Title: Numerical Standard Errors Computation in R
Description: Collection of functions designed to calculate numerical standard error (NSE) of univariate time series as described in Ardia et al. (2018) <doi:10.1515/jtse-2017-0011> and Ardia and Bluteau (2017) <doi:10.21105/joss.00172>.
Author: David Ardia [aut] (<https://orcid.org/0000-0003-2823-782X>),
Keven Bluteau [aut, cre] (<https://orcid.org/0000-0003-2990-4807>)
Maintainer: Keven Bluteau <keven.bluteau@hec.ca>
Diff between nse versions 1.19 dated 2018-09-13 and 1.20 dated 2021-04-25
nse-1.19/nse/tests |only nse-1.20/nse/DESCRIPTION | 24 nse-1.20/nse/MD5 | 34 - nse-1.20/nse/NEWS | 100 +-- nse-1.20/nse/R/RcppExports.R | 14 nse-1.20/nse/R/kernel_addon.R | 160 ++--- nse-1.20/nse/R/nse.R | 1223 +++++++++++++++++++--------------------- nse-1.20/nse/build/partial.rdb |binary nse-1.20/nse/inst/CITATION | 64 +- nse-1.20/nse/inst/COPYRIGHTS | 20 nse-1.20/nse/man/nse.Rd | 10 nse-1.20/nse/man/nse.andrews.Rd | 16 nse-1.20/nse/man/nse.boot.Rd | 9 nse-1.20/nse/man/nse.cos.Rd | 6 nse-1.20/nse/man/nse.geyer.Rd | 12 nse-1.20/nse/man/nse.hiruk.Rd | 5 nse-1.20/nse/man/nse.nw.Rd | 6 nse-1.20/nse/man/nse.spec0.Rd | 19 18 files changed, 860 insertions(+), 862 deletions(-)
Title: Relational Data Models
Description: Provides tools for working with multiple related
tables, stored as data frames or in a relational database. Multiple
tables (data and metadata) are stored in a compound object, which can
then be manipulated with a pipe-friendly syntax.
Author: Tobias Schieferdecker [aut],
Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
Darko Bergant [aut],
Katharina Brunner [ctb],
James Wondrasek [ctb],
energie360° AG [fnd],
cynkra GmbH [fnd, cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between dm versions 0.1.12 dated 2021-02-15 and 0.1.13 dated 2021-04-25
DESCRIPTION | 19 MD5 | 236 ++++++----- NAMESPACE | 22 + NEWS.md | 33 + R/datamodelr-code.R | 3 R/db-helpers.R | 27 + R/db-interface.R | 12 R/dm-from-src.R | 19 R/draw-dm.R | 78 ++- R/error-helpers.R | 91 ++++ R/foreign-keys.R | 21 - R/learn.R | 4 R/primary-keys.R | 6 R/rows-db.R | 25 + R/rows-dm.R | 2 R/rows-truncate.R | 4 R/schema.R |only R/zoom.R | 22 - README.md | 26 - build/vignette.rds |binary inst/doc/dm.html | 288 ++++++++++---- inst/doc/howto-dm-copy.R | 4 inst/doc/howto-dm-copy.Rmd | 14 inst/doc/howto-dm-copy.html | 376 ++++++++++++++---- inst/doc/howto-dm-db.R | 4 inst/doc/howto-dm-db.Rmd | 14 inst/doc/howto-dm-db.html | 377 ++++++++++++++----- inst/doc/howto-dm-df.Rmd | 8 inst/doc/howto-dm-df.html | 27 - inst/doc/howto-dm-rows.R | 4 inst/doc/howto-dm-rows.Rmd | 18 inst/doc/howto-dm-rows.html | 33 + inst/doc/howto-dm-theory.R | 14 inst/doc/howto-dm-theory.Rmd | 32 - inst/doc/howto-dm-theory.html | 76 ++- inst/doc/tech-dm-cdm.Rmd | 4 inst/doc/tech-dm-cdm.html | 17 inst/doc/tech-dm-class.R | 24 - inst/doc/tech-dm-class.Rmd | 38 - inst/doc/tech-dm-class.html | 75 ++- inst/doc/tech-dm-draw.R | 13 inst/doc/tech-dm-draw.Rmd | 26 - inst/doc/tech-dm-draw.html | 27 + inst/doc/tech-dm-filter.R | 30 - inst/doc/tech-dm-filter.Rmd | 42 +- inst/doc/tech-dm-filter.html | 213 +++++----- inst/doc/tech-dm-join.R | 24 - inst/doc/tech-dm-join.Rmd | 36 - inst/doc/tech-dm-join.html | 91 ++-- inst/doc/tech-dm-low-level.Rmd | 16 inst/doc/tech-dm-low-level.html | 13 inst/doc/tech-dm-naming.Rmd | 6 inst/doc/tech-dm-naming.html | 2 inst/doc/tech-dm-zoom.R | 84 ++-- inst/doc/tech-dm-zoom.Rmd | 88 ++-- inst/doc/tech-dm-zoom.html | 121 +++--- man/copy_dm_to.Rd | 9 man/decompose_table.Rd | 2 man/dm_add_fk.Rd | 2 man/dm_add_pk.Rd | 2 man/dm_draw.Rd | 69 --- man/dm_enum_fk_candidates.Rd | 2 man/dm_filter.Rd | 2 man/dm_financial.Rd | 2 man/dm_from_src.Rd | 4 man/dm_get_all_fks.Rd | 2 man/dm_get_all_pks.Rd | 2 man/dm_get_fk.Rd | 2 man/dm_get_pk.Rd | 2 man/dm_mutate_tbl.Rd | 2 man/dm_ptype.Rd | 2 