Title: Wrap R Functions for Debugging and Ease of Use
Description: Provides 'DebugFnW()' to capture function context on error for
debugging, and 'let()' which converts non-standard evaluation interfaces to
standard evaluation interfaces.
'DebugFnW()' captures the calling function and arguments prior to the
call causing the exception, while
the classic 'options(error=dump.frames)' form captures at the
moment of the exception
itself (thus function arguments may not be at their starting values).
'let()' rebinds (possibly unbound) names to names.
Author: John Mount, Nina Zumel
Maintainer: John Mount <jmount@win-vector.com>
Diff between wrapr versions 0.1.1 dated 2017-03-14 and 0.1.2 dated 2017-04-13
DESCRIPTION | 13 +++----- MD5 | 22 ++++++++------ NAMESPACE | 3 + NEWS.md | 4 ++ R/atblock.R |only R/let.R | 74 +++++++++++++++++++++++++++++++++++++------------ inst/doc/DebugFnW.html | 6 +-- inst/doc/let.Rmd | 3 - inst/doc/let.html | 5 +-- man/ateval.Rd |only man/beval.Rd |only man/let.Rd | 11 +++++-- man/letprep.Rd |only vignettes/let.Rmd | 3 - 14 files changed, 98 insertions(+), 46 deletions(-)
Title: A Systematic Data Wrangling Idiom
Description: Supports systematic scrutiny, modification, and integration of
data. The function status() counts rows that have missing values in
grouping columns (returned by na() ), have non-unique combinations of
grouping columns (returned by dup() ), and that are not locally sorted
(returned by unsorted() ). Functions enumerate() and itemize() give
sorted unique combinations of columns, with or without occurrence counts,
respectively. Function ignore() drops columns in x that are present in y,
and informative() drops columns in x that are entirely NA. Data that have
defined unique combinations of grouping values behave more predictably
during merge operations.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between wrangle versions 0.3 dated 2017-02-20 and 0.4 dated 2017-04-13
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/enumerate.Rd | 2 +- man/itemize.Rd | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: A Data Specification Format and Interface
Description: Creates a data specification that describes the columns of a
table (data.frame). Provides methods to read, write, and update the
specification. Checks whether a table matches its specification. See
specification.data.frame(),read.spec(), write.spec(), as.csv.spec(),
respecify.character(), and %matches%.data.frame().
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between spec versions 0.1.1 dated 2017-03-12 and 0.1.3 dated 2017-04-13
DESCRIPTION | 6 +-- MD5 | 11 +++--- NAMESPACE | 1 R/spec.R | 51 +++++++++++++++++++++++++++++-- man/grapes-matches-grapes-.data.frame.Rd | 5 +-- man/print.spec.Rd |only man/specification.data.frame.Rd | 17 ++++++++++ 7 files changed, 79 insertions(+), 12 deletions(-)
Title: Exemplar Data Sets for SGP Analyses
Description: Data sets utilized by the SGP Package as exemplars for users to conduct their own SGP analyses.
Author: Damian W. Betebenner [aut, cre],
Adam Van Iwaarden [aut],
Ben Domingue [aut]
Maintainer: Damian W. Betebenner <dbetebenner@nciea.org>
Diff between SGPdata versions 16.0-0.0 dated 2017-03-15 and 17.0-0.0 dated 2017-04-13
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- data/sgpData.rda |binary data/sgpData_INSTRUCTOR_NUMBER.rda |binary data/sgpData_LONG.rda |binary inst/CITATION | 4 ++-- inst/NEWS | 4 ++++ man/SGPdata-package.Rd | 4 ++-- man/sgpData.Rd | 4 ++-- 9 files changed, 22 insertions(+), 18 deletions(-)
Title: An R Interface to the Onigmo Regular Expression Library
Description: Provides an alternative to R's built-in functionality for handling
regular expressions, based on the Onigmo library. Offers first-class
compiled regex objects, partial matching and function-based substitutions,
amongst other features.
Author: Jon Clayden, based on Onigmo by K. Kosako and K. Takata
Maintainer: Jon Clayden <code@clayden.org>
Diff between ore versions 1.5.0 dated 2016-09-09 and 1.6.0 dated 2017-04-13
ore-1.5.0/ore/src/onig/enc/cp1251.c |only ore-1.5.0/ore/src/onig/enc/cp932.c |only ore-1.5.0/ore/src/onig/enc/iso8859_1.c |only ore-1.5.0/ore/src/onig/enc/iso8859_10.c |only ore-1.5.0/ore/src/onig/enc/iso8859_11.c |only ore-1.5.0/ore/src/onig/enc/iso8859_13.c |only ore-1.5.0/ore/src/onig/enc/iso8859_14.c |only ore-1.5.0/ore/src/onig/enc/iso8859_15.c |only ore-1.5.0/ore/src/onig/enc/iso8859_16.c |only ore-1.5.0/ore/src/onig/enc/iso8859_2.c |only ore-1.5.0/ore/src/onig/enc/iso8859_3.c |only ore-1.5.0/ore/src/onig/enc/iso8859_4.c |only ore-1.5.0/ore/src/onig/enc/iso8859_5.c |only ore-1.5.0/ore/src/onig/enc/iso8859_6.c |only ore-1.5.0/ore/src/onig/enc/iso8859_7.c |only ore-1.5.0/ore/src/onig/enc/iso8859_8.c |only ore-1.5.0/ore/src/onig/enc/iso8859_9.c |only ore-1.5.0/ore/src/onig/enc/koi8.c |only ore-1.5.0/ore/src/onig/enc/sjis.c |only ore-1.5.0/ore/src/onig/enc/utf16_be.c |only ore-1.5.0/ore/src/onig/enc/utf16_le.c |only ore-1.5.0/ore/src/onig/enc/utf32_be.c |only ore-1.5.0/ore/src/onig/enc/utf32_le.c |only ore-1.5.0/ore/src/onig/enc/utf8.c |only ore-1.5.0/ore/src/onig/oniggnu.h |only ore-1.5.0/ore/src/onig/onigposix.h |only ore-1.5.0/ore/src/onig/oniguruma.h |only ore-1.6.0/ore/DESCRIPTION | 12 ore-1.6.0/ore/LICENCE | 2 ore-1.6.0/ore/MD5 | 162 ore-1.6.0/ore/NAMESPACE | 2 ore-1.6.0/ore/NEWS | 15 ore-1.6.0/ore/R/match.R | 21 ore-1.6.0/ore/R/ore.R | 4 ore-1.6.0/ore/R/zzz.R | 6 ore-1.6.0/ore/README.md | 2 ore-1.6.0/ore/configure | 251 ore-1.6.0/ore/configure.ac | 58 ore-1.6.0/ore/man/ore.ismatch.Rd | 6 ore-1.6.0/ore/man/ore.search.Rd | 7 ore-1.6.0/ore/src/Makevars | 4 ore-1.6.0/ore/src/compile.c | 44 ore-1.6.0/ore/src/compile.h | 2 ore-1.6.0/ore/src/match.c | 70 ore-1.6.0/ore/src/match.h | 11 ore-1.6.0/ore/src/onig/config.h.in | 30 ore-1.6.0/ore/src/onig/config.h.win | 9 ore-1.6.0/ore/src/onig/enc/ascii.c | 57 ore-1.6.0/ore/src/onig/enc/big5.c | 247 ore-1.6.0/ore/src/onig/enc/cp949.c |only ore-1.6.0/ore/src/onig/enc/euc_jp.c | 168 ore-1.6.0/ore/src/onig/enc/euc_kr.c | 94 ore-1.6.0/ore/src/onig/enc/euc_tw.c | 126 ore-1.6.0/ore/src/onig/enc/gb18030.c | 153 ore-1.6.0/ore/src/onig/enc/gbk.c |only ore-1.6.0/ore/src/onig/enc/iso_8859.h |only ore-1.6.0/ore/src/onig/enc/iso_8859_1.c |only ore-1.6.0/ore/src/onig/enc/iso_8859_10.c |only ore-1.6.0/ore/src/onig/enc/iso_8859_11.c |only ore-1.6.0/ore/src/onig/enc/iso_8859_13.c |only ore-1.6.0/ore/src/onig/enc/iso_8859_14.c |only ore-1.6.0/ore/src/onig/enc/iso_8859_15.c |only ore-1.6.0/ore/src/onig/enc/iso_8859_16.c |only ore-1.6.0/ore/src/onig/enc/iso_8859_2.c |only ore-1.6.0/ore/src/onig/enc/iso_8859_3.c |only ore-1.6.0/ore/src/onig/enc/iso_8859_4.c |only ore-1.6.0/ore/src/onig/enc/iso_8859_5.c |only ore-1.6.0/ore/src/onig/enc/iso_8859_6.c |only ore-1.6.0/ore/src/onig/enc/iso_8859_7.c |only ore-1.6.0/ore/src/onig/enc/iso_8859_8.c |only ore-1.6.0/ore/src/onig/enc/iso_8859_9.c |only ore-1.6.0/ore/src/onig/enc/jis/props.kwd |only ore-1.6.0/ore/src/onig/enc/koi8_r.c | 22 ore-1.6.0/ore/src/onig/enc/koi8_u.c |only ore-1.6.0/ore/src/onig/enc/shift_jis.c |only ore-1.6.0/ore/src/onig/enc/unicode.c | 332 ore-1.6.0/ore/src/onig/enc/unicode/casefold.h |10693 +++++++++++++---------- ore-1.6.0/ore/src/onig/enc/unicode/name2ctype.h |10899 ++++++++++++++++-------- ore-1.6.0/ore/src/onig/enc/us_ascii.c |only ore-1.6.0/ore/src/onig/enc/utf_16be.c |only ore-1.6.0/ore/src/onig/enc/utf_16le.c |only ore-1.6.0/ore/src/onig/enc/utf_32be.c |only ore-1.6.0/ore/src/onig/enc/utf_32le.c |only ore-1.6.0/ore/src/onig/enc/utf_8.c |only ore-1.6.0/ore/src/onig/enc/windows_1250.c |only ore-1.6.0/ore/src/onig/enc/windows_1251.c |only ore-1.6.0/ore/src/onig/enc/windows_1252.c |only ore-1.6.0/ore/src/onig/enc/windows_1253.c |only ore-1.6.0/ore/src/onig/enc/windows_1254.c |only ore-1.6.0/ore/src/onig/enc/windows_1257.c |only ore-1.6.0/ore/src/onig/enc/windows_31j.c |only ore-1.6.0/ore/src/onig/onigmo.h |only ore-1.6.0/ore/src/onig/onigmognu.h |only ore-1.6.0/ore/src/onig/onigmoposix.h |only ore-1.6.0/ore/src/onig/regcomp.c | 780 - ore-1.6.0/ore/src/onig/regenc.c | 186 ore-1.6.0/ore/src/onig/regenc.h | 156 ore-1.6.0/ore/src/onig/regerror.c | 86 ore-1.6.0/ore/src/onig/regexec.c | 1826 ++-- ore-1.6.0/ore/src/onig/regext.c | 22 ore-1.6.0/ore/src/onig/reggnu.c | 36 ore-1.6.0/ore/src/onig/regint.h | 452 ore-1.6.0/ore/src/onig/regparse.c | 1969 ++-- ore-1.6.0/ore/src/onig/regparse.h | 72 ore-1.6.0/ore/src/onig/regposerr.c | 29 ore-1.6.0/ore/src/onig/regposix.c | 35 ore-1.6.0/ore/src/onig/regsyntax.c | 39 ore-1.6.0/ore/src/onig/regversion.c | 29 ore-1.6.0/ore/src/onig/st.c | 2260 ++++ ore-1.6.0/ore/src/onig/st.h | 184 ore-1.6.0/ore/src/print.c | 9 ore-1.6.0/ore/src/subst.c | 7 ore-1.6.0/ore/src/zzz.c | 35 ore-1.6.0/ore/tests/testthat/test-10-match.R | 1 114 files changed, 20332 insertions(+), 11390 deletions(-)
Title: Scrapes Data from Fitbit
Description: Scrapes data from Fitbit <http://www.fitbit.com>. This does not use the official
API, but instead uses the API that the web dashboard uses to generate the graphs
displayed on the dashboard after login at <http://www.fitbit.com>.
