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Title: Convert Data from and to 'GeoJSON' or 'TopoJSON'
Description: Convert data to 'GeoJSON' or 'TopoJSON' from various R classes,
including vectors, lists, data frames, shape files, and spatial classes.
geojsonio does not aim to replace packages like 'sp', 'rgdal', 'rgeos',
but rather aims to be a high level client to simplify conversions of data
from and to 'GeoJSON' and 'TopoJSON'.
Author: Scott Chamberlain [aut, cre],
Andy Teucher [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between geojsonio versions 0.2.0 dated 2016-07-13 and 0.3.0 dated 2017-01-27
DESCRIPTION | 25 +-- LICENSE | 2 MD5 | 63 ++++---- NAMESPACE | 11 + NEWS.md | 31 ++++ R/as.location.R | 2 R/construction.R | 12 - R/crs_convert.R |only R/file_to_geojson.r | 84 ++++++----- R/geojson_json.R | 151 +++++++++++++++---- R/geojson_list.R | 258 ++++++++++++++++++++++++++++------ R/geojson_read.R | 47 +++--- R/geojson_sp.R | 2 R/geojson_style.R | 2 R/geojson_write.r | 157 +++++++++++++++----- R/geojsonio-package.r | 2 R/mapleaflet.R | 2 R/zzz.r | 41 +++-- README.md | 2 build/vignette.rds |binary man/file_to_geojson.Rd | 57 +++++-- man/geojson_json.Rd | 40 +++++ man/geojson_list.Rd | 41 +++++ man/geojson_read.Rd | 54 +++++-- man/geojson_sp.Rd | 2 man/geojson_write.Rd | 18 +- tests/testthat/helper-geojsonio.R | 2 tests/testthat/test-crs_convert.R |only tests/testthat/test-file_to_geojson.R | 119 +++++++++++++++ tests/testthat/test-geojson_json.R | 2 tests/testthat/test-lint.R | 52 +++--- tests/testthat/test-sf_classes.R |only tests/testthat/test-spatial_methods.R | 4 tests/testthat/test-validate.R | 40 ++--- 34 files changed, 988 insertions(+), 337 deletions(-)
Title: An API Wrapper for the Bureau of Labor Statistics (BLS)
Description: Scrapes various data from the Bureau of Labor Statistics, which is the statistical branch of the United States Department of Labor. The package has additional functions to help parse, analyze and visualize the data.
Author: Kris Eberwein [aut, cre]
Maintainer: Kris Eberwein <eberwein@knights.ucf.edu>
Diff between blscrapeR versions 2.0.0 dated 2016-12-17 and 2.1.1 dated 2017-01-27
DESCRIPTION | 6 +- MD5 | 43 ++++++++++--------- NEWS.md | 16 +++++++ R/county_map.R | 6 +- R/county_map_merc.R |only R/get_bls_state.R | 39 +++++++++++------ R/maps.R | 21 ++++++++- R/state_map.R | 4 - README.md | 66 ++++++------------------------ data/county_map_data.rda |binary data/county_map_merc.rda |only data/datalist |only data/state_map_data.rda |binary inst/doc/Employment_and_Unemployment.html | 4 - inst/doc/Inflation_and_Prices.html | 4 - inst/doc/Mapping_BLS_Data.Rmd | 2 inst/doc/Mapping_BLS_Data.html | 20 ++++----- inst/doc/Pay_and_Benefits.html | 4 - inst/doc/QCEW_API.html | 4 - inst/doc/qcew.html | 4 - man/bls_map_county.Rd | 5 +- man/county_map_data.Rd | 31 ++++++++++++-- man/state_map_data.Rd | 4 - vignettes/Mapping_BLS_Data.Rmd | 2 24 files changed, 159 insertions(+), 126 deletions(-)
Title: Easily Install and Load 'Tidyverse' Packages
Description: The 'tidyverse' is a set of packages that work in harmony
because they share common data representations and 'API' design. This
package is designed to make it easy to install and load multiple
'tidyverse' packages in a single step. Learn more about the 'tidyverse'
at <https://github.com/hadley/tidyverse>.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between tidyverse versions 1.1.0 dated 2017-01-20 and 1.1.1 dated 2017-01-27
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- NAMESPACE | 1 + NEWS.md | 6 ++++++ R/tidyverse.R | 1 + inst/doc/manifesto.html | 4 ++-- 6 files changed, 22 insertions(+), 14 deletions(-)
Title: Simple Imputation
Description: Easy to use interfaces to a number of imputation methods
that fit in the not-a-pipe operator of the 'magrittr' package.
Author: Mark van der Loo [aut, cre]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between simputation versions 0.2.0 dated 2016-12-30 and 0.2.1 dated 2017-01-27
simputation-0.2.0/simputation/man/impute_.Rd |only simputation-0.2.1/simputation/DESCRIPTION | 13 simputation-0.2.1/simputation/MD5 | 46 - simputation-0.2.1/simputation/NAMESPACE | 11 simputation-0.2.1/simputation/NEWS | 19 simputation-0.2.1/simputation/R/hotdeck.R | 145 +++- simputation-0.2.1/simputation/R/linearmodels.R | 315 ++++------ simputation-0.2.1/simputation/R/multivariate.R |only simputation-0.2.1/simputation/R/proxy.R |only simputation-0.2.1/simputation/R/simputation-pkg.R | 10 simputation-0.2.1/simputation/R/treemodels.R | 97 ++- simputation-0.2.1/simputation/R/utils.R | 148 ++++ simputation-0.2.1/simputation/inst/doc/intro.R | 24 simputation-0.2.1/simputation/inst/doc/intro.Rmd | 65 +- simputation-0.2.1/simputation/inst/doc/intro.html | 123 +++ simputation-0.2.1/simputation/man/impute_hotdeck.Rd |only simputation-0.2.1/simputation/man/impute_lm.Rd |only simputation-0.2.1/simputation/man/impute_median.Rd |only simputation-0.2.1/simputation/man/impute_multivariate.Rd |only simputation-0.2.1/simputation/man/impute_proxy.Rd |only simputation-0.2.1/simputation/man/impute_tree.Rd |only simputation-0.2.1/simputation/man/na.roughfix.Rd |only simputation-0.2.1/simputation/man/print.simputation.capabilities.Rd |only simputation-0.2.1/simputation/man/reexports.Rd |only simputation-0.2.1/simputation/man/simputation.Rd | 5 simputation-0.2.1/simputation/man/simputation_capabilities.Rd |only simputation-0.2.1/simputation/tests/testthat/test_em.R |only simputation-0.2.1/simputation/tests/testthat/test_lm.R | 19 simputation-0.2.1/simputation/tests/testthat/test_tree.R | 29 simputation-0.2.1/simputation/tests/testthat/test_utils.R | 36 - simputation-0.2.1/simputation/vignettes/intro.Rmd | 65 +- 31 files changed, 846 insertions(+), 324 deletions(-)
Title: Robust Gaussian Stochastic Process Emulation
Description: Robust parameter estimation and prediction of Gaussian stochastic process emulators.
Important functions : rgasp(), predict.rgasp().
Author: Mengyang Gu [aut, cre], Jesus Palomo [aut], James Berger [aut]
Maintainer: Mengyang Gu <mgu6@jhu.edu>
Diff between RobustGaSP versions 0.5.2 dated 2016-09-16 and 0.5.3 dated 2017-01-27
CHANGELOG | 10 ++++++- DESCRIPTION | 10 +++---- MD5 | 12 ++++---- R/functions.R | 4 ++ R/rgasp.R | 65 +++++++++++++++++++++++++++++++++------------- build/partial.rdb |binary man/RobustGaSP-package.Rd | 13 ++++++++- 7 files changed, 82 insertions(+), 32 deletions(-)
Title: Quantitative Analysis of Textual Data
Description: A fast, flexible toolset for for the management, processing, and
quantitative analysis of textual data in R.
