Title: Time-Varying Effect Models
Description: Fits time-varying effect models (TVEM). These are a kind of application of varying-coefficient models in the context of longitudinal data, allowing the strength of linear, logistic, or Poisson regression relationships to change over time. These models are described further in Tan, Shiyko, Li, Li & Dierker (2012) <doi:10.1037/a0025814>. We thank Kaylee Litson, Patricia Berglund, and Yajnaseni Chakraborti for their valuable help with testing the package and documentation. The development of this package was part of a research project supported by National Institutes of Health grants P50 DA039838 from the National Institute of Drug Abuse and 1R01 CA229542-01 from the National Cancer Institute and the NIH Office of Behavioral and Social Science Research. Content is solely the responsibility of the authors and does not necessarily represent the official views of the funding institutions mentioned above. This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
Author: John J. Dziak [aut, cre] (<https://orcid.org/0000-0003-0762-5495>),
Donna L. Coffman [aut] (<https://orcid.org/0000-0001-6305-6579>),
Runze Li [aut] (<https://orcid.org/0000-0002-0154-2202>),
Kaylee Litson [aut] (<https://orcid.org/0000-0003-1296-4811>),
Yajnaseni Chakraborti [aut]
Maintainer: John J. Dziak <dziakj1@gmail.com>
Diff between tvem versions 1.3 dated 2021-08-05 and 1.3.1 dated 2021-10-14
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/tvem.r | 6 +++++- build/vignette.rds |binary inst/doc/vignette-tvem.Rmd | 4 ++-- inst/doc/vignette-tvem.html | 8 ++++---- man/tvem.Rd | 6 +++++- vignettes/vignette-tvem.Rmd | 4 ++-- 8 files changed, 29 insertions(+), 21 deletions(-)
Title: Text Plots
Description: Visualise complex relations in texts. This is done by providing functionalities for displaying
text co-occurrence networks, text correlation networks, dependency relationships as well as text clustering and semantic text 'embeddings'.
Feel free to join the effort of providing interesting text visualisations.
Author: Jan Wijffels [aut, cre, cph],
BNOSAC [cph],
Sacha Epskamp [ctb, cph] (code in R/matrix_reduction.R adapted from the
qgraph package version 1.4.0 which is GPL-2 licensed),
Ingo Feinerer and Kurt Hornik [ctb, cph] (partial code in
R/textplot_corlines.R adapted from the tm package version 0.4 which
is GPL-2 licensed)
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between textplot versions 0.2.0 dated 2021-08-18 and 0.2.1 dated 2021-10-14
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/textplot_biterms.R | 2 +- build/vignette.rds |binary inst/doc/textplot-examples.pdf |binary 6 files changed, 15 insertions(+), 10 deletions(-)
Title: The Ramer-Douglas-Peucker Algorithm
Description: Pretty fast implementation of the Ramer-Douglas-Peucker algorithm for reducing the number of points on a 2D curve.
Urs Ramer (1972), "An iterative procedure for the polygonal approximation of plane curves" <doi:10.1016/S0146-664X(72)80017-0>.
David H. Douglas and Thomas K. Peucker (1973), "Algorithms for the Reduction of the Number of Points Required to Represent a Digitized Line or its Caricature" <doi:10.3138/FM57-6770-U75U-7727>.
Author: Robert Dahl Jacobsen [aut, cre]
Maintainer: Robert Dahl Jacobsen <cran@dahl-jacobsen.dk>
Diff between RDP versions 0.1.8 dated 2021-09-25 and 0.2.0 dated 2021-10-14
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/RcppExports.R | 3 +++ build/partial.rdb |binary man/RamerDouglasPeucker.Rd | 4 ++++ src/RamerDouglasPeucker.cpp | 1 - src/wrapper.cpp | 7 +++++-- tests/testthat/test-RamerDouglasPeucker.R | 12 +++++++++--- 8 files changed, 31 insertions(+), 16 deletions(-)
Title: Variance Function Program
Description: Variance function estimation for models proposed by W. Sadler in his variance function program
('VFP', <http://www.aacb.asn.au/resources/useful-tools/variance-function-program-v14>). Here, the idea is
to fit multiple variance functions to a data set and consequently assess which function reflects
the relationship 'Var ~ Mean' best. For 'in-vitro diagnostic' ('IVD') assays modeling this relationship
is of great importance when individual test-results are used for defining follow-up treatment of patients.
Author: Andre Schuetzenmeister [cre, aut],
Florian Dufey [aut],
Andrea Geistanger [ctb]
Maintainer: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Diff between VFP versions 1.3 dated 2020-06-16 and 1.3.1 dated 2021-10-14
DESCRIPTION | 8 ++-- MD5 | 18 ++++----- build/vignette.rds |binary inst/doc/VFP_package_vignette.html | 53 +++++++++++++++++++--------- inst/doc/VFP_package_vignette.rmd | 38 ++++++++++---------- man/VFP-Package.Rd | 4 +- vignettes/VFP_package_vignette.rmd | 38 ++++++++++---------- vignettes/figures/deriveCx_examples_2-1.png |binary vignettes/figures/deriveCx_examples_3-1.png |binary vignettes/figures/deriveCx_examples_4-1.png |binary 10 files changed, 89 insertions(+), 70 deletions(-)
Title: UK Flood Estimation
Description: Functions to implement the methods of the Flood Estimation Handbook (FEH), associated updates and the revitalised flood hydrograph model (ReFH). Currently the package uses NRFA peak flow dataset version 10. Aside from FEH functionality, further hydrological functions are available. Most of the methods implemented in this package are described in one or more of the following: "Flood Estimation Handbook", Centre for Ecology & Hydrology (1999, ISBN:0 948540 94 X). "Flood Estimation Handbook Supplementary Report No. 1", Kjeldsen (2007, ISBN:0 903741 15 7). "Regional Frequency Analysis - an approach based on L-moments", Hosking & Wallis (1997, ISBN: 978 0 521 01940 8). "Proposal of the extreme rank plot for extreme value analysis: with an emphasis on flood frequency studies", Hammond (2019, <doi:10.2166/nh.2019.157>). "Making better use of local data in flood frequency estimation", Environment Agency (2017, ISBN: 978 1 84911 387 8). "Improving the FEH statistical procedures for flood frequency estimation", Environment Agency (2008, ISBN: 978 1 84432 920 5). "Low flow estimation in the United Kingdom", Institute of Hydrology (1992, ISBN 0 948540 45 1). Wallingford HydroSolutions, (2016, <http://software.hydrosolutions.co.uk/winfap4/Urban-Adjustment-Procedure-Technical-Note.pdf>). Data from the UK National River Flow Archive (<https://nrfa.ceh.ac.uk/>, terms and conditions: <https://nrfa.ceh.ac.uk/costs-terms-and-conditions>.
Author: Anthony Hammond
Maintainer: Anthony Hammond <agqhammond@gmail.com>
Diff between UKFE versions 0.1.9 dated 2021-10-05 and 0.2.0 dated 2021-10-14
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/All.R | 26 ++++++++++++++++++++++---- data/AMSP.RData |binary data/NRFAData.RData |binary data/QMEDData.RData |binary 6 files changed, 30 insertions(+), 12 deletions(-)
Title: Framework for Specifying and Simulating Individual Based Models
Description: A framework which provides users a set of useful primitive elements for
specifying individual based simulation models, with special attention models for
infectious disease epidemiology. Users build models by specifying variables for
each characteristic of individuals in the simulated population by using data
structures exposed by the package. The package provides efficient methods for
finding subsets of individuals based on these variables, or cohorts. Cohorts can
then be targeted for variable updates or scheduled for events. Variable updates
queued during a time step are executed at the end of a discrete time step, and
the code places no restrictions on how individuals are allowed to interact.
These data structures are designed to provide an intuitive way for users to turn
their conceptual model of a system into executable code, which is fast and
memory efficient.
Author: Giovanni Charles [aut, cre] (<https://orcid.org/0000-0002-7024-1200>),
Sean L. Wu [aut] (<https://orcid.org/0000-0002-5781-9493>),
Peter Winskill [aut] (<https://orcid.org/0000-0003-3001-4959>),
Imperial College of Science, Technology and Medicine [cph]
Maintainer: Giovanni Charles <giovanni.charles@gmail.com>
Diff between individual versions 0.1.4 dated 2021-07-29 and 0.1.6 dated 2021-10-14
individual-0.1.4/individual/tests/testthat/helper-event.R |only individual-0.1.4/individual/tests/testthat/test-variables.R |only individual-0.1.6/individual/DESCRIPTION | 21 individual-0.1.6/individual/MD5 | 83 +- individual-0.1.6/individual/NEWS.md |only individual-0.1.6/individual/R/RcppExports.R | 16 individual-0.1.6/individual/R/bitset.R | 23 individual-0.1.6/individual/R/categorical_variable.R | 6 individual-0.1.6/individual/R/double_variable.R | 42 - individual-0.1.6/individual/R/integer_variable.R | 42 - individual-0.1.6/individual/R/targeted_event.R | 36 - individual-0.1.6/individual/README.md | 91 ++ individual-0.1.6/individual/inst/doc/API.Rmd | 2 individual-0.1.6/individual/inst/doc/API.html | 4 individual-0.1.6/individual/inst/doc/Contributing.Rmd | 2 individual-0.1.6/individual/inst/doc/Contributing.html | 2 individual-0.1.6/individual/inst/doc/Tutorial.R | 2 individual-0.1.6/individual/inst/doc/Tutorial.Rmd | 2 individual-0.1.6/individual/inst/doc/Tutorial.html | 4 individual-0.1.6/individual/inst/include/CategoricalVariable.h | 170 +++-- individual-0.1.6/individual/inst/include/DoubleVariable.h | 222 ++++--- individual-0.1.6/individual/inst/include/Event.h | 314 ++++++--- individual-0.1.6/individual/inst/include/IntegerVariable.h | 316 +++++----- individual-0.1.6/individual/inst/include/IterableBitset.h | 55 + individual-0.1.6/individual/inst/include/Variable.h | 2 individual-0.1.6/individual/man/Bitset.Rd | 16 individual-0.1.6/individual/man/IntegerVariable.Rd | 4 individual-0.1.6/individual/man/TargetedEvent.Rd | 5 individual-0.1.6/individual/man/figures |only individual-0.1.6/individual/src/RcppExports.cpp | 56 + individual-0.1.6/individual/src/bitset.cpp | 22 individual-0.1.6/individual/src/categorical_variable.cpp | 2 individual-0.1.6/individual/src/double_variable.cpp | 13 individual-0.1.6/individual/src/event.cpp | 25 individual-0.1.6/individual/src/integer_variable.cpp | 23 individual-0.1.6/individual/tests/testthat/helper-targetedevent.R |only individual-0.1.6/individual/tests/testthat/test-bitset.R | 79 +- individual-0.1.6/individual/tests/testthat/test-categoricalvariable.R |only individual-0.1.6/individual/tests/testthat/test-cpp.R | 5 individual-0.1.6/individual/tests/testthat/test-doublevariable.R |only individual-0.1.6/individual/tests/testthat/test-events.R | 176 ----- individual-0.1.6/individual/tests/testthat/test-integervariable.R |only individual-0.1.6/individual/tests/testthat/test-simulation-e2e.R | 2 individual-0.1.6/individual/tests/testthat/test-targetedevent.R |only individual-0.1.6/individual/vignettes/API.Rmd | 2 individual-0.1.6/individual/vignettes/Contributing.Rmd | 2 individual-0.1.6/individual/vignettes/Tutorial.Rmd | 2 47 files changed, 1135 insertions(+), 756 deletions(-)
Title: Datasets for Spatial Analysis
Description: Diverse spatial datasets for demonstrating, benchmarking and teaching spatial data analysis.
It includes R data of class sf (defined by the package 'sf'), Spatial ('sp'), and nb ('spdep').
Unlike other spatial data packages such as 'rnaturalearth' and 'maps',
it also contains data stored in a range of file formats including GeoJSON, ESRI Shapefile and GeoPackage.
Some of the datasets are designed to illustrate specific analysis techniques.
cycle_hire() and cycle_hire_osm(), for example, is designed to illustrate point pattern analysis techniques.
Author: Roger Bivand [aut] (<https://orcid.org/0000-0003-2392-6140>),
Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>),
Robin Lovelace [aut] (<https://orcid.org/0000-0001-5679-6536>),
Mark Monmonier [ctb] (author of the state.vbm dataset),
Greg Snow [ctb] (author of the state.vbm dataset)
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between spData versions 0.3.10 dated 2021-06-18 and 2.0.1 dated 2021-10-14
DESCRIPTION | 6 +++--- MD5 | 5 ++++- inst/raster |only 3 files changed, 7 insertions(+), 4 deletions(-)
Title: Parallel GLM
Description: Provides a parallel estimation method for generalized
linear models without compiling with a multithreaded LAPACK or BLAS.
