear mixed model. First, each position on the genome is detected in order to obtain a negative logarithm P-value curve against genome position. Then, all the peaks on each effect (additive or dominant) curve are viewed as potential QTL, all the effects of the potential QTL are included in a multi-QTL model, their effects are estimated by empirical Bayes in doubled haploid population or by adaptive lasso in F2 population, and true QTL are identified by likelihood radio test. See Wen et al. (2018) <doi:10.1093/bib/bby058>.
Author: Zhang Ya-Wen, Wen Yang-Jun, Wang Shi-Bo, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Diff between QTL.gCIMapping versions 3.1 dated 2018-10-17 and 3.2 dated 2019-11-11
QTL.gCIMapping-3.1/QTL.gCIMapping/data/f2data.rda |only QTL.gCIMapping-3.1/QTL.gCIMapping/inst/extdata/GCIM_Cov.csv |only QTL.gCIMapping-3.1/QTL.gCIMapping/inst/extdata/GCIM_Cov.txt |only QTL.gCIMapping-3.1/QTL.gCIMapping/man/f2data.Rd |only QTL.gCIMapping-3.2/QTL.gCIMapping/DESCRIPTION | 15 QTL.gCIMapping-3.2/QTL.gCIMapping/MD5 | 38 QTL.gCIMapping-3.2/QTL.gCIMapping/NAMESPACE | 11 QTL.gCIMapping-3.2/QTL.gCIMapping/R/Dodata.R |only QTL.gCIMapping-3.2/QTL.gCIMapping/R/QTL.gCIMapping.R | 603 ------ QTL.gCIMapping-3.2/QTL.gCIMapping/R/Readdata.R |only QTL.gCIMapping-3.2/QTL.gCIMapping/R/WangF.R | 1051 +++++------ QTL.gCIMapping-3.2/QTL.gCIMapping/R/WenF.r | 1126 ++++-------- QTL.gCIMapping-3.2/QTL.gCIMapping/data/DHdata.rda |only QTL.gCIMapping-3.2/QTL.gCIMapping/data/F2data.rda |only QTL.gCIMapping-3.2/QTL.gCIMapping/inst/doc/instruction.pdf |binary QTL.gCIMapping-3.2/QTL.gCIMapping/inst/extdata/ICIM_Cov.csv |only QTL.gCIMapping-3.2/QTL.gCIMapping/inst/extdata/ICIM_Cov.txt |only QTL.gCIMapping-3.2/QTL.gCIMapping/man/DHdata.Rd |only QTL.gCIMapping-3.2/QTL.gCIMapping/man/Dodata.Rd |only QTL.gCIMapping-3.2/QTL.gCIMapping/man/F2data.Rd |only QTL.gCIMapping-3.2/QTL.gCIMapping/man/QTL.gCIMapping.Rd | 25 QTL.gCIMapping-3.2/QTL.gCIMapping/man/Readdata.Rd |only QTL.gCIMapping-3.2/QTL.gCIMapping/man/WangF.Rd | 9 QTL.gCIMapping-3.2/QTL.gCIMapping/man/WangS.Rd | 16 QTL.gCIMapping-3.2/QTL.gCIMapping/man/WenF.Rd | 9 QTL.gCIMapping-3.2/QTL.gCIMapping/man/WenS.Rd | 15 QTL.gCIMapping-3.2/QTL.gCIMapping/man/markerinsert.Rd | 4 27 files changed, 1110 insertions(+), 1812 deletions(-)
More information about QTL.gCIMapping at CRAN
Permanent link
Title: Sensitivity Analysis of Neural Networks
Description: Analysis functions to quantify inputs importance in neural network models.
Functions are available for calculating and plotting the inputs importance and obtaining
the activation function of each neuron layer and its derivatives. The importance of a given
input is defined as the distribution of the derivatives of the output with respect to that
input in each training data point.
Author: José Portela González [aut],
Antonio Muñoz San Roque [aut],
Jaime Pizarroso Gonzalo [ctb, cre]
Maintainer: Jaime Pizarroso Gonzalo <jpizarroso@comillas.edu>
Diff between NeuralSens versions 0.0.9 dated 2019-10-03 and 0.1.0 dated 2019-11-11
DESCRIPTION | 14 ++-- MD5 | 37 ++++++---- NAMESPACE | 2 R/ActFunc.R | 4 - R/CombineSens.R |only R/SensAnalysisMLP.R | 155 ++++++++++++++++++++++++++++++++------------- R/SensFeaturePlot.R |only R/SensTimePlot.R | 92 ++++++++++++++++---------- R/SensitivityPlots.R | 40 ++++++----- R/data.R | 37 ++++++++++ data/DAILY_DEMAND_TR.rdata |binary data/DAILY_DEMAND_TV.rdata |binary data/simdata.rdata |only man/CombineSens.Rd |only man/DAILY_DEMAND_TR.Rd | 2 man/DAILY_DEMAND_TV.Rd | 2 man/DerActFunc.Rd | 4 - man/SensAnalysisMLP.Rd | 9 +- man/SensFeaturePlot.Rd |only man/SensTimePlot.Rd | 39 ++++++----- man/SensitivityPlots.Rd | 2 man/logo |only man/simdata.Rd |only 23 files changed, 291 insertions(+), 148 deletions(-)
Title: Hilbert Similarity Index for High Dimensional Data
Description: Quantifying similarity between high-dimensional single cell samples is challenging, and usually requires
some simplifying hypothesis to be made. By transforming the high dimensional space into a high dimensional grid,
the number of cells in each sub-space of the grid is characteristic of a given sample. Using a Hilbert curve
each sample can be visualized as a simple density plot, and the distance between samples can be calculated from
the distribution of cells using the Jensen-Shannon distance. Bins that correspond to significant differences
between samples can identified using a simple bootstrap procedure.
Author: Yann Abraham [aut, cre],
Marilisa Neri [aut],
John Skilling [ctb]
Maintainer: Yann Abraham <yann.abraham@gmail.com>
Diff between hilbertSimilarity versions 0.4.2 dated 2019-11-05 and 0.4.3 dated 2019-11-11
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- README.md | 6 ++++++ inst/doc/comparing_samples.html | 4 ++-- inst/doc/identifying_effects.html | 16 ++++++++-------- src/mapping.cpp | 12 ++++++++---- 6 files changed, 33 insertions(+), 23 deletions(-)
More information about hilbertSimilarity at CRAN
Permanent link
Title: 'NoSQL' Database Connector
Description: Simplified document database manipulation and analysis,
including support for many 'NoSQL' databases, including document
databases ('Elasticsearch', 'CouchDB', 'MongoDB'),
'key-value' databases ('Redis'), and (with limitations)
SQLite/json1.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Rich FitzJohn [aut],
Jeroen Ooms [aut],
Ralf Herold [aut] (<https://orcid.org/0000-0002-8148-6748>)
Maintainer: Scott Chamberlain <sckott@protonmail.com>
Diff between nodbi versions 0.3.0 dated 2019-09-18 and 0.4.0 dated 2019-11-11
DESCRIPTION | 6 ++-- MD5 | 22 +++++++------- NEWS.md | 9 ++++++ R/create.R | 12 ++------ R/delete.R | 1 R/get.R | 17 ++++++++--- R/query.R | 63 ++++++++++++++++++++++++++---------------- man/docdb_create.Rd | 2 - man/docdb_delete.Rd | 1 man/docdb_get.Rd | 2 + man/docdb_query.Rd | 1 tests/testthat/test-couchdb.R | 4 ++ 12 files changed, 88 insertions(+), 52 deletions(-)
Title: Hexagonal Binning Routines
Description: Binning and plotting functions for hexagonal bins.
Author: Dan Carr <dcarr@voxel.galaxy.gmu.edu>, ported by Nicholas
Lewin-Koh and Martin Maechler <maechler@stat.math.ethz.ch>,
contains copies of lattice functions written by Deepayan Sarkar
<deepayan.sarkar@r-project.org>
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between hexbin versions 1.27.3 dated 2019-05-14 and 1.28.0 dated 2019-11-11
DESCRIPTION | 6 +++--- MD5 | 17 +++++++++-------- R/hexViewport.R | 7 ++++++- R/hexbin.s4.R | 9 +++++---- build/vignette.rds |binary inst/doc/hexagon_binning.R | 6 +++--- inst/doc/hexagon_binning.Rnw | 38 +++++++++++++++++++++----------------- inst/doc/hexagon_binning.pdf |binary vignettes/hexagon_binning.Rnw | 38 +++++++++++++++++++++----------------- vignettes/references.bib |only 10 files changed, 68 insertions(+), 53 deletions(-)
Title: Tools for Spatial Data
Description: For curve, surface and function fitting with an emphasis
on splines, spatial data, geostatistics, and spatial statistics. The major methods
include cubic, and thin plate splines, Kriging, and compactly supported
covariance functions for large data sets. The splines and Kriging methods are
supported by functions that can determine the smoothing parameter
(nugget and sill variance) and other covariance function parameters by cross
validation and also by restricted maximum likelihood. For Kriging
there is an easy to use function that also estimates the correlation
scale (range parameter). A major feature is that any covariance function
implemented in R and following a simple format can be used for
spatial prediction. There are also many useful functions for plotting
and working with spatial data as images. This package also contains
an implementation of sparse matrix methods for large spatial data
sets and currently requires the sparse matrix (spam) package. Use
help(fields) to get started and for an overview. The fields source
code is deliberately commented and provides useful explanations of
numerical details as a companion to the manual pages. The commented
source code can be viewed by expanding source code version
and looking in the R subdirectory. The reference for fields can be generated
by the citation function in R and has DOI <doi:10.5065/D6W957CT>. Development
of this package was supported in part by the National Science Foundation Grant
1417857 and the National Center for Atmospheric Research. See the Fields URL
for a vignette on using this package and some background on spatial statistics.
