Title: Fit Continuous-Time State-Space and Latent Variable Models for
Filtering Argos Satellite (and Other) Telemetry Data and
Estimating Movement Behaviour
Description: Fits continuous-time random walk and correlated random walk state-space models to filter animal tracking data ('Argos', processed light-level 'geolocation', 'GPS'). Template Model Builder ('TMB') is used for fast estimation. The 'Argos' data can be: (older) least squares-based locations; (newer) Kalman filter-based locations with error ellipse information; or a mixture of both. The models estimate two sets of location states corresponding to: 1) each observation, which are (usually) irregularly timed; and 2) user-specified time intervals (regular or irregular). Latent variable models are provided to estimate move persistence along tracks as an index of behaviour. 'Jonsen I', 'McMahon CR', 'Patterson TA', 'Auger-Methe M', 'Harcourt R', 'Hindell MA', 'Bestley S' (2019) Movement responses to environment: fast inference of variation among southern elephant seals with a mixed effects model. Ecology 100:e02566 <doi:10.1002/ecy.2566>.
Author: Ian Jonsen [aut, cre],
Toby Patterson [aut, ctb]
Maintainer: Ian Jonsen <ian.jonsen@mq.edu.au>
Diff between foieGras versions 0.2.2 dated 2019-07-03 and 0.4.0 dated 2019-10-07
foieGras-0.2.2/foieGras/R/foieGras-deprecated.R |only foieGras-0.2.2/foieGras/R/plot.foieGras.R |only foieGras-0.2.2/foieGras/R/print.foieGras.R |only foieGras-0.2.2/foieGras/R/util.R |only foieGras-0.2.2/foieGras/data/fit.RData |only foieGras-0.2.2/foieGras/data/rope.RData |only foieGras-0.2.2/foieGras/man/fit.Rd |only foieGras-0.2.2/foieGras/man/foieGras-deprecated.Rd |only foieGras-0.2.2/foieGras/man/plot.foieGras.Rd |only foieGras-0.2.2/foieGras/man/print.foieGras.Rd |only foieGras-0.2.2/foieGras/man/rope.Rd |only foieGras-0.4.0/foieGras/DESCRIPTION | 33 - foieGras-0.4.0/foieGras/LICENSE |only foieGras-0.4.0/foieGras/MD5 | 99 ++-- foieGras-0.4.0/foieGras/NAMESPACE | 46 +- foieGras-0.4.0/foieGras/NEWS.md | 11 foieGras-0.4.0/foieGras/R/emf.R |only foieGras-0.4.0/foieGras/R/fit_mpm.R |only foieGras-0.4.0/foieGras/R/fit_ssm.R | 76 +-- foieGras-0.4.0/foieGras/R/fmap.R |only foieGras-0.4.0/foieGras/R/foieGras-package.R | 40 + foieGras-0.4.0/foieGras/R/grab.R | 205 +++++---- foieGras-0.4.0/foieGras/R/join.R |only foieGras-0.4.0/foieGras/R/mpmf.R |only foieGras-0.4.0/foieGras/R/osar.r |only foieGras-0.4.0/foieGras/R/plot.fG_osar.R |only foieGras-0.4.0/foieGras/R/plot.fG_ssm.R |only foieGras-0.4.0/foieGras/R/prefilter.R | 168 +++++-- foieGras-0.4.0/foieGras/R/print.ssm.R |only foieGras-0.4.0/foieGras/R/sfilter.R | 190 ++++++-- foieGras-0.4.0/foieGras/R/wrap_lon.r |only foieGras-0.4.0/foieGras/README.md | 14 foieGras-0.4.0/foieGras/build/vignette.rds |binary foieGras-0.4.0/foieGras/data/ellie.RData |binary foieGras-0.4.0/foieGras/data/ellies.RData |only foieGras-0.4.0/foieGras/data/fmpm.RData |only foieGras-0.4.0/foieGras/data/fssm.RData |only foieGras-0.4.0/foieGras/inst/doc/foiegras-basics.R | 138 +++--- foieGras-0.4.0/foieGras/inst/doc/foiegras-basics.Rmd | 181 ++++--- foieGras-0.4.0/foieGras/inst/doc/foiegras-basics.html | 364 ++++++++-------- foieGras-0.4.0/foieGras/man/ellie.Rd | 2 foieGras-0.4.0/foieGras/man/ellies.Rd |only foieGras-0.4.0/foieGras/man/emf.Rd |only foieGras-0.4.0/foieGras/man/fit_mpm.Rd |only foieGras-0.4.0/foieGras/man/fit_ssm.Rd | 51 +- foieGras-0.4.0/foieGras/man/fmap.Rd |only foieGras-0.4.0/foieGras/man/fmpm.Rd |only foieGras-0.4.0/foieGras/man/fssm.Rd |only foieGras-0.4.0/foieGras/man/grab.Rd | 13 foieGras-0.4.0/foieGras/man/join.Rd |only foieGras-0.4.0/foieGras/man/mpmf.Rd |only foieGras-0.4.0/foieGras/man/osar.Rd |only foieGras-0.4.0/foieGras/man/plot.fG_osar.Rd |only foieGras-0.4.0/foieGras/man/plot.fG_ssm.Rd |only foieGras-0.4.0/foieGras/man/prefilter.Rd | 32 - foieGras-0.4.0/foieGras/man/print.ssm.Rd |only foieGras-0.4.0/foieGras/man/sfilter.Rd | 15 foieGras-0.4.0/foieGras/man/wrap_lon.Rd | 8 foieGras-0.4.0/foieGras/src/Makevars |only foieGras-0.4.0/foieGras/src/Makevars.win |only foieGras-0.4.0/foieGras/src/TMB |only foieGras-0.4.0/foieGras/src/foieGras.cpp | 185 -------- foieGras-0.4.0/foieGras/tests/testthat/test-fit_mpm.R |only foieGras-0.4.0/foieGras/tests/testthat/test-fit_ssm.R | 157 ++++-- foieGras-0.4.0/foieGras/tests/testthat/test-fmap.R |only foieGras-0.4.0/foieGras/tests/testthat/test-grab.R | 26 - foieGras-0.4.0/foieGras/tests/testthat/test-join.R |only foieGras-0.4.0/foieGras/tests/testthat/test-osar.R |only foieGras-0.4.0/foieGras/tests/testthat/test-plot.R | 17 foieGras-0.4.0/foieGras/tests/testthat/test-prefilter.R | 20 foieGras-0.4.0/foieGras/vignettes/foiegras-basics.Rmd | 181 ++++--- 71 files changed, 1325 insertions(+), 947 deletions(-)
Title: Relevance-Integrated Statistical Inference Engine
Description: A framework of methods to perform customized inference at individual level
by taking contextual covariates into account. Three main functions are provided
in this package: (i) LASER(): it generates specially-designed artificial relevant
samples for a given case; (ii) g2l.proc(): computes customized fdr(z|x); and (iii)
rEB.proc(): performs empirical Bayes inference based on LASERs. The details can be
found in Mukhopadhyay, S., and Wang, K (2019, Technical Report).
Author: Subhadeep Mukhopadhyay, Kaijun Wang
Maintainer: Kaijun Wang <kwang2@fredhutch.org>
Diff between LPRelevance versions 2.0 dated 2019-09-06 and 2.1 dated 2019-10-07
LPRelevance-2.0/LPRelevance/data/RAZOR.rda |only LPRelevance-2.0/LPRelevance/man/RAZOR.Rd |only LPRelevance-2.1/LPRelevance/DESCRIPTION | 10 LPRelevance-2.1/LPRelevance/MD5 | 34 - LPRelevance-2.1/LPRelevance/R/Finite.rEB.R | 173 +++---- LPRelevance-2.1/LPRelevance/R/LASER.R | 75 +-- LPRelevance-2.1/LPRelevance/R/LP.post.conv.R | 8 LPRelevance-2.1/LPRelevance/R/LPcden.R | 57 -- LPRelevance-2.1/LPRelevance/R/LPregression.R |only LPRelevance-2.1/LPRelevance/R/eLP.poly.predict.R |only LPRelevance-2.1/LPRelevance/R/g2l.infer.R | 376 ++++++++--------- LPRelevance-2.1/LPRelevance/R/g2l.infer.boot.R | 56 +- LPRelevance-2.1/LPRelevance/R/g2l.proc.R | 16 LPRelevance-2.1/LPRelevance/R/rEB.proc.R | 234 +++++----- LPRelevance-2.1/LPRelevance/build/partial.rdb |binary LPRelevance-2.1/LPRelevance/data/funnel.rda |only LPRelevance-2.1/LPRelevance/man/LASER.Rd | 8 LPRelevance-2.1/LPRelevance/man/LPRelevance-package.Rd | 6 LPRelevance-2.1/LPRelevance/man/funnel.Rd |only LPRelevance-2.1/LPRelevance/man/g2l.proc.Rd | 9 LPRelevance-2.1/LPRelevance/man/rEB.proc.Rd | 8 21 files changed, 522 insertions(+), 548 deletions(-)
Title: An R Wrapper for 'TooManyCells'
Description: An R wrapper for using 'TooManyCells', a command line program for clustering, visualizing, and quantifying cell clade relationships. See <https://gregoryschwartz.github.io/too-many-cells/> for more details.
Author: Gregory W. Schwartz
Maintainer: Gregory W. Schwartz <gsch@pennmedicine.upenn.edu>
Diff between TooManyCellsR versions 0.1.0.0 dated 2019-03-05 and 0.1.1.0 dated 2019-10-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/TooManyCellsR.R | 25 ++++++++++++++++++++++++- man/tooManyCells.Rd | 9 ++++++++- 4 files changed, 38 insertions(+), 8 deletions(-)
Title: Linear Model Evaluation with Randomized Residuals in a
Permutation Procedure
Description: Linear model calculations are made for many random versions of data.
Using residual randomization in a permutation procedure, sums of squares are
calculated over many permutations to generate empirical probability distributions
for evaluating model effects. This packaged is described by
Collyer & Adams (2018) <doi:10.1111/2041-210X.13029>. Additionally, coefficients, statistics, fitted values, and residuals generated over many
permutations can be used for various procedures including pairwise tests, prediction, classification, and
model comparison. This package should provide most tools one could need for the analysis of
high-dimensional data, especially in ecology and evolutionary biology, but certainly other fields, as well.
Author: Michael Collyer [aut, cre],
Dean Adams [aut]
Maintainer: Michael Collyer <mlcollyer@gmail.com>
Diff between RRPP versions 0.4.2 dated 2019-05-19 and 0.4.3 dated 2019-10-07
DESCRIPTION | 18 +++++---- MD5 | 18 ++++----- NEWS.md | 25 ++++++++++--- R/RRPP.support.code.r | 79 +++++++++++++++++++++--------------------- R/lm.rrpp.r | 12 +++--- R/shared.support.code.r | 5 +- R/trajectory.analysis.r | 4 +- build/vignette.rds |binary inst/doc/ANOVA.vs.MANOVA.html | 4 +- inst/doc/Using.RRPP.html | 20 +++++----- 10 files changed, 104 insertions(+), 81 deletions(-)
Title: Psychometric Functions from the Waller Lab
Description: Computes fungible coefficients and Monte Carlo data. Underlying theory for these functions is described in the following publications:
Waller, N. (2008). Fungible Weights in Multiple Regression. Psychometrika, 73(4), 691-703, <DOI:10.1007/s11336-008-9066-z>.
Waller, N. & Jones, J. (2009). Locating the Extrema of Fungible Regression Weights.
Psychometrika, 74(4), 589-602, <DOI:10.1007/s11336-008-9087-7>.
Waller, N. G. (2016). Fungible Correlation Matrices:
A Method for Generating Nonsingular, Singular, and Improper Correlation Matrices for
Monte Carlo Research. Multivariate Behavioral Research, 51(4), 554-568, <DOI:10.1080/00273171.2016.1178566>.