Author: Benjamin Christoffersen [cre, aut]
(<https://orcid.org/0000-0002-7182-1346>),
Anthony Williams [cph],
Boost developers [cph]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>
Diff between parglm versions 0.1.6 dated 2020-08-10 and 0.1.7 dated 2021-10-14
DESCRIPTION | 15 +-- MD5 | 35 +++---- NEWS.md | 18 ++- R/parglm.R | 2 README.md | 2 build/vignette.rds |binary src/LAPACK_wrappers.cpp | 90 +++---------------- src/LAPACK_wrappers.h | 98 +++++++++++++++++++-- src/R_BLAS_LAPACK.cpp | 29 ++++++ src/R_BLAS_LAPACK.h | 4 src/RcppExports.cpp | 5 + src/constant.h |only src/family.cpp | 36 ++++--- src/family.h | 134 +++++++++++++++++------------ src/parallel_glm.cpp | 206 +++++++++++++++++++++++++++------------------ src/parallel_qr.cpp | 55 +++++++++--- src/parallel_qr.h | 7 + src/thread_pool.h | 12 ++ tests/testthat/test_misc.R | 2 19 files changed, 472 insertions(+), 278 deletions(-)
Title: Create, Modify and Visualize Multi-Layered Networks
Description: Allows the user to create graph with multiple layers. The user can also modify the layers, the nodes, and the edges. The graph can also be visualized.
Zaynab Hammoud and Frank Kramer (2018) <doi:10.3390/genes9110519>.
More about multilayered graphs and their usage can be found in our review paper:
Zaynab Hammoud and Frank Kramer (2020) <doi:10.1186/s41044-020-00046-0>.
Author: Zaynab Hammoud
Maintainer: Zaynab Hammoud <zaynabhassanhammoud@gmail.com>
Diff between mully versions 2.1.33 dated 2021-06-02 and 2.1.34 dated 2021-10-14
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/mully_constructor.R | 2 ++ R/mully_import.R | 10 ++++------ R/mully_visualization.R | 18 ++++++++++++++---- inst/doc/mully-pdf.pdf |binary inst/doc/mully-vignette.html | 4 ++-- man/importGraphCSV.Rd | 2 +- 8 files changed, 33 insertions(+), 23 deletions(-)
Title: Mixtures of Exponential-Distance Models with Covariates
Description: Implements a model-based clustering method for categorical life-course sequences relying on mixtures of exponential-distance models introduced by Murphy et al. (2021) <doi:10.1111/rssa.12712>. A range of flexible precision parameter settings corresponding to weighted generalisations of the Hamming distance metric are considered, along with the potential inclusion of a noise component. Gating covariates can be supplied in order to relate sequences to baseline characteristics. Sampling weights are also accommodated. The models are fitted using the EM algorithm and tools for visualising the results are also provided.
Author: Keefe Murphy [aut, cre] (<https://orcid.org/0000-0002-7709-3159>),
Thomas Brendan Murphy [ctb] (<https://orcid.org/0000-0002-5668-7046>),
Raffaella Piccarreta [ctb],
Isobel Claire Gormley [ctb] (<https://orcid.org/0000-0001-7713-681X>)
Maintainer: Keefe Murphy <keefe.murphy@mu.ie>
Diff between MEDseq versions 1.3.0 dated 2021-07-15 and 1.3.1 dated 2021-10-14
DESCRIPTION | 12 - MD5 | 29 +-- NAMESPACE | 4 R/Functions.R | 382 +++++++++++++++++++++++++++++++++++++++++++------- R/Hidden_Functions.R | 34 ++++ R/MEDseq.R | 4 build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.md | 16 +- inst/doc/MEDseq.html | 8 - man/MEDseq-package.Rd | 4 man/MEDseq_compare.Rd | 2 man/MEDseq_control.Rd | 8 - man/plot.MEDseq.Rd | 12 + man/wKModes.Rd |only vignettes/bio_mod.rda |binary 16 files changed, 430 insertions(+), 85 deletions(-)
Title: Cross-Validated Covariance Matrix Estimation
Description: An efficient cross-validated approach for covariance matrix
estimation, particularly useful in high-dimensional settings. This
method relies upon the theory of loss-based estimator selection to
identify the optimal estimator of the covariance matrix from among a
prespecified set of candidates.
Author: Philippe Boileau [aut, cre, cph]
(<https://orcid.org/0000-0002-4850-2507>),
Nima Hejazi [aut] (<https://orcid.org/0000-0002-7127-2789>),
Brian Collica [aut] (<https://orcid.org/0000-0003-1127-2557>),
Jamarcus Liu [ctb],
Mark van der Laan [ctb, ths] (<https://orcid.org/0000-0003-1432-5511>),
Sandrine Dudoit [ctb, ths] (<https://orcid.org/0000-0002-6069-8629>)
Maintainer: Philippe Boileau <philippe_boileau@berkeley.edu>
Diff between cvCovEst versions 1.0.0 dated 2021-07-25 and 1.0.1 dated 2021-10-14
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 5 +++++ R/estimators.R | 8 +++----- R/thresholdingFunctions.R | 31 +++++++++++++------------------ README.md | 25 ++++++++++++++++++++----- build/partial.rdb |binary inst/doc/using_cvCovEst.html | 12 ++++++------ 8 files changed, 57 insertions(+), 44 deletions(-)
Title: Creates Co-Occurrence Matrices of Spatial Data
Description: Builds co-occurrence matrices based on spatial raster data.
It includes creation of weighted co-occurrence matrices (wecoma) and
integrated co-occurrence matrices
(incoma; Vadivel et al. (2007) <doi:10.1016/j.patrec.2007.01.004>).
Author: Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>),
Maximillian H.K. Hesselbarth [ctb] (Co-author of underlying C++ code
for get_class_index_map(), get_unique_values(), and rcpp_get_coma()
functions),
Marco Sciaini [ctb] (Co-author of underlying C++ code for
get_class_index_map(), get_unique_values(), and rcpp_get_coma()
functions),
Sebastian Hanss [ctb] (Co-author of underlying C++ code for
get_class_index_map(), get_unique_values(), and rcpp_get_coma()
functions)
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between comat versions 0.9.1 dated 2021-04-19 and 0.9.2 dated 2021-10-14
DESCRIPTION | 6 +- MD5 | 18 +++---- README.md | 16 +++++- build/vignette.rds |binary inst/doc/coma.html | 4 - inst/doc/incoma.html | 4 - inst/doc/wecoma.html | 4 - inst/include/comat_RcppExports.h | 63 +++++++++++++++++++++++++ src/RcppExports.cpp | 98 +++++++++++++++++++++++++++++++++++---- src/create_neighborhood.cpp | 6 -- 10 files changed, 187 insertions(+), 32 deletions(-)
Title: Statistical Methods for Phenology Analysis in Temperate Fruit
Trees
Description: The phenology of plants (i.e. the timing of their annual life
phases) depends on climatic cues. For temperate trees and many other plants,
spring phases, such as leaf emergence and flowering, have been found to result
from the effects of both cool (chilling) conditions and heat. Fruit tree
scientists (pomologists) have developed some metrics to quantify chilling
and heat (e.g. see Luedeling (2012) <doi:10.1016/j.scienta.2012.07.011>).
'chillR' contains functions for processing temperature records into
chilling (Chilling Hours, Utah Chill Units and Chill Portions) and heat units
(Growing Degree Hours). Regarding chilling metrics, Chill Portions are often
considered the most promising, but they are difficult to calculate. This package
makes it easy. 'chillR' also contains procedures for conducting a PLS analysis
relating phenological dates (e.g. bloom dates) to either mean temperatures or
mean chill and heat accumulation rates, based on long-term weather and phenology
records (Luedeling and Gassner (2012) <doi:10.1016/j.agrformet.2011.10.020>).
As of version 0.65, it also includes functions for generating weather
scenarios with a weather generator, for conducting climate change analyses
for temperature-based climatic metrics and for plotting results from such
analyses. Since version 0.70, 'chillR' contains a function for interpolating
hourly temperature records.
Author: Eike Luedeling [aut, cre] (<https://orcid.org/0000-0002-7316-3631>)
Maintainer: Eike Luedeling <eike@eikeluedeling.com>
Diff between chillR versions 0.72.4 dated 2021-05-13 and 0.72.5 dated 2021-10-14
DESCRIPTION | 12 ++-- MD5 | 20 +++--- NAMESPACE | 1 R/daylength.R | 4 - R/temperature_generation.R | 1 inst/doc/PhenoFlex.html | 61 ++++++++++---------- inst/doc/hourly_temperatures.html | 114 +++++++++++++++++++------------------- src/RcppExports.cpp | 5 + tests/testthat/test_PhenoFlex.R | 2 tests/testthat/test_chifull.R | 2 vignettes/Chilling_references.bib | 2 11 files changed, 115 insertions(+), 109 deletions(-)
Title: Rational Approximations of Fractional Stochastic Partial
Differential Equations
Description: Functions that compute rational approximations of fractional elliptic stochastic partial differential equations. The package also contains functions for common statistical usage of these approximations. The main reference for the methods is Bolin and Kirchner (2020) <doi:10.1080/10618600.2019.1665537>, which can be generated by the citation function in R.
Author: David Bolin [cre, aut]
Maintainer: David Bolin <davidbolin@gmail.com>
Diff between rSPDE versions 0.6.2 dated 2021-02-23 and 0.6.3 dated 2021-10-14
rSPDE-0.6.2/rSPDE/R/factional.computations.R |only rSPDE-0.6.2/rSPDE/R/factional.operators.R |only rSPDE-0.6.2/rSPDE/vignettes/rspde.bib |only rSPDE-0.6.3/rSPDE/DESCRIPTION | 8 rSPDE-0.6.3/rSPDE/MD5 | 23 rSPDE-0.6.3/rSPDE/NEWS.md | 3 rSPDE-0.6.3/rSPDE/R/fractional.computations.R |only rSPDE-0.6.3/rSPDE/R/fractional.operators.R |only rSPDE-0.6.3/rSPDE/build/vignette.rds |binary rSPDE-0.6.3/rSPDE/inst/doc/rspde.Rmd | 36 + rSPDE-0.6.3/rSPDE/inst/doc/rspde.html | 710 +++++++++++--------------- rSPDE-0.6.3/rSPDE/man/fractional.operators.Rd | 2 rSPDE-0.6.3/rSPDE/man/matern.operators.Rd | 2 rSPDE-0.6.3/rSPDE/man/rSPDE.loglike.Rd | 9 rSPDE-0.6.3/rSPDE/vignettes/rspde.Rmd | 36 + 15 files changed, 396 insertions(+), 433 deletions(-)
Title: Projection Pursuit Classification Forest
Description: Implements projection pursuit forest algorithm for supervised classification.
Author: Natalia da Silva, Eun-Kyung Lee, Di Cook
Maintainer: Natalia da Silva <natalia.dasilva@fcea.edu.uy>
Diff between PPforest versions 0.1.1 dated 2018-06-11 and 0.1.2 dated 2021-10-14
DESCRIPTION | 8 MD5 | 24 +- NEWS.md | 6 R/PPforest.R | 40 ++- R/trees_pred.R | 15 - build/vignette.rds |binary inst/doc/PPforest-vignette.R | 30 +- inst/doc/PPforest-vignette.Rmd | 23 +- inst/doc/PPforest-vignette.html | 444 +++++++++++++++------------------------- man/PPforest.Rd | 7 man/trees_pred.Rd | 6 src/RcppExports.cpp | 5 vignettes/PPforest-vignette.Rmd | 23 +- 13 files changed, 276 insertions(+), 355 deletions(-)
Title: 'DataSHIELD' Client for 'MOLGENIS Armadillo'
Description: 'DataSHIELD' is an infrastructure and series of R packages that
enables the remote and 'non-disclosive' analysis of sensitive research data.
This package is the 'DataSHIELD' interface implementation to analyze data
shared on a 'MOLGENIS Armadillo' server. 'MOLGENIS Armadillo' is a
light-weight 'DataSHIELD' server using a file store and an 'RServe' server.
Author: Sido Haakma [aut, cre] (<https://orcid.org/0000-0003-1278-9144>),
Tommy de Boer [aut] (<https://orcid.org/0000-0002-4492-7225>),
Fleur Kelpin [aut] (<https://orcid.org/0000-0003-1527-5130>),
MOLGENIS org [cph, fnd]
Maintainer: Sido Haakma <s.haakma@rug.nl>
Diff between DSMolgenisArmadillo versions 1.3.6 dated 2021-10-12 and 1.3.7 dated 2021-10-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 8 ++++++++ R/ArmadilloResult.R | 3 ++- tests/testthat/test-ArmadilloResult.R | 22 ++++++++++++++++++++++ 5 files changed, 39 insertions(+), 8 deletions(-)
More information about DSMolgenisArmadillo at CRAN
Permanent link
Title: Tools for CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable monitoring of the climate
system by providing essential climate variables related to the energy and water
cycle of the atmosphere (<http://www.cmsaf.eu>). It is a joint cooperation of eight
National Meteorological and Hydrological Services.
