Title: Trust, but Verify
Description: Declarative template-based framework for verifying that objects
meet structural requirements, and auto-composing error messages when they do
not.
Author: Brodie Gaslam [aut, cre],
Paxdiablo [cph] (Hash table implementation in src/pfhash.h),
R Core Team [cph] (Used/adapted several code snippets from R sources,
see src/misc-alike.c and src/valname.c)
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between vetr versions 0.2.9 dated 2020-03-06 and 0.2.10 dated 2020-05-13
DESCRIPTION | 6 +-- MD5 | 22 ++++++------ NEWS.md | 4 ++ build/vignette.rds |binary inst/doc/alike.R | 60 ++++++++++++++++----------------- inst/doc/alike.html | 31 +++++++++-------- inst/doc/vetr.R | 56 +++++++++++++++--------------- inst/doc/vetr.html | 21 ++++++----- tests/run.R | 2 - tests/unitizer/alike.R | 2 - tests/unitizer/alike.unitizer/data.rds |binary tests/valgrind/run.R | 2 + 12 files changed, 108 insertions(+), 98 deletions(-)
Title: Calculate MIMS Dissolved Gas Concentrations Without Getting a
Headache
Description: Calculate dissolved gas concentrations from raw MIMS
(Membrane Inlet Mass Spectrometer) signal data. Use mimsy() on
a formatted CSV file to return dissolved gas concentrations
(mg and microMole) of N2, O2, Ar based on
gas solubility at temperature, pressure, and salinity. See references
Benson and Krause (1984) <DOI:10.4319/lo.1992.37.6.1307>, Garcia and
Gordon (1992) <DOI:10.4319/lo.1984.29.3.0620>, Stull (1947)
<DOI:10.1021/ie50448a022>, and Hamme and Emerson (2004)
<DOI:10.1016/j.dsr.2004.06.009> for more information. Easily save the
output to a nicely-formatted multi-tab 'Excel' workbook with mimsy.save().
Supports dual-temperature standard calibration for dual-bath MIMS setups.
Author: Michelle Catherine Kelly [aut, cre],
Kevin Nevorski [ctb],
Amy M. Marcarelli [ctb]
Maintainer: Michelle Catherine Kelly <mckelly1@mtu.edu>
Diff between mimsy versions 0.4.3 dated 2020-01-28 and 0.6.0 dated 2020-05-13
mimsy-0.4.3/mimsy/vignettes/data.csv |only mimsy-0.6.0/mimsy/DESCRIPTION | 20 mimsy-0.6.0/mimsy/MD5 | 23 mimsy-0.6.0/mimsy/NEWS.md | 12 mimsy-0.6.0/mimsy/R/mimsy.R | 737 +++++-- mimsy-0.6.0/mimsy/README.md | 6 mimsy-0.6.0/mimsy/inst/doc/mimsy.R | 64 mimsy-0.6.0/mimsy/inst/doc/mimsy.Rmd | 85 mimsy-0.6.0/mimsy/inst/doc/mimsy.html | 2487 +++++++++++++++++++++++- mimsy-0.6.0/mimsy/inst/extdata/data_oneTemp.csv |only mimsy-0.6.0/mimsy/inst/extdata/data_twoTemp.csv |only mimsy-0.6.0/mimsy/vignettes/data_oneTemp.csv |only mimsy-0.6.0/mimsy/vignettes/data_twoTemp.csv |only mimsy-0.6.0/mimsy/vignettes/excel.png |binary mimsy-0.6.0/mimsy/vignettes/mimsy.Rmd | 85 15 files changed, 3185 insertions(+), 334 deletions(-)
Title: Machine Learning Models and Tools
Description: Meta-package for statistical and machine learning with a unified
interface for model fitting, prediction, performance assessment, and
presentation of results. Approaches for model fitting and prediction of
numerical, categorical, or censored time-to-event outcomes include
traditional regression models, regularization methods, tree-based methods,
support vector machines, neural networks, ensembles, data preprocessing,
filtering, and model tuning and selection. Performance metrics are provided
for model assessment and can be estimated with independent test sets, split
sampling, cross-validation, or bootstrap resampling. Resample estimation
can be executed in parallel for faster processing and nested in cases of
model tuning and selection. Modeling results can be summarized with
descriptive statistics; calibration curves; variable importance; partial
dependence plots; confusion matrices; and ROC, lift, and other performance
curves.
Author: Brian J Smith [aut, cre]
Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>
Diff between MachineShop versions 2.2.0 dated 2020-03-18 and 2.3.0 dated 2020-05-13
MachineShop-2.2.0/MachineShop/R/deprecated.R |only MachineShop-2.2.0/MachineShop/man/deprecated.Rd |only MachineShop-2.3.0/MachineShop/DESCRIPTION | 13 MachineShop-2.3.0/MachineShop/MD5 | 76 MachineShop-2.3.0/MachineShop/NAMESPACE | 19 MachineShop-2.3.0/MachineShop/NEWS.md | 31 MachineShop-2.3.0/MachineShop/R/AllClasses.R | 40 MachineShop-2.3.0/MachineShop/R/ML_BARTMachineModel.R | 10 MachineShop-2.3.0/MachineShop/R/ML_NNetModel.R | 8 MachineShop-2.3.0/MachineShop/R/ML_StackedModel.R | 7 MachineShop-2.3.0/MachineShop/R/ML_SuperModel.R | 7 MachineShop-2.3.0/MachineShop/R/ModelFrame.R | 51 MachineShop-2.3.0/MachineShop/R/ModelRecipe.R | 12 MachineShop-2.3.0/MachineShop/R/ModeledInput.R | 53 MachineShop-2.3.0/MachineShop/R/TrainedInputs.R | 100 MachineShop-2.3.0/MachineShop/R/TrainedModels.R | 6 MachineShop-2.3.0/MachineShop/R/coerce.R | 16 MachineShop-2.3.0/MachineShop/R/confusion.R | 30 MachineShop-2.3.0/MachineShop/R/fit.R | 7 MachineShop-2.3.0/MachineShop/R/performance_curve.R | 35 MachineShop-2.3.0/MachineShop/R/print.R | 32 MachineShop-2.3.0/MachineShop/R/resample.R | 86 MachineShop-2.3.0/MachineShop/R/settings.R | 26 MachineShop-2.3.0/MachineShop/R/summary.R | 2 MachineShop-2.3.0/MachineShop/R/survival.R | 17 MachineShop-2.3.0/MachineShop/R/utils.R | 26 MachineShop-2.3.0/MachineShop/build/vignette.rds |binary MachineShop-2.3.0/MachineShop/inst/doc/MLModels.html | 4 MachineShop-2.3.0/MachineShop/inst/doc/UsersGuide.R | 139 MachineShop-2.3.0/MachineShop/inst/doc/UsersGuide.Rmd | 492 +- MachineShop-2.3.0/MachineShop/inst/doc/UsersGuide.html | 2364 +++++----- MachineShop-2.3.0/MachineShop/man/BARTMachineModel.Rd | 2 MachineShop-2.3.0/MachineShop/man/SelectedInput.Rd | 16 MachineShop-2.3.0/MachineShop/man/TunedInput.Rd | 1 MachineShop-2.3.0/MachineShop/man/settings.Rd | 8 MachineShop-2.3.0/MachineShop/tests/testthat/Rplots.pdf |binary MachineShop-2.3.0/MachineShop/tests/testthat/test-settings.R | 12 MachineShop-2.3.0/MachineShop/tests/testthat/test-survival.txt | 176 MachineShop-2.3.0/MachineShop/vignettes/UsersGuide.Rmd | 492 +- MachineShop-2.3.0/MachineShop/vignettes/bibliography.bib | 20 40 files changed, 2440 insertions(+), 1996 deletions(-)
Title: Lysate and Secretome Peptide Feature Plotter
Description: Creates plots of peptides from shotgun proteomics analysis of secretome and lysate samples. These plots contain associated protein features and scores for potential secretion and truncation.
Author: Rafael Dellen, with contributions of Fabian Kruse
Maintainer: Gereon Poschmann <gereon.poschmann@hhu.de>
Diff between LSPFP versions 1.0.0 dated 2016-05-19 and 1.0.3 dated 2020-05-13
LSPFP-1.0.0/LSPFP/inst |only LSPFP-1.0.3/LSPFP/ChangeLog |only LSPFP-1.0.3/LSPFP/DESCRIPTION | 13 LSPFP-1.0.3/LSPFP/MD5 | 24 LSPFP-1.0.3/LSPFP/R/download_funct_lspfp.R | 1190 ++++++++++----------- LSPFP-1.0.3/LSPFP/R/feature_funct_lspfp.R | 1005 +++++++++++------ LSPFP-1.0.3/LSPFP/R/gffxtract_lspfp.R | 12 LSPFP-1.0.3/LSPFP/R/math_lspfp.R | 2 LSPFP-1.0.3/LSPFP/R/print_lspfp.R | 1094 +++++++++---------- LSPFP-1.0.3/LSPFP/R/score_funct_lspfp.R | 16 LSPFP-1.0.3/LSPFP/R/wrapper_lspfp.R | 1407 ++++++++++++------------- LSPFP-1.0.3/LSPFP/build/partial.rdb |binary LSPFP-1.0.3/LSPFP/man/printSelectedPeptides.Rd | 162 +- LSPFP-1.0.3/LSPFP/man/wrapperLSPFP.Rd | 433 +++---- 14 files changed, 2882 insertions(+), 2476 deletions(-)
Title: Differential Risk Hotspots in a Linear Network
Description: Performs the identification of differential risk hotspots (Briz-Redon et al. 2019) <doi:10.1016/j.aap.2019.105278> along a linear network. Given a marked point pattern lying on the linear network, the method implemented uses a network-constrained version of kernel density estimation (McSwiggan et al. 2017) <doi:10.1111/sjos.12255> to approximate the probability of occurrence across space for the type of event specified by the user through the marks of the pattern (Kelsall and Diggle 1995) <doi:10.2307/3318678>. The goal is to detect microzones of the linear network where the type of event indicated by the user is overrepresented.
Author: Alvaro Briz-Redon
Maintainer: Alvaro Briz-Redon <alvaro.briz@uv.es>
Diff between DRHotNet versions 1.1 dated 2019-09-15 and 1.2 dated 2020-05-13
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/DRHotspots_k_n.R | 15 +++++++++++---- R/RelativeProbabilityNetwork.R | 4 ++-- R/Sensitivity_k_n.R | 2 +- man/DRHotspots_k_n.Rd | 9 ++++++--- man/Sensitivity_k_n.Rd | 2 +- 7 files changed, 30 insertions(+), 20 deletions(-)
Title: Some Empiric and Nonparametric Copula Models
Description: Provides S4 classes and methods to fit several copula models: The classic empirical checkerboard copula and the empirical checkerboard copula with known margins, see Cuberos, Masiello and Maume-Deschamps (2019) <doi:10.1080/03610926.2019.1586936> are proposed. These two models allow to fit copulas in high dimension with a small number of observations, and they are always proper copulas. Some flexibility is added via a possibility to differentiate the checkerboard parameter by dimension. The last model consist of the implementation of the Copula Recursive Tree algorithm proposed by Laverny, Maume-Deschamps, Masiello and Rullière (2020) <arXiv:2005.02912>, including the localised dimension reduction, which fits a copula by recursive splitting of the copula domain. We also provide an efficient way of mixing copulas, allowing to bag the algorithm into a forest, and a generic way of measuring d-dimensional boxes with a copula.
Author: Oskar Laverny [aut, cre] (<https://orcid.org/0000-0002-7508-999X>)
Maintainer: Oskar Laverny <oskar.laverny@gmail.com>
Diff between cort versions 0.3.0 dated 2020-04-01 and 0.3.1 dated 2020-05-13
cort-0.3.0/cort/R/Box.R |only cort-0.3.0/cort/R/WeightedBox.R |only cort-0.3.0/cort/R/utils-pipe.R |only cort-0.3.0/cort/man/pipe.Rd |only cort-0.3.0/cort/src/code.cpp |only cort-0.3.0/cort/tests/testthat/test-Box.R |only cort-0.3.0/cort/tests/testthat/test-WeightedBox.R |only cort-0.3.1/cort/DESCRIPTION | 18 cort-0.3.1/cort/MD5 | 98 - cort-0.3.1/cort/NAMESPACE | 2 cort-0.3.1/cort/NEWS.md | 58 cort-0.3.1/cort/R/ConvexCombCopula.R | 8 cort-0.3.1/cort/R/Cort.R | 644 ++++------- cort-0.3.1/cort/R/CortForest.R | 159 +- cort-0.3.1/cort/R/RcppExports.R | 36 cort-0.3.1/cort/R/cbCopula.R | 63 - cort-0.3.1/cort/R/cbkmCopula.R | 12 cort-0.3.1/cort/R/data.R |only cort-0.3.1/cort/R/empiricalCopula.R | 4 cort-0.3.1/cort/R/generics.R | 28 cort-0.3.1/cort/R/utils.R | 55 cort-0.3.1/cort/README.md | 20 cort-0.3.1/cort/build/partial.rdb |binary cort-0.3.1/cort/data |only cort-0.3.1/cort/inst/REFERENCES.bib | 10 cort-0.3.1/cort/inst/WORDLIST | 15 cort-0.3.1/cort/inst/doc/vignette01_ecb.html | 12 cort-0.3.1/cort/inst/doc/vignette02_cort_clayton.R | 20 cort-0.3.1/cort/inst/doc/vignette02_cort_clayton.Rmd | 23 cort-0.3.1/cort/inst/doc/vignette02_cort_clayton.html | 601 ---------- cort-0.3.1/cort/inst/doc/vignette03_ecbkm.html | 12 cort-0.3.1/cort/inst/doc/vignette04_bootstrap_varying_m.R | 4 cort-0.3.1/cort/inst/doc/vignette04_bootstrap_varying_m.Rmd | 4 cort-0.3.1/cort/inst/doc/vignette04_bootstrap_varying_m.html | 90 + cort-0.3.1/cort/man/Cort-Class.Rd | 16 cort-0.3.1/cort/man/CortForest-Class.Rd | 15 cort-0.3.1/cort/man/cbkmCopula-Class.Rd | 2 cort-0.3.1/cort/man/clayton_data.Rd |only cort-0.3.1/cort/man/constraint_infl-methods.Rd | 2 cort-0.3.1/cort/man/funcdep_data.Rd |only cort-0.3.1/cort/man/impossible_data.Rd |only cort-0.3.1/cort/man/quad_norm-methods.Rd | 2 cort-0.3.1/cort/man/recoveryourself_data.Rd |only cort-0.3.1/cort/src/RcppExports.cpp | 137 ++ cort-0.3.1/cort/src/bivRho.cpp |only cort-0.3.1/cort/src/bivTau.cpp |only cort-0.3.1/cort/src/cortMonteCarlo.cpp |only cort-0.3.1/cort/src/dCort.cpp |only cort-0.3.1/cort/src/dcbCopula.cpp |only cort-0.3.1/cort/src/lossFunc.cpp |only cort-0.3.1/cort/src/pCort.cpp |only cort-0.3.1/cort/src/pcbCopula.cpp |only cort-0.3.1/cort/src/projectOnTwoDims.cpp |only cort-0.3.1/cort/src/quadProd.cpp |only cort-0.3.1/cort/tests/testthat/test-Cort.R | 13 cort-0.3.1/cort/tests/testthat/test-CortForest.R | 4 cort-0.3.1/cort/tests/testthat/test-cbCopula.R | 4 cort-0.3.1/cort/tests/testthat/test-vCopula.R | 31 cort-0.3.1/cort/vignettes/vignette02_cort_clayton.Rmd | 23 cort-0.3.1/cort/vignettes/vignette04_bootstrap_varying_m.Rmd | 4 60 files changed, 921 insertions(+), 1328 deletions(-)
Title: Mesh Topology and Visualization for Spatial Data
Description: Gives direct access to generic 3D tools and provides a full suite
of mesh-creation and 3D plotting functions. By extending the 'rgl' package
conversion and visualization functions for the 'mesh3d' class a wide variety of
complex spatial data can be brought into 3D scenes. These tools allow for
spatial raster, polygons, and lines that are common in 'GIS' contexts to be
converted into mesh forms with high flexibility and the ability to integrate
disparate data types. Vector and raster data can be seamlessly combined as
meshes, and surfaces can be set to have material properties based on data
values or with image textures. Textures and other data combinations use
projection transformations to map between coordinate systems, and objects can
be easily visualized in an interactive scene at any stage. This package relies
on the 'RTriangle' package for high-quality triangular meshing which is
licensed restrictively under 'CC BY-NC-SA 4.0'.
