Title: Missing Morphometric Data Simulation and Estimation
Description: Functions for simulating missing morphometric
data randomly, with taxonomic bias and with anatomical bias. LOST also
includes functions for estimating linear and geometric morphometric data.
Author: J. Arbour,
C. Brown
Maintainer: J. Arbour <jessica.arbour@mtsu.edu>
Diff between LOST versions 2.0.2 dated 2020-04-14 and 2.1.1 dated 2024-07-03
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++++++--------- NAMESPACE | 2 +- R/align.missing.R | 2 ++ R/bilat.align.R |only R/byclade.R | 4 ++-- R/how.many.missing.R | 2 +- R/missing.data.R | 2 +- R/unbend.spine.R |only R/unbend.tps.poly.R |only data/darters.rda |only man/LOST-package.Rd | 9 --------- man/bilat.align.Rd |only man/complete.specimens.Rd | 2 +- man/darters.Rd |only man/missing.specimens.Rd | 2 +- man/unbend.spine.Rd |only man/unbend.tps.poly.Rd |only 18 files changed, 30 insertions(+), 29 deletions(-)
Title: Tools for Working with Posterior Distributions
Description: Provides useful tools for both users and developers of packages
for fitting Bayesian models or working with output from Bayesian models.
The primary goals of the package are to:
(a) Efficiently convert between many different useful formats of
draws (samples) from posterior or prior distributions.
(b) Provide consistent methods for operations commonly performed on draws,
for example, subsetting, binding, or mutating draws.
(c) Provide various summaries of draws in convenient formats.
(d) Provide lightweight implementations of state of the art posterior
inference diagnostics. References: Vehtari et al. (2021)
<doi:10.1214/20-BA1221>.
Author: Paul-Christian Buerkner [aut, cre],
Jonah Gabry [aut],
Matthew Kay [aut],
Aki Vehtari [aut],
Mans Magnusson [ctb],
Rok Česnovar [ctb],
Ben Lambert [ctb],
Ozan Adiguezel [ctb],
Jacob Socolar [ctb],
Noa Kallioinen [ctb]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Diff between posterior versions 1.5.0 dated 2023-10-31 and 1.6.0 dated 2024-07-03
posterior-1.5.0/posterior/man/set_variables.Rd |only posterior-1.6.0/posterior/DESCRIPTION | 20 posterior-1.6.0/posterior/MD5 | 172 ++-- posterior-1.6.0/posterior/NAMESPACE | 20 posterior-1.6.0/posterior/NEWS.md | 27 posterior-1.6.0/posterior/R/as_draws_rvars.R | 58 - posterior-1.6.0/posterior/R/convergence.R | 2 posterior-1.6.0/posterior/R/draws-index.R | 281 ------- posterior-1.6.0/posterior/R/extract_variable.R | 38 posterior-1.6.0/posterior/R/extract_variable_array.R |only posterior-1.6.0/posterior/R/extract_variable_matrix.R | 58 + posterior-1.6.0/posterior/R/for_each_draw.R | 3 posterior-1.6.0/posterior/R/gpd.R | 41 - posterior-1.6.0/posterior/R/misc.R | 7 posterior-1.6.0/posterior/R/pareto_smooth.R | 381 +++++++--- posterior-1.6.0/posterior/R/posterior-package.R | 3 posterior-1.6.0/posterior/R/rename_variables.R | 2 posterior-1.6.0/posterior/R/rvar-.R | 101 -- posterior-1.6.0/posterior/R/rvar-bind.R | 4 posterior-1.6.0/posterior/R/rvar-cast.R | 30 posterior-1.6.0/posterior/R/rvar-dist.R | 2 posterior-1.6.0/posterior/R/rvar-factor.R | 15 posterior-1.6.0/posterior/R/rvar-math.R | 27 posterior-1.6.0/posterior/R/rvar-rfun.R | 2 posterior-1.6.0/posterior/R/subset_draws.R | 111 +- posterior-1.6.0/posterior/R/thin_draws.R | 49 + posterior-1.6.0/posterior/R/variable-indices.R |only posterior-1.6.0/posterior/R/variables.R |only posterior-1.6.0/posterior/R/weight_draws.R | 58 + posterior-1.6.0/posterior/R/zzz.R | 6 posterior-1.6.0/posterior/README.md | 2 posterior-1.6.0/posterior/build/vignette.rds |binary posterior-1.6.0/posterior/inst/doc/pareto_diagnostics.R |only posterior-1.6.0/posterior/inst/doc/pareto_diagnostics.Rmd |only posterior-1.6.0/posterior/inst/doc/pareto_diagnostics.html |only posterior-1.6.0/posterior/inst/doc/posterior.Rmd | 4 posterior-1.6.0/posterior/inst/doc/posterior.html | 330 ++++---- posterior-1.6.0/posterior/inst/doc/rvar.Rmd | 10 posterior-1.6.0/posterior/inst/doc/rvar.html | 113 +- posterior-1.6.0/posterior/man/diagnostics.Rd | 2 posterior-1.6.0/posterior/man/draws-index.Rd | 35 posterior-1.6.0/posterior/man/draws_array.Rd | 4 posterior-1.6.0/posterior/man/draws_df.Rd | 4 posterior-1.6.0/posterior/man/draws_list.Rd | 4 posterior-1.6.0/posterior/man/draws_matrix.Rd | 4 posterior-1.6.0/posterior/man/draws_rvars.Rd | 4 posterior-1.6.0/posterior/man/ess_basic.Rd | 4 posterior-1.6.0/posterior/man/ess_bulk.Rd | 4 posterior-1.6.0/posterior/man/ess_quantile.Rd | 4 posterior-1.6.0/posterior/man/ess_sd.Rd | 4 posterior-1.6.0/posterior/man/ess_tail.Rd | 4 posterior-1.6.0/posterior/man/extract_variable.Rd | 18 posterior-1.6.0/posterior/man/extract_variable_array.Rd |only posterior-1.6.0/posterior/man/extract_variable_matrix.Rd | 16 posterior-1.6.0/posterior/man/for_each_draw.Rd | 3 posterior-1.6.0/posterior/man/mcse_mean.Rd | 4 posterior-1.6.0/posterior/man/mcse_quantile.Rd | 4 posterior-1.6.0/posterior/man/mcse_sd.Rd | 4 posterior-1.6.0/posterior/man/pareto_diags.Rd | 72 + posterior-1.6.0/posterior/man/pareto_khat.Rd | 53 + posterior-1.6.0/posterior/man/pareto_smooth.Rd | 54 - posterior-1.6.0/posterior/man/posterior-package.Rd | 30 posterior-1.6.0/posterior/man/ps_convergence_rate.Rd |only posterior-1.6.0/posterior/man/ps_khat_threshold.Rd |only posterior-1.6.0/posterior/man/ps_min_ss.Rd |only posterior-1.6.0/posterior/man/ps_tail_length.Rd |only posterior-1.6.0/posterior/man/rdo.Rd | 2 posterior-1.6.0/posterior/man/rename_variables.Rd | 2 posterior-1.6.0/posterior/man/rhat.Rd | 2 posterior-1.6.0/posterior/man/rhat_basic.Rd | 4 posterior-1.6.0/posterior/man/rhat_nested.Rd | 4 posterior-1.6.0/posterior/man/rstar.Rd | 6 posterior-1.6.0/posterior/man/rvar-matmult.Rd | 8 posterior-1.6.0/posterior/man/subset_draws.Rd | 46 - posterior-1.6.0/posterior/man/thin_draws.Rd | 25 posterior-1.6.0/posterior/man/variables-set.Rd |only posterior-1.6.0/posterior/man/variables.Rd |only posterior-1.6.0/posterior/man/weight_draws.Rd | 18 posterior-1.6.0/posterior/man/weights.draws.Rd | 3 posterior-1.6.0/posterior/tests/testthat/test-as_draws.R | 3 posterior-1.6.0/posterior/tests/testthat/test-extract_variable.R | 8 posterior-1.6.0/posterior/tests/testthat/test-extract_variable_array.R |only posterior-1.6.0/posterior/tests/testthat/test-extract_variable_matrix.R | 11 posterior-1.6.0/posterior/tests/testthat/test-pareto_smooth.R | 89 +- posterior-1.6.0/posterior/tests/testthat/test-remove_variables.R | 2 posterior-1.6.0/posterior/tests/testthat/test-rstar.R | 1 posterior-1.6.0/posterior/tests/testthat/test-rvar-cast.R | 23 posterior-1.6.0/posterior/tests/testthat/test-rvar-math.R | 9 posterior-1.6.0/posterior/tests/testthat/test-subset_draws.R | 71 + posterior-1.6.0/posterior/tests/testthat/test-thin_draws.R | 22 posterior-1.6.0/posterior/tests/testthat/test-variables.R | 52 + posterior-1.6.0/posterior/tests/testthat/test-weight_draws.R | 11 posterior-1.6.0/posterior/vignettes/pareto_diagnostics.Rmd |only posterior-1.6.0/posterior/vignettes/posterior.Rmd | 4 posterior-1.6.0/posterior/vignettes/rvar.Rmd | 10 95 files changed, 1679 insertions(+), 1069 deletions(-)
Title: Gene Locus Plot with Gene Annotations
Description: Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots.
Author: Myles Lewis [aut, cre]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between locuszoomr versions 0.3.0 dated 2024-04-16 and 0.3.1 dated 2024-07-03
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 6 ++++++ R/genetrack_ly.R | 6 ++++-- R/locus.R | 6 +++++- R/locus_plotly.R | 17 +++++++++++++---- R/scatter_plotly.R | 28 +++++++++++++++++----------- build/vignette.rds |binary man/genetrack_ly.Rd | 3 +++ man/locus_plotly.Rd | 4 +++- man/scatter_plotly.Rd | 8 +++++++- 11 files changed, 71 insertions(+), 33 deletions(-)
Title: Statistical Methods for Graphs
Description: Contains statistical methods to analyze graphs, such as graph parameter estimation,
model selection based on the Graph Information Criterion, statistical tests to discriminate two or more populations of graphs,
correlation between graphs, and clustering of graphs.
References: Takahashi et al. (2012) <doi:10.1371/journal.pone.0049949>, Fujita et al. (2017) <doi:10.3389/fnins.2017.00066>,
Fujita et al. (2017) <doi:10.1016/j.csda.2016.11.016>, Fujita et al. (2019) <doi:10.1093/comnet/cnz028>.
Author: Grover E. Castro Guzman [aut],
Diogo R. da Costa [aut],
Taiane C. Ramos [aut],
Suzana S. Santos [aut],
Eduardo S. Lira [aut],
Andre Fujita [aut, cre]
Maintainer: Andre Fujita <andrefujita@usp.br>
Diff between statGraph versions 1.0.1 dated 2024-05-04 and 1.0.2 dated 2024-07-03
statGraph-1.0.1/statGraph/R/showResults.R |only statGraph-1.0.2/statGraph/DESCRIPTION | 10 +- statGraph-1.0.2/statGraph/MD5 | 60 ++++++++-------- statGraph-1.0.2/statGraph/NAMESPACE | 1 statGraph-1.0.2/statGraph/R/GIC.R | 6 - statGraph-1.0.2/statGraph/R/anogva.R | 4 - statGraph-1.0.2/statGraph/R/graph.acf.R | 2 statGraph-1.0.2/statGraph/R/graph.cem.R | 10 +- statGraph-1.0.2/statGraph/R/graph.dist.R | 3 statGraph-1.0.2/statGraph/R/graph.entropy.R | 10 +- statGraph-1.0.2/statGraph/R/graph.hclust.R | 2 statGraph-1.0.2/statGraph/R/graph.kmeans.R | 9 -- statGraph-1.0.2/statGraph/R/graph.model.selection.R | 7 - statGraph-1.0.2/statGraph/R/graph.models.R | 4 - statGraph-1.0.2/statGraph/R/graph.mult.scaling.R | 6 - statGraph-1.0.2/statGraph/R/graph.param.estimator.R | 14 +-- statGraph-1.0.2/statGraph/R/graph.spectral.density.R | 18 ++-- statGraph-1.0.2/statGraph/R/graph.takahashi.test.R | 4 - statGraph-1.0.2/statGraph/R/print.statGraph.R |only statGraph-1.0.2/statGraph/R/sp.anogva.R | 17 ++-- statGraph-1.0.2/statGraph/man/anogva.Rd | 2 statGraph-1.0.2/statGraph/man/graph.acf.Rd | 2 statGraph-1.0.2/statGraph/man/graph.cem.Rd | 2 statGraph-1.0.2/statGraph/man/graph.dist.Rd | 2 statGraph-1.0.2/statGraph/man/graph.entropy.Rd | 2 statGraph-1.0.2/statGraph/man/graph.hclust.Rd | 2 statGraph-1.0.2/statGraph/man/graph.model.selection.Rd | 2 statGraph-1.0.2/statGraph/man/graph.mult.scaling.Rd | 2 statGraph-1.0.2/statGraph/man/graph.param.estimator.Rd | 2 statGraph-1.0.2/statGraph/man/graph.spectral.density.Rd | 4 - statGraph-1.0.2/statGraph/man/graph.takahashi.test.Rd | 2 statGraph-1.0.2/statGraph/man/sp.anogva.Rd | 6 - 32 files changed, 104 insertions(+), 113 deletions(-)
Title: Portfolio Analysis, Including Numerical Methods for Optimization
of Portfolios
Description: Portfolio optimization and analysis routines and graphics.