Author: Kenneth Benoit [aut, cre],
Paul Nulty [ctb],
Kohei Watanabe [ctb],
Adam Obeng [ctb],
Haiyan Wang [ctb],
Benjamin Lauderdale [ctb],
Will Lowe [ctb]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda versions 0.9.9-3 dated 2017-01-10 and 0.9.9-17 dated 2017-01-27
quanteda-0.9.9-17/quanteda/DESCRIPTION | 39 quanteda-0.9.9-17/quanteda/MD5 | 237 +++-- quanteda-0.9.9-17/quanteda/NAMESPACE | 18 quanteda-0.9.9-17/quanteda/NEWS.md | 28 quanteda-0.9.9-17/quanteda/R/RcppExports.R | 16 quanteda-0.9.9-17/quanteda/R/character-methods.R | 2 quanteda-0.9.9-17/quanteda/R/collocations.R | 4 quanteda-0.9.9-17/quanteda/R/convert.R | 16 quanteda-0.9.9-17/quanteda/R/corpus-methods-quanteda.R | 38 quanteda-0.9.9-17/quanteda/R/corpus.R | 4 quanteda-0.9.9-17/quanteda/R/corpuszip.R | 112 -- quanteda-0.9.9-17/quanteda/R/dfm-classes.R | 184 ---- quanteda-0.9.9-17/quanteda/R/dfm-deprecated.R | 6 quanteda-0.9.9-17/quanteda/R/dfm-methods.R | 12 quanteda-0.9.9-17/quanteda/R/dfm-print.R |only quanteda-0.9.9-17/quanteda/R/dfm.R | 161 ++- quanteda-0.9.9-17/quanteda/R/dfm_compress.R | 46 - quanteda-0.9.9-17/quanteda/R/dfm_lookup.R | 9 quanteda-0.9.9-17/quanteda/R/dfm_select.R | 307 +++---- quanteda-0.9.9-17/quanteda/R/dfm_trim.R | 30 quanteda-0.9.9-17/quanteda/R/dfm_weight.R | 2 quanteda-0.9.9-17/quanteda/R/dictionaries-deprecated.R | 6 quanteda-0.9.9-17/quanteda/R/dictionaries.R | 241 +++-- quanteda-0.9.9-17/quanteda/R/fcm-methods.R | 190 ++-- quanteda-0.9.9-17/quanteda/R/fcm.R | 99 +- quanteda-0.9.9-17/quanteda/R/nfunctions.R | 8 quanteda-0.9.9-17/quanteda/R/nsyllable.R | 2 quanteda-0.9.9-17/quanteda/R/regex2fixed.R | 35 quanteda-0.9.9-17/quanteda/R/selectFeatures-old.R | 4 quanteda-0.9.9-17/quanteda/R/selectFeatures.R | 19 quanteda-0.9.9-17/quanteda/R/sequences.R | 22 quanteda-0.9.9-17/quanteda/R/textmodel-NB.R | 28 quanteda-0.9.9-17/quanteda/R/textmodel-wordfish.R | 8 quanteda-0.9.9-17/quanteda/R/textmodel-wordshoal.R | 179 ++-- quanteda-0.9.9-17/quanteda/R/textstat_keyness.R |only quanteda-0.9.9-17/quanteda/R/textstat_simil.R | 17 quanteda-0.9.9-17/quanteda/R/toLower.R | 19 quanteda-0.9.9-17/quanteda/R/tokenize.R | 8 quanteda-0.9.9-17/quanteda/R/tokens.R | 30 quanteda-0.9.9-17/quanteda/R/tokens_compound.R | 3 quanteda-0.9.9-17/quanteda/R/tokens_lookup.R | 56 + quanteda-0.9.9-17/quanteda/R/tokens_ngrams.R | 5 quanteda-0.9.9-17/quanteda/README.md | 16 quanteda-0.9.9-17/quanteda/data/data_char_inaugural.RData |binary quanteda-0.9.9-17/quanteda/data/data_corpus_inaugural.RData |binary quanteda-0.9.9-17/quanteda/data/inaugCorpus.RData |binary quanteda-0.9.9-17/quanteda/data/inaugTexts.RData |binary quanteda-0.9.9-17/quanteda/demo/quanteda.R | 10 quanteda-0.9.9-17/quanteda/inst/doc/LitVignette.R | 8 quanteda-0.9.9-17/quanteda/inst/doc/LitVignette.Rmd | 12 quanteda-0.9.9-17/quanteda/inst/doc/LitVignette.html | 16 quanteda-0.9.9-17/quanteda/inst/doc/design.R | 4 quanteda-0.9.9-17/quanteda/inst/doc/design.Rmd | 4 quanteda-0.9.9-17/quanteda/inst/doc/design.html | 4 quanteda-0.9.9-17/quanteda/inst/doc/plotting.html | 6 quanteda-0.9.9-17/quanteda/inst/doc/quickstart.html | 100 +- quanteda-0.9.9-17/quanteda/man/compress.Rd | 6 quanteda-0.9.9-17/quanteda/man/convert-wrappers.Rd | 6 quanteda-0.9.9-17/quanteda/man/convert.Rd | 10 quanteda-0.9.9-17/quanteda/man/dfm.Rd | 15 quanteda-0.9.9-17/quanteda/man/dfm_compress.Rd | 6 quanteda-0.9.9-17/quanteda/man/dfm_lookup.Rd | 8 quanteda-0.9.9-17/quanteda/man/dfm_select.Rd | 42 - quanteda-0.9.9-17/quanteda/man/dfm_trim.Rd | 18 quanteda-0.9.9-17/quanteda/man/dfm_weight.Rd | 2 quanteda-0.9.9-17/quanteda/man/dictionary.Rd | 15 quanteda-0.9.9-17/quanteda/man/docnames.Rd | 5 quanteda-0.9.9-17/quanteda/man/fcm.Rd | 12 quanteda-0.9.9-17/quanteda/man/head.dfm.Rd | 4 quanteda-0.9.9-17/quanteda/man/keyness.Rd |only quanteda-0.9.9-17/quanteda/man/ntoken.Rd | 8 quanteda-0.9.9-17/quanteda/man/print.dfm.Rd | 20 quanteda-0.9.9-17/quanteda/man/selectFeatures.Rd | 45 - quanteda-0.9.9-17/quanteda/man/selectFeaturesOLD.Rd | 4 quanteda-0.9.9-17/quanteda/man/sequences.Rd | 17 quanteda-0.9.9-17/quanteda/man/textmodel_wordfish.Rd | 2 quanteda-0.9.9-17/quanteda/man/textmodel_wordshoal.Rd | 17 quanteda-0.9.9-17/quanteda/man/texts.Rd | 10 quanteda-0.9.9-17/quanteda/man/textstat_keyness.Rd |only quanteda-0.9.9-17/quanteda/man/toLower.Rd | 4 quanteda-0.9.9-17/quanteda/man/tokenize.Rd | 8 quanteda-0.9.9-17/quanteda/man/tokens.Rd | 8 quanteda-0.9.9-17/quanteda/man/tokens_hash.Rd | 2 quanteda-0.9.9-17/quanteda/man/tokens_lookup.Rd | 38 quanteda-0.9.9-17/quanteda/src/RcppExports.cpp | 102 -- quanteda-0.9.9-17/quanteda/src/dist_parallel.cpp | 4 quanteda-0.9.9-17/quanteda/src/fcm.cpp | 70 - quanteda-0.9.9-17/quanteda/src/quanteda.h | 46 - quanteda-0.9.9-17/quanteda/src/sequences_mt.cpp | 216 +++-- quanteda-0.9.9-17/quanteda/src/tokens_detect_mt.cpp | 40 quanteda-0.9.9-17/quanteda/src/tokens_lookup_mt.cpp | 81 + quanteda-0.9.9-17/quanteda/src/tokens_ngrams_mt.cpp | 278 ++++-- quanteda-0.9.9-17/quanteda/src/tokens_replace_mt.cpp | 58 - quanteda-0.9.9-17/quanteda/src/tokens_select_mt.cpp | 107 +- quanteda-0.9.9-17/quanteda/src/utility.cpp | 43 - quanteda-0.9.9-17/quanteda/src/wordfish.cpp | 412 +++++----- quanteda-0.9.9-17/quanteda/tests/data/dictionaries/issue-459.cat |only quanteda-0.9.9-17/quanteda/tests/data/dictionaries/mary.dic | 4 quanteda-0.9.9-17/quanteda/tests/data/dictionaries/mary.lc3 | 4 quanteda-0.9.9-17/quanteda/tests/data/dictionaries/mary.yml |only quanteda-0.9.9-17/quanteda/tests/testthat/test-collocations.R |only quanteda-0.9.9-17/quanteda/tests/testthat/test-convert.R | 6 quanteda-0.9.9-17/quanteda/tests/testthat/test-corpus-compress.R | 40 quanteda-0.9.9-17/quanteda/tests/testthat/test-corpus.R | 31 quanteda-0.9.9-17/quanteda/tests/testthat/test-dfm.R | 125 ++- quanteda-0.9.9-17/quanteda/tests/testthat/test-dfm_lookup.R | 53 + quanteda-0.9.9-17/quanteda/tests/testthat/test-dfm_select.R |only quanteda-0.9.9-17/quanteda/tests/testthat/test-dictionaries.R |only quanteda-0.9.9-17/quanteda/tests/testthat/test-fcm.R | 117 ++ quanteda-0.9.9-17/quanteda/tests/testthat/test-fcm_methods.R |only quanteda-0.9.9-17/quanteda/tests/testthat/test-regex2fixed.R | 14 quanteda-0.9.9-17/quanteda/tests/testthat/test-sequences.R |only quanteda-0.9.9-17/quanteda/tests/testthat/test-textmodel_NB.R |only quanteda-0.9.9-17/quanteda/tests/testthat/test-texts.R |only quanteda-0.9.9-17/quanteda/tests/testthat/test-textstat_dist.R | 40 quanteda-0.9.9-17/quanteda/tests/testthat/test-textstat_keyness.R |only quanteda-0.9.9-17/quanteda/tests/testthat/test-tokens.R | 58 + quanteda-0.9.9-17/quanteda/tests/testthat/test-tokens_lookup.R | 107 ++ quanteda-0.9.9-17/quanteda/tests/testthat/test-tokens_ngrams.R | 29 quanteda-0.9.9-17/quanteda/tests/testthat/test-tolower.R | 8 quanteda-0.9.9-17/quanteda/tests/testthat/test-wordfish.R |only quanteda-0.9.9-17/quanteda/tests/testthat/test_dfm-compress.R |only quanteda-0.9.9-17/quanteda/tests/testthat/test_similarity.R | 2 quanteda-0.9.9-17/quanteda/tests/testthat/test_tokenizer.R | 10 quanteda-0.9.9-17/quanteda/vignettes/LitVignette.Rmd | 12 quanteda-0.9.9-17/quanteda/vignettes/design.Rmd | 4 quanteda-0.9.9-3/quanteda/man/corpuszip.Rd |only quanteda-0.9.9-3/quanteda/tests/testthat/test-corpuszip.R |only quanteda-0.9.9-3/quanteda/tests/testthat/testCollocations.R |only 129 files changed, 2755 insertions(+), 2128 deletions(-)
Title: Latent Variable Models
Description: Estimation and simulation of latent variable models.