Author: Douglas Nychka [aut, cre],
Reinhard Furrer [aut],
John Paige [aut],
Stephan Sain [aut],
Florian Gerber [aut],
Matthew Iverson [aut],
University Corporation for Atmospheric Research [cph]
Maintainer: Douglas Nychka <douglasnychka@gmail.com>
Diff between fields versions 9.9 dated 2019-10-13 and 10.0 dated 2019-11-11
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- man/rdist.earth.Rd | 10 +++++++--- man/registeredC.Rd | 7 +++++++ src/init.c | 4 ++++ 5 files changed, 26 insertions(+), 11 deletions(-)
Title: R Graphics Devices for Vector Graphics Output
Description: Vector Graphics devices for Microsoft
PowerPoint and Excel. Functions extending package 'officer' are provided to
embed 'DrawingML' graphics into 'Microsoft PowerPoint' presentations and
'Microsoft Excel' workbooks.
Author: David Gohel [aut, cre],
Bob Rudis [ctb] (the javascript code used by function set_attr),
Francois Brunetti [ctb] (clipping algorithms)
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between rvg versions 0.2.1 dated 2019-06-25 and 0.2.2 dated 2019-11-11
rvg-0.2.1/rvg/inst/templates |only rvg-0.2.2/rvg/DESCRIPTION | 13 ++-- rvg-0.2.2/rvg/MD5 | 25 ++++---- rvg-0.2.2/rvg/NAMESPACE | 9 +- rvg-0.2.2/rvg/R/dml_pptx.R | 6 + rvg-0.2.2/rvg/R/fonts.R | 55 +++++++++-------- rvg-0.2.2/rvg/R/ph_with_vg.R | 87 ++++++++-------------------- rvg-0.2.2/rvg/build |only rvg-0.2.2/rvg/inst/doc |only rvg-0.2.2/rvg/man/dml.Rd | 3 rvg-0.2.2/rvg/man/dml_pptx.Rd | 7 +- rvg-0.2.2/rvg/man/ph_with.dml.Rd | 12 +-- rvg-0.2.2/rvg/man/ph_with_vg.Rd | 29 +-------- rvg-0.2.2/rvg/tests/testthat/test-officer.R | 2 rvg-0.2.2/rvg/vignettes |only 15 files changed, 108 insertions(+), 140 deletions(-)
Title: Creates the MCC-F1 Curve and Calculates the MCC-F1 Metric and
the Best Threshold
Description: The MCC-F1 analysis is a method to evaluate the performance of binary classifications.
The MCC-F1 curve is more reliable than the Receiver Operating Characteristic (ROC) curve and the Precision-Recall (PR)curve under imbalanced ground truth.
The MCC-F1 analysis also provides the MCC-F1 metric that integrates classifier performance over varying thresholds, and the best threshold of binary classification.
Author: Chang Cao [aut, cre],
Michael Hoffman [aut],
Davide Chicco [aut]
Maintainer: Chang Cao <kirin.cao@mail.utoronto.ca>
Diff between mccf1 versions 1.0 dated 2018-08-13 and 1.1 dated 2019-11-11
mccf1-1.0/mccf1/man/plot.mccf1.Rd |only mccf1-1.1/mccf1/DESCRIPTION | 12 ++-- mccf1-1.1/mccf1/MD5 | 12 ++-- mccf1-1.1/mccf1/NAMESPACE | 11 ++-- mccf1-1.1/mccf1/R/mccf1.R | 85 ++++++++++++++++------------------ mccf1-1.1/mccf1/man/autoplot.mccf1.Rd |only mccf1-1.1/mccf1/man/mccf1.Rd | 26 ++++++---- mccf1-1.1/mccf1/man/summary.mccf1.Rd | 17 +++--- 8 files changed, 83 insertions(+), 80 deletions(-)
Title: Water Resources System Simulator
Description: Water resources system simulator is a tool for simulation and analysis of large-scale water resources systems. 'WRSS' proposes functions and methods for construction, simulation and analysis of primary storage and hydropower water resources features (e.g. reservoirs, aquifers, and etc.) based on Standard Operating Policy (SOP).
Author: Rezgar Arabzadeh; Parisa Aberi; Kaveh Panaghi; Shahab Araghinejad; Majid Montaseri
Maintainer: Rezgar Arabzadeh <rezgararabzadeh@ut.ac.ir>
Diff between WRSS versions 2.3 dated 2019-04-01 and 3.0 dated 2019-11-11
WRSS-2.3/WRSS/R/WRSS-internal.R |only WRSS-3.0/WRSS/DESCRIPTION | 8 +-- WRSS-3.0/WRSS/MD5 | 31 ++++++++---- WRSS-3.0/WRSS/NAMESPACE | 12 +++- WRSS-3.0/WRSS/R/GOF.R |only WRSS-3.0/WRSS/R/GOF.base.R |only WRSS-3.0/WRSS/R/GOF.default.R |only WRSS-3.0/WRSS/R/cap_design.R |only WRSS-3.0/WRSS/R/cap_design.base.R |only WRSS-3.0/WRSS/R/cap_design.default.R |only WRSS-3.0/WRSS/R/createReservoir.default.R | 66 ++++++++++++++++----------- WRSS-3.0/WRSS/R/reservoirRouting.R | 44 +++++++++++++++--- WRSS-3.0/WRSS/R/sim.base.R | 2 WRSS-3.0/WRSS/man/GOF.Rd |only WRSS-3.0/WRSS/man/GOF.base.Rd |only WRSS-3.0/WRSS/man/GOF.default.Rd |only WRSS-3.0/WRSS/man/WRSS-package.Rd | 21 ++++---- WRSS-3.0/WRSS/man/cap_design.Rd |only WRSS-3.0/WRSS/man/cap_design.base.Rd |only WRSS-3.0/WRSS/man/cap_design.default.Rd |only WRSS-3.0/WRSS/man/createReservoir.Rd | 1 WRSS-3.0/WRSS/man/createReservoir.base.Rd | 1 WRSS-3.0/WRSS/man/createReservoir.default.Rd | 1 23 files changed, 127 insertions(+), 60 deletions(-)
Title: Basic Functions to Check Readability, Consistency, and Content
of an Individual Participant Data File
Description: Basic checks to be carried out with an individual level participant data from randomised controlled trial. This
checks files for existence, read access and individual columns for formats. The checks on format is currently implemented for gender and age formats.
Author: Sheeja Manchira Krishnan
Maintainer: Sheeja Manchira Krishnan <sheejamk@gmail.com>
Diff between IPDFileCheck versions 0.4.0 dated 2019-10-15 and 0.5.0 dated 2019-11-11
DESCRIPTION | 15 MD5 | 71 - NAMESPACE | 61 - R/IPDdataFilecheck.R | 1610 ++++++++++++++--------------- R/globals.R | 2 build/vignette.rds |binary inst/doc/User_Guide.R | 189 +-- inst/doc/User_Guide.Rmd | 55 inst/doc/User_Guide.html | 630 +++++------ man/calculateAgeFromBirthYear.Rd | 48 man/calculateAgeFromDob.Rd | 54 man/checkColumnExists.Rd | 44 man/checkColumnNoForPatternInColumnname.Rd |only man/checkLoadPackages.Rd | 40 man/cohensD.Rd | 44 man/convertStdDateFormat.Rd | 48 man/descriptiveStatisticsDataColumn.Rd | 48 man/getColumnNoForNames.Rd | 44 man/getColumnNoForPatternInColumnname.Rd | 44 man/getConentdInCols.Rd | 44 man/getModeForVector.Rd | 40 man/getSEM.Rd | 40 man/presentMeanSdRemoveNAText.Rd | 48 man/representCategoricalData.Rd | 48 man/representCategoricalDataText.Rd | 48 man/returnSubgroupOmitNA.Rd | 48 man/testAge.Rd | 48 man/testColumnContents.Rd | 52 man/testDataColumnNames.Rd | 44 man/testDataNumeric.Rd | 56 - man/testDataNumericNorange.Rd | 48 man/testDataString.Rd | 48 man/testDataStringRestriction.Rd | 54 man/testFileExistenceReadability.Rd | 40 man/testGender.Rd | 52 tests/testthat/testthat.R | 1118 ++++++++++---------- vignettes/User_Guide.Rmd | 55 37 files changed, 2438 insertions(+), 2540 deletions(-)
Title: Average Bioequivalence with Expanding Limits (ABEL)
Description: Performs comparative bioavailability calculations for the EMA's Average Bioequivalence
with Expanding Limits (ABEL). Implemented are 'Method A' and 'Method B', detection of outliers.
If the design allows, assessment of the empiric Type I Error and iteratively adjusting alpha to
control the consumer risk.
Average Bioequivalence (ABE) - optionally with tighter (EMA: NTIDs) or wider limits (GCC: Cmax) -
is implemented as well.
Author: Helmut Schütz [aut, cre] (<https://orcid.org/0000-0002-1167-7880>),
Michael Tomashevskiy [ctb],
Detlew Labes [ctb] (<https://orcid.org/0000-0003-2169-426X>)
Maintainer: Helmut Schütz <helmut.schuetz@bebac.at>
Diff between replicateBE versions 1.0.11 dated 2019-08-25 and 1.0.12 dated 2019-11-11
DESCRIPTION | 10 MD5 | 20 NEWS.md | 21 - R/CV.calc.R | 9 README.md | 73 +++ build/partial.rdb |binary inst/doc/vignette.R | 49 +- inst/doc/vignette.Rmd | 351 +++++++++-------- inst/doc/vignette.html | 988 +++++++++++++++++++++---------------------------- vignettes/toparrow.png |only vignettes/vignette.Rmd | 351 +++++++++-------- vignettes/vignette.css |only 12 files changed, 939 insertions(+), 933 deletions(-)
Title: Manipulation of Microsoft Word and PowerPoint Documents
Description: Access and manipulate 'Microsoft Word' and 'Microsoft PowerPoint' documents from R.
The package focuses on tabular and graphical reporting from R; it also provides two functions
that let users get document content into data objects. A set of functions
lets add and remove images, tables and paragraphs of text in new or existing documents.
