Title: Example Data from the Multi-Modal MRI 'Reproducibility' Resource
Description: Multi-modal magnetic resonance imaging ('MRI')
data from the 'Kirby21' 'reproducibility' study
<https://www.nitrc.org/projects/multimodal/>, including functional
and structural imaging.
Author: John Muschelli <muschellij2@gmail.com>
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between kirby21.base versions 1.7.0 dated 2018-08-13 and 1.7.3 dated 2020-07-02
DESCRIPTION | 11 ++++--- MD5 | 30 +++++++++++---------- NEWS.md | 4 ++ R/copy_kirby21_data.R | 37 ++++++++++++++++++++++--- R/delete_kirby21_data.R | 18 +++++++++++- R/download_kirby21_data.R | 60 +++++++++++++++++++++++++----------------- R/get_image_filenames.R | 2 - R/modality_df.R | 1 man/copy_kirby21_data.Rd | 29 ++++++++++++++++++-- man/delete_kirby21_data.Rd | 16 ++++++++++- man/download_kirby21_data.Rd | 18 +++++++++++- man/get_image_filenames_df.Rd | 10 +++++-- man/get_par_filenames.Rd | 7 +++- man/kirby21_demog.Rd | 4 ++ man/subject_id_to_visit_id.Rd | 4 ++ tests |only 16 files changed, 189 insertions(+), 62 deletions(-)
Title: Models for Data from Unmarked Animals
Description: Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates.
Author: Richard Chandler [aut],
Ken Kellner [aut],
Ian Fiske [aut],
David Miller [aut],
Andy Royle [cre, aut],
Jeff Hostetler [aut],
Rebecca Hutchinson [aut],
Adam Smith [aut],
Marc Kery [ctb],
Mike Meredith [ctb],
Auriel Fournier [ctb],
Ariel Muldoon [ctb],
Chris Baker [ctb]
Maintainer: Andy Royle <aroyle@usgs.gov>
Diff between unmarked versions 1.0.0 dated 2020-05-04 and 1.0.1 dated 2020-07-02
DESCRIPTION | 8 - MD5 | 49 ++++--- NEWS | 5 R/getDesign.R | 144 ++++++++++++----------- R/occuRN.R | 4 R/unmarkedFit.R | 32 +++-- R/unmarkedFrame.R | 13 +- R/utils.R | 24 +++ build/vignette.rds |binary inst/csv/csv_factor_test.csv |only inst/doc/cap-recap.pdf |binary inst/doc/colext.pdf |binary inst/doc/distsamp.pdf |binary inst/doc/spp-dist.pdf |binary inst/doc/unmarked.pdf |binary inst/unitTests/runit.colext.R | 29 ++++ inst/unitTests/runit.gdistsamp.R | 215 ++++++++++++++++++++++++----------- inst/unitTests/runit.occuMS.R | 106 ++++++++++------- inst/unitTests/runit.occuMulti.R | 61 +++++---- inst/unitTests/runit.occuRN.R | 18 ++ inst/unitTests/runit.pcountOpen.R | 41 ++++++ inst/unitTests/runit.predict.R | 7 + inst/unitTests/runit.unmarkedFrame.R | 72 +++++++++++ inst/unitTests/runit.utils.R | 17 ++ man/occuTTD.Rd | 11 + src/init.c | 4 26 files changed, 616 insertions(+), 244 deletions(-)
Title: R Interface to NLopt
Description: Solve optimization problems using an R interface to NLopt. NLopt is a
free/open-source library for nonlinear optimization, providing a common
interface for a number of different free optimization routines available
online as well as original implementations of various other algorithms.
See <http://ab-initio.mit.edu/wiki/index.php/NLopt_Introduction> for more
information on the available algorithms. During installation of nloptr on
Unix-based systems, the installer checks whether the NLopt library is
installed on the system. If the NLopt library cannot be found, the code
is compiled using the NLopt source included in the nloptr package.
Author: Jelmer Ypma [aut, cre],
Steven G. Johnson [aut] (author of the NLopt C library),
Hans W. Borchers [ctb],
Dirk Eddelbuettel [ctb],
Brian Ripley [ctb] (build process on multiple OS),
Kurt Hornik [ctb] (build process on multiple OS),
Julien Chiquet [ctb],
Avraham Adler [ctb] (removal deprecated calls from tests,
<https://orcid.org/0000-0002-3039-0703>)
Maintainer: Jelmer Ypma <uctpjyy@ucl.ac.uk>
Diff between nloptr versions 1.2.2.1 dated 2020-03-11 and 1.2.2.2 dated 2020-07-02
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- configure | 17 ++++------------- configure.ac | 3 +++ 4 files changed, 14 insertions(+), 20 deletions(-)
Title: Simulated Predicted Probabilities for Multinomial Logit Models
Description: Functions to easily return simulated predicted probabilities and
first differences for multinomial logit models. It takes a specified
scenario and a multinomial model to predict probabilities with a set of
coefficients, drawn from a simulated sampling distribution. The simulated
predictions allow for meaningful plots with means and confidence intervals.
The methodological approach is based on the principles laid out by King,
Tomz, and Wittenberg (2000) <doi:10.2307/2669316> and Hanmer and Ozan Kalkan
(2016) <doi:10.1111/j.1540-5907.2012.00602.x>.
Author: Manuel Neumann [aut, cre]
Maintainer: Manuel Neumann <manuel.neumann@mzes.uni-mannheim.de>
Diff between MNLpred versions 0.0.2 dated 2020-03-04 and 0.0.3 dated 2020-07-02
DESCRIPTION | 15 MD5 | 45 +- NAMESPACE | 4 NEWS.md | 7 R/gles-data.R |only R/mnl_fd2_ova.R | 55 +-- R/mnl_fd_ova.R | 26 - R/mnl_pred_ova.R | 64 ++- README.md | 318 +++++++++++------- build/vignette.rds |binary data |only inst/doc/OVA_Predictions_For_MNL.R | 99 ++--- inst/doc/OVA_Predictions_For_MNL.Rmd | 140 ++++---- inst/doc/OVA_Predictions_For_MNL.html | 412 ++++++++++++++---------- man/figures/README-first_differences_plot-1.png |binary man/figures/README-prediction_plot1-1.png |binary man/figures/README-prediction_plot2-1.png |binary man/figures/README-static_fd_plot-1.png |binary man/gles.Rd |only man/mnl_fd2_ova.Rd | 136 +++---- man/mnl_fd_ova.Rd | 155 ++++----- man/mnl_pred_ova.Rd | 141 +++----- tests/testthat/test_inputvariants.R | 95 +++-- vignettes/OVA_Predictions_For_MNL.Rmd | 140 ++++---- vignettes/bibliography.bib | 36 +- 25 files changed, 1031 insertions(+), 857 deletions(-)
Title: moDel Agnostic Language for Exploration and eXplanation
Description: Unverified black box model is the path to the failure. Opaqueness leads to distrust.
Distrust leads to ignoration. Ignoration leads to rejection.
DALEX package xrays any model and helps to explore and explain its behaviour.
Machine Learning (ML) models are widely used and have various applications in classification
or regression. Models created with boosting, bagging, stacking or similar techniques are often
used due to their high performance. But such black-box models usually lack of direct interpretability.
DALEX package contains various methods that help to understand the link between input variables
and model output. Implemented methods help to explore model on the level of a single instance
as well as a level of the whole dataset.
All model explainers are model agnostic and can be compared across different models.
DALEX package is the cornerstone for 'DrWhy.AI' universe of packages for visual model exploration.
Find more details in (Biecek 2018) <arXiv:1806.08915>.
Author: Przemyslaw Biecek [aut, cre] (<https://orcid.org/0000-0001-8423-1823>),
Szymon Maksymiuk [aut],
Hubert Baniecki [aut] (<https://orcid.org/0000-0001-6661-5364>)
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between DALEX versions 1.2.1 dated 2020-04-25 and 1.3.0 dated 2020-07-02
DESCRIPTION | 8 - MD5 | 54 +++++------ NAMESPACE | 2 R/data_fifa.R | 5 - R/explain.R | 76 ++++++++++----- R/misc_loss_functions.R | 145 +++++++++++++++++------------- R/misc_yhat.R | 14 ++ R/model_info.R | 83 ++++++++++++----- R/model_parts.R | 10 +- R/model_performance.R | 71 ++++++++++++++ R/model_profile.R | 11 +- R/model_variable_effect.R | 4 R/plot_model_performance.R | 20 ++-- R/predict_diagnostics.R | 2 R/predict_parts.R | 2 R/print_model_performance.R | 2 data/fifa.rda |binary man/explain.Rd | 16 +-- man/loss_functions.Rd | 5 + man/model_info.Rd | 31 +++--- man/model_parts.Rd | 9 + man/model_profile.Rd | 6 - man/plot.model_performance.Rd | 7 + man/predict_parts.Rd | 2 man/variable_effect.Rd | 4 tests/testthat/test_explain.R | 2 tests/testthat/test_model_performance.R | 3 tests/testthat/test_variable_importance.R | 12 +- 28 files changed, 399 insertions(+), 207 deletions(-)
Title: Cognitive Diagnostic Computerized Adaptive Testing
Description: Provides a set of functions for conducting cognitive diagnostic computerized adaptive testing applications (Chen (2009) <doi:10.1007/s11336-009-9123-2>). It includes different item selection rules such us the global discrimination index (Kaplan, de la Torre, and Barrada (2015) <doi:10.1177/0146621614554650>) and the nonparametric selection method (Chang, Chiu, and Tsai (2019) <doi:10.1177/0146621618813113>), as well as several stopping rules. Functions for generating item banks and responses are also provided. To guide item bank calibration, model comparison at the item level can be conducted using the two-step likelihood ratio test statistic by Sorrel, de la Torre, Abad and Olea (2017) <doi:10.1027/1614-2241/a000131>.
Author: Miguel A. Sorrel [aut, cre, cph],
Pablo Nájera [aut, cph],
Francisco J. Abad [aut, cph]
Maintainer: Miguel A. Sorrel <miguel.sorrel@uam.es>
Diff between cdcatR versions 1.0.0 dated 2020-06-13 and 1.0.1 dated 2020-07-02
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 3 +++ R/helper.R | 2 +- 4 files changed, 11 insertions(+), 8 deletions(-)
Title: Variable Importance via Oscillations
Description: Provides an easy to calculate local variable importance measure based on Ceteris Paribus profile
and global variable importance measure based on Partial Dependence Profiles.
Author: Anna Kozak [aut, cre],
Przemyslaw Biecek [aut, ths]
Maintainer: Anna Kozak <anna1993kozak@gmail.com>
Diff between vivo versions 0.1.2 dated 2020-02-27 and 0.2.0 dated 2020-07-02
vivo-0.1.2/vivo/inst/doc/vignette_apartments.R |only vivo-0.1.2/vivo/inst/doc/vignette_apartments.Rmd |only vivo-0.1.2/vivo/inst/doc/vignette_apartments.html |only vivo-0.1.2/vivo/vignettes/vignette_apartments.Rmd |only vivo-0.2.0/vivo/DESCRIPTION | 19 -- vivo-0.2.0/vivo/MD5 | 47 ++-- vivo-0.2.0/vivo/NAMESPACE | 2 vivo-0.2.0/vivo/NEWS.md | 6 vivo-0.2.0/vivo/R/calculate_weight.R | 29 +-- vivo-0.2.0/vivo/R/global_variable_importance.R |only vivo-0.2.0/vivo/R/local_variable_importance.R | 67 +++++-- vivo-0.2.0/vivo/R/plot_global_importance.R |only vivo-0.2.0/vivo/R/plot_local_importance.R | 142 +++++++++++++-- vivo-0.2.0/vivo/README.md | 112 +++-------- vivo-0.2.0/vivo/build/vignette.rds |binary vivo-0.2.0/vivo/inst/doc/vignette_apartments_global.R |only vivo-0.2.0/vivo/inst/doc/vignette_apartments_global.Rmd |only vivo-0.2.0/vivo/inst/doc/vignette_apartments_global.html |only vivo-0.2.0/vivo/inst/doc/vignette_apartments_local.R |only vivo-0.2.0/vivo/inst/doc/vignette_apartments_local.Rmd |only vivo-0.2.0/vivo/inst/doc/vignette_apartments_local.html |only vivo-0.2.0/vivo/man/calculate_variable_split.Rd | 3 vivo-0.2.0/vivo/man/calculate_weight.Rd | 7 vivo-0.2.0/vivo/man/figures/vivo.png |only vivo-0.2.0/vivo/man/global_variable_importance.Rd |only vivo-0.2.0/vivo/man/local_variable_importance.Rd | 18 + vivo-0.2.0/vivo/man/plot.global_importance.Rd |only vivo-0.2.0/vivo/man/plot.local_importance.Rd | 29 ++- vivo-0.2.0/vivo/tests/testthat/objects_for_tests.R | 46 ++++ vivo-0.2.0/vivo/tests/testthat/test_measure.R | 9 vivo-0.2.0/vivo/tests/testthat/test_plot.R | 130 +++++++++++++ vivo-0.2.0/vivo/vignettes/vignette_apartments_global.Rmd |only vivo-0.2.0/vivo/vignettes/vignette_apartments_local.Rmd |only 33 files changed, 487 insertions(+), 179 deletions(-)
Title: Advanced Statistical Methods to Model and Adjust for Bias in
Meta-Analysis
Description: The following methods are implemented to evaluate how sensitive the results of a meta-analysis are to potential bias in meta-analysis and to support Schwarzer et al. (2015) <DOI:10.1007/978-3-319-21416-0>, Chapter 5 'Small-Study Effects in Meta-Analysis':
- Copas selection model described in Copas & Shi (2001) <DOI:10.1177/096228020101000402>;
- limit meta-analysis by Rücker et al. (2011) <DOI:10.1093/biostatistics/kxq046>;
- upper bound for outcome reporting bias by Copas & Jackson (2004) <DOI:10.1111/j.0006-341X.2004.00161.x>;
- imputation methods for missing binary data by Gamble & Hollis (2005) <DOI:10.1016/j.jclinepi.2004.09.013> and Higgins et al. (2008) <DOI:10.1177/1740774508091600>.
