Title: Robust Data-Driven Statistical Inference in
Regression-Discontinuity Designs
Description: Regression-discontinuity (RD) designs are quasi-experimental research designs popular in social, behavioral and natural sciences. The RD design is usually employed to study the (local) causal effect of a treatment, intervention or policy. This package provides tools for data-driven graphical and analytical statistical inference in RD designs: rdrobust() to construct local-polynomial point estimators and robust confidence intervals for average treatment effects at the cutoff in Sharp, Fuzzy and Kink RD settings, rdbwselect() to perform bandwidth selection for the different procedures implemented, and rdplot() to conduct exploratory data analysis (RD plots).
Author: Sebastian Calonico <scalonico@bus.miami.edu>, Matias D. Cattaneo <cattaneo@umich.edu>, Max H. Farrell <max.farrell@chicagobooth.edu>, Rocio Titiunik <titiunik@umich.edu>
Maintainer: Sebastian Calonico <scalonico@bus.miami.edu>
Diff between rdrobust versions 0.99.3 dated 2018-07-12 and 0.99.4 dated 2018-09-26
DESCRIPTION | 8 ++--- MD5 | 22 +++++++------- R/functions.R | 2 - R/rdbwselect.R | 24 ++++++--------- R/rdbwselect_2014.R | 2 - R/rdplot.R | 60 +++++++++++++++++++------------------- R/rdrobust.R | 73 ++++++++++++++++++++++------------------------- man/rdbwselect.Rd | 4 +- man/rdplot.Rd | 19 +++++++++--- man/rdrobust-package.Rd | 4 +- man/rdrobust.Rd | 4 +- man/rdrobust_RDsenate.Rd | 2 - 12 files changed, 114 insertions(+), 110 deletions(-)
Title: Access to the Neotoma Paleoecological Database Through R
Description: Access paleoecological datasets from the Neotoma Paleoecological
Database using the published API (<http://api.neotomadb.org/>). The functions
in this package access various pre-built API functions and attempt to return
the results from Neotoma in a usable format for researchers and the public.
Author: Simon J. Goring [aut, cre],
Gavin L. Simpson [aut],
Jeremiah P. Marsicek [ctb],
Karthik Ram [aut],
Luke Sosalla [ctb]
Maintainer: Simon J. Goring <goring@wisc.edu>
Diff between neotoma versions 1.7.0 dated 2017-06-21 and 1.7.2 dated 2018-09-26
DESCRIPTION | 20 ++- MD5 | 60 ++++++----- NAMESPACE | 4 NEWS | 8 + R/ages.R | 2 R/compile_downloads.R | 5 R/counts.R | 2 R/depths.R | 2 R/get_chroncontrol.R | 6 - R/get_dataset.R | 6 - R/get_download.R | 171 +++++++++++++++++---------------- R/get_site.R | 2 R/param_check.R | 5 R/read_methods.R | 26 ++--- R/taxa.R |only README.md | 2 man/ages.Rd | 2 man/compile_downloads.Rd | 2 man/compile_taxa.Rd | 3 man/counts.Rd | 2 man/depths.Rd | 2 man/download.Rd | 1 man/get_chroncontrol.dataset_list.Rd | 4 man/get_chroncontrol.download_list.Rd | 4 man/get_dataset.Rd | 4 man/get_dataset.default.Rd | 6 - man/get_download.Rd | 6 - man/get_site.Rd | 2 man/read.tilia.Rd | 7 - man/taxa.Rd |only man/write_agefile.Rd | 3 tests/testthat/test_neotoma.R | 172 ++++++++++++++++++++-------------- 32 files changed, 298 insertions(+), 243 deletions(-)
Title: Loading NONMEM Output Files and Simulate with Parameter
Uncertainty
Description: Loading NONMEM (NONlinear Mixed-Effect Modeling, <http://www.iconplc.com/innovation/solutions/nonmem/> ) output files and simulate with parameter uncertainty.
