Title: Modeling, Analysis, Validation and Visualization of Observer
Performance Studies in Diagnostic Radiology
Description: Tools for quantitative assessment of medical imaging systems, radiologists or computer aided ('CAD') algorithms. Implements methods described in a book: 'Chakraborty' 'DP' (2017), "Observer Performance Methods for Diagnostic Imaging - Foundations, Modeling, and Applications with R-Based Examples", Taylor-Francis <https://www.crcpress.com/9781482214840> and its Online Appendices <https://github.com/dpc10ster/onlinebookk21778>. Data collection paradigms include receiver operating characteristic ('ROC') and its location specific extensions, primarily free-response 'ROC' ('FROC'). 'ROC' data consists of a single rating per image, where the rating is the perceived confidence level the image is of a diseased patient. 'FROC' data consists of a variable number (including zero) of mark-rating pairs per image, where a mark is the location of a clinically reportable suspicious region and the rating is the corresponding confidence level that it is a true lesion. The software supersedes the current Windows version of 'JAFROC' software <http://www.devchakraborty.com>. 'RJafroc' is derived from it being an enhanced R version of original Windows 'JAFROC'. Implemented are a number of figures of merit quantifying performance, functions for visualizing operating characteristics; three ROC ratings data curve-fitting algorithms: the 'binormal' model ('BM'), the contaminated binormal model ('CBM') and the radiological search model ('RSM'). Unlike the 'BM', the 'CBM' and the 'RSM' predict proper ROC curves that do not cross the chance diagonal or display inappropriate hooks near the upper right corner of the plots. 'RSM' fitting additionally yields measures of search and lesion-classification performances, in addition to the usual case-classification performance measured by the area under the 'ROC' curve. Search performance is the ability to find lesions while avoiding finding non-lesions. Lesion-classification performance is the ability to discriminate between found lesions and non-lesions. For fully crossed study designs, termed multiple-reader multiple-case, significance testing of reader-averaged figure-of-merit differences between modalities is implemented via both 'Dorfman', 'Berbaum' and 'Metz' ('DBM') and the 'Obuchowski' and 'Rockette' ('OR') methods. Single treatment analysis allows comparison of performance of a group of radiologists to a specified value, or comparison of 'CAD' performance to a group of radiologists interpreting the same cases. Sample size estimation tools are provided for 'ROC' and 'FROC' studies that allow estimation of relevant variances from a pilot study to predict required numbers of readers and cases in a pivotal study. Utility and data file manipulation functions allow data to be read in any of the currently used input formats, including Excel, and the results of the analysis can be viewed in text or Excel output files. 'RJafroc' is used extensively in the cited book and its online appendices.
Author: Dev Chakraborty [cre, aut, cph],
Xuetong Zhai [aut],
Lucy D'Agostino McGowan [ctb],
Alejandro RodriguezRuiz [ctb]
Maintainer: Dev Chakraborty <dpc10ster@gmail.com>
Diff between RJafroc versions 1.0.1 dated 2018-02-18 and 1.0.2 dated 2018-05-31
RJafroc-1.0.1/RJafroc/inst/doc |only RJafroc-1.0.1/RJafroc/man/SsFROCPowerGivenJK.Rd |only RJafroc-1.0.2/RJafroc/DESCRIPTION | 21 RJafroc-1.0.2/RJafroc/MD5 | 43 - RJafroc-1.0.2/RJafroc/NAMESPACE | 1 RJafroc-1.0.2/RJafroc/NEWS.md | 9 RJafroc-1.0.2/RJafroc/R/DfExtractDataset.R | 53 +- RJafroc-1.0.2/RJafroc/R/DfReadDataFile.R | 2 RJafroc-1.0.2/RJafroc/R/DfSaveDataFile.R | 4 RJafroc-1.0.2/RJafroc/R/PlotRsmOperatingCharacteristics.R | 5 RJafroc-1.0.2/RJafroc/R/SsFROCPowerGivenJK.R | 234 +++++----- RJafroc-1.0.2/RJafroc/R/SsPowerTable.R | 2 RJafroc-1.0.2/RJafroc/R/SsSampleSizeKGivenJ.R | 2 RJafroc-1.0.2/RJafroc/R/StSignificanceTestingCadVsRadiologists.R | 49 +- RJafroc-1.0.2/RJafroc/R/StSignificanceTestingCrossedModalities.R | 4 RJafroc-1.0.2/RJafroc/man/DfExtractDataset.Rd | 8 RJafroc-1.0.2/RJafroc/man/DfReadDataFile.Rd | 2 RJafroc-1.0.2/RJafroc/man/DfSaveDataFile.Rd | 4 RJafroc-1.0.2/RJafroc/man/RJafroc-package.Rd | 10 RJafroc-1.0.2/RJafroc/man/SsPowerTable.Rd | 2 RJafroc-1.0.2/RJafroc/man/SsSampleSizeKGivenJ.Rd | 2 RJafroc-1.0.2/RJafroc/man/StSignificanceTestingCadVsRadiologists.Rd | 24 - RJafroc-1.0.2/RJafroc/man/StSignificanceTestingCrossedModalities.Rd | 2 23 files changed, 278 insertions(+), 205 deletions(-)
Title: R Bindings to 'hiredis'
Description: A 'hiredis' wrapper that includes support for
transactions, pipelining, blocking subscription, serialisation of
all keys and values, 'Redis' error handling with R errors.