man/dm_set_colors.Rd |only man/dm_zoom_to.Rd | 23 - man/enum_pk_candidates.Rd | 2 man/reunite_parent_child.Rd | 2 man/rows-db.Rd | 2 man/rows-dm.Rd | 4 man/sql_schema_create.Rd |only man/sql_schema_drop.Rd |only man/sql_schema_exists.Rd |only man/sql_schema_list.Rd |only tests/testthat/_snaps/check-cardinalities.md | 6 tests/testthat/_snaps/dm.md | 1 tests/testthat/_snaps/draw-dm/nycflight-dm-types.svg |only tests/testthat/_snaps/error-helpers.md | 41 +- tests/testthat/_snaps/examine-constraints.md | 11 tests/testthat/_snaps/paste.md | 12 tests/testthat/_snaps/rows-db.md | 96 ++-- tests/testthat/_snaps/rows-dm.md | 21 - tests/testthat/helper-config-db.R | 4 tests/testthat/helper-expectations.R | 19 tests/testthat/helper-skip.R | 4 tests/testthat/test-bind.R | 11 tests/testthat/test-db-helpers.R | 48 +- tests/testthat/test-db-interface.R | 81 ++++ tests/testthat/test-disambiguate.R | 2 tests/testthat/test-dm.R | 16 tests/testthat/test-dplyr.R | 2 tests/testthat/test-draw-dm.R | 91 ++-- tests/testthat/test-error-helpers.R | 11 tests/testthat/test-examine-constraints.R | 1 tests/testthat/test-flatten.R | 9 tests/testthat/test-foreign-keys.R | 16 tests/testthat/test-learn.R | 114 ++--- tests/testthat/test-rows-db.R | 32 + tests/testthat/test-rows-dm.R | 2 tests/testthat/test-schema.R |only tests/testthat/test-select-tbl.R | 1 tests/testthat/test-zoom.R | 1 vignettes/howto-dm-copy.Rmd | 14 vignettes/howto-dm-db.Rmd | 14 vignettes/howto-dm-df.Rmd | 8 vignettes/howto-dm-rows.Rmd | 18 vignettes/howto-dm-theory.Rmd | 32 - vignettes/setup/setup.R | 5 vignettes/tech-dm-cdm.Rmd | 4 vignettes/tech-dm-class.Rmd | 38 - vignettes/tech-dm-draw.Rmd | 26 - vignettes/tech-dm-filter.Rmd | 42 +- vignettes/tech-dm-join.Rmd | 36 - vignettes/tech-dm-low-level.Rmd | 16 vignettes/tech-dm-naming.Rmd | 6 vignettes/tech-dm-zoom.Rmd | 88 ++-- 123 files changed, 2524 insertions(+), 1544 deletions(-)
Title: Sleep Cycle Detection
Description: Sleep cycles are largely detected according to the originally proposed criteria by Feinberg & Floyd (1979) <doi:10.1111/j.1469-8986.1979.tb02991.x> as described in Blume & Cajochen (2021) <doi:10.1016/j.mex.2021.101318>.
Author: Christine Blume [aut, cre] (<https://orcid.org/0000-0003-2328-9612>)
Maintainer: Christine Blume <christine.blume@sbg.ac.at>
Diff between SleepCycles versions 1.1.1 dated 2021-03-29 and 1.1.2 dated 2021-04-25
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/load_prep.R | 4 ++-- build/partial.rdb |binary 5 files changed, 14 insertions(+), 9 deletions(-)
Title: Detecting Politeness Features in Text
Description: Detecting markers of politeness in English natural language. This package allows researchers to easily visualize and quantify politeness between groups of documents. This package combines prior research on the linguistic markers of politeness. We thank the Spencer Foundation, the Hewlett Foundation, and Harvard's Institute for Quantitative Social Science for support.
Author: Mike Yeomans, Alejandro Kantor, Dustin Tingley
Maintainer: Mike Yeomans <mk.yeomans@gmail.com>
Diff between politeness versions 0.7.7 dated 2021-03-01 and 0.7.8 dated 2021-04-25
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NAMESPACE | 4 ++++ R/dictTools.R | 8 ++++---- R/sysdata.rda |binary inst/doc/politeness.html | 6 +++--- 6 files changed, 19 insertions(+), 15 deletions(-)
Title: Measuring Concreteness in Natural Language
Description: Models for detecting concreteness in natural language. This package is built in support of Yeomans (2021) <doi:10.1016/j.obhdp.2020.10.008>, which reviews linguistic models of concreteness in several domains. Here, we provide an implementation of the best-performing domain-general model (from Brysbaert et al., (2014) <doi:10.3758/s13428-013-0403-5>) as well as two pre-trained models for the feedback and plan-making domains.
