Title: Plot Columns of Two Matrices Against Each Other Using 'ggplot2'
Description: A quick and easy way of plotting the columns of two matrices or
data frames against each other using 'ggplot2'. Although 'ggmatplot' doesn't
provide the same flexibility as 'ggplot2', it can be used as a workaround for
having to wrangle wide format data into long format for plotting with
'ggplot2'.
Author: Xuan Liang [aut, cre] ,
Francis K. C. Hui [aut] ,
Emi Tanaka [aut] ,
Dilinie Seimon [aut]
Maintainer: Xuan Liang <xuan.liang@anu.edu.au>
Diff between ggmatplot versions 0.1.1 dated 2022-01-11 and 0.1.2 dated 2022-05-16
ggmatplot-0.1.1/ggmatplot/R/validateNumParams.R |only ggmatplot-0.1.2/ggmatplot/DESCRIPTION | 11 ggmatplot-0.1.2/ggmatplot/MD5 | 89 +- ggmatplot-0.1.2/ggmatplot/NEWS.md | 10 ggmatplot-0.1.2/ggmatplot/R/errorplotstats.R | 15 ggmatplot-0.1.2/ggmatplot/R/ggmatplot.R | 434 ++-------- ggmatplot-0.1.2/ggmatplot/R/matclean.R | 37 ggmatplot-0.1.2/ggmatplot/R/utils.R |only ggmatplot-0.1.2/ggmatplot/README.md | 67 - ggmatplot-0.1.2/ggmatplot/build/vignette.rds |binary ggmatplot-0.1.2/ggmatplot/inst/doc/ggmatplot.R | 2 ggmatplot-0.1.2/ggmatplot/inst/doc/ggmatplot.Rmd | 4 ggmatplot-0.1.2/ggmatplot/inst/doc/ggmatplot.html | 29 ggmatplot-0.1.2/ggmatplot/man/figures/README-both-1.png |binary ggmatplot-0.1.2/ggmatplot/man/figures/README-boxplot-1.png |binary ggmatplot-0.1.2/ggmatplot/man/figures/README-density-1.png |binary ggmatplot-0.1.2/ggmatplot/man/figures/README-dotplot-1.png |binary ggmatplot-0.1.2/ggmatplot/man/figures/README-ecdf-1.png |binary ggmatplot-0.1.2/ggmatplot/man/figures/README-errorplot-1.png |binary ggmatplot-0.1.2/ggmatplot/man/figures/README-histogram-1.png |binary ggmatplot-0.1.2/ggmatplot/man/figures/README-line-1.png |binary ggmatplot-0.1.2/ggmatplot/man/figures/README-point-1.png |binary ggmatplot-0.1.2/ggmatplot/man/figures/README-point-columns-1.png |binary ggmatplot-0.1.2/ggmatplot/man/figures/README-point-columns-2.png |binary ggmatplot-0.1.2/ggmatplot/man/figures/README-violin-1.png |binary ggmatplot-0.1.2/ggmatplot/man/ggmatplot.Rd | 7 ggmatplot-0.1.2/ggmatplot/tests/testthat/_snaps |only ggmatplot-0.1.2/ggmatplot/tests/testthat/test_errorplotstats.R | 4 ggmatplot-0.1.2/ggmatplot/tests/testthat/test_ggmatplot_baseplots.R | 20 ggmatplot-0.1.2/ggmatplot/tests/testthat/test_ggmatplot_parameters.R | 32 ggmatplot-0.1.2/ggmatplot/tests/testthat/test_matclean.R | 47 - ggmatplot-0.1.2/ggmatplot/tests/testthat/test_pivotlonger.R | 11 ggmatplot-0.1.2/ggmatplot/vignettes/ggmatplot.Rmd | 4 33 files changed, 345 insertions(+), 478 deletions(-)
Title: Helper Functions to Install and Maintain TeX Live, and Compile
LaTeX Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] ,
RStudio, PBC [cph],
Christophe Dervieux [ctb] ,
Devon Ryan [ctb] ,
Ethan Heinzen [ctb],
Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.38 dated 2022-03-28 and 0.39 dated 2022-05-16
DESCRIPTION | 10 ++--- MD5 | 16 ++++---- R/install.R | 93 +++++++++++++++++++++++++++++++++++-------------- R/latex.R | 2 - R/tlmgr.R | 10 +---- README.md | 7 +-- inst/NEWS.Rd | 2 - man/install_tinytex.Rd | 25 +++++++++---- man/tinytex-package.Rd | 4 +- 9 files changed, 108 insertions(+), 61 deletions(-)
Title: Optimal Test Design Approach to Fixed and Adaptive Test
Construction
Description: Uses the optimal test design approach by Birnbaum (1968, ISBN:9781593119348) and
van der Linden (2018) <doi:10.1201/9781315117430> to construct fixed, adaptive, and parallel tests.
Supports the following mixed-integer programming (MIP) solver packages: 'lpsymphony', 'Rsymphony',
'gurobi', 'lpSolve', and 'Rglpk'. The 'gurobi' package is not available from CRAN; see <https://www.gurobi.com/downloads/>.
Author: Seung W. Choi [aut, cre] ,
Sangdon Lim [aut]
Maintainer: Seung W. Choi <schoi@austin.utexas.edu>
Diff between TestDesign versions 1.3.2 dated 2022-04-29 and 1.3.3 dated 2022-05-16
TestDesign-1.3.2/TestDesign/data/itemcontent_fatigue_data.rda |only TestDesign-1.3.2/TestDesign/inst/extdata/itemcontent_fatigue_95.csv |only TestDesign-1.3.3/TestDesign/DESCRIPTION | 10 TestDesign-1.3.3/TestDesign/MD5 | 86 +- TestDesign-1.3.3/TestDesign/NAMESPACE | 2 TestDesign-1.3.3/TestDesign/NEWS.md | 7 TestDesign-1.3.3/TestDesign/R/datasets.R | 4 TestDesign-1.3.3/TestDesign/R/shadow_class.R | 1 TestDesign-1.3.3/TestDesign/R/solver_functions.R | 1 TestDesign-1.3.3/TestDesign/R/static_class.R | 1 TestDesign-1.3.3/TestDesign/data/constraints_bayes.rda |binary TestDesign-1.3.3/TestDesign/data/constraints_bayes_data.rda |binary TestDesign-1.3.3/TestDesign/data/constraints_fatigue.rda |binary TestDesign-1.3.3/TestDesign/data/constraints_fatigue_data.rda |binary TestDesign-1.3.3/TestDesign/data/constraints_reading.rda |binary TestDesign-1.3.3/TestDesign/data/constraints_reading_data.rda |binary TestDesign-1.3.3/TestDesign/data/constraints_science.rda |binary TestDesign-1.3.3/TestDesign/data/constraints_science_data.rda |binary TestDesign-1.3.3/TestDesign/data/itemattrib_bayes.rda |binary TestDesign-1.3.3/TestDesign/data/itemattrib_bayes_data.rda |binary TestDesign-1.3.3/TestDesign/data/itemattrib_fatigue.rda |binary TestDesign-1.3.3/TestDesign/data/itemattrib_fatigue_data.rda |binary TestDesign-1.3.3/TestDesign/data/itemattrib_reading.rda |binary TestDesign-1.3.3/TestDesign/data/itemattrib_reading_data.rda |binary TestDesign-1.3.3/TestDesign/data/itemattrib_science.rda |binary TestDesign-1.3.3/TestDesign/data/itemattrib_science_data.rda |binary TestDesign-1.3.3/TestDesign/data/itempool_bayes.rda |binary TestDesign-1.3.3/TestDesign/data/itempool_bayes_data.rda |binary TestDesign-1.3.3/TestDesign/data/itempool_fatigue.rda |binary TestDesign-1.3.3/TestDesign/data/itempool_fatigue_data.rda |binary TestDesign-1.3.3/TestDesign/data/itempool_reading.rda |binary TestDesign-1.3.3/TestDesign/data/itempool_reading_data.rda |binary TestDesign-1.3.3/TestDesign/data/itempool_science.rda |binary TestDesign-1.3.3/TestDesign/data/itempool_science_data.rda |binary TestDesign-1.3.3/TestDesign/data/itempool_se_bayes_data.rda |binary TestDesign-1.3.3/TestDesign/data/itemtext_fatigue_data.rda |only TestDesign-1.3.3/TestDesign/data/resp_fatigue_data.rda |binary TestDesign-1.3.3/TestDesign/data/stimattrib_reading.rda |binary TestDesign-1.3.3/TestDesign/data/stimattrib_reading_data.rda |binary TestDesign-1.3.3/TestDesign/inst/extdata/example_datasets.R | 4 TestDesign-1.3.3/TestDesign/inst/extdata/itemtext_fatigue_95.csv |only TestDesign-1.3.3/TestDesign/inst/shiny/server.r | 359 ++++------ TestDesign-1.3.3/TestDesign/inst/shiny/styles.css | 8 TestDesign-1.3.3/TestDesign/inst/shiny/ui.r | 48 - TestDesign-1.3.3/TestDesign/man/dataset_fatigue.Rd | 4 TestDesign-1.3.3/TestDesign/man/runAssembly.Rd | 2 46 files changed, 247 insertions(+), 290 deletions(-)
Title: A Flexible Approach for Causal Inference with Multiple
Treatments and Clustered Survival Outcomes
Description: Random-intercept accelerated failure time (AFT) model utilizing Bayesian additive regression trees (BART) for drawing causal inferences about multiple treatments while accounting for the multilevel survival data structure. It also includes an interpretable sensitivity analysis approach to evaluate how the drawn causal conclusions might be altered in response to the potential magnitude of departure from the no unmeasured confounding assumption.
Author: Liangyuan Hu [aut],
Jiayi Ji [aut, cre]
Maintainer: Jiayi Ji <jj869@sph.rutgers.edu>
Diff between riAFTBART versions 0.3.1 dated 2022-05-16 and 0.3.2 dated 2022-05-16
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/cal_PEHE.R | 25 +++++++++++++------------ man/cal_PEHE.Rd | 2 +- 4 files changed, 21 insertions(+), 20 deletions(-)
Title: Planning and Analysing Survival Studies under Non-Proportional
Hazards
Description: Piecewise constant hazard functions are used to flexibly model survival distributions with non-proportional hazards and
to simulate data from the specified distributions. A function to calculate weighted log-rank tests for the comparison of two
hazard functions is included. Also, a function to calculate a test using the maximum of a set of test statistics from weighted
log-rank tests (MaxCombo test) is provided. This test utilizes the asymptotic multivariate normal joint distribution of the
separate test statistics. The correlation is estimated from the data. These methods are described in Ristl et al. (2021)
<doi:10.1002/pst.2062>.
Finally, a function is provided for the estimation and inferential statistics of various parameters that quantify the difference
between two survival curves. Eligible parameters are differences in survival probabilities, log survival probabilities,
complementary log log (cloglog) transformed survival probabilities, quantiles of the survival functions, log transformed quantiles,
restricted mean survival times, as well as an average hazard ratio, the Cox model score statistic (logrank statistic), and the
Cox-model hazard ratio. Adjustments for multiple testing and simultaneous confidence intervals are calculated using a multivariate
normal approximation to the set of selected parameters.
Author: Robin Ristl [aut, cre],
Nicolas Ballarini [ctb]
Maintainer: Robin Ristl <robin.ristl@meduniwien.ac.at>
Diff between nph versions 2.0 dated 2020-01-10 and 2.1 dated 2022-05-16
nph-2.0/nph/R/additional_functions.R |only nph-2.0/nph/R/continuous_functions.R |only nph-2.0/nph/R/paket_nph_1-9.R |only nph-2.0/nph/inst/shiny/server/additional_functions.R |only nph-2.0/nph/inst/shiny/server/continuous_functions.R |only nph-2.0/nph/inst/shiny/server/paket_nph_1-9.R |only nph-2.1/nph/DESCRIPTION | 30 nph-2.1/nph/MD5 | 63 nph-2.1/nph/NAMESPACE | 60 nph-2.1/nph/R/additional_functions_1-1.R |only nph-2.1/nph/R/continuous_functions_1-1.R |only nph-2.1/nph/R/paket_nph_2-1_1.R |only nph-2.1/nph/R/simultane_Inferenz_Funktionen_nph_1-3.R |only nph-2.1/nph/build/vignette.rds |binary nph-2.1/nph/data |only nph-2.1/nph/inst/CITATION |only nph-2.1/nph/inst/doc/examples.R | 6 nph-2.1/nph/inst/doc/examples.html | 1658 +++++++++++++-- nph-2.1/nph/inst/doc/usage.R | 14 nph-2.1/nph/inst/doc/usage.html | 770 ++++-- nph-2.1/nph/inst/shiny/server/additional_functions_1-1.R |only nph-2.1/nph/inst/shiny/server/continuous_functions_1-1.R |only nph-2.1/nph/inst/shiny/server/paket_nph_2-1_1.R |only nph-2.1/nph/man/logrank.maxtest.Rd | 58 nph-2.1/nph/man/logrank.test.Rd | 48 nph-2.1/nph/man/m2r.Rd | 6 nph-2.1/nph/man/nph_gui.Rd | 4 nph-2.1/nph/man/nphparams.Rd |only nph-2.1/nph/man/pchaz.Rd | 28 nph-2.1/nph/man/pembro.Rd |only nph-2.1/nph/man/plot.mixpch.Rd | 6 nph-2.1/nph/man/plot.nphparams.Rd |only nph-2.1/nph/man/plot_diagram.Rd | 2 nph-2.1/nph/man/plot_shhr.Rd | 2 nph-2.1/nph/man/plot_subgroups.Rd | 6 nph-2.1/nph/man/pop_pchaz.Rd | 24 nph-2.1/nph/man/print.nphparams.Rd |only nph-2.1/nph/man/rSurv_conditional_fun.Rd | 13 nph-2.1/nph/man/rSurv_fun.Rd | 6 nph-2.1/nph/man/sample_conditional_fun.Rd | 10 nph-2.1/nph/man/sample_fun.Rd | 10 nph-2.1/nph/man/subpop_pchaz.Rd | 38 42 files changed, 2310 insertions(+), 552 deletions(-)
Title: Creating Demographic Table
Description: Functions for creating demographic table with simple summary
statistics, with optional comparison(s) over one or more groups.
