Title: R-Friendly Threading in C++
Description: Provides a C++11-style thread class and thread pool that can safely
be interrupted from R. See Nagler (2021) <doi:10.18637/jss.v097.c01>.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between RcppThread versions 0.5.4 dated 2019-10-19 and 1.0.0 dated 2021-02-01
DESCRIPTION | 10 +++++----- LICENSE | 2 +- MD5 | 23 ++++++++++++----------- NEWS.md | 14 +++++++++----- R/RcppThread-package.R | 4 ++++ README.md | 18 +++++++++++++----- build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 24 +++++++++++++++--------- inst/doc/RcppThread-vignette.pdf |binary inst/include/RcppThread/Rcout.hpp | 1 - inst/include/RcppThread/ThreadPool.hpp | 16 +++++++++------- man/RcppThread.Rd | 6 +++++- 13 files changed, 73 insertions(+), 45 deletions(-)
Title: M-Quantile Regression Coefficients Modeling
Description: Parametric modeling of M-quantile regression coefficient functions.
Author: Paolo Frumento <paolo.frumento@unipi.it>
Maintainer: Paolo Frumento <paolo.frumento@unipi.it>
Diff between Mqrcm versions 1.1 dated 2020-02-28 and 1.2 dated 2021-02-01
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ NAMESPACE | 2 +- NEWS.md | 16 +++++----------- R/Mqrcm.R | 30 ++++++++++++++++++------------ man/Mqrcm-package.Rd | 8 ++++---- man/iMqr.Rd | 4 ++-- 7 files changed, 42 insertions(+), 42 deletions(-)
Title: A 'dplyr' Interface for Crunch
Description: In order to facilitate analysis of datasets hosted on the Crunch
data platform <https://crunch.io/>, the 'crplyr' package implements 'dplyr'
methods on top of the Crunch backend. The usual methods 'select', 'filter',
'group_by', 'summarize', and 'collect' are implemented in such a way as to
perform as much computation on the server and pull as little data locally
as possible.
Author: Greg Freedman Ellis [aut, cre],
Jonathan Keane [aut],
Neal Richardson [aut],
Mike Malecki [aut],
Gordon Shotwell [aut]
Maintainer: Greg Freedman Ellis <greg@crunch.io>
Diff between crplyr versions 0.3.7 dated 2021-01-12 and 0.3.8 dated 2021-02-01
DESCRIPTION | 6 +-- MD5 | 20 ++++++++-- NEWS.md | 5 ++ tests/testthat/app.crunch.io/api/datasets/mtcars/cube-1d4e27.json |only tests/testthat/app.crunch.io/api/datasets/mtcars/cube-7b6f9f.json |only tests/testthat/app.crunch.io/api/datasets/mtcars/cube-7c5896.json |only tests/testthat/app.crunch.io/api/datasets/mtcars/cube-7d83f8.json |only tests/testthat/app.crunch.io/api/datasets/mtcars/cube-9bbacb.json |only tests/testthat/app.crunch.io/api/datasets/mtcars/cube-b067f8.json |only tests/testthat/app.crunch.io/api/datasets/mtcars/cube-bc4017.json |only tests/testthat/app.crunch.io/api/datasets/mtcars/cube-cd2668.json |only tests/testthat/app.crunch.io/api/datasets/mtcars/cube-e41475.json |only vignettes/plotting/0/api/datasets/5c9336/README.md | 10 +++-- vignettes/plotting/0/api/datasets/5c9336/cube-169e06.json |only vignettes/plotting/0/api/datasets/5c9336/cube-1add39.json |only vignettes/plotting/0/api/datasets/5c9336/cube-8cbca1.json |only vignettes/plotting/0/api/datasets/5c9336/cube-a9f318.json |only vignettes/plotting/0/api/datasets/5c9336/cube-c7c07d.json |only 18 files changed, 30 insertions(+), 11 deletions(-)
Title: Archetypes for Targets
Description: Function-oriented Make-like declarative workflows for
Statistics and data science are supported in the 'targets' R package.
As an extension to 'targets', the 'tarchetypes' package provides
convenient user-side functions to make 'targets' easier to use.
By establishing reusable archetypes for common kinds of
targets and pipelines, these functions help express complicated
reproducible workflows concisely and compactly.
The methods in this package were influenced by the 'drake' R package
by Will Landau (2018) <doi:10.21105/joss.00550>.
Author: William Michael Landau [aut, cre]
(<https://orcid.org/0000-0003-1878-3253>),
Samantha Oliver [rev] (<https://orcid.org/0000-0001-5668-1165>),
Tristan Mahr [rev] (<https://orcid.org/0000-0002-8890-5116>),
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Diff between tarchetypes versions 0.0.2 dated 2021-02-01 and 0.0.4 dated 2021-02-01
DESCRIPTION | 6 - MD5 | 125 ++++++++++++------------- NEWS.md | 7 + R/tar_change.R | 2 R/tar_combine.R | 2 R/tar_combine_raw.R | 2 R/tar_eval.R | 10 +- R/tar_eval_raw.R | 10 +- R/tar_files.R | 149 +----------------------------- R/tar_files_input.R | 16 +-- R/tar_files_input_raw.R | 16 +-- R/tar_files_raw.R |only R/tar_force.R | 2 R/tar_formats.R | 3 R/tar_knit.R | 32 +++--- R/tar_knit_raw.R | 33 +++--- R/tar_knitr_deps.R | 4 R/tar_knitr_deps_expr.R | 4 R/tar_map.R | 2 R/tar_plan.R | 18 --- R/tar_render.R | 19 ++- R/tar_render_raw.R | 22 ++-- R/tar_render_rep.R | 11 +- R/tar_render_rep_raw.R | 11 +- R/tar_rep.R | 2 R/tar_rep_raw.R | 2 R/tar_skip.R | 2 R/tar_sub.R | 13 -- R/tar_sub_raw.R | 13 -- man/tar_change.Rd | 2 man/tar_combine.Rd | 2 man/tar_combine_raw.Rd | 2 man/tar_eval.Rd | 10 +- man/tar_eval_raw.Rd | 10 +- man/tar_files.Rd | 15 +-- man/tar_files_input.Rd | 16 +-- man/tar_files_input_raw.Rd | 16 +-- man/tar_files_raw.Rd | 41 +------- man/tar_force.Rd | 2 man/tar_formats.Rd | 3 man/tar_knit.Rd | 32 +++--- man/tar_knit_raw.Rd | 33 +++--- man/tar_knitr_deps.Rd | 4 man/tar_knitr_deps_expr.Rd | 4 man/tar_map.Rd | 2 man/tar_plan.Rd | 18 --- man/tar_render.Rd | 19 ++- man/tar_render_raw.Rd | 22 ++-- man/tar_render_rep.Rd | 11 +- man/tar_render_rep_raw.Rd | 11 +- man/tar_rep.Rd | 2 man/tar_rep_raw.Rd | 2 man/tar_skip.Rd | 2 man/tar_sub.Rd | 13 -- man/tar_sub_raw.Rd | 13 -- tests/testthat/helper-utils.R | 5 + tests/testthat/test-tar_knit.R | 4 tests/testthat/test-tar_knit_raw.R | 4 tests/testthat/test-tar_knitr_deps.R | 1 tests/testthat/test-tar_knitr_deps_expr.R | 1 tests/testthat/test-tar_render.R | 3 tests/testthat/test-tar_render_raw.R | 5 + tests/testthat/test-tar_render_rep.R | 4 tests/testthat/test-tar_sub.R | 6 - 64 files changed, 340 insertions(+), 538 deletions(-)
Title: Spatio-Temporal Under-Five Mortality Methods for Estimation
Description: Provides methods for spatial and spatio-temporal smoothing of demographic and health indicators using survey data, with particular focus on estimating and projecting under-five mortality rates, described in Mercer et al. (2015) <doi:10.1214/15-AOAS872>, Li et al. (2019) <doi:10.1371/journal.pone.0210645> and Li et al. (2020) <arXiv:2007.05117>.
Author: Zehang R Li [cre, aut],
Bryan D Martin [aut],
Yuan Hsiao [aut],
Jessica Godwin [aut],
Jon Wakefield [aut],
Samuel J Clark [aut],
Geir-Arne Fuglstad [aut],
Andrea Riebler [aut]
Maintainer: Zehang R Li <lizehang@gmail.com>
Diff between SUMMER versions 1.0.0 dated 2020-07-09 and 1.1.0 dated 2021-02-01
SUMMER-1.0.0/SUMMER/data/datalist |only SUMMER-1.1.0/SUMMER/DESCRIPTION | 17 - SUMMER-1.1.0/SUMMER/MD5 | 89 ++--- SUMMER-1.1.0/SUMMER/NEWS.md | 11 SUMMER-1.1.0/SUMMER/R/BRFSS.R | 4 SUMMER-1.1.0/SUMMER/R/fitINLA2.R | 37 +- SUMMER-1.1.0/SUMMER/R/fitspace.R | 371 +++++++++++++++------- SUMMER-1.1.0/SUMMER/R/getBirths.R | 46 ++ SUMMER-1.1.0/SUMMER/R/getDiag.R | 11 SUMMER-1.1.0/SUMMER/R/projINLA.R | 18 - SUMMER-1.1.0/SUMMER/build/vignette.rds |binary SUMMER-1.1.0/SUMMER/inst/doc/summer-vignette.html | 201 +++++++---- SUMMER-1.1.0/SUMMER/inst/doc/u5mr-vignette.html | 95 ++++- SUMMER-1.1.0/SUMMER/inst/doc/u5mr-vignette2.html | 68 +++- SUMMER-1.1.0/SUMMER/man/BRFSS.Rd | 9 SUMMER-1.1.0/SUMMER/man/DemoData.Rd | 4 SUMMER-1.1.0/SUMMER/man/DemoData2.Rd | 4 SUMMER-1.1.0/SUMMER/man/DemoMap.Rd | 4 SUMMER-1.1.0/SUMMER/man/DemoMap2.Rd | 4 SUMMER-1.1.0/SUMMER/man/KenData.Rd | 4 SUMMER-1.1.0/SUMMER/man/KingCounty.Rd | 4 SUMMER-1.1.0/SUMMER/man/MalawiData.Rd | 4 SUMMER-1.1.0/SUMMER/man/MalawiMap.Rd | 4 SUMMER-1.1.0/SUMMER/man/getAdjusted.Rd | 23 + SUMMER-1.1.0/SUMMER/man/getBirths.Rd | 30 + SUMMER-1.1.0/SUMMER/man/getCounts.Rd | 3 SUMMER-1.1.0/SUMMER/man/getDiag.Rd | 9 SUMMER-1.1.0/SUMMER/man/getDirect.Rd | 15 SUMMER-1.1.0/SUMMER/man/getDirectList.Rd | 15 SUMMER-1.1.0/SUMMER/man/getSmoothed.Rd | 22 - SUMMER-1.1.0/SUMMER/man/hatchPlot.Rd | 28 + SUMMER-1.1.0/SUMMER/man/iid.new.Rd | 6 SUMMER-1.1.0/SUMMER/man/iid.new.pc.Rd | 6 SUMMER-1.1.0/SUMMER/man/mapPlot.Rd | 28 + SUMMER-1.1.0/SUMMER/man/plot.SUMMERproj.Rd | 24 + SUMMER-1.1.0/SUMMER/man/ridgePlot.Rd | 40 +- SUMMER-1.1.0/SUMMER/man/rst.Rd | 12 SUMMER-1.1.0/SUMMER/man/rw.new.Rd | 6 SUMMER-1.1.0/SUMMER/man/rw.new.pc.Rd | 6 SUMMER-1.1.0/SUMMER/man/simhyper.Rd | 10 SUMMER-1.1.0/SUMMER/man/smoothCluster.Rd | 102 ++++-- SUMMER-1.1.0/SUMMER/man/smoothDirect.Rd | 78 +++- SUMMER-1.1.0/SUMMER/man/smoothSurvey.Rd | 88 ++++- SUMMER-1.1.0/SUMMER/man/st.new.Rd | 6 SUMMER-1.1.0/SUMMER/man/st.new.pc.Rd | 6 SUMMER-1.1.0/SUMMER/man/tcpPlot.Rd | 18 - 46 files changed, 1134 insertions(+), 456 deletions(-)
Title: Models for Non Linear Causality Detection in Time Series
Description: Models for non-linear time series analysis and causality detection. The main functionalities of this package consist of an implementation of the classical causality test (C.W.J.Granger 1980) <doi:10.1016/0165-1889(80)90069-X>, and a non-linear version of it based on feed-forward neural networks. This package contains also an implementation of the Transfer Entropy <doi:10.1103/PhysRevLett.85.461>, and the continuous Transfer Entropy using an approximation based on the k-nearest neighbors <doi:10.1103/PhysRevE.69.066138>. There are also some other useful tools, like the VARNN (Vector Auto-Regressive Neural Network) prediction model, the Augmented test of stationarity, and the discrete and continuous entropy and mutual information.
