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Title: Performs Bayesian Variable Selection on the Covariates in a
Semi-Competing Risks Model
Description: Contains four functions used in the DIC-tau_g procedure. SCRSELECT() and SCRSELECTRUN() uses Stochastic Search Variable Selection to select important
covariates in the three hazard functions of a semi-competing risks model. These functions perform the Gibbs sampler for variable selection and a Metropolis-Hastings-Green sampler for the number of split points and parameters for the
three baseline hazard function. The function SCRSELECT() returns the posterior sample of all quantities sampled in the Gibbs sampler after a burn-in period to a desired
file location, while the function SCRSELECTRUN() returns posterior values of important quantities to the DIC-Tau_g procedure in a list.
The function DICTAUG() returns a list containing the DIC values for the unique models visited by the DIC-Tau_g grid search.
The function ReturnModel() uses SCRSELECTRUN() and DICTAUG() to return a summary of the posterior coefficient vectors for the optimal model along with saving this posterior sample to a desired path location.
Author: Andrew Chapple [aut, cre]
Maintainer: Andrew Chapple <Andrew.G.Chapple@rice.edu>
Diff between SCRSELECT versions 1.1-1 dated 2017-04-07 and 1.1-2 dated 2017-04-10
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/DICTAUG.R | 3 ++- R/ReturnModel.R | 2 +- R/SCRSELECT.R | 3 ++- man/DICTAUG.Rd | 1 + man/ReturnModel.Rd | 1 + man/SCRSELECT.Rd | 1 + 8 files changed, 18 insertions(+), 13 deletions(-)
Title: A Simple XML Tree Parser and Generator
Description: Provides a simple XML tree parser/generator. It includes functions to read XML files into R objects, get information out
of and into nodes, and write R objects back to XML code. It's not as powerful as the 'XML' package and doesn't aim to
be, but for simple XML handling it could be useful. It was originally developed for the R GUI and IDE 'RKWard'
<https://rkward.kde.org>, to make plugin development easier.
Author: Meik Michalke [aut, cre]
Maintainer: Meik Michalke <meik.michalke@hhu.de>
Diff between XiMpLe versions 0.03-23 dated 2015-11-24 and 0.10-1 dated 2017-04-10
ChangeLog | 22 DESCRIPTION | 30 - MD5 | 79 +- NAMESPACE | 10 R/00_class_01_XiMpLe.node.R | 92 +-- R/00_class_02_XiMpLe.doc.R | 78 +- R/00_class_03_XiMpLe.validity.R |only R/01_method_01_pasteXML.R | 23 R/01_method_02_node.R | 2 R/01_method_03_show.R | 2 R/01_method_04_validXML.R |only R/01_method_05_XMLgenerators.R |only R/XMLTree.R | 2 R/XMLValidity.R |only R/XiMpLe-internal.R | 141 ++++- R/XiMpLe-package.R | 16 R/parseXMLTree.R | 17 R/pasteXMLTag.R | 122 ++-- R/zzz_is_get_utils.R | 29 - README.md |only inst/CITATION | 12 inst/NEWS.Rd | 31 + inst/doc/XiMpLe_vignette.R |only inst/doc/XiMpLe_vignette.Rnw | 2 inst/doc/XiMpLe_vignette.pdf |binary man/XMLGetters-methods.Rd | 72 +- man/XMLNode.Rd | 8 man/XMLTree.Rd | 11 man/XMLValidity.Rd |only man/XMLgenerators.Rd |only man/XiMpLe-package.Rd | 19 man/XiMpLe.doc-class.Rd | 38 + man/XiMpLe.node-class.Rd | 61 +- man/XiMpLe.validity-class.Rd |only man/node.Rd | 11 man/parseXMLTree.Rd | 1 man/pasteXML-methods.Rd | 4 man/pasteXMLTag.Rd | 1 man/show-methods.Rd | 3 man/validXML.Rd |only tests/testthat/sample_RSS_parsed.RData |binary tests/testthat/sample_XML_tree_changed.RData |binary tests/testthat/sample_XML_tree_changed_value.RData |binary tests/testthat/sample_XML_validity.RData |only tests/testthat/tests.R | 579 ++++++++++++++------- vignettes/XiMpLe_vignette.Rnw | 2 46 files changed, 1012 insertions(+), 508 deletions(-)
Title: Analysis of Music and Speech
Description: Analyze music and speech, extract features like MFCCs, handle wave files and their representation in various ways, read mp3, read midi, perform steps of a transcription, ...
Also contains functions ported from the 'rastamat' 'Matlab' package.
Author: Uwe Ligges <ligges@statistik.tu-dortmund.de> with contributions
from Sebastian Krey, Olaf Mersmann, Sarah Schnackenberg, Guillaume Guenard,
Andrea Preusser, Anita Thieler, Johanna Mielke and Claus Weihs, as well as code fragments
and ideas from the former package 'sound' by Matthias Heymann
and functions from 'rastamat' by Daniel P. W. Ellis.
The included parts of the libmad MPEG audio decoder library are
authored by Underbit Technologies.
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>
Diff between tuneR versions 1.3.1 dated 2016-10-20 and 1.3.2 dated 2017-04-10
DESCRIPTION | 8 ++++---- MD5 | 11 ++++++----- NAMESPACE | 2 +- R/Waveforms.R | 4 ++-- R/readMP3.R | 2 +- src/init.c |only src/readmp3.c | 10 ++++++---- 7 files changed, 20 insertions(+), 17 deletions(-)
Title: React Helpers
Description: Make it easy to use 'react' in R with helper
dependency functions, embedded 'Babel' transpiler,
and examples. Please note the separate 'react'
BSD license <https://github.com/facebook/react/blob/master/LICENSE>
when using 'react' in your projects.
Author: Facebook Inc [aut, cph] (React library in lib,
https://facebook.github.io/react; see AUTHORS for full list of
contributors),
Kent Russell [aut, cre] (R interface)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>
Diff between reactR versions 0.1.0 dated 2016-11-05 and 0.1.2 dated 2017-04-10
DESCRIPTION | 10 +++++----- LICENSE | 2 +- MD5 | 28 +++++++++++++++++----------- NEWS.md |only R/babel.R | 7 ++++++- R/meta.R | 3 ++- README.md | 3 +++ build/getreact.R | 23 ++++++++++++++++++++++- inst/doc/intro_reactR.html | 10 +++++----- inst/examples/antd.R |only inst/examples/blueprint.R |only inst/examples/office-fabric.R |only inst/examples/victory-chart.R |only inst/www/babel |only inst/www/react/react-dom.min.js | 7 +++++-- inst/www/react/react.min.js | 8 ++------ man/babel_transform.Rd | 1 - man/html_dependency_react.Rd | 1 - 18 files changed, 68 insertions(+), 35 deletions(-)
Title: Interface to the 'USGS' 'BISON' 'API'
Description: Interface to the 'USGS' 'BISON' (<https://bison.usgs.gov/>)
'API', a 'database' for species occurrence data. Data comes from
species in the United States from participating data providers. You can get
data via 'taxonomic' and location based queries. A simple function
is provided to help visualize data.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rbison versions 0.5.0 dated 2016-10-05 and 0.5.4 dated 2017-04-10
DESCRIPTION | 18 +-- LICENSE | 2 MD5 | 62 ++++++------ NAMESPACE | 6 - NEWS.md | 20 +++ R/bison.R | 196 +++++++++++++++++++++------------------ R/bison_providers.R | 46 +++++---- R/bison_solr.r | 185 +++++++++++++++++++----------------- R/bison_stats.R | 32 +++--- R/bison_tax.R | 51 +++++----- R/bisonmap.R | 24 +++- R/citation_datause.R | 74 ++++++++------ R/rbison-package.R | 9 - R/zzz.R | 63 +++++++++--- README.md | 18 +-- build/vignette.rds |binary man/all_states.Rd | 1 man/bison.Rd | 120 ++++++++++++----------- man/bison_datause.Rd | 3 man/bison_providers.Rd | 12 +- man/bison_solr.Rd | 136 +++++++++++++++++++-------- man/bison_stats.Rd | 20 ++- man/bison_tax.Rd | 36 +++---- man/bisonmap.Rd | 4 man/fips.Rd | 1 man/is.bison.Rd | 1 man/is.bison_solr.Rd | 1 man/rbison-package.Rd | 13 +- tests/testthat/test-bison_solr.R | 11 +- tools |only 30 files changed, 681 insertions(+), 484 deletions(-)
Title: The Generalized DINA Model Framework
Description: A set of psychometric tools for cognitive diagnostic analyses
for both dichotomous and polytomous responses. Various cognitive diagnosis
models can be estimated, include the generalized deterministic inputs, noisy
and gate (G-DINA) model by de la Torre (2011) <DOI:10.1007/s11336-011-9207-7>,
the sequential G-DINA model by Ma and de la Torre (2016) <DOI:10.1111/bmsp.12070>, and many other models they subsume. Joint attribute distribution can
be saturated, higher-order or structured. Q-matrix validation, item and model
fit statistics, model comparison at test and item level and differential item
functioning can also be conducted. A graphical user interface is also provided.
Author: Wenchao Ma [aut, cre],
Jimmy de la Torre [aut]
Maintainer: Wenchao Ma <wenchao.ma@rutgers.edu>
Diff between GDINA versions 1.2.1 dated 2017-02-12 and 1.4.1 dated 2017-04-10
GDINA-1.2.1/GDINA/R/alpha.R |only GDINA-1.2.1/GDINA/R/eta.loc.R |only GDINA-1.2.1/GDINA/R/exportedUtils.R |only GDINA-1.2.1/GDINA/R/internalExtract.R |only GDINA-1.2.1/GDINA/R/rowCount.R |only GDINA-1.2.1/GDINA/src/SE.cpp |only GDINA-1.4.1/GDINA/DESCRIPTION | 38 - GDINA-1.4.1/GDINA/MD5 | 118 ++-- GDINA-1.4.1/GDINA/NAMESPACE | 14 GDINA-1.4.1/GDINA/NEWS.md | 24 + GDINA-1.4.1/GDINA/R/ExportedFuncs.R |only GDINA-1.4.1/GDINA/R/GDI.R | 23 GDINA-1.4.1/GDINA/R/GDINA.R | 408 +++++++++-------- GDINA-1.4.1/GDINA/R/HO.R | 117 +++- GDINA-1.4.1/GDINA/R/HOsupplement.R | 177 ++++++- GDINA-1.4.1/GDINA/R/RcppExports.R | 16 GDINA-1.4.1/GDINA/R/anova.GDINA.R | 55 -- GDINA-1.4.1/GDINA/R/autoGDINA.R | 18 GDINA-1.4.1/GDINA/R/dif.R | 115 +++- GDINA-1.4.1/GDINA/R/ecpe.R | 10 GDINA-1.4.1/GDINA/R/extract.GDINA.R | 352 ++++++++------ GDINA-1.4.1/GDINA/R/frac20.R | 2 GDINA-1.4.1/GDINA/R/hoparm.R | 79 ++- GDINA-1.4.1/GDINA/R/itemfit.R | 35 - GDINA-1.4.1/GDINA/R/itemparm.GDINA.R | 61 +- GDINA-1.4.1/GDINA/R/modelcomp.R | 30 - GDINA-1.4.1/GDINA/R/monocheck.R | 6 GDINA-1.4.1/GDINA/R/personparm.GDINA.R | 20 GDINA-1.4.1/GDINA/R/plotIRF.GDINA.R | 19 GDINA-1.4.1/GDINA/R/plotPVAF.Qval.R | 21 GDINA-1.4.1/GDINA/R/print.GDINA.R | 108 +++- GDINA-1.4.1/GDINA/R/s3GDINA.R | 25 - GDINA-1.4.1/GDINA/R/score.R |only GDINA-1.4.1/GDINA/R/simGDINA.R | 11 GDINA-1.4.1/GDINA/R/summary.GDINA.R | 52 -- GDINA-1.4.1/GDINA/R/utils.R | 301 ++++++------ GDINA-1.4.1/GDINA/inst/CITATION | 9 GDINA-1.4.1/GDINA/inst/shiny/server.R | 39 - GDINA-1.4.1/GDINA/inst/shiny/ui.R | 16 GDINA-1.4.1/GDINA/man/GDINA.Rd | 198 ++++---- GDINA-1.4.1/GDINA/man/LC2LG.Rd |only GDINA-1.4.1/GDINA/man/attributepattern.Rd | 2 GDINA-1.4.1/GDINA/man/autoGDINA.Rd | 2 GDINA-1.4.1/GDINA/man/bdiagMatrix.Rd | 2 GDINA-1.4.1/GDINA/man/cjoint.Rd | 2 GDINA-1.4.1/GDINA/man/dif.Rd | 9 GDINA-1.4.1/GDINA/man/ecpe.Rd | 11 GDINA-1.4.1/GDINA/man/extract.Rd | 105 ++-- GDINA-1.4.1/GDINA/man/frac20.Rd | 2 GDINA-1.4.1/GDINA/man/hoparm.Rd | 4 GDINA-1.4.1/GDINA/man/itemparm.Rd | 13 GDINA-1.4.1/GDINA/man/mesaplot.Rd | 11 GDINA-1.4.1/GDINA/man/personparm.Rd | 2 GDINA-1.4.1/GDINA/man/rowCount.Rd | 6 GDINA-1.4.1/GDINA/man/rowMatch.Rd | 2 GDINA-1.4.1/GDINA/man/score.Rd |only GDINA-1.4.1/GDINA/man/simGDINA.Rd | 2 GDINA-1.4.1/GDINA/man/unique_only.Rd | 2 GDINA-1.4.1/GDINA/man/unrestrQ.Rd |only GDINA-1.4.1/GDINA/src/Lik.cpp | 4 GDINA-1.4.1/GDINA/src/NgRg.cpp | 12 GDINA-1.4.1/GDINA/src/RcppExports.cpp | 43 - GDINA-1.4.1/GDINA/src/aggregateCol.cpp |only GDINA-1.4.1/GDINA/src/init.c |only GDINA-1.4.1/GDINA/src/scorep.cpp | 7 GDINA-1.4.1/GDINA/tests/testthat/test-likelihood.R | 223 +++++++++ GDINA-1.4.1/GDINA/tests/testthat/test-scorefunctions.R |only 67 files changed, 1850 insertions(+), 1133 deletions(-)
Title: Seasonal/Sequential (Instants/Durations, Even or not) Time
Series
Description: Objects to manipulate sequential and seasonal time series. Sequential time series based on time instants and time durations are handled. Both can be regularly or unevenly spaced (overlapping durations are allowed). Only POSIX* format are used for dates and times. The following classes are provided : 'POSIXcti', 'POSIXctp', 'TimeIntervalDataFrame', 'TimeInstantDataFrame', 'SubtimeDataFrame' ; methods to switch from a class to another and to modify the time support of series (hourly time series to daily time series for instance) are also defined. Tools provided can be used for instance to handle environmental monitoring data (not always produced on a regular time base).