Numeric variables are summarized in means, standard deviations,
medians, inter-quartile-ranges (IQR), skewness, Shapiro-Wilk
normality test and ranges, and compared using two-sample t-test,
Wilcoxon test, ANOVA and/or Kruskal-Wallis test. Logical and
factor variables are summarized in counts and percentages and
compared using chi-squared test and/or Fisher's exact test.
Author: Tingting Zhan [aut, cre, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between DemographicTable versions 0.1.1 dated 2022-04-20 and 0.1.2 dated 2022-05-16
DESCRIPTION | 31 +++++++-------- MD5 | 32 +++++++-------- NEWS.md | 2 R/DemographicTable.R | 71 +++++++++++++++++------------------ R/DemographicTable_info.R | 17 ++------ R/adjustColWidths.R | 12 ++--- R/class1List.R | 20 ++++----- R/pval_shapiro.R | 6 +- R/summaryText.R | 10 ++-- man/DemographicTable-package.Rd | 16 ++----- man/DemographicTable.Rd | 45 ++++++++++++---------- man/as_flextable.DemographicTable.Rd | 8 +-- man/class1List.Rd | 11 ++--- man/colWidth.Rd | 6 +- man/nchar_lf.Rd | 8 +-- man/pval_shapiro.Rd | 8 +-- man/summaryText.Rd | 2 17 files changed, 154 insertions(+), 151 deletions(-)
More information about DemographicTable at CRAN
Permanent link
Title: Universal Storage Engine for Sparse and Dense Multidimensional
Arrays
Description: The universal storage engine 'TileDB' introduces a
powerful on-disk format for multi-dimensional arrays. It supports
dense and sparse arrays, dataframes and key-values stores, cloud
storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression,
encryption and checksum filters, uses a fully multi-threaded
implementation, supports parallel I/O, data versioning ('time
travel'), metadata and groups. It is implemented as an embeddable
cross-platform C++ library with APIs from several languages, and
integrations.
Author: TileDB, Inc. [aut, cph],
Dirk Eddelbuettel [cre]
Maintainer: Dirk Eddelbuettel <dirk@tiledb.com>
Diff between tiledb versions 0.12.0 dated 2022-04-13 and 0.13.0 dated 2022-05-16
DESCRIPTION | 6 MD5 | 48 +++-- NAMESPACE | 8 NEWS.md | 35 +++ R/ArraySchema.R | 18 +- R/Filestore.R |only R/Filter.R | 21 +- R/Group.R | 9 - R/Query.R | 9 - R/RcppExports.R | 44 +++- R/TileDBArray.R | 21 -- build/vignette.rds |binary inst/include/tiledb.h | 2 inst/tinytest/test_filestore.R |only inst/tinytest/test_filter.R | 56 ++++++ inst/tinytest/test_group.R | 9 - man/tiledb_array_schema_check.Rd | 8 man/tiledb_filestore_buffer_export.Rd |only man/tiledb_filestore_buffer_import.Rd |only man/tiledb_filestore_schema_create.Rd |only man/tiledb_filestore_size.Rd |only man/tiledb_filestore_uri_export.Rd |only man/tiledb_filestore_uri_import.Rd |only man/tiledb_filter.Rd | 3 man/tiledb_group_member.Rd | 7 src/Makevars.win | 1 src/RcppExports.cpp | 144 ++++++++++++---- src/libtiledb.cpp | 301 ++++++++++++++++++++++++---------- tools/tiledbVersion.txt | 4 29 files changed, 556 insertions(+), 198 deletions(-)
Title: Simulate from ODE-Based Models
Description: Fast simulation from ordinary differential equation
(ODE) based models typically employed in quantitative pharmacology and
systems biology.
Author: Kyle T Baron [aut, cre] ,
Bill Gillespie [ctb],
Charles Margossian [ctb],
Devin Pastoor [ctb],
Bill Denney [ctb] ,
Dilawar Singh [ctb],
Felicien Le Louedec [ctb] ,
Timothy Waterhouse [ctb] ,
Metrum Research Group [cph]
Maintainer: Kyle T Baron <kyleb@metrumrg.com>
Diff between mrgsolve versions 1.0.3 dated 2022-03-21 and 1.0.4 dated 2022-05-16
DESCRIPTION | 6 +-- MD5 | 33 +++++++++-------- NAMESPACE | 6 +++ R/class_evd.R | 7 +-- R/data_set.R | 39 ++++++++++++++------- R/events.R | 1 R/utils.R | 76 ++++++++++++++++++++++++----------------- inst/WORDLIST | 1 inst/mrgx/mrgx.h | 20 +++++----- inst/stories.yaml |only man/evd.Rd | 4 +- man/expand.idata.Rd | 24 ++++++++---- man/lctran.Rd | 27 +++++++++++--- src/devtran.cpp | 2 - src/mrgsolve.cpp | 16 ++++---- tests/testthat/test-data_set.R | 13 +++++-- tests/testthat/test-evd.R | 20 ++++++++++ tests/testthat/test-rng.R | 13 +++++-- 18 files changed, 203 insertions(+), 105 deletions(-)
Title: High Dimensional Geometry, Set Operations, Projection, and
Inference Using Kernel Density Estimation, Support Vector
Machines, and Convex Hulls
Description: Estimates the shape and volume of high-dimensional datasets and performs set operations: intersection / overlap, union, unique components, inclusion test, and hole detection. Uses stochastic geometry approach to high-dimensional kernel density estimation, support vector machine delineation, and convex hull generation. Applications include modeling trait and niche hypervolumes and species distribution modeling.
Author: Benjamin Blonder, with contributions from Cecina Babich Morrow, David J. Harris, Stuart Brown, Gregoire Butruille, Alex Laini, and Dan Chen
Maintainer: Benjamin Blonder <benjamin.blonder@berkeley.edu>
Diff between hypervolume versions 3.0.2 dated 2022-01-31 and 3.0.3 dated 2022-05-16
DESCRIPTION | 12 MD5 | 34 - R/get_centroid.R | 4 R/get_centroid_weighted.R | 134 ++-- R/hypervolume_estimate_probability.R | 2 R/hypervolume_expectation.R | 138 ++-- R/hypervolume_join.R | 4 R/hypervolume_n_occupancy.R | 744 +++++++++++++------------- R/hypervolume_n_occupancy_permute.R | 784 ++++++++++++++-------------- R/hypervolume_plot.R | 978 +++++++++++++++++------------------ R/hypervolume_prune.R | 2 R/hypervolume_segment.R | 2 R/kdtree_build.R | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Hypervolume-Resampling.html | 334 +++++++++++ man/expectation_convex.Rd | 4 man/quercus.Rd | 4 18 files changed, 1735 insertions(+), 1449 deletions(-)
Title: Classification with Parallel Factor Analysis
Description: Classification using Richard A. Harshman's Parallel Factor Analysis (Parafac) model-1 fit to a three-way or four-way data tensor/array. See Harshman (1994) <doi:10.1016/0167-9473(94)90132-5>. Uses Parafac factor weights from one mode of this model as predictors to tune parameters for one or more classification methods via a k-fold cross-validation procedure. Supports penalized logistic regression, support vector machine, random forest, and feed-forward neural network. Supports binary and multiclass classification. Predicts class labels or class probabilities and calculates multiple classification performance measures. Parallel computing is implemented via the 'parallel' and 'doParallel' packages.
Author: Matthew A. Snodgress <snodg031@umn.edu>
Maintainer: Matthew A. Snodgress <snodg031@umn.edu>
Diff between cpfa versions 1.0-1 dated 2022-04-08 and 1.0-2 dated 2022-05-16
DESCRIPTION | 12 +++++++----- MD5 | 27 ++++++++++++++++----------- R/cpfa.R | 2 +- R/cpm.R | 2 +- R/kcv.nn.R | 2 +- R/kcv.plr.R | 2 +- R/kcv.rf.R | 2 +- R/kcv.svm.R | 2 +- R/predict.cpfa.R | 2 +- build |only inst |only man/cpfa.Rd | 22 +++++++++++++--------- man/cpm.Rd | 4 +++- man/predict.cpfa.Rd | 12 ++++++++++-- vignettes |only 15 files changed, 56 insertions(+), 35 deletions(-)
Title: Bayesian Regularization for Feed-Forward Neural Networks
Description: Bayesian regularization for feed-forward neural networks.
Author: Paulino Perez Rodriguez, Daniel Gianola
Maintainer: Paulino Perez Rodriguez <perpdgo@colpos.mx>
Diff between brnn versions 0.9.1 dated 2022-04-25 and 0.9.2 dated 2022-05-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/brnn.R | 2 +- inst/history.txt | 3 +++ src/win/util_win.c | 9 +++++---- 5 files changed, 17 insertions(+), 13 deletions(-)
Title: Selection of K in K-Means Clustering
Description: Selection of k in k-means clustering based on Pham et al. paper
``Selection of k in k-means clustering''.
Author: Daniel Rodriguez
Maintainer: Daniel Rodriguez <daniel.rodriguez.perez@gmail.com>
Diff between kselection versions 0.2.0 dated 2015-02-11 and 0.2.1 dated 2022-05-16
DESCRIPTION | 12 ++++++---- MD5 | 26 +++++++++++------------ NAMESPACE | 6 ++++- R/pham.R | 6 +++++ man/get_f_k.Rd | 10 ++++---- man/get_k_threshold.Rd | 9 +++----- man/kselection-package.Rd | 9 +++----- man/kselection.Rd | 27 +++++++++++++++--------- man/num_clusters.Rd | 10 ++++---- man/num_clusters_all.Rd | 10 ++++---- man/set_k_threshold.Rd | 11 ++++----- tests/testthat/testPham.R | 14 ++++++------ tests/testthat/testPhamFix.R | 2 - tests/testthat/testPhamKmeans.R | 45 +++++----------------------------------- 14 files changed, 90 insertions(+), 107 deletions(-)
Title: Group Sorted L1 Penalized Estimation
Description: Group SLOPE is a penalized linear regression method that is used
for adaptive selection of groups of significant predictors in a
high-dimensional linear model.
The Group SLOPE method can control the (group) false discovery rate at a
user-specified level (i.e., control the expected proportion of irrelevant
among all selected groups of predictors).
Author: Alexej Gossmann [aut, cre],
Damian Brzyski [aut],
Weijie Su [aut],
Malgorzata Bogdan [aut],
Ewout van den Berg [ctb] ,
Emmanuel Candes [ctb] ,
Chiara Sabatti [ctb] ,
Evan Patterson [ctb]
Maintainer: Alexej Gossmann <alexej.go@googlemail.com>
Diff between grpSLOPE versions 0.3.0 dated 2020-04-07 and 0.3.1 dated 2022-05-16
DESCRIPTION | 13 - MD5 | 27 +- NEWS.md | 4 R/optimization.R | 6 build/partial.rdb |only build/vignette.rds |binary inst/doc/basic-usage.R | 32 +- inst/doc/basic-usage.html | 346 ++++++++++++++++++++------------ man/SLOPE_solver.Rd | 15 + man/admmSolverGroupSLOPE.Rd | 18 + man/grpSLOPE.Rd | 20 + man/proxGroupSortedL1.Rd | 2 man/proximalGradientSolverGroupSLOPE.Rd | 20 + src/RcppExports.cpp | 5 tests/testthat/test_grpSLOPE.R | 72 ++++++ 15 files changed, 397 insertions(+), 183 deletions(-)
Title: Bayesian Dynamic Borrowing with Propensity Score
Description: A tool which aims to help evaluate the effect of external borrowing using an integrated approach described in Lewis et al., (2019) <doi:10.1080/19466315.2018.1497533> that combines propensity score and Bayesian dynamic borrowing methods.
