Title: Zero-Inflated Poisson Hidden (Semi-)Markov Models
Description: Fit zero-inflated Poisson hidden (semi-)Markov models with or without covariates by directly minimizing the negative log likelihood function using the gradient descent algorithm. Multiple starting values should be used to avoid local minima.
Author: Zekun (Jack) Xu, Ye Liu
Maintainer: Zekun (Jack) Xu <zekunxu@gmail.com>
Diff between ziphsmm versions 1.0.6 dated 2017-06-07 and 1.0.7 dated 2017-09-23
DESCRIPTION | 8 MD5 | 30 NAMESPACE | 6 R/RcppExports.R | 128 +++ R/dist_learn.R |only R/fasthmmfit.cont.R |only R/hmmsim.R | 3 R/hmmsim.cont.R |only R/hmmsim2.cont.R |only R/hmmviterbi.cont.R |only R/hmmviterbi2.cont.R |only R/package.R | 4 man/dist_learn.Rd |only man/fasthmmfit.cont.Rd |only man/hmmsim.Rd | 3 man/hmmsim.cont.Rd |only man/hmmsim2.cont.Rd |only man/hmmviterbi.cont.Rd |only man/hmmviterbi2.cont.Rd |only man/package-ziphsmm.Rd | 4 src/RcppExports.cpp | 481 ++++++++++++- src/rcpparma_hello_world.cpp | 1563 ++++++++++++++++++++++++++++++++++++++++--- 22 files changed, 2095 insertions(+), 135 deletions(-)
Title: Global Sensitivity Analysis of Model Outputs
Description: A collection of functions for factor screening, global sensitivity analysis and reliability sensitivity analysis. Most of the functions have to be applied on model with scalar output, but several functions support multi-dimensional outputs.
Author: Gilles Pujol, Bertrand Iooss, Alexandre Janon with contributions from Khalid Boumhaout, Sebastien Da Veiga, Thibault Delage, Jana Fruth, Laurent Gilquin, Joseph Guillaume, Loic Le Gratiet, Paul Lemaitre, Barry L. Nelson, Filippo Monari, Roelof Oomen, Bernardo Ramos, Olivier Roustant, Eunhye Song, Jeremy Staum, Taieb Touati, Frank Weber
Maintainer: Bertrand Iooss <biooss@yahoo.fr>
Diff between sensitivity versions 1.14.0 dated 2017-02-10 and 1.15.0 dated 2017-09-23
sensitivity-1.14.0/sensitivity/R/sobolCert.R |only sensitivity-1.14.0/sensitivity/man/sobolCert.Rd |only sensitivity-1.14.0/sensitivity/src/Makevars |only sensitivity-1.14.0/sensitivity/src/as.cpp |only sensitivity-1.14.0/sensitivity/src/as.h |only sensitivity-1.14.0/sensitivity/src/lbfgs-b.f |only sensitivity-1.14.0/sensitivity/src/rglueas.cpp |only sensitivity-1.15.0/sensitivity/DESCRIPTION | 10 sensitivity-1.15.0/sensitivity/MD5 | 45 +- sensitivity-1.15.0/sensitivity/NAMESPACE | 10 sensitivity-1.15.0/sensitivity/NEWS | 14 sensitivity-1.15.0/sensitivity/R/PLIquantile.r | 2 sensitivity-1.15.0/sensitivity/R/PoincareConstant.R | 2 sensitivity-1.15.0/sensitivity/R/PoincareOptimal.R | 2 sensitivity-1.15.0/sensitivity/R/base.R | 6 sensitivity-1.15.0/sensitivity/R/sobolMultOut.R | 9 sensitivity-1.15.0/sensitivity/R/support.R | 181 ++++++++--- sensitivity-1.15.0/sensitivity/man/PLIquantile.Rd | 7 sensitivity-1.15.0/sensitivity/man/PoincareConstant.Rd | 11 sensitivity-1.15.0/sensitivity/man/PoincareOptimal.Rd | 7 sensitivity-1.15.0/sensitivity/man/plot.support.Rd |only sensitivity-1.15.0/sensitivity/man/sensitivity-package.Rd | 12 sensitivity-1.15.0/sensitivity/man/shapleyPermEx.Rd | 24 - sensitivity-1.15.0/sensitivity/man/shapleyPermRand.Rd | 23 - sensitivity-1.15.0/sensitivity/man/sobolMultOut.Rd | 16 sensitivity-1.15.0/sensitivity/man/sobolSmthSpl.Rd | 89 ++--- sensitivity-1.15.0/sensitivity/man/support.Rd | 177 +++++----- sensitivity-1.15.0/sensitivity/src/registerDynamicSymbol.cpp |only 28 files changed, 400 insertions(+), 247 deletions(-)
Title: Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column- and row- wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions.
