Title: Tools for Reading SDMX Data and Metadata
Description: Set of classes and methods to read data and metadata documents
exchanged through the Statistical Data and Metadata Exchange (SDMX) framework,
currently focusing on the SDMX XML standard format (SDMX-ML).
Author: Emmanuel Blondel [aut, cre] (<https://orcid.org/0000-0002-5870-5762>),
Matthieu Stigler [ctb],
Eric Persson [ctb]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between rsdmx versions 0.5-11 dated 2018-02-14 and 0.5-12 dated 2018-06-28
DESCRIPTION | 14 MD5 | 52 +-- R/Class-SDMXCode.R | 23 + R/Class-SDMXStructureType.R | 27 - R/SDMXCode-methods.R | 42 ++ R/SDMXCodelists-methods.R | 14 R/SDMXComponents-methods.R | 12 R/SDMXConcept-methods.R | 27 + R/SDMXData-methods.R | 2 R/SDMXServiceProvider-methods.R | 81 ++++- R/readSDMX.R | 2 R/rsdmx.R | 4 README.md | 11 inst/extdata/SDMXStructureSpecificDataExample_2.1.xml | 284 +++++++++--------- man/SDMXCode.Rd | 8 man/rsdmx.Rd | 4 tests/testthat/test_CompactData.R | 2 tests/testthat/test_CrossSectionalData.R | 2 tests/testthat/test_Data.R | 6 tests/testthat/test_DataFlows.R | 2 tests/testthat/test_DataStructureDefinition.R | 4 tests/testthat/test_DataStructures.R | 4 tests/testthat/test_GenericData.R | 6 tests/testthat/test_Main.R | 3 tests/testthat/test_Main_Helpers.R | 97 ++++++ tests/testthat/test_MessageGroup.R | 2 tests/testthat/test_StructureSpecificData.R | 2 27 files changed, 511 insertions(+), 226 deletions(-)
Title: Systematic Conservation Prioritization in R
Description: Conservation prioritization using integer
programming techniques. To solve large-scale problems, users
should install the 'gurobi' optimizer
(available from <http://www.gurobi.com/>).
Author: Jeffrey O Hanson [aut],
Richard Schuster [aut, cre],
Nina Morrell [aut],
Matthew Strimas-Mackey [aut],
Matthew E Watts [aut],
Peter Arcese [aut],
Joeseph Bennett [aut],
Hugh P Possingham [aut]
Maintainer: Richard Schuster <mail@richard-schuster.com>
Diff between prioritizr versions 4.0.1 dated 2018-05-26 and 4.0.2 dated 2018-06-28
prioritizr-4.0.1/prioritizr/tests/testthat/test_add_binary_stack.R |only prioritizr-4.0.2/prioritizr/DESCRIPTION | 6 prioritizr-4.0.2/prioritizr/MD5 | 318 - prioritizr-4.0.2/prioritizr/NAMESPACE | 342 - prioritizr-4.0.2/prioritizr/R/ConservationProblem-proto.R | 6 prioritizr-4.0.2/prioritizr/R/RcppExports.R | 342 - prioritizr-4.0.2/prioritizr/R/add_absolute_targets.R | 8 prioritizr-4.0.2/prioritizr/R/add_cuts_portfolio.R | 80 prioritizr-4.0.2/prioritizr/R/add_feature_contiguity_constraints.R | 4 prioritizr-4.0.2/prioritizr/R/add_locked_in_constraints.R | 2 prioritizr-4.0.2/prioritizr/R/add_locked_out_constraints.R | 2 prioritizr-4.0.2/prioritizr/R/add_loglinear_targets.R | 53 prioritizr-4.0.2/prioritizr/R/add_manual_locked_constraints.R | 6 prioritizr-4.0.2/prioritizr/R/add_manual_targets.R | 1 prioritizr-4.0.2/prioritizr/R/add_pool_portfolio.R | 71 prioritizr-4.0.2/prioritizr/R/add_relative_targets.R | 5 prioritizr-4.0.2/prioritizr/R/feature_representation.R | 2 prioritizr-4.0.2/prioritizr/R/internal.R | 19 prioritizr-4.0.2/prioritizr/R/problem.R | 58 prioritizr-4.0.2/prioritizr/build/vignette.rds |binary prioritizr-4.0.2/prioritizr/inst/doc/gurobi_installation.html | 914 +- prioritizr-4.0.2/prioritizr/inst/doc/prioritizr.Rmd | 11 prioritizr-4.0.2/prioritizr/inst/doc/prioritizr.html | 3058 ++++------ prioritizr-4.0.2/prioritizr/inst/doc/publication_record.html | 411 - prioritizr-4.0.2/prioritizr/inst/doc/saltspring.html | 919 +-- prioritizr-4.0.2/prioritizr/inst/doc/tasmania.Rmd | 6 prioritizr-4.0.2/prioritizr/inst/doc/tasmania.html | 1282 ++-- prioritizr-4.0.2/prioritizr/inst/doc/zones.html | 1871 +++--- prioritizr-4.0.2/prioritizr/man/ArrayParameter-class.Rd | 200 prioritizr-4.0.2/prioritizr/man/Collection-class.Rd | 182 prioritizr-4.0.2/prioritizr/man/ConservationModifier-class.Rd | 256 prioritizr-4.0.2/prioritizr/man/ConservationProblem-class.Rd | 562 - prioritizr-4.0.2/prioritizr/man/Constraint-class.Rd | 32 prioritizr-4.0.2/prioritizr/man/Decision-class.Rd | 34 prioritizr-4.0.2/prioritizr/man/MiscParameter-class.Rd | 166 prioritizr-4.0.2/prioritizr/man/Objective-class.Rd | 26 prioritizr-4.0.2/prioritizr/man/OptimizationProblem-class.Rd | 248 prioritizr-4.0.2/prioritizr/man/OptimizationProblem-methods.Rd | 344 - prioritizr-4.0.2/prioritizr/man/Parameter-class.Rd | 118 prioritizr-4.0.2/prioritizr/man/Parameters-class.Rd | 180 prioritizr-4.0.2/prioritizr/man/Penalty-class.Rd | 34 prioritizr-4.0.2/prioritizr/man/Portfolio-class.Rd | 132 prioritizr-4.0.2/prioritizr/man/ScalarParameter-class.Rd | 182 prioritizr-4.0.2/prioritizr/man/Solver-class.Rd | 134 prioritizr-4.0.2/prioritizr/man/Target-class.Rd | 32 prioritizr-4.0.2/prioritizr/man/add_absolute_targets.Rd | 316 - 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prioritizr-4.0.2/prioritizr/man/add_max_cover_objective.Rd | 312 - prioritizr-4.0.2/prioritizr/man/add_max_features_objective.Rd | 256 prioritizr-4.0.2/prioritizr/man/add_max_phylo_objective.Rd | 436 - prioritizr-4.0.2/prioritizr/man/add_max_utility_objective.Rd | 238 prioritizr-4.0.2/prioritizr/man/add_min_set_objective.Rd | 196 prioritizr-4.0.2/prioritizr/man/add_neighbor_constraints.Rd | 392 - prioritizr-4.0.2/prioritizr/man/add_pool_portfolio.Rd | 193 prioritizr-4.0.2/prioritizr/man/add_proportion_decisions.Rd | 146 prioritizr-4.0.2/prioritizr/man/add_relative_targets.Rd | 307 - prioritizr-4.0.2/prioritizr/man/add_rsymphony_solver.Rd | 156 prioritizr-4.0.2/prioritizr/man/add_semicontinuous_decisions.Rd | 162 prioritizr-4.0.2/prioritizr/man/add_shuffle_portfolio.Rd | 166 prioritizr-4.0.2/prioritizr/man/array_parameters.Rd | 254 prioritizr-4.0.2/prioritizr/man/as.Rd | 58 prioritizr-4.0.2/prioritizr/man/as.list.Rd | 38 prioritizr-4.0.2/prioritizr/man/binary_stack.Rd | 82 prioritizr-4.0.2/prioritizr/man/boundary_matrix.Rd | 194 prioritizr-4.0.2/prioritizr/man/branch_matrix.Rd | 90 prioritizr-4.0.2/prioritizr/man/category_layer.Rd | 88 prioritizr-4.0.2/prioritizr/man/category_vector.Rd | 94 prioritizr-4.0.2/prioritizr/man/compile.Rd | 116 prioritizr-4.0.2/prioritizr/man/connected_matrix.Rd | 226 prioritizr-4.0.2/prioritizr/man/connectivity_matrix.Rd | 198 prioritizr-4.0.2/prioritizr/man/constraints.Rd | 182 prioritizr-4.0.2/prioritizr/man/decisions.Rd | 164 prioritizr-4.0.2/prioritizr/man/distribute_load.Rd | 142 prioritizr-4.0.2/prioritizr/man/fast_extract.Rd | 164 prioritizr-4.0.2/prioritizr/man/feature_abundances.Rd | 290 prioritizr-4.0.2/prioritizr/man/feature_names.Rd | 86 prioritizr-4.0.2/prioritizr/man/feature_representation.Rd | 442 - 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Title: Nested Association Mapping
Description: Designed for association studies in nested association mapping (NAM) panels, experimental and random panels. The method is described by Xavier et al. (2015) <doi:10.1093/bioinformatics/btv448>. It includes tools for genome-wide associations of multiple populations, marker quality control, population genetics analysis, genome-wide prediction, solving mixed models and finding variance components through likelihood and Bayesian methods.