Author: Mike Yeomans
Maintainer: Mike Yeomans <mk.yeomans@gmail.com>
Diff between doc2concrete versions 0.5.2 dated 2021-01-13 and 0.5.3 dated 2021-04-25
doc2concrete-0.5.2/doc2concrete/man/gramstem.Rd |only doc2concrete-0.5.2/doc2concrete/man/ngrammer.Rd |only doc2concrete-0.5.3/doc2concrete/DESCRIPTION | 10 - doc2concrete-0.5.3/doc2concrete/LICENSE | 2 doc2concrete-0.5.3/doc2concrete/MD5 | 21 +-- doc2concrete-0.5.3/doc2concrete/R/ngramComponents.R | 77 +++++-------- doc2concrete-0.5.3/doc2concrete/R/ngramTokens.R | 17 +- doc2concrete-0.5.3/doc2concrete/inst/doc/doc2concrete.R | 2 doc2concrete-0.5.3/doc2concrete/inst/doc/doc2concrete.Rmd | 6 - doc2concrete-0.5.3/doc2concrete/inst/doc/doc2concrete.html | 16 +- doc2concrete-0.5.3/doc2concrete/man/overlaps.Rd | 2 doc2concrete-0.5.3/doc2concrete/man/stemmer.Rd |only doc2concrete-0.5.3/doc2concrete/vignettes/doc2concrete.Rmd | 6 - 13 files changed, 76 insertions(+), 83 deletions(-)
Title: Simple Methods for Calculating Value at Risk and Expected
Shortfall
Description: Enables the user to calculate Value at Risk (VaR)
and Expected Shortfall (ES) by means of various types of historical
simulation. Currently plain-, age-, volatility-weighted- and filtered
historical simulation are implemented in this package. Volatility weighting
can be carried out via an exponentially weighted moving average model
(EWMA) or other GARCH-type models. The methods of the package are described in
Gurrola-Perez, P. and Murphy, D. (2015)
<https://EconPapers.repec.org/RePEc:boe:boeewp:0525>.
Author: Sebastian Letmathe [aut, cre] (Paderborn University, Germany)
Maintainer: Sebastian Letmathe <sebastian.letmathe@uni-paderborn.de>
Diff between quarks versions 1.0.5 dated 2021-03-01 and 1.0.6 dated 2021-04-25
DESCRIPTION | 18 ++-- MD5 | 35 ++++--- NAMESPACE | 1 NEWS.md | 8 + R/fhs.R |only R/hs.R | 9 +- R/plot.quarks.R | 2 R/rollcast.R | 136 +++++++++++++++++++++++-------- R/vwhs.R | 49 +++++++++-- README.md | 63 ++++++++++---- data/DAX30.rda |binary man/fhs.Rd |only man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |only man/figures/README-unnamed-chunk-6-1.png |only man/figures/README-unnamed-chunk-7-1.png |only man/hs.Rd | 8 - man/rollcast.Rd | 76 +++++++++++++---- man/vwhs.Rd | 26 ++++- 21 files changed, 319 insertions(+), 112 deletions(-)
Title: Administrative Boundaries of Spain
Description: Administrative Boundaries of Spain at several levels (CCAA,
Provinces, Municipalities) based on the GISCO Eurostat database
<https://ec.europa.eu/eurostat/web/gisco> and 'CartoBase SIANE'
from 'Instituto Geografico Nacional' <https://www.ign.es/>.
It also provides a 'leaflet' plugin and the ability of
downloading and processing static tiles.
Author: Diego Hernangómez [aut, cre, cph]
(<https://orcid.org/0000-0001-8457-4658>),
EuroGeographics [cph] (for the administrative boundaries.),
Instituto Geográfico Nacional [cph] (for the administrative
boundaries.)
Maintainer: Diego Hernangómez <diego.hernangomezherrero@gmail.com>
Diff between mapSpain versions 0.2.2 dated 2021-04-17 and 0.2.3 dated 2021-04-25
mapSpain-0.2.2/mapSpain/build |only mapSpain-0.2.2/mapSpain/inst/doc |only mapSpain-0.2.2/mapSpain/vignettes |only mapSpain-0.2.3/mapSpain/DESCRIPTION | 11 +--- mapSpain-0.2.3/mapSpain/MD5 | 37 +++++--------- mapSpain-0.2.3/mapSpain/NEWS.md | 18 ++++++ mapSpain-0.2.3/mapSpain/R/addProviderEspTiles.R | 7 +- mapSpain-0.2.3/mapSpain/R/esp_dict.R | 8 +++ mapSpain-0.2.3/mapSpain/R/esp_getTiles.R | 7 +- mapSpain-0.2.3/mapSpain/R/esp_get_can_box.R | 9 ++- mapSpain-0.2.3/mapSpain/R/esp_get_capimun.R | 4 + mapSpain-0.2.3/mapSpain/R/utils_names.R | 2 mapSpain-0.2.3/mapSpain/R/utils_tiles.R | 10 +++ mapSpain-0.2.3/mapSpain/inst/tinytest/test_esp_dict.R | 13 +++- mapSpain-0.2.3/mapSpain/inst/tinytest/test_esp_getTiles.R | 4 - mapSpain-0.2.3/mapSpain/man/addProviderEspTiles.Rd | 10 +-- mapSpain-0.2.3/mapSpain/man/esp_getTiles.Rd | 4 + mapSpain-0.2.3/mapSpain/man/esp_get_can_box.Rd | 9 ++- mapSpain-0.2.3/mapSpain/man/esp_get_capimun.Rd | 4 + 19 files changed, 102 insertions(+), 55 deletions(-)
Title: PKPD, PBPK, and Systems Pharmacology Modeling Tools
Description: Complete work flow for the analysis of pharmacokinetic pharmacodynamic (PKPD), physiologically-based pharmacokinetic (PBPK) and systems pharmacology models including: creation of ordinary differential equation-based models, pooled parameter estimation, individual/population based simulations, rule-based simulations for clinical trial design and modeling assays, deployment with a customizable 'Shiny' app, and non-compartmental analysis. System-specific analysis templates can be generated and each element includes integrated reporting with 'PowerPoint' and 'Word'.