Author: Manos Papadakis, Michail Tsagris, Marios Dimitriadis, Stefanos Fafalios, Ioannis Tsamardinos, Matteo Fasiolo, Giorgos Borboudakis, John Burkardt, Changliang Zou and Kleanthi Lakiotaki
Maintainer: Manos Papadakis <papadakm95@gmail.com>
Diff between Rfast versions 1.8.3 dated 2017-09-21 and 1.8.4 dated 2017-09-23
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- man/Rfast-package.Rd | 4 ++-- src/Order.cpp | 23 +++++++++-------------- src/binarysearch.cpp | 22 ++++++++++++++++------ src/geom_regs.cpp | 3 +-- src/sort_mat.cpp | 10 +--------- src/sort_mat_p.cpp | 10 +--------- src/sort_mat_stable.cpp | 10 +--------- src/sort_mat_stable_p.cpp | 10 +--------- 10 files changed, 45 insertions(+), 73 deletions(-)
Title: Data Science Labs
Description: Datasets and functions that facilitate data analysis labs in data science courses and workshops.
Author: Rafael A. Irizarry
Maintainer: Rafael A. Irizarry <rafa@jimmy.harvard.edu>
Diff between dslabs versions 0.1.0 dated 2017-07-14 and 0.2.0 dated 2017-09-23
DESCRIPTION | 6 +- MD5 | 27 ++++++++-- NAMESPACE | 3 + R/admissions.R |only R/divorce_margarine.R |only R/ds_theme_set.R | 5 - R/research_funding_rates.R |only R/rfalling_object.R |only data/admissions.rda |only data/divorce_margarine.rda |only data/research_funding_rates.rda |only inst/extdata/fertility-two-countries-example.csv |only inst/extdata/life-expectancy-and-fertility-two-countries-example.csv |only inst/script/make-admissions.R |only inst/script/make-divorce_margarine.R |only inst/script/make-gapminder-rdas.R | 3 + inst/script/make-research_funding_rates.R |only inst/script/save-gapminder-example-csv.R |only man/admissions.Rd |only man/divorce_margarine.Rd |only man/ds_theme_set.Rd | 4 - man/research_funding_rates.Rd |only man/rfalling_object.Rd |only 23 files changed, 34 insertions(+), 14 deletions(-)
Title: Public Subject Attention via Wikipedia Page View Statistics
Description: Public attention is an interesting field of study. The
internet not only allows to access information in no time on
virtually any subject but via page access statistics gathered
by website authors the subject of attention as well can be
studied.
