Title: Tools for Analyzing MCMC Simulations from Bayesian Inference
Description: Tools for assessing and diagnosing convergence of
Markov Chain Monte Carlo simulations, as well as for graphically display
results from full MCMC analysis. The package also facilitates the graphical
interpretation of models by providing flexible functions to plot the
results against observed variables.
Author: Xavier Fernández i Marín <xavier.fim@gmail.com>
Maintainer: Xavier Fernández i Marín <xavier.fim@gmail.com>
Diff between ggmcmc versions 1.1.1 dated 2019-01-23 and 1.2 dated 2019-02-15
DESCRIPTION | 14 - MD5 | 94 ++++---- NEWS | 32 ++ R/functions.R | 5 R/ggs.R | 9 R/ggs_caterpillar.R | 17 + R/ggs_density.R | 10 R/ggs_separation.R | 2 R/ggs_traceplot.R | 17 + build/vignette.rds |binary inst/doc/using_ggmcmc.R | 20 - inst/doc/using_ggmcmc.Rmd | 45 +-- inst/doc/using_ggmcmc.html | 502 ++++++++++++-------------------------------- inst/doc/v70i09.pdf |binary man/ac.Rd | 1 man/calc_bin.Rd | 1 man/ci.Rd | 1 man/custom.sort.Rd | 1 man/get_family.Rd | 1 man/ggmcmc.Rd | 5 man/ggs.Rd | 10 man/ggs_Rhat.Rd | 1 man/ggs_autocorrelation.Rd | 1 man/ggs_caterpillar.Rd | 5 man/ggs_chain.Rd | 1 man/ggs_compare_partial.Rd | 1 man/ggs_crosscorrelation.Rd | 4 man/ggs_density.Rd | 6 man/ggs_geweke.Rd | 1 man/ggs_histogram.Rd | 1 man/ggs_pairs.Rd | 1 man/ggs_ppmean.Rd | 1 man/ggs_ppsd.Rd | 1 man/ggs_rocplot.Rd | 1 man/ggs_running.Rd | 5 man/ggs_separation.Rd | 1 man/ggs_traceplot.Rd | 6 man/gl_unq.Rd | 1 man/radon.Rd | 1 man/roc_calc.Rd | 1 man/s.Rd | 1 man/s.binary.Rd | 1 man/s.y.rep.Rd | 1 man/sde0f.Rd | 1 man/y.Rd | 1 man/y.binary.Rd | 1 vignettes/bibliography.bib | 8 vignettes/using_ggmcmc.Rmd | 45 +-- 48 files changed, 359 insertions(+), 527 deletions(-)
Title: Fast Nearest Neighbor Search Algorithms and Applications
Description: Cover-tree and kd-tree fast k-nearest neighbor search algorithms and related applications
including KNN classification, regression and information measures are implemented.
Author: Alina Beygelzimer, Sham Kakadet and John Langford (cover tree library),
Sunil Arya and David Mount (ANN library 1.1.2 for the kd-tree approach), Shengqiao Li
Maintainer: Shengqiao Li <lishengqiao@yahoo.com>
Diff between FNN versions 1.1.2.2 dated 2018-12-10 and 1.1.3 dated 2019-02-15
ChangeLog | 3 +++ DESCRIPTION | 13 +++++-------- MD5 | 6 +++--- src/KNN_mutual_information.cpp | 10 ++++++++-- 4 files changed, 19 insertions(+), 13 deletions(-)
Title: Statistical Methods for Phenology Analysis in Temperate Fruit
Trees
Description: The phenology of plants (i.e. the timing of their annual life
phases) depends on climatic cues. For temperate trees and many other plants,
spring phases, such as leaf emergence and flowering, have been found to result
from the effects of both cool (chilling) conditions and heat. Fruit tree
scientists (pomologists) have developed some metrics to quantify chilling
and heat (e.g. see Luedeling (2012) <doi.org/10.1016/j.scienta.2012.07.011>).
'chillR' contains functions for processing temperature records into
chilling (Chilling Hours, Utah Chill Units and Chill Portions) and heat units
(Growing Degree Hours). Regarding chilling metrics, Chill Portions are often
considered the most promising, but they are difficult to calculate. This package
makes it easy. 'chillR' also contains procedures for conducting a PLS analysis
relating phenological dates (e.g. bloom dates) to either mean temperatures or
mean chill and heat accumulation rates, based on long-term weather and phenology
records (Luedeling and Gassner (2012) <doi.org/10.1016/j.agrformet.2011.10.020>).
As of version 0.65, it also includes functions for generating weather
scenarios with a weather generator, for conducting climate change analyses
for temperature-based climatic metrics and for plotting results from such
analyses. Since version 0.70, 'chillR' contains a function for interpolating
hourly temperature records.
Author: Eike Luedeling
Maintainer: Eike Luedeling <eike@eikeluedeling.com>
Diff between chillR versions 0.70.12 dated 2018-12-18 and 0.70.14 dated 2019-02-15
DESCRIPTION | 12 +- MD5 | 30 +++--- NAMESPACE | 3 R/check_temperature_scenario.R | 4 R/getClimateWizardData.R | 131 ++++++++++++++++++++-------- R/getClimateWizard_scenarios.R |only R/handle_cimis.R | 23 ++-- R/make_daily_chill_plot.R | 166 ++++++++++++++++++++++++++++++++++++ R/patch_daily_temperatures.R | 2 R/runn_mean.R | 2 inst/doc/hourly_temperatures.html | 30 +++++- man/getClimateWizardData.Rd | 19 ++-- man/getClimateWizard_scenarios.Rd |only man/handle_cimis.Rd | 23 ++-- man/make_daily_chill_plot2.Rd |only man/patch_daily_temperatures.Rd | 4 man/plot_climateWizard_scenarios.Rd |only vignettes/Chilling_references.bib | 1 18 files changed, 355 insertions(+), 95 deletions(-)
Title: Psychometric Meta-Analysis Toolkit
Description: Tools for computing bare-bones and psychometric meta-analyses and for generating psychometric data for use in meta-analysis simulations. Supports bare-bones, individual-correction, and artifact-distribution methods for meta-analyzing correlations and d values. Includes tools for converting effect sizes, computing sporadic artifact corrections, reshaping meta-analytic databases, computing multivariate corrections for range variation, and more. Bugs can be reported to <https://github.com/psychmeta/psychmeta/issues> or <issues@psychmeta.com>.
Author: Jeffrey A. Dahlke [aut, cre],
Brenton M. Wiernik [aut],
Michael T. Brannick [ctb] (Testing),
Jack Kostal [ctb] (Code for reshape_mat2dat function),
Sean Potter [ctb] (Testing; Code for cumulative and leave1out plots),
John Sakaluk [ctb] (Code for funnel and forest plots),
Yuejia (Mandy) Teng [ctb] (Testing)
Maintainer: Jeffrey A. Dahlke <dahlk068@umn.edu>
Diff between psychmeta versions 2.3.0 dated 2019-01-09 and 2.3.1 dated 2019-02-15
DESCRIPTION | 10 MD5 | 113 ++++- NEWS | 15 R/convert_es.R | 6 R/convert_ma.R | 4 R/create_ad.R | 14 R/estimate_mixture.R | 34 + R/estimate_u.R | 4 R/filters.R | 2 R/heterogeneity.R | 767 +++++++++++++++++++++++++-------------- R/ma_d.R | 8 R/ma_d_bb.R | 33 - R/ma_d_ic.R | 6 R/ma_r.R | 25 - R/ma_r_bb.R | 39 - R/ma_r_ic.R | 26 - R/methods_print.R | 143 ++++++- R/output.R | 189 +++++---- R/plotting.R | 4 R/simulate_d.R | 4 R/var_error.R | 17 R/wt_stat.R | 195 ++++----- inst/doc/overview.html | 8 man/dot-attenuate_r_bvdrr.Rd |only man/dot-attenuate_r_bvirr.Rd |only man/dot-attenuate_r_rb.Rd |only man/dot-attenuate_r_uvdrr.Rd |only man/dot-attenuate_r_uvirr.Rd |only man/dot-convert_metatab.Rd |only man/dot-correct_r_bvdrr.Rd |only man/dot-correct_r_bvirr.Rd |only man/dot-correct_r_rb.Rd |only man/dot-correct_r_uvdrr.Rd |only man/dot-correct_r_uvirr.Rd |only man/dot-create_ad_int.Rd |only man/dot-descriptives_database.Rd |only man/dot-estimate_attenuation.Rd |only man/dot-heterogeneity.Rd |only man/dot-identify_ma_cols.Rd |only man/dot-integrate_dmod.Rd |only man/dot-lambda_bvirr.Rd |only man/dot-ma_artifacts.Rd |only man/dot-ma_bootstrap.Rd |only man/dot-ma_cumulative.Rd |only man/dot-ma_d_bb.Rd |only man/dot-ma_d_bb_boot.Rd |only man/dot-ma_generic.Rd |only man/dot-ma_generic_boot.Rd |only man/dot-ma_leave1out.Rd |only man/dot-ma_r_bb.Rd |only man/dot-ma_r_bb_boot.Rd |only man/dot-ma_r_ic.Rd |only man/dot-ma_r_ic_boot.Rd |only man/dot-ma_r_icts_boot.Rd |only man/dot-ma_r_icvgx_boot.Rd |only man/dot-ma_r_icvgy_boot.Rd |only man/dot-ma_r_order2.Rd |only man/dot-ma_r_order2_ad_boot.Rd |only man/dot-ma_r_order2_bb_boot.Rd |only man/dot-ma_r_order2_ic_boot.Rd |only man/dot-metabulate.Rd |only man/dot-plot_forest_meta.Rd |only man/dot-plot_funnel.Rd |only man/dot-print.lm_mat.Rd |only man/dot-print.summary.lm_mat.Rd |only man/dot-rbeta.Rd |only man/dot-refine_var_rr.Rd |only man/dot-tau_squared_m_solver.Rd |only man/dot-tau_squared_r_solver.Rd |only man/format_num.Rd | 15 man/heterogeneity.Rd | 31 - man/limits_tau.Rd | 11 man/limits_tau2.Rd |only man/ma_d.Rd | 36 - man/metabulate.Rd | 17 man/mix_dist.Rd | 12 man/plot_forest.Rd | 2 man/plot_funnel.Rd | 2 man/var_error_d.Rd | 4 man/var_error_r.Rd | 4 man/wt_cov.Rd | 2 81 files changed, 1103 insertions(+), 699 deletions(-)
Title: A 'Neo4J' Driver
Description: A Modern and Flexible 'Neo4J' Driver, allowing you to query
data on a 'Neo4J' server and handle the results in R. It's modern in
the sense it provides a driver
that can be easily integrated in a data analysis workflow, especially by
providing an API working smoothly with other data analysis and graph
packages. It's flexible in the way it returns the results, by
trying to stay as close as
possible to the way 'Neo4J' returns data. That way, you have the control
over the way you will compute the results. At the same time, the result
is not too complex, so that the "heavy lifting" of data wrangling is not
left to the user.
