Title: Gene-Based Segregation Test
Description: Implements the gene-based segregation test(GESE) and the weighted GESE test for identifying genes with causal variants of large effects for family-based sequencing data. The methods are described in Qiao, D. Lange, C., Laird, N.M., Won, S., Hobbs, B., et al. 2016. Gene-based segregation method for identifying rare variants for family-based sequencing studies. More details can be found at <http://scholar.harvard.edu/dqiao/gese>.
Author: Dandi Qiao, Michael H. Cho
Maintainer: Dandi Qiao <redaq@channing.harvard.edu>
Diff between GESE versions 1.0 dated 2016-08-05 and 2.0.0 dated 2016-11-16
DESCRIPTION | 10 +++++----- MD5 | 28 ++++++++++++++-------------- R/GESE.R | 12 ++++++++---- R/condSegProbF.R | 14 +++++++++++--- R/getPvalue_resampling.R | 4 ++-- R/getSegInfo.R | 2 +- R/segProb.R | 8 ++++---- build/partial.rdb |binary inst/doc/my-vignette.R | 6 +++--- inst/doc/my-vignette.Rmd | 12 ++++++------ inst/doc/my-vignette.pdf |binary man/GESE-package.Rd | 2 +- man/GESE.Rd | 9 ++++++--- man/condSegProbF.Rd | 2 +- vignettes/my-vignette.Rmd | 12 ++++++------ 15 files changed, 68 insertions(+), 53 deletions(-)
Title: Residual Diagnostics for Hierarchical (Multi-Level / Mixed)
Regression Models
Description: The 'DHARMa' package uses a simulation-based approach to create
readily interpretable scaled (quantile) residuals from fitted generalized linear mixed
models. Currently supported are all 'merMod' classes from 'lme4' ('lmerMod', 'glmerMod'),
'glm' (including 'negbin' from 'MASS', but excluding quasi-distributions) and 'lm' model
classes. Alternatively, externally created simulations, e.g. posterior predictive simulations
from Bayesian software such as 'JAGS', 'STAN', or 'Bugs' can be processed as well.
The resulting residuals are standardized to values between 0 and 1 and can be interpreted
as intuitively as residuals from a linear regression. The package also provides a number of
plot and test functions for typical model misspecification problem, such as
over/underdispersion, zero-inflation, and spatial and temporal autocorrelation.
Author: Florian Hartig [aut, cre]
Maintainer: Florian Hartig <florian.hartig@biologie.uni-regensburg.de>
Diff between DHARMa versions 0.1.0 dated 2016-08-26 and 0.1.1 dated 2016-11-16
DHARMa-0.1.0/DHARMa/R/testOverdispersionParametric.R |only DHARMa-0.1.1/DHARMa/DESCRIPTION | 22 +- DHARMa-0.1.1/DHARMa/MD5 | 40 ++- DHARMa-0.1.1/DHARMa/NAMESPACE | 2 DHARMa-0.1.1/DHARMa/NEWS | 14 + DHARMa-0.1.1/DHARMa/R/DHARMa.R | 57 ++++- DHARMa-0.1.1/DHARMa/R/benchmarkPvalues.R |only DHARMa-0.1.1/DHARMa/R/createData.R | 87 ++++--- DHARMa-0.1.1/DHARMa/R/plotResiduals.R | 6 DHARMa-0.1.1/DHARMa/R/simulateResiduals.R | 10 DHARMa-0.1.1/DHARMa/R/testsParametric.R |only DHARMa-0.1.1/DHARMa/inst/doc/DHARMa.R | 6 DHARMa-0.1.1/DHARMa/inst/doc/DHARMa.Rmd | 125 ++++++----- DHARMa-0.1.1/DHARMa/inst/doc/DHARMa.html | 132 ++++++------ DHARMa-0.1.1/DHARMa/inst/examples/benchmarkUniformityHelp.R | 2 DHARMa-0.1.1/DHARMa/man/DHARMa.Rd | 4 DHARMa-0.1.1/DHARMa/man/benchmarkP.Rd |only DHARMa-0.1.1/DHARMa/man/benchmarkUniformity.Rd | 2 DHARMa-0.1.1/DHARMa/man/createDHARMa.Rd |only DHARMa-0.1.1/DHARMa/man/testOverdispersionParametric.Rd | 2 DHARMa-0.1.1/DHARMa/tests/testthat/Rplots.pdf |only DHARMa-0.1.1/DHARMa/tests/testthat/testModelTypes.R | 70 ++++-- DHARMa-0.1.1/DHARMa/vignettes/DHARMa.Rmd | 125 ++++++----- DHARMa-0.1.1/DHARMa/vignettes/ECDFmotivation.pdf |only DHARMa-0.1.1/DHARMa/vignettes/ECDFmotivation.png |only 25 files changed, 412 insertions(+), 294 deletions(-)
Title: Validation Tools for Artificial Neural Networks
Description: Methods and tools for analysing and validating the outputs
and modelled functions of artificial neural networks (ANNs) in terms
of predictive, replicative and structural validity. Also provides a
method for fitting feed-forward ANNs with a single hidden layer.