Jones, J. A. & Waller, N. G. (2015). The normal-theory and asymptotic distribution-free (ADF)
covariance matrix of standardized regression coefficients: theoretical extensions
and finite sample behavior. Psychometrika, 80, 365-378, <DOI:10.1007/s11336-013-9380-y>.
Waller, N. G. (2018). Direct Schmid-Leiman transformations and rank-deficient loadings matrices. Psychometrika, 83, 858-870. <DOI:10.1007/s11336-017-9599-0>.
Author: Niels Waller [aut, cre],
Jeff Jones [ctb],
Casey Giordano [ctb]
Maintainer: Niels Waller <nwaller@umn.edu>
Diff between fungible versions 1.86 dated 2019-05-14 and 1.91 dated 2019-10-07
DESCRIPTION | 8 - MD5 | 78 +++++++----- NAMESPACE | 12 + R/BiFAD.R | 6 R/Box20.R | 23 +++ R/Box26.R | 37 ++++- R/GenerateBoxData.R | 85 +++++++++---- R/Ledermann.R |only R/ThurstoneBox20.R |only R/ThurstoneBox26.R |only R/faEKC.R |only R/faMain.R | 301 ++++++++++++++++++++++++++++-------------------- R/faScores.R |only R/faSort.R | 256 ++++++++++++++++++++-------------------- R/faX.R | 28 +++- R/fals.R | 9 - R/genPhi.R |only R/print.faMain.R |only R/simFA.R |only R/smoothKB.R | 8 - R/summary.faMain.R |only data/ThurstoneBox20.rda |only data/ThurstoneBox26.rda |only inst/CITATION | 4 man/BiFAD.Rd | 16 -- man/Box20.Rd | 23 +++ man/Box26.Rd | 47 ++++++- man/GenerateBoxData.Rd | 25 +++ man/Ledermann.Rd |only man/SLi.Rd | 23 +-- man/SchmidLeiman.Rd | 16 -- man/ThurstoneBox20.Rd |only man/ThurstoneBox26.Rd |only man/faAlign.Rd | 9 - man/faEKC.Rd |only man/faMain.Rd | 27 +--- man/faScores.Rd |only man/faSort.Rd | 15 +- man/faStandardize.Rd | 9 - man/faX.Rd | 9 - man/fals.Rd | 14 +- man/fapa.Rd | 9 - man/fareg.Rd | 9 - man/genPhi.Rd |only man/orderFactors.Rd | 9 - man/print.faMain.Rd |only man/promaxQ.Rd | 9 - man/simFA.Rd |only man/smoothKB.Rd | 2 man/summary.faMain.Rd |only 50 files changed, 704 insertions(+), 422 deletions(-)
Title: Integration to 'Apache' 'Arrow'
Description: 'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language
development platform for in-memory data. It specifies a standardized
language-independent columnar memory format for flat and hierarchical data,
organized for efficient analytic operations on modern hardware. This
package provides an interface to the 'Arrow C++' library.
Author: Romain François [aut] (<https://orcid.org/0000-0002-2444-4226>),
Jeroen Ooms [aut],
Neal Richardson [aut, cre],
Javier Luraschi [ctb],
Jeffrey Wong [ctb],
Apache Arrow [aut, cph]
Maintainer: Neal Richardson <neal@ursalabs.org>
Diff between arrow versions 0.14.1.1 dated 2019-08-08 and 0.15.0 dated 2019-10-07
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arrow-0.15.0/arrow/NEWS.md | 24 arrow-0.15.0/arrow/R/array-data.R |only arrow-0.15.0/arrow/R/array.R | 121 arrow-0.15.0/arrow/R/arrow-package.R | 43 arrow-0.15.0/arrow/R/arrowExports.R | 320 ++ arrow-0.15.0/arrow/R/buffer.R | 74 arrow-0.15.0/arrow/R/chunked-array.R |only arrow-0.15.0/arrow/R/compression.R | 142 - arrow-0.15.0/arrow/R/compute.R | 4 arrow-0.15.0/arrow/R/csv.R | 441 +-- arrow-0.15.0/arrow/R/dictionary.R | 53 arrow-0.15.0/arrow/R/enums.R | 42 arrow-0.15.0/arrow/R/feather.R | 246 - arrow-0.15.0/arrow/R/field.R |only arrow-0.15.0/arrow/R/filesystem.R |only arrow-0.15.0/arrow/R/io.R | 355 -- arrow-0.15.0/arrow/R/json.R | 176 - arrow-0.15.0/arrow/R/list.R |only arrow-0.15.0/arrow/R/memory-pool.R |only arrow-0.15.0/arrow/R/message.R | 62 arrow-0.15.0/arrow/R/parquet.R | 484 ++- arrow-0.15.0/arrow/R/read-record-batch.R |only arrow-0.15.0/arrow/R/read-table.R |only arrow-0.15.0/arrow/R/record-batch-reader.R |only arrow-0.15.0/arrow/R/record-batch-writer.R |only arrow-0.15.0/arrow/R/record-batch.R |only arrow-0.15.0/arrow/R/schema.R |only arrow-0.15.0/arrow/R/struct.R |only arrow-0.15.0/arrow/R/table.R |only arrow-0.15.0/arrow/R/type.R |only arrow-0.15.0/arrow/R/util.R |only arrow-0.15.0/arrow/R/write-arrow.R |only arrow-0.15.0/arrow/README.md | 176 - arrow-0.15.0/arrow/build |only arrow-0.15.0/arrow/configure | 34 arrow-0.15.0/arrow/inst/doc |only arrow-0.15.0/arrow/man/ArrayData.Rd |only arrow-0.15.0/arrow/man/ChunkedArray.Rd |only arrow-0.15.0/arrow/man/Codec.Rd |only arrow-0.15.0/arrow/man/CsvReadOptions.Rd |only arrow-0.15.0/arrow/man/CsvTableReader.Rd |only arrow-0.15.0/arrow/man/DataType.Rd | 115 arrow-0.15.0/arrow/man/DictionaryType.Rd |only arrow-0.15.0/arrow/man/FeatherTableReader.Rd | 39 arrow-0.15.0/arrow/man/FeatherTableWriter.Rd | 35 arrow-0.15.0/arrow/man/Field.Rd |only arrow-0.15.0/arrow/man/FileStats.Rd |only arrow-0.15.0/arrow/man/FileSystem.Rd |only arrow-0.15.0/arrow/man/FixedWidthType.Rd |only arrow-0.15.0/arrow/man/InputStream.Rd |only arrow-0.15.0/arrow/man/MemoryPool.Rd |only arrow-0.15.0/arrow/man/Message.Rd |only arrow-0.15.0/arrow/man/MessageReader.Rd | 18 arrow-0.15.0/arrow/man/OutputStream.Rd |only arrow-0.15.0/arrow/man/ParquetFileReader.Rd |only arrow-0.15.0/arrow/man/ParquetReaderProperties.Rd |only arrow-0.15.0/arrow/man/RecordBatch.Rd |only arrow-0.15.0/arrow/man/RecordBatchReader.Rd |only arrow-0.15.0/arrow/man/RecordBatchWriter.Rd |only arrow-0.15.0/arrow/man/Schema.Rd |only arrow-0.15.0/arrow/man/Selector.Rd |only arrow-0.15.0/arrow/man/Table.Rd |only arrow-0.15.0/arrow/man/array.Rd | 55 arrow-0.15.0/arrow/man/arrow-package.Rd | 1 arrow-0.15.0/arrow/man/buffer.Rd | 25 arrow-0.15.0/arrow/man/compression.Rd |only arrow-0.15.0/arrow/man/data-type.Rd |only arrow-0.15.0/arrow/man/default_memory_pool.Rd | 8 arrow-0.15.0/arrow/man/dictionary.Rd | 18 arrow-0.15.0/arrow/man/enums.Rd |only arrow-0.15.0/arrow/man/make_readable_file.Rd |only arrow-0.15.0/arrow/man/mmap_create.Rd | 2 arrow-0.15.0/arrow/man/read_delim_arrow.Rd | 61 arrow-0.15.0/arrow/man/read_feather.Rd | 16 arrow-0.15.0/arrow/man/read_json_arrow.Rd | 18 arrow-0.15.0/arrow/man/read_parquet.Rd | 25 arrow-0.15.0/arrow/man/read_record_batch.Rd | 12 arrow-0.15.0/arrow/man/read_schema.Rd | 2 arrow-0.15.0/arrow/man/read_table.Rd | 26 arrow-0.15.0/arrow/man/type.Rd | 2 arrow-0.15.0/arrow/man/write_arrow.Rd | 20 arrow-0.15.0/arrow/man/write_feather.Rd | 6 arrow-0.15.0/arrow/man/write_parquet.Rd | 72 arrow-0.15.0/arrow/src/Makevars.in | 5 arrow-0.15.0/arrow/src/array.cpp | 13 arrow-0.15.0/arrow/src/array_from_vector.cpp | 53 arrow-0.15.0/arrow/src/array_to_vector.cpp |only arrow-0.15.0/arrow/src/arrowExports.cpp | 1381 ++++++++-- arrow-0.15.0/arrow/src/arrow_types.h | 21 arrow-0.15.0/arrow/src/buffer.cpp | 6 arrow-0.15.0/arrow/src/chunkedarray.cpp | 20 arrow-0.15.0/arrow/src/compression.cpp | 10 arrow-0.15.0/arrow/src/compute.cpp | 7 arrow-0.15.0/arrow/src/csv.cpp | 17 arrow-0.15.0/arrow/src/datatype.cpp | 4 arrow-0.15.0/arrow/src/feather.cpp | 4 arrow-0.15.0/arrow/src/filesystem.cpp |only arrow-0.15.0/arrow/src/parquet.cpp | 254 + arrow-0.15.0/arrow/src/recordbatch.cpp | 28 arrow-0.15.0/arrow/src/recordbatchwriter.cpp | 21 arrow-0.15.0/arrow/src/symbols.cpp | 10 arrow-0.15.0/arrow/src/table.cpp | 90 arrow-0.15.0/arrow/tests/testthat/helper-arrow.R | 2 arrow-0.15.0/arrow/tests/testthat/helper-parquet.R |only arrow-0.15.0/arrow/tests/testthat/test-Array.R | 169 - arrow-0.15.0/arrow/tests/testthat/test-RecordBatch.R | 93 arrow-0.15.0/arrow/tests/testthat/test-Table.R | 135 arrow-0.15.0/arrow/tests/testthat/test-array-data.R |only arrow-0.15.0/arrow/tests/testthat/test-arrow.R | 17 arrow-0.15.0/arrow/tests/testthat/test-buffer-reader.R |only arrow-0.15.0/arrow/tests/testthat/test-buffer.R | 41 arrow-0.15.0/arrow/tests/testthat/test-chunked-array.R |only arrow-0.15.0/arrow/tests/testthat/test-compressed.R | 24 arrow-0.15.0/arrow/tests/testthat/test-csv.R |only arrow-0.15.0/arrow/tests/testthat/test-data-type.R |only arrow-0.15.0/arrow/tests/testthat/test-feather.R | 71 arrow-0.15.0/arrow/tests/testthat/test-field.R | 14 arrow-0.15.0/arrow/tests/testthat/test-filesystem.R |only arrow-0.15.0/arrow/tests/testthat/test-json.R | 24 arrow-0.15.0/arrow/tests/testthat/test-message-reader.R |only arrow-0.15.0/arrow/tests/testthat/test-message.R | 22 arrow-0.15.0/arrow/tests/testthat/test-parquet.R | 49 arrow-0.15.0/arrow/tests/testthat/test-read-record-batch.R |only arrow-0.15.0/arrow/tests/testthat/test-read-write.R | 41 arrow-0.15.0/arrow/tests/testthat/test-record-batch-reader.R |only arrow-0.15.0/arrow/tests/testthat/test-schema.R | 38 arrow-0.15.0/arrow/tests/testthat/test-thread-pool.R |only arrow-0.15.0/arrow/tests/testthat/test-type.R | 6 arrow-0.15.0/arrow/tools/autobrew |only arrow-0.15.0/arrow/tools/ubsan.supp |only arrow-0.15.0/arrow/vignettes |only 219 files changed, 4386 insertions(+), 2169 deletions(-)
Title: Access the Bioconductor Project Package Repository
Description: A convenient tool to install and update Bioconductor packages.