Author: Peter Meissner [aut, cre], R Core Team [ctb]
Maintainer: Peter Meissner <retep.meissner@gmail.com>
Diff between wikipediatrend versions 1.1.10 dated 2016-03-20 and 1.1.14 dated 2017-09-23
wikipediatrend-1.1.10/wikipediatrend/build |only wikipediatrend-1.1.10/wikipediatrend/inst/doc |only wikipediatrend-1.1.10/wikipediatrend/tests/testthat/test.csv |only wikipediatrend-1.1.10/wikipediatrend/vignettes |only wikipediatrend-1.1.14/wikipediatrend/DESCRIPTION | 24 wikipediatrend-1.1.14/wikipediatrend/MD5 | 103 +-- wikipediatrend-1.1.14/wikipediatrend/NAMESPACE | 79 +- wikipediatrend-1.1.14/wikipediatrend/NEWS | 343 +++++----- wikipediatrend-1.1.14/wikipediatrend/R/wp_cache.R | 2 wikipediatrend-1.1.14/wikipediatrend/R/wp_date_functions.r | 2 wikipediatrend-1.1.14/wikipediatrend/R/wp_get_data.R | 2 wikipediatrend-1.1.14/wikipediatrend/R/wp_linked_pages.R | 50 + wikipediatrend-1.1.14/wikipediatrend/R/wp_load_and_save.r | 4 wikipediatrend-1.1.14/wikipediatrend/R/wp_plot.R |only wikipediatrend-1.1.14/wikipediatrend/R/wp_prepare_urls.R | 2 wikipediatrend-1.1.14/wikipediatrend/R/wp_trend.R | 23 wikipediatrend-1.1.14/wikipediatrend/README.md | 323 +-------- wikipediatrend-1.1.14/wikipediatrend/man/html.Rd | 33 wikipediatrend-1.1.14/wikipediatrend/man/html2.Rd | 33 wikipediatrend-1.1.14/wikipediatrend/man/plot.wp_df.Rd |only wikipediatrend-1.1.14/wikipediatrend/man/prev_month_end.Rd | 23 wikipediatrend-1.1.14/wikipediatrend/man/prev_month_start.Rd | 23 wikipediatrend-1.1.14/wikipediatrend/man/print.wp_df.Rd | 33 wikipediatrend-1.1.14/wikipediatrend/man/read_utf8_csv.Rd | 33 wikipediatrend-1.1.14/wikipediatrend/man/toUTF8.Rd | 29 wikipediatrend-1.1.14/wikipediatrend/man/wp_add_to_cache.Rd | 29 wikipediatrend-1.1.14/wikipediatrend/man/wp_cache.Rd | 29 wikipediatrend-1.1.14/wikipediatrend/man/wp_cache_default.Rd | 23 wikipediatrend-1.1.14/wikipediatrend/man/wp_cache_file.Rd | 23 wikipediatrend-1.1.14/wikipediatrend/man/wp_cache_load.Rd | 29 wikipediatrend-1.1.14/wikipediatrend/man/wp_cache_reset.Rd | 23 wikipediatrend-1.1.14/wikipediatrend/man/wp_check_date_inputs.Rd | 37 - wikipediatrend-1.1.14/wikipediatrend/man/wp_date.Rd | 152 ++-- wikipediatrend-1.1.14/wikipediatrend/man/wp_day.Rd | 62 - wikipediatrend-1.1.14/wikipediatrend/man/wp_download_data.Rd | 33 wikipediatrend-1.1.14/wikipediatrend/man/wp_expand_ts.Rd | 43 - wikipediatrend-1.1.14/wikipediatrend/man/wp_get_cache.Rd | 23 wikipediatrend-1.1.14/wikipediatrend/man/wp_get_data.Rd | 29 wikipediatrend-1.1.14/wikipediatrend/man/wp_http_header.Rd | 23 wikipediatrend-1.1.14/wikipediatrend/man/wp_jsons_to_df.Rd | 35 - wikipediatrend-1.1.14/wikipediatrend/man/wp_linked_pages.Rd | 37 - wikipediatrend-1.1.14/wikipediatrend/man/wp_load.Rd | 31 wikipediatrend-1.1.14/wikipediatrend/man/wp_month.Rd | 66 - wikipediatrend-1.1.14/wikipediatrend/man/wp_prepare_urls.Rd | 41 - wikipediatrend-1.1.14/wikipediatrend/man/wp_save.Rd | 33 wikipediatrend-1.1.14/wikipediatrend/man/wp_save_cache.Rd | 29 wikipediatrend-1.1.14/wikipediatrend/man/wp_set_cache_file.Rd | 29 wikipediatrend-1.1.14/wikipediatrend/man/wp_set_print_options.Rd | 29 wikipediatrend-1.1.14/wikipediatrend/man/wp_trend.Rd | 102 +- wikipediatrend-1.1.14/wikipediatrend/man/wp_wday.Rd | 68 - wikipediatrend-1.1.14/wikipediatrend/man/wp_year.Rd | 58 - wikipediatrend-1.1.14/wikipediatrend/man/wp_yearmonth.Rd | 33 wikipediatrend-1.1.14/wikipediatrend/man/write_utf8_csv.Rd | 33 wikipediatrend-1.1.14/wikipediatrend/tests/testthat/test_aux.R |only wikipediatrend-1.1.14/wikipediatrend/tests/testthat/test_caching_gathering.R | 68 - 55 files changed, 1064 insertions(+), 1350 deletions(-)
More information about wikipediatrend at CRAN
Permanent link
Title: Functional Linear Mixed Models for Irregularly or Sparsely
Sampled Data
Description: Estimation of functional linear mixed models for irregularly or
sparsely sampled data based on functional principal component analysis.
