Title: Binary Classification via GMDH-Type Neural Network Algorithms
Description: Performs binary classification via Group Method of Data Handling (GMDH) - type neural network algorithms. There exist two main algorithms available in GMDH() and dceGMDH() functions. GMDH() performs classification via GMDH algorithm for a binary response and returns important variables. dceGMDH() performs classification via diverse classifiers ensemble based on GMDH (dce-GMDH) algorithm. Also, the package produces a well-formatted table of descriptives for a binary response. Moreover, it produces confusion matrix, its related statistics and scatter plot (2D and 3D) with classification labels of binary classes to assess the prediction performance. All 'GMDH2' functions are designed for a binary response. See Dag O. and Yozgatligil C. (2016, ISSN:2073-4859) and Kondo T. and Ueno J. (2016, ISSN:1349-4198) for the details of GMDH algorithms.
Author: Osman Dag [aut, cre], Erdem Karabulut [aut], Reha Alpar [aut]
Maintainer: Osman Dag <osman.dag@hacettepe.edu.tr>
Diff between GMDH2 versions 1.3 dated 2018-05-15 and 1.4 dated 2018-06-23
DESCRIPTION | 13 ++++---- MD5 | 28 +++++++++--------- R/GMDH.R | 75 ++++++++++++++++++++++--------------------------- R/dceGMDH.R | 59 +++++++++++++++----------------------- R/plot.GMDHplot.R | 2 - man/GMDH.Rd | 42 ++++++++++++++++----------- man/GMDH2.Rd | 4 +- man/Table.Rd | 2 + man/confMat.Rd | 30 +++++++++++-------- man/cplot2d.Rd | 31 +++++++++++--------- man/cplot3d.Rd | 30 +++++++++++-------- man/dceGMDH.Rd | 43 +++++++++++++++------------- man/plot.GMDHplot.Rd | 28 +++++++++++------- man/predict.GMDH.Rd | 31 +++++++++++--------- man/predict.dceGMDH.Rd | 31 +++++++++++--------- 15 files changed, 237 insertions(+), 212 deletions(-)
Title: Read and Write from the System Clipboard
Description: Simple utility functions to read from and write to the Windows,
OS X, and X11 clipboards.
Author: Matthew Lincoln [aut, cre],
Louis Maddox [ctb],
Steve Simpson [ctb],
Jennifer Bryan [ctb]
Maintainer: Matthew Lincoln <matthew.d.lincoln@gmail.com>
Diff between clipr versions 0.4.0 dated 2017-11-03 and 0.4.1 dated 2018-06-23
DESCRIPTION | 8 +- MD5 | 13 ++-- NEWS.md | 5 + R/flat_str.R | 9 +++ README.md | 105 +++++++++++++++++++++++++++++--------- tests/testthat/setup.R |only tests/testthat/test-diagnostics.R |only tests/testthat/test-systems.R |only tests/testthat/test_render.R | 68 ++++++++++-------------- 9 files changed, 137 insertions(+), 71 deletions(-)
Title: Patches to Use 'dplyr' on Remote Data Sources
Description: Patches to use 'dplyr' on remote data sources ('SQL' databases,
'Spark' 2.0.0 and above) in a reliable "generic" fashion (generic meaning
user code works similarly on all such sources, without needing per-source
adaption). Due to the fluctuating nature of 'dplyr'/'dbplyr'/'rlang' 'APIs' this package
is going into maintenance mode. Most of the 'replyr' functions are already
done better by one of the non-monolithic replacement packages: 'wrapr', 'seplyr', 'rquery',
or 'cdata'.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between replyr versions 0.9.5 dated 2018-05-20 and 0.9.6 dated 2018-06-23
DESCRIPTION | 10 +++++----- MD5 | 37 +++++++++++++++++++------------------ NAMESPACE | 1 + NEWS.md | 4 ++++ R/joinController.R | 12 ++++++++++-- README.md | 8 ++++---- build/vignette.rds |binary inst/doc/DependencySorting.R | 2 +- inst/doc/DependencySorting.Rmd | 2 +- inst/doc/DependencySorting.html | 27 ++++++++++++++++----------- inst/doc/ParametricExample.html | 6 +++--- inst/doc/coalesce.html | 10 +++++----- inst/doc/joinController.html | 20 ++++++++++---------- inst/doc/letExample.html | 8 ++++---- inst/doc/replyr.html | 12 ++++++------ inst/doc/summary.html | 10 +++++----- man/example_employeeAndDate.Rd |only man/makeJoinDiagramSpec.Rd | 2 +- man/topoSortTables.Rd | 2 +- vignettes/DependencySorting.Rmd | 2 +- 20 files changed, 97 insertions(+), 78 deletions(-)
Title: Project MOSAIC Data Sets
Description: Data sets from Project MOSAIC (<http://mosaic-web.org>) used
to teach mathematics, statistics, computation and modeling. Funded by the
NSF, Project MOSAIC is a community of educators working to tie together
aspects of quantitative work that students in science, technology,
engineering and mathematics will need in their professional lives, but
which are usually taught in isolation, if at all.