Author: Martin Morgan [aut] (<https://orcid.org/0000-0002-5874-8148>),
Marcel Ramos [ctb, cre] (<https://orcid.org/0000-0002-3242-0582>)
Maintainer: Marcel Ramos <marcel.ramos@roswellpark.org>
Diff between BiocManager versions 1.30.4 dated 2018-11-13 and 1.30.7 dated 2019-10-07
DESCRIPTION | 10 MD5 | 46 - NEWS | 73 ++ R/BiocManager-pkg.R | 20 R/available.R | 9 R/inet.R |only R/install.R | 32 - R/repositories.R | 8 R/utilities.R | 13 R/valid.R | 39 + R/version.R | 142 +++-- R/zzz.R | 7 README.md |only build/vignette.rds |binary inst/doc/BiocManager.R | 21 inst/doc/BiocManager.Rmd | 158 +++++ inst/doc/BiocManager.html | 1023 ++++++++++++++----------------------- man/BiocManager-pkg.Rd | 12 man/install.Rd | 7 man/valid.Rd | 7 tests/testthat.R | 2 tests/testthat/test_install.R | 4 tests/testthat/test_repositories.R | 12 tests/testthat/test_version.R | 76 ++ vignettes/BiocManager.Rmd | 158 +++++ 25 files changed, 1124 insertions(+), 755 deletions(-)
Title: Padé Approximant Coefficients
Description: Given a vector of Taylor series coefficients of sufficient length as input, the function returns the numerator and denominator coefficients for the Padé approximant of appropriate order.
Author: Avraham Adler [aut, cph, cre] (<https://orcid.org/0000-0002-3039-0703>)
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between Pade versions 0.1-4 dated 2015-07-29 and 0.1.5 dated 2019-10-07
DESCRIPTION | 16 ++++++++-------- MD5 | 8 ++++---- README.md | 48 +++++++++++++++++++++++++++++++++++++++++++++--- inst/NEWS.Rd | 13 +++++++++++++ man/Pade.Rd | 6 +++--- 5 files changed, 73 insertions(+), 18 deletions(-)
Title: Utility Functions for Conducting and Interpreting Meta-Analyses
Description: Contains functions to estimate the proportion of effects stronger than a threshold
of scientific importance (function prop_stronger), to nonparametrically characterize the distribution of effects in a meta-analysis (calib_ests, pct_pval),
to make effect size conversions (r_to_d, r_to_z, z_to_r), to compute and format inference in a meta-analysis (format_CI, format_stat, tau_CI), to scrape results from
existing meta-analyses for re-analysis (scrape_meta, parse_CI_string).
Author: Maya B. Mathur, Rui Wang, Tyler J. VanderWeele
Maintainer: Maya B. Mathur <mmathur@stanford.edu>
Diff between MetaUtility versions 1.2.0 dated 2019-04-10 and 2.0.0 dated 2019-10-07
DESCRIPTION | 18 - MD5 | 13 NAMESPACE | 4 R/functions.R | 689 ++++++++++++++++++++++++++++++++++------------ man/calib_ests.Rd |only man/pct_pval.Rd |only man/prop_stronger.Rd | 204 +++++++------ man/prop_stronger_sign.Rd |only man/r_to_d.Rd | 2 9 files changed, 658 insertions(+), 272 deletions(-)
Title: Generalized Correlations and Plausible Causal Paths
Description: Since causal paths from data are important for all sciences, the
package provides many sophisticated functions. causeSummary()
gives easy-to-interpret causal paths. Let Z denote control variables and compare
two flipped kernel regressions: X=f(Y, Z)+e1 and Y=g(X,Z)+e2. Our criterion Cr1
says that if |e1*Y|>|e2*X| then variation in X is more "exogenous or independent"
than in Y and causal path is X to Y. Criterion Cr2 requires |e2|<|e1|. These
inequalities between many absolute value are quantified by four orders of
stochastic dominance. Our third criterion Cr3 for the causal path X to Y
requires new generalized partial correlations to satisfy |r*(x|y,z)|< |r*(y|x,z)|.
The function parcorMany() reports generalized partials between the first
variable and all others. The package provides additional R tools for
causal assessment, "outlier detection," and for numerical integration by the
trapezoidal rule, stochastic dominance, pillar 3D charts, etc. We also provide
functions for bootstrap-based statistical inference for causal paths.
Author: Prof. H. D. Vinod, Fordham University, NY.
Maintainer: H. D. Vinod <vinod@fordham.edu>
Diff between generalCorr versions 1.1.2 dated 2018-07-12 and 1.1.3 dated 2019-10-07
DESCRIPTION | 47 +++---- MD5 | 226 +++++++++++++++++++------------------ NAMESPACE | 5 NEWS | 5 R/NLhat.R |only R/abs_res.R | 2 R/abs_stdapd.R | 3 R/abs_stdapdC.R | 3 R/abs_stdres.R | 2 R/abs_stdresC.R | 4 R/abs_stdrhserC.R | 4 R/abs_stdrhserr.R | 3 R/allPairs.R | 19 ++- R/bigfp.R | 6 R/bootPairs.R | 1 R/bootQuantile.R | 5 R/bootSign.R | 5 R/bootSignPcent.R | 5 R/bootSummary.R | 5 R/causeSummary.R | 10 + R/causeSummary0.R | 3 R/cofactor.R | 1 R/comp_portfo2.R | 6 R/generalCorrInfo.R | 8 + R/get0outliers.R | 1 R/getSeq.R |only R/gmcmtx0.R | 16 +- R/gmcmtxBlk.R |only R/gmcmtxZ.R | 7 - R/gmcxy_np.R | 6 R/heurist.R | 1 R/kern.R | 5 R/kern_ctrl.R | 5 R/mag.R | 2 R/mag_ctrl.R | 2 R/minor.R | 1 R/parcorMany.R | 6 R/parcorMtx.R | 2 R/parcorSilent.R | 3 R/parcor_ijk.R | 5 R/parcor_ridg.R | 5 R/pcause.R | 5 R/pillar3D.R |only R/prelec2.R | 8 - R/probSign.R | 5 R/rstar.R | 12 - R/silentMtx.R | 4 R/silentMtx0.R | 3 R/silentPairs.R | 4 R/silentPairs0.R | 3 R/some0Pairs.R | 5 R/someCPairs.R | 6 R/someCPairs2.R | 17 +- R/someMagPairs.R | 2 R/somePairs.R | 5 R/somePairs2.R | 9 - R/stdres.R | 2 R/stochdom2.R | 5 R/wtdpapb.R | 4 build/vignette.rds |binary inst/doc/generalCorr-vignette.pdf |binary inst/doc/generalCorr-vignette2.pdf |binary inst/doc/generalCorr-vignette3.pdf |binary man/NLhat.Rd |only man/abs_res.Rd | 4 man/abs_stdapd.Rd | 6 man/abs_stdapdC.Rd | 6 man/abs_stdres.Rd | 4 man/abs_stdresC.Rd | 6 man/abs_stdrhserC.Rd | 6 man/abs_stdrhserr.Rd | 6 man/allPairs.Rd | 24 ++- man/bigfp.Rd | 9 - man/bootPairs.Rd | 1 man/bootQuantile.Rd | 10 - man/bootSign.Rd | 10 - man/bootSignPcent.Rd | 10 - man/bootSummary.Rd | 10 - man/causeSummary.Rd | 20 +-- man/causeSummary0.Rd | 14 -- man/cofactor.Rd | 1 man/comp_portfo2.Rd | 13 -- man/generalCorrInfo.Rd | 9 + man/get0outliers.Rd | 1 man/getSeq.Rd |only man/gmcmtx0.Rd | 21 ++- man/gmcmtxBlk.Rd |only man/gmcmtxZ.Rd | 9 - man/gmcxy_np.Rd | 9 - man/heurist.Rd | 1 man/kern.Rd | 11 - man/kern_ctrl.Rd | 14 -- man/mag.Rd | 3 man/mag_ctrl.Rd | 3 man/minor.Rd | 1 man/parcorMany.Rd | 10 - man/parcorMtx.Rd | 6 man/parcorSilent.Rd | 7 - man/parcor_ijk.Rd | 5 man/parcor_ridg.Rd | 6 man/pcause.Rd | 7 - man/pillar3D.Rd |only man/prelec2.Rd | 8 - man/probSign.Rd | 10 - man/rstar.Rd | 12 - man/silentMtx.Rd | 14 -- man/silentMtx0.Rd | 13 -- man/silentPairs.Rd | 11 - man/silentPairs0.Rd | 10 - man/some0Pairs.Rd | 16 -- man/someCPairs.Rd | 13 -- man/someCPairs2.Rd | 28 ++-- man/someMagPairs.Rd | 3 man/somePairs.Rd | 12 - man/somePairs2.Rd | 16 -- man/stdres.Rd | 4 man/stochdom2.Rd | 8 - man/wtdpapb.Rd | 5 118 files changed, 503 insertions(+), 507 deletions(-)
Title: Dose Response Data Analysis using the 4 Parameter Logistic (4pl)
Model
Description: Models the relationship between dose levels and responses in a pharmacological experiment using the 4 Parameter Logistic model. Traditional packages on dose-response modelling such as 'drc' and 'nplr' often draw errors due to convergence failure especially when data have outliers or non-logistic shapes. This package provides robust estimation methods that are less affected by outliers and other initialization methods that work well for data lacking logistic shapes. We provide the bounds on the parameters of the 4PL model that prevent parameter estimates from diverging or converging to zero and base their justification in a statistical principle. These methods are used as remedies to convergence failure problems. Gadagkar, S. R. and Call, G. B. (2015) <doi:10.1016/j.vascn.2014.08.006> Ritz, C. and Baty, F. and Streibig, J. C. and Gerhard, D. (2015) <doi:10.1371/journal.pone.0146021>.
Author: Justin T. Landis [aut, cre],
Hyowon An [aut],
Aubrey G. Bailey [aut],
Dirk P. Dittmer [aut],
James S. Marron [aut]
Maintainer: Justin T. Landis <jtlandis314@gmail.com>
Diff between dr4pl versions 1.1.8 dated 2019-02-24 and 1.1.11 dated 2019-10-07
DESCRIPTION | 8 - MD5 | 32 +++--- NEWS.md | 14 ++ R/base.R | 6 - R/initialization.R | 8 - R/main.R | 188 ++++++++++++++++++++++++++++++++++++---- README.md | 62 ++++++------- build/partial.rdb |binary build/vignette.rds |binary data/drc_error_1.rda |binary data/drc_error_2.rda |binary data/drc_error_3.rda |binary data/drc_error_4.rda |binary inst/doc/walk_through_in_R.html | 43 +++++---- man/FindInitialParms.Rd | 2 man/dr4pl.Rd | 37 ++++++- man/dr4plEst.Rd | 6 + 17 files changed, 301 insertions(+), 105 deletions(-)
Title: Design Shaded Contour Lines (or Tanaka) Maps
Description: The Tanaka method enhances the representation of topography on a map using shaded contour lines. In this simplified implementation of the method, north-west white contours represent illuminated topography and south-east black contours represent shaded topography. See Tanaka (1950) <doi:10.2307/211219>.
