Title: Penn World Table (Version 9.x)
Description: The Penn World Table 9.x (<http://www.ggdc.net/pwt/>) provides information
on relative levels of income, output, inputs, and productivity
for 182 countries between 1950 and 2017.
Author: Achim Zeileis [aut, cre] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between pwt9 versions 9.0-0 dated 2017-01-04 and 9.1-0 dated 2019-06-12
DESCRIPTION | 19 ++++++++++--------- MD5 | 14 ++++++++------ NEWS | 8 ++++++++ data/datalist | 1 + data/pwt9.0.rda |binary data/pwt9.1.rda |only inst/CITATION | 33 ++++++++++----------------------- man/pwt9.0.Rd | 8 +++++--- man/pwt9.1.Rd |only 9 files changed, 42 insertions(+), 41 deletions(-)
Title: API Wrapper for Quandl.com
Description: Functions for interacting directly with the Quandl API to offer data in a number of formats usable in R, downloading a zip with all data from a Quandl database, and the ability to search. This R package uses the Quandl API. For more information go to <https://www.quandl.com/docs/api>. For more help on the package itself go to <https://www.quandl.com/help/r>.
Author: Dave Dotson [cre],
Raymond McTaggart [aut],
Gergely Daroczi [aut],
Clement Leung [aut],
Quandl Inc. [cph]
Maintainer: Dave Dotson <dave@quandl.com>
Diff between Quandl versions 2.9.1 dated 2018-08-14 and 2.10.0 dated 2019-06-12
ChangeLog | 6 ++ DESCRIPTION | 22 ++++---- MD5 | 18 ++++--- NAMESPACE | 2 R/Quandldatatable.R | 64 ++++++++++++++++++++++++++ man/Quandl.datatable.bulk_download_to_file.Rd |only man/Quandl.datatable.bulk_download_url.Rd |only tests/testthat/test-api.r | 2 tests/testthat/test-datatable-helper.r | 24 +++++++++ tests/testthat/test-datatable.r | 43 +++++++++++++++++ tests/testthat/test-get.r | 4 - 11 files changed, 164 insertions(+), 21 deletions(-)
Title: Load Census TIGER/Line Shapefiles
Description: Download TIGER/Line shapefiles from the United States Census Bureau
(<https://www.census.gov/geo/maps-data/data/tiger-line.html>) and load into R as 'SpatialDataFrame' or 'sf' objects.
Author: Kyle Walker [aut, cre],
Bob Rudis [ctb]
Maintainer: Kyle Walker <kyle.walker@tcu.edu>
Diff between tigris versions 0.7 dated 2018-04-14 and 0.8.2 dated 2019-06-12
DESCRIPTION | 11 LICENSE | 4 MD5 | 157 +- NAMESPACE | 147 +- NEWS | 108 - R/enumeration_units.R | 1902 ++++++++++++++--------------- R/fips_codes.R | 50 R/geocode.R | 340 ++--- R/helpers.R | 1254 +++++++++---------- R/landmarks.R | 236 +-- R/legislative.R | 489 +++---- R/metro_areas.R | 647 ++++----- R/national.R | 333 ++--- R/native.R | 613 ++++----- R/places.R | 265 ++-- R/pumas.R | 177 +- R/states.R | 369 ++--- R/tigris-package.R | 114 - R/transportation.R | 524 ++++--- R/utils.R | 296 ++-- R/water.R | 367 ++--- R/zzz.R | 90 - README.md | 166 +- man/address_ranges.Rd |only man/alaska_native_regional_corporations.Rd | 68 - man/append_geoid.Rd | 68 - man/area_water.Rd | 92 - man/block_groups.Rd | 135 +- man/blocks.Rd | 136 +- man/call_geolocator.Rd | 52 man/call_geolocator_latlon.Rd | 52 man/coastline.Rd | 106 - man/combined_statistical_areas.Rd | 72 - man/congressional_districts.Rd | 113 - man/core_based_statistical_areas.Rd | 78 - man/counties.Rd | 164 +- man/county_subdivisions.Rd | 107 - man/divisions.Rd | 76 - man/filter_place.Rd | 48 man/filter_state.Rd | 48 man/fips_codes.Rd | 64 man/geo_join.Rd | 115 - man/grep_place.Rd | 44 man/grep_state.Rd | 44 man/is_tigris.Rd | 34 man/landmarks.Rd | 89 - man/linear_water.Rd | 96 - man/list_counties.Rd | 38 man/list_places.Rd | 42 man/list_states.Rd | 42 man/lookup_code.Rd | 94 - man/metro_divisions.Rd | 55 man/military.Rd | 67 - man/nation.Rd | 76 - man/native_areas.Rd | 108 - man/new_england.Rd | 107 - man/places.Rd | 114 - man/primary_roads.Rd | 79 - man/primary_secondary_roads.Rd | 95 - man/pumas.Rd | 124 - man/rails.Rd | 77 - man/rbind_tigris.Rd | 70 - man/regions.Rd | 76 - man/roads.Rd | 131 + man/school_districts.Rd | 122 - man/state_legislative_districts.Rd | 104 - man/states.Rd | 106 - man/tigris-exports.Rd | 30 man/tigris.Rd | 58 man/tigris_cache_dir.Rd | 58 man/tigris_type.Rd | 36 man/tracts.Rd | 152 +- man/tribal_block_groups.Rd | 106 - man/tribal_census_tracts.Rd | 96 - man/tribal_subdivisions_national.Rd | 86 - man/urban_areas.Rd | 64 man/voting_districts.Rd | 82 - man/zctas.Rd | 131 + tests/testthat.R | 8 tests/testthat/test_lookup_helper.R | 26 80 files changed, 6711 insertions(+), 6509 deletions(-)
Title: Load US Census Boundary and Attribute Data as 'tidyverse' and
'sf'-Ready Data Frames
Description: An integrated R interface to the decennial US Census and American Community Survey APIs and
the US Census Bureau's geographic boundary files. Allows R users to return Census and ACS data as
tidyverse-ready data frames, and optionally returns a list-column with feature geometry for many
geographies.
Author: Kyle Walker [aut, cre],
Kris Eberwein [ctb],
Matt Herman [ctb]
Maintainer: Kyle Walker <kyle.walker@tcu.edu>
Diff between tidycensus versions 0.9 dated 2019-01-09 and 0.9.2 dated 2019-06-12
DESCRIPTION | 15 +++--- MD5 | 20 ++++---- NAMESPACE | 1 R/acs.R | 125 +++++++++++++++++++++++++++++++++++++++++---------- R/census.R | 76 +++++++++++++++++++++++++------ R/helpers.R | 4 + R/search_variables.R | 2 R/significance.R |only R/utils.R | 25 ++++------ README.md | 2 man/get_acs.Rd | 4 - man/significance.Rd |only 12 files changed, 202 insertions(+), 72 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 4.5.1 dated 2019-05-17 and 4.6.0 dated 2019-06-12
DESCRIPTION | 8 - MD5 | 12 +- R/ss.aipe.cv.R | 170 +++++++++++++++++++++--------------------- R/ss.aipe.cv.sensitivity.R | 136 +++++++++++++++++---------------- R/ss.aipe.sm.R | 148 +++++++++++++++++++----------------- man/ss.aipe.cv.Rd | 2 man/ss.aipe.cv.sensitivity.Rd | 3 7 files changed, 246 insertions(+), 233 deletions(-)
Title: Diversity Dynamics using Fossil Sampling Data
Description: Functions to describe sampling and diversity dynamics of fossil occurrence datasets (e.g. from the Paleobiology Database). The package includes methods to calculate range- and occurrence-based metrics of taxonomic richness, extinction and origination rates, along with traditional sampling measures. A powerful subsampling tool is also included that implements frequently used sampling standardization methods in a multiple bin-framework. The plotting of time series and the occurrence data can be simplified by the functions incorporated in the package, as well other calculations, such as environmental affinities and extinction selectivity testing. Details can be found in: Kocsis, A.T.; Reddin, C.J.; Alroy, J. and Kiessling, W. (2019) <doi:10.1101/423780>.