Author: Klaus K. Holst [aut, cre],
Brice Ozenne [ctb],
Thomas Gerds [ctb]
Maintainer: Klaus K. Holst <kkho@biostat.ku.dk>
Diff between lava versions 1.4.6 dated 2016-12-20 and 1.4.7 dated 2017-01-27
lava-1.4.6/lava/R/sim.R |only lava-1.4.6/lava/R/survival.R |only lava-1.4.7/lava/DESCRIPTION | 8 ++-- lava-1.4.7/lava/MD5 | 43 +++++++++++------------- lava-1.4.7/lava/NAMESPACE | 5 -- lava-1.4.7/lava/NEWS | 5 ++ lava-1.4.7/lava/R/addhook.R | 1 lava-1.4.7/lava/R/backdoor.R | 14 +++++-- lava-1.4.7/lava/R/eventTime.R | 1 lava-1.4.7/lava/R/lava-package.R | 1 lava-1.4.7/lava/R/logo.R | 4 +- lava-1.4.7/lava/R/path.R | 2 - lava-1.4.7/lava/R/regression.R | 5 +- lava-1.4.7/lava/R/sim.default.R | 32 +++++++++++++---- lava-1.4.7/lava/R/sim.lvm.R |only lava-1.4.7/lava/R/spaghetti.R | 26 +++++++------- lava-1.4.7/lava/R/utils.R | 14 +++---- lava-1.4.7/lava/R/zorg.R | 10 +++++ lava-1.4.7/lava/inst/doc/reference.pdf |binary lava-1.4.7/lava/man/backdoor.Rd | 4 +- lava-1.4.7/lava/man/org.Rd | 5 ++ lava-1.4.7/lava/man/sim.Rd | 7 ++- lava-1.4.7/lava/man/sim.default.Rd | 18 ++++++++-- lava-1.4.7/lava/tests/testthat/test-inference.R | 2 - 24 files changed, 131 insertions(+), 76 deletions(-)
Title: Prediction of Therapeutic Success
Description: In personalized medicine, one wants to know, for a given patient and his or her outcome for a predictor (pre-treatment variable), how likely it is that a treatment will be more beneficial than an alternative treatment. This package allows for the quantification of the predictive causal association (i.e., the association between the predictor variable and the individual causal effect of the treatment) and related metrics. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Ariel Alonso & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between EffectTreat versions 0.2 dated 2015-07-07 and 0.3 dated 2017-01-27
DESCRIPTION | 9 ++++----- MD5 | 6 +++--- NAMESPACE | 1 - NEWS | 2 +- 4 files changed, 8 insertions(+), 10 deletions(-)
Title: Bayesian Regression Models using Stan
Description: Fit Bayesian generalized (non-)linear multilevel models
using Stan for full Bayesian inference. A wide range of distributions
and link functions are supported, allowing users to fit -- among others --
linear, robust linear, binomial, Poisson, survival, response times, ordinal,
zero-inflated, hurdle, and even non-linear models all in a
multilevel context. Further modeling options include auto-correlation
and smoothing terms, user defined dependence structures, censored data,
meta-analytic standard errors, and quite a few more.
In addition, all parameters of the response distribution can be predicted
in order to perform distributional regression.
Prior specifications are flexible and explicitly encourage
users to apply prior distributions that actually reflect their beliefs.
In addition, model fit can easily be assessed and compared with
posterior predictive checks and leave-one-out cross-validation.
Author: Paul-Christian Bürkner [aut, cre]
Maintainer: Paul-Christian Bürkner <paul.buerkner@gmail.com>
Diff between brms versions 1.3.1 dated 2016-12-21 and 1.4.0 dated 2017-01-27
brms-1.3.1/brms/man/cov_fixed.Rd |only brms-1.3.1/brms/man/ngrps.brmsfit.Rd |only brms-1.3.1/brms/tests/testthat/tests.stan-helpers.R |only brms-1.4.0/brms/DESCRIPTION | 26 brms-1.4.0/brms/MD5 | 223 ++-- brms-1.4.0/brms/NAMESPACE | 33 brms-1.4.0/brms/R/brm.R | 100 + brms-1.4.0/brms/R/brmsfit-helpers.R | 351 +++--- brms-1.4.0/brms/R/brmsfit-methods.R | 442 ++++---- brms-1.4.0/brms/R/brmsformula.R | 509 +++++---- brms-1.4.0/brms/R/correlations.R | 156 +- brms-1.4.0/brms/R/data-helpers.R | 254 ++-- brms-1.4.0/brms/R/distributions.R | 68 + brms-1.4.0/brms/R/extract_draws.R | 73 - brms-1.4.0/brms/R/families.R | 426 ++++--- brms-1.4.0/brms/R/fitted.R | 388 ++++--- brms-1.4.0/brms/R/formula-helpers.R | 283 +++-- brms-1.4.0/brms/R/generics.R | 118 +- brms-1.4.0/brms/R/linear_predictor.R | 20 brms-1.4.0/brms/R/loglik.R | 51 brms-1.4.0/brms/R/make_stancode.R | 100 - brms-1.4.0/brms/R/make_standata.R | 177 +-- brms-1.4.0/brms/R/misc-methods.R | 38 brms-1.4.0/brms/R/misc.R | 71 + brms-1.4.0/brms/R/plots.R | 30 brms-1.4.0/brms/R/predict.R | 32 brms-1.4.0/brms/R/priors.R | 208 ++- brms-1.4.0/brms/R/rename.R | 138 +- brms-1.4.0/brms/R/stan-helpers.R | 311 +++-- brms-1.4.0/brms/R/stan-predictor.R | 109 + brms-1.4.0/brms/R/sysdata.rda |binary brms-1.4.0/brms/R/validate.R | 714 ++++++------- brms-1.4.0/brms/R/zzz.R | 4 brms-1.4.0/brms/README.md | 95 + brms-1.4.0/brms/inst/NEWS.Rd | 77 + brms-1.4.0/brms/inst/chunks/fun_asym_laplace.stan |only brms-1.4.0/brms/inst/chunks/fun_logm1.stan |only brms-1.4.0/brms/inst/doc/brms_distreg.R | 26 brms-1.4.0/brms/inst/doc/brms_distreg.Rmd | 33 brms-1.4.0/brms/inst/doc/brms_distreg.html | 24 brms-1.4.0/brms/inst/doc/brms_families.Rmd | 17 brms-1.4.0/brms/inst/doc/brms_families.html | 15 brms-1.4.0/brms/inst/doc/brms_monotonic.R | 41 brms-1.4.0/brms/inst/doc/brms_monotonic.Rmd | 40 brms-1.4.0/brms/inst/doc/brms_monotonic.html | 33 brms-1.4.0/brms/inst/doc/brms_nonlinear.R | 45 brms-1.4.0/brms/inst/doc/brms_nonlinear.Rmd | 49 brms-1.4.0/brms/inst/doc/brms_nonlinear.html | 37 brms-1.4.0/brms/inst/doc/brms_overview.ltx | 4 brms-1.4.0/brms/inst/doc/brms_overview.pdf |binary brms-1.4.0/brms/inst/doc/brms_phylogenetics.R | 60 - brms-1.4.0/brms/inst/doc/brms_phylogenetics.Rmd | 66 - brms-1.4.0/brms/inst/doc/brms_phylogenetics.html | 62 - brms-1.4.0/brms/man/LOO.Rd | 24 brms-1.4.0/brms/man/VarCorr.brmsfit.Rd | 2 brms-1.4.0/brms/man/WAIC.Rd | 26 brms-1.4.0/brms/man/addition-terms.Rd |only brms-1.4.0/brms/man/brm.Rd | 74 - brms-1.4.0/brms/man/brmsfamily.Rd | 99 + brms-1.4.0/brms/man/brmsformula.Rd | 198 ++- brms-1.4.0/brms/man/compare_ic.Rd |only brms-1.4.0/brms/man/cor_ar.Rd | 19 brms-1.4.0/brms/man/cor_arma.Rd | 16 brms-1.4.0/brms/man/cor_arr.Rd | 14 brms-1.4.0/brms/man/cor_brms.Rd | 3 brms-1.4.0/brms/man/cor_bsts.Rd | 7 brms-1.4.0/brms/man/cor_fixed.Rd |only brms-1.4.0/brms/man/cor_ma.Rd | 10 brms-1.4.0/brms/man/expp1.Rd |only brms-1.4.0/brms/man/fitted.brmsfit.Rd | 9 brms-1.4.0/brms/man/get_prior.Rd | 24 brms-1.4.0/brms/man/hypothesis.Rd | 4 brms-1.4.0/brms/man/is.brmsfit.Rd |only brms-1.4.0/brms/man/is.brmsformula.Rd |only brms-1.4.0/brms/man/is.brmsprior.Rd |only brms-1.4.0/brms/man/is.brmsterms.Rd |only brms-1.4.0/brms/man/is.cor_brms.Rd |only brms-1.4.0/brms/man/log_lik.brmsfit.Rd | 9 brms-1.4.0/brms/man/logm1.Rd |only brms-1.4.0/brms/man/make_stancode.Rd | 44 brms-1.4.0/brms/man/make_standata.Rd | 39 brms-1.4.0/brms/man/marginal_effects.Rd | 46 brms-1.4.0/brms/man/marginal_smooths.Rd | 13 brms-1.4.0/brms/man/ngrps.Rd |only brms-1.4.0/brms/man/nsamples.Rd |only brms-1.4.0/brms/man/parnames.Rd | 5 brms-1.4.0/brms/man/parse_bf.Rd |only brms-1.4.0/brms/man/plot.brmsfit.Rd | 4 brms-1.4.0/brms/man/pp_check.brmsfit.Rd | 23 brms-1.4.0/brms/man/predict.brmsfit.Rd | 9 brms-1.4.0/brms/man/residuals.brmsfit.Rd | 9 brms-1.4.0/brms/man/set_prior.Rd | 74 - brms-1.4.0/brms/man/stanplot.Rd | 6 brms-1.4.0/brms/man/update.brmsfit.Rd | 2 brms-1.4.0/brms/tests/testthat/tests.brm.R | 59 + brms-1.4.0/brms/tests/testthat/tests.brmsfit-helpers.R | 124 -- brms-1.4.0/brms/tests/testthat/tests.brmsfit-methods.R | 71 - brms-1.4.0/brms/tests/testthat/tests.brmsformula.R | 56 - brms-1.4.0/brms/tests/testthat/tests.data-helpers.R | 127 +- brms-1.4.0/brms/tests/testthat/tests.distributions.R | 2 brms-1.4.0/brms/tests/testthat/tests.families.R | 42 brms-1.4.0/brms/tests/testthat/tests.fitted.R | 70 - brms-1.4.0/brms/tests/testthat/tests.loglik.R | 25 brms-1.4.0/brms/tests/testthat/tests.make_stancode.R | 928 ++++++++++------- brms-1.4.0/brms/tests/testthat/tests.make_standata.R | 309 +++-- brms-1.4.0/brms/tests/testthat/tests.misc.R | 5 brms-1.4.0/brms/tests/testthat/tests.plots.R | 8 brms-1.4.0/brms/tests/testthat/tests.predict.R | 19 brms-1.4.0/brms/tests/testthat/tests.priors.R | 174 --- brms-1.4.0/brms/tests/testthat/tests.rename.R | 47 brms-1.4.0/brms/tests/testthat/tests.stan_functions.R | 29 brms-1.4.0/brms/tests/testthat/tests.validate.R | 290 ----- brms-1.4.0/brms/vignettes/brms_distreg.Rmd | 33 brms-1.4.0/brms/vignettes/brms_families.Rmd | 17 brms-1.4.0/brms/vignettes/brms_monotonic.Rmd | 40 brms-1.4.0/brms/vignettes/brms_nonlinear.Rmd | 49 brms-1.4.0/brms/vignettes/brms_overview.ltx | 4 brms-1.4.0/brms/vignettes/brms_phylogenetics.Rmd | 66 - brms-1.4.0/brms/vignettes/children |only brms-1.4.0/brms/vignettes/inhaler_plot.pdf |binary brms-1.4.0/brms/vignettes/kidney_marginal_effects.pdf |binary brms-1.4.0/brms/vignettes/kidney_plot.pdf |binary 122 files changed, 5540 insertions(+), 4043 deletions(-)
Title: Flights that Departed NYC in 2013
Description: Airline on-time data for all flights departing NYC in 2013.
Also includes useful 'metadata' on airlines, airports, weather, and planes.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between nycflights13 versions 0.2.1 dated 2016-12-29 and 0.2.2 dated 2017-01-27
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NAMESPACE | 1 + NEWS.md | 4 ++++ R/flights.R | 4 ++++ man/airlines.Rd | 1 - man/airports.Rd | 1 - man/flights.Rd | 1 - man/planes.Rd | 1 - man/weather.Rd | 1 - 10 files changed, 22 insertions(+), 18 deletions(-)
Title: Access Elevation Data from Various APIs
Description: Several web services are available that provide access to elevation
data. This package provides access to several of those services and
returns elevation data either as a SpatialPointsDataFrame from
point elevation services or as a raster object from raster
elevation services. Currently, the package supports access to the
Mapzen Elevation Service <https://mapzen.com/documentation/elevation/elevation-service/>,
Mapzen Terrain Service <https://mapzen.com/documentation/terrain-tiles/>,
Amazon Web Services Terrain Tiles <https://aws.amazon.com/public-datasets/terrain/> and the USGS
Elevation Point Query Service <http://ned.usgs.gov/epqs/>.
Author: Jeffrey Hollister [aut, cre],
Tarak Shah [ctb]
Maintainer: Jeffrey Hollister <hollister.jeff@epa.gov>
Diff between elevatr versions 0.1.0 dated 2017-01-26 and 0.1.1 dated 2017-01-27
elevatr-0.1.0/elevatr/inst/doc/Introduction.R |only elevatr-0.1.0/elevatr/inst/doc/Introduction.Rmd |only elevatr-0.1.0/elevatr/inst/doc/Introduction.html |only elevatr-0.1.1/elevatr/DESCRIPTION | 6 - elevatr-0.1.1/elevatr/MD5 | 11 +-- elevatr-0.1.1/elevatr/inst/doc/introduction_to_elevatr.R | 21 +----- elevatr-0.1.1/elevatr/inst/doc/introduction_to_elevatr.Rmd | 37 +++-------- elevatr-0.1.1/elevatr/inst/doc/introduction_to_elevatr.html | 40 +++--------- 8 files changed, 33 insertions(+), 82 deletions(-)
Title: Unicode Symbols at the R Prompt
Description: A small subset of Unicode symbols, that are useful
when building command line applications. They fall back to
alternatives on terminals that do not support Unicode.
Many symbols were taken from the 'figures' 'npm' package
(see <https://github.com/sindresorhus/figures>).
Author: Gábor Csárdi [aut, cre],
Sindre Sorhus [aut]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between clisymbols versions 1.0.0 dated 2015-06-08 and 1.1.0 dated 2017-01-27
DESCRIPTION | 13 +++++++------ MD5 | 8 ++++---- R/symbols.R | 22 +++++++++++++++++----- inst/NEWS.md | 4 ++++ inst/README.md | 8 +++++++- 5 files changed, 39 insertions(+), 16 deletions(-)
Title: Zero-Inflated Poisson Hidden (Semi-)Markov Models
Description: Fit zero-inflated Poisson hidden (semi-)Markov models with or without covariates by directly maximizing the log likelihood function. 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 1.0.1 dated 2017-01-15 and 1.0.2 dated 2017-01-27
DESCRIPTION | 10 MD5 | 18 - NAMESPACE | 2 R/RcppExports.R | 10 R/hmmsim2.R |only R/hsmmsim2.R |only R/package.R | 4 man/hmmsim2.Rd |only man/hsmmsim2.Rd |only man/package-ziphsmm.Rd | 4 src/RcppExports.cpp | 225 +++++++------ src/rcpparma_hello_world.cpp | 737 +++++++++++++++++++++++++++++++++++++++++-- 12 files changed, 879 insertions(+), 131 deletions(-)
Title: Forecasting Using Smoothing Functions
Description: The set of smoothing functions used for time series analysis and in forecasting.
Currently the package includes exponential smoothing models and SARIMA in state-space
form + several simulation functions.