Author: Randall Pruim <rpruim@calvin.edu>, Daniel Kaplan
<kaplan@macalester.edu>, Nicholas Horton <nhorton@amherst.edu>
Maintainer: Randall Pruim <rpruim@calvin.edu>
Diff between mosaicData versions 0.16.0 dated 2018-01-28 and 0.17.0 dated 2018-06-23
DESCRIPTION | 10 MD5 | 80 +- NEWS.md | 4 R/BirthsDoc.R | 125 +++ R/GoosePermitsDoc.R | 14 R/Weather.R | 7 R/datasetsDoc.R | 165 +---- data/Births.rda |binary data/Births2015.rda |binary data/Births78.rda |binary man/Alcohol.Rd | 12 man/Birthdays.Rd | 32 - man/Births.Rd | 22 man/Births2015.Rd | 30 man/Births78.Rd | 26 man/CPS85.Rd | 28 man/Cards.Rd | 2 man/CoolingWater.Rd | 16 man/Countries.Rd | 10 man/Dimes.Rd | 4 man/Galton.Rd | 19 man/Gestation.Rd | 70 +- man/GoosePermits.Rd | 24 man/HELPfull.Rd | 1580 +++++++++++++++++++++++++------------------------- man/HELPmiss.Rd | 78 +- man/HELPrct.Rd | 85 +- man/HeatX.Rd | 24 man/KidsFeet.Rd | 20 man/Marriage.Rd | 36 - man/Mites.Rd | 8 man/RailTrail.Rd | 36 - man/Riders.Rd | 46 - man/SAT.Rd | 33 - man/SaratogaHouses.Rd | 6 man/SnowGR.Rd | 54 - man/SwimRecords.Rd | 14 man/TenMileRace.Rd | 21 man/Utilities.Rd | 32 - man/Utilities2.Rd | 50 - man/Weather.Rd | 33 - man/Whickham.Rd | 12 41 files changed, 1459 insertions(+), 1409 deletions(-)
Title: Improved Standard Evaluation Interfaces for Common Data
Manipulation Tasks
Description: The 'seplyr' (standard evaluation plying) package supplies improved
standard evaluation adapter methods for important common 'dplyr' data manipulation tasks.
In addition the 'seplyr' package supplies several new "key operations
bound together" methods. These include 'group_summarize()' (which
combines grouping, arranging and calculation in an atomic unit),
'add_group_summaries()' (which joins grouped summaries into a 'data.frame'
in a well documented manner), 'add_group_indices()' (which adds
per-group identifiers to a 'data.frame' without depending on row-order),
'partition_mutate_qt()' (which optimizes mutate sequences), and 'if_else_device()'
(which simulates per-row if-else blocks in expression sequences).
Author: John Mount [aut, cre],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between seplyr versions 0.5.5 dated 2018-03-13 and 0.5.6 dated 2018-06-23
DESCRIPTION | 14 +++---- MD5 | 40 +++++++++++---------- NAMESPACE | 5 ++ NEWS.md | 4 ++ R/complete_se.R |only R/stmtPlanner.R | 4 +- README.md | 2 - build/vignette.rds |binary inst/doc/MutatePartitioner.html | 4 +- inst/doc/named_map_builder.Rmd | 2 - inst/doc/named_map_builder.html | 6 +-- inst/doc/rename_se.Rmd | 2 - inst/doc/rename_se.html | 6 +-- inst/doc/seplyr.Rmd | 2 - inst/doc/seplyr.html | 8 ++-- inst/doc/using_seplyr.Rmd | 2 - inst/doc/using_seplyr.html | 74 ++++++++++++++++++++-------------------- man/complete_se.Rd |only vignettes/named_map_builder.Rmd | 2 - vignettes/rename_se.Rmd | 2 - vignettes/seplyr.Rmd | 2 - vignettes/using_seplyr.Rmd | 2 - 22 files changed, 97 insertions(+), 86 deletions(-)
Title: Schumaker Shape-Preserving Spline
Description: This is a shape preserving spline <doi:10.1137/0720057>
which is guaranteed to be monotonic and concave or convex if the
data is monotonic and concave or convex. It does not use any
optimisation and is therefore quick and smoothly converges to a
fixed point in economic dynamics problems including value function
iteration. It also automatically gives the first two derivatives
of the spline and options for determining behaviour when evaluated
outside the interpolation domain.
Author: Stuart Baumann [aut, cre], Margaryta Klymak[aut]
Maintainer: Stuart Baumann <Stuart@StuartBaumann.com>
Diff between schumaker versions 1.0 dated 2017-05-20 and 1.1 dated 2018-06-23
schumaker-1.0/schumaker/vignettes/schumaker.md |only schumaker-1.1/schumaker/DESCRIPTION | 24 ++-- schumaker-1.1/schumaker/LICENSE | 4 schumaker-1.1/schumaker/MD5 | 21 +-- schumaker-1.1/schumaker/R/Schumaker.R | 10 + schumaker-1.1/schumaker/build/vignette.rds |binary schumaker-1.1/schumaker/inst/doc/schumaker.R | 42 ++++++- schumaker-1.1/schumaker/inst/doc/schumaker.Rmd | 57 +++++++++- schumaker-1.1/schumaker/inst/doc/schumaker.html | 133 +++++++++++++++--------- schumaker-1.1/schumaker/man/Schumaker.Rd | 5 schumaker-1.1/schumaker/tests |only schumaker-1.1/schumaker/vignettes/schumaker.Rmd | 57 +++++++++- 12 files changed, 260 insertions(+), 93 deletions(-)
Title: Analyze Multinomial Processing Tree Models
Description: Provides a user-friendly way for the analysis of multinomial processing tree (MPT) models (e.g., Riefer, D. M., and Batchelder, W. H. [1988]. Multinomial modeling and the measurement of cognitive processes. Psychological Review, 95, 318-339) for single and multiple datasets. The main functions perform model fitting and model selection. Model selection can be done using AIC, BIC, or the Fisher Information Approximation (FIA) a measure based on the Minimum Description Length (MDL) framework. The model and restrictions can be specified in external files or within an R script in an intuitive syntax or using the context-free language for MPTs. The 'classical' .EQN file format for model files is also supported. Besides MPTs, this package can fit a wide variety of other cognitive models such as SDT models (see fit.model). It also supports multicore fitting and FIA calculation (using the snowfall package), can generate or bootstrap data for simulations, and plot predicted versus observed data.