Author: Youssef Hmamouche [aut, cre]
Maintainer: Youssef Hmamouche <hmamoucheyussef@gmail.com>
Diff between NlinTS versions 1.4.4 dated 2020-10-26 and 1.4.5 dated 2021-02-01
NlinTS-1.4.4/NlinTS/src/layer.cpp |only NlinTS-1.4.5/NlinTS/DESCRIPTION | 10 NlinTS-1.4.5/NlinTS/MD5 | 45 +- NlinTS-1.4.5/NlinTS/R/modules.R | 28 - NlinTS-1.4.5/NlinTS/build/partial.rdb |binary NlinTS-1.4.5/NlinTS/inst/include/dense.h | 82 ++-- NlinTS-1.4.5/NlinTS/inst/include/layer.h | 50 +- NlinTS-1.4.5/NlinTS/inst/include/network.h | 86 ++-- NlinTS-1.4.5/NlinTS/inst/include/nlinCausalityTest.h | 20 - NlinTS-1.4.5/NlinTS/inst/include/utils.h | 24 - NlinTS-1.4.5/NlinTS/inst/include/varnn.h | 28 - NlinTS-1.4.5/NlinTS/inst/include/varnnExport.h | 20 - NlinTS-1.4.5/NlinTS/man/nlin_causality.test.Rd | 12 NlinTS-1.4.5/NlinTS/man/varmlp.Rd | 26 - NlinTS-1.4.5/NlinTS/src/causalityTest.cpp | 6 NlinTS-1.4.5/NlinTS/src/dense.cpp | 224 +++++++---- NlinTS-1.4.5/NlinTS/src/fdist.cpp | 2 NlinTS-1.4.5/NlinTS/src/module.cpp | 7 NlinTS-1.4.5/NlinTS/src/network.cpp | 355 ++++++++++++++----- NlinTS-1.4.5/NlinTS/src/nlinCausalityTest.cpp | 19 - NlinTS-1.4.5/NlinTS/src/struct.cpp | 28 - NlinTS-1.4.5/NlinTS/src/utils.cpp | 159 ++++++++ NlinTS-1.4.5/NlinTS/src/varnn.cpp | 104 ++--- NlinTS-1.4.5/NlinTS/src/varnnExport.cpp | 33 - 24 files changed, 926 insertions(+), 442 deletions(-)
Title: Homemade Deep Learning Library
Description: Allows to build and train different flavors of Neural Networks.
In particular, it can be used to build fairly complex computational graphs,
which ca be automatically differentiated and optimized with gradient descent
methods.
Author: Filippo Monari [aut, cre]
Maintainer: Filippo Monari <ingfimo@gmail.com>
Diff between modello versions 0.1 dated 2021-02-01 and 0.1.1 dated 2021-02-01
modello-0.1.1/modello/DESCRIPTION | 8 modello-0.1.1/modello/MD5 | 148 ++++---- modello-0.1.1/modello/R/dataLoaders.R | 6 modello-0.1.1/modello/R/graphs.R | 8 modello-0.1.1/modello/R/modules.R | 40 +- modello-0.1.1/modello/R/numbers.R | 42 +- modello-0.1.1/modello/R/numbers_math.R | 112 ++---- modello-0.1.1/modello/R/utils.R | 58 +-- modello-0.1.1/modello/man/DataLoader.Seq.Rd | 4 modello-0.1.1/modello/man/DataSet.Array.Rd | 4 modello-0.1.1/modello/man/DataSet.Seq.Rd | 4 modello-0.1.1/modello/man/abs.modello_number.Rd | 2 modello-0.1.1/modello/man/adam.opt.Rd | 2 modello-0.1.1/modello/man/bin.entropy.Rd | 2 modello-0.1.1/modello/man/bind.Rd | 4 modello-0.1.1/modello/man/cos.modello_number.Rd | 2 modello-0.1.1/modello/man/cosh.modello_number.Rd | 2 modello-0.1.1/modello/man/cross.entropy.Rd | 2 modello-0.1.1/modello/man/dim.modello_number.Rd | 2 modello-0.1.1/modello/man/dot-graph.Rd | 16 modello-0.1.1/modello/man/dot-k.Rd | 2 modello-0.1.1/modello/man/dot-modello_number.Rd | 2 modello-0.1.1/modello/man/dot-number.Rd | 84 ++--- modello-0.1.1/modello/man/exp.modello_number.Rd | 2 modello-0.1.1/modello/man/gemm.Rd | 2 modello-0.1.1/modello/man/gemv.Rd | 2 modello-0.1.1/modello/man/ger.Rd | 2 modello-0.1.1/modello/man/grapes-.-grapes.Rd | 2 modello-0.1.1/modello/man/grapes-.T-grapes.Rd | 2 modello-0.1.1/modello/man/grapes-T.-grapes.Rd | 2 modello-0.1.1/modello/man/grapes-T.T-grapes.Rd | 2 modello-0.1.1/modello/man/graph.close.Rd | 2 modello-0.1.1/modello/man/graph.open.Rd | 2 modello-0.1.1/modello/man/invMat.Rd | 2 modello-0.1.1/modello/man/is.graph.Rd | 2 modello-0.1.1/modello/man/is.number.Rd | 2 modello-0.1.1/modello/man/is.opt.Rd | 2 modello-0.1.1/modello/man/ldbeta.Rd | 2 modello-0.1.1/modello/man/ldexp.Rd | 2 modello-0.1.1/modello/man/ldgamma.Rd | 2 modello-0.1.1/modello/man/ldlaplace.Rd | 2 modello-0.1.1/modello/man/ldmvnorm.Rd | 2 modello-0.1.1/modello/man/ldnorm.Rd | 2 modello-0.1.1/modello/man/length.modello_number.Rd | 2 modello-0.1.1/modello/man/lkh.norm.Rd | 2 modello-0.1.1/modello/man/log.modello_number.Rd | 2 modello-0.1.1/modello/man/mae.Rd | 2 modello-0.1.1/modello/man/module.lm.Rd | 12 modello-0.1.1/modello/man/module.logistic.Rd | 38 ++ modello-0.1.1/modello/man/module.softmax.Rd | 38 ++ modello-0.1.1/modello/man/mse.Rd | 2 modello-0.1.1/modello/man/plus-.modello_number.Rd | 2 modello-0.1.1/modello/man/pop.Rd | 4 modello-0.1.1/modello/man/pow-.modello_number.Rd | 2 modello-0.1.1/modello/man/relu.Rd | 2 modello-0.1.1/modello/man/sgd.opt.Rd | 2 modello-0.1.1/modello/man/sgdwm.opt.Rd | 2 modello-0.1.1/modello/man/sigmoid.Rd | 2 modello-0.1.1/modello/man/sin.modello_number.Rd | 2 modello-0.1.1/modello/man/sinh.modello_number.Rd | 2 modello-0.1.1/modello/man/slash-.modello_number.Rd | 2 modello-0.1.1/modello/man/softmax.Rd | 2 modello-0.1.1/modello/man/ssq.Rd | 2 modello-0.1.1/modello/man/sub-.modello_number.Rd | 2 modello-0.1.1/modello/man/subset-.modello_number.Rd | 2 modello-0.1.1/modello/man/sum.modello_number.Rd | 2 modello-0.1.1/modello/man/swish.Rd | 2 modello-0.1.1/modello/man/tan.modello_number.Rd | 2 modello-0.1.1/modello/man/tanh.modello_number.Rd | 2 modello-0.1.1/modello/man/times-.modello_number.Rd | 2 modello-0.1.1/modello/src/Makevars | 57 +++ modello-0.1.1/modello/src/Rfuns.c | 331 -------------------- modello-0.1.1/modello/src/math.f95 | 141 -------- modello-0.1/modello/src/Makefile |only modello-0.1/modello/src/Makefile.win |only modello-0.1/modello/src/Makevars.win |only modello-0.1/modello/src/dataio.f95 |only 77 files changed, 438 insertions(+), 825 deletions(-)
Title: Calculating Linkage Disequilibrium (LD) in Human Population
Groups of Interest
Description: Provides access to the 'LDlink' API (<https://ldlink.nci.nih.gov/?tab=apiaccess>)
using the R console. This programmatic access facilitates researchers who are
interested in performing batch queries in 1000 Genomes Project (2015) <doi:10.1038/nature15393>
data using 'LDlink'. 'LDlink' is an interactive and powerful suite of web-based tools for querying
germline variants in human population groups of interest. For more details, please see
Machiela et al. (2015) <doi:10.1093/bioinformatics/btv402>.
Author: Timothy A. Myers [aut, cre],
Stephen J. Chanock [aut],
Mitchell J. Machiela [aut]
Maintainer: Timothy A. Myers <myersta@mail.nih.gov>
Diff between LDlinkR versions 1.0.2 dated 2020-03-02 and 1.1.1 dated 2021-02-01
LDlinkR-1.0.2/LDlinkR/inst/doc/LDlinkR_vignette_v8-2_TM.R |only LDlinkR-1.0.2/LDlinkR/inst/doc/LDlinkR_vignette_v8-2_TM.Rmd |only LDlinkR-1.0.2/LDlinkR/inst/doc/LDlinkR_vignette_v8-2_TM.html |only LDlinkR-1.0.2/LDlinkR/vignettes/LDlinkR_vignette_v8-2_TM.Rmd |only LDlinkR-1.1.1/LDlinkR/DESCRIPTION | 28 - LDlinkR-1.1.1/LDlinkR/MD5 | 69 +-- LDlinkR-1.1.1/LDlinkR/NAMESPACE | 3 LDlinkR-1.1.1/LDlinkR/NEWS.md |only LDlinkR-1.1.1/LDlinkR/R/LDexpress.R |only LDlinkR-1.1.1/LDlinkR/R/LDhap.R | 3 LDlinkR-1.1.1/LDlinkR/R/LDmatrix.R | 3 LDlinkR-1.1.1/LDlinkR/R/LDpair.R | 5 LDlinkR-1.1.1/LDlinkR/R/LDpop.R | 3 LDlinkR-1.1.1/LDlinkR/R/LDproxy.R | 3 LDlinkR-1.1.1/LDlinkR/R/LDproxy_batch.R | 7 LDlinkR-1.1.1/LDlinkR/R/LDtrait.R |only LDlinkR-1.1.1/LDlinkR/R/SNPchip.R | 2 LDlinkR-1.1.1/LDlinkR/R/SNPclip.R | 2 LDlinkR-1.1.1/LDlinkR/R/list_chips.R | 3 LDlinkR-1.1.1/LDlinkR/R/list_gtex_tissues.R |only LDlinkR-1.1.1/LDlinkR/R/list_pop.R | 3 LDlinkR-1.1.1/LDlinkR/README.md | 227 ++++++++++- LDlinkR-1.1.1/LDlinkR/build/vignette.rds |binary LDlinkR-1.1.1/LDlinkR/inst/WORDLIST |only LDlinkR-1.1.1/LDlinkR/inst/doc/LDlinkR.R |only LDlinkR-1.1.1/LDlinkR/inst/doc/LDlinkR.Rmd |only LDlinkR-1.1.1/LDlinkR/inst/doc/LDlinkR.html |only LDlinkR-1.1.1/LDlinkR/man/LDexpress.Rd |only LDlinkR-1.1.1/LDlinkR/man/LDhap.Rd | 6 LDlinkR-1.1.1/LDlinkR/man/LDlinkR-package.Rd | 11 LDlinkR-1.1.1/LDlinkR/man/LDmatrix.Rd | 6 LDlinkR-1.1.1/LDlinkR/man/LDpair.Rd | 8 LDlinkR-1.1.1/LDlinkR/man/LDpop.Rd | 6 LDlinkR-1.1.1/LDlinkR/man/LDproxy.Rd | 6 LDlinkR-1.1.1/LDlinkR/man/LDproxy_batch.Rd | 4 LDlinkR-1.1.1/LDlinkR/man/LDtrait.Rd |only LDlinkR-1.1.1/LDlinkR/man/SNPchip.Rd | 4 LDlinkR-1.1.1/LDlinkR/man/SNPclip.Rd | 4 LDlinkR-1.1.1/LDlinkR/man/list_chips.Rd | 6 LDlinkR-1.1.1/LDlinkR/man/list_gtex_tissues.Rd |only LDlinkR-1.1.1/LDlinkR/man/list_pop.Rd | 6 LDlinkR-1.1.1/LDlinkR/tests/spelling.R |only LDlinkR-1.1.1/LDlinkR/tests/testthat/test-ldexpress.R |only LDlinkR-1.1.1/LDlinkR/tests/testthat/test-ldtrait.R |only LDlinkR-1.1.1/LDlinkR/vignettes/LDlinkR.Rmd |only 45 files changed, 341 insertions(+), 87 deletions(-)
Title: Provides an R Interface to 'Enrichr'
Description: Provides an R interface to all 'Enrichr' databases. 'Enrichr' is a web-based tool for analysing gene sets and returns any enrichment of common annotated biological features. Quoting from their website 'Enrichment analysis is a computational method for inferring knowledge about an input gene set by comparing it to annotated gene sets representing prior biological knowledge.' See <https://maayanlab.cloud/Enrichr/> for further details.
Author: Wajid Jawaid [aut, cre]
Maintainer: Wajid Jawaid <wj241@alumni.cam.ac.uk>
Diff between enrichR versions 2.1 dated 2019-08-29 and 3.0 dated 2021-02-01
DESCRIPTION | 12 - MD5 | 39 +-- NAMESPACE | 18 + NEWS.md |only R/enrichR-package.r | 2 R/functions.R | 324 +++++++++++++++++++++++---- README.md | 162 +++++++------ build/vignette.rds |binary inst/doc/enrichR.R | 36 +-- inst/doc/enrichR.Rmd | 26 +- inst/doc/enrichR.html | 423 ++++++++++++++++++++++++++++++------ man/dot-onAttach.Rd | 9 man/enrichr.Rd | 16 - man/genes790.Rd | 4 man/getEnrichr.Rd | 6 man/listEnrichrDbs.Rd | 7 man/listEnrichrSites.Rd |only man/plotEnrich.Rd |only man/printEnrich.Rd | 36 ++- man/setEnrichrSite.Rd |only tools/README-unnamed-chunk-12-1.png |only tools/README-unnamed-chunk-13-1.png |only tools/README-unnamed-chunk-14-1.png |only vignettes/enrichR.Rmd | 26 +- 24 files changed, 884 insertions(+), 262 deletions(-)
Title: Evapotranspiration and Energy Fluxes Spatial Analysis
Description: Spatial modeling of energy balance and actual
evapotranspiration using satellite images and meteorological data.
Options of satellite are: Landsat-8 (with and without thermal bands),
Sentinel-2 and MODIS. Respectively spatial resolutions are 30, 100,
10 and 250 meters. User can use data from a single meteorological
station or a grid of meteorological stations (using any spatial
interpolation method). Silva, Teixeira, and Manzione (2019) <doi:10.1016/j.envsoft.2019.104497>.
