Title: Treemap Visualization
Description: A treemap is a space-filling visualization of hierarchical
structures. This package offers great flexibility to draw treemaps.
Author: Martijn Tennekes [aut, cre],
Peter Ellis [ctb]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between treemap versions 2.4-1 dated 2016-03-26 and 2.4-2 dated 2017-01-03
DESCRIPTION | 14 +++++++++----- MD5 | 16 ++++++++-------- NEWS | 4 ++++ R/dens2col.R | 8 +++++--- R/tmColorsLegend.R | 8 ++++---- R/treemap.R | 8 +++++--- R/value2col.R | 9 +++++---- build/vignette.rds |binary man/treemap.Rd | 9 ++++++--- 9 files changed, 46 insertions(+), 30 deletions(-)
Title: A Set of RStudio Addins
Description: A set of RStudio addins that are designed to be used in
combination with user-defined RStudio keyboard shortcuts. These
addins either:
1) insert text at a cursor position (e.g. insert
operators %>%, <<-, %$%, etc.),
2) replace symbols in selected pieces of text (e.g., convert
backslashes to forward slashes which results in stings like
"c:\data\" converted into "c:/data/") or
3) enclose text with special symbols (e.g., converts "bold" into
"**bold**") which is convenient for editing R Markdown files.
Author: Vilmantas Gegzna [aut, cre, cph]
Maintainer: Vilmantas Gegzna <GegznaV@gmail.com>
Diff between spAddins versions 0.1.5 dated 2016-07-13 and 0.1.7 dated 2017-01-03
DESCRIPTION | 10 +++--- MD5 | 36 +++++++++++----------- NAMESPACE | 2 + R/Replace_addins.R | 15 +++++---- R/enclose_addins.R | 64 +++++++++++++++++++++++++++++++++++++--- R/insert_Line_addins.R | 9 +++-- README.md | 41 +++++++++++++++++++------ build/vignette.rds |binary inst/rstudio/addins.dcf | 35 +++++++++++++++++++++ man/Back2ForwardSlash.Rd | 3 + man/enclose_with_asterisk.Rd | 4 +- man/enclose_with_asterisk2.Rd | 2 + man/enclose_with_backtick.Rd | 4 +- man/enclose_with_dollar.Rd | 2 + man/enclose_with_dollar2.Rd | 2 + man/enclose_with_tilde.Rd |only man/enclose_with_tilde2.Rd |only man/enclose_with_underscore.Rd | 4 +- man/enclose_with_underscore2.Rd | 4 +- vignettes/v1_workflow.Rmd | 33 +++++++++++--------- 20 files changed, 206 insertions(+), 64 deletions(-)
Title: Helper Functions for QCA in R
Description: Helper functions for Qualitative Comparative Analysis: evaluate and
plot Boolean formulae on fuzzy set score data, apply Boolean operations, compute
consistency and coverage measures.
Author: Jirka Lewandowski <jirka.lewandowski@wzb.eu> [aut, cre]
Maintainer: Jirka Lewandowski <jirka.lewandowski@wzb.eu>
Diff between QCAtools versions 0.2.2 dated 2016-07-21 and 0.2.3 dated 2017-01-03
DESCRIPTION | 9 ++++----- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 4 ++-- R/QCAtools-package.r | 2 +- R/boolean.R | 4 ++-- R/xyplot.R | 8 ++++---- README.md | 10 +--------- man/QCAtools.Rd | 2 +- man/boolean.Rd | 3 ++- man/consistency.Rd | 8 +++++--- man/evaluate_dnf.Rd | 5 +++-- man/format_dnf.Rd | 2 +- man/formula_to_function.Rd | 3 ++- man/plot.qca.Rd | 6 +++--- man/xyplot.Rd | 5 +++-- 15 files changed, 48 insertions(+), 51 deletions(-)
Title: 'NatureServe' Interface
Description: Interface to 'NatureServe' (<http://www.natureserve.org>).
Includes methods to get data, image metadata, search taxonomic names,
and make maps.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between natserv versions 0.1.0 dated 2016-12-15 and 0.1.4 dated 2017-01-03
DESCRIPTION | 9 +++++---- LICENSE | 2 +- MD5 | 12 ++++++------ NEWS.md | 9 +++++++++ R/http.R | 16 ++-------------- R/ns_search.R | 2 +- README.md | 2 ++ 7 files changed, 26 insertions(+), 26 deletions(-)
Title: Query Cache for HTTP Clients
Description: In order to improve performance for HTTP API clients, 'httpcache'
provides simple tools for caching and invalidating cache. It includes the
HTTP verb functions GET, PUT, PATCH, POST, and DELETE, which are drop-in
replacements for those in the 'httr' package. These functions are cache-aware
and provide default settings for cache invalidation suitable for RESTful
APIs; the package also enables custom cache-management strategies.
Finally, 'httpcache' includes a basic logging framework to facilitate the
measurement of HTTP request time and cache performance.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson <neal.p.richardson@gmail.com>
Diff between httpcache versions 0.1.8 dated 2016-08-29 and 1.0.0 dated 2017-01-03
httpcache-0.1.8/httpcache/tests/testthat/helper-mocks.R |only httpcache-1.0.0/httpcache/DESCRIPTION | 12 httpcache-1.0.0/httpcache/MD5 | 45 +-- httpcache-1.0.0/httpcache/NAMESPACE | 9 httpcache-1.0.0/httpcache/R/cache.R | 72 ++++- httpcache-1.0.0/httpcache/R/download.R |only httpcache-1.0.0/httpcache/R/http-verbs.R | 72 +++-- httpcache-1.0.0/httpcache/R/load-cache.R |only httpcache-1.0.0/httpcache/R/log.R | 36 ++ httpcache-1.0.0/httpcache/inst/doc/httpcache.R | 66 ---- httpcache-1.0.0/httpcache/inst/doc/httpcache.Rmd | 70 ----- httpcache-1.0.0/httpcache/inst/doc/httpcache.html | 16 - httpcache-1.0.0/httpcache/man/buildCacheKey.Rd |only httpcache-1.0.0/httpcache/man/cache-api.Rd |only httpcache-1.0.0/httpcache/man/cached-http-verbs.Rd | 2 httpcache-1.0.0/httpcache/man/cachedDownload.Rd |only httpcache-1.0.0/httpcache/man/cachedPOST.Rd |only httpcache-1.0.0/httpcache/man/saveCache.Rd |only httpcache-1.0.0/httpcache/tests/testthat.R | 2 httpcache-1.0.0/httpcache/tests/testthat/helper.R | 6 httpcache-1.0.0/httpcache/tests/testthat/test-cache-query-params.R | 30 +- httpcache-1.0.0/httpcache/tests/testthat/test-cache.R | 136 +++++++--- httpcache-1.0.0/httpcache/tests/testthat/test-cached-post.R |only httpcache-1.0.0/httpcache/tests/testthat/test-download.R |only httpcache-1.0.0/httpcache/tests/testthat/test-drop-cache.R | 17 - httpcache-1.0.0/httpcache/tests/testthat/test-load-cache.R |only httpcache-1.0.0/httpcache/tests/testthat/test-logging.R | 60 ++-- httpcache-1.0.0/httpcache/tests/testthat/test-zzz-helper.R | 20 - httpcache-1.0.0/httpcache/vignettes/httpcache.Rmd | 70 ----- 29 files changed, 373 insertions(+), 368 deletions(-)
Title: Create Graph Diagrams and Flowcharts Using R
Description: Create graph diagrams and flowcharts using R.