Author: Brian G. Peterson [cre, aut, cph],
Peter Carl [aut, cph],
Ross Bennett [ctb, cph],
Kris Boudt [ctb, cph],
Xinran Zhao [ctb],
R. Douglas Martin [ctb],
Guy Yollin [ctb],
Hezky Varon [ctb],
Xiaokang Feng [ctb],
Yifu Kang [ctb]
Maintainer: Brian G. Peterson <brian@braverock.com>
Diff between PortfolioAnalytics versions 1.1.0 dated 2018-05-17 and 2.0.0 dated 2024-07-03
DESCRIPTION | 46 MD5 | 275 ++-- NAMESPACE | 24 R/EntropyProg.R | 8 R/ac_ranking.R | 6 R/applyFUN.R | 12 R/backtest.plot.R |only R/black_litterman.R | 6 R/chart.RiskReward.R | 2 R/chart.Weights.R | 4 R/charts.DE.R | 14 R/charts.GenSA.R | 14 R/charts.PSO.R | 14 R/charts.ROI.R | 14 R/charts.RP.R | 16 R/charts.efficient.frontier.R | 245 +++- R/charts.groups.R | 6 R/charts.multiple.R | 6 R/charts.risk.R | 11 R/constrained_objective.R | 3 R/constraint_fn_map.R | 6 R/constraints.R | 77 - R/constraintsFUN.R | 2 R/constraints_ROI.R | 2 R/custom.covRob.R |only R/equal.weight.R | 2 R/extract.efficient.frontier.R | 224 +++ R/extractrisk.R |only R/extractstats.R | 67 - R/generics.R | 92 + R/inverse.volatility.weight.R | 2 R/meucci_moments.R | 2 R/meucci_ranking.R | 2 R/moment.functions.R | 13 R/objective.R | 8 R/objectiveFUN.R | 2 R/opt.outputMvo.R |only R/optFUN.R | 2 R/optimize.portfolio.R | 1806 +++++++++++++++++++++++++++++- R/plotFrontiers.R |only R/portfolio.R | 10 R/random_portfolios.R | 4 R/stat.factor.model.R | 4 R/trailingFUN.R | 2 R/utility.combine.R | 2 R/utils.R | 2 R/zzz.R | 10 README | 91 + build/vignette.rds |binary data/indexes.rda |binary demo/00Index | 2 demo/demo_cvxrPortfolioAnalytics.R |only demo/demo_robustCovMatForPA.R |only inst/doc/ROI_vignette.pdf |binary inst/doc/custom_moments_objectives.R | 29 inst/doc/custom_moments_objectives.Rnw | 1 inst/doc/custom_moments_objectives.pdf |binary inst/doc/cvxrPortfolioAnalytics.pdf |only inst/doc/cvxrPortfolioAnalytics.pdf.asis |only inst/doc/portfolio_vignette.R | 1 inst/doc/portfolio_vignette.pdf |binary inst/doc/risk_budget_optimization.R | 1 inst/doc/risk_budget_optimization.pdf |binary inst/doc/robustCovMatForPA.pdf |only inst/doc/robustCovMatForPA.pdf.asis |only man/BlackLittermanFormula.Rd | 2 man/EntropyProg.Rd | 6 man/MycovRobMcd.Rd |only man/MycovRobTSGS.Rd |only man/ac.ranking.Rd | 2 man/add.constraint.Rd | 12 man/add.objective.Rd | 25 man/add.sub.portfolio.Rd | 16 man/backtest.plot.Rd |only man/barplotGroupWeights.Rd | 16 man/black.litterman.Rd | 4 man/box_constraint.Rd | 13 man/chart.Concentration.Rd | 17 man/chart.EF.Weights.Rd | 38 man/chart.EfficientFrontier.Rd | 106 + man/chart.EfficientFrontierCompare.Rd |only man/chart.EfficientFrontierOverlay.Rd | 30 man/chart.GroupWeights.Rd | 17 man/chart.RiskBudget.Rd | 49 man/chart.RiskReward.Rd | 114 + man/chart.Weights.Rd | 130 +- man/constrained_objective.Rd | 25 man/constraint.Rd | 13 man/constraint_ROI.Rd | 8 man/create.EfficientFrontier.Rd | 29 man/custom.covRob.MM.Rd |only man/custom.covRob.Mcd.Rd |only man/custom.covRob.Rocke.Rd |only man/custom.covRob.TSGS.Rd |only man/diversification_constraint.Rd | 9 man/etl_milp_opt.Rd | 11 man/etl_opt.Rd | 11 man/extractEfficientFrontier.Rd | 10 man/extractGroups.Rd | 2 man/extract_risk.Rd |only man/factor_exposure_constraint.Rd | 12 man/fn_map.Rd | 4 man/gmv_opt.Rd | 13 man/gmv_opt_leverage.Rd | 11 man/gmv_opt_ptc.Rd | 12 man/gmv_opt_toc.Rd | 12 man/group_constraint.Rd | 15 man/indexes.Rd | 2 man/leverage_exposure_constraint.Rd | 9 man/maxret_milp_opt.Rd | 10 man/meaneqs.efficient.frontier.Rd |only man/meanetl.efficient.frontier.Rd | 10 man/meanrisk.efficient.frontier.Rd |only man/meanvar.efficient.frontier.Rd | 12 man/meucci.moments.Rd | 2 man/meucci.ranking.Rd | 2 man/minmax_objective.Rd | 12 man/mult.portfolio.spec.Rd | 2 man/objective.Rd | 11 man/opt.outputMvo.Rd |only man/optimize.portfolio.Rd | 143 +- man/optimize.portfolio.parallel.Rd | 16 man/optimize.portfolio.rebalancing.Rd | 56 man/pHist.Rd | 2 man/plot.Rd | 93 + man/plotFrontiers.Rd |only man/portfolio.moments.bl.Rd | 11 man/portfolio.spec.Rd | 13 man/portfolio_risk_objective.Rd | 10 man/position_limit_constraint.Rd | 34 man/print.optimize.portfolio.Rd | 3 man/quadratic_utility_objective.Rd | 7 man/random_portfolios.Rd | 11 man/regime.portfolios.Rd | 2 man/return_constraint.Rd | 9 man/return_objective.Rd | 10 man/risk_budget_objective.Rd | 16 man/rp_transform.Rd | 21 man/set.portfolio.moments.Rd | 11 man/statistical.factor.model.Rd | 2 man/transaction_cost_constraint.Rd | 10 man/turnover_constraint.Rd | 9 man/turnover_objective.Rd | 10 man/weight_concentration_objective.Rd | 10 man/weight_sum_constraint.Rd | 9 vignettes/PA.bib | 23 vignettes/custom_moments_objectives.Rnw | 1 vignettes/cvxrPortfolioAnalytics.Rmd |only vignettes/cvxrPortfolioAnalytics.pdf.asis |only vignettes/robustCovMatForPA.Rmd |only vignettes/robustCovMatForPA.pdf.asis |only vignettes/robustRef.bib |only vignettes/todo_notes.Rmd |only vignettes/todo_notes.html |only 154 files changed, 3822 insertions(+), 780 deletions(-)
More information about PortfolioAnalytics at CRAN
Permanent link
Title: Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian
Models
Description: Efficient approximate leave-one-out cross-validation (LOO)
for Bayesian models fit using Markov chain Monte Carlo, as
described in Vehtari, Gelman, and Gabry (2017)
<doi:10.1007/s11222-016-9696-4>.
The approximation uses Pareto smoothed importance sampling (PSIS),
a new procedure for regularizing importance weights.
As a byproduct of the calculations, we also obtain approximate
standard errors for estimated predictive errors and for the comparison
of predictive errors between models. The package also provides methods
for using stacking and other model weighting techniques to average
Bayesian predictive distributions.
Author: Aki Vehtari [aut],
Jonah Gabry [cre, aut],
Mans Magnusson [aut],
Yuling Yao [aut],
Paul-Christian Buerkner [aut],
Topi Paananen [aut],
Andrew Gelman [aut],
Ben Goodrich [ctb],
Juho Piironen [ctb],
Bruno Nicenboim [ctb],
Leevi Lindgren [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between loo versions 2.7.0 dated 2024-02-24 and 2.8.0 dated 2024-07-03
DESCRIPTION | 14 - MD5 | 124 +++++----- NEWS.md | 14 + R/E_loo.R | 30 +- R/diagnostics.R | 10 R/helpers.R | 8 R/loo-glossary.R | 8 R/loo-package.R | 4 R/loo.R | 4 R/loo_model_weights.R | 2 R/loo_moment_matching.R | 42 ++- R/loo_subsample.R | 16 - R/psis.R | 2 R/split_moment_matching.R | 13 - R/waic.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/loo2-elpd.html | 6 inst/doc/loo2-example.Rmd | 12 inst/doc/loo2-example.html | 28 +- inst/doc/loo2-large-data.Rmd | 10 inst/doc/loo2-large-data.html | 27 +- inst/doc/loo2-lfo.Rmd | 10 inst/doc/loo2-lfo.html | 103 ++++---- inst/doc/loo2-mixis.Rmd | 4 inst/doc/loo2-mixis.html | 31 +- inst/doc/loo2-moment-matching.Rmd | 10 inst/doc/loo2-moment-matching.html | 22 - inst/doc/loo2-non-factorized.Rmd | 8 inst/doc/loo2-non-factorized.html | 29 +- inst/doc/loo2-weights.Rmd | 4 inst/doc/loo2-weights.html | 12 inst/doc/loo2-with-rstan.Rmd | 10 inst/doc/loo2-with-rstan.html | 16 - man/E_loo.Rd | 10 man/compare.Rd | 7 man/loo-glossary.Rd | 15 - man/loo-package.Rd | 13 - man/loo.Rd | 9 man/loo_compare.Rd | 7 man/loo_model_weights.Rd | 9 man/pareto-k-diagnostic.Rd | 16 - man/psis.Rd | 9 man/psis_approximate_posterior.Rd | 7 man/psislw.Rd | 7 man/sis.Rd | 7 man/waic.Rd | 9 tests/testthat/reference-results/moment_match_loo_1.rds |binary tests/testthat/reference-results/moment_match_loo_2.rds |binary tests/testthat/reference-results/moment_match_loo_3.rds |binary tests/testthat/reference-results/moment_match_var_and_cov.rds |binary tests/testthat/test_E_loo.R | 7 tests/testthat/test_loo_moment_matching.R | 6 tests/testthat/test_psis.R | 5 tests/testthat/test_tisis.R | 4 vignettes/loo2-example.Rmd | 12 vignettes/loo2-large-data.Rmd | 10 vignettes/loo2-lfo.Rmd | 10 vignettes/loo2-mixis.Rmd | 4 vignettes/loo2-moment-matching.Rmd | 10 vignettes/loo2-non-factorized.Rmd | 8 vignettes/loo2-weights.Rmd | 4 vignettes/loo2-with-rstan.Rmd | 10 63 files changed, 481 insertions(+), 369 deletions(-)
Title: Simple Peak Alignment for Gas-Chromatography Data
Description: Aligns peak based on peak retention times and matches homologous peaks
across samples. The underlying alignment procedure comprises three sequential steps.
(1) Full alignment of samples by linear transformation of retention times to
maximise similarity among homologous peaks (2) Partial alignment of peaks within
a user-defined retention time window to cluster homologous peaks (3) Merging rows
that are likely representing homologous substances (i.e. no sample shows peaks in
both rows and the rows have similar retention time means). The algorithm is described in detail
in Ottensmann et al., 2018 <doi:10.1371/journal.pone.0198311>.