Author: Alencar Xavier, William Muir, Katy Rainey, Shizhong Xu.
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between NAM versions 1.6 dated 2018-05-11 and 1.6.1 dated 2018-06-28
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- R/snp.R | 25 +++---------------------- inst/doc/gwa_description.pdf |binary inst/doc/vignette1.Rmd | 14 +++++++------- inst/doc/vignette1.html | 18 +++++++++--------- inst/doc/vignette2.html | 4 ++-- man/NAM-package.Rd | 6 +++--- man/gwas.Rd | 10 +++++----- man/wgr.Rd | 7 ------- src/Functions.cpp | 2 -- vignettes/vignette1.Rmd | 14 +++++++------- 12 files changed, 52 insertions(+), 80 deletions(-)
Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS.
Useful for estimating linear models with multiple group fixed effects, and for
estimating linear models which uses factors with many levels as pure control variables.
Includes support for instrumental variables, conditional F statistics for weak instruments,
robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure [aut, cre]
Maintainer: Simen Gaure <Simen.Gaure@frisch.uio.no>
Diff between lfe versions 2.7-2383 dated 2018-06-18 and 2.8 dated 2018-06-28
DESCRIPTION | 20 - MD5 | 55 +-- NAMESPACE | 4 R/bccorr.R | 6 R/btrap.R | 12 R/fixedse.R |only R/kaczmarz.R | 11 R/nlexpect.R | 30 + build/autoconf/config.guess | 679 +++++++++++++++++++++++--------------------- build/autoconf/config.sub | 284 ++++++++---------- build/autoconf/install-sh | 23 - build/vignette.rds |binary configure | 98 +----- configure.ac | 5 inst/NEWS.Rd | 6 inst/doc/biascorrection.pdf |binary inst/doc/identification.pdf |binary inst/doc/lfehow.pdf |binary inst/doc/speed.pdf |binary man/diammatrix.Rd |only man/fixedse.Rd |only man/nlexpect.Rd | 10 src/config.h | 2 src/config.h.in | 2 src/demean.c | 24 + tests/mlhs.R | 10 tests/mlhs.Rout.save | 251 +++++++++------- tests/onefac.R | 4 tests/onefac.Rout.save | 36 +- tests/weights.Rout.save | 8 30 files changed, 816 insertions(+), 764 deletions(-)
Title: Work with Hyperspectral Data, i.e. Spectra + Meta Information
(Spatial, Time, Concentration, ...)
Description: Comfortable ways to work with hyperspectral data sets.
I.e. spatially or time-resolved spectra, or spectra with any other kind
of information associated with each of the spectra. The spectra can be data
as obtained in XRF, UV/VIS, Fluorescence, AES, NIR, IR, Raman, NMR, MS,
etc. More generally, any data that is recorded over a discretized variable,
e.g. absorbance = f (wavelength), stored as a vector of absorbance values
for discrete wavelengths is suitable.
Author: Claudia Beleites [aut, cre, dtc],
Valter Sergo [aut],
Alois Bonifacio [ctb, dtc],
Marcel Dahms [ctb],
Björn Egert [ctb],
Simon Fuller [ctb],
Vilmantas Gegzna [ctb],
Rustam Guliev [ctb],
Bryan Hanson [ctb],
Michael Hermes [ctb],
Martin Kammer [dtc],
Roman Kiselev [ctb],
Sebastian Mellor [ctb]
Maintainer: Claudia Beleites <chemometrie@beleites.de>
Diff between hyperSpec versions 0.99-20171005 dated 2017-10-06 and 0.99-20180627 dated 2018-06-28
DESCRIPTION | 12 +- MD5 | 85 ++++++++++---------- NAMESPACE | 8 + R/bind.R | 37 ++++++-- R/mark.peak.R | 2 R/merge.R | 101 ++++++++++++++++++++++-- R/plotspc.R | 25 +++-- R/qplot.R | 33 +++---- R/qplotmixmap.R | 25 ++++- R/read.spc.R | 44 +++++----- R/read.spe.R | 93 ++++++++++++++++++++-- R/spc.fit.poly.R | 43 +++++++++- R/spc.rubberband.R | 23 +++++ R/sysdata.rda |binary R/wl2i.R | 167 +++++++++++++++++++++++++++++++--------- build/vignette.rds |binary data/barbiturates.rda |binary data/flu.rda |binary data/laser.rda |binary data/paracetamol.rda |binary inst/doc/baseline.pdf |binary inst/doc/chondro.pdf |binary inst/doc/chondro.pdf.asis | 60 +++++++++++++- inst/doc/fileio.pdf |binary inst/doc/fileio.pdf.asis | 5 - inst/doc/flu.pdf |binary inst/doc/hyperspec.R | 150 +++++++++++++++++++++-------------- inst/doc/hyperspec.Rnw | 48 +++++++++-- inst/doc/hyperspec.pdf |binary inst/doc/laser.pdf |binary inst/doc/plotting.pdf |binary man/bind.Rd | 22 +++-- man/merge.Rd | 21 ++++- man/plotspc.Rd | 2 man/qplotmap.Rd | 3 man/qplotmixmap.Rd | 3 man/qplotspc.Rd | 4 man/read.spe.Rd | 2 man/read.spe.xml.Rd |only man/wl2i.Rd | 4 vignettes/chondro.pdf.asis | 60 +++++++++++++- vignettes/fileio.pdf.asis | 5 - vignettes/hyperspec.Rnw | 48 +++++++++-- vignettes/strukturhyperspec.pdf |binary 44 files changed, 853 insertions(+), 282 deletions(-)
Title: Google's Compact Language Detector 3
Description: Google's Compact Language Detector 3 is a neural network model for language
identification and the successor of 'cld2' (available from CRAN). The algorithm is still
experimental and takes a novel approach to language detection with different properties
and outcomes. It can be useful to combine this with the Bayesian classifier results
from 'cld2'. See <https://github.com/google/cld3#readme> for more information.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
Google Inc [cph] (CLD3 C++ library)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between cld3 versions 1.0 dated 2017-06-07 and 1.1 dated 2018-06-28
DESCRIPTION | 13 +++++++------ MD5 | 17 +++++++++-------- NEWS |only R/RcppExports.R | 6 +++--- cleanup | 1 + src/Makevars.in | 13 ++++++++----- src/Makevars.win | 22 +++++++++++++++------- src/RcppExports.cpp | 12 ++++++------ src/wrapper.cpp | 3 ++- tools/winlibs.R | 14 +++++++------- 10 files changed, 58 insertions(+), 43 deletions(-)
Title: Constrained Generalized Additive Model
Description: A constrained generalized additive model is fitted by the cgam routine. Given a set of predictors, each of which may have a shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The ShapeSelect routine chooses a subset of predictor variables and describes the component relationships with the response. For each predictor, the user needs only specify a set of possible shape or order restrictions. A model selection method chooses the shapes and orderings of the relationships as well as the variables. The cone information criterion (CIC) is used to select the best combination of variables and shapes. A genetic algorithm may be used when the set of possible models is large. In addition, the cgam routine implements a two-dimensional isotonic regression using warped-plane splines without additivity assumptions. It can also fit a convex or concave regression surface with triangle splines without additivity assumptions. See Mary C. Meyer (2013)<doi:10.1080/10485252.2013.797577> for more details.