Author: Cesar de Oliveira Ferreira Silva [cre]
(<https://orcid.org/0000-0002-5152-6497>),
Antonio Heriberto de Castro Teixeira [aut],
Rodrigo Lilla Manzione [ctb] (<https://orcid.org/0000-0002-0754-2641>)
Maintainer: Cesar de Oliveira Ferreira Silva <cesaroliveira.f.silva@gmail.com>
Diff between agriwater versions 1.0.0 dated 2019-01-30 and 1.0.1 dated 2021-02-01
DESCRIPTION | 16 LICENSE | 4 MD5 | 88 - R/landsat8_grid.R | 233 ++++- R/landsat8_single.R | 1945 ++++++++++++++++++++++++-------------------- R/landsat8_thermal_grid.R | 379 ++++++-- R/landsat8_thermal_single.R | 390 ++++++-- R/modis_grid.R | 798 +++++++++--------- R/modis_single.R | 60 + R/sentinel2_grid.R | 884 +++++++++---------- R/sentinel2_single.R | 215 ++++ README.md | 5 build/vignette.rds |binary inst/doc/agriwater.R | 2 inst/doc/agriwater.Rmd | 1704 +++++++++++++++++++------------------- inst/doc/agriwater.html | 325 ++++--- man/albedo_l8.Rd | 34 man/albedo_modis.Rd | 28 man/albedo_s2.Rd | 28 man/evapo_l8.Rd | 54 - man/evapo_l8_grid.Rd | 42 man/evapo_l8t.Rd | 54 - man/evapo_l8t_grid.Rd | 42 man/evapo_modis.Rd | 102 -- man/evapo_modis_grid.Rd | 42 man/evapo_s2.Rd | 54 - man/evapo_s2_grid.Rd | 42 man/kc_l8.Rd | 50 - man/kc_l8_grid.Rd | 42 man/kc_l8t.Rd | 50 - man/kc_l8t_grid.Rd | 42 man/kc_modis.Rd | 96 -- man/kc_modis_grid.Rd | 42 man/kc_s2.Rd | 50 - man/kc_s2_grid.Rd | 42 man/radiation_l8.Rd | 54 - man/radiation_l8_grid.Rd | 42 man/radiation_l8t.Rd | 54 - man/radiation_l8t_grid.Rd | 42 man/radiation_modis.Rd | 104 -- man/radiation_modis_grid.Rd | 42 man/radiation_s2.Rd | 54 - man/radiation_s2_grid.Rd | 42 man/reflectance_l8.Rd | 34 vignettes/agriwater.Rmd | 1704 +++++++++++++++++++------------------- 45 files changed, 5578 insertions(+), 4578 deletions(-)
Title: Bayesian Models for Data from Unmarked Animals using 'Stan'
Description: Fit Bayesian hierarchical models of animal abundance and occurrence
via the 'rstan' package, the R interface to the 'Stan' C++ library.
Supported models include single-season occupancy, dynamic occupancy, and
N-mixture abundance models. Covariates on model parameters are specified
using a formula-based interface similar to package 'unmarked', while also
allowing for estimation of random slope and intercept terms. References:
Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>;
Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.
Author: Ken Kellner [cre, aut]
Maintainer: Ken Kellner <contact@kenkellner.com>
Diff between ubms versions 1.0.1 dated 2021-01-19 and 1.0.2 dated 2021-02-01
DESCRIPTION | 8 MD5 | 48 ++--- NAMESPACE | 1 NEWS.md | 12 + R/ubmsFit-methods.R | 1 R/utils.R | 4 inst/doc/ubms.html | 188 +++++++++++----------- inst/stan/include/fixed_priors_single_season.stan | 4 src/simz.cpp | 20 +- tests/testthat/test_colext.R | 29 ++- tests/testthat/test_distsamp.R | 30 ++- tests/testthat/test_fit.R | 12 + tests/testthat/test_fitlist.R | 11 + tests/testthat/test_linpred.R | 14 + tests/testthat/test_multinomPois.R | 56 ++++-- tests/testthat/test_occu.R | 27 ++- tests/testthat/test_occuRN.R | 25 ++ tests/testthat/test_occuTTD.R | 22 +- tests/testthat/test_pcount.R | 24 +- tests/testthat/test_plot_marginal.R | 10 + tests/testthat/test_ranef.R | 10 + tests/testthat/test_residuals.R | 10 + tests/testthat/test_submodel.R | 4 tests/testthat/test_ubmsFit_methods.R | 11 + tests/testthat/test_utils.R | 10 + 25 files changed, 391 insertions(+), 200 deletions(-)
Title: Apply Functions to Multiple Multidimensional Arrays or Vectors
Description: The base apply function and its variants, as well as the related
functions in the 'plyr' package, typically apply user-defined functions to a
single argument (or a list of vectorized arguments in the case of mapply). The
'multiApply' package extends this paradigm with its only function, Apply, which
efficiently applies functions taking one or a list of multiple unidimensional
or multidimensional arrays (or combinations thereof) as input. The input
arrays can have different numbers of dimensions as well as different dimension
lengths, and the applied function can return one or a list of unidimensional or
multidimensional arrays as output. This saves development time by preventing the
R user from writing often error-prone and memory-inefficient loops dealing with
multiple complex arrays. Also, a remarkable feature of Apply is the transparent
use of multi-core through its parameter 'ncores'. In contrast to the base apply
function, this package suggests the use of 'target dimensions' as opposite
to the 'margins' for specifying the dimensions relevant to the function to be
applied.
Author: BSC-CNS [aut, cph],
Nicolau Manubens [aut],
Alasdair Hunter [aut],
Nuria Perez [cre]
Maintainer: Nuria Perez <nuria.perez@bsc.es>
Diff between multiApply versions 2.1.2 dated 2021-01-21 and 2.1.3 dated 2021-02-01
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/Apply.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Estimation Methods for Markets in Equilibrium and Disequilibrium
Description: Provides estimation methods for markets in equilibrium and
disequilibrium. Specifically, it supports the estimation of an equilibrium and
four disequilibrium models with both correlated and independent shocks.
It also provides post-estimation analysis tools, such as aggregation and
marginal effects calculations. The estimation methods are based on full
information maximum likelihood techniques given in Maddala and Nelson (1974)
<doi:10.2307/1914215>. They are implemented using the analytic derivative
expressions calculated in Karapanagiotis (2020) <doi:10.2139/ssrn.3525622>.
The equilibrium estimation constitutes a special case of
a system of simultaneous equations. The disequilibrium models, instead, replace
the market clearing condition with a short side rule and
allow for different specifications of price dynamics.
Author: Pantelis Karapanagiotis [aut, cre]
(<https://orcid.org/0000-0001-9871-1908>)
Maintainer: Pantelis Karapanagiotis <pikappa.devel@gmail.com>
Diff between diseq versions 0.1.2 dated 2021-01-29 and 0.1.3 dated 2021-02-01
DESCRIPTION | 13 - MD5 | 32 +-- NAMESPACE | 2 NEWS.md | 32 ++- R/diseq.R | 2 R/market_model.R | 6 README.md | 5 build/partial.rdb |binary configure | 296 ++++++++++--------------------- configure.ac | 50 +++-- inst/doc/basic_usage.html | 8 inst/doc/market_clearing_assessment.html | 8 man/maximize_log_likelihood.Rd | 6 src/Makevars.in | 2 src/Makevars.win | 3 src/RcppExports.cpp | 1 src/equilibrium.cpp | 117 +++++------- 17 files changed, 268 insertions(+), 315 deletions(-)
Title: Kriging-Based Optimization for Computer Experiments
Description: Efficient Global Optimization (EGO) algorithm as described in "Roustant et al. (2012)" <doi:10.18637/jss.v051.i01> and adaptations for problems with noise ("Picheny and Ginsbourger, 2012") <doi:10.1016/j.csda.2013.03.018>, parallel infill, and problems with constraints.
Author: Victor Picheny [aut, cre],
David Ginsbourger Green [aut],
Olivier Roustant [aut],
Mickael Binois [ctb],
Sebastien Marmin [ctb],
Tobias Wagner [ctb]
Maintainer: Victor Picheny <victor.picheny@toulouse.inra.fr>
Diff between DiceOptim versions 2.1.0 dated 2021-01-27 and 2.1.1 dated 2021-02-01
DESCRIPTION | 8 MD5 | 12 - R/DiceOptim-package.R | 476 ++++++++++++++++++++++++------------------------- R/TREGO.nsteps.R | 23 +- R/easyEGO.R | 8 man/easyEGO.Rd | 8 src/packagename_init.c | 3 7 files changed, 275 insertions(+), 263 deletions(-)
Title: Censored and Truncated Quantile Regression
Description: Estimation of quantile regression models for survival data.
Author: Paolo Frumento
Maintainer: Paolo Frumento <paolo.frumento@unipi.it>
Diff between ctqr versions 1.1 dated 2020-03-15 and 2.0 dated 2021-02-01
ctqr-1.1/ctqr/R/ctqr.R |only ctqr-2.0/ctqr/DESCRIPTION | 14 ++--- ctqr-2.0/ctqr/MD5 | 18 +++--- ctqr-2.0/ctqr/NAMESPACE | 2 ctqr-2.0/ctqr/NEWS.md | 16 +++--- ctqr-2.0/ctqr/R/A0_first_step.R |only ctqr-2.0/ctqr/R/A1_main_function.R |only ctqr-2.0/ctqr/R/A2_aux_functions.R |only ctqr-2.0/ctqr/man/ctqr-internal.Rd | 12 +++- ctqr-2.0/ctqr/man/ctqr-package.Rd | 18 +++--- ctqr-2.0/ctqr/man/ctqr.Rd | 97 +++++++++++++++++++++++-------------- ctqr-2.0/ctqr/man/ctqr.control.Rd | 2 12 files changed, 108 insertions(+), 71 deletions(-)
Title: Dynamic Function-Oriented 'Make'-Like Declarative Workflows
Description: As a pipeline toolkit for Statistics and data science in R,
the 'targets' package brings together function-oriented programming and
'Make'-like declarative workflows.
It analyzes the dependency relationships among the tasks of a workflow,
skips steps that are already up to date, runs the necessary
computation with optional parallel workers, abstracts files as
R objects, and provides tangible evidence that the results match
the underlying code and data. The methodology in this package
borrows from GNU 'Make' (2015, ISBN:978-9881443519)
and 'drake' (2018, <doi:10.21105/joss.00550>).
Author: William Michael Landau [aut, cre]
(<https://orcid.org/0000-0003-1878-3253>),
Matthew T. Warkentin [ctb],
Samantha Oliver [rev] (<https://orcid.org/0000-0001-5668-1165>),
Tristan Mahr [rev] (<https://orcid.org/0000-0002-8890-5116>),
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Diff between targets versions 0.0.2 dated 2021-01-21 and 0.1.0 dated 2021-02-01
DESCRIPTION | 17 - MD5 | 255 ++++++++++++++-------------- NAMESPACE | 8 NEWS.md | 31 +++ R/class_active.R | 2 R/class_branch.R | 4 R/class_builder.R | 18 - R/class_inspection.R | 2 R/class_meta.R | 4 R/class_pattern.R | 9 R/class_patternview.R | 14 - R/class_progress.R | 154 +++++++++------- R/class_reporter.R | 8 R/class_stem.R | 5 R/class_summary.R | 4 R/class_target.R | 13 + R/class_timestamp.R | 2 R/class_verbose.R | 2 R/class_visnetwork.R | 4 R/class_visual.R | 8 R/tar_branches.R | 8 R/tar_cancel.R | 4 R/tar_deduplicate.R | 6 R/tar_delete.R | 13 - R/tar_destroy.R | 14 - R/tar_dir.R | 3 R/tar_edit.R | 2 R/tar_envir.R | 4 R/tar_glimpse.R | 16 - R/tar_group.R | 4 R/tar_invalidate.R | 8 R/tar_load.R | 16 - R/tar_make.R | 8 R/tar_make_clustermq.R | 8 R/tar_make_future.R | 8 R/tar_manifest.R | 8 R/tar_meta.R | 14 - R/tar_name.R | 6 R/tar_network.R | 10 - R/tar_objects.R | 6 R/tar_option_get.R | 4 R/tar_option_reset.R | 4 R/tar_option_set.R | 4 R/tar_outdated.R | 10 - R/tar_path.R | 6 R/tar_progress.R | 29 ++- R/tar_progress_branches.R |only R/tar_prune.R | 14 - R/tar_read.R | 10 - R/tar_renv.R | 6 R/tar_script.R | 14 - R/tar_seed.R | 6 R/tar_sitrep.R | 10 - R/tar_target.R | 6 R/tar_target_raw.R | 6 R/tar_test.R | 31 ++- R/tar_traceback.R | 6 R/tar_validate.R | 6 R/tar_visnetwork.R | 14 - R/tar_watch.R | 210 ++++++++++++++--------- R/tar_workspace.R | 8 R/tar_workspaces.R | 6 R/utils_assert.R | 13 - R/utils_callr.R | 6 R/utils_cli.R | 12 + R/utils_data.R | 4 R/utils_path.R | 26 ++ build/partial.rdb |binary inst/WORDLIST | 3 man/tar_branches.Rd | 8 man/tar_cancel.Rd | 4 man/tar_deduplicate.Rd | 6 man/tar_delete.Rd | 8 man/tar_destroy.Rd | 6 man/tar_dir.Rd | 3 man/tar_envir.Rd | 4 man/tar_glimpse.Rd | 8 man/tar_group.Rd | 4 man/tar_invalidate.Rd | 8 man/tar_load.Rd | 8 man/tar_load_raw.Rd | 8 man/tar_make.Rd | 6 man/tar_make_clustermq.Rd | 8 man/tar_make_future.Rd | 8 man/tar_manifest.Rd | 6 man/tar_meta.Rd | 14 + man/tar_name.Rd | 6 man/tar_network.Rd | 8 man/tar_objects.Rd | 6 man/tar_option_get.Rd | 4 man/tar_option_reset.Rd | 4 man/tar_option_set.Rd | 4 man/tar_outdated.Rd | 8 man/tar_path.Rd | 6 man/tar_progress.Rd | 24 +- man/tar_progress_branches.Rd |only man/tar_prune.Rd | 10 - man/tar_read.Rd | 4 man/tar_read_raw.Rd | 6 man/tar_renv.Rd | 4 man/tar_script.Rd | 4 man/tar_seed.Rd | 6 man/tar_sitrep.Rd | 8 man/tar_target.Rd | 6 man/tar_target_raw.Rd | 6 man/tar_test.Rd | 7 man/tar_traceback.Rd | 6 man/tar_validate.Rd | 6 man/tar_visnetwork.Rd | 6 man/tar_watch.Rd | 22 -- man/tar_watch_app_ui.Rd | 2 man/tar_watch_server.Rd | 4 man/tar_watch_ui.Rd | 4 man/tar_workspace.Rd | 6 man/tar_workspaces.Rd | 6 tests/interactive/test-reporter.R | 2 tests/interactive/test-tar_watch.R | 29 +++ tests/testthat/test-class_builder.R | 22 +- tests/testthat/test-class_clustermq.R | 6 tests/testthat/test-class_inspection.R | 8 tests/testthat/test-class_patternview.R | 4 tests/testthat/test-class_progress.R | 137 +++++++++++---- tests/testthat/test-class_stem.R | 4 tests/testthat/test-class_torch.R | 5 tests/testthat/test-class_url.R | 10 - tests/testthat/test-tar_cancel.R | 6 tests/testthat/test-tar_make_clustermq.R | 2 tests/testthat/test-tar_progress.R | 23 ++ tests/testthat/test-tar_progress_branches.R |only tests/testthat/test-utils_assert.R | 8 130 files changed, 1055 insertions(+), 725 deletions(-)
Title: System Native Font Finding
Description: Provides system native access to the font catalogue. As font
handling varies between systems it is difficult to correctly locate
installed fonts across different operating systems. The 'systemfonts'
package provides bindings to the native libraries on Windows, macOS and
Linux for finding font files that can then be used further by e.g. graphic
devices. The main use is intended to be from compiled code but 'systemfonts'
also provides access from R.