Author: Knut Sveidqvist [aut, cph] (mermaid.js library in htmlwidgets/lib,
http://github.com/knsv/mermaid/),
Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib,
http://d3js.org),
Chris Pettitt [aut, cph] (dagre-d3.js library in htmlwidgets/lib,
http://github.com/cpettitt/dagre-d3),
Mike Daines [aut, cph] (viz.js library in htmlwidgets/lib,
http://github.com/mdaines/viz.js/),
Andrei Kashcha [aut, cph] (vivagraphjs library in htmlwidgets/lib,
https://github.com/anvaka/VivaGraphJS),
Richard Iannone [aut, cre] (R interface)
Maintainer: Richard Iannone <riannone@me.com>
Diff between DiagrammeR versions 0.8.4 dated 2016-07-17 and 0.9.0 dated 2017-01-03
DiagrammeR-0.8.4/DiagrammeR/R/combine_edges.R |only DiagrammeR-0.8.4/DiagrammeR/R/combine_nodes.R |only DiagrammeR-0.8.4/DiagrammeR/R/country_graph.R |only DiagrammeR-0.8.4/DiagrammeR/R/create_edges.R |only DiagrammeR-0.8.4/DiagrammeR/R/create_nodes.R |only DiagrammeR-0.8.4/DiagrammeR/R/get_connected_components.R |only DiagrammeR-0.8.4/DiagrammeR/R/get_nodes.R |only DiagrammeR-0.8.4/DiagrammeR/R/get_s_connected_components.R |only DiagrammeR-0.8.4/DiagrammeR/R/rescale_edge_attrs_ws.R |only DiagrammeR-0.8.4/DiagrammeR/R/rescale_node_attrs_ws.R |only DiagrammeR-0.8.4/DiagrammeR/R/reverse_edge_direction.R |only DiagrammeR-0.8.4/DiagrammeR/inst/examples |only DiagrammeR-0.8.4/DiagrammeR/inst/img/simple-graph.png |only DiagrammeR-0.8.4/DiagrammeR/man/combine_edges.Rd |only DiagrammeR-0.8.4/DiagrammeR/man/combine_nodes.Rd |only DiagrammeR-0.8.4/DiagrammeR/man/country_graph.Rd |only DiagrammeR-0.8.4/DiagrammeR/man/create_edges.Rd |only DiagrammeR-0.8.4/DiagrammeR/man/create_nodes.Rd |only 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DiagrammeR-0.9.0/DiagrammeR/R/create_subgraph_ws.R | 185 + DiagrammeR-0.9.0/DiagrammeR/R/delete_edge.R | 269 +- DiagrammeR-0.9.0/DiagrammeR/R/delete_edges_ws.R | 108 - DiagrammeR-0.9.0/DiagrammeR/R/delete_global_graph_attrs.R |only DiagrammeR-0.9.0/DiagrammeR/R/delete_node.R | 205 - DiagrammeR-0.9.0/DiagrammeR/R/delete_nodes_ws.R | 88 DiagrammeR-0.9.0/DiagrammeR/R/do_bfs.R |only DiagrammeR-0.9.0/DiagrammeR/R/do_dfs.R | 339 --- DiagrammeR-0.9.0/DiagrammeR/R/drop_edge_attrs.R |only DiagrammeR-0.9.0/DiagrammeR/R/drop_node_attrs.R |only DiagrammeR-0.9.0/DiagrammeR/R/edge_count.R | 49 DiagrammeR-0.9.0/DiagrammeR/R/edge_info.R | 108 - DiagrammeR-0.9.0/DiagrammeR/R/edge_present.R | 52 DiagrammeR-0.9.0/DiagrammeR/R/edge_rel.R | 67 DiagrammeR-0.9.0/DiagrammeR/R/export_csv.R | 35 DiagrammeR-0.9.0/DiagrammeR/R/export_graph.R | 182 + DiagrammeR-0.9.0/DiagrammeR/R/from_adj_matrix.R |only DiagrammeR-0.9.0/DiagrammeR/R/from_igraph.R |only DiagrammeR-0.9.0/DiagrammeR/R/generate_dot.R |only 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DiagrammeR-0.9.0/DiagrammeR/R/utils.R |only DiagrammeR-0.9.0/DiagrammeR/R/visnetwork.R | 82 DiagrammeR-0.9.0/DiagrammeR/R/vivagraph.R | 110 - DiagrammeR-0.9.0/DiagrammeR/README.md | 325 +-- DiagrammeR-0.9.0/DiagrammeR/inst/extdata |only DiagrammeR-0.9.0/DiagrammeR/inst/img/graph_functions_1.png |binary DiagrammeR-0.9.0/DiagrammeR/inst/img/graph_functions_2.png |binary DiagrammeR-0.9.0/DiagrammeR/inst/img/graph_functions_3.png |binary DiagrammeR-0.9.0/DiagrammeR/inst/img/graph_functions_4.png |binary DiagrammeR-0.9.0/DiagrammeR/inst/img/graph_functions_5.png |binary DiagrammeR-0.9.0/DiagrammeR/inst/img/graph_functions_6.png |binary DiagrammeR-0.9.0/DiagrammeR/inst/img/graph_functions_7.png |binary DiagrammeR-0.9.0/DiagrammeR/inst/img/graph_functions_8.png |binary DiagrammeR-0.9.0/DiagrammeR/inst/img/graph_functions_9.png |only DiagrammeR-0.9.0/DiagrammeR/inst/img/simple_graph.png |only DiagrammeR-0.9.0/DiagrammeR/man/DiagrammeR.Rd | 2 DiagrammeR-0.9.0/DiagrammeR/man/DiagrammeROutput.Rd 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DiagrammeR-0.9.0/DiagrammeR/man/is_graph_connected.Rd | 6 DiagrammeR-0.9.0/DiagrammeR/man/is_graph_directed.Rd | 6 DiagrammeR-0.9.0/DiagrammeR/man/is_graph_empty.Rd | 2 DiagrammeR-0.9.0/DiagrammeR/man/join_edge_attrs.Rd | 29 DiagrammeR-0.9.0/DiagrammeR/man/join_node_attrs.Rd | 51 DiagrammeR-0.9.0/DiagrammeR/man/layout_nodes_w_string.Rd |only DiagrammeR-0.9.0/DiagrammeR/man/mermaid.Rd | 33 DiagrammeR-0.9.0/DiagrammeR/man/mk_cond.Rd |only DiagrammeR-0.9.0/DiagrammeR/man/mutate_edge_attrs.Rd |only DiagrammeR-0.9.0/DiagrammeR/man/mutate_node_attrs.Rd |only DiagrammeR-0.9.0/DiagrammeR/man/node_count.Rd | 54 DiagrammeR-0.9.0/DiagrammeR/man/node_info.Rd | 53 DiagrammeR-0.9.0/DiagrammeR/man/node_present.Rd | 55 DiagrammeR-0.9.0/DiagrammeR/man/node_type.Rd | 41 DiagrammeR-0.9.0/DiagrammeR/man/nudge_node_positions_ws.Rd |only DiagrammeR-0.9.0/DiagrammeR/man/pipe.Rd |only DiagrammeR-0.9.0/DiagrammeR/man/recode_edge_attrs.Rd |only DiagrammeR-0.9.0/DiagrammeR/man/recode_node_attrs.Rd |only 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DiagrammeR-0.9.0/DiagrammeR/tests/testthat/test-node_type.R | 226 +- DiagrammeR-0.9.0/DiagrammeR/tests/testthat/test-predecessors_successors.R | 60 DiagrammeR-0.9.0/DiagrammeR/tests/testthat/test-render_graph_series.R | 201 + DiagrammeR-0.9.0/DiagrammeR/tests/testthat/test-rescale_node_edge_attrs.R |only DiagrammeR-0.9.0/DiagrammeR/tests/testthat/test-selections.R | 921 ++++---- DiagrammeR-0.9.0/DiagrammeR/tests/testthat/test-series_info.R | 128 - DiagrammeR-0.9.0/DiagrammeR/tests/testthat/test-set_get_graph_attrs.R |only DiagrammeR-0.9.0/DiagrammeR/tests/testthat/test-set_get_node_edge_attrs.R |only DiagrammeR-0.9.0/DiagrammeR/tests/testthat/test-set_node_attr_to_display.R |only DiagrammeR-0.9.0/DiagrammeR/tests/testthat/test-set_node_positions.R |only DiagrammeR-0.9.0/DiagrammeR/tests/testthat/test-similarity_measures.R |only DiagrammeR-0.9.0/DiagrammeR/tests/testthat/test-transform_graph.R |only DiagrammeR-0.9.0/DiagrammeR/tests/testthat/test-traversals.R | 495 ++-- DiagrammeR-0.9.0/DiagrammeR/tests/testthat/test-traversals_copying_attr_vals.R |only 427 files changed, 15504 insertions(+), 13670 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 0.6.10 dated 2016-08-02 and 0.6.11 dated 2017-01-03
ChangeLog | 71 +++++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 10 +++--- MD5 | 49 +++++++++++++++---------------- NAMESPACE | 9 +++++ R/digest.R | 38 +++++++++++++----------- R/hmac.R | 6 +-- R/sha1.R | 18 +++++------ R/zzz.R | 4 +- README.md | 4 +- build/vignette.rds |binary inst/doc/sha1.html | 4 +- man/makeRaw.Rd |only man/sha1.rd | 2 - src/crc32.c | 10 +++--- src/digest.c | 20 ++++++------ src/pmurhash.c | 6 +-- src/raes.c | 22 ++++++------- src/sha2.c | 52 ++++++++++++++++++++------------ src/xxhash.c | 44 +++++++++++++-------------- tests/AESTest.R | 2 + tests/AESTest.Rout.save | 11 ++++-- tests/digestTest.R | 3 + tests/digestTest.Rout.save | 21 ++++++++----- tests/hmacTest.R | 6 +++ tests/hmacTest.Rout.save | 20 ++++++++---- tests/load-unload.R | 40 ++++++++++++------------- 26 files changed, 297 insertions(+), 175 deletions(-)
Title: Pricing of Variable Annuities
Description: Pricing of variable annuity life insurance
contracts by means of Monte Carlo methods. Monte Carlo is used to price
the contract in case the policyholder cannot surrender while
Least Squares Monte Carlo is used if the insured can surrender.
This package implements the pricing framework and algorithm described in
Bacinello et al. (2011) <doi:10.1016/j.insmatheco.2011.05.003>.
It also implements the state-dependent fee structure
discussed in Bernard et al. (2014) <doi:10.1017/asb.2014.13>.
Author: Ivan Zoccolan [aut, cre]
Maintainer: Ivan Zoccolan <ivan.zoccolan@gmail.com>
Diff between valuer versions 1.1.0 dated 2016-12-12 and 1.1.1 dated 2017-01-03
DESCRIPTION | 15 +++++++------ MD5 | 45 +++++++++++++++++++++------------------ NAMESPACE | 1 R/help_for_data_objects.R | 48 +++++++++++++++++++++++++++++++++++------- R/payoffs.R | 5 +++- R/utils.R | 8 +++++++ R/va_pricing_engine.R | 4 +-- R/va_pricing_engine2.R | 4 +-- R/va_pricing_engine4.R | 4 +-- R/va_pricing_engine5.R |only README.md | 15 +++++++++---- data/financials_BZ2016bis.rda |only inst/doc/Introduction.Rmd | 6 ++++- inst/doc/Introduction.html | 3 ++ man/financials_BBM2010.Rd | 2 - man/financials_BMOP2011.Rd | 2 - man/financials_BZ2016.Rd | 12 +++++++--- man/financials_BZ2016bis.Rd |only man/mortality_BBM2010.Rd | 2 - man/mortality_BMOP2011.Rd | 2 - man/va_sde_engine.Rd | 4 +-- man/va_sde_engine2.Rd | 4 +-- man/va_sde_engine3.Rd |only src/calc_account.cpp | 13 +++-------- vignettes/Introduction.Rmd | 6 ++++- vignettes/News.Rmd |only 26 files changed, 139 insertions(+), 66 deletions(-)
Title: Thematic Maps
Description: Thematic maps are geographical maps in which spatial data distributions are visualized. This package offers a flexible, layer-based, and easy to use approach to create thematic maps, such as choropleths and bubble maps.