Author: Vladislav Navel
Maintainer: Vladislav Navel <vnavel@yahoo.fr>
Diff between timetools versions 1.11.1 dated 2017-03-31 and 1.11.4 dated 2017-04-10
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/TimeInstantDataFrame.R | 3 +-- R/TimeIntervalDataFrame.R | 3 +-- man/POSIXcti-class.Rd | 7 +------ man/POSIXctp-class.Rd | 7 +------ man/POSIXst-class.Rd | 7 +------ man/TimeInstantDataFrame-class.Rd | 3 ++- man/TimeIntervalDataFrame-class.Rd | 3 ++- man/timetools-package.Rd | 4 ++-- 10 files changed, 24 insertions(+), 39 deletions(-)
Title: L1-Norm PCA Methods
Description: Implementations of several methods for principal component analysis
using the L1 norm. The package depends on COIN-OR Clp version >=
1.12.0. The methods implemented are
PCA-L1 (Kwak 2008) <DOI:10.1109/TPAMI.2008.114>,
L1-PCA (Ke and Kanade 2003, 2005) <DOI:10.1109/CVPR.2005.309>,
L1-PCA* (Brooks, Dula, and Boone 2013) <DOI:10.1016/j.csda.2012.11.007>,
L1-PCAhp (Visentin, Prestwich and Armagan 2016)
<DOI:10.1007/978-3-319-46227-1_37>,
wPCA (Park and Klabjan 2016),
awPCA (Park and Klabjan 2016),
PCA-Lp (Kwak 2014) <DOI:10.1109/TCYB.2013.2262936>, and
SharpEl1-PCA (Brooks and Dula, submitted).
Author: Sapan Jot <sapan.madaan@gmail.com>, Paul Brooks
<jpbrooks@vcu.edu>,
Andrea Visentin <andrea.visentin@insight-centre.org>,
Young Woong Park <ywpark@mail.smu.edu>,
and Yi-Hui Zhou <yihui_zhou@ncsu.edu>
Maintainer: Paul Brooks <jpbrooks@vcu.edu>
Diff between pcaL1 versions 1.5 dated 2017-03-12 and 1.5.1 dated 2017-04-10
ChangeLog | 10 +++ DESCRIPTION | 10 +-- MD5 | 38 ++++++------- NEWS | 6 +- configure | 18 +++--- configure.ac | 2 man/awl1pca.Rd | 20 +++---- man/l1pca.Rd | 13 ++-- man/l1pcahp.Rd | 16 ++--- man/l1pcastar.Rd | 6 +- man/pcaL1-package.Rd | 4 - man/pcal1.Rd | 12 ++-- man/pcalp.Rd | 8 +- man/sharpel1pca.Rd | 16 ++--- man/wl1pca.Rd | 18 +++--- src/l1projection.c | 142 +++++++++++++++++++++++++-------------------------- src/l1projection_R.c | 9 --- src/pcal1.c | 27 +++++++++ src/sharpel1pca.c | 32 +++++++++-- src/type.h | 2 20 files changed, 229 insertions(+), 180 deletions(-)
Title: Data-Limited Methods Toolkit
Description: Development, simulation testing, and implementation of management procedures for data-limited fisheries (see Carruthers et al (2014) <doi:10.1016/j.fishres.2013.12.014>).
Author: Tom Carruthers [aut, cre],
Adrian Hordyk [aut]
Maintainer: Tom Carruthers <t.carruthers@fisheries.ubc.ca>
Diff between DLMtool versions 3.2.2 dated 2016-10-17 and 3.2.3 dated 2017-04-10
DLMtool-3.2.2/DLMtool/R/ClassMeths.r |only DLMtool-3.2.2/DLMtool/build |only DLMtool-3.2.2/DLMtool/data/DLMdat.RData |only DLMtool-3.2.2/DLMtool/data/PorgMSE.rda |only DLMtool-3.2.2/DLMtool/data/SnapMSE.rda |only DLMtool-3.2.2/DLMtool/data/datalist |only DLMtool-3.2.2/DLMtool/data/ourMSE.rda |only DLMtool-3.2.2/DLMtool/inst/doc |only DLMtool-3.2.2/DLMtool/man/ChooseSelect.rd |only DLMtool-3.2.2/DLMtool/man/DLM_general-class.Rd |only DLMtool-3.2.2/DLMtool/man/DLMdat.Rd |only DLMtool-3.2.2/DLMtool/man/DoOpt.Rd |only DLMtool-3.2.2/DLMtool/man/KalmanFilter.Rd |only DLMtool-3.2.2/DLMtool/man/LBSPRSim.Rd |only DLMtool-3.2.2/DLMtool/man/OptFun.Rd |only DLMtool-3.2.2/DLMtool/man/PorgMSE.Rd |only DLMtool-3.2.2/DLMtool/man/SnapMSE.Rd |only DLMtool-3.2.2/DLMtool/man/VPA.Rd |only DLMtool-3.2.2/DLMtool/man/comp.Rd |only DLMtool-3.2.2/DLMtool/man/ourMSE.Rd |only DLMtool-3.2.2/DLMtool/man/plot-methods.Rd |only DLMtool-3.2.2/DLMtool/man/summary-methods.Rd |only DLMtool-3.2.2/DLMtool/vignettes |only DLMtool-3.2.3/DLMtool/DESCRIPTION | 27 DLMtool-3.2.3/DLMtool/MD5 | 512 - DLMtool-3.2.3/DLMtool/NAMESPACE | 452 - DLMtool-3.2.3/DLMtool/NEWS.md |only DLMtool-3.2.3/DLMtool/R/ChooseEffort.r |only DLMtool-3.2.3/DLMtool/R/ChooseSelect.r |only DLMtool-3.2.3/DLMtool/R/DLM_input.R | 1453 ++-- DLMtool-3.2.3/DLMtool/R/DLM_output.R | 6462 ++++++++++++------- DLMtool-3.2.3/DLMtool/R/DLMtool-package.R |only DLMtool-3.2.3/DLMtool/R/DataObj.r | 1081 +-- DLMtool-3.2.3/DLMtool/R/DefineClasses.r |only DLMtool-3.2.3/DLMtool/R/LBSPR_MPs.r |only DLMtool-3.2.3/DLMtool/R/MSEObj.r | 5264 +++++++++------ DLMtool-3.2.3/DLMtool/R/MiscFuns.r | 1839 +++-- DLMtool-3.2.3/DLMtool/R/MiscInt.r | 1307 +-- DLMtool-3.2.3/DLMtool/R/RcppExports.R | 137 DLMtool-3.2.3/DLMtool/R/XLloadfuns.r | 190 DLMtool-3.2.3/DLMtool/R/dataObjects.r |only DLMtool-3.2.3/DLMtool/R/runMSE.r | 2379 ++++-- DLMtool-3.2.3/DLMtool/R/runMSErobust.r |only DLMtool-3.2.3/DLMtool/README.md |only DLMtool-3.2.3/DLMtool/data/Albacore.rda |only DLMtool-3.2.3/DLMtool/data/Atlantic_mackerel.rda |only DLMtool-3.2.3/DLMtool/data/Blue_shark.rda |only DLMtool-3.2.3/DLMtool/data/Bluefin_tuna.rda |only DLMtool-3.2.3/DLMtool/data/Bluefin_tuna_WAtl.rda |only DLMtool-3.2.3/DLMtool/data/Butterfish.rda |only DLMtool-3.2.3/DLMtool/data/China_rockfish.rda |only DLMtool-3.2.3/DLMtool/data/Cobia.rda |only DLMtool-3.2.3/DLMtool/data/DecE_Dom.rda |only DLMtool-3.2.3/DLMtool/data/DecE_HDom.rda |only DLMtool-3.2.3/DLMtool/data/DecE_NDom.rda |only DLMtool-3.2.3/DLMtool/data/Example_datafile.rda |only DLMtool-3.2.3/DLMtool/data/Feasibility.rda |only DLMtool-3.2.3/DLMtool/data/Feasibility2.rda |only DLMtool-3.2.3/DLMtool/data/FlatE_Dom.rda |only DLMtool-3.2.3/DLMtool/data/FlatE_HDom.rda |only DLMtool-3.2.3/DLMtool/data/FlatE_NDom.rda |only DLMtool-3.2.3/DLMtool/data/Generic_DecE.rda |only DLMtool-3.2.3/DLMtool/data/Generic_FlatE.rda |only DLMtool-3.2.3/DLMtool/data/Generic_IncE.rda |only DLMtool-3.2.3/DLMtool/data/Generic_fleet.rda |only DLMtool-3.2.3/DLMtool/data/Generic_obs.rda |only DLMtool-3.2.3/DLMtool/data/Gulf_blue_tilefish.rda |only DLMtool-3.2.3/DLMtool/data/Herring.rda |only DLMtool-3.2.3/DLMtool/data/Imprecise_Biased.rda |only DLMtool-3.2.3/DLMtool/data/Imprecise_Unbiased.rda |only DLMtool-3.2.3/DLMtool/data/IncE_Dom.rda |only DLMtool-3.2.3/DLMtool/data/IncE_HDom.rda |only DLMtool-3.2.3/DLMtool/data/IncE_NDom.rda |only DLMtool-3.2.3/DLMtool/data/Low_Effort_Non_Target.rda |only DLMtool-3.2.3/DLMtool/data/Mackerel.rda |only DLMtool-3.2.3/DLMtool/data/Perfect_Info.rda |only DLMtool-3.2.3/DLMtool/data/Porgy.rda |only DLMtool-3.2.3/DLMtool/data/Precise_Biased.rda |only DLMtool-3.2.3/DLMtool/data/Precise_Unbiased.rda |only DLMtool-3.2.3/DLMtool/data/Red_snapper.rda |only DLMtool-3.2.3/DLMtool/data/Rockfish.rda |only DLMtool-3.2.3/DLMtool/data/Simulation_1.rda |only DLMtool-3.2.3/DLMtool/data/Snapper.rda |only DLMtool-3.2.3/DLMtool/data/Sole.rda |only DLMtool-3.2.3/DLMtool/data/Target_All_Fish.rda |only DLMtool-3.2.3/DLMtool/data/Targeting_Small_Fish.rda |only DLMtool-3.2.3/DLMtool/data/Toothfish.rda |only DLMtool-3.2.3/DLMtool/data/mypars.rda |only DLMtool-3.2.3/DLMtool/data/ourReefFish.rda |binary DLMtool-3.2.3/DLMtool/man/Albacore.Rd |only DLMtool-3.2.3/DLMtool/man/Atlantic_mackerel.Rd |only DLMtool-3.2.3/DLMtool/man/AvC.Rd | 30 DLMtool-3.2.3/DLMtool/man/BK.Rd | 36 DLMtool-3.2.3/DLMtool/man/BK_CC.Rd | 39 DLMtool-3.2.3/DLMtool/man/BK_ML.Rd | 37 DLMtool-3.2.3/DLMtool/man/BlankSelPlot.Rd |only DLMtool-3.2.3/DLMtool/man/Blue_shark.Rd |only DLMtool-3.2.3/DLMtool/man/Bluefin_tuna.Rd |only DLMtool-3.2.3/DLMtool/man/Bluefin_tuna_WAtl.Rd |only DLMtool-3.2.3/DLMtool/man/Butterfish.Rd |only DLMtool-3.2.3/DLMtool/man/CC1.Rd | 45 DLMtool-3.2.3/DLMtool/man/CC4.Rd | 46 DLMtool-3.2.3/DLMtool/man/CSRA.Rd | 95 DLMtool-3.2.3/DLMtool/man/CSRAfunc.Rd | 123 DLMtool-3.2.3/DLMtool/man/Can.Rd | 27 DLMtool-3.2.3/DLMtool/man/Cant.Rd | 23 DLMtool-3.2.3/DLMtool/man/CheckConverg.Rd | 30 DLMtool-3.2.3/DLMtool/man/China_rockfish.Rd |only DLMtool-3.2.3/DLMtool/man/ChooseEffort.Rd | 25 DLMtool-3.2.3/DLMtool/man/ChooseSelect.Rd |only DLMtool-3.2.3/DLMtool/man/Cobia.Rd |only DLMtool-3.2.3/DLMtool/man/CompSRA.Rd | 34 DLMtool-3.2.3/DLMtool/man/CompSRA4010.Rd | 34 DLMtool-3.2.3/DLMtool/man/Converge.Rd |only DLMtool-3.2.3/DLMtool/man/Cplot.Rd | 53 DLMtool-3.2.3/DLMtool/man/DAAC.Rd | 34 DLMtool-3.2.3/DLMtool/man/DBSRA.Rd | 58 DLMtool-3.2.3/DLMtool/man/DBSRA4010.Rd | 35 DLMtool-3.2.3/DLMtool/man/DBSRA_40.Rd | 39 DLMtool-3.2.3/DLMtool/man/DBSRA_ML.Rd | 36 DLMtool-3.2.3/DLMtool/man/DCAC.Rd | 39 DLMtool-3.2.3/DLMtool/man/DCAC4010.Rd | 41 DLMtool-3.2.3/DLMtool/man/DCAC_40.Rd | 36 DLMtool-3.2.3/DLMtool/man/DCAC_ML.Rd | 37 DLMtool-3.2.3/DLMtool/man/DD.Rd | 43 DLMtool-3.2.3/DLMtool/man/DD4010.Rd | 31 DLMtool-3.2.3/DLMtool/man/DDe.Rd | 40 DLMtool-3.2.3/DLMtool/man/DDe75.Rd | 41 DLMtool-3.2.3/DLMtool/man/DDes.Rd | 52 DLMtool-3.2.3/DLMtool/man/DLMDataDir.Rd | 18 DLMtool-3.2.3/DLMtool/man/DLM_data-class.Rd | 253 DLMtool-3.2.3/DLMtool/man/DLM_fease-class.Rd | 89 DLMtool-3.2.3/DLMtool/man/DLMtool-package.Rd | 63 DLMtool-3.2.3/DLMtool/man/DOM.Rd | 30 DLMtool-3.2.3/DLMtool/man/DTe40.Rd | 43 DLMtool-3.2.3/DLMtool/man/DTe50.Rd | 43 DLMtool-3.2.3/DLMtool/man/DecE_Dom.Rd |only DLMtool-3.2.3/DLMtool/man/DecE_HDom.Rd |only DLMtool-3.2.3/DLMtool/man/DecE_NDom.Rd |only DLMtool-3.2.3/DLMtool/man/DepF.Rd | 31 DLMtool-3.2.3/DLMtool/man/DynF.Rd | 56 DLMtool-3.2.3/DLMtool/man/EtargetLopt.Rd | 39 DLMtool-3.2.3/DLMtool/man/Example_datafile.Rd |only DLMtool-3.2.3/DLMtool/man/FMSYopt.Rd |only DLMtool-3.2.3/DLMtool/man/FMSYref.Rd | 32 DLMtool-3.2.3/DLMtool/man/FMSYref50.Rd | 36 DLMtool-3.2.3/DLMtool/man/FMSYref75.Rd | 35 DLMtool-3.2.3/DLMtool/man/Fadapt.Rd | 53 DLMtool-3.2.3/DLMtool/man/Fdem.Rd | 39 DLMtool-3.2.3/DLMtool/man/Fdem_CC.Rd | 38 DLMtool-3.2.3/DLMtool/man/Fdem_ML.Rd | 37 DLMtool-3.2.3/DLMtool/man/Fease.Rd | 28 DLMtool-3.2.3/DLMtool/man/Fease_xl.Rd | 53 DLMtool-3.2.3/DLMtool/man/Feasibility.Rd |only DLMtool-3.2.3/DLMtool/man/Feasibility2.Rd |only DLMtool-3.2.3/DLMtool/man/FlatE_Dom.Rd |only DLMtool-3.2.3/DLMtool/man/FlatE_HDom.Rd |only DLMtool-3.2.3/DLMtool/man/FlatE_NDom.Rd |only DLMtool-3.2.3/DLMtool/man/Fleet-class.Rd | 96 DLMtool-3.2.3/DLMtool/man/Fratio.Rd | 42 DLMtool-3.2.3/DLMtool/man/Fratio4010.Rd | 35 DLMtool-3.2.3/DLMtool/man/Fratio_CC.Rd | 40 DLMtool-3.2.3/DLMtool/man/Fratio_ML.Rd | 38 DLMtool-3.2.3/DLMtool/man/GB_CC.Rd | 36 DLMtool-3.2.3/DLMtool/man/GB_slope.Rd | 46 DLMtool-3.2.3/DLMtool/man/GB_target.Rd | 40 DLMtool-3.2.3/DLMtool/man/Gcontrol.Rd | 51 DLMtool-3.2.3/DLMtool/man/Generic_DecE.Rd |only DLMtool-3.2.3/DLMtool/man/Generic_FlatE.Rd |only DLMtool-3.2.3/DLMtool/man/Generic_IncE.Rd |only DLMtool-3.2.3/DLMtool/man/Generic_fleet.Rd |only DLMtool-3.2.3/DLMtool/man/Generic_obs.Rd |only DLMtool-3.2.3/DLMtool/man/Gulf_blue_tilefish.Rd |only DLMtool-3.2.3/DLMtool/man/HDAAC.Rd | 34 DLMtool-3.2.3/DLMtool/man/Herring.Rd |only DLMtool-3.2.3/DLMtool/man/IT10.Rd | 41 DLMtool-3.2.3/DLMtool/man/IT5.Rd | 41 DLMtool-3.2.3/DLMtool/man/ITM.Rd | 34 DLMtool-3.2.3/DLMtool/man/ITe10.Rd | 42 DLMtool-3.2.3/DLMtool/man/ITe5.Rd | 42 DLMtool-3.2.3/DLMtool/man/Imprecise_Biased.Rd |only DLMtool-3.2.3/DLMtool/man/Imprecise_Unbiased.Rd |only DLMtool-3.2.3/DLMtool/man/IncE_Dom.Rd |only DLMtool-3.2.3/DLMtool/man/IncE_HDom.Rd |only DLMtool-3.2.3/DLMtool/man/IncE_NDom.Rd |only DLMtool-3.2.3/DLMtool/man/Input.Rd | 41 DLMtool-3.2.3/DLMtool/man/Islope1.Rd | 59 DLMtool-3.2.3/DLMtool/man/Islope4.Rd | 59 DLMtool-3.2.3/DLMtool/man/Itarget1.Rd | 61 DLMtool-3.2.3/DLMtool/man/Itarget4.Rd | 61 DLMtool-3.2.3/DLMtool/man/ItargetE1.Rd | 61 DLMtool-3.2.3/DLMtool/man/ItargetE4.Rd | 59 DLMtool-3.2.3/DLMtool/man/Jplot.Rd | 84 DLMtool-3.2.3/DLMtool/man/Kplot.Rd | 54 DLMtool-3.2.3/DLMtool/man/L2A.Rd | 40 DLMtool-3.2.3/DLMtool/man/L95target.Rd | 47 DLMtool-3.2.3/DLMtool/man/LBSPR.Rd | 41 DLMtool-3.2.3/DLMtool/man/LBSPR_ItEff.Rd | 36 DLMtool-3.2.3/DLMtool/man/LBSPR_ItSel.Rd | 35 DLMtool-3.2.3/DLMtool/man/LBSPR_ItTAC.Rd | 36 DLMtool-3.2.3/DLMtool/man/Low_Effort_Non_Target.Rd |only DLMtool-3.2.3/DLMtool/man/LstepCC1.Rd | 67 DLMtool-3.2.3/DLMtool/man/LstepCC4.Rd | 67 DLMtool-3.2.3/DLMtool/man/LstepCE1.Rd | 58 DLMtool-3.2.3/DLMtool/man/LstepCE2.Rd | 57 DLMtool-3.2.3/DLMtool/man/Ltarget1.Rd | 60 DLMtool-3.2.3/DLMtool/man/Ltarget4.Rd | 60 DLMtool-3.2.3/DLMtool/man/LtargetE1.Rd | 50 DLMtool-3.2.3/DLMtool/man/LtargetE4.Rd | 50 DLMtool-3.2.3/DLMtool/man/MCD.Rd | 30 DLMtool-3.2.3/DLMtool/man/MCD4010.Rd | 31 DLMtool-3.2.3/DLMtool/man/ML2D.Rd | 44 DLMtool-3.2.3/DLMtool/man/MPStats.Rd | 46 DLMtool-3.2.3/DLMtool/man/MRnoreal.Rd | 28 DLMtool-3.2.3/DLMtool/man/MRreal.Rd | 28 DLMtool-3.2.3/DLMtool/man/MSE-class.Rd | 213 DLMtool-3.2.3/DLMtool/man/Mackerel.Rd |only DLMtool-3.2.3/DLMtool/man/NAor0.Rd | 21 DLMtool-3.2.3/DLMtool/man/NFref.Rd | 29 DLMtool-3.2.3/DLMtool/man/NOAA_plot.Rd | 38 DLMtool-3.2.3/DLMtool/man/Needed.Rd | 25 DLMtool-3.2.3/DLMtool/man/OM-class.Rd | 288 DLMtool-3.2.3/DLMtool/man/OM_xl.Rd | 57 DLMtool-3.2.3/DLMtool/man/Observation-class.Rd | 149 DLMtool-3.2.3/DLMtool/man/OneRep.Rd |only DLMtool-3.2.3/DLMtool/man/Perfect_Info.Rd |only DLMtool-3.2.3/DLMtool/man/Porgy.Rd |only DLMtool-3.2.3/DLMtool/man/Pplot.Rd | 90 DLMtool-3.2.3/DLMtool/man/Pplot2.Rd |only DLMtool-3.2.3/DLMtool/man/Precise_Biased.Rd |only DLMtool-3.2.3/DLMtool/man/Precise_Unbiased.Rd |only DLMtool-3.2.3/DLMtool/man/Range.Rd |only DLMtool-3.2.3/DLMtool/man/Rcontrol.Rd | 46 DLMtool-3.2.3/DLMtool/man/Rcontrol2.Rd | 49 DLMtool-3.2.3/DLMtool/man/Red_snapper.Rd |only DLMtool-3.2.3/DLMtool/man/Required.Rd | 18 DLMtool-3.2.3/DLMtool/man/Rockfish.Rd |only DLMtool-3.2.3/DLMtool/man/SBT1.Rd | 54 DLMtool-3.2.3/DLMtool/man/SBT2.Rd | 63 DLMtool-3.2.3/DLMtool/man/SPMSY.Rd | 41 DLMtool-3.2.3/DLMtool/man/SPSRA.Rd | 34 DLMtool-3.2.3/DLMtool/man/SPSRA_ML.Rd | 39 DLMtool-3.2.3/DLMtool/man/SPmod.Rd | 45 DLMtool-3.2.3/DLMtool/man/SPslope.Rd | 55 DLMtool-3.2.3/DLMtool/man/Sam.Rd | 37 DLMtool-3.2.3/DLMtool/man/SelectFun.Rd |only DLMtool-3.2.3/DLMtool/man/Sense.Rd | 44 DLMtool-3.2.3/DLMtool/man/SetRecruitCycle.Rd | 51 DLMtool-3.2.3/DLMtool/man/Simulation_1.Rd |only DLMtool-3.2.3/DLMtool/man/SketchFun.Rd |only DLMtool-3.2.3/DLMtool/man/Snapper.Rd |only DLMtool-3.2.3/DLMtool/man/Sole.Rd |only DLMtool-3.2.3/DLMtool/man/Splot.Rd | 84 DLMtool-3.2.3/DLMtool/man/Stock-class.Rd | 123 DLMtool-3.2.3/DLMtool/man/Sub.Rd | 40 DLMtool-3.2.3/DLMtool/man/TAC.Rd | 43 DLMtool-3.2.3/DLMtool/man/TACfilter.Rd |only DLMtool-3.2.3/DLMtool/man/Target_All_Fish.Rd |only DLMtool-3.2.3/DLMtool/man/Targeting_Small_Fish.Rd |only DLMtool-3.2.3/DLMtool/man/Toothfish.Rd |only DLMtool-3.2.3/DLMtool/man/Tplot.Rd | 23 DLMtool-3.2.3/DLMtool/man/Tplot2.Rd | 29 DLMtool-3.2.3/DLMtool/man/TradePlot.Rd | 58 DLMtool-3.2.3/DLMtool/man/TwoSidedFun.Rd |only DLMtool-3.2.3/DLMtool/man/VOI.Rd | 40 DLMtool-3.2.3/DLMtool/man/VOI2.Rd | 47 DLMtool-3.2.3/DLMtool/man/VOIplot.Rd | 88 DLMtool-3.2.3/DLMtool/man/YPR.Rd | 37 DLMtool-3.2.3/DLMtool/man/YPR_CC.Rd | 37 DLMtool-3.2.3/DLMtool/man/YPR_ML.Rd | 35 DLMtool-3.2.3/DLMtool/man/alphaconv.Rd |only DLMtool-3.2.3/DLMtool/man/avail.Rd | 21 DLMtool-3.2.3/DLMtool/man/barplot.MSE.Rd | 83 DLMtool-3.2.3/DLMtool/man/betaconv.Rd |only DLMtool-3.2.3/DLMtool/man/boxplot.DLM_data.Rd | 30 DLMtool-3.2.3/DLMtool/man/boxplot.MSE.Rd | 98 DLMtool-3.2.3/DLMtool/man/checkMSE.Rd |only DLMtool-3.2.3/DLMtool/man/condmet.Rd |only DLMtool-3.2.3/DLMtool/man/curE.Rd | 32 DLMtool-3.2.3/DLMtool/man/curE75.Rd | 32 DLMtool-3.2.3/DLMtool/man/cv.Rd |only DLMtool-3.2.3/DLMtool/man/doprojPI.Rd |only DLMtool-3.2.3/DLMtool/man/doprojPI_cpp.Rd |only DLMtool-3.2.3/DLMtool/man/genLenComp.Rd |only DLMtool-3.2.3/DLMtool/man/getAFC.Rd | 40 DLMtool-3.2.3/DLMtool/man/getEffhist.Rd |only DLMtool-3.2.3/DLMtool/man/getFMSY.Rd |only DLMtool-3.2.3/DLMtool/man/getFMSY2.Rd |only DLMtool-3.2.3/DLMtool/man/getFref.Rd |only DLMtool-3.2.3/DLMtool/man/getFref2.Rd |only DLMtool-3.2.3/DLMtool/man/getSlope1.Rd |only DLMtool-3.2.3/DLMtool/man/getSlope2.Rd |only DLMtool-3.2.3/DLMtool/man/getSlopeFun.Rd |only DLMtool-3.2.3/DLMtool/man/getclass.Rd |only DLMtool-3.2.3/DLMtool/man/getmov.Rd | 44 DLMtool-3.2.3/DLMtool/man/getmov2.Rd |only DLMtool-3.2.3/DLMtool/man/getq.Rd | 95 DLMtool-3.2.3/DLMtool/man/getq2.Rd |only DLMtool-3.2.3/DLMtool/man/getroot.Rd |only DLMtool-3.2.3/DLMtool/man/gettempvar.Rd |only DLMtool-3.2.3/DLMtool/man/initialize-methods.Rd | 57 DLMtool-3.2.3/DLMtool/man/joinMSE.Rd | 21 DLMtool-3.2.3/DLMtool/man/lmmodel-class.Rd | 33 DLMtool-3.2.3/DLMtool/man/makePerf.Rd | 31 DLMtool-3.2.3/DLMtool/man/makeTransparent.Rd |only DLMtool-3.2.3/DLMtool/man/matlenlim.Rd | 33 DLMtool-3.2.3/DLMtool/man/matlenlim2.Rd | 33 DLMtool-3.2.3/DLMtool/man/mconv.Rd |only DLMtool-3.2.3/DLMtool/man/minlenLopt1.Rd | 44 DLMtool-3.2.3/DLMtool/man/movfit.Rd | 35 DLMtool-3.2.3/DLMtool/man/movfit_Rcpp.Rd |only DLMtool-3.2.3/DLMtool/man/mypars.Rd |only DLMtool-3.2.3/DLMtool/man/optQ_cpp.Rd |only DLMtool-3.2.3/DLMtool/man/ourReefFish.Rd | 104 DLMtool-3.2.3/DLMtool/man/plot-DLM_data.Rd |only DLMtool-3.2.3/DLMtool/man/plot-MSE.Rd |only DLMtool-3.2.3/DLMtool/man/plotFun.Rd | 32 DLMtool-3.2.3/DLMtool/man/plotOFL.Rd | 29 DLMtool-3.2.3/DLMtool/man/projOpt_cpp.Rd |only DLMtool-3.2.3/DLMtool/man/qopt.Rd | 98 DLMtool-3.2.3/DLMtool/man/replic8.Rd | 22 DLMtool-3.2.3/DLMtool/man/runInMP.Rd | 31 DLMtool-3.2.3/DLMtool/man/runMSE.Rd | 96 DLMtool-3.2.3/DLMtool/man/runMSErobust.Rd | 139 DLMtool-3.2.3/DLMtool/man/sampy.Rd |only DLMtool-3.2.3/DLMtool/man/sdconv.Rd |only DLMtool-3.2.3/DLMtool/man/setup.Rd |only DLMtool-3.2.3/DLMtool/man/slotlim.Rd | 36 DLMtool-3.2.3/DLMtool/man/summary-DLM_data.Rd |only DLMtool-3.2.3/DLMtool/man/summary-MSE.Rd |only DLMtool-3.2.3/DLMtool/man/tdlnorm.Rd |only DLMtool-3.2.3/DLMtool/man/trlnorm.Rd |only DLMtool-3.2.3/DLMtool/man/updateMSE.Rd | 21 DLMtool-3.2.3/DLMtool/man/wormplot.Rd | 34 DLMtool-3.2.3/DLMtool/man/writeCSV.Rd | 32 DLMtool-3.2.3/DLMtool/src/DLMtool_init.c |only DLMtool-3.2.3/DLMtool/src/RcppExports.cpp | 117 DLMtool-3.2.3/DLMtool/src/doprojPI_cpp.cpp |only DLMtool-3.2.3/DLMtool/src/genLenComp.cpp |only DLMtool-3.2.3/DLMtool/src/movefit_Rcpp.cpp |only DLMtool-3.2.3/DLMtool/src/optQ_cpp.cpp |only DLMtool-3.2.3/DLMtool/src/projOpt_cpp.cpp |only 342 files changed, 16905 insertions(+), 12284 deletions(-)
Title: Fitting Linear Models with Endogenous Regressors using Latent
Instrumental Variables
Description: Fits linear models with endogenous regressor using latent
instrumental variable approaches. The methods included in the package
are Lewbel's (1997) <doi:10.2307/2171884> higher moments approach as well as Lewbel's (2012) <doi:10.1080/07350015.2012.643126>
heteroskedasticity approach, Park and Gupta's (2012) <doi:10.1287/mksc.1120.0718>joint estimation method
that uses Gaussian copula and Kim and Frees's (2007) <doi:10.1007/s11336-007-9008-1> multilevel generalized
method of moment approach that deals with endogeneity in a multilevel setting.
These are statistical techniques to address the endogeneity problem where no
external instrumental variables are needed.
This version:
- solves an error occurring when using the multilevelIV() function with two levels, random intercept.
- returns the AIC and BIC for copulaCorrection() (method 1) and latentIV() methods.
- residuals and fitted values can be saved by users for latentIV() and copulaCorrection() methods.
- improves the summary methods for copulaCorrection() and multilevelIV() functions.