Author: Thomas Lin Pedersen [aut, cre]
(<https://orcid.org/0000-0002-5147-4711>),
Jeroen Ooms [aut] (<https://orcid.org/0000-0002-4035-0289>),
Devon Govett [aut] (Author of font-manager),
RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@rstudio.com>
Diff between systemfonts versions 0.3.2 dated 2020-09-29 and 1.0.0 dated 2021-02-01
DESCRIPTION | 9 - MD5 | 64 ++++++----- NAMESPACE | 1 NEWS.md | 12 ++ R/cpp11.R | 32 +++-- R/font_fallback.R |only R/font_info.R | 2 R/register_font.R | 10 - R/sysdata.rda |binary R/zzz.R | 7 + README.md | 30 ++--- build/vignette.rds |binary configure | 25 ++-- inst/doc/c_interface.Rmd | 61 +++++++++++ inst/doc/c_interface.html | 109 +++++++++++++++++++ inst/include/systemfonts.h | 40 ++++++- man/font_fallback.Rd |only man/font_info.Rd | 2 src/Makevars.in | 4 src/Makevars.win | 8 - src/caches.cpp | 8 + src/caches.h | 2 src/cpp11.cpp | 13 ++ src/emoji.cpp | 85 +++++++++++++++ src/emoji.h | 8 + src/font_fallback.cpp |only src/font_fallback.h |only src/font_matching.cpp | 3 src/font_metrics.cpp | 67 ++++++++++++ src/font_metrics.h | 3 src/ft_cache.cpp | 63 +++++++++++ src/ft_cache.h | 6 + src/types.h | 2 src/win/FontManagerWindows.cpp | 225 ++++++++++++++++++++++++++++++++++++----- vignettes/c_interface.Rmd | 61 +++++++++++ 35 files changed, 845 insertions(+), 117 deletions(-)
Title: Core Functionality of the 'spatstat' Package
Description: This is a subset of the original 'spatstat' package,
containing all of the user-level code from 'spatstat',
except for the code for linear networks.
Author: Adrian Baddeley [aut, cre],
Rolf Turner [aut],
Ege Rubak [aut],
Kasper Klitgaard Berthelsen [ctb],
Ottmar Cronie [ctb],
Tilman Davies [ctb],
Julian Gilbey [ctb],
Yongtao Guan [ctb],
Ute Hahn [ctb],
Kassel Hingee [ctb],
Abdollah Jalilian [ctb],
Marie-Colette van Lieshout [ctb],
Greg McSwiggan [ctb],
Tuomas Rajala [ctb],
Suman Rakshit [ctb],
Dominic Schuhmacher [ctb],
Rasmus Plenge Waagepetersen [ctb],
Hangsheng Wang [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.core versions 1.65-0 dated 2021-01-22 and 1.65-5 dated 2021-02-01
DESCRIPTION | 14 ++- MD5 | 168 +++++++++++++++++++-------------------- NEWS |only R/detpointprocfamilyfun.R | 6 - R/interactions.R | 14 +-- R/markcorr.R | 8 - inst/doc/packagesizes.txt | 1 man/AreaInter.Rd | 10 -- man/BadGey.Rd | 4 man/Concom.Rd | 4 man/DiggleGatesStibbard.Rd | 4 man/Extract.fasp.Rd | 4 man/Fest.Rd | 2 man/Finhom.Rd | 5 - man/Gcross.Rd | 6 - man/Gest.Rd | 2 man/Gfox.Rd | 3 man/Ginhom.Rd | 5 - man/Gres.Rd | 6 - man/Hardcore.Rd | 8 - man/Jdot.Rd | 6 - man/Jinhom.Rd | 5 - man/Kcross.Rd | 13 +-- man/Kdot.Rd | 8 - man/Kinhom.Rd | 2 man/Kmodel.dppm.Rd | 13 +-- man/Kres.Rd | 6 - man/MultiStrauss.Rd | 4 man/PairPiece.Rd | 6 - man/Poisson.Rd | 4 man/SatPiece.Rd | 8 - man/Smooth.Rd | 10 +- man/Strauss.Rd | 8 - man/StraussHard.Rd | 4 man/Triplets.Rd | 6 - man/allstats.Rd | 2 man/alltypes.Rd | 13 +-- man/bw.diggle.Rd | 2 man/bw.scott.Rd | 2 man/density.ppp.Rd | 8 - man/detpointprocfamilyfun.Rd | 14 +-- man/diagnose.ppm.Rd | 4 man/dppapproxpcf.Rd | 24 +++-- man/envelope.Rd | 45 +++++----- man/envelope.pp3.Rd | 2 man/harmonise.fv.Rd | 4 man/hierpair.family.Rd | 18 +--- man/hybrid.family.Rd | 16 +-- man/inforder.family.Rd | 10 -- man/isf.object.Rd |only man/kppm.Rd | 8 + man/lgcp.estK.Rd | 10 +- man/markcorr.Rd | 14 +-- man/ord.family.Rd | 19 ---- man/pairsat.family.Rd | 5 - man/pairwise.family.Rd | 3 man/plot.fasp.Rd | 2 man/plot.plotppm.Rd | 2 man/ppm.Rd | 61 ++++++-------- man/ppm.object.Rd | 6 - man/ppm.ppp.Rd | 109 ------------------------- man/predict.dppm.Rd | 15 +-- man/predict.ppm.Rd | 4 man/print.ppm.Rd | 6 - man/profilepl.Rd | 12 +- man/qqplot.ppm.Rd | 28 +++--- man/quad.ppm.Rd | 2 man/quadrat.test.Rd | 7 - man/rdpp.Rd | 11 -- man/reload.or.compute.Rd | 2 man/relrisk.Rd | 13 +-- man/rho2hat.Rd | 4 man/rmh.default.Rd | 2 man/rmh.ppm.Rd | 10 +- man/spatstat.core-deprecated.Rd | 3 man/spatstat.core-internal.Rd | 6 + man/spatstat.core-package.Rd | 7 - man/summary.ppm.Rd | 8 - man/triplet.family.Rd | 3 man/update.detpointprocfamily.Rd | 11 -- man/vargamma.estK.Rd | 11 +- tests/testsAtoC.R | 13 ++- tests/testsD.R | 18 +++- tests/testsK.R | 14 ++- tests/testsL.R | 15 ++- tests/testsM.R | 6 + 86 files changed, 433 insertions(+), 578 deletions(-)
Title: Markdown Reference Manuals
Description: The native R functionalities only allow PDF exports of reference manuals. This shall be extended by converting the package documentation files into markdown files and combining them into a markdown version of the package reference manual.
Author: Julian Busch [aut, cre]
Maintainer: Julian Busch <jb@quants.ch>
Diff between Rd2md versions 0.0.2 dated 2017-05-22 and 0.0.5 dated 2021-02-01
Rd2md-0.0.2/Rd2md/R/00_ReferenceManual.R |only Rd2md-0.0.2/Rd2md/inst/doc/Introduction.pdf |only Rd2md-0.0.5/Rd2md/DESCRIPTION | 10 +-- Rd2md-0.0.5/Rd2md/MD5 | 46 +++++++++-------- Rd2md-0.0.5/Rd2md/NEWS | 24 +++++++++ Rd2md-0.0.5/Rd2md/R/Rd2markdown.R | 71 ++++++++++++--------------- Rd2md-0.0.5/Rd2md/R/Rd2md-package.R | 38 +++++++------- Rd2md-0.0.5/Rd2md/R/ReferenceManual.R |only Rd2md-0.0.5/Rd2md/R/parseRd.R | 49 +++++++++--------- Rd2md-0.0.5/Rd2md/R/parseTag.R | 56 +++++++++++---------- Rd2md-0.0.5/Rd2md/R/utils.R | 42 +++++++++++++++ Rd2md-0.0.5/Rd2md/README.md | 26 ++------- Rd2md-0.0.5/Rd2md/build/vignette.rds |binary Rd2md-0.0.5/Rd2md/inst/doc/Introduction.R | 7 +- Rd2md-0.0.5/Rd2md/inst/doc/Introduction.Rmd | 56 ++++++++++++++++++--- Rd2md-0.0.5/Rd2md/inst/doc/Introduction.html |only Rd2md-0.0.5/Rd2md/man/Rd2markdown.Rd | 7 +- Rd2md-0.0.5/Rd2md/man/Rd2md-package.Rd | 9 +-- Rd2md-0.0.5/Rd2md/man/RdTags.Rd | 1 Rd2md-0.0.5/Rd2md/man/ReferenceManual.Rd | 42 +++++++++++---- Rd2md-0.0.5/Rd2md/man/fetchRdDB.Rd |only Rd2md-0.0.5/Rd2md/man/parseRd.Rd | 9 +-- Rd2md-0.0.5/Rd2md/man/parseTag.Rd | 27 ++++++---- Rd2md-0.0.5/Rd2md/man/simpleCap.Rd | 1 Rd2md-0.0.5/Rd2md/man/stripWhite.Rd | 1 Rd2md-0.0.5/Rd2md/man/trim.Rd |only Rd2md-0.0.5/Rd2md/vignettes/Introduction.Rmd | 56 ++++++++++++++++++--- 27 files changed, 365 insertions(+), 213 deletions(-)
Title: Enhanced 'R Markdown' Format for 'Word' and 'PowerPoint'
Description: Allows production of 'Microsoft' corporate documents from 'R Markdown' by
reusing formatting defined in 'Microsoft Word' documents. You can reuse table styles,
list styles but also add column sections, landscape oriented pages. Table and image
captions as well as cross-references are transformed into 'Microsoft Word' fields,
allowing documents edition and merging without issue with references; the syntax
conforms to the 'bookdown' cross-reference definition. Objects generated by
the 'officer' package are also supported in the 'knitr' chunks.
'Microsoft PowerPoint' presentations also benefit from this as well as the
ability to produce editable vector graphics in 'PowerPoint' and also to
define placeholder where content is to be added.
Author: David Gohel [aut, cre, cph],
Institut für Qualitätssicherung und Transparenz im Gesundheitswesen
[fnd],
Noam Ross [aut] (rmarkdown implementation for rvg),
ArData [cph]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between officedown versions 0.2.0 dated 2020-06-29 and 0.2.1 dated 2021-02-01
officedown-0.2.0/officedown/inst/doc/captions.R |only officedown-0.2.0/officedown/inst/doc/captions.Rmd |only officedown-0.2.0/officedown/inst/doc/captions.html |only officedown-0.2.0/officedown/inst/doc/lists.R |only officedown-0.2.0/officedown/inst/doc/lists.Rmd |only officedown-0.2.0/officedown/inst/doc/lists.html |only officedown-0.2.0/officedown/inst/doc/officer.R |only officedown-0.2.0/officedown/inst/doc/officer.Rmd |only officedown-0.2.0/officedown/inst/doc/officer.html |only officedown-0.2.0/officedown/inst/doc/tables.R |only officedown-0.2.0/officedown/inst/doc/tables.Rmd |only officedown-0.2.0/officedown/inst/doc/tables.html |only officedown-0.2.0/officedown/inst/doc/yaml.R |only officedown-0.2.0/officedown/inst/doc/yaml.Rmd |only officedown-0.2.0/officedown/inst/doc/yaml.html |only officedown-0.2.0/officedown/vignettes/captions.Rmd |only officedown-0.2.0/officedown/vignettes/lists.Rmd |only officedown-0.2.0/officedown/vignettes/officer.Rmd |only officedown-0.2.0/officedown/vignettes/tables.Rmd |only officedown-0.2.0/officedown/vignettes/yaml.Rmd |only officedown-0.2.1/officedown/DESCRIPTION | 13 ++-- officedown-0.2.1/officedown/MD5 | 41 ++++---------- officedown-0.2.1/officedown/NEWS.md | 8 ++ officedown-0.2.1/officedown/R/rdocx_document.R | 39 ++++++++++++-- officedown-0.2.1/officedown/R/rdocx_post_proc.R | 58 --------------------- officedown-0.2.1/officedown/R/rpptx_document.R | 3 - officedown-0.2.1/officedown/README.md | 21 +++++-- officedown-0.2.1/officedown/build/vignette.rds |binary officedown-0.2.1/officedown/inst/doc/overview.Rmd |only officedown-0.2.1/officedown/inst/doc/overview.html |only officedown-0.2.1/officedown/man/rdocx_document.Rd | 2 officedown-0.2.1/officedown/man/rpptx_document.Rd | 3 - officedown-0.2.1/officedown/vignettes/overview.Rmd |only 33 files changed, 80 insertions(+), 108 deletions(-)
Title: Functions for Behavioral Science Researchers
Description: Miscellaneous functions to simplify and expedite
analyses of experimental data. Examples include a function
that plots sample means of groups in a factorial experimental design,
a function that conducts robust regressions with bootstrapped samples,
and a function that conducts robust two-way analysis of variance.