Author: Adam T. Kocsis, John Alroy, Carl J. Reddin, Wolfgang Kiessling
Maintainer: Adam T. Kocsis <adam.t.kocsis@gmail.com>
Diff between divDyn versions 0.7.1 dated 2019-02-19 and 0.8.0 dated 2019-06-12
divDyn-0.7.1/divDyn/data/bins.RData |only divDyn-0.7.1/divDyn/man/bins.Rd |only divDyn-0.8.0/divDyn/DESCRIPTION | 10 divDyn-0.8.0/divDyn/MD5 | 105 divDyn-0.8.0/divDyn/NAMESPACE | 4 divDyn-0.8.0/divDyn/R/affinity.R | 66 divDyn-0.8.0/divDyn/R/cleaning.R | 74 divDyn-0.8.0/divDyn/R/data.R | 11 divDyn-0.8.0/divDyn/R/diversityDynamics.r | 433 ++-- divDyn-0.8.0/divDyn/R/fadLad.R | 110 - divDyn-0.8.0/divDyn/R/georange.R | 10 divDyn-0.8.0/divDyn/R/indices.R | 2 divDyn-0.8.0/divDyn/R/modeltab.R | 36 divDyn-0.8.0/divDyn/R/plotting.R | 134 + divDyn-0.8.0/divDyn/R/rateSplit.R | 28 divDyn-0.8.0/divDyn/R/repmatch.R |only divDyn-0.8.0/divDyn/R/sampstat.R | 97 divDyn-0.8.0/divDyn/R/singletons.R | 38 divDyn-0.8.0/divDyn/R/slice.R |only divDyn-0.8.0/divDyn/R/subsample.R | 3159 ++++++++++++++++-------------- divDyn-0.8.0/divDyn/R/subtrials.R |only divDyn-0.8.0/divDyn/R/tabinate.R | 72 divDyn-0.8.0/divDyn/R/utility.R |only divDyn-0.8.0/divDyn/R/zzz.R | 2 divDyn-0.8.0/divDyn/build/vignette.rds |binary divDyn-0.8.0/divDyn/data/corals.RData |binary divDyn-0.8.0/divDyn/data/keys.RData |binary divDyn-0.8.0/divDyn/data/stages.RData |binary divDyn-0.8.0/divDyn/data/stratkeys.RData |binary divDyn-0.8.0/divDyn/data/tens.RData |only divDyn-0.8.0/divDyn/inst/CITATION | 12 divDyn-0.8.0/divDyn/inst/NEWS | 36 divDyn-0.8.0/divDyn/inst/doc/handout.R | 1507 +++++++------- divDyn-0.8.0/divDyn/inst/doc/handout.Rmd | 248 +- divDyn-0.8.0/divDyn/inst/doc/handout.pdf |binary divDyn-0.8.0/divDyn/man/affinity.Rd | 14 divDyn-0.8.0/divDyn/man/binstat.Rd | 19 divDyn-0.8.0/divDyn/man/cleansp.Rd | 4 divDyn-0.8.0/divDyn/man/corals.Rd | 2 divDyn-0.8.0/divDyn/man/divDyn.Rd | 28 divDyn-0.8.0/divDyn/man/fadlad.Rd | 31 divDyn-0.8.0/divDyn/man/georange.Rd | 4 divDyn-0.8.0/divDyn/man/indices.Rd | 2 divDyn-0.8.0/divDyn/man/keys.Rd | 3 divDyn-0.8.0/divDyn/man/modeltab.Rd | 5 divDyn-0.8.0/divDyn/man/omit.Rd | 18 divDyn-0.8.0/divDyn/man/ratesplit.Rd | 6 divDyn-0.8.0/divDyn/man/repmatch.Rd |only divDyn-0.8.0/divDyn/man/slice.Rd |only divDyn-0.8.0/divDyn/man/stratkeys.Rd | 2 divDyn-0.8.0/divDyn/man/subsample.Rd | 41 divDyn-0.8.0/divDyn/man/subtrial.Rd | 30 divDyn-0.8.0/divDyn/man/sumstat.Rd | 4 divDyn-0.8.0/divDyn/man/survivors.Rd | 4 divDyn-0.8.0/divDyn/man/tabinate.Rd | 6 divDyn-0.8.0/divDyn/man/tens.Rd |only divDyn-0.8.0/divDyn/man/tsbars.Rd |only divDyn-0.8.0/divDyn/man/tsplot.Rd | 4 divDyn-0.8.0/divDyn/vignettes/handout.Rmd | 248 +- 59 files changed, 3623 insertions(+), 3046 deletions(-)
Title: Modeling Over Dispersed Binomial Outcome Data Using BMD and ABD
Description: Contains Probability Mass Functions, Cumulative Mass Functions, Negative Log Likelihood value, parameter estimation and modeling data using Binomial Mixture Distributions (BMD) (Manoj et al (2013) <doi:10.5539/ijsp.v2n2p24>) and Alternate Binomial Distributions (ABD) (Paul (1985) <doi:10.1080/03610928508828990>).
Author: Amalan Mahendran [aut, cre] (<https://orcid.org/0000-0002-0643-9052>),
Pushpakanthie Wijekoon [aut, ctb]
(<https://orcid.org/0000-0003-4242-1017>)
Maintainer: Amalan Mahendran <amalan0595@gmail.com>
Diff between fitODBOD versions 1.3.0 dated 2019-05-07 and 1.4.0 dated 2019-06-12
DESCRIPTION | 11 ++++++----- MD5 | 32 ++++++++++++++++---------------- R/AddBin.R | 2 +- R/Data.R | 6 +++--- R/Gamma.R | 2 +- R/Gbeta1.R | 6 +++--- R/Kumaraswamy.R | 11 ++++------- man/Epidemic_Cold.Rd | 4 ++-- man/EstMLEGammaBin.Rd | 2 +- man/EstMLEMcGBB.Rd | 4 ++-- man/NegLLKumBin.Rd | 1 + man/dKumBin.Rd | 4 +--- man/fitAddBin.Rd | 2 +- man/fitBin.Rd | 2 +- man/fitKumBin.Rd | 2 +- man/fitMcGBB.Rd | 2 +- man/pKumBin.Rd | 4 +--- 17 files changed, 46 insertions(+), 51 deletions(-)
Title: Vehicular Emissions Inventories
Description: Elaboration of vehicular emissions inventories,
consisting in four stages, pre-processing activity data, preparing
emissions factors, estimating the emissions and post-processing of emissions
in maps and databases. More details in Ibarra-Espinosa et al (2018) <doi:10.5194/gmd-11-2209-2018>.
Before using VEIN you need to know the vehicular composition of your study area, in other words,
the combination of of type of vehicles, size and fuel of the fleet. Then, it is recommended to
start with the function inventory to create a structure of directories and template scripts.