Author: Timothée Giraud [cre, aut] (<https://orcid.org/0000-0002-1932-3323>)
Maintainer: Timothée Giraud <timothee.giraud@cnrs.fr>
Diff between tanaka versions 0.1.0 dated 2019-03-08 and 0.1.1 dated 2019-10-07
DESCRIPTION | 14 ++--- MD5 | 24 ++++---- NAMESPACE | 27 ++++++++- NEWS.md |only R/legend.R | 118 +++++++++++++++++++++++++++++-------------- R/package.R | 13 +++- R/tanaka.R | 117 ++++++++++++++++++++++++++++++++---------- R/tanaka_contour.R | 95 ++++++++++++++++++++-------------- README.md | 64 +++++++++++++++++++++-- man/tanaka-package.Rd |only man/tanaka.Rd | 25 +++++---- man/tanaka_contour.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/test_tanaka.R | 53 ++++++++++++++----- 14 files changed, 395 insertions(+), 157 deletions(-)
Title: Epistemic Network Analysis
Description: ENA (Shaffer, D. W. (2017) Quantitative Ethnography. ISBN: 0578191687) is a method used to identify meaningful and quantifiable patterns in discourse or reasoning. ENA moves beyond the traditional frequency-based assessments by examining the structure of the co-occurrence, or connections in coded data. Moreover, compared to other methodological approaches, ENA has the novelty of (1) modeling whole networks of connections and (2) affording both quantitative and qualitative comparisons between different network models. Shaffer, D.W., Collier, W., & Ruis, A.R. (2016) <doi:10.18608/jla.2016.33.3>.
Author: Cody L Marquart [aut, cre] (<https://orcid.org/0000-0002-3387-6792>),
Zachari Swiecki [aut],
Wesley Collier [aut],
Brendan Eagan [aut],
Roman Woodward [aut],
David Williamson Shaffer [aut]
Maintainer: Cody L Marquart <cody.marquart@wisc.edu>
Diff between rENA versions 0.1.6.1 dated 2019-05-09 and 0.2.0.0 dated 2019-10-07
rENA-0.1.6.1/rENA/R/adj.mat.to.dir.R |only rENA-0.1.6.1/rENA/R/do_optimization.R |only rENA-0.1.6.1/rENA/R/egr.positions.R |only rENA-0.1.6.1/rENA/R/ena.conversation.R |only rENA-0.1.6.1/rENA/R/ena.get.conversation.R |only rENA-0.1.6.1/rENA/R/ena.plot.groups.R |only rENA-0.1.6.1/rENA/R/ena.plot.nodes.R |only rENA-0.1.6.1/rENA/R/ena.plot.set.R |only rENA-0.1.6.1/rENA/R/ena.plot.units.R |only rENA-0.1.6.1/rENA/R/ena.split.codes.R |only rENA-0.1.6.1/rENA/R/equiload.positions.R |only rENA-0.1.6.1/rENA/R/full.opt.R |only rENA-0.1.6.1/rENA/R/full_opt_soln.R |only rENA-0.1.6.1/rENA/R/get_cor.R |only rENA-0.1.6.1/rENA/R/get_optimized_node_positions.R |only rENA-0.1.6.1/rENA/R/group.stats.R |only rENA-0.1.6.1/rENA/R/lagpad.R |only rENA-0.1.6.1/rENA/R/lm_.R |only rENA-0.1.6.1/rENA/R/log.R |only rENA-0.1.6.1/rENA/R/lws.positions.R |only rENA-0.1.6.1/rENA/R/make.adj.matrices.R |only rENA-0.1.6.1/rENA/R/make.adjacency.labels.R |only rENA-0.1.6.1/rENA/R/make.network.node.R |only rENA-0.1.6.1/rENA/R/merge.columns.R |only rENA-0.1.6.1/rENA/R/old.accumulation.R |only rENA-0.1.6.1/rENA/R/r6.to.json.R |only rENA-0.1.6.1/rENA/R/rotate.R |only rENA-0.1.6.1/rENA/R/rotationPlusSvdWrapper.R |only rENA-0.1.6.1/rENA/R/scale_soln.R |only rENA-0.1.6.1/rENA/R/sphere.norm.R |only rENA-0.1.6.1/rENA/man/cohens.d.Rd |only rENA-0.1.6.1/rENA/man/group.stats.Rd |only rENA-0.1.6.1/rENA/src/dfvector_to_ut.cpp |only rENA-0.1.6.1/rENA/src/eq_pos.cpp |only rENA-0.1.6.1/rENA/src/lws_lsq_positions_c.cpp |only rENA-0.1.6.1/rENA/src/lws_positions_es_c.cpp |only rENA-0.1.6.1/rENA/src/merge_columns_c.cpp |only rENA-0.1.6.1/rENA/src/ref_window_df.cpp |only rENA-0.1.6.1/rENA/src/ref_window_parallel.cpp |only rENA-0.1.6.1/rENA/src/ref_window_sum.cpp |only rENA-0.1.6.1/rENA/src/svector_to_ut.cpp |only rENA-0.1.6.1/rENA/src/vector_to_ut.cpp |only rENA-0.1.6.1/rENA/src/vector_to_ut_full.cpp |only rENA-0.2.0.0/rENA/DESCRIPTION | 16 rENA-0.2.0.0/rENA/MD5 | 222 +-- rENA-0.2.0.0/rENA/NAMESPACE | 42 rENA-0.2.0.0/rENA/NEWS.md |only rENA-0.2.0.0/rENA/R/ENAdata.R | 319 +--- rENA-0.2.0.0/rENA/R/ENAplot.R | 65 rENA-0.2.0.0/rENA/R/ENAset.R | 15 rENA-0.2.0.0/rENA/R/RcppExports.R | 122 - rENA-0.2.0.0/rENA/R/accumulate.data.R | 322 ++-- rENA-0.2.0.0/rENA/R/cohens.d.R | 5 rENA-0.2.0.0/rENA/R/connection.matrix.R |only rENA-0.2.0.0/rENA/R/ena.R | 262 +-- rENA-0.2.0.0/rENA/R/ena.accumulate.data.R | 96 - rENA-0.2.0.0/rENA/R/ena.accumulate.data.file.R | 35 rENA-0.2.0.0/rENA/R/ena.conversations.R | 17 rENA-0.2.0.0/rENA/R/ena.correlations.R | 8 rENA-0.2.0.0/rENA/R/ena.group.R | 2 rENA-0.2.0.0/rENA/R/ena.make.set.R | 239 +++ rENA-0.2.0.0/rENA/R/ena.plot.R | 13 rENA-0.2.0.0/rENA/R/ena.plot.group.R | 39 rENA-0.2.0.0/rENA/R/ena.plot.network.R | 74 - rENA-0.2.0.0/rENA/R/ena.plot.points.R | 64 rENA-0.2.0.0/rENA/R/ena.plot.subtraction.R |only rENA-0.2.0.0/rENA/R/ena.plot.trajectory.R | 100 - rENA-0.2.0.0/rENA/R/ena.plotter.R |only rENA-0.2.0.0/rENA/R/ena.rotate.by.mean.R | 115 - rENA-0.2.0.0/rENA/R/ena.set.R |only rENA-0.2.0.0/rENA/R/ena.set.creator.R |only rENA-0.2.0.0/rENA/R/ena.svd.R | 26 rENA-0.2.0.0/rENA/R/ena.update.set.R | 1 rENA-0.2.0.0/rENA/R/ena.writeup.R | 5 rENA-0.2.0.0/rENA/R/lws.positions.sq.R | 31 rENA-0.2.0.0/rENA/R/namesToAdjacencyKey.R | 7 rENA-0.2.0.0/rENA/R/rENA.R | 9 rENA-0.2.0.0/rENA/R/utils.R |only rENA-0.2.0.0/rENA/R/utils.classes.R |only rENA-0.2.0.0/rENA/R/utils.matrix.R |only rENA-0.2.0.0/rENA/R/utils.plot.R |only rENA-0.2.0.0/rENA/README.md | 42 rENA-0.2.0.0/rENA/build/vignette.rds |binary rENA-0.2.0.0/rENA/demo/fullExample.R | 15 rENA-0.2.0.0/rENA/inst/CITATION | 4 rENA-0.2.0.0/rENA/inst/_pkgdown.yml |only rENA-0.2.0.0/rENA/inst/doc/getting-started.R | 39 rENA-0.2.0.0/rENA/inst/doc/getting-started.Rmd | 48 rENA-0.2.0.0/rENA/inst/doc/getting-started.html | 80 - rENA-0.2.0.0/rENA/inst/doc/means-rotation.R | 9 rENA-0.2.0.0/rENA/inst/doc/means-rotation.Rmd | 9 rENA-0.2.0.0/rENA/inst/doc/means-rotation.html | 27 rENA-0.2.0.0/rENA/inst/include/rENA_RcppExports.h | 127 + rENA-0.2.0.0/rENA/inst/rmd/methods.rmd | 20 rENA-0.2.0.0/rENA/man/add_group.Rd |only rENA-0.2.0.0/rENA/man/add_network.Rd |only rENA-0.2.0.0/rENA/man/add_nodes.Rd |only rENA-0.2.0.0/rENA/man/add_points.Rd |only rENA-0.2.0.0/rENA/man/add_trajectory.Rd |only rENA-0.2.0.0/rENA/man/as.ena.matrix.Rd |only rENA-0.2.0.0/rENA/man/as.ena.metadata.Rd |only rENA-0.2.0.0/rENA/man/as.matrix.ena.connections.Rd |only rENA-0.2.0.0/rENA/man/as.matrix.ena.line.weights.Rd |only rENA-0.2.0.0/rENA/man/as.matrix.ena.matrix.Rd |only rENA-0.2.0.0/rENA/man/as.matrix.ena.nodes.Rd |only rENA-0.2.0.0/rENA/man/as.matrix.ena.points.Rd |only rENA-0.2.0.0/rENA/man/as.matrix.ena.rotation.matrix.Rd |only rENA-0.2.0.0/rENA/man/as.matrix.row.connections.Rd |only rENA-0.2.0.0/rENA/man/as_trajectory.Rd |only rENA-0.2.0.0/rENA/man/cash-.ena.metadata.Rd |only rENA-0.2.0.0/rENA/man/cash-.ena.points.Rd |only rENA-0.2.0.0/rENA/man/cash-.line.weights.Rd |only rENA-0.2.0.0/rENA/man/clear.Rd |only rENA-0.2.0.0/rENA/man/connection.matrix.Rd |only rENA-0.2.0.0/rENA/man/ena.Rd | 98 - rENA-0.2.0.0/rENA/man/ena.accumulate.data.Rd | 6 rENA-0.2.0.0/rENA/man/ena.conversations.Rd | 4 rENA-0.2.0.0/rENA/man/ena.group.Rd | 3 rENA-0.2.0.0/rENA/man/ena.make.set.Rd | 14 rENA-0.2.0.0/rENA/man/ena.plot.Rd | 10 rENA-0.2.0.0/rENA/man/ena.plot.group.Rd | 31 rENA-0.2.0.0/rENA/man/ena.plot.network.Rd | 37 rENA-0.2.0.0/rENA/man/ena.plot.points.Rd | 30 rENA-0.2.0.0/rENA/man/ena.plot.trajectory.Rd | 25 rENA-0.2.0.0/rENA/man/ena.plotter.Rd |only rENA-0.2.0.0/rENA/man/ena.set.creator.Rd |only rENA-0.2.0.0/rENA/man/figures |only rENA-0.2.0.0/rENA/man/find_code_cols.Rd |only rENA-0.2.0.0/rENA/man/find_dimension_cols.Rd |only rENA-0.2.0.0/rENA/man/find_meta_cols.Rd |only rENA-0.2.0.0/rENA/man/fun_cohens.d.Rd |only rENA-0.2.0.0/rENA/man/fun_skip_sphere_norm.Rd |only rENA-0.2.0.0/rENA/man/fun_sphere_norm.Rd |only rENA-0.2.0.0/rENA/man/means_rotate.Rd |only rENA-0.2.0.0/rENA/man/merge_columns_c.Rd |only rENA-0.2.0.0/rENA/man/namesToAdjacencyKey.Rd | 4 rENA-0.2.0.0/rENA/man/plot.ena.set.Rd |only rENA-0.2.0.0/rENA/man/prepare_trajectory_data.Rd |only rENA-0.2.0.0/rENA/man/print.ena.set.Rd |only rENA-0.2.0.0/rENA/man/project_in.Rd |only rENA-0.2.0.0/rENA/man/remove_meta_data.Rd |only rENA-0.2.0.0/rENA/man/scale.ena.set.Rd |only rENA-0.2.0.0/rENA/man/show.Rd |only rENA-0.2.0.0/rENA/man/with_means.Rd |only rENA-0.2.0.0/rENA/man/with_trajectory.Rd |only rENA-0.2.0.0/rENA/src/Makevars | 2 rENA-0.2.0.0/rENA/src/RcppExports.cpp | 517 +++---- rENA-0.2.0.0/rENA/src/ena.cpp | 705 +++------- rENA-0.2.0.0/rENA/tests/testthat/test-rotation_matrix.R |only rENA-0.2.0.0/rENA/tests/testthat/test.connection.matrix.R |only rENA-0.2.0.0/rENA/tests/testthat/test.ena.accumulate.data.file.R | 119 + rENA-0.2.0.0/rENA/tests/testthat/test.ena.accumulations.R | 459 +++--- rENA-0.2.0.0/rENA/tests/testthat/test.ena.make.set.R | 232 ++- rENA-0.2.0.0/rENA/tests/testthat/test.ena.make.set.old.R |only rENA-0.2.0.0/rENA/tests/testthat/test.ena.plot.set.R | 358 ++--- rENA-0.2.0.0/rENA/tests/testthat/test.ena.use.cases.R | 442 +++--- rENA-0.2.0.0/rENA/tests/testthat/test.util.classes.R |only rENA-0.2.0.0/rENA/tests/testthat/test.util.matrices.R |only rENA-0.2.0.0/rENA/tests/testthat/test.utils.R |only rENA-0.2.0.0/rENA/tests/testthat/test.weighted.single.window.R | 7 rENA-0.2.0.0/rENA/vignettes/getting-started.Rmd | 48 rENA-0.2.0.0/rENA/vignettes/means-rotation.Rmd | 9 162 files changed, 3081 insertions(+), 2770 deletions(-)
Title: Automated Backtesting of Portfolios over Multiple Datasets
Description: Automated backtesting of multiple portfolios over multiple
datasets of stock prices in a rolling-window fashion. Intended for
researchers and practitioners to backtest a set of different portfolios,
as well as by a course instructor to assess the students in their portfolio
design in a fully automated and convenient manner, with results conveniently
formatted in tables and plots. Each portfolio design is easily defined as a
function that takes as input a window of the stock prices and outputs the
portfolio weights. Multiple portfolios can be easily specified as a list
of functions or as files in a folder. Multiple datasets can be conveniently
extracted randomly from different markets, different time periods, and
different subsets of the stock universe. The results can be later assessed
and ranked with tables based on a number of performance criteria (e.g.,
expected return, volatility, Sharpe ratio, drawdown, turnover rate, return
on investment, computational time, etc.), as well as plotted in a number of
ways with nice barplots and boxplots.