Author: Jin Kim [aut, cre] (<https://orcid.org/0000-0002-5013-3958>)
Maintainer: Jin Kim <jin.m.kim@yale.edu>
Diff between kim versions 0.2.35 dated 2021-01-06 and 0.2.71 dated 2021-02-01
DESCRIPTION | 14 +++--- MD5 | 68 +++++++++++++++++++----------- NAMESPACE | 10 ++++ NEWS.md | 8 +++ R/compare_datasets.R | 2 R/compare_groups.R | 3 - R/correlation_matrix.R | 14 +++--- R/desc_stats.R | 85 ++++++++++++++++++++++++++++++-------- R/desc_stats_by_group.R | 46 ++++++++++++-------- R/find_duplicates.R |only R/ggsave_quick.R |only R/histogram.R | 5 ++ R/histogram_by_group.R | 8 ++- R/histogram_w_outlier_bins.R |only R/onAttach.R | 16 +++---- R/prep.R | 73 +++++++++++++++++++++++++------- R/print_loop_progress.R |only R/read_csv.R |only R/read_sole_csv.R |only R/rel_pos_of_value_in_vector.R |only R/rel_value_of_pos_in_vector.R |only R/scatterplot.R | 84 ++++++++++++++++++++----------------- R/setup_r_env.R | 6 +- R/start_kim.R |only R/top_median_or_bottom.R | 8 +-- R/update_kim.R | 38 ++++++++++++++-- R/write_csv.R |only README.md | 10 ++-- inst/CITATION | 4 - man/compare_datasets.Rd | 2 man/desc_stats.Rd | 14 +++++- man/find_duplicates.Rd |only man/ggsave_quick.Rd |only man/histogram_by_group.Rd | 6 ++ man/histogram_w_outlier_bins.Rd |only man/prep.Rd | 18 +++++++- man/print_loop_progress.Rd |only man/read_csv.Rd |only man/read_sole_csv.Rd |only man/rel_pos_of_value_in_vector.Rd |only man/rel_value_of_pos_in_vector.Rd |only man/scatterplot.Rd | 28 ++++++++++-- man/start_kim.Rd |only man/update_kim.Rd | 20 ++++++++ man/write_csv.Rd |only 45 files changed, 420 insertions(+), 170 deletions(-)
Title: Functions for Tabular Reporting
Description: Create pretty tables for 'HTML', 'PDF', 'Microsoft Word' and 'Microsoft PowerPoint'
documents from 'R Markdown'. Functions are provided to let users create tables, modify and format
their content. It also extends package 'officer' that does not contain any feature for customized
tabular reporting.
Author: David Gohel [aut, cre],
Quentin Fazilleau [ctb],
Maxim Nazarov [ctb] (rmarkdown for docx output),
Titouan Robert [ctb],
Michael Barrowman [ctb] (inline footnotes),
Atsushi Yasumoto [ctb] (support for bookdown cross reference),
Paul Julian [ctb] (support for gam objects)
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between flextable versions 0.6.2 dated 2021-01-25 and 0.6.3 dated 2021-02-01
flextable-0.6.2/flextable/man/glance_gam.Rd |only flextable-0.6.2/flextable/man/tidy_gam.Rd |only flextable-0.6.3/flextable/DESCRIPTION | 6 flextable-0.6.3/flextable/MD5 | 248 +++++----- flextable-0.6.3/flextable/NAMESPACE | 1 flextable-0.6.3/flextable/NEWS.md | 18 flextable-0.6.3/flextable/R/05_content.R | 18 flextable-0.6.3/flextable/R/as_flextable.R | 10 flextable-0.6.3/flextable/R/as_flextable_gam.R | 9 flextable-0.6.3/flextable/R/chunk_images.R | 8 flextable-0.6.3/flextable/R/compose.R | 16 flextable-0.6.3/flextable/R/defaults.R | 23 flextable-0.6.3/flextable/R/flextable_sizes.R | 3 flextable-0.6.3/flextable/R/format_fun.R | 18 flextable-0.6.3/flextable/R/formatters.R | 31 + flextable-0.6.3/flextable/R/latex_chunks.R | 32 - flextable-0.6.3/flextable/R/latex_str.R | 4 flextable-0.6.3/flextable/build/vignette.rds |binary flextable-0.6.3/flextable/inst/doc/overview.Rmd | 13 flextable-0.6.3/flextable/inst/doc/overview.html | 10 flextable-0.6.3/flextable/man/as_flextable.gam.Rd | 6 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Title: Univariate GARCH-MIDAS, Double-Asymmetric GARCH-MIDAS and
MEM-MIDAS
Description: Adds the MIxing-Data Sampling (MIDAS, Ghysels et al. (2007) <doi:10.1080/07474930600972467>) components to a variety of GARCH and MEM (Engle (2002) <doi:10.1002/jae.683>) models, with the aim of predicting the volatility with additional low-frequency (that is, MIDAS) terms. The estimation takes place through simple functions, which provide in-sample and (if present) and out-of-sample evaluations. 'rumidas' also offers a summary tool, which synthesizes the main information of the estimated model. There is also the possibility of generating one-step-ahead and multi-step-ahead forecasts.
Author: Vincenzo Candila [aut, cre]
Maintainer: Vincenzo Candila <vincenzo.candila@uniroma1.it>
Diff between rumidas versions 0.1.0 dated 2020-09-22 and 0.1.1 dated 2021-02-01
DESCRIPTION | 8 MD5 | 94 - NAMESPACE | 27 NEWS.md |only R/data.R | 28 R/functions.R | 208 ++ R/midas_functions.R | 3415 ++++++++++++++++++++++++++++++++++--- build/partial.rdb |binary data/vix.rda |only inst/CITATION | 2 inst/REFERENCES.bib | 41 man/DAGM_X_cond_vol.Rd |only man/DAGM_X_cond_vol_no_skew.Rd |only man/DAGM_X_loglik.Rd |only man/DAGM_X_loglik_no_skew.Rd |only man/DAGM_X_long_run_vol.Rd |only man/DAGM_X_long_run_vol_no_skew.Rd |only man/DAGM_cond_vol.Rd | 5 man/DAGM_cond_vol_no_skew.Rd | 5 man/DAGM_loglik.Rd | 9 man/DAGM_loglik_no_skew.Rd | 9 man/DAGM_long_run_vol.Rd | 5 man/DAGM_long_run_vol_no_skew.Rd | 5 man/GM_X_cond_vol.Rd |only man/GM_X_cond_vol_no_skew.Rd |only man/GM_X_loglik.Rd |only man/GM_X_loglik_no_skew.Rd |only man/GM_X_long_run_vol.Rd |only man/GM_X_long_run_vol_no_skew.Rd |only man/GM_cond_vol.Rd | 7 man/GM_cond_vol_no_skew.Rd | 9 man/GM_loglik.Rd | 7 man/GM_loglik_no_skew.Rd | 9 man/GM_long_run_vol.Rd | 7 man/GM_long_run_vol_no_skew.Rd | 7 man/MEM_MIDAS_X_loglik.Rd |only man/MEM_MIDAS_X_loglik_no_skew.Rd |only man/MEM_MIDAS_X_lr_pred.Rd |only man/MEM_MIDAS_X_lr_pred_no_skew.Rd |only man/MEM_MIDAS_X_pred.Rd |only man/MEM_MIDAS_X_pred_no_skew.Rd |only man/MEM_MIDAS_loglik.Rd | 2 man/MEM_MIDAS_loglik_no_skew.Rd | 10 man/MEM_MIDAS_lr_pred_no_skew.Rd | 2 man/MEM_MIDAS_pred_no_skew.Rd | 2 man/MEM_QMLE_sd.Rd | 2 man/MEM_X_loglik.Rd |only man/MEM_X_loglik_no_skew.Rd |only man/MEM_X_pred.Rd |only man/MEM_X_pred_no_skew.Rd |only man/MEM_loglik.Rd | 2 man/MEM_loglik_no_skew.Rd | 2 man/MEM_pred.Rd | 2 man/MEM_pred_no_skew.Rd | 2 man/beta_function.Rd | 4 man/exp_almon.Rd |only man/multi_step_ahead_pred.Rd |only man/mv_into_mat.Rd | 15 man/sum_X_f.Rd |only man/ugmfit.Rd | 61 man/umemfit.Rd | 43 man/vix.Rd |only 62 files changed, 3669 insertions(+), 387 deletions(-)
Title: Adaptive Empirical Pattern Transformation
Description: Designed for optimal use in performing fast,
accurate walking strides segmentation from high-density
data collected from a wearable accelerometer worn
during continuous walking activity.
Author: Marta Karas [aut, cre] (<https://orcid.org/0000-0001-5889-3970>),
Jacek Urbanek [aut] (<https://orcid.org/0000-0002-1890-8899>),
Ciprian Crainiceanu [aut],
John Muschelli [ctb] (<https://orcid.org/0000-0001-6469-1750>),
Adi Gherman [ctb]
Maintainer: Marta Karas <marta.karass@gmail.com>
Diff between adept versions 1.1.2 dated 2019-06-18 and 1.2 dated 2021-02-01
DESCRIPTION | 12 MD5 | 44 - NAMESPACE | 5 NEWS.md | 6 R/segmentPattern.R | 130 ++-- R/segmentWalking.R |only README.md | 32 build/vignette.rds |binary inst/CITATION |only inst/doc/adept-intro.R | 52 - inst/doc/adept-intro.html | 999 +++++++++++++++---------------- inst/doc/adept-strides-segmentation.R | 68 +- inst/doc/adept-strides-segmentation.Rmd | 4 inst/doc/adept-strides-segmentation.html | 981 +++++++++++++++--------------- man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-5-2.png |binary man/figures/README-unnamed-chunk-5-3.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/segmentPattern.Rd | 39 - man/segmentWalking.Rd |only man/similarityMatrix.Rd | 2 tests/testthat/test-segmentPattern.R | 94 -- tests/testthat/test-segmentWalking.R |only vignettes/adept-strides-segmentation.Rmd | 4 25 files changed, 1242 insertions(+), 1230 deletions(-)
Title: Japanese Utility Functions and Data
Description: Some data treated by the Japanese R user require
unique operations and processing. These are caused by address, Kanji,
and traditional year representations. 'zipangu' transforms specific
to Japan into something more general one.
Author: Shinya Uryu [aut, cre] (<https://orcid.org/0000-0002-0493-6186>),
Hiroaki Yutani [ctb] (<https://orcid.org/0000-0002-3385-7233>),
Kazuhiro Maeda [ctb],
Mao Kobayashi [ctb]
Maintainer: Shinya Uryu <suika1127@gmail.com>
Diff between zipangu versions 0.2.1 dated 2020-07-07 and 0.2.2 dated 2021-02-01
DESCRIPTION | 21 ++-- MD5 | 33 +++--- NAMESPACE | 4 NEWS.md | 15 +++ R/convert-jyear.R | 123 ++++++++++++++++--------- R/jholiday.R | 30 +++--- R/kansuji.R | 200 +++++++++++++++++++++++++++++++++++++++-- R/label-kansuji.R |only README.md | 58 +++++------ build/zipangu.pdf |binary man/find_date_by_wday.Rd | 2 man/is_jholiday.Rd | 4 man/jholiday.Rd | 8 - man/kansuji.Rd | 30 ++++++ man/label_kansuji.Rd |only tests/testthat/test-jholiday.R | 68 ++++++++----- tests/testthat/test-jyear.R | 20 +++- tests/testthat/test-kanji.R | 20 ++++ tests/testthat/test-label.R |only 19 files changed, 489 insertions(+), 147 deletions(-)
Title: Single Transferable Vote Counting
Description: Implementations of the Single Transferable Vote counting
system. By default, it uses the Cambridge method for surplus allocation
and Droop method for quota calculation. Fractional surplus allocation
and the Hare quota are available as options.
Author: John Emerson [cre, aut],
Saksham Chandra [aut],
Lilla Orr [aut],
Efim Abrikosov [ctb],
Shadie Khubba [ctb],
William Meyerson [ctb],
Shylee Ezroni [ctb],
Junchao Ma [ctb]
Maintainer: John Emerson <john.emerson@yale.edu>
Diff between STV versions 1.0.1 dated 2019-03-07 and 1.0.2 dated 2021-02-01
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/validate_clean_ballots.R | 5 ++++- man/stv.Rd | 10 ++++++++-- 5 files changed, 25 insertions(+), 11 deletions(-)
Title: Group Ordinal Method for Multiple Criteria Decision-Making
Description: Implementation of SAPEVO-M, a Group Ordinal Method for Multiple Criteria Decision-Making (MCDM). SAPEVO-M is an acronym for Simple Aggregation of Preferences Expressed by Ordinal Vectors Group Decision Making. This method provides alternatives ranking given decision makers' preferences: criteria preferences and alternatives preferences for each criterion.This method is described in Gomes et al. (2020) <doi: 10.1590/0101-7438.2020.040.00226524 >.