Author: Cory Nissen <corynissen@gmail.com> [aut, cre]
Maintainer: Cory Nissen <corynissen@gmail.com>
Diff between fitbitScraper versions 0.1.7 dated 2016-05-19 and 0.1.8 dated 2017-04-13
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- NEWS.md | 6 ++++++ R/get_activity_data.R | 13 +------------ R/get_daily_data.R | 31 ++++++++++++++++++++++++------- R/login.R | 3 +-- README.md | 9 ++++++--- build/vignette.rds |binary inst/doc/fitbitScraper-examples.html | 13 ++++++------- man/get_activity_data.Rd | 13 +------------ man/get_daily_data.Rd | 3 +-- man/get_intraday_data.Rd | 1 - man/get_premium_export.Rd | 1 - man/get_sleep_data.Rd | 1 - man/get_weight_data.Rd | 1 - man/login.Rd | 1 - 16 files changed, 65 insertions(+), 69 deletions(-)
Title: Represent Ordered Lists and Pairs as Strings
Description: Interconverts between ordered lists and compact string notation.
Useful for capturing code lists, and pair-wise codes and decodes, for text storage.
Analogous to factor levels and labels. Generics encode() and decode()
perform interconversion, while codes() and decodes() extract components of an encoding.
The function encoded() checks whether something is interpretable as an encoding.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between encode versions 0.2 dated 2017-02-18 and 0.3 dated 2017-04-13
DESCRIPTION | 14 +++++++------- MD5 | 2 +- 2 files changed, 8 insertions(+), 8 deletions(-)
More information about SeerMapper2010Regs at CRAN
Permanent link
Title: Utilities for the Simulation and Analysis of Random Fields
Description: Various utilities are provided that might be used in spatial statistics and elsewhere. It delivers a method for solving linear equations that checks the sparsity of the matrix before any algorithm is used. Furthermore, it includes the Struve functions.
Author: Martin Schlather [aut, cre], Reinhard Furrer [ctb], Martin Kroll [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFieldsUtils versions 0.3.21 dated 2017-04-06 and 0.3.23 dated 2017-04-13
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/zzz.R | 2 +- inst/include/Basic_utils.h | 2 +- src/Basic_utils.h | 2 +- src/init_RandomFieldsUtils.c | 2 +- src/maths.cc | 5 +++++ src/scalar.cc | 3 ++- src/solve.cc | 7 ++++++- 9 files changed, 29 insertions(+), 18 deletions(-)
More information about RandomFieldsUtils at CRAN
Permanent link
Title: Ridge Estimation of Precision Matrices from High-Dimensional
Data
Description: Proper L2-penalized ML estimators for the
precision matrix as well as supporting functions to employ these estimators
in a graphical modeling setting.
Author: Carel F.W. Peeters [cre, aut], Anders Ellern Bilgrau [aut], Wessel N. van Wieringen [aut]
Maintainer: Carel F.W. Peeters <cf.peeters@vumc.nl>
Diff between rags2ridges versions 2.1.1 dated 2016-08-18 and 2.2 dated 2017-04-13
DESCRIPTION | 11 MD5 | 57 + NAMESPACE | 11 R/RcppExports.R | 30 R/rags2ridges.R | 1360 +++++++++++++++++++++++++------------------ R/rags2ridgesDepr.R |only R/rags2ridgesMisc.R | 16 R/rags2ridgesVariants.r |only README.md | 8 data |only inst/CITATION | 4 inst/NEWS.Rd | 12 inst/include |only man/ADdata.Rd |only man/Communities.Rd |only man/DiffGraph.Rd |only man/GGMblockTest.Rd | 2 man/GGMnetworkStats.Rd | 4 man/GGMnetworkStats.fused.Rd | 2 man/Ugraph.Rd | 6 man/Union.Rd |only man/edgeHeat.Rd | 2 man/momentS.Rd |only man/optPenalty.LOOCV.Rd | 2 man/optPenalty.LOOCVauto.Rd | 2 man/optPenalty.kCV.Rd |only man/optPenalty.kCVauto.Rd |only man/optPenaltyPchordal.Rd |only man/pruneMatrix.Rd |only man/rags2ridges-package.Rd | 6 man/ridgePchordal.Rd |only man/ridgePsign.Rd |only man/sparsify.Rd | 4 man/support4ridgeP.Rd |only src/RcppExports.cpp | 750 ++++++++++++++++++++--- src/rags2ridges.cpp | 6 src/registerDynamicSymbol.c |only src/ridgePchordal.h |only 38 files changed, 1567 insertions(+), 728 deletions(-)
Title: A Test Environment for HTTP Requests
Description: Testing code and packages that communicate with remote servers can
be painful. Dealing with authentication, bootstrapping server state,
cleaning up objects that may get created during the test run, network
flakiness, and other complications can make testing seem too costly to
bother with. But it doesn't need to be that hard. This package enables one
to test all of the logic on the R sides of the API in your package without
requiring access to the remote service. Importantly, it provides three test
contexts that mock the network connection in different ways, and it offers
additional expectations to assert that HTTP requests were--or were
not--made. Using these tools, one can test that code is making the intended
requests and that it handles the expected responses correctly, all without
depending on a connection to a remote API.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson <neal.p.richardson@gmail.com>
Diff between httptest versions 1.2.0 dated 2017-03-22 and 1.3.0 dated 2017-04-13
DESCRIPTION | 8 ++--- MD5 | 42 +++++++++++++++------------- NAMESPACE | 4 ++ NEWS.md | 7 ++++ R/capture-requests.R |only R/expect-header.R | 21 +++++++++++--- R/expect-json.R | 8 ++--- R/expect-request.R | 4 +- R/fake-http.R | 6 ++-- R/mock-api.R | 48 +++++++++++++++++++-------------- R/offline.R | 8 ++--- R/public.R | 2 - R/without-internet.R | 2 - README.md | 2 + man/buildMockURL.Rd | 2 - man/capture_requests.Rd |only man/expect_header.Rd | 2 - man/expect_json_equivalent.Rd | 2 - man/skip_if_disconnected.Rd | 8 ++--- man/with_fake_HTTP.Rd | 2 - man/with_mock_API.Rd | 4 +- man/with_trace.Rd |only tests/testthat/test-capture-requests.R |only tests/testthat/test-mock-api.R | 6 ++++ 24 files changed, 114 insertions(+), 74 deletions(-)
Title: Analysis of Factorial Experiments
Description: Convenience functions for analyzing factorial experiments using ANOVA or
mixed models. aov_ez(), aov_car(), and aov_4() allow specification of
between, within (i.e., repeated-measures), or mixed between-within (i.e.,
split-plot) ANOVAs for data in long format (i.e., one observation per row),
aggregating multiple observations per individual and cell of the design.
mixed() fits mixed models using lme4::lmer() and computes p-values for all
fixed effects using either Kenward-Roger or Satterthwaite approximation for
degrees of freedom (LMM only), parametric bootstrap (LMMs and GLMMs), or
likelihood ratio tests (LMMs and GLMMs). afex uses type 3 sums of squares
as default (imitating commercial statistical software).