Author: Craig Gower-Page [cre],
Matt Secrest [ctb],
Yichen Lu [aut],
Aijing Lin [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Craig Gower-Page <craig.gower-page@roche.com>
Diff between psborrow versions 0.1.0 dated 2021-06-04 and 0.2.0 dated 2022-05-16
psborrow-0.1.0/psborrow/LICENCE |only psborrow-0.1.0/psborrow/inst/doc/user_guide.R |only psborrow-0.1.0/psborrow/inst/doc/user_guide.Rmd |only psborrow-0.2.0/psborrow/DESCRIPTION | 52 psborrow-0.2.0/psborrow/MD5 | 93 - psborrow-0.2.0/psborrow/NAMESPACE | 94 - psborrow-0.2.0/psborrow/NEWS.md |only psborrow-0.2.0/psborrow/R/add_cov.R | 586 +++++-- psborrow-0.2.0/psborrow/R/add_mcmc.R | 472 +++--- psborrow-0.2.0/psborrow/R/add_time.R | 540 ++++--- psborrow-0.2.0/psborrow/R/apply_mcmc.R |only psborrow-0.2.0/psborrow/R/get_summary.R | 688 ++++++--- psborrow-0.2.0/psborrow/R/match_cov.R | 80 - psborrow-0.2.0/psborrow/R/run_mcmc.R | 367 ++-- psborrow-0.2.0/psborrow/R/simu_cov.R | 214 +- psborrow-0.2.0/psborrow/R/simu_time.R | 120 - psborrow-0.2.0/psborrow/R/utils.R | 828 ++++++----- psborrow-0.2.0/psborrow/R/zzz.R |only psborrow-0.2.0/psborrow/build/vignette.rds |binary psborrow-0.2.0/psborrow/inst/doc/analysis.html |only psborrow-0.2.0/psborrow/inst/doc/analysis.html.asis |only psborrow-0.2.0/psborrow/inst/doc/user_guide.html | 1249 +++++++++++------ psborrow-0.2.0/psborrow/inst/doc/user_guide.html.asis |only psborrow-0.2.0/psborrow/man/add_cov.Rd | 46 psborrow-0.2.0/psborrow/man/add_mcmc.Rd | 62 psborrow-0.2.0/psborrow/man/add_time.Rd | 54 psborrow-0.2.0/psborrow/man/apply_mcmc.Rd |only psborrow-0.2.0/psborrow/man/c-.covClass-method.Rd | 61 psborrow-0.2.0/psborrow/man/fix_col_names.Rd |only psborrow-0.2.0/psborrow/man/is_psborrow_dev.Rd |only psborrow-0.2.0/psborrow/man/match_cov.Rd | 72 psborrow-0.2.0/psborrow/man/plot_bias.Rd | 12 psborrow-0.2.0/psborrow/man/plot_hr.Rd | 14 psborrow-0.2.0/psborrow/man/plot_mse.Rd | 14 psborrow-0.2.0/psborrow/man/plot_power.Rd | 12 psborrow-0.2.0/psborrow/man/plot_type1error.Rd | 10 psborrow-0.2.0/psborrow/man/ps_message.Rd |only psborrow-0.2.0/psborrow/man/run_mcmc.Rd | 72 psborrow-0.2.0/psborrow/man/run_mcmc_p.Rd | 86 - psborrow-0.2.0/psborrow/man/set_cov.Rd | 52 psborrow-0.2.0/psborrow/man/set_event.Rd | 120 + psborrow-0.2.0/psborrow/man/set_n.Rd | 6 psborrow-0.2.0/psborrow/man/set_prior.Rd | 18 psborrow-0.2.0/psborrow/man/simu_cov.Rd | 88 - psborrow-0.2.0/psborrow/man/simu_time.Rd | 100 - psborrow-0.2.0/psborrow/man/valid_mcmc.Rd | 50 psborrow-0.2.0/psborrow/tests |only psborrow-0.2.0/psborrow/vignettes/analysis.Rmd |only psborrow-0.2.0/psborrow/vignettes/analysis.html.asis |only psborrow-0.2.0/psborrow/vignettes/build.R |only psborrow-0.2.0/psborrow/vignettes/user_guide.Rmd | 829 +++++++---- psborrow-0.2.0/psborrow/vignettes/user_guide.html.asis |only 52 files changed, 4293 insertions(+), 2868 deletions(-)
Title: Multilevel Mediation Analysis
Description: Do multilevel mediation analysis with generalized additive multilevel models. The analysis method is described in Yu and Li (2020), "Third-Variable Effect Analysis with Multilevel Additive Models", PLoS ONE 15(10): e0241072.
Author: Qingzhao Yu, Bin Li
Maintainer: Qingzhao Yu <qyu@lsuhsc.edu>
Diff between mlma versions 6.1-1 dated 2021-07-06 and 6.2-1 dated 2022-05-16
DESCRIPTION | 8 - MD5 | 14 +-- inst/doc/MLMAvignette.Rmd | 2 inst/doc/MLMAvignette.html | 14 ++- man/joint.effect.Rd | 2 man/mlma-package.Rd | 6 + vignettes/MLMAvignette.Rmd | 2 vignettes/vignette.bib | 189 +++++++++++++++++++++++++-------------------- 8 files changed, 138 insertions(+), 99 deletions(-)
Title: Rcmdr Receiver Operator Characteristic Plug-in Package
Description: Rcmdr GUI extension plug-in for Receiver Operator Characteristic tools from pROC package. Also it ads a Rcmdr GUI extension for Hosmer and Lemeshow GOF test from the package ResourceSelection.
Author: Daniel-Corneliu Leucuta [aut, cre],
Mihaela Hedesiu [ctb],
Andrei Achimas [ctb],
Oana Almasan [ctb]
Maintainer: Daniel-Corneliu Leucuta <danny.ldc@gmail.com>
Diff between RcmdrPlugin.ROC versions 1.0-18 dated 2015-02-26 and 1.0-19 dated 2022-05-16
RcmdrPlugin.ROC-1.0-18/RcmdrPlugin.ROC/R/vROCR.R |only RcmdrPlugin.ROC-1.0-19/RcmdrPlugin.ROC/DESCRIPTION | 14 +++++----- RcmdrPlugin.ROC-1.0-19/RcmdrPlugin.ROC/MD5 | 13 ++++----- RcmdrPlugin.ROC-1.0-19/RcmdrPlugin.ROC/NAMESPACE | 7 ++--- RcmdrPlugin.ROC-1.0-19/RcmdrPlugin.ROC/inst/CHANGES | 1 RcmdrPlugin.ROC-1.0-19/RcmdrPlugin.ROC/inst/etc/menus.txt | 6 ++-- RcmdrPlugin.ROC-1.0-19/RcmdrPlugin.ROC/man/RcmdrPlugin.ROC-internal.Rd | 1 RcmdrPlugin.ROC-1.0-19/RcmdrPlugin.ROC/man/RcmdrPlugin.ROC-package.Rd | 8 ++--- 8 files changed, 25 insertions(+), 25 deletions(-)
More information about RcmdrPlugin.ROC at CRAN
Permanent link
Title: Rcmdr Coin Plug-in
Description: Rcmdr GUI extension plug-in for coin package (Conditional Inference Procedures in a Permutation Test Framework).
Author: Daniel-Corneliu Leucuta <danny.ldc@gmail.com>
Maintainer: Daniel-Corneliu Leucuta <danny.ldc@gmail.com>
Diff between RcmdrPlugin.coin versions 1.0-22 dated 2014-09-14 and 1.0-23 dated 2022-05-16
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NAMESPACE | 1 + NEWS | 4 ++++ man/RcmdrPlugin.coin-package.Rd | 8 ++++---- 5 files changed, 19 insertions(+), 14 deletions(-)
More information about RcmdrPlugin.coin at CRAN
Permanent link
Title: Providing Data from the US Department of Housing and Urban
Development
Description: Provides functions to access data from the US Department of Housing and Urban Development <https://www.huduser.gov/portal/dataset/fmr-api.html>.
Author: Paul Richardson
Maintainer: Paul Richardson <p.richardson.54391@gmail.com>
Diff between hudr versions 1.0.0 dated 2022-03-29 and 1.1.0 dated 2022-05-16
DESCRIPTION | 10 ++-- MD5 | 12 ++--- R/hudr.R | 102 ++++++++++++++++++++++--------------------- man/get_hud_fmr_data.Rd | 8 +-- man/get_hud_fmr_statedata.Rd | 6 +- man/get_hud_il_data.Rd | 8 +-- man/get_hud_il_statedata.Rd | 6 +- 7 files changed, 78 insertions(+), 74 deletions(-)
Title: Partially Observed Integrated Functional Depth
Description: Applications to visualization, outlier detection and classification. Software companion for Elías, Antonio, Jiménez, Raúl, Paganoni, Anna M. and Sangalli, Laura M., (2022), "Integrated Depth for Partially Observed Functional Data". Journal of Computational and Graphical Statistics. <doi:10.1080/10618600.2022.2070171>.
Author: Antonio Elias [aut, cre],
Raul Jimenez [ctb],
Anna M. Paganoni [ctb],
Laura M. Sangalli [ctb]
Maintainer: Antonio Elias <antonioefz91@gmail.com>
Diff between fdaPOIFD versions 1.0.2 dated 2021-08-04 and 1.0.3 dated 2022-05-16
DESCRIPTION | 8 ++++---- MD5 | 5 +++-- NEWS.md | 3 +++ inst/CITATION |only 4 files changed, 10 insertions(+), 6 deletions(-)
Title: Eigenvectors from Eigenvalues Sparse Principal Component
Analysis (EESPCA)
Description: Contains logic for computing sparse principal components via the EESPCA method,
which is based on an approximation of the eigenvector/eigenvalue identity.
Includes logic to support execution of the TPower and rifle sparse PCA methods,
as well as logic to estimate the sparsity parameters used by EESPCA, TPower and rifle
via cross-validation to minimize the out-of-sample reconstruction error.
H. Robert Frost (2021) <doi:10.1080/10618600.2021.1987254>.
Author: H. Robert Frost
Maintainer: H. Robert Frost <rob.frost@dartmouth.edu>
Diff between EESPCA versions 0.5.0 dated 2021-10-13 and 0.6.0 dated 2022-05-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/EESPCA.R | 33 +++++++++++++++++++++++++-------- inst/doc/EESPCA_Example.pdf |binary man/EESPCA-package.Rd | 5 ++--- 5 files changed, 35 insertions(+), 19 deletions(-)
Title: Electroencephalography Toolkit Datasets
Description: Contains the example EEG data used in the package eegkit. Also contains code for easily creating larger EEG datasets from the EEG Database on the UCI Machine Learning Repository.
Author: Nathaniel E. Helwig <helwig@umn.edu>
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
Diff between eegkitdata versions 1.0 dated 2014-09-09 and 1.1 dated 2022-05-16
DESCRIPTION | 12 +-- MD5 | 14 ++-- NAMESPACE | 4 - R/geteegdata.R | 140 +++++++++++++++++++++++----------------------- data/eegdata.rda |binary man/eegdata.Rd | 2 man/eegkitdata-package.Rd | 2 man/geteegdata.Rd | 6 - 8 files changed, 91 insertions(+), 89 deletions(-)
Title: Small Area Estimation Evaluation
Description: Allows users to produce diagnostic procedures and graphic tools for the evaluation of Small Area estimators.
Author: Andrea Fasulo [aut, cre]
Maintainer: Andrea Fasulo <fasulo@istat.it>
Diff between SAEval versions 0.1.4 dated 2022-05-05 and 0.1.5 dated 2022-05-16
DESCRIPTION | 6 ++--- MD5 | 6 ++--- R/cinterval.R | 63 +++++++++++++++++++++++++++++-------------------------- man/cinterval.Rd | 2 - 4 files changed, 41 insertions(+), 36 deletions(-)
Title: Seismic Time Series Analysis Tools
Description: Multiple interactive codes to view and analyze seismic data, via spectrum analysis, wavelet transforms, particle motion, hodograms. Includes general time-series tools, plotting, filtering, interactive display.
Author: Jonathan M. Lees [aut, cre],
Jake Anderson [ctb],
Leonard Lisapaly [ctb],
Dave Harris [aut, cph]
Maintainer: Jonathan M. Lees <jonathan.lees@unc.edu>
Diff between RSEIS versions 4.0-3 dated 2021-08-02 and 4.1-1 dated 2022-05-16
DESCRIPTION | 8 ++++---- MD5 | 42 ++++++++++++++++++++++++------------------ R/DISTxsec.R |only R/FILT.SEISN.R | 22 ++++++++++++++++++---- R/GET.seis.R | 17 +++++++++++++++-- R/GLUE.GET.seis.R | 8 ++++++++ R/JGET.seis.R | 20 ++++++++++++++++++-- R/PLOT.SEISN.R | 9 +++++++-- R/SEIS2list.R |only R/butfilt.R | 10 +++++++--- R/combineSEIS.R |only R/swig.R | 8 +++++--- man/DISTxsec.Rd |only man/FILT.SEISN.Rd | 11 ++++++++--- man/GET.seis.Rd | 13 +++++++++++-- man/Mine.seis.Rd | 3 ++- man/PLOT.SEISN.Rd | 6 ++++-- man/SEIS2list.Rd |only man/combineSEIS.Rd |only man/distseisnXY.Rd | 8 ++++---- man/getseis24.Rd | 3 ++- man/longfft.Rd | 3 ++- man/makeDB.Rd | 10 +++++++--- man/swig.Rd | 5 ++++- src/ARAIC.c | 13 ++++++------- 25 files changed, 156 insertions(+), 63 deletions(-)
Title: Intensity Analysis of Spatial Point Patterns on Complex Networks
Description: Tools to analyze point patterns in space occurring over planar network structures derived from graph-related intensity measures for undirected, directed, and mixed networks.