Author: John Harrold [aut, cre] (<https://orcid.org/0000-0003-2052-4373>)
Maintainer: John Harrold <john.m.harrold@gmail.com>
Diff between ubiquity versions 1.0.4 dated 2021-04-18 and 1.0.5 dated 2021-04-25
DESCRIPTION | 6 +-- MD5 | 44 ++++++++++++------------ NAMESPACE | 2 + R/ubiquity.r | 54 ++++++++++++++++++++++++++++++ README.md | 24 +++++++------ build/partial.rdb |binary inst/doc/Deployment.html | 4 +- inst/doc/Estimation.html | 4 +- inst/doc/Language.Rmd | 43 ++++++++++++++++++++++-- inst/doc/Language.html | 30 +++++++++++++--- inst/doc/NCA.html | 42 +++++++++++------------ inst/doc/Reporting.Rmd | 35 ++++++------------- inst/doc/Reporting.html | 59 +++++++++++++++++++-------------- inst/doc/Simulation.Rmd | 2 - inst/doc/Simulation.html | 16 ++++---- inst/doc/Titration.html | 16 ++++---- inst/ubinc/perl/build_system.pl | 4 +- inst/ubinc/scripts/ubiquity_fcns.R | 54 ++++++++++++++++++++++++++++++ inst/ubinc/templates/ubiquity_server.R | 5 +- man/tic.Rd |only man/toc.Rd |only vignettes/Language.Rmd | 43 ++++++++++++++++++++++-- vignettes/Reporting.Rmd | 35 ++++++------------- vignettes/Simulation.Rmd | 2 - 24 files changed, 363 insertions(+), 161 deletions(-)
Title: Estimation of Entropy, Mutual Information and Related Quantities
Description: Implements various estimators of entropy for discrete random
variables, including the shrinkage estimator by Hausser and Strimmer (2009),
the maximum likelihood and the Millow-Madow estimator, various Bayesian
estimators, and the Chao-Shen estimator. It also offers an R interface to the
NSB estimator. Furthermore, the package provides functions for estimating the
Kullback-Leibler divergence, the chi-squared divergence, mutual information,
and the chi-squared divergence of independence. It also computes the
G statistic and the chi-squared statistic and corresponding p-values.
Furthermore, there are functions for discretizing continuous random variables.
Author: Jean Hausser and Korbinian Strimmer
Maintainer: Korbinian Strimmer <strimmerlab@gmail.com>
Diff between entropy versions 1.2.1 dated 2014-11-14 and 1.3.0 dated 2021-04-25
DESCRIPTION | 28 ++++++++++++----------- MD5 | 32 ++++++++++++++------------ NAMESPACE | 6 ++++- NEWS | 11 +++++++++ R/Gstat.R |only man/Gstat.Rd |only man/KL.plugin.Rd | 49 +++++++++++++++++++++++++--------------- man/discretize.Rd | 2 - man/entropy-internal.Rd | 10 +++++--- man/entropy.ChaoShen.Rd | 2 - man/entropy.Dirichlet.Rd | 14 +++++------ man/entropy.MillerMadow.Rd | 2 - man/entropy.Rd | 2 - man/entropy.empirical.Rd | 54 +++++++++++++++++++++++++++++---------------- man/entropy.package.Rd | 10 +++++--- man/entropy.plugin.Rd | 9 +++---- man/entropy.shrink.Rd | 16 ++++++------- man/mi.plugin.Rd | 16 ++++++------- 18 files changed, 157 insertions(+), 106 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-31 0.1.1
2021-03-30 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-22 0.4.1
2021-03-28 0.3.1
2021-03-27 0.3.0
2021-02-27 0.2.0
2021-02-01 0.1.0
2021-01-21 0.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-02-23 0.3.3
2021-02-17 0.3.2
2020-07-21 0.3.1
2020-07-09 0.3.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-24 1.8
2021-01-27 1.7
2020-10-20 1.6.5
2020-01-30 1.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-27 0.1.1
2021-02-27 0.1.0
2021-02-01 0.0.2
2021-02-01 0.0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-23 1.5.2
2020-07-27 1.5.1
2020-07-24 1.5.0
Title: Record Linkage and Epidemiological Case Definitions in R
Description: An R package for record linkage and implementing epidemiological case definitions in R.