Author: Raquel Coutinho [aut, cre],
Marcos dos Santos [aut]
Maintainer: Raquel Coutinho <rdouradocoutinho@gmail.com>
Diff between sapevom versions 0.1.0 dated 2020-12-07 and 0.2.0 dated 2021-02-01
DESCRIPTION | 12 +++++++----- MD5 | 7 ++++++- build |only inst |only vignettes |only 5 files changed, 13 insertions(+), 6 deletions(-)
Title: Piecewise Constant Hazard Models for Censored and Truncated Data
Description: Piecewise constant hazard models for survival data.
The package allows for right-censored, left-truncated, and interval-censored data.
Author: Paolo Frumento
Maintainer: Paolo Frumento <paolo.frumento@unipi.it>
Diff between pch versions 1.4 dated 2020-02-27 and 2.0 dated 2021-02-01
pch-1.4/pch/R/pch.R |only pch-2.0/pch/DESCRIPTION | 20 ++--- pch-2.0/pch/MD5 | 19 ++--- pch-2.0/pch/NAMESPACE | 5 - pch-2.0/pch/NEWS.md | 17 ++-- pch-2.0/pch/R/pchreg_ct.R |only pch-2.0/pch/R/pchreg_ic.R |only pch-2.0/pch/R/pchreg_main.R |only pch-2.0/pch/R/splinex_and_utilities.R |only pch-2.0/pch/man/pch-internal.Rd | 16 +++- pch-2.0/pch/man/pchreg.Rd | 126 ++++++++++++++++++++++------------ pch-2.0/pch/man/predict.pch.Rd | 36 +++++---- pch-2.0/pch/man/splinex.Rd | 20 ++--- 13 files changed, 160 insertions(+), 99 deletions(-)
Title: Detecting Outliers in Network Meta-Analysis
Description: A set of functions providing several outlier (i.e., studies with extreme findings) and influential detection measures and methodologies in network meta-analysis:
- Simple outlier and influential deletion measures provided: (a) Raw, (b) Standardized, (c) Studentized residuals; (d) Mahalanobis distance and (c) leverage.
- Outlier and influential detection measures by considering study deletion (Shift the mean): (a) Raw (b) Standardized, (c) Studentized deleted residuals;
(d) Cook distance; (e) Ratio of variance-covariance matrix; (f) weight leave one out; (g) leverage leave one out; (h) heterogeneity leave one out;
(i) R heterogeneity; (k) R Q total; (l) R Q heterogeneity (m); R Q inconsistency and (n) statistic that indicate the effect that deleting each study has on the treatment estimates.
- Plots for outlier and influential detection simply and deletion measures (all the above measures) and Q-Q plot for network meta-analysis.
- Forward Search algorithm in network meta-analysis.
- Forward plots for the monitoring statistics in each step of Forward search algorithm:
(a) P-scores; (b) z-values for difference of direct and indirect evidence with back-calculation method;
(c) Standardized residuals; (d) heterogeneity variance estimator; (e) cook distance; (f) ratio of variances;
(g) Q statistics.
- Forward plots for summary estimates and their confidence intervals in each step of forward search algorithm.
Author: Maria Petropoulou [aut, cre] (<https://orcid.org/0000-0002-7147-3644>),
Guido Schwarzer [aut] (<https://orcid.org/0000-0001-6214-9087>),
Agapios Panos [aut],
Dimitris Mavridis [aut] (<https://orcid.org/0000-0003-1041-4592>)
Maintainer: Maria Petropoulou <petropoulou@imbi.uni-freiburg.de>
Diff between NMAoutlier versions 0.1.13 dated 2019-02-01 and 0.1.17 dated 2021-02-01
DESCRIPTION | 46 ++++----- MD5 | 59 +++++++---- NAMESPACE | 8 + NEWS | 23 ++++ R/Gupta2013.R | 44 ++++---- R/NMAoutlier-internal.R | 2 R/NMAoutlier-package.R | 125 +++++++++++++++--------- R/NMAoutlier.R | 124 +++++++++++------------- R/NMAoutlier.measures.R |only R/Qnetplot.R |only R/Schoenberg2013.R | 30 ++--- R/fwdplot.R | 150 +++-------------------------- R/fwdplotest.R | 68 ++----------- R/help_plot.R |only R/measplot.R |only R/netmet.R | 8 - R/plotesthelper.R |only R/plothelper.R |only R/print.NMAoutlier.R | 12 +- R/print.NMAoutlier.measures.R |only R/res_multi.R |only man/Gupta2013.Rd | 34 +++--- man/InitialSubset.Rd | 16 ++- man/NMAoutlier-package.Rd | 126 +++++++++++++++--------- man/NMAoutlier.Rd | 124 +++++++++++++----------- man/NMAoutlier.measures.Rd |only man/Qnetplot.Rd |only man/Schoenberg2013.Rd | 20 +-- man/figures/Estimates.png |only man/figures/LRT.png |only man/figures/Mahalanobis.png |only man/figures/Q-Q.png |only man/figures/Qinc.png |only man/fwdplot.Rd | 212 +++++++++++++++++++++--------------------- man/fwdplotest.Rd | 21 +--- man/measplot.Rd |only man/netmet.Rd | 13 ++ man/plotesthelper.Rd |only man/plothelper.Rd |only man/res_multi.Rd |only 40 files changed, 621 insertions(+), 644 deletions(-)
Title: Moving-Window and Direct Data Aggregation
Description: Data aggregation via moving window or direct methods. Aggregate a
fine-resolution raster to a grid. The moving window method smooths the surface
using a specified function within a moving window of a specified size and shape
prior to aggregation. The direct method simply aggregates to the grid using the
specified function.
Author: Laura Graham [aut, cre] (<https://orcid.org/0000-0002-3611-7281>),
Felix Eigenbrod [ctb] (Input on initial conceptual development),
Marco Sciaini [ctb] (Input on package development and structure)
Maintainer: Laura Graham <LauraJaneEGraham@gmail.com>
Diff between grainchanger versions 0.3.1 dated 2021-01-29 and 0.3.2 dated 2021-02-01
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 3 +++ inst/doc/grainchanger.html | 6 +++--- tests/testthat/test-winmove_agg.R | 4 ++++ 5 files changed, 17 insertions(+), 10 deletions(-)
Title: Binary Expansion Testing
Description: Nonparametric detection of nonuniformity and dependence with Binary Expansion Testing (BET). See Kai Zhang (2019) BET on Independence, Journal of the American Statistical Association, 114:528, 1620-1637, <DOI:10.1080/01621459.2018.1537921> and Zhigen Zhao, Michael Baiocchi, Kai Zhang. SorBET: A Fast and Powerful Algorithm to Test Dependence of Variables.
Author: Wan Zhang [aut, cre],
Zhigen Zhao [aut],
Michael Baiocchi [aut],
Kai Zhang [aut]
Maintainer: Wan Zhang <wanz63@live.unc.edu>
Diff between BET versions 0.3.2 dated 2021-01-28 and 0.3.3 dated 2021-02-01
DESCRIPTION | 6 MD5 | 30 ++-- NAMESPACE | 22 +-- R/RcppExports.R | 30 ++-- R/plot.R | 382 ++++++++++++++++++++++++++--------------------------- build/partial.rdb |binary man/BET.Rd | 112 +++++++-------- man/BET_package.Rd | 44 +++--- man/BETs.Rd | 110 +++++++-------- man/Beast.Rd | 128 ++++++++--------- man/bet.plot.Rd | 62 ++++---- man/star.Rd | 38 ++--- man/symm.Rd | 70 ++++----- src/BET3.cpp | 30 +++- src/Makevars | 4 src/Makevars.win | 2 16 files changed, 545 insertions(+), 525 deletions(-)
Title: Teaching Hydrological Modelling with the GR Rainfall-Runoff
Models ('Shiny' Interface Included)
Description: Add-on package to the 'airGR' package that simplifies its use and is aimed at being used for teaching hydrology. The package provides 1) three functions that allow to complete very simply a hydrological modelling exercise 2) plotting functions to help students to explore observed data and to interpret the results of calibration and simulation of the GR ('Génie rural') models 3) a 'Shiny' graphical interface that allows for displaying the impact of model parameters on hydrographs and models internal variables.
Author: Olivier Delaigue [aut, cre] (<https://orcid.org/0000-0002-7668-8468>),
Laurent Coron [aut] (<https://orcid.org/0000-0002-1503-6204>),
Pierre Brigode [aut] (<https://orcid.org/0000-0001-8257-0741>),
Guillaume Thirel [ctb] (<https://orcid.org/0000-0002-1444-1830>)
Maintainer: Olivier Delaigue <airGR@inrae.fr>
Diff between airGRteaching versions 0.2.9.25 dated 2020-10-19 and 0.2.10.112 dated 2021-02-01
DESCRIPTION | 15 INDEX | 69 MD5 | 118 NAMESPACE | 105 NEWS.md | 844 +-- R/CalGR.R | 173 R/PrepGR.R | 149 R/ShinyGR.R | 329 - R/SimGR.R | 221 - R/Utils.R | 1671 +++---- R/as.data.frame.airGRt.R | 110 R/dyplot.CalGR.R | 18 R/dyplot.PrepGR.R | 18 R/dyplot.R | 8 R/dyplot.SimGR.R | 18 R/dyplot.default.R | 230 - R/plot.CalGR.R | 220 - R/plot.PrepGR.R | 98 R/plot.SimGR.R | 24 README.md | 192 build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 96 inst/ShinyGR/server.R | 2176 +++++----- inst/ShinyGR/ui.R | 483 +- inst/ShinyGR/www/css/bootstrap.min_Cerulean.css | 287 - inst/ShinyGR/www/css/bootstrap.min_Cyborg.css | 70 inst/ShinyGR/www/css/bootstrap.min_Flatly.css | 178 inst/ShinyGR/www/css/bootstrap.min_Inrae.css | 381 - inst/ShinyGR/www/css/bootstrap.min_Saclay.css | 373 - inst/ShinyGR/www/css/bootstrap.min_United.css | 176 inst/ShinyGR/www/css/bootstrap.min_Yeti.css | 178 inst/ShinyGR/www/fig/ShinyGR_dyplot.html | 46 inst/ShinyGR/www/fig/airGRteaching_GUI_Description.png |only inst/ShinyGR/www/fig/airGRteaching_GUI_MD_theme-Cerulean_550x300.png |only inst/ShinyGR/www/fig/airGRteaching_GUI_MD_theme-Cyborg_544x300.png |only inst/ShinyGR/www/fig/airGRteaching_GUI_MD_theme-Flatly_550x300.png |only inst/ShinyGR/www/fig/airGRteaching_GUI_MD_theme-Inrae_550x300.png |only inst/ShinyGR/www/fig/airGRteaching_GUI_MD_theme-RStudio_550x300.png |only inst/ShinyGR/www/fig/airGRteaching_GUI_MD_theme-Saclay_550x300.png |only inst/ShinyGR/www/fig/airGRteaching_GUI_MD_theme-United_550x300.png |only inst/ShinyGR/www/fig/airGRteaching_GUI_MD_theme-Yeti_550x300.png |only inst/ShinyGR/www/fig/logo_R_CMJN.svg | 64 inst/ShinyGR/www/fig/sheet_W1110010_thumbnail.png |binary inst/ShinyGR/www/tab_about.html |only inst/ShinyGR/www/tab_about.md | 146 inst/ShinyGR/www/tab_about.rmd |only inst/ShinyGR/www/tab_authors.html |only inst/ShinyGR/www/tab_authors.md | 256 - inst/ShinyGR/www/tab_authors.rmd |only inst/ShinyGR/www/tab_fun.html |only inst/ShinyGR/www/tab_fun.md | 595 +- inst/ShinyGR/www/tab_fun.rmd |only inst/ShinyGR/www/tab_fun_files/figure-html/unnamed-chunk-10-1.png |binary inst/ShinyGR/www/tab_fun_files/figure-html/unnamed-chunk-11-1.png |only inst/ShinyGR/www/tab_fun_files/figure-html/unnamed-chunk-12-1.png |only inst/ShinyGR/www/tab_fun_files/figure-html/unnamed-chunk-8-1.png |binary inst/doc/get_started.R | 114 inst/doc/get_started.html | 835 ++- inst/doc/get_started.rmd | 376 - man/CalGR.Rd | 165 man/PrepGR.Rd | 201 man/ShinyGR.Rd | 243 - man/SimGR.Rd | 194 man/airGRteaching.Rd | 201 man/as.data.frame.airGRt.Rd | 138 man/dyplot.default.Rd | 162 man/plot.Rd | 159 vignettes/get_started.rmd | 376 - 69 files changed, 7028 insertions(+), 6271 deletions(-)
Title: Variance-Adjusted Mahalanobis
Description: Contains logic for cell-specific gene set scoring of single cell RNA sequencing data.