This package is based on the following research: Eckardt and Mateu (2018) <doi:10.1080/10618600.2017.1391695>. Eckardt and Mateu (2021) <doi:10.1007/s11749-020-00720-4>.
Author: Pol Llagostera [aut, cre],
Matthias Eckardt [aut]
Maintainer: Pol Llagostera <pol.llagostera@udl.cat>
Diff between intensitynet versions 1.0.0 dated 2022-01-26 and 1.3.0 dated 2022-05-16
intensitynet-1.0.0/intensitynet/man/AllEdgeIntensities.intensitynet.Rd |only intensitynet-1.0.0/intensitynet/man/CalculateEventIntensities.Rd |only intensitynet-1.0.0/intensitynet/man/CalculateEventIntensities.intensitynetDir.Rd |only intensitynet-1.0.0/intensitynet/man/CalculateEventIntensities.intensitynetMix.Rd |only intensitynet-1.0.0/intensitynet/man/CalculateEventIntensities.intensitynetUnd.Rd |only intensitynet-1.0.0/intensitynet/man/PathIntensity.Rd |only intensitynet-1.0.0/intensitynet/man/PathIntensity.intensitynet.Rd |only intensitynet-1.0.0/intensitynet/man/ShortestPathIntensity.Rd |only intensitynet-1.0.0/intensitynet/man/ShortestPathIntensity.intensitynet.Rd |only intensitynet-1.3.0/intensitynet/DESCRIPTION | 8 intensitynet-1.3.0/intensitynet/MD5 | 95 - intensitynet-1.3.0/intensitynet/NAMESPACE | 16 intensitynet-1.3.0/intensitynet/NEWS.md | 41 intensitynet-1.3.0/intensitynet/R/intensitynet.R | 522 +++++----- intensitynet-1.3.0/intensitynet/R/intensitynetDir.R | 71 - intensitynet-1.3.0/intensitynet/R/intensitynetMix.R | 73 - intensitynet-1.3.0/intensitynet/R/intensitynetUnd.R | 64 - intensitynet-1.3.0/intensitynet/R/netTools.R | 479 ++++++--- intensitynet-1.3.0/intensitynet/README.md | 19 intensitynet-1.3.0/intensitynet/data/dir_intnet_chicago.rda |binary intensitynet-1.3.0/intensitynet/data/mix_intnet_chicago.rda |binary intensitynet-1.3.0/intensitynet/data/und_intnet_chicago.rda |binary intensitynet-1.3.0/intensitynet/man/ApplyWindow.Rd | 58 - intensitynet-1.3.0/intensitynet/man/ApplyWindow.intensitynet.Rd | 58 - intensitynet-1.3.0/intensitynet/man/EdgeIntensitiesAndProportions.intensitynet.Rd |only intensitynet-1.3.0/intensitynet/man/EdgeIntensity.intensitynet.Rd | 48 intensitynet-1.3.0/intensitynet/man/GeoreferencedGgplot2.netTools.Rd | 47 intensitynet-1.3.0/intensitynet/man/GeoreferencedPlot.netTools.Rd | 27 intensitynet-1.3.0/intensitynet/man/NodeGeneralCorrelation.Rd | 78 - intensitynet-1.3.0/intensitynet/man/NodeGeneralCorrelation.intensitynet.Rd | 22 intensitynet-1.3.0/intensitynet/man/NodeLocalCorrelation.Rd | 74 - intensitynet-1.3.0/intensitynet/man/NodeLocalCorrelation.intensitynet.Rd | 12 intensitynet-1.3.0/intensitynet/man/PathTotalWeight.Rd |only intensitynet-1.3.0/intensitynet/man/PathTotalWeight.intensitynet.Rd |only intensitynet-1.3.0/intensitynet/man/PlotHeatmap.Rd | 104 + intensitynet-1.3.0/intensitynet/man/PlotHeatmap.intensitynet.Rd | 104 + intensitynet-1.3.0/intensitynet/man/PlotNeighborhood.Rd | 54 - intensitynet-1.3.0/intensitynet/man/PlotNeighborhood.intensitynet.Rd | 54 - intensitynet-1.3.0/intensitynet/man/PointToSegment.netTools.Rd | 36 intensitynet-1.3.0/intensitynet/man/PointToSegment_deprecated.netTools.Rd |only intensitynet-1.3.0/intensitynet/man/RelateEventsToNetwork.Rd |only intensitynet-1.3.0/intensitynet/man/RelateEventsToNetwork.intensitynetDir.Rd |only intensitynet-1.3.0/intensitynet/man/RelateEventsToNetwork.intensitynetMix.Rd |only intensitynet-1.3.0/intensitynet/man/RelateEventsToNetwork.intensitynetUnd.Rd |only intensitynet-1.3.0/intensitynet/man/ShortestNodeDistance.intensitynet.Rd | 46 intensitynet-1.3.0/intensitynet/man/ShortestPath.Rd |only intensitynet-1.3.0/intensitynet/man/ShortestPath.intensitynet.Rd |only intensitynet-1.3.0/intensitynet/man/dir_intnet_chicago.Rd | 42 intensitynet-1.3.0/intensitynet/man/figures/README-example-1.png |binary intensitynet-1.3.0/intensitynet/man/intensitynet.Rd | 19 intensitynet-1.3.0/intensitynet/man/mix_intnet_chicago.Rd | 42 intensitynet-1.3.0/intensitynet/man/plot.intensitynetDir.Rd | 10 intensitynet-1.3.0/intensitynet/man/plot.intensitynetMix.Rd | 10 intensitynet-1.3.0/intensitynet/man/plot.intensitynetUnd.Rd | 10 intensitynet-1.3.0/intensitynet/man/und_intnet_chicago.Rd | 42 intensitynet-1.3.0/intensitynet/tests/testthat/test-directed.R | 11 intensitynet-1.3.0/intensitynet/tests/testthat/test-mixed.R | 11 intensitynet-1.3.0/intensitynet/tests/testthat/test-undirected.R | 11 58 files changed, 1432 insertions(+), 986 deletions(-)
Title: Quickly Explore Your Data Using 'ggplot2' and 'table1' Summary
Tables
Description: Quickly and easily perform exploratory data analysis by uploading your
data as a 'csv' file. Start generating insights using 'ggplot2' plots and
'table1' tables with descriptive stats, all using an easy-to-use point and click
'Shiny' interface.
Author: Samer Mouksassi [aut, cre] ,
Dean Attali [aut],
Benjamin Rich [aut] ,
Michael Sachs [aut]
Maintainer: Samer Mouksassi <samermouksassi@gmail.com>
Diff between ggquickeda versions 0.2.1 dated 2021-06-22 and 0.2.2 dated 2022-05-16
DESCRIPTION | 16 MD5 | 36 NAMESPACE | 1 NEWS.md | 14 R/ggkm.R | 1 README.md | 7 build/vignette.rds |binary inst/doc/AdditionalPlotsStats.html | 298 +++++- inst/doc/Visualizing_Summary_Data.html | 301 +++++- inst/doc/ggquickeda.html | 258 +++++ inst/shinyapp/global.R | 306 ++++++ inst/shinyapp/rsconnect/rstudio.studyexplorer.io/samer.mouksassi/ggquickeda.dcf | 5 inst/shinyapp/server.R | 470 +++++----- inst/shinyapp/ui.R | 235 +++-- man/figures/ggquickedahex.png |binary vignettes/remdesivirfig3.csv | 4 vignettes/sumdata3.png |binary vignettes/sumdata7.png |binary vignettes/sumdata8.png |binary 19 files changed, 1525 insertions(+), 427 deletions(-)
Title: Ornstein-Uhlenbeck Models for Phylogenetic Comparative
Hypotheses
Description: Fit and compare Ornstein-Uhlenbeck models for evolution along a phylogenetic tree.
Author: Aaron A. King [aut, cre],
Marguerite A. Butler [ctb]
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between ouch versions 2.17 dated 2021-05-16 and 2.18 dated 2022-05-16
DESCRIPTION | 16 +++++----- MD5 | 43 +++++++++++++++------------- R/brown.R | 2 - R/geospiza.R |only R/hansen.R | 2 + R/package.R | 5 +++ data/anolis.ssd.rda |binary data/bimac.rda |binary data/geospiza.rda |only inst/CITATION | 72 +++++++++++++++++++++++++----------------------- man/anolis_ssd.Rd | 2 + man/bimac.Rd | 2 + man/bootstrap.Rd | 1 man/brown.Rd | 1 man/coef.Rd | 2 - man/geospiza.Rd |only man/hansen.Rd | 64 ++++++++++++++++++++++-------------------- man/macros/citations.Rd | 8 +++-- man/ouchtree.Rd | 1 man/package.Rd | 10 ++++++ man/paint.Rd | 1 man/plot.Rd | 1 src/covar-matrix.c | 16 +++++----- src/weight-matrix.c | 12 ++++---- 24 files changed, 148 insertions(+), 113 deletions(-)
Title: Functions for Optimal Matching
Description: Distance based bipartite matching using minimum cost flow, oriented
to matching of treatment and control groups in observational studies (Hansen
and Klopfer 2006 <doi:10.1198/106186006X137047>). Routines are provided to
generate distances from generalised linear models (propensity score
matching), formulas giving variables on which to limit matched distances,
stratified or exact matching directives, or calipers, alone or in
combination.
Author: Ben Hansen [aut],
Mark Fredrickson [aut],
Josh Errickson [cre, aut],
Josh Buckner [aut],
Adam Rauh [ctb]
Maintainer: Josh Errickson <jerrick@umich.edu>
Diff between optmatch versions 0.10.2 dated 2022-05-14 and 0.10.3 dated 2022-05-16
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 10 +++++----- inst/doc/fullmatch-vignette.html | 4 ++-- inst/doc/matching-from-foreign-software.html | 4 ++-- inst/doc/matching-within-subgroups.html | 4 ++-- 6 files changed, 19 insertions(+), 19 deletions(-)
Title: Bayesian Inference for Directed Acyclic Graphs
Description: Implementation of a collection of MCMC methods for Bayesian structure learning
of directed acyclic graphs (DAGs), both from continuous and discrete data. For efficient
inference on larger DAGs, the space of DAGs is pruned according to the data. To filter
the search space, the algorithm employs a hybrid approach, combining constraint-based
learning with search and score. A reduced search space is initially defined on the basis
of a skeleton obtained by means of the PC-algorithm, and then iteratively improved with
search and score. Search and score is then performed following two approaches:
Order MCMC, or Partition MCMC.
The BGe score is implemented for continuous data and the BDe score is implemented
for binary data or categorical data. The algorithms may provide the maximum a posteriori
(MAP) graph or a sample (a collection of DAGs) from the posterior distribution given the data.
All algorithms are also applicable for structure learning and sampling for dynamic Bayesian networks.
References:
J. Kuipers, P. Suter, G. Moffa (2022) <doi:10.1080/10618600.2021.2020127>,
N. Friedman and D. Koller (2003) <doi:10.1023/A:1020249912095>,
J. Kuipers and G. Moffa (2017) <doi:10.1080/01621459.2015.1133426>,
M. Kalisch et al. (2012) <doi:10.18637/jss.v047.i11>,
D. Geiger and D. Heckerman (2002) <doi:10.1214/aos/1035844981>.
Author: Polina Suter [aut, cre], Jack Kuipers [aut]
Maintainer: Polina Suter <polina.suter@bsse.ethz.ch>
Diff between BiDAG versions 2.0.6 dated 2022-05-09 and 2.0.7 dated 2022-05-16
BiDAG-2.0.6/BiDAG/man/scoreagainstDBN3.Rd |only BiDAG-2.0.7/BiDAG/DESCRIPTION | 6 BiDAG-2.0.7/BiDAG/MD5 | 59 +++---- BiDAG-2.0.7/BiDAG/R/bidag2coda.R | 19 +- BiDAG-2.0.7/BiDAG/R/extractors.R | 8 - BiDAG-2.0.7/BiDAG/R/graphhelpfns.R | 24 ++- BiDAG-2.0.7/BiDAG/R/initpar.R | 36 ++-- BiDAG-2.0.7/BiDAG/R/performanceassess.R | 74 ++++++++- BiDAG-2.0.7/BiDAG/R/plotfns.R | 5 BiDAG-2.0.7/BiDAG/R/plotusingrgraphviz.R | 239 +++++++++++++++++------------- BiDAG-2.0.7/BiDAG/R/scoreagainstDBN.R | 24 +-- BiDAG-2.0.7/BiDAG/R/summary.R | 2 BiDAG-2.0.7/BiDAG/R/wrappers.R | 25 +-- BiDAG-2.0.7/BiDAG/man/bidag2coda.Rd | 9 - BiDAG-2.0.7/BiDAG/man/bidag2codalist.Rd | 10 - BiDAG-2.0.7/BiDAG/man/compareDAGs.Rd | 6 BiDAG-2.0.7/BiDAG/man/compareDBNs.Rd | 2 BiDAG-2.0.7/BiDAG/man/edgep.Rd | 4 BiDAG-2.0.7/BiDAG/man/getDAG.Rd | 2 BiDAG-2.0.7/BiDAG/man/getMCMCscore.Rd | 2 BiDAG-2.0.7/BiDAG/man/getSpace.Rd | 2 BiDAG-2.0.7/BiDAG/man/getTrace.Rd | 2 BiDAG-2.0.7/BiDAG/man/itercomp.Rd | 2 BiDAG-2.0.7/BiDAG/man/learnBN.Rd | 14 - BiDAG-2.0.7/BiDAG/man/modelp.Rd | 6 BiDAG-2.0.7/BiDAG/man/plotDBN.Rd | 6 BiDAG-2.0.7/BiDAG/man/plotdiffsDBN.Rd | 8 - BiDAG-2.0.7/BiDAG/man/plotpcor.Rd | 5 BiDAG-2.0.7/BiDAG/man/sampleBN.Rd | 11 - BiDAG-2.0.7/BiDAG/man/samplecomp.Rd | 4 BiDAG-2.0.7/BiDAG/man/scoreparameters.Rd | 5 31 files changed, 371 insertions(+), 250 deletions(-)
Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including
functions modelled on base graphics (plot3d(), etc.) as well as functions for
constructing representations of geometric objects (cube3d(), etc.). Output
may be on screen using OpenGL, or to various standard 3D file formats including
WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Duncan Murdoch [aut, cre],
Daniel Adler [aut],
Oleg Nenadic [ctb],
Simon Urbanek [ctb],
Ming Chen [ctb],
Albrecht Gebhardt [ctb],
Ben Bolker [ctb],
Gabor Csardi [ctb],
Adam Strzelecki [ctb],
Alexander Senger [ctb],
The R Core Team [ctb, cph],
Dirk Ed [...truncated...]