Author: Colin Fay [cre, aut] (<https://orcid.org/0000-0001-7343-1846>),
ThinkR [cph],
Neo4J [spn]
Maintainer: Colin Fay <contact@colinfay.me>
Diff between neo4r versions 0.1.0 dated 2019-01-27 and 0.1.1 dated 2019-02-15
neo4r-0.1.0/neo4r/man/convert_to.Rd |only neo4r-0.1.1/neo4r/DESCRIPTION | 6 neo4r-0.1.1/neo4r/MD5 | 37 neo4r-0.1.1/neo4r/NAMESPACE | 8 neo4r-0.1.1/neo4r/NEWS.md | 6 neo4r-0.1.1/neo4r/R/R6.R | 2 neo4r-0.1.1/neo4r/R/api_result_parsing.R | 28 neo4r-0.1.1/neo4r/R/con_pane_rstudio.R | 3 neo4r-0.1.1/neo4r/R/convert_to.R | 128 neo4r-0.1.1/neo4r/R/unnest_them.R | 47 neo4r-0.1.1/neo4r/R/utils.R |only neo4r-0.1.1/neo4r/inst/tests/testthat/a_movie.cypher |only neo4r-0.1.1/neo4r/inst/tests/testthat/movies_graph.RDS |only neo4r-0.1.1/neo4r/inst/tests/testthat/movies_rows.RDS |only neo4r-0.1.1/neo4r/inst/tests/testthat/test-connection.R | 4 neo4r-0.1.1/neo4r/inst/tests/testthat/test-context-formule1.R | 1542 +++++----- neo4r-0.1.1/neo4r/inst/tests/testthat/test-movies.R |only neo4r-0.1.1/neo4r/inst/tests/testthat/test-query.R | 11 neo4r-0.1.1/neo4r/man/figures/README-unnamed-chunk-16-1.png |binary neo4r-0.1.1/neo4r/man/figures/README-unnamed-chunk-17-1.png |binary neo4r-0.1.1/neo4r/man/figures/README-unnamed-chunk-18-1.png |only neo4r-0.1.1/neo4r/man/send_cypher.Rd | 4 neo4r-0.1.1/neo4r/man/unnest_relationships.Rd | 4 23 files changed, 948 insertions(+), 882 deletions(-)
Title: A Grammar of Animated Graphics
Description: The grammar of graphics as implemented in the 'ggplot2' package has
been successful in providing a powerful API for creating static
visualisation. In order to extend the API for animated graphics this package
provides a completely new set of grammar, fully compatible with 'ggplot2'
for specifying transitions and animations in a flexible and extensible way.
Author: Thomas Lin Pedersen [aut, cre],
David Robinson [aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between gganimate versions 1.0.0 dated 2019-01-02 and 1.0.1 dated 2019-02-15
DESCRIPTION | 8 +++--- MD5 | 39 +++++++++++++++---------------- NAMESPACE | 1 NEWS.md |only R/animate.R | 1 R/ggplot2_reimpl.R | 1 R/shadow-mark.R | 2 + R/transition-.R | 22 +++++++++++------ R/transition-components.R | 2 - R/transition-events.R | 2 - R/transition-filter.R | 2 - R/transition-layers.R | 4 +-- R/transition-states.R | 2 - R/transition-time.R | 2 - R/transition_reveal.R | 2 - R/transmuters.R | 9 +++++++ R/view-follow.R | 3 ++ inst/doc/gganimate.html | 4 +-- man/figures/README-unnamed-chunk-2-1.gif |binary man/figures/README-unnamed-chunk-4-1.gif |binary vignettes/extra/talks.Rmd | 4 +-- 21 files changed, 67 insertions(+), 43 deletions(-)
Title: Quickly Create Elegant Regression Results Tables and Plots when
Modelling
Description: Generate regression results tables and plots in final
format for publication. Explore models and export directly to PDF
and 'Word' using 'RMarkdown'.
Author: Ewen Harrison [aut, cre],
Tom Drake [aut],
Riinu Ots [aut]
Maintainer: Ewen Harrison <ewen.harrison@ed.ac.uk>
Diff between finalfit versions 0.8.9 dated 2018-12-18 and 0.9.0 dated 2019-02-15
DESCRIPTION | 10 LICENCE | 2 MD5 | 102 +++++----- NAMESPACE | 2 NEWS.md | 7 R/ff_glimpse.R | 8 R/ff_interaction.R | 2 R/ff_label.R | 1 R/ff_merge.R | 8 R/ff_metrics.R | 26 -- R/ff_remove_ref.R |only R/finalfit.R | 36 +-- R/finalfit_internal_functions.R | 51 +++-- R/fit2df.R | 11 - R/glmmixed.R | 11 - R/lmmixed.R | 32 +-- R/or_plot.R | 7 R/summaryfactorlist.R | 4 R/surv_plot.R | 2 README.md | 2 build/vignette.rds |binary inst/doc/bootstrap.Rmd | 4 inst/doc/bootstrap.html | 26 +- inst/doc/data_prep.R |only inst/doc/data_prep.Rmd |only inst/doc/data_prep.html |only inst/doc/export.Rmd | 10 inst/doc/export.html | 14 - inst/doc/finalfit.R | 3 inst/doc/finalfit.Rmd | 33 +-- inst/doc/finalfit.html | 33 +-- inst/doc/missing.Rmd | 6 inst/doc/missing.html | 10 inst/doc/tables_gallery.R |only inst/doc/tables_gallery.Rmd |only inst/doc/tables_gallery.html |only man/dependent_label.Rd | 3 man/ff_formula.Rd | 16 + man/ff_interaction.Rd | 4 man/ff_metrics.Rd | 25 -- man/ff_remove_ref.Rd |only man/finalfit.Rd | 36 +-- man/fit2df.Rd | 2 man/glmmixed.Rd | 7 man/lmmixed.Rd | 28 +- man/p_tidy.Rd | 1 man/round_tidy.Rd | 7 man/summary_factorlist.Rd | 4 tests/testthat/Rplots.pdf |binary vignettes/bootstrap.Rmd | 4 vignettes/data_prep.Rmd |only vignettes/export.Rmd | 10 vignettes/export_cache/html/__packages | 1 vignettes/export_cache/html/unnamed-chunk-8_7b1d29257e73baaeb9bec379b79b6c81.RData |binary vignettes/finalfit.Rmd | 33 +-- vignettes/missing.Rmd | 6 vignettes/tables_gallery.Rmd |only 57 files changed, 342 insertions(+), 308 deletions(-)
Title: Tidy Data Validation Reports
Description: Tools for creating data validation pipelines and tidy reports. This
package offers a framework for exploring and validating data frame like
objects using 'dplyr' grammar of data manipulation.
Author: Evgeni Chasnovski [aut, cre]
Maintainer: Evgeni Chasnovski <evgeni.chasnovski@gmail.com>
Diff between ruler versions 0.1.4 dated 2018-12-05 and 0.2.0 dated 2019-02-15
DESCRIPTION | 6 - MD5 | 48 +++++++-------- NEWS.md | 14 ++++ R/expose.R | 18 ++++- R/packs.R | 4 - R/rules.R | 107 +++++++++++++++++++++++++---------- R/utils.R | 2 build/vignette.rds |binary inst/doc/design-and-format.html | 4 - inst/doc/rule-packs.Rmd | 4 - inst/doc/rule-packs.html | 41 +++++++++++-- inst/doc/validation.R | 6 - inst/doc/validation.Rmd | 8 +- inst/doc/validation.html | 58 +++++++++++++----- man/cell-pack.Rd | 4 - man/column-pack.Rd | 4 - man/rules.Rd | 74 ++++++++++++++++-------- tests/testthat/helper-expose-data.R | 12 +-- tests/testthat/test-expose-helpers.R | 10 +-- tests/testthat/test-expose.R | 36 +++++------ tests/testthat/test-exposure.R | 8 +- tests/testthat/test-rules.R | 39 +++++++++--- tests/testthat/test-utils.R | 14 ++-- vignettes/rule-packs.Rmd | 4 - vignettes/validation.Rmd | 8 +- 25 files changed, 355 insertions(+), 178 deletions(-)
Title: Interface to the 'Open Tree of Life' API
Description: An interface to the 'Open Tree of Life' API to retrieve
phylogenetic trees, information about studies used to assemble the synthetic
tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The
'Open Tree of Life' aims at assembling a comprehensive phylogenetic tree for all
named species.