Author: Guido Schwarzer [cre, aut] (<https://orcid.org/0000-0001-6214-9087>),
James R. Carpenter [aut] (<https://orcid.org/0000-0003-3890-6206>),
Gerta Rücker [aut] (<https://orcid.org/0000-0002-2192-2560>)
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between metasens versions 0.4-0 dated 2019-08-06 and 0.4-1 dated 2020-07-02
metasens-0.4-0/metasens/NEWS |only metasens-0.4-1/metasens/DESCRIPTION | 10 +-- metasens-0.4-1/metasens/MD5 | 46 ++++++++--------- metasens-0.4-1/metasens/NEWS.md |only metasens-0.4-1/metasens/R/copas.R | 7 +- metasens-0.4-1/metasens/R/forest.orbbound.R | 4 - metasens-0.4-1/metasens/R/funnel.limitmeta.R | 8 +- metasens-0.4-1/metasens/R/limitmeta.R | 14 +---- metasens-0.4-1/metasens/R/metamiss.R | 6 +- metasens-0.4-1/metasens/R/plot.copas.R | 5 + metasens-0.4-1/metasens/man/Crowther2003.Rd | 6 +- metasens-0.4-1/metasens/man/Moore1998.Rd | 6 +- metasens-0.4-1/metasens/man/copas.Rd | 19 +++++-- metasens-0.4-1/metasens/man/forest.orbbound.Rd | 18 ++++-- metasens-0.4-1/metasens/man/funnel.limitmeta.Rd | 44 +++++++++++----- metasens-0.4-1/metasens/man/limitmeta.Rd | 13 +++- metasens-0.4-1/metasens/man/metamiss.Rd | 16 ++++- metasens-0.4-1/metasens/man/orbbound.Rd | 3 - metasens-0.4-1/metasens/man/plot.copas.Rd | 22 +++++--- metasens-0.4-1/metasens/man/print.copas.Rd | 11 ++-- metasens-0.4-1/metasens/man/print.limitmeta.Rd | 10 ++- metasens-0.4-1/metasens/man/print.orbbound.Rd | 21 +++++-- metasens-0.4-1/metasens/man/print.summary.copas.Rd | 14 +++-- metasens-0.4-1/metasens/man/print.summary.limitmeta.Rd | 27 +++++++-- metasens-0.4-1/metasens/man/summary.copas.Rd | 3 - 25 files changed, 215 insertions(+), 118 deletions(-)
Title: Construct Modeling Packages
Description: Building modeling packages is hard. A large amount
of effort generally goes into providing an implementation for a new
method that is efficient, fast, and correct, but often less emphasis
is put on the user interface. A good interface requires specialized
knowledge about S3 methods and formulas, which the average package
developer might not have. The goal of 'hardhat' is to reduce the
burden around building new modeling packages by providing
functionality for preprocessing, predicting, and validating input.
Author: Davis Vaughan [aut, cre],
Max Kuhn [aut],
RStudio [cph]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between hardhat versions 0.1.3 dated 2020-05-20 and 0.1.4 dated 2020-07-02
DESCRIPTION | 51 +- MD5 | 69 +- NEWS.md | 24 + R/blueprint-formula-default.R | 266 ++++++----- R/blueprint-formula.R | 67 ++ R/compat-lifecycle.R |only R/forge.R | 2 R/hardhat-example-data.R |only R/model-matrix.R | 92 +++ README.md | 21 build/hardhat.pdf |binary build/vignette.rds |binary data |only inst/doc/forge.R | 86 +-- inst/doc/forge.Rmd | 104 ++-- inst/doc/forge.html | 434 +++++++++--------- inst/doc/mold.R | 72 +-- inst/doc/mold.Rmd | 76 +-- inst/doc/mold.html | 550 +++++++++++------------ inst/doc/package.R | 71 +- inst/doc/package.Rmd | 71 +- inst/doc/package.html | 273 ++++++----- man/contr_one_hot.Rd |only man/default_formula_blueprint.Rd | 140 +++-- man/forge.Rd | 2 man/get_levels.Rd | 2 man/hardhat-example-data.Rd |only man/model_offset.Rd | 4 man/new-blueprint.Rd | 15 man/new-default-blueprint.Rd | 15 tests/testthat/out/print-blueprint-formula-1.txt | 2 tests/testthat/out/print-blueprint-formula-2.txt | 2 tests/testthat/test-forge-formula.R | 340 +++++++++++--- tests/testthat/test-model-offset.R | 11 tests/testthat/test-mold-formula.R | 462 ++++++++++++++----- vignettes/forge.Rmd | 104 ++-- vignettes/mold.Rmd | 76 +-- vignettes/package.Rmd | 71 +- 38 files changed, 2192 insertions(+), 1383 deletions(-)
Title: R Parallel Implementation of Local Outlier Factor(LOF)
Description: R parallel implementation of Local Outlier Factor(LOF) which uses multiple CPUs to significantly speed up the LOF computation for large datasets. (Note: The overall performance depends on the computers especially the number of the cores).It also supports multiple k values to be calculated in parallel, as well as various distance measures in addition to the default Euclidean distance.
Author: Yingsong Hu, Wayne Murray and Yin Shan, Australia.
Maintainer: Yingsong Hu <yingsonghu@hotmail.com>
Diff between Rlof versions 1.1.1 dated 2015-09-17 and 1.1.2 dated 2020-07-02
DESCRIPTION | 7 +++---- MD5 | 12 ++++++------ NAMESPACE | 6 +++--- R/Rlof.R | 47 +++++++++++++++++++++-------------------------- man/Rlof-package.Rd | 2 +- src/distance.c | 28 ++++++++++++++++++++++++++-- src/distance.h | 12 +++++------- 7 files changed, 65 insertions(+), 49 deletions(-)
Title: Landscape Epidemiology and Evolution
Description: A stochastic, spatially-explicit, demo-genetic model simulating the spread and evolution
of a plant pathogen in a heterogeneous landscape to assess resistance deployment strategies.
It is based on a spatial geometry for describing the landscape and allocation of different cultivars,
a dispersal kernel for the dissemination of the pathogen, and a SEIR
('Susceptible-Exposed-Infectious-Removed’) structure with a discrete time step.
It provides a useful tool to assess the performance of a wide range of deployment options with
respect to their epidemiological, evolutionary and economic outcomes.
Loup Rimbaud, Julien Papaïx, Jean-François Rey, Luke G Barrett,
Peter H Thrall (2018) <doi:10.1371/journal.pcbi.1006067>.
Author: Loup Rimbaud [aut],
Julien Papaix [aut],
Jean-Francois Rey [cre],
Jean-Loup Gaussen [ctb]
Maintainer: Jean-Francois Rey <jean-francois.rey@inrae.fr>
Diff between landsepi versions 1.0.0 dated 2020-07-01 and 1.0.1 dated 2020-07-02
DESCRIPTION | 8 ++++---- MD5 | 38 +++++++++++++++++++------------------- R/landsepi.R | 4 ++-- build/vignette.rds |binary configure | 30 +++++++++++++++--------------- configure.ac | 6 +++--- inst/doc/landscape_dispersal.Rmd | 6 ++---- inst/doc/landscape_dispersal.html | 7 ++----- inst/doc/list_of_parameters.Rnw | 5 +++-- inst/doc/list_of_parameters.pdf |binary inst/doc/run_exp_design.Rmd | 18 ++++++++---------- inst/doc/run_exp_design.html | 25 ++++++++++++++----------- inst/doc/run_simple_simul.Rmd | 32 ++++++++++++++++---------------- inst/doc/run_simple_simul.html | 36 +++++++++++++++++++++++------------- man/landsepi-package.Rd | 4 ++-- src/Model.cpp | 2 +- vignettes/landscape_dispersal.Rmd | 6 ++---- vignettes/list_of_parameters.Rnw | 5 +++-- vignettes/run_exp_design.Rmd | 18 ++++++++---------- vignettes/run_simple_simul.Rmd | 32 ++++++++++++++++---------------- 20 files changed, 143 insertions(+), 139 deletions(-)
Title: Functions to Compute Compositional Turnover Using Zeta Diversity
Description: Functions to compute compositional turnover using zeta-diversity,
the number of species shared by multiple assemblages. The package includes
functions to compute zeta-diversity for a specific number of
assemblages and to compute zeta-diversity for a range of numbers of
assemblages. It also includes functions to explain how zeta-diversity
varies with distance and with differences in environmental variables
between assemblages, using generalised linear models, linear models
with negative constraints, generalised additive models,shape
constrained additive models, and I-splines.
Author: Guillaume Latombe [aut, cre],
Melodie A. McGeoch [aut],
David A. Nipperess [aut],
Cang Hui [aut]
Maintainer: Guillaume Latombe <latombe.guillaume@gmail.com>
Diff between zetadiv versions 1.1.1 dated 2018-05-17 and 1.2.0 dated 2020-07-02
zetadiv-1.1.1/zetadiv/R/unexported.functions.from.scam.1.2.R |only zetadiv-1.2.0/zetadiv/DESCRIPTION | 22 zetadiv-1.2.0/zetadiv/MD5 | 71 zetadiv-1.2.0/zetadiv/NAMESPACE | 55 zetadiv-1.2.0/zetadiv/R/zetadiv.R | 1597 ++++++++--- zetadiv-1.2.0/zetadiv/inst |only zetadiv-1.2.0/zetadiv/man/Ispline.Rd | 76 zetadiv-1.2.0/zetadiv/man/Marion.env.Rd | 68 zetadiv-1.2.0/zetadiv/man/Marion.species.Rd | 68 zetadiv-1.2.0/zetadiv/man/Plot.ispline.Rd | 139 zetadiv-1.2.0/zetadiv/man/Plot.zeta.ddecay.Rd | 94 zetadiv-1.2.0/zetadiv/man/Plot.zeta.ddecays.Rd | 94 zetadiv-1.2.0/zetadiv/man/Plot.zeta.decline.Rd | 96 zetadiv-1.2.0/zetadiv/man/Plot.zeta.scale.min.dist.Rd | 101 zetadiv-1.2.0/zetadiv/man/Plot.zeta.scale.regular.Rd | 103 zetadiv-1.2.0/zetadiv/man/Predict.msgdm.Rd | 138 zetadiv-1.2.0/zetadiv/man/Reg.ispline.Rd |only zetadiv-1.2.0/zetadiv/man/Return.ispline.Rd |only zetadiv-1.2.0/zetadiv/man/Zeta.ddecay.Rd | 227 - zetadiv-1.2.0/zetadiv/man/Zeta.ddecays.Rd | 169 - zetadiv-1.2.0/zetadiv/man/Zeta.decline.ex.Rd | 177 - zetadiv-1.2.0/zetadiv/man/Zeta.decline.mc.Rd | 227 - zetadiv-1.2.0/zetadiv/man/Zeta.msgdm.Rd | 329 +- zetadiv-1.2.0/zetadiv/man/Zeta.order.ex.Rd | 129 zetadiv-1.2.0/zetadiv/man/Zeta.order.mc.Rd | 179 - zetadiv-1.2.0/zetadiv/man/Zeta.order.mc.mult.Rd |only zetadiv-1.2.0/zetadiv/man/Zeta.sam.sensitivity.Rd | 181 - zetadiv-1.2.0/zetadiv/man/Zeta.scale.min.dist.Rd | 171 - zetadiv-1.2.0/zetadiv/man/Zeta.scale.regular.Rd | 145 zetadiv-1.2.0/zetadiv/man/Zeta.varpart.Rd | 186 - zetadiv-1.2.0/zetadiv/man/bird.env.coarse.Rd | 90 zetadiv-1.2.0/zetadiv/man/bird.env.fine.Rd | 90 zetadiv-1.2.0/zetadiv/man/bird.spec.coarse.Rd | 62 zetadiv-1.2.0/zetadiv/man/bird.spec.fine.Rd | 62 zetadiv-1.2.0/zetadiv/man/glm.cons.Rd | 165 - zetadiv-1.2.0/zetadiv/man/glm.fit.cons.Rd | 129 zetadiv-1.2.0/zetadiv/man/pie.neg.Rd | 126 zetadiv-1.2.0/zetadiv/man/rescale.min.dist.Rd | 115 zetadiv-1.2.0/zetadiv/man/rescale.regular.Rd | 88 39 files changed, 3514 insertions(+), 2255 deletions(-)
Title: Scoring the EQ-5D Descriptive System
Description: EQ-5D is a standard instrument (<https://euroqol.org/eq-5d-instruments/>) that measures the quality of life
often used in clinical and economic evaluations of health care technologies. Both adult versions of EQ-5D (EQ-5D-3L and EQ-5D-5L)
contain a descriptive system and visual analog scale. The descriptive system measures the patient's health in 5 dimensions:
the 5L versions has 5 levels and 3L version has 3 levels. The descriptive system scores are usually converted to index values
using country specific values sets (that incorporates the country preferences). This package allows the calculation of both descriptive system
scores to the index value scores. The value sets for EQ-5D-3L are from the references mentioned in the website <https://euroqol.org/eq-5d-instruments/eq-5d-3l-about/valuation/>
The value sets for EQ-5D-3L for a total of 31 countries are used for the valuation (see the user guide for a complete list of references).
The value sets for EQ-5D-5L are obtained from references mentioned in the <https://euroqol.org/eq-5d-instruments/eq-5d-5l-about/valuation-standard-value-sets/> and other sources.
The value sets for EQ-5D-5L for a total of 17 countries are used for the valuation (see the user guide for a complete list of references).
The package can also be used to map 5L scores to 3L index values for 10 countries: Denmark, France, Germany, Japan, Netherlands, Spain, Thailand, UK, USA, and Zimbabwe.
The value set and method for mapping are obtained from Van Hout et al (2012) <doi: 10.1016/j.jval.2012.02.008>.
Author: Sheeja Manchira Krishnan [aut, cre]
Maintainer: Sheeja Manchira Krishnan <sheejamk@gmail.com>
Diff between valueEQ5D versions 0.5.1 dated 2020-01-23 and 0.5.2 dated 2020-07-02
DESCRIPTION | 6 MD5 | 90 +- NAMESPACE | 48 - R/basic_checks.R | 279 +++--- R/data.R | 306 +++---- R/eq5d.R | 1341 +++++++++++++++++---------------- R/globals.R | 14 R/sysdata.rda |binary build/vignette.rds |binary data/EQ5D3L_indexvalues.df.rda |binary data/EQ5D3L_tariffs_TTO.df.rda |binary data/EQ5D5L_indexvalues.df.rda |binary data/EQ5D5L_tariffs.df.rda |binary inst/doc/User_Guide.R | 165 +--- inst/doc/User_Guide.Rmd | 409 +++++----- inst/doc/User_Guide.html | 1279 +++++++++++++++---------------- inst/shiny/app.R | 444 +++++----- man/EQ5D3L_indexvalues.df.Rd | 190 ++-- man/EQ5D3L_tariffs_TTO.df.Rd | 134 +-- man/EQ5D3L_tariffs_VAS.df.Rd | 75 - man/EQ5D5L_crosswalk_indexvalues.df.Rd | 44 - man/EQ5D5L_indexvalues.df.Rd | 111 +- man/EQ5D5L_tariffs.df.Rd | 106 +- man/Probability_matrix_crosswalk.df.Rd | 38 man/checkColumnExist.Rd | 45 - man/checkScores3L.Rd | 58 - man/checkScores5L.Rd | 56 - man/convertNumberToIndividualDigits.Rd | 40 man/descriptiveStatDataColumn.Rd | 48 - man/dot-correctImplausibleOrdering.Rd | 40 man/getColNumExistingColNames.Rd | 48 - man/getColumnNoColNames.Rd | 44 - man/getFrequencyTable.Rd | 40 man/getModeForVec.Rd | 40 man/map5Lto3L.Rd | 81 + man/map5Lto3LInd.Rd | 70 - man/replaceSpaceUnderscore.Rd | 40 man/subsetGenderAgeToGroup.Rd | 52 - man/testDataNumNorange.Rd | 44 - man/testFileExistRead.Rd | 40 man/value3L.Rd | 76 - man/value3LInd.Rd | 70 - man/value5L.Rd | 77 - man/value5LInd.Rd | 66 - tests/testthat/testthat.R | 934 +++++++++++----------- vignettes/User_Guide.Rmd | 409 +++++----- 46 files changed, 3829 insertions(+), 3668 deletions(-)
Title: Connect to 'AWS Athena' using R 'AWS SDK' 'paws' ('DBI'
Interface)
Description: Designed to be compatible with the 'R' package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this the 'R' 'AWS' Software Development Kit ('SDK') 'paws'
<https://github.com/paws-r/paws> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between noctua versions 1.7.0 dated 2020-05-14 and 1.7.1 dated 2020-07-02
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 9 ++++++++- R/Connection.R | 4 +++- R/File_Parser.R | 39 ++++++++++++++++++++++++++++++++++++--- R/Options.R | 3 ++- R/Result.R | 21 +++++++++++---------- build/vignette.rds |binary man/dbClearResult.Rd | 4 ++++ man/dbFetch.Rd | 3 +-- man/dbGetQuery.Rd | 4 ++++ man/noctua_options.Rd | 3 ++- tests/testthat/test-metadata.R | 2 +- 13 files changed, 88 insertions(+), 36 deletions(-)
Title: 'HTMLWidget' Wrapper of 'UpSet.js' for Exploring Large Set
Intersections
Description: 'UpSet.js' is a re-implementation of 'UpSetR' to create interactive set visualizations for more than three sets.