Author: Meinolf Ottensmann [aut, cre] ,
Martin Stoffel [aut],
Hazel J. Nichols [aut],
Joseph I. Hoffman [aut]
Maintainer: Meinolf Ottensmann <meinolf.ottensmann@web.de>
Diff between GCalignR versions 1.0.6 dated 2024-01-22 and 1.0.7 dated 2024-07-03
DESCRIPTION | 10 MD5 | 22 NEWS.md | 8 R/GCalignR.R | 3 README.md | 13 build/vignette.rds |binary inst/doc/GCalignR_How_does_the_Algorithm_work.html | 25 inst/doc/GCalignR_step_by_step.R | 2 inst/doc/GCalignR_step_by_step.Rmd | 9 inst/doc/GCalignR_step_by_step.html | 1656 +-------------------- man/GCalignR.Rd | 20 vignettes/GCalignR_step_by_step.Rmd | 9 12 files changed, 206 insertions(+), 1571 deletions(-)
Title: Bayesian Global Vector Autoregressions
Description: Estimation of Bayesian Global Vector Autoregressions (BGVAR) with different prior setups and the possibility to introduce stochastic volatility. Built-in priors include the Minnesota, the stochastic search variable selection and Normal-Gamma (NG) prior. For a reference see also Crespo Cuaresma, J., Feldkircher, M. and F. Huber (2016) "Forecasting with Global Vector Autoregressive Models: a Bayesian Approach", Journal of Applied Econometrics, Vol. 31(7), pp. 1371-1391 <doi:10.1002/jae.2504>. Post-processing functions allow for doing predictions, structurally identify the model with short-run or sign-restrictions and compute impulse response functions, historical decompositions and forecast error variance decompositions. Plotting functions are also available. The package has a companion paper: Boeck, M., Feldkircher, M. and F. Huber (2022) "BGVAR: Bayesian Global Vector Autoregressions with Shrinkage Priors in R", Journal of Statistical Software, Vol. 104(9), pp. 1-28 <doi:10.18 [...truncated...]
Author: Maximilian Boeck [aut, cre] ,
Martin Feldkircher [aut] ,
Florian Huber [aut] ,
Darjus Hosszejni [ctb]
Maintainer: Maximilian Boeck <maximilian.boeck@unibocconi.it>
Diff between BGVAR versions 2.5.5 dated 2023-12-13 and 2.5.6 dated 2024-07-03
DESCRIPTION | 8 MD5 | 20 - NEWS | 3 R/bgvar-package.R | 1 R/utils.R | 134 +++++---- build/vignette.rds |binary inst/doc/examples.R | 4 inst/doc/examples.Rmd | 4 inst/doc/examples.html | 660 ++++++++++++++++++++++++------------------------- man/BGVAR-package.Rd | 1 vignettes/examples.Rmd | 4 11 files changed, 426 insertions(+), 413 deletions(-)
Title: Processing DAS Data Files
Description: Process and summarize DAS data files.
These files are typically, but do not have to be
DAS <https://swfsc-publications.fisheries.noaa.gov/publications/TM/SWFSC/NOAA-TM-NMFS-SWFSC-305.PDF> data
produced by the Southwest Fisheries Science Center (SWFSC) program 'WinCruz'.
This package standardizes and streamlines basic DAS data processing,
and includes a PDF with the DAS data format requirements expected by the package.
Author: Sam Woodman [aut, cre]
Maintainer: Sam Woodman <sam.woodman@noaa.gov>
Diff between swfscDAS versions 0.6.2 dated 2023-08-10 and 0.6.3 dated 2024-07-03
DESCRIPTION | 28 - MD5 | 32 - NEWS.md | 9 R/das_chop_equallength.R | 8 R/das_format_pdf.R | 2 R/swfscDAS-package.R | 5 README.md | 48 -- build/vignette.rds |binary inst/doc/DAS_data_join.R | 2 inst/doc/DAS_data_join.html | 66 +- inst/doc/swfscDAS.R | 2 inst/doc/swfscDAS.Rmd | 6 inst/doc/swfscDAS.html | 1005 ++++++++++++++++++++++---------------------- man/das_chop_equallength.Rd | 8 man/das_format_pdf.Rd | 2 man/swfscDAS-package.Rd | 2 vignettes/swfscDAS.Rmd | 6 17 files changed, 609 insertions(+), 622 deletions(-)
Title: Tools to Visualize 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 (<https://www.cmsaf.eu>). It is a joint cooperation of eight
National Meteorological and Hydrological Services.
The 'cmsafvis' R-package provides a collection of R-operators for the analysis and
visualization of CM SAF NetCDF data.
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 cmsafvis versions 1.2.7 dated 2024-05-03 and 1.2.8 dated 2024-07-03
DESCRIPTION | 10 ++-- MD5 | 18 ++++---- NEWS.md | 8 +++ R/anomaly_map.R | 10 ++++ R/create_country_mask.R | 15 +----- R/plot_abs_map.R | 82 +++++++++++++++++++++++++++++--------- R/plot_abs_map_mean.R | 73 +++++++++++++++++++++++++++------ R/plot_warming_stripes.R | 9 ++-- R/quicklook.R | 2 inst/extdata/quicklook_config.yml | 60 +++++++++++++++++++++++++++ 10 files changed, 223 insertions(+), 64 deletions(-)
Title: Tailored Knowledge Catalog
Description: Facilitate the management of data from knowledge
resources that are frequently used alone or together
in research environments.
In 'TKCat', knowledge resources are manipulated as modeled database (MDB)
objects. These objects provide access to the data tables along with a general
description of the resource and a detail data model documenting the
tables, their fields and their relationships.
These MDBs are then gathered in catalogs that can be easily
explored an shared.
Finally, 'TKCat' provides tools to easily subset, filter and combine MDBs and
create new catalogs suited for specific needs.
Author: Patrice Godard [aut, cre, cph]
Maintainer: Patrice Godard <patrice.godard@gmail.com>
Diff between TKCat versions 1.1.8 dated 2024-05-23 and 1.1.11 dated 2024-07-03
DESCRIPTION | 8 +- MD5 | 38 +++++----- R/KMR.R | 10 +- R/chMDB.R | 10 ++ R/chTKCat.R | 5 + R/fileMDB.R | 10 ++ R/memoMDB.R | 10 ++ R/shiny-helpers.R | 9 +- build/vignette.rds |binary inst/doc/TKCat-KMR-POK.html | 4 - inst/doc/TKCat.R | 20 ++++- inst/doc/TKCat.Rmd | 22 ++++-- inst/doc/TKCat.html | 150 +++++++++++++++++++++-------------------- inst/pkgdown.yml | 4 - man/list_feature_properties.Rd | 2 man/list_measurement_units.Rd | 2 man/list_property_values.Rd | 2 man/list_table_features.Rd | 2 man/list_table_types.Rd | 2 vignettes/TKCat.Rmd | 22 ++++-- 20 files changed, 208 insertions(+), 124 deletions(-)
Title: Tutorials for "R for Data Science"
Description: When assigned "R for Data Science" (Wickham, Çetinkaya-Rundel,
and Grolemund (2023, ISBN: 1492097402)), students should read the book and
type in all the associated R commands themselves. Sadly, that never happens.
These tutorials allow students to demonstrate (and their instructors
to be sure) that all work has been completed. See Kane (2023)
<https://ppbds.github.io/tutorial.helpers/articles/instructions.html> from
the 'tutorial.helpers' package for a background discussion.
Author: David Kane [aut, cre, cph]
Maintainer: David Kane <dave.kane@gmail.com>
Diff between r4ds.tutorials versions 0.2.0 dated 2024-02-22 and 0.3.0 dated 2024-07-03
r4ds.tutorials-0.2.0/r4ds.tutorials/inst/tutorials/02-rstudio-and-code/images/untitled_script.png |only r4ds.tutorials-0.2.0/r4ds.tutorials/inst/tutorials/02-rstudio-and-code/images/visual-editing-options.png |only r4ds.tutorials-0.2.0/r4ds.tutorials/inst/tutorials/04-rstudio-and-github/images/rstudio_panes.jpg |only r4ds.tutorials-0.2.0/r4ds.tutorials/inst/tutorials/04-rstudio-and-github_es |only r4ds.tutorials-0.2.0/r4ds.tutorials/inst/tutorials/10-exploratory-data-analysis/data |only r4ds.tutorials-0.2.0/r4ds.tutorials/inst/tutorials/10-exploratory-data-analysis/images |only r4ds.tutorials-0.2.0/r4ds.tutorials/inst/tutorials/20-spreadsheets_es |only r4ds.tutorials-0.2.0/r4ds.tutorials/inst/tutorials/28-quarto |only r4ds.tutorials-0.3.0/r4ds.tutorials/DESCRIPTION | 21 r4ds.tutorials-0.3.0/r4ds.tutorials/MD5 | 95 r4ds.tutorials-0.3.0/r4ds.tutorials/NEWS.md | 10 r4ds.tutorials-0.3.0/r4ds.tutorials/README.md | 9 r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/00-introduction/tutorial.Rmd | 132 r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/01-data-visualization/tutorial.Rmd | 1318 +++++--- r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/02-rstudio-and-code/images/visual-editing-options.jpg |only r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/02-rstudio-and-code/tutorial.Rmd | 652 ++-- r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/03-data-transformation/tutorial.Rmd | 30 r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/04-rstudio-and-github/images/quarto-1-example.txt |only r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/04-rstudio-and-github/images/quarto-2-example.txt | 4 r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/04-rstudio-and-github/images/rs_panes.jpg |only r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/04-rstudio-and-github/tutorial.Rmd | 605 +-- r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/05-data-tidying/tutorial.Rmd | 1 r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/06-terminal/tutorial.Rmd | 266 - r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/07-data-import/tutorial.Rmd | 14 r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/08-getting-help/tutorial.Rmd | 39 r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/09-layers/tutorial.Rmd | 26 r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/10-exploratory-data-analysis/tutorial.Rmd | 732 ---- r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/11-communication/tutorial.Rmd | 657 ---- r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/12-logical-vectors/tutorial.Rmd | 928 +---- r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/13-numbers/tutorial.Rmd | 30 r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/14-strings/tutorial.Rmd | 647 +++ r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/15-regular-expressions/tutorial.Rmd | 10 r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/16-factors/tutorial.Rmd | 10 r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/17-dates-and-times/tutorial.Rmd | 254 - r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/21-databases/tutorial.Rmd | 1259 +++++-- r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/22-arrow/data |only r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/22-arrow/tutorial.Rmd | 1217 +++---- r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/26-iteration/tutorial.Rmd | 1624 +++++----- r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/27-a-field-guide-to-base-R/data |only r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/27-a-field-guide-to-base-R/tutorial.Rmd | 503 +-- r4ds.tutorials-0.3.0/r4ds.tutorials/inst/tutorials/28-quarto-websites |only 41 files changed, 5531 insertions(+), 5562 deletions(-)
More information about r4ds.tutorials at CRAN
Permanent link
Title: Template Model Builder: A General Random Effect Tool Inspired by
'ADMB'
Description: With this tool, a user should be able to quickly implement
complex random effect models through simple C++ templates. The package combines
'CppAD' (C++ automatic differentiation), 'Eigen' (templated matrix-vector
library) and 'CHOLMOD' (sparse matrix routines available from R) to obtain
an efficient implementation of the applied Laplace approximation with exact
derivatives. Key features are: Automatic sparseness detection, parallelism
through 'BLAS' and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph],
Brad Bell [cph],
Hans Skaug [ctb],
Arni Magnusson [ctb],
Casper Berg [ctb],
Anders Nielsen [ctb],
Martin Maechler [ctb],
Theo Michelot [ctb],
Mollie Brooks [ctb],
Alex Forrence [ctb],
Christoffer Moesgaard Albertsen [...truncated...]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between TMB versions 1.9.13 dated 2024-06-28 and 1.9.14 dated 2024-07-03
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 6 ++++++ inst/include/expm.hpp | 6 +++--- 4 files changed, 16 insertions(+), 10 deletions(-)
Title: Handling Taxonomic Lists
Description: Handling taxonomic lists through objects of class 'taxlist'.
This package provides functions to import species lists from 'Turboveg'
(<https://www.synbiosys.alterra.nl/turboveg/>) and the possibility to create
backups from resulting R-objects.
Also quick displays are implemented as summary-methods.