Includes an automatically generated 'R6' interface to the full
'hiredis' 'API'. Generated functions are faithful to the
'hiredis' documentation while attempting to match R's argument
semantics. Serialisation must be explicitly done by the user, but
both binary and text-mode serialisation is supported.
Author: Rich FitzJohn [aut, cre]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Diff between redux versions 1.0.0 dated 2017-05-15 and 1.1.0 dated 2018-05-31
redux-1.0.0/redux/inst/doc/low_level.Rmd |only redux-1.0.0/redux/inst/doc/low_level.html |only redux-1.0.0/redux/vignettes/low_level.Rmd |only redux-1.1.0/redux/DESCRIPTION | 15 - redux-1.1.0/redux/MD5 | 91 +++++----- redux-1.1.0/redux/NAMESPACE | 2 redux-1.1.0/redux/NEWS.md |only redux-1.1.0/redux/R/connection.R | 6 redux-1.1.0/redux/R/hiredis.R | 28 ++- redux-1.1.0/redux/R/redis_api.R | 10 - redux-1.1.0/redux/R/storr.R |only redux-1.1.0/redux/R/util.R | 4 redux-1.1.0/redux/R/util_assert.R | 6 redux-1.1.0/redux/R/zzz.R | 2 redux-1.1.0/redux/README.md | 27 ++ redux-1.1.0/redux/build/vignette.rds |binary redux-1.1.0/redux/configure | 2 redux-1.1.0/redux/inst/doc/redux.Rmd | 72 +++---- redux-1.1.0/redux/inst/doc/redux.html | 74 ++++---- redux-1.1.0/redux/man/hiredis.Rd | 31 +++ redux-1.1.0/redux/man/redis.Rd | 2 redux-1.1.0/redux/man/redis_connection.Rd | 6 redux-1.1.0/redux/man/storr_redis_api.Rd |only redux-1.1.0/redux/src/conversions.c | 2 redux-1.1.0/redux/src/subscribe.c | 5 redux-1.1.0/redux/tests/testthat/helper-common.R | 19 +- redux-1.1.0/redux/tests/testthat/helper-publisher.R | 4 redux-1.1.0/redux/tests/testthat/helper-redux.R | 3 redux-1.1.0/redux/tests/testthat/test-aaa.R | 3 redux-1.1.0/redux/tests/testthat/test-conversions.R | 12 - redux-1.1.0/redux/tests/testthat/test-interface.R | 24 +- redux-1.1.0/redux/tests/testthat/test-print.R | 3 redux-1.1.0/redux/tests/testthat/test-redis-commands.R | 7 redux-1.1.0/redux/tests/testthat/test-redis-socket.R | 1 redux-1.1.0/redux/tests/testthat/test-redis.R | 19 +- redux-1.1.0/redux/tests/testthat/test-scan.R | 15 - redux-1.1.0/redux/tests/testthat/test-storr.R |only redux-1.1.0/redux/tests/testthat/test-tools.R | 24 +- redux-1.1.0/redux/tests/testthat/test-util.R | 9 redux-1.1.0/redux/tests/testthat/test-zzz-commands-generic.R | 44 ++-- redux-1.1.0/redux/tests/testthat/test-zzz-commands-geo.R | 12 - redux-1.1.0/redux/tests/testthat/test-zzz-commands-hash.R | 28 +-- redux-1.1.0/redux/tests/testthat/test-zzz-commands-hyperloglog.R | 6 redux-1.1.0/redux/tests/testthat/test-zzz-commands-list.R | 34 +-- redux-1.1.0/redux/tests/testthat/test-zzz-commands-scripting.R | 5 redux-1.1.0/redux/tests/testthat/test-zzz-commands-set.R | 34 +-- redux-1.1.0/redux/tests/testthat/test-zzz-commands-sorted-set.R | 40 ++-- redux-1.1.0/redux/tests/testthat/test-zzz-commands-string.R | 50 ++--- redux-1.1.0/redux/tests/testthat/test-zzz-subscribe.R | 10 - redux-1.1.0/redux/vignettes/redux.Rmd | 72 +++---- 50 files changed, 487 insertions(+), 376 deletions(-)
Title: Multivariate Normal and t Distributions
Description: Computes multivariate normal and t probabilities, quantiles,
random deviates and densities.