Author: Mary C. Meyer and Xiyue Liao
Maintainer: Xiyue Liao <liaoxiyue2011@gmail.com>
Diff between cgam versions 1.10 dated 2018-04-11 and 1.11 dated 2018-06-28
ChangeLog | 8 + DESCRIPTION | 12 +- MD5 | 16 +-- NAMESPACE | 10 + R/cgam.R | 302 ++++++++++++++++++++++++++++++++++++++++++++++++++++++---- R/cgamm.R |only man/cgam.Rd | 54 +++++++++- man/cgamm.Rd |only man/s.decr.Rd | 8 + man/s.incr.Rd | 8 + 10 files changed, 376 insertions(+), 42 deletions(-)
Title: Reproducible Data Retrieval from the Roper Center Data Archive
Description: Reproducible, programmatic retrieval of datasets from the
Roper Center data archive. The Roper Center for Public Opinion
Research <https://ropercenter.cornell.edu> maintains the largest
archive of public opinion data in existence, but researchers using
these datasets are caught in a bind. The Center's terms and conditions
bar redistribution of downloaded datasets, but to ensure that one's
work can be reproduced, assessed, and built upon by others, one must
provide access to the raw data one employed. The `ropercenter`
package cuts this knot by providing registered users with programmatic,
reproducible access to Roper Center datasets from within R.
Author: Frederick Solt [aut, cre]
Maintainer: Frederick Solt <frederick-solt@uiowa.edu>
Diff between ropercenter versions 0.1.0 dated 2017-03-17 and 0.2.0 dated 2018-06-28
DESCRIPTION | 11 +-- MD5 | 22 +++--- NAMESPACE | 8 ++ NEWS.md | 7 ++ R/read_ascii.R |only R/roper_download.R | 122 ++++++++++++++++++++++--------------- README.md | 4 - build/vignette.rds |binary inst/doc/ropercenter-vignette.R | 19 +++++ inst/doc/ropercenter-vignette.Rmd | 40 +++++++++++- inst/doc/ropercenter-vignette.html | 35 ++++++++-- man/read_ascii.Rd |only vignettes/ropercenter-vignette.Rmd | 40 +++++++++++- 13 files changed, 231 insertions(+), 77 deletions(-)
Title: Mixed-Frequency GARCH Models
Description: Estimating GARCH-MIDAS (MIxed-DAta-Sampling) models (Engle, Ghysels, Sohn, 2013, <doi:10.1162/REST_a_00300>) and related statistical inference, accompanying the paper "Two are better than one: volatility forecasting using multiplicative component GARCH models" by Conrad and Kleen (2018, Working Paper, <doi:10.2139/ssrn.2752354>). The GARCH-MIDAS model decomposes the conditional variance of (daily) stock returns into a short- and long-term component, where the latter may depend on an exogenous covariate sampled at a lower frequency.
Author: Onno Kleen [aut, cre]
Maintainer: Onno Kleen <r@onnokleen.de>
Diff between mfGARCH versions 0.1.4 dated 2018-06-19 and 0.1.5 dated 2018-06-28
DESCRIPTION | 6 MD5 | 24 +- NEWS.md | 3 R/data.R | 24 ++ R/fit_mfgarch.R | 315 +++++++++++++++++++++++++++++--------- R/helper_functions.R | 43 ++++- R/simulate_mfgarch.R | 3 R/simulate_mfgarch_diffusion.R | 3 data/df_mfgarch.rda |only man/df_mfgarch.Rd |only man/fit_mfgarch.Rd | 20 ++ man/simulate_mfgarch.Rd | 4 man/simulate_mfgarch_diffusion.Rd | 4 tests/testthat/test-estimation.R | 9 + 14 files changed, 361 insertions(+), 97 deletions(-)
Title: Simulation of Correlated Data with Multiple Variable Types
Description: Generate continuous (normal or non-normal), binary, ordinal, and count (Poisson or Negative
Binomial) variables with a specified correlation matrix. It can also produce a single continuous
variable. This package can be used to simulate data sets that mimic real-world situations (i.e.
clinical or genetic data sets, plasmodes). All variables are generated from standard normal
variables with an imposed intermediate correlation matrix. Continuous variables are simulated
by specifying mean, variance, skewness, standardized kurtosis, and fifth and sixth standardized
cumulants using either Fleishman's third-order (<DOI:10.1007/BF02293811>) or Headrick's
fifth-order (<DOI:10.1016/S0167-9473(02)00072-5>) polynomial transformation. Binary and
ordinal variables are simulated using a modification of the ordsample() function from 'GenOrd'.
Count variables are simulated using the inverse cdf method. There are two simulation pathways
which differ primarily according to the calculation of the intermediate correlation matrix. In
Correlation Method 1, the intercorrelations involving count variables are determined using a
simulation based, logarithmic correlation correction (adapting Yahav and Shmueli's 2012 method,
<DOI:10.1002/asmb.901>). In Correlation Method 2, the count variables are treated as ordinal
(adapting Barbiero and Ferrari's 2015 modification of GenOrd, <DOI:10.1002/asmb.2072>).
There is an optional error loop that corrects the final correlation matrix to be within a
user-specified precision value of the target matrix. The package also includes functions to
calculate standardized cumulants for theoretical distributions or from real data sets, check
if a target correlation matrix is within the possible correlation bounds (given the distributions
of the simulated variables), summarize results (numerically or graphically), to verify valid power
method pdfs, and to calculate lower standardized kurtosis bounds.
Author: Allison Cynthia Fialkowski
Maintainer: Allison Cynthia Fialkowski <allijazz@uab.edu>
Diff between SimMultiCorrData versions 0.2.1 dated 2017-11-09 and 0.2.2 dated 2018-06-28
DESCRIPTION | 12 +- MD5 | 178 ++++++++++++++++++++--------------------- NEWS.md | 7 + R/SimMultiCorrData.R | 8 - R/calc_lower_skurt.R | 13 ++ R/calc_theory.R | 8 - R/cdf_prob.R | 6 + R/chat_nb.R | 2 R/chat_pois.R | 2 R/error_loop.R | 12 +- R/error_vars.R | 4 R/find_constants.R | 18 ++-- R/findintercorr.R | 4 R/findintercorr2.R | 16 +-- R/findintercorr_cat_nb.R | 2 R/findintercorr_cat_pois.R | 2 R/findintercorr_cont.R | 6 - R/findintercorr_cont_nb.R | 2 R/findintercorr_cont_pois.R | 2 R/findintercorr_nb.R | 6 - R/findintercorr_pois.R | 10 +- R/findintercorr_pois_nb.R | 8 - R/fleish_Hessian.R | 2 R/fleish_skurt_check.R | 2 R/max_count_support.R | 4 R/nonnormvar1.R | 6 + R/pdf_check.R | 6 + R/plot_cdf.R | 10 +- R/plot_pdf_ext.R | 8 - R/plot_pdf_theory.R | 10 +- R/plot_sim_cdf.R | 10 +- R/plot_sim_ext.R | 8 - R/plot_sim_pdf_ext.R | 8 - R/plot_sim_pdf_theory.R | 12 +- R/plot_sim_theory.R | 10 +- R/poly_skurt_check.R | 2 R/rcorrvar.R | 42 +++++---- R/rcorrvar2.R | 42 +++++---- R/stats_pdf.R | 5 - R/valid_corr.R | 33 ++++--- R/valid_corr2.R | 33 ++++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/benefits.html | 4 inst/doc/dist_comp.html | 8 - inst/doc/errorloop.html | 4 inst/doc/functions.html | 10 +- inst/doc/method_comp.html | 4 inst/doc/sixth_validpdf.html | 14 +-- inst/doc/variable_types.html | 4 inst/doc/workflow.html | 22 ++--- man/SimMultiCorrData.Rd | 8 - man/calc_lower_skurt.Rd | 10 +- man/calc_theory.Rd | 8 - man/cdf_prob.Rd | 5 - man/chat_nb.Rd | 2 man/chat_pois.Rd | 2 man/error_loop.Rd | 12 +- man/error_vars.Rd | 4 man/find_constants.Rd | 15 +-- man/findintercorr.Rd | 6 - man/findintercorr2.Rd | 4 man/findintercorr_cat_nb.Rd | 4 man/findintercorr_cat_pois.Rd | 4 man/findintercorr_cont.Rd | 6 - man/findintercorr_cont_nb.Rd | 4 man/findintercorr_cont_pois.Rd | 4 man/findintercorr_nb.Rd | 8 - man/findintercorr_pois.Rd | 12 +- man/findintercorr_pois_nb.Rd | 10 +- man/fleish_Hessian.Rd | 2 man/fleish_skurt_check.Rd | 2 man/max_count_support.Rd | 4 man/nonnormvar1.Rd | 3 man/pdf_check.Rd | 3 man/plot_cdf.Rd | 12 +- man/plot_pdf_ext.Rd | 8 - man/plot_pdf_theory.Rd | 10 +- man/plot_sim_cdf.Rd | 10 +- man/plot_sim_ext.Rd | 8 - man/plot_sim_pdf_ext.Rd | 8 - man/plot_sim_pdf_theory.Rd | 12 +- man/plot_sim_theory.Rd | 10 +- man/poly_skurt_check.Rd | 2 man/rcorrvar.Rd | 19 ++-- man/rcorrvar2.Rd | 21 ++-- man/stats_pdf.Rd | 2 man/valid_corr.Rd | 10 +- man/valid_corr2.Rd | 10 +- vignettes/Bibliography.bib | 30 +++--- 90 files changed, 529 insertions(+), 436 deletions(-)
More information about SimMultiCorrData at CRAN
Permanent link
Title: Analysis of Ecotoxicology
Description: A simple approach to using a probit or logit analysis to calculate
lethal concentration (LC) or time (LT) and the appropriate fiducial
confidence limits desired for selected LC or LT for
ecotoxicology studies (Finney 1971; Wheeler et al. 2006;
Robertson et al. 2007). The simplicity of 'ecotox' comes from the
syntax it implies within its functions which are similar to functions
like glm() and lm(). In addition to the simplicity of the syntax,
a comprehensive data frame is produced which gives the user a
predicted LC or LT value for the desired level and a suite of important
parameters such as fiducial confidence limits and slope.