Author: Jona Cederbaum
Maintainer: Jona Cederbaum <Jona.Cederbaum@stat.uni-muenchen.de>
Diff between sparseFLMM versions 0.1.1 dated 2017-06-08 and 0.2.0 dated 2017-09-23
DESCRIPTION | 6 +- MD5 | 10 ++-- R/call_all_functions.R | 5 +- R/get_cross_products.R | 114 +++++++++++++++++++++++++------------------------ R/zzz.R | 16 +++--- man/acoustic.Rd | 2 6 files changed, 79 insertions(+), 74 deletions(-)
Title: Interactive Collapsible Tree Diagrams using 'D3.js'
Description: Interactive Reingold-Tilford tree diagrams created using 'D3.js', where every node can be expanded and collapsed by clicking on it.
Tooltips and color gradients can be mapped to nodes using a numeric column in the source data frame.
See 'collapsibleTree' website for more information and examples.
Author: Adeel Khan [aut, cre],
Dhrumin Shah [ctb],
Mike Bostock [ctb, cph] (D3.js library, http://d3js.org)
Maintainer: Adeel Khan <AdeelK@gwu.edu>
Diff between collapsibleTree versions 0.1.5 dated 2017-07-23 and 0.1.6 dated 2017-09-23
collapsibleTree-0.1.5/collapsibleTree/inst/htmlwidgets/lib/d3-4.5.0 |only collapsibleTree-0.1.5/collapsibleTree/man/collapsibleTree.Node.Rd |only collapsibleTree-0.1.5/collapsibleTree/man/collapsibleTree.data.frame.Rd |only collapsibleTree-0.1.6/collapsibleTree/DESCRIPTION | 6 collapsibleTree-0.1.6/collapsibleTree/MD5 | 39 +-- collapsibleTree-0.1.6/collapsibleTree/NAMESPACE | 3 collapsibleTree-0.1.6/collapsibleTree/R/collapsibleTree.R | 78 ++++-- collapsibleTree-0.1.6/collapsibleTree/R/collapsibleTree.data.frame.R | 81 +++--- collapsibleTree-0.1.6/collapsibleTree/R/collapsibleTree.data.tree.R | 122 ++++------ collapsibleTree-0.1.6/collapsibleTree/R/collapsibleTreeNetwork.R |only collapsibleTree-0.1.6/collapsibleTree/R/collapsibleTreeSummary.R | 95 +++++-- collapsibleTree-0.1.6/collapsibleTree/README.md | 67 +++++ collapsibleTree-0.1.6/collapsibleTree/inst/examples/01rmd/Example01.html | 26 +- collapsibleTree-0.1.6/collapsibleTree/inst/examples/03shiny/app.R | 22 + collapsibleTree-0.1.6/collapsibleTree/inst/examples/04rmd |only collapsibleTree-0.1.6/collapsibleTree/inst/htmlwidgets/collapsibleTree.js | 27 +- collapsibleTree-0.1.6/collapsibleTree/inst/htmlwidgets/collapsibleTree.yaml | 6 collapsibleTree-0.1.6/collapsibleTree/inst/htmlwidgets/lib/d3-4.10.2 |only collapsibleTree-0.1.6/collapsibleTree/man/collapsibleTree.Rd | 110 +++++++-- collapsibleTree-0.1.6/collapsibleTree/man/collapsibleTreeNetwork.Rd |only collapsibleTree-0.1.6/collapsibleTree/man/collapsibleTreeSummary.Rd | 29 +- collapsibleTree-0.1.6/collapsibleTree/tests/testthat/test-error.R | 1 collapsibleTree-0.1.6/collapsibleTree/tests/testthat/test-network.R |only 23 files changed, 475 insertions(+), 237 deletions(-)
More information about collapsibleTree at CRAN
Permanent link
Title: Tools for Analysing UK Politics
Description: Provides various tools for analysing UK political data, including creating political cartograms and retrieving data.