Author: Ivan Svetunkov [aut, cre] (Research Associate at Lancaster Centre for
Forecasting, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>
Diff between smooth versions 1.5.2 dated 2016-12-18 and 1.6.0 dated 2017-01-27
DESCRIPTION | 8 MD5 | 74 +-- NAMESPACE | 7 NEWS | 23 + R/autoces.R | 19 R/autossarima.R | 54 +- R/ces.R | 301 +++++++++------ R/error-measures.R | 38 + R/es.R | 744 ++++++++++++++++++++++---------------- R/ges.R | 272 ++++++++----- R/iss.R | 10 R/methods.R | 26 - R/simes.R | 2 R/sma.R | 36 - R/ssarima.R | 297 +++++++++------ R/ssfunctions.R | 544 +++++++++++++++++---------- R/stepwise.R |only build/vignette.rds |binary inst/doc/ces.html | 83 ++-- inst/doc/es.html | 70 +-- inst/doc/ges.html | 38 - inst/doc/simulate.html | 72 +-- inst/doc/sma.html | 8 inst/doc/smooth-Documentation.pdf |binary inst/doc/smooth.html | 4 inst/doc/ssarima.html | 44 +- man/autoces.Rd | 23 - man/autossarima.Rd | 15 man/ces.Rd | 13 man/error-measures.Rd | 15 man/es.Rd | 12 man/ges.Rd | 17 man/ssarima.Rd | 17 man/stepwise.Rd |only src/ssgeneralfun.cpp | 32 + tests/testthat/test_ces.R | 8 tests/testthat/test_es.R | 18 tests/testthat/test_ges.R | 6 tests/testthat/test_ssarima.R | 6 39 files changed, 1837 insertions(+), 1119 deletions(-)
Title: A Method to Download Department of Education College Scorecard
Data
Description: A method to download Department of Education College
Scorecard data using the public API
<https://collegescorecard.ed.gov/data/documentation/>. It is based on
the 'dplyr' model of piped commands to select and filter data in a
single chained function call. An API key from the U.S. Department of
Education is required.
Author: Benjamin Skinner [aut, cre]
Maintainer: Benjamin Skinner <b.skinner@vanderbilt.edu>
Diff between rscorecard versions 0.3.1 dated 2017-01-14 and 0.3.5 dated 2017-01-27
DESCRIPTION | 18 ++++++++------- LICENSE | 2 - MD5 | 14 +++++------ NEWS.md | 10 ++++++++ R/api_convert.R | 10 ++++++++ R/filter.R | 5 ++-- inst/doc/introduction.html | 47 ++++++++++++++++++++------------------- tests/testthat/test-filter.R | 51 +++++++++++++++++++++++++++++++++++++------ 8 files changed, 110 insertions(+), 47 deletions(-)
Title: Goodness of Fit Tests for High-Dimensional Linear Regression
Models
Description: Performs goodness of fits tests for both high and low-dimensional linear models.
It can test for a variety of model misspecifications including nonlinearity and heteroscedasticity.
In addition one can test the significance of potentially large groups of variables, and also
produce p-values for the significance of individual variables in high-dimensional linear
regression.
Author: Rajen Shah [aut, cre],
Peter Buhlmann [aut]
Maintainer: Rajen Shah <r.shah@statslab.cam.ac.uk>
Diff between RPtests versions 0.1.2 dated 2016-11-07 and 0.1.3 dated 2017-01-27
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/RPtest.R | 53 ++++++++++++++++++++++++++++++++++------------------- R/resid_gen.R | 5 +++-- man/RPtest.Rd | 10 ++++++++-- 5 files changed, 52 insertions(+), 30 deletions(-)
Title: Power/Sample Size Calculation for Mediation Analysis
Description: Functions to
calculate power and sample size for testing
(1) mediation effects;
(2) the slope in a simple linear regression;
(3) odds ratio in a simple logistic regression;
(4) mean change for longitudinal study with 2 time points;
(5) interaction effect in 2-way ANOVA; and
(6) the slope in a simple Poisson regression.
Author: Weiliang Qiu <stwxq@channing.harvard.edu>
Maintainer: Weiliang Qiu <stwxq@channing.harvard.edu>
Diff between powerMediation versions 0.2.4 dated 2015-05-08 and 0.2.6 dated 2017-01-27
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 37 +++++++++++++++++++++++++++++++++++++ R/powerMediation.R | 24 ++++++++++++++---------- man/minEffect.SLR.Rd | 5 +++-- man/power.SLR.Rd | 5 +++-- man/powerMediation.Sobel.Rd | 6 +----- man/ss.SLR.Rd | 5 +++-- man/ssMediation.Sobel.Rd | 6 +----- 9 files changed, 74 insertions(+), 38 deletions(-)
More information about powerMediation at CRAN
Permanent link
Title: L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation
in GLMs and in the Cox Model
Description: Fitting possibly high dimensional penalized
regression models. The penalty structure can be any combination
of an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a
positivity constraint on the regression coefficients. The
supported regression models are linear, logistic and Poisson
regression and the Cox Proportional Hazards model.
Cross-validation routines allow optimization of the tuning
parameters.
Author: Jelle Goeman, Rosa Meijer, Nimisha Chaturvedi, Matthew Lueder
Maintainer: Jelle Goeman <j.j.goeman@lumc.nl>
Diff between penalized versions 0.9-47 dated 2016-05-27 and 0.9-49 dated 2017-01-27
.Rinstignore |only ChangeLog | 7 DESCRIPTION | 15 MD5 | 71 - NAMESPACE | 48 R/Brent.R | 298 ++-- R/breslow.R | 142 +- R/checkinput.R | 656 +++++----- R/contrasts.R | 68 - R/core.R | 3065 ++++++++++++++++++++++-------------------------- R/cox.R | 369 ++--- R/cvl.R | 274 ++-- R/linear.R | 120 - R/logit.R | 116 - R/onattach.R | 6 R/penalized.R | 322 ++--- R/penfit.R | 175 +- R/plotpath.R | 92 - R/poisson.R | 110 - README |only build/vignette.rds |binary inst/CITATION | 56 inst/doc/penalized.R | 700 +++++----- inst/doc/penalized.Rnw | 1100 ++++++++--------- man/breslow.Rd | 100 - man/contrasts.Rd | 120 - man/cvl.Rd | 272 ++-- man/nki70.Rd | 62 man/penalized.Rd | 196 +-- man/penfit.Rd | 142 +- man/plotpath.Rd | 74 - man/predict.Rd | 80 - src |only vignettes/penalized.Rnw | 1100 ++++++++--------- vignettes/penalized.bib | 354 ++--- 35 files changed, 5069 insertions(+), 5241 deletions(-)
Title: Tools to Work with Mixture Components
Description: A collection of tools implemented to facilitate the analysis of the components of a finite mixture distributions. The package has some functions to generate random samples coming from a finite mixture. The package provides a C++ implementation for the construction of a hierarchy over the components of a given finite mixture.
Author: Marc Comas-Cufí [aut, cre],
Josep Antoni Martín-Fernández [aut],
Glòria Mateu-Figueras [aut]
Maintainer: Marc Comas-Cufí <mcomas@imae.udg.edu>
Diff between mixpack versions 0.3.4 dated 2015-12-08 and 0.3.6 dated 2017-01-27
DESCRIPTION | 11 MD5 | 57 +-- NAMESPACE | 34 +- R/RcppExports.R | 2 R/coda.R | 86 ++--- R/combining_partitions.R | 485 +++++++++++++++---------------- R/mixpack-package.r | 10 R/mixpack.R | 4 R/mixture_function.R | 7 R/zzz.R | 6 README.md | 28 + build |only inst |only man/clr_coordinates.Rd | 30 - man/clr_mixnorm.Rd | 46 +- man/cluster_partition.Rd | 34 +- man/dmixnorm.Rd | 56 +-- man/dmixnorm_solution.Rd | 52 +-- man/get_hierarchical_partition.Rd | 66 ++-- man/get_random_hierarchical_partition.Rd | 30 - man/ilr_basis.Rd | 30 - man/ilr_coordinates.Rd | 30 - man/merge_components.Rd | 44 +- man/merge_step.Rd | 66 ++-- man/mixpack.Rd | 22 - man/rmixnorm.Rd | 102 +++--- man/rmixnorm_solution.Rd | 52 +-- src/RcppExports.cpp | 114 +++---- src/merging_components.cpp | 27 + vignettes |only 30 files changed, 783 insertions(+), 748 deletions(-)
Title: The MBESS R Package
Description: Implements methods that useful in designing research studies and analyzing data, with
particular emphasis on methods that are developed for or used within the behavioral,
educational, and social sciences (broadly defined). That being said, many of the methods
implemented within MBESS are applicable to a wide variety of disciplines. MBESS has a
suite of functions for a variety of related topics, such as effect sizes, confidence intervals
for effect sizes (including standardized effect sizes and noncentral effect sizes), sample size
planning (from the accuracy in parameter estimation [AIPE], power analytic, equivalence, and
minimum-risk point estimation perspectives), mediation analysis, various properties of
distributions, and a variety of utility functions. MBESS (pronounced 'em-bes') was originally
an acronym for 'Methods for the Behavioral, Educational, and Social Sciences,' but at this
point MBESS contains methods applicable and used in a wide variety of fields and is an
orphan acronym, in the sense that what was an acronym is now literally its name. MBESS has
greatly benefited from others, see <http://nd.edu/~kkelley/site/MBESS.html> for a detailed
list of those that have contributed and other details.