Author: Henrik Singmann [aut, cre],
Ben Bolker [aut],
Jake Westfall [aut],
Frederik Aust [aut],
Søren Højsgaard [ctb],
John Fox [ctb],
Michael A. Lawrence [ctb],
Ulf Mertens [ctb],
Jonathan Love [ctb]
Maintainer: Henrik Singmann <singmann+afex@gmail.com>
Diff between afex versions 0.16-1 dated 2016-04-03 and 0.17-8 dated 2017-04-13
afex-0.16-1/afex/inst/doc/anova_posthoc.R |only afex-0.16-1/afex/inst/doc/anova_posthoc.Rmd |only afex-0.16-1/afex/inst/doc/anova_posthoc.html |only afex-0.16-1/afex/man/allFit.Rd |only afex-0.16-1/afex/vignettes/anova_posthoc.Rmd |only afex-0.17-8/afex/DESCRIPTION | 62 - afex-0.17-8/afex/MD5 | 108 +- afex-0.17-8/afex/NAMESPACE | 21 afex-0.17-8/afex/NEWS | 82 + afex-0.17-8/afex/R/afex-package.R | 14 afex-0.17-8/afex/R/allFit.R | 66 + afex-0.17-8/afex/R/aov_car.R | 112 +- afex-0.17-8/afex/R/deprecated.R | 6 afex-0.17-8/afex/R/ems.R | 2 afex-0.17-8/afex/R/fhch2010-data.R |only afex-0.17-8/afex/R/helpers.R | 66 - afex-0.17-8/afex/R/methods.afex_aov.R | 31 afex-0.17-8/afex/R/mixed.R | 741 +++++++------- afex-0.17-8/afex/R/nice.R | 137 +- afex-0.17-8/afex/R/reexport.R |only afex-0.17-8/afex/R/sk2011.1-data.R | 4 afex-0.17-8/afex/R/utils.R |only afex-0.17-8/afex/R/zzz.R | 31 afex-0.17-8/afex/build/vignette.rds |binary afex-0.17-8/afex/data/fhch2010.rda |only afex-0.17-8/afex/inst/doc/afex_anova_example.R |only afex-0.17-8/afex/inst/doc/afex_anova_example.Rmd |only afex-0.17-8/afex/inst/doc/afex_anova_example.html |only afex-0.17-8/afex/inst/doc/afex_mixed_example.R |only afex-0.17-8/afex/inst/doc/afex_mixed_example.Rmd |only afex-0.17-8/afex/inst/doc/afex_mixed_example.html |only afex-0.17-8/afex/inst/extdata |only afex-0.17-8/afex/man/afex-package.Rd | 15 afex-0.17-8/afex/man/afex_aov-methods.Rd | 18 afex-0.17-8/afex/man/afex_options.Rd | 22 afex-0.17-8/afex/man/all_fit.Rd |only afex-0.17-8/afex/man/aov_car.Rd | 98 - afex-0.17-8/afex/man/compare.2.vectors.Rd | 1 afex-0.17-8/afex/man/deprecated.Rd | 5 afex-0.17-8/afex/man/ems.Rd | 9 afex-0.17-8/afex/man/fhch2010.Rd |only afex-0.17-8/afex/man/ks2013.3.Rd | 1 afex-0.17-8/afex/man/md_12.1.Rd | 1 afex-0.17-8/afex/man/md_15.1.Rd | 1 afex-0.17-8/afex/man/md_16.1.Rd | 1 afex-0.17-8/afex/man/md_16.4.Rd | 1 afex-0.17-8/afex/man/mixed.Rd | 174 ++- afex-0.17-8/afex/man/nice.Rd | 48 afex-0.17-8/afex/man/obk.long.Rd | 1 afex-0.17-8/afex/man/reexports.Rd |only afex-0.17-8/afex/man/round_ps.Rd | 1 afex-0.17-8/afex/man/set_sum_contrasts.Rd | 5 afex-0.17-8/afex/man/sk2011.1.Rd | 5 afex-0.17-8/afex/man/sk2011.2.Rd | 21 afex-0.17-8/afex/tests/testthat/afex_aov_16_1.rda |only afex-0.17-8/afex/tests/testthat/mixed_with_dot.rda |only afex-0.17-8/afex/tests/testthat/test-afex_aov.R | 6 afex-0.17-8/afex/tests/testthat/test-aov_car-basic.R | 19 afex-0.17-8/afex/tests/testthat/test-aov_car-bugs.R | 24 afex-0.17-8/afex/tests/testthat/test-aov_car-structural.R | 41 afex-0.17-8/afex/tests/testthat/test-lmerTest-support.R |only afex-0.17-8/afex/tests/testthat/test-lsmeans-interface.R | 8 afex-0.17-8/afex/tests/testthat/test-mixed-bugs.R | 24 afex-0.17-8/afex/tests/testthat/test-mixed-mw.R | 28 afex-0.17-8/afex/tests/testthat/test-mixed-structure.R | 180 ++- afex-0.17-8/afex/vignettes/afex_anova_example.Rmd |only afex-0.17-8/afex/vignettes/afex_mixed_example.Rmd |only 67 files changed, 1399 insertions(+), 842 deletions(-)
Title: Identification of Conditionally Essential Genes in Transposon
Sequencing Studies
Description: Identification of conditionally essential genes using high-throughput sequencing data from transposon mutant libraries.
Author: Lili Zhao <zhaolili@umich.edu>
Maintainer: Lili Zhao <zhaolili@umich.edu>
Diff between Tnseq versions 0.1.1 dated 2017-02-09 and 0.1.2 dated 2017-04-13
Tnseq-0.1.1/Tnseq/R/Tnseq.R |only Tnseq-0.1.1/Tnseq/man/Tnseq.rd |only Tnseq-0.1.2/Tnseq/DESCRIPTION | 8 ++++---- Tnseq-0.1.2/Tnseq/MD5 | 10 +++++----- Tnseq-0.1.2/Tnseq/NAMESPACE | 2 +- Tnseq-0.1.2/Tnseq/R/CombineNBEst.R | 4 +++- Tnseq-0.1.2/Tnseq/R/TnseqDiff.R |only Tnseq-0.1.2/Tnseq/man/TnseqDiff.rd |only 8 files changed, 13 insertions(+), 11 deletions(-)
Title: Non-Parametric Concordance Coefficient
Description: A non-parametric test for multi-observer concordance and
differences between concordances in (un)balanced data.
Author: Rowan Kuiper [cre, aut],
Remco Hoogenboezem [aut],
Sjoerd Huisman [ctb],
Pieter Sonneveld [ths],
Mark van Duin [ths]
Maintainer: Rowan Kuiper <r.kuiper.emc@gmail.com>
Diff between nopaco versions 0.99.9 dated 2017-03-19 and 1.0.3 dated 2017-04-13
nopaco-0.99.9/nopaco/configure |only nopaco-0.99.9/nopaco/configure.ac |only nopaco-0.99.9/nopaco/configure.win |only nopaco-0.99.9/nopaco/inst/COPYRIGHTS |only nopaco-0.99.9/nopaco/src/densehash |only nopaco-0.99.9/nopaco/src/exactdistribution202.cpp |only nopaco-0.99.9/nopaco/src/exactdistribution202.h |only nopaco-0.99.9/nopaco/src/exactdistribution_base.cpp |only nopaco-0.99.9/nopaco/src/exactdistribution_base.h |only nopaco-1.0.3/nopaco/DESCRIPTION | 24 -- nopaco-1.0.3/nopaco/MD5 | 70 ++---- nopaco-1.0.3/nopaco/NEWS |only nopaco-1.0.3/nopaco/R/allGenerics.R | 2 nopaco-1.0.3/nopaco/R/concordance.test.R | 9 nopaco-1.0.3/nopaco/R/dataDoc.R |only nopaco-1.0.3/nopaco/R/onLoad.R | 4 nopaco-1.0.3/nopaco/R/zzz.R | 67 ++++-- nopaco-1.0.3/nopaco/build |only nopaco-1.0.3/nopaco/data |only nopaco-1.0.3/nopaco/inst/CITATION |only nopaco-1.0.3/nopaco/inst/doc |only nopaco-1.0.3/nopaco/man/coef-methods.Rd | 3 nopaco-1.0.3/nopaco/man/concordance.test.Rd | 3 nopaco-1.0.3/nopaco/man/convertionMethods.Rd | 4 nopaco-1.0.3/nopaco/man/getPsi-methods.Rd | 9 nopaco-1.0.3/nopaco/man/scores.Rd |only nopaco-1.0.3/nopaco/src/Makevars | 1 nopaco-1.0.3/nopaco/src/Makevars.win |only nopaco-1.0.3/nopaco/src/exactdistribution.cpp |only nopaco-1.0.3/nopaco/src/exactdistribution.h |only nopaco-1.0.3/nopaco/src/getPsi.cpp | 223 ++++++++------------ nopaco-1.0.3/nopaco/src/getPsi.h | 23 +- nopaco-1.0.3/nopaco/src/register.cpp | 18 + nopaco-1.0.3/nopaco/src/samplePsi.cpp | 177 ++++++--------- nopaco-1.0.3/nopaco/src/samplePsi.h | 10 nopaco-1.0.3/nopaco/vignettes |only 36 files changed, 327 insertions(+), 320 deletions(-)
Title: Incidence Estimation Tools
Description: Tools for estimating incidence from biomarker data in cross-
sectional surveys, and for calibrating tests for recent infection.
Implements and extends the method of Kassanjee et al. (2012)
<doi:10.1097/EDE.0b013e3182576c07>.