Author: Henrik Singmann [aut, cre],
David Kellen [aut],
Quentin Gronau [aut],
Christian Mueller [ctb],
Akhil S Bhel [ctb]
Maintainer: Henrik Singmann <singmann+mptinr@gmail.com>
Diff between MPTinR versions 1.10.3 dated 2015-07-27 and 1.11.0 dated 2018-06-23
DESCRIPTION | 7 MD5 | 15 - R/RcppExports.R | 22 +- build/partial.rdb |only build/vignette.rds |binary inst/doc/mptinr_introduction.pdf |binary man/MPTinR-package.Rd | 69 +++----- man/prediction.plot.Rd | 332 +++++++++++++++++++-------------------- src/RcppExports.cpp | 33 ++- 9 files changed, 240 insertions(+), 238 deletions(-)
Title: Partitioning of Individual Autozygosity into Multiple
Homozygous-by-Descent Classes
Description: Functions to identify Homozygous-by-Descent (HBD) segments associated with runs of homozygosity (ROH) and to
estimate individual autozygosity (or inbreeding coefficient). HBD segments and autozygosity are assigned to multiple HBD classes
with a model-based approach relying on a mixture of exponential distributions. The rate of the exponential distribution is distinct
for each HBD class and defines the expected length of the HBD segments. These HBD classes are therefore related to the age of the
segments (longer segments and smaller rates for recent autozygosity / recent common ancestor). The functions allow to estimate the
parameters of the model (rates of the exponential distributions, mixing proportions), to estimate global and local autozygosity
probabilities and to identify HBD segments with the Viterbi decoding. The method is fully described in Druet and Gautier (2017)
<doi:10.1111/mec.14324>.
Author: Tom Druet, Naveen Kumar Kadri, Amandine Bertrand and Mathieu Gautier
Maintainer: Tom Druet <tom.druet@uliege.be>
Diff between RZooRoH versions 0.1.0 dated 2018-06-19 and 0.1.1 dated 2018-06-23
RZooRoH-0.1.0/RZooRoH/build |only RZooRoH-0.1.0/RZooRoH/inst/doc |only RZooRoH-0.1.0/RZooRoH/vignettes |only RZooRoH-0.1.1/RZooRoH/DESCRIPTION | 7 +++---- RZooRoH-0.1.1/RZooRoH/MD5 | 9 ++------- RZooRoH-0.1.1/RZooRoH/R/zooroh.R | 6 +++--- 6 files changed, 8 insertions(+), 14 deletions(-)
Title: Response Time Distributions
Description: Provides response time distributions (density/PDF,
distribution function/CDF, quantile function, and random
generation): (a) Ratcliff diffusion model (Ratcliff &
McKoon, 2008, <doi:10.1162/neco.2008.12-06-420>) based on C
code by Andreas and Jochen Voss and (b) linear ballistic
accumulator (LBA; Brown & Heathcote, 2008,
<doi:10.1016/j.cogpsych.2007.12.002>) with different
distributions underlying the drift rate.
Author: Henrik Singmann [aut, cre] (<https://orcid.org/0000-0002-4842-3657>),
Scott Brown [aut],
Matthew Gretton [aut],
Andrew Heathcote [aut],
Andreas Voss [ctb],
Jochen Voss [ctb],
Andrew Terry [ctb]
Maintainer: Henrik Singmann <singmann+rtdists@gmail.com>
Diff between rtdists versions 0.8-1 dated 2017-12-23 and 0.8-3 dated 2018-06-23
DESCRIPTION | 38 ++++++++++----------- MD5 | 18 +++++----- NEWS | 6 ++- R/rtdists-package.R | 4 +- build/vignette.rds |binary inst/doc/reanalysis_rr98.html | 62 +++++++++++++++++------------------ man/rtdists-package.Rd | 4 +- tests/testthat/test-diffusion-math.R | 1 tests/testthat/test-diffusion-rcpp.R | 9 +++-- tests/testthat/test-lba-bugs.R | 8 ++-- 10 files changed, 79 insertions(+), 71 deletions(-)
Title: Depth-Based Classification and Calculation of Data Depth
Description: Contains procedures for depth-based supervised learning, which are entirely non-parametric, in particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014 <doi:10.1007/s00362-012-0488-4>). The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.