Record linkage is implemented either through a multistage deterministic approach or a probabilistic approach.
Matching records are assigned to unique groups. There are mechanisms to address missing data and conflicting matches across linkage stages.
Track and assign events (e.g. sample collection) and periods (e.g. hospital admission) to unique groups based on a case definition.
The tracking process permits several options such as episode lengths and recurrence.
Duplicate events or records can then be identified for removal or further analyses.
Author: Olisaeloka Nsonwu
Maintainer: Olisaeloka Nsonwu <olisa.nsonwu@gmail.com>
Diff between diyar versions 0.2.0 dated 2020-09-17 and 0.3.0 dated 2021-04-25
diyar-0.2.0/diyar/man/combns.Rd |only diyar-0.2.0/diyar/man/to_s4.Rd |only diyar-0.3.0/diyar/DESCRIPTION | 31 diyar-0.3.0/diyar/MD5 | 114 - diyar-0.3.0/diyar/NAMESPACE | 46 diyar-0.3.0/diyar/NEWS.md | 261 ++- diyar-0.3.0/diyar/R/bridge_episode_group.R | 2 diyar-0.3.0/diyar/R/bridge_record_group.R | 40 diyar-0.3.0/diyar/R/classes.R | 972 +++++++++++- diyar-0.3.0/diyar/R/conv_funcs.R | 431 +++++ diyar-0.3.0/diyar/R/d_labels.R |only diyar-0.3.0/diyar/R/data.R | 8 diyar-0.3.0/diyar/R/dev_funcs.R | 2 diyar-0.3.0/diyar/R/episode_group.R | 1814 +++++++++++++++--------- diyar-0.3.0/diyar/R/err_checks.R | 1594 ++++++++++++++++----- diyar-0.3.0/diyar/R/number_line.R | 438 +++-- diyar-0.3.0/diyar/R/overlap.R | 241 ++- diyar-0.3.0/diyar/R/panes.R |only diyar-0.3.0/diyar/R/predefined_tests.R |only diyar-0.3.0/diyar/R/record_group.R | 1139 +++++++++------ diyar-0.3.0/diyar/R/schema.R |only diyar-0.3.0/diyar/R/set_operations.R | 30 diyar-0.3.0/diyar/R/sub_criteria.R |only diyar-0.3.0/diyar/R/to_s4.R | 124 - diyar-0.3.0/diyar/README.md | 241 +-- diyar-0.3.0/diyar/build/vignette.rds |binary diyar-0.3.0/diyar/data/overlap_methods.RData |only diyar-0.3.0/diyar/inst/doc/episodes.R | 1173 ++++++--------- diyar-0.3.0/diyar/inst/doc/episodes.Rmd | 1595 +++++++-------------- diyar-0.3.0/diyar/inst/doc/episodes.html | 1810 +++++++---------------- diyar-0.3.0/diyar/inst/doc/links.R | 635 +++----- diyar-0.3.0/diyar/inst/doc/links.Rmd | 699 ++++----- diyar-0.3.0/diyar/inst/doc/links.html | 1212 ++++++---------- diyar-0.3.0/diyar/inst/doc/number_line.R | 308 ---- diyar-0.3.0/diyar/inst/doc/number_line.Rmd | 427 ----- diyar-0.3.0/diyar/inst/doc/number_line.html | 451 +---- diyar-0.3.0/diyar/man/custom_sort.Rd | 56 diyar-0.3.0/diyar/man/diyar_label.Rd |only diyar-0.3.0/diyar/man/epid-class.Rd | 53 diyar-0.3.0/diyar/man/episodes.Rd | 206 +- diyar-0.3.0/diyar/man/links.Rd | 133 + diyar-0.3.0/diyar/man/links_wf_probabilistic.Rd |only diyar-0.3.0/diyar/man/number_line-class.Rd | 29 diyar-0.3.0/diyar/man/number_line.Rd | 130 - diyar-0.3.0/diyar/man/overlaps.Rd | 35 diyar-0.3.0/diyar/man/pane-class.Rd |only diyar-0.3.0/diyar/man/partitions.Rd |only diyar-0.3.0/diyar/man/patient_list.Rd | 8 diyar-0.3.0/diyar/man/pid-class.Rd | 41 diyar-0.3.0/diyar/man/predefined_tests.Rd | 60 diyar-0.3.0/diyar/man/schema.Rd |only diyar-0.3.0/diyar/man/set_operations.Rd | 28 diyar-0.3.0/diyar/man/sub_criteria.Rd | 95 - diyar-0.3.0/diyar/man/windows.Rd | 49 diyar-0.3.0/diyar/vignettes/episodes.Rmd | 1595 +++++++-------------- diyar-0.3.0/diyar/vignettes/fig_e1.png |only diyar-0.3.0/diyar/vignettes/fig_e10.png |only diyar-0.3.0/diyar/vignettes/fig_e11.png |only diyar-0.3.0/diyar/vignettes/fig_e12.png |only diyar-0.3.0/diyar/vignettes/fig_e2.png |only diyar-0.3.0/diyar/vignettes/fig_e3.png |only diyar-0.3.0/diyar/vignettes/fig_e4.png |only diyar-0.3.0/diyar/vignettes/fig_e5.png |only diyar-0.3.0/diyar/vignettes/fig_e6.png |only diyar-0.3.0/diyar/vignettes/fig_e7.png |only diyar-0.3.0/diyar/vignettes/fig_e8.png |only diyar-0.3.0/diyar/vignettes/fig_e9.png |only diyar-0.3.0/diyar/vignettes/fig_n1.png |only diyar-0.3.0/diyar/vignettes/fig_p1.png |only diyar-0.3.0/diyar/vignettes/fig_p2.png |only diyar-0.3.0/diyar/vignettes/links.Rmd | 699 ++++----- diyar-0.3.0/diyar/vignettes/number_line.Rmd | 427 ----- 72 files changed, 9755 insertions(+), 9727 deletions(-)
Title: Bayesian Inference of Vector Autoregressive Models
Description: Assists in the set-up of algorithms for Bayesian inference of vector autoregressive (VAR) models. Functions for posterior simulation, forecasting, impulse response analysis and forecast error variance decomposition are largely based on the introductory texts of Chan, Koop, Poirier and Tobias (2019, ISBN: 9781108437493), Koop and Korobilis (2010) <doi:10.1561/0800000013> and Luetkepohl (2006, ISBN: 9783540262398).