This is a 'htmlwidget' wrapper around the 'JavaScript' library 'UpSet.js'.
Author: Samuel Gratzl [aut, cre]
Maintainer: Samuel Gratzl <sam@sgratzl.com>
Diff between upsetjs versions 1.3.1 dated 2020-06-21 and 1.6.0 dated 2020-07-02
DESCRIPTION | 8 - MD5 | 50 +++++++----- NAMESPACE | 4 R/attributes.R | 2 R/data.R | 82 ++++++++++++-------- R/queries.R | 8 - R/selection.R | 4 R/style.R | 69 +++++++++++++++-- R/upsetjs.R | 61 +++++++++++++++ R/utils.R | 29 +++++-- build/vignette.rds |binary inst/doc/basic.html | 70 ++++++++--------- inst/doc/colors.html | 18 ++-- inst/doc/combinationModes.html | 18 ++-- inst/doc/got.R |only inst/doc/got.Rmd |only inst/doc/got.html |only inst/doc/kmap.R |only inst/doc/kmap.Rmd |only inst/doc/kmap.html |only inst/doc/venn.Rmd | 166 ++++++++++++++++++++--------------------- inst/doc/venn.html | 18 ++-- inst/htmlwidgets/upsetjs.js | 2 man/chartKarnaughMapLabels.Rd |only man/chartKarnaughMapLayout.Rd |only man/chartTheme.Rd | 7 + man/fromExpression.Rd | 5 - man/upsetjsKarnaughMap.Rd |only man/upsetjsKarnaughMapProxy.Rd |only vignettes/got.Rmd |only vignettes/kmap.Rmd |only vignettes/venn.Rmd | 166 ++++++++++++++++++++--------------------- 32 files changed, 480 insertions(+), 307 deletions(-)
Title: Tidy Quantitative Financial Analysis
Description: Bringing business and financial analysis to the 'tidyverse'. The 'tidyquant'
package provides a convenient wrapper to various 'xts', 'zoo', 'quantmod', 'TTR'
and 'PerformanceAnalytics' package
functions and returns the objects in the tidy 'tibble' format. The main
advantage is being able to use quantitative functions with the 'tidyverse'
functions including 'purrr', 'dplyr', 'tidyr', 'ggplot2', 'lubridate', etc. See
the 'tidyquant' website for more information, documentation and examples.
Author: Matt Dancho [aut, cre],
Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between tidyquant versions 1.0.0 dated 2020-03-04 and 1.0.1 dated 2020-07-02
tidyquant-1.0.0/tidyquant/R/dplyr-colwise-summarise.R |only tidyquant-1.0.0/tidyquant/R/dplyr-summarise.R |only tidyquant-1.0.0/tidyquant/man/summarise_by_time.Rd |only tidyquant-1.0.1/tidyquant/DESCRIPTION | 11 tidyquant-1.0.1/tidyquant/MD5 | 95 - tidyquant-1.0.1/tidyquant/NAMESPACE | 4 tidyquant-1.0.1/tidyquant/NEWS.md | 31 tidyquant-1.0.1/tidyquant/R/deprecated.R | 13 tidyquant-1.0.1/tidyquant/R/excel-financial-math-functions.R | 13 tidyquant-1.0.1/tidyquant/R/excel-if-functions.R | 1 tidyquant-1.0.1/tidyquant/R/excel-pivot-table.R | 6 tidyquant-1.0.1/tidyquant/R/excel-stat-mutation-functions.R | 3 tidyquant-1.0.1/tidyquant/R/excel-stat-summary-functions.R | 3 tidyquant-1.0.1/tidyquant/R/ggplot-geom_bbands.R | 16 tidyquant-1.0.1/tidyquant/R/ggplot-geom_ma.R | 18 tidyquant-1.0.1/tidyquant/R/tq_get.R | 23 tidyquant-1.0.1/tidyquant/R/zzz.R | 37 tidyquant-1.0.1/tidyquant/README.md | 80 - tidyquant-1.0.1/tidyquant/inst/doc/TQ00-introduction-to-tidyquant.R | 1 tidyquant-1.0.1/tidyquant/inst/doc/TQ00-introduction-to-tidyquant.Rmd | 22 tidyquant-1.0.1/tidyquant/inst/doc/TQ00-introduction-to-tidyquant.html | 64 - tidyquant-1.0.1/tidyquant/inst/doc/TQ01-core-functions-in-tidyquant.R | 2 tidyquant-1.0.1/tidyquant/inst/doc/TQ01-core-functions-in-tidyquant.Rmd | 2 tidyquant-1.0.1/tidyquant/inst/doc/TQ01-core-functions-in-tidyquant.html | 300 ++--- tidyquant-1.0.1/tidyquant/inst/doc/TQ02-quant-integrations-in-tidyquant.R | 2 tidyquant-1.0.1/tidyquant/inst/doc/TQ02-quant-integrations-in-tidyquant.Rmd | 2 tidyquant-1.0.1/tidyquant/inst/doc/TQ02-quant-integrations-in-tidyquant.html | 548 +++++---- tidyquant-1.0.1/tidyquant/inst/doc/TQ03-scaling-and-modeling-with-tidyquant.R | 2 tidyquant-1.0.1/tidyquant/inst/doc/TQ03-scaling-and-modeling-with-tidyquant.Rmd | 2 tidyquant-1.0.1/tidyquant/inst/doc/TQ03-scaling-and-modeling-with-tidyquant.html | 421 ++++--- tidyquant-1.0.1/tidyquant/inst/doc/TQ04-charting-with-tidyquant.html | 526 ++++----- tidyquant-1.0.1/tidyquant/inst/doc/TQ05-performance-analysis-with-tidyquant.R | 3 tidyquant-1.0.1/tidyquant/inst/doc/TQ05-performance-analysis-with-tidyquant.Rmd | 4 tidyquant-1.0.1/tidyquant/inst/doc/TQ05-performance-analysis-with-tidyquant.html | 567 +++++----- tidyquant-1.0.1/tidyquant/inst/doc/TQ06-excel-in-r.html | 29 tidyquant-1.0.1/tidyquant/man/FANG.Rd | 6 tidyquant-1.0.1/tidyquant/man/deprecated.Rd | 1 tidyquant-1.0.1/tidyquant/man/excel_financial_math_functions.Rd | 13 tidyquant-1.0.1/tidyquant/man/excel_if_functions.Rd | 1 tidyquant-1.0.1/tidyquant/man/excel_stat_mutation_functions.Rd | 3 tidyquant-1.0.1/tidyquant/man/excel_stat_summary_functions.Rd | 3 tidyquant-1.0.1/tidyquant/man/geom_bbands.Rd | 18 tidyquant-1.0.1/tidyquant/man/geom_ma.Rd | 18 tidyquant-1.0.1/tidyquant/man/theme_tq.Rd | 2 tidyquant-1.0.1/tidyquant/man/tq_get.Rd | 4 tidyquant-1.0.1/tidyquant/vignettes/TQ00-introduction-to-tidyquant.Rmd | 22 tidyquant-1.0.1/tidyquant/vignettes/TQ01-core-functions-in-tidyquant.Rmd | 2 tidyquant-1.0.1/tidyquant/vignettes/TQ02-quant-integrations-in-tidyquant.Rmd | 2 tidyquant-1.0.1/tidyquant/vignettes/TQ03-scaling-and-modeling-with-tidyquant.Rmd | 2 tidyquant-1.0.1/tidyquant/vignettes/TQ05-performance-analysis-with-tidyquant.Rmd | 4 50 files changed, 1605 insertions(+), 1347 deletions(-)
Title: Connect to 'AWS Athena' using 'Boto3' ('DBI' Interface)
Description: Designed to be compatible with the R package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this 'Python' 'Boto3' Software Development Kit ('SDK')
<https://boto3.amazonaws.com/v1/documentation/api/latest/index.html> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between RAthena versions 1.9.0 dated 2020-05-14 and 1.9.1 dated 2020-07-02
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NEWS.md | 9 ++++++++- R/Connection.R | 4 +++- R/File_Parser.R | 41 ++++++++++++++++++++++++++++++++++++++--- R/Options.R | 3 ++- R/Result.R | 18 ++++++++++-------- build/vignette.rds |binary man/RAthena_options.Rd | 3 ++- man/dbClearResult.Rd | 4 ++++ man/dbGetQuery.Rd | 4 ++++ tests/testthat/test-metadata.R | 2 +- 12 files changed, 88 insertions(+), 32 deletions(-)
Title: Port of the 'Scilab' 'n1qn1' Modules for Un-constrained BFGS
Optimization
Description: Provides 'Scilab' 'n1qn1', or Quasi-Newton BFGS
"qn" without constraints and 'qnbd' or Quasi-Newton BFGS with constraints.
This takes more memory than traditional L-BFGS. The n1qn1 routine is useful since it allows prespecification of a Hessian.
If the Hessian is near enough the truth in optimization it can speed up the optimization problem. Both algorithms are described in the
'Scilab' optimization documentation located at
<https://www.scilab.org/sites/default/files/optimization_in_scilab.pdf>.
Author: Matthew Fidler [aut, cre],
Wenping Wang [aut],
Claude Lemarechal [aut, ctb],
Joseph Bonnans [ctb],
Jean-Charles Gilbert [ctb],
Claudia Sagastizabal [ctb],
Stephen L. Campbell, [ctb],
Jean-Philippe Chancelier [ctb],
Ramine Nikoukhah [ctb],
Dirk Eddelbuettel [ctb],
Bruno Jofret [ctb],
INRIA [cph]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between n1qn1 versions 6.0.1-8 dated 2020-06-29 and 6.0.1-9 dated 2020-07-02
n1qn1-6.0.1-8/n1qn1/man/qnbd.Rd |only n1qn1-6.0.1-8/n1qn1/src/qnbd.f |only n1qn1-6.0.1-8/n1qn1/src/rlbd.f |only n1qn1-6.0.1-8/n1qn1/src/zqnbd.f |only n1qn1-6.0.1-9/n1qn1/DESCRIPTION | 10 - n1qn1-6.0.1-9/n1qn1/MD5 | 16 -- n1qn1-6.0.1-9/n1qn1/NAMESPACE | 1 n1qn1-6.0.1-9/n1qn1/R/n1qn1.R | 64 ---------- n1qn1-6.0.1-9/n1qn1/src/Makevars.in | 2 n1qn1-6.0.1-9/n1qn1/src/RcppExpMod.cpp | 207 --------------------------------- n1qn1-6.0.1-9/n1qn1/src/init.c | 10 - 11 files changed, 12 insertions(+), 298 deletions(-)
Title: Generalized Linear Mixed Models using Template Model Builder
Description: Fit linear and generalized linear mixed models with various
extensions, including zero-inflation. The models are fitted using maximum
likelihood estimation via 'TMB' (Template Model Builder). Random effects are
assumed to be Gaussian on the scale of the linear predictor and are integrated
out using the Laplace approximation. Gradients are calculated using automatic
differentiation.
Author: Arni Magnusson [aut] (<https://orcid.org/0000-0003-2769-6741>),
Hans Skaug [aut],
Anders Nielsen [aut] (<https://orcid.org/0000-0001-9683-9262>),
Casper Berg [aut] (<https://orcid.org/0000-0002-3812-5269>),
Kasper Kristensen [aut],
Martin Maechler [aut] (<https://orcid.org/0000-0002-8685-9910>),
Koen van Bentham [aut],
Ben Bolker [aut] (<https://orcid.org/0000-0002-2127-0443>),
Nafis Sadat [ctb] (<https://orcid.org/0000-0001-5715-616X>),
Daniel Lüdecke [ctb] (<https://orcid.org/0000-0002-8895-3206>),
Russ Lenth [ctb],
Joseph O'Brien [ctb] (<https://orcid.org/0000-0001-9851-5077>),
Mollie Brooks [aut, cre] (<https://orcid.org/0000-0001-6963-8326>)
Maintainer: Mollie Brooks <mollieebrooks@gmail.com>
Diff between glmmTMB versions 1.0.1 dated 2020-03-15 and 1.0.2.1 dated 2020-07-02
DESCRIPTION | 12 +-- MD5 | 95 +++++++++++++------------ NAMESPACE | 7 + R/emmeans.R | 51 ++++++++----- R/family.R | 2 R/glmmTMB.R | 121 +++++++++++++++++++++++++------- R/methods.R | 70 ++++++++++++++---- R/predict.R | 14 ++- R/utils.R | 47 ++++++++---- inst/NEWS.Rd | 49 ++++++++++-- inst/doc/covstruct.R | 2 inst/doc/covstruct.html | 16 ++-- inst/doc/covstruct.rmd | 16 ++-- inst/doc/glmmTMB.Rnw | 42 +++++------ inst/doc/glmmTMB.pdf |binary inst/doc/mcmc.html | 4 - inst/doc/miscEx.html | 4 - inst/doc/model_evaluation.R | 63 ++++++---------- inst/doc/model_evaluation.Rnw | 62 ++++++---------- inst/doc/model_evaluation.pdf |binary inst/doc/parallel.html | 53 +++++++------- inst/doc/sim.html | 4 - inst/doc/troubleshooting.R | 53 ++++++++++++++ inst/doc/troubleshooting.html | 59 +++++++++++++++ inst/doc/troubleshooting.rmd | 57 +++++++++++++++ inst/example_files/mk_examples.R |only inst/example_files/salamander1.rds |only inst/other_methods/extract.R | 6 - inst/test_data/Makefile |only inst/test_data/models.rda |binary inst/vignette_data/model_evaluation.rda |binary man/bootmer_methods.Rd | 6 + man/downstream_methods.Rd | 56 ++++++++------ man/fitTMB.Rd |only man/getXReTrms.Rd | 4 - man/glmmTMB.Rd | 5 + man/glmmTMBControl.Rd | 9 +- man/mkTMBStruc.Rd | 5 + man/nbinom2.Rd | 2 man/ranef.glmmTMB.Rd | 6 - man/reexports.Rd |only man/splitForm.Rd | 3 man/weights.glmmTMB.Rd | 2 src/glmmTMB.cpp | 35 ++++++--- tests/testthat/test-altopt.R |only tests/testthat/test-methods.R | 27 +++++-- tests/testthat/test-sparseX.R |only tests/testthat/test-utils.R | 10 ++ vignettes/covstruct.rmd | 16 ++-- vignettes/glmmTMB.Rnw | 42 +++++------ vignettes/model_evaluation.Rnw | 62 ++++++---------- vignettes/troubleshooting.rmd | 57 +++++++++++++++ 52 files changed, 850 insertions(+), 406 deletions(-)
Title: Path Algorithm for Generalized Lasso Problems
Description: Computes the solution path for generalized lasso problems. Important use cases are the fused lasso over an arbitrary graph, and trend fitting of any given polynomial order. Specialized implementations for the latter two subproblems are given to improve stability and speed.