Author: Greer B. Humphrey [aut, cre]
Maintainer: Greer B. Humphrey <greer.humphrey@student.adelaide.edu.au>
Diff between validann versions 1.1.0 dated 2016-11-08 and 1.2.0 dated 2016-11-16
validann |only 1 file changed
Title: Datensätze und Übungsmaterial zu 'Large-Scale Assessment mit R'
Description: Dieses R-Paket stellt Zusatzmaterial in Form von Daten, Funktionen
und R-Hilfe-Seiten für den Herausgeberband Breit, S. und Schreiner,
C. (Hrsg.). (2016). "Large-Scale Assessment mit R: Methodische Grundlagen
der österreichischen Bildungsstandardüberprüfung." Wien: facultas.
(ISBN: 978-3-7089-1343-8, <https://www.bifie.at/node/3770>) zur
Verfügung.
Author: Thomas Kiefer [aut, cre], Alexander Robitzsch [aut], Matthias
Trendtel [aut], Robert Fellinger [aut]
Maintainer: Thomas Kiefer <t.kiefer@bifie.at>
Diff between LSAmitR versions 0.5-3 dated 2016-09-09 and 1.0-0 dated 2016-11-16
LSAmitR-0.5-3/LSAmitR/man/02_Stichprobenziehung__20160908.Rd |only LSAmitR-0.5-3/LSAmitR/man/03_StandardSetting__20160908.Rd |only LSAmitR-0.5-3/LSAmitR/man/07_ProduktiveKomp__20160902.Rd |only LSAmitR-0.5-3/LSAmitR/man/08_Missings__20160908.Rd |only LSAmitR-0.5-3/LSAmitR/man/09_FairerVergleich__20160908.Rd |only LSAmitR-1.0-0/LSAmitR/DESCRIPTION | 21 LSAmitR-1.0-0/LSAmitR/MD5 | 70 +- LSAmitR-1.0-0/LSAmitR/data/datenKapitel01.rda |binary LSAmitR-1.0-0/LSAmitR/data/datenKapitel02.rda |binary LSAmitR-1.0-0/LSAmitR/data/datenKapitel03.rda |binary LSAmitR-1.0-0/LSAmitR/data/datenKapitel04.rda |binary LSAmitR-1.0-0/LSAmitR/data/datenKapitel05.rda |binary LSAmitR-1.0-0/LSAmitR/data/datenKapitel06.rda |binary LSAmitR-1.0-0/LSAmitR/data/datenKapitel07.rda |binary LSAmitR-1.0-0/LSAmitR/data/datenKapitel08.rda |binary LSAmitR-1.0-0/LSAmitR/data/datenKapitel09.rda |binary LSAmitR-1.0-0/LSAmitR/data/datenKapitel10.rda |binary LSAmitR-1.0-0/LSAmitR/man/00_Konzeption__20160908.Rd | 26 - LSAmitR-1.0-0/LSAmitR/man/01_Testkonstruktion__20160908.Rd | 79 +-- LSAmitR-1.0-0/LSAmitR/man/02_Stichprobenziehung__20161115.Rd |only LSAmitR-1.0-0/LSAmitR/man/03_StandardSetting__20161111.Rd |only LSAmitR-1.0-0/LSAmitR/man/04_DIF__20160908.Rd | 68 +- LSAmitR-1.0-0/LSAmitR/man/05_Testdesign__20160908.Rd | 76 +-- LSAmitR-1.0-0/LSAmitR/man/06_Skalierung__20160908.Rd | 81 +-- LSAmitR-1.0-0/LSAmitR/man/07_ProduktiveKomp__20161111.Rd |only LSAmitR-1.0-0/LSAmitR/man/08_Missings__20161111.Rd |only LSAmitR-1.0-0/LSAmitR/man/09_FairerVergleich__20161111.Rd |only LSAmitR-1.0-0/LSAmitR/man/10_Reporting__20160908.Rd | 76 +-- LSAmitR-1.0-0/LSAmitR/man/11_Validierung__20160908.Rd | 22 LSAmitR-1.0-0/LSAmitR/man/LSAmitR-methods.Rd | 16 LSAmitR-1.0-0/LSAmitR/man/LSAmitR-package.Rd | 45 + LSAmitR-1.0-0/LSAmitR/man/datenKapitel01.Rd | 263 ++++++++-- LSAmitR-1.0-0/LSAmitR/man/datenKapitel02.Rd | 131 ++++- LSAmitR-1.0-0/LSAmitR/man/datenKapitel03.Rd | 239 ++++++++- LSAmitR-1.0-0/LSAmitR/man/datenKapitel04.Rd | 161 +++++- LSAmitR-1.0-0/LSAmitR/man/datenKapitel05.Rd | 276 ++++++++++- LSAmitR-1.0-0/LSAmitR/man/datenKapitel06.Rd | 275 ++++++++++ LSAmitR-1.0-0/LSAmitR/man/datenKapitel07.Rd | 275 ++++++++++ LSAmitR-1.0-0/LSAmitR/man/datenKapitel08.Rd | 266 ++++++++++ LSAmitR-1.0-0/LSAmitR/man/datenKapitel09.Rd | 122 ++++ LSAmitR-1.0-0/LSAmitR/man/datenKapitel10.Rd | 256 +++++++++- 41 files changed, 2408 insertions(+), 436 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-08-18 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-07 1.0-4