Author: Ken Kelley [aut, cre]
Maintainer: Ken Kelley <kkelley@nd.edu>
Diff between MBESS versions 4.1.0 dated 2016-09-23 and 4.2.0 dated 2017-01-27
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/mediation.R | 18 ++++++------------ 3 files changed, 13 insertions(+), 19 deletions(-)
Title: Add Even More Interactivity to Interactive Charts
Description: Like package 'manipulate' does for static graphics, this package
helps to easily add controls like sliders, pickers, checkboxes, etc. that
can be used to modify the input data or the parameters of an interactive
chart created with package 'htmlwidgets'.
Author: Francois Guillem [aut, cre],
RTE [cph],
JJ Allaire [ctb]
Maintainer: Francois Guillem <francois.guillem@rte-france.com>
Diff between manipulateWidget versions 0.5.0 dated 2017-01-19 and 0.5.1 dated 2017-01-27
DESCRIPTION | 12 +++++++----- MD5 | 22 +++++++++++----------- NAMESPACE | 13 ++++++++++--- NEWS.md | 12 ++++++++++++ R/controls.R | 20 ++++++++++---------- R/controlsUtils.R | 15 ++++++++++++--- R/manipulateWidget.R | 18 +++++++++--------- R/mwControlsUI.R | 20 ++++++++++++-------- R/mwServer.R | 32 +++++++++++++++++--------------- R/mwUI.R | 33 ++++++++++++++++++--------------- R/zzz.R | 7 +++---- man/mwUI.Rd | 7 ++++++- 12 files changed, 127 insertions(+), 84 deletions(-)
More information about manipulateWidget at CRAN
Permanent link
Title: Landsat 8 Imagery Rescaled to Reflectance, Radiance and/or
Temperature
Description: Functions for converted Landsat 8 multispectral satellite imagery
rescaled to the top of atmosphere (TOA) reflectance, radiance
and/or at satellite brightness temperature using radiometric
rescaling coefficients provided in the metadata file (MTL file).
Author: Alexandre dos Santos
Maintainer: Alexandre dos Santos <alexandre.santos@cas.ifmt.edu.br>
Diff between landsat8 versions 0.1-9 dated 2015-07-26 and 0.1-10 dated 2017-01-27
DESCRIPTION | 15 ++++++++------- MD5 | 12 ++++++------ R/land8tools.R | 2 +- man/radconv.Rd | 2 +- man/reflconv.Rd | 2 +- man/reflconvS.Rd | 2 +- man/tempconv.Rd | 2 +- 7 files changed, 19 insertions(+), 18 deletions(-)
Title: Global Summary Daily Weather Data in R
Description: Provides automated downloading, parsing, cleaning, unit conversion
and formatting of Global Surface Summary of the Day (GSOD) weather data from
the from the USA National Climatic Data Center (NCDC) for use in R. All
units are converted from from United States Customary System (USCS) units to
International System of Units (SI). Stations may be individually checked for
number of missing days defined by the user, where stations with too many
missing observations are omitted. Only stations with valid reported latitude
and longitude values are permitted in the final data. Additional useful
variables, saturation vapour pressure (es), actual vapour pressure (ea) and
relative humidity are calculated from the original data and included in the
final data set. The resulting data include station identification
information, state, country, latitude, longitude, elevation, weather
observations and associated flags. Data may be automatically saved to disk.
File output may be returned as a comma-separated values (CSV) or GeoPackage
(GPKG) file. Additional data are included with this R package: a list of
elevation values for stations between -60 and 60 degrees latitude derived
from the Shuttle Radar Topography Measuring Mission (SRTM). For information
on the GSOD data from NCDC, please see the GSOD readme.txt file available
from, <http://www1.ncdc.noaa.gov/pub/data/gsod/readme.txt>.
Author: Adam Sparks [aut, cre],
Tomislav Hengl [aut],
Andrew Nelson [aut]
Maintainer: Adam Sparks <adamhsparks@gmail.com>
Diff between GSODR versions 1.0.0 dated 2017-01-19 and 1.0.1 dated 2017-01-27
DESCRIPTION | 11 - MD5 | 67 +++--- NEWS.md | 9 R/GSODR.R | 93 +++++++- R/data.R | 57 +++-- R/get_GSOD.R | 45 ++-- R/get_station_list.R | 4 R/nearest_stations.R | 14 - R/reformat_GSOD.R | 6 README.md | 27 +- build/vignette.rds |binary inst/doc/GSODR.Rmd | 5 inst/doc/GSODR.html | 5 inst/doc/Specified_stations_for_a_range_of_years.Rmd | 17 - inst/doc/Specified_stations_for_a_range_of_years.html | 19 - inst/doc/Working_with_spatial_and_climate_data.R |only inst/doc/Working_with_spatial_and_climate_data.Rmd | 88 +++++--- inst/doc/Working_with_spatial_and_climate_data.html | 82 ++++--- inst/paper/paper.bib | 35 --- inst/paper/paper.md | 187 +----------------- inst/paper/paper.pdf |only man/GSODR.Rd | 93 +++++++- man/SRTM_GSOD_elevation.Rd | 42 ++-- man/country_list.Rd | 13 - man/get_GSOD.Rd | 44 ++-- man/get_station_list.Rd | 4 man/nearest_stations.Rd | 14 - man/reformat_GSOD.Rd | 6 tests/testthat/test-get_GSOD.R | 59 ++--- tests/testthat/test-get_station_list.R |only tests/testthat/test-process_gz.R | 1 vignettes/GSODR.Rmd | 5 vignettes/GSODR.md | 7 vignettes/Specified_stations_for_a_range_of_years.Rmd | 17 - vignettes/Specified_stations_for_a_range_of_years.md |only vignettes/Working_with_spatial_and_climate_data.Rmd | 88 +++++--- vignettes/Working_with_spatial_and_climate_data.md |only 37 files changed, 588 insertions(+), 576 deletions(-)
Title: Extreme Value Statistics and Quantile Estimation
Description: Code to fit, plot and compare several (extreme value)
distribution functions. Can also compute (truncated) distribution quantile estimates and
draw a plot with return periods on a linear scale.
Author: Berry Boessenkool
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between extremeStat versions 0.6.0 dated 2016-12-13 and 1.3.0 dated 2017-01-27
extremeStat-0.6.0/extremeStat/R/distLextremePlot.R |only extremeStat-0.6.0/extremeStat/R/distLgof.R |only extremeStat-0.6.0/extremeStat/R/distLgofPlot.R |only extremeStat-0.6.0/extremeStat/R/distLplot.R |only extremeStat-0.6.0/extremeStat/R/distLprint.R |only extremeStat-0.6.0/extremeStat/man/distLextremePlot.Rd |only extremeStat-0.6.0/extremeStat/man/distLgof.Rd |only extremeStat-0.6.0/extremeStat/man/distLgofPlot.Rd |only extremeStat-0.6.0/extremeStat/man/distLplot.Rd |only extremeStat-0.6.0/extremeStat/man/distLprint.Rd |only extremeStat-1.3.0/extremeStat/DESCRIPTION | 15 extremeStat-1.3.0/extremeStat/MD5 | 76 + extremeStat-1.3.0/extremeStat/NAMESPACE | 12 extremeStat-1.3.0/extremeStat/NEWS | 40 extremeStat-1.3.0/extremeStat/R/deprecated.R |only extremeStat-1.3.0/extremeStat/R/distLexBoot.R | 170 ++-- extremeStat-1.3.0/extremeStat/R/distLextreme.R | 228 ++--- extremeStat-1.3.0/extremeStat/R/distLfit.R | 452 ++++++----- extremeStat-1.3.0/extremeStat/R/distLquantile.R | 356 ++++---- extremeStat-1.3.0/extremeStat/R/distLweights.R |only extremeStat-1.3.0/extremeStat/R/extremeStat-package.R | 175 ++-- extremeStat-1.3.0/extremeStat/R/plotLexBoot.R |only extremeStat-1.3.0/extremeStat/R/plotLextreme.R |only extremeStat-1.3.0/extremeStat/R/plotLfit.R |only extremeStat-1.3.0/extremeStat/R/plotLquantile.R |only extremeStat-1.3.0/extremeStat/R/plotLweights.R |only extremeStat-1.3.0/extremeStat/R/printL.R |only extremeStat-1.3.0/extremeStat/R/q_gpd.R | 228 +++-- extremeStat-1.3.0/extremeStat/R/q_weighted.R |only extremeStat-1.3.0/extremeStat/data/weightp.rda |only extremeStat-1.3.0/extremeStat/inst/doc/extremeStat.R | 96 +- extremeStat-1.3.0/extremeStat/inst/doc/extremeStat.Rmd | 184 ++-- extremeStat-1.3.0/extremeStat/inst/doc/extremeStat.html | 229 ++--- extremeStat-1.3.0/extremeStat/man/annMax.Rd | 58 - extremeStat-1.3.0/extremeStat/man/distLexBoot.Rd | 140 +-- extremeStat-1.3.0/extremeStat/man/distLextreme.Rd | 193 ++-- extremeStat-1.3.0/extremeStat/man/distLfit.Rd | 246 +++-- extremeStat-1.3.0/extremeStat/man/distLquantile.Rd | 420 +++++----- extremeStat-1.3.0/extremeStat/man/distLweights.Rd |only extremeStat-1.3.0/extremeStat/man/extremeStat-deprecated.Rd |only extremeStat-1.3.0/extremeStat/man/extremeStat.Rd | 135 +-- extremeStat-1.3.0/extremeStat/man/plotLexBoot.Rd |only extremeStat-1.3.0/extremeStat/man/plotLextreme.Rd |only extremeStat-1.3.0/extremeStat/man/plotLfit.Rd |only extremeStat-1.3.0/extremeStat/man/plotLquantile.Rd |only extremeStat-1.3.0/extremeStat/man/plotLweights.Rd |only extremeStat-1.3.0/extremeStat/man/printL.Rd |only extremeStat-1.3.0/extremeStat/man/q_gpd.Rd | 423 +++++----- extremeStat-1.3.0/extremeStat/man/q_weighted.Rd |only extremeStat-1.3.0/extremeStat/man/weightp.Rd |only extremeStat-1.3.0/extremeStat/tests/testthat/test-fit.R |only extremeStat-1.3.0/extremeStat/tests/testthat/test-gof.R |only extremeStat-1.3.0/extremeStat/tests/testthat/test-quantile.R | 175 +++- extremeStat-1.3.0/extremeStat/vignettes/extremeStat.Rmd | 184 ++-- extremeStat-1.3.0/extremeStat/vignettes/qq.Rdata |binary 55 files changed, 2401 insertions(+), 1834 deletions(-)
Title: Epidemiological Tool for Contact Tracing
Description: Routines for epidemiological contact tracing
and visualisation of network of contacts.