Author: Miguel Alvarez [aut, cre] ,
Zachary Foster [ctb] ,
Sam Levin [rev],
Margaret Siple [rev]
Maintainer: Miguel Alvarez <kamapu78@gmail.com>
Diff between taxlist versions 0.2.4 dated 2023-03-12 and 0.3.0 dated 2024-07-03
taxlist-0.2.4/taxlist/man/sort_backups.Rd |only taxlist-0.3.0/taxlist/DESCRIPTION | 28 +-- taxlist-0.3.0/taxlist/MD5 | 75 +++++--- taxlist-0.3.0/taxlist/NAMESPACE | 11 + taxlist-0.3.0/taxlist/NEWS.md | 34 ++++ taxlist-0.3.0/taxlist/R/backup_object.R | 112 ++++++++++--- taxlist-0.3.0/taxlist/R/df2taxlist.R | 2 taxlist-0.3.0/taxlist/R/id_generator.R | 2 taxlist-0.3.0/taxlist/R/imports.R | 2 taxlist-0.3.0/taxlist/R/insert_rows.R |only taxlist-0.3.0/taxlist/R/internal.R | 60 ------- taxlist-0.3.0/taxlist/R/levels.R | 2 taxlist-0.3.0/taxlist/R/match_names.R | 6 taxlist-0.3.0/taxlist/R/merge_taxa.R | 56 +++--- taxlist-0.3.0/taxlist/R/merge_to_parent.R |only taxlist-0.3.0/taxlist/R/parents.R |only taxlist-0.3.0/taxlist/R/print_name.R | 185 +++++++++++++--------- taxlist-0.3.0/taxlist/R/prune_levels.R |only taxlist-0.3.0/taxlist/R/replace_x.R | 37 ---- taxlist-0.3.0/taxlist/R/sysdata.rda |only taxlist-0.3.0/taxlist/R/taxlist-package.R | 40 ---- taxlist-0.3.0/taxlist/R/taxlist2df.R |only taxlist-0.3.0/taxlist/R/tv2taxlist.R | 5 taxlist-0.3.0/taxlist/build/partial.rdb |binary taxlist-0.3.0/taxlist/build/vignette.rds |binary taxlist-0.3.0/taxlist/data/Easplist.rda |binary taxlist-0.3.0/taxlist/inst/doc/taxlist-intro.html | 6 taxlist-0.3.0/taxlist/man/backup_object.Rd | 58 +++++- taxlist-0.3.0/taxlist/man/coerce-methods.Rd | 3 taxlist-0.3.0/taxlist/man/collapse_names.Rd |only taxlist-0.3.0/taxlist/man/df2taxlist.Rd | 2 taxlist-0.3.0/taxlist/man/figures/logo.png |binary taxlist-0.3.0/taxlist/man/id_generator.Rd | 2 taxlist-0.3.0/taxlist/man/insert_rows.Rd |only taxlist-0.3.0/taxlist/man/levels.Rd | 3 taxlist-0.3.0/taxlist/man/match_names.Rd | 6 taxlist-0.3.0/taxlist/man/merge_taxa.Rd | 35 +++- taxlist-0.3.0/taxlist/man/merge_to_parent.Rd |only taxlist-0.3.0/taxlist/man/parents.Rd |only taxlist-0.3.0/taxlist/man/print_name.Rd | 12 + taxlist-0.3.0/taxlist/man/prune_levels.Rd |only taxlist-0.3.0/taxlist/man/replace_x.Rd | 18 -- taxlist-0.3.0/taxlist/man/taxlist-package.Rd | 49 ++--- taxlist-0.3.0/taxlist/man/taxlist2df.Rd |only taxlist-0.3.0/taxlist/man/tv2taxlist.Rd | 5 45 files changed, 487 insertions(+), 369 deletions(-)
Title: Seamless 'Nonmem' Simulation Platform
Description: A complete and seamless 'Nonmem' simulation interface from within R. Turns 'Nonmem' control streams into simulation control streams, executes them with specified simulation input data and returns the results. The simulation is performed by 'Nonmem', eliminating time spent and risks of re-implementation of models in other tools.
Author: Philip Delff [aut, cre]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMsim versions 0.1.0 dated 2024-02-22 and 0.1.1 dated 2024-07-03
NMsim-0.1.0/NMsim/R/NMreadCov.R |only NMsim-0.1.0/NMsim/man/NMreadCov.Rd |only NMsim-0.1.0/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_default_01/NMsimData_xgxr021_default_01.rds |only NMsim-0.1.0/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_default_01/NMsim_xgxr021_default_01.ext |only NMsim-0.1.0/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_default_01/NMsim_xgxr021_default_01.lst |only NMsim-0.1.0/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_default_01/NMsim_xgxr021_default_01.mod |only NMsim-0.1.0/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_default_01/NMsim_xgxr021_default_01.tab |only NMsim-0.1.0/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_default_01/NMsim_xgxr021_default_01.xml |only NMsim-0.1.0/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_default_01/NMsim_xgxr021_default_01_input.rds |only NMsim-0.1.0/NMsim/tests/testthat/testOutput |only NMsim-0.1.1/NMsim/DESCRIPTION | 16 NMsim-0.1.1/NMsim/MD5 | 340 ++--- NMsim-0.1.1/NMsim/NAMESPACE | 2 NMsim-0.1.1/NMsim/NEWS.md | 89 + NMsim-0.1.1/NMsim/R/NMcreateDoses.R | 6 NMsim-0.1.1/NMsim/R/NMcreateMatLines.R | 7 NMsim-0.1.1/NMsim/R/NMexec.R | 15 NMsim-0.1.1/NMsim/R/NMexecDirectory.R | 14 NMsim-0.1.1/NMsim/R/NMreadSim.R | 31 NMsim-0.1.1/NMsim/R/NMreadSimModTab.R | 142 +- NMsim-0.1.1/NMsim/R/NMreplaceInits.R | 20 NMsim-0.1.1/NMsim/R/NMseed.R |only NMsim-0.1.1/NMsim/R/NMsim.R | 636 ++++++---- NMsim-0.1.1/NMsim/R/NMsimRes_utils.R | 16 NMsim-0.1.1/NMsim/R/NMsim_EBE.R |only NMsim-0.1.1/NMsim/R/NMsim_VarCov.R | 146 +- NMsim-0.1.1/NMsim/R/NMsim_default.R | 2 NMsim-0.1.1/NMsim/R/NMsim_helpers.R |only NMsim-0.1.1/NMsim/R/NMsim_known.R | 149 -- NMsim-0.1.1/NMsim/R/NMsim_typical.R | 25 NMsim-0.1.1/NMsim/R/NMupdateInits.R | 77 + NMsim-0.1.1/NMsim/R/addEVID2.R | 24 NMsim-0.1.1/NMsim/R/modifyHelpers.R |only NMsim-0.1.1/NMsim/R/padZeros.R |only NMsim-0.1.1/NMsim/R/readParsWide.R |only NMsim-0.1.1/NMsim/R/seedFunDefault.R |only NMsim-0.1.1/NMsim/R/typicalize.R |only NMsim-0.1.1/NMsim/README.md | 80 - NMsim-0.1.1/NMsim/inst/examples/R/testrun_NMsim.R | 56 NMsim-0.1.1/NMsim/inst/examples/derived |only NMsim-0.1.1/NMsim/man/NMreadSim.Rd | 21 NMsim-0.1.1/NMsim/man/NMreadSimModTab.Rd | 12 NMsim-0.1.1/NMsim/man/NMreadSimModTabOne.Rd | 10 NMsim-0.1.1/NMsim/man/NMseed.Rd |only NMsim-0.1.1/NMsim/man/NMsim.Rd | 224 ++- NMsim-0.1.1/NMsim/man/NMsim_EBE.Rd |only NMsim-0.1.1/NMsim/man/NMsim_VarCov.Rd | 8 NMsim-0.1.1/NMsim/man/NMsim_known.Rd | 32 NMsim-0.1.1/NMsim/man/NMupdateInits.Rd | 8 NMsim-0.1.1/NMsim/man/addEVID2.Rd | 24 NMsim-0.1.1/NMsim/man/cleanStrings.Rd |only NMsim-0.1.1/NMsim/man/figures/README-simple-sim-1.png |only NMsim-0.1.1/NMsim/man/figures/README-unnamed-chunk-5-1.png |binary NMsim-0.1.1/NMsim/man/figures/README-unnamed-chunk-6-1.png |only NMsim-0.1.1/NMsim/man/padZeros.Rd |only NMsim-0.1.1/NMsim/man/readParsWide.Rd |only NMsim-0.1.1/NMsim/tests/testthat/simres |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_default_01/NMsimData_xgxr021_default_01.csv | 10 NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_default_01/NMsimData_xgxr021_default_01.fst |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_default_01/xgxr021_default_01.ext |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_default_01/xgxr021_default_01.lst |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_default_01/xgxr021_default_01.mod |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_default_01/xgxr021_default_01.tab |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_default_01/xgxr021_default_01.xml |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_default_01/xgxr021_default_01_input.rds |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_default_01_paths.rds |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_default_01_paths_res.fst |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_known_01 |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_known_01_paths.rds |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_known_01_paths_res.fst |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail_MetaData.rds |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail_paths.rds |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/xgxr021.ctl |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/xgxr021_sd1_NMreadSim |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/xgxr025.mod | 3 NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/xgxr033.coi |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/xgxr033.cor |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/xgxr033.cov |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/xgxr033.dir1 |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/xgxr033.ext |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/xgxr033.lst |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/xgxr033.mod |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/xgxr033.msf |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/xgxr033.phi |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/xgxr033.shk |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/xgxr033.xml |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/xgxr033_ETAS.msf |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/xgxr033_input.rds |only NMsim-0.1.1/NMsim/tests/testthat/testData/nonmem/xgxr033_res.txt |only NMsim-0.1.1/NMsim/tests/testthat/testReference/NMreadSim_01.rds |binary NMsim-0.1.1/NMsim/tests/testthat/testReference/NMreadSim_02.rds |only NMsim-0.1.1/NMsim/tests/testthat/testReference/NMseed_01.rds |only NMsim-0.1.1/NMsim/tests/testthat/testReference/NMseed_02.rds |only NMsim-0.1.1/NMsim/tests/testthat/testReference/NMseed_03.rds |only NMsim-0.1.1/NMsim/tests/testthat/testReference/NMsim_01.rds |binary NMsim-0.1.1/NMsim/tests/testthat/testReference/NMsim_02.rds |only NMsim-0.1.1/NMsim/tests/testthat/testReference/NMsim_03.rds |only NMsim-0.1.1/NMsim/tests/testthat/testReference/NMsim_05.rds |only NMsim-0.1.1/NMsim/tests/testthat/testReference/NMsim_06.rds |only NMsim-0.1.1/NMsim/tests/testthat/testReference/NMsim_09.rds |only NMsim-0.1.1/NMsim/tests/testthat/testReference/NMsim_10.rds |only NMsim-0.1.1/NMsim/tests/testthat/testReference/NMsim_11.rds |only NMsim-0.1.1/NMsim/tests/testthat/testReference/NMsim_EBE_03.rds |only NMsim-0.1.1/NMsim/tests/testthat/testReference/NMsim_VarCov_04.rds |only NMsim-0.1.1/NMsim/tests/testthat/testReference/rbind_NMsimRes_01.rds |only NMsim-0.1.1/NMsim/tests/testthat/test_NMcreateDoses.R | 2 NMsim-0.1.1/NMsim/tests/testthat/test_NMreadSim.R | 106 + NMsim-0.1.1/NMsim/tests/testthat/test_NMseed.R |only NMsim-0.1.1/NMsim/tests/testthat/test_NMsim.R | 92 + NMsim-0.1.1/NMsim/tests/testthat/test_rbind_NMsimRes.R |only 111 files changed, 1549 insertions(+), 896 deletions(-)
Title: Linear Mixed-Effects Models using 'Eigen' and S4
Description: Fit linear and generalized linear mixed-effects models.
The models and their components are represented using S4 classes and
methods. The core computational algorithms are implemented using the
'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Douglas Bates [aut] ,
Martin Maechler [aut] ,
Ben Bolker [aut, cre] ,
Steven Walker [aut] ,
Rune Haubo Bojesen Christensen [ctb]
,
Henrik Singmann [ctb] ,
Bin Dai [ctb],
Fabian Scheipl [ctb] ,
Gabor Grothendieck [ctb],
Peter Green [ctb] ,
John Fox [c [...truncated...]
Maintainer: Ben Bolker <bbolker+lme4@gmail.com>
Diff between lme4 versions 1.1-35.4 dated 2024-06-19 and 1.1-35.5 dated 2024-07-03
lme4-1.1-35.4/lme4/inst/tinytest |only lme4-1.1-35.5/lme4/DESCRIPTION | 10 - lme4-1.1-35.5/lme4/MD5 | 35 ++-- lme4-1.1-35.5/lme4/R/predict.R | 40 +--- lme4-1.1-35.5/lme4/inst/NEWS.Rd | 20 ++ lme4-1.1-35.5/lme4/inst/doc/PLSvGLS.pdf |binary lme4-1.1-35.5/lme4/inst/doc/Theory.pdf |binary lme4-1.1-35.5/lme4/inst/doc/lmer.R | 187 +++++++++++++++++++++++ lme4-1.1-35.5/lme4/inst/doc/lmer.pdf |binary lme4-1.1-35.5/lme4/man/grouseticks.Rd | 3 lme4-1.1-35.5/lme4/man/lmerControl.Rd | 2 lme4-1.1-35.5/lme4/man/modular.Rd | 2 lme4-1.1-35.5/lme4/man/plots.thpr.Rd | 6 lme4-1.1-35.5/lme4/man/predict.merMod.Rd | 13 - lme4-1.1-35.5/lme4/man/residuals.merMod.Rd | 2 lme4-1.1-35.5/lme4/man/simulate.merMod.Rd | 6 lme4-1.1-35.5/lme4/tests/predict_basis.R | 12 - lme4-1.1-35.5/lme4/tests/predsim.R | 2 lme4-1.1-35.5/lme4/tests/testthat/test-predict.R | 3 19 files changed, 258 insertions(+), 85 deletions(-)
Title: A 'Future' API for Parallel Processing using 'mirai'
Description: Implementation of the 'Future' API <doi:10.32614/RJ-2021-048> on top of the 'mirai' package <doi:10.5281/zenodo.7912722>. This allows you to process futures, as defined by the 'future' package, in parallel out of the box, on your local machine or across remote machines. Contrary to back-ends relying on the 'parallel' package (e.g. 'multisession') and socket connections, 'mirai_cluster' and 'mirai_multisession', provided here, can run more than 125 parallel R processes.