Author: Daniel P. Palomar [cre, aut],
Rui Zhou [aut]
Maintainer: Daniel P. Palomar <daniel.p.palomar@gmail.com>
Diff between portfolioBacktest versions 0.2.0 dated 2019-08-23 and 0.2.1 dated 2019-10-07
DESCRIPTION | 15 - MD5 | 57 ++-- NAMESPACE | 34 ++ NEWS.md | 13 R/backtestLeaderboard.R | 2 R/backtestSummary.R | 25 + R/param_tuning.R | 40 +- R/plotsNtables.R | 245 +++++++++++++++++- R/portfolioBacktest-package.R | 1 R/portfolioBacktest.R | 45 ++- R/stockDataDownload.R | 2 data/SP500_symbols.RData |binary inst/CITATION | 4 inst/doc/PortfolioBacktest.html | 434 ++++++++++++++++---------------- man/backtestBoxPlot.Rd | 6 man/backtestChartCumReturns.Rd |only man/backtestChartDrawdown.Rd |only man/backtestChartStackedBar.Rd |only man/backtestSelector.Rd | 2 man/backtestSummary.Rd | 2 man/backtestTable.Rd | 2 man/plotPerformanceVsParams.Rd | 2 man/portfolioBacktest-package.Rd | 1 man/portfolioBacktest.Rd | 2 man/summaryBarPlot.Rd | 4 tests/testthat/SP500symbols_check.RData |binary tests/testthat/bt_check.RData |binary tests/testthat/portfolio_files/0001.R | 3 tests/testthat/portfolio_files/0003.R | 3 tests/testthat/test-errorControl.R | 27 + tests/testthat/test-portfolioBacktest.R | 5 31 files changed, 681 insertions(+), 295 deletions(-)
More information about portfolioBacktest at CRAN
Permanent link
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization and Stochastic dominance. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 0.4.5 dated 2019-09-09 and 0.4.6 dated 2019-10-07
DESCRIPTION | 8 MD5 | 74 ++-- NAMESPACE | 15 R/ANOVA.R | 7 R/ARMA.R | 7 R/ARMA_optim.R | 3 R/Binary_ANOVA.R | 20 - R/Boost.R | 8 R/Causation.R | 3 R/Dependence.R | 48 +- R/FSD.R | 45 +- R/LPM_UPM_VaR.R | 8 R/Multivariate_Regression.R | 71 +--- R/NNS_Distance.R | 13 R/Partial_Moments.R | 33 + R/Partition_Map.R | 14 R/Regression.R | 128 ++++--- R/SD_Efficient_Set.R | 106 +++--- R/SSD.R | 7 R/Seasonality_Test.R | 2 R/Stack.R | 321 ++++++++----------- R/TSD.R | 7 R/Uni_SD_Routines.R | 106 +++--- R/dy_d_wrt.R | 147 ++++---- R/gvload.R | 5 inst/doc/NNSvignette_Classification.html | 12 inst/doc/NNSvignette_Clustering_and_Regression.html | 71 ++-- inst/doc/NNSvignette_Correlation_and_Dependence.R | 60 +++ inst/doc/NNSvignette_Correlation_and_Dependence.Rmd | 64 +++ inst/doc/NNSvignette_Correlation_and_Dependence.html | 84 ++++ inst/doc/NNSvignette_Forecasting.html | 10 man/LPM.ratio.Rd | 13 man/NNS.ANOVA.Rd | 2 man/NNS.dep.Rd | 36 -- man/NNS.reg.Rd | 12 man/NNS.stack.Rd | 4 man/PM.matrix.Rd | 3 vignettes/NNSvignette_Correlation_and_Dependence.Rmd | 64 +++ 38 files changed, 976 insertions(+), 665 deletions(-)
Title: Continuous-Time Movement Modeling
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data.
The package is described in Calabrese et al (2016) <doi:10.1111/2041-210X.12559>, with models and methods based on those introduced in
Fleming & Calabrese et al (2014) <doi:10.1086/675504>,
Fleming et al (2014) <doi:10.1111/2041-210X.12176>,
Fleming et al (2015) <doi:10.1103/PhysRevE.91.032107>,
Fleming et al (2015) <doi:10.1890/14-2010.1>,
Fleming et al (2016) <doi:10.1890/15-1607>,
Péron & Fleming et al (2016) <doi:10.1186/s40462-016-0084-7>,
Fleming & Calabrese (2017) <doi:10.1111/2041-210X.12673>,
Péron et al (2017) <doi:10.1002/ecm.1260>,
Fleming et al (2017) <doi:10.1016/j.ecoinf.2017.04.008>,
Fleming et al (2018) <doi:10.1002/eap.1704>,
Winner & Noonan et al (2018) <doi:10.1111/2041-210X.13027>,
and
Fleming et al (2019) <doi:10.1111/2041-210X.13270>.
Author: Christen H. Fleming [aut, cre],
Justin M. Calabrese [aut],
Xianghui Dong [ctb],
Kevin Winner [ctb],
Guillaume Péron [ctb],
Michael J. Noonan [ctb],
Bart Kranstauber [ctb],
Eliezer Gurarie [ctb],
Kamran Safi [ctb],
Paul C. Cross [dtc],
Thomas Mueller [dtc],
Rogério C. de Paula [dtc],
Thomas Akre [dtc],
Jonathan Drescher-Lehman [dtc]
Maintainer: Christen H. Fleming <flemingc@si.edu>
Diff between ctmm versions 0.5.6 dated 2019-05-15 and 0.5.7 dated 2019-10-07
DESCRIPTION | 22 +- MD5 | 157 ++++++++++---------- NAMESPACE | 20 +- NEWS.md | 57 +++++++ R/1.R | 7 R/acf.R | 2 R/color.R | 1 R/covm.R | 88 +++++++---- R/ctmm.R | 4 R/cv.R |only R/diffusion.R |only R/emulate.R | 45 ++++- R/export.R | 56 ++++++- R/extent.R | 3 R/kalman.R | 85 ++++++++-- R/kde.R | 345 +++++++++++++++++++++++++++++++++---------- R/krige.R | 218 +++++++++++++++++---------- R/likelihood.R | 150 ++++++++++++------- R/mag.R |only R/matrix.R | 13 - R/mean.R | 2 R/optim.R | 21 +- R/outlier.R | 93 +++++++++-- R/overlap.R | 103 ------------- R/parameters.R | 101 +++++++++--- R/plot.telemetry.R | 9 - R/projection.R | 24 +++ R/select.R | 111 +++++++++----- R/speed.R | 6 R/speeds.R | 4 R/split.R | 18 ++ R/stats.R | 41 ++++- R/str.R |only R/summary.ctmm.R | 2 R/telemetry.R | 361 ++++++++++++++++++++++++++-------------------- R/uere.R | 62 ++++++- R/units.R | 8 - R/variogram.R | 149 ++++++++++++++---- TODO | 27 ++- build/vignette.rds |binary data/datalist | 1 data/pelican.rda |only inst/doc/akde.html | 29 ++- inst/doc/error.R | 32 ++-- inst/doc/error.Rmd | 59 ++++--- inst/doc/error.html | 138 ++++++++++------- inst/doc/periodogram.R | 4 inst/doc/periodogram.Rmd | 5 inst/doc/periodogram.html | 161 ++++++++++---------- inst/doc/variogram.R | 3 inst/doc/variogram.Rmd | 3 inst/doc/variogram.html | 82 +++++----- man/akde.Rd | 36 ++-- man/as.telemetry.Rd | 33 +++- man/bandwidth.Rd | 14 - man/buffalo.Rd | 2 man/coati.Rd | 2 man/ctmm-FAQ.Rd | 9 - man/ctmm-package.Rd | 70 +++++--- man/ctmm.boot.Rd | 13 + man/ctmm.fit.Rd | 47 +++-- man/export.Rd | 10 + man/gazelle.Rd | 2 man/mean.variogram.Rd | 4 man/occurrence.Rd | 22 +- man/optimizer.Rd |only man/outlie.Rd | 22 +- man/overlap.Rd | 4 man/pelican.Rd |only man/periodogram.Rd | 8 - man/plot.telemetry.Rd | 2 man/projection.Rd | 2 man/residuals.Rd | 14 + man/simulate.ctmm.Rd | 8 - man/speed.Rd | 8 - man/summary.ctmm.Rd | 4 man/turtle.Rd | 2 man/uere.Rd | 22 +- man/variogram.Rd | 15 + man/wolf.Rd | 2 vignettes/error.Rmd | 59 ++++--- vignettes/periodogram.Rmd | 5 vignettes/variogram.Rmd | 3 83 files changed, 2194 insertions(+), 1182 deletions(-)
Title: Produce Charts that you See on the Fingertips Website
Description: Use Fingertips charts to recreate the visualisations
that are displayed on the Fingertips website (<http://fingertips.phe.org.uk/>).