The 'cmsafops' R-package provides a collection of R-operators for the analysis and
manipulation of CM SAF NetCDF formatted data. Other CF conform NetCDF data with time,
longitude and latitude dimension should be applicable, but there is no guarantee for
an error-free application.
CM SAF climate data records are provided for free via (<https://wui.cmsaf.eu/safira>).
Detailed information and test data are provided on the CM SAF webpage
(<http://www.cmsaf.eu/R_toolbox>).
Author: Steffen Kothe [aut, cre],
Danny Parsons [ctb]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsafops versions 1.2.0 dated 2021-09-06 and 1.2.1 dated 2021-10-14
DESCRIPTION | 19 MD5 | 609 +++++++++++++++---------------- NAMESPACE | 1 NEWS.md | 4 R/arith_wrapper.R | 20 - R/arithc_wrapper.R | 226 +++++------ R/calc_field.R | 73 +-- R/calc_overlapping_time.R | 319 ++++++++-------- R/calc_timx_result.R | 14 R/calc_trend.R | 141 +++---- R/calc_trend_advanced.R | 251 ++++++------ R/check_infile.R | 18 R/cmsaf.abs.R | 298 +++++++-------- R/cmsaf.add.R | 8 R/cmsaf.addc.R | 6 R/cmsaf.adjust.two.files.R | 36 + R/cmsaf.detrend.R | 14 R/cmsaf.div.R | 8 R/cmsaf.divc.R | 6 R/cmsaf.mk.test.R | 13 R/cmsaf.mul.R | 8 R/cmsaf.mulc.R | 6 R/cmsaf.regres.R | 14 R/cmsaf.stats.R | 13 R/cmsaf.stats.station.data.R | 422 ++++++++++----------- R/cmsaf.sub.R | 8 R/cmsaf.sub.rel.R | 24 - R/cmsaf.subc.R | 6 R/cmsaf.transform.coordinate.system.R | 217 +++++------ R/dayavg.R | 130 +++--- R/daymax.R | 122 +++--- R/daymean.R | 130 +++--- R/daymin.R | 6 R/daypctl.R | 6 R/dayrange.R | 14 R/daysd.R | 6 R/daysum.R | 120 +++--- R/dayvar.R | 6 R/dayx_wrapper.R | 302 +++++++-------- R/divdpm.R | 6 R/extract.level.R | 15 R/extract.period.R | 15 R/fld_cor_covar_wrapper.R | 284 +++++++------- R/fldcor.R | 8 R/fldcovar.R | 8 R/fldmax.R | 6 R/fldmean.R | 6 R/fldmin.R | 6 R/fldrange.R | 6 R/fldsd.R | 124 +++--- R/fldsum.R | 6 R/fldx_wrapper.R | 210 +++++----- R/getTimeRange.R | 77 +-- R/get_basename.R |only R/get_climatology.R | 57 +- R/get_time_bnds_from_file.R | 16 R/gridboxmax.R | 6 R/gridboxmean.R | 6 R/gridboxmin.R | 6 R/gridboxrange.R | 6 R/gridboxsd.R | 6 R/gridboxsum.R | 6 R/gridboxvar.R | 6 R/gridboxx_wrapper.R | 556 ++++++++++++++-------------- R/hourmean.R | 122 +++--- R/hoursum.R | 6 R/hourx_wrapper.R | 237 ++++++------ R/is_url.R |only R/mermean.R | 6 R/merx_wrapper.R | 217 +++++------ R/mon.anomaly.R | 18 R/mon.anomaly.climatology.R | 355 +++++++++--------- R/mon_num_above.R | 6 R/mon_num_below.R | 6 R/mon_num_equal.R | 6 R/mon_num_wrapper.R | 11 R/monavg.R | 6 R/mondaymean.R | 393 ++++++++++---------- R/monmax.R | 6 R/monmean.R | 6 R/monmin.R | 6 R/monpctl.R | 6 R/monsd.R | 6 R/monsum.R | 6 R/monvar.R | 6 R/monx_wrapper.R | 340 ++++++++--------- R/muldpm.R | 6 R/multimonmean.R | 13 R/multimonsum.R | 13 R/ncinfo.R | 9 R/num_above.R | 6 R/num_below.R | 6 R/num_equal.R | 6 R/num_wrapper.R | 11 R/read_file.R | 161 ++++---- R/read_file_all.R | 143 +++---- R/read_ncvar.R | 13 R/remap.R | 21 - R/runmax.R | 6 R/runmean.R | 6 R/runmin.R | 128 +++--- R/runrange.R | 6 R/runsd.R | 6 R/runsum.R | 6 R/runx_wrapper.R | 309 +++++++-------- R/seas.anomaly.R | 14 R/seasmean.R | 6 R/seassd.R | 6 R/seassum.R | 6 R/seasvar.R | 128 +++--- R/seasx_wrapper.R | 321 ++++++++-------- R/sellonlatbox.R | 18 R/selmon.R | 15 R/selperiod.R | 353 +++++++++-------- R/selpoint.R | 20 - R/selpoint.multi.R | 29 - R/seltime.R | 15 R/selyear.R | 15 R/tim_cor_covar_wrapper.R | 20 - R/timavg.R | 6 R/timcor.R | 8 R/timcovar.R | 8 R/timcumsum.R | 25 - R/timmax.R | 6 R/timmean.R | 6 R/timmin.R | 6 R/timpctl.R | 6 R/timsd.R | 6 R/timselmean.R | 6 R/timselsum.R | 6 R/timselx_wrapper.R | 11 R/timsum.R | 6 R/timx_wrapper.R | 164 ++++---- R/trend.R | 10 R/trend_advanced.R | 16 R/wfldmean.R | 7 R/xdpm_wrapper.R | 243 ++++++------ R/ydaymax.R | 6 R/ydaymean.R | 14 R/ydaymin.R | 6 R/ydayrange.R | 6 R/ydaysd.R | 6 R/ydaysum.R | 6 R/ydayx_wrapper.R | 268 ++++++------- R/ydrunmean.R | 6 R/ydrunsd.R | 6 R/ydrunsum.R | 6 R/ydrunx_wrapper.R | 97 ++-- R/year.anomaly.R | 16 R/yearmax.R | 124 +++--- R/yearmean.R | 14 R/yearmin.R | 122 +++--- R/yearrange.R | 6 R/yearsd.R | 6 R/yearsum.R | 13 R/yearvar.R | 122 +++--- R/yearx_wrapper.R | 257 ++++++------- R/ymonmax.R | 6 R/ymonmean.R | 6 R/ymonmin.R | 6 R/ymonsd.R | 6 R/ymonsum.R | 6 R/ymonx_wrapper.R | 258 ++++++------- R/yseasmax.R | 6 R/yseasmean.R | 6 R/yseasmin.R | 6 R/yseassd.R | 6 R/yseasx_wrapper.R | 256 ++++++------- R/zonmean.R | 124 +++--- R/zonsum.R | 124 +++--- R/zonx_wrapper.R | 229 +++++------ build/partial.rdb |binary inst/WORDLIST | 1 man/calc_overlapping_time.Rd | 15 man/cmsaf.abs.Rd | 13 man/cmsaf.add.Rd | 10 man/cmsaf.addc.Rd | 6 man/cmsaf.adjust.two.files.Rd | 10 man/cmsaf.detrend.Rd | 6 man/cmsaf.div.Rd | 10 man/cmsaf.divc.Rd | 6 man/cmsaf.mk.test.Rd | 6 man/cmsaf.mul.Rd | 10 man/cmsaf.mulc.Rd | 6 man/cmsaf.regres.Rd | 6 man/cmsaf.stats.Rd | 10 man/cmsaf.stats.station.data.Rd | 12 man/cmsaf.sub.Rd | 10 man/cmsaf.sub.rel.Rd | 10 man/cmsaf.subc.Rd | 6 man/cmsaf.transform.coordinate.system.Rd | 5 man/dayavg.Rd | 13 man/daymax.Rd | 13 man/daymean.Rd | 13 man/daymin.Rd | 13 man/daypctl.Rd | 6 man/dayrange.Rd | 13 man/daysd.Rd | 13 man/daysum.Rd | 13 man/dayvar.Rd | 13 man/divdpm.Rd | 13 man/extract.level.Rd | 6 man/extract.period.Rd | 6 man/fldcor.Rd | 10 man/fldcovar.Rd | 10 man/fldmax.Rd | 13 man/fldmean.Rd | 13 man/fldmin.Rd | 13 man/fldrange.Rd | 13 man/fldsd.Rd | 13 man/fldsum.Rd | 13 man/get_basename.Rd |only man/gridboxmax.Rd | 6 man/gridboxmean.Rd | 6 man/gridboxmin.Rd | 6 man/gridboxrange.Rd | 6 man/gridboxsd.Rd | 6 man/gridboxsum.Rd | 6 man/gridboxvar.Rd | 6 man/hourmean.Rd | 13 man/hoursum.Rd | 13 man/mermean.Rd | 13 man/mon.anomaly.Rd | 13 man/mon.anomaly.climatology.Rd | 6 man/mon_num_above.Rd | 6 man/mon_num_below.Rd | 6 man/mon_num_equal.Rd | 6 man/monavg.Rd | 13 man/mondaymean.Rd | 13 man/monmax.Rd | 13 man/monmean.Rd | 13 man/monmin.Rd | 13 man/monpctl.Rd | 6 man/monsd.Rd | 13 man/monsum.Rd | 13 man/monvar.Rd | 13 man/muldpm.Rd | 13 man/multimonmean.Rd | 6 man/multimonsum.Rd | 6 man/ncinfo.Rd | 123 +++--- man/num_above.Rd | 6 man/num_below.Rd | 6 man/num_equal.Rd | 6 man/read_file.Rd | 5 man/read_ncvar.Rd | 5 man/remap.Rd | 10 man/runmax.Rd | 6 man/runmean.Rd | 6 man/runmin.Rd | 6 man/runrange.Rd | 6 man/runsd.Rd | 6 man/runsum.Rd | 6 man/seas.anomaly.Rd | 6 man/seasmean.Rd | 13 man/seassd.Rd | 13 man/seassum.Rd | 13 man/seasvar.Rd | 13 man/sellonlatbox.Rd | 6 man/selmon.Rd | 6 man/selperiod.Rd | 6 man/selpoint.Rd | 6 man/selpoint.multi.Rd | 6 man/seltime.Rd | 6 man/selyear.Rd | 6 man/timavg.Rd | 13 man/timcor.Rd | 10 man/timcovar.Rd | 10 man/timcumsum.Rd | 6 man/timmax.Rd | 13 man/timmean.Rd | 13 man/timmin.Rd | 13 man/timpctl.Rd | 6 man/timsd.Rd | 13 man/timselmean.Rd | 6 man/timselsum.Rd | 6 man/timsum.Rd | 13 man/trend.Rd | 6 man/trend_advanced.Rd | 10 man/wfldmean.Rd | 13 man/ydaymax.Rd | 13 man/ydaymean.Rd | 13 man/ydaymin.Rd | 13 man/ydayrange.Rd | 13 man/ydaysd.Rd | 13 man/ydaysum.Rd | 13 man/ydrunmean.Rd | 6 man/ydrunsd.Rd | 6 man/ydrunsum.Rd | 6 man/year.anomaly.Rd | 6 man/yearmax.Rd | 13 man/yearmean.Rd | 13 man/yearmin.Rd | 13 man/yearrange.Rd | 13 man/yearsd.Rd | 13 man/yearsum.Rd | 13 man/yearvar.Rd | 13 man/ymonmax.Rd | 13 man/ymonmean.Rd | 13 man/ymonmin.Rd | 13 man/ymonsd.Rd | 13 man/ymonsum.Rd | 13 man/yseasmax.Rd | 13 man/yseasmean.Rd | 13 man/yseasmin.Rd | 13 man/yseassd.Rd | 13 man/zonmean.Rd | 13 man/zonsum.Rd | 13 307 files changed, 7144 insertions(+), 5686 deletions(-)
Title: A Toolbox for CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable monitoring of the climate
system by providing essential climate variables related to the energy and water
cycle of the atmosphere (<http://www.cmsaf.eu>). It is a joint cooperation of eight
National Meteorological and Hydrological Services.
The 'cmsaf' R-package includes a 'shiny' based interface for an easy application of
the 'cmsafops' and 'cmsafvis' packages - the CM SAF R Toolbox. The Toolbox offers an
easy way to prepare, manipulate, analyse and visualize CM SAF NetCDF formatted data.