Author: Francois Michonneau [aut, cre]
(<https://orcid.org/0000-0002-9092-966X>),
Joseph Brown [aut] (<https://orcid.org/0000-0002-3835-8062>),
David Winter [aut] (<https://orcid.org/0000-0002-6165-0029>),
Scott Chamberlain [rev] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between rotl versions 3.0.6 dated 2019-01-20 and 3.0.7 dated 2019-02-15
DESCRIPTION | 6 MD5 | 22 +-- NEWS.md | 5 R/tol.R | 32 +++- README.md | 176 +++++++++++++++++--------- inst/doc/data_mashups.html | 4 inst/doc/how-to-use-rotl.html | 4 inst/doc/meta-analysis.R | 4 inst/doc/meta-analysis.Rmd | 6 inst/doc/meta-analysis.html | 284 +++++++++++++++++++++--------------------- man/tol_induced_subtree.Rd | 32 +++- vignettes/meta-analysis.Rmd | 6 12 files changed, 343 insertions(+), 238 deletions(-)
Title: Analytic Hierarchy Process for Survey Data
Description: The Analytic Hierarchy Process is a versatile multi-criteria decision-making tool introduced by Saaty (1987) <doi:10.1016/0270-0255(87)90473-8> that allows decision-makers to weigh attributes and evaluate alternatives presented to them. This package provides a consistent methodology for researchers to reformat data and run analytic hierarchy process in R on data that are formatted using the survey data entry mode. It is optimized for performing the analytic hierarchy process with many decision-makers, and provides tools and options for researchers to aggregate individual preferences and test multiple options. It also allows researchers to quantify, visualize and correct for inconsistency in the decision-maker's comparisons.
Author: Frankie Cho [aut, cre]
Maintainer: Frankie Cho <htcho@connect.hku.hk>
Diff between ahpsurvey versions 0.3.0 dated 2018-12-17 and 0.4.0 dated 2019-02-15
DESCRIPTION | 13 MD5 | 36 +- NAMESPACE | 1 NEWS.md | 18 + R/ahp.R | 111 +++++- R/ahp_RI.R |only R/ahp_cr.R | 26 + R/data.R | 3 README.md | 41 +- build/partial.rdb |binary inst/REFERENCES.bib | 8 inst/doc/my-vignette.R | 65 +++ inst/doc/my-vignette.Rmd | 98 +++++- inst/doc/my-vignette.html | 699 ++++++++++++++++++++++++------------------- man/ahp.Rd | 9 man/ahp.aggjudge.Rd | 2 man/ahp.cr.Rd | 4 man/ahp.ri.Rd |only vignettes/REFERENCES_vig.bib | 8 vignettes/my-vignette.Rmd | 98 +++++- 20 files changed, 848 insertions(+), 392 deletions(-)
Title: Bayesian Structure Learning in Graphical Models using
Birth-Death MCMC
Description: Statistical tools for Bayesian structure learning in undirected graphical models for continuous, discrete, and mixed data. The package is implemented the recent improvements in the Bayesian graphical models literature, including Mohammadi and Wit (2015) <doi:10.1214/14-BA889>, Letac et al. (2018) <arXiv:1706.04416>, Dobra and Mohammadi (2018) <doi:10.1214/18-AOAS1164>, Mohammadi et al. (2017) <doi:10.1111/rssc.12171>. To speed up the computations, the BDMCMC sampling algorithms are implemented in parallel using OpenMP in C++.
Author: Reza Mohammadi [aut, cre] <https://orcid.org/0000-0001-9538-0648>,
Ernst Wit [aut],
Adrian Dobra [ctb]
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between BDgraph versions 2.54 dated 2019-01-21 and 2.55 dated 2019-02-15
DESCRIPTION | 10 +-- MD5 | 18 +++--- R/bdgraph.sim.R | 11 --- R/gnorm.R | 2 R/graph.sim.R | 142 ++++++++++++++++++++++--------------------------- inst/doc/vignette.pdf |binary man/BDgraph-package.Rd | 4 - man/bdgraph.Rd | 2 man/bdgraph.sim.Rd | 6 +- man/graph.sim.Rd | 6 +- 10 files changed, 92 insertions(+), 109 deletions(-)
Title: Model-Averaged Tail Area Wald (MATA-Wald) Confidence Interval
Description: Calculates Model-Averaged Tail Area Wald
(MATA-Wald) confidence intervals, which are constructed using
single-model estimators and model weights. See Turek and Fletcher
(2012) <doi:10.1016/j.csda.2012.03.002> for details.
Author: Daniel Turek [aut, cre]
Maintainer: Daniel Turek <danielturek@gmail.com>
Diff between MATA versions 0.3 dated 2015-04-18 and 0.4 dated 2019-02-15
DESCRIPTION | 27 +++++++++------ MD5 | 8 ++-- NAMESPACE | 2 - R/MATA_package_source.R | 49 ++++++++++++++++------------ man/mata.wald.Rd | 82 +++++++++++++++++++++++++----------------------- 5 files changed, 94 insertions(+), 74 deletions(-)
Title: Machine Learning Models and Tools
Description: Meta-package for statistical and machine learning with a common interface for model fitting, prediction, performance assessment, and presentation of results. Supports predictive modeling of numerical, categorical, and censored time-to-event outcomes and resample (bootstrap and cross-validation) estimation of model performance.
Author: Brian J Smith [aut, cre]
Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>
Diff between MachineShop versions 1.1.0 dated 2019-01-23 and 1.2.0 dated 2019-02-15
MachineShop-1.1.0/MachineShop/R/metrics.R |only MachineShop-1.2.0/MachineShop/DESCRIPTION | 10 MachineShop-1.2.0/MachineShop/MD5 | 99 MachineShop-1.2.0/MachineShop/NAMESPACE | 20 MachineShop-1.2.0/MachineShop/NEWS.md | 13 MachineShop-1.2.0/MachineShop/R/AllClasses.R | 296 - MachineShop-1.2.0/MachineShop/R/ML_StackedModel.R | 2 MachineShop-1.2.0/MachineShop/R/ML_SuperModel.R | 2 MachineShop-1.2.0/MachineShop/R/MachineShop-package.R | 1 MachineShop-1.2.0/MachineShop/R/ModelFrame.R | 18 MachineShop-1.2.0/MachineShop/R/append.R |only MachineShop-1.2.0/MachineShop/R/calibration.R | 75 MachineShop-1.2.0/MachineShop/R/confusion.R | 64 MachineShop-1.2.0/MachineShop/R/convert.R | 57 MachineShop-1.2.0/MachineShop/R/lift.R | 49 MachineShop-1.2.0/MachineShop/R/metricinfo.R | 6 MachineShop-1.2.0/MachineShop/R/metrics-factor.R |only MachineShop-1.2.0/MachineShop/R/metrics-numeric.R |only MachineShop-1.2.0/MachineShop/R/performance.R | 71 MachineShop-1.2.0/MachineShop/R/performance_curve.R |only MachineShop-1.2.0/MachineShop/R/plots.R | 145 MachineShop-1.2.0/MachineShop/R/predict.R | 8 MachineShop-1.2.0/MachineShop/R/resample.R | 5 MachineShop-1.2.0/MachineShop/R/response.R | 7 MachineShop-1.2.0/MachineShop/R/show.R | 18 MachineShop-1.2.0/MachineShop/R/summary.R | 47 MachineShop-1.2.0/MachineShop/R/survival.R | 6 MachineShop-1.2.0/MachineShop/R/tune.R | 25 MachineShop-1.2.0/MachineShop/R/utils.R | 119 MachineShop-1.2.0/MachineShop/README.md | 2174 -------- MachineShop-1.2.0/MachineShop/build/vignette.rds |binary MachineShop-1.2.0/MachineShop/inst/doc/Introduction.R | 604 +- MachineShop-1.2.0/MachineShop/inst/doc/Introduction.Rmd | 1032 ++- MachineShop-1.2.0/MachineShop/inst/doc/Introduction.html | 2685 +++++++--- MachineShop-1.2.0/MachineShop/inst/doc/MLModels.html | 28 MachineShop-1.2.0/MachineShop/man/MLControl.Rd | 6 MachineShop-1.2.0/MachineShop/man/MachineShop-package.Rd | 3 MachineShop-1.2.0/MachineShop/man/SurvMatrix.Rd |only MachineShop-1.2.0/MachineShop/man/calibration.Rd | 9 MachineShop-1.2.0/MachineShop/man/confusion.Rd | 8 MachineShop-1.2.0/MachineShop/man/figures/README-unnamed-chunk-18-1.png |binary MachineShop-1.2.0/MachineShop/man/figures/README-unnamed-chunk-19-1.png |binary MachineShop-1.2.0/MachineShop/man/lift.Rd | 4 MachineShop-1.2.0/MachineShop/man/metrics.Rd | 101 MachineShop-1.2.0/MachineShop/man/performance.Rd | 50 MachineShop-1.2.0/MachineShop/man/performance_curve.Rd |only MachineShop-1.2.0/MachineShop/man/plot-methods.Rd | 27 MachineShop-1.2.0/MachineShop/man/predict.Rd | 10 MachineShop-1.2.0/MachineShop/man/summary-methods.Rd | 7 MachineShop-1.2.0/MachineShop/man/tune-methods.Rd | 6 MachineShop-1.2.0/MachineShop/tests/testthat/Rplots.pdf |binary MachineShop-1.2.0/MachineShop/tests/testthat/helper-models.R | 9 MachineShop-1.2.0/MachineShop/vignettes/Introduction.Rmd | 1032 ++- MachineShop-1.2.0/MachineShop/vignettes/bibliography.bib | 8 54 files changed, 4959 insertions(+), 4007 deletions(-)
Title: Bayesian Regression with Time-Varying Coefficients
Description: Bayesian dynamic regression models where the regression
coefficients can vary over time as random walks.
Gaussian, Poisson, and binomial observations are supported.
The Markov chain Monte Carlo computations are done using
Hamiltonian Monte Carlo provided by Stan, using a state space representation
of the model in order to marginalise over the coefficients for efficient sampling.
For non-Gaussian models, walker uses the importance sampling type estimators based on
approximate marginal MCMC as in Vihola, Helske, Franks (2017, <arXiv:1609.02541>).