2013-01-16 1.0-3
2012-12-24 1.0-2
2012-12-16 1.0-1
2012-07-05 1.0-0
2011-12-03 0.9-4
2011-12-02 0.9-3
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)
higher moments approach as well as Lewbel's (2012) heteroskedasticity approach, Park and Gupta's (2012) joint estimation method that uses Gaussian
copula and Kim and Frees's (2007) 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.
Author: Raluca Gui,
Markus Meierer,
Rene Algesheimer
Maintainer: Raluca Gui <raluca.gui@business.uzh.ch>
Diff between REndo versions 1.0 dated 2015-12-08 and 1.1 dated 2016-11-16
REndo-1.0/REndo/R/LIV_loglik.R |only REndo-1.0/REndo/R/generics_liv.R |only REndo-1.0/REndo/R/hmlewbel.R |only REndo-1.0/REndo/R/liv.R |only REndo-1.0/REndo/data/dataHMLewbel.RData |only REndo-1.0/REndo/data/dataLIV.RData |only REndo-1.0/REndo/man/dataHMLewbel.Rd |only REndo-1.0/REndo/man/dataLIV.Rd |only REndo-1.0/REndo/man/hmlewbel.Rd |only REndo-1.0/REndo/man/liv-class.Rd |only REndo-1.0/REndo/man/liv.Rd |only REndo-1.1/REndo/DESCRIPTION | 33 +++---- REndo-1.1/REndo/MD5 | 86 ++++++++++++++----- REndo-1.1/REndo/NAMESPACE | 21 +++- REndo-1.1/REndo/R/checkAssumptions.R | 6 - REndo-1.1/REndo/R/cop_Cont1.R |only REndo-1.1/REndo/R/cop_Cont2.R |only REndo-1.1/REndo/R/cop_Discrete.R |only REndo-1.1/REndo/R/cop_bootsSE.R |only REndo-1.1/REndo/R/cop_logLik.R |only REndo-1.1/REndo/R/cop_pStar.R |only REndo-1.1/REndo/R/copulaCorrection.R |only REndo-1.1/REndo/R/copulaCorrection_class.R |only REndo-1.1/REndo/R/f_heterogenIV.R |only REndo-1.1/REndo/R/f_multilevelGMM.R |only REndo-1.1/REndo/R/heterogenIV.R |only REndo-1.1/REndo/R/heterogenIV_class.R |only REndo-1.1/REndo/R/higherMomentsIV.R |only REndo-1.1/REndo/R/internalIV.R | 24 ++--- REndo-1.1/REndo/R/latentIV.R |only REndo-1.1/REndo/R/latentIV_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/R/methods_copulaCorrection.R |only REndo-1.1/REndo/R/methods_latentIV.R |only REndo-1.1/REndo/R/methods_multilevelIV.R |only REndo-1.1/REndo/R/multilevelIV.R |only REndo-1.1/REndo/R/multilevelIV_class.R |only REndo-1.1/REndo/R/tScores.R |only REndo-1.1/REndo/README.md | 8 + REndo-1.1/REndo/data/dataCopC1.RData |only REndo-1.1/REndo/data/dataCopC2.RData |only REndo-1.1/REndo/data/dataCopDis.RData |only REndo-1.1/REndo/data/dataHigherMoments.RData |only REndo-1.1/REndo/data/dataLatentIV.RData |only REndo-1.1/REndo/data/tScores.RData |only REndo-1.1/REndo/man/boots.Rd |only REndo-1.1/REndo/man/checkAssumptions.Rd | 2 REndo-1.1/REndo/man/coef-copulaREndo-method.Rd |only REndo-1.1/REndo/man/coef-heterogenREndo-method.Rd |only REndo-1.1/REndo/man/coef-livREndo-method.Rd |only REndo-1.1/REndo/man/coef-mixedREndo-method.Rd |only REndo-1.1/REndo/man/copulaCont1.Rd |only REndo-1.1/REndo/man/copulaCorrection.Rd |only REndo-1.1/REndo/man/copulaDiscrete.Rd |only REndo-1.1/REndo/man/copulaMethod2.Rd |only REndo-1.1/REndo/man/copulaPStar.Rd |only REndo-1.1/REndo/man/copulaRendo-class.Rd |only REndo-1.1/REndo/man/dataCopC1.Rd |only REndo-1.1/REndo/man/dataCopC2.Rd |only REndo-1.1/REndo/man/dataCopDis.Rd |only REndo-1.1/REndo/man/dataHigherMoments.Rd |only REndo-1.1/REndo/man/dataLatentIV.Rd |only REndo-1.1/REndo/man/heterogenIV.Rd |only REndo-1.1/REndo/man/heterogenREndo-class.Rd |only REndo-1.1/REndo/man/higherMomentsIV.Rd |only REndo-1.1/REndo/man/internalIV.Rd | 20 ++-- REndo-1.1/REndo/man/latentIV.Rd |only REndo-1.1/REndo/man/livREndo-class.Rd |only REndo-1.1/REndo/man/logL.Rd | 4 REndo-1.1/REndo/man/logLL.Rd |only REndo-1.1/REndo/man/mixedREndo.Rd |only REndo-1.1/REndo/man/multilevelGMM.Rd |only REndo-1.1/REndo/man/multilevelIV.Rd |only REndo-1.1/REndo/man/summary-copulaREndo-method.Rd |only REndo-1.1/REndo/man/summary-heterogenREndo-method.Rd |only REndo-1.1/REndo/man/summary-livREndo-method.Rd |only REndo-1.1/REndo/man/summary-mixedREndo-method.Rd |only REndo-1.1/REndo/man/tScores.Rd |only 79 files changed, 132 insertions(+), 72 deletions(-)
Title: Quick Wraps 2
Description: A collection of (wrapper) functions the creator found useful
for quickly placing data summaries and formatted regression results into
'.Rnw' or '.Rmd' files. Functions for generating commonly used graphics,
such as receiver operating curves or Bland-Altman plots, are also provided
by 'qwraps2'. 'qwraps2' is a updated version of a package 'qwraps'. The
original version 'qwraps' was never submitted to CRAN but can be found at
<https://github.com/dewittpe/qwraps/>. The implementation and limited scope
of the functions within 'qwraps2' <https://github.com/dewittpe/qwraps2/> is
fundamentally different from 'qwraps'.
Author: Peter DeWitt [aut, cre],
Tell Bennett [ctb]
Maintainer: Peter DeWitt <dewittpe@gmail.com>
Diff between qwraps2 versions 0.2.2 dated 2016-09-27 and 0.2.3 dated 2016-11-16
DESCRIPTION | 8 +- MD5 | 36 +++++----- NAMESPACE | 3 R/confusion_matrix.R | 24 +----- R/ll.R |only R/n_perc.R | 6 - R/qable.R | 57 +++++++++++++++- R/qacf.R | 102 ++++++++++++++++++++++++++++- R/summary_table.R | 4 - README.md | 6 - build/vignette.rds |binary inst/doc/summary-statistics.R | 2 inst/doc/summary-statistics.Rmd | 8 +- inst/doc/summary-statistics.html | 136 ++++++++++++++++++++++++++++++--------- man/confusion_matrix.Rd | 24 +----- man/ll.Rd |only man/qable.Rd | 45 ++++++++++++ man/qacf.Rd | 44 ++++++++++++ tests/testthat/test-n_perc.R | 1 vignettes/summary-statistics.Rmd | 8 +- 20 files changed, 401 insertions(+), 113 deletions(-)
Title: Statistical Toolbox for Radiometric Geochronology
Description: An R implementation of Ken Ludwig's popular Isoplot add-in to Microsoft Excel. Currently plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using the 'York' approach. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith') plots. Deconvolves finite mixtures and minimum ages from heteroscedastic data. Future versions will include functionality for the Rb-Sr, Sm-Nd, Re-Os, Lu-Hf and U-series dating methods. A graphical user interface is provided as an RStudio Shiny app at <http://isoplotr.london-geochron.com>. Offline access to this interface will be provided at a later point in time.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between IsoplotR versions 0.7 dated 2016-08-13 and 0.8 dated 2016-11-16