Author: H. Robert Frost
Maintainer: H. Robert Frost <rob.frost@dartmouth.edu>
Diff between VAM versions 0.4.0 dated 2021-01-14 and 0.5.0 dated 2021-02-01
DESCRIPTION | 8 ++-- MD5 | 34 +++++++++++------ NEWS |only R/VAM.R | 9 +++- build/vignette.rds |binary inst/doc/VAM_PBMC3K_Hallmark_LogNormalization.Rnw |only inst/doc/VAM_PBMC3K_Hallmark_LogNormalization.pdf |binary inst/doc/VAM_PBMC3K_LogNormalization.Rnw |only inst/doc/VAM_PBMC3K_LogNormalization.pdf |binary inst/doc/VAM_PBMC3K_SCTransform.Rnw |only inst/doc/VAM_PBMC3K_SCTransform.pdf |binary inst/doc/VAM_pbmc_small.R | 23 ++++++----- inst/doc/VAM_pbmc_small.Rnw | 13 ++++-- inst/doc/VAM_pbmc_small.pdf |binary man/VAM-package.Rd | 8 ++-- man/VAMForSeurat.Rd | 6 +-- vignettes/VAM_PBMC3K_Hallmark_LogNormalization.Rnw |only vignettes/VAM_PBMC3K_Hallmark_LogNormalization_tmp.pdf |only vignettes/VAM_PBMC3K_LogNormalization.Rnw |only vignettes/VAM_PBMC3K_LogNormalization_tmp.pdf |only vignettes/VAM_PBMC3K_SCTransform.Rnw |only vignettes/VAM_PBMC3K_SCTransform_tmp.pdf |only vignettes/VAM_pbmc_small.Rnw | 13 ++++-- 23 files changed, 68 insertions(+), 46 deletions(-)
Title: Shape Constrained Additive Models
Description: Routines for generalized additive modelling under shape
constraints on the component functions of the linear predictor
(Pya and Wood, 2015) <doi:10.1007/s11222-013-9448-7>.
Models can contain multiple shape constrained (univariate
and/or bivariate) and unconstrained terms. The routines of gam()
in package 'mgcv' are used for setting up the model matrix,
printing and plotting the results. Penalized likelihood
maximization based on Newton-Raphson method is used to fit a
model with multiple smoothing parameter selection by GCV or
UBRE/AIC.
Author: Natalya Pya <nat.pya@gmail.com>
Maintainer: Natalya Pya <nat.pya@gmail.com>
Diff between scam versions 1.2-9 dated 2020-12-09 and 1.2-10 dated 2021-02-01
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/plot.r | 1 + build/partial.rdb |binary 5 files changed, 13 insertions(+), 8 deletions(-)
Title: Create Reports Using R and 'asciidoc'
Description: Inspired by Karl Broman`s reader on using 'knitr'
with 'asciidoc'
(<http://kbroman.org/knitr_knutshell/pages/asciidoc.html>), this is
merely a wrapper to 'knitr' and 'asciidoc'.
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between rasciidoc versions 3.0.1 dated 2021-01-25 and 3.0.2 dated 2021-02-01
DESCRIPTION | 10 +++--- MD5 | 18 ++++++------ NEWS.md | 4 ++ R/render.R | 18 +++++++----- R/zzz.R | 1 inst/NEWS.rd |only inst/doc/An_Introduction_to_rasciidoc.html | 28 +++++++++---------- inst/runit_tests/runit-render.R | 42 +++++++++++++++-------------- inst/vignettes_code |only man/rasciidoc.Rd | 3 +- man/render.Rd | 3 +- 11 files changed, 72 insertions(+), 55 deletions(-)
Title: SPatially aUTomatic deNoising for Ims toolKit
Description: A set of tools for the peak filtering of mass spectrometry
imaging data (MSI or IMS) based on spatial distribution of signal. Given a
region-of-interest (ROI), representing the spatial region where the informative
signal is expected to be localized, a series of filters determine which peak
signals are characterized by an implausible spatial distribution. The filters
reduce the dataset dimensionality and increase its information vs noise ratio,
improving the quality of the unsupervised analysis results, reducing data
dimensionality and simplifying the chemical interpretation.
Author: Paolo Inglese [aut, cre],
Goncalo Correia [aut, ctb]
Maintainer: Paolo Inglese <p.inglese@outlook.com>
Diff between SPUTNIK versions 1.3 dated 2020-03-23 and 1.3.1 dated 2021-02-01
DESCRIPTION | 8 MD5 | 135 +-- NAMESPACE | 132 +-- NEWS | 118 +- R/add_rem_border.R | 110 +- R/construct_funcs.R | 260 +++--- R/data_funcs.R | 190 ++-- R/examples/filter_count.R | 72 - R/examples/filter_csr.R | 64 - R/examples/filter_global.R | 66 - R/examples/filter_split.R | 50 - R/examples/graph_funcs.R | 66 - R/examples/msImage_binOtsu.R | 16 R/examples/msImage_closeImage.R | 22 R/examples/msImage_invertImage.R | 16 R/examples/msImage_plot.R | 16 R/examples/msImage_removeSmallObjects.R | 18 R/examples/msImage_smoothImage.R | 16 R/examples/msiDataset_binKmeans.R | 30 R/examples/msiDataset_getters.R | 36 R/examples/msiDataset_transform.R | 46 - R/examples/sparseness.R | 36 R/filter_count.R | 318 +++---- R/filter_csr.R | 452 +++++----- R/filter_global.R | 230 ++--- R/filter_split.R | 460 +++++----- R/generic_funcs.R | 62 - R/graph_funcs.R | 611 +++++++------- R/is_funcs.R | 258 +++--- R/ms.image_class.R | 94 +- R/ms.image_methods.R | 570 ++++++------- R/msi.dataset_class.R | 148 +-- R/msi.dataset_funcs.R | 864 ++++++++++---------- R/msi.dataset_methods.R | 1221 ++++++++++++++--------------- R/mz_funcs.R | 430 +++++----- R/sparseness_funcs.R | 254 +++--- inst |only man/CSRPeaksFilter.Rd | 276 +++--- man/NMI.Rd | 62 - man/SSIM.Rd | 70 - man/applyPeaksFilter-msi.dataset-method.Rd | 116 +- man/binKmeans-msi.dataset-method.Rd | 74 - man/binKmeans2-msi.dataset-method.Rd | 122 +- man/binOtsu-ms.image-method.Rd | 56 - man/binSupervised-msi.dataset-method.Rd | 102 +- man/bladderMALDIRompp2010.Rd | 56 - man/closeImage-ms.image-method.Rd | 66 - man/countPixelsFilter.Rd | 230 ++--- man/createPeaksFilter.Rd | 76 - man/getIntensityMat-msi.dataset-method.Rd | 78 - man/getMZ-msi.dataset-method.Rd | 76 - man/getShapeMSI-msi.dataset-method.Rd | 76 - man/gini.index.Rd | 110 +- man/globalPeaksFilter.Rd | 208 ++-- man/invertImage-ms.image-method.Rd | 56 - man/ms.image-class.Rd | 46 - man/msImage.Rd | 70 - man/msi.dataset-class.Rd | 70 - man/msiDataset.Rd | 96 +- man/normIntensity-msi.dataset-method.Rd | 190 ++-- man/ovarianDESIDoria2016.Rd | 56 - man/plot.Rd | 58 - man/refAndROIimages.Rd | 276 +++--- man/removeSmallObjects-ms.image-method.Rd | 70 - man/scatter.ratio.Rd | 94 +- man/smoothImage-ms.image-method.Rd | 62 - man/spatial.chaos.Rd | 112 +- man/splitPeaksFilter.Rd | 240 ++--- man/varTransform-msi.dataset-method.Rd | 110 +- 69 files changed, 5488 insertions(+), 5467 deletions(-)
Title: 'sf'-Based Interface to the 'HERE' REST APIs
Description: Interface to the 'HERE' REST APIs <https://developer.here.com/develop/rest-apis>:
(1) geocode and autosuggest addresses or reverse geocode POIs using the 'Geocoder' API;
(2) route directions, travel distance or time matrices and isolines using the 'Routing', 'Matrix Routing' and 'Isoline Routing' APIs;
(3) request real-time traffic flow and incident information from the 'Traffic' API;
(4) find request public transport connections and nearby stations from the 'Public Transit' API;
(5) request intermodal routes using the 'Intermodal Routing' API;
(6) get weather forecasts, reports on current weather conditions, astronomical
information and alerts at a specific location from the 'Destination Weather' API.
Locations, routes and isolines are returned as 'sf' objects.
Author: Merlin Unterfinger [aut, cre] (<https://orcid.org/0000-0003-2020-2366>),
Daniel Possenriede [ctb] (<https://orcid.org/0000-0002-6738-9845>)
Maintainer: Merlin Unterfinger <info@munterfinger.ch>
Diff between hereR versions 0.6.0 dated 2021-01-04 and 0.6.1 dated 2021-02-01
hereR-0.6.0/hereR/man/unset_proxy.Rd |only hereR-0.6.1/hereR/DESCRIPTION | 6 hereR-0.6.1/hereR/MD5 | 97 ++--- hereR-0.6.1/hereR/NEWS.md | 9 hereR-0.6.1/hereR/R/authentication.R | 4 hereR-0.6.1/hereR/R/autosuggest.R | 45 +- hereR-0.6.1/hereR/R/checks.R | 7 hereR-0.6.1/hereR/R/connection.R | 62 ++- hereR-0.6.1/hereR/R/defunct.R | 4 hereR-0.6.1/hereR/R/flow.R | 34 +- hereR-0.6.1/hereR/R/geocode.R | 87 ++--- hereR-0.6.1/hereR/R/incident.R | 40 -- hereR-0.6.1/hereR/R/intermodal_route.R | 131 +++++-- hereR-0.6.1/hereR/R/isoline.R | 61 ++- hereR-0.6.1/hereR/R/reverse_geocode.R | 30 + hereR-0.6.1/hereR/R/route.R | 55 ++- hereR-0.6.1/hereR/R/route_matrix.R | 96 +++-- hereR-0.6.1/hereR/R/station.R | 40 +- hereR-0.6.1/hereR/R/sysdata.rda |binary hereR-0.6.1/hereR/R/utils.R | 36 +- hereR-0.6.1/hereR/R/weather.R | 53 +-- hereR-0.6.1/hereR/README.md | 14 hereR-0.6.1/hereR/inst/doc/geocoder.html | 12 hereR-0.6.1/hereR/inst/doc/intermodal.html | 133 ++++--- hereR-0.6.1/hereR/inst/doc/routing.html | 97 +++-- hereR-0.6.1/hereR/inst/doc/transit.html | 121 ++++--- hereR-0.6.1/hereR/inst/doc/weather.Rmd | 2 hereR-0.6.1/hereR/inst/doc/weather.html | 170 +++++----- hereR-0.6.1/hereR/inst/figure/logo.R | 16 hereR-0.6.1/hereR/man/hereR-defunct.Rd | 8 hereR-0.6.1/hereR/man/route.Rd | 2 hereR-0.6.1/hereR/man/set_key.Rd | 2 hereR-0.6.1/hereR/man/weather.Rd | 2 hereR-0.6.1/hereR/tests/testthat/test-autosuggest.R | 4 hereR-0.6.1/hereR/tests/testthat/test-connection.R | 8 hereR-0.6.1/hereR/tests/testthat/test-flow.R | 4 hereR-0.6.1/hereR/tests/testthat/test-geocode.R | 8 hereR-0.6.1/hereR/tests/testthat/test-get_content.R | 1 hereR-0.6.1/hereR/tests/testthat/test-incident.R | 10 hereR-0.6.1/hereR/tests/testthat/test-intermodal_route.R | 4 hereR-0.6.1/hereR/tests/testthat/test-isoline.R | 4 hereR-0.6.1/hereR/tests/testthat/test-reverse_geocode.R | 12 hereR-0.6.1/hereR/tests/testthat/test-route.R | 4 hereR-0.6.1/hereR/tests/testthat/test-route_matrix.R | 6 hereR-0.6.1/hereR/tests/testthat/test-station.R | 4 hereR-0.6.1/hereR/tests/testthat/test-weather_alerts.R | 4 hereR-0.6.1/hereR/tests/testthat/test-weather_forecast_astronomy.R | 4 hereR-0.6.1/hereR/tests/testthat/test-weather_forecast_hourly.R | 4 hereR-0.6.1/hereR/tests/testthat/test-weather_observation.R | 4 hereR-0.6.1/hereR/vignettes/weather.Rmd | 2 50 files changed, 931 insertions(+), 632 deletions(-)
Title: Locate Errors with Validation Rules
Description: Errors in data can be located and removed using validation rules from package 'validate'.
Author: Edwin de Jonge [aut, cre] (<https://orcid.org/0000-0002-6580-4718>),
Mark van der Loo [aut]
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Diff between errorlocate versions 0.5.1 dated 2020-11-27 and 0.9.8 dated 2021-02-01
DESCRIPTION | 8 MD5 | 76 ++++---- NEWS.md | 22 ++ R/MipRules.R | 50 ++--- R/addnoise.R | 10 - R/categorical.R | 4 R/conditional.R | 2 R/dnf.R | 6 R/errorlocalizer.R | 208 ++++++++++++++++------ R/errorlocate-package.r | 12 - R/errorlocation.R | 26 +- R/expr_manip.R | 43 ++++ R/inspect_mip.R | 2 R/linear.R | 14 - R/locate-errors.R | 51 ++++- R/log_extract.R | 85 +++++---- R/mip_lpsolve.R | 47 ++++- R/replace-errors.R | 51 +++-- R/soft-rule.R | 10 - R/utils.R | 9 inst/doc/inspect_mip.html | 260 +--------------------------- man/ErrorLocalizer-class.Rd | 2 man/FHLocalizer-class.Rd | 2 man/MipRules-class.Rd | 12 - man/add_noise.Rd | 2 man/errorlocate-package.Rd | 14 - man/errorlocation.Rd | 18 - man/errors_removed.Rd | 4 man/inspect_mip.Rd | 4 man/is_linear.Rd | 2 man/locate_errors.Rd | 68 ++++++- man/replace_errors.Rd | 64 +++++- man/translate_mip_lp.Rd | 2 tests/testthat/test-dnf.R | 17 + tests/testthat/test-errorlocation-print.txt | 2 tests/testthat/test-expr-manip.R | 22 ++ tests/testthat/test-locate_errors.R | 39 +++- tests/testthat/test-replace-errors.R | 4 tests/testthat/test-soft-rule.R | 8 39 files changed, 745 insertions(+), 537 deletions(-)
Title: Create Interactive Trelliscope Displays
Description: Trelliscope is a scalable, flexible, interactive approach to visualizing data (Hafen, 2013 <doi:10.1109/LDAV.2013.6675164>). This package provides methods that make it easy to create a Trelliscope display specification for TrelliscopeJS. High-level functions are provided for creating displays from within 'tidyverse' or 'ggplot2' workflows. Low-level functions are also provided for creating new interfaces.