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between walker versions 0.2.3-1 dated 2018-11-09 and 0.2.4 dated 2019-02-15
DESCRIPTION | 8 MD5 | 72 NAMESPACE | 100 R/RcppExports.R | 22 R/plot_coefs.R | 122 R/plot_fit.R | 36 R/plot_predict.R | 152 R/pp_check.R | 42 R/predict.R | 152 R/print_fit.R | 22 R/rw.R | 178 R/stanmodels.R | 80 R/walker.R | 1071 +- R/walker_rw1.R | 494 - README.md | 72 build/vignette.rds |binary cleanup.win | 18 exec/rw1_model.stan | 286 exec/rw_glm_model.stan | 406 exec/walker_glm.stan | 426 - exec/walker_lm.stan | 284 inst/chunks/common_functions.stan | 498 - inst/chunks/license.stan | 28 inst/doc/walker.R | 134 inst/doc/walker.html | 673 - man/plot_coefs.Rd | 52 man/plot_fit.Rd | 40 man/plot_predict.Rd | 100 man/pp_check.walker_fit.Rd | 34 man/predict.walker_fit.Rd | 56 man/print.walker_fit.Rd | 32 man/rw1.Rd | 50 man/rw2.Rd | 56 man/walker.Rd | 228 man/walker_glm.Rd | 228 man/walker_rw1.Rd | 224 src/include/models.hpp |15770 +++++++++++++++++++------------------- 37 files changed, 11123 insertions(+), 11123 deletions(-)
Title: Preliminary Visualisation of Data
Description: Create preliminary exploratory data visualisations of an entire
dataset to identify problems or unexpected features using 'ggplot2'.
Author: Nicholas Tierney [aut, cre] (<https://orcid.org/0000-0003-1460-8722>),
Sean Hughes [rev] (<https://orcid.org/0000-0002-9409-9405>, Sean Hughes
reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/87),
Mara Averick [rev] (Mara Averick reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/87),
Stuart Lee [ctb],
Earo Wang [ctb],
Nic Crane [ctb]
Maintainer: Nicholas Tierney <nicholas.tierney@gmail.com>
Diff between visdat versions 0.5.2 dated 2018-12-10 and 0.5.3 dated 2019-02-15
DESCRIPTION | 14 - MD5 | 75 +++--- NEWS.md | 9 R/internals.R | 42 +-- R/vis-cor.R | 14 - R/vis-dat.R | 3 R/vis-expect.R | 17 - build/vignette.rds |binary inst/WORDLIST |only inst/doc/using_visdat.html | 90 +++++--- man/figures/README-vis-compare-iris-1.png |binary man/figures/README-vis-guess-messy-df-1.png |binary man/figures/logo.png |only tests/figs/comparing-vis/vis-compare-vanilla.svg | 66 +++--- tests/figs/deps.txt | 9 tests/figs/test-vis-dat-one-col/vis-miss-with-one-col-cluster.svg | 54 ++-- tests/figs/test-vis-dat-one-col/vis-miss-with-one-col-no-show-pct-in-columns.svg | 54 ++-- tests/figs/test-vis-dat-one-col/vis-miss-with-one-col-show-pct-in-columns.svg | 54 ++-- tests/figs/test-vis-dat-one-col/vis-miss-with-one-col-show-pct.svg | 50 ++-- tests/figs/test-vis-dat-one-col/vis-miss-with-one-col-sort-rows.svg | 54 ++-- tests/figs/test-vis-dat-one-col/vis-miss-with-one-col-vanilla.svg | 54 ++-- tests/figs/vis-cor/vis-cor-vanilla.svg | 80 +++---- tests/figs/vis-dat/vis-dat-colourblind-safe-palette.svg | 110 +++++----- tests/figs/vis-dat/vis-dat-qualitative-palette.svg | 110 +++++----- tests/figs/vis-dat/vis-dat-sort-type.svg | 106 ++++----- tests/figs/vis-dat/vis-dat-vanilla.svg | 106 ++++----- tests/figs/vis-expect/vis-expect-show-perc-true.svg | 62 ++--- tests/figs/vis-expect/vis-expect-vanilla.svg | 66 +++--- tests/figs/vis-guess/vis-guess-cb-safe.svg | 110 +++++----- tests/figs/vis-guess/vis-guess-default.svg | 106 ++++----- tests/figs/vis-guess/vis-guess-qual.svg | 110 +++++----- tests/figs/vis-guess/vis-guess-vanilla.svg | 106 ++++----- tests/figs/vis-miss/vis-miss-cluster.svg | 96 ++++---- tests/figs/vis-miss/vis-miss-no-show-percent-in-columns.svg | 96 ++++---- tests/figs/vis-miss/vis-miss-show-percent-in-columns.svg | 96 ++++---- tests/figs/vis-miss/vis-miss-show-percent.svg | 92 ++++---- tests/figs/vis-miss/vis-miss-sort-rows.svg | 96 ++++---- tests/figs/vis-miss/vis-miss-vanilla.svg | 96 ++++---- tests/spelling.R |only tests/testthat/test-vismiss-legend.R | 7 40 files changed, 1171 insertions(+), 1139 deletions(-)
Title: Read Ethoscope Data
Description: Handling of behavioural data from the Ethoscope platform
(Geissmann, Garcia Rodriguez, Beckwith, French, Jamasb and Gilestro (2017) <DOI:10.1371/journal.pbio.2003026>).
Ethoscopes (<http://gilestrolab.github.io/ethoscope/>) are an open source/open hardware framework made of
interconnected raspberry pis (<https://www.raspberrypi.org>) designed to quantify the behaviour of multiple
small animals in a distributed and real-time fashion. The default tracking algorithm records primary variables
such as xy coordinates, dimensions and speed.
This package is part of the rethomics framework <http://rethomics.github.io/>.
Author: Quentin Geissmann [aut, cre]
Maintainer: Quentin Geissmann <qgeissmann@gmail.com>
Diff between scopr versions 0.3.2 dated 2018-05-29 and 0.3.3 dated 2019-02-15
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- man/load_ethoscope.Rd | 4 ++-- tests/testthat/test-link_ethocope_metadata.R | 2 +- tests/testthat/test-link_ethoscope_metadata_remote.R | 2 +- 5 files changed, 13 insertions(+), 13 deletions(-)
Title: R We There Yet? Visualizing MCMC Convergence in Phylogenetics
Description: Implements various tests, visualizations, and metrics
for diagnosing convergence of MCMC chains in phylogenetics. It implements
and automates many of the functions of the AWTY package in the R
environment.
Author: Dan Warren [aut, cre],
Anthony Geneva [aut],
Rob Lanfear [aut],
Luke Harmon [ctb],
April Wright [ctb],
Diego Mallo [ctb],
Klaus Schliep [ctb]
Maintainer: Dan Warren <dan.l.warren@gmail.com>
Diff between rwty versions 1.0.1 dated 2016-06-22 and 1.0.2 dated 2019-02-15
rwty-1.0.1/rwty/R/print.rwty.trees.R |only rwty-1.0.1/rwty/man/print.rwty.trees.Rd |only rwty-1.0.2/rwty/DESCRIPTION | 31 + rwty-1.0.2/rwty/MD5 | 160 ++++++---- rwty-1.0.2/rwty/NAMESPACE | 5 rwty-1.0.2/rwty/R/analyze.rwty.R | 203 +++++++----- rwty-1.0.2/rwty/R/check.chains.R | 16 - rwty-1.0.2/rwty/R/clade.freq.R | 8 rwty-1.0.2/rwty/R/combine.ptables.R | 12 rwty-1.0.2/rwty/R/cumulative.freq.R | 4 rwty-1.0.2/rwty/R/load.multi.R | 34 +- rwty-1.0.2/rwty/R/load.trees.R | 174 +++++++--- rwty-1.0.2/rwty/R/makeplot.acsf.cumulative.R | 12 rwty-1.0.2/rwty/R/makeplot.acsf.sliding.R | 12 rwty-1.0.2/rwty/R/makeplot.all.params.R | 2 rwty-1.0.2/rwty/R/makeplot.asdsf.R | 27 + rwty-1.0.2/rwty/R/makeplot.autocorr.R | 11 rwty-1.0.2/rwty/R/makeplot.pairs.R | 25 + rwty-1.0.2/rwty/R/makeplot.param.R | 26 + rwty-1.0.2/rwty/R/makeplot.pseudo.ess.R | 4 rwty-1.0.2/rwty/R/makeplot.splitfreq.matrix.R | 11 rwty-1.0.2/rwty/R/makeplot.splitfreqs.cumulative.R | 6 rwty-1.0.2/rwty/R/makeplot.splitfreqs.sliding.R | 6 rwty-1.0.2/rwty/R/makeplot.topology.R | 23 + rwty-1.0.2/rwty/R/makeplot.treespace.R | 10 rwty-1.0.2/rwty/R/parse.clades.R | 2 rwty-1.0.2/rwty/R/print.rwty.chain.R |only rwty-1.0.2/rwty/R/slide.freq.R | 6 rwty-1.0.2/rwty/R/topological.approx.ess.R | 34 +- rwty-1.0.2/rwty/R/topological.autocorr.R | 287 +++++++++--------- rwty-1.0.2/rwty/R/topological.pseudo.ess.R | 4 rwty-1.0.2/rwty/R/tree.dist.matrix.R | 2 rwty-1.0.2/rwty/R/treespace.R | 4 rwty-1.0.2/rwty/build |only rwty-1.0.2/rwty/data/fungus.RData |binary rwty-1.0.2/rwty/data/salamanders.RData |binary rwty-1.0.2/rwty/inst |only rwty-1.0.2/rwty/man/analyze.rwty.Rd | 15 rwty-1.0.2/rwty/man/check.chains.Rd | 7 rwty-1.0.2/rwty/man/clade.freq.Rd | 5 rwty-1.0.2/rwty/man/combine.ptables.Rd | 7 rwty-1.0.2/rwty/man/cumulative.freq.Rd | 5 rwty-1.0.2/rwty/man/estimate.autocorr.m.Rd | 1 rwty-1.0.2/rwty/man/fungus.Rd | 1 rwty-1.0.2/rwty/man/load.multi.Rd | 9 rwty-1.0.2/rwty/man/load.trees.Rd | 18 - rwty-1.0.2/rwty/man/makeplot.acsf.cumulative.Rd | 7 rwty-1.0.2/rwty/man/makeplot.acsf.sliding.Rd | 10 rwty-1.0.2/rwty/man/makeplot.all.params.Rd | 3 rwty-1.0.2/rwty/man/makeplot.asdsf.Rd | 7 rwty-1.0.2/rwty/man/makeplot.autocorr.Rd | 7 rwty-1.0.2/rwty/man/makeplot.pairs.Rd | 3 rwty-1.0.2/rwty/man/makeplot.param.Rd | 5 rwty-1.0.2/rwty/man/makeplot.pseudo.ess.Rd | 5 rwty-1.0.2/rwty/man/makeplot.splitfreq.matrix.Rd | 7 rwty-1.0.2/rwty/man/makeplot.splitfreqs.cumulative.Rd | 7 rwty-1.0.2/rwty/man/makeplot.splitfreqs.sliding.Rd | 7 rwty-1.0.2/rwty/man/makeplot.topology.Rd | 3 rwty-1.0.2/rwty/man/makeplot.treespace.Rd | 6 rwty-1.0.2/rwty/man/parse.clades.Rd | 1 rwty-1.0.2/rwty/man/print.rwty.chain.Rd |only rwty-1.0.2/rwty/man/salamanders.Rd | 1 rwty-1.0.2/rwty/man/slide.freq.Rd | 7 rwty-1.0.2/rwty/man/topological.approx.ess.Rd | 7 rwty-1.0.2/rwty/man/topological.autocorr.Rd | 5 rwty-1.0.2/rwty/man/topological.pseudo.ess.Rd | 5 rwty-1.0.2/rwty/man/tree.dist.matrix.Rd | 3 rwty-1.0.2/rwty/man/treespace.Rd | 5 rwty-1.0.2/rwty/vignettes |only 69 files changed, 809 insertions(+), 531 deletions(-)
Title: Read Excel Files
Description: Import excel files into R. Supports '.xls' via the
embedded 'libxls' C library <https://github.com/evanmiller/libxls> and
'.xlsx' via the embedded 'RapidXML' C++ library
<http://rapidxml.sourceforge.net>. Works on Windows, Mac and Linux
without external dependencies.