Other CF conform NetCDF data with time, longitude and latitude dimension should be
applicable, but there is no guarantee for an error-free application.
CM SAF climate data records are provided for free via (<https://wui.cmsaf.eu/safira>).
Detailed information and test data are provided on the CM SAF webpage
(<http://www.cmsaf.eu/R_toolbox>).
Author: Steffen Kothe [aut, cre],
Danny Parsons [ctb]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsaf versions 3.2.0 dated 2021-09-06 and 3.3.0 dated 2021-10-14
DESCRIPTION | 23 - MD5 | 14 NEWS.md | 4 build/partial.rdb |binary inst/toolbox/global.R | 2 inst/toolbox/server.R | 923 +++++++++++++++++++++++++++++++++++++++------ inst/toolbox/ui.R | 108 ++++- inst/toolbox/www/style.css | 532 ++++++++++++------------- 8 files changed, 1211 insertions(+), 395 deletions(-)
Title: Moment Condition Based Estimation of Linear Dynamic Panel Data
Models
Description: Linear dynamic panel data modeling based on linear and
nonlinear moment conditions as proposed by
Holtz-Eakin, Newey, and Rosen (1988) <doi:10.2307/1913103>,
Ahn and Schmidt (1995) <doi:10.1016/0304-4076(94)01641-C>,
and Arellano and Bover (1995) <doi:10.1016/0304-4076(94)01642-D>.
Estimation of the model parameters relies on the Generalized
Method of Moments (GMM), numerical optimization (when nonlinear
moment conditions are employed) and the computation of closed
form solutions (when estimation is based on linear moment
conditions). One-step, two-step and iterated estimation is
available. of closed form solutions. For inference and specification
testing, Windmeijer (2005) <doi:10.1016/j.jeconom.2004.02.005>
and doubly corrected standard errors
(Hwang, Kang, Lee, 2021 <doi:10.1016/j.jeconom.2020.09.010>)
are available. Additionally, serial correlation tests, tests for
overidentification, and Wald tests are provided. Functions for
visualizing panel data structures and modeling results obtained
from GMM estimation are also available. The plot methods include
functions to plot unbalanced panel structure, coefficient ranges
and coefficient paths across GMM iterations (the latter is
implemented according to the plot shown in
Hansen and Lee, 2021 <doi:10.3982/ECTA16274>).
Author: Markus Fritsch [aut, cre],
Joachim Schnurbus [aut],
Andrew Adrian Yu Pua [aut]
Maintainer: Markus Fritsch <Markus.Fritsch@uni-Passau.de>
Diff between pdynmc versions 0.9.5 dated 2021-08-13 and 0.9.6 dated 2021-10-14
DESCRIPTION | 16 MD5 | 72 +-- NAMESPACE | 124 ++--- NEWS.md | 30 + R/pdynmc_estFct.R | 136 ++++-- R/pdynmc_specTestFcst.R | 53 +- README.md | 5 build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 2 inst/doc/pdynmc-intro.pdf |binary inst/doc/pdynmc-introLong.pdf |binary inst/doc/pdynmc-pres-in-a-nutshell.pdf |binary inst/tests/arguments_for_StepByStepFunctionChecksABdata.R | 6 inst/tests/arguments_for_StepByStepFunctionChecksMaxG.R |only man/case.names.pdynmc.Rd | 152 +++--- man/coef.pdynmc.Rd | 150 +++--- man/data.info.Rd | 102 ++-- man/dummy.coef.pdynmc.Rd | 150 +++--- man/fitted.pdynmc.Rd | 164 +++---- man/model.matrix.pdynmc.Rd | 152 +++--- man/mtest.fct.Rd | 14 man/ninst.Rd | 146 +++--- man/ninst.pdynmc.Rd | 146 +++--- man/optimIn.Rd | 152 +++--- man/optimIn.pdynmc.Rd | 158 +++---- man/pdynmc.Rd | 14 man/plot.pdynmc.Rd | 310 +++++++------- man/print.pdynmc.Rd | 152 +++--- man/print.summary.pdynmc.Rd | 166 +++---- man/residuals.pdynmc.Rd | 164 +++---- man/summary.pdynmc.Rd | 146 +++--- man/variable.names.pdynmc.Rd | 148 +++--- man/vcov.pdynmc.Rd | 156 +++---- man/wald.fct.Rd | 8 man/wmat.Rd | 148 +++--- man/wmat.pdynmc.Rd | 156 +++---- tests/testthat/test-stdErr.R |only 38 files changed, 1804 insertions(+), 1694 deletions(-)
Title: Linguistic Typology and Mapping
Description: Provides R with the Glottolog database <https://glottolog.org/> and some more abilities for purposes of linguistic mapping. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <https://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://docs.ropensci.org/lingtypology/> and package vignette. Maps created by this package can be used both for the investigation and linguistic teaching. In addition, package provides an ability to download data from typological databases such as WALS, AUTOTYP and some others and to create your own database website.
Author: George Moroz [aut, cre] (<https://orcid.org/0000-0003-1990-6083>),
Kirill Koncha [ctb] (<https://orcid.org/0000-0003-0676-2658>),
Mikhail Leonov [ctb],
Anna Smirnova [ctb]
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between lingtypology versions 1.1.5 dated 2021-05-15 and 1.1.6 dated 2021-10-14
DESCRIPTION | 10 +- MD5 | 110 +++++++++++++------------ NAMESPACE | 4 NEWS | 15 ++- R/aff.lang.R | 4 R/area.lang.R | 4 R/bantu.R |only R/bantu.feature.R |only R/country.lang.R |only R/eurasianphonology.R | 2 R/eurasianphonology.feature.R | 2 R/glottolog.R | 12 +- R/gltc.lang.R | 2 R/is.glottolog.R | 2 R/iso.lang.R | 2 R/lang.aff.R | 2 R/lang.gltc.R | 2 R/lang.iso.R | 2 R/lat.lang.R | 4 R/long.lang.R | 4 R/soundcomparisons.feature.R | 3 R/subc.lang.R |only R/url.lang.R | 3 build/vignette.rds |binary data/bantu.RData |only data/glottolog.RData |binary inst/doc/lingtypology_creating_maps.Rmd | 4 inst/doc/lingtypology_creating_maps.html | 8 - inst/doc/lingtypology_db_API.html | 4 inst/doc/lingtypology_dplyr.html | 4 inst/doc/lingtypology_glottolog_functions.R | 11 ++ inst/doc/lingtypology_glottolog_functions.Rmd | 32 ++++++- inst/doc/lingtypology_glottolog_functions.html | 41 +++++++-- inst/doc/lingtypology_intro.Rmd | 2 inst/doc/lingtypology_intro.html | 6 - man/aff.lang.Rd | 4 man/area.lang.Rd | 4 man/bantu.Rd |only man/bantu.feature.Rd |only man/country.lang.Rd |only man/eurasianphonology.Rd | 2 man/eurasianphonology.feature.Rd | 2 man/glottolog.Rd | 12 +- man/gltc.lang.Rd | 2 man/is.glottolog.Rd | 2 man/iso.lang.Rd | 2 man/lang.aff.Rd | 2 man/lang.gltc.Rd | 2 man/lang.iso.Rd | 2 man/lat.lang.Rd | 4 man/long.lang.Rd | 4 man/subc.lang.Rd |only man/url.lang.Rd | 5 - tests/testthat/test-aff-lang.R | 4 tests/testthat/test-bantu-feature.R |only tests/testthat/test-country-lang.R |only tests/testthat/test-lang-aff.R | 15 +-- tests/testthat/test-mapfeature.R | 1 tests/testthat/test-subc-lang.R |only vignettes/lingtypology_creating_maps.Rmd | 4 vignettes/lingtypology_glottolog_functions.Rmd | 32 ++++++- vignettes/lingtypology_intro.Rmd | 2 62 files changed, 260 insertions(+), 148 deletions(-)
Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model
(Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>;
Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>). Both Cayley, footrule,
Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be
analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well
as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the
posterior distributions of parameters are provided. The package also provides functions for estimating
the partition function (normalizing constant) of the Mallows rank model, both with the importance
sampling algorithm of Vitelli et al. and asymptotic approximation with the IPFP algorithm
(Mukherjee, Annals of Statistics, 2016 <doi:10.1214/15-AOS1389>).
Author: Oystein Sorensen [aut, cre] (<https://orcid.org/0000-0003-0724-3542>),
Valeria Vitelli [aut] (<https://orcid.org/0000-0002-6746-0453>),
Marta Crispino [aut],
Qinghua Liu [aut],
Cristina Mollica [aut],
Luca Tardella [aut]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between BayesMallows versions 1.0.2 dated 2021-06-04 and 1.0.3 dated 2021-10-14
DESCRIPTION | 8 MD5 | 246 ++--- NAMESPACE | 58 - NEWS.md | 283 +++--- R/BayesMallows.R | 64 - R/RcppExports.R | 386 ++++----- R/all_topological_sorts.R | 44 - R/assess_convergence.R | 396 ++++----- R/assign_cluster.R | 164 +-- R/compute_consensus.R | 414 ++++----- R/compute_mallows.R | 848 ++++++++++---------- R/compute_mallows_mixtures.R | 90 +- R/compute_posterior_intervals.R | 256 +++--- R/data.R | 62 - R/estimate_partition_function.R | 214 ++--- R/expected_dist.R | 108 +- R/generate_constraints.R | 162 +-- R/generate_initial_ranking.R | 312 +++---- R/generate_transitive_closure.R | 214 ++--- R/label_switching.R | 42 R/lik_db_mix.R | 146 +-- R/misc.R | 144 +-- R/misc_expected_dist.R | 222 ++--- R/misc_likelihood.R | 151 +-- R/obs_freq.R | 24 R/plot.BayesMallows.R | 282 +++--- R/plot_elbow.R | 134 +-- R/plot_top_k.R | 168 +-- R/predict_top_k.R | 126 +- R/print.BayesMallows.R | 52 - R/print.BayesMallowsMixtures.R | 58 - R/rank_conversion.R | 178 ++-- R/rank_distance.R | 80 - R/rank_freq_distr.R | 56 - R/sample_mallows.R | 284 +++--- R/tidy_mcmc.R | 506 +++++------ build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 30 inst/REFERENCES.bib | 552 ++++++------- inst/doc/BayesMallows.pdf.asis | 4 inst/examples/compute_consensus_example.R | 128 +-- inst/examples/compute_mallows_example.R | 240 ++--- inst/examples/compute_mallows_mixtures_example.R | 122 +- inst/examples/compute_posterior_intervals_example.R | 56 - inst/examples/estimate_partition_function_example.R | 130 +-- inst/examples/expected_dist_example.R | 12 inst/examples/generate_constraints_example.R | 42 inst/examples/generate_initial_ranking_example.R | 148 +-- inst/examples/generate_transitive_closure_example.R | 106 +- inst/examples/label_switching_example.R | 150 +-- inst/examples/lik_db_mix_example.R | 96 +- inst/examples/obs_freq_example.R | 230 ++--- inst/examples/plot.BayesMallows_example.R | 98 +- inst/examples/plot_top_k_example.R | 42 inst/examples/rank_distance_example.R | 30 inst/examples/rank_freq_distr_example.R | 12 inst/examples/sample_mallows_example.R | 98 +- man/BayesMallows.Rd | 66 - man/assess_convergence.Rd | 76 - man/assign_cluster.Rd | 90 +- man/asymptotic_partition_function.Rd | 82 - man/beach_preferences.Rd | 38 man/compute_consensus.Rd | 214 ++--- man/compute_importance_sampling_estimate.Rd | 56 - man/compute_mallows.Rd | 726 ++++++++--------- man/compute_mallows_mixtures.Rd | 180 ++-- man/compute_posterior_intervals.Rd | 154 +-- man/dot-generate_transitive_closure.Rd | 32 man/estimate_partition_function.Rd | 270 +++--- man/expected_dist.Rd | 58 - man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/generate_constraints.Rd | 112 +- man/generate_initial_ranking.Rd | 310 +++---- man/generate_transitive_closure.Rd | 204 ++-- man/get_partition_function.Rd | 76 - man/get_rank_distance.Rd | 68 - man/label_switching.Rd | 198 ++-- man/lik_db_mix.Rd | 190 ++-- man/log_expected_dist.Rd | 50 - man/obs_freq.Rd | 260 +++--- man/plot.BayesMallows.Rd | 162 +-- man/plot_elbow.Rd | 188 ++-- man/plot_top_k.Rd | 116 +- man/potato_true_ranking.Rd | 38 man/potato_visual.Rd | 42 man/potato_weighing.Rd | 42 man/predict_top_k.Rd | 64 - man/print.BayesMallows.Rd | 34 man/print.BayesMallowsMixtures.Rd | 34 man/rank_conversion.Rd | 120 +- man/rank_distance.Rd | 106 +- man/rank_freq_distr.Rd | 60 - man/rmallows.Rd | 94 +- man/run_mcmc.Rd | 218 ++--- man/sample_mallows.Rd | 238 ++--- man/sushi_rankings.Rd | 40 man/validate_permutation.Rd | 36 src/RcppExports.cpp | 5 src/run_mcmc.cpp | 3 tests/testthat.R | 10 tests/testthat/test_assess_convergence.R | 28 tests/testthat/test_compute_consensus.R | 325 +++---- tests/testthat/test_compute_mallows.R | 357 ++++---- tests/testthat/test_distance_function.R | 224 ++--- tests/testthat/test_estimate_partition_function.R | 88 +- tests/testthat/test_expected_dist.R | 30 tests/testthat/test_generate_ranking.R | 136 +-- tests/testthat/test_lik_db_mix.R | 122 +- tests/testthat/test_mcmc_function.R | 80 - tests/testthat/test_misc_cpp.R | 102 +- tests/testthat/test_misc_functions.R | 46 - tests/testthat/test_partition_function.R | 242 ++--- tests/testthat/test_plot.R | 20 tests/testthat/test_plot_elbow.R | 24 tests/testthat/test_plot_top_k.R | 166 +-- tests/testthat/test_print.R | 40 tests/testthat/test_random_number_seed.R | 100 +- tests/testthat/test_rank_conversion.R | 52 - tests/testthat/test_rank_freq_distr.R | 122 +- tests/testthat/test_sample_mallows.R | 68 - tests/testthat/test_transitive_closure.R | 100 +- vignettes/BayesMallows.pdf.asis | 4 124 files changed, 8457 insertions(+), 8487 deletions(-)
Title: Computation and Plots of Influence Functions for Risk and
Performance Measures
Description: Computes the influence functions time series of the returns for the risk and
performance measures as mentioned in Chen and Martin (2018)
<https://www.ssrn.com/abstract=3085672>, as well as in Zhang et al. (2019)
<https://www.ssrn.com/abstract=3415903>. Also evaluates estimators influence
functions at a set of parameter values and plots them to display the shapes of
the influence functions.