Author: Henrik Bengtsson [aut, cre, cph]
,
Charlie Gao [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future.mirai versions 0.2.1 dated 2024-05-15 and 0.2.2 dated 2024-07-03
DESCRIPTION | 14 +++++++------- MD5 | 12 ++++++------ NEWS.md | 10 +++++++++- R/MiraiFuture-class.R | 2 +- README.md | 6 +++--- man/future.mirai.Rd | 4 ++-- tests/mirai_cluster,worker-termination.R | 9 +++++++++ 7 files changed, 37 insertions(+), 20 deletions(-)
Title: Tidy Finance Helper Functions
Description: Helper functions for empirical research in financial economics,
addressing a variety of topics covered in Scheuch, Voigt, and Weiss (2023) <doi:10.1201/b23237>.
The package is designed to provide shortcuts for issues extensively discussed in the book,
facilitating easier application of its concepts. For more information and resources
related to the book, visit <https://www.tidy-finance.org/r/index.html>.
Author: Christoph Scheuch [aut, cre] ,
Stefan Voigt [aut] ,
Patrick Weiss [aut]
Maintainer: Christoph Scheuch <christoph.scheuch@gmail.com>
Diff between tidyfinance versions 0.2.0 dated 2024-05-29 and 0.2.1 dated 2024-07-03
DESCRIPTION | 6 +- MD5 | 48 +++++++++--------- NAMESPACE | 1 NEWS.md | 18 +++++++ R/check_supported_type.R | 7 +- R/create_summary_statistics.R | 17 +++--- R/download_data.R | 6 +- R/download_data_factors.R | 27 ++++++---- R/download_data_macro_predictors.R | 29 ++++++----- R/download_data_wrds.R | 6 +- R/download_data_wrds_clean_trace.R | 9 +-- R/download_data_wrds_compustat.R | 22 +++++--- R/download_data_wrds_crsp.R | 61 +++++++++++++----------- R/estimate_model.R | 6 +- R/global_variables.R | 3 - R/list_supported_types.R | 28 +++++++++-- README.md | 7 ++ build/partial.rdb |binary build/vignette.rds |binary man/download_data_macro_predictors.Rd | 3 - man/download_data_wrds_clean_trace.Rd | 3 - man/download_data_wrds_compustat.Rd | 18 +++++-- man/download_data_wrds_crsp.Rd | 19 ++++--- man/list_supported_types.Rd | 16 +++++- tests/testthat/test-create_summary_statistics.R | 12 ++-- 25 files changed, 234 insertions(+), 138 deletions(-)
Title: The Weyl Algebra
Description: A suite of routines for Weyl algebras. Notation follows
Coutinho (1995, ISBN 0-521-55119-6, "A Primer of Algebraic
D-Modules"). Uses 'disordR' discipline
(Hankin 2022 <doi:10.48550/arXiv.2210.03856>). To cite
the package in publications, use Hankin
2022 <doi:10.48550/arXiv.2212.09230>.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between weyl versions 0.0-4 dated 2023-09-29 and 0.0-5 dated 2024-07-03
weyl-0.0-4/weyl/build/stage23.rdb |only weyl-0.0-4/weyl/build/weyl.pdf |only weyl-0.0-4/weyl/inst/weyl_arxiv.bib |only weyl-0.0-5/weyl/DESCRIPTION | 16 - weyl-0.0-5/weyl/MD5 | 53 ++-- weyl-0.0-5/weyl/NAMESPACE | 2 weyl-0.0-5/weyl/build/partial.rdb |binary weyl-0.0-5/weyl/build/vignette.rds |binary weyl-0.0-5/weyl/data/dot.rda |binary weyl-0.0-5/weyl/data/x_and_d.rda |binary weyl-0.0-5/weyl/inst/doc/borcherds.Rmd | 19 - weyl-0.0-5/weyl/inst/doc/borcherds.html | 197 ++++++++++------ weyl-0.0-5/weyl/inst/doc/weyl.R | 2 weyl-0.0-5/weyl/inst/doc/weyl.Rmd | 15 - weyl-0.0-5/weyl/inst/doc/weyl.html | 348 ++++++++++++++++++++---------- weyl-0.0-5/weyl/inst/read.me | 5 weyl-0.0-5/weyl/inst/weyl_arxiv.Rnw | 8 weyl-0.0-5/weyl/man/Ops.Rd | 33 +- weyl-0.0-5/weyl/man/degree.Rd | 14 - weyl-0.0-5/weyl/man/derivation.Rd | 14 - weyl-0.0-5/weyl/man/dim.Rd | 6 weyl-0.0-5/weyl/man/dot.Rd | 3 weyl-0.0-5/weyl/man/grade.Rd | 4 weyl-0.0-5/weyl/man/weyl-package.Rd | 2 weyl-0.0-5/weyl/man/x_and_d.Rd | 8 weyl-0.0-5/weyl/tests/testthat/test_aab.R | 4 weyl-0.0-5/weyl/vignettes/borcherds.Rmd | 19 - weyl-0.0-5/weyl/vignettes/weyl.Rmd | 15 - weyl-0.0-5/weyl/vignettes/weyl.bib | 28 ++ 29 files changed, 518 insertions(+), 297 deletions(-)
Title: Seeded Sequential LDA for Topic Modeling
Description: Seeded Sequential LDA can classify sentences of texts into pre-define topics with a small number of seed words (Watanabe & Baturo, 2023) <doi:10.1177/08944393231178605>.
Implements Seeded LDA (Lu et al., 2010) <doi:10.1109/ICDMW.2011.125> and Sequential LDA (Du et al., 2012) <doi:10.1007/s10115-011-0425-1> with the distributed LDA algorithm (Newman, et al., 2009) for parallel computing.
Author: Kohei Watanabe [aut, cre, cph],
Phan Xuan-Hieu [aut, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between seededlda versions 1.3.1 dated 2024-06-25 and 1.3.2 dated 2024-07-03
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ man/textmodel_lda.Rd | 2 +- src/array.h | 12 +++++------- src/lda.cpp | 1 - 6 files changed, 18 insertions(+), 17 deletions(-)
Title: Consensus Pathway Analysis
Description: Provides a set of functions to perform pathway analysis and meta analysis from multiple gene expression datasets, as well as visualization of the results (Nguyen et al. (2024) <doi:10.1002/cpz1.1036>). The package is a wrapper of the following packages: Ritchie et al. (2015) <doi:10.1093/nar/gkv007>, Love et al. (2014) <doi:10.1186/s13059-014-0550-8>, Robinson et al. (2010) <doi:10.1093/bioinformatics/btp616>, Korotkevich et al. (2016) <arxiv:10.1101/060012>, Efron et al. (2015) <https://CRAN.R-project.org/package=GSA>, and Gu, Z. (2012) <https://CRAN.R-project.org/package=CePa>.
Author: Ha Nguyen [aut, cre],
Phi Bya [aut],
Zeynab Maghsoudi [aut],
Tin Nguyen [fnd]
Maintainer: Ha Nguyen <hvn0006@auburn.edu>
Diff between RCPA versions 0.2.2 dated 2024-04-15 and 0.2.3 dated 2024-07-03
DESCRIPTION | 16 ++++++++-------- MD5 | 8 ++++---- R/annotation.R | 2 +- build/vignette.rds |binary inst/doc/RCPA.html | 6 +----- 5 files changed, 14 insertions(+), 18 deletions(-)
Title: Methods and Classes for the OMOP Common Data Model
Description: Provides definitions of core classes and methods used by analytic
pipelines that query the OMOP (Observational Medical Outcomes Partnership)
common data model.
Author: Marti Catala [aut, cre] ,
Edward Burn [aut] ,
Mike Du [ctb] ,
Yuchen Guo [ctb] ,
Adam Black [ctb] ,
Marta Alcalde-Herraiz [ctb] ,
Nuria Mercade-Besora [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between omopgenerics versions 0.2.2 dated 2024-06-19 and 0.2.3 dated 2024-07-03
DESCRIPTION | 23 ++- MD5 | 49 +++---- NAMESPACE | 5 R/classCdmReference.R | 25 +++ R/classCodelist.R | 3 R/classCodelistWithDetails.R |only R/classCohortTable.R | 13 + R/classSummarisedResult.R | 2 R/methodBind.R | 2 R/methodSuppress.R | 170 ++++++++++++------------ R/overwriteClasses.R | 11 + inst/doc/a02_concept_set.html | 4 inst/doc/reexport.Rmd | 174 ++++++++++++------------- inst/doc/reexport.html | 2 man/emptyCodelistWithDetails.Rd |only man/newCodelistWithDetails.Rd |only man/omopgenerics-package.Rd | 3 man/print.codelist_with_details.Rd |only man/suppress.summarised_result.Rd | 2 man/validateNameLevel.Rd | 8 - tests/testthat/test-cdmFromTables.R | 16 ++ tests/testthat/test-classCodelist.R | 69 ++++++--- tests/testthat/test-classCodelistWithDetails.R |only tests/testthat/test-classCohortTable.R | 35 +++++ tests/testthat/test-classSummarisedResult.R | 42 +++++- tests/testthat/test-methodSuppress.R | 63 +++++++++ tests/testthat/test-overwriteClasses.R | 31 ++++ vignettes/reexport.Rmd | 174 ++++++++++++------------- 28 files changed, 599 insertions(+), 327 deletions(-)
Title: Score and Plot the Healthy Eating Index from NHANES Data
Description: Calculate and visualize Healthy Eating Index (HEI) scores
from National Health and Nutrition Examination Survey 24-hour dietary
recall data utilizing three methods recommended by the National Cancer
Institute (2024)
<https://epi.grants.cancer.gov/hei/hei-methods-and-calculations.html#:~:text=To%20use%20the%20simple%20HEI,the%20total%20scores%20across%20individuals.>.
Effortlessly analyze HEI scores across different demographic groups
and years.
Author: Vijetha Ramdas [aut, cre],
Berkeley Ho [aut],
Abhra Sarkar [aut]
Maintainer: Vijetha Ramdas <vramdas06@gmail.com>
Diff between heiscore versions 0.0.1 dated 2024-05-10 and 0.1.1 dated 2024-07-03
DESCRIPTION | 12 MD5 | 25 NEWS.md | 14 R/app.R | 185 R/cleanDataset.R | 2 R/mainScoringFunction.R | 148 R/plotScore.R | 180 R/selectDataset.R | 14 README.md |19670 +++++++++++++++++++++++++++++++++++++++++++++++- man/figures |only man/plotScore.Rd | 58 man/runShinyApp.Rd | 13 man/score.Rd | 54 man/selectDataset.Rd | 10 14 files changed, 19988 insertions(+), 397 deletions(-)
Title: Globally-Applicable Area Disaggregated General Ecosystem Toolbox
V3
Description: A framework to assist creation of marine ecosystem models,
generating either 'R' or 'C++' code which can then be optimised using
the 'TMB' package and standard 'R' tools. Principally designed to
reproduce gadget2 models in 'TMB', but can be extended beyond
gadget2's capabilities.
Kasper Kristensen, Anders Nielsen, Casper W. Berg, Hans Skaug, Bradley M. Bell (2016) <doi:10.18637/jss.v070.i05> "TMB: Automatic Differentiation and Laplace Approximation.".
Begley, J., & Howell, D. (2004) <https://core.ac.uk/download/pdf/225936648.pdf> "An overview of Gadget, the globally applicable area-disaggregated general ecosystem toolbox. ICES.".
Author: Jamie Lentin [aut, cre] ,
Bjarki Thor Elvarsson [aut] ,
William Butler [aut] ,
Marine and Freshwater Research Institute [cph]
Maintainer: Jamie Lentin <lentinj@shuttlethread.com>
Diff between gadget3 versions 0.11-1 dated 2024-03-19 and 0.12-1 dated 2024-07-03
DESCRIPTION | 10 MD5 | 63 ++-- NEWS.md | 5 R/aab_env.R | 6 R/action_age.R | 98 +----- R/action_naturalmortality.R | 4 R/action_spawn.R | 19 - R/run_tmb.R | 2 R/step.R | 40 ++ build/vignette.rds |binary inst/doc/incorporating-observation-data.R | 6 inst/doc/incorporating-observation-data.html | 187 +++++++++---- inst/doc/introduction-single-stock.R | 24 - inst/doc/introduction-single-stock.html | 383 ++++++++++++++++++++------- inst/doc/model-customisation.R | 2 inst/doc/model-customisation.html | 3 inst/doc/model-debugging.R | 20 - inst/doc/model-debugging.html | 68 +++- inst/doc/model-structure.R | 2 inst/doc/model-structure.html | 208 ++++++++++---- inst/doc/multiple-substocks.R | 18 - inst/doc/multiple-substocks.html | 122 ++++++-- inst/doc/random-effects.R | 8 inst/doc/random-effects.html | 76 ++++- inst/doc/writing_actions.R | 4 inst/doc/writing_actions.html | 99 +++++- man/aab_env.Rd | 14 man/run_tmb.Rd | 4 man/step.Rd | 25 + tests/test-action_age.R | 6 tests/test-action_naturalmortality.R | 52 +++ tests/test-action_spawn-multipleoutputs.R |only tests/test-step.R | 30 ++ 33 files changed, 1122 insertions(+), 486 deletions(-)
Title: Functional Data Analysis and Empirical Dynamics
Description: A versatile package that provides implementation of various
methods of Functional Data Analysis (FDA) and Empirical Dynamics. The core of this
package is Functional Principal Component Analysis (FPCA), a key technique for
functional data analysis, for sparsely or densely sampled random trajectories
and time courses, via the Principal Analysis by Conditional Estimation
(PACE) algorithm. This core algorithm yields covariance and mean functions,
eigenfunctions and principal component (scores), for both functional data and
derivatives, for both dense (functional) and sparse (longitudinal) sampling designs.