Author: Raluca Gui,
Markus Meierer,
Rene Algesheimer
Maintainer: Raluca Gui <raluca.gui@business.uzh.ch>
Diff between REndo versions 1.1 dated 2016-11-16 and 1.2 dated 2017-04-10
REndo-1.1/REndo/R/f_heterogenIV.R |only REndo-1.1/REndo/R/heterogenIV.R |only REndo-1.1/REndo/R/heterogenIV_class.R |only REndo-1.1/REndo/R/latetnIV_loglik.R |only REndo-1.1/REndo/R/method_heterogenIV.R |only REndo-1.1/REndo/README.md |only REndo-1.1/REndo/man/coef-heterogenREndo-method.Rd |only REndo-1.1/REndo/man/heterogenIV.Rd |only REndo-1.1/REndo/man/heterogenREndo-class.Rd |only REndo-1.1/REndo/man/summary-heterogenREndo-method.Rd |only REndo-1.2/REndo/DESCRIPTION | 43 +++++-- REndo-1.2/REndo/MD5 | 111 +++++++++---------- REndo-1.2/REndo/NAMESPACE | 7 - REndo-1.2/REndo/R/cop_Cont1.R | 7 - REndo-1.2/REndo/R/cop_Cont2.R | 2 REndo-1.2/REndo/R/cop_Discrete.R | 10 - REndo-1.2/REndo/R/cop_bootsSE.R | 29 +++- REndo-1.2/REndo/R/copulaCorrection.R | 59 ++++++---- REndo-1.2/REndo/R/copulaCorrection_class.R | 25 +++- REndo-1.2/REndo/R/f_hetErrorsIV.R |only REndo-1.2/REndo/R/hetErrorsIV.R |only REndo-1.2/REndo/R/hetErrorsIV_class.R |only REndo-1.2/REndo/R/higherMomentsIV.R | 9 - REndo-1.2/REndo/R/latentIV.R | 51 +++++--- REndo-1.2/REndo/R/latentIV_class.R | 22 +++ REndo-1.2/REndo/R/latentIV_loglik.R |only REndo-1.2/REndo/R/methods_copulaCorrection.R | 103 +++++++++++------ REndo-1.2/REndo/R/methods_hetErrorsIV.R |only REndo-1.2/REndo/R/methods_latentIV.R | 10 + REndo-1.2/REndo/R/methods_multilevelIV.R | 45 +++++-- REndo-1.2/REndo/R/mixedGMM.R |only REndo-1.2/REndo/R/multilevelIV.R | 12 +- REndo-1.2/REndo/R/multilevelIV_class.R | 1 REndo-1.2/REndo/man/boots.Rd | 1 REndo-1.2/REndo/man/checkAssumptions.Rd | 1 REndo-1.2/REndo/man/coef-copulaREndo-method.Rd | 1 REndo-1.2/REndo/man/coef-hetREndo-method.Rd |only REndo-1.2/REndo/man/coef-livREndo-method.Rd | 1 REndo-1.2/REndo/man/coef-mixedREndo-method.Rd | 2 REndo-1.2/REndo/man/copulaCont1.Rd | 1 REndo-1.2/REndo/man/copulaCorrection.Rd | 33 +++-- REndo-1.2/REndo/man/copulaDiscrete.Rd | 9 - REndo-1.2/REndo/man/copulaMethod2.Rd | 1 REndo-1.2/REndo/man/copulaPStar.Rd | 1 REndo-1.2/REndo/man/copulaRendo-class.Rd | 14 ++ REndo-1.2/REndo/man/dataCopC1.Rd | 10 - REndo-1.2/REndo/man/dataCopC2.Rd | 12 +- REndo-1.2/REndo/man/dataCopDis.Rd | 10 - REndo-1.2/REndo/man/dataHigherMoments.Rd | 8 - REndo-1.2/REndo/man/dataLatentIV.Rd | 8 - REndo-1.2/REndo/man/hetErrorsIV.Rd |only REndo-1.2/REndo/man/hetREndo-class.Rd |only REndo-1.2/REndo/man/higherMomentsIV.Rd | 16 +- REndo-1.2/REndo/man/internalIV.Rd | 1 REndo-1.2/REndo/man/latentIV.Rd | 28 ++-- REndo-1.2/REndo/man/livREndo-class.Rd | 20 ++- REndo-1.2/REndo/man/logL.Rd | 9 - REndo-1.2/REndo/man/logLL.Rd | 1 REndo-1.2/REndo/man/mixedGMM.Rd |only REndo-1.2/REndo/man/mixedREndo.Rd | 2 REndo-1.2/REndo/man/multilevelGMM.Rd | 1 REndo-1.2/REndo/man/multilevelIV.Rd | 13 +- REndo-1.2/REndo/man/summary-copulaREndo-method.Rd | 1 REndo-1.2/REndo/man/summary-hetREndo-method.Rd |only REndo-1.2/REndo/man/summary-livREndo-method.Rd | 1 REndo-1.2/REndo/man/summary-mixedREndo-method.Rd | 6 - REndo-1.2/REndo/man/tScores.Rd | 1 67 files changed, 454 insertions(+), 305 deletions(-)
Title: Compute the Rectangular Statistical Cartogram
Description: Provides an interface and a C++ implementation of the RecMap MP2
construction heuristic (see 'citation("recmap")' for details). This algorithm
draws maps according to a given statistical value (e.g. election results,
population or epidemiological data). The basic idea of the RecMap algorithm is
that each map region (e.g. different countries) is represented by a
rectangle. The area of each rectangle represents the statistical value given
as input (maintain zero cartographic error). Documentation about RecMap is
provided by a vignette included in this package.
Author: Christian Panse [aut, cre]
Maintainer: Christian Panse <Christian.Panse@gmail.com>
Diff between recmap versions 0.5.16 dated 2017-01-15 and 0.5.20 dated 2017-04-10
DESCRIPTION | 17 +++++++++++------ MD5 | 40 +++++++++++++++++++++++----------------- NAMESPACE | 2 +- R/RcppExports.R | 4 ++-- R/recmap.R | 39 ++++++++++++++++++++++++++------------- README.md | 49 ++++++++++++++++++++++++++++++++++++------------- build/partial.rdb |binary inst/CITATION | 15 +++++++++++++++ inst/NEWS.Rd | 14 +++++++++++++- inst/doc/recmap.R | 2 +- inst/doc/recmap.Rmd | 2 +- inst/doc/recmap.html | 24 ++++++++++++------------ inst/shiny-examples |only man/recmap.Rd | 13 ++++++++++--- man/sp2recmap.Rd | 28 ++++++++++++++++++++++++++++ src/RcppExports.cpp | 7 ++++--- src/Rrecmap.cpp | 21 +++++++++++++++++---- src/recmap.h | 20 ++++++++++++++------ src/recmap_init.c |only vignettes/recmap.Rmd | 2 +- 20 files changed, 215 insertions(+), 84 deletions(-)
Title: Generic Reproducible Parallel Backend for 'foreach' Loops
Description: Provides functions to perform
reproducible parallel foreach loops, using independent
random streams as generated by L'Ecuyer's combined
multiple-recursive generator [L'Ecuyer (1999), <DOI:10.1287/opre.47.1.159>].
It enables to easily convert standard %dopar% loops into
fully reproducible loops, independently of the number
of workers, the task scheduling strategy, or the chosen
parallel environment and associated foreach backend.
Author: Renaud Gaujoux
Maintainer: Renaud Gaujoux <renaud@tx.technion.ac.il>
Diff between doRNG versions 1.6 dated 2014-03-07 and 1.6.6 dated 2017-04-10
DESCRIPTION | 20 ++++----- MD5 | 38 +++++++++--------- NAMESPACE | 13 +++--- NEWS | 24 ++++++++--- R/doRNG-package.R | 11 +---- R/doRNG.R | 76 +++++++++++++++++++++++++++---------- build/vignette.rds |binary inst/REFERENCES.bib | 86 +++++++++++++++++++++--------------------- inst/doc/doRNG-unitTests.R | 2 inst/doc/doRNG-unitTests.Rnw | 35 ++++++++--------- inst/doc/doRNG-unitTests.pdf |binary inst/doc/doRNG.R | 81 ++++++++++++--------------------------- inst/doc/doRNG.pdf |binary inst/unitTests/runit.dorng.R | 31 ++++++++++++++- man/doRNG-package.Rd | 56 +++++++++++++-------------- man/doRNG.Rd | 34 +++++++--------- man/doRNGversion.Rd | 52 ++++++++++++++----------- man/infoDoRNG.Rd | 39 +++++++++---------- man/registerDoRNG.Rd | 48 +++++++++++------------ vignettes/doRNG-unitTests.Rnw | 35 ++++++++--------- 20 files changed, 367 insertions(+), 314 deletions(-)
Title: Bias and Uncertainty Corrected Sample Size
Description: Implements a method of correcting for publication bias and
uncertainty when planning sample sizes in a future study from an original study. See Anderson, Kelley, & Maxwell (submitted, revised and resubmitted).
Author: Samantha F. Anderson <sander10@nd.edu>, Ken Kelley <kkelley@nd.edu>
Maintainer: Ken Kelley <kkelley@nd.edu>
Diff between BUCSS versions 0.0.1 dated 2016-12-13 and 0.0.2 dated 2017-04-10
DESCRIPTION | 12 +-- MD5 | 36 +++++----- R/BUCSS.R |only R/ss.power.ba.R | 141 +++++++++++++++++++-------------------- R/ss.power.ba.general.R | 141 +++++++++++++++++++-------------------- R/ss.power.dt.r | 116 ++++++++++++++------------------ R/ss.power.it.R | 148 +++++++++++++++++++---------------------- R/ss.power.spa.general.R | 145 +++++++++++++++++++--------------------- R/ss.power.spa.r | 144 +++++++++++++++++++--------------------- R/ss.power.wa.general.R | 125 ++++++++++++++++------------------- R/ss.power.wa.r | 124 ++++++++++++++++------------------ man/BUCSS-package.Rd |only man/ss.power.ba.Rd | 150 ++++++++++++++++++++---------------------- man/ss.power.ba.general.Rd | 150 ++++++++++++++++++++---------------------- man/ss.power.dt.Rd | 125 +++++++++++++++-------------------- man/ss.power.it.Rd | 157 +++++++++++++++++++++----------------------- man/ss.power.spa.Rd | 153 ++++++++++++++++++++---------------------- man/ss.power.spa.general.Rd | 154 +++++++++++++++++++++---------------------- man/ss.power.wa.Rd | 133 +++++++++++++++++-------------------- man/ss.power.wa.general.Rd | 134 +++++++++++++++++-------------------- 20 files changed, 1097 insertions(+), 1191 deletions(-)
Title: Function Collection Related to Plotting and Hydrology
Description: Draw horizontal histograms, color scattered points by 3rd dimension,
enhance date- and log-axis plots, zoom in X11 graphics, trace errors and warnings,
use the unit hydrograph in a linear storage cascade, convert lists to data.frames and arrays,
fit multiple functions.
Author: Berry Boessenkool
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between berryFunctions versions 1.14.0 dated 2017-01-17 and 1.15.0 dated 2017-04-10
berryFunctions-1.14.0/berryFunctions/R/dataDWD.R |only berryFunctions-1.14.0/berryFunctions/R/readDWD.R |only berryFunctions-1.14.0/berryFunctions/man/readDWD.Rd |only berryFunctions-1.15.0/berryFunctions/DESCRIPTION | 10 berryFunctions-1.15.0/berryFunctions/MD5 | 256 ++- berryFunctions-1.15.0/berryFunctions/NAMESPACE | 15 berryFunctions-1.15.0/berryFunctions/NEWS | 44 berryFunctions-1.15.0/berryFunctions/R/almost.equal.R |only berryFunctions-1.15.0/berryFunctions/R/anhang.R | 20 berryFunctions-1.15.0/berryFunctions/R/approx2.R | 4 berryFunctions-1.15.0/berryFunctions/R/berryFunctions-package.R | 11 berryFunctions-1.15.0/berryFunctions/R/checkFile.R | 2 berryFunctions-1.15.0/berryFunctions/R/climateGraph.R | 4 berryFunctions-1.15.0/berryFunctions/R/colPoints.R | 128 + berryFunctions-1.15.0/berryFunctions/R/colPointsLegend.R | 2 berryFunctions-1.15.0/berryFunctions/R/createFun.R | 4 berryFunctions-1.15.0/berryFunctions/R/createPres.R |only berryFunctions-1.15.0/berryFunctions/R/exTime.R | 22 berryFunctions-1.15.0/berryFunctions/R/getColumn.R | 6 berryFunctions-1.15.0/berryFunctions/R/l2df.R | 78 - berryFunctions-1.15.0/berryFunctions/R/legendmt.R |only berryFunctions-1.15.0/berryFunctions/R/logHist.R | 11 berryFunctions-1.15.0/berryFunctions/R/newFilename.R |only berryFunctions-1.15.0/berryFunctions/R/pdfpng.R |only berryFunctions-1.15.0/berryFunctions/R/popleaf.R |only berryFunctions-1.15.0/berryFunctions/R/seasonality.R | 331 +++-- berryFunctions-1.15.0/berryFunctions/R/seqR.R | 4 berryFunctions-1.15.0/berryFunctions/R/smallPlot.R | 41 berryFunctions-1.15.0/berryFunctions/R/traceCall.R | 42 berryFunctions-1.15.0/berryFunctions/README.md |only berryFunctions-1.15.0/berryFunctions/build/vignette.rds |binary berryFunctions-1.15.0/berryFunctions/inst/doc/berryFunctions.Rmd | 652 +++++----- berryFunctions-1.15.0/berryFunctions/inst/doc/berryFunctions.html | 10 berryFunctions-1.15.0/berryFunctions/inst/extdata/Anhang.pdf |only berryFunctions-1.15.0/berryFunctions/inst/extdata/camera1.jpg |only berryFunctions-1.15.0/berryFunctions/inst/extdata/camera2.png |only berryFunctions-1.15.0/berryFunctions/inst/extdata/ccby.png |only berryFunctions-1.15.0/berryFunctions/inst/extdata/solitaire.txt | 6 berryFunctions-1.15.0/berryFunctions/man/TFtest.Rd | 79 - berryFunctions-1.15.0/berryFunctions/man/addAlpha.Rd | 85 - berryFunctions-1.15.0/berryFunctions/man/addFade.Rd | 85 - berryFunctions-1.15.0/berryFunctions/man/addRows.Rd | 69 - berryFunctions-1.15.0/berryFunctions/man/almost.equal.Rd |only berryFunctions-1.15.0/berryFunctions/man/anhang.Rd | 52 berryFunctions-1.15.0/berryFunctions/man/approx2.Rd | 119 - berryFunctions-1.15.0/berryFunctions/man/around.Rd | 83 - berryFunctions-1.15.0/berryFunctions/man/berryFunctions-package.Rd | 87 - berryFunctions-1.15.0/berryFunctions/man/betaPlot.Rd | 147 +- berryFunctions-1.15.0/berryFunctions/man/betaPlotComp.Rd | 125 - berryFunctions-1.15.0/berryFunctions/man/checkFile.Rd | 119 - berryFunctions-1.15.0/berryFunctions/man/ci.Rd | 113 - berryFunctions-1.15.0/berryFunctions/man/ciBand.Rd | 187 +- berryFunctions-1.15.0/berryFunctions/man/circle.Rd | 95 - berryFunctions-1.15.0/berryFunctions/man/classify.Rd | 147 +- berryFunctions-1.15.0/berryFunctions/man/colPoints.Rd | 448 +++--- berryFunctions-1.15.0/berryFunctions/man/colPointsHist.Rd | 163 +- berryFunctions-1.15.0/berryFunctions/man/colPointsLegend.Rd | 247 +-- berryFunctions-1.15.0/berryFunctions/man/combineFiles.Rd | 115 - berryFunctions-1.15.0/berryFunctions/man/compareFiles.Rd | 85 - berryFunctions-1.15.0/berryFunctions/man/convertUmlaut.Rd | 75 - berryFunctions-1.15.0/berryFunctions/man/createFun.Rd | 71 - berryFunctions-1.15.0/berryFunctions/man/createPres.Rd |only berryFunctions-1.15.0/berryFunctions/man/dataDWD.Rd | 86 - berryFunctions-1.15.0/berryFunctions/man/dataStr.Rd | 67 - berryFunctions-1.15.0/berryFunctions/man/distance.Rd | 99 - berryFunctions-1.15.0/berryFunctions/man/divPal.Rd | 99 - berryFunctions-1.15.0/berryFunctions/man/dupes.Rd | 131 -- berryFunctions-1.15.0/berryFunctions/man/exTime.Rd | 25 berryFunctions-1.15.0/berryFunctions/man/exp4p.Rd | 131 -- berryFunctions-1.15.0/berryFunctions/man/expReg.Rd | 175 +- berryFunctions-1.15.0/berryFunctions/man/funSource.Rd | 95 - berryFunctions-1.15.0/berryFunctions/man/funTinn.Rd | 61 berryFunctions-1.15.0/berryFunctions/man/funnelPlot.Rd | 310 ++-- berryFunctions-1.15.0/berryFunctions/man/getColumn.Rd | 157 +- berryFunctions-1.15.0/berryFunctions/man/getName.Rd | 99 - berryFunctions-1.15.0/berryFunctions/man/gof.Rd | 15 berryFunctions-1.15.0/berryFunctions/man/googleLink2pdf.Rd | 7 berryFunctions-1.15.0/berryFunctions/man/groupHist.Rd | 105 - berryFunctions-1.15.0/berryFunctions/man/headtail.Rd | 137 +- berryFunctions-1.15.0/berryFunctions/man/horizHist.Rd | 163 +- berryFunctions-1.15.0/berryFunctions/man/insertRows.Rd | 123 - berryFunctions-1.15.0/berryFunctions/man/instGit.Rd | 107 - berryFunctions-1.15.0/berryFunctions/man/is.error.Rd | 83 - berryFunctions-1.15.0/berryFunctions/man/l2array.Rd | 7 berryFunctions-1.15.0/berryFunctions/man/l2df.Rd | 164 +- berryFunctions-1.15.0/berryFunctions/man/legendmt.Rd |only berryFunctions-1.15.0/berryFunctions/man/library2.Rd | 83 - berryFunctions-1.15.0/berryFunctions/man/lim0.Rd | 115 - berryFunctions-1.15.0/berryFunctions/man/linLogHist.Rd | 195 +- berryFunctions-1.15.0/berryFunctions/man/linLogTrans.Rd | 301 ++-- berryFunctions-1.15.0/berryFunctions/man/linReg.Rd | 181 +- berryFunctions-1.15.0/berryFunctions/man/locArrow.Rd | 83 - berryFunctions-1.15.0/berryFunctions/man/locLine.Rd | 79 - berryFunctions-1.15.0/berryFunctions/man/logAxis.Rd | 205 +-- berryFunctions-1.15.0/berryFunctions/man/logHist.Rd | 11 berryFunctions-1.15.0/berryFunctions/man/logSpaced.Rd | 109 - berryFunctions-1.15.0/berryFunctions/man/logVals.Rd | 157 +- berryFunctions-1.15.0/berryFunctions/man/lsMem.Rd | 81 - berryFunctions-1.15.0/berryFunctions/man/lsc.Rd | 307 ++-- berryFunctions-1.15.0/berryFunctions/man/mReg.Rd | 560 ++++---- berryFunctions-1.15.0/berryFunctions/man/monthAxis.Rd | 257 +-- berryFunctions-1.15.0/berryFunctions/man/monthLabs.Rd | 99 - berryFunctions-1.15.0/berryFunctions/man/movAv.Rd | 221 +-- berryFunctions-1.15.0/berryFunctions/man/movAvLines.Rd | 95 - berryFunctions-1.15.0/berryFunctions/man/na9.Rd | 89 - berryFunctions-1.15.0/berryFunctions/man/nameSample.Rd | 133 +- berryFunctions-1.15.0/berryFunctions/man/newFilename.Rd |only berryFunctions-1.15.0/berryFunctions/man/normPlot.Rd | 141 +- berryFunctions-1.15.0/berryFunctions/man/owa.Rd | 163 +- berryFunctions-1.15.0/berryFunctions/man/panelDim.Rd | 169 +- berryFunctions-1.15.0/berryFunctions/man/pdfpng.Rd |only berryFunctions-1.15.0/berryFunctions/man/popleaf.Rd |only berryFunctions-1.15.0/berryFunctions/man/pretty2.Rd | 93 - berryFunctions-1.15.0/berryFunctions/man/quantileBands.Rd | 161 +- berryFunctions-1.15.0/berryFunctions/man/quantileMean.Rd | 221 +-- berryFunctions-1.15.0/berryFunctions/man/rainbow2.Rd | 77 - berryFunctions-1.15.0/berryFunctions/man/removeSpace.Rd | 97 - berryFunctions-1.15.0/berryFunctions/man/rescale.Rd | 83 - berryFunctions-1.15.0/berryFunctions/man/runAxis.Rd | 79 - berryFunctions-1.15.0/berryFunctions/man/seasonality.Rd | 341 ++--- berryFunctions-1.15.0/berryFunctions/man/seqPal.Rd | 127 - berryFunctions-1.15.0/berryFunctions/man/seqR.Rd | 87 - berryFunctions-1.15.0/berryFunctions/man/showPal.Rd | 59 berryFunctions-1.15.0/berryFunctions/man/smallPlot.Rd | 321 ++-- berryFunctions-1.15.0/berryFunctions/man/smoothLines.Rd | 113 - berryFunctions-1.15.0/berryFunctions/man/sortDF.Rd | 79 - berryFunctions-1.15.0/berryFunctions/man/spiralDate.Rd | 193 +- berryFunctions-1.15.0/berryFunctions/man/spiralDateAnim.Rd | 119 - berryFunctions-1.15.0/berryFunctions/man/superPos.Rd | 191 +- berryFunctions-1.15.0/berryFunctions/man/tableColVal.Rd | 163 +- berryFunctions-1.15.0/berryFunctions/man/textField.Rd | 291 ++-- berryFunctions-1.15.0/berryFunctions/man/timer.Rd | 85 - berryFunctions-1.15.0/berryFunctions/man/toupper1.Rd | 65 berryFunctions-1.15.0/berryFunctions/man/traceCall.Rd | 94 - berryFunctions-1.15.0/berryFunctions/man/truncMessage.Rd | 85 - berryFunctions-1.15.0/berryFunctions/man/tryStack.Rd | 7 berryFunctions-1.15.0/berryFunctions/man/unitHydrograph.Rd | 149 +- berryFunctions-1.15.0/berryFunctions/man/yearSample.Rd | 73 - berryFunctions-1.15.0/berryFunctions/vignettes/berryFunctions.Rmd | 652 +++++----- 139 files changed, 7492 insertions(+), 7392 deletions(-)
More information about berryFunctions at CRAN
Permanent link
Title: Effects under Linear, Logistic and Poisson Regression Models
with Transformed Variables
Description: Computation of effects under linear, logistic and Poisson regression models with transformed variables. Logarithm and power transformations are allowed. Effects can be displayed both numerically and graphically in both the original and the transformed space of the variables.
Author: Jose Barrera-Gomez and Xavier Basagana
Maintainer: Jose Barrera-Gomez <jose.barrera@isglobal.org>
Diff between tlm versions 0.1.4 dated 2016-05-04 and 0.1.5 dated 2017-04-10
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++------------ NEWS | 13 +++++++++++++ R/tlm.R | 4 ++++ build/vignette.rds |binary inst/doc/tlm-manual.pdf |binary inst/doc/tlm.Rnw | 10 +++++----- inst/doc/tlm.pdf |binary man/MY.Rd | 11 ++++++----- man/effect.Rd | 8 ++++---- man/tlm-package.Rd | 4 ++-- man/tlm.Rd | 31 ++++++++++++++++++++++--------- vignettes/tlm.Rnw | 10 +++++----- 13 files changed, 78 insertions(+), 47 deletions(-)
Title: Genetic Analysis of Populations with Mixed Reproduction
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the 'adegenet' package.
Author: Zhian N. Kamvar [cre, aut],
Javier F. Tabima [aut],
Sydney E. Everhart [ctb, dtc],
Jonah C. Brooks [aut],
Stacy A. Krueger-Hadfield [ctb],
Erik Sotka [ctb],
Brian J. Knaus [ctb],
Niklaus J. Grunwald [ths]
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>
Diff between poppr versions 2.3.0 dated 2016-11-23 and 2.4.0 dated 2017-04-10
DESCRIPTION | 13 - MD5 | 235 +++++++++++----------- NAMESPACE | 4 NEWS | 76 +++++++ R/Index_calculations.r | 4 R/bitwise.r | 105 ++++++++- R/bruvo.r | 1 R/classes.r | 11 - R/file_handling.r | 69 +++++- R/ia_jackknife.R |only R/internal.r | 368 +++++++++++++---------------------- R/internal_methods.R | 2 R/methods.r | 29 ++ R/mlg.r | 87 +++++--- R/poppr.R | 161 +++++++++++++++ R/round_robin.R | 196 +++++++++++++----- R/sandbox.r | 37 --- R/visualizations.r | 57 ++++- README.md | 12 - build/vignette.rds |binary inst/doc/algo.Rnw | 8 inst/doc/algo.pdf |binary inst/doc/mlg.html | 22 +- inst/doc/poppr_manual.R | 4 inst/doc/poppr_manual.Rmd | 4 inst/doc/poppr_manual.html | 39 +-- man/Aeut.Rd | 3 man/MLG-accessors.Rd | 33 +-- man/MLG-class.Rd | 10 man/MLG-method.Rd | 19 - man/Pinf.Rd | 3 man/Pram.Rd | 3 man/aboot.Rd | 1 man/bitwise.dist.Rd | 28 +- man/bitwise.ia.Rd | 7 man/bootgen-class.Rd | 3 man/bootgen-methods.Rd | 3 man/bruvo.boot.Rd | 7 man/bruvo.dist.Rd | 7 man/bruvo.msn.Rd | 7 man/bruvomat-class.Rd | 2 man/bruvomat-methods.Rd | 5 man/clonecorrect.Rd | 1 man/coercion-methods.Rd | 11 - man/cutoff_predictor.Rd | 7 man/diss.dist.Rd | 7 man/diversity_boot.Rd | 7 man/diversity_ci.Rd | 7 man/diversity_stats.Rd | 7 man/filter_stats.Rd | 7 man/fix_replen.Rd | 7 man/genclone-class.Rd | 22 +- man/genclone-method.Rd | 5 man/genetic_distance.Rd | 19 - man/genind2genalex.Rd | 7 man/genotype_curve.Rd | 25 +- man/getfile.Rd | 1 man/grapes-greater-than-grapes.Rd | 1 man/greycurve.Rd | 1 man/ia.Rd | 7 man/imsn.Rd | 8 man/incomp.Rd | 1 man/info_table.Rd | 1 man/informloci.Rd | 1 man/is.clone.Rd | 3 man/jack.ia.Rd |only man/levels-methods.Rd | 1 man/locus_table.Rd | 7 man/missingno.Rd | 7 man/mlg.Rd | 58 ++++- man/mlg.filter.Rd | 5 man/mll-method.Rd | 17 - man/mll.custom.Rd | 7 man/mll.reset-method.Rd | 7 man/monpop.Rd | 3 man/old2new_genclone.Rd | 1 man/partial_clone.Rd | 5 man/pgen.Rd | 9 man/plot_filter_stats.Rd | 7 man/plot_poppr_msn.Rd | 7 man/poppr-package.Rd | 11 - man/poppr.Rd | 7 man/poppr.all.Rd | 7 man/poppr.amova.Rd | 3 man/poppr.msn.Rd | 9 man/poppr_has_parallel.Rd | 1 man/popsub.Rd | 1 man/private_alleles.Rd | 1 man/psex.Rd | 107 +++++++--- man/rare_allele_correction.Rd | 8 man/read.genalex.Rd | 7 man/recode_polyploids.Rd | 1 man/rraf.Rd | 10 man/rrmlg.Rd | 7 man/samp.ia.Rd | 7 man/shufflepop.Rd | 7 man/snpclone-coercion-methods.Rd | 1 man/snpclone-method.Rd | 7 man/test_replen.Rd | 7 man/unique-methods.Rd | 3 man/win.ia.Rd | 44 +++- src/bitwise_distance.c | 21 + src/init.c |only src/mlg_clustering.c | 2 src/mlg_counter.c | 7 src/msn.c | 2 src/permut_shuffler.c | 14 - src/poppr_distance.c | 56 +++-- tests/testthat/test-genclone.R | 13 + tests/testthat/test-genotype_curve.R |only tests/testthat/test-import.R | 49 ++++ tests/testthat/test-jackia.R |only tests/testthat/test-mlg.R | 64 ++++++ tests/testthat/test-plots.R | 88 +++++++- tests/testthat/test-poppr.R | 10 tests/testthat/test-round-robin.R | 80 ++++++- tests/testthat/test-snpclone.R | 53 ++++- tests/testthat/test-values.R | 28 ++ tests/testthat/test-winia.R |only vignettes/algo.Rnw | 8 vignettes/poppr_manual.Rmd | 4 vignettes/small_logo.png |only 122 files changed, 1824 insertions(+), 920 deletions(-)
Title: Lexicons for Text Analysis
Description: A collection of lexical hash tables, dictionaries, and
word lists.