Author: Taylor B. Arnold and Ryan J. Tibshirani
Maintainer: Taylor Arnold <taylor.arnold@acm.org>
Diff between genlasso versions 1.4 dated 2019-07-11 and 1.5 dated 2020-07-02
genlasso-1.4/genlasso/src/genlasso_init.c |only genlasso-1.5/genlasso/DESCRIPTION | 15 +- genlasso-1.5/genlasso/MD5 | 67 ++++++------ genlasso-1.5/genlasso/NAMESPACE | 6 - genlasso-1.5/genlasso/R/downdateT.R | 11 -- genlasso-1.5/genlasso/R/downdateW.R | 7 - genlasso-1.5/genlasso/R/dualpathFused.R | 2 genlasso-1.5/genlasso/R/dualpathFusedL1.R | 2 genlasso-1.5/genlasso/R/dualpathFusedL1X.R | 2 genlasso-1.5/genlasso/R/dualpathFusedX.R | 2 genlasso-1.5/genlasso/R/dualpathSvd.R | 2 genlasso-1.5/genlasso/R/dualpathTall.R | 45 +++++--- genlasso-1.5/genlasso/R/dualpathTrendX.R | 2 genlasso-1.5/genlasso/R/dualpathWide.R | 2 genlasso-1.5/genlasso/R/dualpathWideSparse.R | 3 genlasso-1.5/genlasso/R/fusedlasso.R | 5 genlasso-1.5/genlasso/R/fusedlasso1d.R | 2 genlasso-1.5/genlasso/R/fusedlasso2d.R | 2 genlasso-1.5/genlasso/R/genlasso.R | 6 - genlasso-1.5/genlasso/R/getDtfPosSparse.R | 2 genlasso-1.5/genlasso/R/getDtfSparse.R | 2 genlasso-1.5/genlasso/R/maketri2.R | 9 - genlasso-1.5/genlasso/R/maketri3.R | 9 - genlasso-1.5/genlasso/R/maketri4.R | 7 - genlasso-1.5/genlasso/R/plot.trendfilter.R | 1 genlasso-1.5/genlasso/R/trendfilter.R | 2 genlasso-1.5/genlasso/R/updateT.R | 9 - genlasso-1.5/genlasso/R/updateW.R | 7 - genlasso-1.5/genlasso/README.md |only genlasso-1.5/genlasso/build/vignette.rds |binary genlasso-1.5/genlasso/inst/doc/article.Rnw | 2 genlasso-1.5/genlasso/inst/doc/article.pdf |binary genlasso-1.5/genlasso/src/init.c |only genlasso-1.5/genlasso/src/matrixcomps.c | 145 +++++++++++++-------------- genlasso-1.5/genlasso/vignettes/article.Rnw | 2 genlasso-1.5/genlasso/vignettes/bibfile.bib | 13 +- 36 files changed, 203 insertions(+), 190 deletions(-)
Title: Modelling Multivariate Data with Additive Bayesian Networks
Description: Bayesian network analysis is a form of probabilistic graphical models which derives from empirical data a directed acyclic graph, DAG, describing the dependency structure between random variables. An additive Bayesian network model consists of a form of a DAG where each node comprises a generalized linear model, GLM. Additive Bayesian network models are equivalent to Bayesian multivariate regression using graphical modelling, they generalises the usual multivariable regression, GLM, to multiple dependent variables. 'abn' provides routines to help determine optimal Bayesian network models for a given data set, where these models are used to identify statistical dependencies in messy, complex data. The additive formulation of these models is equivalent to multivariate generalised linear modelling (including mixed models with iid random effects). The usual term to describe this model selection process is structure discovery. The core functionality is concerned with model selection - determining the most robust empirical model of data from interdependent variables. Laplace approximations are used to estimate goodness of fit metrics and model parameters, and wrappers are also included to the INLA package which can be obtained from <http://www.r-inla.org>. The computing library JAGS <http://mcmc-jags.sourceforge.net> is used to simulate 'abn'-like data. A comprehensive set of documented case studies, numerical accuracy/quality assurance exercises, and additional documentation are available from the 'abn' website <http://r-bayesian-networks.org>.
Author: Gilles Kratzer [aut, cre] (<https://orcid.org/0000-0002-5929-8935>),
Fraser Ian Lewis [aut],
Reinhard Furrer [ctb] (<https://orcid.org/0000-0002-6319-2332>),
Marta Pittavino [ctb] (<https://orcid.org/0000-0002-1232-1034>)
Maintainer: Gilles Kratzer <gilles.kratzer@gmail.com>
Diff between abn versions 2.2.1 dated 2020-06-15 and 2.2.2 dated 2020-07-02
abn-2.2.1/abn/tests/testhat.R |only abn-2.2.2/abn/DESCRIPTION | 14 +++---- abn-2.2.2/abn/MD5 | 35 ++++++++++-------- abn-2.2.2/abn/inst/Code_vignette |only abn-2.2.2/abn/man/build_score_cache.Rd | 8 ++-- abn-2.2.2/abn/man/fitabn.Rd | 53 ++++++++++++++-------------- abn-2.2.2/abn/man/mostprobable.Rd | 46 +++++------------------- abn-2.2.2/abn/man/simulate-abn.Rd | 2 - abn-2.2.2/abn/src/irls_binomial.cpp | 2 + abn-2.2.2/abn/src/irls_binomial_br.cpp | 2 + abn-2.2.2/abn/src/irls_binomial_fast.cpp | 2 + abn-2.2.2/abn/src/irls_binomial_fast_br.cpp | 2 + abn-2.2.2/abn/src/irls_gaussian.cpp | 2 - abn-2.2.2/abn/src/irls_gaussian_fast.cpp | 1 abn-2.2.2/abn/src/irls_poisson.cpp | 2 + abn-2.2.2/abn/src/irls_poisson_fast.cpp | 2 + abn-2.2.2/abn/tests/Examples |only abn-2.2.2/abn/tests/testthat.R |only abn-2.2.2/abn/tests/testthat.Rout.save |only abn-2.2.2/abn/tests/testthat/Rplots.pdf |binary 20 files changed, 84 insertions(+), 89 deletions(-)
Title: Motif Analyses of Bipartite Networks
Description: Counts occurrences of motifs in bipartite networks, as well as the number of
times each node or link appears in each unique position within motifs. Has support for both
binary and weighted motifs: can calculate the mean weight of motifs and the standard deviation
of their mean weights. Intended for use in ecology, but its methods are general and can be
applied to any bipartite network.
Author: Benno Simmons [aut, cre],
Michelle Sweering [aut],
Maybritt Schillinger [aut],
Riccardo Di Clemente [aut]
Maintainer: Benno Simmons <benno.simmons@gmail.com>
Diff between bmotif versions 2.0.0 dated 2019-12-11 and 2.0.1 dated 2020-07-02
DESCRIPTION | 10 +-- MD5 | 20 +++---- NEWS | 6 ++ build/vignette.rds |binary inst/doc/bmotif-dictionary.html | 28 +++++++--- tests/testthat/test_check_motif.R | 2 tests/testthat/test_link_positions.R | 12 ++-- tests/testthat/test_link_positions_weights.R | 20 +++---- tests/testthat/test_mean_weight.R | 20 +++---- tests/testthat/test_normalise_node_positions.R | 69 ++++++++++++++++--------- tests/testthat/test_sd.R | 58 ++++++++++----------- 11 files changed, 144 insertions(+), 101 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-29 0.4
2020-04-20 0.3
2012-12-11 0.2
2011-04-04 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-17 1.2.1
2012-04-21 1.2
2012-03-19 1.1
2011-04-15 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-10 1.0.2
2014-11-05 1.0.1
2014-11-03 1.0
Title: Placido Analysis of Corneal Irregularity
Description: Analysis of corneal data obtained from a Placido disk corneal
topographer with calculation of irregularity indices. A corneal topographer is
an ophthalmic clinical device that obtains measurements in the cornea (the anterior
part of the eye). A Placido disk corneal topographer makes use of the Placido disk
(Rowsey et al. (1981), <doi:10.1001/archopht.1981.03930011093022>, Rand et al.
(1997), <doi:10.1016/S0886-3350(99)00355-7>), which produce a circular pattern
of measurement nodes. The raw information measured by such a topographer is
used by practitioners to analyze curvatures, to study optical aberrations, or
to diagnose specific conditions of the eye. The rPACI package allows the
calculation of the corneal irregularity indices described in Castro-Luna et al. (2020),
<doi:10.1016/j.clae.2019.12.006>; Ramos-Lopez et al. (2013), <doi:10.1097/OPX.0b013e3182843f2a>;
and Ramos-Lopez et al. (2011), <doi:10.1097/OPX.0b013e3182843f2a>.
It provides a simple interface to read corneal topography data files as exported by a typical
Placido disk topographer, to compute the irregularity indices mentioned before,
and to display summary plots that are easy to interpret for a clinician.
Author: Darío Ramos-López [aut, cre],
Ana D. Maldonado [aut]
Maintainer: Darío Ramos-López <dario.ramos.lopez@urjc.es>
Diff between rPACI versions 0.1.1 dated 2019-02-11 and 0.1.2 dated 2020-07-02
DESCRIPTION | 18 ++++---- MD5 | 15 +++---- NAMESPACE | 14 +++++- R/rPACI.R | 91 ++++++++++++++++++++++++++++++++++--------- R/sysdata.rda |only demo/rPACIdemo.R | 7 +-- man/analyzeFolder.Rd | 11 ++++- man/computePlacidoIndices.Rd | 8 ++- man/plotSingleCornea.Rd | 3 - 9 files changed, 121 insertions(+), 46 deletions(-)
Title: Assessing Skill of Climate Forecasts on Seasonal-to-Decadal
Timescales
Description: Exploits dynamical seasonal forecasts in order to provide
information relevant to stakeholders at the seasonal timescale. The package
contains process-based methods for forecast calibration, bias correction,
statistical and stochastic downscaling, optimal forecast combination and
multivariate verification, as well as basic and advanced tools to obtain
tailored products. This package was developed in the context of the
ERA4CS project MEDSCOPE and the H2020 S2S4E project.
Doblas-Reyes et al. (2005) <doi:10.1111/j.1600-0870.2005.00104.x>.
Mishra et al. (2018) <doi:10.1007/s00382-018-4404-z>.
Sanchez-Garcia et al. (2019) <doi:10.5194/asr-16-165-2019>.
Straus et al. (2007) <doi:10.1175/JCLI4070.1>.
Terzago et al. (2018) <doi:10.5194/nhess-18-2825-2018>.
Torralba et al. (2017) <doi:10.1175/JAMC-D-16-0204.1>.
D'Onofrio et al. (2014) <doi:10.1175/JHM-D-13-096.1>.
Van Schaeybroeck et al. (2019) <doi:10.1016/B978-0-12-812372-0.00010-8>.
Yiou et al. (2013) <doi:10.1007/s00382-012-1626-3>.
Author: Nuria Perez-Zanon [aut, cre] (<https://orcid.org/0000-0001-8568-3071>),
Louis-Philippe Caron [aut] (<https://orcid.org/0000-0001-5221-0147>),
Carmen Alvarez-Castro [aut],
Jost von Hardenberg [aut] (<https://orcid.org/0000-0002-5312-8070>),
Llorenç LLedo [aut],
Nicolau Manubens [aut],
Eroteida Sanchez-Garcia [aut],
Bert van Schaeybroeck [aut],
Veronica Torralba [aut],
Deborah Verfaillie [aut],
Lauriane Batte [ctb],
Filippo Cali Quaglia [ctb],
Chihchung Chou [ctb],
Nicola Cortesi [ctb],
Susanna Corti [ctb],
Paolo Davini [ctb],
Marta Dominguez [ctb],
Federico Fabiano [ctb],
Ignazio Giuntoli [ctb],
Raul Marcos [ctb],
Niti Mishra [ctb],
Jesus Peña [ctb],
Francesc Roura-Adserias [ctb],
Silvia Terzago [ctb],
Danila Volpi [ctb],
BSC-CNS [cph]
Maintainer: Nuria Perez-Zanon <nuria.perez@bsc.es>
Diff between CSTools versions 3.0.0 dated 2020-02-11 and 3.1.0 dated 2020-07-02
DESCRIPTION | 25 + MD5 | 91 +++-- NAMESPACE | 18 + NEWS.md | 27 + R/CST_Anomaly.R | 44 ++ R/CST_BiasCorrection.R | 29 + R/CST_Calibration.R | 26 - R/CST_EnsClustering.R | 70 +++- R/CST_QuantileMapping.R | 12 R/CST_RFTemp.R |only R/CST_RainFARM.R | 6 R/CST_RegimesAssign.R |only R/CST_SaveExp.R | 231 ++++++++----- R/CST_WeatherRegimes.R |only R/PlotCombinedMap.R | 24 + R/PlotForecastPDF.R | 7 R/PlotPDFsOLE.R |only R/PlotTriangles4Categories.R |only build/vignette.rds |binary inst/doc/BestEstimateIndex_vignette.Rmd | 306 ++++++++++-------- inst/doc/BestEstimateIndex_vignette.html | 104 ++++-- inst/doc/ENSclustering_vignette.Rmd |only inst/doc/ENSclustering_vignette.html |only inst/doc/MultiModelSkill_vignette.Rmd | 2 inst/doc/MultiModelSkill_vignette.html | 2 inst/doc/PlotForecastPDF.R | 37 +- inst/doc/PlotForecastPDF.Rmd | 47 ++ inst/doc/PlotForecastPDF.html | 51 ++- inst/doc/WeatherRegimes_vignette.Rmd |only inst/doc/WeatherRegimes_vignette.html |only man/CST_Anomaly.Rd | 15 man/CST_BiasCorrection.Rd | 4 man/CST_Calibration.Rd | 4 man/CST_EnsClustering.Rd | 16 man/CST_QuantileMapping.Rd | 12 man/CST_RFTemp.Rd |only man/CST_RegimesAssign.Rd |only man/CST_WeatherRegimes.Rd |only man/Calibration.Rd | 12 man/EnsClustering.Rd | 11 man/PlotCombinedMap.Rd | 11 man/PlotPDFsOLE.Rd |only man/PlotTriangles4Categories.Rd |only man/RFTemp.Rd |only man/RegimesAssign.Rd |only man/SaveExp.Rd |only man/WeatherRegimes.Rd |only vignettes/BestEstimateIndex_vignette.Rmd | 306 ++++++++++-------- vignettes/ENSclustering_vignette.Rmd |only vignettes/Figures/EnsClus_4clus_both_mem_std_Fig1.png |only vignettes/Figures/EnsClus_4clus_both_mem_std_Fig2.png |only vignettes/Figures/Obs_Persistence.png |only vignettes/Figures/PlotForecastPDF_ex1.png |only vignettes/Figures/PlotForecastPDF_ex2.png |only vignettes/Figures/PlotForecastPDF_ex3.png |only vignettes/Figures/PlotForecastPDF_ex4.png |only vignettes/Figures/observed_regimes.png |only vignettes/Figures/predicted_regimes.png |only vignettes/MultiModelSkill_vignette.Rmd | 2 vignettes/PlotForecastPDF.Rmd | 47 ++ vignettes/WeatherRegimes_vignette.Rmd |only 61 files changed, 1076 insertions(+), 523 deletions(-)
Title: Bayesian Seemingly Unrelated Regression
Description: Bayesian seemingly unrelated regression with general variable selection and dense/sparse covariance matrix. The sparse seemingly unrelated regression is described in Banterle et al. (2018) <doi:10.1101/467019>.