Finney, D.J. (1971, ISBN: 052108041X);
Wheeler, M.W., Park, R.M., and Bailer, A.J. (2006) <doi:10.1897/05-320R.1>;
Robertson, J.L., Savin, N.E., Russell, R.M., and Preisler, H.K.
(2007, ISBN: 0849323312).
Author: Benjamin L Hlina [aut, cre]
Maintainer: Benjamin L Hlina <benjamin.hlina@gmail.com>
Diff between ecotox versions 1.3.1 dated 2018-03-20 and 1.3.2 dated 2018-06-28
DESCRIPTION | 8 +- MD5 | 32 +++++----- R/LCx.R | 127 +++++++++++++++++++++++++--------------- R/LTx.R | 126 ++++++++++++++++++++++++++------------- R/lampreytime.R | 3 R/lampreytox.R | 3 README.md | 8 +- man/LC_logit.Rd | 14 ++-- man/LC_probit.Rd | 16 ++--- man/LT_logit.Rd | 14 ++-- man/LT_probit.Rd | 14 ++-- man/lampreytime.Rd | 2 man/lampreytox.Rd | 2 tests/testthat/test-LC_logit.R | 37 +++++++++++ tests/testthat/test-LC_probit.R | 36 ++++++++++- tests/testthat/test-LT_logit.R | 51 +++++++++++++++- tests/testthat/test-LT_probit.R | 48 ++++++++++++++- 17 files changed, 394 insertions(+), 147 deletions(-)
Title: Wrappers for Tools in Other Packages for IDE Friendliness
Description: Set of tools aimed at wrapping some of the functionalities of the
packages tools, utils and codetools into a nicer format so that an IDE can use
them.
Author: Philippe Grosjean [aut, cre],
Romain Francois [aut]
Maintainer: Philippe Grosjean <phgrosjean@sciviews.org>
Diff between svTools versions 0.9-4 dated 2014-03-02 and 0.9-5 dated 2018-06-28
DESCRIPTION | 19 +++++++++---------- MD5 | 6 +++--- NAMESPACE | 10 +++++++--- man/svTools-package.Rd | 6 +++--- 4 files changed, 22 insertions(+), 19 deletions(-)
Title: Functions to Ease Interactions Between R and IDE or Code Editors
Description: Function for the GUI API to interact with external IDE/code editors.
Author: Philippe Grosjean [aut, cre]
Maintainer: Philippe Grosjean <phgrosjean@sciviews.org>
Diff between svIDE versions 0.9-52 dated 2014-03-03 and 0.9-54 dated 2018-06-28
DESCRIPTION | 12 ++-- MD5 | 16 +++--- NAMESPACE | 39 +++++++++------ NEWS | 13 ++++- R/createSyntaxFile.R | 124 ++++++++++++++++++++++++------------------------- R/guiDDEInstall.R | 4 - R/makeIconGallery.R | 11 +--- man/makeIconGallery.Rd | 6 +- man/svIDE-package.Rd | 6 +- 9 files changed, 124 insertions(+), 107 deletions(-)
Title: Freshing Up your 'ggplot2' Plots
Description: Functions for working with legends and axis lines of 'ggplot2',
facets that repeat axis lines on all panels, and some 'knitr' extensions.
Author: Stefan McKinnon Edwards [aut, ctb, cre]
(<https://orcid.org/0000-0002-4628-8148>),
Baptiste Auguie [ctb] (For g_legend and grid_arrange_shared_legend),
Shaun Jackman [ctb] (For grid_arrange_shared_legend),
Hadley Wickham [ctb] (ggplot2 functions),
Winston Chang [ctb] (ggplot2 functions)
Maintainer: Stefan McKinnon Edwards <sme@iysik.com>
Diff between lemon versions 0.3.3 dated 2018-01-31 and 0.4.1 dated 2018-06-28
lemon-0.3.3/lemon/vignettes/ggext-lemon.png |only lemon-0.4.1/lemon/DESCRIPTION | 18 +- lemon-0.4.1/lemon/MD5 | 49 +++--- lemon-0.4.1/lemon/NAMESPACE | 4 lemon-0.4.1/lemon/R/brackets.R | 8 - lemon-0.4.1/lemon/R/geom-pointline.r | 144 ++++++++++++------- lemon-0.4.1/lemon/R/geom-siderange.r |only lemon-0.4.1/lemon/R/ggplot2.r | 14 + lemon-0.4.1/lemon/R/gtable_show-.r | 8 - lemon-0.4.1/lemon/R/legends.r | 78 ++++++++++ lemon-0.4.1/lemon/build/vignette.rds |binary lemon-0.4.1/lemon/inst/doc/capped-axes.html | 76 +++++----- lemon-0.4.1/lemon/inst/doc/facet-rep-labels.html | 52 +++--- lemon-0.4.1/lemon/inst/doc/geoms.R |only lemon-0.4.1/lemon/inst/doc/geoms.Rmd |only lemon-0.4.1/lemon/inst/doc/geoms.html |only lemon-0.4.1/lemon/inst/doc/gtable_show_lemonade.html | 136 ++++++++--------- lemon-0.4.1/lemon/inst/doc/legends.R | 8 - lemon-0.4.1/lemon/inst/doc/legends.Rmd | 8 - lemon-0.4.1/lemon/inst/doc/legends.html | 142 +++++++++--------- lemon-0.4.1/lemon/inst/doc/lemon_print.html | 17 +- lemon-0.4.1/lemon/inst/examples/geom-pointline-ex.r | 63 +------- lemon-0.4.1/lemon/inst/examples/geom-siderange-ex.r |only lemon-0.4.1/lemon/man/geom_pointpath.Rd | 87 +++-------- lemon-0.4.1/lemon/man/geom_siderange.Rd |only lemon-0.4.1/lemon/man/gtable_show.Rd | 2 lemon-0.4.1/lemon/man/guidebox_as_column.Rd |only lemon-0.4.1/lemon/man/lemon-ggproto.Rd | 3 lemon-0.4.1/lemon/vignettes/geoms.Rmd |only lemon-0.4.1/lemon/vignettes/legends.Rmd | 8 - 30 files changed, 508 insertions(+), 417 deletions(-)
Title: Interface to 'Dygraphs' Interactive Time Series Charting Library
Description: An R interface to the 'dygraphs' JavaScript charting library
(a copy of which is included in the package). Provides rich facilities
for charting time-series data in R, including highly configurable
series- and axis-display and interactive features like zoom/pan and
series/point highlighting.