Author: Alex Welte [aut],
Eduard Grebe [cre, aut],
Avery McIntosh [aut],
Petra Bäumler [aut],
Reshma Kassanjee [ctb],
Hilmarie Brand [ctb],
Cari Van Schalkwyk [ctb],
Yuruo Li [ctb],
Simon Daniel [ctb],
Stefano Ongarello [aut],
Yusuke Asai [ctb]
Maintainer: Eduard Grebe <eduardgrebe@sun.ac.za>
Diff between inctools versions 1.0.7 dated 2016-09-13 and 1.0.10 dated 2017-04-13
DESCRIPTION | 18 ++--- MD5 | 34 +++++----- NAMESPACE | 3 R/calibration_frr.R | 118 ++++++++++++++++++++++++----------- R/calibration_mdri.R | 128 +++++++++++++++++++++----------------- build/vignette.rds |binary inst/doc/EstimatingIncidence.html | 6 - inst/doc/Introduction.html | 2 inst/doc/SurveyDesign.html | 2 inst/doc/TestCalibration.html | 12 +-- man/excalibdata.Rd | 1 man/frrcal.Rd | 1 man/inccounts.Rd | 1 man/incpower.Rd | 1 man/incprecision.Rd | 1 man/incprops.Rd | 1 man/mdrical.Rd | 1 man/prevcounts.Rd | 1 18 files changed, 194 insertions(+), 137 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 and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.7.700.0.0 dated 2017-02-08 and 0.7.800.2.0 dated 2017-04-13
ChangeLog | 26 DESCRIPTION | 20 MD5 | 1019 +++++----- NAMESPACE | 28 build/vignette.rds |binary inst/NEWS.Rd | 16 inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-unitTests.pdf |binary inst/include/armadillo | 18 inst/include/armadillo_bits/BaseCube_bones.hpp | 18 inst/include/armadillo_bits/BaseCube_meat.hpp | 18 inst/include/armadillo_bits/Base_bones.hpp | 18 inst/include/armadillo_bits/Base_meat.hpp | 18 inst/include/armadillo_bits/Col_bones.hpp | 18 inst/include/armadillo_bits/Col_meat.hpp | 18 inst/include/armadillo_bits/Cube_bones.hpp | 18 inst/include/armadillo_bits/Cube_meat.hpp | 18 inst/include/armadillo_bits/GenCube_bones.hpp | 18 inst/include/armadillo_bits/GenCube_meat.hpp | 18 inst/include/armadillo_bits/GenSpecialiser.hpp | 18 inst/include/armadillo_bits/Gen_bones.hpp | 18 inst/include/armadillo_bits/Gen_meat.hpp | 18 inst/include/armadillo_bits/GlueCube_bones.hpp | 18 inst/include/armadillo_bits/GlueCube_meat.hpp | 18 inst/include/armadillo_bits/Glue_bones.hpp | 18 inst/include/armadillo_bits/Glue_meat.hpp | 18 inst/include/armadillo_bits/Mat_bones.hpp | 19 inst/include/armadillo_bits/Mat_meat.hpp | 19 inst/include/armadillo_bits/OpCube_bones.hpp | 18 inst/include/armadillo_bits/OpCube_meat.hpp | 18 inst/include/armadillo_bits/Op_bones.hpp | 18 inst/include/armadillo_bits/Op_meat.hpp | 18 inst/include/armadillo_bits/Proxy.hpp | 18 inst/include/armadillo_bits/ProxyCube.hpp | 18 inst/include/armadillo_bits/Row_bones.hpp | 18 inst/include/armadillo_bits/Row_meat.hpp | 18 inst/include/armadillo_bits/SizeCube_bones.hpp | 18 inst/include/armadillo_bits/SizeCube_meat.hpp | 18 inst/include/armadillo_bits/SizeMat_bones.hpp | 18 inst/include/armadillo_bits/SizeMat_meat.hpp | 18 inst/include/armadillo_bits/SpBase_bones.hpp | 18 inst/include/armadillo_bits/SpBase_meat.hpp | 18 inst/include/armadillo_bits/SpCol_bones.hpp | 22 inst/include/armadillo_bits/SpCol_meat.hpp | 20 inst/include/armadillo_bits/SpGlue_bones.hpp | 18 inst/include/armadillo_bits/SpGlue_meat.hpp | 18 inst/include/armadillo_bits/SpMat_bones.hpp | 20 inst/include/armadillo_bits/SpMat_iterators_meat.hpp | 22 inst/include/armadillo_bits/SpMat_meat.hpp | 20 inst/include/armadillo_bits/SpOp_bones.hpp | 18 inst/include/armadillo_bits/SpOp_meat.hpp | 18 inst/include/armadillo_bits/SpProxy.hpp | 19 inst/include/armadillo_bits/SpRow_bones.hpp | 20 inst/include/armadillo_bits/SpRow_meat.hpp | 20 inst/include/armadillo_bits/SpSubview_bones.hpp | 20 inst/include/armadillo_bits/SpSubview_iterators_meat.hpp | 19 inst/include/armadillo_bits/SpSubview_meat.hpp | 20 inst/include/armadillo_bits/SpValProxy_bones.hpp | 21 inst/include/armadillo_bits/SpValProxy_meat.hpp | 19 inst/include/armadillo_bits/access.hpp | 18 inst/include/armadillo_bits/arma_cmath.hpp | 18 inst/include/armadillo_bits/arma_config.hpp | 18 inst/include/armadillo_bits/arma_forward.hpp | 18 inst/include/armadillo_bits/arma_ostream_bones.hpp | 18 inst/include/armadillo_bits/arma_ostream_meat.hpp | 19 inst/include/armadillo_bits/arma_rng.hpp | 18 inst/include/armadillo_bits/arma_rng_cxx11.hpp | 18 inst/include/armadillo_bits/arma_rng_cxx98.hpp | 18 inst/include/armadillo_bits/arma_static_check.hpp | 18 inst/include/armadillo_bits/arma_str.hpp | 18 inst/include/armadillo_bits/arma_version.hpp | 24 inst/include/armadillo_bits/arrayops_bones.hpp | 18 inst/include/armadillo_bits/arrayops_meat.hpp | 27 inst/include/armadillo_bits/auxlib_bones.hpp | 20 inst/include/armadillo_bits/auxlib_meat.hpp | 23 inst/include/armadillo_bits/compiler_setup.hpp | 24 inst/include/armadillo_bits/compiler_setup_post.hpp | 18 inst/include/armadillo_bits/cond_rel_bones.hpp | 18 inst/include/armadillo_bits/cond_rel_meat.hpp | 18 inst/include/armadillo_bits/config.hpp | 19 inst/include/armadillo_bits/config.hpp.cmake | 19 inst/include/armadillo_bits/constants.hpp | 18 inst/include/armadillo_bits/constants_old.hpp | 18 inst/include/armadillo_bits/debug.hpp | 19 inst/include/armadillo_bits/def_arpack.hpp | 20 inst/include/armadillo_bits/def_atlas.hpp | 18 inst/include/armadillo_bits/def_blas.hpp | 18 inst/include/armadillo_bits/def_hdf5.hpp | 18 inst/include/armadillo_bits/def_lapack.hpp | 20 inst/include/armadillo_bits/def_superlu.hpp | 21 inst/include/armadillo_bits/diagmat_proxy.hpp | 18 inst/include/armadillo_bits/diagview_bones.hpp | 18 inst/include/armadillo_bits/diagview_meat.hpp | 18 inst/include/armadillo_bits/diskio_bones.hpp | 21 inst/include/armadillo_bits/diskio_meat.hpp | 79 inst/include/armadillo_bits/distr_param.hpp | 18 inst/include/armadillo_bits/eGlueCube_bones.hpp | 18 inst/include/armadillo_bits/eGlueCube_meat.hpp | 18 inst/include/armadillo_bits/eGlue_bones.hpp | 18 inst/include/armadillo_bits/eGlue_meat.hpp | 18 inst/include/armadillo_bits/eOpCube_bones.hpp | 18 inst/include/armadillo_bits/eOpCube_meat.hpp | 24 inst/include/armadillo_bits/eOp_bones.hpp | 18 inst/include/armadillo_bits/eOp_meat.hpp | 23 inst/include/armadillo_bits/eglue_core_bones.hpp | 18 inst/include/armadillo_bits/eglue_core_meat.hpp | 18 inst/include/armadillo_bits/eop_aux.hpp | 18 inst/include/armadillo_bits/eop_core_bones.hpp | 18 inst/include/armadillo_bits/eop_core_meat.hpp | 18 inst/include/armadillo_bits/fft_engine.hpp | 56 inst/include/armadillo_bits/field_bones.hpp | 19 inst/include/armadillo_bits/field_meat.hpp | 19 inst/include/armadillo_bits/fn_accu.hpp | 19 inst/include/armadillo_bits/fn_all.hpp | 18 inst/include/armadillo_bits/fn_any.hpp | 18 inst/include/armadillo_bits/fn_approx_equal.hpp | 18 inst/include/armadillo_bits/fn_as_scalar.hpp | 18 inst/include/armadillo_bits/fn_chol.hpp | 18 inst/include/armadillo_bits/fn_clamp.hpp | 18 inst/include/armadillo_bits/fn_cond.hpp | 18 inst/include/armadillo_bits/fn_conv.hpp | 18 inst/include/armadillo_bits/fn_conv_to.hpp | 18 inst/include/armadillo_bits/fn_cor.hpp | 19 inst/include/armadillo_bits/fn_cov.hpp | 19 inst/include/armadillo_bits/fn_cross.hpp | 18 inst/include/armadillo_bits/fn_cumprod.hpp | 18 inst/include/armadillo_bits/fn_cumsum.hpp | 18 inst/include/armadillo_bits/fn_det.hpp | 18 inst/include/armadillo_bits/fn_diagmat.hpp | 18 inst/include/armadillo_bits/fn_diagvec.hpp | 18 inst/include/armadillo_bits/fn_diff.hpp | 18 inst/include/armadillo_bits/fn_dot.hpp | 19 inst/include/armadillo_bits/fn_eig_gen.hpp | 18 inst/include/armadillo_bits/fn_eig_pair.hpp | 18 inst/include/armadillo_bits/fn_eig_sym.hpp | 19 inst/include/armadillo_bits/fn_eigs_gen.hpp | 19 inst/include/armadillo_bits/fn_eigs_sym.hpp | 19 inst/include/armadillo_bits/fn_elem.hpp | 18 inst/include/armadillo_bits/fn_eps.hpp | 19 inst/include/armadillo_bits/fn_expmat.hpp | 18 inst/include/armadillo_bits/fn_eye.hpp | 18 inst/include/armadillo_bits/fn_fft.hpp | 18 inst/include/armadillo_bits/fn_fft2.hpp | 18 inst/include/armadillo_bits/fn_find.hpp | 18 inst/include/armadillo_bits/fn_find_unique.hpp | 18 inst/include/armadillo_bits/fn_flip.hpp | 18 inst/include/armadillo_bits/fn_hist.hpp | 18 inst/include/armadillo_bits/fn_histc.hpp | 18 inst/include/armadillo_bits/fn_index_max.hpp | 18 inst/include/armadillo_bits/fn_index_min.hpp | 18 inst/include/armadillo_bits/fn_inplace_strans.hpp | 19 inst/include/armadillo_bits/fn_inplace_trans.hpp | 18 inst/include/armadillo_bits/fn_interp1.hpp | 18 inst/include/armadillo_bits/fn_inv.hpp | 18 inst/include/armadillo_bits/fn_join.hpp | 18 inst/include/armadillo_bits/fn_kmeans.hpp | 18 inst/include/armadillo_bits/fn_kron.hpp | 19 inst/include/armadillo_bits/fn_log_det.hpp | 20 inst/include/armadillo_bits/fn_logmat.hpp | 18 inst/include/armadillo_bits/fn_lu.hpp | 18 inst/include/armadillo_bits/fn_max.hpp | 18 inst/include/armadillo_bits/fn_mean.hpp | 18 inst/include/armadillo_bits/fn_median.hpp | 18 inst/include/armadillo_bits/fn_min.hpp | 18 inst/include/armadillo_bits/fn_misc.hpp | 18 inst/include/armadillo_bits/fn_n_unique.hpp | 19 inst/include/armadillo_bits/fn_nonzeros.hpp | 18 inst/include/armadillo_bits/fn_norm.hpp | 18 inst/include/armadillo_bits/fn_normalise.hpp | 18 inst/include/armadillo_bits/fn_numel.hpp | 18 inst/include/armadillo_bits/fn_ones.hpp | 18 inst/include/armadillo_bits/fn_orth_null.hpp | 18 inst/include/armadillo_bits/fn_pinv.hpp | 19 inst/include/armadillo_bits/fn_polyfit.hpp | 18 inst/include/armadillo_bits/fn_polyval.hpp | 18 inst/include/armadillo_bits/fn_princomp.hpp | 19 inst/include/armadillo_bits/fn_prod.hpp | 18 inst/include/armadillo_bits/fn_qr.hpp | 18 inst/include/armadillo_bits/fn_qz.hpp | 19 inst/include/armadillo_bits/fn_randg.hpp | 18 inst/include/armadillo_bits/fn_randi.hpp | 18 inst/include/armadillo_bits/fn_randn.hpp | 18 inst/include/armadillo_bits/fn_randu.hpp | 18 inst/include/armadillo_bits/fn_range.hpp | 18 inst/include/armadillo_bits/fn_rank.hpp | 20 inst/include/armadillo_bits/fn_regspace.hpp | 18 inst/include/armadillo_bits/fn_repmat.hpp | 19 inst/include/armadillo_bits/fn_reshape.hpp | 18 inst/include/armadillo_bits/fn_resize.hpp | 18 inst/include/armadillo_bits/fn_schur.hpp | 18 inst/include/armadillo_bits/fn_shift.hpp | 18 inst/include/armadillo_bits/fn_shuffle.hpp | 19 inst/include/armadillo_bits/fn_size.hpp | 18 inst/include/armadillo_bits/fn_solve.hpp | 18 inst/include/armadillo_bits/fn_sort.hpp | 18 inst/include/armadillo_bits/fn_sort_index.hpp | 18 inst/include/armadillo_bits/fn_speye.hpp | 19 inst/include/armadillo_bits/fn_spones.hpp | 18 inst/include/armadillo_bits/fn_sprandn.hpp | 18 inst/include/armadillo_bits/fn_sprandu.hpp | 18 inst/include/armadillo_bits/fn_spsolve.hpp | 19 inst/include/armadillo_bits/fn_sqrtmat.hpp | 18 inst/include/armadillo_bits/fn_stddev.hpp | 18 inst/include/armadillo_bits/fn_strans.hpp | 18 inst/include/armadillo_bits/fn_sum.hpp | 18 inst/include/armadillo_bits/fn_svd.hpp | 18 inst/include/armadillo_bits/fn_svds.hpp | 18 inst/include/armadillo_bits/fn_syl_lyap.hpp | 18 inst/include/armadillo_bits/fn_symmat.hpp | 18 inst/include/armadillo_bits/fn_toeplitz.hpp | 18 inst/include/armadillo_bits/fn_trace.hpp | 19 inst/include/armadillo_bits/fn_trans.hpp | 18 inst/include/armadillo_bits/fn_trapz.hpp | 18 inst/include/armadillo_bits/fn_trig.hpp | 18 inst/include/armadillo_bits/fn_trimat.hpp | 18 inst/include/armadillo_bits/fn_trunc_exp.hpp | 18 inst/include/armadillo_bits/fn_trunc_log.hpp | 18 inst/include/armadillo_bits/fn_unique.hpp | 19 inst/include/armadillo_bits/fn_var.hpp | 18 inst/include/armadillo_bits/fn_vectorise.hpp | 18 inst/include/armadillo_bits/fn_zeros.hpp | 18 inst/include/armadillo_bits/glue_atan2_bones.hpp | 18 inst/include/armadillo_bits/glue_atan2_meat.hpp | 18 inst/include/armadillo_bits/glue_conv_bones.hpp | 18 inst/include/armadillo_bits/glue_conv_meat.hpp | 29 inst/include/armadillo_bits/glue_cor_bones.hpp | 19 inst/include/armadillo_bits/glue_cor_meat.hpp | 19 inst/include/armadillo_bits/glue_cov_bones.hpp | 19 inst/include/armadillo_bits/glue_cov_meat.hpp | 19 inst/include/armadillo_bits/glue_cross_bones.hpp | 18 inst/include/armadillo_bits/glue_cross_meat.hpp | 18 inst/include/armadillo_bits/glue_hist_bones.hpp | 18 inst/include/armadillo_bits/glue_hist_meat.hpp | 18 inst/include/armadillo_bits/glue_histc_bones.hpp | 18 inst/include/armadillo_bits/glue_histc_meat.hpp | 18 inst/include/armadillo_bits/glue_hypot_bones.hpp | 18 inst/include/armadillo_bits/glue_hypot_meat.hpp | 18 inst/include/armadillo_bits/glue_join_bones.hpp | 18 inst/include/armadillo_bits/glue_join_meat.hpp | 18 inst/include/armadillo_bits/glue_kron_bones.hpp | 19 inst/include/armadillo_bits/glue_kron_meat.hpp | 19 inst/include/armadillo_bits/glue_max_bones.hpp | 18 inst/include/armadillo_bits/glue_max_meat.hpp | 18 inst/include/armadillo_bits/glue_min_bones.hpp | 18 inst/include/armadillo_bits/glue_min_meat.hpp | 18 inst/include/armadillo_bits/glue_mixed_bones.hpp | 18 inst/include/armadillo_bits/glue_mixed_meat.hpp | 18 inst/include/armadillo_bits/glue_polyfit_bones.hpp | 18 inst/include/armadillo_bits/glue_polyfit_meat.hpp | 18 inst/include/armadillo_bits/glue_polyval_bones.hpp | 18 inst/include/armadillo_bits/glue_polyval_meat.hpp | 18 inst/include/armadillo_bits/glue_relational_bones.hpp | 18 inst/include/armadillo_bits/glue_relational_meat.hpp | 18 inst/include/armadillo_bits/glue_solve_bones.hpp | 18 inst/include/armadillo_bits/glue_solve_meat.hpp | 18 inst/include/armadillo_bits/glue_times_bones.hpp | 18 inst/include/armadillo_bits/glue_times_meat.hpp | 18 inst/include/armadillo_bits/glue_toeplitz_bones.hpp | 18 inst/include/armadillo_bits/glue_toeplitz_meat.hpp | 18 inst/include/armadillo_bits/glue_trapz_bones.hpp | 18 inst/include/armadillo_bits/glue_trapz_meat.hpp | 18 inst/include/armadillo_bits/gmm_diag_bones.hpp | 18 inst/include/armadillo_bits/gmm_diag_meat.hpp | 18 inst/include/armadillo_bits/gmm_misc_bones.hpp | 18 inst/include/armadillo_bits/gmm_misc_meat.hpp | 18 inst/include/armadillo_bits/hdf5_misc.hpp | 20 inst/include/armadillo_bits/include_atlas.hpp | 18 inst/include/armadillo_bits/include_hdf5.hpp | 18 inst/include/armadillo_bits/include_superlu.hpp | 32 inst/include/armadillo_bits/injector_bones.hpp | 18 inst/include/armadillo_bits/injector_meat.hpp | 18 inst/include/armadillo_bits/memory.hpp | 18 inst/include/armadillo_bits/mtGlueCube_bones.hpp | 18 