Author: Sergio Ibarra-Espinosa [aut, cre]
(<https://orcid.org/0000-0002-3162-1905>),
Daniel Schuch [ctb] (<https://orcid.org/0000-0001-5977-4519>)
Maintainer: Sergio Ibarra-Espinosa <sergio.ibarra@usp.br>
Diff between vein versions 0.7.0 dated 2019-03-26 and 0.7.8 dated 2019-06-12
vein-0.7.0/vein/man/emis_wrf.Rd |only vein-0.7.8/vein/DESCRIPTION | 10 vein-0.7.8/vein/MD5 | 148 +++--- vein-0.7.8/vein/NAMESPACE | 16 vein-0.7.8/vein/NEWS.md | 53 ++ vein-0.7.8/vein/R/EmissionFactors.R | 16 vein-0.7.8/vein/R/Emissions.R | 16 vein-0.7.8/vein/R/Speed.R | 16 vein-0.7.8/vein/R/Vehicles.R | 17 vein-0.7.8/vein/R/add_polid.R |only vein-0.7.8/vein/R/age.R | 6 vein-0.7.8/vein/R/age_hdv.R | 33 - vein-0.7.8/vein/R/age_ldv.R | 10 vein-0.7.8/vein/R/age_moto.R | 17 vein-0.7.8/vein/R/cold_mileage.R | 4 vein-0.7.8/vein/R/ef_cetesb.R | 21 vein-0.7.8/vein/R/ef_china.R |only vein-0.7.8/vein/R/ef_evap.R | 87 +++ vein-0.7.8/vein/R/ef_fun.R | 2 vein-0.7.8/vein/R/ef_hdv_speed.R | 9 vein-0.7.8/vein/R/ef_ldv_speed.R | 18 vein-0.7.8/vein/R/ef_nitro.R | 213 ++++++++- vein-0.7.8/vein/R/emis.R | 13 vein-0.7.8/vein/R/emis_chem.R |only vein-0.7.8/vein/R/emis_dist.R | 7 vein-0.7.8/vein/R/emis_grid.R | 21 vein-0.7.8/vein/R/emis_hot_td.R | 141 ++++-- vein-0.7.8/vein/R/emis_to_streets.R |only vein-0.7.8/vein/R/emis_wrf.R | 232 +++++----- vein-0.7.8/vein/R/fe2015.R | 3 vein-0.7.8/vein/R/grid_emis.R | 1 vein-0.7.8/vein/R/long_to_wide.R |only vein-0.7.8/vein/R/make_grid.R | 5 vein-0.7.8/vein/R/pollutants.R |only vein-0.7.8/vein/R/remove_units.R |only vein-0.7.8/vein/R/speciate.R | 74 ++- vein-0.7.8/vein/R/split_emis.R | 26 + vein-0.7.8/vein/R/sysdata.rda |binary vein-0.7.8/vein/R/to_latex.R |only vein-0.7.8/vein/R/wide_to_long.R |only vein-0.7.8/vein/data/fe2015.rda |binary vein-0.7.8/vein/data/pollutants.rda |only vein-0.7.8/vein/demo/VEIN.R | 2 vein-0.7.8/vein/inst/README.Rmd | 76 ++- vein-0.7.8/vein/inst/README.html | 306 +++++++++++--- vein-0.7.8/vein/man/add_polid.Rd |only vein-0.7.8/vein/man/age.Rd | 5 vein-0.7.8/vein/man/age_hdv.Rd | 2 vein-0.7.8/vein/man/age_ldv.Rd | 2 vein-0.7.8/vein/man/age_moto.Rd | 2 vein-0.7.8/vein/man/ef_cetesb.Rd | 17 vein-0.7.8/vein/man/ef_china.Rd |only vein-0.7.8/vein/man/ef_evap.Rd | 17 vein-0.7.8/vein/man/ef_fun.Rd | 2 vein-0.7.8/vein/man/ef_hdv_speed.Rd | 5 vein-0.7.8/vein/man/ef_ldv_speed.Rd | 13 vein-0.7.8/vein/man/ef_nitro.Rd | 41 + vein-0.7.8/vein/man/emis.Rd | 17 vein-0.7.8/vein/man/emis_chem.Rd |only vein-0.7.8/vein/man/emis_dist.Rd | 2 vein-0.7.8/vein/man/emis_grid.Rd | 6 vein-0.7.8/vein/man/emis_hot_td.Rd | 45 +- vein-0.7.8/vein/man/emis_to_streets.Rd |only vein-0.7.8/vein/man/emis_wrf-deprecated.Rd |only vein-0.7.8/vein/man/fe2015.Rd | 3 vein-0.7.8/vein/man/long_to_wide.Rd |only vein-0.7.8/vein/man/make_grid.Rd | 5 vein-0.7.8/vein/man/pollutants.Rd |only vein-0.7.8/vein/man/remove_units.Rd |only vein-0.7.8/vein/man/speciate.Rd | 9 vein-0.7.8/vein/man/split_emis.Rd | 10 vein-0.7.8/vein/man/to_latex.Rd |only vein-0.7.8/vein/man/vein-deprecated.Rd | 13 vein-0.7.8/vein/man/wide_to_long.Rd |only vein-0.7.8/vein/tests/testthat/test-EmissionFactors.R | 2 vein-0.7.8/vein/tests/testthat/test-EmissionFactorsList.R | 2 vein-0.7.8/vein/tests/testthat/test-Emissions.R | 2 vein-0.7.8/vein/tests/testthat/test-EmissionsArray.R | 2 vein-0.7.8/vein/tests/testthat/test-ef_cetesb.R | 2 vein-0.7.8/vein/tests/testthat/test-ef_china.R |only vein-0.7.8/vein/tests/testthat/test-ef_fun.R | 2 vein-0.7.8/vein/tests/testthat/test-ef_ldv_speed.R | 111 +++++ vein-0.7.8/vein/tests/testthat/test-ef_nitro.R | 2 vein-0.7.8/vein/tests/testthat/test-emis.R | 2 vein-0.7.8/vein/tests/testthat/test-emis_chem.R |only vein-0.7.8/vein/tests/testthat/test-emis_post.R | 2 vein-0.7.8/vein/tests/testthat/test-split_emis.R |only 87 files changed, 1406 insertions(+), 558 deletions(-)
Title: The Generalized DINA Model Framework
Description: A set of psychometric tools for cognitive diagnosis modeling based on the generalized deterministic inputs, noisy and gate (G-DINA) model by de la Torre (2011) <DOI:10.1007/s11336-011-9207-7> and its extensions, including the sequential G-DINA model by Ma and de la Torre (2016) <DOI:10.1111/bmsp.12070> for polytomous responses, and the polytomous G-DINA model by Chen and de la Torre <DOI:10.1177/0146621613479818> for polytomous attributes. Joint attribute distribution can be independent, saturated, higher-order, loglinear smoothed or structured. Q-matrix validation, item and model fit statistics, model comparison at test and item level and differential item functioning can also be conducted. A graphical user interface is also provided.
Author: Wenchao Ma [aut, cre, cph],
Jimmy de la Torre [aut, cph],
Miguel Sorrel [ctb],
Zhehan Jiang [ctb]
Maintainer: Wenchao Ma <wenchao.ma@ua.edu>
Diff between GDINA versions 2.5.2 dated 2019-05-10 and 2.6.0 dated 2019-06-12
DESCRIPTION | 8 +- MD5 | 18 +++--- NEWS.md | 8 ++ R/M2.R | 133 ++++++++++++++++++++++++++++++--------------- R/SingleGroup_Estimation.R | 2 R/extract.R | 1 README.md | 15 ++--- inst/CITATION | 4 - inst/doc/GDINA.html | 4 - man/modelfit.Rd | 16 ++--- 10 files changed, 130 insertions(+), 79 deletions(-)
Title: Tools for Survey Statistics in Educational Assessment
Description: Contains tools for survey statistics (especially in educational
assessment) for datasets with replication designs (jackknife,
bootstrap, replicate weights; see Kolenikov, 2010;
Pfefferman & Rao, 2009a, 2009b, <doi:10.1016/S0169-7161(09)70003-3>,
<doi:10.1016/S0169-7161(09)70037-9>); Shao, 1996,
<doi:10.1080/02331889708802523>).
Descriptive statistics, linear and logistic regression,
path models for manifest variables with measurement error
correction and two-level hierarchical regressions for weighted
samples are included. Statistical inference can be conducted for
multiply imputed datasets and nested multiply imputed datasets
and is in particularly suited for the analysis of plausible values
(for details see George, Oberwimmer & Itzlinger-Bruneforth, 2016;
Bruneforth, Oberwimmer & Robitzsch, 2016; Robitzsch, Pham &
Yanagida, 2016; <doi:10.17888/fdb-demo:bistE813I-16a>).
The package development was supported by BIFIE (Federal Institute for
Educational Research, Innovation and Development of the Austrian
School System; Salzburg, Austria).