Author: Maria Noremark [aut],
Stefan Widgren [aut, cre]
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between EpiContactTrace versions 0.9.1 dated 2015-07-03 and 0.10.0 dated 2017-01-27
DESCRIPTION | 10 MD5 | 51 +- NAMESPACE | 2 NEWS | 16 R/report.r | 811 +++++++++++++++++------------------- R/trace.r | 58 +- R/tree.r | 8 man/ContactTrace-class.Rd | 3 man/Contacts-class.Rd | 4 man/EpiContactTrace-package.Rd | 4 man/InDegree-methods.Rd | 2 man/IngoingContactChain-methods.Rd | 2 man/NetworkStructure-methods.Rd | 2 man/NetworkSummary-methods.Rd | 2 man/OutDegree-methods.Rd | 2 man/OutgoingContactChain-methods.Rd | 3 man/Report-methods.Rd | 4 man/ReportObject.Rd | 2 man/ShortestPaths-methods.Rd | 2 man/Trace.Rd | 18 man/build_tree.Rd | 2 man/is_wholenumber.Rd |only man/plot-methods.Rd | 2 man/position_tree.Rd | 8 man/show-methods.Rd | 2 man/transfers.Rd | 4 src/trace.cpp | 198 ++++---- 27 files changed, 637 insertions(+), 585 deletions(-)
More information about EpiContactTrace at CRAN
Permanent link
Title: Integrative Analysis of Omics Data in Terms of Network,
Evolution and Ontology
Description: The focus of the dnet is to make sense of omics data (such as gene expression and mutations) from different angles including: integration with molecular networks, enrichments using ontologies, and relevance to gene evolutionary ages. Integration is achieved to identify a gene subnetwork from the whole gene network whose nodes/genes are labelled with informative data (such as the significant levels of differential expression or survival risks). To help make sense of identified gene networks, enrichment analysis is also supported using a wide variety of pre-compiled ontologies and phylostratific gene age information in major organisms including: human, mouse, rat, chicken, C.elegans, fruit fly, zebrafish and arabidopsis. Add-on functionalities are supports for calculating semantic similarity between ontology terms (and between genes) and for calculating network affinity based on random walk; both can be done via high-performance parallel computing.
Author: Hai Fang and Julian Gough
Maintainer: Hai Fang <hfang@well.ox.ac.uk>
Diff between dnet versions 1.0.9 dated 2016-05-31 and 1.0.10 dated 2017-01-27
DESCRIPTION | 15 ++--- MD5 | 110 +++++++++++++++++++-------------------- NAMESPACE | 2 R/dCheckParallel.r | 12 ++-- R/dDAGgeneSim.r | 2 R/dDAGtermSim.r | 2 R/dPvalAggregate.r | 25 +++++++- R/dRWR.r | 2 R/dRWRcontact.r | 2 R/dRWRpipeline.r | 2 data/TCGA_mutations.RData |binary data/ig.HPPA.RData |binary data/org.Hs.egHPPA.RData |binary inst/NEWS | 12 ++++ inst/staticdocs/INSTALLATIONs.md | 18 +++--- man/dBUMfit.Rd | 2 man/dBUMscore.Rd | 2 man/dCheckParallel.Rd | 12 ++-- man/dCommSignif.Rd | 2 man/dContrast.Rd | 2 man/dDAGancestor.Rd | 2 man/dDAGannotate.Rd | 2 man/dDAGgeneSim.Rd | 16 ++--- man/dDAGinduce.Rd | 2 man/dDAGlevel.Rd | 2 man/dDAGreverse.Rd | 2 man/dDAGroot.Rd | 2 man/dDAGtermSim.Rd | 16 ++--- man/dDAGtip.Rd | 2 man/dEnricher.Rd | 2 man/dEnricherView.Rd | 2 man/dFDRscore.Rd | 2 man/dFunArgs.Rd | 2 man/dGSEA.Rd | 2 man/dGSEAview.Rd | 2 man/dGSEAwrite.Rd | 2 man/dNetConfidence.Rd | 2 man/dNetFind.Rd | 2 man/dNetInduce.Rd | 2 man/dNetPipeline.Rd | 2 man/dNetReorder.Rd | 2 man/dPvalAggregate.Rd | 29 +++++++--- man/dRDataLoader.Rd | 2 man/dRWR.Rd | 12 +--- man/dRWRcontact.Rd | 12 +--- man/dRWRpipeline.Rd | 12 +--- man/dSVDsignif.Rd | 2 man/visBoxplotAdv.Rd | 2 man/visDAG.Rd | 2 man/visGSEA.Rd | 2 man/visNet.Rd | 2 man/visNetAnimate.Rd | 2 man/visNetArc.Rd | 4 - man/visNetCircle.Rd | 8 +- man/visNetMul.Rd | 2 man/visNetReorder.Rd | 2 56 files changed, 212 insertions(+), 177 deletions(-)
Title: Create Compact Hash Digests of R Objects
Description: Implementation of a function 'digest()' for the creation
of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256',
'crc32', 'xxhash' and 'murmurhash' algorithms) permitting easy comparison of R
language objects, as well as a function 'hmac()' to create hash-based
message authentication code. Please note that this package is not meant to
be deployed for cryptographic purposes for which more comprehensive (and
widely tested) libraries such as 'OpenSSL' should be used.
Author: Dirk Eddelbuettel <edd@debian.org> with contributions
by Antoine Lucas, Jarek Tuszynski, Henrik Bengtsson, Simon Urbanek,
Mario Frasca, Bryan Lewis, Murray Stokely, Hannes Muehleisen,
Duncan Murdoch, Jim Hester, Wush Wu, Qiang Kou, Thierry Onkelinx,
Michel Lang and Viliam Simko.
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between digest versions 0.6.11 dated 2017-01-03 and 0.6.12 dated 2017-01-27
ChangeLog | 21 ++++++ DESCRIPTION | 8 +- MD5 | 14 ++-- NAMESPACE | 2 R/sha1.R | 164 ++++++++++++++++++++++++++++++++++++++++------------- inst/doc/sha1.html | 4 - man/sha1.rd | 49 ++++++++++----- tests/sha1Test.R | 11 ++- 8 files changed, 202 insertions(+), 71 deletions(-)
Title: Manipulate DESCRIPTION Files
Description: Tools to read, write, create, and manipulate DESCRIPTION files.
It is intended for packages that create or manipulate other packages.