inst/include/armadillo_bits/mtGlueCube_meat.hpp | 18 inst/include/armadillo_bits/mtGlue_bones.hpp | 18 inst/include/armadillo_bits/mtGlue_meat.hpp | 18 inst/include/armadillo_bits/mtOpCube_bones.hpp | 18 inst/include/armadillo_bits/mtOpCube_meat.hpp | 18 inst/include/armadillo_bits/mtOp_bones.hpp | 18 inst/include/armadillo_bits/mtOp_meat.hpp | 18 inst/include/armadillo_bits/mtSpOp_bones.hpp | 19 inst/include/armadillo_bits/mtSpOp_meat.hpp | 19 inst/include/armadillo_bits/mul_gemm.hpp | 18 inst/include/armadillo_bits/mul_gemm_mixed.hpp | 18 inst/include/armadillo_bits/mul_gemv.hpp | 18 inst/include/armadillo_bits/mul_herk.hpp | 18 inst/include/armadillo_bits/mul_syrk.hpp | 18 inst/include/armadillo_bits/newarp_DenseGenMatProd_bones.hpp | 22 inst/include/armadillo_bits/newarp_DenseGenMatProd_meat.hpp | 22 inst/include/armadillo_bits/newarp_DoubleShiftQR_bones.hpp | 22 inst/include/armadillo_bits/newarp_DoubleShiftQR_meat.hpp | 22 inst/include/armadillo_bits/newarp_EigsSelect.hpp | 22 inst/include/armadillo_bits/newarp_GenEigsSolver_bones.hpp | 22 inst/include/armadillo_bits/newarp_GenEigsSolver_meat.hpp | 23 inst/include/armadillo_bits/newarp_SortEigenvalue.hpp | 22 inst/include/armadillo_bits/newarp_SparseGenMatProd_bones.hpp | 22 inst/include/armadillo_bits/newarp_SparseGenMatProd_meat.hpp | 22 inst/include/armadillo_bits/newarp_SymEigsSolver_bones.hpp | 22 inst/include/armadillo_bits/newarp_SymEigsSolver_meat.hpp | 23 inst/include/armadillo_bits/newarp_TridiagEigen_bones.hpp | 22 inst/include/armadillo_bits/newarp_TridiagEigen_meat.hpp | 23 inst/include/armadillo_bits/newarp_UpperHessenbergEigen_bones.hpp | 22 inst/include/armadillo_bits/newarp_UpperHessenbergEigen_meat.hpp | 23 inst/include/armadillo_bits/newarp_UpperHessenbergQR_bones.hpp | 22 inst/include/armadillo_bits/newarp_UpperHessenbergQR_meat.hpp | 22 inst/include/armadillo_bits/newarp_cx_attrib.hpp | 22 inst/include/armadillo_bits/op_all_bones.hpp | 18 inst/include/armadillo_bits/op_all_meat.hpp | 18 inst/include/armadillo_bits/op_any_bones.hpp | 18 inst/include/armadillo_bits/op_any_meat.hpp | 18 inst/include/armadillo_bits/op_chol_bones.hpp | 18 inst/include/armadillo_bits/op_chol_meat.hpp | 18 inst/include/armadillo_bits/op_clamp_bones.hpp | 18 inst/include/armadillo_bits/op_clamp_meat.hpp | 18 inst/include/armadillo_bits/op_cor_bones.hpp | 19 inst/include/armadillo_bits/op_cor_meat.hpp | 19 inst/include/armadillo_bits/op_cov_bones.hpp | 19 inst/include/armadillo_bits/op_cov_meat.hpp | 19 inst/include/armadillo_bits/op_cumprod_bones.hpp | 18 inst/include/armadillo_bits/op_cumprod_meat.hpp | 18 inst/include/armadillo_bits/op_cumsum_bones.hpp | 18 inst/include/armadillo_bits/op_cumsum_meat.hpp | 18 inst/include/armadillo_bits/op_cx_scalar_bones.hpp | 18 inst/include/armadillo_bits/op_cx_scalar_meat.hpp | 18 inst/include/armadillo_bits/op_diagmat_bones.hpp | 18 inst/include/armadillo_bits/op_diagmat_meat.hpp | 18 inst/include/armadillo_bits/op_diagvec_bones.hpp | 18 inst/include/armadillo_bits/op_diagvec_meat.hpp | 18 inst/include/armadillo_bits/op_diff_bones.hpp | 18 inst/include/armadillo_bits/op_diff_meat.hpp | 18 inst/include/armadillo_bits/op_dot_bones.hpp | 18 inst/include/armadillo_bits/op_dot_meat.hpp | 18 inst/include/armadillo_bits/op_dotext_bones.hpp | 18 inst/include/armadillo_bits/op_dotext_meat.hpp | 18 inst/include/armadillo_bits/op_expmat_bones.hpp | 18 inst/include/armadillo_bits/op_expmat_meat.hpp | 18 inst/include/armadillo_bits/op_fft_bones.hpp | 18 inst/include/armadillo_bits/op_fft_meat.hpp | 18 inst/include/armadillo_bits/op_find_bones.hpp | 19 inst/include/armadillo_bits/op_find_meat.hpp | 19 inst/include/armadillo_bits/op_find_unique_bones.hpp | 18 inst/include/armadillo_bits/op_find_unique_meat.hpp | 18 inst/include/armadillo_bits/op_flip_bones.hpp | 18 inst/include/armadillo_bits/op_flip_meat.hpp | 18 inst/include/armadillo_bits/op_hist_bones.hpp | 18 inst/include/armadillo_bits/op_hist_meat.hpp | 18 inst/include/armadillo_bits/op_htrans_bones.hpp | 18 inst/include/armadillo_bits/op_htrans_meat.hpp | 19 inst/include/armadillo_bits/op_index_max_bones.hpp | 18 inst/include/armadillo_bits/op_index_max_meat.hpp | 18 inst/include/armadillo_bits/op_index_min_bones.hpp | 18 inst/include/armadillo_bits/op_index_min_meat.hpp | 18 inst/include/armadillo_bits/op_inv_bones.hpp | 18 inst/include/armadillo_bits/op_inv_meat.hpp | 18 inst/include/armadillo_bits/op_logmat_bones.hpp | 18 inst/include/armadillo_bits/op_logmat_meat.hpp | 18 inst/include/armadillo_bits/op_max_bones.hpp | 18 inst/include/armadillo_bits/op_max_meat.hpp | 18 inst/include/armadillo_bits/op_mean_bones.hpp | 18 inst/include/armadillo_bits/op_mean_meat.hpp | 18 inst/include/armadillo_bits/op_median_bones.hpp | 18 inst/include/armadillo_bits/op_median_meat.hpp | 18 inst/include/armadillo_bits/op_min_bones.hpp | 18 inst/include/armadillo_bits/op_min_meat.hpp | 18 inst/include/armadillo_bits/op_misc_bones.hpp | 18 inst/include/armadillo_bits/op_misc_meat.hpp | 18 inst/include/armadillo_bits/op_nonzeros_bones.hpp | 18 inst/include/armadillo_bits/op_nonzeros_meat.hpp | 18 inst/include/armadillo_bits/op_norm_bones.hpp | 18 inst/include/armadillo_bits/op_norm_meat.hpp | 18 inst/include/armadillo_bits/op_normalise_bones.hpp | 18 inst/include/armadillo_bits/op_normalise_meat.hpp | 18 inst/include/armadillo_bits/op_orth_null_bones.hpp | 18 inst/include/armadillo_bits/op_orth_null_meat.hpp | 18 inst/include/armadillo_bits/op_pinv_bones.hpp | 19 inst/include/armadillo_bits/op_pinv_meat.hpp | 20 inst/include/armadillo_bits/op_princomp_bones.hpp | 19 inst/include/armadillo_bits/op_princomp_meat.hpp | 20 inst/include/armadillo_bits/op_prod_bones.hpp | 18 inst/include/armadillo_bits/op_prod_meat.hpp | 18 inst/include/armadillo_bits/op_range_bones.hpp | 18 inst/include/armadillo_bits/op_range_meat.hpp | 18 inst/include/armadillo_bits/op_relational_bones.hpp | 18 inst/include/armadillo_bits/op_relational_meat.hpp | 18 inst/include/armadillo_bits/op_repmat_bones.hpp | 19 inst/include/armadillo_bits/op_repmat_meat.hpp | 19 inst/include/armadillo_bits/op_reshape_bones.hpp | 18 inst/include/armadillo_bits/op_reshape_meat.hpp | 18 inst/include/armadillo_bits/op_resize_bones.hpp | 18 inst/include/armadillo_bits/op_resize_meat.hpp | 18 inst/include/armadillo_bits/op_shift_bones.hpp | 18 inst/include/armadillo_bits/op_shift_meat.hpp | 18 inst/include/armadillo_bits/op_shuffle_bones.hpp | 19 inst/include/armadillo_bits/op_shuffle_meat.hpp | 19 inst/include/armadillo_bits/op_sort_bones.hpp | 18 inst/include/armadillo_bits/op_sort_index_bones.hpp | 18 inst/include/armadillo_bits/op_sort_index_meat.hpp | 18 inst/include/armadillo_bits/op_sort_meat.hpp | 18 inst/include/armadillo_bits/op_sqrtmat_bones.hpp | 18 inst/include/armadillo_bits/op_sqrtmat_meat.hpp | 18 inst/include/armadillo_bits/op_stddev_bones.hpp | 18 inst/include/armadillo_bits/op_stddev_meat.hpp | 18 inst/include/armadillo_bits/op_strans_bones.hpp | 18 inst/include/armadillo_bits/op_strans_meat.hpp | 19 inst/include/armadillo_bits/op_sum_bones.hpp | 18 inst/include/armadillo_bits/op_sum_meat.hpp | 18 inst/include/armadillo_bits/op_symmat_bones.hpp | 