Author: Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>),
Jennifer Bryan [aut, cre] (<https://orcid.org/0000-0002-6983-2759>),
RStudio [cph, fnd] (Copyright holder of all R code and all C/C++ code
without explicit copyright attribution),
Marcin Kalicinski [ctb, cph] (Author of included RapidXML code),
Komarov Valery [ctb, cph] (Author of included libxls code),
Christophe Leitienne [ctb, cph] (Author of included libxls code),
Bob Colbert [ctb, cph] (Author of included libxls code),
David Hoerl [ctb, cph] (Author of included libxls code),
Evan Miller [ctb, cph] (Author of included libxls code)
Maintainer: Jennifer Bryan <jenny@rstudio.com>
Diff between readxl versions 1.2.0 dated 2018-12-19 and 1.3.0 dated 2019-02-15
DESCRIPTION | 11 - MD5 | 34 +-- NEWS.md | 9 build/vignette.rds |binary inst/doc/cell-and-column-types.html | 382 +++++++++++++++++++----------------- inst/doc/sheet-geometry.html | 234 ++++++++++++---------- src/XlsCell.h | 3 src/endian.c | 18 - src/libxls/endian.h | 3 src/libxls/ole.h | 18 - src/libxls/xls.h | 28 +- src/libxls/xlstool.h | 31 +- src/libxls/xlstypes.h | 1 src/ole.c | 218 ++++++++++++-------- src/unix/config.h | 19 + src/windows/config.h | 20 + src/xls.c | 128 ++++++------ src/xlstool.c | 30 -- 18 files changed, 639 insertions(+), 548 deletions(-)
Title: Tools at the Intersection of 'purrr' and 'dplyr'
Description: Some functions at the intersection of 'dplyr' and 'purrr' that
formerly lived in 'purrr'.
Author: Lionel Henry [aut, cre],
Hadley Wickham [ctb],
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between purrrlyr versions 0.0.3 dated 2018-05-29 and 0.0.4 dated 2019-02-15
purrrlyr-0.0.3/purrrlyr/src/Makevars |only purrrlyr-0.0.3/purrrlyr/src/Makevars.win |only purrrlyr-0.0.4/purrrlyr/DESCRIPTION | 11 ++--- purrrlyr-0.0.4/purrrlyr/MD5 | 36 ++++++++-------- purrrlyr-0.0.4/purrrlyr/NAMESPACE | 1 purrrlyr-0.0.4/purrrlyr/NEWS.md | 8 +++ purrrlyr-0.0.4/purrrlyr/R/dmap.R | 17 ++++--- purrrlyr-0.0.4/purrrlyr/R/dplyr.R |only purrrlyr-0.0.4/purrrlyr/R/rows.R | 21 +-------- purrrlyr-0.0.4/purrrlyr/R/utils.R | 6 -- purrrlyr-0.0.4/purrrlyr/README.md | 2 purrrlyr-0.0.4/purrrlyr/man/by_row.Rd | 8 +-- purrrlyr-0.0.4/purrrlyr/man/by_slice.Rd | 4 - purrrlyr-0.0.4/purrrlyr/man/dmap.Rd | 27 ++++++------ purrrlyr-0.0.4/purrrlyr/src/fast-copy.cpp | 13 +++++- purrrlyr-0.0.4/purrrlyr/src/map.c | 17 ++++--- purrrlyr-0.0.4/purrrlyr/src/rows-formatter.cpp | 28 ++++++------ purrrlyr-0.0.4/purrrlyr/src/utils.cpp | 8 ++- purrrlyr-0.0.4/purrrlyr/tests/testthat/helper-rows.R |only purrrlyr-0.0.4/purrrlyr/tests/testthat/test-dmap.R | 2 purrrlyr-0.0.4/purrrlyr/tests/testthat/test-rows.R | 41 ++----------------- 21 files changed, 114 insertions(+), 136 deletions(-)
Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Anpanman [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 0.7.7 dated 2019-02-03 and 0.7.9 dated 2019-02-15
DESCRIPTION | 10 - MD5 | 33 ++-- NAMESPACE | 2 NEWS.md | 8 R/DToption.R | 15 - R/cox2.R | 2 R/label.R | 4 README.md | 330 +++++++---------------------------------- inst/doc/jstable.html | 64 +++---- man/LabelepiDisplay.Rd | 4 man/opt.data.Rd | 3 man/opt.roc.Rd | 3 man/opt.simpledown.Rd | 3 man/opt.tb1.Rd | 3 man/opt.tbreg.Rd | 3 tests/testthat/test-DToption.R |only tests/testthat/test-label.R | 2 tests/testthat/test-regtable.R | 24 ++ 18 files changed, 161 insertions(+), 352 deletions(-)
Title: Instantaneous Rate of Green Up
Description: Fits a double logistic function to NDVI time series and calculates
instantaneous rate of green (IRG) according to methods described
in Bischoff et al. (2012) <doi:10.1086/667590>.
Author: Alec L. Robitaille [aut, cre] (<https://orcid.org/0000-0002-4706-1762>)
Maintainer: Alec L. Robitaille <robit.alec@gmail.com>
Diff between irg versions 0.1.0 dated 2019-01-04 and 0.1.1 dated 2019-02-15
DESCRIPTION | 8 MD5 | 14 NEWS.md | 28 R/model.R | 2 inst/doc/getting-started-with-irg.Rmd | 22 inst/doc/getting-started-with-irg.html | 84 inst/extdata/ndvi.csv | 3795 +++++++++++---------------------- vignettes/getting-started-with-irg.Rmd | 22 8 files changed, 1328 insertions(+), 2647 deletions(-)
Title: A Grammar of Data Manipulation
Description: A fast, consistent tool for working with data frame like objects,
both in memory and out of memory.
Author: Hadley Wickham [aut, cre] (<https://orcid.org/0000-0003-4757-117X>),
Romain François [aut] (<https://orcid.org/0000-0002-2444-4226>),
Lionel Henry [aut],
Kirill Müller [aut] (<https://orcid.org/0000-0002-1416-3412>),
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between dplyr versions 0.8.0 dated 2019-02-14 and 0.8.0.1 dated 2019-02-15
DESCRIPTION | 6 +++--- MD5 | 6 +++--- build/dplyr.pdf |binary inst/include/dplyr/hybrid/vector_result/ntile.h | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Work with Open Road Traffic Casualty Data from Great Britain
Description: Tools to help download, process and analyse the UK road collision data collected using the
'STATS19' form. The data are provided as 'CSV' files with detailed road safety data about the
circumstances of car crashes and other incidents on the roads resulting in
casualties in Great Britain from 1979, the types
(including make and model) of vehicles involved and the consequential casualties. The
statistics relate only to personal casualties on public roads that are reported
to the police, and subsequently recorded, using the 'STATS19' accident reporting form. See
the Department for Transportation website
<https://data.gov.uk/dataset/cb7ae6f0-4be6-4935-9277-47e5ce24a11f/road-safety-data> for more
information on these data.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>),
Malcolm Morgan [aut],
Layik Hama [aut] (<https://orcid.org/0000-0003-1912-4890>),
Mark Padgham [aut] (<https://orcid.org/0000-0003-2172-5265>),
David Ranzolin [rev],
Adam Sparks [rev, ctb] (<https://orcid.org/0000-0002-0061-8359>)
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between stats19 versions 0.1.1 dated 2019-01-17 and 0.2.0 dated 2019-02-15
DESCRIPTION | 19 MD5 | 31 NEWS.md |only R/format.R | 7 R/get.R | 13 README.md | 73 build/vignette.rds |binary inst/CITATION | 25 inst/doc/blog.R |only inst/doc/blog.Rmd |only inst/doc/blog.html |only inst/doc/stats19.R | 2 inst/doc/stats19.Rmd | 2 inst/doc/stats19.html | 4978 +++++++++++++++++++++++++++---- man/figures/README-crash-date-plot-1.png |binary man/get_stats19.Rd | 4 vignettes/blog.Rmd |only vignettes/references.bib | 35 vignettes/stats19.Rmd | 2 19 files changed, 4542 insertions(+), 649 deletions(-)
Title: Data Structures, Summaries, and Visualisations for Missing Data
Description: Missing values are ubiquitous in data and need to be explored and
handled in the initial stages of analysis. 'naniar' provides data structures
and functions that facilitate the plotting of missing values and examination
of imputations. This allows missing data dependencies to be explored with
minimal deviation from the common work patterns of 'ggplot2' and tidy data.