Author: Dan Vanderkam [aut, cph] (dygraphs library in htmlwidgets/lib,
http://dygraphs.com/),
Petr Shevtsov [cre, cph],
JJ Allaire [aut],
RStudio [cph],
Jonathan Owen [aut, cph],
Daniel Gromer [aut, cph],
Benoit Thieurmel [aut, cph],
Kent Laukhuf [ctb],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/htmlwidgets/lib/jquery/AUTHORS.txt)
Maintainer: Petr Shevtsov <petr.shevtsov@gmail.com>
Diff between dygraphs versions 1.1.1.4 dated 2017-01-04 and 1.1.1.5 dated 2018-06-28
dygraphs-1.1.1.4/dygraphs/inst/examples/examples.html |only dygraphs-1.1.1.4/dygraphs/inst/examples/plotters |only dygraphs-1.1.1.4/dygraphs/inst/plugins/candlestick.js |only dygraphs-1.1.1.4/dygraphs/man/dyCandlestick.Rd |only dygraphs-1.1.1.5/dygraphs/DESCRIPTION | 23 + dygraphs-1.1.1.5/dygraphs/MD5 | 95 ++++--- dygraphs-1.1.1.5/dygraphs/NAMESPACE | 15 + dygraphs-1.1.1.5/dygraphs/R/candlestick.R | 21 - dygraphs-1.1.1.5/dygraphs/R/dependency.R | 9 dygraphs-1.1.1.5/dygraphs/R/group.R |only dygraphs-1.1.1.5/dygraphs/R/options.R | 25 ++ dygraphs-1.1.1.5/dygraphs/R/plotters.R |only dygraphs-1.1.1.5/dygraphs/R/series.R | 119 +++++++++- dygraphs-1.1.1.5/dygraphs/inst/NEWS | 9 dygraphs-1.1.1.5/dygraphs/inst/htmlwidgets/dygraphs.js | 20 + dygraphs-1.1.1.5/dygraphs/inst/htmlwidgets/dygraphs.yaml | 4 dygraphs-1.1.1.5/dygraphs/inst/htmlwidgets/lib/dygraphs/shapes.js |only dygraphs-1.1.1.5/dygraphs/inst/plotters |only dygraphs-1.1.1.5/dygraphs/man/Plotters.Rd |only dygraphs-1.1.1.5/dygraphs/man/dyAnnotation.Rd | 1 dygraphs-1.1.1.5/dygraphs/man/dyAxis.Rd | 1 dygraphs-1.1.1.5/dygraphs/man/dyCSS.Rd | 1 dygraphs-1.1.1.5/dygraphs/man/dyCallbacks.Rd | 1 dygraphs-1.1.1.5/dygraphs/man/dyCrosshair.Rd | 1 dygraphs-1.1.1.5/dygraphs/man/dyDataHandler.Rd | 1 dygraphs-1.1.1.5/dygraphs/man/dyDependency.Rd | 1 dygraphs-1.1.1.5/dygraphs/man/dyEvent.Rd | 1 dygraphs-1.1.1.5/dygraphs/man/dyGroup.Rd |only dygraphs-1.1.1.5/dygraphs/man/dyHighlight.Rd | 1 dygraphs-1.1.1.5/dygraphs/man/dyLegend.Rd | 1 dygraphs-1.1.1.5/dygraphs/man/dyLimit.Rd | 1 dygraphs-1.1.1.5/dygraphs/man/dyOptions.Rd | 36 +-- dygraphs-1.1.1.5/dygraphs/man/dyPlotter.Rd | 1 dygraphs-1.1.1.5/dygraphs/man/dyPlugin.Rd | 1 dygraphs-1.1.1.5/dygraphs/man/dyRangeSelector.Rd | 1 dygraphs-1.1.1.5/dygraphs/man/dyRebase.Rd | 1 dygraphs-1.1.1.5/dygraphs/man/dyRibbon.Rd | 1 dygraphs-1.1.1.5/dygraphs/man/dyRoller.Rd | 1 dygraphs-1.1.1.5/dygraphs/man/dySeries.Rd | 17 - dygraphs-1.1.1.5/dygraphs/man/dySeriesData.Rd | 1 dygraphs-1.1.1.5/dygraphs/man/dyShading.Rd | 1 dygraphs-1.1.1.5/dygraphs/man/dyUnzoom.Rd | 1 dygraphs-1.1.1.5/dygraphs/man/dygraph-shiny.Rd | 1 dygraphs-1.1.1.5/dygraphs/man/dygraph.Rd | 1 dygraphs-1.1.1.5/dygraphs/man/dygraphs-exports.Rd | 3 45 files changed, 291 insertions(+), 127 deletions(-)
Title: Connecting to Various Database Platforms
Description: An R 'DataBase Interface' ('DBI') compatible interface to various database platforms ('PostgreSQL', 'Oracle', 'Microsoft SQL Server',
'Amazon Redshift', 'Microsoft Parallel Database Warehouse', 'IBM Netezza', 'Apache Impala', and 'Google BigQuery'). Also includes support for
fetching data as 'ffdf' objects. Uses 'Java Database Connectivity' ('JDBC') to connect to databases.
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut],
Observational Health Data Science and Informatics [cph],
Microsoft Inc. [cph] (SQL Server JDBC driver),
PostgreSQL Global Development Group [cph] (PostgreSQL JDBC driver),
Starschema Ltd. [cph] (BigQuery JDBC driver),
Oracle Inc. [cph] (Oracle JDBC driver),
Amazon Inc. [cph] (RedShift JDBC driver)
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between DatabaseConnector versions 2.1.2 dated 2018-05-24 and 2.1.3 dated 2018-06-28
DESCRIPTION | 10 MD5 | 68 NAMESPACE | 4 NEWS | 14 R/Connect.R | 22 R/DBI.R | 65 R/InsertTable.R | 75 R/RStudio.R | 25 README.md | 22 build/DatabaseConnector.pdf |13216 +++++----- build/vignette.rds |binary inst/doc/UsingDatabaseConnector.pdf |binary man/dbAppendTable-DatabaseConnectorConnection-character-data.frame-method.Rd |only man/dbClearResult-DatabaseConnectorResult-method.Rd | 4 man/dbColumnInfo-DatabaseConnectorResult-method.Rd | 22 man/dbCreateTable-DatabaseConnectorConnection-character-data.frame-method.Rd |only man/dbDisconnect-DatabaseConnectorConnection-method.Rd | 13 man/dbExecute-DatabaseConnectorConnection-character-method.Rd | 18 man/dbExistsTable-DatabaseConnectorConnection-character-method.Rd | 12 man/dbFetch-DatabaseConnectorResult-method.Rd | 4 man/dbGetQuery-DatabaseConnectorConnection-character-method.Rd | 21 man/dbGetRowCount-DatabaseConnectorResult-method.Rd | 4 man/dbGetRowsAffected-DatabaseConnectorResult-method.Rd | 4 man/dbGetStatement-DatabaseConnectorResult-method.Rd | 4 man/dbHasCompleted-DatabaseConnectorResult-method.Rd | 4 man/dbIsValid-DatabaseConnectorConnection-method.Rd | 19 man/dbListFields-DatabaseConnectorConnection-character-method.Rd | 26 man/dbListTables-DatabaseConnectorConnection-method.Rd | 12 man/dbQuoteIdentifier-DatabaseConnectorConnection-character-method.Rd | 10 man/dbQuoteString-DatabaseConnectorConnection-character-method.Rd | 4 man/dbReadTable-DatabaseConnectorConnection-character-method.Rd | 12 man/dbRemoveTable-DatabaseConnectorConnection-character-method.Rd | 12 man/dbSendQuery-DatabaseConnectorConnection-character-method.Rd | 10 man/dbSendStatement-DatabaseConnectorConnection-character-method.Rd | 12 man/dbUnloadDriver-DatabaseConnectorDriver-method.Rd | 10 man/dbWriteTable-DatabaseConnectorConnection-character-data.frame-method.Rd | 12 36 files changed, 7852 insertions(+), 5918 deletions(-)
More information about DatabaseConnector at CRAN
Permanent link
Title: Representative and Adequate Prioritization Toolkit in R
Description: Biodiversity is in crisis. The overarching aim of conservation
is to preserve biodiversity patterns and processes. To this end, protected
areas are established to buffer species and preserve biodiversity processes.
But resources are limited and so protected areas must be cost-effective.
This package contains tools to generate plans for protected areas
(prioritizations), using spatially explicit targets for biodiversity
patterns and processes. To obtain solutions in a feasible amount of time,
this package uses the commercial 'Gurobi' software package (obtained from
<http://www.gurobi.com/>). For more information on using
this package, see Hanson et al. (2017) <doi:10.1111/2041-210X.12862>.