Author: Marco Banterle [aut],
Zhi Zhao [aut, cre],
Leonardo Bottolo [ctb],
Sylvia Richardson [ctb],
Waldir Leoncio [ctb],
Alex Lewin [aut],
Manuela Zucknick [ctb]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
Diff between BayesSUR versions 1.1-2 dated 2020-04-27 and 1.2-0 dated 2020-07-02
BayesSUR-1.1-2/BayesSUR/R/getEstimator.R |only BayesSUR-1.1-2/BayesSUR/R/plot.Estimator.R |only BayesSUR-1.1-2/BayesSUR/R/plot.Network.R |only BayesSUR-1.1-2/BayesSUR/R/plot.ResponseGraph.R |only BayesSUR-1.1-2/BayesSUR/man/getEstimator.Rd |only BayesSUR-1.1-2/BayesSUR/man/plot.Estimator.Rd |only BayesSUR-1.1-2/BayesSUR/man/plot.Network.Rd |only BayesSUR-1.1-2/BayesSUR/man/plot.ResponseGraph.Rd |only BayesSUR-1.2-0/BayesSUR/DESCRIPTION | 16 - BayesSUR-1.2-0/BayesSUR/MD5 | 62 +++--- BayesSUR-1.2-0/BayesSUR/NAMESPACE | 8 BayesSUR-1.2-0/BayesSUR/R/BayesSUR.R | 6 BayesSUR-1.2-0/BayesSUR/R/example_GDSC.R | 55 ++--- BayesSUR-1.2-0/BayesSUR/R/get.estimator.R |only BayesSUR-1.2-0/BayesSUR/R/plot.BayesSUR.R | 16 - BayesSUR-1.2-0/BayesSUR/R/plot.CPO.R | 4 BayesSUR-1.2-0/BayesSUR/R/plot.MCMCdiag.R | 4 BayesSUR-1.2-0/BayesSUR/R/plot.Manhattan.R | 4 BayesSUR-1.2-0/BayesSUR/R/plot.estimator.R |only BayesSUR-1.2-0/BayesSUR/R/plot.network.R |only BayesSUR-1.2-0/BayesSUR/R/plot.response.graph.R |only BayesSUR-1.2-0/BayesSUR/R/targetGene.R | 43 +--- BayesSUR-1.2-0/BayesSUR/data/example_GDSC.rda |binary BayesSUR-1.2-0/BayesSUR/inst/doc/BayesSUR.pdf |binary BayesSUR-1.2-0/BayesSUR/man/BayesSUR.Rd | 6 BayesSUR-1.2-0/BayesSUR/man/example_GDSC.Rd | 55 ++--- BayesSUR-1.2-0/BayesSUR/man/get.estimator.Rd |only BayesSUR-1.2-0/BayesSUR/man/plot.CPO.Rd | 4 BayesSUR-1.2-0/BayesSUR/man/plot.MCMCdiag.Rd | 4 BayesSUR-1.2-0/BayesSUR/man/plot.Manhattan.Rd | 4 BayesSUR-1.2-0/BayesSUR/man/plot.estimator.Rd |only BayesSUR-1.2-0/BayesSUR/man/plot.network.Rd |only BayesSUR-1.2-0/BayesSUR/man/plot.response.graph.Rd |only BayesSUR-1.2-0/BayesSUR/man/targetGene.Rd | 43 +--- BayesSUR-1.2-0/BayesSUR/src/ESS_Sampler.h | 22 +- BayesSUR-1.2-0/BayesSUR/src/HRR_Chain.cpp | 197 +++++++++++---------- BayesSUR-1.2-0/BayesSUR/src/HRR_Chain.h | 2 BayesSUR-1.2-0/BayesSUR/src/SUR_Chain.cpp | 16 + BayesSUR-1.2-0/BayesSUR/src/distr.cpp | 4 BayesSUR-1.2-0/BayesSUR/src/drive.cpp | 41 ++-- 40 files changed, 309 insertions(+), 307 deletions(-)
Title: FROC Analysis by Bayesian Approaches
Description: Execute BayesianFROC::fit_GUI_Shiny() (or fit_GUI_Shiny_MRMC()) for a graphical user interface via Shiny. Provides new methods for the so-called Free-response Receiver Operating Characteristic (FROC) analysis. The ultimate aim of FROC analysis is to compare observer performances, which means comparing characteristics, such as area under the curve (AUC) or figure of merit (FOM). In this package, we only use the notion of AUC for modality comparison, where by "modality", we mean imaging methods such as Magnetic Resonance Imaging (MRI), Computed Tomography (CT), Positron Emission Tomography (PET), ..., etc. So there is a problem that which imaging method is better to detect lesions from shadows in radiographs. To solve modality comparison issues, this package provides new methods using hierarchical Bayesian models proposed by the author of this package. Using this package, one can obtain at least one conclusion that which imaging methods are better for finding lesions in radiographs with the case of your data. Fitting FROC statistical models is sometimes not so good, it can easily confirm by drawing FROC curves and comparing these curves and the points constructed by False Positive fractions (FPFs) and True Positive Fractions (TPFs), we can validate the goodness of fit intuitively. Such validation is also implemented by the Chi square goodness of fit statistics in the Bayesian context which means that the parameter is not deterministic, thus by integrating it with the posterior predictive measure, we get a desired value. To compare modalities (imaging methods: MRI, CT, PET, ... , etc), we evaluate AUCs for each modality. FROC is developed by Dev Chakraborty, his FROC model in his 1989 paper relies on the maximal likelihood methodology. The author modified and provided the alternative Bayesian FROC model. Strictly speaking, his model does not coincide with models in this package. In FROC context, we means by multiple reader and multiple case (MRMC) the case of the number of reader or modality is two or more. The MRMC data is available for functions of this package. I hope that medical researchers use not only the frequentist method but also alternative Bayesian methods. In medical research, many problems are considered under only frequentist methods, such as the notion of p-values. But p-value is sometimes misunderstood. Bayesian methods provide very simple, direct, intuitive answer for research questions. Combining frequentist methods with Bayesian methods, we can obtain more reliable answer for research questions. Please execute the following R scripts from the R (R studio) console, demo(demo_MRMC, package = "BayesianFROC"); demo(demo_srsc, package = "BayesianFROC"); demo(demo_stan, package = "BayesianFROC"); demo(demo_drawcurves_srsc, package = "BayesianFROC"); demo_Bayesian_FROC(); demo_Bayesian_FROC_without_pause(). References: Dev Chakraborty (1989) <doi:10.1118/1.596358> Maximum likelihood analysis of free - response receiver operating characteristic (FROC) data. Pre-print: Issei Tsunoda; Bayesian Models for free-response receiver operating characteristic analysis.
Author: Issei Tsunoda [aut, cre]
Maintainer: Issei Tsunoda <tsunoda.issei1111@gmail.com>
Diff between BayesianFROC versions 0.2.3 dated 2020-04-27 and 0.3.0 dated 2020-07-02
BayesianFROC-0.2.3/BayesianFROC/R/plot_curve_and_hit_rate_and_false_rate_simultaneously.R |only BayesianFROC-0.3.0/BayesianFROC/DESCRIPTION | 15 BayesianFROC-0.3.0/BayesianFROC/MD5 | 238 - BayesianFROC-0.3.0/BayesianFROC/NEWS.md | 65 BayesianFROC-0.3.0/BayesianFROC/R/AFROC.R | 57 BayesianFROC-0.3.0/BayesianFROC/R/BayesianFROC.R | 427 ++ BayesianFROC-0.3.0/BayesianFROC/R/ConfirmConvergence.R | 2 BayesianFROC-0.3.0/BayesianFROC/R/CoronaVirus_Disease_2019.R | 97 BayesianFROC-0.3.0/BayesianFROC/R/DrawCurves.R | 14 BayesianFROC-0.3.0/BayesianFROC/R/StartupMessage.R | 99 BayesianFROC-0.3.0/BayesianFROC/R/Test_Null_Hypothesis_that_all_modalities_are_same.R | 4 BayesianFROC-0.3.0/BayesianFROC/R/When_install.R |only BayesianFROC-0.3.0/BayesianFROC/R/chi_square_goodness_of_fit.R | 47 BayesianFROC-0.3.0/BayesianFROC/R/convertFromJafroc.R | 8 BayesianFROC-0.3.0/BayesianFROC/R/document_dataset_MRMC.R | 2 BayesianFROC-0.3.0/BayesianFROC/R/download.R |only BayesianFROC-0.3.0/BayesianFROC/R/draw_latent_distribution.R | 121 BayesianFROC-0.3.0/BayesianFROC/R/error_message_on_imaging_device_rhat_values.R | 12 BayesianFROC-0.3.0/BayesianFROC/R/extract_EAP_by_array.R | 4 BayesianFROC-0.3.0/BayesianFROC/R/extract_data_frame_from_dataList_MRMC.R | 4 BayesianFROC-0.3.0/BayesianFROC/R/fffaaabbb.R | 48 BayesianFROC-0.3.0/BayesianFROC/R/fit_Bayesian_FROC.R | 158 BayesianFROC-0.3.0/BayesianFROC/R/fit_GUI_Shiny.R | 1643 +++++----- BayesianFROC-0.3.0/BayesianFROC/R/fit_MRMC_versionTWO.R | 164 BayesianFROC-0.3.0/BayesianFROC/R/get_posterior_variance.R | 22 BayesianFROC-0.3.0/BayesianFROC/R/metadata.R | 9 BayesianFROC-0.3.0/BayesianFROC/R/methods.R | 2 BayesianFROC-0.3.0/BayesianFROC/R/p_value_of_the_Bayesian_sense_for_chi_square_goodness_of_fit.R | 16 BayesianFROC-0.3.0/BayesianFROC/R/plotFROC.R | 126 BayesianFROC-0.3.0/BayesianFROC/R/ppp.R | 2 BayesianFROC-0.3.0/BayesianFROC/R/snippet_for_BayesianFROC.R | 150 BayesianFROC-0.3.0/BayesianFROC/R/stanfitExtended.R | 28 BayesianFROC-0.3.0/BayesianFROC/R/summary_EAP_CI_srsc.R | 88 BayesianFROC-0.3.0/BayesianFROC/R/validation_MRMC_Create_dataList_MRMC_Hit_from_rate_etc.R | 34 BayesianFROC-0.3.0/BayesianFROC/R/validation_error_srsc.R | 16 BayesianFROC-0.3.0/BayesianFROC/README.md | 104 BayesianFROC-0.3.0/BayesianFROC/build/vignette.rds |binary BayesianFROC-0.3.0/BayesianFROC/demo/00Index | 4 BayesianFROC-0.3.0/BayesianFROC/demo/demo_SBC.R |only BayesianFROC-0.3.0/BayesianFROC/demo/demo_for_traditional_FROC_models_with_multinomial_distribution.R |only BayesianFROC-0.3.0/BayesianFROC/inst/CITATION | 8 BayesianFROC-0.3.0/BayesianFROC/inst/doc/Very_Very_Very_Brief_Description_MRMC.R | 42 BayesianFROC-0.3.0/BayesianFROC/inst/doc/Very_Very_Very_Brief_Description_MRMC.Rmd | 198 + BayesianFROC-0.3.0/BayesianFROC/inst/doc/Very_Very_Very_Brief_Description_MRMC.html | 175 - BayesianFROC-0.3.0/BayesianFROC/inst/extdata/Model_srsc_multinomial.stan |only 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BayesianFROC-0.3.0/BayesianFROC/man/Draw_a_simulated_data_set.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/Draw_a_simulated_data_set_and_Draw_posterior_samples.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/Draw_an_area_of_AUC_for_srsc.Rd | 2 BayesianFROC-0.3.0/BayesianFROC/man/Empirical_FROC_via_ggplot.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/Simulation_Based_Calibration_histogram.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/Simulation_Based_Calibration_single_reader_single_modality_via_rstan_sbc.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/Test_Null_Hypothesis_that_all_modalities_are_same.Rd | 10 BayesianFROC-0.3.0/BayesianFROC/man/check_hit_is_less_than_NL.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/check_rhat.Rd | 2 BayesianFROC-0.3.0/BayesianFROC/man/chi_square_at_replicated_data_and_MCMC_samples_MRMC.Rd | 14 BayesianFROC-0.3.0/BayesianFROC/man/chi_square_goodness_of_fit.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/chi_square_goodness_of_fit_from_input_all_param.Rd | 2 BayesianFROC-0.3.0/BayesianFROC/man/chi_square_goodness_of_fit_from_input_all_param_MRMC.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/comparison.Rd | 2 BayesianFROC-0.3.0/BayesianFROC/man/convertFromJafroc.Rd | 8 BayesianFROC-0.3.0/BayesianFROC/man/create_dataList_MRMC.Rd | 34 BayesianFROC-0.3.0/BayesianFROC/man/dataList.one.modality.Rd | 2 BayesianFROC-0.3.0/BayesianFROC/man/draw.CFP.CTP.from.dataList.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/draw_latent_noise_distribution.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/draw_latent_signal_distribution.Rd | 2 BayesianFROC-0.3.0/BayesianFROC/man/error_MRMC.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/error_message_on_imaging_device_rhat_values.Rd | 5 BayesianFROC-0.3.0/BayesianFROC/man/error_srsc.Rd | 10 BayesianFROC-0.3.0/BayesianFROC/man/extractAUC.Rd | 2 BayesianFROC-0.3.0/BayesianFROC/man/extract_EAP_CI.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/extract_EAP_by_array.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/extract_data_frame_from_dataList_MRMC.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/extract_estimates_MRMC.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/extract_parameters_from_replicated_models.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/fit_Bayesian_FROC.Rd | 30 BayesianFROC-0.3.0/BayesianFROC/man/fit_GUI_Shiny.Rd | 6 BayesianFROC-0.3.0/BayesianFROC/man/fit_MRMC.Rd | 16 BayesianFROC-0.3.0/BayesianFROC/man/fit_MRMC_versionTWO.Rd | 26 BayesianFROC-0.3.0/BayesianFROC/man/fit_Null_hypothesis_model_to_.Rd | 12 BayesianFROC-0.3.0/BayesianFROC/man/fit_a_model_to.Rd | 104 BayesianFROC-0.3.0/BayesianFROC/man/fit_srsc.Rd | 15 BayesianFROC-0.3.0/BayesianFROC/man/get_posterior_variance.Rd | 24 BayesianFROC-0.3.0/BayesianFROC/man/get_samples_from_Posterior_Predictive_distribution.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/ggplotFROC.EAP.Rd | 6 BayesianFROC-0.3.0/BayesianFROC/man/ggplotFROC.Rd | 6 BayesianFROC-0.3.0/BayesianFROC/man/give_name_srsc_data.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/grapes-greater-than-greater-than-grapes.Rd | 8 BayesianFROC-0.3.0/BayesianFROC/man/initial_values_specification_for_stan_in_case_of_MRMC.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/make_true_parameter_MRMC.Rd | 2 BayesianFROC-0.3.0/BayesianFROC/man/metadata_to_DrawCurve_MRMC.Rd | 2 BayesianFROC-0.3.0/BayesianFROC/man/p_value_of_the_Bayesian_sense_for_chi_square_goodness_of_fit.Rd | 15 BayesianFROC-0.3.0/BayesianFROC/man/pairs_plot_if_divergent_transition_occurred.Rd | 2 BayesianFROC-0.3.0/BayesianFROC/man/plot-stanfitExtended-missing-method.Rd | 42 BayesianFROC-0.3.0/BayesianFROC/man/plot_FPF_and_TPF_from_a_dataset.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/plot_curve_and_hit_rate_and_false_rate_simultaneously.Rd | 5 BayesianFROC-0.3.0/BayesianFROC/man/ppp.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/ppp_MRMC.Rd | 2 BayesianFROC-0.3.0/BayesianFROC/man/ppp_srsc.Rd | 2 BayesianFROC-0.3.0/BayesianFROC/man/replicate_model_MRMC.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/snippet_for_BayesianFROC.Rd | 11 BayesianFROC-0.3.0/BayesianFROC/man/sortAUC.Rd | 2 BayesianFROC-0.3.0/BayesianFROC/man/stanfitExtended.Rd | 24 BayesianFROC-0.3.0/BayesianFROC/man/summarize_MRMC.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/summary_AUC_comparison_MRMC.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/summary_AUC_comparison_MRMC_with_crayon.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/summary_AUC_comparison_MRMC_without_crayon.Rd | 4 BayesianFROC-0.3.0/BayesianFROC/man/summary_EAP_CI_srsc.Rd | 2 BayesianFROC-0.3.0/BayesianFROC/man/validation.dataset_srsc.Rd | 14 BayesianFROC-0.3.0/BayesianFROC/vignettes/Very_Very_Very_Brief_Description_MRMC.Rmd | 198 + 123 files changed, 3835 insertions(+), 1802 deletions(-)
Title: Hierarchical Cluster Analysis of Nominal Data
Description: Similarity measures for hierarchical clustering of objects characterized by
nominal (categorical) variables. Evaluation criteria for nominal data clustering.