Author: Michael D. Sumner [aut, cre],
Miles McBain [ctb]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between anglr versions 0.5.0 dated 2020-04-28 and 0.6.0 dated 2020-05-13
anglr-0.5.0/anglr/R/globe.r |only anglr-0.6.0/anglr/DESCRIPTION | 16 anglr-0.6.0/anglr/MD5 | 109 anglr-0.6.0/anglr/NAMESPACE | 17 anglr-0.6.0/anglr/NEWS.md | 367 - anglr-0.6.0/anglr/R/DEL0-model.R | 63 anglr-0.6.0/anglr/R/GET-things.R | 132 anglr-0.6.0/anglr/R/QUAD-model.R | 1 anglr-0.6.0/anglr/R/as.mesh3d.R | 31 anglr-0.6.0/anglr/R/copy_down.R | 3 anglr-0.6.0/anglr/R/de-normalize.R | 300 - anglr-0.6.0/anglr/R/dot3d.R | 9 anglr-0.6.0/anglr/R/globe.R |only anglr-0.6.0/anglr/R/make_local.R | 110 anglr-0.6.0/anglr/R/mesh_plot.R | 4 anglr-0.6.0/anglr/R/persp3d.R | 130 anglr-0.6.0/anglr/R/plot3d.R | 2 anglr-0.6.0/anglr/R/polygon-finder-for-triangles.R | 170 anglr-0.6.0/anglr/R/raster-utils.R |only anglr-0.6.0/anglr/R/sf_extent.R |only anglr-0.6.0/anglr/R/shade3d.R | 204 anglr-0.6.0/anglr/R/utils-pipe.R | 22 anglr-0.6.0/anglr/R/utils.R | 757 +-- anglr-0.6.0/anglr/R/wire3d.R | 172 anglr-0.6.0/anglr/README.md | 15 anglr-0.6.0/anglr/build/vignette.rds |binary anglr-0.6.0/anglr/inst/doc/anglr.R | 76 anglr-0.6.0/anglr/inst/doc/anglr.html | 812 +-- anglr-0.6.0/anglr/inst/docs-vign/old_readme_rant.Rmd | 158 anglr-0.6.0/anglr/inst/docs-vign/vignettes-dev/rangl-examples.Rmd | 512 +- anglr-0.6.0/anglr/inst/docs-vign/vignettes-dev/setup.R | 152 anglr-0.6.0/anglr/inst/docs-vign/vignettes-dev/spatial-normal-forms.Rmd | 620 +- anglr-0.6.0/anglr/inst/extdata/2017-04-30_16021834_steinbruch-export.gpx | 2346 +++++----- anglr-0.6.0/anglr/inst/extdata/longname-readme | 4 anglr-0.6.0/anglr/man/DEL0.Rd | 11 anglr-0.6.0/anglr/man/as.mesh3d.Rd | 13 anglr-0.6.0/anglr/man/copy_down.Rd | 2 anglr-0.6.0/anglr/man/dot3d.Rd | 9 anglr-0.6.0/anglr/man/globe.Rd | 5 anglr-0.6.0/anglr/man/pipe.Rd | 24 anglr-0.6.0/anglr/man/plot3d.Rd | 2 anglr-0.6.0/anglr/man/reproj.Rd | 18 anglr-0.6.0/anglr/man/sf_data_zoo.Rd | 18 anglr-0.6.0/anglr/man/sf_extent.Rd |only anglr-0.6.0/anglr/man/simpleworld.Rd | 26 anglr-0.6.0/anglr/tests/testthat.R | 8 anglr-0.6.0/anglr/tests/testthat/Rplots.pdf | 6 anglr-0.6.0/anglr/tests/testthat/test-DEL0.R | 98 anglr-0.6.0/anglr/tests/testthat/test-RTriangle.R | 24 anglr-0.6.0/anglr/tests/testthat/test-TRI.R | 14 anglr-0.6.0/anglr/tests/testthat/test-as.mesh3d.R | 186 anglr-0.6.0/anglr/tests/testthat/test-copy-down.R | 92 anglr-0.6.0/anglr/tests/testthat/test-extent-example.R | 42 anglr-0.6.0/anglr/tests/testthat/test-mesh-sanity.R | 234 anglr-0.6.0/anglr/tests/testthat/test-mesh_plot.R | 98 anglr-0.6.0/anglr/tests/testthat/test-plot3d.R | 40 anglr-0.6.0/anglr/tests/testthat/test-sanity.R | 92 anglr-0.6.0/anglr/tests/testthat/test-silicate-sanity.R | 62 58 files changed, 4310 insertions(+), 4128 deletions(-)
Title: Enhanced Database Interactivity
Description: Facilitates interaction with ODBC data sources, by remembering and hiding communication settings and supporting parameterised multi-statement SQL with embedded R.
Author: Mike Lee
Maintainer: Mike Lee <random.deviate@gmail.com>
Diff between SQRL versions 0.7.1 dated 2020-03-14 and 0.7.2 dated 2020-05-13
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/SQRL.R | 3 ++- man/SQRL-package.Rd | 15 ++++++++++----- man/sqrlParams.Rd | 10 +++++++--- 5 files changed, 27 insertions(+), 17 deletions(-)
Title: Generates Facts Sourced from the Wikipedia Main Page
Description: Displays random facts from the Wikipedia homepage.
Intended to keep users interested during long waiting periods.
Author: Keith McNulty [aut, cre]
Maintainer: Keith McNulty <keith.mcnulty@gmail.com>
Diff between wikifacts versions 0.1.0 dated 2019-08-01 and 0.2 dated 2020-05-13
DESCRIPTION | 13 ++---- MD5 | 22 +++++----- NEWS.md | 7 ++- R/wiki_didyouknow.R | 56 +++++++++++++++++--------- R/wiki_inthenews.R | 58 ++++++++++++++++++--------- R/wiki_onthisday.R | 57 ++++++++++++++++++-------- R/wiki_randomfact.R | 19 +++++--- README.md | 104 +++++++++++++++++++++++++++++++++++++++++-------- man/wiki_didyouknow.Rd | 13 +++--- man/wiki_inthenews.Rd | 13 +++--- man/wiki_onthisday.Rd | 13 +++--- man/wiki_randomfact.Rd | 13 +++--- 12 files changed, 272 insertions(+), 116 deletions(-)
Title: Predicting Categorical and Continuous Outcomes Using One in Ten
Rule
Description: Predicts categorical or continuous outcomes while concentrating on four key points. These are Cross-validation, Accuracy, Regression and Rule of Ten or "one in ten rule" (CARRoT). It performs the cross-validation specified number of times by partitioning the input into training and test set and fitting linear/multinomial/binary regression models to the training set. All regression models satisfying a rule of ten events per variable are fitted and the ones with the best predictive power are given as an output. Best predictive power is understood as highest accuracy in case of binary/multinomial outcomes, smallest absolute and relative errors in case of continuous outcomes. For binary case there is also an option of finding a regression model which gives the highest AUROC (Area Under Receiver Operating Curve) value. The option of parallel toolbox is also available. Methods are described in Peduzzi et al. (1996) <doi:10.1016/S0895-4356(96)00236-3> and Rhemtulla et al. (2012) <doi:10.1037/a0029315>.
Author: Alina Bazarova [aut, cre],
Marko Raseta [aut]
Maintainer: Alina Bazarova <a.bazarova@uni-koeln.de>
Diff between CARRoT versions 2.5.0 dated 2020-03-26 and 2.5.1 dated 2020-05-13
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NAMESPACE | 3 +++ R/carrot_functions.R | 17 +++++++++++------ build/partial.rdb |binary man/cub.Rd | 5 +++++ man/find_int.Rd | 3 +++ man/quadr.Rd | 3 +++ 8 files changed, 35 insertions(+), 16 deletions(-)
Title: Apps for Teaching Statistics, R Programming, and Shiny App
Development
Description: Contains apps and gadgets for teaching data analysis and
statistics concepts along with how to implement them in R. Includes
tools to make app development easier and faster by nesting apps together.
Author: Jason Freels [aut, cre],
Bradley Boehmke [ctb]
Maintainer: Jason Freels <auburngrads@live.com>
Diff between teachingApps versions 1.0.4 dated 2018-06-10 and 1.0.8 dated 2020-05-13
teachingApps-1.0.4/teachingApps/inst/apps/htmlwidgets_shiny |only teachingApps-1.0.4/teachingApps/man/figures |only teachingApps-1.0.8/teachingApps/DESCRIPTION | 26 - teachingApps-1.0.8/teachingApps/MD5 | 252 ++++++++-- teachingApps-1.0.8/teachingApps/NAMESPACE | 81 +-- teachingApps-1.0.8/teachingApps/R/RcppExports.R | 45 + teachingApps-1.0.8/teachingApps/R/basic.distribution.R |only teachingApps-1.0.8/teachingApps/R/bound.roots.R |only teachingApps-1.0.8/teachingApps/R/distribution-egeng.R |only teachingApps-1.0.8/teachingApps/R/distribution-geng.R |only teachingApps-1.0.8/teachingApps/R/distribution-gets.R |only teachingApps-1.0.8/teachingApps/R/distribution-goma.R |only teachingApps-1.0.8/teachingApps/R/distribution-igau.R |only teachingApps-1.0.8/teachingApps/R/expand.vec.R |only teachingApps-1.0.8/teachingApps/R/generic.distribution.R |only teachingApps-1.0.8/teachingApps/R/quant.R |only teachingApps-1.0.8/teachingApps/R/teachingApp.R | 14 teachingApps-1.0.8/teachingApps/R/wqmf.phibf.R |only teachingApps-1.0.8/teachingApps/R/wqmf.phisl.R |only teachingApps-1.0.8/teachingApps/inst/apps/acceptance_mtbf/global.R | 2 teachingApps-1.0.8/teachingApps/inst/apps/cdf_ace |only teachingApps-1.0.8/teachingApps/inst/apps/chaz_ace |only teachingApps-1.0.8/teachingApps/inst/apps/confidence_intervals_simulation/global.R | 2 teachingApps-1.0.8/teachingApps/inst/apps/confidence_intervals_simulation/server.R | 31 - teachingApps-1.0.8/teachingApps/inst/apps/confidence_intervals_simulation/server3.R |only teachingApps-1.0.8/teachingApps/inst/apps/distribution_egeng |only teachingApps-1.0.8/teachingApps/inst/apps/distribution_egeng_functions |only teachingApps-1.0.8/teachingApps/inst/apps/distribution_gamma/gamma-func.Rmd | 29 + teachingApps-1.0.8/teachingApps/inst/apps/distribution_gamma/gamma-props.Rmd | 30 - teachingApps-1.0.8/teachingApps/inst/apps/distribution_gamma_functions/server.R | 37 - teachingApps-1.0.8/teachingApps/inst/apps/distribution_geng |only teachingApps-1.0.8/teachingApps/inst/apps/distribution_geng_functions |only teachingApps-1.0.8/teachingApps/inst/apps/distribution_goma |only teachingApps-1.0.8/teachingApps/inst/apps/distribution_igau |only teachingApps-1.0.8/teachingApps/inst/apps/distribution_lev/lev-props.Rmd | 18 teachingApps-1.0.8/teachingApps/inst/apps/distribution_lev_functions/server.R | 37 - teachingApps-1.0.8/teachingApps/inst/apps/distribution_levgets |only teachingApps-1.0.8/teachingApps/inst/apps/distribution_logistic_functions/server.R | 37 - teachingApps-1.0.8/teachingApps/inst/apps/distribution_loglogistic_functions/server.R | 37 - teachingApps-1.0.8/teachingApps/inst/apps/distribution_norgets |only teachingApps-1.0.8/teachingApps/inst/apps/distribution_normal_functions/server.R | 37 - teachingApps-1.0.8/teachingApps/inst/apps/distribution_sev_functions/server.R | 37 - teachingApps-1.0.8/teachingApps/inst/apps/distribution_sevgets |only teachingApps-1.0.8/teachingApps/inst/apps/distribution_weibull_functions/server.R | 37 - teachingApps-1.0.8/teachingApps/inst/apps/haz_ace |only teachingApps-1.0.8/teachingApps/inst/apps/location_scale/server.R | 2 teachingApps-1.0.8/teachingApps/inst/apps/maximum_likelihood/background1.Rmd | 2 teachingApps-1.0.8/teachingApps/inst/apps/maximum_likelihood/background1.md |only teachingApps-1.0.8/teachingApps/inst/apps/maximum_likelihood/example2_1.Rmd | 146 ++++- teachingApps-1.0.8/teachingApps/inst/apps/maximum_likelihood_simulation/server.R | 4 teachingApps-1.0.8/teachingApps/inst/apps/pdf_ace |only teachingApps-1.0.8/teachingApps/inst/apps/probability_functions/backgroundsurv.Rmd |only teachingApps-1.0.8/teachingApps/inst/apps/probability_functions/rfuncssurv.Rmd |only teachingApps-1.0.8/teachingApps/inst/apps/probability_functions/server.R | 55 -- teachingApps-1.0.8/teachingApps/inst/apps/probability_functions/ui.R | 109 ++-- teachingApps-1.0.8/teachingApps/inst/apps/probability_functions2 |only teachingApps-1.0.8/teachingApps/inst/apps/quan_ace |only teachingApps-1.0.8/teachingApps/inst/apps/rel_ace |only teachingApps-1.0.8/teachingApps/inst/figure |only teachingApps-1.0.8/teachingApps/inst/gadget_test.Rmd |only teachingApps-1.0.8/teachingApps/inst/gadget_test.html |only teachingApps-1.0.8/teachingApps/inst/include |only teachingApps-1.0.8/teachingApps/inst/teachingApps/css/teachingApps.css | 8 teachingApps-1.0.8/teachingApps/inst/test.Rhtml |only teachingApps-1.0.8/teachingApps/inst/test.html |only teachingApps-1.0.8/teachingApps/man/Extended-Generalized-Gamma.Rd |only teachingApps-1.0.8/teachingApps/man/Generalized-Gamma.Rd |only teachingApps-1.0.8/teachingApps/man/Gomphertz-Makeham.Rd |only teachingApps-1.0.8/teachingApps/man/Inverse-Gaussian.Rd |only teachingApps-1.0.8/teachingApps/man/add_logo.Rd | 9 teachingApps-1.0.8/teachingApps/man/add_options.Rd | 10 teachingApps-1.0.8/teachingApps/man/add_update.Rd | 4 teachingApps-1.0.8/teachingApps/man/beta4.Rd | 4 teachingApps-1.0.8/teachingApps/man/gadget_clean_columns.Rd | 11 teachingApps-1.0.8/teachingApps/man/gadget_lm.Rd | 12 teachingApps-1.0.8/teachingApps/man/gets.Rd |only teachingApps-1.0.8/teachingApps/man/sev.Rd | 3 teachingApps-1.0.8/teachingApps/man/sgpdfl.Rd |only teachingApps-1.0.8/teachingApps/man/sgquan.Rd |only teachingApps-1.0.8/teachingApps/man/spgeng.Rd |only teachingApps-1.0.8/teachingApps/man/spmlgeng.Rd |only teachingApps-1.0.8/teachingApps/man/teachingApp.Rd | 16 teachingApps-1.0.8/teachingApps/man/teachingApps-package.Rd | 6 teachingApps-1.0.8/teachingApps/src/0-done-0_POSTKP_flnf_dlgama.cpp |only teachingApps-1.0.8/teachingApps/src/0-done-0_SGPDFL.cpp |only teachingApps-1.0.8/teachingApps/src/0-done-0_SGPDFL_gpdfl.cpp |only teachingApps-1.0.8/teachingApps/src/0-done-0_SGPDFL_gpdfl_pdfggl.cpp |only teachingApps-1.0.8/teachingApps/src/0-done-0_SGPDFL_gpdfl_usrpdf.cpp |only teachingApps-1.0.8/teachingApps/src/0-done-0_SGQUAN.cpp |only teachingApps-1.0.8/teachingApps/src/0-done-0_SGQUAN_gquant.cpp |only teachingApps-1.0.8/teachingApps/src/0-done-0_SGQUAN_gquant_qugamm.cpp |only teachingApps-1.0.8/teachingApps/src/0-done-0_SLSINF_lsinf_lsint_norint_wqm_dxerc.cpp |only teachingApps-1.0.8/teachingApps/src/0-done-0_SPGENG.cpp |only teachingApps-1.0.8/teachingApps/src/0-done-0_SPGENG_gcdf.cpp |only teachingApps-1.0.8/teachingApps/src/0-done-0_SPGENG_gcdf_pbgg.cpp |only teachingApps-1.0.8/teachingApps/src/0-done-0_SPGENG_gcdf_pbmlgg_gaminc.cpp |only teachingApps-1.0.8/teachingApps/src/0-done-0_SPGENG_gcdf_wqm_zgtran.cpp |only teachingApps-1.0.8/teachingApps/src/0-done-0_SPGENG_gcdf_wqm_zgtran_usrcdf.cpp |only teachingApps-1.0.8/teachingApps/src/0-done-0_UTILITY_dexpc.cpp |only teachingApps-1.0.8/teachingApps/src/0-done-0_UTILITY_dlogc.cpp |only teachingApps-1.0.8/teachingApps/src/0-done-0_UTILITY_dsign.cpp |only teachingApps-1.0.8/teachingApps/src/0-done-0_UTILITY_dsqrtc.cpp |only teachingApps-1.0.8/teachingApps/src/0-done-0_UTILITY_wqm_pinv.cpp |only teachingApps-1.0.8/teachingApps/src/0-done-0_UTILITY_wqm_quant.cpp |only teachingApps-1.0.8/teachingApps/src/Makevars | 3 teachingApps-1.0.8/teachingApps/src/Makevars.win |only teachingApps-1.0.8/teachingApps/src/RcppExports.cpp | 83 +++ teachingApps-1.0.8/teachingApps/src/SPMLGENG.cpp |only teachingApps-1.0.8/teachingApps/src/SPMLGENG_gcdfml.cpp |only teachingApps-1.0.8/teachingApps/src/SPMLGENG_gcdfml_pbmlgg.cpp |only teachingApps-1.0.8/teachingApps/src/beta_funcs.cpp | 19 teachingApps-1.0.8/teachingApps/src/heads |only teachingApps-1.0.8/teachingApps/src/sev.cpp | 11 113 files changed, 879 insertions(+), 427 deletions(-)
Title: Construct and Compare scGRN from Single-Cell Transcriptomic Data
Description: A workflow based on machine learning methods to construct and compare single-cell gene regulatory networks (scGRN) using single-cell RNA-seq (scRNA-seq) data collected from different conditions. Uses principal component regression, tensor decomposition, and manifold alignment, to accurately identify even subtly shifted gene expression programs.