Author: Jeffrey O Hanson [aut, cre],
Jonathan R Rhodes [aut],
Hugh P Possingham [aut],
Richard A Fuller [aut]
Maintainer: Jeffrey O Hanson <jeffrey.hanson@uqconnect.edu.au>
Diff between raptr versions 0.1.1 dated 2017-11-20 and 0.1.2 dated 2018-06-28
DESCRIPTION | 17 MD5 | 80 - NEWS.md | 15 R/DemandPoints.R | 15 R/GurobiOpts.R | 54 R/RapResults.R | 6 R/RapSolved.R | 54 R/RapUnsolved.R | 8 R/generics.R | 26 R/misc.R | 23 R/raptr.R | 4 README.md | 16 build/vignette.rds |binary inst/CITATION | 13 inst/doc/raptr.html | 2182 ++++++++++++++-------------- man/GurobiOpts-class.Rd | 22 man/GurobiOpts.Rd | 24 man/RapUnsolved.Rd | 8 man/calcSpeciesAverageInPus.Rd | 2 man/is.GurobiInstalled.Rd | 2 man/make.DemandPoints.Rd | 15 man/raptr.Rd | 4 man/update.Rd | 24 src/dump_object.cpp | 12 src/functions.cpp | 198 +- src/rcpp_Polygons2PolySet.cpp | 114 - src/rcpp_append_model_object.cpp | 80 - src/rcpp_calcBoundaryDF.cpp | 403 ++--- src/rcpp_extract_model_object.cpp | 200 +- src/rcpp_generate_model_object.cpp | 2034 +++++++++++++------------- src/rcpp_groupcombine.cpp | 72 src/rcpp_groupmean.cpp | 74 src/rcpp_proportion_held.cpp | 74 src/rcpp_rrap_proportion_held.cpp | 112 - src/rcpp_rrap_squared_distance.cpp | 96 - src/rcpp_squared_distance.cpp | 48 src/rcpp_sum_duplicates.cpp | 94 - tests/testthat/test-01-rapr-internal-test.R | 2 tests/testthat/test-07-DemandPoints.R | 10 tests/testthat/test-11-RapUnsolved.R | 105 - tests/testthat/test-13-rap.R | 40 41 files changed, 3294 insertions(+), 3088 deletions(-)
Title: Optimum Contribution Selection and Population Genetics
Description: A framework for the optimization of breeding programs via optimum contribution selection and mate allocation. An easy to use set of function for computation of optimum contributions of selection candidates, and of the population genetic parameters to be optimized. These parameters can be estimated using pedigree or genotype information, and include kinships, kinships at native haplotype segments, and breed composition of crossbred individuals. They are suitable for managing genetic diversity, removing introgressed genetic material, and accelerating genetic gain. Additionally, functions are provided for computing genetic contributions from ancestors, inbreeding coefficients, the native effective size, the native genome equivalent, pedigree completeness, and for preparing and plotting pedigrees.
Author: Robin Wellmann
Maintainer: Robin Wellmann <r.wellmann@uni-hohenheim.de>
Diff between optiSel versions 2.0 dated 2017-12-15 and 2.0.1 dated 2018-06-28
optiSel-2.0.1/optiSel/DESCRIPTION | 8 - optiSel-2.0.1/optiSel/MD5 | 57 ++++---- optiSel-2.0.1/optiSel/R/NPOpopALT.R |only optiSel-2.0.1/optiSel/R/agecont.R | 3 optiSel-2.0.1/optiSel/R/characterizeClasses.R | 2 optiSel-2.0.1/optiSel/R/checkbc.R | 2 optiSel-2.0.1/optiSel/R/checkphen.R | 4 optiSel-2.0.1/optiSel/R/fun4Kin.R | 4 optiSel-2.0.1/optiSel/R/fun4KinatN.R | 2 optiSel-2.0.1/optiSel/R/gettraits.R | 2 optiSel-2.0.1/optiSel/R/pPOpop.R |only optiSel-2.0.1/optiSel/R/param4candes.R | 4 optiSel-2.0.1/optiSel/R/pedIBDatN.R | 4 optiSel-2.0.1/optiSel/R/prePed.R | 9 + optiSel-2.0.1/optiSel/R/segIBDatN.R | 4 optiSel-2.0.1/optiSel/build/partial.rdb |binary optiSel-2.0.1/optiSel/build/vignette.rds |binary optiSel-2.0.1/optiSel/data/Cattle.rda |binary optiSel-2.0.1/optiSel/data/ExamplePed.rda |binary optiSel-2.0.1/optiSel/data/PedigWithErrors.rda |binary optiSel-2.0.1/optiSel/data/Phen.rda |binary optiSel-2.0.1/optiSel/data/map.rda |binary optiSel-2.0.1/optiSel/inst/doc/ocs-vignette.html | 156 +++++++++++------------ optiSel-2.0.1/optiSel/inst/doc/ped-vignette.html | 8 - optiSel-2.0.1/optiSel/inst/doc/seg-vignette.html | 4 optiSel-2.0.1/optiSel/man/candes.Rd | 4 optiSel-2.0.1/optiSel/man/optiSel-package.Rd | 2 optiSel-2.0.1/optiSel/man/opticont.Rd | 16 +- optiSel-2.0.1/optiSel/man/pedIBDatN.Rd | 10 - optiSel-2.0.1/optiSel/man/segIBDatN.Rd | 10 - optiSel-2.0/optiSel/R/NPOpop.R |only 31 files changed, 163 insertions(+), 152 deletions(-)
Title: Evaluation of Indicator Performances for Assessing Ecosystem
States
Description: An implementation of the 7-step approach suggested by Otto et al.
(2018) <doi:10.1016/j.ecolind.2017.05.045> to validate ecological state indicators
and to select a suite of complimentary and well performing indicators.
This suite can be then used to assess the current state of the system
in comparison to a reference period. However, the tools in this package
are very generic and can be used to test any type of indicator (e.g. social
or economic indicators).
Author: Saskia A. Otto [aut, cre],
Rene Plonus [aut],
Steffen Funk [aut],
Alexander Keth [aut]
Maintainer: Saskia A. Otto <saskia.a.otto@gmail.com>
Diff between INDperform versions 0.1.0 dated 2018-06-14 and 0.1.1 dated 2018-06-28
INDperform-0.1.0/INDperform/man/figures/Logo.png |only INDperform-0.1.0/INDperform/tests/figs |only INDperform-0.1.1/INDperform/DESCRIPTION | 9 INDperform-0.1.1/INDperform/MD5 | 38 INDperform-0.1.1/INDperform/R/plot_trend.R | 1 INDperform-0.1.1/INDperform/R/select_model.R | 2 INDperform-0.1.1/INDperform/README.md | 31 INDperform-0.1.1/INDperform/man/figures/INDperform_cheatsheet.png |only INDperform-0.1.1/INDperform/man/figures/logo.png |only INDperform-0.1.1/INDperform/man/select_model.Rd | 2 INDperform-0.1.1/INDperform/tests/testthat/Rplots.pdf |only INDperform-0.1.1/INDperform/tests/testthat/test_model_gamm.R | 21 INDperform-0.1.1/INDperform/tests/testthat/test_plots.R | 486 +++++----- 13 files changed, 303 insertions(+), 287 deletions(-)
Title: Flexible Gaussian Cluster Simulator
Description: Clustering is a central task in big data analyses and clusters are often Gaussian or near Gaussian. However, a flexible Gaussian cluster simulation tool with precise control over the size, variance, and spacing of the clusters in NXN dimensional space does not exist. This is why we created 'clusterlab'. The algorithm first creates X points equally spaced on the circumference of a circle in 2D space. These form the centers of each cluster to be simulated. Additional samples are added by adding Gaussian noise to each cluster center and concatenating the new sample co-ordinates. Then if the feature space is greater than 2D, the generated points are considered principal component scores and projected into N dimensional space using linear combinations using fixed eigenvectors. Through using vector rotations and scalar multiplication clusterlab can generate complex patterns of Gaussian clusters and outliers. The algorithm is highly customizable and well suited to testing class discovery tools across a range of fields.
Author: Christopher R John
Maintainer: Christopher R John <chris.r.john86@gmail.com>
Diff between clusterlab versions 0.0.2.1 dated 2018-06-27 and 0.0.2.2 dated 2018-06-28
DESCRIPTION | 6 ++--- MD5 | 8 +++---- inst/doc/introduction.Rmd | 25 +++++++++++------------ inst/doc/introduction.html | 47 ++++++++++++++++++++++----------------------- vignettes/introduction.Rmd | 25 +++++++++++------------ 5 files changed, 54 insertions(+), 57 deletions(-)
Title: Management of GUI Widgets, Windows, and Other GUI Resources
Description: High level management of widgets, windows and other graphical resources.