Author: BIFIE [aut], Alexander Robitzsch [aut, cre],
Konrad Oberwimmer [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between BIFIEsurvey versions 3.2-25 dated 2019-04-16 and 3.3-12 dated 2019-06-12
BIFIEsurvey-3.2-25/BIFIEsurvey/R/bifie_NMIcombine_results.R |only BIFIEsurvey-3.2-25/BIFIEsurvey/R/bifie_NMIcombine_results_extract_parameters.R |only BIFIEsurvey-3.2-25/BIFIEsurvey/R/bifie_data_pv_vars_create_datlist.R |only BIFIEsurvey-3.2-25/BIFIEsurvey/R/bifie_lavaan_survey_NMIcombine.R |only BIFIEsurvey-3.2-25/BIFIEsurvey/R/bifie_lavaan_survey_combine_fit_measures.R |only BIFIEsurvey-3.2-25/BIFIEsurvey/R/bifie_nmi_error_message.R |only BIFIEsurvey-3.2-25/BIFIEsurvey/inst/include |only BIFIEsurvey-3.3-12/BIFIEsurvey/DESCRIPTION | 10 - BIFIEsurvey-3.3-12/BIFIEsurvey/MD5 | 56 ++++------ BIFIEsurvey-3.3-12/BIFIEsurvey/R/BIFIE.cdata.select.R | 29 +---- BIFIEsurvey-3.3-12/BIFIEsurvey/R/BIFIE.data.R | 15 +- BIFIEsurvey-3.3-12/BIFIEsurvey/R/BIFIE.data.jack.R | 24 +--- BIFIEsurvey-3.3-12/BIFIEsurvey/R/BIFIE.hist.R | 22 +-- BIFIEsurvey-3.3-12/BIFIEsurvey/R/BIFIE.lavaan.survey.R | 12 +- BIFIEsurvey-3.3-12/BIFIEsurvey/R/BIFIE.logistreg.R | 9 - BIFIEsurvey-3.3-12/BIFIEsurvey/R/BIFIE.survey.R | 5 BIFIEsurvey-3.3-12/BIFIEsurvey/R/BIFIE.univar.R | 42 ++----- BIFIEsurvey-3.3-12/BIFIEsurvey/R/BIFIE_NMIcombine_results.R |only BIFIEsurvey-3.3-12/BIFIEsurvey/R/BIFIE_NMIcombine_results_extract_parameters.R |only BIFIEsurvey-3.3-12/BIFIEsurvey/R/BIFIE_create_pseudogroup.R | 12 +- BIFIEsurvey-3.3-12/BIFIEsurvey/R/BIFIE_data_pv_vars_create_datlist.R |only BIFIEsurvey-3.3-12/BIFIEsurvey/R/BIFIE_lavaan_survey_NMIcombine.R |only BIFIEsurvey-3.3-12/BIFIEsurvey/R/BIFIE_lavaan_survey_combine_fit_measures.R |only BIFIEsurvey-3.3-12/BIFIEsurvey/R/BIFIE_nmi_error_message.R |only BIFIEsurvey-3.3-12/BIFIEsurvey/R/BIFIE_table_multiple_groupings.R | 5 BIFIEsurvey-3.3-12/BIFIEsurvey/R/RcppExports.R | 2 BIFIEsurvey-3.3-12/BIFIEsurvey/R/bifie_data_select_pv_vars.R | 6 - BIFIEsurvey-3.3-12/BIFIEsurvey/README.md | 4 BIFIEsurvey-3.3-12/BIFIEsurvey/build/partial.rdb |binary BIFIEsurvey-3.3-12/BIFIEsurvey/inst/NEWS | 11 + BIFIEsurvey-3.3-12/BIFIEsurvey/man/BIFIE.derivedParameters.Rd | 6 - BIFIEsurvey-3.3-12/BIFIEsurvey/man/BIFIE.lavaan.survey.Rd | 4 BIFIEsurvey-3.3-12/BIFIEsurvey/man/BIFIE.twolevelreg.Rd | 4 BIFIEsurvey-3.3-12/BIFIEsurvey/man/BIFIE.waldtest.Rd | 4 BIFIEsurvey-3.3-12/BIFIEsurvey/src/RcppExports.cpp | 2 35 files changed, 134 insertions(+), 150 deletions(-)
Title: An R Port of the 'ImageJ' Plugin 'Auto Threshold'
Description: Algorithms for automatically finding appropriate thresholds for
numerical data, with special functions for thresholding images. Provides the
'ImageJ' 'Auto Threshold' plugin functionality to R users. See
<http://imagej.net/Auto_Threshold> and Landini et al. (2017)
<DOI:10.1111/jmi.12474>.
Author: Rory Nolan [aut, cre, trl] (<https://orcid.org/0000-0002-5239-4043>),
Luis Alvarez [ctb] (<https://orcid.org/0000-0003-1316-1906>),
Sergi Padilla-Parra [ctb, ths]
(<https://orcid.org/0000-0002-8010-9481>),
Gabriel Landini [ctb, cph] (<https://orcid.org/0000-0002-9689-0989>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between autothresholdr versions 1.3.2 dated 2019-05-30 and 1.3.3 dated 2019-06-12
DESCRIPTION | 8 - MD5 | 34 +++---- NEWS.md | 76 +++++++++------- R/autothresholdr.R | 2 R/class_constructors.R | 10 +- R/stack_thresh.R | 32 +++---- R/thresh.R | 76 ++++++++++------ R/utils.R | 16 ++- inst/doc/finding-thresholds.html | 4 inst/doc/thresholding-image-stacks.html | 4 inst/doc/thresholding-images.html | 4 man/mean_stack_thresh.Rd | 10 +- man/med_stack_thresh.Rd | 10 +- tests/spelling.R | 9 + tests/testthat/test_auto_thresh_methods.R | 6 - tests/testthat/test_stack_thresh.R | 53 +++++++---- tests/testthat/test_thresh.R | 136 +++++++++++++++++++----------- tests/testthat/test_utils.R | 20 ++-- 18 files changed, 301 insertions(+), 209 deletions(-)
More information about autothresholdr at CRAN
Permanent link
Title: Statistical Framework to Define Subgroups in Complex Datasets
Description: High-dimensional datasets that do not exhibit a clear intrinsic clustered structure pose a challenge to conventional clustering algorithms. For this reason, we developed an unsupervised framework that helps scientists to better subgroup their datasets based on visual cues, please see Gao S, Mutter S, Casey A, Makinen V-P (2018) Numero: a statistical framework to define multivariable subgroups in complex population-based datasets, Int J Epidemiology, dyy113, <doi:10.1093/ije/dyy113>. The framework includes the necessary functions to construct a self-organizing map of the data, to evaluate the statistical significance of the observed data patterns, and to visualize the results.