Author: Evan Odell [aut, cre]
Maintainer: Evan Odell <evanodell91@gmail.com>
Diff between parlitools versions 0.2.0 dated 2017-08-10 and 0.2.1 dated 2017-09-23
DESCRIPTION | 13 LICENSE | 2 MD5 | 96 - NAMESPACE | 25 R/current_mps.R | 118 - R/data.R | 286 +-- R/mps_on_date.R | 242 +-- R/parlitools-package.R | 37 R/parlitools_tidy.R | 216 +- build/vignette.rds |binary data/council_data.rda |binary data/datalist | 16 data/leave_votes_west.rda |binary inst/CITATION | 20 inst/doc/bes-2015.Rmd | 222 +- inst/doc/bes-2015.html | 1066 ++++++------- inst/doc/bes-2017.Rmd | 282 +-- inst/doc/bes-2017.html | 1376 +++++++++--------- inst/doc/census-11.Rmd | 418 ++--- inst/doc/census-11.html | 2442 ++++++++++++++++---------------- inst/doc/introduction.R | 211 +- inst/doc/introduction.Rmd | 382 ++--- inst/doc/introduction.html | 525 +++--- inst/doc/mapping-local-authorities.R | 98 - inst/doc/mapping-local-authorities.Rmd | 134 - inst/doc/mapping-local-authorities.html | 308 ++-- inst/doc/using-cartograms.R | 120 - inst/doc/using-cartograms.Rmd | 168 +- inst/doc/using-cartograms.html | 340 ++-- man/bes_2015.Rd | 50 man/bes_2017.Rd | 50 man/census_11.Rd | 34 man/council_data.Rd | 80 - man/current_mps.Rd | 50 man/leave_votes_west.Rd | 55 man/local_hex_map.Rd | 50 man/mps_on_date.Rd | 63 man/parlitools.Rd | 20 man/party_colour.Rd | 46 man/west_hex_map.Rd | 54 tests/testthat.R | 8 tests/testthat/test_current_mps.R | 26 tests/testthat/test_mps_on_date.R | 53 vignettes/bes-2015.Rmd | 222 +- vignettes/bes-2017.Rmd | 282 +-- vignettes/census-11.Rmd | 418 ++--- vignettes/introduction.Rmd | 382 ++--- vignettes/mapping-local-authorities.Rmd | 134 - vignettes/using-cartograms.Rmd | 168 +- 49 files changed, 5675 insertions(+), 5733 deletions(-)
Title: Everyone's Statistical Software
Description: A framework that brings together an abundance of common
statistical models found across packages into a unified interface, and
provides a common architecture for estimation and interpretation, as well
as bridging functions to absorb increasingly more models into the
collective library. Zelig allows each individual package, for each
statistical model, to be accessed by a common uniformly structured call and
set of arguments. Moreover, Zelig automates all the surrounding building
blocks of a statistical work-flow--procedures and algorithms that may be
essential to one user's application but which the original package
developer did not use in their own research and might not themselves
support. These include bootstrapping, jackknifing, and re-weighting of data.