18 inst/include/armadillo_bits/op_symmat_meat.hpp | 18 inst/include/armadillo_bits/op_toeplitz_bones.hpp | 18 inst/include/armadillo_bits/op_toeplitz_meat.hpp | 18 inst/include/armadillo_bits/op_trimat_bones.hpp | 19 inst/include/armadillo_bits/op_trimat_meat.hpp | 19 inst/include/armadillo_bits/op_unique_bones.hpp | 19 inst/include/armadillo_bits/op_unique_meat.hpp | 19 inst/include/armadillo_bits/op_var_bones.hpp | 18 inst/include/armadillo_bits/op_var_meat.hpp | 18 inst/include/armadillo_bits/op_vectorise_bones.hpp | 18 inst/include/armadillo_bits/op_vectorise_meat.hpp | 18 inst/include/armadillo_bits/operator_cube_div.hpp | 18 inst/include/armadillo_bits/operator_cube_minus.hpp | 18 inst/include/armadillo_bits/operator_cube_plus.hpp | 18 inst/include/armadillo_bits/operator_cube_relational.hpp | 18 inst/include/armadillo_bits/operator_cube_schur.hpp | 18 inst/include/armadillo_bits/operator_cube_times.hpp | 18 inst/include/armadillo_bits/operator_div.hpp | 19 inst/include/armadillo_bits/operator_minus.hpp | 19 inst/include/armadillo_bits/operator_ostream.hpp | 18 inst/include/armadillo_bits/operator_plus.hpp | 19 inst/include/armadillo_bits/operator_relational.hpp | 18 inst/include/armadillo_bits/operator_schur.hpp | 19 inst/include/armadillo_bits/operator_times.hpp | 19 inst/include/armadillo_bits/podarray_bones.hpp | 18 inst/include/armadillo_bits/podarray_meat.hpp | 18 inst/include/armadillo_bits/promote_type.hpp | 19 inst/include/armadillo_bits/restrictors.hpp | 18 inst/include/armadillo_bits/running_stat_bones.hpp | 18 inst/include/armadillo_bits/running_stat_meat.hpp | 18 inst/include/armadillo_bits/running_stat_vec_bones.hpp | 18 inst/include/armadillo_bits/running_stat_vec_meat.hpp | 18 inst/include/armadillo_bits/sp_auxlib_bones.hpp | 21 inst/include/armadillo_bits/sp_auxlib_meat.hpp | 20 inst/include/armadillo_bits/span.hpp | 19 inst/include/armadillo_bits/spdiagview_bones.hpp | 18 inst/include/armadillo_bits/spdiagview_meat.hpp | 18 inst/include/armadillo_bits/spglue_join_bones.hpp | 18 inst/include/armadillo_bits/spglue_join_meat.hpp | 18 inst/include/armadillo_bits/spglue_minus_bones.hpp | 18 inst/include/armadillo_bits/spglue_minus_meat.hpp | 19 inst/include/armadillo_bits/spglue_plus_bones.hpp | 18 inst/include/armadillo_bits/spglue_plus_meat.hpp | 19 inst/include/armadillo_bits/spglue_times_bones.hpp | 18 inst/include/armadillo_bits/spglue_times_meat.hpp | 19 inst/include/armadillo_bits/spop_diagmat_bones.hpp | 18 inst/include/armadillo_bits/spop_diagmat_meat.hpp | 18 inst/include/armadillo_bits/spop_htrans_bones.hpp | 18 inst/include/armadillo_bits/spop_htrans_meat.hpp | 19 inst/include/armadillo_bits/spop_max_bones.hpp | 19 inst/include/armadillo_bits/spop_max_meat.hpp | 19 inst/include/armadillo_bits/spop_mean_bones.hpp | 21 inst/include/armadillo_bits/spop_mean_meat.hpp | 21 inst/include/armadillo_bits/spop_min_bones.hpp | 19 inst/include/armadillo_bits/spop_min_meat.hpp | 19 inst/include/armadillo_bits/spop_misc_bones.hpp | 18 inst/include/armadillo_bits/spop_misc_meat.hpp | 18 inst/include/armadillo_bits/spop_strans_bones.hpp | 18 inst/include/armadillo_bits/spop_strans_meat.hpp | 19 inst/include/armadillo_bits/spop_sum_bones.hpp | 18 inst/include/armadillo_bits/spop_sum_meat.hpp | 19 inst/include/armadillo_bits/spop_symmat_bones.hpp | 18 inst/include/armadillo_bits/spop_symmat_meat.hpp | 18 inst/include/armadillo_bits/spop_trimat_bones.hpp | 18 inst/include/armadillo_bits/spop_trimat_meat.hpp | 18 inst/include/armadillo_bits/spop_var_bones.hpp | 19 inst/include/armadillo_bits/spop_var_meat.hpp | 19 inst/include/armadillo_bits/strip.hpp | 18 inst/include/armadillo_bits/subview_bones.hpp | 19 inst/include/armadillo_bits/subview_cube_bones.hpp | 18 inst/include/armadillo_bits/subview_cube_each_bones.hpp | 18 inst/include/armadillo_bits/subview_cube_each_meat.hpp | 18 inst/include/armadillo_bits/subview_cube_meat.hpp | 18 inst/include/armadillo_bits/subview_each_bones.hpp | 18 inst/include/armadillo_bits/subview_each_meat.hpp | 18 inst/include/armadillo_bits/subview_elem1_bones.hpp | 18 inst/include/armadillo_bits/subview_elem1_meat.hpp | 18 inst/include/armadillo_bits/subview_elem2_bones.hpp | 18 inst/include/armadillo_bits/subview_elem2_meat.hpp | 18 inst/include/armadillo_bits/subview_field_bones.hpp | 18 inst/include/armadillo_bits/subview_field_meat.hpp | 18 inst/include/armadillo_bits/subview_meat.hpp | 20 inst/include/armadillo_bits/traits.hpp | 18 inst/include/armadillo_bits/typedef_elem.hpp | 18 inst/include/armadillo_bits/typedef_elem_check.hpp | 18 inst/include/armadillo_bits/typedef_mat.hpp | 18 inst/include/armadillo_bits/typedef_mat_fixed.hpp | 18 inst/include/armadillo_bits/unwrap.hpp | 18 inst/include/armadillo_bits/unwrap_cube.hpp | 18 inst/include/armadillo_bits/unwrap_spmat.hpp | 18 inst/include/armadillo_bits/upgrade_val.hpp | 18 inst/include/armadillo_bits/wall_clock_bones.hpp | 18 inst/include/armadillo_bits/wall_clock_meat.hpp | 22 inst/include/armadillo_bits/wrapper_arpack.hpp | 20 inst/include/armadillo_bits/wrapper_atlas.hpp | 18 inst/include/armadillo_bits/wrapper_blas.hpp | 18 inst/include/armadillo_bits/wrapper_lapack.hpp | 20 inst/include/armadillo_bits/wrapper_superlu.hpp | 21 inst/include/armadillo_bits/xtrans_mat_bones.hpp | 18 inst/include/armadillo_bits/xtrans_mat_meat.hpp | 18 inst/include/armadillo_bits/xvec_htrans_bones.hpp | 18 inst/include/armadillo_bits/xvec_htrans_meat.hpp | 18 src/fastLm.cpp | 10 src/init.c |only 511 files changed, 6739 insertions(+), 3787 deletions(-)
Title: North Temperate Lakes - Microbial Observatory 16S Time Series
Data and Functions
Description: Analyses of OTU tables produced by 16S sequencing, as well as example data. It contains the data and scripts used in the paper Linz, et al. (2017) "Bacterial community composition and dynamics spanning five years in freshwater bog lakes" (Manuscript submitted, preprint available at <http://biorxiv.org/content/early/2017/04/12/127035>).
Author: Alexandra Linz
Maintainer: Alexandra Linz <amlinz16@gmail.com>
Diff between OTUtable versions 1.0.0 dated 2016-03-17 and 1.1.0 dated 2017-04-13
OTUtable-1.0.0/OTUtable/man/clean_taxonomy.Rd |only OTUtable-1.1.0/OTUtable/DESCRIPTION | 10 +-- OTUtable-1.1.0/OTUtable/MD5 | 22 ++++--- OTUtable-1.1.0/OTUtable/NAMESPACE | 2 OTUtable-1.1.0/OTUtable/R/data_processing.R | 20 ++++++ OTUtable-1.1.0/OTUtable/R/format_mothur_output.R | 56 +++++++++++++++++-- OTUtable-1.1.0/OTUtable/data/metadata.rda |binary OTUtable-1.1.0/OTUtable/data/otu_table.rda |binary OTUtable-1.1.0/OTUtable/data/taxonomy.rda |binary OTUtable-1.1.0/OTUtable/man/OTUtable-package.Rd | 14 ++-- OTUtable-1.1.0/OTUtable/man/clean_TaxAss_taxonomy.Rd |only OTUtable-1.1.0/OTUtable/man/clean_mothur_taxonomy.Rd |only OTUtable-1.1.0/OTUtable/man/filter_otus.Rd |only OTUtable-1.1.0/OTUtable/man/reduce_names.Rd | 14 ++-- 14 files changed, 104 insertions(+), 34 deletions(-)
Title: Individual Tree Crowns Segmentation
Description: Three methods for Individual Tree Crowns (ITCs) delineation on remote sensing data: one is based on LiDAR data in x,y,z format and one on imagery data in raster format.