Author: Martijn Tennekes [aut, cre],
Joel Gombin [ctb],
Sebastian Jeworutzki [ctb],
Kent Russell [ctb],
Richard Zijdeman [ctb]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between tmap versions 1.6-1 dated 2016-10-29 and 1.8 dated 2017-01-03
tmap-1.6-1/tmap/R/append_data.R |only tmap-1.6-1/tmap/R/approx_areas.R |only tmap-1.6-1/tmap/R/bb.R |only tmap-1.6-1/tmap/R/calc_densities.R |only tmap-1.6-1/tmap/R/cartogram.R |only tmap-1.6-1/tmap/R/col2hex.R |only tmap-1.6-1/tmap/R/crop_shape.R |only tmap-1.6-1/tmap/R/end_of_the_world.R |only tmap-1.6-1/tmap/R/geocode_OSM.R |only tmap-1.6-1/tmap/R/get_IDs.R |only tmap-1.6-1/tmap/R/get_asp_ratio.R |only tmap-1.6-1/tmap/R/get_proj4_code.R |only tmap-1.6-1/tmap/R/get_raster_data.R |only tmap-1.6-1/tmap/R/is_projected.R |only tmap-1.6-1/tmap/R/kde2D.R |only tmap-1.6-1/tmap/R/line_functions.R |only tmap-1.6-1/tmap/R/map2scale.R |only tmap-1.6-1/tmap/R/map_coloring.R |only tmap-1.6-1/tmap/R/read_GPX.R |only tmap-1.6-1/tmap/R/read_osm.R |only tmap-1.6-1/tmap/R/read_shape.R |only tmap-1.6-1/tmap/R/sample_dots.R |only tmap-1.6-1/tmap/R/sbind.R |only tmap-1.6-1/tmap/R/set_projection.R |only tmap-1.6-1/tmap/R/smooth_map.R |only tmap-1.6-1/tmap/R/smooth_raster_cover.R |only tmap-1.6-1/tmap/R/split_shps.R |only tmap-1.6-1/tmap/R/to_raster.R |only tmap-1.6-1/tmap/man/append_data.Rd |only tmap-1.6-1/tmap/man/approx_areas.Rd |only tmap-1.6-1/tmap/man/bb.Rd |only tmap-1.6-1/tmap/man/calc_densities.Rd |only tmap-1.6-1/tmap/man/cartogram.Rd |only tmap-1.6-1/tmap/man/crop_shape.Rd |only tmap-1.6-1/tmap/man/double_line.Rd |only tmap-1.6-1/tmap/man/geocode_OSM.Rd |only tmap-1.6-1/tmap/man/get_IDs.Rd |only tmap-1.6-1/tmap/man/get_asp_ratio.Rd |only tmap-1.6-1/tmap/man/get_proj4.Rd |only tmap-1.6-1/tmap/man/map_coloring.Rd |only tmap-1.6-1/tmap/man/points_to_raster.Rd |only tmap-1.6-1/tmap/man/poly_to_raster.Rd |only tmap-1.6-1/tmap/man/read_GPX.Rd |only tmap-1.6-1/tmap/man/read_osm.Rd |only tmap-1.6-1/tmap/man/read_shape.Rd |only tmap-1.6-1/tmap/man/rev_geocode_OSM.Rd |only tmap-1.6-1/tmap/man/sample_dots.Rd |only tmap-1.6-1/tmap/man/sbind.Rd |only tmap-1.6-1/tmap/man/set_projection.Rd |only tmap-1.6-1/tmap/man/smooth_map.Rd |only tmap-1.6-1/tmap/man/smooth_raster_cover.Rd |only tmap-1.6-1/tmap/man/split_shapes.Rd |only tmap-1.6-1/tmap/man/tm_raster.Rd |only tmap-1.6-1/tmap/man/write_shape.Rd |only tmap-1.6-1/tmap/vignettes/tmap-modes_files |only tmap-1.8/tmap/DESCRIPTION | 16 tmap-1.8/tmap/MD5 | 228 +-- tmap-1.8/tmap/NAMESPACE | 76 - tmap-1.8/tmap/NEWS | 9 tmap-1.8/tmap/R/add_data_to_gps.R |only tmap-1.8/tmap/R/animation_tmap.R | 3 tmap-1.8/tmap/R/cat2pal.R | 2 tmap-1.8/tmap/R/facet_functions.R |only tmap-1.8/tmap/R/get_sp_coordinates.R | 6 tmap-1.8/tmap/R/grid_shp.R | 89 - tmap-1.8/tmap/R/gridplot.R | 14 tmap-1.8/tmap/R/meta_plot.R | 6 tmap-1.8/tmap/R/meta_plot_items.R | 17 tmap-1.8/tmap/R/num2pal.R | 99 - tmap-1.8/tmap/R/onLoad.R | 11 tmap-1.8/tmap/R/pkg.R | 39 tmap-1.8/tmap/R/plot_all.R | 10 tmap-1.8/tmap/R/plot_map.R | 34 tmap-1.8/tmap/R/preprocess_facet_layout.R |only tmap-1.8/tmap/R/preprocess_gt.R | 17 tmap-1.8/tmap/R/preprocess_shapes.R | 98 + tmap-1.8/tmap/R/print_tmap.R | 597 ++++------ tmap-1.8/tmap/R/process_color.R | 45 tmap-1.8/tmap/R/process_color_aes.R | 15 tmap-1.8/tmap/R/process_facet_layout.R | 222 +-- tmap-1.8/tmap/R/process_fill.R | 18 tmap-1.8/tmap/R/process_gps.R |only tmap-1.8/tmap/R/process_layers.R | 4 tmap-1.8/tmap/R/process_lines.R | 14 tmap-1.8/tmap/R/process_meta.R | 91 - tmap-1.8/tmap/R/process_raster.R | 8 tmap-1.8/tmap/R/process_shapes.R | 58 tmap-1.8/tmap/R/process_symbols.R | 16 tmap-1.8/tmap/R/process_tm.R | 72 - tmap-1.8/tmap/R/qtm.R | 35 tmap-1.8/tmap/R/save_tmap.R | 3 tmap-1.8/tmap/R/theme_ps.R | 2 tmap-1.8/tmap/R/tm_layers.R | 50 tmap-1.8/tmap/R/tm_layout.R | 20 tmap-1.8/tmap/R/tm_misc_elements.R | 26 tmap-1.8/tmap/R/tm_shape.R | 20 tmap-1.8/tmap/R/tm_view.R | 16 tmap-1.8/tmap/R/tmap_arrange.R |only tmap-1.8/tmap/R/tmap_mode.R | 4 tmap-1.8/tmap/R/view_tmap.R | 163 +- tmap-1.8/tmap/R/xxx_raster.R |only tmap-1.8/tmap/R/xxx_scales.R |only tmap-1.8/tmap/build/check_for_non_ASCII.R |only tmap-1.8/tmap/build/create_NLD.R |only tmap-1.8/tmap/build/create_NLD_dasy.R |only tmap-1.8/tmap/build/create_europe_world.R |only tmap-1.8/tmap/build/create_land.R |only tmap-1.8/tmap/build/create_metro.R |only tmap-1.8/tmap/build/create_rivers.R |only tmap-1.8/tmap/build/roxygen.r |only tmap-1.8/tmap/build/vignette.rds |binary tmap-1.8/tmap/inst/doc/tmap-modes.html | 2 tmap-1.8/tmap/inst/doc/tmap-nutshell.R | 8 tmap-1.8/tmap/inst/doc/tmap-nutshell.Rmd | 53 tmap-1.8/tmap/inst/doc/tmap-nutshell.html | 275 +--- tmap-1.8/tmap/man/Shapes.Rd | 2 tmap-1.8/tmap/man/polygons.Rd | 20 tmap-1.8/tmap/man/qtm.Rd | 4 tmap-1.8/tmap/man/raster.Rd |only tmap-1.8/tmap/man/tm_facets.Rd | 15 tmap-1.8/tmap/man/tm_grid.Rd | 2 tmap-1.8/tmap/man/tm_iso.Rd | 6 tmap-1.8/tmap/man/tm_layout.Rd | 26 tmap-1.8/tmap/man/tm_lines.Rd | 31 tmap-1.8/tmap/man/tm_scale_bar.Rd | 8 tmap-1.8/tmap/man/tm_shape.Rd | 28 tmap-1.8/tmap/man/tm_symbols.Rd | 83 - tmap-1.8/tmap/man/tm_text.Rd | 2 tmap-1.8/tmap/man/tm_view.Rd | 20 tmap-1.8/tmap/man/tmap-package.Rd | 44 tmap-1.8/tmap/man/tmap_arrange.Rd |only tmap-1.8/tmap/man/tmap_mode.Rd | 1 tmap-1.8/tmap/vignettes/tmap-nutshell.Rmd | 53 tmap-1.8/tmap/vignettes/tmap-nutshell_files/figure-html/unnamed-chunk-10-1.png |binary tmap-1.8/tmap/vignettes/tmap-nutshell_files/figure-html/unnamed-chunk-11-1.png |binary tmap-1.8/tmap/vignettes/tmap-nutshell_files/figure-html/unnamed-chunk-12-1.png |binary tmap-1.8/tmap/vignettes/tmap-nutshell_files/figure-html/unnamed-chunk-13-1.png |binary tmap-1.8/tmap/vignettes/tmap-nutshell_files/figure-html/unnamed-chunk-14-1.png |binary tmap-1.8/tmap/vignettes/tmap-nutshell_files/figure-html/unnamed-chunk-14-2.png |binary tmap-1.8/tmap/vignettes/tmap-nutshell_files/figure-html/unnamed-chunk-15-1.png |binary tmap-1.8/tmap/vignettes/tmap-nutshell_files/figure-html/unnamed-chunk-16-1.png |binary tmap-1.8/tmap/vignettes/tmap-nutshell_files/figure-html/unnamed-chunk-17-1.png |binary tmap-1.8/tmap/vignettes/tmap-nutshell_files/figure-html/unnamed-chunk-21-1.png |binary tmap-1.8/tmap/vignettes/tmap-nutshell_files/figure-html/unnamed-chunk-22-1.png |binary tmap-1.8/tmap/vignettes/tmap-nutshell_files/figure-html/unnamed-chunk-23-1.png |binary tmap-1.8/tmap/vignettes/tmap-nutshell_files/figure-html/unnamed-chunk-3-1.png |binary tmap-1.8/tmap/vignettes/tmap-nutshell_files/figure-html/unnamed-chunk-4-1.png |binary tmap-1.8/tmap/vignettes/tmap-nutshell_files/figure-html/unnamed-chunk-6-1.png |binary tmap-1.8/tmap/vignettes/tmap-nutshell_files/figure-html/unnamed-chunk-7-1.png |binary tmap-1.8/tmap/vignettes/tmap-nutshell_files/figure-html/unnamed-chunk-8-1.png |binary tmap-1.8/tmap/vignettes/tmap-nutshell_files/figure-html/unnamed-chunk-9-1.png |binary 151 files changed, 1220 insertions(+), 1736 deletions(-)
Title: R Graphics Devices for Vector Graphics Output
Description: Vector Graphics devices for 'SVG', 'DrawingML' for
Microsoft Word, PowerPoint and Excel.