Author: Franz X. Mohr [aut, cre]
Maintainer: Franz X. Mohr <bvartools@outlook.com>
Diff between bvartools versions 0.1.0 dated 2020-09-18 and 0.2.0 dated 2021-04-25
DESCRIPTION | 26 + MD5 | 109 ++++--- NAMESPACE | 9 NEWS.md | 10 R/RcppExports.R | 14 R/add_priors.R | 603 ----------------------------------------- R/add_priors.bvarmodel.R |only R/add_priors.bvecmodel.R |only R/add_priors.dfmodel.R |only R/bvarpost.R | 8 R/bvartools.R | 14 R/bvecpost.R | 6 R/data.R | 24 + R/dfm.R |only R/dfmpost.R |only R/draw_posterior.R | 23 - R/gen_dfm.R |only R/inclusion_prior.R | 4 R/minnesota_prior.R | 2 R/plot.bvarirf.R | 3 R/plot.dfm.R |only R/predict.bvar.R | 32 +- R/ssvs_prior.R | 2 R/summary.dfm.R |only R/thin_posterior.dfm.R |only build/partial.rdb |only build/vignette.rds |binary data/bem_dfmdata.rda |only inst/doc/bvartools.Rmd | 2 inst/doc/bvartools.html | 96 +++--- inst/doc/bvec.html | 23 + inst/doc/model-comparison.html | 23 + inst/doc/ssvs.html | 23 + man/add_priors.Rd | 155 ---------- man/add_priors.bvarmodel.Rd |only man/add_priors.bvecmodel.Rd |only man/add_priors.dfmodel.Rd |only man/bem_dfmdata.Rd |only man/bvar.Rd | 4 man/bvarpost.Rd | 8 man/bvartools.Rd | 14 man/bvecpost.Rd | 6 man/bvs.Rd | 2 man/dfm.Rd |only man/dfmpost.Rd |only man/draw_posterior.Rd | 9 man/gen_dfm.Rd |only man/inclusion_prior.Rd | 4 man/irf.Rd | 3 man/kalman_dk.Rd | 2 man/minnesota_prior.Rd | 2 man/post_coint_kls.Rd | 2 man/post_coint_kls_sur.Rd | 2 man/ssvs.Rd | 2 man/ssvs_prior.Rd | 2 man/summary.dfm.Rd |only man/thin_posterior.dfm.Rd |only src/RcppExports.cpp | 12 src/bvs.cpp | 2 src/dfmalg.cpp |only src/kalman_dk.cpp | 2 src/post_coint_kls.cpp | 2 src/post_coint_kls_sur.cpp | 2 src/post_normal.cpp | 12 src/svss.cpp | 2 vignettes/bvartools.Rmd | 2 66 files changed, 388 insertions(+), 921 deletions(-)
Title: Analyses of Phylogenetics and Evolution
Description: Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
Author: Emmanuel Paradis [aut, cre, cph]
(<https://orcid.org/0000-0003-3092-2199>),
Simon Blomberg [aut, cph] (<https://orcid.org/0000-0003-1062-0839>),
Ben Bolker [aut, cph] (<https://orcid.org/0000-0002-2127-0443>),
Joseph Brown [aut, cph] (<https://orcid.org/0000-0002-3835-8062>),
Santiago Claramunt [aut, cph] (<https://orcid.org/0000-0002-8926-5974>),
Julien Claude [aut, cph] (<https://orcid.org/0000-0002-9267-1228>),
Hoa Sien Cuong [aut, cph],
Richard Desper [aut, cph],
Gilles Didier [aut, cph] (<https://orcid.org/0000-0003-0596-9112>),
Benoit Durand [aut, cph],
Julien Dutheil [aut, cph] (<https://orcid.org/0000-0001-7753-4121>),
RJ Ewing [aut, cph],
Olivier Gascuel [aut, cph],
Thomas Guillerme [aut, cph] (<https://orcid.org/0000-0003-4325-1275>),
Christoph Heibl [aut, cph] (<https://orcid.org/0000-0002-7655-3299>),
Anthony Ives [aut, cph] (<https://orcid.org/0000-0001-9375-9523>),
Bradley Jones [aut, cph] (<https://orcid.org/0000-0003-4498-1069>),
Franz Krah [aut, cph] (<https://orcid.org/0000-0001-7866-7508>),