IsoplotR-0.7/IsoplotR/man/botev.Rd |only IsoplotR-0.8/IsoplotR/DESCRIPTION | 8 - IsoplotR-0.8/IsoplotR/MD5 | 87 ++++++++------- IsoplotR-0.8/IsoplotR/NAMESPACE | 19 +++ IsoplotR-0.8/IsoplotR/R/ArAr.R | 10 - IsoplotR-0.8/IsoplotR/R/UPb.R | 30 ++--- IsoplotR-0.8/IsoplotR/R/UThHe.R | 2 IsoplotR-0.8/IsoplotR/R/age.R | 171 ++++++++++++++++++------------ IsoplotR-0.8/IsoplotR/R/agespectrum.R | 45 ++++--- IsoplotR-0.8/IsoplotR/R/botev.R | 18 --- IsoplotR-0.8/IsoplotR/R/cad.R | 46 ++++---- IsoplotR-0.8/IsoplotR/R/central.R |only IsoplotR-0.8/IsoplotR/R/concordia.R | 44 +++---- IsoplotR-0.8/IsoplotR/R/constants.R | 41 +++++-- IsoplotR-0.8/IsoplotR/R/discordia.R | 8 - IsoplotR-0.8/IsoplotR/R/documentation.R | 37 +++++- IsoplotR-0.8/IsoplotR/R/fissiontracks.R |only IsoplotR-0.8/IsoplotR/R/helioplot.R | 77 ------------- IsoplotR-0.8/IsoplotR/R/io.R | 88 ++++++++++++--- IsoplotR-0.8/IsoplotR/R/isochron.R | 21 +-- IsoplotR-0.8/IsoplotR/R/kde.R | 92 ++++++++++------ IsoplotR-0.8/IsoplotR/R/mds.R | 32 ++--- IsoplotR-0.8/IsoplotR/R/peakfit.R |only IsoplotR-0.8/IsoplotR/R/radialplot.R |only IsoplotR-0.8/IsoplotR/R/regression.R | 8 - IsoplotR-0.8/IsoplotR/R/toolbox.R | 20 ++- IsoplotR-0.8/IsoplotR/R/weightedmean.R | 122 +++++++++++++++------ IsoplotR-0.8/IsoplotR/data/examples.rda |binary IsoplotR-0.8/IsoplotR/inst/FT1.csv |only IsoplotR-0.8/IsoplotR/inst/FT2.csv |only IsoplotR-0.8/IsoplotR/inst/FT3.csv |only IsoplotR-0.8/IsoplotR/inst/MountTom.csv |only IsoplotR-0.8/IsoplotR/inst/constants.json | 16 ++ IsoplotR-0.8/IsoplotR/man/age.Rd | 138 ++++++++++++++---------- IsoplotR-0.8/IsoplotR/man/agespectrum.Rd | 36 +++--- IsoplotR-0.8/IsoplotR/man/cad.Rd | 33 +++-- IsoplotR-0.8/IsoplotR/man/central.Rd | 57 +++++++--- IsoplotR-0.8/IsoplotR/man/concordia.Rd | 10 - IsoplotR-0.8/IsoplotR/man/examples.Rd | 38 +++++- IsoplotR-0.8/IsoplotR/man/helioplot.Rd | 2 IsoplotR-0.8/IsoplotR/man/isochron.Rd | 18 +-- IsoplotR-0.8/IsoplotR/man/kde.Rd | 74 ++++++++---- IsoplotR-0.8/IsoplotR/man/lambda.Rd | 14 +- IsoplotR-0.8/IsoplotR/man/mds.Rd | 33 +++-- IsoplotR-0.8/IsoplotR/man/peakfit.Rd |only IsoplotR-0.8/IsoplotR/man/radialplot.Rd |only IsoplotR-0.8/IsoplotR/man/read.data.Rd | 43 +++++-- IsoplotR-0.8/IsoplotR/man/settings.Rd | 4 IsoplotR-0.8/IsoplotR/man/weightedmean.Rd | 58 ++++++---- IsoplotR-0.8/IsoplotR/man/yorkfit.Rd | 8 - 50 files changed, 974 insertions(+), 634 deletions(-)
Title: Toolkits to Develop Individual-Based Models in Infectious
Disease
Description: It provides a generic set of tools for initializing a synthetic
population with each individual in specific disease states, and
making transitions between those disease states according to the rates
calculated on each timestep. The new version 1.0.0 has C++ code
integration to make the functions run faster. It has also a higher level
function to actually run the transitions for the number of timesteps
that users specify. Additional functions will follow for changing
attributes on demographic, health belief and movement.