Author: Song Gao [aut],
Stefan Mutter [aut],
Aaron E. Casey [aut],
Ville-Petteri Makinen [aut, cre]
Maintainer: Ville-Petteri Makinen <vpmakine@gmail.com>
Diff between Numero versions 1.1.1 dated 2018-11-24 and 1.2.0 dated 2019-06-12
Numero-1.1.1/Numero/inst/doc/NumeroGuide.R |only Numero-1.1.1/Numero/inst/doc/NumeroGuide.html |only Numero-1.1.1/Numero/inst/doc/NumeroGuide.rmd |only Numero-1.1.1/Numero/inst/extdata/README.txt |only Numero-1.1.1/Numero/inst/extdata/finndiane_dataset.txt |only Numero-1.1.1/Numero/src/koho.engine.histogram.cpp |only Numero-1.1.1/Numero/src/koho.enginebuffer.diffuse.cpp |only Numero-1.1.1/Numero/src/koho.trainer.euclidean.cpp |only Numero-1.1.1/Numero/vignettes/Numero.bib |only Numero-1.1.1/Numero/vignettes/NumeroGuide.rmd |only Numero-1.1.1/Numero/vignettes/apa-old-doi-prefix.csl |only Numero-1.1.1/Numero/vignettes/legumes.jpg |only Numero-1.1.1/Numero/vignettes/pipeline.svg |only Numero-1.1.1/Numero/vignettes/split.jpg |only Numero-1.1.1/Numero/vignettes/step1.jpg |only Numero-1.1.1/Numero/vignettes/step2.jpg |only Numero-1.1.1/Numero/vignettes/step3.jpg |only Numero-1.1.1/Numero/vignettes/step4.jpg |only Numero-1.1.1/Numero/vignettes/subgroups.svg |only Numero-1.1.1/Numero/vignettes/trainingColorings.svg |only Numero-1.2.0/Numero/DESCRIPTION | 11 Numero-1.2.0/Numero/MD5 | 180 ++++++------ Numero-1.2.0/Numero/NAMESPACE | 14 Numero-1.2.0/Numero/R/nroAggregate.R | 59 ++- Numero-1.2.0/Numero/R/nroColorize.R | 94 ++++-- Numero-1.2.0/Numero/R/nroDestratify.R |only Numero-1.2.0/Numero/R/nroImpute.R |only Numero-1.2.0/Numero/R/nroKmeans.R | 56 ++- Numero-1.2.0/Numero/R/nroKohonen.R | 32 +- Numero-1.2.0/Numero/R/nroLabel.R | 31 +- Numero-1.2.0/Numero/R/nroMatch.R | 59 ++- Numero-1.2.0/Numero/R/nroPair.R |only Numero-1.2.0/Numero/R/nroPermute.R | 144 ++++++--- Numero-1.2.0/Numero/R/nroPlot.R | 201 ++++++++----- Numero-1.2.0/Numero/R/nroPostprocess.R |only Numero-1.2.0/Numero/R/nroPreprocess.R | 252 +++++++++++------ Numero-1.2.0/Numero/R/nroPrune.R |only Numero-1.2.0/Numero/R/nroRcppMatrix.R |only Numero-1.2.0/Numero/R/nroSummary.R | 249 +++++++++------- Numero-1.2.0/Numero/R/nroTrain.R | 69 +++- Numero-1.2.0/Numero/R/numero.clean.R |only Numero-1.2.0/Numero/R/numero.create.R |only Numero-1.2.0/Numero/R/numero.evaluate.R |only Numero-1.2.0/Numero/R/numero.plot.R |only Numero-1.2.0/Numero/R/numero.prepare.R |only Numero-1.2.0/Numero/R/numero.quality.R |only Numero-1.2.0/Numero/R/numero.subgroup.R |only Numero-1.2.0/Numero/R/numero.summary.R |only Numero-1.2.0/Numero/README.md | 19 + Numero-1.2.0/Numero/build/vignette.rds |binary Numero-1.2.0/Numero/inst/doc/intro.R |only Numero-1.2.0/Numero/inst/doc/intro.html |only Numero-1.2.0/Numero/inst/doc/intro.rmd |only Numero-1.2.0/Numero/inst/extdata/finndiane.readme.txt |only Numero-1.2.0/Numero/inst/extdata/finndiane.txt |only Numero-1.2.0/Numero/man/nroAggregate.Rd | 66 +++- Numero-1.2.0/Numero/man/nroColorize.Rd | 87 ++++- Numero-1.2.0/Numero/man/nroDestratify.Rd |only Numero-1.2.0/Numero/man/nroImpute.Rd |only Numero-1.2.0/Numero/man/nroKmeans.Rd | 56 ++- Numero-1.2.0/Numero/man/nroKohonen.Rd | 41 ++ Numero-1.2.0/Numero/man/nroLabel.Rd | 58 +++ Numero-1.2.0/Numero/man/nroMatch.Rd | 80 +++-- Numero-1.2.0/Numero/man/nroPair.Rd |only Numero-1.2.0/Numero/man/nroPermute.Rd | 85 ++++- Numero-1.2.0/Numero/man/nroPlot.Rd | 79 ++++- Numero-1.2.0/Numero/man/nroPostprocess.Rd |only Numero-1.2.0/Numero/man/nroPreprocess.Rd | 63 +++- Numero-1.2.0/Numero/man/nroPrune.Rd |only Numero-1.2.0/Numero/man/nroRcppMatrix.Rd |only Numero-1.2.0/Numero/man/nroSummary.Rd | 64 +++- Numero-1.2.0/Numero/man/nroTrain.Rd | 62 +++- Numero-1.2.0/Numero/man/numero.clean.Rd |only Numero-1.2.0/Numero/man/numero.create.Rd |only Numero-1.2.0/Numero/man/numero.evaluate.Rd |only Numero-1.2.0/Numero/man/numero.plot.Rd |only Numero-1.2.0/Numero/man/numero.prepare.Rd |only Numero-1.2.0/Numero/man/numero.quality.Rd |only Numero-1.2.0/Numero/man/numero.subrgoup.Rd |only Numero-1.2.0/Numero/man/numero.summary.Rd |only Numero-1.2.0/Numero/src/Numero_init.c | 18 - Numero-1.2.0/Numero/src/abacus.destratify.cpp | 128 +++++--- Numero-1.2.0/Numero/src/abacus.h | 6 Numero-1.2.0/Numero/src/abacus.local.h | 3 Numero-1.2.0/Numero/src/abacus.matrix.column.cpp | 6 Numero-1.2.0/Numero/src/abacus.matrix.row.cpp | 4 Numero-1.2.0/Numero/src/abacus.statistic.cpp | 13 Numero-1.2.0/Numero/src/abacus.transform.cpp | 6 Numero-1.2.0/Numero/src/koho.engine.average.cpp | 21 + Numero-1.2.0/Numero/src/koho.engine.histograms.cpp |only Numero-1.2.0/Numero/src/koho.engine.insert.cpp | 8 Numero-1.2.0/Numero/src/koho.engine.shuffle.cpp | 25 - Numero-1.2.0/Numero/src/koho.enginebuffer.prepare.cpp | 40 +- Numero-1.2.0/Numero/src/koho.h | 43 ++ Numero-1.2.0/Numero/src/koho.local.h | 28 + Numero-1.2.0/Numero/src/koho.model.cpp | 4 Numero-1.2.0/Numero/src/koho.model.distances.cpp | 2 Numero-1.2.0/Numero/src/koho.model.train.cpp | 24 + Numero-1.2.0/Numero/src/koho.trainer.cpp | 13 Numero-1.2.0/Numero/src/koho.trainer.distance.cpp | 4 Numero-1.2.0/Numero/src/koho.trainer.distances.cpp | 12 Numero-1.2.0/Numero/src/koho.trainer.euclid.cpp |only Numero-1.2.0/Numero/src/koho.trainer.pearson.cpp |only Numero-1.2.0/Numero/src/koho.transformation.cpp | 51 +-- Numero-1.2.0/Numero/src/nro.h | 4 Numero-1.2.0/Numero/src/nro.matrix2reals.cpp | 11 Numero-1.2.0/Numero/src/nro.reals2topology.cpp | 8 Numero-1.2.0/Numero/src/nro.reals2vector.cpp | 6 Numero-1.2.0/Numero/src/nro.vector2reals.cpp | 7 Numero-1.2.0/Numero/src/nro.vector2sizes.cpp | 11 Numero-1.2.0/Numero/src/nro_destratify.cpp |only Numero-1.2.0/Numero/src/nro_diffuse.cpp | 14 Numero-1.2.0/Numero/src/nro_figure.cpp | 2 Numero-1.2.0/Numero/src/nro_impute.cpp |only Numero-1.2.0/Numero/src/nro_kohonen.cpp | 5 Numero-1.2.0/Numero/src/nro_label.cpp | 2 Numero-1.2.0/Numero/src/nro_match.cpp | 5 Numero-1.2.0/Numero/src/nro_pair.cpp |only Numero-1.2.0/Numero/src/nro_permute.cpp | 44 ++ Numero-1.2.0/Numero/src/nro_train.cpp | 35 +- Numero-1.2.0/Numero/vignettes/intro.rmd |only 121 files changed, 1934 insertions(+), 890 deletions(-)
Title: Creates and Manages Folder Functions for Portable Large-Scale R
Analysis
Description: If you find yourself working on multiple different projects in R, you'll want a
series of folders pointing to raw data, processed data, plot results, intermediate table
outputs, etc. This package makes it easier to do that by providing a quick and easy way
to create and use functions for project-level directories.
Author: Nathan C. Sheffield [aut, cre],
Michal Stolarczyk [ctb],
Vince Reuter [ctb]
Maintainer: Nathan C. Sheffield <nathan@code.databio.org>
Diff between folderfun versions 0.1.1 dated 2019-03-05 and 0.1.2 dated 2019-06-12
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 5 ++++- R/folderfun.R | 6 ++++-- inst/doc/intro.html | 4 ++-- tests/testthat/helper-all.R | 6 ++++++ tests/testthat/test_setff.R | 12 ++++++------ 7 files changed, 32 insertions(+), 21 deletions(-)
Title: Fit, Simulate and Diagnose Models for Network Evolution Based on
Exponential-Family Random Graph Models
Description: An integrated set of extensions to the 'ergm' package to analyze and simulate network evolution based on exponential-family random graph models (ERGM). 'tergm' is a part of the 'statnet' suite of packages for network analysis.