In particular, Zelig automatically generates predicted and simulated
quantities of interest (such as relative risk ratios, average treatment
effects, first differences and predicted and expected values) to interpret
and visualize complex models.
Author: Christine Choirat [aut],
Christopher Gandrud [aut, cre],
James Honaker [aut],
Kosuke Imai [aut],
Gary King [aut],
Olivia Lau [aut],
IQSS Harvard University [cph]
Maintainer: Christopher Gandrud <zelig.zee@gmail.com>
Diff between Zelig versions 5.1-3 dated 2017-08-06 and 5.1-4 dated 2017-09-23
DESCRIPTION | 8 +++--- MD5 | 27 ++++++++++---------- NAMESPACE | 10 +++---- NEWS.md | 32 +++++++++++++++++------- R/model-logit.R | 27 +++++++++----------- R/model-relogit.R | 56 +++++++++++++++++++++++++++++++++++++----- R/model-zelig.R | 31 +++++++++++++++-------- R/utils.R | 21 +++++++++++++++ man/Zelig-class.Rd | 2 + man/Zelig-logit-class.Rd | 2 - man/Zelig-relogit-class.Rd | 2 + man/or_summary.Rd |only tests/testthat/test-arima.R | 1 tests/testthat/test-relogit.R | 46 +++++++++++++++++++++++++++++++++- tests/testthat/test-utils.R | 7 ++++- 15 files changed, 205 insertions(+), 67 deletions(-)
Title: Utility Functions for 'spatstat'
Description: Contains utility functions for the 'spatstat' package
which may also be useful for other purposes.
Author: Adrian Baddeley [aut, cre],
Rolf Turner [aut],
Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.utils versions 1.7-0 dated 2017-08-09 and 1.7-1 dated 2017-09-23
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/resolve.defaults.R | 6 +++--- inst/doc/packagesizes.txt | 2 +- 4 files changed, 11 insertions(+), 11 deletions(-)
More information about spatstat.utils at CRAN
Permanent link
Title: Phylogenetic Methods for Multiple Gene Data
Description: Toolkit for the analysis of multiple gene data. Apex implements
the new S4 classes 'multidna', 'multiphyDat' and associated methods to handle
aligned DNA sequences from multiple genes.
Author: Thibaut Jombart [aut, cre],
Zhian Namir Kamvar [aut],
Klaus Schliep [aut],
Eric Archer [aut],
Rebecca Harris [aut]
Maintainer: Thibaut Jombart <thibautjombart@gmail.com>
Diff between apex versions 1.0.2 dated 2016-03-31 and 1.0.3 dated 2017-09-23
apex-1.0.2/apex/vignettes/apex.md |only apex-1.0.3/apex/DESCRIPTION | 12 apex-1.0.3/apex/MD5 | 67 ++--- apex-1.0.3/apex/R/add.gaps.R | 20 - apex-1.0.3/apex/R/multiphyDat.constructor.R | 2 apex-1.0.3/apex/build/vignette.rds |binary apex-1.0.3/apex/inst/doc/apex.html | 248 +++++++++++++++---- apex-1.0.3/apex/man/accessors.Rd | 41 +-- apex-1.0.3/apex/man/add.gaps.Rd | 1 apex-1.0.3/apex/man/apex.Rd | 1 apex-1.0.3/apex/man/concatenate.Rd | 1 apex-1.0.3/apex/man/dist.multidna.Rd | 7 apex-1.0.3/apex/man/getTree.Rd | 7 apex-1.0.3/apex/man/initialize-multidna-method.Rd | 7 apex-1.0.3/apex/man/initialize-multiphyDat-method.Rd | 9 apex-1.0.3/apex/man/multidna.Rd | 4 apex-1.0.3/apex/man/multidna2alignment.Rd | 7 apex-1.0.3/apex/man/multidna2genind.Rd | 7 apex-1.0.3/apex/man/multidna2multiphyDat.Rd | 7 apex-1.0.3/apex/man/multiphyDat.Rd | 4 apex-1.0.3/apex/man/plot-multidna-ANY-method.Rd | 1 apex-1.0.3/apex/man/readfiles.Rd | 11 apex-1.0.3/apex/man/rm.gaps.Rd | 1 apex-1.0.3/apex/man/show-multidna-method.Rd | 1 apex-1.0.3/apex/man/show-multiphyDat-method.Rd | 1 apex-1.0.3/apex/man/subset.multidna.Rd | 1 apex-1.0.3/apex/vignettes/figs/concat-1.png |binary apex-1.0.3/apex/vignettes/figs/concat-2.png |binary apex-1.0.3/apex/vignettes/figs/handling-1.png |binary apex-1.0.3/apex/vignettes/figs/handling-2.png |binary apex-1.0.3/apex/vignettes/figs/multidnaclass-1.png |binary apex-1.0.3/apex/vignettes/figs/multidnaclass-2.png |binary apex-1.0.3/apex/vignettes/figs/plotMultiPhylo-1.png |binary apex-1.0.3/apex/vignettes/figs/plotPhyloSingle-1.png |binary apex-1.0.3/apex/vignettes/figs/readfiles-1.png |binary 35 files changed, 301 insertions(+), 167 deletions(-)
Title: Downloading Time Series from ALFRED Database for Various
Vintages
Description: Provides direct access to the ALFRED (<https://alfred.stlouisfed.org>) and FRED (<https://fred.stlouisfed.org>) databases.
Its functions return tidy data frames for different releases of the specified time series.
Note that this product uses the FRED© API but is not endorsed or certified by the Federal Reserve Bank of St. Louis.
Author: Onno Kleen [aut, cre]
Maintainer: Onno Kleen <r@onnokleen.de>
Diff between alfred versions 0.1.1 dated 2017-06-10 and 0.1.3 dated 2017-09-23
DESCRIPTION | 8 MD5 | 12 NAMESPACE | 5 NEWS.md | 1 R/get_alfred_series.R | 80 +-- build/vignette.rds |binary inst/doc/alfred.html | 1275 ++++++++++++++++++++++++++++++++++++++++++++++++-- 7 files changed, 1292 insertions(+), 89 deletions(-)
Title: Efficient Phylogenetics on Large Trees
Description: Efficient tree manipulation functions including pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distance matrices. Calculation of phylogenetic signal and mean trait depth (trait conservatism). Ancestral state reconstruction and hidden character prediction of discrete characters, using Maximum Likelihood and Maximum Parsimony methods. Simulating and fitting models of trait evolution, and generating random trees using birth-death models.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@zoology.ubc.ca>
Diff between castor versions 1.1 dated 2017-06-02 and 1.2 dated 2017-09-23
castor-1.1/castor/R/fit_random_tree_model.R |only castor-1.1/castor/R/map_tip_or_node_names_to_indices.R |only castor-1.2/castor/DESCRIPTION | 10 castor-1.2/castor/MD5 | 126 castor-1.2/castor/NAMESPACE | 11 castor-1.2/castor/R/RcppExports.R | 108 castor-1.2/castor/R/asr_max_parsimony.R | 6 castor-1.2/castor/R/auxiliary_routines.R |only castor-1.2/castor/R/collapse_tree_at_resolution.R | 42 castor-1.2/castor/R/count_clades_over_time.R | 57 castor-1.2/castor/R/date_tree_PL.R |only castor-1.2/castor/R/fit_tree_model.R |only castor-1.2/castor/R/generate_random_tree.R | 92 castor-1.2/castor/R/generate_tree_with_evolving_rates.R |only castor-1.2/castor/R/get_subtree_with_tips.R | 25 castor-1.2/castor/R/get_trait_depth.R | 