Author: David Gohel [aut, cre],
Bob Rudis [ctb] (the javascript code used by function set_attr),
Francois Brunetti [ctb] (clipping algorithms)
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between rvg versions 0.1.1 dated 2016-11-02 and 0.1.2 dated 2017-01-03
DESCRIPTION | 6 +++--- MD5 | 48 ++++++++++++++++++++++++------------------------ NEWS | 5 +++++ R/RcppExports.R | 12 ++++++------ R/dml_docx.R | 27 +++++++++++++++++++++++---- R/dml_pptx.R | 16 ++++++++++++---- R/dml_xlsx.R | 16 ++++++++++++---- R/dsvg.R | 4 +++- R/dsvg_view.R | 10 ++++++---- R/write_docx.R | 4 +++- R/write_pptx.R | 8 ++++---- R/write_xlsx.R | 6 ++++-- man/dml_docx.Rd | 26 +++++++++++++++++++++----- man/dml_pptx.Rd | 10 +++++++--- man/dml_xlsx.Rd | 10 +++++++--- man/dsvg.Rd | 4 +++- man/dsvg_view.Rd | 2 ++ man/write_docx.Rd | 2 ++ man/write_pptx.Rd | 2 ++ man/write_xlsx.Rd | 2 ++ src/RcppExports.cpp | 24 ++++++++++++------------ src/body_pr.cpp | 7 +++---- src/docx.cpp | 24 ++++++++++++------------ src/pptx.cpp | 19 +++++++++---------- src/xlsx.cpp | 15 +++++++-------- 25 files changed, 194 insertions(+), 115 deletions(-)
Title: Build Regular Expressions in a Human Readable Way
Description: Build regular expressions piece by piece using human readable code.
This package is designed for interactive use. For package development, use
the rebus.* dependencies.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between rebus versions 0.1-0 dated 2015-12-16 and 0.1-2 dated 2017-01-03
DESCRIPTION | 11 MD5 | 80 +- NAMESPACE | 1554 +++++++++++++++++++++++------------------- NEWS | 8 R/export-base.R | 576 +++++++-------- R/export-datetimes.R | 176 ++-- R/export-numbers.R | 40 - R/export-unicode.R | 1215 ++++++++++++++++++-------------- R/imports.R | 12 R/regex-package.R | 156 ++-- README.md | 223 +++--- man/Anchors.Rd | 22 man/Backreferences.Rd | 54 - man/CharacterClasses.Rd | 68 - man/ClassGroups.Rd | 68 - man/Concatenation.Rd | 22 man/DateTime.Rd | 134 +-- man/IsoClasses.Rd | 26 man/SpecialCharacters.Rd | 43 - man/Unicode.Rd | 1038 ++++++++++++++-------------- man/UnicodeGeneralCategory.Rd |only man/UnicodeOperators.Rd |only man/UnicodeProperty.Rd |only man/WordBoundaries.Rd | 22 man/as.regex.Rd | 20 man/capture.Rd | 23 man/char_class.Rd | 21 man/escape_special.Rd | 18 man/exactly.Rd | 18 man/format.regex.Rd | 20 man/get_weekdays.Rd | 20 man/literal.Rd | 18 man/lookahead.Rd | 24 man/modify_mode.Rd | 30 man/number_range.Rd | 18 man/or.Rd | 22 man/rebus.Rd | 174 ++-- man/recursive.Rd | 18 man/regex.Rd | 18 man/repeated.Rd | 26 man/roman.Rd | 20 man/whole_word.Rd |only tests |only 43 files changed, 3209 insertions(+), 2847 deletions(-)
Title: Comprehensive Research Synthesis Tools for Systematic Reviews
and Meta- Analysis
Description: Functionalities for facilitating systematic reviews, data
extractions, and meta-analyses. It includes a GUI (graphical user interface)
to help screen the abstracts and titles of bibliographic data; tools to assign
screening effort across multiple collaborators/reviewers and to assess inter-
reviewer reliability; tools to help automate the download and retrieval of
journal PDF articles from online databases; figure and image extractions
from PDFs; web scraping of citations; automated and manual data extraction
from scatter-plot and bar-plot images; PRISMA (Preferred Reporting Items for
Systematic Reviews and Meta-Analyses) flow diagrams; simple imputation tools
to fill gaps in incomplete or missing study parameters; generation of random
effects sizes for Hedges' d, log response ratio, odds ratio, and correlation
coefficients for Monte Carlo experiments; covariance equations for modelling
dependencies among multiple effect sizes (e.g., effect sizes with a common
control); and finally summaries that replicate analyses and outputs from
widely used but no longer updated meta-analysis software. Funding for this
package was supported by National Science Foundation (NSF) grants
DBI-1262545 and DEB-1451031.
Author: Marc J. Lajeunesse [aut, cre]
Maintainer: Marc J. Lajeunesse <lajeunesse@usf.edu>
Diff between metagear versions 0.2 dated 2015-08-19 and 0.3 dated 2017-01-03
metagear-0.2/metagear/vignettes/metagear_basic_vignette_v0.2.Rmd |only metagear-0.3/metagear/DESCRIPTION | 47 - metagear-0.3/metagear/MD5 | 161 ++- metagear-0.3/metagear/NAMESPACE | 15 metagear-0.3/metagear/NEWS.md | 26 metagear-0.3/metagear/R/MA_effectsTable.R | 59 - metagear-0.3/metagear/R/MA_phylogenetic.R |only metagear-0.3/metagear/R/MA_utils.R |only metagear-0.3/metagear/R/PDF_download.R | 24 metagear-0.3/metagear/R/PDF_extractImages.R |only metagear-0.3/metagear/R/PDF_utils.R | 418 +++++----- metagear-0.3/metagear/R/PDFs_collect.R | 81 + metagear-0.3/metagear/R/abstract_screener.R | 344 +++++--- metagear-0.3/metagear/R/chachi.R |only metagear-0.3/metagear/R/covariance_commonControl.R | 15 metagear-0.3/metagear/R/effort_distribute.R | 11 metagear-0.3/metagear/R/effort_summary.R | 4 metagear-0.3/metagear/R/figure_barPlot.R | 2 metagear-0.3/metagear/R/figure_detectAllPoints.R | 4 metagear-0.3/metagear/R/figure_detectAxis.R | 4 metagear-0.3/metagear/R/figure_read.R | 2 metagear-0.3/metagear/R/figure_utils.R | 4 metagear-0.3/metagear/R/impute_SD.R | 7 metagear-0.3/metagear/R/isPDF.R | 29 metagear-0.3/metagear/R/metagear.R | 42 - metagear-0.3/metagear/R/plot_PRISMA.R | 62 - metagear-0.3/metagear/R/plot_PRISMA_utils.R | 177 ++-- metagear-0.3/metagear/R/random_r.R | 2 metagear-0.3/metagear/R/random_utils.R | 6 metagear-0.3/metagear/R/replicate_MetaWin2.0.R | 185 +++- metagear-0.3/metagear/R/scrape_bibliography.R |only metagear-0.3/metagear/R/scrape_utils.R |only metagear-0.3/metagear/build |only metagear-0.3/metagear/inst/CITATION | 23 metagear-0.3/metagear/inst/doc |only metagear-0.3/metagear/man/Kam_et_al_2003_Fig2.Rd | 8 metagear-0.3/metagear/man/Kortum_and_Acymyan_2013_Fig4.Rd | 4 metagear-0.3/metagear/man/MA_effectsTable.Rd | 31 metagear-0.3/metagear/man/PDF_download.Rd | 20 metagear-0.3/metagear/man/PDF_extractImages.Rd |only metagear-0.3/metagear/man/PDFs_collect.Rd | 50 - metagear-0.3/metagear/man/abstract_screener.Rd | 84 +- metagear-0.3/metagear/man/browse_DOI.Rd | 15 metagear-0.3/metagear/man/chachi.Rd |only metagear-0.3/metagear/man/covariance_commonControl.Rd | 30 metagear-0.3/metagear/man/effort_distribute.Rd | 35 metagear-0.3/metagear/man/effort_initialize.Rd | 15 metagear-0.3/metagear/man/effort_merge.Rd | 21 metagear-0.3/metagear/man/effort_redistribute.Rd | 24 metagear-0.3/metagear/man/effort_summary.Rd | 30 metagear-0.3/metagear/man/example_references_metagear.Rd | 4 metagear-0.3/metagear/man/figure_add.Rd | 14 metagear-0.3/metagear/man/figure_barPlot.Rd | 30 metagear-0.3/metagear/man/figure_detectAllPoints.Rd | 12 metagear-0.3/metagear/man/figure_detectAxis.Rd | 14 metagear-0.3/metagear/man/figure_display.Rd | 10 metagear-0.3/metagear/man/figure_displayDetectedPoints.Rd | 10 metagear-0.3/metagear/man/figure_displayDetections.Rd | 8 metagear-0.3/metagear/man/figure_extractDetectedPoints.Rd | 12 metagear-0.3/metagear/man/figure_read.Rd | 2 metagear-0.3/metagear/man/figure_removeOutlyingPoints.Rd | 8 metagear-0.3/metagear/man/figure_scatterPlot.Rd | 24 metagear-0.3/metagear/man/figure_transformByColors.Rd | 10 metagear-0.3/metagear/man/figure_transformToBinary.Rd | 8 metagear-0.3/metagear/man/figure_write.Rd | 2 metagear-0.3/metagear/man/impute_SD.Rd | 38 metagear-0.3/metagear/man/impute_missingness.Rd | 7 metagear-0.3/metagear/man/isPDF.Rd | 8 metagear-0.3/metagear/man/metagear-package.Rd | 53 + metagear-0.3/metagear/man/plot_PRISMA.Rd | 26 metagear-0.3/metagear/man/random_N.Rd | 16 metagear-0.3/metagear/man/random_OR.Rd | 19 metagear-0.3/metagear/man/random_RR.Rd | 25 metagear-0.3/metagear/man/random_d.Rd | 21 metagear-0.3/metagear/man/random_missingness.Rd | 10 metagear-0.3/metagear/man/random_pairedN.Rd | 8 metagear-0.3/metagear/man/random_r.Rd | 21 metagear-0.3/metagear/man/replicate_MetaWin2.0.Rd | 22 metagear-0.3/metagear/man/scrape_bibliography.Rd |only metagear-0.3/metagear/tests |only metagear-0.3/metagear/vignettes/metagear_basic_vignette_v0.31.Rmd |only metagear-0.3/metagear/vignettes/metagear_basic_vignette_v0.31.pdf.asis |only 82 files changed, 1616 insertions(+), 947 deletions(-)
Title: Gaussian Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimation
Description: Gaussian finite mixture models fitted via EM algorithm for model-based clustering, classification, and density estimation, including Bayesian regularization, dimension reduction for visualisation, and resampling-based inference.