For sparse designs, it provides fitted continuous trajectories with confidence bands,
even for subjects with very few longitudinal observations. PACE is a viable and
flexible alternative to random effects modeling of longitudinal data. There is also a
Matlab version (PACE) that contains some methods not available on fdapace and vice
versa. Updates to fdapace were supported by grants from [...truncated...]
Author: Yidong Zhou [cre, aut] ,
Han Chen [aut],
Su I Iao [aut],
Poorbita Kundu [aut],
Hang Zhou [aut],
Satarupa Bhattacharjee [aut],
Cody Carroll [aut] ,
Yaqing Chen [aut],
Xiongtao Dai [aut],
Jianing Fan [aut],
Alvaro Gajardo [aut],
Pantelis Z. Hadjipantel [...truncated...]
Maintainer: Yidong Zhou <ydzhou@ucdavis.edu>
Diff between fdapace versions 0.5.9 dated 2022-08-16 and 0.6.0 dated 2024-07-03
fdapace-0.5.9/fdapace/R/FLM1.R |only fdapace-0.5.9/fdapace/man/FLM1.Rd |only fdapace-0.6.0/fdapace/DESCRIPTION | 39 +- fdapace-0.6.0/fdapace/MD5 | 41 +- fdapace-0.6.0/fdapace/NAMESPACE | 2 fdapace-0.6.0/fdapace/NEWS | 11 fdapace-0.6.0/fdapace/R/CreateDesignPlot.R | 2 fdapace-0.6.0/fdapace/R/CreateModeOfVarPlot.R | 8 fdapace-0.6.0/fdapace/R/FLM.R | 370 +++++++++++----------- fdapace-0.6.0/fdapace/R/FLMCI.R |only fdapace-0.6.0/fdapace/R/MakeGPFunctionalData.R | 4 fdapace-0.6.0/fdapace/R/NormCurveToArea.R | 12 fdapace-0.6.0/fdapace/R/pkgname.R | 135 ++++---- fdapace-0.6.0/fdapace/R/plot.FPCA.R | 4 fdapace-0.6.0/fdapace/README.md | 2 fdapace-0.6.0/fdapace/build/vignette.rds |binary fdapace-0.6.0/fdapace/inst/CITATION |only fdapace-0.6.0/fdapace/inst/doc/dynFPCA.html | 309 +++++++++--------- fdapace-0.6.0/fdapace/inst/doc/fdapaceVig.html | 303 +++++++++--------- fdapace-0.6.0/fdapace/man/FLM.Rd | 13 fdapace-0.6.0/fdapace/man/FLMCI.Rd |only fdapace-0.6.0/fdapace/man/MakeGPFunctionalData.Rd | 4 fdapace-0.6.0/fdapace/man/NormCurvToArea.Rd | 12 fdapace-0.6.0/fdapace/man/fdapace.Rd | 133 ++++--- 24 files changed, 753 insertions(+), 651 deletions(-)
Title: Download Crypto Currency Data from 'CoinMarketCap' without 'API'
Description: Retrieves crypto currency information and historical prices as well as information on the exchanges they are listed on. Historical data contains daily open, high, low and close values for all crypto currencies. All data is scraped from <https://coinmarketcap.com> via their 'web-api'.
Author: Sebastian Stoeckl [aut, cre] ,
Jesse Vent [ctb]
Maintainer: Sebastian Stoeckl <sebastian.stoeckl@uni.li>
Diff between crypto2 versions 2.0.0 dated 2024-06-13 and 2.0.1 dated 2024-07-03
DESCRIPTION | 6 +-- MD5 | 8 ++-- NEWS.md | 4 ++ R/crypto_info.R | 2 - README.md | 98 +++++++++++++++++++++++++++++--------------------------- 5 files changed, 64 insertions(+), 54 deletions(-)
Title: A Robust Interface to ArcGIS 'Geocoding Services'
Description: A very fast and robust interface to ArcGIS 'Geocoding
Services'. Provides capabilities for reverse geocoding, finding
address candidates, character-by-character search autosuggestion, and
batch geocoding. The public 'ArcGIS World Geocoder' is accessible for
free use via 'arcgisgeocode' for all services except batch geocoding.
'arcgisgeocode' also integrates with 'arcgisutils' to provide access
to custom locators or private 'ArcGIS World Geocoder' hosted on
'ArcGIS Enterprise'. Learn more in the 'Geocode service' API reference
<https://developers.arcgis.com/rest/geocode/api-reference/overview-world-geocoding-service.htm>.
Author: Josiah Parry [aut, cre]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between arcgisgeocode versions 0.1.0 dated 2024-05-25 and 0.2.0 dated 2024-07-03
DESCRIPTION | 8 +-- MD5 | 18 ++++---- NEWS.md |only R/core-batch-geocode.R | 45 ++++++++++++++++++--- R/extendr-wrappers.R | 1 R/sysdata.rda |only man/arcgisgeocode-package.Rd | 12 ++++- src/rust/Cargo.lock | 76 ++++++++++++++++++------------------- src/rust/Cargo.toml | 2 src/rust/src/parse_custom_attrs.rs | 7 +++ src/rust/vendor.tar.xz |binary 11 files changed, 108 insertions(+), 61 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-06-05 1.0.1
Title: Retrieve Data on European Union Law
Description: Access to data on European Union laws and court decisions made easy with pre-defined 'SPARQL' queries and 'GET' requests. See Ovadek (2021) <doi:10.1080/2474736X.2020.1870150> .
Author: Michal Ovadek [aut, cre, cph]
Maintainer: Michal Ovadek <michal.ovadek@gmail.com>
Diff between eurlex versions 0.4.7 dated 2024-02-27 and 0.4.8 dated 2024-07-03
eurlex-0.4.7/eurlex/man/elx_council_votes.Rd |only eurlex-0.4.8/eurlex/DESCRIPTION | 12 ++-- eurlex-0.4.8/eurlex/MD5 | 21 +++---- eurlex-0.4.8/eurlex/NAMESPACE | 1 eurlex-0.4.8/eurlex/NEWS.md | 8 ++ eurlex-0.4.8/eurlex/R/elx_council_votes.R | 62 +++++++++++------------ eurlex-0.4.8/eurlex/R/elx_download_xml.R | 1 eurlex-0.4.8/eurlex/README.md | 15 +++++ eurlex-0.4.8/eurlex/inst/doc/sparql-queries.Rmd | 2 eurlex-0.4.8/eurlex/inst/doc/sparql-queries.html | 9 +-- eurlex-0.4.8/eurlex/man/elx_download_xml.Rd | 1 eurlex-0.4.8/eurlex/vignettes/sparql-queries.Rmd | 2 12 files changed, 78 insertions(+), 56 deletions(-)
Title: Indices of Effect Size
Description: Provide utilities to work with indices of effect size for a wide
variety of models and hypothesis tests (see list of supported models using
the function 'insight::supported_models()'), allowing computation of and
conversion between indices such as Cohen's d, r, odds, etc.
References: Ben-Shachar et al. (2020) <doi:10.21105/joss.02815>.
Author: Mattan S. Ben-Shachar [aut, cre]
,
Dominique Makowski [aut] ,
Daniel Luedecke [aut] ,
Indrajeet Patil [aut] ,
Brenton M. Wiernik [aut] ,
Remi Theriault [aut] ,
Ken Kelley [ctb],
David Stanley [ctb],
Aaron Caldwell [ctb] ,
Jessica Burnett [rev] ,
Johan [...truncated...]
Maintainer: Mattan S. Ben-Shachar <mattansb@msbstats.info>
Diff between effectsize versions 0.8.8 dated 2024-05-12 and 0.8.9 dated 2024-07-03
DESCRIPTION | 10 - MD5 | 76 +++++------ NEWS.md | 6 R/cohens_d.R | 6 R/cohens_g.R | 14 -- R/common_language.R | 8 - R/convert_between_common_language.R | 18 ++ R/convert_between_odds_to_probs.R | 44 +++--- R/effectsize.htest.R | 2 R/eta_squared-main.R | 90 ++++++------- R/eta_squared-methods.R | 35 ++--- R/interpret.R | 37 ++++- R/interpret_bf.R | 46 ++---- R/interpret_cohens_d.R | 2 R/interpret_cohens_g.R | 2 R/interpret_ess_rhat.R | 10 - R/interpret_oddsratio.R | 10 - R/interpret_p.R | 5 R/interpret_pd.R | 2 R/interpret_r.R | 15 +- R/interpret_r2.R | 2 R/rank_ANOVA.R | 11 - R/rank_diff.R | 18 +- R/repeated_measures_d.R | 12 - R/utils.R | 2 R/utils_ci.R | 16 +- R/utils_interpret.R | 2 R/utils_validate_input_data.R | 5 inst/doc/effectsize.html | 226 ++++++++++++++++----------------- inst/doc/from_test_statistics.html | 118 ++++++++--------- inst/doc/standardized_differences.html | 19 +- inst/doc/statistical_power.html | 42 +++--- man/effectsize_CIs.Rd | 12 + man/interpret.Rd | 11 + man/interpret_bf.Rd | 2 man/interpret_p.Rd | 5 man/interpret_r.Rd | 11 + tests/testthat/test-interpret.R | 11 + tests/testthat/test-rankES.R | 2 39 files changed, 523 insertions(+), 442 deletions(-)
Title: Open Perimetry Interface
Description: Implementation of the Open Perimetry Interface (OPI) for simulating and controlling visual field machines using R. The OPI is a standard for interfacing with visual field testing machines (perimeters) first started as an open source project with support of Haag-Streit in 2010. It specifies basic functions that allow many visual field tests to be constructed. As of February 2022 it is fully implemented on the Haag-Streit Octopus 900 and 'CrewT ImoVifa' ('Topcon Tempo') with partial implementations on the Centervue Compass, Kowa AP 7000 and Android phones. It also has a cousin: the R package 'visualFields', which has tools for analysing and manipulating visual field data.