Author: Daniel Osorio [aut, cre] (<https://orcid.org/0000-0003-4424-8422>),
Yan Zhong [aut, ctb],
Guanxun Li [aut, ctb],
Jianhua Huang [aut, ctb],
James Cai [aut, ctb, ths] (<https://orcid.org/0000-0002-8081-6725>)
Maintainer: Daniel Osorio <dcosorioh@tamu.edu>
Diff between scTenifoldNet versions 1.2.1 dated 2020-04-09 and 1.2.2 dated 2020-05-13
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/manifoldAlignment.R | 2 +- R/scTenifoldNet.R | 4 ++++ 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Bayesian Mixing Models in R
Description: Creates and runs Bayesian mixing models to analyze
biological tracer data (i.e. stable isotopes, fatty acids), which estimate the
proportions of source (prey) contributions to a mixture (consumer). 'MixSIAR'
is not one model, but a framework that allows a user to create a mixing model
based on their data structure and research questions, via options for fixed/
random effects, source data types, priors, and error terms. 'MixSIAR' incorporates
several years of advances since 'MixSIR' and 'SIAR'.
Author: Brian Stock [cre, aut],
Brice Semmens [aut],
Eric Ward [ctb],
Andrew Parnell [ctb],
Andrew Jackson [ctb],
Donald Phillips [ctb]
Maintainer: Brian Stock <b1stock@ucsd.edu>
Diff between MixSIAR versions 3.1.10 dated 2018-04-12 and 3.1.11 dated 2020-05-13
MixSIAR-3.1.10/MixSIAR/R/build_mix_win.R |only MixSIAR-3.1.10/MixSIAR/R/build_source_win.R |only MixSIAR-3.1.10/MixSIAR/R/create_mixsiar_envir.R |only MixSIAR-3.1.10/MixSIAR/R/mixsiar_gui.R |only MixSIAR-3.1.10/MixSIAR/man/build_mix_win.Rd |only MixSIAR-3.1.10/MixSIAR/man/build_source_win.Rd |only MixSIAR-3.1.10/MixSIAR/man/mixsiar.Rd |only MixSIAR-3.1.10/MixSIAR/man/mixsiar_gui.Rd |only MixSIAR-3.1.11/MixSIAR/DESCRIPTION | 31 MixSIAR-3.1.11/MixSIAR/MD5 | 173 +-- MixSIAR-3.1.11/MixSIAR/NAMESPACE | 2 MixSIAR-3.1.11/MixSIAR/NEWS.md | 27 MixSIAR-3.1.11/MixSIAR/R/calc_area.R | 8 MixSIAR-3.1.11/MixSIAR/R/combine_sources.R | 5 MixSIAR-3.1.11/MixSIAR/R/compare_models.R | 5 MixSIAR-3.1.11/MixSIAR/R/load_discr_data.R | 1 MixSIAR-3.1.11/MixSIAR/R/load_mix_data.R | 4 MixSIAR-3.1.11/MixSIAR/R/load_source_data.R | 3 MixSIAR-3.1.11/MixSIAR/R/mixsiar.R |only MixSIAR-3.1.11/MixSIAR/R/output_JAGS.R | 51 - MixSIAR-3.1.11/MixSIAR/R/plot_continuous_var.R | 7 MixSIAR-3.1.11/MixSIAR/R/plot_data.R | 25 MixSIAR-3.1.11/MixSIAR/R/plot_data_one_iso.R | 4 MixSIAR-3.1.11/MixSIAR/R/plot_data_two_iso.R | 6 MixSIAR-3.1.11/MixSIAR/R/plot_intervals.R | 2 MixSIAR-3.1.11/MixSIAR/R/plot_prior.R | 24 MixSIAR-3.1.11/MixSIAR/R/run_model.R | 33 MixSIAR-3.1.11/MixSIAR/R/summary_stat.R | 2 MixSIAR-3.1.11/MixSIAR/R/write_JAGS_model.R | 6 MixSIAR-3.1.11/MixSIAR/README.md | 272 ----- MixSIAR-3.1.11/MixSIAR/build/vignette.rds |binary MixSIAR-3.1.11/MixSIAR/inst/CITATION | 22 MixSIAR-3.1.11/MixSIAR/inst/doc/cladocera_ex.R | 36 MixSIAR-3.1.11/MixSIAR/inst/doc/cladocera_ex.Rmd | 14 MixSIAR-3.1.11/MixSIAR/inst/doc/cladocera_ex.html | 409 ++++++-- MixSIAR-3.1.11/MixSIAR/inst/doc/geese_ex.R | 32 MixSIAR-3.1.11/MixSIAR/inst/doc/geese_ex.Rmd | 8 MixSIAR-3.1.11/MixSIAR/inst/doc/geese_ex.html | 407 ++++++-- MixSIAR-3.1.11/MixSIAR/inst/doc/isopod_ex.R | 38 MixSIAR-3.1.11/MixSIAR/inst/doc/isopod_ex.Rmd | 14 MixSIAR-3.1.11/MixSIAR/inst/doc/isopod_ex.html | 407 ++++++-- MixSIAR-3.1.11/MixSIAR/inst/doc/killerwhale_ex.R | 32 MixSIAR-3.1.11/MixSIAR/inst/doc/killerwhale_ex.Rmd | 16 MixSIAR-3.1.11/MixSIAR/inst/doc/killerwhale_ex.html | 465 ++++++--- MixSIAR-3.1.11/MixSIAR/inst/doc/lake_ex.R | 40 MixSIAR-3.1.11/MixSIAR/inst/doc/lake_ex.Rmd | 14 MixSIAR-3.1.11/MixSIAR/inst/doc/lake_ex.html | 407 ++++++-- MixSIAR-3.1.11/MixSIAR/inst/doc/wolves_ex.R | 47 MixSIAR-3.1.11/MixSIAR/inst/doc/wolves_ex.Rmd | 37 MixSIAR-3.1.11/MixSIAR/inst/doc/wolves_ex.html | 498 +++++++--- MixSIAR-3.1.11/MixSIAR/inst/example_scripts/mixsiar_script_alligator.R | 24 MixSIAR-3.1.11/MixSIAR/inst/example_scripts/mixsiar_script_alligator_length_ind.R |only MixSIAR-3.1.11/MixSIAR/inst/example_scripts/mixsiar_script_cladocera.R | 4 MixSIAR-3.1.11/MixSIAR/inst/example_scripts/mixsiar_script_geese.R | 4 MixSIAR-3.1.11/MixSIAR/inst/example_scripts/mixsiar_script_isopod.R | 4 MixSIAR-3.1.11/MixSIAR/inst/example_scripts/mixsiar_script_killerwhale.R | 4 MixSIAR-3.1.11/MixSIAR/inst/example_scripts/mixsiar_script_lake.R | 4 MixSIAR-3.1.11/MixSIAR/inst/example_scripts/mixsiar_script_mantis.R | 9 MixSIAR-3.1.11/MixSIAR/inst/example_scripts/mixsiar_script_palmyra.R | 4 MixSIAR-3.1.11/MixSIAR/inst/example_scripts/mixsiar_script_snail.R | 4 MixSIAR-3.1.11/MixSIAR/inst/example_scripts/mixsiar_script_stormpetrel.R | 4 MixSIAR-3.1.11/MixSIAR/inst/example_scripts/mixsiar_script_wolves.R | 11 MixSIAR-3.1.11/MixSIAR/man/calc_area.Rd | 7 MixSIAR-3.1.11/MixSIAR/man/combine_sources.Rd | 1 MixSIAR-3.1.11/MixSIAR/man/compare_models.Rd | 3 MixSIAR-3.1.11/MixSIAR/man/load_mix_data.Rd | 10 MixSIAR-3.1.11/MixSIAR/man/load_source_data.Rd | 2 MixSIAR-3.1.11/MixSIAR/man/mixsiar_env.Rd |only MixSIAR-3.1.11/MixSIAR/man/output_JAGS.Rd | 61 - MixSIAR-3.1.11/MixSIAR/man/plot_data.Rd | 12 MixSIAR-3.1.11/MixSIAR/man/plot_data_one_iso.Rd | 12 MixSIAR-3.1.11/MixSIAR/man/plot_data_two_iso.Rd | 14 MixSIAR-3.1.11/MixSIAR/man/plot_intervals.Rd | 11 MixSIAR-3.1.11/MixSIAR/man/plot_prior.Rd | 9 MixSIAR-3.1.11/MixSIAR/man/run_model.Rd | 16 MixSIAR-3.1.11/MixSIAR/man/summary_stat.Rd | 12 MixSIAR-3.1.11/MixSIAR/man/write_JAGS_model.Rd | 9 MixSIAR-3.1.11/MixSIAR/tests/testthat/test_ex1_wolves.R | 3 MixSIAR-3.1.11/MixSIAR/tests/testthat/test_ex2_geese.R | 3 MixSIAR-3.1.11/MixSIAR/tests/testthat/test_ex3_lake.R | 3 MixSIAR-3.1.11/MixSIAR/tests/testthat/test_ex4_palmyra.R | 3 MixSIAR-3.1.11/MixSIAR/tests/testthat/test_ex5_killerwhale.R | 6 MixSIAR-3.1.11/MixSIAR/tests/testthat/test_ex6_snail.R | 3 MixSIAR-3.1.11/MixSIAR/tests/testthat/test_ex7_stormpetrel.R | 3 MixSIAR-3.1.11/MixSIAR/tests/testthat/test_ex8_cladocera.R | 3 MixSIAR-3.1.11/MixSIAR/tests/testthat/test_ex9_isopod.R | 3 MixSIAR-3.1.11/MixSIAR/tests/testthat/test_run_model.R | 31 MixSIAR-3.1.11/MixSIAR/vignettes/cladocera_ex.Rmd | 14 MixSIAR-3.1.11/MixSIAR/vignettes/geese_ex.Rmd | 8 MixSIAR-3.1.11/MixSIAR/vignettes/isopod_ex.Rmd | 14 MixSIAR-3.1.11/MixSIAR/vignettes/killerwhale_ex.Rmd | 16 MixSIAR-3.1.11/MixSIAR/vignettes/lake_ex.Rmd | 14 MixSIAR-3.1.11/MixSIAR/vignettes/wolves_ex.Rmd | 37 93 files changed, 2655 insertions(+), 1398 deletions(-)
Title: GOV.UK Style Templates for R Markdown
Description: A suite of custom R Markdown formats and templates
for authoring web pages styled with the GOV.UK Design System.
Author: Crown Copyright 2019 [cph],
Duncan Garmonsway [aut, cre]
Maintainer: Duncan Garmonsway <duncan.garmonsway@digital.cabinet-office.gov.uk>
Diff between govdown versions 0.8.0 dated 2020-01-09 and 0.9.1 dated 2020-05-13
DESCRIPTION | 10 - MD5 | 42 ++--- NAMESPACE | 1 NEWS.md | 11 + R/govdown-format.R | 1 R/unstrap.R |only README.md | 5 inst/rmarkdown/resources/alpha-banner.html | 20 +- inst/rmarkdown/resources/beta-banner.html | 20 +- inst/rmarkdown/resources/favicon-custom.html | 12 - inst/rmarkdown/resources/favicon.html | 12 - inst/rmarkdown/resources/google-analytics.html | 20 +- inst/rmarkdown/resources/govuk.html | 175 ++++++++++------------ inst/rmarkdown/resources/govuk.lua | 4 inst/rmarkdown/resources/header-content.html | 12 - inst/rmarkdown/resources/logo-svg.html | 8 - inst/rmarkdown/resources/navbar-item-active.html | 12 - inst/rmarkdown/resources/navbar-item-other.html | 12 - inst/rmarkdown/resources/navbar-links.html | 14 - inst/rmarkdown/resources/navbar-service-name.html | 8 - inst/rmarkdown/resources/navbar.html | 34 ++-- man/govdown_document.Rd | 30 ++- man/unstrap.Rd |only 23 files changed, 242 insertions(+), 221 deletions(-)
Title: Reimplementations of Functions Introduced Since R-3.0.0
Description: Functions introduced or changed since R v3.0.0 are re-implemented in this
package. The backports are conditionally exported in order to let R resolve
the function name to either the implemented backport, or the respective base
version, if available. Package developers can make use of new functions or
arguments by selectively importing specific backports to
support older installations.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
R Core Team [aut]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between backports versions 1.1.6 dated 2020-04-05 and 1.1.7 dated 2020-05-13
DESCRIPTION | 6 +++--- MD5 | 12 +++++++++--- NAMESPACE | 2 ++ NEWS.md | 8 ++++++-- R/deparse1.R |only R/list2DF.R |only man/deparse1.Rd |only man/list2DF.Rd |only tests/test_deparse1.R |only tests/test_list2DF.R |only 10 files changed, 20 insertions(+), 8 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent access to
information contained in various R models, like model formulas, model terms,
information about random effects, data that was used to fit the model or
data from response variables. 'insight' mainly revolves around two types
of functions: Functions that find (the names of) information, starting with
'find_', and functions that get the underlying data, starting with 'get_'.