Author: Chris Fraley [aut],
Adrian E. Raftery [aut],
Luca Scrucca [aut, cre],
Thomas Brendan Murphy [ctb],
Michael Fop [ctb]
Maintainer: Luca Scrucca <luca.scrucca@unipg.it>
Diff between mclust versions 5.2 dated 2016-03-31 and 5.2.1 dated 2017-01-03
DESCRIPTION | 12 +++--- MD5 | 14 +++---- R/mclust.R | 4 +- build/vignette.rds |binary inst/NEWS | 3 + inst/doc/mclust.Rmd | 2 - inst/doc/mclust.html | 99 +++++++++++++++++++++++++-------------------------- vignettes/mclust.Rmd | 2 - 8 files changed, 69 insertions(+), 67 deletions(-)
Title: Advanced Tables for Markdown/HTML
Description: Tables with state-of-the-art layout elements such as row spanners,
column spanners, table spanners, zebra striping, and more. While allowing
advanced layout, the underlying css-structure is simple in order to maximize
compatibility with word processors such as 'MS Word' or 'LibreOffice'. The package
also contains a few text formatting functions that help outputting text
compatible with HTML/'LaTeX'.
Author: Max Gordon <max@gforge.se>
Maintainer: Max Gordon <max@gforge.se>
Diff between htmlTable versions 1.7 dated 2016-10-19 and 1.8 dated 2017-01-03
htmlTable-1.7/htmlTable/tests/visual_tests/word_test.html |only htmlTable-1.8/htmlTable/DESCRIPTION | 12 htmlTable-1.8/htmlTable/MD5 | 144 htmlTable-1.8/htmlTable/NAMESPACE | 76 htmlTable-1.8/htmlTable/NEWS | 169 htmlTable-1.8/htmlTable/R/concatHtmlTables.R |only htmlTable-1.8/htmlTable/R/data-SCB.R | 28 htmlTable-1.8/htmlTable/R/deprecated.R | 78 htmlTable-1.8/htmlTable/R/htmlTable.R | 2201 - htmlTable-1.8/htmlTable/R/htmlTable_helpers.R | 1956 htmlTable-1.8/htmlTable/R/htmlTable_render.R | 512 htmlTable-1.8/htmlTable/R/interactiveTable.R | 474 htmlTable-1.8/htmlTable/R/txtFrmt.R | 602 htmlTable-1.8/htmlTable/README.md | 2358 - htmlTable-1.8/htmlTable/build/vignette.rds |binary htmlTable-1.8/htmlTable/inst/doc/general.R | 343 htmlTable-1.8/htmlTable/inst/doc/general.Rmd | 635 htmlTable-1.8/htmlTable/inst/doc/general.html | 8357 ++-- htmlTable-1.8/htmlTable/inst/doc/tables.R | 450 htmlTable-1.8/htmlTable/inst/doc/tables.Rmd | 830 htmlTable-1.8/htmlTable/inst/doc/tables.html |20466 +++++----- htmlTable-1.8/htmlTable/inst/examples/data-SCB_example.R | 60 htmlTable-1.8/htmlTable/inst/examples/htmlTable_example.R | 143 htmlTable-1.8/htmlTable/inst/examples/interactiveTable_example.R | 38 htmlTable-1.8/htmlTable/inst/html_components/button.html | 4 htmlTable-1.8/htmlTable/inst/javascript/button.js | 48 htmlTable-1.8/htmlTable/inst/javascript/toggler.js | 80 htmlTable-1.8/htmlTable/man/SCB.Rd | 104 htmlTable-1.8/htmlTable/man/concatHtmlTables.Rd |only htmlTable-1.8/htmlTable/man/htmlTable.Rd | 828 htmlTable-1.8/htmlTable/man/interactiveTable.Rd | 152 htmlTable-1.8/htmlTable/man/outputInt.Rd | 40 htmlTable-1.8/htmlTable/man/prAddCells.Rd | 104 htmlTable-1.8/htmlTable/man/prAddSemicolon2StrEnd.Rd | 56 htmlTable-1.8/htmlTable/man/prAttr4RgroupAdd.Rd | 46 htmlTable-1.8/htmlTable/man/prConvertDfFactors.Rd | 38 htmlTable-1.8/htmlTable/man/prGetAlign.Rd | 46 htmlTable-1.8/htmlTable/man/prGetCgroupHeader.Rd | 144 htmlTable-1.8/htmlTable/man/prGetRgroupLine.Rd | 108 htmlTable-1.8/htmlTable/man/prGetRowlabelPos.Rd | 76 htmlTable-1.8/htmlTable/man/prGetScriptString.Rd | 40 htmlTable-1.8/htmlTable/man/prGetStyle.Rd | 68 htmlTable-1.8/htmlTable/man/prGetThead.Rd | 184 htmlTable-1.8/htmlTable/man/prMergeClr.Rd | 46 htmlTable-1.8/htmlTable/man/prPrepareAlign.Rd | 86 htmlTable-1.8/htmlTable/man/prPrepareCgroup.Rd | 90 htmlTable-1.8/htmlTable/man/prPrepareColors.Rd | 50 htmlTable-1.8/htmlTable/man/prPrepareCss.Rd | 68 htmlTable-1.8/htmlTable/man/prSkipRownames.Rd | 40 htmlTable-1.8/htmlTable/man/prTblNo.Rd | 64 htmlTable-1.8/htmlTable/man/pvalueFormatter.Rd | 38 htmlTable-1.8/htmlTable/man/splitLines4Table.Rd | 38 htmlTable-1.8/htmlTable/man/tblNoLast.Rd | 52 htmlTable-1.8/htmlTable/man/tblNoNext.Rd | 52 htmlTable-1.8/htmlTable/man/txtInt.Rd | 72 htmlTable-1.8/htmlTable/man/txtMergeLines.Rd | 78 htmlTable-1.8/htmlTable/man/txtPval.Rd | 98 htmlTable-1.8/htmlTable/man/txtRound.Rd | 114 htmlTable-1.8/htmlTable/tests/testInteractive.R | 54 htmlTable-1.8/htmlTable/tests/testthat.R | 6 htmlTable-1.8/htmlTable/tests/testthat/test-htmlTable-input_checks.R |only htmlTable-1.8/htmlTable/tests/testthat/test-htmlTable.R | 768 htmlTable-1.8/htmlTable/tests/testthat/test-htmlTable_cgroup.R | 228 htmlTable-1.8/htmlTable/tests/testthat/test-htmlTable_dates.R | 91 htmlTable-1.8/htmlTable/tests/testthat/test-htmlTable_rgroup_tspanner.R | 462 htmlTable-1.8/htmlTable/tests/testthat/test-htmlTable_total.R | 118 htmlTable-1.8/htmlTable/tests/testthat/test-interactiveTable.R | 632 htmlTable-1.8/htmlTable/tests/testthat/test-txtFrmt.R | 296 htmlTable-1.8/htmlTable/tests/testthat/test-txtMergeLines.R | 48 htmlTable-1.8/htmlTable/tests/visual_tests/htmlTable_vtests.R | 230 htmlTable-1.8/htmlTable/tests/visual_tests/pandoc_test.Rmd | 58 htmlTable-1.8/htmlTable/tests/visual_tests/word_test.Rmd | 84 htmlTable-1.8/htmlTable/vignettes/custom.css | 324 htmlTable-1.8/htmlTable/vignettes/general.Rmd | 635 htmlTable-1.8/htmlTable/vignettes/tables.Rmd | 830 75 files changed, 24017 insertions(+), 23931 deletions(-)
Title: Digital PCR Analysis
Description: Analysis, visualisation and simulation of digital polymerase chain
reaction (dPCR). Supports data formats of commerical systems (Bio-Rad QX100 and
QX200; Fluidigm BioMark) and other systems.