Author: Magnus Astrand
Maintainer: Magnus Astrand <magnus.astrand@astrazeneca.com>
Diff between nonmem2R versions 0.1.9 dated 2018-04-05 and 0.1.10 dated 2018-09-26
DESCRIPTION | 9 MD5 | 27 +- NAMESPACE | 19 + NEWS | 22 ++ R/LoadNonmemOutput.R | 69 ++++++ R/VPCs_ggplot.R | 483 ++++++++++++++++++++++++++++++++++++++++++--- R/qqnorm_geom.R |only inst/extdata/DV_matrix.csv |only inst/extdata/run001.lst | 41 +-- inst/extdata/run001.mod |only inst/extdata/sdtab |only man/StatQQVPC.Rd |only man/StatQQnorm.Rd |only man/modload.Rd |only man/print.modload.Rd |only man/stat_QQVPC.Rd |only man/stat_QQnorm.Rd |only man/sumoR.Rd | 2 man/vpcfig2.Rd | 16 - man/vpcfig3.Rd |only 20 files changed, 616 insertions(+), 72 deletions(-)
Title: Biodiversity Data Visualizations
Description: Provides a set of functions to create basic visualizations to quickly
preview different aspects of biodiversity information such as inventory
completeness, extent of coverage (taxonomic, temporal and geographic), gaps
and biases.
Author: Vijay Barve <vijay.barve@gmail.com>, Javier Otegui
<javier.otegui@gmail.com>
Maintainer: Vijay Barve <vijay.barve@gmail.com>
Diff between bdvis versions 0.2.20 dated 2018-02-12 and 0.2.22 dated 2018-09-26
DESCRIPTION | 12 ++++++------ MD5 | 30 +++++++++++++++--------------- NAMESPACE | 1 + NEWS | 3 ++- R/mapgrid.R | 15 ++++++++++----- man/bdcalendarheat.Rd | 1 + man/bdsummary.Rd | 1 + man/bdwebmap.Rd | 1 + man/chronohorogram.Rd | 1 + man/fixstr.Rd | 1 + man/format_bdvis.Rd | 1 + man/getcellid.Rd | 1 + man/gettaxo.Rd | 1 + man/mapgrid.Rd | 8 ++++++-- man/taxotree.Rd | 1 + man/tempolar.Rd | 1 + 16 files changed, 50 insertions(+), 29 deletions(-)
Title: Adjacency-Constrained Clustering of a Block-Diagonal Similarity
Matrix
Description: Implements a constrained version of hierarchical agglomerative
clustering, in which each observation is associated to a position, and
only adjacent clusters can be merged. Typical application fields in
bioinformatics include Genome-Wide Association Studies or Hi-C data
analysis, where the similarity between items is a decreasing function of
their genomic distance. Taking advantage of this feature, the implemented
algorithm is time and memory efficient. This algorithm is described in
Chapter 4 of Alia Dehman (2015)
<https://hal.archives-ouvertes.fr/tel-01288568v1>.