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between rgl versions 0.108.3 dated 2021-11-21 and 0.108.3.2 dated 2022-05-16
DESCRIPTION | 6 MD5 | 18 NEWS.md | 8 R/zzz.R | 2 inst/doc/WebGL.html | 1657 ++++++++++++++++++++++++-- inst/doc/pkgdown.html | 246 +++ inst/doc/rgl.html | 1329 ++++++++++++++++---- inst/doc/transparency.html | 281 ++++ inst/htmlwidgets/lib/rglClass/rglClass.min.js | 8 src/init.cpp | 28 10 files changed, 3179 insertions(+), 404 deletions(-)
Title: Integrating Ecosystem Remote Sensing Products to Derive EBV
Indicators
Description: Essential Biodiversity Variables (EBV) are state variables with dimensions on time, space, and biological organization that document biodiversity change. Freely available ecosystem remote sensing products (ERSP) are downloaded and integrated with data for national or regional domains to derive indicators for EBV in the class ecosystem structure (Pereira et al., 2013) <doi:10.1126/science.1229931>, including horizontal ecosystem extents, fragmentation, and information-theory indices. To process ERSP, users must provide a polygon or geographic administrative data map. Downloadable ERSP include Global Surface Water (Peckel et al., 2016) <doi:10.1038/nature20584>, Forest Change (Hansen et al., 2013) <doi:10.1126/science.1244693>, and Continuous Tree Cover data (Sexton et al., 2013) <doi:10.1080/17538947.2013.786146>.
Author: Wilson Lara Henao [aut, cre],
Victor Gutierrez-Velez [aut],
Ivan Gonzalez [ctb],
Maria C. Londono [ctb]
Maintainer: Wilson Lara Henao <wilarhen@gmail.com>
Diff between ecochange versions 2.8 dated 2022-04-09 and 2.9 dated 2022-05-16
DESCRIPTION | 12 +-- MD5 | 40 +++++----- NAMESPACE | 24 +++--- NEWS | 12 +++ R/echanges.R | 4 - R/getrsp.R | 12 --- R/internal.R | 3 R/plot.EBVstats.R | 29 +++---- R/plot.Indicator.R | 111 +++++++++++++++------------- R/plot.echanges.R | 157 +++++++++++++++++++++++++++++++--------- R/rsp2ebv.R | 9 -- R/sampleIndicator.R | 26 +++++- build/vignette.rds |binary inst/doc/EcochangeTutorial.R | 7 - inst/doc/EcochangeTutorial.Rmd | 9 -- inst/doc/EcochangeTutorial.html | 11 +- man/getrsp.Rd | 2 man/plot.Indicator.Rd | 21 +++-- man/plot.echanges.Rd | 29 ++++--- man/rsp2ebv.Rd | 2 vignettes/EcochangeTutorial.Rmd | 9 -- 21 files changed, 326 insertions(+), 203 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-09-28 1.4.2.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-02-06 2.0.4
2010-10-21 1.2.0
2010-10-18 1.1.5
2010-10-05 1.1.4
2010-09-28 1.1.3
2010-09-14 1.1.2
2010-09-13 1.1.1
2010-09-09 1.1.0
2010-08-24 1.0.3
2010-08-20 1.0.2
2010-08-18 1.0.1
2010-08-10 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-07-04 1.3
2010-11-28 1.2
2010-01-14 1.1
2009-07-18 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-29 0.5.4
2021-10-31 0.5.1
2021-07-22 0.4.3
2021-07-14 0.4.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-06-19 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-07-02 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-03 1.0
Title: Hyperbolic Geometry
Description: Hyperbolic geometry in the hyperboloid model and the Poincaré model. The methods are based on the gyrovector space theory developed by A. A. Ungar that can be found in the book 'Analytic Hyperbolic Geometry: Mathematical Foundations And Applications' <doi:10.1142/5914>. The package provides functions to plot three-dimensional hyperbolic polyhedra, to plot hyperbolic tilings of the Poincaré disk, and to construct and plot Delaunay hyperbolic triangulations of the Poincaré disk. They are constructed with the help of the C++ library 'CGAL'.
Author: Stephane Laurent
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between gyro versions 0.2.0 dated 2022-03-15 and 1.0.0 dated 2022-05-16
gyro-0.2.0/gyro/inst/essais |only gyro-1.0.0/gyro/DESCRIPTION | 20 - gyro-1.0.0/gyro/MD5 | 59 ++-- gyro-1.0.0/gyro/NAMESPACE | 72 ++-- gyro-1.0.0/gyro/NEWS.md | 9 gyro-1.0.0/gyro/R/RcppExports.R |only gyro-1.0.0/gyro/R/gyro.R | 456 +++++++++++++++++++++++++------ gyro-1.0.0/gyro/R/hdelaunay.R |only gyro-1.0.0/gyro/R/internal.R | 12 gyro-1.0.0/gyro/R/tiling.R |only gyro-1.0.0/gyro/README.md | 21 + gyro-1.0.0/gyro/inst/approx_sqrt.R |only gyro-1.0.0/gyro/inst/doc/getstarted.Rmd | 9 gyro-1.0.0/gyro/inst/doc/getstarted.html | 58 +++ gyro-1.0.0/gyro/man/PhiMU.Rd |only gyro-1.0.0/gyro/man/PhiUM.Rd |only gyro-1.0.0/gyro/man/gyroABt.Rd | 54 ++- gyro-1.0.0/gyro/man/gyromidpoint.Rd |only gyro-1.0.0/gyro/man/gyrosegment.Rd | 123 +++++--- gyro-1.0.0/gyro/man/gyrotriangle.Rd | 183 ++++++------ gyro-1.0.0/gyro/man/gyrotube.Rd | 102 +++--- gyro-1.0.0/gyro/man/hdelaunay.Rd |only gyro-1.0.0/gyro/man/hreflection.Rd |only gyro-1.0.0/gyro/man/plotGyrohull3d.Rd | 353 ++++++++++++----------- gyro-1.0.0/gyro/man/plotHdelaunay.Rd |only gyro-1.0.0/gyro/man/tiling.Rd |only gyro-1.0.0/gyro/src |only gyro-1.0.0/gyro/vignettes/getstarted.Rmd | 9 28 files changed, 1002 insertions(+), 538 deletions(-)
Title: Streaming Events and their Early Classification
Description: Implements event extraction and early classification of events in data streams in R.
It has the functionality to generate 2-dimensional data streams with events belonging to
2 classes. These events can be extracted and features computed. The event features extracted
from incomplete-events can be classified using a partial-observations-classifier
(Kandanaarachchi et al. 2018) <doi:10.1371/journal.pone.0236331>.
Author: Sevvandi Kandanaarachchi [aut, cre]
Maintainer: Sevvandi Kandanaarachchi <sevvandik@gmail.com>
Diff between eventstream versions 0.1.0 dated 2019-12-06 and 0.1.1 dated 2022-05-16
eventstream-0.1.0/eventstream/data/datalist |only eventstream-0.1.1/eventstream/DESCRIPTION | 12 - eventstream-0.1.1/eventstream/MD5 | 84 +++++----- eventstream-0.1.1/eventstream/NAMESPACE | 2 eventstream-0.1.1/eventstream/R/NO2_2010-data.R | 2 eventstream-0.1.1/eventstream/R/NO2_2011-data.R | 2 eventstream-0.1.1/eventstream/R/NO2_2012-data.R | 2 eventstream-0.1.1/eventstream/R/NO2_2013-data.R | 2 eventstream-0.1.1/eventstream/R/NO2_2014-data.R | 2 eventstream-0.1.1/eventstream/R/NO2_2015-data.R | 2 eventstream-0.1.1/eventstream/R/NO2_2016-data.R | 2 eventstream-0.1.1/eventstream/R/NO2_2017-data.R | 2 eventstream-0.1.1/eventstream/R/NO2_2018-data.R | 2 eventstream-0.1.1/eventstream/R/NO2_2019-data.R | 2 eventstream-0.1.1/eventstream/R/event_functions_2d.R | 2 eventstream-0.1.1/eventstream/R/gen_functions.R | 51 +++++- eventstream-0.1.1/eventstream/R/gen_stream.R | 15 + eventstream-0.1.1/eventstream/R/stream_from_files.R | 2 eventstream-0.1.1/eventstream/R/tune_event_detection.R |only eventstream-0.1.1/eventstream/R/utils.R | 6 eventstream-0.1.1/eventstream/README.md | 65 ++++--- eventstream-0.1.1/eventstream/man/NO2_2010.Rd | 8 eventstream-0.1.1/eventstream/man/NO2_2011.Rd | 8 eventstream-0.1.1/eventstream/man/NO2_2012.Rd | 8 eventstream-0.1.1/eventstream/man/NO2_2013.Rd | 8 eventstream-0.1.1/eventstream/man/NO2_2014.Rd | 8 eventstream-0.1.1/eventstream/man/NO2_2015.Rd | 8 eventstream-0.1.1/eventstream/man/NO2_2016.Rd | 8 eventstream-0.1.1/eventstream/man/NO2_2017.Rd | 8 eventstream-0.1.1/eventstream/man/NO2_2018.Rd | 8 eventstream-0.1.1/eventstream/man/NO2_2019.Rd | 8 eventstream-0.1.1/eventstream/man/extract_event_ftrs.Rd | 18 +- eventstream-0.1.1/eventstream/man/figures/README-extract-1.png |binary eventstream-0.1.1/eventstream/man/figures/README-extract-2.png |binary eventstream-0.1.1/eventstream/man/figures/README-getdat-1.png |binary eventstream-0.1.1/eventstream/man/figures/README-references.bib | 17 +- eventstream-0.1.1/eventstream/man/gen_stream.Rd | 18 +- eventstream-0.1.1/eventstream/man/get_clusters.Rd | 11 + eventstream-0.1.1/eventstream/man/get_features.Rd | 9 - eventstream-0.1.1/eventstream/man/real_details.Rd | 6 eventstream-0.1.1/eventstream/man/real_stream.Rd | 4 eventstream-0.1.1/eventstream/man/stream_from_files.Rd | 2 eventstream-0.1.1/eventstream/man/td_logistic.Rd | 13 + eventstream-0.1.1/eventstream/man/tune_cpdbee_2D.Rd |only eventstream-0.1.1/eventstream/man/tune_cpdbee_3D.Rd |only 45 files changed, 286 insertions(+), 151 deletions(-)
Title: A Flexible Approach for Causal Inference with Multiple
Treatments and Clustered Survival Outcomes
Description: Random-intercept accelerated failure time (AFT) model utilizing Bayesian additive regression trees (BART) for drawing causal inferences about multiple treatments while accounting for the multilevel survival data structure. It also includes an interpretable sensitivity analysis approach to evaluate how the drawn causal conclusions might be altered in response to the potential magnitude of departure from the no unmeasured confounding assumption.
Author: Liangyuan Hu [aut],
Jiayi Ji [aut, cre]
Maintainer: Jiayi Ji <jj869@sph.rutgers.edu>
Diff between riAFTBART versions 0.3.0 dated 2022-04-10 and 0.3.1 dated 2022-05-16
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/cal_PEHE.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Multivariate Normal Distribution
Description: Calculates and differentiates probabilities and density of (conditional) multivariate normal distribution using methods described in A. Genz (2004) <doi:10.1023/B:STCO.0000035304.20635.31>, A. Genz, F. Bretz (2009) <doi:10.1007/978-3-642-01689-9> and E. Kossova, B. Potanin (2018) <https:ideas.repec.org/a/ris/apltrx/0346.html>.