When working with 'PowerPoint' presentations, slides can be added or removed; shapes inside
slides can also be added or removed. When working with 'Word' documents, a cursor can be
used to help insert or delete content at a specific location in the document. The package
does not require any installation of Microsoft products to be able to write Microsoft files.
Author: David Gohel [aut, cre],
Frank Hangler [ctb] (function body_replace_all_text),
Liz Sander [ctb] (several documentation fixes),
Anton Victorson [ctb] (fixes xml structures),
Jon Calder [ctb] (update vignettes),
John Harrold [ctb] (fuction annotate_base),
John Muschelli [ctb] (google doc compatibility)
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between officer versions 0.3.5 dated 2019-06-23 and 0.3.6 dated 2019-11-11
officer-0.3.5/officer/R/ppt_ph_add.R |only officer-0.3.5/officer/inst/doc/officer_reader.R |only officer-0.3.5/officer/inst/doc/officer_reader.Rmd |only officer-0.3.5/officer/inst/doc/officer_reader.html |only officer-0.3.5/officer/inst/doc/powerpoint.R |only officer-0.3.5/officer/inst/doc/powerpoint.Rmd |only officer-0.3.5/officer/inst/doc/powerpoint.html |only officer-0.3.5/officer/inst/doc/word.R |only officer-0.3.5/officer/inst/doc/word.Rmd |only officer-0.3.5/officer/inst/doc/word.html |only officer-0.3.5/officer/man/stext.Rd |only officer-0.3.5/officer/vignettes/officer_reader.Rmd |only officer-0.3.5/officer/vignettes/powerpoint.Rmd |only officer-0.3.5/officer/vignettes/word.Rmd |only officer-0.3.6/officer/DESCRIPTION | 17 officer-0.3.6/officer/MD5 | 181 +- officer-0.3.6/officer/NAMESPACE | 16 officer-0.3.6/officer/NEWS | 21 officer-0.3.6/officer/R/block_list.R | 7 officer-0.3.6/officer/R/core_properties.R | 15 officer-0.3.6/officer/R/cot_objects.R | 62 officer-0.3.6/officer/R/docx_add.R | 7 officer-0.3.6/officer/R/docx_add_chunk.R | 36 officer-0.3.6/officer/R/docx_footnotes.R | 3 officer-0.3.6/officer/R/docx_img.R | 40 officer-0.3.6/officer/R/fortify_docx.R | 5 officer-0.3.6/officer/R/fortify_pptx.R | 21 officer-0.3.6/officer/R/fpar.R | 2 officer-0.3.6/officer/R/pack_folder.R | 7 officer-0.3.6/officer/R/ph_location.R | 323 +++-- officer-0.3.6/officer/R/ppt_classes.R | 11 officer-0.3.6/officer/R/ppt_ph_manipulate.R | 355 ++++- officer-0.3.6/officer/R/ppt_ph_with_methods.R | 636 +++------- officer-0.3.6/officer/R/pptx_informations.R |only officer-0.3.6/officer/R/pptx_slide_manip.R |only officer-0.3.6/officer/R/read_docx.R | 14 officer-0.3.6/officer/R/read_pptx.R | 401 ------ officer-0.3.6/officer/R/read_xlsx.R | 2 officer-0.3.6/officer/R/utils.R | 28 officer-0.3.6/officer/README.md | 8 officer-0.3.6/officer/build/vignette.rds |binary officer-0.3.6/officer/inst/doc/overview.Rmd |only officer-0.3.6/officer/inst/doc/overview.html |only officer-0.3.6/officer/inst/template/core.xml |only officer-0.3.6/officer/man/add_slide.Rd | 14 officer-0.3.6/officer/man/annotate_base.Rd | 20 officer-0.3.6/officer/man/block_list.Rd | 7 officer-0.3.6/officer/man/body_add_blocks.Rd | 3 officer-0.3.6/officer/man/body_add_toc.Rd | 4 officer-0.3.6/officer/man/color_scheme.Rd | 11 officer-0.3.6/officer/man/docx_summary.Rd | 6 officer-0.3.6/officer/man/external_img.Rd | 16 officer-0.3.6/officer/man/fortify_location.Rd |only officer-0.3.6/officer/man/fpar.Rd | 2 officer-0.3.6/officer/man/layout_properties.Rd | 11 officer-0.3.6/officer/man/layout_summary.Rd | 15 officer-0.3.6/officer/man/length.rpptx.Rd |only officer-0.3.6/officer/man/location_eval.Rd | 18 officer-0.3.6/officer/man/move_slide.Rd | 19 officer-0.3.6/officer/man/officer.Rd | 1 officer-0.3.6/officer/man/on_slide.Rd | 15 officer-0.3.6/officer/man/ph_add_fpar.Rd | 29 officer-0.3.6/officer/man/ph_add_par.Rd | 26 officer-0.3.6/officer/man/ph_add_text.Rd | 66 - officer-0.3.6/officer/man/ph_empty.Rd | 12 officer-0.3.6/officer/man/ph_from_xml.Rd | 2 officer-0.3.6/officer/man/ph_hyperlink.Rd | 29 officer-0.3.6/officer/man/ph_location.Rd | 33 officer-0.3.6/officer/man/ph_location_fullsize.Rd | 14 officer-0.3.6/officer/man/ph_location_label.Rd | 30 officer-0.3.6/officer/man/ph_location_left.Rd | 16 officer-0.3.6/officer/man/ph_location_right.Rd | 16 officer-0.3.6/officer/man/ph_location_template.Rd |only officer-0.3.6/officer/man/ph_location_type.Rd | 34 officer-0.3.6/officer/man/ph_remove.Rd | 53 officer-0.3.6/officer/man/ph_slidelink.Rd | 32 officer-0.3.6/officer/man/ph_with.Rd | 132 +- officer-0.3.6/officer/man/ph_with_fpars_at.Rd | 27 officer-0.3.6/officer/man/ph_with_gg.Rd | 21 officer-0.3.6/officer/man/ph_with_img.Rd | 26 officer-0.3.6/officer/man/ph_with_table.Rd | 22 officer-0.3.6/officer/man/ph_with_text.Rd | 29 officer-0.3.6/officer/man/ph_with_ul.Rd | 14 officer-0.3.6/officer/man/pptx_summary.Rd | 5 officer-0.3.6/officer/man/print.rpptx.Rd |only officer-0.3.6/officer/man/read_pptx.Rd | 48 officer-0.3.6/officer/man/remove_slide.Rd | 13 officer-0.3.6/officer/man/slide_size.Rd |only officer-0.3.6/officer/man/slide_summary.Rd | 30 officer-0.3.6/officer/man/slip_in_footnote.Rd | 3 officer-0.3.6/officer/man/slip_in_seqfield.Rd | 5 officer-0.3.6/officer/man/slip_in_text.Rd | 8 officer-0.3.6/officer/src/rpr.cpp | 2 officer-0.3.6/officer/tests/testthat/docs_dir/test_empty.pptx |only officer-0.3.6/officer/tests/testthat/test-block_list.R | 10 officer-0.3.6/officer/tests/testthat/test-doc-summary.R | 8 officer-0.3.6/officer/tests/testthat/test-docx-footnotes.R | 3 officer-0.3.6/officer/tests/testthat/test-docx-insert.R | 17 officer-0.3.6/officer/tests/testthat/test-fp-text.R | 6 officer-0.3.6/officer/tests/testthat/test-missing-tableStyles.R |only officer-0.3.6/officer/tests/testthat/test-pptx-add-at.R | 6 officer-0.3.6/officer/tests/testthat/test-pptx-add.R | 2 officer-0.3.6/officer/tests/testthat/test-pptx-misc.R | 2 officer-0.3.6/officer/tests/testthat/test-pptx-selections.R | 8 officer-0.3.6/officer/vignettes/overview.Rmd |only 105 files changed, 1589 insertions(+), 1630 deletions(-)
Title: An Extended Mixed-Effects Framework for Meta-Analysis
Description: A collection of functions to perform various meta-analytical models
through a unified mixed-effects framework, including standard univariate
fixed and random-effects meta-analysis and meta-regression, and non-standard
extensions such as multivariate, multilevel, longitudinal, and dose-response
models.
Author: Antonio Gasparrini [aut, cre],
Francesco Sera [aut]
Maintainer: Antonio Gasparrini <antonio.gasparrini@lshtm.ac.uk>
Diff between mixmeta versions 1.0.3 dated 2019-08-27 and 1.0.5 dated 2019-11-11
DESCRIPTION | 8 ++-- MD5 | 78 ++++++++++++++++++++++++------------------------ NEWS.md | 10 +++++- README.md | 4 +- inst/CITATION | 10 +++--- inst/NEWS | 10 +++++- man/alcohol.Rd | 2 - man/bcg.Rd | 2 - man/berkey98.Rd | 2 - man/blup.Rd | 2 - man/blup.mixmeta.Rd | 2 - man/dbs.Rd | 2 - man/fibrinogen.Rd | 2 - man/gliomas.Rd | 2 - man/hsls.Rd | 2 - man/hyp.Rd | 2 - man/inputna.Rd | 2 - man/logLik.mixmeta.Rd | 2 - man/mixmeta-package.Rd | 2 - man/mixmeta.Rd | 2 - man/mixmeta.control.Rd | 2 - man/mixmeta.fixed.Rd | 2 - man/mixmeta.ml.Rd | 2 - man/mixmeta.mm.Rd | 2 - man/mixmeta.vc.Rd | 2 - man/mixmetaCovStruct.Rd | 2 - man/mixmetaFormula.Rd | 2 - man/mixmetaObject.Rd | 2 - man/mixmetaSim.Rd | 2 - man/ml.igls.Rd | 2 - man/ml.loglik.fn.Rd | 2 - man/ml.newton.Rd | 2 - man/p53.Rd | 2 - man/predict.mixmeta.Rd | 2 - man/qtest.Rd | 2 - man/qtest.mixmeta.Rd | 2 - man/school.Rd | 2 - man/smoking.Rd | 2 - man/summary.mixmeta.Rd | 2 - man/thrombolytic.Rd | 2 - 40 files changed, 103 insertions(+), 85 deletions(-)
Title: Implementation of Multi Objective Decision Analysis
Description: Aides in the multi objective decision analysis process by simplifying
the creation of value hierarchy tree plots, calculating and plotting single and
multi attribute value function scores, and conducting sensitivity analysis. Linear,
exponential, and categorical single attribute value functions are supported. For
details see Parnell (2013, ISBN:978-1-118-17313-8) Kirkwood (1997, ISBN:0-534-51692-0).