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>,
Shengyu Zhang <syzhang@uw.edu>,
Douglas Martin <doug@amath.washington.edu>
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between RPEIF versions 1.2.3 dated 2021-06-09 and 1.2.4 dated 2021-10-14
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- NAMESPACE | 2 +- NEWS.md | 3 +++ README.md | 2 +- build/vignette.rds |binary 6 files changed, 17 insertions(+), 14 deletions(-)
Title: Administrative Boundaries of Spain
Description: Administrative Boundaries of Spain at several levels
(Autonomous Communities, Provinces, Municipalities) based on the
'GISCO' 'Eurostat' database <https://ec.europa.eu/eurostat/web/gisco>
and 'CartoBase SIANE' from 'Instituto Geografico Nacional'
<https://www.ign.es/>. It also provides a 'leaflet' plugin and the
ability of downloading and processing static tiles.
Author: Diego Hernangómez [aut, cre, cph]
(<https://orcid.org/0000-0001-8457-4658>, rOpenSpain)
Maintainer: Diego Hernangómez <diego.hernangomezherrero@gmail.com>
Diff between mapSpain versions 0.3.1 dated 2021-09-10 and 0.4.0 dated 2021-10-14
DESCRIPTION | 49 ++--- MD5 | 159 +++++++++--------- NAMESPACE | 2 NEWS.md | 32 ++- R/addProviderEspTiles.R | 8 R/data.R | 12 - R/esp_cache.R | 20 +- R/esp_cache_clear.R | 8 R/esp_check_access.R |only R/esp_getTiles.R | 174 +++++++++++++------- R/esp_get_can_box.R | 59 +++--- R/esp_get_capimun.R | 22 +- R/esp_get_ccaa.R | 47 +---- R/esp_get_country.R | 12 + R/esp_get_gridmap.R | 2 R/esp_get_hydrobasin.R | 29 +-- R/esp_get_hypsobath.R | 55 ++++-- R/esp_get_munic.R | 40 ++-- R/esp_get_nuts.R | 75 +++----- R/esp_get_prov.R | 39 +++- R/esp_get_railway.R | 32 ++- R/esp_get_rivers.R | 34 ++- R/esp_get_roads.R | 25 +- R/layer_spatraster.R |only R/utils_siane.R | 198 ++++++++++------------- R/utils_tiles.R | 82 +++++---- README.md | 155 +++++++++--------- inst/WORDLIST | 4 inst/doc/mapSpain.R | 198 ++++++++++++----------- inst/doc/mapSpain.Rmd | 222 +++++++++++++------------- inst/doc/mapSpain.html | 256 +++++++++++++++--------------- inst/examples/esp_get_gridmap.R | 68 ++++--- inst/examples/esp_munic_sf.R | 37 ++-- inst/examples/esp_nuts_sf.R | 33 +-- man/addProviderEspTiles.Rd | 1 man/esp_check_access.Rd |only man/esp_clear_cache.Rd | 2 man/esp_codelist.Rd | 4 man/esp_getTiles.Rd | 20 +- man/esp_get_can_box.Rd | 59 +++--- man/esp_get_capimun.Rd | 26 +-- man/esp_get_ccaa.Rd | 33 +-- man/esp_get_country.Rd | 12 + man/esp_get_gridmap.Rd | 87 ++++------ man/esp_get_hydrobasin.Rd | 29 +-- man/esp_get_hypsobath.Rd | 55 ++++-- man/esp_get_munic.Rd | 40 ++-- man/esp_get_nuts.Rd | 77 ++++----- man/esp_get_prov.Rd | 39 +++- man/esp_get_railway.Rd | 32 ++- man/esp_get_rivers.Rd | 34 ++- man/esp_get_roads.Rd | 25 +- man/esp_munic.sf.Rd | 37 ++-- man/esp_nuts.sf.Rd | 33 +-- man/figures/lifecycle-experimental.svg |only man/layer_spatraster.Rd |only man/leaflet.providersESP.df.Rd | 7 man/mapSpain-package.Rd | 2 man/pobmun19.Rd | 4 tests/testthat.R | 8 tests/testthat/test-addProviderEspTiles.R | 3 tests/testthat/test-esp_cache.R |only tests/testthat/test-esp_getTiles.R | 184 ++++++++++++++++----- tests/testthat/test-esp_get_capimun.R | 7 tests/testthat/test-esp_get_ccaa.R | 17 + tests/testthat/test-esp_get_country.R | 4 tests/testthat/test-esp_get_gridmap.R | 40 ++-- tests/testthat/test-esp_get_hydrobasin.R | 56 +++--- tests/testthat/test-esp_get_hypsobath.R | 50 ++--- tests/testthat/test-esp_get_munic.R | 13 + tests/testthat/test-esp_get_nuts.R | 108 ++++++------ tests/testthat/test-esp_get_prov.R | 15 + tests/testthat/test-esp_get_railway.R | 32 +-- tests/testthat/test-esp_get_rivers.R | 64 +++---- tests/testthat/test-esp_get_roads.R | 33 +-- tests/testthat/test-layer_spatraster.R |only vignettes/basic-1.png |binary vignettes/basic-2.png |binary vignettes/basic-3.png |binary vignettes/choro-1.png |binary vignettes/giscoR-1.png |binary vignettes/mapSpain.Rmd | 222 +++++++++++++------------- vignettes/thematic-1.png |binary vignettes/tile-1.png |binary 84 files changed, 2009 insertions(+), 1693 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-01 1.10.0
Title: Plotting, Smoothing and Growth Trait Extraction for Longitudinal
Data
Description: Assists in producing longitudinal or profile plots of measured
traits. These allow checks to be made for anomalous data and growth patterns
in the data to be explored. Smoothing of growth trends for individual plants
using smoothing splines is available for removing transient effects. There
are tools for diagnosing the adequacy of trait smoothing, either using this
package or other packages, such as those that fit nonlinear growth models.
A range of per-unit (pot, plant, plot) growth traits can be extracted from
longitudinal data, including single time-point smoothed trait values and
their growth rates, interval growth rates and other growth statistics, such
as maximum growth. The package is particularly suited to preparing data from
high-throughput phenotyping facilities, such as imaging data from a Lemna-Tec Scananalyzer 3D
(see <https://www.youtube.com/watch?v=MRAF_mAEa7E/> for more
information). The package 'growthPheno' can also be installed from
<http://chris.brien.name/rpackages/>.
Author: Chris Brien [aut, cre] (<https://orcid.org/0000-0003-0581-1817>)
Maintainer: Chris Brien <chris.brien@adelaide.edu.au>
Diff between growthPheno versions 1.0-30 dated 2020-12-12 and 1.0-34 dated 2021-10-14
growthPheno-1.0-30/growthPheno/R/PVA.v2.r |only growthPheno-1.0-30/growthPheno/tests/testthat/testthat-problems.rds |only growthPheno-1.0-34/growthPheno/DESCRIPTION | 8 growthPheno-1.0-34/growthPheno/MD5 | 55 ++-- growthPheno-1.0-34/growthPheno/R/PVA.v3.r |only growthPheno-1.0-34/growthPheno/R/S3methodsDeprecations.r | 38 +-- growthPheno-1.0-34/growthPheno/R/dataLongi_v9.r | 117 ++-------- growthPheno-1.0-34/growthPheno/build/partial.rdb |binary growthPheno-1.0-34/growthPheno/build/vignette.rds |binary growthPheno-1.0-34/growthPheno/data/RiceRaw.dat.rda |binary growthPheno-1.0-34/growthPheno/data/cart.dat.rda |binary growthPheno-1.0-34/growthPheno/data/exampleData.rda |binary growthPheno-1.0-34/growthPheno/data/tomato.dat.rda |binary growthPheno-1.0-34/growthPheno/inst/News.Rd | 24 +- growthPheno-1.0-34/growthPheno/inst/doc/Rice.pdf |binary growthPheno-1.0-34/growthPheno/inst/doc/Tomato.pdf |binary growthPheno-1.0-34/growthPheno/inst/doc/growthPheno-manual.pdf |binary growthPheno-1.0-34/growthPheno/man/RiceRaw.dat.Rd | 4 growthPheno-1.0-34/growthPheno/man/getTimesSubset.Rd | 9 growthPheno-1.0-34/growthPheno/man/growthPheno-deprecated.Rd | 12 + growthPheno-1.0-34/growthPheno/man/growthPheno-pkg.Rd | 2 growthPheno-1.0-34/growthPheno/man/longitudinalPrime.Rd | 2 growthPheno-1.0-34/growthPheno/man/plotAnom.Rd | 4 growthPheno-1.0-34/growthPheno/man/plotCorrmatrix.Rd | 50 ++-- growthPheno-1.0-34/growthPheno/man/plotDeviationsBoxes.Rd | 12 - growthPheno-1.0-34/growthPheno/man/plotImagetimes.Rd | 11 growthPheno-1.0-34/growthPheno/man/plotLongitudinal.Rd | 7 growthPheno-1.0-34/growthPheno/man/plotMedianDeviations.Rd | 16 + growthPheno-1.0-34/growthPheno/tests/testthat/testCorrPlot.r | 3 growthPheno-1.0-34/growthPheno/tests/testthat/testProbeSmooth.r | 61 +++-- 30 files changed, 222 insertions(+), 213 deletions(-)
Title: R Bindings for Gtk 2.8.0 and Above
Description: Facilities in the R language for programming
graphical interfaces using Gtk, the Gimp Tool Kit.
Author: Michael Lawrence <michafla@gene.com> and Duncan Temple Lang <duncan@wald.ucdavis.edu>
Maintainer: ORPHANED
Diff between RGtk2 versions 2.20.36.1 dated 2021-10-11 and 2.20.36.2 dated 2021-10-14
RGtk2-2.20.36.1/RGtk2/configure.in |only RGtk2-2.20.36.2/RGtk2/DESCRIPTION | 8 +++++--- RGtk2-2.20.36.2/RGtk2/MD5 | 4 ++-- RGtk2-2.20.36.2/RGtk2/configure.ac |only 4 files changed, 7 insertions(+), 5 deletions(-)
Title: Post Processing of (Half-)Hourly Eddy-Covariance Measurements
Description: Standard and extensible Eddy-Covariance data post-processing
(Wutzler et al. (2018) <doi:10.5194/bg-15-5015-2018>)
includes
uStar-filtering, gap-filling, and flux-partitioning.
The Eddy-Covariance (EC) micrometeorological technique quantifies continuous
exchange fluxes of gases, energy, and momentum between an ecosystem and the atmosphere.
It is important for understanding ecosystem dynamics and upscaling exchange fluxes.