Author: Christophe Ambroise [aut],
Shubham Chaturvedi [aut],
Alia Dehman [aut],
Michel Koskas [aut],
Pierre Neuvial [aut, cre],
Guillem Rigaill [aut],
Nathalie Vialaneix [aut]
Maintainer: Pierre Neuvial <pierre.neuvial@math.univ-toulouse.fr>
Diff between adjclust versions 0.5.6 dated 2018-02-08 and 0.5.7 dated 2018-09-26
adjclust-0.5.6/adjclust/src/registerDynamicSymbol.c |only adjclust-0.5.7/adjclust/DESCRIPTION | 18 adjclust-0.5.7/adjclust/MD5 | 67 - adjclust-0.5.7/adjclust/NAMESPACE | 42 + adjclust-0.5.7/adjclust/NEWS.md | 12 adjclust-0.5.7/adjclust/R/adjclust.R | 138 ++- adjclust-0.5.7/adjclust/R/chac.R | 122 ++- adjclust-0.5.7/adjclust/R/helpers.R | 391 +++++++++- adjclust-0.5.7/adjclust/R/hicClust.R | 169 ++-- adjclust-0.5.7/adjclust/R/plotSim.R |only adjclust-0.5.7/adjclust/R/snpClust.R | 109 +- adjclust-0.5.7/adjclust/README.md | 32 adjclust-0.5.7/adjclust/build/vignette.rds |binary adjclust-0.5.7/adjclust/inst/doc/hicClust.R | 5 adjclust-0.5.7/adjclust/inst/doc/hicClust.Rmd | 12 adjclust-0.5.7/adjclust/inst/doc/hicClust.html | 83 +- adjclust-0.5.7/adjclust/inst/doc/notesCHAC.Rmd | 31 adjclust-0.5.7/adjclust/inst/doc/notesCHAC.html | 14 adjclust-0.5.7/adjclust/inst/doc/snpClust.html | 53 - adjclust-0.5.7/adjclust/inst/extdata/hic_imr90_40_XX.rda |binary adjclust-0.5.7/adjclust/inst/system/create_hic_chrXchrX.R | 12 adjclust-0.5.7/adjclust/man/adjClust.Rd | 1 adjclust-0.5.7/adjclust/man/chac.Rd | 6 adjclust-0.5.7/adjclust/man/figures/README-hicClust-1.png |binary adjclust-0.5.7/adjclust/man/figures/README-hicClust-2.png |binary adjclust-0.5.7/adjclust/man/figures/README-hicClust-3.png |only adjclust-0.5.7/adjclust/man/figures/README-snpClust-2.png |binary adjclust-0.5.7/adjclust/man/figures/README-snpClust-3.png |only adjclust-0.5.7/adjclust/man/hicClust.Rd | 25 adjclust-0.5.7/adjclust/man/plotSim.Rd |only adjclust-0.5.7/adjclust/man/select.Rd |only adjclust-0.5.7/adjclust/src/init.c |only adjclust-0.5.7/adjclust/tests/testthat/test_ascendingCompatibility.R | 6 adjclust-0.5.7/adjclust/tests/testthat/test_dense_sparse_comparison.R | 18 adjclust-0.5.7/adjclust/tests/testthat/test_hicClust.R | 18 adjclust-0.5.7/adjclust/tests/testthat/test_snpClust_NA-in-LD.R | 2 adjclust-0.5.7/adjclust/vignettes/hicClust.Rmd | 12 adjclust-0.5.7/adjclust/vignettes/notesCHAC.Rmd | 31 38 files changed, 1084 insertions(+), 345 deletions(-)
Title: Mixtures of von Mises-Fisher Distributions
Description: Fit and simulate mixtures of von Mises-Fisher distributions.
Author: Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>),
Bettina Grün [aut] (<https://orcid.org/0000-0001-7265-4773>)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between movMF versions 0.2-3 dated 2018-09-10 and 0.2-4 dated 2018-09-26
DESCRIPTION | 10 ++--- MD5 | 14 +++---- build/partial.rdb |binary inst/NEWS.Rd | 6 +++ inst/doc/movMF.Rnw | 22 +++++------ inst/doc/movMF.pdf |binary vignettes/movMF.Rnw | 22 +++++------ vignettes/vMF.bib | 99 ++++++++++++++++++++++++++++++++++++++++++++++++++-- 8 files changed, 137 insertions(+), 36 deletions(-)
Title: Statistical Trending for Medical Devices Surveillance
Description: A collection of common statistical algorithms used in active
surveillance of medical device events. Context includes post-market
surveillance, pharmacovigilance, signal detection and trending, and
regulatory reporting. Primary inputs are device-event time series. Outputs
include trending results with the ability to run multiple algorithms at
once. This package works well with the 'mds' package, but does not require
it.