Author: Alan Genz [aut],
Frank Bretz [aut],
Tetsuhisa Miwa [aut],
Xuefei Mi [aut],
Friedrich Leisch [ctb],
Fabian Scheipl [ctb],
Bjoern Bornkamp [ctb],
Martin Maechler [ctb],
Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mvtnorm versions 1.0-7 dated 2018-01-25 and 1.0-8 dated 2018-05-31
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/mvt.R | 8 ++++++-- inst/NEWS | 7 +++++++ inst/doc/MVT_Rnews.pdf |binary man/qmvnorm.Rd | 8 +++++++- man/qmvt.Rd | 8 +++++++- 7 files changed, 38 insertions(+), 15 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-20 1.0
Title: Simple Key Value Stores
Description: Creates and manages simple key-value stores. These can
use a variety of approaches for storing the data. This package
implements the base methods and support for file system, in-memory
and DBI-based database stores.
Author: Rich FitzJohn [aut, cre]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Diff between storr versions 1.1.3 dated 2017-12-15 and 1.2.0 dated 2018-05-31
storr-1.1.3/storr/vignettes/src |only storr-1.2.0/storr/DESCRIPTION | 11 storr-1.2.0/storr/MD5 | 94 +++--- storr-1.2.0/storr/NAMESPACE | 2 storr-1.2.0/storr/NEWS.md | 7 storr-1.2.0/storr/R/base64.R | 17 + storr-1.2.0/storr/R/defunct.R | 1 storr-1.2.0/storr/R/driver_dbi.R | 49 ++- storr-1.2.0/storr/R/driver_environment.R | 8 storr-1.2.0/storr/R/driver_external.R | 4 storr-1.2.0/storr/R/driver_rds.R | 189 ++++++++++++- storr-1.2.0/storr/R/driver_remote.R |only storr-1.2.0/storr/R/exceptions.R | 3 storr-1.2.0/storr/R/hash.R | 58 +++ storr-1.2.0/storr/R/multistorr.R |only storr-1.2.0/storr/R/spec.R | 23 + storr-1.2.0/storr/R/storr.R | 166 +++++++++++ storr-1.2.0/storr/R/storr_copy.R | 3 storr-1.2.0/storr/R/traits.R | 1 storr-1.2.0/storr/R/utils.R | 68 ++++ storr-1.2.0/storr/README.md | 4 storr-1.2.0/storr/build/vignette.rds |binary storr-1.2.0/storr/inst/doc/external.html | 21 - storr-1.2.0/storr/inst/doc/storr.Rmd | 10 storr-1.2.0/storr/inst/doc/storr.html | 28 - storr-1.2.0/storr/inst/spec/test-driver.R | 10 storr-1.2.0/storr/inst/spec/test-export.R | 11 storr-1.2.0/storr/inst/spec/test-external.R | 1 storr-1.2.0/storr/inst/spec/test-storr.R | 14 storr-1.2.0/storr/man/driver_remote.Rd |only storr-1.2.0/storr/man/encode64.Rd | 6 storr-1.2.0/storr/man/storr.Rd | 26 + storr-1.2.0/storr/man/storr_dbi.Rd | 11 storr-1.2.0/storr/man/storr_external.Rd | 2 storr-1.2.0/storr/man/storr_multistorr.Rd |only storr-1.2.0/storr/man/storr_rds.Rd | 30 ++ storr-1.2.0/storr/tests/testthat/base64_reference.csv |only storr-1.2.0/storr/tests/testthat/helper-remote.R |only storr-1.2.0/storr/tests/testthat/helper-storr.R | 26 + storr-1.2.0/storr/tests/testthat/test-auto.R | 43 +- storr-1.2.0/storr/tests/testthat/test-base64.R | 43 -- storr-1.2.0/storr/tests/testthat/test-defunct.R |only storr-1.2.0/storr/tests/testthat/test-driver-dbi.R | 22 + storr-1.2.0/storr/tests/testthat/test-driver-environment.R | 9 storr-1.2.0/storr/tests/testthat/test-driver-multistorr.R |only storr-1.2.0/storr/tests/testthat/test-driver-rds.R | 100 ++++++ storr-1.2.0/storr/tests/testthat/test-driver-remote.R |only storr-1.2.0/storr/tests/testthat/test-hash.R | 7 storr-1.2.0/storr/tests/testthat/test-spec.R | 10 storr-1.2.0/storr/tests/testthat/test-storr.R | 91 ++++++ storr-1.2.0/storr/tests/testthat/test-util.R | 4 storr-1.2.0/storr/vignettes/storr.Rmd | 10 52 files changed, 1039 insertions(+), 204 deletions(-)
Title: Exploring Heterogeneity in Meta-Analysis using Random Forests