Author: Bogdan Potanin [aut, cre, ctb]
Maintainer: Bogdan Potanin <bogdanpotanin@gmail.com>
Diff between mnorm versions 1.0.0 dated 2022-05-11 and 1.0.1 dated 2022-05-16
DESCRIPTION | 10 +++--- MD5 | 12 +++---- src/cmnorm.cpp | 53 ++++++++++++++++++-------------- src/dmnorm.cpp | 84 ++++++++++++++++++++++++++++++++------------------- src/halton.cpp | 20 ++++++++---- src/pmnorm.cpp | 93 ++++++++++++++++++++++++++++++++------------------------- src/qmnorm.cpp | 19 +++++++---- 7 files changed, 174 insertions(+), 117 deletions(-)
Title: Download Data from Kobotoolbox to R
Description: Wrapper for 'Kobotoolbox' APIs ver 2 mentioned at <https://support.kobotoolbox.org/api.html>, to download data from 'Kobotoolbox' to R. Small and simple package that adds immense convenience for the data professionals using 'Kobotoolbox'.
Author: Asitav Sen [aut, cre, cph]
Maintainer: Asitav Sen <hello@asitavsen.com>
Diff between KoboconnectR versions 1.0.0 dated 2022-03-29 and 1.1.0 dated 2022-05-16
DESCRIPTION | 6 - MD5 | 30 ++--- NAMESPACE | 5 NEWS.md | 4 R/Koboconnect.R | 168 +++++++++++++++++-------------- R/other.R | 102 ++++++++++++++++++ README.md | 17 ++- inst/doc/Usage.R | 4 inst/doc/Usage.Rmd | 18 +++ inst/doc/Usage.html | 12 ++ man/kobo_df_download.Rd |only man/kobo_export_create.Rd | 32 ++++- man/kobo_exports.Rd | 2 man/kobotools_kpi_data.Rd | 2 tests/testthat/test-kobo_df_download.R |only tests/testthat/test-kobo_export_create.R | 32 +++++ vignettes/Usage.Rmd | 18 +++ 17 files changed, 348 insertions(+), 104 deletions(-)
Title: Differential Gene Expression (DGE) Analysis Results Data Object
Description: Provides a flexible container to manage and annotate Differential Gene
Expression (DGE) analysis results (Smythe et. al (2015) <doi:10.1093/nar/gkv007>).
The DGEobj has data slots for row (gene), col (samples), assays (matrix n-rows
by m-samples dimensions) and metadata (not keyed to row, col, or assays).
A set of accessory functions to deposit, query and retrieve subsets of a data
workflow has been provided. Attributes are used to capture metadata such as
species and gene model, including reproducibility information such that a 3rd
party can access a DGEobj history to see how each data object was created or
modified. Since the DGEobj is customizable and extensible it is not limited
to RNA-seq analysis types of workflows -- it can accommodate nearly any data
analysis workflow that starts from a matrix of assays (rows) by samples (columns).
Author: John Thompson [aut],
Connie Brett [aut, cre],
Isaac Neuhaus [aut],
Ryan Thompson [aut]
Maintainer: Connie Brett <connie@aggregate-genius.com>
Diff between DGEobj versions 1.1.1 dated 2022-05-10 and 1.1.2 dated 2022-05-16
DESCRIPTION | 10 ++-- MD5 | 97 +++++++++++++++++++-------------------- NEWS.md | 6 ++ R/addItem.R | 8 ++- R/annotate.R | 6 +- R/attributes.R | 10 +--- R/get.R | 9 +-- R/init.R | 13 ++--- R/reset.R | 4 - R/rmItem.R | 2 R/subset.R | 4 - R/types.R | 8 +-- R/utils.R | 10 +--- inst/doc/DGEobj_Overview.Rmd | 66 +++++++++++++------------- inst/doc/DGEobj_Overview.html | 68 +++++++++++++-------------- inst/miniObj.RDS |only man/addItem.Rd | 4 - man/addItems.Rd | 4 + man/annotateDGEobj.Rd | 3 - man/as.list.DGEobj.Rd | 2 man/baseType.Rd | 2 man/baseTypes.Rd | 2 man/getAttributes.Rd | 2 man/getBaseType.Rd | 2 man/getItem.Rd | 2 man/getItems.Rd | 2 man/getType.Rd | 2 man/initDGEobj.Rd | 13 ++--- man/inventory.Rd | 4 - man/newType.Rd | 2 man/print.DGEobj.Rd | 4 - man/resetDGEobj.Rd | 4 - man/rmItem.Rd | 2 man/setAttributes.Rd | 2 man/showAttributes.Rd | 4 - man/showMeta.Rd | 2 man/showTypes.Rd | 2 man/subset.DGEobj.Rd | 4 - tests/testthat/setup.R | 12 ++++ tests/testthat/test_addItem.R | 1 tests/testthat/test_annotate.R | 1 tests/testthat/test_attributes.R | 1 tests/testthat/test_get.R | 1 tests/testthat/test_init.R | 1 tests/testthat/test_reset.R | 2 tests/testthat/test_rmItem.R | 1 tests/testthat/test_subset.R | 1 tests/testthat/test_types.R | 1 tests/testthat/test_utils.R | 1 vignettes/DGEobj_Overview.Rmd | 66 +++++++++++++------------- 50 files changed, 245 insertions(+), 235 deletions(-)
Title: Easy Data Wrangling
Description: A lightweight package to easily manipulate, clean, transform,
and prepare your data for analysis. It also forms the data wrangling
backend for the packages in the 'easystats' ecosystem.
Author: Dominique Makowski [aut] ,
Daniel Luedecke [aut] ,
Indrajeet Patil [aut, cre] ,
Mattan S. Ben-Shachar [aut] ,
Brenton M. Wiernik [aut] ,
Etienne Bacher [ctb]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between datawizard versions 0.4.0 dated 2022-03-30 and 0.4.1 dated 2022-05-16
datawizard-0.4.0/datawizard/R/convert_data_to_numeric.R |only datawizard-0.4.0/datawizard/R/data_findcols.R |only datawizard-0.4.0/datawizard/man/convert_data_to_numeric.Rd |only datawizard-0.4.0/datawizard/tests/testthat/test-convert_data_to_numeric.R |only datawizard-0.4.1/datawizard/DESCRIPTION | 15 datawizard-0.4.1/datawizard/MD5 | 342 - datawizard-0.4.1/datawizard/NAMESPACE | 443 +- datawizard-0.4.1/datawizard/NEWS.md | 373 + datawizard-0.4.1/datawizard/R/adjust.R | 408 +- datawizard-0.4.1/datawizard/R/backports.R | 32 datawizard-0.4.1/datawizard/R/center.R | 462 +- datawizard-0.4.1/datawizard/R/convert_na_to.R | 403 +- datawizard-0.4.1/datawizard/R/convert_to_na.R | 270 - datawizard-0.4.1/datawizard/R/data.R | 42 datawizard-0.4.1/datawizard/R/data_addprefix.R | 56 datawizard-0.4.1/datawizard/R/data_cut.R | 672 +-- datawizard-0.4.1/datawizard/R/data_extract.R | 278 - datawizard-0.4.1/datawizard/R/data_find.R |only datawizard-0.4.1/datawizard/R/data_group.R |only datawizard-0.4.1/datawizard/R/data_match.R | 309 - datawizard-0.4.1/datawizard/R/data_merge.R | 776 ++-- datawizard-0.4.1/datawizard/R/data_partition.R | 162 datawizard-0.4.1/datawizard/R/data_read.R |only datawizard-0.4.1/datawizard/R/data_recode.R |only datawizard-0.4.1/datawizard/R/data_relocate.R | 266 - datawizard-0.4.1/datawizard/R/data_remove.R | 50 datawizard-0.4.1/datawizard/R/data_rename.R | 248 - datawizard-0.4.1/datawizard/R/data_rescale.R | 352 - datawizard-0.4.1/datawizard/R/data_reshape.R | 484 +- datawizard-0.4.1/datawizard/R/data_restoretype.R | 138 datawizard-0.4.1/datawizard/R/data_reverse.R | 404 +- datawizard-0.4.1/datawizard/R/data_rotate.R | 196 - datawizard-0.4.1/datawizard/R/data_select.R | 78 datawizard-0.4.1/datawizard/R/data_shift.R |only datawizard-0.4.1/datawizard/R/data_tabulate.R |only datawizard-0.4.1/datawizard/R/data_to_factor.R |only datawizard-0.4.1/datawizard/R/data_to_numeric.R |only datawizard-0.4.1/datawizard/R/demean.R | 802 ++-- datawizard-0.4.1/datawizard/R/describe_distribution.R | 996 ++--- datawizard-0.4.1/datawizard/R/format.R | 130 datawizard-0.4.1/datawizard/R/format_text.R | 230 - datawizard-0.4.1/datawizard/R/normalize.R | 354 - datawizard-0.4.1/datawizard/R/ranktransform.R | 310 - datawizard-0.4.1/datawizard/R/reexports.R | 38 datawizard-0.4.1/datawizard/R/remove_empty.R | 204 - datawizard-0.4.1/datawizard/R/replace_nan_inf.R | 82 datawizard-0.4.1/datawizard/R/rescale_weights.R | 420 +- datawizard-0.4.1/datawizard/R/reshape_ci.R | 248 - datawizard-0.4.1/datawizard/R/select_helpers.R | 499 +- datawizard-0.4.1/datawizard/R/skewness_kurtosis.R | 920 ++-- datawizard-0.4.1/datawizard/R/smoothness.R | 262 - datawizard-0.4.1/datawizard/R/standardize.R | 673 +-- datawizard-0.4.1/datawizard/R/standardize.models.R |only datawizard-0.4.1/datawizard/R/unnormalize.R |only datawizard-0.4.1/datawizard/R/unstandardize.R | 376 +- datawizard-0.4.1/datawizard/R/utils.R | 13 datawizard-0.4.1/datawizard/R/utils_data.R | 128 datawizard-0.4.1/datawizard/R/utils_standardize_center.R | 780 ++-- datawizard-0.4.1/datawizard/R/utils_strings.R | 38 datawizard-0.4.1/datawizard/R/visualisation_recipe.R | 174 datawizard-0.4.1/datawizard/R/weighted_mean_median_sd_mad.R | 208 - datawizard-0.4.1/datawizard/R/winsorize.R | 136 datawizard-0.4.1/datawizard/README.md | 1141 +++--- datawizard-0.4.1/datawizard/build/vignette.rds |binary datawizard-0.4.1/datawizard/inst/CITATION | 32 datawizard-0.4.1/datawizard/inst/WORDLIST | 174 datawizard-0.4.1/datawizard/inst/doc/standardize_data.R | 576 +-- datawizard-0.4.1/datawizard/inst/doc/standardize_data.Rmd | 900 ++-- datawizard-0.4.1/datawizard/inst/doc/standardize_data.html | 1876 ++++------ datawizard-0.4.1/datawizard/man/adjust.Rd | 265 - datawizard-0.4.1/datawizard/man/center.Rd | 336 - datawizard-0.4.1/datawizard/man/convert_na_to.Rd | 280 - datawizard-0.4.1/datawizard/man/convert_to_na.Rd | 192 - datawizard-0.4.1/datawizard/man/data_cut.Rd | 394 +- datawizard-0.4.1/datawizard/man/data_extract.Rd | 247 - datawizard-0.4.1/datawizard/man/data_group.Rd |only datawizard-0.4.1/datawizard/man/data_match.Rd | 204 - datawizard-0.4.1/datawizard/man/data_merge.Rd | 386 +- datawizard-0.4.1/datawizard/man/data_partition.Rd | 100 datawizard-0.4.1/datawizard/man/data_read.Rd |only datawizard-0.4.1/datawizard/man/data_recode.Rd |only datawizard-0.4.1/datawizard/man/data_relocate.Rd | 213 - 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Title: Identification and Estimation using Group Testing
Description: Methods for the group testing identification problem: 1) Operating
characteristics (e.g., expected number of tests) for commonly used
hierarchical and array-based algorithms, and 2) Optimal testing
configurations for these same algorithms. Methods for the group testing
estimation problem: 1) Estimation and inference procedures for an overall
prevalence, and 2) Regression modeling for commonly used hierarchical and
array-based algorithms.