The package has a consistent syntax and works with many different model
objects, where otherwise functions to access these information are missing.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Dominique Makowski [aut, ctb] (<https://orcid.org/0000-0001-5375-9967>),
Indrajeet Patil [aut, ctb] (<https://orcid.org/0000-0003-1995-6531>),
Philip Waggoner [aut, ctb] (<https://orcid.org/0000-0002-7825-7573>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between insight versions 0.8.3 dated 2020-04-20 and 0.8.4 dated 2020-05-13
insight-0.8.3/insight/tests/testthat/test-BBmm.R |only insight-0.8.3/insight/tests/testthat/test-BBreg.R |only insight-0.8.4/insight/DESCRIPTION | 12 insight-0.8.4/insight/MD5 | 86 +-- insight-0.8.4/insight/NAMESPACE | 9 insight-0.8.4/insight/NEWS.md | 21 insight-0.8.4/insight/R/clean_names.R | 8 insight-0.8.4/insight/R/clean_parameters.R | 26 + insight-0.8.4/insight/R/compute_variances.R | 20 insight-0.8.4/insight/R/find_algorithm.R | 6 insight-0.8.4/insight/R/find_formula.R | 24 - insight-0.8.4/insight/R/find_parameters.R | 18 insight-0.8.4/insight/R/find_statistic.R | 5 insight-0.8.4/insight/R/fish.R | 1 insight-0.8.4/insight/R/get_parameters.R | 70 +-- insight-0.8.4/insight/R/get_statistic.R | 5 insight-0.8.4/insight/R/get_varcov.R | 15 insight-0.8.4/insight/R/get_variances.R | 11 insight-0.8.4/insight/R/helper_functions.R | 20 insight-0.8.4/insight/R/is_model.R | 10 insight-0.8.4/insight/R/is_model_supported.R | 1 insight-0.8.4/insight/R/model_info.R | 15 insight-0.8.4/insight/R/n_obs.R | 9 insight-0.8.4/insight/R/null_model.R | 30 - insight-0.8.4/insight/R/utils_model_info.R | 10 insight-0.8.4/insight/build/partial.rdb |binary insight-0.8.4/insight/build/vignette.rds |binary insight-0.8.4/insight/inst/WORDLIST | 1 insight-0.8.4/insight/inst/doc/insight.html | 320 ++++++-------- insight-0.8.4/insight/man/clean_names.Rd | 2 insight-0.8.4/insight/man/get_parameters.Rd | 3 insight-0.8.4/insight/man/get_statistic.Rd | 2 insight-0.8.4/insight/man/get_variance.Rd | 11 insight-0.8.4/insight/man/null_model.Rd | 58 +- insight-0.8.4/insight/tests/testthat/test-BayesFactorBF.R | 15 insight-0.8.4/insight/tests/testthat/test-MCMCglmm.R | 1 insight-0.8.4/insight/tests/testthat/test-aovlist.R | 20 insight-0.8.4/insight/tests/testthat/test-blmer.R | 1 insight-0.8.4/insight/tests/testthat/test-brms.R | 24 - insight-0.8.4/insight/tests/testthat/test-gbm.R | 1 insight-0.8.4/insight/tests/testthat/test-glmmTMB.R | 45 + insight-0.8.4/insight/tests/testthat/test-lmer.R | 1 insight-0.8.4/insight/tests/testthat/test-rstanarm.R | 1 insight-0.8.4/insight/tests/testthat/test-spatial.R | 4 insight-0.8.4/insight/tests/testthat/test-zeroinfl.R | 12 45 files changed, 575 insertions(+), 379 deletions(-)
Title: Read and Write 'FreeSurfer' Neuroimaging File Formats
Description: Provides functions to read and write data from neuroimaging files in 'FreeSurfer' <http://freesurfer.net/> binary formats. This includes, but is not limited to, the following file formats: 1) MGH/MGZ format files, which can contain multi-dimensional images or other data. Typically they contain time-series of three-dimensional brain scans acquired by magnetic resonance imaging (MRI). They can also contain vertex-wise measures of surface morphometry data. The MGH format is named after the Massachusetts General Hospital, and the MGZ format is a compressed version of the same format. 2) 'FreeSurfer' morphometry data files in binary 'curv' format. These contain vertex-wise surface measures, i.e., one scalar value for each vertex of a brain surface mesh. These are typically values like the cortical thickness or brain surface area at each vertex. 3) Annotation file format. This contains a brain surface parcellation derived from a cortical atlas. 4) Surface file format. Contains a brain surface mesh, given by a list of vertices and a list of faces.
Author: Tim Schäfer [aut, cre] (<https://orcid.org/0000-0002-3683-8070>)
Maintainer: Tim Schäfer <ts+code@rcmd.org>
Diff between freesurferformats versions 0.1.9 dated 2020-04-14 and 0.1.10 dated 2020-05-13
freesurferformats-0.1.10/freesurferformats/DESCRIPTION | 16 freesurferformats-0.1.10/freesurferformats/MD5 | 114 +- freesurferformats-0.1.10/freesurferformats/NAMESPACE | 22 freesurferformats-0.1.10/freesurferformats/R/gifti_writer.R |only freesurferformats-0.1.10/freesurferformats/R/gifti_writer_freesurfer.R |only freesurferformats-0.1.10/freesurferformats/R/gifti_xml_tools.R |only freesurferformats-0.1.10/freesurferformats/R/mghheader.R | 2 freesurferformats-0.1.10/freesurferformats/R/nifti2mgh.R |only freesurferformats-0.1.10/freesurferformats/R/read_fs_curv.R | 60 + freesurferformats-0.1.10/freesurferformats/R/read_fs_label.R | 44 freesurferformats-0.1.10/freesurferformats/R/read_fs_mgh.R | 5 freesurferformats-0.1.10/freesurferformats/R/read_fs_surface.R | 159 +++ freesurferformats-0.1.10/freesurferformats/R/read_fs_volume.R |only freesurferformats-0.1.10/freesurferformats/R/read_nisurface.R | 11 freesurferformats-0.1.10/freesurferformats/R/rotate3d.R |only freesurferformats-0.1.10/freesurferformats/R/write_fs_curv.R | 43 freesurferformats-0.1.10/freesurferformats/R/write_fs_surface.R | 268 +++++ freesurferformats-0.1.10/freesurferformats/build/vignette.rds |binary freesurferformats-0.1.10/freesurferformats/inst/doc/freesurferformats.html | 509 +++++++--- freesurferformats-0.1.10/freesurferformats/inst/doc/freesurferformats_header.html | 311 +++++- freesurferformats-0.1.10/freesurferformats/inst/doc/freesurferformats_write.html | 351 +++++- freesurferformats-0.1.10/freesurferformats/man/cdata.Rd |only freesurferformats-0.1.10/freesurferformats/man/check_data_and_settings_consistency.Rd |only freesurferformats-0.1.10/freesurferformats/man/faces.tris.to.quad.Rd | 5 freesurferformats-0.1.10/freesurferformats/man/flip2D.Rd |only freesurferformats-0.1.10/freesurferformats/man/flip3D.Rd |only freesurferformats-0.1.10/freesurferformats/man/fs.get.morph.file.ext.for.format.Rd | 2 freesurferformats-0.1.10/freesurferformats/man/fs.get.morph.file.format.from.filename.Rd | 4 freesurferformats-0.1.10/freesurferformats/man/gifti_writer.Rd |only freesurferformats-0.1.10/freesurferformats/man/gifti_xml.Rd |only freesurferformats-0.1.10/freesurferformats/man/gifti_xml_add_global_metadata.Rd |only freesurferformats-0.1.10/freesurferformats/man/gifti_xml_write.Rd |only freesurferformats-0.1.10/freesurferformats/man/nifti.space.info.Rd | 2 freesurferformats-0.1.10/freesurferformats/man/nifti.time.info.Rd | 2 freesurferformats-0.1.10/freesurferformats/man/nifti.transform.type.name.Rd | 2 freesurferformats-0.1.10/freesurferformats/man/ply.header.lines.Rd |only freesurferformats-0.1.10/freesurferformats/man/read.element.counts.ply.header.Rd |only freesurferformats-0.1.10/freesurferformats/man/read.fs.curv.Rd | 6 freesurferformats-0.1.10/freesurferformats/man/read.fs.curv.asc.Rd | 3 freesurferformats-0.1.10/freesurferformats/man/read.fs.label.Rd | 8 freesurferformats-0.1.10/freesurferformats/man/read.fs.mgh.Rd | 4 freesurferformats-0.1.10/freesurferformats/man/read.fs.morph.Rd | 10 freesurferformats-0.1.10/freesurferformats/man/read.fs.morph.gii.Rd |only freesurferformats-0.1.10/freesurferformats/man/read.fs.surface.Rd | 5 freesurferformats-0.1.10/freesurferformats/man/read.fs.surface.asc.Rd | 6 freesurferformats-0.1.10/freesurferformats/man/read.fs.surface.gii.Rd |only freesurferformats-0.1.10/freesurferformats/man/read.fs.surface.ply.Rd |only freesurferformats-0.1.10/freesurferformats/man/read.fs.surface.vtk.Rd | 8 freesurferformats-0.1.10/freesurferformats/man/read.fs.volume.Rd |only freesurferformats-0.1.10/freesurferformats/man/read.fs.volume.nii.Rd |only freesurferformats-0.1.10/freesurferformats/man/read.fs.weight.Rd | 2 freesurferformats-0.1.10/freesurferformats/man/read_nisurface.Rd | 3 freesurferformats-0.1.10/freesurferformats/man/read_nisurfacefile.Rd | 3 freesurferformats-0.1.10/freesurferformats/man/rotate2D.Rd |only freesurferformats-0.1.10/freesurferformats/man/rotate3D.Rd |only freesurferformats-0.1.10/freesurferformats/man/rotate90.Rd |only freesurferformats-0.1.10/freesurferformats/man/write.fs.curv.Rd | 2 freesurferformats-0.1.10/freesurferformats/man/write.fs.mgh.Rd | 2 freesurferformats-0.1.10/freesurferformats/man/write.fs.morph.Rd | 10 freesurferformats-0.1.10/freesurferformats/man/write.fs.surface.Rd | 13 freesurferformats-0.1.10/freesurferformats/man/write.fs.surface.asc.Rd | 3 freesurferformats-0.1.10/freesurferformats/man/write.fs.surface.gii.Rd |only freesurferformats-0.1.10/freesurferformats/man/write.fs.surface.obj.Rd |only freesurferformats-0.1.10/freesurferformats/man/write.fs.surface.off.Rd |only freesurferformats-0.1.10/freesurferformats/man/write.fs.surface.ply.Rd |only freesurferformats-0.1.10/freesurferformats/man/write.fs.surface.vtk.Rd | 3 freesurferformats-0.1.10/freesurferformats/man/write.fs.weight.Rd | 2 freesurferformats-0.1.10/freesurferformats/man/xml_node_gifti_MD.Rd |only freesurferformats-0.1.10/freesurferformats/tests/testthat/helper-functions-for-tests.R |only freesurferformats-0.1.10/freesurferformats/tests/testthat/test-read-fs-mgh.R | 34 freesurferformats-0.1.10/freesurferformats/tests/testthat/test-read-fs-surface.R | 9 freesurferformats-0.1.10/freesurferformats/tests/testthat/test-write-fs-surface.R | 57 - freesurferformats-0.1.9/freesurferformats/R/mgh2nii.R |only freesurferformats-0.1.9/freesurferformats/man/fs.volume.from.oro.nifti.Rd |only 74 files changed, 1706 insertions(+), 419 deletions(-)
More information about freesurferformats at CRAN
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Title: Distributed Lag Non-Linear Models
Description: Collection of functions for distributed lag linear and non-linear models.
Author: Antonio Gasparrini [aut, cre],
Ben Armstrong [aut],
Fabian Scheipl [ctb]
Maintainer: Antonio Gasparrini <antonio.gasparrini@lshtm.ac.uk>
Diff between dlnm versions 2.3.9 dated 2019-03-11 and 2.4.1 dated 2020-05-13
DESCRIPTION | 8 ++++---- MD5 | 36 ++++++++++++++++++------------------ NEWS.md | 22 +++++++++++++++++++++- R/crosspred.R | 14 ++++++-------- R/exphist.R | 4 ++-- R/getcoef.R | 2 +- R/getvcov.R | 2 +- README.md | 4 ++-- build/vignette.rds |binary inst/NEWS | 26 +++++++++++++++++++++++--- inst/doc/dlnmExtended.pdf |binary inst/doc/dlnmOverview.pdf |binary inst/doc/dlnmPenalized.pdf |binary inst/doc/dlnmTS.Rnw | 2 +- inst/doc/dlnmTS.pdf |binary man/crosspred.Rd | 6 +++--- man/crossreduce.Rd | 2 +- man/exphist.Rd | 2 +- vignettes/dlnmTS.Rnw | 2 +- 19 files changed, 85 insertions(+), 47 deletions(-)
Title: Causal Modeling with Coincidence Analysis
Description: Provides comprehensive functionalities for causal modeling with Coincidence Analysis (CNA), which is a configurational comparative method of causal data analysis that was first introduced in Baumgartner (2009) <doi:10.1177/0049124109339369>, and generalized in Baumgartner & Ambuehl (2018) <doi:10.1017/psrm.2018.45>. CNA is related to Qualitative Comparative Analysis (QCA), but contrary to the latter, it is custom-built for uncovering causal structures with multiple outcomes and it builds causal models from the bottom up by gradually combining single factors to complex dependency structures until the requested thresholds of model fit are met. The new functionalities provided by this package version include functions for evaluating and benchmarking the correctness of CNA's output, a function determining whether a solution is an INUS model, a function bringing non-INUS expressions into INUS form, and a function for identifying cyclic models. The package vignette has been updated accordingly.
Author: Mathias Ambuehl [aut, cre, cph],
Michael Baumgartner [aut, cph],
Ruedi Epple [ctb],
Veli-Pekka Parkkinen [ctb],
Alrik Thiem [ctb]
Maintainer: Mathias Ambuehl <mathias.ambuehl@consultag.ch>
Diff between cna versions 2.2.2 dated 2019-12-06 and 2.2.3 dated 2020-05-13
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/truthTab.r | 31 +++++++++++++++++++++++-------- inst/NEWS | 4 ++++ inst/doc/cna_vignette.pdf |binary man/cna-package.Rd | 4 ++-- man/cna.Rd | 3 +-- man/condition.Rd | 6 +++--- 8 files changed, 44 insertions(+), 26 deletions(-)
Title: Estimation and Hypothesis Testing for Threshold Regression
Description: Threshold regression models are also called two-phase regression, broken-stick regression, split-point regression, structural change models, and regression kink models, with and without interaction terms. Methods for both continuous and discontinuous threshold models are included, but the support for the former is much greater. This package is described in Fong, Huang, Gilbert and Permar (2017) chngpt: threshold regression model estimation and inference, BMC Bioinformatics, in press, DOI:10.1186/s12859-017-1863-x.
Author: Youyi Fong [cre],
Adam Elder [aut],
Hyunju Son [aut],
Zonglin He [aut],
Tao Yang [aut]
Maintainer: Youyi Fong <youyifong@gmail.com>
Diff between chngpt versions 2020.2-26 dated 2020-02-27 and 2020.5-13 dated 2020-05-13
ChangeLog | 6 ++++++ DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/chngptm.R | 33 ++++++++++++++++++++++----------- inst/doc/chngpt-vignette.pdf |binary inst/unitTests/runit.chngptm.linear.R | 16 +++++++++++++++- man/chngptm.Rd | 9 +++++++-- man/double.hinge.Rd | 2 ++ src/fastgrid.cc | 6 ++++-- src/fastgrid2.cc | 10 ++++++---- 10 files changed, 75 insertions(+), 33 deletions(-)
Title: Retrieving Information of Proteins from Uniprot
Description: Connect to Uniprot <https://www.uniprot.org/> to retrieve information about proteins using their accession number such information could be name or taxonomy information, For detailed information kindly read the publication <https://www.sciencedirect.com/science/article/pii/S1874391919303859>.
Author: Mohamed Soudy [aut, cre],
Ali Mostafa [aut]
Maintainer: Mohamed Soudy <MohmedSoudy2009@gmail.com>
Diff between UniprotR versions 1.2.4 dated 2020-03-19 and 1.2.5 dated 2020-05-13
UniprotR-1.2.4/UniprotR/build |only UniprotR-1.2.4/UniprotR/inst/doc |only UniprotR-1.2.4/UniprotR/vignettes |only UniprotR-1.2.5/UniprotR/DESCRIPTION | 8 +++----- UniprotR-1.2.5/UniprotR/MD5 | 13 ++++--------- UniprotR-1.2.5/UniprotR/R/GetproteinNetwork.R | 6 ++++++ UniprotR-1.2.5/UniprotR/R/PlotProteinTaxa.R | 2 +- UniprotR-1.2.5/UniprotR/R/plotGoannotation.R | 8 +++++++- 8 files changed, 21 insertions(+), 16 deletions(-)
Title: Latent Variable Analysis
Description: Fit a variety of latent variable models, including confirmatory
factor analysis, structural equation modeling and latent growth curve models.