Description: Conduct random forests-based meta-analysis, obtain partial dependence plots for metaforest and classic meta-analyses, and cross-validate and tune metaforest- and classic meta-analyses in conjunction with the caret package. A requirement of classic meta-analysis is that the studies being aggregated are conceptually similar, and ideally, close replications. However, in many fields, there is substantial heterogeneity between studies on the same topic. Classic meta-analysis lacks the power to assess more than a handful of univariate moderators. MetaForest, by contrast, has substantial power to explore heterogeneity in meta-analysis. It can identify important moderators from a larger set of potential candidates, even with as little as 20 studies (Van Lissa, in preparation). This is an appealing quality, because many meta-analyses have small sample sizes. Moreover, MetaForest yields a measure of variable importance which can be used to identify important moderators, and offers partial prediction plots to explore the shape of the marginal relationship between moderators and effect size.
Author: Caspar J. van Lissa
Maintainer: Caspar J. van Lissa <c.j.vanlissa@gmail.com>
Diff between metaforest versions 0.1.0 dated 2017-09-09 and 0.1.2 dated 2018-05-31
metaforest-0.1.0/metaforest/man/extract_proximity.MetaForest.Rd |only metaforest-0.1.2/metaforest/DESCRIPTION | 11 metaforest-0.1.2/metaforest/MD5 | 25 metaforest-0.1.2/metaforest/NAMESPACE | 19 metaforest-0.1.2/metaforest/NEWS.md |only metaforest-0.1.2/metaforest/R/ClusterMF.R | 2 metaforest-0.1.2/metaforest/R/MetaForest.R | 2 metaforest-0.1.2/metaforest/R/ModelInfo_mf.R |only metaforest-0.1.2/metaforest/R/ModelInfo_rma.R |only metaforest-0.1.2/metaforest/R/PartialDependence.R | 485 ++++++++-- metaforest-0.1.2/metaforest/R/WeightedScatter.R |only metaforest-0.1.2/metaforest/R/extract_proximity.MetaForest.R | 18 metaforest-0.1.2/metaforest/R/plot.MetaForest.R | 10 metaforest-0.1.2/metaforest/man/ModelInfo_mf.Rd |only metaforest-0.1.2/metaforest/man/ModelInfo_rma.Rd |only metaforest-0.1.2/metaforest/man/PartialDependence.Rd | 67 + metaforest-0.1.2/metaforest/man/WeightedScatter.Rd |only metaforest-0.1.2/metaforest/man/extract_proximity.Rd |only 18 files changed, 535 insertions(+), 104 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-08-19 0.1
Title: Phylogenetic Linear Regression
Description: Provides functions for fitting phylogenetic linear models and phylogenetic generalized linear models. The computation uses an algorithm that is linear in the number of tips in the tree. The package also provides functions for simulating continuous or binary traits along the tree. Other tools include functions to test the adequacy of a population tree.
Author: Lam Si Tung Ho [aut, cre],
Cecile Ane [aut],
Robert Lachlan [ctb],
Kelsey Tarpinian [ctb],
Rachel Feldman [ctb],
Qing Yu [ctb],
Wouter van der Bijl [ctb]
Maintainer: Lam Si Tung Ho <lamho86@gmail.com>
Diff between phylolm versions 2.5 dated 2016-10-17 and 2.6 dated 2018-05-31
DESCRIPTION | 15 ++++++---- MD5 | 19 +++++++------ NAMESPACE | 3 +- R/OU1d.R | 5 +++ R/phyloglm.R | 41 +++++++++++++++-------------- R/phylolm.R | 61 +++++++++++++++++++++++++------------------- README.md | 7 +++-- man/phyloglm.Rd | 7 ++++- man/phylolm-package.Rd | 6 ++-- man/phylolm.Rd | 5 +++ src/registerDynamicSymbol.c |only 11 files changed, 103 insertions(+), 66 deletions(-)
Title: Penalized Precision Matrix Estimation via ADMM
Description: Estimates a penalized precision matrix via the alternating direction method of multipliers (ADMM) algorithm. It currently supports a general elastic-net penalty that allows for both ridge and lasso-type penalties as special cases. This package is an alternative to the 'glasso' package.