Author: Michal Burdukiewicz [cre, aut],
Stefan Roediger [aut],
Bart Jacobs [aut],
Piotr Sobczyk [ctb]
Maintainer: Michal Burdukiewicz <michalburdukiewicz@gmail.com>
Diff between dpcR versions 0.3 dated 2016-03-15 and 0.4 dated 2017-01-03
dpcR-0.3/dpcR/R/analyze_pooled.R |only dpcR-0.3/dpcR/R/extract_dpcr.R |only dpcR-0.3/dpcR/R/sim_ddpcr.R |only dpcR-0.3/dpcR/R/test_ratio.R |only dpcR-0.3/dpcR/data/datalist |only dpcR-0.3/dpcR/man/analyze_pooled.Rd |only dpcR-0.3/dpcR/man/ddpcr-class.Rd |only dpcR-0.3/dpcR/man/read_raw.Rd |only dpcR-0.3/dpcR/man/sim_ddpcr.Rd |only dpcR-0.3/dpcR/man/test_ratio.Rd |only dpcR-0.4/dpcR/CHANGELOG | 121 dpcR-0.4/dpcR/DESCRIPTION | 45 dpcR-0.4/dpcR/MD5 | 349 dpcR-0.4/dpcR/NAMESPACE | 222 dpcR-0.4/dpcR/R/AUCtest.R | 136 dpcR-0.4/dpcR/R/BioradCNV.R | 32 dpcR-0.4/dpcR/R/White.R | 170 dpcR-0.4/dpcR/R/adpcr2panel.R | 154 dpcR-0.4/dpcR/R/adpcr2ppp.R | 168 dpcR-0.4/dpcR/R/binarize.R | 87 dpcR-0.4/dpcR/R/bind_dpcr.R | 422 dpcR-0.4/dpcR/R/bioamp.R | 154 dpcR-0.4/dpcR/R/calc_breaks.R | 20 dpcR-0.4/dpcR/R/calc_coordinates.R | 107 dpcR-0.4/dpcR/R/calc_lambda.R | 48 dpcR-0.4/dpcR/R/classes.R | 562 dpcR-0.4/dpcR/R/compare_dens.R | 118 dpcR-0.4/dpcR/R/count_test-class.R | 292 dpcR-0.4/dpcR/R/create_dpcr.R | 150 dpcR-0.4/dpcR/R/dPCRmethyl.R | 32 dpcR-0.4/dpcR/R/ddpcRquant.R |only dpcR-0.4/dpcR/R/df2dpcr.R |only dpcR-0.4/dpcR/R/dpcR-package.R | 143 dpcR-0.4/dpcR/R/dpcReport_gui.R | 22 dpcR-0.4/dpcR/R/dpcr2df.R |only dpcR-0.4/dpcR/R/dpcr_calculator.R | 35 dpcR-0.4/dpcR/R/dpcr_density.R | 200 dpcR-0.4/dpcR/R/dpcr_density_gui.R | 24 dpcR-0.4/dpcR/R/dpcr_density_table.R | 87 dpcR-0.4/dpcR/R/extract_run.R |only dpcR-0.4/dpcR/R/fit_adpcr.R | 62 dpcR-0.4/dpcR/R/fl.R | 2 dpcR-0.4/dpcR/R/get_k_n.R | 24 dpcR-0.4/dpcR/R/hsm.R |only dpcR-0.4/dpcR/R/limit_cq.R | 350 dpcR-0.4/dpcR/R/many_peaks.R | 38 dpcR-0.4/dpcR/R/moments.R | 196 dpcR-0.4/dpcR/R/num2int.R | 40 dpcR-0.4/dpcR/R/pds.R | 164 dpcR-0.4/dpcR/R/pds_raw.R | 193 dpcR-0.4/dpcR/R/plot_distr.R | 92 dpcR-0.4/dpcR/R/plot_panel.R | 274 dpcR-0.4/dpcR/R/plot_vf_circ.R | 6 dpcR-0.4/dpcR/R/plot_vic_fam.R | 262 dpcR-0.4/dpcR/R/print_summary.R | 67 dpcR-0.4/dpcR/R/qdpcr.R | 190 dpcR-0.4/dpcR/R/qpcr2pp.R | 238 dpcR-0.4/dpcR/R/qpcr_analyser.R | 320 dpcR-0.4/dpcR/R/read_amp.R |only dpcR-0.4/dpcR/R/read_dpcr.R | 560 dpcR-0.4/dpcR/R/rename_dpcr.R | 75 dpcR-0.4/dpcR/R/rtadpcr.R | 62 dpcR-0.4/dpcR/R/safe_efficiency.R | 20 dpcR-0.4/dpcR/R/show_dpcr.R | 84 dpcR-0.4/dpcR/R/sim_adpcr.R | 201 dpcR-0.4/dpcR/R/sim_ddpcr_bkm.R | 596 dpcR-0.4/dpcR/R/sim_dpcr.R |only dpcR-0.4/dpcR/R/simulations.R | 130 dpcR-0.4/dpcR/R/six_panels.R | 39 dpcR-0.4/dpcR/R/summary_dpcr.R | 214 dpcR-0.4/dpcR/R/test_counts.R | 491 dpcR-0.4/dpcR/R/test_counts_gui.R | 22 dpcR-0.4/dpcR/R/test_panel.R | 114 dpcR-0.4/dpcR/R/test_peaks.R | 210 dpcR-0.4/dpcR/R/test_pooled.R |only dpcR-0.4/dpcR/R/valid_amp.R | 10 dpcR-0.4/dpcR/R/y_val_conf.R | 26 dpcR-0.4/dpcR/README.md | 60 dpcR-0.4/dpcR/build/vignette.rds |binary dpcR-0.4/dpcR/data/BioradCNV.rda |binary dpcR-0.4/dpcR/data/White.rda |binary dpcR-0.4/dpcR/data/dPCRmethyl.rda |binary dpcR-0.4/dpcR/data/many_peaks.rda |binary dpcR-0.4/dpcR/data/pds.rda |binary dpcR-0.4/dpcR/data/pds_raw.rda |binary dpcR-0.4/dpcR/data/six_panels.rda |binary dpcR-0.4/dpcR/inst/CITATION | 36 dpcR-0.4/dpcR/inst/doc/overview.R | 496 dpcR-0.4/dpcR/inst/doc/overview.Rmd | 923 - dpcR-0.4/dpcR/inst/doc/overview.html | 1889 +- dpcR-0.4/dpcR/inst/dpcReport/about.Rmd | 109 dpcR-0.4/dpcR/inst/dpcReport/about.md | 143 dpcR-0.4/dpcR/inst/dpcReport/data_summary/data_summary_table1.md | 28 dpcR-0.4/dpcR/inst/dpcReport/data_summary/summary_input.R | 10 dpcR-0.4/dpcR/inst/dpcReport/download_report1.md | 22 dpcR-0.4/dpcR/inst/dpcReport/dpcr.bib | 167 dpcR-0.4/dpcR/inst/dpcReport/ga.js |only dpcR-0.4/dpcR/inst/dpcReport/input_file1.md | 40 dpcR-0.4/dpcR/inst/dpcReport/input_file2.md | 6 dpcR-0.4/dpcR/inst/dpcReport/plot_panel/plot_panel.R | 24 dpcR-0.4/dpcR/inst/dpcReport/plot_panel/plot_panel0.md | 6 dpcR-0.4/dpcR/inst/dpcReport/plot_panel/plot_panel1.md | 10 dpcR-0.4/dpcR/inst/dpcReport/plot_panel/plot_panel2.md | 2 dpcR-0.4/dpcR/inst/dpcReport/plot_panel/subpanel_summary.R | 44 dpcR-0.4/dpcR/inst/dpcReport/plot_panel/test_panel.R | 14 dpcR-0.4/dpcR/inst/dpcReport/prob_distr/get_kn.R | 20 dpcR-0.4/dpcR/inst/dpcReport/prob_distr/plot_density.R | 28 dpcR-0.4/dpcR/inst/dpcReport/prob_distr/prob_distr1.md | 6 dpcR-0.4/dpcR/inst/dpcReport/prob_distr/prob_distr2.md | 16 dpcR-0.4/dpcR/inst/dpcReport/prob_distr/prob_distr3.md | 10 dpcR-0.4/dpcR/inst/dpcReport/prob_distr/prob_distr4.md | 24 dpcR-0.4/dpcR/inst/dpcReport/prob_distr/single_run_moments.R | 6 dpcR-0.4/dpcR/inst/dpcReport/r_code_gen.R | 231 dpcR-0.4/dpcR/inst/dpcReport/report.css | 214 dpcR-0.4/dpcR/inst/dpcReport/report_template.Rmd | 343 dpcR-0.4/dpcR/inst/dpcReport/server.R | 1148 - dpcR-0.4/dpcR/inst/dpcReport/server_data.R | 250 dpcR-0.4/dpcR/inst/dpcReport/summary_plots/data_summary_scatterchart1.md | 10 dpcR-0.4/dpcR/inst/dpcReport/summary_plots/data_summary_scatterchart2.md | 6 dpcR-0.4/dpcR/inst/dpcReport/summary_plots/summary_exprep_plot.R | 30 dpcR-0.4/dpcR/inst/dpcReport/summary_plots/summary_plot.R | 22 dpcR-0.4/dpcR/inst/dpcReport/test_counts/test_counts1.md | 10 dpcR-0.4/dpcR/inst/dpcReport/test_counts/test_counts2.md | 10 dpcR-0.4/dpcR/inst/dpcReport/test_counts/test_counts3.md | 2 dpcR-0.4/dpcR/inst/dpcReport/test_counts/test_counts_group.R | 8 dpcR-0.4/dpcR/inst/dpcReport/test_counts/test_counts_plot.R | 48 dpcR-0.4/dpcR/inst/dpcReport/test_counts/test_counts_res.R | 16 dpcR-0.4/dpcR/inst/dpcReport/ui.R | 268 dpcR-0.4/dpcR/inst/dpcr_density_gui/server.R | 146 dpcR-0.4/dpcR/inst/dpcr_density_gui/ui.R | 48 dpcR-0.4/dpcR/inst/test_counts_gui/readme.md | 20 dpcR-0.4/dpcR/inst/test_counts_gui/server.R | 92 dpcR-0.4/dpcR/inst/test_counts_gui/ui.R | 54 dpcR-0.4/dpcR/man/BioradCNV.Rd | 48 dpcR-0.4/dpcR/man/White.Rd | 186 dpcR-0.4/dpcR/man/adpcr-class.Rd | 113 dpcR-0.4/dpcR/man/adpcr2panel.Rd | 90 dpcR-0.4/dpcR/man/adpcr2ppp.Rd | 124 dpcR-0.4/dpcR/man/binarize.Rd | 72 dpcR-0.4/dpcR/man/bind_dpcr-methods.Rd | 132 dpcR-0.4/dpcR/man/bioamp.Rd | 107 dpcR-0.4/dpcR/man/calc_coordinates.Rd | 64 dpcR-0.4/dpcR/man/compare_dens.Rd | 74 dpcR-0.4/dpcR/man/count_test-class.Rd | 134 dpcR-0.4/dpcR/man/create_dpcr.Rd | 182 dpcR-0.4/dpcR/man/dPCRmethyl.Rd | 50 dpcR-0.4/dpcR/man/ddpcRquant.Rd |only dpcR-0.4/dpcR/man/df2dpcr.Rd |only dpcR-0.4/dpcR/man/dpcR-package.Rd | 122 dpcR-0.4/dpcR/man/dpcReport.Rd | 40 dpcR-0.4/dpcR/man/dpcr-class.Rd | 133 dpcR-0.4/dpcR/man/dpcr2df-methods.Rd |only dpcR-0.4/dpcR/man/dpcr_density.Rd | 152 dpcR-0.4/dpcR/man/dpcr_density_gui.Rd | 46 dpcR-0.4/dpcR/man/dpcr_density_table.Rd | 110 dpcR-0.4/dpcR/man/extract_dpcr.Rd | 114 dpcR-0.4/dpcR/man/extract_run.Rd |only dpcR-0.4/dpcR/man/limit_cq.Rd | 198 dpcR-0.4/dpcR/man/many_peaks.Rd | 46 dpcR-0.4/dpcR/man/moments-methods.Rd | 116 dpcR-0.4/dpcR/man/num2int.Rd | 44 dpcR-0.4/dpcR/man/pds.Rd | 184 dpcR-0.4/dpcR/man/pds_raw.Rd | 216 dpcR-0.4/dpcR/man/plot.qdpcr.Rd | 88 dpcR-0.4/dpcR/man/plot_panel.Rd | 217 dpcR-0.4/dpcR/man/plot_vic_fam.Rd | 148 dpcR-0.4/dpcR/man/qdpcr-class.Rd | 66 dpcR-0.4/dpcR/man/qpcr2pp.Rd | 222 dpcR-0.4/dpcR/man/qpcr_analyser.Rd | 228 dpcR-0.4/dpcR/man/read_BioMark.Rd | 67 dpcR-0.4/dpcR/man/read_QX100.Rd | 67 dpcR-0.4/dpcR/man/read_QX200.Rd |only dpcR-0.4/dpcR/man/read_amp.Rd |only dpcR-0.4/dpcR/man/read_dpcr.Rd | 83 dpcR-0.4/dpcR/man/read_redf.Rd |only dpcR-0.4/dpcR/man/rename_dpcr.Rd | 52 dpcR-0.4/dpcR/man/rtadpcr-class.Rd | 76 dpcR-0.4/dpcR/man/show-methods.Rd | 80 dpcR-0.4/dpcR/man/sim_adpcr.Rd | 234 dpcR-0.4/dpcR/man/sim_dpcr.Rd |only dpcR-0.4/dpcR/man/six_panels.Rd | 49 dpcR-0.4/dpcR/man/summary-methods.Rd | 186 dpcR-0.4/dpcR/man/test_counts.Rd | 176 dpcR-0.4/dpcR/man/test_counts_gui.Rd | 46 dpcR-0.4/dpcR/man/test_panel.Rd | 164 dpcR-0.4/dpcR/man/test_peaks.Rd | 180 dpcR-0.4/dpcR/man/test_pooled.Rd |only dpcR-0.4/dpcR/vignettes/dpcr.bib | 7114 +++++----- dpcR-0.4/dpcR/vignettes/overview.Rmd | 923 - dpcR-0.4/dpcR/vignettes/workflow.svg |only 190 files changed, 14949 insertions(+), 14801 deletions(-)
Title: HTTP Client
Description: A simple HTTP client, with tools for making HTTP requests,
and mocking HTTP requests. The package is built on R6, and takes
inspiration from Ruby's 'faraday' gem (<https://rubygems.org/gems/faraday>).