Author: Nicholas Tierney [aut, cre] (<https://orcid.org/0000-0003-1460-8722>),
Di Cook [aut] (<https://orcid.org/0000-0002-3813-7155>),
Miles McBain [aut] (<https://orcid.org/0000-0003-2865-2548>),
Colin Fay [aut] (<https://orcid.org/0000-0001-7343-1846>),
Mitchell O'Hara-Wild [ctb],
Jim Hester [ctb],
Luke Smith [ctb]
Maintainer: Nicholas Tierney <nicholas.tierney@gmail.com>
Diff between naniar versions 0.4.1 dated 2018-11-20 and 0.4.2 dated 2019-02-15
DESCRIPTION | 17 +-- MD5 | 123 ++++++++++++----------- NAMESPACE | 1 NEWS.md | 26 ++++ R/geom-miss-point.R | 4 R/geom2plotly.R |only R/gg-miss-case.R | 4 R/gg-miss-var.R | 2 R/miss-complete-x-pct-prop.R | 8 - R/miss-prop-pct-summary.R | 2 R/miss-scan-count.R | 2 R/miss-x-cumsum.R | 2 R/miss-x-run.R | 2 R/miss-x-span.R | 2 R/miss-x-summary.R | 6 - R/miss-x-table.R | 4 R/n-prop-miss-complete-rows.R | 8 - R/nabular.R | 2 R/naniar-package.R | 2 R/prop-pct-var-case-miss-complete.R | 8 - R/replace-with-na.R | 2 R/shadow-recode.R | 6 - R/shadows.R | 2 README.md | 12 +- build/vignette.rds |binary inst/WORDLIST |only inst/doc/exploring-imputed-values.html | 55 ++++++++-- inst/doc/getting-started-w-naniar.html | 110 ++++++++++++-------- inst/doc/naniar-visualisation.html | 147 +++++++++++++++++----------- inst/doc/replace-with-na.html | 42 ++++++-- inst/doc/special-missing-values.html | 32 +++++- man/figures/README-facet-by-month-1.png |binary man/figures/README-geom-miss-point-1.png |binary man/figures/README-gg-miss-span-1.png |binary man/figures/README-gg-miss-upset-1.png |binary man/figures/README-gg-miss-var-1.png |binary man/figures/README-regular-geom-point-1.png |binary man/figures/README-shadow-impute-1.png |binary man/figures/README-shadow-w-ggplot-1.png |binary man/figures/logo.png |only man/miss-complete-case-pct.Rd | 2 man/miss-complete-case-prop.Rd | 2 man/miss-complete-var-pct.Rd | 2 man/miss-complete-var-prop.Rd | 2 man/miss_case_summary.Rd | 2 man/miss_case_table.Rd | 2 man/miss_prop_summary.Rd | 2 man/miss_scan_count.Rd | 2 man/miss_summary.Rd | 2 man/miss_var_run.Rd | 2 man/miss_var_span.Rd | 2 man/miss_var_summary.Rd | 2 man/miss_var_table.Rd | 2 man/n_complete_row.Rd | 2 man/n_miss_row.Rd | 2 man/naniar.Rd | 2 man/pct-miss-complete-case.Rd | 2 man/pct-miss-complete-var.Rd | 2 man/plotly_helpers.Rd |only man/prop-miss-complete-case.Rd | 2 man/prop-miss-complete-var.Rd | 2 man/prop_complete_row.Rd | 2 man/prop_miss_row.Rd | 2 man/replace_with_na.Rd | 2 tests/spelling.R |only 65 files changed, 423 insertions(+), 256 deletions(-)
Title: Kaplan-Meier Plot with 'ggplot2'
Description: The function 'jskm()' creates publication quality Kaplan-Meier plot with at risk tables below. 'svyjskm()' provides plot for weighted Kaplan-Meier estimator.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Anpanman [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jskm versions 0.2.7 dated 2019-02-01 and 0.3.0 dated 2019-02-15
DESCRIPTION | 8 - MD5 | 26 ++- NAMESPACE | 2 NEWS.md | 16 ++ R/jskm.R | 9 - R/svyjskm.R | 118 ++++++++++++++ README.md | 56 +++---- inst/doc/jskm.html | 376 ++++++++++------------------------------------- man/figures |only man/svyjskm.Rd | 13 + tests/testthat/test-km.R | 9 - 11 files changed, 284 insertions(+), 349 deletions(-)
Title: 'DBHYDRO' Hydrologic and Water Quality Data
Description: Client for programmatic access to the South Florida Water
Management District's 'DBHYDRO' database at
<https://www.sfwmd.gov/science-data/dbhydro>, with functions
for accessing hydrologic and water quality data.
Author: Joseph Stachelek [aut, cre] (<https://orcid.org/0000-0002-5924-2464>)
Maintainer: Joseph Stachelek <stachel2@msu.edu>
Diff between dbhydroR versions 0.2-6 dated 2018-07-19 and 0.2-7 dated 2019-02-15
DESCRIPTION | 8 MD5 | 16 - NEWS.md | 6 R/dbhydro_get.R | 3 build/vignette.rds |binary inst/doc/dbhydroR.html | 401 +++++++++++++++++++++++++++++++++++++++---------- man/get_dbkey.Rd | 4 man/get_hydro.Rd | 3 man/get_wq.Rd | 8 9 files changed, 353 insertions(+), 96 deletions(-)
Title: Efficient Phylogenetics on Large Trees
Description: Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@zoology.ubc.ca>
Diff between castor versions 1.3.4 dated 2018-08-16 and 1.3.5 dated 2019-02-15
DESCRIPTION | 12 MD5 | 45 NAMESPACE | 4 R/RcppExports.R | 172 R/asr_mk_model.R | 49 R/auxiliary_routines.R | 45 R/fit_musse.R |only R/fit_tree_model.R | 26 R/generate_tree_with_evolving_rates.R | 11 R/get_subtree_with_tips.R | 1 R/get_transition_index_matrix.R | 5 R/hsp_mk_model.R | 234 - R/simulate_musse.R |only man/asr_mk_model.Rd | 20 man/find_farthest_tips.Rd | 2 man/find_nearest_tips.Rd | 2 man/fit_musse.Rd |only man/fit_tree_model.Rd | 33 man/generate_tree_with_evolving_rates.Rd | 57 man/get_random_mk_transition_matrix.Rd | 2 man/get_transition_index_matrix.Rd |only man/hsp_mk_model.Rd | 20 man/simulate_diversification_model.Rd | 34 man/simulate_musse.Rd |only src/RcppExports.cpp | 318 + src/phylogenetics_cpp_routines.cpp | 6118 +++++++++++++++++++++++++++---- 26 files changed, 6032 insertions(+), 1178 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-04 1.1.14
2014-11-25 1.1.13
2013-11-27 1.1.12
2012-06-30 1.1.09
2011-11-09 1.1.06
2011-09-02 1.1.04
2011-03-21 1.0.8
2010-12-23 1.0.6
2010-05-01 1.0
Title: Tokenization, Parts of Speech Tagging, Lemmatization and
Dependency Parsing with the 'UDPipe' 'NLP' Toolkit
Description: This natural language processing toolkit provides language-agnostic
'tokenization', 'parts of speech tagging', 'lemmatization' and 'dependency
parsing' of raw text. Next to text parsing, the package also allows you to train
annotation models based on data of 'treebanks' in 'CoNLL-U' format as provided
at <http://universaldependencies.org/format.html>. The techniques are explained
in detail in the paper: 'Tokenizing, POS Tagging, Lemmatizing and Parsing UD 2.0
with UDPipe', available at <doi:10.18653/v1/K17-3009>.
Author: Jan Wijffels [aut, cre, cph],
BNOSAC [cph],
Institute of Formal and Applied Linguistics, Faculty of Mathematics and
Physics, Charles University in Prague, Czech Republic [cph],
Milan Straka [ctb, cph],
Jana Straková [ctb, cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between udpipe versions 0.8 dated 2018-12-09 and 0.8.1 dated 2019-02-15
DESCRIPTION | 6 - MD5 | 26 ++-- NAMESPACE | 2 NEWS.md | 6 + R/nlp_collocation.R | 8 - R/utils.R | 89 ++++++++++++++++ build/vignette.rds |binary inst/doc/udpipe-annotation.html | 90 ++++++++++++++-- inst/doc/udpipe-train.html | 88 ++++++++++++++-- inst/doc/udpipe-tryitout.html | 86 ++++++++++++++- inst/doc/udpipe-usecase-postagging-lemmatisation.html | 98 +++++++++++++++--- inst/doc/udpipe-usecase-topicmodelling.html | 88 ++++++++++++++-- man/keywords_collocation.Rd | 8 - man/paste.data.frame.Rd |only man/strsplit.data.frame.Rd |only 15 files changed, 517 insertions(+), 78 deletions(-)
Title: The R to MOSEK Optimization Interface
Description: This is a generic meta-package designed to make the optimization
facilities of MOSEK available from the R-language. The interface supports
large-scale optimization of many kinds: Mixed-integer and continuous linear,
second-order cone, exponential cone and power cone optimization, as well as
continuous semidefinite optimization. Rmosek and the R-language are
open-source projects. MOSEK is a proprietary product, but
unrestricted trial and academic licenses are available.
Author: MOSEK ApS
Maintainer: Henrik A. Friberg <haf@mosek.com>
Diff between Rmosek versions 1.3.1 dated 2019-01-23 and 1.3.2 dated 2019-02-15
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 7 +++++++ R/builder.R | 47 ++++++++++++++++++++++++++++++++--------------- R/export.R | 2 +- man/export.Rd | 12 ++++++++++-- 6 files changed, 59 insertions(+), 27 deletions(-)
Title: Data Analysis of Liquid-Liquid Systems
Description: Analyses experimental data from liquid-liquid phase diagrams and
provide a simple way to obtain its parameters, producing a simplified report. Designed
initially to analyse Aqueous Two-Phases Systems, the package will include (every
other update) new functions in order to comprise useful tools in liquid-liquid
analysis.