Author: Josh Deehr [aut, cre],
Christopher Smith [aut],
Jason Freels [aut],
Emily Meyer [aut]
Maintainer: Josh Deehr <josh.deehr@gmail.com>
Diff between DecisionAnalysis versions 0.1.0 dated 2018-07-30 and 1.0.0 dated 2019-11-11
DESCRIPTION | 10 MD5 | 6 build/vignette.rds |binary inst/doc/MultiObjectiveDecisionAnalysisinR.html | 2859 ++++++++++++++++++++++-- 4 files changed, 2721 insertions(+), 154 deletions(-)
More information about DecisionAnalysis at CRAN
Permanent link
Title: Rank Preserving Structural Failure Time Models
Description: Implements methods described by the paper Robins and Tsiatis (1991) <DOI:10.1080/03610929108830654>. These use g-estimation to estimate the causal effect of a treatment in a two-armed randomised control trial where non-compliance exists and is measured, under an assumption of an accelerated failure time model and no unmeasured confounders.
Author: Simon Bond [aut, cre] (primary author of code, secondary author of
vignette),
Annabel Allison [aut] (primary author of vignette, secondary author of
code)
Maintainer: Simon Bond <simon.bond@addenbrookes.nhs.uk>
Diff between rpsftm versions 1.2.5 dated 2019-04-03 and 1.2.6 dated 2019-11-11
DESCRIPTION | 9 MD5 | 28 NAMESPACE | 1 NEWS.md | 6 R/cox.zph.R |only README.md | 28 build/vignette.rds |binary inst/doc/rpsftm_vignette.Rmd | 4 inst/doc/rpsftm_vignette.html | 563 ++++++---- man/cox.zph.Rd |only tests/testthat/test_rpsftm.R | 4 tools/README-unnamed-chunk-2-1.png |binary vignettes/rpsftm_vignette.Rmd | 4 vignettes/rpsftm_vignette_files/figure-html/unnamed-chunk-5-1.png |binary vignettes/rpsftm_vignette_files/figure-html/unnamed-chunk-7-1.png |binary vignettes/rpsftm_vignette_files/figure-html/unnamed-chunk-9-1.png |binary 16 files changed, 440 insertions(+), 207 deletions(-)
Title: Miscellaneous Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics
paradigm. Specialization of method ggplot(): accept and convert on the fly
time series data. Geom: "table", "plot" and "grob" add insets to plots
using native data coordinates, while "table_npc", "plot_npc" and "grob_npc"
do the same using "npc" coordinates through new aesthetics "npcx" and "npcy".
Statistics: locate and tag peaks and valleys; count observations in different
quadrants of a plot; select observations based on 2D density; label with the
equation of a polynomial fitted with lm() or other types of models; labels
with P-value, R^2 or adjusted R^2 or information criteria for fitted models;
label with ANOVA table for fitted models; label with summary for fitted
models. Model fit classes for which suitable methods are provided by package
'broom' are supported. Scales and stats to build volcano and quadrant plots
based on outcomes, fold changes, p-values and false discovery rates.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>),
Kamil Slowikowski [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggpmisc versions 0.3.1 dated 2019-04-02 and 0.3.2 dated 2019-11-11
ggpmisc-0.3.1/ggpmisc/R/renamed.R |only ggpmisc-0.3.1/ggpmisc/inst/CITATION |only ggpmisc-0.3.1/ggpmisc/man/renamed.Rd |only ggpmisc-0.3.2/ggpmisc/DESCRIPTION | 27 ggpmisc-0.3.2/ggpmisc/MD5 | 130 ggpmisc-0.3.2/ggpmisc/NAMESPACE | 21 ggpmisc-0.3.2/ggpmisc/NEWS | 37 ggpmisc-0.3.2/ggpmisc/R/example-data.R |only ggpmisc-0.3.2/ggpmisc/R/geom-grob.R | 2 ggpmisc-0.3.2/ggpmisc/R/geom-margin-arrow.r | 2 ggpmisc-0.3.2/ggpmisc/R/geom-margin-grob.r | 2 ggpmisc-0.3.2/ggpmisc/R/geom-margin-point.r | 3 ggpmisc-0.3.2/ggpmisc/R/geom-plot.R | 2 ggpmisc-0.3.2/ggpmisc/R/geom-quadrant-lines.R |only ggpmisc-0.3.2/ggpmisc/R/geom-table.R | 22 ggpmisc-0.3.2/ggpmisc/R/geom-text-npc.r | 7 ggpmisc-0.3.2/ggpmisc/R/on-attach.R | 4 ggpmisc-0.3.2/ggpmisc/R/outcome2factor.r |only ggpmisc-0.3.2/ggpmisc/R/scale-colour-outcome.r |only ggpmisc-0.3.2/ggpmisc/R/scale-continuous-Pvalue.r |only ggpmisc-0.3.2/ggpmisc/R/scale-continuous-logFC.r |only ggpmisc-0.3.2/ggpmisc/R/scale-shape-outcome.r |only ggpmisc-0.3.2/ggpmisc/R/stat-apply.R | 79 ggpmisc-0.3.2/ggpmisc/R/stat-dens2d-filter.r | 9 ggpmisc-0.3.2/ggpmisc/R/stat-dens2d-labels.r | 21 ggpmisc-0.3.2/ggpmisc/R/stat-fit-broom-tb.R | 129 ggpmisc-0.3.2/ggpmisc/R/stat-fit-broom.R | 398 ++ ggpmisc-0.3.2/ggpmisc/R/stat-fit-deviations.R | 47 ggpmisc-0.3.2/ggpmisc/R/stat-fit-residuals.R | 35 ggpmisc-0.3.2/ggpmisc/R/stat-peaks.R | 71 ggpmisc-0.3.2/ggpmisc/R/stat-poly-eq.R | 235 + ggpmisc-0.3.2/ggpmisc/R/stat-quadrant-counts.R | 84 ggpmisc-0.3.2/ggpmisc/README.md | 160 - ggpmisc-0.3.2/ggpmisc/build/vignette.rds |binary ggpmisc-0.3.2/ggpmisc/data |only ggpmisc-0.3.2/ggpmisc/inst/doc/user-guide.R | 122 ggpmisc-0.3.2/ggpmisc/inst/doc/user-guide.Rmd | 188 + ggpmisc-0.3.2/ggpmisc/inst/doc/user-guide.html | 1505 +++++----- ggpmisc-0.3.2/ggpmisc/man/FC_format.Rd |only ggpmisc-0.3.2/ggpmisc/man/FC_name.Rd |only ggpmisc-0.3.2/ggpmisc/man/figures/README-readme-03-1.png |binary ggpmisc-0.3.2/ggpmisc/man/figures/README-readme-04-1.png |binary ggpmisc-0.3.2/ggpmisc/man/figures/README-readme-05-1.png |binary ggpmisc-0.3.2/ggpmisc/man/figures/README-readme-06-1.png |binary ggpmisc-0.3.2/ggpmisc/man/figures/README-unnamed-chunk-1-1.png |only ggpmisc-0.3.2/ggpmisc/man/geom_grob.Rd | 5 ggpmisc-0.3.2/ggpmisc/man/geom_plot.Rd | 5 ggpmisc-0.3.2/ggpmisc/man/geom_quadrant_lines.Rd |only ggpmisc-0.3.2/ggpmisc/man/geom_table.Rd | 24 ggpmisc-0.3.2/ggpmisc/man/geom_text_npc.Rd | 6 ggpmisc-0.3.2/ggpmisc/man/geom_x_margin_arrow.Rd | 5 ggpmisc-0.3.2/ggpmisc/man/geom_x_margin_grob.Rd | 5 ggpmisc-0.3.2/ggpmisc/man/geom_x_margin_point.Rd | 5 ggpmisc-0.3.2/ggpmisc/man/ggpmisc-ggproto.Rd | 11 ggpmisc-0.3.2/ggpmisc/man/ggpmisc-package.Rd | 3 ggpmisc-0.3.2/ggpmisc/man/outcome2factor.Rd |only ggpmisc-0.3.2/ggpmisc/man/quadrant_example.df.Rd |only ggpmisc-0.3.2/ggpmisc/man/reverselog_trans.Rd |only ggpmisc-0.3.2/ggpmisc/man/scale_colour_outcome.Rd |only ggpmisc-0.3.2/ggpmisc/man/scale_shape_outcome.Rd |only ggpmisc-0.3.2/ggpmisc/man/scale_x_logFC.Rd |only ggpmisc-0.3.2/ggpmisc/man/scale_y_Pvalue.Rd |only ggpmisc-0.3.2/ggpmisc/man/stat_apply.Rd | 57 ggpmisc-0.3.2/ggpmisc/man/stat_dens2d_filter.Rd | 10 ggpmisc-0.3.2/ggpmisc/man/stat_dens2d_labels.Rd | 23 ggpmisc-0.3.2/ggpmisc/man/stat_fit_augment.Rd | 97 ggpmisc-0.3.2/ggpmisc/man/stat_fit_deviations.Rd | 50 ggpmisc-0.3.2/ggpmisc/man/stat_fit_glance.Rd | 130 ggpmisc-0.3.2/ggpmisc/man/stat_fit_residuals.Rd | 38 ggpmisc-0.3.2/ggpmisc/man/stat_fit_tb.Rd | 88 ggpmisc-0.3.2/ggpmisc/man/stat_fit_tidy.Rd | 85 ggpmisc-0.3.2/ggpmisc/man/stat_peaks.Rd | 31 ggpmisc-0.3.2/ggpmisc/man/stat_poly_eq.Rd | 112 ggpmisc-0.3.2/ggpmisc/man/stat_quadrant_counts.Rd | 73 ggpmisc-0.3.2/ggpmisc/man/symmetric_limits.Rd |only ggpmisc-0.3.2/ggpmisc/man/volcano_example.df.Rd |only ggpmisc-0.3.2/ggpmisc/man/xy_outcomes2factor.Rd |only ggpmisc-0.3.2/ggpmisc/vignettes/user-guide.Rmd | 188 + 78 files changed, 3089 insertions(+), 1304 deletions(-)
Title: Download Stats of R Packages
Description: Monthly download stats of 'CRAN' and 'Bioconductor' packages.