Author: Oleksii Pokotylo [aut, cre],
Pavlo Mozharovskyi [aut],
Rainer Dyckerhoff [aut],
Stanislav Nagy [aut]
Maintainer: Oleksii Pokotylo <alexey.pokotylo@gmail.com>
Diff between ddalpha versions 1.3.3 dated 2018-04-30 and 1.3.4 dated 2018-06-23
ddalpha-1.3.3/ddalpha/R/depth.fd.R |only ddalpha-1.3.3/ddalpha/R/dknn.R |only ddalpha-1.3.3/ddalpha/R/getdata.R |only ddalpha-1.3.4/ddalpha/DESCRIPTION | 8 ddalpha-1.3.4/ddalpha/MD5 | 118 ddalpha-1.3.4/ddalpha/R/ddalpha-internal.r | 3468 +++++------ ddalpha-1.3.4/ddalpha/R/depth.fd.r |only ddalpha-1.3.4/ddalpha/R/dknn.r |only ddalpha-1.3.4/ddalpha/R/getdata.r |only ddalpha-1.3.4/ddalpha/data/baby.txt.gz |binary ddalpha-1.3.4/ddalpha/data/banknoten.txt.gz |binary ddalpha-1.3.4/ddalpha/data/biomed.txt.gz |binary ddalpha-1.3.4/ddalpha/data/bloodtransfusion.txt.gz |binary ddalpha-1.3.4/ddalpha/data/breast_cancer_wisconsin.txt.gz |binary ddalpha-1.3.4/ddalpha/data/bupa.txt.gz |binary ddalpha-1.3.4/ddalpha/data/chemdiab_1vs2.txt.gz |binary ddalpha-1.3.4/ddalpha/data/chemdiab_1vs3.txt.gz |binary ddalpha-1.3.4/ddalpha/data/chemdiab_2vs3.txt.gz |binary ddalpha-1.3.4/ddalpha/data/cloud.txt.gz |binary ddalpha-1.3.4/ddalpha/data/crabB_MvsF.txt.gz |binary ddalpha-1.3.4/ddalpha/data/crabF_BvsO.txt.gz |binary ddalpha-1.3.4/ddalpha/data/crabM_BvsO.txt.gz |binary ddalpha-1.3.4/ddalpha/data/crabO_MvsF.txt.gz |binary ddalpha-1.3.4/ddalpha/data/crab_BvsO.txt.gz |binary ddalpha-1.3.4/ddalpha/data/crab_MvsF.txt.gz |binary ddalpha-1.3.4/ddalpha/data/cricket_CvsP.txt.gz |binary ddalpha-1.3.4/ddalpha/data/diabetes.txt.gz |binary ddalpha-1.3.4/ddalpha/data/ecoli_cpvsim.txt.gz |binary ddalpha-1.3.4/ddalpha/data/ecoli_cpvspp.txt.gz |binary ddalpha-1.3.4/ddalpha/data/ecoli_imvspp.txt.gz |binary ddalpha-1.3.4/ddalpha/data/gemsen_MvsF.txt.gz |binary ddalpha-1.3.4/ddalpha/data/glass.txt.gz |binary ddalpha-1.3.4/ddalpha/data/groessen_MvsF.txt.gz |binary ddalpha-1.3.4/ddalpha/data/haberman.txt.gz |binary ddalpha-1.3.4/ddalpha/data/heart.txt.gz |binary ddalpha-1.3.4/ddalpha/data/hemophilia.txt.gz |binary ddalpha-1.3.4/ddalpha/data/indian_liver_patient_1vs2.txt.gz |binary ddalpha-1.3.4/ddalpha/data/indian_liver_patient_FvsM.txt.gz |binary ddalpha-1.3.4/ddalpha/data/iris_setosavsversicolor.txt.gz |binary ddalpha-1.3.4/ddalpha/data/iris_setosavsvirginica.txt.gz |binary ddalpha-1.3.4/ddalpha/data/iris_versicolorvsvirginica.txt.gz |binary ddalpha-1.3.4/ddalpha/data/irish_ed_MvsF.txt.gz |binary ddalpha-1.3.4/ddalpha/data/kidney.txt.gz |binary ddalpha-1.3.4/ddalpha/data/pima.txt.gz |binary ddalpha-1.3.4/ddalpha/data/plasma_retinol_MvsF.txt.gz |binary ddalpha-1.3.4/ddalpha/data/segmentation.txt.gz |binary ddalpha-1.3.4/ddalpha/data/socmob_IvsNI.txt.gz |binary ddalpha-1.3.4/ddalpha/data/socmob_WvsB.txt.gz |binary ddalpha-1.3.4/ddalpha/data/tae.txt.gz |binary ddalpha-1.3.4/ddalpha/data/tennis_MvsF.txt.gz |binary ddalpha-1.3.4/ddalpha/data/tips_DvsN.txt.gz |binary ddalpha-1.3.4/ddalpha/data/tips_MvsF.txt.gz |binary ddalpha-1.3.4/ddalpha/data/uscrime_SvsN.txt.gz |binary ddalpha-1.3.4/ddalpha/data/vertebral_column.txt.gz |binary ddalpha-1.3.4/ddalpha/data/veteran_lung_cancer.txt.gz |binary ddalpha-1.3.4/ddalpha/data/vowel_MvsF.txt.gz |binary ddalpha-1.3.4/ddalpha/data/wine_1vs2.txt.gz |binary ddalpha-1.3.4/ddalpha/data/wine_1vs3.txt.gz |binary ddalpha-1.3.4/ddalpha/data/wine_2vs3.txt.gz |binary ddalpha-1.3.4/ddalpha/man/ddalpha-package.Rd | 252 ddalpha-1.3.4/ddalpha/man/ddalphaf.classify.Rd | 128 ddalpha-1.3.4/ddalpha/man/ddalphaf.train.Rd | 290 ddalpha-1.3.4/ddalpha/src/ZonoidDepth.cpp | 7 63 files changed, 2137 insertions(+), 2134 deletions(-)
Title: Transformation Trees and Forests
Description: Recursive partytioning of transformation models with
corresponding random forest for conditional transformation models
as described in 'Transformation Forests' (Hothorn and Zeileis, 2017, <arXiv:1701.02110>)
and 'Top-Down Transformation Choice' (Hothorn, 2018, <DOI:10.1177/1471082X17748081>).