(Aubinet et al. (2012) <doi:10.1007/978-94-007-2351-1>).
This package inputs pre-processed (half-)hourly data and supports further processing.
First, a quality-check and filtering is performed based on the relationship between
measured flux and friction
velocity (uStar) to discard biased data
(Papale et al. (2006) <doi:10.5194/bg-3-571-2006>).
Second, gaps in the data are filled based on information from environmental conditions
(Reichstein et al. (2005) <doi:10.1111/j.1365-2486.2005.001002.x>).
Third, the net flux of carbon dioxide is partitioned
into its gross fluxes in and out of the ecosystem by night-time
based and day-time based approaches
(Lasslop et al. (2010) <doi:10.1111/j.1365-2486.2009.02041.x>).
Author: Department for Biogeochemical Integration at MPI-BGC, Jena, Germany
[cph],
Thomas Wutzler [aut, cre],
Markus Reichstein [aut],
Antje Maria Moffat [aut, trl],
Olaf Menzer [ctb],
Mirco Migliavacca [aut],
Kerstin Sickel [ctb, trl],
Ladislav <U+0160>igut [ctb]
Maintainer: Thomas Wutzler <twutz@bgc-jena.mpg.de>
Diff between REddyProc versions 1.2.2 dated 2020-03-18 and 1.3.0 dated 2021-10-14
DESCRIPTION | 21 MD5 | 311 +++-- NAMESPACE | 22 NEWS.md | 29 R/CheckVal.R | 38 R/DataFunctions.R | 21 R/EddyPartitioning.R | 37 R/EddyPlotting.R | 2 R/EddyUStarFilterChangePointDetection.R | 70 - R/EddyUStarFilterDP.R | 58 - R/FileHandling.R | 19 R/FileHandlingFormats.R | 217 ++++ R/GeoFunctions.R | 2 R/LRC_base.R | 44 R/PartitioningLasslop10.R | 23 R/PartitioningLasslop10Nighttime.R | 1 R/aEddy.R | 45 R/estimate_vpd_from_dew.R |only R/imports.R | 13 R/variableNames.R | 6 build/vignette.rds |binary inst/WORDLIST | 292 ++--- inst/doc/DEGebExample.R | 26 inst/doc/DEGebExample.html | 60 - inst/doc/aggUncertainty.Rmd | 211 +++- inst/doc/aggUncertainty.html | 278 +++-- inst/doc/bigleaf.Rmd | 1 inst/doc/bigleaf.html | 103 + inst/doc/gapFilling.R | 10 inst/doc/gapFilling.html | 30 inst/doc/uStarCases.R | 26 inst/doc/uStarCases.html | 68 - inst/doc/useCase.Rmd | 14 inst/doc/useCase.html | 187 +-- inst/genData/REddyProc-package.Rd | 214 ++-- inst/genData/deleteRdList.txt | 5 man/BerkeleyJulianDateToPOSIXct.Rd | 6 man/LightResponseCurveFitter_computeCost.Rd | 2 man/LightResponseCurveFitter_computeLRCGradient.Rd | 2 man/LightResponseCurveFitter_fitLRC.Rd | 4 man/LightResponseCurveFitter_getOptimizedParameterPositions.Rd | 2 man/LightResponseCurveFitter_getParameterInitials.Rd | 2 man/LightResponseCurveFitter_getParameterNames.Rd | 2 man/LightResponseCurveFitter_getPriorLocation.Rd | 2 man/LightResponseCurveFitter_getPriorScale.Rd | 2 man/LightResponseCurveFitter_isParameterInBounds.Rd | 2 man/LightResponseCurveFitter_optimLRC.Rd | 2 man/LightResponseCurveFitter_optimLRCBounds.Rd | 8 man/LightResponseCurveFitter_optimLRCOnAdjustedPrior.Rd | 2 man/LightResponseCurveFitter_predictGPP.Rd | 2 man/LightResponseCurveFitter_predictLRC.Rd | 2 man/LogisticSigmoidLRCFitter_predictGPP.Rd | 2 man/NonrectangularLRCFitter_getParameterNames.Rd | 2 man/NonrectangularLRCFitter_predictGPP.Rd | 2 man/POSIXctToBerkeleyJulianDate.Rd | 6 man/REddyProc-package.Rd | 214 ++-- man/RectangularLRCFitter_predictGPP.Rd | 2 man/estimate_vpd_from_dew.Rd |only man/extract_FN15.Rd |only man/fCalcAVPfromVMFandPress.Rd | 2 man/fCalcETfromLE.Rd | 2 man/fCalcExtRadiation.Rd | 2 man/fCalcPotRadiation.Rd | 2 man/fCalcRHfromAVPandTair.Rd | 2 man/fCalcSVPfromTair.Rd | 2 man/fCalcVPDfromRHandTair.Rd | 2 man/fCheckHHTimeSeries.Rd | 2 man/fConvertCtoK.Rd | 2 man/fConvertGlobalToVisible.Rd | 2 man/fConvertKtoC.Rd | 2 man/fConvertTimeToPosix.Rd | 2 man/fConvertVisibleWm2toPhotons.Rd | 2 man/fLloydTaylor.Rd | 2 man/fLoadEuroFlux16.Rd | 2 man/fLoadFluxnet15.Rd |only man/fLoadTXTIntoDataframe.Rd | 2 man/fWriteDataframeToFile.Rd | 2 man/filterLongRuns.Rd | 2 man/filterLongRunsInVector.Rd | 2 man/getAmerifluxToBGC05VariableNameMapping.Rd | 2 man/getBGC05ToAmerifluxVariableNameMapping.Rd | 2 man/getExamplePath.Rd | 2 man/getFilledExampleDETha98Data.Rd | 2 man/getREddyProcExampleDir.Rd | 2 man/getTZone.Rd | 2 man/get_timestep_hours.Rd |only man/partGLControl.Rd | 11 man/partGLControlLasslopCompatible.Rd | 2 man/partGLExtractStandardData.Rd | 2 man/partitionNEEGL.Rd | 8 man/read_from_fluxnet15.Rd |only man/renameVariablesInDataframe.Rd | 2 man/sEddyProc_initialize.Rd | 10 man/sEddyProc_sApplyUStarScen.Rd | 9 man/sEddyProc_sCalcPotRadiation.Rd | 2 man/sEddyProc_sEstUstarThold.Rd | 2 man/sEddyProc_sEstUstarThreshold.Rd | 2 man/sEddyProc_sEstUstarThresholdDistribution.Rd | 2 man/sEddyProc_sEstimateUstarScenarios.Rd | 6 man/sEddyProc_sExportData.Rd | 2 man/sEddyProc_sExportResults.Rd | 2 man/sEddyProc_sFillInit.Rd | 2 man/sEddyProc_sFillLUT.Rd | 2 man/sEddyProc_sFillMDC.Rd | 2 man/sEddyProc_sFillVPDFromDew.Rd |only man/sEddyProc_sGLFluxPartition.Rd | 2 man/sEddyProc_sGLFluxPartitionUStarScens.Rd | 17 man/sEddyProc_sGetData.Rd | 2 man/sEddyProc_sGetEstimatedUstarThresholdDistribution.Rd | 2 man/sEddyProc_sGetUstarScenarios.Rd | 2 man/sEddyProc_sGetUstarSuffixes.Rd |only man/sEddyProc_sMDSGapFill.Rd | 2 man/sEddyProc_sMDSGapFillAfterUStarDistr.Rd | 2 man/sEddyProc_sMDSGapFillAfterUstar.Rd | 2 man/sEddyProc_sMDSGapFillUStarScens.Rd | 2 man/sEddyProc_sMRFluxPartition.Rd | 2 man/sEddyProc_sMRFluxPartitionUStarScens.Rd | 2 man/sEddyProc_sPlotDailySums.Rd | 2 man/sEddyProc_sPlotDailySumsY.Rd | 2 man/sEddyProc_sPlotDiurnalCycle.Rd | 2 man/sEddyProc_sPlotFingerprint.Rd | 2 man/sEddyProc_sPlotFingerprintY.Rd | 2 man/sEddyProc_sPlotHHFluxes.Rd | 2 man/sEddyProc_sPlotHHFluxesY.Rd | 2 man/sEddyProc_sPlotNEEVersusUStarForSeason.Rd | 2 man/sEddyProc_sSetLocationInfo.Rd | 2 man/sEddyProc_sSetUStarSeasons.Rd | 2 man/sEddyProc_sSetUstarScenarios.Rd | 2 man/sEddyProc_sTKFluxPartition.Rd | 2 man/sEddyProc_sTKFluxPartitionUStarScens.Rd | 2 man/sEddyProc_update_ustarthreshold_columns.Rd |only man/sEddyProc_useAnnualUStarThresholds.Rd | 2 man/sEddyProc_useSeaonsalUStarThresholds.Rd | 2 man/usControlUstarEst.Rd | 2 man/usControlUstarSubsetting.Rd | 2 man/usCreateSeasonFactorMonth.Rd | 2 man/usCreateSeasonFactorMonthWithinYear.Rd | 2 man/usCreateSeasonFactorYday.Rd | 2 man/usCreateSeasonFactorYdayYear.Rd | 2 man/usEstUstarThreshold.Rd | 7 man/usEstUstarThresholdSingleFw1Binned.Rd | 2 man/usEstUstarThresholdSingleFw2Binned.Rd | 2 man/usGetAnnualSeasonUStarMap.Rd | 2 man/usGetSeasonalSeasonUStarMap.Rd | 2 man/usGetYearOfSeason.Rd | 2 src/RcppExports.cpp | 5 src/whichValueGreaterEqualC.cpp | 3 tests/testthat/test_FileHandlingFormats.R |only tests/testthat/test_LightResponseCurveFitter.R | 187 +++ tests/testthat/test_UStarFilter.R | 120 +- tests/testthat/test_binWithEqualValues.R | 46 tests/testthat/test_checkval.R |only tests/testthat/test_estimate_vpd_from_dew.R |only tests/testthat/test_fConvertTimeToPosix.R | 9 tests/testthat/test_gapfilling.R | 1 tests/testthat/test_partGL.R | 36 tests/testthat/test_plotFingerprint.R | 12 tests/testthat/test_sEddyProc.R | 526 +++++----- tests/testthat/test_sEddyProc_Partitioning.R | 286 ++--- vignettes/aggUncertainty.Rmd | 211 +++- vignettes/bigleaf.Rmd | 1 vignettes/plots |only vignettes/useCase.Rmd | 14 163 files changed, 2831 insertions(+), 1614 deletions(-)
Title: Multiscalar Territorial Analysis
Description: Build multiscalar territorial analysis based on various contexts.
Author: Ronan Ysebaert [aut],
Nicolas Lambert [aut],
Timothée Giraud [aut, cre]
Maintainer: Timothée Giraud <timothee.giraud@cnrs.fr>
Diff between MTA versions 0.3.0 dated 2021-01-20 and 0.4.0 dated 2021-10-14
MTA-0.3.0/MTA/data |only MTA-0.4.0/MTA/DESCRIPTION | 13 MTA-0.4.0/MTA/MD5 | 75 MTA-0.4.0/MTA/NAMESPACE | 2 MTA-0.4.0/MTA/NEWS | 12 MTA-0.4.0/MTA/R/bidev.R | 5 MTA-0.4.0/MTA/R/gdev.R | 52 MTA-0.4.0/MTA/R/map_bidev.R | 56 MTA-0.4.0/MTA/R/map_mst.R | 65 MTA-0.4.0/MTA/R/mas.R | 9 MTA-0.4.0/MTA/R/mst.R | 6 MTA-0.4.0/MTA/R/package.R | 19 MTA-0.4.0/MTA/R/plot_bidev.R | 7 MTA-0.4.0/MTA/R/plot_mst.R | 3 MTA-0.4.0/MTA/R/sdev.R | 31 MTA-0.4.0/MTA/R/tdev.R | 72 MTA-0.4.0/MTA/build/vignette.rds |binary MTA-0.4.0/MTA/inst/cardist.txt |only MTA-0.4.0/MTA/inst/doc/MTA.R | 6 MTA-0.4.0/MTA/inst/doc/MTA.Rmd | 20 MTA-0.4.0/MTA/inst/doc/MTA.html | 479 +++--- MTA-0.4.0/MTA/inst/doc/MTA_Scenario.R | 637 +++----- MTA-0.4.0/MTA/inst/doc/MTA_Scenario.Rmd | 641 +++----- MTA-0.4.0/MTA/inst/doc/MTA_Scenario.html | 2334 ++++++++++++++----------------- MTA-0.4.0/MTA/inst/metroparis.gpkg |only MTA-0.4.0/MTA/man/bidev.Rd | 5 MTA-0.4.0/MTA/man/cardist.Rd | 5 MTA-0.4.0/MTA/man/com.Rd | 4 MTA-0.4.0/MTA/man/ept.Rd | 3 MTA-0.4.0/MTA/man/gdev.Rd | 50 MTA-0.4.0/MTA/man/map_bidev.Rd | 38 MTA-0.4.0/MTA/man/map_mst.Rd | 64 MTA-0.4.0/MTA/man/mas.Rd | 5 MTA-0.4.0/MTA/man/mst.Rd | 6 MTA-0.4.0/MTA/man/plot_bidev.Rd | 3 MTA-0.4.0/MTA/man/plot_mst.Rd | 3 MTA-0.4.0/MTA/man/sdev.Rd | 30 MTA-0.4.0/MTA/man/tdev.Rd | 50 MTA-0.4.0/MTA/vignettes/MTA.Rmd | 20 MTA-0.4.0/MTA/vignettes/MTA_Scenario.Rmd | 641 +++----- 40 files changed, 2583 insertions(+), 2888 deletions(-)
Title: Simple 'ggplot2' Visualisation with Less Brainpower
Description: Wrapper functions to make 'ggplot2' and 'leaflet' visualisation easier with less brainpower required.