Download stats of 'CRAN' packages is from the 'RStudio' 'CRAN mirror', see <http://cranlogs.r-pkg.org>.
'Bioconductor' package download stats is at <https://bioconductor.org/packages/stats/>.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between dlstats versions 0.1.0 dated 2017-08-07 and 0.1.2 dated 2019-11-11
dlstats-0.1.0/dlstats/README.md |only dlstats-0.1.2/dlstats/DESCRIPTION | 12 dlstats-0.1.2/dlstats/MD5 | 31 +- dlstats-0.1.2/dlstats/R/bioc_stats.R | 25 +- dlstats-0.1.2/dlstats/R/cran_stats.R | 18 - dlstats-0.1.2/dlstats/R/plot_bioc_stats.R | 26 +- dlstats-0.1.2/dlstats/build/vignette.rds |binary dlstats-0.1.2/dlstats/inst/doc/dlstats.R | 19 - dlstats-0.1.2/dlstats/inst/doc/dlstats.Rmd | 32 +- dlstats-0.1.2/dlstats/inst/doc/dlstats.html | 328 ++++++++++++++------------- dlstats-0.1.2/dlstats/man/biocApp.Rd | 1 dlstats-0.1.2/dlstats/man/bioc_stats.Rd | 8 dlstats-0.1.2/dlstats/man/cranApp.Rd | 1 dlstats-0.1.2/dlstats/man/cran_stats.Rd | 8 dlstats-0.1.2/dlstats/man/plot_bioc_stats.Rd | 1 dlstats-0.1.2/dlstats/man/plot_cran_stats.Rd | 1 dlstats-0.1.2/dlstats/vignettes/dlstats.Rmd | 32 +- 17 files changed, 297 insertions(+), 246 deletions(-)
Title: Uncertainty Intervals and Sensitivity Analysis for Missing Data
Description: Implements functions to derive uncertainty intervals for (i) regression (linear and probit) parameters when outcome is missing not at random (non-ignorable missingness) introduced in Genbaeck, M., Stanghellini, E., de Luna, X. (2015) <doi:10.1007/s00362-014-0610-x> and Genbaeck, M., Ng, N., Stanghellini, E., de Luna, X. (2018) <doi:10.1007/s10433-017-0448-x>; and (ii) double robust and outcome regression estimators of average causal effects (on the treated) with possibly unobserved confounding introduced in Genbaeck, M., de Luna, X. (2018) <doi:10.1111/biom.13001>.
Author: Minna Genbaeck [aut, cre],
Maintainer: Minna Genbaeck <minna.genback@umu.se>
Diff between ui versions 0.1.0 dated 2019-06-19 and 0.1.1 dated 2019-11-11
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- NEWS.md |only R/ui.causal.R | 11 ++++++----- man/ui.causal.Rd | 2 +- 5 files changed, 14 insertions(+), 12 deletions(-)
Title: Stepwise Regression Analysis
Description: Stepwise regression analysis for variable selection can be used to get the best candidate final regression model in univariate or multivariate regression analysis with the 'forward', 'backward' and 'bidirection' steps. Besides, best subset selection is included in this package. Procedure can use Akaike information criterion, corrected Akaike information criterion, Bayesian information criterion, Hannan and Quinn information criterion, corrected Hannan and Quinn information criterion, Schwarz criterion and significance levels as selection criteria. Multicollinearity detection in regression model are performed by checking tolerance value. Continuous variables nested within class effect and weighted stepwise regression are also considered.
Author: Junhui Li,Xiaohuan Lu,Kun Cheng,Wenxin Liu
Maintainer: Junhui Li <junhuili@cau.edu.cn>
Diff between StepReg versions 1.3.1 dated 2019-10-29 and 1.3.2 dated 2019-11-11
DESCRIPTION | 6 +-- MD5 | 6 +-- R/stepwise.R | 86 +++++++++---------------------------------------- man/StepReg-package.Rd | 2 - 4 files changed, 24 insertions(+), 76 deletions(-)
Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 3.2.1 dated 2019-06-03 and 4.0.2 dated 2019-11-11
secr-3.2.1/secr/R/SPACECAP.R |only secr-3.2.1/secr/R/secrloglik.R |only secr-3.2.1/secr/man/SPACECAP.Rd |only secr-3.2.1/secr/src/detectfn.c |only secr-3.2.1/secr/src/init.c |only secr-3.2.1/secr/src/polygon.c |only secr-3.2.1/secr/src/secr.c |only secr-3.2.1/secr/src/sighting.c |only secr-3.2.1/secr/src/simsecr.c |only secr-3.2.1/secr/src/trapping.c |only secr-3.2.1/secr/src/unmarked.c |only secr-3.2.1/secr/src/utils.c |only secr-4.0.2/secr/DESCRIPTION | 13 secr-4.0.2/secr/MD5 | 270 +-- secr-4.0.2/secr/NAMESPACE | 42 secr-4.0.2/secr/NEWS | 50 secr-4.0.2/secr/R/DA.R | 1 secr-4.0.2/secr/R/Dsurface.R | 1 secr-4.0.2/secr/R/Fewstervarn.R | 2 secr-4.0.2/secr/R/LLsurface.secr.R | 17 secr-4.0.2/secr/R/RSE.R |only secr-4.0.2/secr/R/RcppExports.R |only secr-4.0.2/secr/R/Rsurface.R | 8 secr-4.0.2/secr/R/addCovariates.R | 3 secr-4.0.2/secr/R/addTelemetry.R | 243 +-- secr-4.0.2/secr/R/autoini.R | 202 -- secr-4.0.2/secr/R/confint.secr.R | 90 - secr-4.0.2/secr/R/derivedMS.R | 86 - secr-4.0.2/secr/R/empirical.R | 6 secr-4.0.2/secr/R/esa.R | 225 -- secr-4.0.2/secr/R/fastsecrloglik.R |only secr-4.0.2/secr/R/fxi.R | 730 ++++----- secr-4.0.2/secr/R/generalsecrloglik.R |only secr-4.0.2/secr/R/ip.secr.R | 5 secr-4.0.2/secr/R/join2.R | 22 secr-4.0.2/secr/R/loglikhelperfn.R |only secr-4.0.2/secr/R/make.capthist.R | 3 secr-4.0.2/secr/R/make.grid.R | 7 secr-4.0.2/secr/R/make.mask.R | 1 secr-4.0.2/secr/R/mask.check.R | 145 - secr-4.0.2/secr/R/methods.R | 363 +--- secr-4.0.2/secr/R/par.secr.fit.R | 6 secr-4.0.2/secr/R/pdot.R | 191 -- secr-4.0.2/secr/R/plot.popn.R | 18 secr-4.0.2/secr/R/plotMaskEdge.R | 37 secr-4.0.2/secr/R/pmixProfileLL.R | 11 secr-4.0.2/secr/R/preparedata.R |only secr-4.0.2/secr/R/randomHabitat.R | 2 secr-4.0.2/secr/R/regionN.R | 389 ++-- secr-4.0.2/secr/R/reparameterize.R |only secr-4.0.2/secr/R/score.test.R | 61 secr-4.0.2/secr/R/secr.design.MS.R | 13 secr-4.0.2/secr/R/secr.fit.R | 2102 +++++++++++++-------------- secr-4.0.2/secr/R/secr.test.R | 6 secr-4.0.2/secr/R/sim.capthist.R | 273 +-- secr-4.0.2/secr/R/sim.popn.R | 6 secr-4.0.2/secr/R/sim.secr.R | 363 ++-- secr-4.0.2/secr/R/suggest.buffer.R | 12 secr-4.0.2/secr/R/summary.capthist.R | 40 secr-4.0.2/secr/R/summary.secr.R | 2 secr-4.0.2/secr/R/summary.traps.R |only secr-4.0.2/secr/R/trap.builder.R | 26 secr-4.0.2/secr/R/utility.R | 419 ++--- secr-4.0.2/secr/R/verify.R | 87 - secr-4.0.2/secr/R/write.mask.R |only secr-4.0.2/secr/build/vignette.rds |binary secr-4.0.2/secr/data/OVpossum.RData |binary secr-4.0.2/secr/data/deermouse.RData |binary secr-4.0.2/secr/data/hornedlizard.RData |binary secr-4.0.2/secr/data/housemouse.RData |binary secr-4.0.2/secr/data/ovenbird.RData |binary secr-4.0.2/secr/data/ovensong.RData |binary secr-4.0.2/secr/data/possum.RData |binary secr-4.0.2/secr/data/secrdemo.RData |binary secr-4.0.2/secr/data/skink.RData |binary secr-4.0.2/secr/data/stoatDNA.RData |binary secr-4.0.2/secr/inst/doc/index.html | 230 ++ secr-4.0.2/secr/inst/doc/secr-datainput.Rmd | 28 secr-4.0.2/secr/inst/doc/secr-datainput.pdf |binary secr-4.0.2/secr/inst/doc/secr-overview.R | 2 secr-4.0.2/secr/inst/doc/secr-overview.Rmd | 176 +- secr-4.0.2/secr/inst/doc/secr-overview.pdf |binary secr-4.0.2/secr/man/CV.Rd | 18 secr-4.0.2/secr/man/DENSITY.Rd | 4 secr-4.0.2/secr/man/FAQ.Rd | 11 secr-4.0.2/secr/man/LLsurface.Rd | 2 secr-4.0.2/secr/man/PG.Rd | 6 secr-4.0.2/secr/man/Parallel.Rd | 176 -- secr-4.0.2/secr/man/RSE.Rd |only secr-4.0.2/secr/man/addTelemetry.Rd | 2 secr-4.0.2/secr/man/autoini.Rd | 7 secr-4.0.2/secr/man/closedN.Rd | 6 secr-4.0.2/secr/man/confint.secr.Rd | 5 secr-4.0.2/secr/man/coulombe.Rd | 18 secr-4.0.2/secr/man/deermouse.Rd | 31 secr-4.0.2/secr/man/derivedMS.Rd | 12 secr-4.0.2/secr/man/details.Rd | 14 secr-4.0.2/secr/man/discretize.Rd | 3 secr-4.0.2/secr/man/expected.n.Rd | 10 secr-4.0.2/secr/man/fx.total.Rd | 2 secr-4.0.2/secr/man/fxi.Rd | 36 secr-4.0.2/secr/man/hornedlizard.Rd | 2 secr-4.0.2/secr/man/make.systematic.Rd | 15 secr-4.0.2/secr/man/make.traps.Rd | 4 secr-4.0.2/secr/man/mask.check.Rd | 9 secr-4.0.2/secr/man/ovenbird.Rd | 27 secr-4.0.2/secr/man/ovensong.Rd | 8 secr-4.0.2/secr/man/par.secr.fit.Rd | 12 secr-4.0.2/secr/man/plot.capthist.Rd | 9 secr-4.0.2/secr/man/plot.popn.Rd | 4 secr-4.0.2/secr/man/plotmaskedge.Rd | 6 secr-4.0.2/secr/man/pmixProfileLL.Rd | 13 secr-4.0.2/secr/man/possum.Rd | 23 secr-4.0.2/secr/man/print.secr.Rd | 2 secr-4.0.2/secr/man/read.mask.Rd | 9 secr-4.0.2/secr/man/read.traps.Rd | 5 secr-4.0.2/secr/man/region.N.Rd | 8 secr-4.0.2/secr/man/score.test.Rd | 2 secr-4.0.2/secr/man/secr-package.Rd | 27 secr-4.0.2/secr/man/secr.fit.Rd | 41 secr-4.0.2/secr/man/secr.test.Rd | 4 secr-4.0.2/secr/man/secrRNG.Rd | 21 secr-4.0.2/secr/man/sim.secr.Rd | 18 secr-4.0.2/secr/man/snip.Rd | 4 secr-4.0.2/secr/man/stoatDNA.Rd | 28 secr-4.0.2/secr/man/subset.capthist.Rd | 2 secr-4.0.2/secr/man/suggest.buffer.Rd | 3 secr-4.0.2/secr/man/summary.capthist.Rd | 2 secr-4.0.2/secr/man/summary.popn.Rd |only secr-4.0.2/secr/man/trap.builder.Rd | 54 secr-4.0.2/secr/man/troubleshooting.Rd | 2 secr-4.0.2/secr/man/utility.Rd | 2 secr-4.0.2/secr/man/write.Rd | 9 secr-4.0.2/secr/src/Makevars |only secr-4.0.2/secr/src/Makevars.win |only secr-4.0.2/secr/src/RcppExports.cpp |only secr-4.0.2/secr/src/autoini.cpp |only secr-4.0.2/secr/src/detectfn.cpp |only secr-4.0.2/secr/src/getdenom.cpp |only secr-4.0.2/secr/src/geth.cpp |only secr-4.0.2/secr/src/makegk.cpp |only secr-4.0.2/secr/src/makegkpoly.cpp |only secr-4.0.2/secr/src/makelookup.cpp |only secr-4.0.2/secr/src/pdot.cpp |only secr-4.0.2/secr/src/polygon.cpp |only secr-4.0.2/secr/src/prwifastproximity.cpp |only secr-4.0.2/secr/src/prwipolygon.cpp |only secr-4.0.2/secr/src/prwisignal.cpp |only secr-4.0.2/secr/src/prwisimple.cpp |only secr-4.0.2/secr/src/prwisimplefxi.cpp |only secr-4.0.2/secr/src/secr.h | 1381 ++--------------- secr-4.0.2/secr/src/sighting.cpp |only secr-4.0.2/secr/src/sightingchat.cpp |only secr-4.0.2/secr/src/sightingexpectedmusk.cpp |only secr-4.0.2/secr/src/simsecr.cpp |only secr-4.0.2/secr/src/trapping.cpp |only secr-4.0.2/secr/src/utils.cpp |only secr-4.0.2/secr/vignettes/secr-datainput.Rmd | 28 secr-4.0.2/secr/vignettes/secr-overview.Rmd | 176 +- 159 files changed, 4057 insertions(+), 5301 deletions(-)
Title: Tools for Comparing Text Messages Across Time and Media
Description: A collection of tools for measuring the similarity of text messages and tracing the flow of messages over
time and across media.
Author: Kasper Welbers & Wouter van Atteveldt
Maintainer: Kasper Welbers <kasperwelbers@gmail.com>
Diff between RNewsflow versions 1.1.1 dated 2019-07-29 and 1.2.1 dated 2019-11-11
RNewsflow-1.1.1/RNewsflow/LICENSE |only RNewsflow-1.1.1/RNewsflow/R/compare.r |only RNewsflow-1.1.1/RNewsflow/R/quick_compare.r |only RNewsflow-1.2.1/RNewsflow/DESCRIPTION | 14 RNewsflow-1.2.1/RNewsflow/MD5 | 92 +-- RNewsflow-1.2.1/RNewsflow/NAMESPACE | 12 RNewsflow-1.2.1/RNewsflow/NEWS.md |only RNewsflow-1.2.1/RNewsflow/R/RcppExports.R | 4 RNewsflow-1.2.1/RNewsflow/R/compare_documents.r |only RNewsflow-1.2.1/RNewsflow/R/crossprod.r | 111 ++-- RNewsflow-1.2.1/RNewsflow/R/deduplicate.r |only RNewsflow-1.2.1/RNewsflow/R/deprecated.r |only RNewsflow-1.2.1/RNewsflow/R/dtm_functions.r | 4 RNewsflow-1.2.1/RNewsflow/R/feature_preparation.r | 90 +-- RNewsflow-1.2.1/RNewsflow/R/math.r | 2 RNewsflow-1.2.1/RNewsflow/R/networks.r | 274 +++++----- RNewsflow-1.2.1/RNewsflow/R/newsflow.r |only RNewsflow-1.2.1/RNewsflow/build/vignette.rds |binary RNewsflow-1.2.1/RNewsflow/inst/doc/RNewsflow.R | 139 ++--- RNewsflow-1.2.1/RNewsflow/inst/doc/RNewsflow.Rmd | 218 +++---- RNewsflow-1.2.1/RNewsflow/inst/doc/RNewsflow.html | 202 +++---- RNewsflow-1.2.1/RNewsflow/man/as_document_network.Rd |only RNewsflow-1.2.1/RNewsflow/man/compare_documents.Rd |only RNewsflow-1.2.1/RNewsflow/man/create_document_network.Rd |only RNewsflow-1.2.1/RNewsflow/man/create_queries.Rd | 59 +- RNewsflow-1.2.1/RNewsflow/man/delete.duplicates.Rd | 8 RNewsflow-1.2.1/RNewsflow/man/delete_duplicates.Rd |only RNewsflow-1.2.1/RNewsflow/man/directed.network.plot.Rd | 4 RNewsflow-1.2.1/RNewsflow/man/directed_network_plot.Rd |only RNewsflow-1.2.1/RNewsflow/man/document.network.Rd | 2 RNewsflow-1.2.1/RNewsflow/man/document.network.plot.Rd | 2 RNewsflow-1.2.1/RNewsflow/man/document_network_plot.Rd |only RNewsflow-1.2.1/RNewsflow/man/documents.compare.Rd | 14 RNewsflow-1.2.1/RNewsflow/man/filter.window.Rd | 4 RNewsflow-1.2.1/RNewsflow/man/filter_window.Rd |only RNewsflow-1.2.1/RNewsflow/man/network.aggregate.Rd | 2 RNewsflow-1.2.1/RNewsflow/man/network_aggregate.Rd |only RNewsflow-1.2.1/RNewsflow/man/newsflow.compare.Rd | 47 + RNewsflow-1.2.1/RNewsflow/man/newsflow_compare.Rd |only RNewsflow-1.2.1/RNewsflow/man/only.first.match.Rd | 2 RNewsflow-1.2.1/RNewsflow/man/only_first_match.Rd |only RNewsflow-1.2.1/RNewsflow/man/show.window.Rd | 2 RNewsflow-1.2.1/RNewsflow/man/show_window.Rd |only RNewsflow-1.2.1/RNewsflow/man/tcrossprod_sparse.Rd | 62 +- RNewsflow-1.2.1/RNewsflow/man/term.day.dist.Rd | 2 RNewsflow-1.2.1/RNewsflow/man/term_day_dist.Rd |only RNewsflow-1.2.1/RNewsflow/man/term_intersect.Rd | 10 RNewsflow-1.2.1/RNewsflow/man/term_union.Rd | 4 RNewsflow-1.2.1/RNewsflow/src/RcppExports.cpp | 12 RNewsflow-1.2.1/RNewsflow/src/crossprod.cpp | 124 +++- RNewsflow-1.2.1/RNewsflow/src/misc.cpp | 13 RNewsflow-1.2.1/RNewsflow/src/misc.h | 3 RNewsflow-1.2.1/RNewsflow/src/sim_measures.cpp | 50 + RNewsflow-1.2.1/RNewsflow/src/sim_measures.h | 7 RNewsflow-1.2.1/RNewsflow/tests/testthat/test_calculating_similarities.r | 22 RNewsflow-1.2.1/RNewsflow/tests/testthat/test_newsflow.r | 28 - RNewsflow-1.2.1/RNewsflow/vignettes/RNewsflow.Rmd | 218 +++---- 57 files changed, 1099 insertions(+), 764 deletions(-)
Title: Fast Likelihood Calculation for Phylogenetic Comparative Models
Description: Provides a C++ backend for multivariate phylogenetic comparative
models implemented in the R-package 'PCMBase'. Can be used in combination
with 'PCMBase' to enable fast and parallel likelihood calculation. Implements
the pruning likelihood calculation algorithm described in Mitov et al. (2018)
<arXiv:1809.09014>. Uses the 'SPLITT' C++ library for parallel tree traversal
described in Mitov and Stadler (2018) <doi:10.1111/2041-210X.13136>.