Author: Diego F Coelho <diegofcoelho@gmail.com> [aut, cre], Pedro Vitor Oliveira Menezes <pedrod841@hotmail.com> [dtc], Carla Corina dos Santos Porto <carlacorina@hotmail.com.br> [dtc], Jon George Huddleston <Jonathan.Huddleston@brunel.ac.uk> [rev], Elias Basile Tambourgi <eliastam@feq.unicamp.br> [rev]
Maintainer: Diego F Coelho <diegofcoelho@gmail.com>
Diff between LLSR versions 0.0.2.6 dated 2019-01-14 and 0.0.2.12 dated 2019-02-15
LLSR-0.0.2.12/LLSR/DESCRIPTION | 12 +- LLSR-0.0.2.12/LLSR/MD5 | 72 +++++++----- LLSR-0.0.2.12/LLSR/NAMESPACE | 14 ++ LLSR-0.0.2.12/LLSR/R/AQSearch.Binodal.R | 36 +++--- LLSR-0.0.2.12/LLSR/R/AQSearch.Parameter.R | 26 ++-- LLSR-0.0.2.12/LLSR/R/AQSearch.R | 8 - LLSR-0.0.2.12/LLSR/R/AQSearch.Slope.R | 26 ++-- LLSR-0.0.2.12/LLSR/R/AQSearch.Tieline.R | 26 ++-- LLSR-0.0.2.12/LLSR/R/AQSys.CriticalPoint.R |only LLSR-0.0.2.12/LLSR/R/AQSys.LevArmRule.R |only LLSR-0.0.2.12/LLSR/R/AQSys.R | 79 +++++++------- LLSR-0.0.2.12/LLSR/R/AQSys.gsnchk.R | 1 LLSR-0.0.2.12/LLSR/R/AQSys.mathDesc.R | 26 ++++ LLSR-0.0.2.12/LLSR/R/AQSys.mrgsn.R | 58 +++++----- LLSR-0.0.2.12/LLSR/R/AQSysCurve.R | 3 LLSR-0.0.2.12/LLSR/R/AQSysDB.R | 17 +-- LLSR-0.0.2.12/LLSR/R/AQSysDOE.R | 16 ++ LLSR-0.0.2.12/LLSR/R/AQSysEval.R | 79 ++++++++++---- LLSR-0.0.2.12/LLSR/R/AQSysEvalAnimation.R |only LLSR-0.0.2.12/LLSR/R/AQSysFormulas.R | 134 ++++++++++++------------ LLSR-0.0.2.12/LLSR/R/AQSysPlot.R | 28 +++-- LLSR-0.0.2.12/LLSR/R/AQSysUtils.R | 70 ++++++++---- LLSR-0.0.2.12/LLSR/R/CritPointEqSys.R |only LLSR-0.0.2.12/LLSR/R/CritPointPoly.R |only LLSR-0.0.2.12/LLSR/R/CritPointSeq.R |only LLSR-0.0.2.12/LLSR/R/LLSRUtils.R | 81 +++++++++++--- LLSR-0.0.2.12/LLSR/data/llsr_data.rda |binary LLSR-0.0.2.12/LLSR/inst |only LLSR-0.0.2.12/LLSR/man/AQSearch.Binodal.Rd | 12 +- LLSR-0.0.2.12/LLSR/man/AQSys.CritPoint.Rd |only LLSR-0.0.2.12/LLSR/man/AQSys.LevArmRule.Rd |only LLSR-0.0.2.12/LLSR/man/AQSys.Rd | 7 - LLSR-0.0.2.12/LLSR/man/AQSys.plot.Rd | 4 LLSR-0.0.2.12/LLSR/man/AQSysAnima.Rd |only LLSR-0.0.2.12/LLSR/man/AQSysBancroft.Rd | 12 +- LLSR-0.0.2.12/LLSR/man/AQSysDOE.Rd | 6 - LLSR-0.0.2.12/LLSR/man/AQSysEval.Rd | 22 ++- LLSR-0.0.2.12/LLSR/man/AQSysOthmer.Rd | 12 +- LLSR-0.0.2.12/LLSR/man/AQSysPlot.Rd | 8 + LLSR-0.0.2.12/LLSR/man/ExportData.Rd |only LLSR-0.0.2.12/LLSR/man/ExportTemplate.Rd |only LLSR-0.0.2.12/LLSR/tests/testthat/testMainFns.R | 8 - LLSR-0.0.2.6/LLSR/R/AQSys.mrchk.R |only LLSR-0.0.2.6/LLSR/man/AQSys.tielines.Rd |only 44 files changed, 569 insertions(+), 334 deletions(-)
Title: Map Layers and Spatial Utilities for British Columbia
Description: Provides access to various spatial layers for B.C., such as
administrative boundaries, natural resource management boundaries, etc.
All layers are imported from the 'bcmapsdata' package as 'sf' or 'Spatial' objects
through function calls in this package. All layers are in B.C. 'Albers' equal-area projection
<http://spatialreference.org/ref/epsg/nad83-bc-albers/>, which is the B.C.
government standard.
Author: Andy Teucher [aut, cre],
Stephanie Hazlitt [aut],
Sam Albers [aut],
Province of British Columbia [cph]
Maintainer: Andy Teucher <andy.teucher@gov.bc.ca>
Diff between bcmaps versions 0.17.1 dated 2018-03-14 and 0.18.0 dated 2019-02-15
DESCRIPTION | 17 +-- MD5 | 101 +++++++++++---------- NAMESPACE | 3 NEWS.md | 11 +- R/bcmaps.R | 2 R/download_data.R | 6 - R/get_data.R | 22 +++- R/make_shortcuts.R | 14 +-- R/shortcuts.R | 101 +++++++++++++-------- R/utils.R | 40 ++++++++ R/zzz.R | 20 ++-- README.md | 161 +++++++++++------------------------ build/vignette.rds |binary inst/doc/add_points.R | 2 inst/doc/add_points.Rmd | 6 - inst/doc/add_points.html | 98 ++++++++++++--------- man/airzones.Rd | 4 man/available_layers.Rd | 4 man/bc_bbox.Rd |only man/bc_bound.Rd | 4 man/bc_bound_hres.Rd | 4 man/bc_cities.Rd | 4 man/bc_neighbours.Rd |only man/bec_colours.Rd | 3 man/ecoprovinces.Rd | 4 man/ecoregions.Rd | 4 man/ecosections.Rd | 4 man/get_big_data.Rd | 2 man/get_layer.Rd | 2 man/gw_aquifers.Rd | 4 man/hydrozones.Rd | 4 man/make_shortcuts.Rd | 6 - man/municipalities.Rd | 4 man/nr_areas.Rd | 4 man/nr_districts.Rd | 4 man/nr_regions.Rd | 4 man/regional_districts.Rd | 4 man/water_districts.Rd | 4 man/water_precincts.Rd | 4 man/watercourses_15M.Rd | 4 man/watercourses_5M.Rd | 4 man/wsc_drainages.Rd | 4 tests/testthat/test-data_functions.R | 9 + tests/testthat/test-get_big_data.R | 19 ++-- tests/testthat/test-utils.R |only tools/readme/bc_neighbours-1.png |only tools/readme/bec-1.png |binary tools/readme/plot-maps-1.png |binary tools/readme/unnamed-chunk-6-1.png |binary tools/readme/unnamed-chunk-7-1.png |binary tools/readme/unnamed-chunk-8-1.png |only tools/readme/watercourses-1.png |binary vignettes/add_points.Rmd | 6 - vignettes/add_points_files |only 54 files changed, 392 insertions(+), 339 deletions(-)
Title: Storage Management in 'Azure'
Description: Manage storage in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/services/storage>. On the admin side, 'AzureStor' includes features to create, modify and delete storage accounts. On the client side, it includes an interface to blob storage, file storage, and 'Azure Data Lake Storage Gen2': upload and download files and blobs; list containers and files/blobs; create containers; and so on. Authenticated access to storage is supported, via either a shared access key or a shared access signature (SAS).