Author: Yves Rosseel [aut, cre] (<https://orcid.org/0000-0002-4129-4477>),
Terrence D. Jorgensen [aut] (<https://orcid.org/0000-0001-5111-6773>),
Daniel Oberski [ctb],
Jarrett Byrnes [ctb],
Leonard Vanbrabant [ctb],
Victoria Savalei [ctb],
Ed Merkle [ctb],
Michael Hallquist [ctb],
Mijke Rhemtulla [ctb],
Myrsini Katsikatsou [ctb],
Mariska Barendse [ctb],
Florian Scharf [ctb]
Maintainer: Yves Rosseel <Yves.Rosseel@UGent.be>
Diff between lavaan versions 0.6-5 dated 2019-08-28 and 0.6-6 dated 2020-05-13
lavaan-0.6-5/lavaan/R/01RefClass_00lavRefModel.R |only lavaan-0.6-5/lavaan/R/01RefClass_01lavOptim.R |only lavaan-0.6-5/lavaan/R/01RefClass_02lavML.R |only lavaan-0.6-5/lavaan/R/lav_binorm.R |only lavaan-0.6-5/lavaan/R/lav_ols.R |only lavaan-0.6-5/lavaan/R/lav_pearson.R |only lavaan-0.6-5/lavaan/R/lav_polychor.R |only lavaan-0.6-5/lavaan/R/lav_polyserial.R |only lavaan-0.6-5/lavaan/R/lav_probit.R |only lavaan-0.6-6/lavaan/DESCRIPTION | 6 lavaan-0.6-6/lavaan/MD5 | 172 ++++---- lavaan-0.6-6/lavaan/NAMESPACE | 2 lavaan-0.6-6/lavaan/R/00class.R | 2 lavaan-0.6-6/lavaan/R/ctr_mplus2lavaan.R | 199 +++++----- lavaan-0.6-6/lavaan/R/ctr_pml_plrt.R | 2 lavaan-0.6-6/lavaan/R/ctr_pml_plrt2.R | 6 lavaan-0.6-6/lavaan/R/lav_bootstrap.R | 5 lavaan-0.6-6/lavaan/R/lav_bootstrap_lrt.R | 10 lavaan-0.6-6/lavaan/R/lav_bvmix.R |only lavaan-0.6-6/lavaan/R/lav_bvord.R |only lavaan-0.6-6/lavaan/R/lav_bvreg.R |only lavaan-0.6-6/lavaan/R/lav_cor.R | 23 - lavaan-0.6-6/lavaan/R/lav_data.R | 9 lavaan-0.6-6/lavaan/R/lav_dataframe.R | 66 --- lavaan-0.6-6/lavaan/R/lav_efa_extraction.R |only lavaan-0.6-6/lavaan/R/lav_export.R | 13 lavaan-0.6-6/lavaan/R/lav_export_mplus.R | 15 lavaan-0.6-6/lavaan/R/lav_fit_measures.R | 36 + lavaan-0.6-6/lavaan/R/lav_h1_logl.R | 10 lavaan-0.6-6/lavaan/R/lav_integrate.R | 2 lavaan-0.6-6/lavaan/R/lav_matrix.R | 138 ++++++- lavaan-0.6-6/lavaan/R/lav_matrix_rotate.R | 12 lavaan-0.6-6/lavaan/R/lav_model.R | 24 - lavaan-0.6-6/lavaan/R/lav_model_compute.R | 12 lavaan-0.6-6/lavaan/R/lav_model_efa.R | 32 - lavaan-0.6-6/lavaan/R/lav_model_estimate.R | 90 ++++ lavaan-0.6-6/lavaan/R/lav_model_gradient_pml.R | 38 + lavaan-0.6-6/lavaan/R/lav_model_h1_information.R | 20 - lavaan-0.6-6/lavaan/R/lav_model_hessian.R | 14 lavaan-0.6-6/lavaan/R/lav_model_information.R | 9 lavaan-0.6-6/lavaan/R/lav_model_loglik.R | 12 lavaan-0.6-6/lavaan/R/lav_model_vcov.R | 53 ++ lavaan-0.6-6/lavaan/R/lav_muthen1984.R | 188 ++++++--- lavaan-0.6-6/lavaan/R/lav_mvnorm.R | 56 ++ lavaan-0.6-6/lavaan/R/lav_mvnorm_cluster.R | 2 lavaan-0.6-6/lavaan/R/lav_mvnorm_h1.R | 90 +++- lavaan-0.6-6/lavaan/R/lav_mvnorm_missing.R | 148 +++++-- lavaan-0.6-6/lavaan/R/lav_mvnorm_missing_h1.R | 24 + lavaan-0.6-6/lavaan/R/lav_nlminb_constr.R | 1 lavaan-0.6-6/lavaan/R/lav_object_generate.R | 9 lavaan-0.6-6/lavaan/R/lav_object_inspect.R | 112 +++-- lavaan-0.6-6/lavaan/R/lav_object_methods.R | 183 ++++++--- lavaan-0.6-6/lavaan/R/lav_object_print.R | 134 ++++-- lavaan-0.6-6/lavaan/R/lav_objective.R | 73 ++- lavaan-0.6-6/lavaan/R/lav_options.R | 322 +++++++++++++--- lavaan-0.6-6/lavaan/R/lav_partable.R | 235 ++++++------ lavaan-0.6-6/lavaan/R/lav_partable_attributes.R | 22 - lavaan-0.6-6/lavaan/R/lav_partable_bounds.R |only lavaan-0.6-6/lavaan/R/lav_partable_flat.R | 2 lavaan-0.6-6/lavaan/R/lav_partable_from_lm.R | 2 lavaan-0.6-6/lavaan/R/lav_partable_utils.R | 19 lavaan-0.6-6/lavaan/R/lav_partable_vnames.R | 34 + lavaan-0.6-6/lavaan/R/lav_predict.R | 240 +++++++++--- lavaan-0.6-6/lavaan/R/lav_print.R | 99 ++++- lavaan-0.6-6/lavaan/R/lav_representation_lisrel.R | 2 lavaan-0.6-6/lavaan/R/lav_residuals.R | 426 ++++++++++++++++++---- lavaan-0.6-6/lavaan/R/lav_samplestats.R | 49 +- lavaan-0.6-6/lavaan/R/lav_samplestats_gamma.R | 58 ++ lavaan-0.6-6/lavaan/R/lav_samplestats_step1.R | 43 +- lavaan-0.6-6/lavaan/R/lav_samplestats_step2.R | 77 ++- lavaan-0.6-6/lavaan/R/lav_simulate.R | 17 lavaan-0.6-6/lavaan/R/lav_simulate_old.R | 9 lavaan-0.6-6/lavaan/R/lav_standardize.R | 111 ++--- lavaan-0.6-6/lavaan/R/lav_start.R | 147 ++++++- lavaan-0.6-6/lavaan/R/lav_syntax.R | 39 +- lavaan-0.6-6/lavaan/R/lav_tables.R | 6 lavaan-0.6-6/lavaan/R/lav_test.R | 57 ++ lavaan-0.6-6/lavaan/R/lav_test_LRT.R | 155 +++++--- lavaan-0.6-6/lavaan/R/lav_test_diff.R | 2 lavaan-0.6-6/lavaan/R/lav_test_satorra_bentler.R | 24 + lavaan-0.6-6/lavaan/R/lav_test_score.R | 9 lavaan-0.6-6/lavaan/R/lav_test_yuan_bentler.R | 26 + lavaan-0.6-6/lavaan/R/lav_uvord.R |only lavaan-0.6-6/lavaan/R/lav_uvreg.R |only lavaan-0.6-6/lavaan/R/xxx_lavaan.R | 400 ++++++++++---------- lavaan-0.6-6/lavaan/R/xxx_sam.R | 33 + lavaan-0.6-6/lavaan/man/cfa.Rd | 25 - lavaan-0.6-6/lavaan/man/fitMeasures.Rd | 7 lavaan-0.6-6/lavaan/man/growth.Rd | 27 - lavaan-0.6-6/lavaan/man/lavCor.Rd | 33 + lavaan-0.6-6/lavaan/man/lavOptions.Rd | 22 - lavaan-0.6-6/lavaan/man/lavTablesFit.Rd | 2 lavaan-0.6-6/lavaan/man/lavaan.Rd | 28 - lavaan-0.6-6/lavaan/man/parameterEstimates.Rd | 20 - lavaan-0.6-6/lavaan/man/sem.Rd | 27 - 95 files changed, 3401 insertions(+), 1507 deletions(-)
Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package 'pan', 'jomo' is a package for multilevel joint modelling multiple imputation (Carpenter and Kenward, 2013) <doi: 10.1002/9781119942283>.
Novel aspects of 'jomo' are the possibility of handling binary and categorical data through latent normal variables, the option to use cluster-specific covariance matrices and to impute compatibly with the substantive model.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <m.quartagno@ucl.ac.uk>
Diff between jomo versions 2.6-10 dated 2019-10-22 and 2.7-0 dated 2020-05-13
jomo-2.6-10/jomo/src/jomo1clmmC.c |only jomo-2.6-10/jomo/src/jomo1clmmhrC.c |only jomo-2.6-10/jomo/src/jomo1glmerbinC.c |only jomo-2.6-10/jomo/src/jomo1glmerbinhrC.c |only jomo-2.6-10/jomo/src/jomo1lmerC.c |only jomo-2.6-10/jomo/src/jomo1lmerhrC.c |only jomo-2.6-10/jomo/src/jomo2clmmC.c |only jomo-2.6-10/jomo/src/jomo2clmmhrC.c |only jomo-2.6-10/jomo/src/jomo2glmerbinC.c |only jomo-2.6-10/jomo/src/jomo2glmerbinhrC.c |only jomo-2.6-10/jomo/src/jomo2lmerC.c |only jomo-2.6-10/jomo/src/jomo2lmerhrC.c |only jomo-2.6-10/jomo/src/jomocoxC.c |only jomo-2.6-10/jomo/src/jomoglmbinC.c |only jomo-2.6-10/jomo/src/jomolmC.c |only jomo-2.6-10/jomo/src/jomooprobitC.c |only jomo-2.7-0/jomo/DESCRIPTION | 8 jomo-2.7-0/jomo/MD5 | 150 +++---- jomo-2.7-0/jomo/NAMESPACE | 3 jomo-2.7-0/jomo/R/jomo.clmm.MCMCchain.R | 131 ++++-- jomo-2.7-0/jomo/R/jomo.clmm.R | 137 ++++-- jomo-2.7-0/jomo/R/jomo.coxph.MCMCchain.R | 67 ++- jomo-2.7-0/jomo/R/jomo.coxph.R | 69 ++- jomo-2.7-0/jomo/R/jomo.glm.MCMCchain.R | 66 ++- jomo-2.7-0/jomo/R/jomo.glm.R | 70 ++- jomo-2.7-0/jomo/R/jomo.glmer.MCMCchain.R | 129 ++++-- jomo-2.7-0/jomo/R/jomo.glmer.R | 135 ++++-- jomo-2.7-0/jomo/R/jomo.lm.MCMCchain.R | 75 ++- jomo-2.7-0/jomo/R/jomo.lm.R | 141 ++++-- jomo-2.7-0/jomo/R/jomo.lmer.MCMCchain.R | 129 ++++-- jomo-2.7-0/jomo/R/jomo.lmer.R | 136 ++++-- jomo-2.7-0/jomo/R/jomo.polr.MCMCchain.R | 67 ++- jomo-2.7-0/jomo/R/jomo.polr.R | 71 ++- jomo-2.7-0/jomo/R/jomo1cat.MCMCchain.R | 29 + jomo-2.7-0/jomo/R/jomo1cat.R | 38 + jomo-2.7-0/jomo/R/jomo1con.MCMCchain.R | 30 + jomo-2.7-0/jomo/R/jomo1con.R | 32 + jomo-2.7-0/jomo/R/jomo1mix.MCMCchain.R | 29 + jomo-2.7-0/jomo/R/jomo1mix.R | 33 + jomo-2.7-0/jomo/R/jomo1rancat.MCMCchain.R | 29 + jomo-2.7-0/jomo/R/jomo1rancat.R | 32 + jomo-2.7-0/jomo/R/jomo1rancathr.MCMCchain.R | 30 + jomo-2.7-0/jomo/R/jomo1rancathr.R | 32 + jomo-2.7-0/jomo/R/jomo1rancon.MCMCchain.R | 30 + jomo-2.7-0/jomo/R/jomo1rancon.R | 31 + jomo-2.7-0/jomo/R/jomo1ranconhr.MCMCchain.R | 29 + jomo-2.7-0/jomo/R/jomo1ranconhr.R | 31 + jomo-2.7-0/jomo/R/jomo1ranmix.MCMCchain.R | 29 + jomo-2.7-0/jomo/R/jomo1ranmix.R | 32 + jomo-2.7-0/jomo/R/jomo1ranmixhr.MCMCchain.R | 29 + jomo-2.7-0/jomo/R/jomo1ranmixhr.R | 31 + jomo-2.7-0/jomo/R/jomo2com.MCMCchain.R | 60 ++ jomo-2.7-0/jomo/R/jomo2com.R | 60 ++ jomo-2.7-0/jomo/R/jomo2hr.MCMCchain.R | 58 ++ jomo-2.7-0/jomo/R/jomo2hr.R | 59 ++ jomo-2.7-0/jomo/R/md.pattern.mice.R |only jomo-2.7-0/jomo/inst/CITATION | 2 jomo-2.7-0/jomo/man/jomo.clmm.MCMCchain.Rd | 2 jomo-2.7-0/jomo/man/jomo.clmm.Rd | 2 jomo-2.7-0/jomo/man/jomo.coxph.MCMCchain.Rd | 2 jomo-2.7-0/jomo/man/jomo.coxph.Rd | 2 jomo-2.7-0/jomo/man/jomo.glm.MCMCchain.Rd | 2 jomo-2.7-0/jomo/man/jomo.glm.Rd | 2 jomo-2.7-0/jomo/man/jomo.glmer.MCMCchain.Rd | 2 jomo-2.7-0/jomo/man/jomo.glmer.Rd | 2 jomo-2.7-0/jomo/man/jomo.lm.MCMCchain.Rd | 2 jomo-2.7-0/jomo/man/jomo.lm.Rd | 2 jomo-2.7-0/jomo/man/jomo.lmer.MCMCchain.Rd | 2 jomo-2.7-0/jomo/man/jomo.lmer.Rd | 2 jomo-2.7-0/jomo/man/jomo.polr.MCMCchain.Rd | 2 jomo-2.7-0/jomo/man/jomo.polr.Rd | 2 jomo-2.7-0/jomo/man/jomo.smc.MCMCchain.Rd | 2 jomo-2.7-0/jomo/man/jomo.smc.Rd | 2 jomo-2.7-0/jomo/man/jomo1ranconhr.MCMCchain.Rd | 11 jomo-2.7-0/jomo/src/jomo1C.c | 176 ++++---- jomo-2.7-0/jomo/src/jomo1ranC.c | 164 ++++--- jomo-2.7-0/jomo/src/jomo1ranhrC.c | 385 ++++++++++-------- jomo-2.7-0/jomo/src/jomo1ranhrsmcC.c |only jomo-2.7-0/jomo/src/jomo1ransmcC.c |only jomo-2.7-0/jomo/src/jomo1smcC.c |only jomo-2.7-0/jomo/src/jomo2comC.c | 350 ++++++++++------ jomo-2.7-0/jomo/src/jomo2hrC.c | 523 +++++++++++++++---------- jomo-2.7-0/jomo/src/jomo2hrsmcC.c |only jomo-2.7-0/jomo/src/jomo2smcC.c |only jomo-2.7-0/jomo/src/jomo_init.c | 62 -- jomo-2.7-0/jomo/src/pdflib.c | 13 jomo-2.7-0/jomo/src/pdflib.h | 1 87 files changed, 2908 insertions(+), 1188 deletions(-)
Title: Interpreted String Literals
Description: An implementation of interpreted string literals, inspired by
Python's Literal String Interpolation <https://www.python.org/dev/peps/pep-0498/> and Docstrings
<https://www.python.org/dev/peps/pep-0257/> and Julia's Triple-Quoted String Literals
<https://docs.julialang.org/en/v1.3/manual/strings/#Triple-Quoted-String-Literals-1>.
Author: Jim Hester [aut, cre]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between glue versions 1.4.0 dated 2020-04-03 and 1.4.1 dated 2020-05-13
glue-1.4.0/glue/man/glue-vctrs.Rd |only glue-1.4.1/glue/DESCRIPTION | 10 +-- glue-1.4.1/glue/MD5 | 27 ++++---- glue-1.4.1/glue/NAMESPACE | 7 -- glue-1.4.1/glue/NEWS.md | 6 + glue-1.4.1/glue/R/sql.R | 32 +++++----- glue-1.4.1/glue/R/vctrs.R | 88 ++-------------------------- glue-1.4.1/glue/R/zzz.R | 10 +-- glue-1.4.1/glue/build/vignette.rds |binary glue-1.4.1/glue/inst/doc/transformers.R | 28 ++++---- glue-1.4.1/glue/inst/doc/transformers.html | 4 - glue-1.4.1/glue/src/glue.c | 2 glue-1.4.1/glue/src/trim.c | 2 glue-1.4.1/glue/tests/testthat/test-sql.R | 15 ++++ glue-1.4.1/glue/tests/testthat/test-vctrs.R | 8 +- 15 files changed, 94 insertions(+), 145 deletions(-)
Title: Shorten the Distance from Data Visualization Idea to Actual Plot
Description: Streamline the creation of common charts by taking care of a lot of
data preprocessing and plot customization for the user. Provides a
high-level interface to create plots using 'ggplot2'.