Author: David Hodge [aut, cre] (<https://orcid.org/0000-0002-3868-7501>),
Statistics New Zealand [cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between simplevis versions 4.5.0 dated 2021-08-06 and 4.6.0 dated 2021-10-14
simplevis-4.5.0/simplevis/R/internal.R |only simplevis-4.5.0/simplevis/inst/shiny/template1/www/js/iframe-resizer.js |only simplevis-4.5.0/simplevis/inst/shiny/template2/www/js/iframe-resizer.js |only simplevis-4.5.0/simplevis/man/bin_cuts_to_interval_labels.Rd |only simplevis-4.5.0/simplevis/man/sv_interval_breaks_to_interval_labels.Rd |only simplevis-4.5.0/simplevis/man/sv_max_dp.Rd |only simplevis-4.5.0/simplevis/man/theme_x_gridlines.Rd |only simplevis-4.5.0/simplevis/man/theme_xy_gridlines.Rd |only simplevis-4.5.0/simplevis/man/theme_y_gridlines.Rd |only simplevis-4.6.0/simplevis/DESCRIPTION | 10 simplevis-4.6.0/simplevis/MD5 | 168 +++---- simplevis-4.6.0/simplevis/NAMESPACE | 9 simplevis-4.6.0/simplevis/NEWS.md | 19 simplevis-4.6.0/simplevis/R/density_max.R |only simplevis-4.6.0/simplevis/R/font_size.R |only simplevis-4.6.0/simplevis/R/gg_bar.R | 230 +++++----- simplevis-4.6.0/simplevis/R/gg_boxplot.R | 102 +--- simplevis-4.6.0/simplevis/R/gg_density.R | 56 +- simplevis-4.6.0/simplevis/R/gg_hbar.R | 229 +++++---- simplevis-4.6.0/simplevis/R/gg_line.R | 60 +- simplevis-4.6.0/simplevis/R/gg_point.R | 175 +++---- simplevis-4.6.0/simplevis/R/gg_sf.R | 176 ++++--- simplevis-4.6.0/simplevis/R/gg_tile.R | 172 ++++--- simplevis-4.6.0/simplevis/R/imports.R | 1 simplevis-4.6.0/simplevis/R/interval_labels.R |only simplevis-4.6.0/simplevis/R/leaflet_sf.R | 169 ++----- simplevis-4.6.0/simplevis/R/max_digits.R |only simplevis-4.6.0/simplevis/R/numeric_breaks.R |only simplevis-4.6.0/simplevis/R/pal.R | 2 simplevis-4.6.0/simplevis/R/run_app.R | 2 simplevis-4.6.0/simplevis/R/theme.R | 59 +- simplevis-4.6.0/simplevis/R/zero_adjust.R |only simplevis-4.6.0/simplevis/inst/doc/simplevis.html | 99 ++-- simplevis-4.6.0/simplevis/inst/shiny/template1/data/template1.zip |binary simplevis-4.6.0/simplevis/inst/shiny/template1/global.R | 7 simplevis-4.6.0/simplevis/inst/shiny/template1/server.R | 25 - 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Title: Analysis of Geostatistical Count Data using Gaussian Copulas
Description: Provides a variety of functions to analyze and model
geostatistical count data with Gaussian copulas, including
1) data simulation and visualization;
2) correlation structure assessment (here also known as the Normal To Anything);
3) calculate multivariate normal rectangle probabilities;
4) likelihood inference and parallel prediction at predictive locations.
Description of the method is available from: Han and DeOliveira (2018) <doi:10.18637/jss.v087.i13>.
Author: Zifei Han
Maintainer: Zifei Han <hanzifei1@gmail.com>
Diff between gcKrig versions 1.1.6 dated 2021-06-22 and 1.1.7 dated 2021-10-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- build/partial.rdb |binary inst/NEWS.txt | 5 +++++ man/marginal.gc.Rd | 3 ++- 5 files changed, 14 insertions(+), 8 deletions(-)
Title: Double Machine Learning in R
Description: Implementation of the double/debiased machine learning framework of
Chernozhukov et al. (2018) <doi:10.1111/ectj.12097> for partially linear
regression models, partially linear instrumental variable regression models,
interactive regression models and interactive instrumental variable
regression models. 'DoubleML' allows estimation of the nuisance parts in
these models by machine learning methods and computation of the Neyman
orthogonal score functions. 'DoubleML' is built on top of 'mlr3' and the
'mlr3' ecosystem. The object-oriented implementation of 'DoubleML' based on
the 'R6' package is very flexible.
Author: Philipp Bach [aut],
Victor Chernozhukov [aut],
Malte S. Kurz [aut, cre],
Martin Spindler [aut]
Maintainer: Malte S. Kurz <malte.simon.kurz@uni-hamburg.de>
Diff between DoubleML versions 0.3.1 dated 2021-08-02 and 0.4.0 dated 2021-10-14
DESCRIPTION | 11 MD5 | 149 - NAMESPACE | 2 R/datasets.R | 173 + R/double_ml.R | 653 +++++-- R/double_ml_data.R | 418 +++- R/double_ml_iivm.R | 29 R/double_ml_irm.R | 22 R/double_ml_pliv.R | 35 R/helper.R | 37 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Introduction_to_DoubleML.html | 4 man/DoubleML.Rd | 5 man/DoubleMLClusterData.Rd |only man/DoubleMLData.Rd | 2 man/double_ml_data_from_data_frame.Rd | 9 man/double_ml_data_from_matrix.Rd | 4 man/make_pliv_multiway_cluster_CKMS2021.Rd |only tests/testthat/helper-01-helper_functions.R | 6 tests/testthat/helper-03-dgp.R | 18 tests/testthat/helper-04-simdata.R | 65 tests/testthat/helper-05-ml-learner.R | 20 tests/testthat/helper-08-dml_plr.R | 234 +- tests/testthat/helper-09-dml_pliv.R | 105 - tests/testthat/helper-10-dml_irm.R | 118 - tests/testthat/helper-11-dml_iivm.R | 123 - tests/testthat/helper-13-dml_pliv_partial_x.R | 118 - tests/testthat/helper-14-dml_pliv_partial_z.R | 89 tests/testthat/helper-15-dml_pliv_partial_xz.R | 129 - tests/testthat/helper-16-dml_cluster.R |only tests/testthat/print_outputs |only tests/testthat/test-double_ml_active_bindings.R | 99 - tests/testthat/test-double_ml_cluster_not_implemented.R |only tests/testthat/test-double_ml_data.R | 931 +++++----- tests/testthat/test-double_ml_data_active_bindings.R | 563 +++--- tests/testthat/test-double_ml_datasets.R | 21 tests/testthat/test-double_ml_iivm.R | 18 tests/testthat/test-double_ml_iivm_parameter_passing.R | 221 +- tests/testthat/test-double_ml_iivm_trim.R | 36 tests/testthat/test-double_ml_iivm_tuning.R | 2 tests/testthat/test-double_ml_iivm_user_score.R | 2 tests/testthat/test-double_ml_irm.R | 20 tests/testthat/test-double_ml_irm_loaded_mlr3learner.R | 8 tests/testthat/test-double_ml_irm_parameter_passing.R | 180 - tests/testthat/test-double_ml_irm_trim.R | 32 tests/testthat/test-double_ml_irm_tuning.R | 2 tests/testthat/test-double_ml_irm_user_score.R | 8 tests/testthat/test-double_ml_pliv.R | 16 tests/testthat/test-double_ml_pliv_multi_z_parameter_passing.R | 274 +- tests/testthat/test-double_ml_pliv_one_way_cluster.R |only tests/testthat/test-double_ml_pliv_parameter_passing.R | 295 +-- tests/testthat/test-double_ml_pliv_partial_functional_initializer.R | 46 tests/testthat/test-double_ml_pliv_partial_x.R | 47 tests/testthat/test-double_ml_pliv_partial_xz.R | 46 tests/testthat/test-double_ml_pliv_partial_xz_parameter_passing.R | 303 +-- tests/testthat/test-double_ml_pliv_partial_z.R | 37 tests/testthat/test-double_ml_pliv_partial_z_parameter_passing.R | 189 +- tests/testthat/test-double_ml_pliv_tuning.R | 2 tests/testthat/test-double_ml_pliv_two_way_cluster.R |only tests/testthat/test-double_ml_pliv_user_score.R | 8 tests/testthat/test-double_ml_plr.R | 26 tests/testthat/test-double_ml_plr_classifier.R | 85 tests/testthat/test-double_ml_plr_exception_handling.R | 10 tests/testthat/test-double_ml_plr_export_preds.R | 2 tests/testthat/test-double_ml_plr_loaded_mlr3learner.R | 10 tests/testthat/test-double_ml_plr_multitreat.R | 32 tests/testthat/test-double_ml_plr_nocrossfit.R | 27 tests/testthat/test-double_ml_plr_nonorth.R | 2 tests/testthat/test-double_ml_plr_p_adjust.R | 2 tests/testthat/test-double_ml_plr_parameter_passing.R | 292 +-- tests/testthat/test-double_ml_plr_rep_cross_fit.R | 40 tests/testthat/test-double_ml_plr_set_samples.R | 6 tests/testthat/test-double_ml_plr_tuning.R | 2 tests/testthat/test-double_ml_plr_user_score.R | 2 tests/testthat/test-double_ml_print.R |only tests/testthat/test-double_ml_set_sample_splitting.R | 356 ++- 78 files changed, 4044 insertions(+), 2836 deletions(-)
Title: Analysis of Plant Pathogen Pathotype Complexities, Distributions
and Diversity
Description: Analysis of plant pathogen pathotype survey data. Functions
provided calculate distribution of susceptibilities, distribution of
complexities with statistics, pathotype frequency distribution, as well as
diversity indices for pathotypes. This package is meant to be a direct
replacement for Herrmann, Löwer and Schachtel's (1999)
<doi:10.1046/j.1365-3059.1999.00325.x> Habgood-Gilmour Spreadsheet, 'HaGiS',
previously used for pathotype analysis.
Author: Austin G. McCoy [aut, ccp] (<https://orcid.org/0000-0003-2483-4184>),
Zachary Noel [aut, ccp] (<https://orcid.org/0000-0001-6375-8300>),
Adam H. Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>),
Martin Chilvers [aut, ths] (<https://orcid.org/0000-0001-8832-1666>),
Zhian N. Kamvar [ctb, rev] (<https://orcid.org/0000-0003-1458-7108>),
Michigan Soybean Promotion Committee [fnd],
Project GREEEN [fnd],
North Central Soybean Research Program [fnd],
GRDC Project DAQ00186 [fnd]
Maintainer: Adam H. Sparks <adamhsparks@gmail.com>
Diff between hagis versions 3.1.2 dated 2021-09-30 and 3.1.3 dated 2021-10-14
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 14 ++++++++++++++ R/calculate_diversities.R | 4 ++-- README.md | 37 ++++++++++++++++++++++++------------- inst/CITATION | 9 +++++---- inst/WORDLIST | 4 ++++ inst/doc/betadiversity.html | 8 ++++---- inst/doc/hagis.html | 4 ++-- 9 files changed, 66 insertions(+), 36 deletions(-)
Title: Evaluation Metrics for Implicit-Feedback Recommender Systems
Description: Calculates evaluation metrics for implicit-feedback recommender systems
that are based on low-rank matrix factorization models, given the fitted model
matrices and data, thus allowing to compare models from a variety of libraries.
Metrics include P@K (precision-at-k, for top-K recommendations), R@K (recall at k),
AP@K (average precision at k), NDCG@K (normalized discounted cumulative gain at k),
Hit@K (from which the 'Hit Rate' is calculated), RR@K (reciprocal rank at k, from
which the 'MRR' or 'mean reciprocal rank' is calculated), ROC-AUC (area under the
receiver-operating characteristic curve), and PR-AUC (area under the
precision-recall curve).