27 castor-1.2/castor/R/get_trait_stats_over_time.R |only castor-1.2/castor/R/get_tree_span.R |only castor-1.2/castor/R/get_tree_traversal_root_to_tips.R | 5 castor-1.2/castor/R/hsp_mk_model.R | 2 castor-1.2/castor/R/merge_short_edges.R |only castor-1.2/castor/R/multifurcations_to_bifurcations.R | 4 castor-1.2/castor/R/reconstruct_past_diversification.R |only castor-1.2/castor/R/root_at_node.R | 4 castor-1.2/castor/R/root_via_outgroup.R |only castor-1.2/castor/R/simulate_bm_model.R | 63 castor-1.2/castor/R/simulate_diversification_model.R |only castor-1.2/castor/R/simulate_neutral_gene_evolution.R |only castor-1.2/castor/R/trim_tree_at_height.R |only castor-1.2/castor/man/asr_independent_contrasts.Rd | 2 castor-1.2/castor/man/asr_max_parsimony.Rd | 6 castor-1.2/castor/man/asr_mk_model.Rd | 2 castor-1.2/castor/man/asr_squared_change_parsimony.Rd | 2 castor-1.2/castor/man/castor.Rd | 4 castor-1.2/castor/man/collapse_tree_at_resolution.Rd | 42 castor-1.2/castor/man/count_clades_over_time.Rd | 28 castor-1.2/castor/man/count_tips_per_node.Rd | 4 castor-1.2/castor/man/find_nearest_tips.Rd | 2 castor-1.2/castor/man/find_root.Rd | 2 castor-1.2/castor/man/fit_bm_model.Rd | 14 castor-1.2/castor/man/generate_random_tree.Rd | 127 castor-1.2/castor/man/generate_tree_with_evolving_rates.Rd |only castor-1.2/castor/man/get_all_distances_to_root.Rd | 6 castor-1.2/castor/man/get_independent_contrasts.Rd | 2 castor-1.2/castor/man/get_mrca_of_set.Rd | 2 castor-1.2/castor/man/get_pairwise_distances.Rd | 2 castor-1.2/castor/man/get_pairwise_mrcas.Rd | 2 castor-1.2/castor/man/get_subtree_at_node.Rd | 2 castor-1.2/castor/man/get_subtree_with_tips.Rd | 12 castor-1.2/castor/man/get_tips_for_mrcas.Rd | 2 castor-1.2/castor/man/get_trait_acf.Rd | 4 castor-1.2/castor/man/get_trait_depth.Rd | 26 castor-1.2/castor/man/get_trait_stats_over_time.Rd |only castor-1.2/castor/man/get_tree_span.Rd |only castor-1.2/castor/man/hsp_empirical_probabilities.Rd | 2 castor-1.2/castor/man/hsp_independent_contrasts.Rd | 2 castor-1.2/castor/man/hsp_max_parsimony.Rd | 6 castor-1.2/castor/man/hsp_mk_model.Rd | 2 castor-1.2/castor/man/hsp_squared_change_parsimony.Rd | 2 castor-1.2/castor/man/is_monophyletic.Rd | 2 castor-1.2/castor/man/merge_short_edges.Rd |only castor-1.2/castor/man/multifurcations_to_bifurcations.Rd | 7 castor-1.2/castor/man/pick_random_tips.Rd | 2 castor-1.2/castor/man/reconstruct_past_diversification.Rd |only castor-1.2/castor/man/root_at_node.Rd | 3 castor-1.2/castor/man/root_via_outgroup.Rd |only castor-1.2/castor/man/simulate_bm_model.Rd | 41 castor-1.2/castor/man/simulate_diversification_model.Rd |only castor-1.2/castor/man/simulate_mk_model.Rd | 2 castor-1.2/castor/man/simulate_ou_model.Rd | 2 castor-1.2/castor/man/simulate_rou_model.Rd | 2 castor-1.2/castor/man/trim_tree_at_height.Rd |only castor-1.2/castor/man/write_tree.Rd | 2 castor-1.2/castor/src/RcppExports.cpp | 420 + castor-1.2/castor/src/phylogenetics_cpp_routines.cpp | 4438 ++++++++++++- 75 files changed, 5219 insertions(+), 593 deletions(-)