Author: Sai Thein Than Tun [aut, cre]
Maintainer: Sai Thein Than Tun <theinthantun.sai@gmail.com>
Diff between ibmcraftr versions 0.1.0 dated 2016-08-11 and 1.0.0 dated 2016-11-16
DESCRIPTION | 17 +++++++----- MD5 | 21 +++++++++++---- NAMESPACE | 6 ++++ NEWS.md | 16 +++++++++++ R/RcppExports.R |only R/cumprob.R |only R/misc.R |only R/run_state_trans.R |only R/stRCPP.R |only R/state_trans.R | 8 ++--- README.md | 68 ++++++++++++++++++++++++++++++++++++++++--------- man/cumprob.Rd |only man/rate2prob.Rd |only man/run_state_trans.Rd |only man/stRCPP.Rd |only src |only 16 files changed, 108 insertions(+), 28 deletions(-)
Title: Permutation Testing Network Module Preservation Across Datasets
Description: Functions for assessing the replication/preservation of a network
module's topology across datasets through permutation testing.
Author: Scott Ritchie [aut, cre]
Maintainer: Scott Ritchie <sritchie73@gmail.com>
Diff between NetRep versions 1.0.2 dated 2016-07-29 and 1.0.4 dated 2016-11-16
NetRep-1.0.2/NetRep/man/CheckFinite.Rd |only NetRep-1.0.2/NetRep/man/IntermediateProperties.Rd |only NetRep-1.0.2/NetRep/man/IntermediatePropertiesNoData.Rd |only NetRep-1.0.2/NetRep/man/NetProps.Rd |only NetRep-1.0.2/NetRep/man/NetPropsNoData.Rd |only NetRep-1.0.2/NetRep/man/PermutationProcedure.Rd |only NetRep-1.0.2/NetRep/man/PermutationProcedureNoData.Rd |only NetRep-1.0.2/NetRep/man/Scale.Rd |only NetRep-1.0.2/NetRep/man/addGradientLegend.Rd |only NetRep-1.0.2/NetRep/man/any.disk.matrix.Rd |only NetRep-1.0.2/NetRep/man/areColors.Rd |only NetRep-1.0.2/NetRep/man/checkIsMatrix.Rd |only NetRep-1.0.2/NetRep/man/checkPlotArgs.Rd |only NetRep-1.0.2/NetRep/man/combineAnalysesInternal.Rd |only NetRep-1.0.2/NetRep/man/contingencyTable.Rd |only NetRep-1.0.2/NetRep/man/correlation.palette.Rd |only NetRep-1.0.2/NetRep/man/emptyPlot.Rd |only NetRep-1.0.2/NetRep/man/filterInternalProps.Rd |only NetRep-1.0.2/NetRep/man/forceLim.Rd |only NetRep-1.0.2/NetRep/man/getColFromPalette.Rd |only NetRep-1.0.2/NetRep/man/getModuleBreaks.Rd |only NetRep-1.0.2/NetRep/man/getModuleMidPoints.Rd |only NetRep-1.0.2/NetRep/man/insert.nas.Rd |only NetRep-1.0.2/NetRep/man/loadIntoRAM.Rd |only NetRep-1.0.2/NetRep/man/matchsub.Rd |only NetRep-1.0.2/NetRep/man/netPropsInternal.Rd |only NetRep-1.0.2/NetRep/man/network.palette.Rd |only NetRep-1.0.2/NetRep/man/nodeOrderInternal.Rd |only NetRep-1.0.2/NetRep/man/orderAsNumeric.Rd |only NetRep-1.0.2/NetRep/man/permp.Rd |only NetRep-1.0.2/NetRep/man/permutation.Rd |only NetRep-1.0.2/NetRep/man/pkgReqCheck.Rd |only NetRep-1.0.2/NetRep/man/plotBar.Rd |only NetRep-1.0.2/NetRep/man/plotMultiBar.Rd |only NetRep-1.0.2/NetRep/man/plotProps.Rd |only NetRep-1.0.2/NetRep/man/plotSquareHeatmap.Rd |only