Author: Philippe Grosjean [aut, cre]
Maintainer: Philippe Grosjean <phgrosjean@sciviews.org>
Diff between svWidgets versions 0.9-44 dated 2014-03-02 and 0.9-45 dated 2018-06-28
DESCRIPTION | 10 +-- MD5 | 8 +- NAMESPACE | 143 ++++++++++++++++++++++++----------------------- NEWS | 9 ++ man/svWidgets-package.Rd | 4 - 5 files changed, 94 insertions(+), 80 deletions(-)
Title: Toolkit for Item Factor Analysis with 'OpenMx'
Description: Tools, tutorials, and demos of Item Factor Analysis using 'OpenMx'.
Author: Joshua N. Pritikin [cre, aut]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between ifaTools versions 0.14 dated 2017-04-17 and 0.16 dated 2018-06-28
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- R/apps.R | 7 +++++++ R/prior.R | 4 ++-- build/vignette.rds |binary inst/doc/pritikin-schmidt.pdf |binary inst/modelBuilder/server.R | 40 ++++++++++++++++++++-------------------- inst/modelBuilder/ui.R | 3 ++- man/uniquenessPrior.Rd | 4 ++-- 9 files changed, 46 insertions(+), 38 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-09-08 0.4.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-11 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-01-29 1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-03-24 0.5
2017-02-21 0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-01-30 1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-06-07 1.2.1
2018-06-05 1.2.0
2017-12-01 1.1.2
2017-07-18 1.1.1
2017-06-06 1.1.0
2017-03-26 1.0.0
Title: Computing Weighted Topological Overlaps (wTO) & Consensus wTO
Network
Description: Computes the Weighted Topological Overlap with positive and negative signs (wTO) networks (Nowick et al. (2009) <doi:10.1073/pnas.0911376106>) given a data frame containing the mRNA count/ expression/ abundance per sample, and a vector containing the interested nodes of interaction (a subset of the elements of the full data frame). It also computes the cut-off threshold or p-value based on the individuals bootstrap or the values reshuffle per individual. It also allows the construction of a consensus network, based on multiple wTO networks. The package includes a visualization tool for the networks. More about the methodology can be found at <arXiv:1711.04702>.
Author: Deisy Morselli Gysi, Andre Voigt, Tiago Miranda Fragoso, Eivind Almaas and Katja Nowick.
Maintainer: Deisy Morselli Gysi <deisy@bioinf.uni-leipzig.de>
Diff between wTO versions 1.6 dated 2018-05-30 and 1.6.1 dated 2018-06-28
wTO-1.6.1/wTO/DESCRIPTION | 10 + wTO-1.6.1/wTO/MD5 | 58 ++++++--- wTO-1.6.1/wTO/NAMESPACE | 2 wTO-1.6.1/wTO/R/Correlation.Overlap.R | 8 - wTO-1.6.1/wTO/R/Cut.off2.R | 107 +++++++++--------- wTO-1.6.1/wTO/R/ExampledfExpression.R | 12 +- wTO-1.6.1/wTO/R/ExampledfExpression2.R |only wTO-1.6.1/wTO/R/NetVis.R | 2 wTO-1.6.1/wTO/R/metagenomics.R |only wTO-1.6.1/wTO/R/wTO.Complete2.R | 154 +++++++++++++------------- wTO-1.6.1/wTO/R/wTO.Consensus.R | 4 wTO-1.6.1/wTO/R/wTO.aux.each.R | 112 +++++++++--------- wTO-1.6.1/wTO/R/wTOfast.R | 10 - wTO-1.6.1/wTO/build |only wTO-1.6.1/wTO/data/Microarray_Expression1.txt |only wTO-1.6.1/wTO/data/Microarray_Expression2.txt |only wTO-1.6.1/wTO/data/metagenomics_abundance.txt |only wTO-1.6.1/wTO/inst/doc |only wTO-1.6.1/wTO/man/CorrelationOverlap.Rd |only wTO-1.6.1/wTO/man/Microarray_Expression1.Rd |only wTO-1.6.1/wTO/man/Microarray_Expression2.Rd |only wTO-1.6.1/wTO/man/NetVis.Rd | 2 wTO-1.6.1/wTO/man/metagenomics_abundance.Rd |only wTO-1.6.1/wTO/man/wTO.Complete.Rd | 12 +- wTO-1.6.1/wTO/man/wTO.Consensus.Rd | 2 wTO-1.6.1/wTO/man/wTO.fast.Rd | 4 wTO-1.6.1/wTO/vignettes |only wTO-1.6/wTO/data/ExampledfExpression.txt |only wTO-1.6/wTO/man/Correlation.Overlap.Rd |only wTO-1.6/wTO/man/ExampledfExpression.Rd |only 30 files changed, 271 insertions(+), 228 deletions(-)
Title: Functions to Support the ICES Transparent Assessment Framework
Description: Functions to support the ICES Transparent Assessment Framework
<http://taf.ices.dk> to organize data, methods, and results used in ICES
assessments. ICES is an organization facilitating international collaboration
in marine science.
Author: Arni Magnusson [aut, cre],
Colin Millar [aut]
Maintainer: Arni Magnusson <arni.magnusson@ices.dk>
Diff between icesTAF versions 1.6-0 dated 2018-05-15 and 1.6-1 dated 2018-06-28
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS | 22 ++++++++++++++++++++-- R/clean.R | 8 ++------ R/cp.R | 26 ++++++++++++++++++++++++++ R/makeAll.R | 14 ++++++-------- R/makeTAF.R | 2 -- R/sourceAll.R | 14 ++++++-------- R/sourceTAF.R | 24 ++++++++++++++---------- R/write.taf.R | 2 +- man/clean.Rd | 6 ++---- man/cp.Rd | 14 ++++++++++++++ man/makeAll.Rd | 12 ++++++------ man/sourceAll.Rd | 12 ++++++------ man/sourceTAF.Rd | 22 +++++++++++++--------- 15 files changed, 134 insertions(+), 80 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-06-25 1.2.1
2018-04-06 1.0.1
2018-01-29 1.0
Title: Photobiological Calculations
Description: Definitions of classes, methods, operators and functions for use in
photobiology and radiation meteorology and climatology. Calculation of
effective (weighted) and not-weighted irradiances/doses, fluence rates,
transmittance, reflectance, absorptance, absorbance and diverse
ratios and other derived quantities from spectral data. Local maxima and
minima. Conversion between energy- and photon-based units. Wavelength
interpolation. Astronomical calculations related solar angles and day
length. Colours and vision. This package is part of the
'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>),
Titta K. Kotilainen [ctb] (<https://orcid.org/0000-0002-2822-9734>),
Glenn Davis [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiology versions 0.9.20 dated 2018-04-02 and 0.9.21 dated 2018-06-28
DESCRIPTION | 22 MD5 | 162 +- NAMESPACE | 8 NEWS | 21 R/copy.attr.R | 97 + R/fel.spectrum.r | 4 R/head-tail.R | 18 R/mspct.methods.R | 2 R/on-attach.R | 4 R/photobiology.r | 2 R/rbindspct.r | 135 ++ R/spct.classes.r | 835 ++++++++------ R/spct.conversion.R | 3 R/spct.fscale.r | 66 - R/spct.new.r | 62 - R/spct.normalize.r | 133 +- R/spct.operators.r | 104 - R/spct.peaks.r | 201 ++- R/spct.smooth.spct.r | 27 R/spct.trim.r | 12 R/sun.calc.r | 4 R/water.vapour.R | 29 README.md | 103 + build/vignette.rds |binary data/A.illuminant.spct.rda |binary data/D2-FEL-constants.rda |binary data/D65.illuminant.spct.rda |binary data/Ler-leaf-spct.rda |binary data/beesxyz.spct.rda |binary data/black_body.spct.rda |binary data/ccd.spct.rda |binary data/ciev10.spct.rda |binary data/ciev2.spct.rda |binary data/ciexyzCC10.spct.rda |binary data/ciexyzCC2.spct.rda |binary data/ciexyzCMF10.spct.rda |binary data/ciexyzCMF2.spct.rda |binary data/clear.spct.rda |binary data/clear_body.spct.rda |binary data/filter-cps-mspct.rda |binary data/green_leaf.spct.rda |binary data/opaque.spct.rda |binary data/photodiode.spct.rda |binary data/polyester.spct.rda |binary data/sun.daily.data.rda |binary data/sun.daily.spct.rda |binary data/sun.data.rda |binary data/sun.spct.rda |binary data/white-led-spct.rda |binary data/white_body.spct.rda |binary data/yellow.gel.rda |binary inst/doc/userguide1-intro.Rmd | 33 inst/doc/userguide1-intro.html | 288 ++++ inst/doc/userguide2-radiation.R | 12 inst/doc/userguide2-radiation.Rmd | 42 inst/doc/userguide2-radiation.html | 2205 ++++++++++++++++++++----------------- inst/doc/userguide3-astronomy.Rmd | 3 inst/doc/userguide3-astronomy.html | 472 +++++-- man/FEL_spectrum.Rd | 4 man/add_attr2tb.Rd | 2 man/copy_attributes.Rd | 2 man/energy_as_default.Rd | 3 man/findMultipleWl.Rd |only man/find_peaks.Rd | 6 man/fscale.Rd | 7 man/getIdFactor.Rd |only man/getSpctVersion.Rd | 2 man/get_peaks.Rd | 7 man/head_tail.Rd | 19 man/merge_attributes.Rd |only man/normalize.Rd | 58 man/peaks.Rd | 46 man/photobiology-package.Rd | 8 man/setGenericSpct.Rd | 24 man/setIdFactor.Rd |only man/setWhereMeasured.Rd | 2 man/solar_time.Rd | 4 man/source_spct.Rd | 26 man/trim_spct.Rd | 14 man/valleys.Rd | 46 man/water_vp_sat.Rd | 10 vignettes/userguide1-intro.Rmd | 33 vignettes/userguide2-radiation.Rmd | 42 vignettes/userguide3-astronomy.Rmd | 3 84 files changed, 3469 insertions(+), 2008 deletions(-)
Title: An Algorithm for Gene Co-Expression Analysis
Description: Implementation based on Zhang, Jie & Huang, Kun (2014) <doi:10.4137/CIN.S14021> Normalized ImQCM: An Algorithm for Detecting Weak Quasi-Cliques in Weighted Graph with Applications in Gene Co-Expression Module Discovery in Cancers. Cancer informatics, 13, CIN-S14021.