The package name is a play on curl, the widely used command line tool
for HTTP, and this package is built on top of the R package 'curl', an
interface to 'libcurl' (<https://curl.haxx.se/libcurl>).
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between crul versions 0.1.6 dated 2016-12-17 and 0.2.0 dated 2017-01-03
DESCRIPTION | 11 ++-- LICENSE | 2 MD5 | 47 ++++++++++++------ NEWS.md | 17 ++++++ R/body.R |only R/client.R | 106 ++++++++++++------------------------------ R/curl-options.R |only R/handle.R | 5 + R/headers.R |only R/http-headers.R |only R/make_url.R |only R/post-requests.R |only R/query.R |only R/response.R | 26 +++++++++- R/writing-options.R |only R/zzz.R | 20 ------- README.md | 42 ++++++++++++---- inst/doc/crul_vignette.Rmd | 69 +++++++++++++++++---------- inst/doc/crul_vignette.html | 69 +++++++++++++++++---------- inst/vign/crul_vignette.md | 69 +++++++++++++++++---------- man/HttpClient.Rd | 61 +++--------------------- man/HttpResponse.Rd | 2 man/curl-options.Rd |only man/handle.Rd | 5 + man/http-headers.Rd |only man/post-requests.Rd |only man/writing-options.Rd |only tests/testthat/test-headers.R |only tests/testthat/test-paths.R |only tests/testthat/test-query.R |only tests/testthat/test-status.R | 8 +-- vignettes/crul_vignette.Rmd | 69 +++++++++++++++++---------- 32 files changed, 343 insertions(+), 285 deletions(-)
Title: Formula-Driven Table Generation
Description: Computes and displays complex tables of summary statistics.
Output may be in LaTeX, HTML, plain text, or an R
matrix for further processing.
Author: Duncan Murdoch
Maintainer: Duncan Murdoch <murdoch@stats.uwo.ca>
Diff between tables versions 0.7.92 dated 2016-08-11 and 0.8 dated 2017-01-03
DESCRIPTION | 8 + MD5 | 41 +++++---- NAMESPACE | 10 +- R/AllObs.R |only R/Paste.R | 15 ++- R/PlusMinus.R | 13 +- R/pseudo.R | 5 - R/subset.R | 134 ++++++++++++++++++++++-------- R/tabular.R | 119 +++++++++++++++++++-------- build/vignette.rds |binary inst/NEWS | 8 + inst/doc/HTML.html | 92 ++++++++++----------- inst/doc/tables.R | 120 +++++++++++++++++++++------ inst/doc/tables.Rnw | 120 ++++++++++++++++++++++++++- inst/doc/tables.pdf |binary inst/todo.txt |only man/AllObs.Rd |only man/DropEmpty.Rd |only man/Heading.Rd | 11 ++ man/Paste.Rd | 7 + man/PlusMinus.Rd | 8 + man/labels.Rd |only vignettes/tables.Rnw | 120 ++++++++++++++++++++++++++- vignettes/tables.Rout.save | 197 ++++++++++++++++++++++++++++++++++++++------- 24 files changed, 808 insertions(+), 220 deletions(-)
Title: XML-RPC Interface to NEOS
Description: Within this package the XML-RPC API to NEOS <https://neos-server.org/neos/> is implemented. This enables the user to pass optimization problems to NEOS and retrieve results within R.
Author: Bernhard Pfaff [aut, cre]
Maintainer: Bernhard Pfaff <bernhard@pfaffikus.de>
Diff between rneos versions 0.3-1 dated 2016-03-06 and 0.3-2 dated 2017-01-03
DESCRIPTION | 14 +++++++------- MD5 | 26 +++++++++++++------------- R/CreateNeosComm.R | 4 ++-- man/CreateNeosComm.Rd | 2 +- man/CreateXmlString.Rd | 2 +- man/NeosJob-class.Rd | 2 +- man/NeosXml-class.Rd | 2 +- man/NgetFinalResults.Rd | 2 +- man/NgetFinalResultsNonBlocking.Rd | 2 +- man/NgetIntermediateResults.Rd | 2 +- man/NgetIntermediateResultsNonBlocking.Rd | 2 +- man/NgetJobInfo.Rd | 2 +- man/NgetJobStatus.Rd | 2 +- man/NsubmitJob.Rd | 3 ++- 14 files changed, 34 insertions(+), 33 deletions(-)
Title: FTRL Proximal Implementation for Elastic Net Regression
Description: Implementation of Follow The Regularized Leader (FTRL) Proximal algorithm, proposed by McMahan et al. (2013) <doi:10.1145/2487575.2488200>, used for online training of large scale regression models using a mixture of L1 and L2 regularization.
Author: Vilhelm von Ehrenheim [aut, cre]
Maintainer: Vilhelm von Ehrenheim <vonehrenheim@gmail.com>
Diff between FTRLProximal versions 0.1.2 dated 2016-11-11 and 0.3.0 dated 2017-01-03
DESCRIPTION | 10 ++-- MD5 | 43 ++++++++++----------- R/ftrlprox.default.r | 24 +++++++---- R/ftrlprox.formula.r | 10 ++-- R/initialize.ftrlprox.r | 10 ++-- R/predict.ftrlprox.r | 11 +++-- R/print.ftrlprox.r | 2 R/update.ftrlprox.r | 12 +++-- README.md | 19 ++++++--- man/ftrlprox.default.Rd | 8 +-- man/ftrlprox.formula.Rd | 8 +-- man/initialize.ftrlprox.Rd | 8 +-- man/predict.ftrlprox.Rd | 6 +- man/print.ftrlprox.Rd | 3 - src/lognet.c | 4 - src/splognet.c | 2 tests/testthat/test_ftrlprox_formula.r | 61 +++++++++++++++++++++++++++--- tests/testthat/test_ftrlprox_matrix.r | 36 ++++++++++++----- tests/testthat/test_ftrlprox_sparse.r | 9 +--- tests/testthat/test_initialize_ftrlprox.r | 25 ++++++++---- tests/testthat/test_predict.r | 14 ++++++ tests/testthat/test_print.r |only tests/testthat/test_update_ftrlprox.r | 50 ++++++++++++++++++++---- 23 files changed, 264 insertions(+), 111 deletions(-)
Title: A Novel Topology-Based Pathway Enrichment Analysis Approach
Description: We described a novel Topology-based pathway enrichment analysis, which integrated the global position of the nodes and the topological property of the pathways in Kyoto Encyclopedia of Genes and Genomes Database.
We also provide some functions to obtain the latest information about pathways to finish pathway enrichment analysis using this method.
Author: Wei Jiang
Maintainer: Wei Jiang <jiangwei@hrbmu.edu.cn>
Diff between TPEA versions 2.0 dated 2016-10-26 and 3.0 dated 2017-01-03
TPEA-2.0/TPEA/R/AUCSC.R |only TPEA-3.0/TPEA/DESCRIPTION | 8 ++++---- TPEA-3.0/TPEA/INDEX | 2 +- TPEA-3.0/TPEA/MD5 | 20 ++++++++++---------- TPEA-3.0/TPEA/R/AUEC.R |only TPEA-3.0/TPEA/R/TPEA.R | 4 ++-- TPEA-3.0/TPEA/man/AUCSC.Rd | 18 +++++++++--------- TPEA-3.0/TPEA/man/TPEA-package.Rd | 11 ++++++----- TPEA-3.0/TPEA/man/TPEA.Rd | 10 +++++----- TPEA-3.0/TPEA/man/UPDATE.Rd | 2 +- TPEA-3.0/TPEA/man/getPathway.Rd | 2 +- TPEA-3.0/TPEA/man/viewpathway.Rd | 4 ++-- 12 files changed, 41 insertions(+), 40 deletions(-)
Title: Unicode Extensions for the 'rebus' Package
Description: Build regular expressions piece by piece using human readable code.
This package contains Unicode functionality, and is primarily intended to be
used by package developers.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between rebus.unicode versions 0.0-1 dated 2015-12-16 and 0.0-2 dated 2017-01-03
DESCRIPTION | 13 MD5 | 21 NAMESPACE | 1182 +++++----- NEWS |only R/imports.R | 8 R/unicode-classes.R | 3718 ++++++++++++++++----------------- R/unicode-constants.R | 2198 +++++++++---------- R/unicode-general-category-classes.R |only R/unicode-general-category-constants.R |only R/unicode-operators.R |only README.md | 3 man/Unicode.Rd | 3220 ++++++++++++++-------------- man/UnicodeGeneralCategory.Rd |only man/UnicodeOperators.Rd |only man/UnicodeProperty.Rd |only 15 files changed, 5282 insertions(+), 5081 deletions(-)
Title: Suite of Functions to Flexibly Read Data from Files
Description: A set of functions to simplify reading data from files. The main function, reader(), should read most common R datafile types without needing any parameters except the filename. Other functions provide simple ways of handling file paths and extensions, and automatically detecting file format and structure.