Author: Sebastian Fox [aut, cre]
Maintainer: Sebastian Fox <sebastian.fox@phe.gov.uk>
Diff between fingertipscharts versions 0.0.9 dated 2019-09-09 and 0.0.10 dated 2019-10-07
fingertipscharts-0.0.10/fingertipscharts/DESCRIPTION | 13 fingertipscharts-0.0.10/fingertipscharts/MD5 | 79 +- fingertipscharts-0.0.10/fingertipscharts/NAMESPACE | 1 fingertipscharts-0.0.10/fingertipscharts/NEWS.md | 11 fingertipscharts-0.0.10/fingertipscharts/R/data.R |only fingertipscharts-0.0.10/fingertipscharts/R/quick_charts.R | 259 +++----- fingertipscharts-0.0.10/fingertipscharts/R/theme.R | 9 fingertipscharts-0.0.10/fingertipscharts/data |only fingertipscharts-0.0.10/fingertipscharts/inst/doc/quick_charts.R | 210 +++--- fingertipscharts-0.0.10/fingertipscharts/inst/doc/quick_charts.Rmd | 210 +++--- fingertipscharts-0.0.10/fingertipscharts/inst/doc/quick_charts.html | 256 ++++---- fingertipscharts-0.0.10/fingertipscharts/man/area_profiles.Rd | 30 fingertipscharts-0.0.10/fingertipscharts/man/box_plots.Rd | 23 fingertipscharts-0.0.10/fingertipscharts/man/compare_areas.Rd | 30 fingertipscharts-0.0.10/fingertipscharts/man/compare_indicators.Rd | 41 - fingertipscharts-0.0.10/fingertipscharts/man/map.Rd | 33 - fingertipscharts-0.0.10/fingertipscharts/man/mapdata.Rd |only fingertipscharts-0.0.10/fingertipscharts/man/overview.Rd | 24 fingertipscharts-0.0.10/fingertipscharts/man/population.Rd | 30 fingertipscharts-0.0.10/fingertipscharts/man/trends.Rd | 32 - fingertipscharts-0.0.10/fingertipscharts/tests/a-l.R |only fingertipscharts-0.0.10/fingertipscharts/tests/figs/area-profiles-example/area-profiles-example.svg | 261 ++++---- fingertipscharts-0.0.10/fingertipscharts/tests/figs/area-profiles-example/area-profiles-full-example.svg |only fingertipscharts-0.0.10/fingertipscharts/tests/figs/box-plots-example/box-plot-example.svg | 224 ++----- fingertipscharts-0.0.10/fingertipscharts/tests/figs/compare-areas/asc-compare-areas.svg | 28 fingertipscharts-0.0.10/fingertipscharts/tests/figs/compare-areas/desc-compare-areas.svg | 28 fingertipscharts-0.0.10/fingertipscharts/tests/figs/compare-areas/no-top-areas-asc-compare-areas.svg | 28 fingertipscharts-0.0.10/fingertipscharts/tests/figs/compare-areas/no-top-areas-desc-compare-areas.svg | 28 fingertipscharts-0.0.10/fingertipscharts/tests/figs/compare-indicators-example/compare-indicators-example.svg | 292 ++++----- fingertipscharts-0.0.10/fingertipscharts/tests/figs/compare-indicators/compare-indicators-high-r2.svg | 24 fingertipscharts-0.0.10/fingertipscharts/tests/figs/compare-indicators/compare-indicators-highlight.svg | 2 fingertipscharts-0.0.10/fingertipscharts/tests/figs/compare-indicators/compare-indicators-no-highlight.svg | 2 fingertipscharts-0.0.10/fingertipscharts/tests/figs/map-example/map-example.svg | 32 - fingertipscharts-0.0.10/fingertipscharts/tests/figs/map/map-p1.svg | 28 fingertipscharts-0.0.10/fingertipscharts/tests/figs/map/map.svg | 28 fingertipscharts-0.0.10/fingertipscharts/tests/figs/population-example/population-example.svg | 138 ++-- fingertipscharts-0.0.10/fingertipscharts/tests/figs/trends-example/trends-example.svg | 152 ++-- fingertipscharts-0.0.10/fingertipscharts/tests/m-z.R |only fingertipscharts-0.0.10/fingertipscharts/tests/testthat/test-area-profiles.R | 49 - fingertipscharts-0.0.10/fingertipscharts/tests/testthat/test-compare-indicators.R | 3 fingertipscharts-0.0.10/fingertipscharts/tests/testthat/test-examples.R | 312 +++++----- fingertipscharts-0.0.10/fingertipscharts/tests/testthat/test-map.R | 25 fingertipscharts-0.0.10/fingertipscharts/vignettes/quick_charts.Rmd | 210 +++--- fingertipscharts-0.0.9/fingertipscharts/tests/testthat.R |only 44 files changed, 1557 insertions(+), 1628 deletions(-)
More information about fingertipscharts at CRAN
Permanent link
Title: Calculate Quantitative Ethnobotany Indices
Description: Calculate common quantitative ethnobotany indices to assess the cultural significance of plant species based on informant consensus. The package closely follows the paper by Tardio and Pardo-de-Santayana (2008). Tardio, J., and M. Pardo-de-Santayana, 2008. Cultural Importance Indices: A Comparative Analysis Based on the Useful Wild Plants of Southern Cantabria (Northern Spain) 1. Economic Botany, 62(1), 24-39. <doi:10.1007/s12231-007-9004-5>.
Author: Cory Whitney
Maintainer: Cory Whitney <whitney.cory@gmail.com>
Diff between ethnobotanyR versions 0.1.5 dated 2019-08-06 and 0.1.6 dated 2019-10-07
ethnobotanyR-0.1.5/ethnobotanyR/R/ethnoChordUser.R |only ethnobotanyR-0.1.5/ethnobotanyR/R/ethnobotanyChord.R |only ethnobotanyR-0.1.5/ethnobotanyR/man/ethnoChordUser.Rd |only ethnobotanyR-0.1.5/ethnobotanyR/man/ethnobotanyChord.Rd |only ethnobotanyR-0.1.6/ethnobotanyR/DESCRIPTION | 16 - ethnobotanyR-0.1.6/ethnobotanyR/MD5 | 77 ++--- ethnobotanyR-0.1.6/ethnobotanyR/NAMESPACE | 7 ethnobotanyR-0.1.6/ethnobotanyR/NEWS.md | 10 ethnobotanyR-0.1.6/ethnobotanyR/R/CIs.R | 62 ++-- ethnobotanyR-0.1.6/ethnobotanyR/R/CVe.R | 95 ++++--- ethnobotanyR-0.1.6/ethnobotanyR/R/FCs.R | 48 ++- ethnobotanyR-0.1.6/ethnobotanyR/R/FLs.R | 53 ++- ethnobotanyR-0.1.6/ethnobotanyR/R/NUs.R | 58 ++-- ethnobotanyR-0.1.6/ethnobotanyR/R/RFCs.R | 53 ++- ethnobotanyR-0.1.6/ethnobotanyR/R/RIs.R | 59 ++-- ethnobotanyR-0.1.6/ethnobotanyR/R/Radial_plot.R | 63 ++-- ethnobotanyR-0.1.6/ethnobotanyR/R/URs.R | 61 ++-- ethnobotanyR-0.1.6/ethnobotanyR/R/URsum.R | 56 ++-- ethnobotanyR-0.1.6/ethnobotanyR/R/UVs.R | 61 ++-- ethnobotanyR-0.1.6/ethnobotanyR/R/ethnoChord.R | 91 +++--- ethnobotanyR-0.1.6/ethnobotanyR/R/ethnobotanydata.R | 2 ethnobotanyR-0.1.6/ethnobotanyR/R/simple_UVs.R | 61 ++-- ethnobotanyR-0.1.6/ethnobotanyR/README.md | 29 -- ethnobotanyR-0.1.6/ethnobotanyR/inst/doc/ethnobotanyr_vignette.R | 6 ethnobotanyR-0.1.6/ethnobotanyR/inst/doc/ethnobotanyr_vignette.Rmd | 65 +--- ethnobotanyR-0.1.6/ethnobotanyR/inst/doc/ethnobotanyr_vignette.html | 134 ++++++---- ethnobotanyR-0.1.6/ethnobotanyR/man/CIs.Rd | 30 +- ethnobotanyR-0.1.6/ethnobotanyR/man/CVe.Rd | 30 +- ethnobotanyR-0.1.6/ethnobotanyR/man/FCs.Rd | 15 - ethnobotanyR-0.1.6/ethnobotanyR/man/FLs.Rd | 29 +- ethnobotanyR-0.1.6/ethnobotanyR/man/NUs.Rd | 26 + ethnobotanyR-0.1.6/ethnobotanyR/man/RFCs.Rd | 29 +- ethnobotanyR-0.1.6/ethnobotanyR/man/RIs.Rd | 29 +- ethnobotanyR-0.1.6/ethnobotanyR/man/Radial_plot.Rd | 35 +- ethnobotanyR-0.1.6/ethnobotanyR/man/URs.Rd | 30 +- ethnobotanyR-0.1.6/ethnobotanyR/man/URsum.Rd | 28 +- ethnobotanyR-0.1.6/ethnobotanyR/man/UVs.Rd | 12 ethnobotanyR-0.1.6/ethnobotanyR/man/ethnoChord.Rd | 38 +- ethnobotanyR-0.1.6/ethnobotanyR/man/ethnobotanydata.Rd | 4 ethnobotanyR-0.1.6/ethnobotanyR/man/simple_UVs.Rd | 30 +- ethnobotanyR-0.1.6/ethnobotanyR/vignettes/ethnobotanyr_vignette.Rmd | 65 +--- ethnobotanyR-0.1.6/ethnobotanyR/vignettes/references |only 42 files changed, 964 insertions(+), 633 deletions(-)
Title: Fast Adaptive Spectral Clustering for Single and Multi-View Data
Description: A self-tuning spectral clustering method for single or multi-view data. 'Spectrum' uses a new type of adaptive density aware kernel that strengthens connections in the graph based on common nearest neighbours. It uses a tensor product graph data integration and diffusion procedure to integrate different data sources and reduce noise. 'Spectrum' uses either the eigengap or multimodality gap heuristics to determine the number of clusters. The method is sufficiently flexible so that a wide range of Gaussian and non-Gaussian structures can be clustered with automatic selection of K.
Author: Christopher R John, David Watson
Maintainer: Christopher R John <chris.r.john86@gmail.com>
Diff between Spectrum versions 0.8 dated 2019-08-19 and 0.9 dated 2019-10-07
Spectrum-0.8/Spectrum/R/spectrum_functions.R |only Spectrum-0.9/Spectrum/DESCRIPTION | 6 - Spectrum-0.9/Spectrum/MD5 | 47 +++++--- Spectrum-0.9/Spectrum/NAMESPACE | 15 +- Spectrum-0.9/Spectrum/R/core_functions.R |only Spectrum-0.9/Spectrum/R/data.R | 20 +++ Spectrum-0.9/Spectrum/R/kernel_functions.R |only Spectrum-0.9/Spectrum/R/plotting_functions.R |only Spectrum-0.9/Spectrum/R/spectrum.R | 60 ++++------ Spectrum-0.9/Spectrum/data/datalist | 2 Spectrum-0.9/Spectrum/data/missl.rda |only Spectrum-0.9/Spectrum/data/misslfilled.rda |only Spectrum-0.9/Spectrum/inst/doc/Spectrum_vignette.R | 16 ++ Spectrum-0.9/Spectrum/inst/doc/Spectrum_vignette.Rmd | 73 +++++++++---- Spectrum-0.9/Spectrum/inst/doc/Spectrum_vignette.pdf |binary Spectrum-0.9/Spectrum/man/CNN_kernel.Rd | 6 - Spectrum-0.9/Spectrum/man/Spectrum.Rd | 18 +-- Spectrum-0.9/Spectrum/man/cluster_similarity.Rd |only Spectrum-0.9/Spectrum/man/estimate_k.Rd |only Spectrum-0.9/Spectrum/man/harmonise_ids.Rd |only Spectrum-0.9/Spectrum/man/integrate_similarity_matrices.Rd |only Spectrum-0.9/Spectrum/man/kernel_pca.Rd | 8 - Spectrum-0.9/Spectrum/man/mean_imputation.Rd |only Spectrum-0.9/Spectrum/man/missl.Rd |only Spectrum-0.9/Spectrum/man/misslfilled.Rd |only Spectrum-0.9/Spectrum/man/ng_kernel.Rd |only Spectrum-0.9/Spectrum/man/pca.Rd | 2 Spectrum-0.9/Spectrum/man/rbfkernel_b.Rd | 2 Spectrum-0.9/Spectrum/man/sigma_finder.Rd |only Spectrum-0.9/Spectrum/man/tsne.Rd | 2 Spectrum-0.9/Spectrum/man/umap.Rd | 2 Spectrum-0.9/Spectrum/vignettes/Spectrum_vignette.Rmd | 73 +++++++++---- 32 files changed, 231 insertions(+), 121 deletions(-)
Title: NanoString Quality Control Dashboard
Description: NanoString nCounter data are gene expression assays where there is no need for the use of enzymes
or amplification protocols and work with fluorescent barcodes (Geiss et al. (2018) <doi:10.1038/nbt1385>).