NetRep-1.0.2/NetRep/man/plotTriangleHeatmap.Rd |only NetRep-1.0.2/NetRep/man/prettyPath.Rd |only NetRep-1.0.2/NetRep/man/processInput.Rd |only NetRep-1.0.2/NetRep/man/sampleOrderInternal.Rd |only NetRep-1.0.2/NetRep/man/simplifyList.Rd |only NetRep-1.0.2/NetRep/man/sortModuleNames.Rd |only NetRep-1.0.2/NetRep/man/vCat.Rd |only NetRep-1.0.2/NetRep/man/verifyDatasetOrder.Rd |only NetRep-1.0.4/NetRep/ChangeLog |only NetRep-1.0.4/NetRep/DESCRIPTION | 8 NetRep-1.0.4/NetRep/MD5 | 127 -- NetRep-1.0.4/NetRep/R/NetRep.R | 5 NetRep-1.0.4/NetRep/R/RcppExports.R | 253 ----- NetRep-1.0.4/NetRep/R/bigMatrix.R | 1 NetRep-1.0.4/NetRep/R/check-user-input.R | 203 ++-- NetRep-1.0.4/NetRep/R/contingency.R | 99 +- NetRep-1.0.4/NetRep/R/example-data.R | 1 NetRep-1.0.4/NetRep/R/multi-machine.R | 24 NetRep-1.0.4/NetRep/R/networkProperties.R | 101 +- NetRep-1.0.4/NetRep/R/orderNodes.R | 32 NetRep-1.0.4/NetRep/R/orderSamples.R | 21 NetRep-1.0.4/NetRep/R/plot-functions.R | 319 +++--- NetRep-1.0.4/NetRep/R/plot-module.R | 4 NetRep-1.0.4/NetRep/R/plot-topology.R | 1 NetRep-1.0.4/NetRep/R/plot-utils.R | 172 +-- NetRep-1.0.4/NetRep/R/pperm.R | 82 + NetRep-1.0.4/NetRep/R/roxygen-defs.R | 4 NetRep-1.0.4/NetRep/R/utils.R | 249 ++--- NetRep-1.0.4/NetRep/README.md | 66 - NetRep-1.0.4/NetRep/build/vignette.rds |binary NetRep-1.0.4/NetRep/inst/doc/NetRep.Rmd | 5 NetRep-1.0.4/NetRep/inst/doc/NetRep.html | 751 ++++++++-------- NetRep-1.0.4/NetRep/man/NetRep.Rd | 3 NetRep-1.0.4/NetRep/man/bigMatrix.Rd | 1 NetRep-1.0.4/NetRep/man/combineAnalyses.Rd | 1 NetRep-1.0.4/NetRep/man/common_params.Rd | 1 NetRep-1.0.4/NetRep/man/nodeOrder.Rd | 2 NetRep-1.0.4/NetRep/man/orderModules_param.Rd | 1 NetRep-1.0.4/NetRep/man/permutationTest.Rd |only NetRep-1.0.4/NetRep/man/plotTopology.Rd | 1 NetRep-1.0.4/NetRep/man/plot_params.Rd | 1 NetRep-1.0.4/NetRep/man/requiredPerms.Rd |only NetRep-1.0.4/NetRep/man/sampleOrder.Rd | 2 NetRep-1.0.4/NetRep/man/simplify_param.Rd | 1 NetRep-1.0.4/NetRep/src/RcppExports.cpp | 60 - NetRep-1.0.4/NetRep/src/checkFinite.cpp | 23 NetRep-1.0.4/NetRep/src/discProps.cpp | 148 +-- NetRep-1.0.4/NetRep/src/permutations.cpp | 102 +- NetRep-1.0.4/NetRep/src/permutationsNoData.cpp | 94 +- NetRep-1.0.4/NetRep/src/properties.cpp | 128 +- NetRep-1.0.4/NetRep/src/scale.cpp | 19 NetRep-1.0.4/NetRep/vignettes/NetRep.Rmd | 5 88 files changed, 1540 insertions(+), 1581 deletions(-)
Title: Extensions to 'ggplot2' for Radiation Spectra
Description: Additional annotations, stats and scales for plotting "light"
spectra with 'ggplot2', together with specializations of ggplot()
and plot() methods for spectral data stored in objects of the classes
defined in package 'photobiology' and a plot() method for objects of
class "waveband", also defined in package 'photobiology'.