Author: Zhi Huang [aut, cre],
Jie Zhang [aut, ctb],
Kun Huang [aut, ctb],
Zhi Han [aut, ctb]
Maintainer: Zhi Huang <huang898@purdue.edu>
Diff between lmQCM versions 0.1.0 dated 2018-03-19 and 0.1.1 dated 2018-06-28
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/lmQCM.R | 16 ++++++++++++++-- man/lmQCM.Rd | 4 +++- 4 files changed, 25 insertions(+), 11 deletions(-)
Title: Work with 'GitHub' 'Gists'
Description: Work with 'GitHub' 'gists' from 'R' (e.g.,
<http://en.wikipedia.org/wiki/GitHub#Gist>,
<https://help.github.com/articles/about-gists/>). A 'gist'
is simply one or more files with code/text/images/etc. This package allows
the user to create new 'gists', update 'gists' with new files, rename files,
delete files, get and delete 'gists', star and 'un-star' 'gists', fork 'gists',
open a 'gist' in your default browser, get embed code for a 'gist', list
'gist' 'commits', and get rate limit information when 'authenticated'. Some
requests require authentication and some do not. 'Gists' website:
<https://gist.github.com/>.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Ramnath Vaidyanathan [aut],
Karthik Ram [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between gistr versions 0.4.0 dated 2017-04-20 and 0.4.2 dated 2018-06-28
DESCRIPTION | 18 ++-- LICENSE | 2 MD5 | 46 +++++------ NEWS.md | 13 +++ R/gist.R | 14 ++- R/gist_create.R | 22 +---- R/gist_create_git.R | 5 - R/rate_limit.R | 1 R/update.R | 3 R/zzz.R | 15 ++- README.md | 174 +++++++++++++++++++++--------------------- build/vignette.rds |binary inst/examples/example1.md | 2 inst/examples/plots.md | 6 - inst/examples/plots_imgur.md | 6 - inst/examples/rmarkdown_eg.md | 4 man/gist.Rd | 11 ++ man/gist_create.Rd | 66 +++++++-------- man/gist_create_git.Rd | 39 +++++---- man/rate_limit.Rd | 1 man/update.Rd | 2 tests/testthat/test-fork.R | 2 tests/testthat/test-gist.R | 16 +++ tests/testthat/test-star.R | 40 ++++----- 24 files changed, 278 insertions(+), 230 deletions(-)
Title: R Interface to the DataONE REST API
Description: Provides read and write access to data and metadata from
the DataONE network <https://www.dataone.org> of data repositories.
Each DataONE repository implements a consistent repository application
programming interface. Users call methods in R to access these remote
repository functions, such as methods to query the metadata catalog, get
access to metadata for particular data packages, and read the data objects
from the data repository. Users can also insert and update data objects on
repositories that support these methods.
Author: Matthew B. Jones [aut, cre],
Peter Slaughter [aut],
Rob Nahf [aut],
Carl Boettiger [aut],
Chris Jones [aut],
Jordan Read [aut],
Lauren Walker [aut],
Edmund Hart [aut],
Scott Chamberlain [aut],
Regents of the University of California [cph]
Maintainer: Matthew B. Jones <jones@nceas.ucsb.edu>
Diff between dataone versions 2.1.0 dated 2017-08-18 and 2.1.1 dated 2018-06-28
DESCRIPTION | 10 MD5 | 75 ++--- NAMESPACE | 2 NEWS | 13 R/CNode.R | 30 +- R/D1Client.R | 149 +++++++++-- R/D1Node.R | 29 +- R/MNode.R | 204 ++++++++------- R/auth_request.R | 16 - build/vignette.rds |binary inst/doc/dataone-federation.html | 310 +++++++++++++++++++---- inst/doc/dataone-overview.Rmd | 4 inst/doc/dataone-overview.html | 342 ++++++++++++++++++++----- inst/doc/download-data.html | 364 +++++++++++++++++++++------ inst/doc/known-issues.html | 322 +++++++++++++++++++----- inst/doc/searching-dataone.html | 348 ++++++++++++++++++++------ inst/doc/update-package.html | 380 ++++++++++++++++++++++------ inst/doc/upload-data.html | 519 +++++++++++++++++++++++++++------------ man/D1Client-initialize.Rd | 2 man/D1Client.Rd | 3 man/MNode-class.Rd | 2 man/archive.Rd | 2 man/auth_get.Rd | 4 man/createObject.Rd | 2 man/describeObject.Rd | 2 man/downloadObject.Rd |only man/getCapabilities.Rd | 2 man/getChecksum.Rd | 4 man/getPackage.Rd | 8 man/getSystemMetadata.Rd | 4 man/listMemberNodes.Rd | 2 man/ping.Rd | 2 man/uploadDataObject.Rd | 2 tests/testthat/helper-base.R | 1 tests/testthat/test.CNode.R | 26 - tests/testthat/test.D1Client.R | 25 + tests/testthat/test.D1Node.R | 79 ++--- tests/testthat/test.MNode.R | 47 +-- vignettes/dataone-overview.Rmd | 4 39 files changed, 2509 insertions(+), 831 deletions(-)
Title: Multivariate Chebyshev Interpolation
Description: Contains methods for creating multivariate Chebyshev
interpolations of functions on a hypercube. If available through fftw3, the DCT-II/FFT
is used to compute the coefficients, so it is reasonably fast. Some interpolation methods for
multivariate non-Chebyshev grids are also provided, as well as polyharmonic
splines with a linear term.
Author: Simen Gaure [aut, cre]
Maintainer: Simen Gaure <Simen.Gaure@frisch.uio.no>
Diff between chebpol versions 1.3-1789 dated 2015-10-28 and 1.4-1 dated 2018-06-28
DESCRIPTION | 23 +- MD5 | 38 ++-- R/chebpol.R | 141 ++++++++++++++--- build/vignette.rds |binary configure | 394 +++++++++++++++++++++++++++++++++++++++++++------ configure.ac | 60 ++++++- inst/doc/chebpol.R | 92 ++--------- inst/doc/chebpol.Rnw | 95 +++-------- inst/doc/chebpol.pdf |binary man/chebappx.Rd | 5 man/chebeval.Rd | 4 man/chebpol-package.Rd | 27 ++- man/mlappx.Rd | 2 man/polyh.Rd | 32 ++- src/Makevars.in | 4 src/chebpol.c | 228 +++++++++++++++++----------- src/config.h |only src/config.h.in |only tests/all.R | 22 +- tests/all.Rout.save | 67 ++++---- vignettes/chebpol.Rnw | 95 +++-------- 21 files changed, 870 insertions(+), 459 deletions(-)