These are calculated on a per-user basis according to the ranking of items induced
by the model, using efficient multi-threaded routines. Also provides functions
for creating train-test splits for model fitting and evaluation.
Author: David Cortes
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between recometrics versions 0.1.5 dated 2021-09-02 and 0.1.5-2 dated 2021-10-14
DESCRIPTION | 6 MD5 | 14 configure | 1271 +++++++++++++++++---------- configure.ac | 6 inst/doc/Evaluating_recommender_systems.html | 254 ++--- src/Makevars.in | 4 src/Makevars.win | 2 src/recometrics.h | 11 8 files changed, 979 insertions(+), 589 deletions(-)
Title: Read and Write Sparse Matrices in 'SVMLight' and 'LibSVM'
Formats
Description: Read and write labelled sparse matrices in text format as used by
software such as 'SVMLight', 'LibSVM', 'ThunderSVM', 'LibFM', 'xLearn', 'XGBoost', 'LightGBM',
and others. Supports labelled data for regression, classification (binary, multi-class, multi-label),
and ranking (with 'qid' field), and can handle header metadata and comments in files.
Author: David Cortes
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between readsparse versions 0.1.5 dated 2021-09-07 and 0.1.5-1 dated 2021-10-14
DESCRIPTION | 6 +++--- MD5 | 6 +++--- configure | 6 +++--- configure.ac | 4 ++-- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Pattern-Oriented Modeling Framework for Coupled Niche-Population
Paleo-Climatic Models
Description: This extension of the poems pattern-oriented modeling (POM) framework
provides a collection of modules and functions customized for paleontological
time-scales, and optimized for single-generation transitions and large populations,
across multiple generations.
Author: Sean Haythorne [aut],
Julia Pilowsky [aut, cre] (<https://orcid.org/0000-0002-6376-2585>),
Stuart Brown [aut] (<https://orcid.org/0000-0002-0669-1418>),
Damien Fordham [aut] (<https://orcid.org/0000-0003-2137-5592>)
Maintainer: Julia Pilowsky <julia.pilowsky@adelaide.edu.au>
Diff between paleopop versions 2.1.1 dated 2021-04-23 and 2.1.2 dated 2021-10-14
DESCRIPTION | 26 ++++++++++++++++---------- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/PaleoPopModel.R | 2 +- build/vignette.rds |binary inst/doc/bison_example.html | 4 ++-- man/PaleoPopModel.Rd | 2 +- 7 files changed, 30 insertions(+), 20 deletions(-)
Title: Visualizations for 'mlr3'
Description: Provides visualizations for 'mlr3' objects such as tasks,
predictions, resample results or benchmark results via the autoplot()
generic of 'ggplot2'. The returned 'ggplot' objects are intended to
provide sensible defaults, yet can easily be customized to create
camera-ready figures. Visualizations include barplots, boxplots,
histograms, ROC curves, and Precision-Recall curves.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>),
Raphael Sonabend [aut] (<https://orcid.org/0000-0001-9225-4654>),
Marc Becker [aut] (<https://orcid.org/0000-0002-8115-0400>),
Jakob Richter [aut] (<https://orcid.org/0000-0003-4481-5554>),
Damir Pulatov [ctb]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3viz versions 0.5.6 dated 2021-09-14 and 0.5.7 dated 2021-10-14
DESCRIPTION | 24 ++- MD5 | 39 ++++-- NAMESPACE | 3 NEWS.md | 4 R/OptimInstanceSingleCrit.R |only R/TuningInstanceSingleCrit.R | 159 +------------------------ build/partial.rdb |binary man/autoplot.OptimInstanceSingleCrit.Rd |only man/autoplot.TuningInstanceSingleCrit.Rd | 12 + man/mlr3viz-package.Rd | 8 - tests/testthat/_snaps/OptimInstanceSingleCrit |only tests/testthat/test_OptimInstanceSingleCrit.R |only tests/testthat/test_PredictionClust.R | 2 tests/testthat/test_TuningInstanceSingleCrit.R | 5 14 files changed, 77 insertions(+), 179 deletions(-)
Title: Functions to Fit Mixtures of Regressions
Description: Fits mixtures of (possibly multivariate) regressions
(which has been described as doing ANCOVA when you don't
know the levels). Turner (2000) <doi:10.1111/1467-9876.00198>.
Author: Rolf Turner <r.turner@auckland.ac.nz>
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>
Diff between mixreg versions 0.0-6 dated 2018-03-31 and 2.0-10 dated 2021-10-14
mixreg-0.0-6/mixreg/R/bootSam.R |only mixreg-0.0-6/mixreg/R/bootcomp.R |only mixreg-0.0-6/mixreg/R/covmix.R |only mixreg-0.0-6/mixreg/R/plot.mresid.R |only mixreg-0.0-6/mixreg/R/residMix.R |only mixreg-0.0-6/mixreg/R/simmix.R |only mixreg-0.0-6/mixreg/inst/aphids.R |only mixreg-0.0-6/mixreg/inst/aphids.dat |only mixreg-0.0-6/mixreg/man/bootcomp.Rd |only mixreg-0.0-6/mixreg/man/covmix.Rd |only mixreg-0.0-6/mixreg/man/plot.mresid.Rd |only mixreg-0.0-6/mixreg/man/residMix.Rd |only mixreg-2.0-10/mixreg/ChangeLog | 320 ++++++++++++++++++++++++++- mixreg-2.0-10/mixreg/DESCRIPTION | 12 - mixreg-2.0-10/mixreg/MD5 | 86 ++++--- mixreg-2.0-10/mixreg/NAMESPACE | 12 - mixreg-2.0-10/mixreg/R/First.R | 18 + mixreg-2.0-10/mixreg/R/cband.R | 123 +++++----- mixreg-2.0-10/mixreg/R/cint.R |only mixreg-2.0-10/mixreg/R/covMix.R |only mixreg-2.0-10/mixreg/R/covMixMC.R |only mixreg-2.0-10/mixreg/R/distFuns.R |only mixreg-2.0-10/mixreg/R/gfun.R | 17 - mixreg-2.0-10/mixreg/R/hatfun.R | 1 mixreg-2.0-10/mixreg/R/info1.R | 3 mixreg-2.0-10/mixreg/R/info2.R | 3 mixreg-2.0-10/mixreg/R/initRand.R | 7 mixreg-2.0-10/mixreg/R/mixreg.R | 227 +++++++++---------- mixreg-2.0-10/mixreg/R/mixregEngine.R |only mixreg-2.0-10/mixreg/R/ncMcTest.R |only mixreg-2.0-10/mixreg/R/plot.cband.R | 158 ++++++++++--- mixreg-2.0-10/mixreg/R/plot.cint.R |only mixreg-2.0-10/mixreg/R/plot.mixreg.R |only mixreg-2.0-10/mixreg/R/plot.mixresid.R |only mixreg-2.0-10/mixreg/R/qqMix.R | 73 +++--- mixreg-2.0-10/mixreg/R/residuals.mixreg.R |only mixreg-2.0-10/mixreg/R/rmixreg.R |only mixreg-2.0-10/mixreg/R/rmixreg.default.R |only mixreg-2.0-10/mixreg/R/rmixreg.mixreg.R |only mixreg-2.0-10/mixreg/R/stepPlot.R |only mixreg-2.0-10/mixreg/R/visualFit.R |only mixreg-2.0-10/mixreg/build |only mixreg-2.0-10/mixreg/data/aphids.rda |binary mixreg-2.0-10/mixreg/data/kilnAfull.rda |only mixreg-2.0-10/mixreg/data/kilnAoneOut.rda |only mixreg-2.0-10/mixreg/data/kilnAsubset.rda |only mixreg-2.0-10/mixreg/data/kilnB.rda |only mixreg-2.0-10/mixreg/inst/doc |only mixreg-2.0-10/mixreg/man/aphids.Rd | 38 +-- mixreg-2.0-10/mixreg/man/cband.Rd | 134 +++++++---- mixreg-2.0-10/mixreg/man/covMix.Rd |only mixreg-2.0-10/mixreg/man/kilns.Rd |only mixreg-2.0-10/mixreg/man/mixreg-internal.Rd | 19 + mixreg-2.0-10/mixreg/man/mixreg.Rd | 320 ++++++++++++++++++--------- mixreg-2.0-10/mixreg/man/ncMcTest.Rd |only mixreg-2.0-10/mixreg/man/plot.cband.Rd | 93 +++++-- mixreg-2.0-10/mixreg/man/plot.cint.Rd |only mixreg-2.0-10/mixreg/man/plot.mixreg.Rd |only mixreg-2.0-10/mixreg/man/plot.mixresid.Rd |only mixreg-2.0-10/mixreg/man/qqMix.Rd | 85 ++++--- mixreg-2.0-10/mixreg/man/residuals.mixreg.Rd |only mixreg-2.0-10/mixreg/man/rmixreg.Rd |only mixreg-2.0-10/mixreg/man/stepPlot.Rd |only mixreg-2.0-10/mixreg/man/visualFit.Rd |only mixreg-2.0-10/mixreg/vignettes |only 65 files changed, 1227 insertions(+), 522 deletions(-)
Title: Conditioned Latin Hypercube Sampling
Description: Conditioned Latin hypercube sampling, as published by Minasny and McBratney (2006) <DOI:10.1016/j.cageo.2005.12.009>. This method proposes to stratify sampling in presence of ancillary data. An extension of this method, which propose to associate a cost to each individual and take it into account during the optimisation process, is also proposed (Roudier et al., 2012, <DOI:10.1201/b12728>).
Author: Pierre Roudier [aut, cre],
Colby Brugnard [ctb],
Dylan Beaudette [ctb],
Benjamin Louis [ctb],
Kiri Daust [ctb],
David Clifford [ctb]
Maintainer: Pierre Roudier <roudierp@landcareresearch.co.nz>
Diff between clhs versions 0.8.1 dated 2021-05-10 and 0.9.0 dated 2021-10-14
DESCRIPTION | 21 - MD5 | 52 +-- NAMESPACE | 2 NEWS.md | 11 R/RcppExports.R |only R/clhs-data.frame.R | 549 ++++++++++++++++++-------------- R/clhs-package.R | 2 R/clhs.R | 26 - R/plot.R | 2 README.md | 10 build/vignette.rds |binary inst/doc/intro-clhs.R | 12 inst/doc/intro-clhs.Rmd | 14 inst/doc/intro-clhs.html | 32 - man/CppLHS.Rd |only man/clhs.Rd | 29 + man/plot.cLHS_result.Rd | 2 src |only tests/testthat/test-clhs-data.frame.R | 52 ++- tests/testthat/test-clhs-tibble.R | 16 tests/testthat/test-cost-constraint.R | 24 + tests/testthat/test-mandatory_samples.R | 45 ++ tests/testthat/test-method_DLHS.R | 23 + tests/testthat/test-raster.R | 2 tests/testthat/test-sf.R | 4 tests/testthat/test-spdf.R | 4 vignettes/intro-clhs.Rmd | 14 27 files changed, 603 insertions(+), 345 deletions(-)
Title: Analyse Audio Recordings and Automatically Extract Animal
Vocalizations
Description: Contains all the necessary tools to process audio recordings of
various formats (e.g., WAV, WAC, MP3, ZC), filter noisy files,
display audio signals, detect and extract automatically acoustic
features for further analysis such as classification.
Author: Jean Marchal [aut, cre],
Francois Fabianek [aut],
Christopher Scott [aut],
Chris Corben [ctb, cph] (Read ZC files, original C code),
David Riggs [ctb, cph] (Read GUANO metadata, original R code),
Peter Wilson [ctb, cph] (Read ZC files, original R code),
Wildlife Acoustics, inc. [ctb, cph] (Read WAC files, original C code),
Jordan Biserkov [ctb],
WavX, inc. [cph]
Maintainer: Jean Marchal <jean.marchal@wavx.ca>
Diff between bioacoustics versions 0.2.5 dated 2021-01-05 and 0.2.7 dated 2021-10-14
DESCRIPTION | 8 ++- MD5 | 28 ++++++------ NEWS.md | 9 +++ R/write_zc.R | 102 ++++++++++++++++++++++---------------------- configure | 18 +++---- configure.ac | 10 +--- inst/doc/introduction.Rmd | 6 +- inst/doc/introduction.html | 6 +- inst/doc/tutorial.R | 6 +- inst/doc/tutorial.Rmd | 6 +- inst/doc/tutorial.html | 6 +- man/bioacoustics-package.Rd | 1 src/RcppExports.cpp | 5 ++ vignettes/introduction.Rmd | 6 +- vignettes/tutorial.Rmd | 6 +- 15 files changed, 119 insertions(+), 104 deletions(-)