Daniel Lawson [aut, cph] (<https://orcid.org/0000-0002-5311-6213>),
Vincent Lefort [aut, cph],
Pierre Legendre [aut, cph] (<https://orcid.org/0000-0002-3838-3305>),
Jim Lemon [aut, cph],
Guillaume Louvel [aut, cph] (<https://orcid.org/0000-0002-7745-0785>),
Eric Marcon [aut, cph] (<https://orcid.org/0000-0002-5249-321X>),
Rosemary McCloskey [aut, cph] (<https://orcid.org/0000-0002-9772-8553>),
Johan Nylander [aut, cph],
Rainer Opgen-Rhein [aut, cph],
Andrei-Alin Popescu [aut, cph],
Manuela Royer-Carenzi [aut, cph],
Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>),
Korbinian Strimmer [aut, cph] (<https://orcid.org/0000-0001-7917-2056>),
Damien de Vienne [aut, cph] (<https://orcid.org/0000-0001-9532-5251>)
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between ape versions 5.4-1 dated 2020-08-13 and 5.5 dated 2021-04-25
DESCRIPTION | 26 +- MD5 | 135 ++++++----- NAMESPACE | 8 R/CADM.global.R | 52 ++-- R/CADM.post.R | 56 ++-- R/DNA.R | 55 ++-- R/as.bitsplits.R | 6 R/as.phylo.formula.R | 3 R/bind.tree.R | 7 R/biplot.pcoa.R | 8 R/corphylo.R | 4 R/dist.topo.R | 65 ++++- R/howmanytrees.R | 45 ++- R/is.binary.tree.R | 6 R/lmorigin.R | 20 - R/ltt.plot.R | 116 +++++---- R/multi2di.R | 6 R/nj.R | 19 - R/node.dating.R | 16 - R/nodelabels.R | 9 R/pcoa.R | 6 R/print.lmorigin.R | 6 R/read.tree.R | 6 R/root.R | 9 R/rtree.R | 142 +++++++++++ R/write.dna.R | 17 - README.md |only build/partial.rdb |only build/vignette.rds |binary inst/doc/DrawingPhylogenies.R |only inst/doc/DrawingPhylogenies.Rnw |only inst/doc/DrawingPhylogenies.pdf |only inst/doc/MoranI.R | 29 +- inst/doc/MoranI.Rnw | 32 +- inst/doc/MoranI.pdf |binary inst/doc/RandomTopologies.R |only inst/doc/RandomTopologies.Rnw |only inst/doc/RandomTopologies.pdf |only man/ape-internal.Rd | 4 man/as.bitsplits.Rd | 15 - man/as.phylo.Rd | 5 man/as.phylo.formula.Rd | 9 man/base.freq.Rd | 3 man/dist.topo.Rd | 11 man/howmanytrees.Rd | 30 +- man/ltt.plot.Rd | 13 - man/mcconwaysims.test.Rd | 3 man/nodelabels.Rd | 3 man/read.dna.Rd | 4 man/read.gff.Rd | 4 man/read.nexus.data.Rd | 2 man/root.Rd | 2 man/rtree.Rd | 22 + man/seg.sites.Rd | 3 man/slowinskiguyer.test.Rd | 3 man/write.dna.Rd | 2 man/write.nexus.data.Rd | 2 src/NNI.c | 14 - src/ape.c | 28 -- src/bionjs.c | 71 ----- src/bitsplits.c | 89 ------- src/dist_dna.c | 467 +++++++++++++++++++++------------------ src/mvrs.c | 70 ----- src/nj.c | 198 ++++++++-------- src/njs.c | 142 ----------- src/reorder_phylo.c | 79 ------ src/treePop.c | 87 ------- src/triangMtd.c | 70 ----- src/triangMtds.c | 12 - vignettes/DrawingPhylogenies.Rnw |only vignettes/MoranI.Rnw | 32 +- vignettes/RandomTopologies.Rnw |only vignettes/ape.bib | 110 ++++++--- vignettes/ape.sty |only 74 files changed, 1145 insertions(+), 1373 deletions(-)
Title: Operations to Ease Data Analyses Specific to Nigeria
Description: A set of convenience functions as well as geographical/political
data about Nigeria, aimed at simplifying work with data and information that
are specific to the country.