Author: Pavel N. Krivitsky [aut, cre] (<https://orcid.org/0000-0002-9101-3362>),
Mark S. Handcock [aut, ths],
David R. Hunter [ctb],
Steven M. Goodreau [ctb, ths],
Martina Morris [ctb, ths],
Nicole Bohme Carnegie [ctb],
Carter T. Butts [ctb],
Ayn Leslie-Cook [ctb],
Skye Bender-deMoll [ctb],
Li Wang [ctb],
Kirk Li [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between tergm versions 3.6.0 dated 2019-05-15 and 3.6.1 dated 2019-06-12
DESCRIPTION | 14 +++++++------- MD5 | 8 ++++---- inst/CITATION | 4 ++-- inst/NEWS.Rd | 10 ++++++++++ inst/doc/STERGM.pdf |binary 5 files changed, 23 insertions(+), 13 deletions(-)
Title: Stability Measures for Feature Selection
Description: An implementation of many measures for the assessment of the stability
of feature selection. Both simple measures and measures which take into account
the similarities between features are available, see Bommert et al. (2017) <doi:10.1155/2017/7907163>.
Author: Andrea Bommert [aut, cre]
Maintainer: Andrea Bommert <bommert@statistik.tu-dortmund.de>
Diff between stabm versions 1.0.0 dated 2019-02-22 and 1.1.0 dated 2019-06-12
stabm-1.0.0/stabm/man/stabilityZhang.Rd |only stabm-1.1.0/stabm/DESCRIPTION | 8 - stabm-1.1.0/stabm/MD5 | 62 +++++------ stabm-1.1.0/stabm/NAMESPACE | 4 stabm-1.1.0/stabm/R/documentation_stability.R | 3 stabm-1.1.0/stabm/R/list_stability_measures.R | 4 stabm-1.1.0/stabm/R/other_adjusted_measures.R | 2 stabm-1.1.0/stabm/R/stability.R | 11 + stabm-1.1.0/stabm/R/stability_functions_adjusted.R | 10 - stabm-1.1.0/stabm/R/stability_functions_corrected.R | 27 ++++ stabm-1.1.0/stabm/R/stability_functions_uncorrected.R | 24 ++++ stabm-1.1.0/stabm/R/unadjusted_measures.R | 41 +++++++ stabm-1.1.0/stabm/man/stabilityDavis.Rd | 3 stabm-1.1.0/stabm/man/stabilityDice.Rd | 3 stabm-1.1.0/stabm/man/stabilityDocumentation.Rd | 3 stabm-1.1.0/stabm/man/stabilityHamming.Rd |only stabm-1.1.0/stabm/man/stabilityIntersectionCount.Rd | 3 stabm-1.1.0/stabm/man/stabilityIntersectionGreedy.Rd | 3 stabm-1.1.0/stabm/man/stabilityIntersectionMBM.Rd | 3 stabm-1.1.0/stabm/man/stabilityIntersectionMean.Rd | 3 stabm-1.1.0/stabm/man/stabilityJaccard.Rd | 3 stabm-1.1.0/stabm/man/stabilityKappa.Rd | 3 stabm-1.1.0/stabm/man/stabilityLustgarten.Rd | 3 stabm-1.1.0/stabm/man/stabilityNogueira.Rd | 7 - stabm-1.1.0/stabm/man/stabilityNovovicova.Rd | 3 stabm-1.1.0/stabm/man/stabilityOchiai.Rd | 3 stabm-1.1.0/stabm/man/stabilityPhi.Rd | 3 stabm-1.1.0/stabm/man/stabilitySomol.Rd | 3 stabm-1.1.0/stabm/man/stabilityUnadjusted.Rd | 3 stabm-1.1.0/stabm/man/stabilityWald.Rd |only stabm-1.1.0/stabm/man/stabilityYu.Rd |only stabm-1.1.0/stabm/man/stabilityZucknick.Rd | 3 stabm-1.1.0/stabm/tests/testthat/test_stability_adjusted.R | 2 stabm-1.1.0/stabm/tests/testthat/test_stability_unadjusted.R | 19 ++- 34 files changed, 177 insertions(+), 95 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is
licensed under Apache License 2; previous releases were under licensed as
MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under
the GNU GPL version 2 or later, as is the rest of 'Rcpp'. Note that
Armadillo requires a fairly recent compiler; for the g++ family at least
version 4.6.* is required.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates and Binxiang Ni
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.9.400.3.0 dated 2019-05-11 and 0.9.500.2.0 dated 2019-06-12
RcppArmadillo-0.9.400.3.0/RcppArmadillo/inst/include/armadillo_bits/wrapper_arpack.hpp |only RcppArmadillo-0.9.400.3.0/RcppArmadillo/inst/include/armadillo_bits/wrapper_atlas.hpp |only RcppArmadillo-0.9.400.3.0/RcppArmadillo/inst/include/armadillo_bits/wrapper_blas.hpp |only RcppArmadillo-0.9.400.3.0/RcppArmadillo/inst/include/armadillo_bits/wrapper_lapack.hpp |only RcppArmadillo-0.9.400.3.0/RcppArmadillo/inst/include/armadillo_bits/wrapper_superlu.hpp |only RcppArmadillo-0.9.500.2.0/RcppArmadillo/ChangeLog | 22 RcppArmadillo-0.9.500.2.0/RcppArmadillo/DESCRIPTION | 8 RcppArmadillo-0.9.500.2.0/RcppArmadillo/MD5 | 82 - RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/NEWS.Rd | 21 RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/doc/RcppArmadillo-intro.pdf |binary RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/doc/RcppArmadillo-sparseMatrix.pdf |binary RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo | 12 RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/SpMat_meat.hpp | 2 RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/SpProxy.hpp | 44 + RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/SpSubview_meat.hpp | 434 ++-------- RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/arma_config.hpp | 7 RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/arma_version.hpp | 6 RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/auxlib_meat.hpp | 34 RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/compiler_setup.hpp | 54 - RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/config.hpp | 11 RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/config.hpp.cmake | 11 RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/debug.hpp | 1 RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/def_arpack.hpp | 62 + RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/def_blas.hpp | 40 RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/def_lapack.hpp | 272 ++++++ RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/diskio_meat.hpp | 40 RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_fft.hpp | 8 RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_fft2.hpp | 4 RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_normcdf.hpp | 6 RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_normpdf.hpp | 6 RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/fn_size.hpp | 70 + RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_solve_bones.hpp | 57 - RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/glue_solve_meat.hpp | 41 RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/op_cond_meat.hpp | 4 RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/op_misc_meat.hpp | 36 RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/op_pinv_meat.hpp | 44 - RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/sp_auxlib_bones.hpp | 28 RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/sp_auxlib_meat.hpp | 211 +++- RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/spglue_merge_bones.hpp |only RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/spglue_merge_meat.hpp |only RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/sympd_helper.hpp | 127 ++ RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/traits.hpp | 97 -- RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/translate_arpack.hpp |only RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/translate_atlas.hpp |only RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/translate_blas.hpp |only RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/translate_lapack.hpp |only RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/translate_superlu.hpp |only RcppArmadillo-0.9.500.2.0/RcppArmadillo/inst/include/armadillo_bits/typedef_elem.hpp | 45 - 48 files changed, 1263 insertions(+), 684 deletions(-)
Title: Process Map Token Replay Animation
Description: Provides animated process maps based on the 'procesmapR' package.
Cases stored in event logs created with with 'bupaR' S3 class eventlog() are
rendered as tokens (SVG shapes) and animated according to their occurrence
times on top of the process map. For rendering SVG animations ('SMIL') and the
'htmlwidget' package are used.