Author: Gary Chung [aut, cre]
Maintainer: Gary Chung <gchung05@gmail.com>
Diff between mdsstat versions 0.1.0 dated 2018-06-10 and 0.2.0 dated 2018-09-26
DESCRIPTION | 10 - MD5 | 36 ++--- NAMESPACE | 2 NEWS.md | 22 ++- R/data.R | 4 R/dpa.R | 7 - R/qc.R | 12 - R/stats.R | 87 ++++++++++++- build/vignette.rds |binary inst/doc/mdsstat_intro.Rmd | 2 inst/doc/mdsstat_intro.html | 290 +++++++++++++++++++++++++++++++++++++------- man/maude.Rd | 4 man/poisson_rare.Rd | 5 man/prr.Rd | 3 man/run_algos.Rd | 30 ++++ man/shewhart.Rd | 4 tests/testthat/test_dpa.R | 12 - tests/testthat/test_stats.R | 24 +++ vignettes/mdsstat_intro.Rmd | 2 19 files changed, 454 insertions(+), 102 deletions(-)
Title: Medical Devices Surveillance
Description: A set of core functions for handling medical device event data in
the context of post-market surveillance, pharmacovigilance, signal detection
and trending, and regulatory reporting. Primary inputs are data on events by
device and data on exposures by device. Outputs include: standardized
device-event and exposure datasets, defined analyses, and time series.
Author: Gary Chung [aut, cre]
Maintainer: Gary Chung <gchung05@gmail.com>
Diff between mds versions 0.1.0 dated 2018-04-27 and 0.2.0 dated 2018-09-26
mds-0.1.0/mds/NEWS.md |only mds-0.1.0/mds/man/time_series.list.Rd |only mds-0.1.0/mds/man/time_series.mds_da.Rd |only mds-0.1.0/mds/man/time_series.mds_das.Rd |only mds-0.2.0/mds/DESCRIPTION | 8 mds-0.2.0/mds/MD5 | 46 +- mds-0.2.0/mds/R/data.R | 15 mds-0.2.0/mds/R/standardize_device_events.R | 46 ++ mds-0.2.0/mds/R/standardize_exposure.R | 33 + mds-0.2.0/mds/R/time_series.R | 119 ++---- mds-0.2.0/mds/R/utils.R | 6 mds-0.2.0/mds/README.md | 44 ++ mds-0.2.0/mds/build/vignette.rds |binary mds-0.2.0/mds/data/mds_ts.rda |only mds-0.2.0/mds/inst/doc/mds_intro.Rmd | 2 mds-0.2.0/mds/inst/doc/mds_intro.html | 508 +++++++++++++++++++--------- mds-0.2.0/mds/man/char_to_df.Rd | 1 mds-0.2.0/mds/man/convert_date.Rd | 1 mds-0.2.0/mds/man/deviceevent.Rd | 5 mds-0.2.0/mds/man/fNA.Rd | 1 mds-0.2.0/mds/man/input_param_checker.Rd | 1 mds-0.2.0/mds/man/maude.Rd | 4 mds-0.2.0/mds/man/mds_ts.Rd |only mds-0.2.0/mds/man/next_dev.Rd | 1 mds-0.2.0/mds/man/next_ev.Rd | 1 mds-0.2.0/mds/man/time_series.Rd | 104 +++++ mds-0.2.0/mds/vignettes/mds_intro.Rmd | 2 27 files changed, 673 insertions(+), 275 deletions(-)
Title: Continual Reassessment Method (CRM) for Phase I Clinical Trials
Description: Functions for phase I clinical trials using the continual reassessment method.
Author: Qianxing Mo
Maintainer: Qianxing Mo <qianxing.mo@moffitt.org>
Diff between CRM versions 1.1.1 dated 2012-03-01 and 1.2.4 dated 2018-09-26
DESCRIPTION | 13 +++++++------ MD5 | 15 ++++++++------- NAMESPACE | 3 ++- demo/00Index | 1 + demo/crmsim.R | 25 +++++++++++++------------ man/crm.Rd | 4 ++-- man/crmsim.Rd | 30 ++++++++++++++++-------------- src/CRM.c | 2 +- src/registerDynamicSymbol.c |only 9 files changed, 50 insertions(+), 43 deletions(-)
Title: Fast Generators and Iterators for Permutations, Combinations and
Partitions
Description: Fast generators and iterators for permutations, combinations
and partitions. The iterators allow users to generate arrangements in
a memory efficient manner and the generated arrangements are in
lexicographical (dictionary) order. Permutations and combinations can
be drawn with/without replacement and support multisets. It has been
demonstrated that 'arrangements' outperforms most of the existing
packages of similar kind. Some benchmarks could be found at
<https://randy3k.github.io/arrangements/articles/benchmark.html>.