Author: Zdenek Sulc [aut, cre],
Jana Cibulkova [aut],
Hana Rezankova [aut]
Maintainer: Zdenek Sulc <zdenek.sulc@vse.cz>
Diff between nomclust versions 2.1.5 dated 2020-06-22 and 2.1.6 dated 2020-07-02
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/lin1.R | 6 +++--- R/lin1_fx.R | 2 +- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Sorted L1 Penalized Estimation
Description: Efficient implementations for Sorted L-One Penalized Estimation
(SLOPE): generalized linear models regularized with the sorted L1-norm
(Bogdan et al. (2015) <doi:10/gfgwzt>). Supported models include ordinary
least-squares regression, binomial regression, multinomial regression, and
Poisson regression. Both dense and sparse predictor matrices are supported.
In addition, the package features predictor screening rules that enable fast
and efficient solutions to high-dimensional problems.
Author: Johan Larsson [aut, cre] (<https://orcid.org/0000-0002-4029-5945>),
Jonas Wallin [aut] (<https://orcid.org/0000-0003-0381-6593>),
Malgorzata Bogdan [aut],
Ewout van den Berg [aut],
Chiara Sabatti [aut],
Emmanuel Candes [aut],
Evan Patterson [aut],
Weijie Su [aut],
Jerome Friedman [ctb] (code adapted from 'glmnet'),
Trevor Hastie [ctb] (code adapted from 'glmnet'),
Rob Tibshirani [ctb] (code adapted from 'glmnet'),
Balasubramanian Narasimhan [ctb] (code adapted from 'glmnet'),
Noah Simon [ctb] (code adapted from 'glmnet'),
Junyang Qian [ctb] (code adapted from 'glmnet')
Maintainer: Johan Larsson <johan.larsson@stat.lu.se>
Diff between SLOPE versions 0.2.1 dated 2020-04-16 and 0.3.0 dated 2020-07-02
SLOPE-0.2.1/SLOPE/R/deprecated.R |only SLOPE-0.2.1/SLOPE/man/SLOPE_solver.Rd |only SLOPE-0.2.1/SLOPE/man/lambda.Rd |only SLOPE-0.2.1/SLOPE/man/prox_sorted_L1.Rd |only SLOPE-0.2.1/SLOPE/tests/testthat/test-deprecated.R |only SLOPE-0.3.0/SLOPE/DESCRIPTION | 6 SLOPE-0.3.0/SLOPE/MD5 | 118 ++--- SLOPE-0.3.0/SLOPE/NAMESPACE | 3 SLOPE-0.3.0/SLOPE/NEWS.md | 40 + SLOPE-0.3.0/SLOPE/R/SLOPE.R | 254 +++++------ SLOPE-0.3.0/SLOPE/R/caretSLOPE.R | 77 +-- SLOPE-0.3.0/SLOPE/R/coef.R | 22 SLOPE-0.3.0/SLOPE/R/data.R | 5 SLOPE-0.3.0/SLOPE/R/deviance.R | 3 SLOPE-0.3.0/SLOPE/R/plot.R | 58 +- SLOPE-0.3.0/SLOPE/R/plotDiagnostics.R | 5 SLOPE-0.3.0/SLOPE/R/predict.R | 20 SLOPE-0.3.0/SLOPE/R/print.R | 7 SLOPE-0.3.0/SLOPE/R/score.R | 5 SLOPE-0.3.0/SLOPE/R/trainSLOPE.R | 17 SLOPE-0.3.0/SLOPE/R/utils.R | 11 SLOPE-0.3.0/SLOPE/README.md | 4 SLOPE-0.3.0/SLOPE/build/vignette.rds |binary SLOPE-0.3.0/SLOPE/inst/doc/introduction.R | 6 SLOPE-0.3.0/SLOPE/inst/doc/introduction.Rmd | 14 SLOPE-0.3.0/SLOPE/inst/doc/introduction.html | 46 + SLOPE-0.3.0/SLOPE/man/SLOPE.Rd | 123 +++-- SLOPE-0.3.0/SLOPE/man/abalone.Rd | 8 SLOPE-0.3.0/SLOPE/man/bodyfat.Rd | 8 SLOPE-0.3.0/SLOPE/man/caretSLOPE.Rd | 5 SLOPE-0.3.0/SLOPE/man/coef.SLOPE.Rd | 21 SLOPE-0.3.0/SLOPE/man/deviance.SLOPE.Rd | 11 SLOPE-0.3.0/SLOPE/man/heart.Rd | 8 SLOPE-0.3.0/SLOPE/man/plot.SLOPE.Rd | 19 SLOPE-0.3.0/SLOPE/man/plot.TrainedSLOPE.Rd | 5 SLOPE-0.3.0/SLOPE/man/plotDiagnostics.Rd | 5 SLOPE-0.3.0/SLOPE/man/predict.SLOPE.Rd | 16 SLOPE-0.3.0/SLOPE/man/print.SLOPE.Rd | 11 SLOPE-0.3.0/SLOPE/man/score.Rd | 13 SLOPE-0.3.0/SLOPE/man/student.Rd | 8 SLOPE-0.3.0/SLOPE/man/trainSLOPE.Rd | 5 SLOPE-0.3.0/SLOPE/man/wine.Rd | 8 SLOPE-0.3.0/SLOPE/src/SLOPE.cpp | 84 ++- SLOPE-0.3.0/SLOPE/src/regularizationPath.h | 34 - SLOPE-0.3.0/SLOPE/src/rescale.h | 4 SLOPE-0.3.0/SLOPE/src/standardize.h | 4 SLOPE-0.3.0/SLOPE/tests/testthat/test-alpha-scaling.R |only SLOPE-0.3.0/SLOPE/tests/testthat/test-assertions.R | 16 SLOPE-0.3.0/SLOPE/tests/testthat/test-binomial.R | 4 SLOPE-0.3.0/SLOPE/tests/testthat/test-coef.R | 4 SLOPE-0.3.0/SLOPE/tests/testthat/test-diagnostics.R | 2 SLOPE-0.3.0/SLOPE/tests/testthat/test-gaussian.R | 4 SLOPE-0.3.0/SLOPE/tests/testthat/test-lasso.R | 2 SLOPE-0.3.0/SLOPE/tests/testthat/test-multinomial.R | 2 SLOPE-0.3.0/SLOPE/tests/testthat/test-path-behavior.R | 4 SLOPE-0.3.0/SLOPE/tests/testthat/test-plotting.R | 4 SLOPE-0.3.0/SLOPE/tests/testthat/test-poisson.R | 8 SLOPE-0.3.0/SLOPE/tests/testthat/test-predictions.R | 2 SLOPE-0.3.0/SLOPE/tests/testthat/test-screening-algorithms.R | 8 SLOPE-0.3.0/SLOPE/tests/testthat/test-sigma-estimation.R | 6 SLOPE-0.3.0/SLOPE/tests/testthat/test-training.R | 2 SLOPE-0.3.0/SLOPE/vignettes/SLOPE.bib | 11 SLOPE-0.3.0/SLOPE/vignettes/introduction.Rmd | 14 63 files changed, 750 insertions(+), 464 deletions(-)
Title: A Spatial Model of Intra-Tumor Heterogeneity
Description: Implements a three-dimensional stochastic model of cancer growth and mutation similar to the one described in Waclaw et al. (2015) <doi:10.1038/nature14971>. Allows for interactive 3D visualizations of the simulated tumor. Provides a comprehensive summary of the spatial distribution of mutants within the tumor. Contains functions which create synthetic sequencing datasets from the generated tumor.
Author: Phillip B. Nicol
Maintainer: Phillip B. Nicol <philnicol740@gmail.com>
Diff between SITH versions 1.0.0 dated 2020-07-01 and 1.0.1 dated 2020-07-02
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 2 +- NEWS.md | 10 +++++++++- inst/doc/SITH.html | 2 +- src/post_processing.h | 2 +- 6 files changed, 22 insertions(+), 14 deletions(-)
Title: Item-Wise Score-Based DIF Detection
Description: Detection of item-wise Differential Item Functioning (DIF)
in fitted 'mirt', 'multipleGroup' or 'bfactor' models
using score-based structural change tests. Under the hood
the sctest() function from the 'strucchange' package is used.
Author: Dries Debeer [cre, aut]
Maintainer: Dries Debeer <debeer.dries@gmail.com>
Diff between scDIFtest versions 0.1.0 dated 2020-06-26 and 0.1.1 dated 2020-07-02
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/scDIFtest.R | 3 ++- inst/doc/scDIFtest.html | 22 +++++++++++----------- man/scDIFtest.Rd | 3 ++- tests/testthat/test_scDIFtest.R | 10 +++++++--- 6 files changed, 30 insertions(+), 24 deletions(-)
Title: Statistical Analysis of Network Data with R, 2nd Edition
Description: Data sets and code blocks for the book 'Statistical Analysis of
Network Data with R, 2nd Edition'.
Author: Eric Kolaczyk [aut, cre],
Gábor Csárdi [aut],
Carolyn Kolaczyk [ctb]
Maintainer: Eric Kolaczyk <eric.kolaczyk@gmail.com>
Diff between sand versions 1.0.3 dated 2017-03-02 and 2.0.0 dated 2020-07-02
DESCRIPTION | 27 +- MD5 | 45 ++-- NAMESPACE | 24 +- R/sand-package.r | 134 +++++++++++-- data/aidsblog.rda |binary data/fblog.rda |binary data/g.bip.rda |binary data/lazega.rda |binary data/ppi.CC.rda |binary data/strike.rda |only inst/code/chapter1.R | 20 - inst/code/chapter10.R | 431 +++++++++++++++---------------------------- inst/code/chapter11.R |only inst/code/chapter2.R | 250 +++++++++++------------- inst/code/chapter3.R | 106 +++++----- inst/code/chapter4.R | 256 ++++++++++++------------- inst/code/chapter5.R | 196 +++++++++---------- inst/code/chapter6.R | 367 +++++++++++++++++++----------------- inst/code/chapter7.R | 170 +++++++--------- inst/code/chapter8.R | 148 +++++++------- inst/code/chapter9.R | 176 +++++++++-------- man/aaa-sand.Rd | 194 +++++++++---------- man/fblog.Rd | 47 ++-- man/install_sand_packages.Rd | 40 +-- man/strike.Rd |only 25 files changed, 1329 insertions(+), 1302 deletions(-)
Title: Basic Pipe and Open Channel Hydraulics
Description: Functions for basic hydraulic calculations related to
water flow in circular pipes both flowing full (under pressure), and
partially full (gravity flow), and trapezoidal open channels. For
pressure flow this includes friction loss calculations by solving
the Darcy-Weisbach equation for head loss, flow or diameter, and
plotting a Moody diagram. The Darcy-Weisbach friction factor is
calculated using the Colebrook (or Colebrook-White equation),
the basis of the Moody diagram, the original citation being
Colebrook (1939) <doi:10.1680/ijoti.1939.13150>. For gravity flow, the
Manning equation is used, again solving for missing parameters. The
derivation of and solutions using the Darcy-Weisbach equation and the
Manning equation are outlined in many fluid mechanics texts such as
Finnemore and Franzini (2002, ISBN:978-0072432022). For the Manning equation
solutions, this package uses modifications of original code from the 'iemisc'
package by Irucka Embry.