Author: Andrew Turpin [cre, aut, cph] ,
David Lawson [ctb, cph],
Ivan Marin-Franch [ctb, cph],
Matthias Muller [ctb],
Jonathan Denniss [ctb, cph],
Astrid Zeman [ctb],
Giovanni Montesano [ctb]
Maintainer: Andrew Turpin <andrew.turpin@lei.org.au>
Diff between OPI versions 2.11.2 dated 2024-01-24 and 3.0.1 dated 2024-07-03
OPI-2.11.2/OPI/R/compassClient.r |only OPI-2.11.2/OPI/R/daydreamClient.r |only OPI-2.11.2/OPI/R/displayClient.r |only OPI-2.11.2/OPI/R/imoClient.r |only OPI-2.11.2/OPI/R/kowaAP7000Client.r |only OPI-2.11.2/OPI/R/octopus600.r |only OPI-2.11.2/OPI/R/octopus900Client.r |only OPI-2.11.2/OPI/R/opiKineticStimulus.r |only OPI-2.11.2/OPI/R/opiStaticStimulus.r |only OPI-2.11.2/OPI/R/opiTemporalStimulus.r |only OPI-2.11.2/OPI/R/phoneHMD.r |only OPI-2.11.2/OPI/R/simDisplay.r |only OPI-2.11.2/OPI/R/simG.r |only OPI-2.11.2/OPI/R/simH.r |only OPI-2.11.2/OPI/R/simH_RT.r |only OPI-2.11.2/OPI/R/simNo.r |only OPI-2.11.2/OPI/R/simYes.r |only OPI-2.11.2/OPI/man/FT.Rd |only OPI-2.11.2/OPI/man/chooseOpi.Rd |only OPI-2.11.2/OPI/man/dot-OpiEnv.Rd |only OPI-2.11.2/OPI/man/opiDistributor.Rd |only OPI-2.11.2/OPI/man/opiGetParams.Rd |only OPI-2.11.2/OPI/man/opiInitialize.Rd |only OPI-2.11.2/OPI/tests/1.R |only OPI-2.11.2/OPI/tests/2.R |only OPI-2.11.2/OPI/tests/3.R |only OPI-2.11.2/OPI/tests/4.R |only OPI-2.11.2/OPI/tests/5.R |only OPI-3.0.1/OPI/DESCRIPTION | 59 - OPI-3.0.1/OPI/MD5 | 180 +++-- OPI-3.0.1/OPI/NAMESPACE | 25 OPI-3.0.1/OPI/NEWS.md | 27 OPI-3.0.1/OPI/R/Compass.r |only OPI-3.0.1/OPI/R/Display.r |only OPI-3.0.1/OPI/R/ImoVifa.r |only OPI-3.0.1/OPI/R/KTPsi.r |only OPI-3.0.1/OPI/R/KowaAP7000Client.r |only OPI-3.0.1/OPI/R/OPI-package.r | 11 OPI-3.0.1/OPI/R/Octopus600.r |only OPI-3.0.1/OPI/R/Octopus900.r |only OPI-3.0.1/OPI/R/PhoneHMD.r |only OPI-3.0.1/OPI/R/PicoVR.r |only OPI-3.0.1/OPI/R/QUESTP.r | 101 +-- OPI-3.0.1/OPI/R/SimGaussian.r |only OPI-3.0.1/OPI/R/SimHenson.r |only OPI-3.0.1/OPI/R/SimHensonRT.r |only OPI-3.0.1/OPI/R/SimNo.r |only OPI-3.0.1/OPI/R/SimYes.r |only OPI-3.0.1/OPI/R/data-RtDbUnits.r | 9 OPI-3.0.1/OPI/R/data-RtSigmaUnits.r | 11 OPI-3.0.1/OPI/R/fourTwo.r | 129 +-- OPI-3.0.1/OPI/R/full_threshold.r | 106 +-- OPI-3.0.1/OPI/R/mocs.r | 49 - OPI-3.0.1/OPI/R/opi.r | 653 +++++++------------- OPI-3.0.1/OPI/R/zest.r | 33 - OPI-3.0.1/OPI/README.md | 76 +- OPI-3.0.1/OPI/man/KTPsi.Rd |only OPI-3.0.1/OPI/man/MOCS.Rd | 12 OPI-3.0.1/OPI/man/OPI-package.Rd | 14 OPI-3.0.1/OPI/man/QUESTP.Rd | 37 - OPI-3.0.1/OPI/man/RtDbUnits.Rd | 8 OPI-3.0.1/OPI/man/RtSigmaUnits.Rd | 10 OPI-3.0.1/OPI/man/ZEST.Rd | 12 OPI-3.0.1/OPI/man/chooseOPI.Rd |only OPI-3.0.1/OPI/man/dot-opi_env.Rd |only OPI-3.0.1/OPI/man/fourTwo.Rd | 54 - OPI-3.0.1/OPI/man/full_threshold.Rd |only OPI-3.0.1/OPI/man/kowa.presentKinetic.Rd |only OPI-3.0.1/OPI/man/kowa.presentStatic.Rd |only OPI-3.0.1/OPI/man/kowa.presentTemporal.Rd |only OPI-3.0.1/OPI/man/octo900.presentKinetic.Rd |only OPI-3.0.1/OPI/man/octo900.presentStatic.Rd |only OPI-3.0.1/OPI/man/octo900.presentTemporal.Rd |only OPI-3.0.1/OPI/man/open_socket.Rd |only OPI-3.0.1/OPI/man/opiClose.Rd | 104 --- OPI-3.0.1/OPI/man/opiClose_for_Compass.Rd |only OPI-3.0.1/OPI/man/opiClose_for_Display.Rd |only OPI-3.0.1/OPI/man/opiClose_for_ImoVifa.Rd |only OPI-3.0.1/OPI/man/opiClose_for_KowaAP7000.Rd |only OPI-3.0.1/OPI/man/opiClose_for_O600.Rd |only OPI-3.0.1/OPI/man/opiClose_for_Octopus900.Rd |only OPI-3.0.1/OPI/man/opiClose_for_PhoneHMD.Rd |only OPI-3.0.1/OPI/man/opiClose_for_PicoVR.Rd |only OPI-3.0.1/OPI/man/opiClose_for_SimGaussian.Rd |only OPI-3.0.1/OPI/man/opiClose_for_SimHenson.Rd |only OPI-3.0.1/OPI/man/opiClose_for_SimHensonRT.Rd |only OPI-3.0.1/OPI/man/opiClose_for_SimNo.Rd |only OPI-3.0.1/OPI/man/opiClose_for_SimYes.Rd |only OPI-3.0.1/OPI/man/opiInitialise.Rd |only OPI-3.0.1/OPI/man/opiInitialise_for_Compass.Rd |only OPI-3.0.1/OPI/man/opiInitialise_for_Display.Rd |only OPI-3.0.1/OPI/man/opiInitialise_for_ImoVifa.Rd |only OPI-3.0.1/OPI/man/opiInitialise_for_KowaAP7000.Rd |only OPI-3.0.1/OPI/man/opiInitialise_for_O600.Rd |only OPI-3.0.1/OPI/man/opiInitialise_for_Octopus900.Rd |only OPI-3.0.1/OPI/man/opiInitialise_for_PhoneHMD.Rd |only OPI-3.0.1/OPI/man/opiInitialise_for_PicoVR.Rd |only OPI-3.0.1/OPI/man/opiInitialise_for_SimGaussian.Rd |only OPI-3.0.1/OPI/man/opiInitialise_for_SimHenson.Rd |only OPI-3.0.1/OPI/man/opiInitialise_for_SimHensonRT.Rd |only OPI-3.0.1/OPI/man/opiInitialise_for_SimNo.Rd |only OPI-3.0.1/OPI/man/opiInitialise_for_SimYes.Rd |only OPI-3.0.1/OPI/man/opiKineticStimulus.Rd | 74 -- OPI-3.0.1/OPI/man/opiPresent.Rd | 429 ------------- OPI-3.0.1/OPI/man/opiPresent_for_Compass.Rd |only OPI-3.0.1/OPI/man/opiPresent_for_Display.Rd |only OPI-3.0.1/OPI/man/opiPresent_for_ImoVifa.Rd |only OPI-3.0.1/OPI/man/opiPresent_for_KowaAP7000.Rd |only OPI-3.0.1/OPI/man/opiPresent_for_O600.Rd |only OPI-3.0.1/OPI/man/opiPresent_for_Octopus900.Rd |only OPI-3.0.1/OPI/man/opiPresent_for_PhoneHMD.Rd |only OPI-3.0.1/OPI/man/opiPresent_for_PicoVR.Rd |only OPI-3.0.1/OPI/man/opiPresent_for_SimGaussian.Rd |only OPI-3.0.1/OPI/man/opiPresent_for_SimHenson.Rd |only OPI-3.0.1/OPI/man/opiPresent_for_SimHensonRT.Rd |only OPI-3.0.1/OPI/man/opiPresent_for_SimNo.Rd |only OPI-3.0.1/OPI/man/opiPresent_for_SimYes.Rd |only OPI-3.0.1/OPI/man/opiQueryDevice.Rd | 133 ---- OPI-3.0.1/OPI/man/opiQueryDevice_for_Compass.Rd |only OPI-3.0.1/OPI/man/opiQueryDevice_for_Display.Rd |only OPI-3.0.1/OPI/man/opiQueryDevice_for_ImoVifa.Rd |only OPI-3.0.1/OPI/man/opiQueryDevice_for_KowaAP7000.Rd |only OPI-3.0.1/OPI/man/opiQueryDevice_for_O600.Rd |only OPI-3.0.1/OPI/man/opiQueryDevice_for_Octopus900.Rd |only OPI-3.0.1/OPI/man/opiQueryDevice_for_PhoneHMD.Rd |only OPI-3.0.1/OPI/man/opiQueryDevice_for_PicoVR.Rd |only OPI-3.0.1/OPI/man/opiQueryDevice_for_SimGaussian.Rd |only OPI-3.0.1/OPI/man/opiQueryDevice_for_SimHenson.Rd |only OPI-3.0.1/OPI/man/opiQueryDevice_for_SimHensonRT.Rd |only OPI-3.0.1/OPI/man/opiQueryDevice_for_SimNo.Rd |only OPI-3.0.1/OPI/man/opiQueryDevice_for_SimYes.Rd |only OPI-3.0.1/OPI/man/opiSetBackground.Rd | 422 ------------ OPI-3.0.1/OPI/man/opiSetup.Rd |only OPI-3.0.1/OPI/man/opiSetup_for_Compass.Rd |only OPI-3.0.1/OPI/man/opiSetup_for_Display.Rd |only OPI-3.0.1/OPI/man/opiSetup_for_ImoVifa.Rd |only OPI-3.0.1/OPI/man/opiSetup_for_KowaAP7000.Rd |only OPI-3.0.1/OPI/man/opiSetup_for_O600.Rd |only OPI-3.0.1/OPI/man/opiSetup_for_Octopus900.Rd |only OPI-3.0.1/OPI/man/opiSetup_for_PhoneHMD.Rd |only OPI-3.0.1/OPI/man/opiSetup_for_PicoVR.Rd |only OPI-3.0.1/OPI/man/opiSetup_for_SimGaussian.Rd |only OPI-3.0.1/OPI/man/opiSetup_for_SimHenson.Rd |only OPI-3.0.1/OPI/man/opiSetup_for_SimHensonRT.Rd |only OPI-3.0.1/OPI/man/opiSetup_for_SimNo.Rd |only OPI-3.0.1/OPI/man/opiSetup_for_SimYes.Rd |only OPI-3.0.1/OPI/man/opiStaticStimulus.Rd | 100 --- OPI-3.0.1/OPI/man/opiTemporalStimulus.Rd | 68 -- OPI-3.0.1/OPI/tests/testthat |only OPI-3.0.1/OPI/tests/testthat.R |only 150 files changed, 831 insertions(+), 2115 deletions(-)
Title: Efficient Monitoring of Global Biodiversity Portfolios
Description: Biodiversity areas, especially primary forest, serve a
multitude of functions for local economy, regional functionality of
the ecosystems as well as the global health of our planet. Recently,
adverse changes in human land use practices and climatic responses to
increased greenhouse gas emissions, put these biodiversity areas under
a variety of different threats. The present package helps to analyse a
number of biodiversity indicators based on freely available
geographical datasets. It supports computational efficient routines
that allow the analysis of potentially global biodiversity portfolios.
The primary use case of the package is to support evidence based
reporting of an organization's effort to protect biodiversity areas
under threat and to identify regions were intervention is most duly
needed.