Author: Brianna Hitt [aut, cre] ,
Christopher Bilder [aut] ,
Frank Schaarschmidt [aut] ,
Brad Biggerstaff [aut] ,
Christopher McMahan [aut] ,
Joshua Tebbs [aut] ,
Boan Zhang [ctb],
Michael Black [ctb],
Peijie Hou [ctb],
Peng Chen [ctb]
Maintainer: Brianna Hitt <brianna.hitt@huskers.unl.edu>
Diff between binGroup2 versions 1.1.0 dated 2021-03-17 and 1.2.3 dated 2022-05-16
binGroup2-1.1.0/binGroup2/R/convert.config.R |only binGroup2-1.1.0/binGroup2/R/plot.OTC.R |only binGroup2-1.2.3/binGroup2/DESCRIPTION | 21 binGroup2-1.2.3/binGroup2/MD5 | 132 - binGroup2-1.2.3/binGroup2/NAMESPACE | 45 binGroup2-1.2.3/binGroup2/R/AddGenericFunctions.R |only binGroup2-1.2.3/binGroup2/R/DorfmanFunctions.R | 139 + binGroup2-1.2.3/binGroup2/R/Inf.D3.OTC1.R | 240 +- binGroup2-1.2.3/binGroup2/R/Inf.Dorf.OTC1.R | 350 +-- binGroup2-1.2.3/binGroup2/R/NI.D3.OTC1.R | 264 +- binGroup2-1.2.3/binGroup2/R/OTC1.R | 1123 ++------- binGroup2-1.2.3/binGroup2/R/OTC2.R | 526 ++-- binGroup2-1.2.3/binGroup2/R/OTCMethodFunctions.R |only binGroup2-1.2.3/binGroup2/R/SterrettFunctions.R | 914 ++++---- binGroup2-1.2.3/binGroup2/R/SupportingOTCFunctions.R |only binGroup2-1.2.3/binGroup2/R/SupportingOpCharFunctions.R |only binGroup2-1.2.3/binGroup2/R/ThresholdDorfman.R |only binGroup2-1.2.3/binGroup2/R/arrayFunctions.R | 178 - binGroup2-1.2.3/binGroup2/R/binGroup2-package.R | 433 +-- binGroup2-1.2.3/binGroup2/R/designFunctions.R | 757 +++--- binGroup2-1.2.3/binGroup2/R/gtPower.R | 307 +- binGroup2-1.2.3/binGroup2/R/gtReg.R | 1466 +++++++------ binGroup2-1.2.3/binGroup2/R/gtSim.R | 222 - binGroup2-1.2.3/binGroup2/R/gtTest.R | 156 - binGroup2-1.2.3/binGroup2/R/gtWidth.R | 145 - binGroup2-1.2.3/binGroup2/R/halving.R |only binGroup2-1.2.3/binGroup2/R/hierarchicalFunctions.R | 1098 +++------ binGroup2-1.2.3/binGroup2/R/opCharMethodFunctions.R |only binGroup2-1.2.3/binGroup2/R/operatingCharacteristics1.R | 359 --- binGroup2-1.2.3/binGroup2/R/operatingCharacteristics2.R | 656 ++--- binGroup2-1.2.3/binGroup2/build/partial.rdb |binary binGroup2-1.2.3/binGroup2/inst/REFERENCES.bib | 42 binGroup2-1.2.3/binGroup2/man/Accuracy.Rd |only binGroup2-1.2.3/binGroup2/man/CompareConfig.Rd |only binGroup2-1.2.3/binGroup2/man/Config.OTC.Rd |only binGroup2-1.2.3/binGroup2/man/Config.Rd |only binGroup2-1.2.3/binGroup2/man/Config.opChar.Rd |only binGroup2-1.2.3/binGroup2/man/ExpTests.OTC.Rd |only binGroup2-1.2.3/binGroup2/man/ExpTests.Rd |only binGroup2-1.2.3/binGroup2/man/ExpTests.Sterrett.Rd |only binGroup2-1.2.3/binGroup2/man/ExpTests.TOD.Rd |only binGroup2-1.2.3/binGroup2/man/ExpTests.halving.Rd |only binGroup2-1.2.3/binGroup2/man/ExpTests.opChar.Rd |only binGroup2-1.2.3/binGroup2/man/IndProb.Rd |only binGroup2-1.2.3/binGroup2/man/OTC1.Rd | 349 +-- binGroup2-1.2.3/binGroup2/man/OTC2.Rd | 352 +-- binGroup2-1.2.3/binGroup2/man/Sterrett.Rd | 29 binGroup2-1.2.3/binGroup2/man/TOD.Rd |only binGroup2-1.2.3/binGroup2/man/binGroup2.Rd | 329 +- binGroup2-1.2.3/binGroup2/man/coef.gtReg.Rd |only binGroup2-1.2.3/binGroup2/man/designEst.Rd | 48 binGroup2-1.2.3/binGroup2/man/designPower.Rd | 174 - binGroup2-1.2.3/binGroup2/man/expectOrderBeta.Rd | 47 binGroup2-1.2.3/binGroup2/man/formula.gtReg.Rd |only binGroup2-1.2.3/binGroup2/man/gtPower.Rd | 81 binGroup2-1.2.3/binGroup2/man/gtReg.Rd | 389 +-- binGroup2-1.2.3/binGroup2/man/gtRegControl.Rd | 20 binGroup2-1.2.3/binGroup2/man/gtSim.Rd | 154 - binGroup2-1.2.3/binGroup2/man/gtTest.Rd | 60 binGroup2-1.2.3/binGroup2/man/gtWidth.Rd | 41 binGroup2-1.2.3/binGroup2/man/halving.Rd | 60 binGroup2-1.2.3/binGroup2/man/informativeArrayProb.Rd | 26 binGroup2-1.2.3/binGroup2/man/operatingCharacteristics1.Rd | 14 binGroup2-1.2.3/binGroup2/man/operatingCharacteristics2.Rd | 401 +-- binGroup2-1.2.3/binGroup2/man/plot.OTC.Rd | 111 binGroup2-1.2.3/binGroup2/man/pmf.Rd |only binGroup2-1.2.3/binGroup2/man/pmf.Sterrett.Rd |only binGroup2-1.2.3/binGroup2/man/pmf.halving.Rd |only binGroup2-1.2.3/binGroup2/man/predict.gtReg.Rd | 67 binGroup2-1.2.3/binGroup2/man/print.OTC.Rd |only binGroup2-1.2.3/binGroup2/man/print.Sterrett.Rd |only binGroup2-1.2.3/binGroup2/man/print.TOD.Rd |only binGroup2-1.2.3/binGroup2/man/print.designEst.Rd |only binGroup2-1.2.3/binGroup2/man/print.designPower.Rd | 18 binGroup2-1.2.3/binGroup2/man/print.gtReg.Rd |only binGroup2-1.2.3/binGroup2/man/print.gtTest.Rd | 14 binGroup2-1.2.3/binGroup2/man/print.halving.Rd |only binGroup2-1.2.3/binGroup2/man/print.opChar.Rd |only binGroup2-1.2.3/binGroup2/man/print.predict.gtReg.Rd |only binGroup2-1.2.3/binGroup2/man/print.summary.gtReg.Rd | 24 binGroup2-1.2.3/binGroup2/man/residuals.gtReg.Rd |only binGroup2-1.2.3/binGroup2/man/summary.OTC.Rd | 129 - binGroup2-1.2.3/binGroup2/man/summary.gtReg.Rd | 69 binGroup2-1.2.3/binGroup2/man/summary.opChar.Rd | 124 - binGroup2-1.2.3/binGroup2/src/RcppExports.cpp | 5 85 files changed, 6039 insertions(+), 6669 deletions(-)
Title: Generate Bootstrap Prediction Intervals from a 'tidymodels'
Workflow
Description: Provides functions for generating bootstrap prediction
intervals from a 'tidymodels' workflow. 'tidymodels'
<https://www.tidymodels.org/> is a collection of packages for modeling
and machine learning using 'tidyverse' <https://www.tidyverse.org/>
principles. This package is not affiliated with or maintained by
'RStudio' or the 'tidymodels' maintainers.
Author: Mark Rieke [aut, cre]
Maintainer: Mark Rieke <markjrieke@gmail.com>
Diff between workboots versions 0.1.1 dated 2022-04-11 and 0.2.0 dated 2022-05-16
workboots-0.1.1/workboots/inst/doc/Estimating-a-Linear-Prediction-Interval.R |only workboots-0.1.1/workboots/inst/doc/Estimating-a-Linear-Prediction-Interval.Rmd |only workboots-0.1.1/workboots/inst/doc/Estimating-a-Linear-Prediction-Interval.html |only workboots-0.1.1/workboots/inst/doc/Getting-Started.R |only workboots-0.1.1/workboots/inst/doc/Getting-Started.Rmd |only workboots-0.1.1/workboots/inst/doc/Getting-Started.html |only workboots-0.1.1/workboots/man/predict_single_boot.Rd |only workboots-0.1.1/workboots/man/summarise_generic.Rd |only workboots-0.1.1/workboots/man/vi_single_boot.Rd |only workboots-0.1.1/workboots/vignettes/Estimating-a-Linear-Prediction-Interval.Rmd |only workboots-0.1.1/workboots/vignettes/Getting-Started.Rmd |only workboots-0.2.0/workboots/DESCRIPTION | 17 - workboots-0.2.0/workboots/MD5 | 51 ++--- workboots-0.2.0/workboots/NAMESPACE | 3 workboots-0.2.0/workboots/NEWS.md | 10 - workboots-0.2.0/workboots/R/assertions.R | 12 - workboots-0.2.0/workboots/R/globals.R | 3 workboots-0.2.0/workboots/R/predict_boots.R | 96 +++++----- workboots-0.2.0/workboots/R/summarise_boots.R | 91 +++++++-- workboots-0.2.0/workboots/R/vi_boots.R | 12 - workboots-0.2.0/workboots/README.md | 94 ++++++--- workboots-0.2.0/workboots/build/vignette.rds |binary workboots-0.2.0/workboots/inst/doc/Estimating-Linear-Intervals.R |only workboots-0.2.0/workboots/inst/doc/Estimating-Linear-Intervals.Rmd |only workboots-0.2.0/workboots/inst/doc/Estimating-Linear-Intervals.html |only workboots-0.2.0/workboots/inst/doc/Getting-Started-with-workboots.R |only workboots-0.2.0/workboots/inst/doc/Getting-Started-with-workboots.Rmd |only workboots-0.2.0/workboots/inst/doc/Getting-Started-with-workboots.html |only workboots-0.2.0/workboots/man/predict_boots.Rd | 7 workboots-0.2.0/workboots/man/summarise_importance.Rd | 14 - workboots-0.2.0/workboots/man/summarise_predictions.Rd | 20 +- workboots-0.2.0/workboots/man/vi_boots.Rd | 10 - workboots-0.2.0/workboots/tests/testthat/test-predict-boots.R | 30 +++ workboots-0.2.0/workboots/tests/testthat/test-summarise-boots.R | 4 workboots-0.2.0/workboots/vignettes/Estimating-Linear-Intervals.Rmd |only workboots-0.2.0/workboots/vignettes/Getting-Started-with-workboots.Rmd |only 36 files changed, 311 insertions(+), 163 deletions(-)
Title: Multiple Imputation of Covariates by Substantive Model
Compatible Fully Conditional Specification
Description: Implements multiple imputation of missing covariates by
Substantive Model Compatible Fully Conditional Specification.
This is a modification of the popular FCS/chained equations
multiple imputation approach, and allows imputation of missing
covariate values from models which are compatible with the user
specified substantive model.
Author: Jonathan Bartlett [aut, cre],
Ruth Keogh [aut],
Edouard F. Bonneville [aut],
Claus Thorn Ekstroem [ctb]
Maintainer: Jonathan Bartlett <j.w.bartlett@bath.ac.uk>
Diff between smcfcs versions 1.6.1 dated 2022-01-18 and 1.6.2 dated 2022-05-16
DESCRIPTION | 8 MD5 | 80 - NAMESPACE | 22 R/data.r | 286 ++-- R/plot_convergence.R | 426 +++--- R/smcfcs.r | 2338 ++++++++++++++++----------------- R/smcfcs_parallel.r | 342 ++-- README.md | 22 build/partial.rdb |binary build/vignette.rds |binary inst/doc/smcfcs-vignette.R | 96 - inst/doc/smcfcs-vignette.Rmd | 278 +-- inst/doc/smcfcs-vignette.html | 1133 ++++++++++----- inst/doc/smcfcs_coverror-vignette.R | 168 +- inst/doc/smcfcs_coverror-vignette.Rmd | 262 +-- inst/doc/smcfcs_coverror-vignette.html | 935 ++++++++----- man/ex_cc.Rd | 50 man/ex_compet.Rd | 48 man/ex_coxquad.Rd | 50 man/ex_dtsam.Rd | 44 man/ex_lininter.Rd | 44 man/ex_linquad.Rd | 48 man/ex_logisticquad.Rd | 48 man/ex_ncc.Rd | 52 man/ex_poisson.Rd | 46 man/plot.smcfcs.Rd | 118 - man/smcfcs.Rd | 444 +++--- man/smcfcs.casecohort.Rd | 202 +- man/smcfcs.dtsam.Rd | 230 +-- man/smcfcs.nestedcc.Rd | 216 +-- man/smcfcs.parallel.Rd | 164 +- tests/testthat/test_casecohort.r | 166 +- tests/testthat/test_coxph.r | 96 - tests/testthat/test_dtsam.r | 878 ++++++------ tests/testthat/test_errorchecks.R | 487 +++--- tests/testthat/test_measerror.r | 172 +- tests/testthat/test_nestedcc.R | 272 +-- tests/testthat/test_parallel.r | 418 ++--- tests/testthat/test_weibull.r | 126 - vignettes/smcfcs-vignette.Rmd | 278 +-- vignettes/smcfcs_coverror-vignette.Rmd | 262 +-- 41 files changed, 6014 insertions(+), 5341 deletions(-)
Title: Multiple Mediation Analysis
Description: Used for general multiple mediation analysis.