Author: Hong Ooi [aut, cre],
Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>
Diff between AzureStor versions 1.0.0 dated 2018-12-25 and 2.0.0 dated 2019-02-15
AzureStor-1.0.0/AzureStor/R/client.R |only AzureStor-1.0.0/AzureStor/R/storage.R |only AzureStor-1.0.0/AzureStor/inst/doc/intro.R |only AzureStor-2.0.0/AzureStor/DESCRIPTION | 10 AzureStor-2.0.0/AzureStor/MD5 | 77 ++-- AzureStor-2.0.0/AzureStor/NAMESPACE | 65 ++++ AzureStor-2.0.0/AzureStor/NEWS.md | 19 + AzureStor-2.0.0/AzureStor/R/AzureStor.R | 27 + AzureStor-2.0.0/AzureStor/R/add_methods.R | 34 -- AzureStor-2.0.0/AzureStor/R/adls_client_funcs.R | 152 +++++---- AzureStor-2.0.0/AzureStor/R/adls_transfer_internal.R |only AzureStor-2.0.0/AzureStor/R/az_storage.R |only AzureStor-2.0.0/AzureStor/R/azcopy.R |only AzureStor-2.0.0/AzureStor/R/blob_client_funcs.R | 168 ++++++---- AzureStor-2.0.0/AzureStor/R/blob_transfer_internal.R |only AzureStor-2.0.0/AzureStor/R/client_endpoint.R |only AzureStor-2.0.0/AzureStor/R/client_generics.R |only AzureStor-2.0.0/AzureStor/R/file_client_funcs.R | 145 +++++--- AzureStor-2.0.0/AzureStor/R/file_transfer_internal.R |only AzureStor-2.0.0/AzureStor/R/pool.R |only AzureStor-2.0.0/AzureStor/R/storage_utils.R | 47 ++ AzureStor-2.0.0/AzureStor/R/transfer_generics.R |only AzureStor-2.0.0/AzureStor/README.md | 192 +++++++---- AzureStor-2.0.0/AzureStor/build/vignette.rds |binary AzureStor-2.0.0/AzureStor/inst/doc/generics.Rmd |only AzureStor-2.0.0/AzureStor/inst/doc/generics.html |only AzureStor-2.0.0/AzureStor/inst/doc/intro.html | 186 +++++------ AzureStor-2.0.0/AzureStor/inst/doc/intro.rmd | 211 ++++++------- AzureStor-2.0.0/AzureStor/man/adls.Rd | 53 +++ AzureStor-2.0.0/AzureStor/man/adls_filesystem.Rd | 28 + AzureStor-2.0.0/AzureStor/man/az_storage.Rd | 2 AzureStor-2.0.0/AzureStor/man/azcopy.Rd |only AzureStor-2.0.0/AzureStor/man/blob.Rd | 57 +++ AzureStor-2.0.0/AzureStor/man/blob_container.Rd | 32 + AzureStor-2.0.0/AzureStor/man/create_storage_account.Rd | 6 AzureStor-2.0.0/AzureStor/man/file.Rd | 55 +++ AzureStor-2.0.0/AzureStor/man/file_share.Rd | 18 - AzureStor-2.0.0/AzureStor/man/file_transfer.Rd | 98 +++++- AzureStor-2.0.0/AzureStor/man/generics.Rd |only AzureStor-2.0.0/AzureStor/man/pool.Rd |only AzureStor-2.0.0/AzureStor/man/storage_endpoint.Rd | 24 - AzureStor-2.0.0/AzureStor/tests/resources/iris.json |only AzureStor-2.0.0/AzureStor/tests/resources/iris.rds |only AzureStor-2.0.0/AzureStor/tests/testthat/test01_resource.R | 2 AzureStor-2.0.0/AzureStor/tests/testthat/test02_blob.R | 160 ++++++++- AzureStor-2.0.0/AzureStor/tests/testthat/test03_file.R | 103 +++++- AzureStor-2.0.0/AzureStor/tests/testthat/test04_adls.R | 130 ++++++-- AzureStor-2.0.0/AzureStor/tests/testthat/test05_generics.R |only AzureStor-2.0.0/AzureStor/vignettes/generics.Rmd |only AzureStor-2.0.0/AzureStor/vignettes/intro.rmd | 211 ++++++------- 50 files changed, 1558 insertions(+), 754 deletions(-)
Title: Modeling Framework for Cellular Communities in their
Environments
Description: Can be used for simulation of organisms living in
communities. Each organism is represented individually and genome scale
metabolic models determine the uptake and release of compounds. Biological
processes such as movement, diffusion, chemotaxis and kinetics are available
along with data analysis techniques.
Author: Eugen Bauer [aut],
Johannes Zimmermann [aut, cre]
Maintainer: Johannes Zimmermann <j.zimmermann@iem.uni-kiel.de>
Diff between BacArena versions 1.7 dated 2018-05-09 and 1.8 dated 2019-02-15
DESCRIPTION | 10 ++-- LICENSE |only MD5 | 83 ++++++++++++++++++------------------ NEWS | 13 +++++ R/Arena.R | 71 ++++++++++++++++++++---------- R/BacArena.R | 2 R/Organism.R | 83 ++++++++++++++++++++++-------------- R/Stuff.R | 27 +++++++---- README.md | 20 ++++++-- build/vignette.rds |binary data/colpal.rda |binary data/sihumi_test.rda |binary inst/doc/BacArena-Introduction.R | 48 +++++++++----------- inst/doc/BacArena-Introduction.Rmd | 72 ++++++++++++++----------------- inst/doc/BacArena-Introduction.pdf |binary man/Arena-constructor.Rd | 4 - man/NemptyHood.Rd | 6 +- man/Substance-constructor.Rd | 4 - man/addOrg.Rd | 9 ++- man/addSubs.Rd | 6 +- man/chemotaxis.Rd | 8 ++- man/constrain.Rd | 4 - man/consume.Rd | 3 - man/diffusePDE.Rd | 4 - man/emptyHood.Rd | 6 +- man/evalArena.Rd | 12 ++--- man/extractMed.Rd | 3 - man/findFeeding.Rd | 8 +-- man/findFeeding3.Rd | 7 ++- man/findRxnFlux.Rd | 3 - man/findrBiomass.Rd | 2 man/plotCurves.Rd | 4 - man/plotCurves2.Rd | 7 +-- man/plotGrowthCurve.Rd | 4 + man/plotSpecActivity.Rd | 6 +- man/plotSubCurve.Rd | 5 +- man/plotSubUsage.Rd | 3 - man/simBac.Rd | 4 - man/simEnv.Rd | 11 ++-- man/simEnv_par.Rd | 14 +++--- man/simHum.Rd | 9 ++- man/statPheno.Rd | 3 - vignettes/BacArena-Introduction.Rmd | 72 ++++++++++++++----------------- 43 files changed, 374 insertions(+), 286 deletions(-)
Title: Rendering Parameterized SQL and Translation to Dialects
Description: A rendering tool for parameterized SQL that also translates into
different SQL dialects. These dialects include 'Microsoft Sql Server', 'Oracle',
'PostgreSql', 'Amazon RedShift', 'Apache Impala', 'IBM Netezza', 'Google BigQuery', 'Microsoft PDW', and 'SQLite'.
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between SqlRender versions 1.5.3 dated 2018-11-23 and 1.6.0 dated 2019-02-15
DESCRIPTION | 18 MD5 | 64 NAMESPACE | 3 NEWS.md | 24 R/HelperFunctions.R | 24 R/RenderSql.R | 168 +- R/ShinyApps.R | 2 README.md | 6 build/vignette.rds |binary inst/csv/replacementPatterns.csv | 125 + inst/doc/UsingSqlRender.R | 38 inst/doc/UsingSqlRender.Rmd | 53 inst/doc/UsingSqlRender.pdf |binary inst/java/SqlRender.jar |binary inst/shinyApps/SqlDeveloper/server.R | 4 inst/shinyApps/SqlDeveloper/ui.R | 2 java/org/ohdsi/sql/BigQueryTranslate.java | 158 -- java/org/ohdsi/sql/MainClass.java | 2 java/org/ohdsi/sql/SqlRender.java | 2 java/org/ohdsi/sql/SqlSplit.java | 2 java/org/ohdsi/sql/SqlTranslate.java | 88 + java/org/ohdsi/sql/StringUtils.java | 2 man/loadRenderTranslateSql.Rd | 6 man/render.Rd |only man/renderSql.Rd | 32 man/renderSqlFile.Rd | 2 man/splitSql.Rd | 2 man/translate.Rd |only man/translateSingleStatement.Rd |only man/translateSql.Rd | 19 man/translateSqlFile.Rd | 5 tests/testthat/test-renderSql.R | 64 tests/testthat/test-translate-sqlite.R |only tests/testthat/test-translateSql.R | 2117 +++++++++++++++--------------- vignettes/UsingSqlRender.Rmd | 53 35 files changed, 1614 insertions(+), 1471 deletions(-)
Title: Performs Common Linear Algebra Operations Used in Quantum
Computing
Description: Contains basic structures and operations used frequently in quantum computing. Intended to be a convenient tool to help in practicing the linear algebra involved in quantum operations. Has functionality for the creation of arbitrarily sized kets, bras, matrices and implements quantum gates, inner products, and tensor products. Contains all commonly used quantum gates, creates arbitrarily controlled versions of all gates, and can simulate complete or partial measurements of kets. Implements modular arithmetic commonly found in quantum algorithms and can convert functions into equivalent quantum gates. It can also simulate larger applications, including the Quantum Fourier Transform developed by Shor (1999), Shor's algorithm which factors numbers up to 21, Grover's algorithm (1996), and the training of a quantum neural network developed by Schuld (2018) which can classify the MNIST dataset.
Author: Salonik Resch
Maintainer: Salonik Resch <resc0059@umn.edu>
Diff between QuantumOps versions 2.3 dated 2019-01-30 and 2.4 dated 2019-02-15
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++++++++----- NAMESPACE | 6 ++++++ R/GroverDiffusion.R |only R/GroverOracle.R |only R/GroversAlgorithm.R |only R/QFT.R | 4 ++-- R/QuantumMNIST256Classifier.R | 3 +-- R/Rx.R |only R/Ry.R |only R/Rz.R |only man/GroverDiffusion.Rd |only man/GroverOracle.Rd |only man/GroversAlgorithm.Rd |only man/R.Rd | 4 ++-- man/Rx.Rd |only man/Ry.Rd |only man/Rz.Rd |only 18 files changed, 33 insertions(+), 16 deletions(-)
Title: Geographically-Weighted Models
Description: In GWmodel, we introduce techniques from a particular branch of spatial statistics,termed geographically-weighted (GW) models. GW models suit situations when data are not described well by some global model, but where there are spatial regions where a suitably localised calibration provides a better description. GWmodel includes functions to calibrate: GW summary statistics, GW principal components analysis, GW discriminant analysis and various forms of GW regression; some of which are provided in basic and robust (outlier resistant) forms.
Author: Binbin Lu[aut], Paul Harris[aut], Martin Charlton[aut], Chris Brunsdon[aut], Tomoki Nakaya[aut], Isabella Gollini[ctb]
Maintainer: Binbin Lu <binbinlu@whu.edu.cn>
Diff between GWmodel versions 2.0-7 dated 2019-02-02 and 2.0-8 dated 2019-02-15
DESCRIPTION | 8 MD5 | 16 - NAMESPACE | 2 R/GeneralizedGWR.r | 3 R/bw.ggwr.r | 3 R/gwr.multiscale.R | 521 +++++++++++++++++++++++++------------------------- R/zzz.r | 2 man/USelect.rd | 3 man/gwr.multiscale.rd | 14 - 9 files changed, 295 insertions(+), 277 deletions(-)