Author: Ryan Hafen [aut, cre] (<https://orcid.org/0000-0002-5516-8367>),
Barret Schloerke [aut]
Maintainer: Ryan Hafen <rhafen@gmail.com>
Diff between trelliscopejs versions 0.2.5 dated 2020-05-28 and 0.2.6 dated 2021-02-01
DESCRIPTION | 11 ++++++----- MD5 | 19 ++++++++++--------- R/abs-path-checking.R |only R/helpers.R | 10 ++++++---- R/trelliscopejs-package.R | 2 +- README.md | 10 +++++----- build/vignette.rds |binary inst/doc/trelliscopejs.Rmd | 16 ++++++++-------- inst/doc/trelliscopejs.html | 32 +++++++++++++++++++++----------- man/trelliscopejs-package.Rd | 2 +- vignettes/trelliscopejs.Rmd | 16 ++++++++-------- 11 files changed, 66 insertions(+), 52 deletions(-)
Title: Read and Write Rectangular Text Data Quickly
Description: The goal of 'vroom' is to read and write data (like
'csv', 'tsv' and 'fwf') quickly. When reading it uses a quick initial
indexing step, then reads the values lazily , so only the data you
actually use needs to be read. The writer formats the data in
parallel and writes to disk asynchronously from formatting.
Author: Jim Hester [aut, cre] (<https://orcid.org/0000-0002-2739-7082>),
Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>),
https://github.com/mandreyel/ [cph] (mio library),
R Core Team [ctb] (localtime.c code adapted from R),
Jukka Jylänki [cph] (grisu3 implementation),
Mikkel Jørgensen [cph] (grisu3 implementation),
RStudio [cph, fnd]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between vroom versions 1.3.2 dated 2020-09-30 and 1.4.0 dated 2021-02-01
DESCRIPTION | 8 - MD5 | 160 ++++++++++++++++++---------------- NAMESPACE | 3 NEWS.md | 34 +++++++ R/col_types.R | 3 R/cpp11.R | 20 +++- R/problems.R |only R/utils.R | 21 ++++ R/vroom.R | 15 +-- R/vroom_fwf.R | 5 - R/vroom_lines.R | 3 R/vroom_write.R | 30 ++++-- R/zzz.R | 4 README.md | 19 +--- build/vroom.pdf |binary inst/WORDLIST | 1 inst/doc/benchmarks.R | 3 inst/doc/benchmarks.Rmd | 3 inst/doc/benchmarks.html | 10 ++ inst/doc/vroom.html | 12 ++ man/gen_tbl.Rd | 20 +++- man/problems.Rd |only man/vroom.Rd | 28 ++++-- man/vroom_format.Rd | 10 +- man/vroom_fwf.Rd | 28 ++++-- man/vroom_lines.Rd | 4 man/vroom_write.Rd | 18 ++- man/vroom_write_lines.Rd |only src/DateTimeParser.h | 12 +- src/altrep.cc | 69 +++++++++++++- src/collectors.h | 2 src/columns.h | 22 +++- src/cpp11.cpp | 58 ++++++++---- src/delimited_index.cc | 166 +++++++++++++++++++----------------- src/delimited_index.h | 76 ++++++++++++---- src/delimited_index_connection.cc | 13 ++ src/delimited_index_connection.h | 3 src/fixed_width_index.h | 15 ++- src/fixed_width_index_connection.cc | 6 - src/fixed_width_index_connection.h | 2 src/guess_type.cc | 9 - src/index.h | 18 ++- src/index_collection.cc | 14 ++- src/index_collection.h | 13 +- src/iterator.h | 9 + src/parallel.h | 19 ++-- src/utils.h | 8 + src/vroom.cc | 11 ++ src/vroom.h | 4 src/vroom_big_int.cc | 9 + src/vroom_big_int.h | 33 ++++--- src/vroom_chr.cc | 12 ++ src/vroom_chr.h | 18 +++ src/vroom_date.cc | 49 +++++++--- src/vroom_date.h | 34 +++++-- src/vroom_dbl.cc | 13 +- src/vroom_dbl.h | 21 ++-- src/vroom_dttm.cc | 48 +++++++--- src/vroom_dttm.h | 29 +++++- src/vroom_errors.cpp |only src/vroom_errors.h |only src/vroom_fct.cc | 36 ++++++- src/vroom_fct.h | 34 ++++--- src/vroom_fwf.cc | 7 + src/vroom_int.cc | 7 + src/vroom_int.h | 13 ++ src/vroom_lgl.h | 15 ++- src/vroom_num.cc | 26 ++++- src/vroom_num.h | 23 ++++ src/vroom_time.cc | 25 ++++- src/vroom_time.h | 26 ++++- src/vroom_types.h |only src/vroom_vec.h | 49 +++++++++- src/vroom_write.cc | 70 +++++++++++---- tests/testthat/raw.csv |only tests/testthat/test-big-int.R | 18 ++- tests/testthat/test-datetime.R | 45 ++++++--- tests/testthat/test-factor.R | 49 ++++++---- tests/testthat/test-int.R | 18 ++- tests/testthat/test-num.R | 4 tests/testthat/test-problems.R |only tests/testthat/test-vroom.R | 75 ++++++++++++++-- tests/testthat/test-vroom_lines.R | 8 + tests/testthat/test-vroom_write.R | 16 +++ vignettes/benchmarks.Rmd | 3 85 files changed, 1321 insertions(+), 523 deletions(-)
Title: A Test Environment for HTTP Requests
Description: Testing and documenting code that communicates with remote servers
can be painful. Dealing with authentication, server state,
and other complications can make testing seem too costly to
bother with. But it doesn't need to be that hard. This package enables one
to test all of the logic on the R sides of the API in your package without
requiring access to the remote service. Importantly, it provides three
contexts that mock the network connection in different ways, as well as
testing functions to assert that HTTP requests were---or were
not---made. It also allows one to safely record real API responses to use as
test fixtures. The ability to save responses and load them offline also
enables one to write vignettes and other dynamic documents that can be
distributed without access to a live server.
Author: Neal Richardson [aut, cre],
Jonathan Keane [ctb],
Maëlle Salmon [ctb] (<https://orcid.org/0000-0002-2815-0399>)
Maintainer: Neal Richardson <neal.p.richardson@gmail.com>
Diff between httptest versions 3.3.0 dated 2020-01-28 and 4.0.0 dated 2021-02-01
httptest-3.3.0/httptest/tests/testthat/helper.R |only httptest-4.0.0/httptest/DESCRIPTION | 22 httptest-4.0.0/httptest/MD5 | 143 +- httptest-4.0.0/httptest/NAMESPACE | 3 httptest-4.0.0/httptest/NEWS.md | 35 httptest-4.0.0/httptest/R/capture-requests.R | 250 ++--- httptest-4.0.0/httptest/R/content-type.R | 33 httptest-4.0.0/httptest/R/expect-header.R | 25 httptest-4.0.0/httptest/R/expect-json.R | 40 httptest-4.0.0/httptest/R/expect-request.R | 105 +- httptest-4.0.0/httptest/R/fake-http.R | 128 +- httptest-4.0.0/httptest/R/find-redactor.R | 199 ++-- httptest-4.0.0/httptest/R/find-requester.R | 83 - httptest-4.0.0/httptest/R/mock-api.R | 282 ++--- httptest-4.0.0/httptest/R/mock-dir.R |only httptest-4.0.0/httptest/R/mock-paths.R | 58 - httptest-4.0.0/httptest/R/offline.R | 18 httptest-4.0.0/httptest/R/public.R | 8 httptest-4.0.0/httptest/R/redact.R | 154 +-- httptest-4.0.0/httptest/R/trace.R | 179 +-- httptest-4.0.0/httptest/R/use-httptest.R | 102 +- httptest-4.0.0/httptest/R/vignette.R | 89 - httptest-4.0.0/httptest/R/without-internet.R | 55 - httptest-4.0.0/httptest/README.md | 127 -- httptest-4.0.0/httptest/build/vignette.rds |binary httptest-4.0.0/httptest/inst/doc/faq.Rmd |only httptest-4.0.0/httptest/inst/doc/faq.html |only httptest-4.0.0/httptest/inst/doc/httptest.Rmd | 139 +- httptest-4.0.0/httptest/inst/doc/httptest.html | 137 +- httptest-4.0.0/httptest/inst/doc/redacting.Rmd | 38 httptest-4.0.0/httptest/inst/doc/redacting.html | 38 httptest-4.0.0/httptest/inst/doc/vignettes.Rmd | 20 httptest-4.0.0/httptest/inst/doc/vignettes.html | 20 httptest-4.0.0/httptest/man/build_mock_url.Rd | 9 httptest-4.0.0/httptest/man/capture_requests.Rd | 12 httptest-4.0.0/httptest/man/expect_header.Rd | 8 httptest-4.0.0/httptest/man/expect_verb.Rd | 27 httptest-4.0.0/httptest/man/gsub_response.Rd | 4 httptest-4.0.0/httptest/man/mockPaths.Rd | 2 httptest-4.0.0/httptest/man/use_httptest.Rd | 2 httptest-4.0.0/httptest/man/with_fake_http.Rd | 18 httptest-4.0.0/httptest/man/with_mock_api.Rd | 4 httptest-4.0.0/httptest/man/with_mock_dir.Rd |only httptest-4.0.0/httptest/man/without_internet.Rd | 15 httptest-4.0.0/httptest/tests/testthat/api/x(y='1',z='2').json |only httptest-4.0.0/httptest/tests/testthat/example.com/html.R | 101 +- httptest-4.0.0/httptest/tests/testthat/example.com/login-712027-POST.R | 73 + httptest-4.0.0/httptest/tests/testthat/httpbin.org/basic-auth/user/passwd.R | 73 - httptest-4.0.0/httptest/tests/testthat/httpbin.org/cookies.R | 88 + httptest-4.0.0/httptest/tests/testthat/httpbin.org/cookies/set-5b2631.R | 94 + httptest-4.0.0/httptest/tests/testthat/httpbin.org/response-headers-b8a5cc.R | 80 + httptest-4.0.0/httptest/tests/testthat/httpbin.org/status/204.R | 78 + httptest-4.0.0/httptest/tests/testthat/setup.R |only httptest-4.0.0/httptest/tests/testthat/test-capture-requests.R | 396 ++++---- httptest-4.0.0/httptest/tests/testthat/test-content-type.R | 14 httptest-4.0.0/httptest/tests/testthat/test-expect-header.R | 176 ++- httptest-4.0.0/httptest/tests/testthat/test-fake-http.R | 219 ++-- httptest-4.0.0/httptest/tests/testthat/test-find-redactor.R | 169 +-- httptest-4.0.0/httptest/tests/testthat/test-json-equal.R | 40 httptest-4.0.0/httptest/tests/testthat/test-mock-api.R | 422 +++++--- httptest-4.0.0/httptest/tests/testthat/test-mock-dir.R |only httptest-4.0.0/httptest/tests/testthat/test-mock-paths.R | 111 +- httptest-4.0.0/httptest/tests/testthat/test-offline.R | 34 httptest-4.0.0/httptest/tests/testthat/test-public.R | 15 httptest-4.0.0/httptest/tests/testthat/test-redact.R | 488 +++++----- httptest-4.0.0/httptest/tests/testthat/test-trace.R | 30 httptest-4.0.0/httptest/tests/testthat/test-use-httptest.R | 126 +- httptest-4.0.0/httptest/tests/testthat/test-vignette.R | 76 - httptest-4.0.0/httptest/tests/testthat/test-without-internet.R | 148 +-- httptest-4.0.0/httptest/tests/testthat/testpkg/inst/httptest/end-vignette.R | 2 httptest-4.0.0/httptest/tests/testthat/testpkg/inst/httptest/redact.R | 4 httptest-4.0.0/httptest/tests/testthat/testpkg/inst/httptest/request.R | 2 httptest-4.0.0/httptest/tests/testthat/testpkg/inst/httptest/start-vignette.R | 2 httptest-4.0.0/httptest/vignettes/faq.Rmd |only httptest-4.0.0/httptest/vignettes/httptest.Rmd | 139 +- httptest-4.0.0/httptest/vignettes/redacting.Rmd | 38 httptest-4.0.0/httptest/vignettes/vignettes.Rmd | 20 77 files changed, 3253 insertions(+), 2636 deletions(-)
Title: Design Patterns in R
Description: Build robust and maintainable software with object-oriented design
patterns in R. Design patterns abstract and present in neat, well-defined
components and interfaces the experience of many software designers and
architects over many years of solving similar problems. These are solutions
that have withstood the test of time with respect to re-usability,
flexibility, and maintainability. 'R6P' provides abstract base classes with
examples for a few known design patterns. The patterns were selected by
their applicability to analytic projects in R. Using these patterns in R
projects have proven effective in dealing with the complexity that
data-driven applications possess.
Author: Harel Lustiger [aut, cre] (<https://orcid.org/0000-0003-2953-9598>),
Tidylab [cph, fnd]
Maintainer: Harel Lustiger <tidylab@gmail.com>
Diff between R6P versions 0.1.1 dated 2021-01-19 and 0.2.0 dated 2021-02-01
DESCRIPTION | 15 +++++++----- MD5 | 18 +++++++++----- NAMESPACE | 14 ++++++----- NEWS.md | 15 +++++++++--- R/base-NullObject.R |only R/base-ValueObject.R |only README.md | 62 ++++++++++++++++++++++++++++++++++++++------------- inst/REFERENCES.bib | 19 +++++++++++++++ man/NullObject.Rd |only man/Repository.Rd | 3 +- man/Singleton.Rd | 5 ++++ man/ValueObject.Rd |only 12 files changed, 112 insertions(+), 39 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-18 0.1.0