Author: Thomas Neitmann [aut, cre],
Julia Silge [ctb, cph],
David Robinson [ctb, cph]
Maintainer: Thomas Neitmann <th.neitmann@gmail.com>
Diff between ggcharts versions 0.1.0 dated 2020-03-26 and 0.2.0 dated 2020-05-13
ggcharts-0.1.0/ggcharts/R/diverging_bar_chart.R |only ggcharts-0.1.0/ggcharts/R/diverging_lollipop_chart.R |only ggcharts-0.1.0/ggcharts/R/theme_discrete_chart.R |only ggcharts-0.2.0/ggcharts/DESCRIPTION | 16 ggcharts-0.2.0/ggcharts/MD5 | 102 ggcharts-0.2.0/ggcharts/NAMESPACE | 16 ggcharts-0.2.0/ggcharts/NEWS.md |only ggcharts-0.2.0/ggcharts/R/bar_chart.R | 76 ggcharts-0.2.0/ggcharts/R/data.R | 28 ggcharts-0.2.0/ggcharts/R/diverging_chart.R |only ggcharts-0.2.0/ggcharts/R/dumbbell_chart.R | 72 ggcharts-0.2.0/ggcharts/R/ggcharts_global.R |only ggcharts-0.2.0/ggcharts/R/highlight.R |only ggcharts-0.2.0/ggcharts/R/lollipop_chart.R | 83 ggcharts-0.2.0/ggcharts/R/post_process_plot.R | 56 ggcharts-0.2.0/ggcharts/R/pre_process_data.R | 74 ggcharts-0.2.0/ggcharts/R/pyramid_chart.R | 22 ggcharts-0.2.0/ggcharts/R/reorder_within.R | 2 ggcharts-0.2.0/ggcharts/R/theme.R |only ggcharts-0.2.0/ggcharts/R/utils.R | 56 ggcharts-0.2.0/ggcharts/README.md | 15 ggcharts-0.2.0/ggcharts/build/vignette.rds |binary ggcharts-0.2.0/ggcharts/data/popch.rda |only ggcharts-0.2.0/ggcharts/data/popeurope.rda |only ggcharts-0.2.0/ggcharts/inst/WORDLIST | 8 ggcharts-0.2.0/ggcharts/inst/doc/customize.R |only ggcharts-0.2.0/ggcharts/inst/doc/customize.Rmd |only ggcharts-0.2.0/ggcharts/inst/doc/customize.html |only ggcharts-0.2.0/ggcharts/inst/doc/highlight.R | 39 ggcharts-0.2.0/ggcharts/inst/doc/highlight.Rmd | 57 ggcharts-0.2.0/ggcharts/inst/doc/highlight.html | 70 ggcharts-0.2.0/ggcharts/inst/doc/themes.R |only ggcharts-0.2.0/ggcharts/inst/doc/themes.Rmd |only ggcharts-0.2.0/ggcharts/inst/doc/themes.html |only ggcharts-0.2.0/ggcharts/man/bar_chart.Rd | 243 - ggcharts-0.2.0/ggcharts/man/biomedicalrevenue.Rd | 46 ggcharts-0.2.0/ggcharts/man/diverging_bar_chart.Rd | 148 - ggcharts-0.2.0/ggcharts/man/diverging_lollipop_chart.Rd | 160 - ggcharts-0.2.0/ggcharts/man/dumbbell_chart.Rd | 186 - ggcharts-0.2.0/ggcharts/man/figures/README-motivation-1.png |binary ggcharts-0.2.0/ggcharts/man/figures/README-motivation_continued-1.png |binary ggcharts-0.2.0/ggcharts/man/ggcharts_get_default_color.Rd |only ggcharts-0.2.0/ggcharts/man/ggcharts_get_theme.Rd |only ggcharts-0.2.0/ggcharts/man/highlight_spec.Rd |only ggcharts-0.2.0/ggcharts/man/lollipop_chart.Rd | 228 - ggcharts-0.2.0/ggcharts/man/popch.Rd |only ggcharts-0.2.0/ggcharts/man/popeurope.Rd |only ggcharts-0.2.0/ggcharts/man/pyramid_chart.Rd | 108 ggcharts-0.2.0/ggcharts/man/theme_ggcharts.Rd |only ggcharts-0.2.0/ggcharts/man/theme_hermit.Rd |only ggcharts-0.2.0/ggcharts/man/theme_ng.Rd |only ggcharts-0.2.0/ggcharts/man/theme_nightblue.Rd |only ggcharts-0.2.0/ggcharts/tests/figs/bar-chart/horizontal-non-sorted-bar-chart-with-facets.svg | 1160 ++++---- ggcharts-0.2.0/ggcharts/tests/figs/bar-chart/horizontal-non-sorted-bar-chart.svg | 56 ggcharts-0.2.0/ggcharts/tests/figs/bar-chart/horizontal-sorted-bar-chart-2-highlights-different-colors.svg |only ggcharts-0.2.0/ggcharts/tests/figs/bar-chart/horizontal-sorted-bar-chart-with-facets.svg | 1395 +++++----- ggcharts-0.2.0/ggcharts/tests/figs/bar-chart/horizontal-sorted-bar-chart-with-one-highlight.svg |only ggcharts-0.2.0/ggcharts/tests/figs/bar-chart/horizontal-sorted-bar-chart-with-two-highlights-in-the-same-color.svg |only ggcharts-0.2.0/ggcharts/tests/figs/bar-chart/horizontal-sorted-bar-chart.svg | 144 - ggcharts-0.2.0/ggcharts/tests/figs/bar-chart/vertical-non-sorted-bar-chart-with-facets.svg | 1159 ++++---- ggcharts-0.2.0/ggcharts/tests/figs/bar-chart/vertical-non-sorted-bar-chart.svg | 64 ggcharts-0.2.0/ggcharts/tests/figs/bar-chart/vertical-sorted-bar-chart.svg | 144 - ggcharts-0.2.0/ggcharts/tests/testthat/test-bar_chart.R | 41 ggcharts-0.2.0/ggcharts/tests/testthat/test-pre_process_data.R | 2 ggcharts-0.2.0/ggcharts/vignettes/customize.Rmd |only ggcharts-0.2.0/ggcharts/vignettes/highlight.Rmd | 57 ggcharts-0.2.0/ggcharts/vignettes/themes.Rmd |only 67 files changed, 3182 insertions(+), 2951 deletions(-)
Title: Improved Standard Evaluation Interfaces for Common Data
Manipulation Tasks
Description: The 'seplyr' (standard evaluation plying) package supplies improved
standard evaluation adapter methods for important common 'dplyr' data manipulation tasks.
In addition the 'seplyr' package supplies several new "key operations
bound together" methods. These include 'group_summarize()' (which
combines grouping, arranging and calculation in an atomic unit),
'add_group_summaries()' (which joins grouped summaries into a 'data.frame'
in a well documented manner), 'add_group_indices()' (which adds
per-group identifiers to a 'data.frame' without depending on row-order),
'partition_mutate_qt()' (which optimizes mutate sequences), and 'if_else_device()'
(which simulates per-row if-else blocks in expression sequences).
Author: John Mount [aut, cre],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between seplyr versions 0.8.6 dated 2020-04-30 and 0.8.7 dated 2020-05-13
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- NAMESPACE | 1 - NEWS.md | 4 ++++ R/package.R | 2 +- inst/doc/MutatePartitioner.html | 4 ++-- inst/doc/named_map_builder.html | 4 ++-- inst/doc/rename_se.html | 4 ++-- inst/doc/seplyr.html | 4 ++-- inst/doc/using_seplyr.html | 4 ++-- 10 files changed, 30 insertions(+), 27 deletions(-)
Title: Opinionated Approach for Digitizing Semi-Structured Qualitative
GIS Data
Description: Provides a set of functions for taking qualitative GIS data, hand drawn on a map, and
converting it to a simple features object. These tools are focused on data that are drawn on a map
that contains some type of polygon features. For each area identified on the map, the id numbers
of these polygons can be entered as vectors and transformed using qualmap.
Author: Christopher Prener [aut, cre] (<https://orcid.org/0000-0002-4310-9888>)
Maintainer: Christopher Prener <chris.prener@slu.edu>
Diff between qualmap versions 0.1.1 dated 2018-09-12 and 0.2.0 dated 2020-05-13
DESCRIPTION | 8 +- MD5 | 42 +++++++-------- NAMESPACE | 1 NEWS.md | 10 +++ R/qm_combine.R | 7 +- R/qm_create.R | 8 +- R/qm_is_cluster.R | 60 ++++++++++++++++++--- R/qm_summarize.R | 78 +++++++++++++++++----------- R/qm_verify.R |only R/qualmap-package.R | 2 README.md | 55 ++++++++++++++----- build/vignette.rds |binary inst/doc/qualmap.R | 4 - inst/doc/qualmap.html | 48 +++++++++++++---- man/qm_create.Rd | 4 - man/qm_is_cluster.Rd | 15 +++-- man/qm_summarize.Rd | 18 +++++- man/qm_verify.Rd |only man/qualmap.Rd | 3 - man/stLouis.Rd | 6 +- tests/testthat/test_4_qm_create.R | 22 +++---- tests/testthat/test_5_qm_combine.R | 29 +++------- tests/testthat/test_6_qm_summarize.R | 97 ++++++++++++++++++++++++----------- 23 files changed, 338 insertions(+), 179 deletions(-)
Title: Easily Carry Out Latent Profile Analysis (LPA) Using Open-Source
or Commercial Software
Description: An interface to the 'mclust' package to easily
carry out latent profile analysis ("LPA"). Provides functionality to
estimate commonly-specified models. Follows a tidy approach, in that
output is in the form of a data frame that can subsequently be
computed on. Also has functions to interface to the commercial 'MPlus'
software via the 'MplusAutomation' package.
Author: Joshua M Rosenberg [aut, cre],
Caspar van Lissa [aut],
Jennifer A Schmidt [ctb],
Patrick N Beymer [ctb],
Daniel Anderson [ctb],
Matthew J. Schell [ctb]
Maintainer: Joshua M Rosenberg <jmichaelrosenberg@gmail.com>
Diff between tidyLPA versions 1.0.6 dated 2020-03-19 and 1.0.7 dated 2020-05-13
DESCRIPTION | 8 - MD5 | 36 ++-- NEWS.md | 3 R/calc_functions.R | 20 ++ R/estimate-profiles-mplus.R | 23 +-- R/helpers.R | 2 build/vignette.rds |binary inst/doc/Introduction_to_tidyLPA.html | 74 ++++------ inst/doc/benchmarking-mclust-and-mplus.html | 12 - man/curry_mac.Rd | 4 man/empathy.Rd | 4 man/id_edu.Rd | 4 man/pisaUSA15.Rd | 6 man/print.tidyLPA.Rd | 3 tests/testthat.R | 2 tests/testthat/test-compare-fit-stats.R | 69 ++++----- tests/testthat/test-local-estimate-profiles-mplus.R | 6 tests/testthat/test-local-estimate_profiles_mplus2-arguments.R | 5 tests/testthat/test-local-plot-profiles-mplus.R | 12 - 19 files changed, 161 insertions(+), 132 deletions(-)
Title: Moment-Free Estimation of Sharpe Ratios
Description: An efficient moment-free estimator of the Sharpe ratio, or signal-to-noise ratio, for heavy-tailed data (see <arXiv:1505.01333>).
Author: Damien Challet
Maintainer: Damien Challet <damien.challet@gmail.com>
Diff between sharpeRratio versions 1.3 dated 2020-02-12 and 1.4 dated 2020-05-13
sharpeRratio-1.3/sharpeRratio/data |only sharpeRratio-1.3/sharpeRratio/man/a.Rd |only sharpeRratio-1.3/sharpeRratio/man/f.Rd |only sharpeRratio-1.4/sharpeRratio/DESCRIPTION | 10 - sharpeRratio-1.4/sharpeRratio/MD5 | 24 +-- sharpeRratio-1.4/sharpeRratio/NAMESPACE | 11 + sharpeRratio-1.4/sharpeRratio/NEWS | 10 + sharpeRratio-1.4/sharpeRratio/R/RcppExports.R | 31 ++++- sharpeRratio-1.4/sharpeRratio/R/estimateSNR.R | 109 +++++++++++++----- sharpeRratio-1.4/sharpeRratio/R/sysdata.rda |only sharpeRratio-1.4/sharpeRratio/man/computeR0bar.Rd |only sharpeRratio-1.4/sharpeRratio/man/estimateSNR.Rd | 53 +++----- sharpeRratio-1.4/sharpeRratio/man/num_records_down.Rd |only sharpeRratio-1.4/sharpeRratio/man/num_records_up.Rd |only sharpeRratio-1.4/sharpeRratio/src/RcppExports.cpp | 36 +++++ sharpeRratio-1.4/sharpeRratio/src/num_records.cpp | 52 +++++++- 16 files changed, 240 insertions(+), 96 deletions(-)
Title: Access Vegetation Databases and Treat Taxonomy
Description: Handling of vegetation data from different sources (
Turboveg <http://www.synbiosys.alterra.nl/turboveg/>;
the German national repository <http://www.vegetweb.de> and others.
Taxonomic harmonization (given appropriate taxonomic lists,
e.g. the German taxonomic standard list "GermanSL", <http://germansl.infinitenature.org>).
Author: Florian Jansen <florian.jansen@uni-rostock.de>
Maintainer: Florian Jansen <florian.jansen@uni-rostock.de>
Diff between vegdata versions 0.9.7 dated 2019-11-05 and 0.9.8 dated 2020-05-13
DESCRIPTION | 11 +- MD5 | 42 ++++----- R/internal.r | 46 +++++++--- R/tax.child.r | 105 ++++++++--------------- R/tax.names.r | 79 ++++++++++------- R/tax.r | 37 +++----- R/tax.reflist.r | 4 R/taxval.r | 222 +++++++++++++++++++++++++------------------------- R/tv.compRefl.r | 25 ++--- R/tv.coverperc.r | 8 - R/tv.veg.r | 10 +- R/zzz.r | 2 build/vignette.rds |binary data/taxlevels.csv.gz |binary inst/ChangeLog | 6 + inst/doc/vegdata.R | 62 +++++++------ inst/doc/vegdata.Rnw | 94 +++++++++++++-------- inst/doc/vegdata.pdf |binary man/tax.Rd | 31 ++++-- man/taxval.Rd | 3 man/tv.comprefl.Rd | 4 vignettes/vegdata.Rnw | 94 +++++++++++++-------- 22 files changed, 467 insertions(+), 418 deletions(-)
Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models
implemented in package 'mlt'. Available models include Cox models, some parametric
survival models (Weibull, etc.), models for ordered categorical variables,
normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression
(Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory
is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to
transformation models for clustered data is provided (Hothorn, 2019, <arxiv:1910.09219>).
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>),
Brian Ripley [ctb],
Bill Venables [ctb],
Douglas M. Bates [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between tram versions 0.3-2 dated 2020-01-12 and 0.4-0 dated 2020-05-13
DESCRIPTION | 12 - MD5 | 38 ++-- NAMESPACE | 11 - R/helpers.R |only R/internal.R | 5 R/methods.R | 456 ++++++++++++++++++++++++++++++++++++++++++++++++++++- R/models.R | 30 +++ R/tram.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 12 - inst/NEWS.Rd | 23 ++ inst/doc/mtram.pdf |binary inst/doc/tram.pdf |binary man/Aareg.Rd |only man/Colr.Rd | 4 man/Coxph.Rd | 6 man/Lehmann.Rd | 4 man/perm_test.Rd |only man/score_test.Rd |only man/tram.Rd | 2 tests/bugfixes.R | 17 + 22 files changed, 576 insertions(+), 46 deletions(-)
Title: Bayesian Estimation for Finite Mixture of Distributions
Description: Provides statistical tools for Bayesian estimation of finite mixture of distributions, mainly mixture of Gamma, Normal and t-distributions. The package is implemented the Bayesian literature for the finite mixture of distributions, including Mohammadi and et al. (2013) <doi:10.1007/s00180-012-0323-3> and Mohammadi and Salehi-Rad (2012) <doi:10.1080/03610918.2011.588358>.
Author: Reza Mohammadi [aut, cre, cph]
(<https://orcid.org/0000-0001-9538-0648>)
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between bmixture versions 1.4 dated 2019-09-11 and 1.5 dated 2020-05-13
DESCRIPTION | 22 +++++++++++++++------- MD5 | 6 +++--- NEWS | 8 +++++--- man/bmixture-package.Rd | 2 +- 4 files changed, 24 insertions(+), 14 deletions(-)
Title: National Statistical Office of Mongolia's Open Data API Handler
Description: National Statistical Office of Mongolia (NSO) is the national statistical service and an organization of Mongolian government. NSO provides open access and official data via its web site <http://www.1212.mn/> and API <http://opendata.1212.mn/en/doc>. The package NSO1212 has functions for accessing the API service. The functions are compatible with the API v2.0 and get data sets and its detailed informations from the API.