Author: Randy Lai [aut, cre]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between arrangements versions 1.1.3 dated 2018-09-16 and 1.1.4 dated 2018-09-26
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/combinations.R | 2 +- R/partitions.R | 16 ++++++++-------- R/permutations.R | 2 +- man/ipartitions.Rd | 4 ++-- man/ncombinations.Rd | 2 +- man/npartitions.Rd | 2 +- man/npermutations.Rd | 2 +- man/partitions.Rd | 10 +++++----- src/partitions/k_partitions.h | 1 + src/partitions/ordinary_partitions.h | 1 + src/partitions/partitions_utils.h | 10 ++++++++-- 13 files changed, 46 insertions(+), 38 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, Austin Gratton, Wei Jing
Maintainer: Silvia Liverani <liveranis@gmail.com>
Diff between PReMiuM versions 3.2.0 dated 2018-06-15 and 3.2.1 dated 2018-09-26
PReMiuM-3.2.0/PReMiuM/tests/testthat.R |only PReMiuM-3.2.0/PReMiuM/tests/testthat/output_alpha.txt |only PReMiuM-3.2.0/PReMiuM/tests/testthat/output_alphaProp.txt |only PReMiuM-3.2.0/PReMiuM/tests/testthat/output_beta.txt |only PReMiuM-3.2.0/PReMiuM/tests/testthat/output_betaProp.txt |only PReMiuM-3.2.0/PReMiuM/tests/testthat/output_entropy.txt |only PReMiuM-3.2.0/PReMiuM/tests/testthat/output_input.txt |only PReMiuM-3.2.0/PReMiuM/tests/testthat/output_log.txt |only PReMiuM-3.2.0/PReMiuM/tests/testthat/output_logPost.txt |only PReMiuM-3.2.0/PReMiuM/tests/testthat/output_nClusters.txt |only PReMiuM-3.2.0/PReMiuM/tests/testthat/output_nMembers.txt |only PReMiuM-3.2.0/PReMiuM/tests/testthat/output_phi.txt |only PReMiuM-3.2.0/PReMiuM/tests/testthat/output_psi.txt |only PReMiuM-3.2.0/PReMiuM/tests/testthat/output_theta.txt |only PReMiuM-3.2.0/PReMiuM/tests/testthat/output_thetaProp.txt |only PReMiuM-3.2.0/PReMiuM/tests/testthat/output_z.txt |only PReMiuM-3.2.1/PReMiuM/ChangeLog | 8 PReMiuM-3.2.1/PReMiuM/DESCRIPTION | 10 PReMiuM-3.2.1/PReMiuM/MD5 | 48 -- PReMiuM-3.2.1/PReMiuM/NAMESPACE | 2 PReMiuM-3.2.1/PReMiuM/R/generateData.R | 8 PReMiuM-3.2.1/PReMiuM/R/postProcess.R | 5 PReMiuM-3.2.1/PReMiuM/inst/shapes |only PReMiuM-3.2.1/PReMiuM/man/profRegr.Rd | 19 PReMiuM-3.2.1/PReMiuM/src/PReMiuM.cpp | 15 PReMiuM-3.2.1/PReMiuM/src/include/PReMiuMIO.h | 3 PReMiuM-3.2.1/PReMiuM/src/include/PReMiuMModel.h | 3 PReMiuM-3.2.1/PReMiuM/src/include/PReMiuMOptions.h | 14 PReMiuM-3.2.1/PReMiuM/src/include/PReMiuMProposals.h | 299 ++++++++++++-- PReMiuM-3.2.1/PReMiuM/src/postProcess.cpp | 21 PReMiuM-3.2.1/PReMiuM/tests/test-basic1.R |only PReMiuM-3.2.1/PReMiuM/tests/testthat/test-calcAvgRisk.R | 9 PReMiuM-3.2.1/PReMiuM/tests/testthat/test-profRegr.R | 2 33 files changed, 372 insertions(+), 94 deletions(-)
Title: Depth Measures in Multivariate, Regression and Functional
Settings
Description: Tools to compute depth measures and implementations of related
tasks such as outlier detection, data exploration and
classification of multivariate, regression and functional data.