Each barcode is assigned a messenger-RNA/micro-RNA (mRNA/miRNA) which after bonding with its target can be counted.
As a result each count of a specific barcode represents the presence of its target mRNA/miRNA.
'NACHO' (NAnoString quality Control dasHbOard) is able to analyse the exported NanoString nCounter
data and facilitates the user in performing a quality control.
'NACHO' does this by visualising quality control metrics, expression of control genes,
principal components and sample specific size factors in an interactive web application.
Author: Mickaël Canouil [aut, cre] (<https://orcid.org/0000-0002-3396-4549>),
Roderick Slieker [aut] (<https://orcid.org/0000-0003-0961-9152>),
Gerard Bouland [aut]
Maintainer: Mickaël Canouil <mickael.canouil@cnrs.fr>
Diff between NACHO versions 0.5.6 dated 2019-04-29 and 0.6.0 dated 2019-10-07
DESCRIPTION | 17 - MD5 | 149 +++++++------ NAMESPACE | 7 NEWS.md | 37 +++ R/GSE74821.R | 8 R/autoplot.R |only R/details_outlier.R | 3 R/exclude_outliers.R | 2 R/factor_calculation.R | 5 R/find_housekeeping.R | 7 R/format_counts.R | 7 R/format_tag_content.R | 3 R/geometric_housekeeping.R | 10 R/geometric_mean.R | 5 R/geometric_probes.R | 9 R/norm_geo.R | 5 R/norm_glm.R | 5 R/normalise.R | 79 +++---- R/normalise_counts.R | 5 R/print.R |only R/probe_exclusion.R | 5 R/qc_features.R | 5 R/qc_imaging.R | 7 R/qc_limit_detection.R | 7 R/qc_pca.R | 5 R/qc_positive_control.R | 5 R/qc_rcc.R | 7 R/read_rcc.R | 26 +- R/read_tags.R | 7 R/render.R |only R/summarise.R | 137 +++++++----- R/utils-autoplot.R |only R/utils-pipe.R |only R/visualise.R | 233 ++++++++++++++------- build/vignette.rds |binary data/GSE74821.rda |binary inst/CITATION |only inst/doc/NACHO.R | 145 +++++++++---- inst/doc/NACHO.Rmd | 158 +++++++++++--- inst/doc/NACHO.html | 443 +++++++++++++++++++++++++++++++++------- man/GSE74821.Rd | 6 man/autoplot.Rd |only man/autoplot.nacho.Rd |only man/details_outlier.Rd | 13 - man/exclude_outliers.Rd | 4 man/factor_calculation.Rd | 20 - man/find_housekeeping.Rd | 11 man/format_counts.Rd | 11 man/format_tag_content.Rd | 9 man/geometric_housekeeping.Rd | 15 - man/geometric_mean.Rd | 7 man/geometric_probes.Rd | 11 man/norm_geo.Rd | 7 man/norm_glm.Rd | 7 man/normalise.Rd | 79 +++---- man/normalise_counts.Rd | 9 man/pipe.Rd |only man/plot_acbd.Rd |only man/plot_acmc.Rd |only man/plot_cg.Rd |only man/plot_hf.Rd |only man/plot_metrics.Rd |only man/plot_norm.Rd |only man/plot_pca.Rd |only man/plot_pca12.Rd |only man/plot_pcai.Rd |only man/plot_pfnf.Rd |only man/plot_pn.Rd |only man/print.nacho.Rd |only man/probe_exclusion.Rd | 7 man/qc_features.Rd | 9 man/qc_imaging.Rd | 9 man/qc_limit_detection.Rd | 9 man/qc_pca.Rd | 9 man/qc_positive_control.Rd | 7 man/qc_rcc.Rd | 24 -- man/read_rcc.Rd | 7 man/read_tags.Rd | 9 man/render.Rd |only man/summarise.Rd | 62 ++--- man/visualise.Rd | 8 tests/testthat/test-autoplot.R |only tests/testthat/test-normalise.R | 28 +- tests/testthat/test-print.R |only tests/testthat/test-render.R |only tests/testthat/test-summarise.R | 41 +-- tests/testthat/test-visualise.R | 30 +- vignettes/NACHO.Rmd | 158 +++++++++++--- 88 files changed, 1434 insertions(+), 745 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] (<https://orcid.org/0000-0002-7152-6654>),
Dean Attali [aut],
Benjamin Rich [aut] (provided summary stats tables tab code),
Michael Sachs [aut] (provided ggkm code)
Maintainer: Samer Mouksassi <samermouksassi@gmail.com>
Diff between ggquickeda versions 0.1.4 dated 2019-09-03 and 0.1.5 dated 2019-10-07
DESCRIPTION | 6 MD5 | 14 - NEWS.md | 10 inst/doc/AdditionalPlotsStats.html | 4 inst/doc/ggquickeda.html | 4 inst/shinyapp/global.R | 2 inst/shinyapp/server.R | 479 +++++++++++++++++++++++++++++++------ inst/shinyapp/ui.R | 70 +++-- 8 files changed, 484 insertions(+), 105 deletions(-)
Title: Methods for Joint Dimension Reduction and Clustering
Description: A class of methods that combine dimension reduction and clustering of continuous, categorical or mixed-type data. For continuous data, the package contains implementations of factorial K-means (Vichi and Kiers 2001; <DOI:10.1016/S0167-9473(00)00064-5>) and reduced K-means (De Soete and Carroll 1994; <DOI:10.1007/978-3-642-51175-2_24>); both methods that combine principal component analysis with K-means clustering. For categorical data, the package provides MCA K-means (Hwang, Dillon and Takane 2006; <DOI:10.1007/s11336-004-1173-x>), i-FCB (Iodice D'Enza and Palumbo 2013, <DOI:10.1007/s00180-012-0329-x>) and Cluster Correspondence Analysis (van de Velden, Iodice D'Enza and Palumbo 2017; <DOI:10.1007/s11336-016-9514-0>), which combine multiple correspondence analysis with K-means. For mixed-type data, it provides mixed Reduced K-means and mixed Factorial K-means (van de Velden, Iodice D'Enza and Markos 2019; <DOI:10.1002/wics.1456>), which combine PCA for mixed-type data with K-means.
Author: Angelos Markos [aut, cre], Alfonso Iodice D'Enza [aut], Michel van de Velden [ctb]
Maintainer: Angelos Markos <amarkos@gmail.com>
Diff between clustrd versions 1.3.5 dated 2019-09-07 and 1.3.6 dated 2019-10-07
DESCRIPTION | 8 +- MD5 | 22 +++---- R/clusCA.R | 157 ++++++++++++++++++++++++++------------------------ R/cluspca.R | 20 +++--- R/cluspcamix.R | 24 +++++-- R/outOfIndependence.r | 7 -- R/plot.clusmca.R | 10 +-- R/plot.cluspca.R | 8 +- R/plot.cluspcamix.R | 13 ++-- R/summary.cluspca.R | 4 - man/clusmca.Rd | 8 ++ man/plot.cluspca.Rd | 4 - 12 files changed, 159 insertions(+), 126 deletions(-)
Title: Inference of Linear Mixed Models Through MM Algorithm
Description: The main function MMEst() performs (Restricted) Maximum Likelihood in a variance component mixed models using a Min-Max (MM) algorithm (Hunter, D. R., & Lange, K. (2004) <doi:10.1198/0003130042836>).
Author: Fabien Laporte, Tristan Mary-Huard
Maintainer: Fabien Laporte <fabien.laporte@pasteur.fr>
Diff between MM4LMM versions 1.1.5 dated 2019-01-15 and 2.0.1 dated 2019-10-07
DESCRIPTION | 12 - MD5 | 22 +- NAMESPACE | 4 R/AnovaTest.R | 13 + R/MM4LMM-internal.R | 321 +++++++++++++++++++++++++++++++++++--- R/MMEst.R | 3 data/QTLDetectionExample.rda |binary data/VarianceComponentExample.rda |binary man/AnovaTest.Rd | 36 +++- man/MM4LMM-package.Rd | 6 man/MMEst.Rd | 4 src/RemlMM2Mat.h | 4 12 files changed, 366 insertions(+), 59 deletions(-)
Title: Infrastructure for Computing with Basis Functions
Description: Some very simple infrastructure for basis functions.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between basefun versions 1.0-5 dated 2019-06-21 and 1.0-6 dated 2019-10-07
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/intercept.R | 8 ++++---- inst/NEWS.Rd | 9 +++++++++ 4 files changed, 20 insertions(+), 11 deletions(-)
Title: Litter Analysis
Description: Data sets on various litter types like beach litter, riverain
litter, floating litter, and seafloor litter are rapidly growing. This
package offers a simple user interface to analyse these litter data in
a consistent and reproducible way. It also provides functions to
facilitate several kinds of litter analysis, e.g., trend analysis,
power analysis, and baseline analysis. Under the hood, these functions
are also used by the user interface. See Schulz et al. (2019)
<doi:10.1016/j.envpol.2019.02.030> for details.
Author: Dennis Walvoort [aut, cre, cph],
Willem van Loon [aut, cph],
Rijkswaterstaat - The Netherlands [cph, fnd, dtc]
Maintainer: Dennis Walvoort <dennis.Walvoort@wur.nl>
Diff between litteR versions 0.4.1 dated 2019-07-26 and 0.6.2 dated 2019-10-07
litteR-0.4.1/litteR/inst/app/litter-assessment.Rmd |only litteR-0.4.1/litteR/inst/extdata/litter-groups.csv |only litteR-0.4.1/litteR/vignettes/tbl/tab-checks.csv |only litteR-0.6.2/litteR/DESCRIPTION | 10 litteR-0.6.2/litteR/MD5 | 52 litteR-0.6.2/litteR/NAMESPACE | 4 litteR-0.6.2/litteR/NEWS.md | 39 litteR-0.6.2/litteR/R/gui.R | 86 litteR-0.6.2/litteR/R/io.R | 54 litteR-0.6.2/litteR/R/litteR.R | 5 litteR-0.6.2/litteR/R/onLoad.R | 6 litteR-0.6.2/litteR/R/stats.R | 4 litteR-0.6.2/litteR/build/partial.rdb |binary litteR-0.6.2/litteR/inst/app/litter-baseline.Rmd | 2 litteR-0.6.2/litteR/inst/app/litter-main.Rmd | 239 litteR-0.6.2/litteR/inst/app/litter-trend.Rmd | 11 litteR-0.6.2/litteR/inst/doc/litter-manual.R | 34 litteR-0.6.2/litteR/inst/doc/litter-manual.Rmd | 190 litteR-0.6.2/litteR/inst/doc/litter-manual.html | 459 litteR-0.6.2/litteR/inst/extdata/beach-litter-nl-2012-2017-long.csv |22992 +++++----- litteR-0.6.2/litteR/inst/extdata/beach-litter-nl-2012-2017-wide.csv | 192 litteR-0.6.2/litteR/inst/extdata/litter-stats-meta.csv | 5 litteR-0.6.2/litteR/inst/extdata/ospar-groups.csv |only litteR-0.6.2/litteR/inst/extdata/settings.yaml | 20 litteR-0.6.2/litteR/man/litter.Rd | 8 litteR-0.6.2/litteR/man/read_litter_groups.Rd | 3 litteR-0.6.2/litteR/man/theil_sen.Rd | 3 litteR-0.6.2/litteR/vignettes/litter-manual.Rmd | 190 litteR-0.6.2/litteR/vignettes/tbl/settings.csv | 9 29 files changed, 12330 insertions(+), 12287 deletions(-)
Title: Design of Risk Parity Portfolios
Description: Fast design of risk parity portfolios for financial investment.