The analysis method is described in Yu and Li (2022) (ISBN: 9780367365479) "Statistical Methods for Mediation, Confounding and Moderation Analysis Using R and SAS", published by Chapman and Hall/CRC; and Yu et al.(2017) <DOI:10.1016/j.sste.2017.02.001> "Exploring racial disparity in obesity: a mediation analysis considering geo-coded environmental factors", published on Spatial and Spatio-temporal Epidemiology, 21, 13-23.
Author: Qingzhao Yu and Bin Li
Maintainer: Qingzhao Yu <qyu@lsuhsc.edu>
Diff between mma versions 10.5-1 dated 2021-10-25 and 10.6-1 dated 2022-05-16
DESCRIPTION | 12 MD5 | 28 - NAMESPACE | 1 R/mma.r | 6 inst/doc/MMAvignette.Rmd | 2 inst/doc/MMAvignette.html | 175 +++++----- man/mma-package.Rd | 2 vignettes/MMAvignette.Rmd | 2 vignettes/MMAvignette_files/figure-html/unnamed-chunk-10-3.png |binary vignettes/MMAvignette_files/figure-html/unnamed-chunk-13-1.png |binary vignettes/MMAvignette_files/figure-html/unnamed-chunk-16-1.png |binary vignettes/MMAvignette_files/figure-html/unnamed-chunk-19-1.png |binary vignettes/MMAvignette_files/figure-html/unnamed-chunk-22-1.png |binary vignettes/MMAvignette_files/figure-html/unnamed-chunk-23-1.png |binary vignettes/vignettebib.bib | 128 +++---- 15 files changed, 185 insertions(+), 171 deletions(-)
Title: Latent (Variable) Analysis with Bayesian Learning
Description: A variety of models to analyze latent variables based on Bayesian learning: the partially CFA (Chen, Guo, Zhang, & Pan, 2020) <DOI: 10.1037/met0000293>; generalized PCFA; partially confirmatory IRM (Chen, 2020) <DOI: 10.1007/s11336-020-09724-3>; Bayesian regularized EFA <DOI: 10.1080/10705511.2020.1854763>; Fully and partially EFA.
Author: Jinsong Chen [aut, cre, cph]
Maintainer: Jinsong Chen <jinsong.chen@live.com>
Diff between LAWBL versions 1.4.0 dated 2021-04-01 and 1.5.0 dated 2022-05-16
LAWBL-1.4.0/LAWBL/R/Gibbs_pefa_main.R |only LAWBL-1.5.0/LAWBL/DESCRIPTION | 10 LAWBL-1.5.0/LAWBL/MD5 | 50 ++-- LAWBL-1.5.0/LAWBL/NEWS.md | 48 ++-- LAWBL-1.5.0/LAWBL/R/Gibbs_BLR_SSP.R |only LAWBL-1.5.0/LAWBL/R/Init.R | 41 +++ LAWBL-1.5.0/LAWBL/R/LAWBL-package.R | 15 - LAWBL-1.5.0/LAWBL/R/Omega_Phi.R | 72 ++++++ LAWBL-1.5.0/LAWBL/R/pcfa.R | 183 ++++++++++------ LAWBL-1.5.0/LAWBL/R/pcirm.R | 148 ++++++------- LAWBL-1.5.0/LAWBL/R/pefa.R | 365 ++++++++++++++++----------------- LAWBL-1.5.0/LAWBL/R/plot_lawbl.R | 22 + LAWBL-1.5.0/LAWBL/R/sim_lvm.R | 267 +++++++++++++++++------- LAWBL-1.5.0/LAWBL/R/summary.lawbl.R | 218 +++++++++++++++---- LAWBL-1.5.0/LAWBL/README.md | 65 ++++- LAWBL-1.5.0/LAWBL/build/vignette.rds |binary LAWBL-1.5.0/LAWBL/data/sim18cfa1.RData |binary LAWBL-1.5.0/LAWBL/inst/doc/LAWBL.Rmd | 1 LAWBL-1.5.0/LAWBL/inst/doc/LAWBL.html | 241 --------------------- LAWBL-1.5.0/LAWBL/man/LAWBL-package.Rd | 15 + LAWBL-1.5.0/LAWBL/man/pcfa.Rd | 35 ++- LAWBL-1.5.0/LAWBL/man/pcirm.Rd | 17 + LAWBL-1.5.0/LAWBL/man/pefa.Rd | 45 +++- LAWBL-1.5.0/LAWBL/man/plot_lawbl.Rd | 10 LAWBL-1.5.0/LAWBL/man/sim_lvm.Rd | 56 +++-- LAWBL-1.5.0/LAWBL/man/summary.lawbl.Rd | 6 LAWBL-1.5.0/LAWBL/vignettes/LAWBL.Rmd | 1 27 files changed, 1114 insertions(+), 817 deletions(-)
Title: Data Only: The Correlates of State Policy Project Dataset
Description: Contains the Correlates of State Policy Project dataset (+ codebook) assembled by Marty P. Jordan and Matt Grossmann (2020) <http://ippsr.msu.edu/public-policy/correlates-state-policy> used by the 'cspp' package. The Correlates data contains over 3000 variables across more than 100 years that pertain to state politics and policy in the United States.
Author: Caleb Lucas and Joshua McCrain
Maintainer: Caleb Lucas <calebjlucas@gmail.com>
Diff between csppData versions 0.2.5 dated 2022-03-08 and 0.2.61 dated 2022-05-16
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/zzz.R | 2 +- README.md | 2 +- data/codebook.rda |binary data/correlates.rda |binary man/codebook.Rd | 2 +- man/correlates.Rd | 2 +- 8 files changed, 14 insertions(+), 14 deletions(-)
Title: Tools for Reading, Writing, Viewing and Manipulating CIFTI Files
Description: CIFTI files contain brain imaging data in "grayordinates," which
represent the gray matter as cortical surface vertices (left and right) and
subcortical voxels (cerebellum, basal ganglia, and other deep gray matter).
'ciftiTools' provides a unified environment for reading, writing,
visualizing and manipulating CIFTI-format data. It supports the "dscalar,"
"dlabel," and "dtseries" intents. Grayordinate data is read in as a "xifti"
object, which is structured for convenient access to the data and metadata,
and includes support for surface geometry files to enable
spatially-dependent functionality such as static or interactive
visualizations and smoothing.
Author: Amanda Mejia [aut, cre],
Damon Pham [aut] ,
John Muschelli [ctb]
Maintainer: Amanda Mejia <mandy.mejia@gmail.com>
Diff between ciftiTools versions 0.8.0 dated 2022-01-31 and 0.9.0 dated 2022-05-16
ciftiTools-0.8.0/ciftiTools/R/wrappers.R |only ciftiTools-0.9.0/ciftiTools/DESCRIPTION | 10 ciftiTools-0.9.0/ciftiTools/MD5 | 121 +-- ciftiTools-0.9.0/ciftiTools/NAMESPACE | 24 ciftiTools-0.9.0/ciftiTools/NEWS.md | 20 ciftiTools-0.9.0/ciftiTools/R/add_surf.R | 47 - ciftiTools-0.9.0/ciftiTools/R/apply_xifti.R | 5 ciftiTools-0.9.0/ciftiTools/R/combine_xifti.R | 4 ciftiTools-0.9.0/ciftiTools/R/convert_xifti.R | 16 ciftiTools-0.9.0/ciftiTools/R/expect_equal_xifti.R | 5 ciftiTools-0.9.0/ciftiTools/R/fix_gifti_mwalls.R | 36 ciftiTools-0.9.0/ciftiTools/R/info_cifti.R | 6 ciftiTools-0.9.0/ciftiTools/R/is.xifti.R | 11 ciftiTools-0.9.0/ciftiTools/R/make_xifti.R | 4 ciftiTools-0.9.0/ciftiTools/R/make_xifti_components.R | 1 ciftiTools-0.9.0/ciftiTools/R/move_mwall.R | 4 ciftiTools-0.9.0/ciftiTools/R/newdata_xifti.R | 17 ciftiTools-0.9.0/ciftiTools/R/onAttach.R | 17 ciftiTools-0.9.0/ciftiTools/R/read_cifti_separate.R | 19 ciftiTools-0.9.0/ciftiTools/R/read_surf.R | 2 ciftiTools-0.9.0/ciftiTools/R/resample_cifti.R | 215 +++-- ciftiTools-0.9.0/ciftiTools/R/resample_cifti_components.R | 7 ciftiTools-0.9.0/ciftiTools/R/resample_cifti_from_template.R | 35 ciftiTools-0.9.0/ciftiTools/R/resample_gifti.R | 25 ciftiTools-0.9.0/ciftiTools/R/resample_surf.R | 6 ciftiTools-0.9.0/ciftiTools/R/rox_args_docs.R | 4 ciftiTools-0.9.0/ciftiTools/R/separate_cifti.R | 64 + ciftiTools-0.9.0/ciftiTools/R/smooth_cifti.R | 12 ciftiTools-0.9.0/ciftiTools/R/transform_xifti.R | 248 +----- ciftiTools-0.9.0/ciftiTools/R/utils.R | 5 ciftiTools-0.9.0/ciftiTools/R/utils_xifti.R | 183 ++-- ciftiTools-0.9.0/ciftiTools/R/view_comp.R | 83 +- ciftiTools-0.9.0/ciftiTools/R/view_surf.R | 2 ciftiTools-0.9.0/ciftiTools/R/view_xifti.R | 12 ciftiTools-0.9.0/ciftiTools/R/view_xifti_surface.R | 399 +++++----- ciftiTools-0.9.0/ciftiTools/R/view_xifti_volume.R | 314 ++++--- ciftiTools-0.9.0/ciftiTools/R/wb_cmd.R | 2 ciftiTools-0.9.0/ciftiTools/R/write_xifti2.R | 4 ciftiTools-0.9.0/ciftiTools/README.md | 7 ciftiTools-0.9.0/ciftiTools/inst/CITATION | 2 ciftiTools-0.9.0/ciftiTools/man/S3_Math.Rd |only ciftiTools-0.9.0/ciftiTools/man/S3_Ops.Rd |only ciftiTools-0.9.0/ciftiTools/man/S3_Summary.Rd |only ciftiTools-0.9.0/ciftiTools/man/combine_xifti.Rd | 4 ciftiTools-0.9.0/ciftiTools/man/convert_xifti.Rd | 6 ciftiTools-0.9.0/ciftiTools/man/infer_resolution.Rd | 3 ciftiTools-0.9.0/ciftiTools/man/make_xifti.Rd | 5 ciftiTools-0.9.0/ciftiTools/man/resample_cifti_components.Rd | 2 ciftiTools-0.9.0/ciftiTools/man/resample_cifti_wrapper.Rd | 14 ciftiTools-0.9.0/ciftiTools/man/separate_cifti_wrapper.Rd | 2 ciftiTools-0.9.0/ciftiTools/man/smooth_cifti.Rd | 5 ciftiTools-0.9.0/ciftiTools/man/surface_plot_Params.Rd | 5 ciftiTools-0.9.0/ciftiTools/man/transform_xifti.Rd | 84 -- ciftiTools-0.9.0/ciftiTools/man/view_comp.Rd | 29 ciftiTools-0.9.0/ciftiTools/man/view_surf.Rd | 6 ciftiTools-0.9.0/ciftiTools/man/view_xifti_surface.Rd | 19 ciftiTools-0.9.0/ciftiTools/man/view_xifti_surface.draw_mesh.Rd | 3 ciftiTools-0.9.0/ciftiTools/man/view_xifti_surface.mesh_val.Rd | 11 ciftiTools-0.9.0/ciftiTools/man/view_xifti_volume.Rd | 52 + ciftiTools-0.9.0/ciftiTools/man/welcome_msg.Rd |only ciftiTools-0.9.0/ciftiTools/tests/testthat/test-misc.R | 7 ciftiTools-0.9.0/ciftiTools/tests/testthat/test-plotting_sub.R | 2 ciftiTools-0.9.0/ciftiTools/tests/testthat/test-plotting_together.R | 5 ciftiTools-0.9.0/ciftiTools/tests/testthat/test-resampling.R | 12 64 files changed, 1309 insertions(+), 965 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-25 0.4.9
2022-02-16 0.4.4
2022-01-22 0.4.3
2021-10-22 0.4.2
2021-09-07 0.4.1
2021-04-18 0.4.0
2021-03-15 0.3.2
2021-02-03 0.3.1
2021-02-02 0.3.0
2020-12-04 0.2.6
2020-11-18 0.2.5
2020-11-11 0.2.4
2020-11-01 0.2.3
2020-09-23 0.2.2
2020-08-28 0.2.1
2020-07-25 0.2.0
2020-06-05 0.1.6
2020-04-16 0.1.5
2020-03-20 0.1.4
2020-02-20 0.1.3
2020-01-31 0.1.2
2020-01-08 0.1.1
2019-12-22 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-11 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-04-25 0.4.1
2022-01-18 0.4.0
2021-08-03 0.3.3.0
2021-06-09 0.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-21 0.2.4
2021-08-11 0.2.2
2021-03-07 0.2.1
2021-01-27 0.2.0
2020-07-06 0.1.3
2020-01-19 0.1.1
2019-12-15 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-08-20 0.2.0
2021-05-31 0.1.0