Author: Venelin Mitov [aut, cre, cph]
Maintainer: Venelin Mitov <vmitov@gmail.com>
Diff between PCMBaseCpp versions 0.1.5 dated 2019-10-06 and 0.1.6 dated 2019-11-11
DESCRIPTION | 6 +-- MD5 | 40 +++++++++++---------- NEWS.md |only R/BenchmarkRvsCpp.R | 40 +++++++++++++-------- R/Generic.R | 8 +++- README.md | 37 +++++++++++++++---- man/BenchmarkRvsCpp.Rd | 8 +++- man/MiniBenchmarkRvsCpp.Rd | 5 ++ src/Makevars | 6 +-- src/QuadraticPoly.h | 6 +-- src/QuadraticPolyBM.h | 4 +- src/QuadraticPolyBM1D.h | 2 - src/QuadraticPolyCommon.h | 58 +++++++++++++++++++++++++++++-- src/QuadraticPolyDOU.h | 4 +- src/QuadraticPolyJOU.h | 4 +- src/QuadraticPolyMixedGaussian.h | 2 - src/QuadraticPolyMixedGaussian1D.h | 2 - src/QuadraticPolyOU.h | 4 +- src/QuadraticPolyOU1D.h | 2 - src/QuadraticPolyWhite.h | 4 +- src/SPLITT.h | 69 ++++++++++++++++++++++++++++--------- tests/testthat/test-SingularV.R |only 22 files changed, 221 insertions(+), 90 deletions(-)
Title: High Dimensional Numerical and Symbolic Calculus
Description: Efficient C++ optimized functions for numerical and symbolic calculus. It includes basic symbolic arithmetic, tensor calculus, Einstein summing convention, fast computation of the Levi-Civita symbol and generalized Kronecker delta, Taylor series expansion, multivariate Hermite polynomials, accurate high-order derivatives, differential operators (Gradient, Jacobian, Hessian, Divergence, Curl, Laplacian) and Monte Carlo integration in arbitrary orthogonal coordinate systems: cartesian, polar, spherical, cylindrical, parabolic or user defined by custom scale factors.
Author: Emanuele Guidotti [aut, cre] (<https://orcid.org/0000-0002-8961-6623>)
Maintainer: Emanuele Guidotti <emanuele.guidotti@unine.ch>
Diff between calculus versions 0.1.0 dated 2019-11-07 and 0.1.1 dated 2019-11-11
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- README.md | 14 ++++++++++++-- src/calculus.cpp | 8 ++++---- 4 files changed, 25 insertions(+), 15 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-07-11 0.0-9
2012-07-25 0.0-8
2011-06-20 0.0-7
2011-06-15 0.0-6
2010-09-07 0.0-5
2010-04-29 0.0-3
Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance
Spectroscopy data.
Author: Martin Wilson [cre, aut],
John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Diff between spant versions 0.16.0 dated 2019-10-30 and 0.18.0 dated 2019-11-11
DESCRIPTION | 10 ++-- MD5 | 38 ++++++++++-------- NAMESPACE | 4 + NEWS.md | 7 +++ R/fit_display.R | 5 ++ R/fitting.R | 70 ++++++++++++++++++++++++++-------- R/image_reg.R | 71 +++++++++++++++++++++++++++++++++- R/interactive_plotting.R | 27 +++++++------ R/mrs_data_display.R | 22 ++++++++++ R/mrs_data_proc.R | 72 ++++++++++++++++++++++++++++++++++- R/spant.R | 4 + R/varpro_3_para.R | 5 ++ inst/doc/spant-intro.html | 6 +- man/fit_mrs.Rd | 6 -- man/get_mrsi2d_seg.Rd |only man/grid_shift_xy.Rd |only man/mask_xy.Rd |only man/mask_xy_mat.Rd |only man/plot_slice_fit_inter.Rd | 4 + man/resample_img.Rd | 4 + tests/testthat/fit_res_varpro.rds |binary tests/testthat/fit_res_varpro_3p.rds |binary 22 files changed, 293 insertions(+), 62 deletions(-)
Title: Analysis Of The Interpopulation Difference In Degree of Sexual
Dimorphism Using Summary Statistics
Description: Provides two approaches of comparison; the univariate and the multivariate analysis in two or more populations. Since the main obstacle of performing systematic comparisons in anthropological studies is the absence of raw data, the current package offer a solution for this problem by allowing the use of published summary statistics of metric data (mean, standard deviation and sex specific sample size) as illustrated by the works of Greene, D. L. (1989) <doi:10.1002/ajpa.1330790113> and Konigsberg, L. W. (1991) <doi:10.1002/ajpa.1330840110>.
Author: Bassam A. Abulnoor [aut, cre] (<https://orcid.org/0000-0003-4351-2754>),
MennattAllah H. Attia [aut] (<https://orcid.org/0000-0002-2304-532X>),
Lyle W. Konigsberg [ctb, dtc] (<https://orcid.org/0000-0003-4052-1575>)
Maintainer: Bassam A. Abulnoor <bas12@fayoum.edu.eg>
Diff between TestDimorph versions 0.2.0 dated 2019-07-19 and 0.2.1 dated 2019-11-11
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/Tg.R | 2 +- R/pMatrix.R | 2 +- build/partial.rdb |binary 6 files changed, 14 insertions(+), 10 deletions(-)
Title: Geometric Shadow Calculations
Description: Functions for calculating: (1) shadow height, (2) logical shadow flag, (3) shadow footprint, (4) Sky View Factor and (5) radiation load. Basic required inputs include a polygonal layer of obstacle outlines along with their heights (i.e. "extruded polygons"), sun azimuth and sun elevation. The package also provides functions for related preliminary calculations: breaking polygons into line segments, determining azimuth of line segments, shifting segments by azimuth and distance, constructing the footprint of a line-of-sight between an observer and the sun, and creating a 3D grid covering the surface area of extruded polygons.
Author: Michael Dorman [aut, cre],
Evyatar Erell [ctb],
Itai Kloog [ctb],
Adi Vulkan [ctb]
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>
Diff between shadow versions 0.6.2 dated 2019-09-07 and 0.6.3 dated 2019-11-11
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 7 +++++-- inst/doc/introduction.pdf |binary 4 files changed, 11 insertions(+), 8 deletions(-)
Title: Fit Projected 2D Profiles to Galaxy Images
Description: Get data / Define model / ??? / Profit! 'ProFit' is a Bayesian galaxy fitting tool that uses a fast 'C++' image generation library and a flexible interface to a large number of likelihood samplers.
Author: Aaron Robotham [aut, cre] (<https://orcid.org/0000-0003-0429-3579>),
Dan Taranu [aut] (<https://orcid.org/0000-0001-6268-1882>),
Rodrigo Tobar [aut] (<https://orcid.org/0000-0002-1052-0611>)
Maintainer: Aaron Robotham <aaron.robotham@uwa.edu.au>
Diff between ProFit versions 1.3.2 dated 2019-07-23 and 1.3.3 dated 2019-11-11
ProFit-1.3.2/ProFit/data/ExampleInit.tab.gz |only ProFit-1.3.2/ProFit/src/libprofit/profit |only ProFit-1.3.3/ProFit/DESCRIPTION | 8 +- ProFit-1.3.3/ProFit/MD5 | 25 +++--- ProFit-1.3.3/ProFit/build/partial.rdb |binary ProFit-1.3.3/ProFit/build/vignette.rds |binary ProFit-1.3.3/ProFit/configure | 4 - ProFit-1.3.3/ProFit/data/ExampleInit.tab |only ProFit-1.3.3/ProFit/inst/doc/ProFit-Galaxy-Fit-Example.html | 16 ++-- ProFit-1.3.3/ProFit/inst/doc/ProFit-Make-Model-Image.html | 36 +++++----- ProFit-1.3.3/ProFit/inst/doc/ProFit-OpenCL-OpenMP.html | 10 +- ProFit-1.3.3/ProFit/inst/doc/ProFit-PSF-Convolution-Can-Be-Convoluted.html | 10 +- ProFit-1.3.3/ProFit/inst/doc/ProFit-PSF-Fit-Example.html | 16 ++-- ProFit-1.3.3/ProFit/man/ProFit-package.Rd | 4 - ProFit-1.3.3/ProFit/src/libprofit/src/utils.cpp | 11 +-- 15 files changed, 81 insertions(+), 59 deletions(-)
Title: High-Dimensional Regression with Measurement Error
Description: Penalized regression for generalized linear models for
measurement error problems (aka. errors-in-variables). The package
contains a version of the lasso (L1-penalization) which corrects
for measurement error (Sorensen et al. (2015) <doi:10.5705/ss.2013.180>).
It also contains an implementation of the Generalized Matrix Uncertainty
Selector, which is a version the (Generalized) Dantzig Selector for the
case of measurement error (Sorensen et al. (2018) <doi:10.1080/10618600.2018.1425626>).