Author: Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between lexicon versions 0.2.0 dated 2017-03-07 and 0.3.1 dated 2017-04-10
DESCRIPTION | 27 ++-- MD5 | 95 ++++++++-------- NAMESPACE | 2 NEWS | 19 +++ R/available_data.R |only R/hash_sentiment_jockers.R | 7 - R/lexicon-package.R | 1 README.md | 225 +++++++++++++++++++++++++-------------- data/freq_first_names.rda |binary data/freq_last_names.rda |binary inst/CITATION | 4 man/available_data.Rd |only man/common_names.Rd | 1 man/discourse_markers_alemany.Rd | 1 man/dodds_sentiment.Rd | 1 man/freq_first_names.Rd | 1 man/freq_last_names.Rd | 1 man/function_words.Rd | 1 man/grady_augmented.Rd | 1 man/hash_emoticons.Rd | 1 man/hash_grady_pos.Rd | 1 man/hash_lemmas.Rd | 1 man/hash_power.Rd | 1 man/hash_sentiment_huliu.Rd | 1 man/hash_sentiment_jockers.Rd | 3 man/hash_sentiment_nrc.Rd | 1 man/hash_sentiment_sentiword.Rd | 1 man/hash_strength.Rd | 1 man/hash_syllable.Rd | 1 man/hash_valence_shifters.Rd | 1 man/key_abbreviation.Rd | 1 man/key_contractions.Rd | 1 man/key_grade.Rd | 2 man/key_rating.Rd | 1 man/key_sentiment_jockers.Rd | 3 man/lexicon.Rd | 3 man/nrc_emotions.Rd | 1 man/pos_action_verb.Rd | 1 man/pos_adverb.Rd | 1 man/pos_df_pronouns.Rd | 1 man/pos_interjections.Rd | 1 man/pos_preposition.Rd | 1 man/sw_buckley_salton.Rd | 1 man/sw_dolch.Rd | 1 man/sw_fry_100.Rd | 1 man/sw_fry_1000.Rd | 1 man/sw_fry_200.Rd | 1 man/sw_fry_25.Rd | 1 man/sw_onix.Rd | 1 tools |only 50 files changed, 243 insertions(+), 181 deletions(-)
Title: Graph Theory Analysis of Brain MRI Data
Description: A set of tools for performing graph theory analysis of brain MRI
data. It is best suited to data from a Freesurfer analysis (cortical
thickness, volumes, local gyrification index, surface area), but also works
with e.g., tractography data from FSL and fMRI data from DPABI. It contains
a graphical user interface for graph visualization and data exploration and
several functions for generating useful figures.
Author: Christopher G. Watson <cgwatson@bu.edu>
Maintainer: Christopher G. Watson <cgwatson@bu.edu>
Diff between brainGraph versions 0.72.0 dated 2016-10-10 and 1.0.0 dated 2017-04-10
brainGraph-0.72.0/brainGraph/R/SPM.R |only brainGraph-0.72.0/brainGraph/R/auc_diff.R |only brainGraph-0.72.0/brainGraph/R/color_edges.R |only brainGraph-0.72.0/brainGraph/R/color_vertices.R |only brainGraph-0.72.0/brainGraph/R/count_homologous.R |only brainGraph-0.72.0/brainGraph/R/count_interlobar.R |only brainGraph-0.72.0/brainGraph/R/dti_create_mats.R |only brainGraph-0.72.0/brainGraph/R/graph_contract_brain.R |only brainGraph-0.72.0/brainGraph/R/graph_neighborhood_multiple.R |only brainGraph-0.72.0/brainGraph/R/part_coeff.R |only brainGraph-0.72.0/brainGraph/R/permute_group_auc.R |only brainGraph-0.72.0/brainGraph/R/rich_club_attrs.R |only brainGraph-0.72.0/brainGraph/R/rich_club_coeff.R |only brainGraph-0.72.0/brainGraph/R/rich_club_norm.R |only brainGraph-0.72.0/brainGraph/R/rich_core.R |only brainGraph-0.72.0/brainGraph/R/rotation.R |only brainGraph-0.72.0/brainGraph/R/vec_transform.R |only brainGraph-0.72.0/brainGraph/R/within_module_degree_z_score.R |only brainGraph-0.72.0/brainGraph/man/SPM.Rd |only brainGraph-0.72.0/brainGraph/man/aop.Rd |only brainGraph-0.72.0/brainGraph/man/color.edges.Rd |only brainGraph-0.72.0/brainGraph/man/color.vertices.Rd |only brainGraph-0.72.0/brainGraph/man/count_homologous.Rd |only brainGraph-0.72.0/brainGraph/man/count_interlobar.Rd |only brainGraph-0.72.0/brainGraph/man/dti_create_mats.Rd |only brainGraph-0.72.0/brainGraph/man/edge_spatial_dist.Rd |only brainGraph-0.72.0/brainGraph/man/graph.contract.brain.Rd |only brainGraph-0.72.0/brainGraph/man/graph.efficiency.Rd |only brainGraph-0.72.0/brainGraph/man/graph_neighborhood_multiple.Rd |only brainGraph-0.72.0/brainGraph/man/loo.Rd |only brainGraph-0.72.0/brainGraph/man/part.coeff.Rd |only brainGraph-0.72.0/brainGraph/man/permute.group.auc.Rd |only brainGraph-0.72.0/brainGraph/man/rich.club.attrs.Rd |only brainGraph-0.72.0/brainGraph/man/rich.club.coeff.Rd |only brainGraph-0.72.0/brainGraph/man/rich.club.norm.Rd |only brainGraph-0.72.0/brainGraph/man/rich.core.Rd |only brainGraph-0.72.0/brainGraph/man/set.brainGraph.attributes.Rd |only brainGraph-0.72.0/brainGraph/man/vertex_spatial_dist.Rd |only brainGraph-0.72.0/brainGraph/man/within_module_deg_z_score.Rd |only brainGraph-0.72.0/brainGraph/man/write.brainnet.Rd |only brainGraph-1.0.0/brainGraph/DESCRIPTION | 18 brainGraph-1.0.0/brainGraph/MD5 | 213 ++++------ brainGraph-1.0.0/brainGraph/NAMESPACE | 33 - brainGraph-1.0.0/brainGraph/NEWS.md |only brainGraph-1.0.0/brainGraph/R/NBS.R | 82 ++- brainGraph-1.0.0/brainGraph/R/analysis_random_graphs.R | 6 brainGraph-1.0.0/brainGraph/R/assign_lobes.R | 125 ++--- brainGraph-1.0.0/brainGraph/R/boot_global.R | 2 brainGraph-1.0.0/brainGraph/R/brainGraph_GLM.R |only brainGraph-1.0.0/brainGraph/R/brainGraph_init.R | 30 - brainGraph-1.0.0/brainGraph/R/centr_lev.R | 26 - brainGraph-1.0.0/brainGraph/R/choose_edges.R | 56 +- brainGraph-1.0.0/brainGraph/R/color_vertices_edges.R |only brainGraph-1.0.0/brainGraph/R/contract_brainGraph.R |only brainGraph-1.0.0/brainGraph/R/cor_diff_test.R | 4 brainGraph-1.0.0/brainGraph/R/count_edges.R |only brainGraph-1.0.0/brainGraph/R/create_mats.R |only brainGraph-1.0.0/brainGraph/R/edge_asymmetry.R | 44 -- brainGraph-1.0.0/brainGraph/R/get_resid.R | 8 brainGraph-1.0.0/brainGraph/R/graph_attr_dt.R | 7 brainGraph-1.0.0/brainGraph/R/graph_efficiency.R | 80 ++- brainGraph-1.0.0/brainGraph/R/individ_contrib.R | 48 -- brainGraph-1.0.0/brainGraph/R/make_ego_brainGraph.R |only brainGraph-1.0.0/brainGraph/R/make_empty_brainGraph.R | 2 brainGraph-1.0.0/brainGraph/R/permute_group.R | 134 +++--- brainGraph-1.0.0/brainGraph/R/plot_brainGraph.R | 154 +++---- brainGraph-1.0.0/brainGraph/R/plot_brainGraph_gui.R | 3 brainGraph-1.0.0/brainGraph/R/plot_brainGraph_list.R | 3 brainGraph-1.0.0/brainGraph/R/plot_brainGraph_multi.R |only brainGraph-1.0.0/brainGraph/R/plot_corr_mat.R | 17 brainGraph-1.0.0/brainGraph/R/plot_global.R | 2 brainGraph-1.0.0/brainGraph/R/plot_group_means.R | 11 brainGraph-1.0.0/brainGraph/R/plot_perm_diffs.R | 12 brainGraph-1.0.0/brainGraph/R/plot_rich_norm.R | 7 brainGraph-1.0.0/brainGraph/R/plot_vertex_measures.R | 2 brainGraph-1.0.0/brainGraph/R/rich_club.R |only brainGraph-1.0.0/brainGraph/R/set_brainGraph_attributes.R | 120 +++-- brainGraph-1.0.0/brainGraph/R/sim_rand_graph_clust.R | 45 -- brainGraph-1.0.0/brainGraph/R/sim_rand_graph_par.R | 33 - brainGraph-1.0.0/brainGraph/R/spatial_dist.R | 49 +- brainGraph-1.0.0/brainGraph/R/update_brainGraph_gui.R | 58 +- brainGraph-1.0.0/brainGraph/R/utils.R |only brainGraph-1.0.0/brainGraph/R/vertex_attr_dt.R | 65 +-- brainGraph-1.0.0/brainGraph/R/vertex_roles.R |only brainGraph-1.0.0/brainGraph/R/vulnerability.R | 31 - brainGraph-1.0.0/brainGraph/R/write_brainnet.R | 20 brainGraph-1.0.0/brainGraph/data/craddock200.rda |only brainGraph-1.0.0/brainGraph/man/NBS.Rd | 31 - brainGraph-1.0.0/brainGraph/man/analysis_random_graphs.Rd | 9 brainGraph-1.0.0/brainGraph/man/assign_lobes.Rd | 3 brainGraph-1.0.0/brainGraph/man/auc_diff.Rd | 3 brainGraph-1.0.0/brainGraph/man/boot_global.Rd | 7 brainGraph-1.0.0/brainGraph/man/brainGraph_GLM.Rd |only brainGraph-1.0.0/brainGraph/man/brainGraph_GLM_design.Rd |only brainGraph-1.0.0/brainGraph/man/brainGraph_GLM_fit.Rd |only brainGraph-1.0.0/brainGraph/man/brainGraph_init.Rd | 5 brainGraph-1.0.0/brainGraph/man/centr_lev.Rd | 14 brainGraph-1.0.0/brainGraph/man/check.resid.Rd | 7 brainGraph-1.0.0/brainGraph/man/choose.edges.Rd | 13 brainGraph-1.0.0/brainGraph/man/color_vertices_edges.Rd |only brainGraph-1.0.0/brainGraph/man/contract_brainGraph.Rd |only brainGraph-1.0.0/brainGraph/man/cor.diff.test.Rd | 5 brainGraph-1.0.0/brainGraph/man/corr.matrix.Rd | 7 brainGraph-1.0.0/brainGraph/man/count_edges.Rd |only brainGraph-1.0.0/brainGraph/man/craddock200.Rd |only brainGraph-1.0.0/brainGraph/man/create_mats.Rd |only brainGraph-1.0.0/brainGraph/man/delete_all_attr.Rd |only brainGraph-1.0.0/brainGraph/man/edge_asymmetry.Rd | 14 brainGraph-1.0.0/brainGraph/man/efficiency.Rd |only brainGraph-1.0.0/brainGraph/man/get.resid.Rd | 1 brainGraph-1.0.0/brainGraph/man/graph_attr_dt.Rd | 1 brainGraph-1.0.0/brainGraph/man/individ_contrib.Rd |only brainGraph-1.0.0/brainGraph/man/make_ego_brainGraph.Rd |only brainGraph-1.0.0/brainGraph/man/make_empty_brainGraph.Rd | 7 brainGraph-1.0.0/brainGraph/man/permute.group.Rd | 19 brainGraph-1.0.0/brainGraph/man/plot_boot.Rd | 7 brainGraph-1.0.0/brainGraph/man/plot_brainGraph.Rd | 22 - brainGraph-1.0.0/brainGraph/man/plot_brainGraph_gui.Rd | 7 brainGraph-1.0.0/brainGraph/man/plot_brainGraph_list.Rd | 7 brainGraph-1.0.0/brainGraph/man/plot_brainGraph_mni.Rd | 1 brainGraph-1.0.0/brainGraph/man/plot_brainGraph_multi.Rd |only brainGraph-1.0.0/brainGraph/man/plot_corr_mat.Rd | 7 brainGraph-1.0.0/brainGraph/man/plot_global.Rd | 1 brainGraph-1.0.0/brainGraph/man/plot_group_means.Rd | 7 brainGraph-1.0.0/brainGraph/man/plot_perm_diffs.Rd | 7 brainGraph-1.0.0/brainGraph/man/plot_rich_norm.Rd | 10 brainGraph-1.0.0/brainGraph/man/plot_vertex_measures.Rd | 3 brainGraph-1.0.0/brainGraph/man/rich_club_attrs.Rd |only brainGraph-1.0.0/brainGraph/man/rich_club_coeff.Rd |only brainGraph-1.0.0/brainGraph/man/rich_club_norm.Rd |only brainGraph-1.0.0/brainGraph/man/rich_core.Rd |only brainGraph-1.0.0/brainGraph/man/robustness.Rd | 7 brainGraph-1.0.0/brainGraph/man/rotation.Rd | 3 brainGraph-1.0.0/brainGraph/man/set_brainGraph_attr.Rd |only brainGraph-1.0.0/brainGraph/man/sim.rand.graph.clust.Rd | 10 brainGraph-1.0.0/brainGraph/man/sim.rand.graph.par.Rd | 27 - brainGraph-1.0.0/brainGraph/man/small.world.Rd | 7 brainGraph-1.0.0/brainGraph/man/spatial_dist.Rd |only brainGraph-1.0.0/brainGraph/man/update_brainGraph_gui.Rd | 1 brainGraph-1.0.0/brainGraph/man/vec.transform.Rd | 3 brainGraph-1.0.0/brainGraph/man/vertex_attr_dt.Rd | 17 brainGraph-1.0.0/brainGraph/man/vertex_roles.Rd |only brainGraph-1.0.0/brainGraph/man/vulnerability.Rd | 17 brainGraph-1.0.0/brainGraph/man/write_brainnet.Rd |only 144 files changed, 910 insertions(+), 957 deletions(-)
Title: Analyzing Archival Tagging Data
Description: A set of functions to generate, access and analyze standard data products from archival tagging data.
Author: Robert Bauer
Maintainer: Robert Bauer <robert.bauer@ird.fr>
Diff between RchivalTag versions 0.0.2 dated 2017-03-24 and 0.0.3 dated 2017-04-10
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/plot_TS.r | 12 ++++++++---- R/read_PDT.r | 7 ++++--- inst/doc/RchivalTag.pdf |binary 6 files changed, 24 insertions(+), 16 deletions(-)
Title: Weighted Win Loss Statistics and their Variances
Description: Calculate the (weighted) win loss statistics including the win ratio, win difference and win product
and their variances, with which the p-values are also calculated. The variance estimation is based on
Luo et al. (2015) <doi:10.1111/biom.12225> and Luo et al. (2017) <doi:10.1002/sim.7284>. This package also calculates general win loss statistics with
user-specified win loss function with variance estimation based on
Bebu and Lachin (2016) <doi:10.1093/biostatistics/kxv032>.
Author: Xiaodong Luo [aut, cre],
Junshan Qiu [ctb],
Steven Bai [ctb],
Hong Tian [ctb],
Mike Mikailov [ctb],
Sanofi [cph]
Maintainer: Xiaodong Luo <Xiaodong.Luo@sanofi.com>
Diff between WWR versions 1.0.0 dated 2017-02-11 and 1.1.0 dated 2017-04-10
WWR-1.0.0/WWR/src/WWR_Prog.f90 |only WWR-1.1.0/WWR/DESCRIPTION | 18 ++- WWR-1.1.0/WWR/MD5 | 23 ++--- WWR-1.1.0/WWR/NAMESPACE | 18 +-- WWR-1.1.0/WWR/R/genwr.R |only WWR-1.1.0/WWR/R/winratio.R | 62 +++++++------ WWR-1.1.0/WWR/R/wwratio.R | 11 +- WWR-1.1.0/WWR/build/partial.rdb |binary WWR-1.1.0/WWR/man/WWR-package.Rd | 4 WWR-1.1.0/WWR/man/genwr.Rd |only WWR-1.1.0/WWR/man/winratio.Rd | 169 ++++++++++++++++++------------------ WWR-1.1.0/WWR/man/wlogr2.Rd | 103 +++++++++++----------- WWR-1.1.0/WWR/man/wwratio.Rd | 179 +++++++++++++++++++-------------------- WWR-1.1.0/WWR/src/Prog.f90 |only WWR-1.1.0/WWR/src/WWR_init.c |only 15 files changed, 305 insertions(+), 282 deletions(-)
Title: Parameterized Queries Extension for RODBC
Description: An extension for RODBC package adding support for parameterized
queries.
Author: Mateusz Zoltak [aut, cre],
Brian Ripley [aut],
Michael Lapsley [aut],
Will Beasley [ctb],
Juergen Altfeld [ctb]
Maintainer: Mateusz Zoltak <zozlak@zozlak.org>
Diff between RODBCext versions 0.2.7 dated 2016-09-24 and 0.3.0 dated 2017-04-10
DESCRIPTION | 27 MD5 | 42 - NAMESPACE | 2 NEWS | 15 R/odbcFetchRows.R | 79 +- R/odbcGetQueryTimeout.R |only R/odbcSetQueryTimeout.R |only R/odbcValidChannel.R | 46 - R/sqlExecute.R | 376 ++++++------ R/sqlFetchMore.R | 79 +- R/sqlPrepare.R | 52 + build/vignette.rds |binary inst/doc/Parameterized_SQL_queries.Rmd | 977 +++++++++++++++----------------- inst/doc/Parameterized_SQL_queries.html | 57 + man/odbcGetQueryTimeout.Rd |only man/odbcSetQueryTimeout.Rd |only man/sqlExecute.Rd | 11 man/sqlPrepare.Rd | 11 src/RODBC.c | 17 src/RODBCext.c | 98 ++- src/RODBCext.h | 3 tests |only vignettes/Parameterized_SQL_queries.Rmd | 977 +++++++++++++++----------------- 23 files changed, 1521 insertions(+), 1348 deletions(-)
Title: Easy Interface to the Statistical Disclosure Control Package
'sdcTable'
Description: The main function, ProtectTable(), performs table suppression according to a
frequency rule with a data set as the only required input. Within this function,
protectTable(), protectLinkedTables() or runArgusBatchFile() in package 'sdcTable' is called.
Lists of level-hierarchy (parameter 'dimList') and other required input to these functions
are created automatically.
The function, PTgui(), starts a graphical user interface based on the shiny package.
Author: Øyvind Langsrud
Maintainer: Øyvind Langsrud <oyl@ssb.no>
Diff between easySdcTable versions 0.2.1 dated 2017-02-16 and 0.3.0 dated 2017-04-10
DESCRIPTION | 19 +++---- MD5 | 32 ++++++----- NAMESPACE | 9 +++ R/PTwrap.R |only R/ProtectTable.R | 99 +++++++++++++++++++++++++++++++++---- R/ProtectTable1.R | 70 ++++++++++++++++++++++---- R/PtGui.R |only build/vignette.rds |binary inst/doc/easySdcTableVignette.R | 11 ++++ inst/doc/easySdcTableVignette.Rmd | 20 +++++++ inst/doc/easySdcTableVignette.html | 15 +++++ man/EasyData.Rd | 1 man/IncDefault.Rd | 1 man/PTgui.Rd |only man/PTwrap.Rd |only man/ProtectTable.Rd | 49 ++++++++++++++++-- man/ProtectTable1.Rd | 13 ++-- man/sosialFiktiv.Rd | 1 vignettes/easySdcTableVignette.Rmd | 20 +++++++ 19 files changed, 301 insertions(+), 59 deletions(-)
Title: Analyzes Clickstreams Based on Markov Chains
Description: A set of tools to read, analyze and write lists of click sequences
on websites (i.e., clickstream). A click can be represented by a number,
character or string. Clickstreams can be modeled as zero- (only computes
occurrence probabilities), first- or higher-order Markov chains.
Author: Michael Scholz
Maintainer: Michael Scholz <michael.scholz@uni-passau.de>
Diff between clickstream versions 1.1.9 dated 2016-10-14 and 1.2.0 dated 2017-04-10
DESCRIPTION | 15 +++---- MD5 | 57 ++++++++++++++------------- NAMESPACE | 6 ++ NEWS | 7 +++ R/MarkovChain.r | 76 ++++++++++++++++++++++++++++++++++++- R/clickstream-package.R | 6 +- man/MarkovChain-class.Rd | 13 ++---- man/Pattern-class.Rd | 21 ++++------ man/absorbingStates-methods.Rd | 11 ++--- man/as.transactions.Rd | 12 ++--- man/clickstream-package.Rd | 28 +++++-------- man/clusterClickstreams.Rd | 48 +++++++++++------------ man/fitMarkovChain.Rd | 75 +++++++++++++++++------------------- man/frequencies.Rd | 15 ++----- man/hmPlot-methods.Rd |only man/predict-methods.Rd | 51 +++++++++++++----------- man/predict.ClickstreamClusters.Rd | 31 +++++++-------- man/print.ClickstreamClusters.Rd | 20 ++++----- man/print.Clickstreams.Rd | 13 ++---- man/print.MarkovChainSummary.Rd | 14 +++--- man/randomClicks-methods.Rd | 29 +++++++------- man/randomClickstreams.Rd | 29 +++++++------- man/readClickstreams.Rd | 32 +++++++-------- man/show-methods.Rd | 9 ++-- man/states-methods.Rd | 10 ++-- man/summary-methods.Rd | 25 +++++------- man/summary.ClickstreamClusters.Rd | 21 ++++------ man/summary.Clickstreams.Rd | 14 ++---- man/transientStates-methods.Rd | 12 ++--- man/writeClickstreams.Rd | 28 ++++++------- 30 files changed, 400 insertions(+), 328 deletions(-)