Author: Pedro J. Aphalo [aut, cre],
Titta K. Kotilainen [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggspectra versions 0.1.10 dated 2016-09-24 and 0.1.12 dated 2016-11-16
DESCRIPTION | 16 +- MD5 | 92 +++++++------- NAMESPACE | 5 NEWS | 14 ++ R/decoration.R | 17 ++ R/ggspectra.r | 1 R/plot-cps-spct.r | 21 +-- R/plot-filter-spct.r | 75 ++++++----- R/plot-raw-spct.r | 17 +- R/plot-response-spct.r | 52 +++++--- R/plot-source-spct.r | 52 +++++--- R/stat-color.R | 18 ++ R/stat-label-peaks.R |only R/stat-peaks.R | 25 +++ R/stat-wb-contribution.R | 43 +++++- R/stat-wb-irrad.R | 43 +++++- R/stat-wb-label.R | 29 +++- R/stat-wb-mean.R | 42 +++++- R/stat-wb-relative.R | 43 +++++- R/stat-wb-sirrad.R | 43 +++++- R/stat-wb-total.R | 44 +++++- R/stat-wl-strip.R | 31 ++++ R/stat-wl-summary.R | 43 +++++- build/vignette.rds |binary inst/CITATION | 2 inst/doc/plot-methods.R | 14 -- inst/doc/plot-methods.Rmd | 20 +-- inst/doc/plot-methods.html | 91 ++++++-------- inst/doc/user-guide.R | 27 +++- inst/doc/user-guide.Rmd | 78 ++++++++++-- inst/doc/user-guide.html | 283 ++++++++++++++++++++++++++++++++------------ inst/staticdocs/index.r | 1 man/decoration.Rd | 6 man/gg2spectra-ggproto.Rd | 17 ++ man/stat_color.Rd | 26 +++- man/stat_label_peaks.Rd |only man/stat_peaks.Rd | 29 ++++ man/stat_wb_contribution.Rd | 57 +++++++- man/stat_wb_irrad.Rd | 48 ++++++- man/stat_wb_label.Rd | 34 ++++- man/stat_wb_mean.Rd | 52 ++++++-- man/stat_wb_relative.Rd | 54 +++++++- man/stat_wb_sirrad.Rd | 48 ++++++- man/stat_wb_total.Rd | 54 ++++++-- man/stat_wl_strip.Rd | 36 ++++- man/stat_wl_summary.Rd | 43 +++++- vignettes/plot-methods.Rmd | 20 +-- vignettes/user-guide.Rmd | 78 ++++++++++-- 48 files changed, 1424 insertions(+), 460 deletions(-)
Title: Generation of IRT Response Patterns under Computerized Adaptive
Testing
Description: Provides routines for the generation of response patterns under unidimensional dichotomous and polytomous computerized adaptive testing (CAT) framework. It holds many standard functions to estimate ability, select the first item(s) to administer and optimally select the next item, as well as several stopping rules. Options to control for item exposure and content balancing are also available (Magis and Raiche, Random Generation of Response Patterns under Computerized Adaptive Testing with the R Package catR, Journal of Statistical Software, 48 (8), 2012, 1-31 <doi:10.18637/jss.v048.i08>).
Author: David Magis (U Liege, Belgium), Gilles Raiche (UQAM, Canada), Juan Ramon Barrada (U Zaragoza, Spain)
Maintainer: David Magis <david.magis@ulg.ac.be>
Diff between catR versions 3.10 dated 2016-08-26 and 3.11 dated 2016-11-16
DESCRIPTION | 12 ++++----- MD5 | 8 +++--- NEWS | 23 +++++++++++++++++ R/simulateRespondents.R | 60 +++++++++++++++++++++------------------------ man/simulateRespondents.Rd | 17 +++++++----- 5 files changed, 72 insertions(+), 48 deletions(-)
Title: Download or Upload 'Socrata' Data Sets
Description: Provides easier interaction with
Socrata open data portals http://dev.socrata.com.
Users can provide a 'Socrata' data set resource URL,
or a 'Socrata' Open Data API (SoDA) web query,
or a 'Socrata' "human-friendly" URL,
returns an R data frame. Converts dates to 'POSIX'
format and manages throttling by 'Socrata'.
Users can upload data to Socrata portals directly
from R.
Author: Hugh Devlin, Ph. D., Tom Schenk, Jr., and John Malc
Maintainer: "Tom Schenk Jr." <developers@cityofchicago.org>
Diff between RSocrata versions 1.7.0-14 dated 2016-02-11 and 1.7.1-24 dated 2016-11-16
DESCRIPTION | 11 MD5 | 14 NAMESPACE | 1 R/RSocrata.R | 822 +++++++++++++++++++++++++--------------------- README.md | 23 + man/ls.socrata.Rd | 53 +- man/read.socrata.Rd | 5 tests/testthat/test-all.R | 287 +++++++++++++--- 8 files changed, 768 insertions(+), 448 deletions(-)