Author: Pieter Segaert [aut],
Mia Hubert [aut],
Peter Rousseeuw [aut],
Jakob Raymaekers [aut, cre],
Kaveh Vakili [ctb]
Maintainer: Jakob Raymaekers <jakob.raymaekers@kuleuven.be>
Diff between mrfDepth versions 1.0.8 dated 2018-07-07 and 1.0.9 dated 2018-09-26
DESCRIPTION | 21 +++++++++++---------- MD5 | 18 +++++++++--------- R/adjOutl.R | 6 ++++-- R/dirOutl.R | 6 ++++-- R/outlyingness.R | 5 ++++- inst/NEWS.Rd | 8 +++++++- man/adjOutl.Rd | 3 ++- man/dirOutl.Rd | 4 ++-- man/outlyingness.Rd | 2 +- src/Makevars.win | 3 +-- 10 files changed, 45 insertions(+), 31 deletions(-)
Title: Creation of Empirical Density Functions Based on Multivariate
Data
Description: Based on the input data an n-dimensional cube with sub cells of user specified side length is created.
The number of sample points which fall in each sub cube is counted, and with the cell volume and overall sample
size an empirical probability can be computed. A number of cubes of higher resolution can be superimposed. The
basic method stems from J.L. Bentley in "Multidimensional Divide and Conquer".
J. L. Bentley (1980) <doi:10.1145/358841.358850>.
Furthermore a simple kernel density estimation method is made available, as well as an expansion of Bentleys
method, which offers a kernel approach for the grid method.
Author: Martin Wiegand, Saralees Nadarajah
Maintainer: Martin Wiegand <Martin.Wiegand@manchester.ac.uk>
Diff between MEPDF versions 2.0 dated 2018-07-31 and 3.0 dated 2018-09-26
DESCRIPTION | 8 MD5 | 4 R/EPDF.R | 545 ++++++++++++++++++++++++++++++------------------------------ 3 files changed, 283 insertions(+), 274 deletions(-)
Title: Group Sequential Enrichment Design
Description: Provides function to apply "Group sequential enrichment design incorporating subgroup selection" (GSED) method proposed by Magnusson and Turnbull (2013) <doi:10.1002/sim.5738>.
Author: Marie-Karelle Riviere
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between GSED versions 1.8 dated 2018-08-22 and 1.9 dated 2018-09-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/GSED.R | 18 +++++++----------- man/GSED-package.Rd | 4 ++-- 4 files changed, 16 insertions(+), 20 deletions(-)
Title: Analytical Tool for Aquatic Respirometry
Description: Calculates metabolic rate of fish and other aquatic organisms measured using
an intermittent-flow respirometry approach. The tool is used to run a set of graphical
QC tests of raw respirometry data, correct it for background respiration and chamber
effect, filter and extract target values of absolute and mass-specific metabolic rate.
Experimental design should include background respiration tests and measuring of one
or more metabolic rate traits. The package allows a user to import raw respirometry
data obtained from 'AquaResp' (free software), 'AutoResp' ('LoligoSystems'), 'OxyView'
('PreSens'), 'Pyro Oxygen Logger' ('PyroScience') and 'Q-box Aqua' ('QubitSystems').