Author: Ed Maurer [aut, cre], Irucka Embry [aut, ctb] (iemisc code)
Maintainer: Ed Maurer <emaurer@scu.edu>
Diff between hydraulics versions 0.1.0 dated 2020-05-18 and 0.2.0 dated 2020-07-02
DESCRIPTION | 34 ++- MD5 | 29 ++- NAMESPACE | 5 NEWS.md | 16 + R/darcy_weisbach.R | 51 +++-- R/manningc.R |only R/manningt.R |only R/spec_energy_trap.R |only R/water_properties.R | 2 R/xc_circle.R |only R/xc_trap.R |only README.md | 239 +++++++++++++++++++++++++++- man/darcyweisbach.Rd | 11 - man/figures/README-spec-energy-plot-1-1.png |only man/figures/README-xc-plot-circle-1.png |only man/figures/README-xc-plot-trap-1.png |only man/manningc.Rd |only man/manningt.Rd |only man/spec_energy_trap.Rd |only man/waterprops.Rd | 2 man/xc_circle.Rd |only man/xc_trap.Rd |only 22 files changed, 332 insertions(+), 57 deletions(-)
Title: Simulate Expression Data from 'igraph' Networks
Description: Functions to develop simulated continuous data (e.g., gene expression) from a sigma covariance matrix derived from a graph structure in 'igraph' objects. Intended to extend 'mvtnorm' to take 'igraph' structures rather than sigma matrices as input. This allows the use of simulated data that correctly accounts for pathway relationships and correlations. This allows the use of simulated data that correctly accounts for pathway relationships and correlations. Here we present a versatile statistical framework to simulate correlated gene expression data from biological pathways, by sampling from a multivariate normal distribution derived from a graph structure. This package allows the simulation of biological pathways from a graph structure based on a statistical model of gene expression. For example methods to infer biological pathways and gene regulatory networks from gene expression data can be tested on simulated datasets using this framework. This also allows for pathway structures to be considered as a confounding variable when simulating gene expression data to test the performance of genomic analyses.
Author: S. Thomas Kelly [ctb],
S. Thomas Kelly [aut, cre],
Michael A. Black [aut, ths]
Maintainer: S. Thomas Kelly <tom.kelly@riken.jp>
Diff between graphsim versions 0.1.2 dated 2020-03-16 and 1.0.0 dated 2020-07-02
graphsim-0.1.2/graphsim/inst/doc/plots_viral_quantitate.R |only graphsim-0.1.2/graphsim/inst/doc/plots_viral_quantitate.Rmd |only graphsim-0.1.2/graphsim/inst/doc/plots_viral_quantitate.html |only graphsim-0.1.2/graphsim/inst/doc/run_example_pathways.R |only graphsim-0.1.2/graphsim/inst/doc/run_example_pathways.Rmd |only graphsim-0.1.2/graphsim/inst/doc/run_example_pathways.html |only graphsim-0.1.2/graphsim/inst/doc/test_graph_convergent.R |only graphsim-0.1.2/graphsim/inst/doc/test_graph_convergent.Rmd |only graphsim-0.1.2/graphsim/inst/doc/test_graph_convergent.html |only graphsim-0.1.2/graphsim/inst/doc/test_graph_divergent.R |only graphsim-0.1.2/graphsim/inst/doc/test_graph_divergent.Rmd |only graphsim-0.1.2/graphsim/inst/doc/test_graph_divergent.html |only graphsim-0.1.2/graphsim/inst/doc/test_graph_network.R |only graphsim-0.1.2/graphsim/inst/doc/test_graph_network.Rmd |only graphsim-0.1.2/graphsim/inst/doc/test_graph_network.html |only graphsim-0.1.2/graphsim/inst/doc/test_graph_network_inhibiting.R |only graphsim-0.1.2/graphsim/inst/doc/test_graph_network_inhibiting.Rmd |only graphsim-0.1.2/graphsim/inst/doc/test_graph_network_inhibiting.html |only graphsim-0.1.2/graphsim/inst/doc/test_graph_reconvergent.R |only graphsim-0.1.2/graphsim/inst/doc/test_graph_reconvergent.Rmd |only graphsim-0.1.2/graphsim/inst/doc/test_graph_reconvergent.html |only graphsim-0.1.2/graphsim/tests/testthat/Rplots.pdf |only graphsim-0.1.2/graphsim/vignettes/plots_viral_quantitate.Rmd |only graphsim-0.1.2/graphsim/vignettes/run_example_pathways.Rmd |only graphsim-0.1.2/graphsim/vignettes/test_graph_convergent.Rmd |only graphsim-0.1.2/graphsim/vignettes/test_graph_divergent.Rmd |only graphsim-0.1.2/graphsim/vignettes/test_graph_network.Rmd |only graphsim-0.1.2/graphsim/vignettes/test_graph_network_inhibiting.Rmd |only graphsim-0.1.2/graphsim/vignettes/test_graph_network_large.html |only graphsim-0.1.2/graphsim/vignettes/test_graph_reconvergent.Rmd |only graphsim-1.0.0/graphsim/DESCRIPTION | 24 graphsim-1.0.0/graphsim/MD5 | 162 +- graphsim-1.0.0/graphsim/NAMESPACE | 21 graphsim-1.0.0/graphsim/NEWS.md | 20 graphsim-1.0.0/graphsim/R/adjmat.R | 29 graphsim-1.0.0/graphsim/R/commonlink.R | 37 graphsim-1.0.0/graphsim/R/distance.R | 132 +- graphsim-1.0.0/graphsim/R/generate.R | 288 ++++ graphsim-1.0.0/graphsim/R/laplacian.R |only graphsim-1.0.0/graphsim/R/plot_directed.R | 113 + graphsim-1.0.0/graphsim/R/sigma.R | 312 ++++- graphsim-1.0.0/graphsim/R/state.R | 291 ++++ graphsim-1.0.0/graphsim/README.md | 76 + graphsim-1.0.0/graphsim/build/vignette.rds |binary graphsim-1.0.0/graphsim/inst/CITATION | 4 graphsim-1.0.0/graphsim/inst/doc/plots_directed.R | 82 + graphsim-1.0.0/graphsim/inst/doc/plots_directed.Rmd | 238 +++ graphsim-1.0.0/graphsim/inst/doc/plots_directed.html | 610 +++++----- graphsim-1.0.0/graphsim/inst/doc/simulate_expression.R |only graphsim-1.0.0/graphsim/inst/doc/simulate_expression.Rmd |only graphsim-1.0.0/graphsim/inst/doc/simulate_expression.html |only graphsim-1.0.0/graphsim/inst/resources |only graphsim-1.0.0/graphsim/inst/rmarkdown |only graphsim-1.0.0/graphsim/man/Pi3K_AKT_graph.Rd | 6 graphsim-1.0.0/graphsim/man/Pi3K_graph.Rd | 6 graphsim-1.0.0/graphsim/man/RAF_MAP_graph.Rd | 6 graphsim-1.0.0/graphsim/man/TGFBeta_Smad_graph.Rd | 6 graphsim-1.0.0/graphsim/man/generate_expression.Rd | 202 +++ graphsim-1.0.0/graphsim/man/make_adjmatrix_graph.Rd | 26 graphsim-1.0.0/graphsim/man/make_commonlink.Rd | 36 graphsim-1.0.0/graphsim/man/make_distance.Rd | 79 + graphsim-1.0.0/graphsim/man/make_laplacian.Rd |only graphsim-1.0.0/graphsim/man/make_sigma.Rd | 196 +++ graphsim-1.0.0/graphsim/man/make_state_matrix.Rd | 74 + graphsim-1.0.0/graphsim/man/plot_directed.Rd | 103 + graphsim-1.0.0/graphsim/tests/testthat/test_adjmatrix.R | 2 graphsim-1.0.0/graphsim/tests/testthat/test_distance.R | 4 graphsim-1.0.0/graphsim/tests/testthat/test_generate.R | 55 graphsim-1.0.0/graphsim/tests/testthat/test_laplacian.R |only graphsim-1.0.0/graphsim/tests/testthat/test_plot.R | 2 graphsim-1.0.0/graphsim/tests/testthat/test_sigma.R | 39 graphsim-1.0.0/graphsim/tests/testthat/test_state.R | 107 + graphsim-1.0.0/graphsim/vignettes/demo.gif |only graphsim-1.0.0/graphsim/vignettes/demo2.gif |only graphsim-1.0.0/graphsim/vignettes/plots_directed.Rmd | 238 +++ graphsim-1.0.0/graphsim/vignettes/simulate_expression.Rmd |only graphsim-1.0.0/graphsim/vignettes/simulate_expression.md |only graphsim-1.0.0/graphsim/vignettes/simulate_expression_files |only 78 files changed, 2955 insertions(+), 671 deletions(-)
Title: Matrix Completion, Imputation, and Inpainting Methods
Description: Filling in the missing entries of a partially observed data is one of fundamental problems in various disciplines of mathematical science. For many cases, data at our interests have canonical form of matrix in that the problem is posed upon a matrix with missing values to fill in the entries under preset assumptions and models. We provide a collection of methods from multiple disciplines under Matrix Completion, Imputation, and Inpainting. See Davenport and Romberg (2016) <doi:10.1109/JSTSP.2016.2539100> for an overview of the topic.
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kyoustat@gmail.com>
Diff between filling versions 0.2.1 dated 2020-02-04 and 0.2.2 dated 2020-07-02
DESCRIPTION | 10 +++++----- LICENSE |only MD5 | 49 +++++++++++++++++++++++++------------------------ NEWS.md | 11 +++++++---- R/fill_HardImpute.R | 3 ++- R/fill_KNNimpute.R | 2 ++ R/fill_OptSpace.R | 6 ++++-- R/fill_SVDimpute.R | 2 ++ R/fill_SVT.R | 4 +++- R/fill_SoftImpute.R | 2 ++ R/fill_USVT.R | 47 +++++++++++++++++++++++++++++++++++++++++------ R/fill_nuclear.R | 2 ++ R/fill_simple.R | 2 ++ build/partial.rdb |binary man/fill.USVT.Rd | 12 +++++++----- man/fill_HardImpute.Rd | 2 ++ man/fill_KNNimpute.Rd | 2 ++ man/fill_OptSpace.Rd | 6 ++++-- man/fill_SVDimpute.Rd | 2 ++ man/fill_SVT.Rd | 4 +++- man/fill_SoftImpute.Rd | 2 ++ man/fill_nuclear.Rd | 2 ++ man/fill_simple.Rd | 2 ++ man/lena128.Rd | 4 +++- man/lena256.Rd | 4 +++- man/lena64.Rd | 4 +++- 26 files changed, 132 insertions(+), 54 deletions(-)
Title: Diffusion Model of Conflict (DMC) in Reaction Time Tasks
Description: DMC model simulation detailed in Ulrich, R., Schroeter, H., Leuthold, H., & Birngruber, T. (2015). Automatic and controlled stimulus processing in conflict tasks: Superimposed diffusion processes and delta functions. Cognitive Psychology, 78, 148-174. Ulrich et al. (2015) <doi:10.1016/j.cogpsych.2015.02.005>.
Author: Mackenzie G. Ian [cre, aut]
Maintainer: Mackenzie G. Ian <ian.mackenzie@uni-tuebingen.de>
Diff between DMCfun versions 0.12.0 dated 2020-07-01 and 0.12.1 dated 2020-07-02
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/runDMC.cpp | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Comprehensive TIFF I/O with Full Support for 'ImageJ' TIFF Files
Description: General purpose TIFF file I/O for R users.
Currently the only such package with read and write support for TIFF
files with floating point (real-numbered) pixels, and the only package
that can correctly import TIFF files that were saved from 'ImageJ' and
write TIFF files than can be correctly read by 'ImageJ'
<https://imagej.nih.gov/ij/>. Also supports text image I/O.