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between trtf versions 0.3-1 dated 2018-04-23 and 0.3-2 dated 2018-06-23
DESCRIPTION | 10 +++--- MD5 | 20 ++++++------ R/methods.R | 60 +++++++++++++++++++++++++++++--------- R/trees_forests.R | 6 +++ inst/NEWS.Rd | 9 +++++ man/traforest.Rd | 46 +++++++++++++++++++++++++++++ man/trafotree.Rd | 19 +++++++++++- tests/GBSG2-Ex.Rout.save | 46 ++++++++++++++--------------- tests/regtest-traforest.R | 21 +++++++++++++ tests/regtest-traforest.Rout.save | 35 +++++++++++++++++----- tests/regtest-trafotree.Rout.save | 52 ++++++++++++++++---------------- 11 files changed, 237 insertions(+), 87 deletions(-)
Title: Template Model Builder: A General Random Effect Tool Inspired by
'ADMB'
Description: With this tool, a user should be able to quickly implement complex
random effect models through simple C++ templates. The package combines
'CppAD' (C++ automatic differentiation), 'Eigen' (templated matrix-vector
library) and 'CHOLMOD' (sparse matrix routines available from R) to obtain an
efficient implementation of the applied Laplace approximation with exact
derivatives. Key features are: Automatic sparseness detection, parallelism
through 'BLAS' and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph],
Brad Bell [cph],
Hans Skaug [ctb],
Arni Magnusson [ctb],
Casper Berg [ctb],
Anders Nielsen [ctb],
Martin Maechler [ctb],
Theo Michelot [ctb],
Mollie Brooks [ctb],
Alex Forrence [ctb],
Christoffer Moesgaard Albertsen [ctb],
Cole Monnahan [ctb]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between TMB versions 1.7.13 dated 2018-03-22 and 1.7.14 dated 2018-06-23
DESCRIPTION | 10 - MD5 | 82 ++++++++-------- NAMESPACE | 5 NEWS | 15 ++ R/TMB.R | 27 +++-- R/checker.R | 7 + R/normalize.R | 18 ++- R/tmbprofile.R | 42 ++++++-- R/tmbroot.R |only R/utils.R | 7 + inst/include/cppad/local/kasper.hpp | 2 inst/include/distributions_R.hpp | 20 ++- inst/include/tiny_ad/atomic.hpp | 6 - inst/include/tiny_ad/tweedie/tweedie.cpp | 158 ++++++++++--------------------- inst/include/tiny_ad/tweedie/tweedie.hpp | 9 - inst/include/tmb_core.hpp | 34 ++++-- man/MakeADFun.Rd | 1 man/Rinterface.Rd | 1 man/as.list.sdreport.Rd | 1 man/benchmark.Rd | 1 man/checkConsistency.Rd | 1 man/compile.Rd | 1 man/config.Rd | 1 man/confint.tmbprofile.Rd | 1 man/dynlib.Rd | 1 man/gdbsource.Rd | 1 man/newton.Rd | 1 man/newtonOption.Rd | 1 man/normalize.Rd | 1 man/oneStepPredict.Rd | 1 man/openmp.Rd | 1 man/plot.tmbprofile.Rd | 1 man/precompile.Rd | 1 man/print.checkConsistency.Rd | 1 man/print.sdreport.Rd | 1 man/runExample.Rd | 1 man/runSymbolicAnalysis.Rd | 1 man/sdreport.Rd | 1 man/summary.checkConsistency.Rd | 5 man/summary.sdreport.Rd | 1 man/template.Rd | 1 man/tmbprofile.Rd | 4 man/tmbroot.Rd |only 43 files changed, 239 insertions(+), 236 deletions(-)
Title: Analysis of Circadian Behaviours
Description: Use behavioural variables to compute period, rhythmicity and other circadian parameters.
Methods include computation of chi square periodograms (Sokolove and Bushell (1978) <DOI:10.1016/0022-5193(78)90022-X>),
Lomb-Scargle periodograms (Lomb (1976) <DOI:10.1007/BF00648343>, Scargle (1982) <DOI:10.1086/160554>, Ruf (1999) <DOI:10.1076/brhm.30.2.178.1422>),
and autocorrelation-based periodograms.
Author: Quentin Geissmann [aut, cre],
Luis Garcia [aut]
Maintainer: Quentin Geissmann <qgeissmann@gmail.com>
Diff between zeitgebr versions 0.3.2 dated 2018-05-18 and 0.3.3 dated 2018-06-23
zeitgebr-0.3.2/zeitgebr/tests/testthat/prototype_tutorial.R |only zeitgebr-0.3.3/zeitgebr/DESCRIPTION | 12 ++++++------ zeitgebr-0.3.3/zeitgebr/MD5 | 5 ++--- zeitgebr-0.3.3/zeitgebr/R/periodogram.R | 1 - 4 files changed, 8 insertions(+), 10 deletions(-)
Title: Analyzing Real-Time Quantitative PCR Data
Description: Calculates the amplification efficiency and curves from real-time
quantitative PCR (Polymerase Chain Reaction) data. Estimates the relative
expression from PCR data using the double delta CT and the standard curve
methods Livak & Schmittgen (2001) <doi:10.1006/meth.2001.1262>. Tests for
statistical significance using two-group tests and linear regression
Yuan et al. (2006) <doi: 10.1186/1471-2105-7-85>.
Author: Mahmoud Ahmed [aut, cre]
Maintainer: Mahmoud Ahmed <mahmoud.s.fahmy@students.kasralainy.edu.eg>
Diff between pcr versions 1.1.0 dated 2017-11-20 and 1.1.1 dated 2018-06-23
pcr-1.1.0/pcr/inst/doc/qpcr_analysis.pdf |only pcr-1.1.1/pcr/DESCRIPTION | 8 pcr-1.1.1/pcr/MD5 | 16 - pcr-1.1.1/pcr/NEWS.md | 4 pcr-1.1.1/pcr/README.md | 7 pcr-1.1.1/pcr/build/vignette.rds |binary pcr-1.1.1/pcr/inst/doc/qpcr_analysis.R | 51 +-- pcr-1.1.1/pcr/inst/doc/qpcr_analysis.Rmd | 412 ++++++++++++------------------ pcr-1.1.1/pcr/inst/doc/qpcr_analysis.html |only pcr-1.1.1/pcr/vignettes/qpcr_analysis.Rmd | 412 ++++++++++++------------------ 10 files changed, 396 insertions(+), 514 deletions(-)
Title: Generate Useful ROC Curve Charts for Print and Interactive Use
Description: Most ROC curve plots obscure the cutoff values and inhibit
interpretation and comparison of multiple curves. This attempts to address
those shortcomings by providing plotting and interactive tools. Functions
are provided to generate an interactive ROC curve plot for web use, and
print versions. A Shiny application implementing the functions is also
included.