Author: Makhgal Ganbold [aut, cre]
Maintainer: Makhgal Ganbold <makhgal@seas.num.edu.mn>
Diff between NSO1212 versions 1.0.0 dated 2019-02-05 and 1.1.0 dated 2020-05-13
NSO1212-1.0.0/NSO1212/NEWS.md |only NSO1212-1.1.0/NSO1212/DESCRIPTION | 10 +- NSO1212-1.1.0/NSO1212/MD5 | 30 +++--- NSO1212-1.1.0/NSO1212/NEWS |only NSO1212-1.1.0/NSO1212/R/NSO1212-package.r | 4 NSO1212-1.1.0/NSO1212/R/all_tables.R | 26 +++-- NSO1212-1.1.0/NSO1212/R/get_sector_info.R | 34 ++++--- NSO1212-1.1.0/NSO1212/R/get_subsector_info.R | 33 ++++--- NSO1212-1.1.0/NSO1212/R/get_table.R | 110 +++++++++++++----------- NSO1212-1.1.0/NSO1212/R/get_table_info.R | 99 ++++++++++++++++++--- NSO1212-1.1.0/NSO1212/README.md | 6 + NSO1212-1.1.0/NSO1212/man/NSO1212.Rd | 5 - NSO1212-1.1.0/NSO1212/man/all_tables.Rd | 22 +++- NSO1212-1.1.0/NSO1212/man/get_sector_info.Rd | 20 +++- NSO1212-1.1.0/NSO1212/man/get_subsector_info.Rd | 19 ++-- NSO1212-1.1.0/NSO1212/man/get_table.Rd | 36 +++++-- NSO1212-1.1.0/NSO1212/man/get_table_info.Rd | 34 +++++-- 17 files changed, 334 insertions(+), 154 deletions(-)
Title: Collection of Methods to Detect Dichotomous Differential Item
Functioning (DIF)
Description: Provides a collection of standard methods to detect differential item functioning among dichotomously scored items. Methods for uniform and non-uniform DIF, based on test-score or IRT methods, for comparing two or more than two groups of respondents, are available (Magis, Beland, Tuerlinckx and De Boeck,A General Framework and an R Package for the Detection of Dichotomous Differential Item Functioning, Behavior Research Methods, 42, 2010, 847-862 <doi:10.3758/BRM.42.3.847>).
Author: David Magis (U Liege), Sebastien Beland (U Montreal) and Gilles Raiche (UQAM)
Maintainer: David Magis <david.magis@gmail.com>
Diff between difR versions 5.0 dated 2018-05-14 and 5.1 dated 2020-05-13
difR-5.0/difR/data/verbal.txt.gz |only difR-5.0/difR/inst/doc |only difR-5.1/difR/DESCRIPTION | 12 ++++++------ difR-5.1/difR/MD5 | 15 +++++++-------- difR-5.1/difR/NEWS | 10 ++++++++++ difR-5.1/difR/R/LRT.R | 4 ++-- difR-5.1/difR/R/itemPar1PL.r | 3 +-- difR-5.1/difR/build/partial.rdb |binary difR-5.1/difR/data/verbal.txt |only difR-5.1/difR/man/difR-package.Rd | 4 ++-- 10 files changed, 28 insertions(+), 20 deletions(-)
Title: Board Game Graphics
Description: Functions to make board game graphics. By default makes game diagrams, animations, and "Print & Play" layouts for the 'piecepack' <http://www.ludism.org/ppwiki> but can be configured to make graphics for other board game systems.
Author: Trevor L Davis [aut, cre]
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between piecepackr versions 1.2.1 dated 2020-01-09 and 1.3.1 dated 2020-05-13
piecepackr-1.2.1/piecepackr/R/3d_helpers.R |only piecepackr-1.2.1/piecepackr/R/SAT.R |only piecepackr-1.2.1/piecepackr/R/component_opt.R |only piecepackr-1.2.1/piecepackr/R/pnp_functions.R |only piecepackr-1.2.1/piecepackr/R/shadowGrobs.R |only piecepackr-1.2.1/piecepackr/tests/figs/no-regressions-in-figures/icehouse-pieces.svg |only piecepackr-1.2.1/piecepackr/tests/testthat/test-3d_helpers.R |only piecepackr-1.3.1/piecepackr/DESCRIPTION | 17 piecepackr-1.3.1/piecepackr/MD5 | 145 ++- piecepackr-1.3.1/piecepackr/NAMESPACE | 9 piecepackr-1.3.1/piecepackr/NEWS.md | 80 ++ piecepackr-1.3.1/piecepackr/R/basicPieceGrobs.R | 6 piecepackr-1.3.1/piecepackr/R/boards.R |only piecepackr-1.3.1/piecepackr/R/game_systems.R | 278 +++++-- piecepackr-1.3.1/piecepackr/R/geometry.R |only piecepackr-1.3.1/piecepackr/R/grid_fns.R | 60 - piecepackr-1.3.1/piecepackr/R/grob_fn_helpers.R | 62 - piecepackr-1.3.1/piecepackr/R/make_images.R | 31 piecepackr-1.3.1/piecepackr/R/op_grobs_fns.R |only piecepackr-1.3.1/piecepackr/R/op_transform.R |only piecepackr-1.3.1/piecepackr/R/pieceGrob.R | 162 +--- piecepackr-1.3.1/piecepackr/R/piece_opt.R |only piecepackr-1.3.1/piecepackr/R/pips.R |only piecepackr-1.3.1/piecepackr/R/pmap_piece.R |only piecepackr-1.3.1/piecepackr/R/pnp.R |only piecepackr-1.3.1/piecepackr/R/pp_cfg.R | 379 ++++++---- piecepackr-1.3.1/piecepackr/R/rayrender.R |only piecepackr-1.3.1/piecepackr/R/rgl.R |only piecepackr-1.3.1/piecepackr/R/shape_xy.R |only piecepackr-1.3.1/piecepackr/R/write_obj.R |only piecepackr-1.3.1/piecepackr/README.md | 196 ++++- piecepackr-1.3.1/piecepackr/man/basicPieceGrobs.Rd | 8 piecepackr-1.3.1/piecepackr/man/figures/README-breakthrough-1.png |only piecepackr-1.3.1/piecepackr/man/figures/README-dominoes-1.png |only piecepackr-1.3.1/piecepackr/man/game_systems.Rd | 91 ++ piecepackr-1.3.1/piecepackr/man/grid.piece.Rd | 96 +- piecepackr-1.3.1/piecepackr/man/grid_shape_grobs.Rd | 6 piecepackr-1.3.1/piecepackr/man/op_transform.Rd | 15 piecepackr-1.3.1/piecepackr/man/piece.Rd |only piecepackr-1.3.1/piecepackr/man/piece3d.Rd |only piecepackr-1.3.1/piecepackr/man/pmap_piece.Rd |only piecepackr-1.3.1/piecepackr/man/pp_cfg.Rd | 50 + piecepackr-1.3.1/piecepackr/man/save_piece_obj.Rd |only piecepackr-1.3.1/piecepackr/man/save_print_and_play.Rd | 2 piecepackr-1.3.1/piecepackr/tests/figs/3d-helper-function/matchsticks-045.svg | 168 +++- piecepackr-1.3.1/piecepackr/tests/figs/3d-helper-function/oblique-pyramids.svg |only piecepackr-1.3.1/piecepackr/tests/figs/3d-helper-function/op-transform-045.svg | 54 - piecepackr-1.3.1/piecepackr/tests/figs/3d-helper-function/op-transform-135.svg | 54 - piecepackr-1.3.1/piecepackr/tests/figs/3d-helper-function/op-transform-225.svg | 54 - piecepackr-1.3.1/piecepackr/tests/figs/3d-helper-function/op-transform-315.svg | 54 - piecepackr-1.3.1/piecepackr/tests/figs/3d-helper-function/pyramid-tops-larger-on-top.svg |only piecepackr-1.3.1/piecepackr/tests/figs/3d-helper-function/pyramid-tops-smaller-on-top.svg |only piecepackr-1.3.1/piecepackr/tests/figs/3d-helper-function/rotated-tile-faces.svg |only piecepackr-1.3.1/piecepackr/tests/figs/3d-helper-function/simple-points.svg |only piecepackr-1.3.1/piecepackr/tests/figs/3d-helper-function/simple-square.svg |only piecepackr-1.3.1/piecepackr/tests/figs/alpha-and-scale-works |only piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/checkers.svg |only piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/coin-face-r4oval.svg |only piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/coin-face-r4pyramid.svg | 4 piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/dice-d6.svg |only piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/die-face-s2-r5-kite.svg | 4 piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/die-layoutrf-opposites-sum-to-5.svg | 12 piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/dominoes.svg |only piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/king-of-stars.svg |only piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/pawn-back-s2.svg | 4 piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/pawn-face-irregular-convex.svg | 31 piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/pawn-face-s3.svg | 4 piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/preview-5s.svg | 18 piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/preview-6s.svg | 20 piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/preview.svg | 18 piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/pyramid-back-s4-r1.svg | 4 piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/pyramid-face-op.svg |only piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/pyramid-face-s1-r6.svg | 4 piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/pyramid-face-s2-r1.svg | 4 piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/pyramid-layout-s3-r4.svg | 20 piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/pyramid-left-s2-r5.svg | 4 piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/pyramid-right-s3-r2.svg | 4 piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/pyramid-top-s4-r3.svg | 32 piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/rankdie-layoutrf-suitasace.svg | 6 piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/red-joker.svg |only piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/suitrankdie-layoutrf-5suits.svg | 12 piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/suitrankdie-layoutrf-6suits.svg | 12 piecepackr-1.3.1/piecepackr/tests/figs/no-regressions-in-figures/ten-of-clubs.svg |only piecepackr-1.3.1/piecepackr/tests/figs/oblique-projection-works/diagram-op.svg | 51 - piecepackr-1.3.1/piecepackr/tests/figs/oblique-projection-works/die-face-op.svg | 6 piecepackr-1.3.1/piecepackr/tests/figs/oblique-projection-works/matchstick-face-op.svg | 6 piecepackr-1.3.1/piecepackr/tests/figs/oblique-projection-works/pawn-face-op.svg | 54 - piecepackr-1.3.1/piecepackr/tests/figs/oblique-projection-works/pyramid-face-op.svg | 20 piecepackr-1.3.1/piecepackr/tests/figs/oblique-projection-works/pyramid-top-op.svg |only piecepackr-1.3.1/piecepackr/tests/figs/oblique-projection-works/tile-face-op.svg | 6 piecepackr-1.3.1/piecepackr/tests/figs/save-piece-images-works-as-expected/diagram-op-ppgf.svg | 100 +- piecepackr-1.3.1/piecepackr/tests/testthat/test-draw_component.R | 60 + piecepackr-1.3.1/piecepackr/tests/testthat/test-game_systems.R |only piecepackr-1.3.1/piecepackr/tests/testthat/test-obj.R |only piecepackr-1.3.1/piecepackr/tests/testthat/test-op_transform.R |only 95 files changed, 1580 insertions(+), 1017 deletions(-)
Title: Adaptive Sum of Powered Score Test
Description: R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU')
tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests
and gene-based and some pathway based association tests (Pathway based Sum of
Powered Score tests ('SPUpath'), adaptive 'SPUpath' ('aSPUpath') test, 'GEEaSPU'
test for multiple traits - single 'SNP' (single nucleotide polymorphism)
association in generalized estimation equations, 'MTaSPUs' test for multiple
traits - single 'SNP' association with Genome Wide Association Studies ('GWAS')
summary statistics, Gene-based Association Test that uses an extended 'Simes'
procedure ('GATES'), Hybrid Set-based Test ('HYST') and extended version
of 'GATES' test for pathway-based association testing ('GATES-Simes'). ).
The tests can be used with genetic and other data sets with covariates. The
response variable is binary or quantitative. Summary; (1) Single trait-'SNP' set
association with individual-level data ('aSPU', 'aSPUw', 'aSPUr'), (2) Single trait-'SNP'
set association with summary statistics ('aSPUs'), (3) Single trait-pathway
association with individual-level data ('aSPUpath'), (4) Single trait-pathway
association with summary statistics ('aSPUsPath'), (5) Multiple traits-single
'SNP' association with individual-level data ('GEEaSPU'), (6) Multiple traits-
single 'SNP' association with summary statistics ('MTaSPUs'), (7) Multiple traits-'SNP' set association with summary statistics('MTaSPUsSet'), (8) Multiple traits-pathway association with summary statistics('MTaSPUsSetPath').
Author: Il-Youp Kwak and others (See Author(s) in each function manual)
Maintainer: Il-Youp Kwak <ikwak2@cau.ac.kr>
Diff between aSPU versions 1.48 dated 2017-06-24 and 1.49 dated 2020-05-13
DESCRIPTION | 14 MD5 | 94 ++--- NAMESPACE | 37 +- R/GATES2.R | 2 R/GEEaSPU.R | 1 R/GatesSimes.R | 2 R/Hyst.R | 2 R/MTaSPUs.R | 2 R/MTaSPUsSet.R | 2 R/MTaSPUsSetPath.R | 2 R/MTaSPUsSetScore.R | 2 R/aSPU.R | 13 R/aSPUd.R | 2 R/aSPUpath.r | 4 R/aSPUpath2.r | 4 R/aSPUr.R | 2 R/aSPUs.R | 2 R/aSPUsD.R | 4 R/aSPUsPath.r | 2 R/aSPUsPath2.r | 2 R/aSPUw.R | 2 R/estcov.R | 2 R/getlogitp.R | 2 R/minP.R | 2 R/plotPmat.r | 2 R/pruningSNP.R | 2 R/simPathAR1SNP.R | 4 README.md | 16 build/vignette.rds |binary inst/doc/MTaSPUsSet.R | 30 - inst/doc/MTaSPUsSet.html | 705 ++++++++++++++++++++------------------- inst/doc/aSPUstat.R | 20 - inst/doc/aSPUstat.html | 845 ++++++++++++++++++++++++----------------------- man/GEEaSPU.Rd | 11 man/MTaSPUsSet.Rd | 13 man/MTaSPUsSetPath.Rd | 16 man/MTaSPUsSetScore.Rd | 12 man/SAMD11.Rd | 3 man/aSPU.Rd | 14 man/aSPUpath.Rd | 16 man/aSPUpath2.Rd | 16 man/aSPUs.Rd | 3 man/aSPUsPath.Rd | 13 man/aSPUsPath2.Rd | 13 man/aSPUw.Rd | 11 man/plotPmat.Rd | 11 man/simPathAR1Snp.Rd | 19 - man/someGs.Rd | 3 48 files changed, 1106 insertions(+), 895 deletions(-)
Title: Converts Between R Objects and Simple Feature Objects
Description: Converts between R and Simple Feature 'sf' objects, without depending
on the Simple Feature library. Conversion functions are available at both the R level,
and through 'Rcpp'.