Author: Rory Nolan [aut, cre] (<https://orcid.org/0000-0002-5239-4043>),
Kent Johnson [aut],
Simon Urbanek [ctb],
Sergi Padilla-Parra [ths] (<https://orcid.org/0000-0002-8010-9481>),
Jeroen Ooms [rev, ctb] (<https://orcid.org/0000-0002-4035-0289>),
Jon Clayden [rev] (<https://orcid.org/0000-0002-6608-0619>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between ijtiff versions 2.0.5 dated 2020-04-06 and 2.1.0 dated 2020-07-02
DESCRIPTION | 18 +- MD5 | 58 ++++---- NAMESPACE | 1 NEWS.md | 7 R/RcppExports.R | 4 R/class_constructors.R | 101 ++++++++++++++ R/print.R |only R/read.R | 15 +- R/utils.R | 169 +++++------------------- build/vignette.rds |binary inst/WORDLIST | 7 inst/doc/reading-and-writing-images.html | 12 - inst/doc/text-images.html | 4 inst/doc/the-imagej-problem.R | 20 +- inst/doc/the-imagej-problem.Rmd | 22 +-- inst/doc/the-imagej-problem.html | 90 +++++------- inst/img/Rlogo-banana-red_green.tif |binary man/as_EBImage.Rd | 2 man/print.ijtiff_img.Rd |only src/RcppExports.cpp | 13 + src/read.c | 131 +++++++++++------- src/utils.cpp | 24 +++ tests/figs |only tests/spelling.R | 6 tests/testthat/printing_of_Rlogo-banana-red.txt |only tests/testthat/test-graphics.R | 54 ++++--- tests/testthat/test-io.R | 21 +- tests/testthat/test-print.R |only vignettes/the-imagej-problem.Rmd | 22 +-- 29 files changed, 453 insertions(+), 348 deletions(-)
Title: Full Text of 'Scholarly' Articles Across Many Data Sources
Description: Provides a single interface to many sources of full text
'scholarly' data, including 'Biomed Central', Public Library of
Science, 'Pubmed Central', 'eLife', 'F1000Research', 'PeerJ',
'Pensoft', 'Hindawi', 'arXiv' 'preprints', and more. Functionality
included for searching for articles, downloading full or partial
text, downloading supplementary materials, converting to various
data formats.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
rOpenSci [fnd] (https://ropensci.org/)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between fulltext versions 1.4.0 dated 2019-12-13 and 1.5.0 dated 2020-07-02
fulltext-1.4.0/fulltext/R/rbindfill.R |only fulltext-1.4.0/fulltext/inst/vign |only fulltext-1.4.0/fulltext/man/ft_type_sum.Rd |only fulltext-1.5.0/fulltext/DESCRIPTION | 27 fulltext-1.5.0/fulltext/LICENSE | 2 fulltext-1.5.0/fulltext/MD5 | 116 - fulltext-1.5.0/fulltext/NAMESPACE | 12 fulltext-1.5.0/fulltext/NEWS.md | 19 fulltext-1.5.0/fulltext/R/cache_clean.R | 4 fulltext-1.5.0/fulltext/R/chunks.R | 4 fulltext-1.5.0/fulltext/R/defunct.R | 4 fulltext-1.5.0/fulltext/R/ft_abstract.R | 36 fulltext-1.5.0/fulltext/R/ft_get.R | 20 fulltext-1.5.0/fulltext/R/ft_search.R | 19 fulltext-1.5.0/fulltext/R/ft_serialize.R | 4 fulltext-1.5.0/fulltext/R/ft_table.R | 4 fulltext-1.5.0/fulltext/R/fulltext-package.R | 24 fulltext-1.5.0/fulltext/R/plugins_abstract.R | 12 fulltext-1.5.0/fulltext/R/plugins_get.R | 30 fulltext-1.5.0/fulltext/R/plugins_links.R | 4 fulltext-1.5.0/fulltext/R/scopus_utils.R | 103 - fulltext-1.5.0/fulltext/R/zzz.R | 115 - fulltext-1.5.0/fulltext/README.md | 173 -- fulltext-1.5.0/fulltext/build/vignette.rds |binary fulltext-1.5.0/fulltext/inst/doc/formats.Rmd | 15 fulltext-1.5.0/fulltext/inst/doc/formats.html | 476 ++++--- fulltext-1.5.0/fulltext/inst/doc/fulltext.Rmd | 79 - fulltext-1.5.0/fulltext/inst/doc/fulltext.html | 769 ++++++----- fulltext-1.5.0/fulltext/inst/doc/getting_fulltext.Rmd | 46 fulltext-1.5.0/fulltext/inst/doc/getting_fulltext.html | 871 +++++++------ fulltext-1.5.0/fulltext/man/cache_file_info.Rd | 4 fulltext-1.5.0/fulltext/man/ft_abstract.Rd | 26 fulltext-1.5.0/fulltext/man/ft_get.Rd | 4 fulltext-1.5.0/fulltext/man/ft_search.Rd | 13 fulltext-1.5.0/fulltext/man/ft_serialize.Rd | 4 fulltext-1.5.0/fulltext/man/fulltext-package.Rd | 22 fulltext-1.5.0/fulltext/man/scopus_search.Rd | 10 fulltext-1.5.0/fulltext/tests/fixtures |only fulltext-1.5.0/fulltext/tests/testthat/helper-fulltext.R | 15 fulltext-1.5.0/fulltext/tests/testthat/test-caching.R | 1 fulltext-1.5.0/fulltext/tests/testthat/test-ft_abstract.R | 26 fulltext-1.5.0/fulltext/tests/testthat/test-ft_collect.R |only fulltext-1.5.0/fulltext/tests/testthat/test-ft_get.r | 27 fulltext-1.5.0/fulltext/tests/testthat/test-ft_get_utils.R | 20 fulltext-1.5.0/fulltext/tests/testthat/test-ft_links.R | 40 fulltext-1.5.0/fulltext/tests/testthat/test-ft_providers.R | 8 fulltext-1.5.0/fulltext/tests/testthat/test-ft_search.R | 55 fulltext-1.5.0/fulltext/tests/testthat/test-ft_table.R |only fulltext-1.5.0/fulltext/vignettes/formats.Rmd | 15 fulltext-1.5.0/fulltext/vignettes/fulltext.Rmd | 79 - fulltext-1.5.0/fulltext/vignettes/fulltext.Rmd.og |only fulltext-1.5.0/fulltext/vignettes/getting_fulltext.Rmd | 46 fulltext-1.5.0/fulltext/vignettes/getting_fulltext.Rmd.og |only 53 files changed, 1888 insertions(+), 1515 deletions(-)
Title: Tools for Managing SSH and Git Credentials
Description: Setup and retrieve HTTPS and SSH credentials for use with 'git' and
other services. For HTTPS remotes the package interfaces the 'git-credential'
utility which 'git' uses to store HTTP usernames and passwords. For SSH
remotes we provide convenient functions to find or generate appropriate SSH
keys. The package both helps the user to setup a local git installation, and
also provides a back-end for git/ssh client libraries to authenticate with
existing user credentials.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between credentials versions 1.2.0 dated 2020-06-25 and 1.2.1 dated 2020-07-02
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 4 ++++ inst/ask_token.sh | 3 ++- 4 files changed, 12 insertions(+), 7 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-19 0.2.6
2020-01-10 0.2.5
2019-10-22 0.2.4
2018-11-01 0.2.3
2018-10-19 0.2.2
2018-07-16 0.2.1
2018-03-26 0.2.0
2017-11-27 0.1.1
Title: Subgroup Specific Optimal Dose Assignment
Description: Chooses subgroup specific optimal doses in a phase I dose finding clinical trial allowing for subgroup combination and simulates clinical trials under the subgroup specific time to event continual reassessment method. Chapple, A.G., Thall, P.F. (2018) <doi:10.1002/pst.1891>.
Author: Andrew Chapple
Maintainer: Andrew Chapple <achapp@lsuhsc.edu>
Diff between SubTite versions 3.0.1 dated 2020-02-12 and 3.0.2 dated 2020-07-02
DESCRIPTION | 6 +-- MD5 | 6 +-- R/GetSubTite.R | 2 + src/SUBGROUP.cpp | 84 +++++++++++++++++++++++++++++++------------------------ 4 files changed, 56 insertions(+), 42 deletions(-)
Title: River Network Distance Computation and Applications
Description: Reads river network shape files and computes network distances.
Also included are a variety of computation and graphical tools designed
for fisheries telemetry research, such as minimum home range, kernel density
estimation, and clustering analysis using empirical k-functions with
a bootstrap envelope. Tools are also provided for editing the river
networks, meaning there is no reliance on external software.
Author: Matt Tyers [aut, cre]
Maintainer: Matt Tyers <matt.tyers@alaska.gov>
Diff between riverdist versions 0.15.2 dated 2020-06-02 and 0.15.3 dated 2020-07-02
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/apps_of_riverdistance.R | 8 ++++++-- inst/doc/riverdist_vignette.html | 10 +++++----- man/plot.homerange.Rd | 2 +- man/riverdist-package.Rd | 4 ++-- 7 files changed, 28 insertions(+), 20 deletions(-)
Title: Operations to Ease Data Analyses Specific to Nigeria
Description: A set of convenience functions as well as geographical/political
data about Nigeria, aimed at simplifying work with data and information that
are specific to the country.
Author: Victor Ordu [aut, cre] (<https://orcid.org/0000-0003-3716-0668>)
Maintainer: Victor Ordu <victorordu@outlook.com>
Diff between naijR versions 0.1.0 dated 2020-05-21 and 0.1.2 dated 2020-07-02
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- NEWS.md |only R/map_nigeria.R | 8 ++++---- R/political.R | 3 ++- build/vignette.rds |binary inst/doc/nigeria-maps.Rmd | 2 +- inst/doc/nigeria-maps.html | 22 +++++++++++----------- man/map_ng.Rd | 8 ++++---- tests/testthat/test-political.R | 6 ++++++ vignettes/nigeria-maps.Rmd | 2 +- 11 files changed, 43 insertions(+), 35 deletions(-)
Title: Idiograms with Marks and Karyotype Indices
Description: Plot idiograms of karyotypes, plasmids, circular chr. having a set of data.frames
for chromosome data and optionally mark data. Two styles of chromosomes can be used: without or with
visible chromatids (when not circular).
Supports micrometers, cM and Mb or any unit. Two styles of centromeres are available: triangular and rounded;
and seven styles of marks: square, dots, cM, cMLeft, cenStyle, upArrow, downArrow;
its legend (label) can be drawn inline or to the right of karyotypes. Idiograms can also be plotted in
concentric circles. It is possible to calculate chromosome indices by Levan et al. (1964)
<doi:10.1111/j.1601-5223.1964.tb01953.x>, karyotype indices of Watanabe et al. (1999)
<doi:10.1007/PL00013869> and Romero-Zarco (1986) <doi:10.2307/1221906> and classify chromosomes
by morphology Guerra (1986) and Levan et al. (1964).
Author: Fernando Roa [aut, cre],
Mariana PC Telles [ctb]
Maintainer: Fernando Roa <froao@unal.edu.co>
Diff between idiogramFISH versions 1.15.1 dated 2020-06-03 and 1.15.3 dated 2020-07-02
idiogramFISH-1.15.1/idiogramFISH/man/figures/nostoc.jpg |only idiogramFISH-1.15.3/idiogramFISH/DESCRIPTION | 8 idiogramFISH-1.15.3/idiogramFISH/MD5 | 145 +- idiogramFISH-1.15.3/idiogramFISH/NAMESPACE | 3 idiogramFISH-1.15.3/idiogramFISH/NEWS.md | 33 idiogramFISH-1.15.3/idiogramFISH/R/armRatioCI.R | 4 idiogramFISH-1.15.3/idiogramFISH/R/asymmetry.R | 7 idiogramFISH-1.15.3/idiogramFISH/R/checkNameChrDfMarks.R | 10 idiogramFISH-1.15.3/idiogramFISH/R/chrbasicdataHolo.R | 9 idiogramFISH-1.15.3/idiogramFISH/R/chrbasicdatamono.R | 21 idiogramFISH-1.15.3/idiogramFISH/R/citrusSize.R |only idiogramFISH-1.15.3/idiogramFISH/R/dfMarkStyle.R | 10 idiogramFISH-1.15.3/idiogramFISH/R/fixChrNameDupDF.R | 40 idiogramFISH-1.15.3/idiogramFISH/R/genBankReadIF.R | 7 idiogramFISH-1.15.3/idiogramFISH/R/makedfMarkColor.R | 4 idiogramFISH-1.15.3/idiogramFISH/R/makedfMarkColorMycolors.R | 8 idiogramFISH-1.15.3/idiogramFISH/R/mapXY.R | 236 ++++ idiogramFISH-1.15.3/idiogramFISH/R/markdataholo.R | 13 idiogramFISH-1.15.3/idiogramFISH/R/markposDFs.R | 31 idiogramFISH-1.15.3/idiogramFISH/R/namesToColumns.R | 47 idiogramFISH-1.15.3/idiogramFISH/R/newOrderColumn.R | 3 idiogramFISH-1.15.3/idiogramFISH/R/orientation.R | 12 idiogramFISH-1.15.3/idiogramFISH/R/plotIdiograms.R | 487 ++++++-- idiogramFISH-1.15.3/idiogramFISH/R/plotlabelsright.R | 3 idiogramFISH-1.15.3/idiogramFISH/R/robert.R | 21 idiogramFISH-1.15.3/idiogramFISH/R/roundPlotMark.R | 49 idiogramFISH-1.15.3/idiogramFISH/README.md | 10 idiogramFISH-1.15.3/idiogramFISH/build/vignette.rds |binary idiogramFISH-1.15.3/idiogramFISH/inst/doc/AplotIdiogramsVig.R | 15 idiogramFISH-1.15.3/idiogramFISH/inst/doc/AplotIdiogramsVig.Rmd | 32 idiogramFISH-1.15.3/idiogramFISH/inst/doc/AplotIdiogramsVig.html | 49 idiogramFISH-1.15.3/idiogramFISH/inst/doc/BcircularVig.R | 80 + idiogramFISH-1.15.3/idiogramFISH/inst/doc/BcircularVig.Rmd | 82 + idiogramFISH-1.15.3/idiogramFISH/inst/doc/BcircularVig.html | 177 +-- idiogramFISH-1.15.3/idiogramFISH/inst/doc/DphylogenyVig.R | 8 idiogramFISH-1.15.3/idiogramFISH/inst/doc/DphylogenyVig.Rmd | 10 idiogramFISH-1.15.3/idiogramFISH/inst/doc/DphylogenyVig.html | 554 +++++----- idiogramFISH-1.15.3/idiogramFISH/inst/doc/EhumanVig.R | 5 idiogramFISH-1.15.3/idiogramFISH/inst/doc/EhumanVig.Rmd | 6 idiogramFISH-1.15.3/idiogramFISH/inst/doc/EhumanVig.html | 75 - idiogramFISH-1.15.3/idiogramFISH/inst/doc/index.html | 26 idiogramFISH-1.15.3/idiogramFISH/man/armRatioCI.Rd | 4 idiogramFISH-1.15.3/idiogramFISH/man/asymmetry.Rd | 7 idiogramFISH-1.15.3/idiogramFISH/man/checkNameChrDfMarks.Rd | 10 idiogramFISH-1.15.3/idiogramFISH/man/chrbasicdataHolo.Rd | 9 idiogramFISH-1.15.3/idiogramFISH/man/chrbasicdatamono.Rd | 18 idiogramFISH-1.15.3/idiogramFISH/man/citrusSize.Rd |only idiogramFISH-1.15.3/idiogramFISH/man/dfMarkStyle.Rd | 7 idiogramFISH-1.15.3/idiogramFISH/man/figures/README-example-1.png |binary idiogramFISH-1.15.3/idiogramFISH/man/figures/README-example2-1.png |binary idiogramFISH-1.15.3/idiogramFISH/man/figures/README-unnamed-chunk-17-1.png |binary idiogramFISH-1.15.3/idiogramFISH/man/figures/circular.png |only idiogramFISH-1.15.3/idiogramFISH/man/figures/cranmanualbookdown.svg | 2 idiogramFISH-1.15.3/idiogramFISH/man/figures/cranversion.svg | 16 idiogramFISH-1.15.3/idiogramFISH/man/figures/develmanualpkgdown.svg | 2 idiogramFISH-1.15.3/idiogramFISH/man/figures/develmanualvignette.svg | 2 idiogramFISH-1.15.3/idiogramFISH/man/figures/firstplot2.png |only idiogramFISH-1.15.3/idiogramFISH/man/figures/gitbadge.svg | 2 idiogramFISH-1.15.3/idiogramFISH/man/figures/manual.svg | 2 idiogramFISH-1.15.3/idiogramFISH/man/figures/pkgdownver.svg | 2 idiogramFISH-1.15.3/idiogramFISH/man/figures/secondplot2.png |only idiogramFISH-1.15.3/idiogramFISH/man/figures/thirdplot2.png |only idiogramFISH-1.15.3/idiogramFISH/man/genBankReadIF.Rd | 7 idiogramFISH-1.15.3/idiogramFISH/man/makedfMarkColor.Rd | 4 idiogramFISH-1.15.3/idiogramFISH/man/makedfMarkColorMycolors.Rd | 8 idiogramFISH-1.15.3/idiogramFISH/man/markdataholo.Rd | 13 idiogramFISH-1.15.3/idiogramFISH/man/markposDFs.Rd | 28 idiogramFISH-1.15.3/idiogramFISH/man/namesToColumns.Rd | 82 + idiogramFISH-1.15.3/idiogramFISH/man/newOrderColumn.Rd | 3 idiogramFISH-1.15.3/idiogramFISH/man/plotIdiograms.Rd | 189 ++- idiogramFISH-1.15.3/idiogramFISH/man/plotlabelsright.Rd | 3 idiogramFISH-1.15.3/idiogramFISH/man/robert.Rd | 19 idiogramFISH-1.15.3/idiogramFISH/man/yVertoHor.Rd | 24 idiogramFISH-1.15.3/idiogramFISH/vignettes/AplotIdiogramsVig.Rmd | 32 idiogramFISH-1.15.3/idiogramFISH/vignettes/BcircularVig.Rmd | 82 + idiogramFISH-1.15.3/idiogramFISH/vignettes/DphylogenyVig.Rmd | 10 idiogramFISH-1.15.3/idiogramFISH/vignettes/EhumanVig.Rmd | 6 77 files changed, 2028 insertions(+), 905 deletions(-)