The goal of the risk parity portfolio formulation is to equalize or distribute
the risk contributions of the different assets, which is missing if we simply
consider the overall volatility of the portfolio as in the mean-variance
Markowitz portfolio. In addition to the vanilla formulation, where the risk
contributions are perfectly equalized subject to no shortselling and budget
constraints, many other formulations are considered that allow for box
constraints and shortselling, as well as the inclusion of additional
objectives like the expected return and overall variance. See vignette for
a detailed documentation and comparison, with several illustrative examples.
The package is based on the papers:
Y. Feng, and D. P. Palomar (2015). SCRIP: Successive Convex Optimization Methods
for Risk Parity Portfolio Design. IEEE Trans. on Signal Processing, vol. 63,
no. 19, pp. 5285-5300. <doi:10.1109/TSP.2015.2452219>.
F. Spinu (2013), An Algorithm for Computing Risk Parity Weights.
<doi:10.2139/ssrn.2297383>.
T. Griveau-Billion, J. Richard, and T. Roncalli (2013). A fast algorithm for computing
High-dimensional risk parity portfolios. <arXiv:1311.4057>.
Author: Ze Vinicius [aut],
Daniel P. Palomar [cre, aut]
Maintainer: Daniel P. Palomar <daniel.p.palomar@gmail.com>
Diff between riskParityPortfolio versions 0.2.0 dated 2019-08-31 and 0.2.1 dated 2019-10-07
riskParityPortfolio-0.2.0/riskParityPortfolio/tests/testthat/test-Constraints.R |only riskParityPortfolio-0.2.1/riskParityPortfolio/DESCRIPTION | 12 riskParityPortfolio-0.2.1/riskParityPortfolio/MD5 | 14 riskParityPortfolio-0.2.1/riskParityPortfolio/NEWS.md | 5 riskParityPortfolio-0.2.1/riskParityPortfolio/README.md | 2 riskParityPortfolio-0.2.1/riskParityPortfolio/inst/CITATION | 4 riskParityPortfolio-0.2.1/riskParityPortfolio/inst/doc/RiskParityPortfolio.html | 503 +++++----- riskParityPortfolio-0.2.1/riskParityPortfolio/tests/testthat/test-constraints.R |only riskParityPortfolio-0.2.1/riskParityPortfolio/tests/testthat/test-pyrb.R | 4 9 files changed, 324 insertions(+), 220 deletions(-)
More information about riskParityPortfolio at CRAN
Permanent link
Title: Bayesian Object Oriented Modeling
Description: A C++ library for Bayesian modeling, with an emphasis on Markov
chain Monte Carlo. Although boom contains a few R utilities (mainly plotting
functions), its primary purpose is to install the BOOM C++ library on your
system so that other packages can link against it.
Author: Steven L. Scott is the sole author and creator of the BOOM project.
Some code in the BOOM libraries has been modified from other open source
projects. These include Cephes (obtained from Netlib, written by Stephen
L. Moshier), NEWUOA (M.J.D Powell, obtained from Powell's web site), and a
modified version of the R math libraries (R core development team). Original
copyright notices have been maintained in all source files. In these cases,
copyright claimed by Steven L. Scott is limited to modifications made to the
original code. Google claims copyright for code written while Steven
L. Scott was employed at Google from 2008 - 2018, but BOOM is not an
officially supported Google project.
Maintainer: Steven L. Scott <steve.the.bayesian@gmail.com>
Diff between Boom versions 0.9.2 dated 2019-09-03 and 0.9.3 dated 2019-10-07
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ inst/include/Models/Policies/IID_DataPolicy.hpp | 15 +++++++-------- inst/include/numopt/Brent.hpp | 14 ++++++++++++++ inst/include/numopt/Integral.hpp | 1 + src/Makevars | 3 +-- src/numopt/Brent.cpp | 7 +++---- 7 files changed, 36 insertions(+), 24 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-10-06 0.1.18
Title: Diagnostics for Pharmacometric Models
Description: Diagnostics for non-linear mixed-effects (population)
models from 'NONMEM' <http://www.iconplc.com/innovation/nonmem/>.
'xpose' facilitates data import, creation of numerical run summary
and provide 'ggplot2'-based graphics for data exploration and model
diagnostics.
Author: Benjamin Guiastrennec [aut, cre, cph],
Andrew C. Hooker [aut, cph],
Sebastian Ueckert [aut, cph],
Mike K. Smith [ctb],
Mats O. Karlsson [aut, cph]
Maintainer: Benjamin Guiastrennec <guiastrennec@gmail.com>
Diff between xpose versions 0.4.4 dated 2019-03-21 and 0.4.5 dated 2019-10-07
xpose-0.4.4/xpose/man/summarize_xpdb.Rd |only xpose-0.4.5/xpose/DESCRIPTION | 17 xpose-0.4.5/xpose/MD5 | 154 +- xpose-0.4.5/xpose/NAMESPACE | 2 xpose-0.4.5/xpose/NEWS.md | 6 xpose-0.4.5/xpose/R/fetch_data.R | 457 +++---- xpose-0.4.5/xpose/R/list_nm_tables.R | 6 xpose-0.4.5/xpose/R/plot_amt.R | 132 +- xpose-0.4.5/xpose/R/plot_distribution.R | 432 +++---- xpose-0.4.5/xpose/R/plot_gof.R | 206 +-- xpose-0.4.5/xpose/R/plot_individuals.R | 158 +- xpose-0.4.5/xpose/R/plot_minimization.R | 242 ++-- xpose-0.4.5/xpose/R/plot_qq.R | 446 +++---- xpose-0.4.5/xpose/R/plot_residuals.R | 494 ++++---- xpose-0.4.5/xpose/R/plot_spaghetti.R | 328 ++--- xpose-0.4.5/xpose/R/plot_vpc.R | 578 ++++----- xpose-0.4.5/xpose/R/print_xpose_data.R | 182 +-- xpose-0.4.5/xpose/R/print_xpose_plot.R | 370 +++--- xpose-0.4.5/xpose/R/prm_table.R | 4 xpose-0.4.5/xpose/R/read_nm_files.R | 15 xpose-0.4.5/xpose/R/read_nm_model.R | 290 ++-- xpose-0.4.5/xpose/R/read_nm_tables.R | 96 + xpose-0.4.5/xpose/R/summarise_nm_model.R | 58 xpose-0.4.5/xpose/R/summary_xpose_data.R | 6 xpose-0.4.5/xpose/R/temporary.R |only xpose-0.4.5/xpose/R/themes_xp.R | 444 +++---- xpose-0.4.5/xpose/R/update_themes.R | 134 +- xpose-0.4.5/xpose/R/utils.R | 718 ++++++------ xpose-0.4.5/xpose/R/vars_list.R | 6 xpose-0.4.5/xpose/R/vars_set.R | 362 +++--- xpose-0.4.5/xpose/R/vpc_data.R | 419 +++---- xpose-0.4.5/xpose/R/vpc_helpers.R | 4 xpose-0.4.5/xpose/R/xpdb_access.R | 40 xpose-0.4.5/xpose/R/xpdb_edits.R | 95 - xpose-0.4.5/xpose/R/xplot_distrib.R | 313 ++--- xpose-0.4.5/xpose/R/xplot_helpers.R | 4 xpose-0.4.5/xpose/R/xplot_qq.R | 267 ++-- xpose-0.4.5/xpose/R/xplot_scatter.R | 404 +++--- xpose-0.4.5/xpose/R/xpose.R | 2 xpose-0.4.5/xpose/R/xpose_data.R | 107 - xpose-0.4.5/xpose/R/xpose_geom.R | 228 +-- xpose-0.4.5/xpose/R/zzz.R | 16 xpose-0.4.5/xpose/README.md | 15 xpose-0.4.5/xpose/build/vignette.rds |binary xpose-0.4.5/xpose/data/xpdb_ex_pk.rda |binary xpose-0.4.5/xpose/inst/doc/access_xpdb_data.html | 10 xpose-0.4.5/xpose/inst/doc/customize_plots.html | 40 xpose-0.4.5/xpose/inst/doc/import_model_outputs.html | 8 xpose-0.4.5/xpose/inst/doc/introduction.html | 18 xpose-0.4.5/xpose/inst/doc/multiple_pages.html | 20 xpose-0.4.5/xpose/inst/doc/vpc.html | 22 xpose-0.4.5/xpose/man/figures/readme_example_figure_1-1.png |binary xpose-0.4.5/xpose/man/figures/readme_example_figure_2-1.png |binary xpose-0.4.5/xpose/man/figures/readme_example_figure_3-1.png |binary xpose-0.4.5/xpose/man/figures/readme_example_figure_4-1.png |binary xpose-0.4.5/xpose/man/figures/readme_example_figure_5-1.png |binary xpose-0.4.5/xpose/man/read_nm_files.Rd | 18 xpose-0.4.5/xpose/man/read_nm_model.Rd | 32 xpose-0.4.5/xpose/man/summarise_xpdb.Rd |only xpose-0.4.5/xpose/man/tidyr_new_interface.Rd |only xpose-0.4.5/xpose/man/update_themes.Rd | 28 xpose-0.4.5/xpose/man/vpc.Rd | 10 xpose-0.4.5/xpose/man/xplot_distrib.Rd | 10 xpose-0.4.5/xpose/man/xplot_qq.Rd | 10 xpose-0.4.5/xpose/man/xplot_scatter.Rd | 10 xpose-0.4.5/xpose/man/xpose-package.Rd | 1 xpose-0.4.5/xpose/man/xpose_data.Rd | 81 - xpose-0.4.5/xpose/tests/testthat/data/ctrl_psn_vpc.RData |binary xpose-0.4.5/xpose/tests/testthat/data/ctrl_special.RData |binary xpose-0.4.5/xpose/tests/testthat/test-console_outputs.R | 1 xpose-0.4.5/xpose/tests/testthat/test-fetch_data.R | 120 +- xpose-0.4.5/xpose/tests/testthat/test-manual_import.R | 4 xpose-0.4.5/xpose/tests/testthat/test-model-summary.R | 10 xpose-0.4.5/xpose/tests/testthat/test-print_xpose_plots.R | 74 - xpose-0.4.5/xpose/tests/testthat/test-update_themes.R | 96 - xpose-0.4.5/xpose/tests/testthat/test-vpc.R | 11 xpose-0.4.5/xpose/tests/testthat/test-xpdb_access.R | 426 +++---- xpose-0.4.5/xpose/tests/testthat/test-xplot_helpers.R | 220 +-- xpose-0.4.5/xpose/tests/testthat/test-xpose-default-plots.R | 240 ++-- xpose-0.4.5/xpose/tests/testthat/test-xpose_data.R | 184 +-- 80 files changed, 5120 insertions(+), 4841 deletions(-)