Author: Oystein Sorensen
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between hdme versions 0.3.1 dated 2019-05-20 and 0.3.2 dated 2019-11-11
DESCRIPTION | 10 MD5 | 31 +- NAMESPACE | 3 NEWS.md | 8 R/cv_corrected_lasso.R | 11 R/cv_gds.R |only R/gds.R | 2 R/helper_functions.R | 24 - R/loss_functions.R |only R/plot.cv_corrected_lasso.R | 24 - R/plot.cv_gds.R |only R/print_methods.R | 19 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/hdme.html | 577 ++++++++++++++++++++--------------------- man/cv_gds.Rd |only man/plot.cv_corrected_lasso.Rd | 4 man/plot.cv_gds.Rd |only man/print.cv_gds.Rd |only tests/testthat/test_cv_gds.R |only 20 files changed, 368 insertions(+), 345 deletions(-)
Title: Multistage Record Linkage and Case Definition for
Epidemiological Analysis
Description: Perform multistage deterministic linkages, apply case definitions to datasets, and deduplicate records.
Records (rows) from datasets are linked by different matching criteria and sub-criteria (columns) in a specified order of certainty.
The linkage process handles missing data and conflicting matches based on this same order of certainty.
For episode grouping, rows of dated events (e.g. sample collection) or interval of events (e.g. hospital admission) are
grouped into chronological episodes beginning with a "Case". The process permits several options such as
episode lengths and recurrence periods which are used to build custom preferences for case assignment (definition).
The record linkage and episode grouping processes assign unique group IDs to matching records or those grouped into episodes.
This then allows for record deduplication or sub-analysis within these groups.
Author: Olisaeloka Nsonwu
Maintainer: Olisaeloka Nsonwu <olisa.nsonwu@gmail.com>
Diff between diyar versions 0.0.1 dated 2019-10-06 and 0.0.2 dated 2019-11-11
DESCRIPTION | 18 MD5 | 54 - NAMESPACE | 8 NEWS.md | 27 R/classes.R |only R/episode_group.R | 551 ++++++++-------- R/number_line.R | 138 ---- R/overlap.R | 7 R/record_group.R | 137 ++-- R/to_s4.R |only README.md | 231 ++----- build/vignette.rds |binary data/patient_list_2.RData |binary inst/doc/episode_group.R | 568 ++++++----------- inst/doc/episode_group.Rmd | 696 ++++++++------------- inst/doc/episode_group.html | 1175 ++++++++++++++---------------------- inst/doc/record_group.R | 190 ++--- inst/doc/record_group.Rmd | 224 +++--- inst/doc/record_group.html | 572 ++++++++--------- man/epid-class.Rd |only man/episode_group.Rd | 253 +++---- man/number_line-class.Rd | 20 man/number_line.Rd | 13 man/pid-class.Rd |only man/record_group.Rd | 85 +- man/to_s4.Rd |only tests/testthat/test-episode_group.R | 171 ++--- tests/testthat/test-record_group.R | 34 - tests/testthat/test-to_s4.R |only vignettes/episode_group.Rmd | 696 ++++++++------------- vignettes/record_group.Rmd | 224 +++--- 31 files changed, 2606 insertions(+), 3486 deletions(-)
Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre],
RStudio [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between renv versions 0.8.2 dated 2019-10-26 and 0.8.3 dated 2019-11-11
renv-0.8.2/renv/R/renv.R |only renv-0.8.2/renv/tests/testthat/test-R.R |only renv-0.8.3/renv/DESCRIPTION | 6 renv-0.8.3/renv/MD5 | 103 ++++++----- renv-0.8.3/renv/NAMESPACE | 3 renv-0.8.3/renv/NEWS.md | 44 ++++ renv-0.8.3/renv/R/R.R | 29 +++ renv-0.8.3/renv/R/actions.R | 46 +++-- renv-0.8.3/renv/R/activate.R |only renv-0.8.3/renv/R/deactivate.R |only renv-0.8.3/renv/R/defer.R | 11 - renv-0.8.3/renv/R/dependencies.R | 82 ++++++--- renv-0.8.3/renv/R/diagnostics.R | 186 ++++++++++++++++++++- renv-0.8.3/renv/R/equip-macos.R |only renv-0.8.3/renv/R/equip.R | 4 renv-0.8.3/renv/R/exit-handlers.R |only renv-0.8.3/renv/R/hydrate.R | 21 +- renv-0.8.3/renv/R/imports.R | 4 renv-0.8.3/renv/R/install.R | 26 ++ renv-0.8.3/renv/R/load.R | 135 ++++++++++++++- renv-0.8.3/renv/R/packages.R | 20 +- renv-0.8.3/renv/R/path.R | 4 renv-0.8.3/renv/R/paths.R | 8 renv-0.8.3/renv/R/project.R | 57 +++++- renv-0.8.3/renv/R/python-conda.R | 8 renv-0.8.3/renv/R/rebuild.R | 2 renv-0.8.3/renv/R/remotes.R | 14 - renv-0.8.3/renv/R/renvignore.R | 10 - renv-0.8.3/renv/R/restore.R | 18 +- renv-0.8.3/renv/R/rtools.R |only renv-0.8.3/renv/R/scope.R | 87 +++++++++ renv-0.8.3/renv/R/snapshot.R | 21 +- renv-0.8.3/renv/R/unload.R |only renv-0.8.3/renv/R/update.R | 2 renv-0.8.3/renv/R/utils-format.R | 12 - renv-0.8.3/renv/R/utils.R | 11 - renv-0.8.3/renv/README.md | 3 renv-0.8.3/renv/inst/doc/renv.html | 4 renv-0.8.3/renv/man/activate.Rd | 2 renv-0.8.3/renv/man/deactivate.Rd | 2 renv-0.8.3/renv/man/dependencies.Rd | 17 + renv-0.8.3/renv/man/diagnostics.Rd |only renv-0.8.3/renv/man/load.Rd | 4 renv-0.8.3/renv/tests/testthat/helper-aaa.R | 14 + renv-0.8.3/renv/tests/testthat/test-actions.R | 8 renv-0.8.3/renv/tests/testthat/test-defer.R | 2 renv-0.8.3/renv/tests/testthat/test-dependencies.R | 24 ++ renv-0.8.3/renv/tests/testthat/test-diagnostics.R |only renv-0.8.3/renv/tests/testthat/test-install.R | 57 ++++++ renv-0.8.3/renv/tests/testthat/test-internal.R |only renv-0.8.3/renv/tests/testthat/test-load.R |only renv-0.8.3/renv/tests/testthat/test-r.R |only renv-0.8.3/renv/tests/testthat/test-records.R | 27 +++ renv-0.8.3/renv/tests/testthat/test-remotes.R | 2 renv-0.8.3/renv/tests/testthat/test-renvignore.R | 35 +++ renv-0.8.3/renv/tests/testthat/test-restore.R | 17 + renv-0.8.3/renv/tests/testthat/test-scope.R | 15 + renv-0.8.3/renv/tests/testthat/test-snapshot.R | 31 +++ renv-0.8.3/renv/tests/testthat/test-update.R | 2 59 files changed, 1029 insertions(+), 211 deletions(-)
Title: Non-Parametric Multiple Change-Point Analysis of Multivariate
Data
Description: Implements various procedures for finding
multiple change-points. Two methods make use of dynamic
programming and pruning, with no distributional
assumptions other than the existence of certain absolute
moments in one method. Hierarchical and exact search methods
are included. All methods return the set of estimated change-
points as well as other summary information.
Author: Nicholas A. James, Wenyu Zhang and David S. Matteson
Maintainer: Wenyu Zhang <wz258@cornell.edu>
Diff between ecp versions 3.1.1 dated 2019-03-18 and 3.1.2 dated 2019-11-11
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS | 7 +++++++ build/vignette.rds |binary inst/CITATION | 20 ++++++++++++++++---- man/e.agglo.Rd | 11 ++++++----- man/e.cp3o.Rd | 16 ++++++++-------- man/e.cp3o_delta.Rd | 16 ++++++++-------- man/e.divisive.Rd | 15 ++++++++------- man/ks.cp3o.Rd | 9 +++++---- man/ks.cp3o_delta.Rd | 9 +++++---- src/Makevars | 2 +- src/Makevars.win | 2 +- src/efast.cpp | 10 ++++------ src/energyChangePoint.cpp | 2 +- 15 files changed, 88 insertions(+), 67 deletions(-)
Title: Open Welfare Data Brazil
Description: Tools for collecting municipal-level data <http://www.transparencia.gov.br/swagger-ui.html> from several Brazilian governmental social programs.
Author: Joao Pedro Oliveira dos Santos [aut, cre]
(<https://orcid.org/0000-0003-1752-265X>)
Maintainer: Joao Pedro Oliveira dos Santos <joaopsantos@pm.me>
Diff between owdbr versions 1.0.1.0 dated 2019-06-20 and 1.0.1.1 dated 2019-11-11
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/uflist.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Compare Baseline Characteristics Between Groups
Description: Compare baseline characteristics between two or more groups. The variables being compared can be factor and numeric variables. The function will automatically judge the type and distribution of the variables, and make statistical description and bivariate analysis.
Author: Zhongheng Zhang,
Sir Run-Run Shaw hospital,
Zhejiang university school of medicine
Maintainer: Zhongheng Zhang <zh_zhang1984@zju.edu.cn>
Diff between CBCgrps versions 2.3 dated 2018-07-27 and 2.4 dated 2019-11-11
CBCgrps-2.3/CBCgrps/man/CBCgrps2.0-package.Rd |only CBCgrps-2.4/CBCgrps/DESCRIPTION | 8 +- CBCgrps-2.4/CBCgrps/MD5 | 12 +-- CBCgrps-2.4/CBCgrps/R/multigrps.R | 74 +++++++++++++++++--- CBCgrps-2.4/CBCgrps/R/twogrps.R | 93 ++++++++++++++++++++------ CBCgrps-2.4/CBCgrps/man/CBCgrps2.4-package.Rd |only CBCgrps-2.4/CBCgrps/man/multigrps.Rd | 26 +++++-- CBCgrps-2.4/CBCgrps/man/twogrps.Rd | 23 ++++-- 8 files changed, 181 insertions(+), 55 deletions(-)