Author: Gábor Csárdi [aut, cre],
Kirill Müller [aut]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between desc versions 1.0.1 dated 2016-09-22 and 1.1.0 dated 2017-01-27
DESCRIPTION | 19 +- MD5 | 158 ++++++++++++-------- NAMESPACE | 22 ++ NEWS.md | 9 + R/assertions.R | 141 +++++++++++++++++ R/authors-at-r.R | 35 +++- R/collate.R | 6 R/deps.R | 20 ++ R/description.R | 308 ++++++++++++++++++++++++++++++++++++--- R/non-oo-api.R | 205 +++++++++++++++++++++++++ R/package-archives.R |only R/remotes.R |only R/str.R | 17 +- R/syntax_checks.R | 10 + R/urls.R |only R/utils.R | 7 R/version.R |only inst/DESCRIPTION | 6 inst/NEWS.md | 9 + inst/README.Rmd | 8 - inst/README.md | 38 ++-- man/check_encoding.Rd | 1 man/check_field.Rd | 1 man/cran_ascii_fields.Rd | 1 man/cran_valid_fields.Rd | 1 man/dep_types.Rd | 1 man/desc.Rd |only man/desc_add_author.Rd | 7 man/desc_add_me.Rd | 8 - man/desc_add_remotes.Rd |only man/desc_add_role.Rd | 7 man/desc_add_to_collate.Rd | 7 man/desc_add_urls.Rd |only man/desc_bump_version.Rd |only man/desc_change_maintainer.Rd | 7 man/desc_clear_remotes.Rd |only man/desc_clear_urls.Rd |only man/desc_del.Rd | 11 - man/desc_del_author.Rd | 7 man/desc_del_collate.Rd | 9 - man/desc_del_dep.Rd | 11 - man/desc_del_deps.Rd | 11 - man/desc_del_from_collate.Rd | 7 man/desc_del_remotes.Rd |only man/desc_del_role.Rd | 7 man/desc_del_urls.Rd |only man/desc_fields.Rd | 11 - man/desc_get.Rd | 16 +- man/desc_get_author.Rd | 7 man/desc_get_authors.Rd | 7 man/desc_get_collate.Rd | 7 man/desc_get_deps.Rd | 11 - man/desc_get_maintainer.Rd | 7 man/desc_get_or_fail.Rd |only man/desc_get_remotes.Rd |only man/desc_get_urls.Rd |only man/desc_get_version.Rd |only man/desc_has_dep.Rd |only man/desc_has_fields.Rd | 10 - man/desc_normalize.Rd | 7 man/desc_print.Rd | 7 man/desc_reformat_fields.Rd | 7 man/desc_reorder_fields.Rd | 7 man/desc_set.Rd | 10 - man/desc_set_authors.Rd | 7 man/desc_set_collate.Rd | 9 - man/desc_set_dep.Rd | 11 - man/desc_set_deps.Rd | 9 - man/desc_set_remotes.Rd |only man/desc_set_urls.Rd |only man/desc_set_version.Rd |only man/desc_to_latex.Rd | 7 man/desc_validate.Rd | 7 man/description.Rd | 164 +++++++++++++++++++- tests/testthat/D1 | 4 tests/testthat/D2 | 3 tests/testthat/D4 |only tests/testthat/files/DESCRIPTION | 4 tests/testthat/fixtures |only tests/testthat/helper.R |only tests/testthat/test-archives.R |only tests/testthat/test-authors.R | 24 +++ tests/testthat/test-create.R | 20 ++ tests/testthat/test-deps.R | 39 ++++ tests/testthat/test-desc.R |only tests/testthat/test-non-oo.R | 18 +- tests/testthat/test-queries.R | 27 +++ tests/testthat/test-remotes.R |only tests/testthat/test-urls.R |only tests/testthat/test-utils.R | 2 tests/testthat/test-versions.R |only 91 files changed, 1324 insertions(+), 267 deletions(-)
Title: Co-Occurrence Network
Description: Read and preprocess fasta format data, and construct the co-occurrence network for downstream analyses. This R package is to construct the co-occurrence network with the algorithm developed by Du (2008) <DOI:10.1101/gr.6969007>. It could be used to transform the data with high-dimension, such as DNA or protein sequence, into co-occurrence networks. Co-occurrence network could not only capture the co-variation pattern between variables, such as the positions in DNA or protein sequences, but also reflect the relationship between samples. Although it is originally used in DNA and protein sequences, it could be also used to other kinds of data, such as RNA, SNP, etc.
Author: Yuanqiang Zou <jerrytsou2001@gmail.com>, Yousong Peng <pys2013@hnu.edu.cn> and Taijiao Jiang <taijiao@moon.ibp.ac.cn>
Maintainer: Yuanqiang Zou <jerrytsou2001@gmail.com>
Diff between cooccurNet versions 0.1.5 dated 2017-01-11 and 0.1.6 dated 2017-01-27
DESCRIPTION | 6 - MD5 | 14 +-- R/cooccurrence.R | 168 +++++++++++++++++++++++++++---------- R/datapreprocess.R | 4 R/gennetwork.R | 38 ++++---- R/networkpvalue.R | 34 ++++--- inst/doc/Extending-cooccurNet.html | 46 +++++----- inst/extdata/changeLog/changeLog | 4 8 files changed, 206 insertions(+), 108 deletions(-)
Title: Wrapper Algorithm for All Relevant Feature Selection
Description: An all relevant feature selection wrapper algorithm.
It finds relevant features by comparing original attributes'
importance with importance achievable at random, estimated
using their permuted copies.
Author: Miron Bartosz Kursa [aut, cre],
Witold Remigiusz Rudnicki [aut]
Maintainer: Miron Bartosz Kursa <M.Kursa@icm.edu.pl>
Diff between Boruta versions 5.1.0 dated 2016-08-16 and 5.2.0 dated 2017-01-27
DESCRIPTION | 16 ++++++++-------- MD5 | 17 +++++++++-------- NAMESPACE | 2 ++ R/Boruta.R | 47 ++++++++++++++++++++++++++++++----------------- R/tools.R | 39 ++++++++++++++++++++++++++++++++++++--- inst/NEWS | 12 +++++++++++- man/Boruta.Rd | 8 ++++---- man/getFormulae.Rd |only man/plot.Boruta.Rd | 2 +- man/plotImpHistory.Rd | 2 +- 10 files changed, 102 insertions(+), 43 deletions(-)
Title: Bayesian Quantile Regression
Description: Bayesian quantile regression using the asymmetric Laplace distribution, both continuous as well as binary dependent variables are supported. The package consists of implementations of the methods of Yu & Moyeed (2001) <doi:10.1016/S0167-7152(01)00124-9>, Benoit & Van den Poel (2012) <doi:10.1002/jae.1216> and Al-Hamzawi, Yu & Benoit (2012) <doi:10.1177/1471082X1101200304>. To speed up the calculations, the Markov Chain Monte Carlo core of all algorithms is programmed in Fortran and called from R.
Author: Dries F. Benoit, Rahim Al-Hamzawi, Keming Yu, Dirk Van den Poel
Maintainer: Dries F. Benoit <Dries.Benoit@UGent.be>
Diff between bayesQR versions 2.2 dated 2014-04-17 and 2.3 dated 2017-01-27
DESCRIPTION | 15 + MD5 | 40 ++--- NAMESPACE | 8 + R/bayesQR.r | 42 +++-- R/bayesQR.single.r | 340 +++++++++++++++++++++++++------------------ R/plot.bayesQR.r | 247 +++++++++++++++++-------------- R/predict.bayesQR.r | 69 ++++---- R/print.bayesQR.r |only R/print.bayesQR.summary.r | 75 +++++---- R/prior.r | 257 ++++++++++++++++---------------- R/summary.bayesQR.r | 30 +-- R/summary.bayesQR.single.r | 94 ++++++----- inst |only man/Churn.Rd | 6 man/bayesQR.Rd | 28 ++- man/plot.bayesQR.Rd | 7 man/predict.bayesQR.Rd | 9 - man/print.bayesQR.Rd | 27 +-- man/print.bayesQR.summary.Rd |only man/summary.bayesQR.Rd | 3 src/QRc_AL_mcmc.f95 | 6 src/QRc_mcmc.f95 | 26 +-- src/setseed.f95 |only 23 files changed, 738 insertions(+), 591 deletions(-)
Title: Verbose Assertions for Tabular Data (Data.frames and
Data.tables)
Description: Simple, flexible, assertions on data.frame or data.table objects with verbose output for vetting. While other assertion packages apply towards more general use-cases, assertable is tailored towards tabular data. It includes functions to check variable names and values, whether the dataset contains all combinations of a given set of unique identifiers, and whether it is a certain length. In addition, assertable includes utility functions to check the existence of target files and to efficiently import multiple tabular data files into one data.table.
Author: Grant Nguyen
Maintainer: Grant Nguyen <gngu@uw.edu>
Diff between assertable versions 0.1.0 dated 2017-01-14 and 0.2.0 dated 2017-01-27
DESCRIPTION | 6 ++-- MD5 | 35 +++++++++++++------------- R/assert_colnames.R | 1 R/assert_ids.R | 30 ++++++++++++++++++---- R/assert_nrows.R | 1 R/check_files.R | 49 ++++++++++++++++++++++++++++--------- R/import_files.R | 28 +++++++++++++++++++-- README.md |only build/vignette.rds |binary inst/doc/assertion_template.Rmd | 4 +-- inst/doc/assertion_template.html | 27 ++++++++++++-------- inst/doc/data_assertion_intro.html | 8 ++++-- inst/doc/file_assertion_intro.Rmd | 2 - inst/doc/file_assertion_intro.html | 32 ++++++++++++------------ man/assert_ids.Rd | 6 ++-- man/check_files.Rd | 10 +++++-- man/import_files.Rd | 10 +++++-- vignettes/assertion_template.Rmd | 4 +-- vignettes/file_assertion_intro.Rmd | 2 - 19 files changed, 173 insertions(+), 82 deletions(-)