Author: Felix Mannhardt [aut, cre],
Gert Janssenswillen [ctb]
Maintainer: Felix Mannhardt <felix.mannhardt@sintef.no>
Diff between processanimateR versions 1.0.0 dated 2018-11-27 and 1.0.1 dated 2019-06-12
DESCRIPTION | 17 MD5 | 69 - NAMESPACE | 3 NEWS.md | 9 R/processanimateR.R | 144 +- README.md | 5 build/vignette.rds |binary inst/doc/use-external-data-to-change-tokens.html | 460 ++++---- inst/doc/use-shiny-selections.Rmd | 1 inst/doc/use-shiny-selections.html | 177 +-- inst/doc/use-timestamp-change-token-aes.R |only inst/doc/use-timestamp-change-token-aes.Rmd |only inst/doc/use-timestamp-change-token-aes.html |only inst/doc/use-token_scales.html | 462 ++++---- inst/doc/use-with-shiny.R | 2 inst/doc/use-with-shiny.Rmd | 2 inst/doc/use-with-shiny.html | 269 ++-- inst/htmlwidgets/lib/es6-promise |only inst/htmlwidgets/lib/fakesmil/smil.user.js | 15 inst/htmlwidgets/lib/leaflet/leaflet.css | 7 inst/htmlwidgets/lib/leaflet/leaflet.min.js | 2 inst/htmlwidgets/lib/leaflet/package-lock.json | 300 ----- inst/htmlwidgets/lib/leaflet/package.json | 4 inst/htmlwidgets/lib/modules/animation_playback_control.js | 18 inst/htmlwidgets/lib/modules/animation_renderer_graphviz.js | 56 - inst/htmlwidgets/lib/modules/animation_renderer_leaflet.js | 12 inst/htmlwidgets/lib/modules/animation_scales.js | 8 inst/htmlwidgets/lib/modules/animation_tokens.js | 162 +- inst/htmlwidgets/lib/svg-pan-zoom/svg-pan-zoom.min.js | 4 inst/htmlwidgets/lib/viz/full.render.js | 39 inst/htmlwidgets/lib/viz/viz.js | 664 ++++++------ inst/htmlwidgets/processanimateR.js | 24 inst/htmlwidgets/processanimateR.yaml | 12 man/animate_process.Rd | 48 man/figures/processanimateR-banner.png |binary vignettes/use-shiny-selections.Rmd | 1 vignettes/use-timestamp-change-token-aes.Rmd |only vignettes/use-with-shiny.Rmd | 2 38 files changed, 1524 insertions(+), 1474 deletions(-)
More information about processanimateR at CRAN
Permanent link
Title: Joint Frailty-Copula Models for Tumour Progression and Death in
Meta-Analysis
Description: Perform likelihood estimation and dynamic prediction under
joint frailty-copula models for tumour progression and death in meta-analysis.
A penalized likelihood method is employed for estimating model parameters, where the baseline hazard functions are modeled by smoothing splines.
The methods are applicable for meta-analytic data combining several studies.
The methods can analyze data having information on both terminal event time (e.g., time-to-death) and non-terminal event time (e.g., time-to-tumour progression).
See Emura et al. (2017) <doi:10.1177/0962280215604510> for likelihood estimation, and
Emura et al. (2018) <doi:10.1177/0962280216688032> for dynamic prediction.
Survival data from ovarian cancer patients are also available.
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between joint.Cox versions 3.2 dated 2019-05-16 and 3.3 dated 2019-06-12
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/splineCox.reg.R | 3 +-- man/joint.Cox-package.Rd | 4 ++-- man/splineCox.reg.Rd | 5 ++++- 5 files changed, 15 insertions(+), 13 deletions(-)
Title: A Swift, Versatile Phylogenomic and High-Throughput Sequencing
Simulator
Description: Simply and efficiently
simulates (i) variants from reference genomes and (ii) reads from both Illumina
<https://www.illumina.com/>
and Pacific Biosciences (PacBio) <https://www.pacb.com/> platforms.
It can either read reference genomes from FASTA files or simulate new ones.
Genomic variants can be simulated using summary statistics, phylogenies,
Variant Call Format (VCF) files, and coalescent simulations—the latter of which
can include selection, recombination, and demographic fluctuations.
'jackalope' can simulate single, paired-end, or mate-pair Illumina reads,
as well as PacBio reads.
These simulations include sequencing errors, mapping qualities, multiplexing,
and optical/polymerase chain reaction (PCR) duplicates.
Simulating Illumina sequencing is based on ART
by Huang et al. (2012) <doi:10.1093/bioinformatics/btr708>.
PacBio sequencing simulation is based on
SimLoRD by Stöcker et al. (2016) <doi:10.1093/bioinformatics/btw286>.
All outputs can be written to standard file formats.
Author: Lucas A. Nell [cph, aut, cre] (<https://orcid.org/0000-0003-3209-0517>)
Maintainer: Lucas A. Nell <lucas@lucasnell.com>
Diff between jackalope versions 0.1.0 dated 2019-06-04 and 0.1.1 dated 2019-06-12
DESCRIPTION | 6 +++--- MD5 | 31 ++++++++++++++++--------------- README.md | 1 + inst/CITATION |only inst/include/pcg/pcg_random.hpp | 16 ++++++++-------- src/RcppExports.cpp | 4 ++-- src/hts_illumina.h | 4 ++-- src/hts_pacbio.h | 4 ++-- src/io.h | 2 +- src/io_fasta.cpp | 2 +- src/io_vcf.cpp | 14 +++++++------- src/io_vcf.h | 2 +- src/mutator.h | 2 +- src/mutator_location.h | 2 +- src/seq_classes_access.cpp | 20 ++++++++++++++++++-- src/seq_classes_ref.h | 2 +- src/seq_classes_var.h | 3 +-- 17 files changed, 66 insertions(+), 49 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-04-28 1.0.6
2019-04-16 1.0.5
2019-03-13 1.0.4
2019-01-16 1.0.3
2019-01-15 1.0.2
2018-10-19 1.0.0
Title: Predicting Economic Variables using Dynamic Factor Models
Description: It contains the tools to implement dynamic factor models to forecast economic variables. The user will be able to construct pseudo real time vintages, use information criteria for determining the number of factors and shocks, estimate the model, and visualize results among other things.
Author: Daiane Marcolino de Mattos [aut, cre],
Pedro Costa Ferreira [aut],
Serge de Valk [aut],
Guilherme Branco Gomes [aut]
Maintainer: Daiane Marcolino de Mattos <daiane.mattos@fgv.br>
Diff between nowcasting versions 1.1.2 dated 2019-06-04 and 1.1.3 dated 2019-06-12
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/Bpanel.R | 13 ++++++++++--- R/method_2s.R | 4 +++- R/nowcast.R | 46 ++++++++++++++++++++++++++++++++++++++++++---- data/NYFED.rda |binary man/Bpanel.Rd | 4 ++++ 7 files changed, 69 insertions(+), 18 deletions(-)
Title: Time Your Codes
Description: Provides a 'timeR' class that makes timing codes easier. One can create 'timeR' objects and use them to record all timings, and extract recordings as data frame for later use.
Author: Yifu Yan
Maintainer: Yifu Yan <yanyifu94@hotmail.com>
Diff between timeR versions 1.0.0 dated 2019-01-25 and 1.1.0 dated 2019-06-12
DESCRIPTION | 10 MD5 | 21 - NAMESPACE | 2 NEWS.md |only R/timer_class.R | 152 +++++++----- R/timer_function.R | 4 README.md | 10 inst/doc/timer-quick-start.R | 8 inst/doc/timer-quick-start.Rmd | 8 inst/doc/timer-quick-start.html | 497 +++++++++++++++++++++++++++++----------- man/timeR.Rd | 48 ++- vignettes/timer-quick-start.Rmd | 8 12 files changed, 547 insertions(+), 221 deletions(-)
Title: Learning Interactions via Hierarchical Group-Lasso
Regularization
Description: Group-Lasso INTERaction-NET. Fits linear pairwise-interaction models that satisfy strong hierarchy: if an interaction coefficient is estimated to be nonzero, then its two associated main effects also have nonzero estimated coefficients. Accommodates categorical variables (factors) with arbitrary numbers of levels, continuous variables, and combinations thereof. Implements the machinery described in the paper "Learning interactions via hierarchical group-lasso regularization" (JCGS 2015, Volume 24, Issue 3). Michael Lim & Trevor Hastie (2015) <DOI:10.1080/10618600.2014.938812>.