Author: Nicholas Cooper
Maintainer: Nicholas Cooper <njcooper@gmx.co.uk>
Diff between reader versions 1.0.5 dated 2015-04-09 and 1.0.6 dated 2017-01-03
DESCRIPTION | 12 ++++++------ MD5 | 44 ++++++++++++++++++++++---------------------- NAMESPACE | 4 +++- R/reader.R | 4 +++- man/cat.path.Rd | 2 +- man/classify.ext.Rd | 2 +- man/column.salvage.Rd | 2 +- man/conv.fixed.width.Rd | 6 ++---- man/file.ncol.Rd | 4 ++-- man/file.nrow.Rd | 4 ++-- man/find.file.Rd | 4 ++-- man/find.id.col.Rd | 10 +++++----- man/force.frame.Rd | 12 ++++++------ man/force.vec.Rd | 6 +++--- man/get.delim.Rd | 6 +++--- man/get.ext.Rd | 2 +- man/is.file.Rd | 4 ++-- man/n.readLines.Rd | 6 +++--- man/parse.args.Rd | 4 ++-- man/reader-package.Rd | 6 +++--- man/reader.Rd | 14 +++++++------- man/rmv.ext.Rd | 6 +++--- man/shift.rownames.Rd | 2 +- 23 files changed, 84 insertions(+), 82 deletions(-)
Title: Miscellaneous Functions for Creating Adaptive Functions and
Scripts
Description: A set of handy functions. Includes a versatile one line progress bar, one
line function timer with detailed output, time delay function, text histogram, object
preview, CRAN package search, simpler package installer, Linux command install check,
a flexible Mode function, top function, simulation of correlated data, and more.
Author: Nicholas Cooper
Maintainer: Nicholas Cooper <njcooper@gmx.co.uk>
Diff between NCmisc versions 1.1.4 dated 2015-04-07 and 1.1.5 dated 2017-01-03
DESCRIPTION | 12 ++-- MD5 | 110 +++++++++++++++++++++--------------------- NAMESPACE | 3 - R/NCmisc.R | 33 ++++++++---- man/Dim.Rd | 2 man/Header.Rd | 4 - man/Mode.Rd | 10 +-- man/NCmisc-package.Rd | 6 +- man/Rfile.index.Rd | 4 - man/Substitute.Rd | 2 man/Unlist.Rd | 4 - man/Z.to.p.Rd | 2 man/check.linux.install.Rd | 2 man/comify.Rd | 4 - man/cor.with.Rd | 6 +- man/dup.pairs.Rd | 6 +- man/estimate.memory.Rd | 2 man/exists.not.function.Rd | 17 +++++- man/extend.pc.Rd | 6 +- man/fakeLines.Rd | 2 man/file.split.Rd | 4 - man/force.percentage.Rd | 4 - man/force.scalar.Rd | 4 - man/get.distinct.cols.Rd | 2 man/getRepositories.Rd | 6 +- man/has.method.Rd | 2 man/headl.Rd | 6 +- man/list.functions.in.file.Rd | 6 +- man/list.to.env.Rd | 6 +- man/loess.scatter.Rd | 22 ++++---- man/loop.tracker.Rd | 10 +-- man/memory.summary.Rd | 6 +- man/must.use.package.Rd | 6 +- man/narm.Rd | 6 +- man/out.of.Rd | 12 ++-- man/p.to.Z.Rd | 4 - man/packages.loaded.Rd | 4 - man/pad.left.Rd | 2 man/pctile.Rd | 2 man/ppa.Rd | 6 +- man/preview.Rd | 8 +-- man/prv.Rd | 4 - man/prv.large.Rd | 4 - man/rmv.spc.Rd | 2 man/search.cran.Rd | 2 man/sim.cor.Rd | 4 - man/simple.date.Rd | 6 +- man/spc.Rd | 2 man/standardize.Rd | 2 man/summarise.r.datasets.Rd | 4 - man/textogram.Rd | 2 man/timeit.Rd | 8 +-- man/toheader.Rd | 2 man/top.Rd | 2 man/wait.Rd | 2 man/which.outlier.Rd | 2 56 files changed, 221 insertions(+), 192 deletions(-)
Title: Machine Learning Tools
Description: A collection of machine learning helper functions, particularly assisting in the Exploratory Data Analysis phase.
Makes heavy use of the 'data.table' package for optimal speed and memory efficiency. Highlights include a versatile bin_data()
function, sparsify() for converting a data.table to sparse matrix format with one-hot encoding, fast evaluation metrics, and
empirical_cdf() for calculating empirical Multivariate Cumulative Distribution Functions.
Author: Ben Gorman
Maintainer: Ben Gorman <bgorman@GormAnalysis.com>
Diff between mltools versions 0.1.0 dated 2016-11-27 and 0.2.0 dated 2017-01-03
DESCRIPTION | 10 +++++----- MD5 | 13 ++++++++----- NAMESPACE | 1 + NEWS.md |only R/date_factor.R |only R/folds.R | 17 +++++++++++++---- README.md | 6 ++++++ man/date_factor.Rd |only man/folds.Rd | 5 ++++- 9 files changed, 37 insertions(+), 15 deletions(-)
Title: Solving Mixed Model Equations in R
Description: Multivariate mixed model solver for multiple random effects allowing the specification of variance covariance structures. ML/REML estimates are obtained using the Average Information (AI), Expectation-Maximization (EM), Newton-Raphson (NR), or Efficient Mixed Model Association (EMMA) algorithms. Designed for genomic prediction and genome wide association studies (GWAS) to include additive, dominance and epistatic relationship structures or other covariance structures in R, but also functional as a regular mixed model program. Multivariate models (multiple responses) can be fitted currently with NR, AI and EMMA algorithms allowing multiple random effects as well. Covariance structures for the residual component is currently supported only for balanced univariate Newton Raphson models.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between sommer versions 2.4 dated 2016-12-01 and 2.5 dated 2017-01-03
CHANGELOG | 11 +++++ DESCRIPTION | 8 ++-- MD5 | 46 ++++++++++++----------- NAMESPACE | 2 - R/MMERM.R | 35 ++++++++++++++++- R/MNR.R | 61 +++++++++++++++++++------------ R/NR.R | 75 ++++++++++++++++++++++++++++++++------ R/NRR.R | 2 - R/fdr.R | 72 +----------------------------------- R/fdr2.R |only R/mmer.R | 98 +++++++++++++++++++++++++++++++++++--------------- R/mmerSNOW.R | 63 +++++++++++++++++++++++++------- R/score.calc.R | 23 +++++++++-- R/score.calcMV.R | 2 + man/MMERM.Rd | 3 + man/NR.Rd | 4 +- man/Technow_data.Rd | 5 ++ man/atcg1234.Rd | 2 - man/cornHybrid.Rd | 41 ++++++++++++++++++++ man/fdr2.Rd |only man/gryphondata.Rd | 6 +-- man/mmer.Rd | 2 - man/score.calc.Rd | 3 + man/sommer-package.Rd | 14 +++++-- vignettes/sommer.html | 22 ++++++----- 25 files changed, 395 insertions(+), 205 deletions(-)
Title: Client to Access 'Openaddresses' Data
Description: 'Openaddresses' (<https://openaddresses.io/>) client. Search,
fetch data, and combine 'datasets'. Outputs are easy to visualize
with base plots, 'ggplot2', or 'leaflet'.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between openadds versions 0.1.0 dated 2016-08-03 and 0.2.0 dated 2017-01-03
DESCRIPTION | 18 +-- LICENSE | 2 MD5 | 45 ++++---- NAMESPACE | 8 - NEWS.md | 25 ++++ R/as_openadd.R | 4 R/caching.R | 25 +++- R/combine.R | 22 ++-- R/list_data.R | 13 +- R/oa_get.R | 123 +++++++++++++---------- R/oa_readme.R | 3 R/oa_search.R | 2 R/openadds-package.R | 1 README.md | 200 +++++++++++++++++++++++++++++++++++++- man/as_openadd.Rd | 4 man/oa_cache.Rd | 4 man/oa_combine.Rd | 4 man/oa_get.Rd | 29 ++--- man/oa_list.Rd | 5 man/oa_search.Rd | 2 tests/testthat/test-oa_combine.R | 8 - tests/testthat/test-oa_get.R | 34 ++++-- tests/testthat/test-oa_get_lots.R |only tests/testthat/test-oa_list.R | 5 24 files changed, 430 insertions(+), 156 deletions(-)
Title: Optimal and Fast Univariate Clustering
Description: A fast dynamic programming algorithm for optimal univariate
clustering. Minimizing the sum of squares of within-cluster distances, the
algorithm guarantees optimality and reproducibility. Its advantage over
heuristic clustering algorithms in efficiency and accuracy is increasingly
pronounced as the number of clusters k increases. With optional weights, the
algorithm can also optimally segment time series and perform peak calling. An
auxiliary function generates histograms that are adaptive to patterns in data.
This package provides a powerful alternative to heuristic methods for
univariate data analysis.
Author: Joe Song [aut, cre], Haizhou Wang [aut]
Maintainer: Joe Song <joemsong@cs.nmsu.edu>
Diff between Ckmeans.1d.dp versions 3.4.6-5 dated 2016-12-05 and 3.4.6-6 dated 2017-01-03
DESCRIPTION | 22 +- MD5 | 40 ++--- NEWS | 18 ++ R/Ckmeans.1d.dp.R | 45 +++-- R/ahist.R | 317 ++++++++++++++++++++++++++++------------- R/visualize.R | 3 build/vignette.rds |binary inst/doc/Ckmeans.1d.dp.R | 2 inst/doc/Ckmeans.1d.dp.Rmd | 10 - inst/doc/Ckmeans.1d.dp.html | 26 +-- inst/doc/ahist.Rmd | 4 inst/doc/ahist.html | 20 +- man/Ckmeans.1d.dp-package.Rd | 14 - man/Ckmeans.1d.dp.Rd | 10 - man/ahist.Rd | 29 +++ man/plot.Ckmeans.1d.dp.Rd | 2 man/print.Ckmeans.1d.dp.Rd | 4 src/Ckmeans.1d.dp.cpp | 19 ++ src/weighted_select_levels.cpp | 4 vignettes/Ckmeans.1d.dp.Rmd | 10 - vignettes/ahist.Rmd | 4 21 files changed, 397 insertions(+), 206 deletions(-)