See Boyd et al (2010) <doi:10.1561/2200000016> for details regarding the estimation method.
Author: Matt Galloway [aut, cre]
Maintainer: Matt Galloway <gall0441@umn.edu>
Diff between ADMMsigma versions 1.0 dated 2018-04-03 and 2.0 dated 2018-05-31
ADMMsigma-1.0/ADMMsigma/man/ADMMsigmac.Rd |only ADMMsigma-1.0/ADMMsigma/man/CVP_ADMMsigmac.Rd |only ADMMsigma-1.0/ADMMsigma/man/CV_ADMMsigmac.Rd |only ADMMsigma-1.0/ADMMsigma/man/CV_RIDGEsigmac.Rd |only ADMMsigma-1.0/ADMMsigma/man/ParallelCV.Rd |only ADMMsigma-1.0/ADMMsigma/man/RIDGEsigmac.Rd |only ADMMsigma-1.0/ADMMsigma/man/plot.ADMMsigma.Rd |only ADMMsigma-1.0/ADMMsigma/man/plot.RIDGEsigma.Rd |only ADMMsigma-1.0/ADMMsigma/man/print.ADMMsigma.Rd |only ADMMsigma-1.0/ADMMsigma/man/print.RIDGEsigma.Rd |only ADMMsigma-2.0/ADMMsigma/DESCRIPTION | 14 ADMMsigma-2.0/ADMMsigma/MD5 | 58 +-- ADMMsigma-2.0/ADMMsigma/NAMESPACE | 13 ADMMsigma-2.0/ADMMsigma/R/ADMMsigma.R | 336 ++++++++++++++------- ADMMsigma-2.0/ADMMsigma/R/Parallel.R | 159 +++++++-- ADMMsigma-2.0/ADMMsigma/R/RIDGEsigma.R | 236 +++++++++----- ADMMsigma-2.0/ADMMsigma/R/RcppExports.R | 135 +++++--- ADMMsigma-2.0/ADMMsigma/R/misc.R | 3 ADMMsigma-2.0/ADMMsigma/man/ADMMc.Rd |only ADMMsigma-2.0/ADMMsigma/man/ADMMsigma.Rd | 77 +++- ADMMsigma-2.0/ADMMsigma/man/CVP_ADMM.Rd |only ADMMsigma-2.0/ADMMsigma/man/CVP_ADMMc.Rd |only ADMMsigma-2.0/ADMMsigma/man/CVP_RIDGE.Rd |only ADMMsigma-2.0/ADMMsigma/man/CVP_RIDGEc.Rd |only ADMMsigma-2.0/ADMMsigma/man/CV_ADMMc.Rd |only ADMMsigma-2.0/ADMMsigma/man/CV_RIDGEc.Rd |only ADMMsigma-2.0/ADMMsigma/man/RIDGEc.Rd |only ADMMsigma-2.0/ADMMsigma/man/RIDGEsigma.Rd | 39 +- ADMMsigma-2.0/ADMMsigma/man/plot.ADMM.Rd |only ADMMsigma-2.0/ADMMsigma/man/plot.RIDGE.Rd |only ADMMsigma-2.0/ADMMsigma/man/print.ADMM.Rd |only ADMMsigma-2.0/ADMMsigma/man/print.RIDGE.Rd |only ADMMsigma-2.0/ADMMsigma/src/CV.cpp | 303 ++++++++++++------ ADMMsigma-2.0/ADMMsigma/src/CVP.cpp | 139 ++++++-- ADMMsigma-2.0/ADMMsigma/src/RcppExports.cpp | 113 ++++--- ADMMsigma-2.0/ADMMsigma/src/Sigma.cpp | 121 +++---- ADMMsigma-2.0/ADMMsigma/src/Sigma.h | 4 ADMMsigma-2.0/ADMMsigma/src/soft.cpp | 47 ++ ADMMsigma-2.0/ADMMsigma/src/soft.h | 5 ADMMsigma-2.0/ADMMsigma/tests/testthat/testADMM.R | 38 ++ ADMMsigma-2.0/ADMMsigma/tests/testthat/testRIDGE.R | 35 +- 41 files changed, 1259 insertions(+), 616 deletions(-)