Author: Michael Lim, Trevor Hastie
Maintainer: Michael Lim <michael626@gmail.com>
Diff between glinternet versions 1.0.8 dated 2018-06-15 and 1.0.9 dated 2019-06-12
DESCRIPTION | 8 +-- MD5 | 12 ++--- R/get_candidates.r | 106 ++++++++++++++++++++++++++++----------------------- R/glinternet.cv.r | 8 +-- R/glinternet.r | 39 ++++++++++++++++-- man/glinternet.Rd | 9 +++- man/glinternet.cv.Rd | 6 +- 7 files changed, 119 insertions(+), 69 deletions(-)
Title: Bayesian Variable Selection in High Dimensional Settings using
Nonlocal Priors
Description: Variable/Feature selection in high or ultra-high dimensional
settings has gained a lot of attention recently specially in cancer genomic
studies. This package provides a Bayesian approach to tackle this problem,
where it exploits mixture of point masses at zero and nonlocal priors to
improve the performance of variable selection and coefficient estimation.
product moment (pMOM) and product inverse moment (piMOM) nonlocal priors
are implemented and can be used for the analyses. This package performs
variable selection for binary response and survival time response datasets
which are widely used in biostatistic and bioinformatics community.
Benefiting from parallel computing ability, it reports necessary outcomes
of Bayesian variable selection such as Highest Posterior Probability Model
(HPPM), Median Probability Model (MPM) and posterior inclusion probability
for each of the covariates in the model. The option to use Bayesian Model
Averaging (BMA) is also part of this package that can be exploited for
predictive power measurements in real datasets.
Author: Amir Nikooienejad [aut, cre], Valen E. Johnson [ths]
Maintainer: Amir Nikooienejad <amir@stat.tamu.edu>
Diff between BVSNLP versions 1.1.5 dated 2018-05-17 and 1.1.8 dated 2019-06-12
DESCRIPTION | 6 +- MD5 | 20 ++++---- NAMESPACE | 3 - R/PreProcess.R | 132 ++++++++++++++++++++++++++++-------------------------- R/bvs.R | 92 +++++++++++++++---------------------- R/matprep.R |only R/predBMA.R | 31 +++++++++--- R/predmat.R |only R/zzz.R | 8 +-- man/PreProcess.Rd | 11 +++- man/bvs.Rd | 52 ++++++++++++--------- man/predBMA.Rd | 25 ++++++---- 12 files changed, 204 insertions(+), 176 deletions(-)
Title: Miscellaneous Functions from Alexey Shipunov
Description: A collection of functions for data manipulation, plotting and statistical computing, to use separately or with the book "Visual Statistics. Use R!": Shipunov (2019) <http://ashipunov.info/shipunov/software/r/r-en.htm>.
Most useful functions are probably Bclust(), Jclust() and BootA() which bootstrap hierarchical clustering; Recode...() which multiple recode in a fast, flexible and simple way; Misclass() which outputs confusion matrix even if classes are not concerted;
Overlap() which calculates overlaps of convex hulls from any projection; and Pleiad() which is fast and flexible correlogram. In fact, there are much more useful functions, please see documentation.
Author: Alexey Shipunov [aut, cre], Paul Murrell [ctb], Marcello D'Orazio [ctb], Stephen Turner [ctb], Eugeny Altshuler [ctb], Roland Rau [ctb], Marcus W Beck [ctb], Sebastian Gibb [ctb], Weiliang Qiu [ctb], Emmanuel Paradis [ctb], Roger Koenker [ctb], R Core Team [ctb]
Maintainer: Alexey Shipunov <dactylorhiza@gmail.com>
Diff between shipunov versions 1.1 dated 2019-05-06 and 1.2 dated 2019-06-12
DESCRIPTION | 11 +- MD5 | 180 ++++++++++++++++++++++++++++---------------- NAMESPACE | 5 - NEWS | 18 +++- R/asmisc.r | 108 -------------------------- R/biokey.r |only R/dnn.r |only R/ellipses.r |only R/fill.r |only R/infill.r | 42 ---------- R/k.r |only R/misclass.r | 1 R/mrbayes.r |only R/mrh.r |only R/ppoints.r |only R/s_value.r |only TODO | 50 +++--------- data |only man/Adj.Rand.Rd | 2 man/Bclabels.Rd | 12 +- man/Bclust.Rd | 16 +-- man/BestOverlap.Rd | 2 man/Biokey.Rd |only man/BootA.Rd | 4 man/BootKNN.Rd | 2 man/BootRF.Rd | 2 man/Boxplots.Rd | 7 - man/Cdate.Rd | 2 man/Classproj.Rd | 11 +- man/Co.test.Rd | 2 man/Coml.Rd | 3 man/DNN.Rd |only man/Dev.Rd | 6 - man/Dotchart.Rd | 4 man/Ellipses.Rd | 41 ++++++++-- man/Ex.pch.Rd | 2 man/Files.Rd | 6 - man/Fill.Rd |only man/Gap.code.Rd | 5 - man/Gen.cl.data.Rd | 2 man/Gower.dist.Rd | 8 - man/Gradd.Rd | 4 man/Hcl2mat.Rd | 13 ++- man/Hclust.match.Rd | 6 - man/Hcoords.Rd | 2 man/Histr.Rd | 4 man/Infill.Rd | 4 man/Jclust.Rd | 14 +-- man/K.Rd | 21 ++--- man/Linechart.Rd | 2 man/Ls.Rd | 2 man/MRH.Rd |only man/Misclass.Rd | 9 +- man/Missing.map.Rd | 3 man/MrBayes.Rd | 61 ++++++++++---- man/Normality.Rd | 2 man/Overlap.Rd | 2 man/Pleiad.Rd | 18 ++-- man/Plot.phylocl.Rd | 8 - man/PlotBest.dist.Rd | 2 man/PlotBest.hclust.Rd | 2 man/PlotBest.mdist.Rd | 7 - man/Points.Rd | 19 +++- man/Read.tri.nts.Rd | 33 ++++++-- man/Recode.Rd | 30 +++++-- man/Root1.Rd | 8 - man/Rostova.tbl.Rd | 4 man/Rresults.Rd | 2 man/S.value.Rd |only man/Saynodynamite.Rd | 6 + man/Str.Rd | 15 ++- man/Tobin.Rd | 2 man/Toclip.Rd | 10 +- man/Topm.Rd | 2 man/Updist.Rd | 10 +- man/VTcoeffs.Rd | 2 man/Write.fasta.Rd | 3 man/Xpager.Rd | 5 - man/atmospheres.Rd |only man/chaetocnema.Rd |only man/classifs.Rd |only man/dolbli.Rd |only man/drosera.Rd |only man/eq.Rd |only man/figures |only man/haltica.Rd |only man/hwc.Rd |only man/keys.Rd |only man/moldino.Rd |only man/pairwise.Eff.Rd | 4 man/pairwise.Rro.test.Rd | 1 man/pairwise.Table2.test.Rd | 2 man/plantago.Rd |only man/salix.Rd |only 94 files changed, 444 insertions(+), 454 deletions(-)
Title: Analysis of Data with Mixed Measurement Error and
Misclassification in Covariates
Description: Implementation of the augmented
Simulation-Extrapolation (SIMEX) algorithm proposed by Yi et al. (2015) <doi:10.1080/01621459.2014.922777>
for analyzing the data with mixed measurement error and misclassification. The main
function provides a similar summary output as that of glm() function. Both parametric and
empirical SIMEX are considered in the package.
Author: Qihuang Zhang <qihuang.zhang@uwaterloo.ca>, Grace Y. Yi <yyi@uwaterloo.ca>
Maintainer: Qihuang Zhang <qihuang.zhang@uwaterloo.ca>
Diff between augSIMEX versions 3.7.2 dated 2019-04-24 and 3.7.3 dated 2019-06-12
DESCRIPTION | 8 ++++---- MD5 | 3 ++- inst |only 3 files changed, 6 insertions(+), 5 deletions(-)