Author: Darius A. Goergen [aut, cre],
Om Prakash Bhandari [aut]
Maintainer: Darius A. Goergen <darius2402@web.de>
Diff between mapme.biodiversity versions 0.7.0 dated 2024-05-31 and 0.8.0 dated 2024-07-03
mapme.biodiversity-0.7.0/mapme.biodiversity/R/calc_active_fire_counts.R |only mapme.biodiversity-0.7.0/mapme.biodiversity/R/get_nasa_firms.R |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/fritz_et_al/Deforestation_Drivers_100m_IIASA.zip |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/fritz_et_al/geo_dr_han_hei_pr1.tif |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/gmw/gmw-extent_1996.gpkg |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/gmw/gmw-extent_1996.zip |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/gmw/gmw-extent_2016.gpkg |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/gmw/gmw-extent_2016.zip |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/gsw_change |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/gsw_occurrence |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/gsw_recurrence |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/gsw_seasonality |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/gsw_transitions |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/nasa_firms |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/nelson_et_al/traveltime-10k_20k.tif |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/nelson_et_al/traveltime-1mio_5mio.tif |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/nelson_et_al/traveltime-200k_500k.tif |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/nelson_et_al/traveltime-20k_110mio.tif |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/nelson_et_al/traveltime-20k_50k.tif |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/nelson_et_al/traveltime-500k_1mio.tif |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/nelson_et_al/traveltime-50k_100k.tif |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/nelson_et_al/traveltime-50k_50mio.tif |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/nelson_et_al/traveltime-5k_10k.tif |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/nelson_et_al/traveltime-5k_110mio.tif |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/soilgrids |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/worldpop/ppp_2000_1km_Aggregated.tif |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/worldpop/ppp_2001_1km_Aggregated.tif |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/worldpop/ppp_2002_1km_Aggregated.tif |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/worldpop/ppp_2003_1km_Aggregated.tif |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/worldpop/ppp_2004_1km_Aggregated.tif |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/worldpop/ppp_2005_1km_Aggregated.tif |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/worldpop/ppp_2006_1km_Aggregated.tif |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/worldpop/ppp_2008_1km_Aggregated.tif |only mapme.biodiversity-0.7.0/mapme.biodiversity/inst/res/worldpop/ppp_2009_1km_Aggregated.tif |only mapme.biodiversity-0.7.0/mapme.biodiversity/man/active_fire_counts.Rd |only mapme.biodiversity-0.7.0/mapme.biodiversity/man/download_or_skip.Rd |only mapme.biodiversity-0.7.0/mapme.biodiversity/man/nasa_firms.Rd |only mapme.biodiversity-0.7.0/mapme.biodiversity/man/unzip_and_remove.Rd |only mapme.biodiversity-0.7.0/mapme.biodiversity/tests/testthat/_snaps/get_nasa_grace.md |only mapme.biodiversity-0.7.0/mapme.biodiversity/tests/testthat/_snaps/get_soilgrids.md |only mapme.biodiversity-0.7.0/mapme.biodiversity/tests/testthat/test-calc_active_fire_counts.R |only mapme.biodiversity-0.7.0/mapme.biodiversity/tests/testthat/test-get_nasa_firms.R |only mapme.biodiversity-0.8.0/mapme.biodiversity/DESCRIPTION | 25 mapme.biodiversity-0.8.0/mapme.biodiversity/MD5 | 368 ++---- mapme.biodiversity-0.8.0/mapme.biodiversity/NAMESPACE | 11 mapme.biodiversity-0.8.0/mapme.biodiversity/NEWS.md | 33 mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_biome.R | 4 mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_burned_area.R |only mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_deforestation_drivers.R | 8 mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_drought_indicator.R | 8 mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_ecoregion.R | 6 mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_elevation.R | 5 mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_fatalities.R | 16 mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_gsw_change.R | 6 mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_gsw_occurrence.R | 6 mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_gsw_recurrence.R | 6 mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_gsw_seasonality.R | 7 mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_gsw_transitions.R | 6 mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_indicators.R | 132 -- mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_landcover.R | 6 mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_mangroves_area.R | 8 mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_population_count.R | 8 mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_precipitation_chirps.R | 6 mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_precipitation_wc.R | 4 mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_soilproperties.R | 57 mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_temperature_max_wc.R | 3 mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_temperature_min_wc.R | 6 mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_traveltime.R | 10 mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_treecover_area.R | 6 mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_treecover_area_and_emissions.R | 6 mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_treecoverloss_emissions.R | 6 mapme.biodiversity-0.8.0/mapme.biodiversity/R/calc_tri.R | 24 mapme.biodiversity-0.8.0/mapme.biodiversity/R/get_chirps.R | 62 - mapme.biodiversity-0.8.0/mapme.biodiversity/R/get_esalandcover.R | 49 mapme.biodiversity-0.8.0/mapme.biodiversity/R/get_fritz_et_al.R | 53 mapme.biodiversity-0.8.0/mapme.biodiversity/R/get_gfw_emissions.R | 27 mapme.biodiversity-0.8.0/mapme.biodiversity/R/get_gfw_lossyear.R | 19 mapme.biodiversity-0.8.0/mapme.biodiversity/R/get_gfw_treecover.R | 19 mapme.biodiversity-0.8.0/mapme.biodiversity/R/get_gmw.R | 99 - mapme.biodiversity-0.8.0/mapme.biodiversity/R/get_gsw.R | 65 - mapme.biodiversity-0.8.0/mapme.biodiversity/R/get_mcd64A1.R |only mapme.biodiversity-0.8.0/mapme.biodiversity/R/get_nasa_grace.R | 20 mapme.biodiversity-0.8.0/mapme.biodiversity/R/get_nasa_srtm.R | 29 mapme.biodiversity-0.8.0/mapme.biodiversity/R/get_nelson_et_al.R | 35 mapme.biodiversity-0.8.0/mapme.biodiversity/R/get_resources.R | 144 +- mapme.biodiversity-0.8.0/mapme.biodiversity/R/get_soilgrids.R | 64 - mapme.biodiversity-0.8.0/mapme.biodiversity/R/get_teow.R | 48 mapme.biodiversity-0.8.0/mapme.biodiversity/R/get_ucdp_ged.R | 64 - mapme.biodiversity-0.8.0/mapme.biodiversity/R/get_worldclim.R | 73 - mapme.biodiversity-0.8.0/mapme.biodiversity/R/get_worldpop.R | 84 - mapme.biodiversity-0.8.0/mapme.biodiversity/R/portfolio.R | 90 + mapme.biodiversity-0.8.0/mapme.biodiversity/R/register.R | 81 - mapme.biodiversity-0.8.0/mapme.biodiversity/R/spatial-utils.R |only mapme.biodiversity-0.8.0/mapme.biodiversity/R/utils.R | 142 -- mapme.biodiversity-0.8.0/mapme.biodiversity/README.md | 120 +- mapme.biodiversity-0.8.0/mapme.biodiversity/inst/doc/quickstart.R | 52 mapme.biodiversity-0.8.0/mapme.biodiversity/inst/doc/quickstart.Rmd | 115 - mapme.biodiversity-0.8.0/mapme.biodiversity/inst/doc/quickstart.html | 594 +++++----- mapme.biodiversity-0.8.0/mapme.biodiversity/inst/doc/terminology.html | 105 + mapme.biodiversity-0.8.0/mapme.biodiversity/inst/extdata/greenhouse_index.geosjon | 515 ++++---- mapme.biodiversity-0.8.0/mapme.biodiversity/inst/extdata/sierra_de_neiba_478140.gpkg |binary mapme.biodiversity-0.8.0/mapme.biodiversity/inst/extdata/sierra_de_neiba_478140_2.gpkg |binary mapme.biodiversity-0.8.0/mapme.biodiversity/inst/res/fritz_et_al/geo_fritz_et_al_100m.tif |only mapme.biodiversity-0.8.0/mapme.biodiversity/inst/res/global_surface_water_change |only mapme.biodiversity-0.8.0/mapme.biodiversity/inst/res/global_surface_water_occurrence |only mapme.biodiversity-0.8.0/mapme.biodiversity/inst/res/global_surface_water_recurrence |only mapme.biodiversity-0.8.0/mapme.biodiversity/inst/res/global_surface_water_seasonality |only mapme.biodiversity-0.8.0/mapme.biodiversity/inst/res/global_surface_water_transitions |only mapme.biodiversity-0.8.0/mapme.biodiversity/inst/res/gmw/gmw_v3_1996_vec.gpkg |only mapme.biodiversity-0.8.0/mapme.biodiversity/inst/res/gmw/gmw_v3_2016_vec.gpkg |only mapme.biodiversity-0.8.0/mapme.biodiversity/inst/res/mcd64a1 |only mapme.biodiversity-0.8.0/mapme.biodiversity/man/biome.Rd | 4 mapme.biodiversity-0.8.0/mapme.biodiversity/man/burned_area.Rd |only mapme.biodiversity-0.8.0/mapme.biodiversity/man/chirps.Rd | 2 mapme.biodiversity-0.8.0/mapme.biodiversity/man/deforestation_drivers.Rd | 6 mapme.biodiversity-0.8.0/mapme.biodiversity/man/drought_indicator.Rd | 4 mapme.biodiversity-0.8.0/mapme.biodiversity/man/ecoregion.Rd | 4 mapme.biodiversity-0.8.0/mapme.biodiversity/man/elevation.Rd | 3 mapme.biodiversity-0.8.0/mapme.biodiversity/man/esalandcover.Rd | 2 mapme.biodiversity-0.8.0/mapme.biodiversity/man/fatalities.Rd | 8 mapme.biodiversity-0.8.0/mapme.biodiversity/man/fritz_et_al.Rd | 2 mapme.biodiversity-0.8.0/mapme.biodiversity/man/gfw_emissions.Rd | 4 mapme.biodiversity-0.8.0/mapme.biodiversity/man/gfw_lossyear.Rd | 2 mapme.biodiversity-0.8.0/mapme.biodiversity/man/gfw_treecover.Rd | 2 mapme.biodiversity-0.8.0/mapme.biodiversity/man/global_surface_water_change.Rd | 2 mapme.biodiversity-0.8.0/mapme.biodiversity/man/gmw.Rd | 7 mapme.biodiversity-0.8.0/mapme.biodiversity/man/gsw_change.Rd | 4 mapme.biodiversity-0.8.0/mapme.biodiversity/man/gsw_occurrence.Rd | 4 mapme.biodiversity-0.8.0/mapme.biodiversity/man/gsw_recurrence.Rd | 4 mapme.biodiversity-0.8.0/mapme.biodiversity/man/gsw_seasonality.Rd | 5 mapme.biodiversity-0.8.0/mapme.biodiversity/man/gsw_transitions.Rd | 4 mapme.biodiversity-0.8.0/mapme.biodiversity/man/landcover.Rd | 4 mapme.biodiversity-0.8.0/mapme.biodiversity/man/make_footprints.Rd |only mapme.biodiversity-0.8.0/mapme.biodiversity/man/mangroves_area.Rd | 4 mapme.biodiversity-0.8.0/mapme.biodiversity/man/mapme.Rd | 32 mapme.biodiversity-0.8.0/mapme.biodiversity/man/mcd64a1.Rd |only mapme.biodiversity-0.8.0/mapme.biodiversity/man/nasa_grace.Rd | 2 mapme.biodiversity-0.8.0/mapme.biodiversity/man/nasa_srtm.Rd | 2 mapme.biodiversity-0.8.0/mapme.biodiversity/man/nelson_et_al.Rd | 2 mapme.biodiversity-0.8.0/mapme.biodiversity/man/population_count.Rd | 6 mapme.biodiversity-0.8.0/mapme.biodiversity/man/portfolio.Rd | 33 mapme.biodiversity-0.8.0/mapme.biodiversity/man/precipitation_chirps.Rd | 3 mapme.biodiversity-0.8.0/mapme.biodiversity/man/precipitation_wc.Rd | 4 mapme.biodiversity-0.8.0/mapme.biodiversity/man/resources.Rd | 3 mapme.biodiversity-0.8.0/mapme.biodiversity/man/soilgrids.Rd | 2 mapme.biodiversity-0.8.0/mapme.biodiversity/man/soilproperties.Rd | 55 mapme.biodiversity-0.8.0/mapme.biodiversity/man/spds_exists.Rd |only mapme.biodiversity-0.8.0/mapme.biodiversity/man/temperature_max_wc.Rd | 3 mapme.biodiversity-0.8.0/mapme.biodiversity/man/temperature_min_wc.Rd | 4 mapme.biodiversity-0.8.0/mapme.biodiversity/man/teow.Rd | 2 mapme.biodiversity-0.8.0/mapme.biodiversity/man/traveltime.Rd | 8 mapme.biodiversity-0.8.0/mapme.biodiversity/man/treecover_area.Rd | 4 mapme.biodiversity-0.8.0/mapme.biodiversity/man/treecover_area_and_emissions.Rd | 4 mapme.biodiversity-0.8.0/mapme.biodiversity/man/treecoverloss_emissions.Rd | 4 mapme.biodiversity-0.8.0/mapme.biodiversity/man/tri.Rd | 23 mapme.biodiversity-0.8.0/mapme.biodiversity/man/ucdp_ged.Rd | 6 mapme.biodiversity-0.8.0/mapme.biodiversity/man/worldclim_precipitation.Rd | 2 mapme.biodiversity-0.8.0/mapme.biodiversity/man/worldpop.Rd | 7 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/_snaps/calc_burned_area.md |only mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/_snaps/calc_population_count.md | 5 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/_snaps/calc_soilproperties.md | 2 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/_snaps/calc_traveltime.md | 3 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-calc_biome.R | 16 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-calc_burned_area.R |only mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-calc_deforestation_drivers.R | 16 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-calc_drought_indicator.R | 11 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-calc_ecoregion.R | 27 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-calc_fatalities.R | 10 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-calc_gsw_change.R | 13 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-calc_gsw_occurrence.R | 13 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-calc_gsw_recurrence.R | 13 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-calc_gsw_seasonality.R | 13 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-calc_gsw_transitions.R | 13 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-calc_indicator.R | 135 -- mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-calc_landcover.R | 12 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-calc_mangroves_area.R | 16 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-calc_population_count.R | 10 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-calc_precipitation_chirps.R | 12 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-calc_precipitation_wc.R | 10 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-calc_soilproperties.R | 17 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-calc_temperature_max_wc.R | 10 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-calc_temperature_min_wc.R | 10 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-calc_traveltime.R | 10 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-calc_treecover_area.R | 27 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-calc_treecover_area_and_emissions.R | 27 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-calc_treecoverloss_emissions.R | 27 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-get_chirps.R | 24 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-get_climaticVariables.R | 45 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-get_esalandcover.R | 33 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-get_fritz_et_al.R | 42 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-get_gfw_emissions.R | 29 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-get_gfw_lossyear.R | 33 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-get_gfw_treecover.R | 32 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-get_gmw.R | 27 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-get_gsw.R | 63 - mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-get_mcd64A1.R |only mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-get_nasa_grace.R | 29 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-get_nasa_srtm.R | 28 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-get_nelson_et_al.R | 29 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-get_resources.R | 7 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-get_soilgrids.R | 59 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-get_teow.R | 29 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-get_ucdp_ged.R | 49 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-get_worldpop.R | 40 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-portfolio.R | 49 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-register.R | 6 mapme.biodiversity-0.8.0/mapme.biodiversity/tests/testthat/test-utils.R | 52 mapme.biodiversity-0.8.0/mapme.biodiversity/vignettes/quickstart.Rmd | 115 - 208 files 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