Author: Victor Ordu [aut, cre] (<https://orcid.org/0000-0003-3716-0668>)
Maintainer: Victor Ordu <victorordu@outlook.com>
Diff between naijR versions 0.1.4 dated 2020-08-25 and 0.2.1 dated 2021-04-25
naijR-0.1.4/naijR/R/lgas_nigeria.R |only naijR-0.1.4/naijR/R/political.R |only naijR-0.1.4/naijR/R/ward_data.R |only naijR-0.1.4/naijR/inst/extdata |only naijR-0.1.4/naijR/inst/ward_data.rda |only naijR-0.1.4/naijR/man/lgas_ng.Rd |only naijR-0.1.4/naijR/tests/testthat/test-lgas_nigeria.R |only naijR-0.1.4/naijR/tests/testthat/test-political.R |only naijR-0.2.1/naijR/DESCRIPTION | 21 naijR-0.2.1/naijR/MD5 | 60 - naijR-0.2.1/naijR/NAMESPACE | 9 naijR-0.2.1/naijR/NEWS.md | 23 naijR-0.2.1/naijR/R/map_nigeria.R | 507 ++++++++---- naijR-0.2.1/naijR/R/regions.R |only naijR-0.2.1/naijR/R/sysdata.rda |only naijR-0.2.1/naijR/README.md | 96 -- naijR-0.2.1/naijR/build/vignette.rds |binary naijR-0.2.1/naijR/data/lgas_nigeria.rda |binary naijR-0.2.1/naijR/inst/doc/nigeria-maps.R | 18 naijR-0.2.1/naijR/inst/doc/nigeria-maps.Rmd | 26 naijR-0.2.1/naijR/inst/doc/nigeria-maps.html | 316 +------ naijR-0.2.1/naijR/man/figures/logo.png |only naijR-0.2.1/naijR/man/fix_region.Rd |only naijR-0.2.1/naijR/man/is_lga.Rd |only naijR-0.2.1/naijR/man/is_state.Rd | 32 naijR-0.2.1/naijR/man/lgas.Rd |only naijR-0.2.1/naijR/man/lgas_nigeria.Rd | 2 naijR-0.2.1/naijR/man/map_ng.Rd | 67 - naijR-0.2.1/naijR/man/states.Rd | 20 naijR-0.2.1/naijR/tests/testthat/data/pvc2015.rds |binary naijR-0.2.1/naijR/tests/testthat/data/pvc2015_badcolumn.rds |only naijR-0.2.1/naijR/tests/testthat/test-map_nigeria.R | 241 ++--- naijR-0.2.1/naijR/tests/testthat/test-numbers.R | 6 naijR-0.2.1/naijR/tests/testthat/test-regions.R |only naijR-0.2.1/naijR/vignettes/nigeria-maps.Rmd | 26 35 files changed, 750 insertions(+), 720 deletions(-)
Title: Sequence Manipulation Utilities
Description: Supports reading and writing sequences for different formats (currently interleaved and sequential formats for 'FASTA' and 'PHYLIP'), file conversion, and manipulation (e.g. filter sequences that contain specify pattern, export consensus sequence from an alignment).
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between seqmagick versions 0.1.4 dated 2020-09-22 and 0.1.5 dated 2021-04-25
DESCRIPTION | 11 +--- MD5 | 8 +-- R/read.R | 40 +++++++++++++-- build/vignette.rds |binary inst/doc/seqmagick.html | 121 +++++++++++++++++------------------------------- 5 files changed, 86 insertions(+), 94 deletions(-)
Title: Portable Emissions (and Other Mobile) Measurement System
Utilities
Description: Utility functions for the handling, analysis and visualisation
of data from portable emissions measurement systems ('PEMS') and other
similar mobile activity monitoring devices. The package includes a dedicated
'pems' data class that manages many of the quality control, unit handling
and data archiving issues that can hinder efforts to standardise 'PEMS'
research.
Author: Karl Ropkins [aut, cre],
Adrian Felipe Ortega Calle [ctb]
Maintainer: Karl Ropkins <karl.ropkins@gmail.com>
Diff between pems.utils versions 0.2.26.4 dated 2018-11-18 and 0.2.29.1 dated 2021-04-25
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Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-18 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-07-05 1.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-07-28 0.1.19
2020-07-20 0.1.17
2020-07-12 0.1.16
2020-07-11 0.1.15
2020-07-05 0.1.14
2020-07-03 0.1.13
Title: Bayesian Emulation of Computer Programs
Description: Allows one to estimate the output of a computer program,
as a function of the input parameters, without actually running it.
The computer program is assumed to be a Gaussian process, whose
parameters are estimated using Bayesian techniques that give a PDF of
expected program output. This PDF is conditional on a training set
of runs, each consisting of a point in parameter space and the model
output at that point. The emphasis is on complex codes that take
weeks or months to run, and that have a large number of undetermined
input parameters; many climate prediction models fall into this
class. The emulator essentially determines Bayesian posterior
estimates of the PDF of the output of a model, conditioned on results
from previous runs and a user-specified prior linear model. The
package includes functionality to evaluate quadratic forms
efficiently.
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between emulator versions 1.2-20 dated 2019-03-19 and 1.2-21 dated 2021-04-25
DESCRIPTION | 15 +- MD5 | 24 +-- build/partial.rdb |binary build/vignette.rds |binary data/expert.estimates.rda |binary data/results.table.rda |binary data/toy.rda |binary inst/doc/emulex.pdf |binary inst/doc/quad_form_test.html | 284 +++++++++++++++++++++---------------------- inst/doc/uncertainty.bib | 6 man/betahat.fun.Rd | 2 man/corr.Rd | 2 vignettes/uncertainty.bib | 6 13 files changed, 166 insertions(+), 173 deletions(-)