Author: Michael C. Sachs [aut, cre],
Robert W. Corty [ctb]
Maintainer: Michael C. Sachs <sachsmc@gmail.com>
Diff between plotROC versions 2.2.0 dated 2017-08-09 and 2.2.1 dated 2018-06-23
DESCRIPTION | 10 MD5 | 70 - NAMESPACE | 94 - NEWS | 6 R/geom_roc.R | 10 R/interactive_roc.R | 14 R/plotROC-package.R | 1 R/style_roc.R | 20 README.md | 2 build/vignette.rds |binary inst/doc/examples.R | 355 ++--- inst/doc/examples.Rmd | 1 inst/doc/examples.html | 2679 ++++++++++++++++++++++-------------------- man/calc_auc.Rd | 50 man/calculate_multi_roc.Rd | 46 man/calculate_roc.Rd | 66 - man/direct_label.Rd | 56 man/export_interactive_roc.Rd | 102 - man/geom_roc.Rd | 280 ++-- man/geom_rocci.Rd | 226 +-- man/getD3.Rd | 24 man/ggroc.Rd | 86 - man/melt_roc.Rd | 62 man/multi_ggroc.Rd | 96 - man/plotROC.Rd | 98 - man/plot_interactive_roc.Rd | 42 man/plot_journal_roc.Rd | 70 - man/roc_key.Rd | 38 man/shiny_plotROC.Rd | 22 man/stat_roc.Rd | 194 +-- man/stat_rocci.Rd | 228 +-- man/style_roc.Rd | 70 - man/verify_d.Rd | 54 tests/testthat/Rplots.pdf |binary tests/testthat/test-calc.R | 116 - vignettes/examples.Rmd | 1 36 files changed, 2774 insertions(+), 2515 deletions(-)
Title: Interactive Cluster Heat Maps Using 'plotly'
Description: Create interactive cluster 'heatmaps' that can be saved as a stand-
alone HTML file, embedded in 'R Markdown' documents or in a 'Shiny' app, and
available in the 'RStudio' viewer pane. Hover the mouse pointer over a cell to
show details or drag a rectangle to zoom. A 'heatmap' is a popular graphical
method for visualizing high-dimensional data, in which a table of numbers
are encoded as a grid of colored cells. The rows and columns of the matrix
are ordered to highlight patterns and are often accompanied by 'dendrograms'.
'Heatmaps' are used in many fields for visualizing observations, correlations,
missing values patterns, and more. Interactive 'heatmaps' allow the inspection
of specific value by hovering the mouse over a cell, as well as zooming into
a region of the 'heatmap' by dragging a rectangle around the relevant area.
This work is based on the 'ggplot2' and 'plotly.js' engine. It produces
similar 'heatmaps' as 'heatmap.2' or 'd3heatmap', with the advantage of speed
('plotly.js' is able to handle larger size matrix), the ability to zoom from
the 'dendrogram' panes, and the placing of factor variables in the sides of the
'heatmap'.
Author: Tal Galili [aut, cre, cph] (https://www.r-statistics.com),
Jonathan Sidi [ctb] (https://github.com/yonicd),
Alan O'Callaghan [ctb] (https://github.com/Alanocallaghan),
Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between heatmaply versions 0.14.1 dated 2018-02-01 and 0.15.0 dated 2018-06-23
ChangeLog | 68 +++++++++++++++++++ DESCRIPTION | 8 +- MD5 | 22 +++--- NEWS | 14 +++ NEWS.md | 16 ++++ R/heatmaply.R | 72 ++++++++++---------- R/heatmapr.R | 25 +++++++ R/plots.R | 12 ++- README.md | 6 - inst/doc/heatmaply.html | 125 +++++++++++++++++------------------ man/heatmaply.Rd | 15 ++-- tests/testthat/test_heatmaply_misc.R | 1 12 files changed, 260 insertions(+), 124 deletions(-)
Title: Create Dummy Variables from Categorical Data
Description: Create dummy variables from categorical data.
This package can convert categorical data (factor and ordered) into
dummy variables and handle multiple columns simultaneously.
This package enables to select whether a dummy variable for base group
is included (for principal component analysis/factor analysis) or
excluded (for regression analysis) by an option.
Author: Toshiaki Ara [aut, cre]
Maintainer: Toshiaki Ara <toshiaki.ara@gmail.com>
Diff between makedummies versions 1.1 dated 2018-04-06 and 1.1.1 dated 2018-06-23
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 11 +++++++++-- R/makedummies.R | 2 ++ man/makedummies.Rd | 2 ++ 5 files changed, 21 insertions(+), 10 deletions(-)
Title: A 'ggplot2' Extension for Plotting Unimodal Distributions
Description: The 'ggdistribute' package is an extension for plotting posterior or other
types of unimodal distributions that require overlaying information about a
distribution's intervals. It makes use of the 'ggproto' system to extend
'ggplot2', providing additional "geoms", "stats", and "positions."
The extensions integrate with existing 'ggplot2' layer elements.