Author: Sergey Morozov [aut, cre],
R.J. Scott McCairns [aut, ths],
Federico Calboli [ctb],
Juha Merila [ths],
Stephen White [dtc],
Daniel Montgomery [dtc],
Laura Almodovar-Acevedo [dtc],
Niclas Kolm [dtc],
Alexander Kotrschal [dtc]
Maintainer: Sergey Morozov <sergey.morozov@helsinki.fi>
Diff between FishResp versions 1.0.0 dated 2018-09-24 and 1.0.1 dated 2018-09-26
FishResp |only 1 file changed
Title: Generalized Pairwise Comparisons
Description: Implementation of the Generalized Pairwise Comparisons. This test
enables to compare two groups of observations in randomized trials(e.g treated
vs. control patients) on several prioritized outcomes. Pairwise comparisons
require consideration of all possible pairs of individuals, one taken from the
treatment group and the other taken from the control group. The outcomes of the
two individuals forming a pair are compared. Thresholds of minimal clinically
significant differences can be defined. It is possible to analyze simultaneously
several outcomes by prioritizing the variables that capture them. The highest
priority is assigned to the variable considered the most clinically relevant.
A natural way of handling uninformative or neutral pairs is to consider the
outcomes in descending order of priority: whenever a pair is uninformative or
neutral for an outcome of higher priority, the outcomes of lower priority are
examined In the case of time-to-event endpoint, four methods to handle censored
observations are available in this package (Gehan, Peto, Efron, and Peron).
Author: Brice Ozenne [aut, cre] (<https://orcid.org/0000-0001-9694-2956>),
Julien Peron [aut]
Maintainer: Brice Ozenne <brice.ozenne@orange.fr>
Diff between BuyseTest versions 1.3.2 dated 2018-05-29 and 1.5.0 dated 2018-09-26
BuyseTest-1.3.2/BuyseTest/R/tableComparison.R |only BuyseTest-1.3.2/BuyseTest/man/BuyseTest_cpp.Rd |only BuyseTest-1.3.2/BuyseTest/tests/testthat/test-BuyseTest-table2Delta.R |only BuyseTest-1.5.0/BuyseTest/DESCRIPTION | 29 BuyseTest-1.5.0/BuyseTest/MD5 | 111 - BuyseTest-1.5.0/BuyseTest/NAMESPACE | 5 BuyseTest-1.5.0/BuyseTest/NEWS | 18 BuyseTest-1.5.0/BuyseTest/R/1-setGeneric.R | 20 BuyseTest-1.5.0/BuyseTest/R/BuyseRes-confint.R | 37 BuyseTest-1.5.0/BuyseTest/R/BuyseRes-object.R | 28 BuyseTest-1.5.0/BuyseTest/R/BuyseRes-summary.R | 28 BuyseTest-1.5.0/BuyseTest/R/BuyseRes_get.R | 312 +++ BuyseTest-1.5.0/BuyseTest/R/BuyseTest-check.R | 85 BuyseTest-1.5.0/BuyseTest/R/BuyseTest-inference.R | 43 BuyseTest-1.5.0/BuyseTest/R/BuyseTest-initialization.R | 438 ++-- BuyseTest-1.5.0/BuyseTest/R/BuyseTest-print.R | 23 BuyseTest-1.5.0/BuyseTest/R/BuyseTest.R | 340 +-- BuyseTest-1.5.0/BuyseTest/R/BuyseTest.options-object.R | 119 - BuyseTest-1.5.0/BuyseTest/R/BuyseTest.options.R | 6 BuyseTest-1.5.0/BuyseTest/R/PairScore.R |only BuyseTest-1.5.0/BuyseTest/R/RcppExports.R | 47 BuyseTest-1.5.0/BuyseTest/R/discreteRoot.R |only BuyseTest-1.5.0/BuyseTest/R/examples/EX_BuyseTest.R | 84 BuyseTest-1.5.0/BuyseTest/R/simBuyseTest.R | 6 BuyseTest-1.5.0/BuyseTest/build |only BuyseTest-1.5.0/BuyseTest/inst/CITATION | 62 BuyseTest-1.5.0/BuyseTest/inst/CR |only BuyseTest-1.5.0/BuyseTest/inst/M2-project |only BuyseTest-1.5.0/BuyseTest/inst/README-save.org |only BuyseTest-1.5.0/BuyseTest/inst/doc |only BuyseTest-1.5.0/BuyseTest/man/BuyseRes-confint.Rd | 4 BuyseTest-1.5.0/BuyseTest/man/BuyseRes-getCount.Rd | 6 BuyseTest-1.5.0/BuyseTest/man/BuyseRes-getPairScore.Rd |only BuyseTest-1.5.0/BuyseTest/man/BuyseRes-getSurvival.Rd |only BuyseTest-1.5.0/BuyseTest/man/BuyseRes-summary.Rd | 2 BuyseTest-1.5.0/BuyseTest/man/BuyseTest.Rd | 66 BuyseTest-1.5.0/BuyseTest/man/GPC_cpp.Rd |only BuyseTest-1.5.0/BuyseTest/man/boot2pvalue.Rd |only BuyseTest-1.5.0/BuyseTest/man/calcIntegralProba_cpp.Rd |only BuyseTest-1.5.0/BuyseTest/man/dicreteRoot.Rd |only BuyseTest-1.5.0/BuyseTest/man/internal-initialization.Rd | 20 BuyseTest-1.5.0/BuyseTest/man/testArgs.Rd | 4 BuyseTest-1.5.0/BuyseTest/src/FCT_buyseTest.cpp | 310 +-- BuyseTest-1.5.0/BuyseTest/src/FCT_calcAllPairs.h | 999 ++++++---- BuyseTest-1.5.0/BuyseTest/src/FCT_calcOnePair.h | 919 ++++----- BuyseTest-1.5.0/BuyseTest/src/FCT_calcStatistic.h | 28 BuyseTest-1.5.0/BuyseTest/src/RcppExports.cpp | 39 BuyseTest-1.5.0/BuyseTest/tests/testthat/test-BuyseTest-CR.R |only BuyseTest-1.5.0/BuyseTest/tests/testthat/test-BuyseTest-PairScore.R |only BuyseTest-1.5.0/BuyseTest/tests/testthat/test-BuyseTest-Pairs.R | 126 - BuyseTest-1.5.0/BuyseTest/tests/testthat/test-BuyseTest-checkValues.R | 105 - BuyseTest-1.5.0/BuyseTest/tests/testthat/test-BuyseTest-correctionTTE.R | 120 - BuyseTest-1.5.0/BuyseTest/tests/testthat/test-BuyseTest-neutralAsUnif.R | 7 BuyseTest-1.5.0/BuyseTest/tests/testthat/test-BuyseTest-operator.R | 8 BuyseTest-1.5.0/BuyseTest/tests/testthat/test-BuyseTest-previousBug.R | 315 +-- BuyseTest-1.5.0/BuyseTest/tests/testthat/test-BuyseTest-resampling.R | 236 -- BuyseTest-1.5.0/BuyseTest/tests/testthat/test-initSurvival.R | 493 +--- BuyseTest-1.5.0/BuyseTest/tests/testthat/test-initThreshold.R | 27 BuyseTest-1.5.0/BuyseTest/tests/testthat/test-otherPackages.R |only BuyseTest-1.5.0/BuyseTest/vignettes |only 60 files changed, 2970 insertions(+), 2705 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-07-26 1.0
Title: Interface to the 'CDK' Libraries
Description: Allows the user to access functionality in the
'CDK', a Java framework for chemoinformatics. This allows the user to load
molecules, evaluate fingerprints, calculate molecular descriptors and so on.
In addition, the 'CDK' API allows the user to view structures in 2D.
Author: Rajarshi Guha [aut, cph],
Zachary Charlop-Powers [cre],
Emma Schymanski [ctb]
Maintainer: ORPHANED
Diff between rcdk versions 3.4.7 dated 2018-04-30 and 3.4.7.1 dated 2018-09-26
DESCRIPTION | 12 ++++++++---- MD5 | 4 ++-- R/rcdk.R | 14 +++++++++----- 3 files changed, 19 insertions(+), 11 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-09-11 1.2.1
2014-01-13 1.2
2013-08-29 1.1