Author: David Cooley [aut, cre],
Michael Sumner [ctb]
Maintainer: David Cooley <david.cooley.au@gmail.com>
Diff between sfheaders versions 0.2.1 dated 2020-03-19 and 0.2.2 dated 2020-05-13
DESCRIPTION | 16 MD5 | 212 ++--- NAMESPACE | 10 NEWS.md | 14 R/RcppExports.R | 160 ++-- R/df.R | 28 R/scratch.R |only R/sf.R | 211 ++++- R/sf_helpers.R |only R/sfc.R | 59 + R/sfg.R | 12 R/utils.R | 21 README.md | 7 inst/include/sfheaders/cast/sfc.hpp | 19 inst/include/sfheaders/cast/sfg.hpp | 198 ++-- inst/include/sfheaders/df/sf.hpp | 85 +- inst/include/sfheaders/df/sfc.hpp | 79 + inst/include/sfheaders/df/sfg.hpp | 2 inst/include/sfheaders/df/utils.hpp | 8 inst/include/sfheaders/sf/linestring/sf_linestring.hpp | 108 +- inst/include/sfheaders/sf/multilinestring/sf_multilinestring.hpp | 122 ++- inst/include/sfheaders/sf/multipoint/sf_multipoint.hpp | 106 +- inst/include/sfheaders/sf/multipolygon/sf_multipolygon.hpp | 141 ++- inst/include/sfheaders/sf/point/sf_point.hpp | 90 +- inst/include/sfheaders/sf/polygon/sf_polygon.hpp | 101 +- inst/include/sfheaders/sf/sf.hpp | 182 ++++ inst/include/sfheaders/sf/sf_utils.hpp | 59 + inst/include/sfheaders/sfc/linestring/sfc_linestring.hpp | 247 +++--- inst/include/sfheaders/sfc/linestring/sfc_linestrings.hpp | 4 inst/include/sfheaders/sfc/m_range.hpp | 141 ++- inst/include/sfheaders/sfc/multilinestring/sfc_multilinestring.hpp | 249 +++--- inst/include/sfheaders/sfc/multilinestring/sfc_multilinestrings.hpp | 4 inst/include/sfheaders/sfc/multipoint/sfc_multipoint.hpp | 246 +++--- inst/include/sfheaders/sfc/multipoint/sfc_multipoints.hpp | 4 inst/include/sfheaders/sfc/multipolygon/sfc_multipolygon.hpp | 201 ++--- inst/include/sfheaders/sfc/multipolygon/sfc_multipolygons.hpp | 4 inst/include/sfheaders/sfc/point/sfc_point.hpp | 113 +- inst/include/sfheaders/sfc/point/sfc_points.hpp | 4 inst/include/sfheaders/sfc/polygon/sfc_polygon.hpp | 184 ++-- inst/include/sfheaders/sfc/polygon/sfc_polygons.hpp | 4 inst/include/sfheaders/sfc/sfc.hpp | 28 inst/include/sfheaders/sfc/sfc_attributes.hpp | 58 + inst/include/sfheaders/sfc/sfc_types.hpp | 11 inst/include/sfheaders/sfc/zm_range.hpp | 220 +++-- inst/include/sfheaders/sfg/linestring/sfg_linestring.hpp | 95 +- inst/include/sfheaders/sfg/linestring/sfg_linestrings.hpp | 4 inst/include/sfheaders/sfg/multilinestring/sfg_multilinestring.hpp | 177 ++-- inst/include/sfheaders/sfg/multilinestring/sfg_multilinestrings.hpp | 4 inst/include/sfheaders/sfg/multipoint/sfg_multipoint.hpp | 99 +- inst/include/sfheaders/sfg/multipoint/sfg_multipoints.hpp | 4 inst/include/sfheaders/sfg/multipolygon/sfg_multipolygon.hpp | 152 ++- inst/include/sfheaders/sfg/multipolygon/sfg_multipolygons.hpp | 4 inst/include/sfheaders/sfg/point/sfg_point.hpp | 103 +- inst/include/sfheaders/sfg/point/sfg_points.hpp | 8 inst/include/sfheaders/sfg/polygon/sfg_polygon.hpp | 141 ++- inst/include/sfheaders/sfg/polygon/sfg_polygons.hpp | 4 inst/include/sfheaders/sfg/sfg.hpp | 28 inst/include/sfheaders/sfg/sfg_dimension.hpp | 56 - inst/include/sfheaders/sfg/sfg_types.hpp | 30 inst/include/sfheaders/utils/lists |only inst/include/sfheaders/utils/sexp/sexp.hpp | 8 inst/include/sfheaders/utils/utils.hpp | 21 inst/include/sfheaders/utils/vectors/vectors.hpp | 63 + man/sf_boxes.Rd |only man/sf_line.Rd |only man/sf_linestring.Rd | 21 man/sf_mline.Rd |only man/sf_mpoly.Rd |only man/sf_mpt.Rd |only man/sf_multilinestring.Rd | 11 man/sf_multipoint.Rd | 11 man/sf_multipolygon.Rd | 11 man/sf_point.Rd | 6 man/sf_poly.Rd |only man/sf_polygon.Rd | 46 + man/sf_pt.Rd |only man/sf_remove_holes.Rd | 2 man/sf_to_df.Rd | 24 src/RcppExports.cpp | 398 ++++++---- src/bbox.cpp | 10 src/cast.cpp | 163 ---- src/lists.cpp |only src/sfg_dimension.cpp | 5 src/to_df.cpp | 30 src/to_sf.cpp | 70 + src/to_sfc.cpp | 82 +- src/to_sfg.cpp | 54 - tests/testthat/test-bbox.R | 204 +++++ tests/testthat/test-df.R | 119 ++ tests/testthat/test-error_handling.R | 98 +- tests/testthat/test-lists.R |only tests/testthat/test-sf.R | 57 - tests/testthat/test-sf_boxes.R |only tests/testthat/test-sf_creator-helpers.R |only tests/testthat/test-sf_linestring.R | 51 - tests/testthat/test-sf_multilinestring.R | 50 - tests/testthat/test-sf_multipoint.R | 42 - tests/testthat/test-sf_multipolygon.R | 38 tests/testthat/test-sf_point.R | 24 tests/testthat/test-sf_polygon.R | 48 - tests/testthat/test-sfc_attributes.R | 8 tests/testthat/test-sfc_linestring.R | 61 - tests/testthat/test-sfc_multilinestring.R | 88 +- tests/testthat/test-sfc_multipoint.R | 61 - tests/testthat/test-sfc_multipolygon.R | 40 - tests/testthat/test-sfc_point.R | 36 tests/testthat/test-sfc_polygon.R | 86 +- tests/testthat/test-sfg_dimension.R | 253 ++++++ tests/testthat/test-sfg_linestring.R | 44 - tests/testthat/test-sfg_multilinestring.R | 48 - tests/testthat/test-sfg_multipoint.R | 38 tests/testthat/test-sfg_multipolygon.R | 40 - tests/testthat/test-sfg_point.R | 38 tests/testthat/test-sfg_polygon.R | 56 - 114 files changed, 4689 insertions(+), 2656 deletions(-)
Title: Assign Treatments, Power Calculations, Balances, Impact
Evaluation of Experiments
Description: Assists in the whole process of designing and evaluating Randomized Control Trials.
Robust treatment assignment by strata/blocks, that handles misfits;
Power calculations of the minimum detectable treatment effect
Balance tables of T-test of covariates;
Balance Regression: (treatment ~ all x variables) with F-test of null model;
Impact_evaluation: Impact evaluation regressions. This function
gives you the option to include control_vars, fixed effect variables,
cluster variables (for robust SE), multiple endogenous variables and
multiple heterogeneous variables (to test treatment effect heterogeneity)
summary_statistics: Function that creates a summary statistics table with statistics
rank observations in n groups: Creates a factor variable with n groups. Each group has
a min and max label attach to each category.
Athey, Susan, and Guido W. Imbens (2017) <arXiv:1607.00698>.
Author: Isidoro Garcia-Urquieta [aut, cre]
Maintainer: Isidoro Garcia-Urquieta <isidoro.gu@gmail.com>
Diff between RCT versions 1.0.0 dated 2020-04-03 and 1.0.2 dated 2020-05-13
DESCRIPTION | 11 ++++---- MD5 | 17 +++++++------ NEWS.md |only R/balance_regression.R | 47 ++++++++++++++++++++++++++++++-------- R/treatment_assign.R | 4 +-- build/vignette.rds |binary man/balance_regression.Rd | 8 ++++-- man/ntile_label.Rd | 2 - man/treatment_assign.Rd | 4 +-- tests/testthat/test_ntile_label.R | 8 ++---- 10 files changed, 66 insertions(+), 35 deletions(-)
Title: The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Dataset
Description: Provides a daily summary of the Coronavirus (COVID-19) cases by state/province. Data source: Johns Hopkins University Center for Systems Science and Engineering (JHU CCSE) Coronavirus <https://systems.jhu.edu/research/public-health/ncov/>.
Author: Rami Krispin [aut, cre]
Maintainer: Rami Krispin <rami.krispin@gmail.com>
Diff between coronavirus versions 0.1.0 dated 2020-02-23 and 0.2.0 dated 2020-05-13
DESCRIPTION | 12 + MD5 | 26 ++- NAMESPACE | 1 NEWS.md | 16 ++ R/data.R | 49 ++++--- R/data_refresh.R |only README.md | 272 +++++++++++++++++++++++++++++++-------- build |only data/coronavirus.rda |binary inst |only man/coronavirus.Rd | 49 ++++--- man/figures/coronavirus.png |only man/figures/total_cases.png |only man/figures/treemap_conf.png |only man/update_dataset.Rd |only tests/testthat/test-data_valid.R | 2 vignettes |only 17 files changed, 328 insertions(+), 99 deletions(-)
Title: Separate a Data Frame by Normalization
Description: Separate a data frame in two based on key columns. The function
unjoin() provides an inside-out version of a nested data frame. This is used
to identify duplication and normalize it (in the database sense) by linking
two tables with the redundancy removed. This is a basic requirement for
detecting topology within spatial structures that has motivated the need for
this package as a building block for workflows within more applied projects.
Author: Michael D. Sumner [aut, cre],
Simon Wotherspoon [ctb],
Hadley Wickham [ctb] (named the concept, provided excellent guidance
via tidyr source code)
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between unjoin versions 0.0.4 dated 2020-03-21 and 0.1.0 dated 2020-05-13
unjoin-0.0.4/unjoin/R/new_unjoin.R |only unjoin-0.1.0/unjoin/DESCRIPTION | 8 unjoin-0.1.0/unjoin/MD5 | 13 - unjoin-0.1.0/unjoin/NAMESPACE | 3 unjoin-0.1.0/unjoin/NEWS.md | 6 unjoin-0.1.0/unjoin/R/unjoin.R | 200 ++++++------------------ unjoin-0.1.0/unjoin/man/unjoin.Rd | 13 - unjoin-0.1.0/unjoin/tests/testthat/test-basic.R | 11 - 8 files changed, 72 insertions(+), 182 deletions(-)
Title: Infers Novel Immunoglobulin Alleles from Sequencing Data
Description: Infers the V genotype of an individual from immunoglobulin (Ig)
repertoire sequencing data (AIRR-Seq, Rep-Seq). Includes detection of
any novel alleles. This information is then used to correct existing V
allele calls from among the sample sequences.
Citations:
Gadala-Maria, et al (2015) <doi:10.1073/pnas.1417683112>.
Gadala-Maria, et al (2019) <doi:10.3389/fimmu.2019.00129>.
Author: Daniel Gadala-Maria [aut],
Susanna Marquez [aut],
Moriah Cohen [aut],
Jason Vander Heiden [aut, cre],
Gur Yaari [aut],
Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@gmail.com>
Diff between tigger versions 0.4.0 dated 2019-07-19 and 1.0.0 dated 2020-05-13
tigger-0.4.0/tigger/data/airrDb.rda |only tigger-0.4.0/tigger/man/airrDb.Rd |only tigger-1.0.0/tigger/DESCRIPTION | 31 tigger-1.0.0/tigger/MD5 | 86 +- tigger-1.0.0/tigger/NAMESPACE | 1 tigger-1.0.0/tigger/NEWS.md | 28 tigger-1.0.0/tigger/R/bayesian.R | 78 +- tigger-1.0.0/tigger/R/data.R | 8 tigger-1.0.0/tigger/R/evidence.R | 177 ++-- tigger-1.0.0/tigger/R/functions.R | 767 +++++++++++---------- tigger-1.0.0/tigger/R/tigger.R | 15 tigger-1.0.0/tigger/build/vignette.rds |binary tigger-1.0.0/tigger/data/AIRRDb.rda |only tigger-1.0.0/tigger/data/SampleGenotype.rda |binary tigger-1.0.0/tigger/data/SampleNovel.rda |binary tigger-1.0.0/tigger/data/datalist | 2 tigger-1.0.0/tigger/inst/doc/Tigger-Vignette.R | 49 - tigger-1.0.0/tigger/inst/doc/Tigger-Vignette.Rmd | 63 - tigger-1.0.0/tigger/inst/doc/Tigger-Vignette.pdf |binary tigger-1.0.0/tigger/man/AIRRDb.Rd |only tigger-1.0.0/tigger/man/GermlineIGHV.Rd | 6 tigger-1.0.0/tigger/man/SampleDb.Rd | 8 tigger-1.0.0/tigger/man/SampleGenotype.Rd | 6 tigger-1.0.0/tigger/man/SampleGermlineIGHV.Rd | 8 tigger-1.0.0/tigger/man/SampleNovel.Rd | 6 tigger-1.0.0/tigger/man/cleanSeqs.Rd | 2 tigger-1.0.0/tigger/man/findNovelAlleles.Rd | 158 ++-- tigger-1.0.0/tigger/man/findUnmutatedCalls.Rd | 8 tigger-1.0.0/tigger/man/generateEvidence.Rd | 96 +- tigger-1.0.0/tigger/man/genotypeFasta.Rd | 4 tigger-1.0.0/tigger/man/getMutCount.Rd | 6 tigger-1.0.0/tigger/man/getMutatedPositions.Rd | 14 tigger-1.0.0/tigger/man/getPopularMutationCount.Rd | 31 tigger-1.0.0/tigger/man/inferGenotype.Rd | 39 - tigger-1.0.0/tigger/man/inferGenotypeBayesian.Rd | 42 - tigger-1.0.0/tigger/man/plotGenotype.Rd | 22 tigger-1.0.0/tigger/man/plotNovel.Rd | 68 + tigger-1.0.0/tigger/man/readIgFasta.Rd | 6 tigger-1.0.0/tigger/man/reassignAlleles.Rd | 29 tigger-1.0.0/tigger/man/selectNovel.Rd | 4 tigger-1.0.0/tigger/man/sortAlleles.Rd | 4 tigger-1.0.0/tigger/man/subsampleDb.Rd | 22 tigger-1.0.0/tigger/man/tigger.Rd | 1 tigger-1.0.0/tigger/man/updateAlleleNames.Rd | 4 tigger-1.0.0/tigger/man/writeFasta.Rd | 8 tigger-1.0.0/tigger/vignettes/Tigger-Vignette.Rmd | 63 - 46 files changed, 1093 insertions(+), 877 deletions(-)
Title: Robust Bootstrap Forecast Densities for GARCH Models
Description: Bootstrap forecast densities for GARCH (Generalized Autoregressive Conditional Heteroskedastic) returns and volatilities using the robust residual-based bootstrap procedure of Trucios, Hotta and Ruiz (2017) <DOI:10.1080/00949655.2017.1359601>.
Author: Carlos Trucios
Maintainer: Carlos Trucios <ctrucios@gmail.com>
Diff between RobGARCHBoot versions 1.0.0 dated 2019-11-04 and 1.0.1 dated 2020-05-13
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ README.md | 16 ++++++++++++++-- man/ROBUSTGARCHloss_RCPP.Rd | 4 ++-- man/RobGARCHBoot-package.Rd | 6 +++--- man/RobGARCHBoot.Rd | 2 +- src/ROBUSTGARCH.cpp | 2 +- 7 files changed, 31 insertions(+), 19 deletions(-)
Title: Read and Write Files to SQLite Databases
Description: Reads and writes files to SQLite databases <https://www.sqlite.org/index.html> as flobs
(a flob is a blob that preserves the file extension).
Author: Sebastian Dalgarno [aut, cre] (<https://orcid.org/0000-0002-3658-4517>),
Joe Thorley [aut] (<https://orcid.org/0000-0002-7683-4592>),
Poisson Consulting [cph, fnd]
Maintainer: Sebastian Dalgarno <seb@poissonconsulting.ca>
Diff between dbflobr versions 0.0.1 dated 2019-08-24 and 0.1.0 dated 2020-05-13
dbflobr-0.0.1/dbflobr/tests/testthat/test-zzz-package.R |only dbflobr-0.1.0/dbflobr/DESCRIPTION | 13 +- dbflobr-0.1.0/dbflobr/MD5 | 59 +++++++---- dbflobr-0.1.0/dbflobr/NAMESPACE | 6 - dbflobr-0.1.0/dbflobr/NEWS.md | 5 dbflobr-0.1.0/dbflobr/R/check.R | 77 +++++++++------ dbflobr-0.1.0/dbflobr/R/chk.R |only dbflobr-0.1.0/dbflobr/R/db.R | 61 +++++++++-- dbflobr-0.1.0/dbflobr/R/dbflob.R | 62 +++++++++--- dbflobr-0.1.0/dbflobr/R/import.R |only dbflobr-0.1.0/dbflobr/R/internal.R | 11 +- dbflobr-0.1.0/dbflobr/R/namespace.R | 2 dbflobr-0.1.0/dbflobr/R/save.R |only dbflobr-0.1.0/dbflobr/R/ui.R |only dbflobr-0.1.0/dbflobr/R/utils.R | 49 ++++----- dbflobr-0.1.0/dbflobr/R/vld.R |only dbflobr-0.1.0/dbflobr/README.md | 32 +++--- dbflobr-0.1.0/dbflobr/build |only dbflobr-0.1.0/dbflobr/inst |only dbflobr-0.1.0/dbflobr/man/add_blob_column.Rd | 2 dbflobr-0.1.0/dbflobr/man/dbflobr-package.Rd | 6 - dbflobr-0.1.0/dbflobr/man/delete_flob.Rd | 2 dbflobr-0.1.0/dbflobr/man/figures |only dbflobr-0.1.0/dbflobr/man/import_all_flobs.Rd |only dbflobr-0.1.0/dbflobr/man/import_flobs.Rd |only dbflobr-0.1.0/dbflobr/man/read_flob.Rd | 2 dbflobr-0.1.0/dbflobr/man/save_all_flobs.Rd |only dbflobr-0.1.0/dbflobr/man/save_flobs.Rd |only dbflobr-0.1.0/dbflobr/man/write_flob.Rd | 2 dbflobr-0.1.0/dbflobr/tests/testthat/test-check.R | 82 ++++++++-------- dbflobr-0.1.0/dbflobr/tests/testthat/test-db.R | 34 ++++-- dbflobr-0.1.0/dbflobr/tests/testthat/test-import.R |only dbflobr-0.1.0/dbflobr/tests/testthat/test-read-write.R |only dbflobr-0.1.0/dbflobr/tests/testthat/test-save.R |only dbflobr-0.1.0/dbflobr/tests/testthat/test-ui.R |only dbflobr-0.1.0/dbflobr/tests/testthat/test-utils.R | 28 ----- dbflobr-0.1.0/dbflobr/vignettes |only 37 files changed, 321 insertions(+), 214 deletions(-)