Author: Joseph M. Burling [aut, cre]
Maintainer: Joseph M. Burling <josephburling@gmail.com>
Diff between ggdistribute versions 1.0.1 dated 2018-05-30 and 1.0.2 dated 2018-06-23
ggdistribute-1.0.1/ggdistribute/man/grapes-help-grapes.Rd |only ggdistribute-1.0.2/ggdistribute/DESCRIPTION | 9 ggdistribute-1.0.2/ggdistribute/MD5 | 55 ggdistribute-1.0.2/ggdistribute/NEWS.md | 6 ggdistribute-1.0.2/ggdistribute/R/data.R | 36 ggdistribute-1.0.2/ggdistribute/R/geom_posterior.R | 204 +-- ggdistribute-1.0.2/ggdistribute/R/ggdistribute-package.R | 172 +- ggdistribute-1.0.2/ggdistribute/R/gghelpers.R | 196 ++- ggdistribute-1.0.2/ggdistribute/R/helpers.R | 127 +- ggdistribute-1.0.2/ggdistribute/R/position_spread.R | 124 -- ggdistribute-1.0.2/ggdistribute/R/stat_posterior_density.R | 103 - ggdistribute-1.0.2/ggdistribute/R/stats.R | 98 - ggdistribute-1.0.2/ggdistribute/R/theme.R | 600 +++------- ggdistribute-1.0.2/ggdistribute/R/zzz.R | 7 ggdistribute-1.0.2/ggdistribute/README.md | 257 +++- ggdistribute-1.0.2/ggdistribute/build/vignette.rds |binary ggdistribute-1.0.2/ggdistribute/inst/doc/geom_posterior.R | 3 ggdistribute-1.0.2/ggdistribute/inst/doc/geom_posterior.Rmd | 7 ggdistribute-1.0.2/ggdistribute/inst/doc/geom_posterior.html | 58 ggdistribute-1.0.2/ggdistribute/man/GeomPosterior.Rd | 78 - ggdistribute-1.0.2/ggdistribute/man/figures/README-candy_wrappers-1.png |binary ggdistribute-1.0.2/ggdistribute/man/figures/README-rainbow_hills-1.png |binary ggdistribute-1.0.2/ggdistribute/man/figures/README-space_ships-1.png |binary ggdistribute-1.0.2/ggdistribute/man/figures/README-turtle_snails-1.png |binary ggdistribute-1.0.2/ggdistribute/man/show_colors.Rd | 2 ggdistribute-1.0.2/ggdistribute/tests/testthat/test_geom_posterior.R | 15 ggdistribute-1.0.2/ggdistribute/tests/testthat/test_position_spread.R | 6 ggdistribute-1.0.2/ggdistribute/tests/testthat/test_stat_density.R | 18 ggdistribute-1.0.2/ggdistribute/vignettes/geom_posterior.Rmd | 7 29 files changed, 1130 insertions(+), 1058 deletions(-)
Title: Trust, but Verify
Description: Declarative template-based framework for verifying that objects
meet structural requirements, and auto-composing error messages when they do
not.
Author: Brodie Gaslam [aut, cre],
Paxdiablo [cph] (Hash table implementation in src/pfhash.h),
R Core Team [cph] (Used/adapted several code snippets from R sources,
see src/misc-alike.c and src/valname.c)
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between vetr versions 0.2.4 dated 2018-03-28 and 0.2.5 dated 2018-06-23
DESCRIPTION | 10 +++--- MD5 | 24 ++++++++-------- NEWS.md | 4 ++ R/abstract.R | 12 ++++++-- README.md | 20 ++++++++----- build/vignette.rds |binary inst/doc/alike.html | 24 ++++++++-------- inst/doc/vetr.html | 16 +++++----- tests/unitizer/abstract.R | 45 ++++++++++-------------------- tests/unitizer/abstract.unitizer/data.rds |binary tests/unitizer/tev.R | 7 ++-- tests/unitizer/tev.unitizer/data.rds |binary vignettes/styles.css | 4 +- 13 files changed, 84 insertions(+), 82 deletions(-)
Title: Basic Robust Statistics
Description: "Essential" Robust Statistics.
Tools allowing to analyze data with robust methods. This includes
regression methodology including model selections and multivariate
statistics where we strive to cover the book "Robust Statistics,
Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.
Author: Martin Maechler [aut, cre],
Peter Rousseeuw [ctb] (Qn and Sn),
Christophe Croux [ctb] (Qn and Sn),
Valentin Todorov [aut] (most robust Cov),
Andreas Ruckstuhl [aut] (nlrob, anova, glmrob),
Matias Salibian-Barrera [aut] (lmrob orig.),
Tobias Verbeke [ctb, fnd] (mc, adjbox),
Manuel Koller [aut] (mc, lmrob, psi-func.),
Eduardo L. T. Conceicao [aut] (MM-, tau-, CM-, and MTL- nlrob),
Maria Anna di Palma [ctb] (initial version of Comedian)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between robustbase versions 0.93-0 dated 2018-04-24 and 0.93-1 dated 2018-06-23
DESCRIPTION | 14 +- MD5 | 164 ++++++++++++++--------------- R/mc.R | 4 build/partial.rdb |binary inst/NEWS.Rd | 18 +++ inst/doc/fastMcd-kmini.pdf |binary inst/doc/lmrob_simulation.R | 18 ++- inst/doc/lmrob_simulation.Rnw | 16 ++ inst/doc/lmrob_simulation.pdf |binary inst/doc/psi_functions.pdf |binary inst/xtraR/plot-psiFun.R | 14 +- man/CrohnD.Rd | 2 man/NOxEmissions.Rd | 2 man/SiegelsEx.Rd | 2 man/aircraft.Rd | 2 man/airmay.Rd | 2 man/alcohol.Rd | 2 man/ambientNOxCH.Rd | 2 man/biomassTill.Rd | 2 man/bushfire.Rd | 2 man/carrots.Rd | 2 man/cloud.Rd | 2 man/coleman.Rd | 2 man/condroz.Rd | 2 man/cushny.Rd | 2 man/delivery.Rd | 2 man/education.Rd | 2 man/epilepsy.Rd | 2 man/exAM.Rd | 2 man/foodstamp.Rd | 2 man/hbk.Rd | 2 man/kootenay.Rd | 2 man/lactic.Rd | 2 man/los.Rd | 2 man/mc.Rd | 22 +++ man/milk.Rd | 2 man/pension.Rd | 2 man/phosphor.Rd | 2 man/pilot.Rd | 2 man/possumDiv.Rd | 2 man/psiFunc.Rd | 7 + man/psi_func-class.Rd | 2 man/pulpfiber.Rd | 2 man/radarImage.Rd | 2 man/salinity.Rd | 2 man/starsCYG.Rd | 2 man/steamUse.Rd | 2 man/telef.Rd | 2 man/toxicity.Rd | 2 man/vaso.Rd | 2 man/wagnerGrowth.Rd | 2 man/wood.Rd | 2 src/lmrob.c | 17 +-- src/mc.c | 35 +++++- src/robustbase.h | 17 +++ tests/lmrob-psifns.R | 4 tests/lmrob-psifns.Rout.save | 8 + tests/mc-etc.R | 2 tests/mc-strict.R | 23 +++- vignettes/lmrob_simulation.Rnw | 16 ++ vignettes/plot-fig-AdB2-1.pdf |binary vignettes/plot-fig-Mscale-all.pdf |binary vignettes/plot-fig-Mscale.pdf |binary vignettes/plot-fig-cpr.pdf |binary vignettes/plot-fig-efficiency-all.pdf |binary vignettes/plot-fig-efficiency.pdf |binary vignettes/plot-fig-emp-level.pdf |binary vignettes/plot-fig-example-design.pdf |binary vignettes/plot-fig-lqq-level.pdf |binary vignettes/plot-fig-max-asymptotic-bias.pdf |binary vignettes/plot-fig-meanscale.pdf |binary vignettes/plot-fig-power-1-0_2.pdf |binary vignettes/plot-fig-power-1-0_4.pdf |binary vignettes/plot-fig-power-1-0_6.pdf |binary vignettes/plot-fig-power-1-0_8.pdf |binary vignettes/plot-fig-power-1-1.pdf |binary vignettes/plot-fig-pred-points.pdf |binary vignettes/plot-fig-psi-functions.pdf |binary vignettes/plot-fig-qscale-all.pdf |binary vignettes/plot-fig-qscale.pdf |binary vignettes/plot-fig-sdAdB2-1.pdf |binary vignettes/plot-fig-sdscale-1.pdf |binary vignettes/plot-fig-sdscale-all.pdf |binary 83 files changed, 319 insertions(+), 158 deletions(-)
Title: 'ggplot2' Based Publication Ready Plots
Description: The 'ggplot2' package is excellent and flexible for elegant data
visualization in R. However the default generated plots requires some formatting
before we can send them for publication. Furthermore, to customize a 'ggplot',
the syntax is opaque and this raises the level of difficulty for researchers
with no advanced R programming skills. 'ggpubr' provides some easy-to-use
functions for creating and customizing 'ggplot2'- based publication ready plots.
Author: Alboukadel Kassambara [aut, cre]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between ggpubr versions 0.1.6 dated 2017-11-14 and 0.1.7 dated 2018-06-23
DESCRIPTION | 29 +++---- MD5 | 58 +++++++------- NAMESPACE | 1 NEWS.md | 21 ++++- R/facet.R | 1 R/ggbarplot.R | 2 R/ggdonutchart.R |only R/ggdotchart.R | 6 - R/ggexport.R | 6 + R/ggscatterhist.R | 2 R/ggtext.R | 7 - R/stat_compare_means.R | 22 +++++ R/utilities.R | 26 +++++- README.md | 2 man/ggboxplot.Rd | 2 man/ggdonutchart.Rd |only man/stat_chull.Rd | 2 man/stat_conf_ellipse.Rd | 2 tools/README-cleveland-dot-plots-1.png |binary tools/README-deviation-graphs-1.png |binary tools/README-deviation-graphs-horizontal-1.png |binary tools/README-ggpubr-1.png |binary tools/README-ggpubr-2.png |binary tools/README-ggpubr-box-plot-dot-plots-strip-charts-1.png |binary tools/README-ggpubr-box-plot-dot-plots-strip-charts-2.png |binary tools/README-ggpubr-box-plot-dot-plots-strip-charts-3.png |binary tools/README-lollipop-chart-1.png |binary tools/README-lollipop-chart-deviation-1.png |binary tools/README-lollipop-chart-rotate-1.png |binary tools/README-ordered-bar-plots-1.png |binary tools/README-ordered-bar-plots-by-groups-1.png |binary 31 files changed, 127 insertions(+), 62 deletions(-)
Title: Simulates LOX Drop Testing
Description: Generates simulated data representing the LOX drop testing
process (also known as impact testing). A simulated process allows for
accelerated study of test behavior. Functions are provided to simulate
trials, test series, and groups of test series. Functions for creating plots
specific to this process are also included. Test attributes and criteria can
be set arbitrarily. This work is not endorsed by or affiliated with NASA.
See "ASTM G86-17, Standard Test Method for Determining Ignition Sensitivity
of Materials to Mechanical Impact in Ambient Liquid Oxygen and Pressurized
Liquid and Gaseous Oxygen Environments" <doi:10.1520/G0086-17>.
Author: Chad Ross [aut, cre]
Maintainer: Chad Ross <chad.ross@gmail.com>
Diff between droptest versions 0.1.0 dated 2018-05-22 and 0.1.1 dated 2018-06-23
DESCRIPTION | 10 +++++----- MD5 | 20 +++++++++++--------- NEWS.md | 7 ++++++- R/dgroups.R | 16 +++++++++------- R/droptest.R | 19 ++++++++++++------- R/dseries.R | 23 ++++++++++++----------- R/dtrials.R | 3 +-- R/gayleplot.R | 6 +++--- data/PREGENTD.RData |only man/D7905.Rd | 8 ++++---- man/PREGENTD.Rd |only man/droptest.Rd | 23 ++++++++++++++--------- 12 files changed, 77 insertions(+), 58 deletions(-)