Author: Michele Dalponte
Maintainer: Michele Dalponte <michele.dalponte@fmach.it>
Diff between itcSegment versions 0.2 dated 2016-05-16 and 0.4 dated 2017-04-13
itcSegment-0.2/itcSegment/vignettes |only itcSegment-0.4/itcSegment/DESCRIPTION | 10 +++++----- itcSegment-0.4/itcSegment/MD5 | 13 +++++++------ itcSegment-0.4/itcSegment/NAMESPACE | 1 + itcSegment-0.4/itcSegment/R/itcIMG.R | 2 +- itcSegment-0.4/itcSegment/R/itcLiDAR.R | 7 ++++--- itcSegment-0.4/itcSegment/R/itcLiDARallo.R |only itcSegment-0.4/itcSegment/man/itcLiDAR.Rd | 5 ++++- itcSegment-0.4/itcSegment/man/itcLiDARallo.Rd |only 9 files changed, 22 insertions(+), 16 deletions(-)
Title: Practical Item Response Theory and Computer-Based Testing in R
Description: An implementation of item response theory and computer-based testing in R.
It is designed for bridging the gap between theoretical advancements in
psychometric research and their applications in practice. Currently, it
consists of five modules: (1) common item response theory functions, (2) estimation procedures,
(3) automated test assembly framework, (4) computerized adaptive testing framework,
(5) multistage testing framework. See detailed documentation at
<https://github.com/xluo11/xxIRT>.
Author: Xiao Luo [aut, cre]
Maintainer: Xiao Luo <xluo1986@gmail.com>
Diff between xxIRT versions 2.0.0 dated 2017-01-10 and 2.0.1 dated 2017-04-13
xxIRT-2.0.0/xxIRT/R/module0_gui_ata.R |only xxIRT-2.0.0/xxIRT/R/module0_gui_cat.R |only xxIRT-2.0.0/xxIRT/R/module0_gui_estimation.R |only xxIRT-2.0.0/xxIRT/R/module0_gui_irt.R |only xxIRT-2.0.0/xxIRT/R/module0_gui_mst.R |only xxIRT-2.0.0/xxIRT/R/module1_3PLmodel.R |only xxIRT-2.0.0/xxIRT/R/module1_commons.R |only xxIRT-2.0.0/xxIRT/R/module1_utilities.R |only xxIRT-2.0.0/xxIRT/R/module2_estimations.R |only xxIRT-2.0.0/xxIRT/README.md |only xxIRT-2.0.0/xxIRT/man/cat.sim.Rd |only xxIRT-2.0.0/xxIRT/man/estimate.3pl.Rd |only xxIRT-2.0.0/xxIRT/man/estimate.items.Rd |only xxIRT-2.0.0/xxIRT/man/estimate.people.Rd |only xxIRT-2.0.0/xxIRT/man/gui.ata.Rd |only xxIRT-2.0.0/xxIRT/man/gui.cat.Rd |only xxIRT-2.0.0/xxIRT/man/gui.estimation.Rd |only xxIRT-2.0.0/xxIRT/man/gui.irt.Rd |only xxIRT-2.0.0/xxIRT/man/gui.mst.Rd |only xxIRT-2.0.0/xxIRT/man/irt.model.3pl.Rd |only xxIRT-2.0.0/xxIRT/man/irt.model.Rd |only xxIRT-2.0.0/xxIRT/man/quadrature.Rd |only xxIRT-2.0.1/xxIRT/DESCRIPTION | 23 xxIRT-2.0.1/xxIRT/MD5 | 62 - xxIRT-2.0.1/xxIRT/NAMESPACE | 89 +- xxIRT-2.0.1/xxIRT/R/module0_model_3pl.R |only xxIRT-2.0.1/xxIRT/R/module1_irt_utils.R |only xxIRT-2.0.1/xxIRT/R/module1_stat_utils.R |only xxIRT-2.0.1/xxIRT/R/module2_estimation.R |only xxIRT-2.0.1/xxIRT/R/module2_estimation_helpers.R |only xxIRT-2.0.1/xxIRT/R/module3_ata.R | 744 ++++++++++++----------- xxIRT-2.0.1/xxIRT/R/module3_ata_helpers.R |only xxIRT-2.0.1/xxIRT/R/module4_cat.R | 501 ++++++++------- xxIRT-2.0.1/xxIRT/R/module4_cat_helpers.R |only xxIRT-2.0.1/xxIRT/R/module5_mst.R | 441 ++++++------- xxIRT-2.0.1/xxIRT/R/module5_mst_helpers.R |only xxIRT-2.0.1/xxIRT/R/module5_mst_simulation.R |only xxIRT-2.0.1/xxIRT/man/ata.Rd | 278 ++++---- xxIRT-2.0.1/xxIRT/man/ataHelpers.Rd |only xxIRT-2.0.1/xxIRT/man/catHelpers.Rd |only xxIRT-2.0.1/xxIRT/man/cat_sim.Rd |only xxIRT-2.0.1/xxIRT/man/estimate_3pl.Rd |only xxIRT-2.0.1/xxIRT/man/estimate_items.Rd |only xxIRT-2.0.1/xxIRT/man/estimate_people.Rd |only xxIRT-2.0.1/xxIRT/man/estimationHelper.Rd |only xxIRT-2.0.1/xxIRT/man/freq.Rd |only xxIRT-2.0.1/xxIRT/man/irt_model.Rd |only xxIRT-2.0.1/xxIRT/man/irt_rescale_3pl.Rd |only xxIRT-2.0.1/xxIRT/man/irt_select.Rd |only xxIRT-2.0.1/xxIRT/man/irt_stats.Rd |only xxIRT-2.0.1/xxIRT/man/model_3pl.Rd |only xxIRT-2.0.1/xxIRT/man/mst.Rd | 235 +++---- xxIRT-2.0.1/xxIRT/man/mstHelpers.Rd |only xxIRT-2.0.1/xxIRT/man/mst_sim.Rd |only xxIRT-2.0.1/xxIRT/man/rmse.Rd | 22 55 files changed, 1213 insertions(+), 1182 deletions(-)
Title: False Discovery Control Procedure Integrating the Prior
Structure Information
Description: Perform more powerful false discovery control (FDR) for microbiome data, taking into account the prior phylogenetic relationship among bacteria species. As a general methodology, it is applicable to any type of (genomic) data with prior structure information.
Author: Jun Chen
Maintainer: Jun Chen <chen.jun2@mayo.edu>
Diff between StructFDR versions 1.1 dated 2017-03-06 and 1.2 dated 2017-04-13
DESCRIPTION | 8 - MD5 | 20 +- NAMESPACE | 2 R/StructFDR.R | 327 ++++++++++++++++++------------------------------ inst/doc/StructFDR.R | 12 + inst/doc/StructFDR.Rmd | 27 +++ inst/doc/StructFDR.html | 37 +++-- man/SimulateData.Rd | 18 +- man/StructFDR.Rd | 17 +- man/TreeFDR.Rd | 20 ++ vignettes/StructFDR.Rmd | 27 +++ 11 files changed, 267 insertions(+), 248 deletions(-)
Title: Solving Ordinary Differential Equations to Understand
Luminescence
Description: A collection of functions to simulate luminescence signals in the
mineral quartz based on published models.
Author: Johannes Friedrich [aut, trl, cre],
Sebastian Kreutzer [aut, ths],
Christoph Schmidt [aut, ths]
Maintainer: Johannes Friedrich <johannes.friedrich@uni-bayreuth.de>
Diff between RLumModel versions 0.2.0 dated 2017-01-20 and 0.2.1 dated 2017-04-13
DESCRIPTION | 12 - MD5 | 57 ++-- NEWS | 14 + R/RLumModel-package.R | 8 R/model_LuminescenceSignals.R | 2 R/read_SEQ2R.R | 4 R/simulate_LM_OSL.R | 2 build/vignette.rds |binary inst/NEWS.Rd | 64 +++-- inst/doc/RLumModel_-_Getting_started_with_RLumModel.pdf |binary inst/doc/RLumModel_-_Using_own_parameter_sets.pdf |binary man/ExampleData.ModelOutput.Rd | 8 man/RLumModel-package.Rd | 3 man/model_LuminescenceSignals.Rd | 12 - man/read_SEQ2R.Rd | 10 src/RLumModel_init.c |only tests/testthat/test-model_LuminescenceSignals.R | 178 +++++++++++++-- tests/testthat/test-read_SEQ2R.R | 8 tests/testthat/test-simulate_CW_OSL.R | 55 ++++ tests/testthat/test-simulate_LM_OSL.R | 65 +++++ tests/testthat/test-simulate_RF.R | 107 +++++++++ tests/testthat/test-simulate_RF_and_heating.R | 88 +++++++ tests/testthat/test-simulate_TL.R | 37 +++ tests/testthat/test-simulate_heating.R | 27 ++ tests/testthat/test-simulate_illumination.R | 46 +++ tests/testthat/test-simulate_irradiation.R | 82 ++++++ tests/testthat/test-simulate_pause.R | 24 ++ tests/testthat/test-translate_sequence.R | 19 + vignettes/RLumModel_-_Getting_started_with_RLumModel.Rmd | 15 - vignettes/RLumModel_-_Using_own_parameter_sets.Rmd | 3 30 files changed, 824 insertions(+), 126 deletions(-)
Title: Analysis of Multivariate Data and Repeated Measures Designs
Description: Implemented are various tests for semi-parametric repeated measures
and general MANOVA designs that do neither assume multivariate normality nor
covariance homogeneity, i.e., the procedures are applicable for a wide range
of general multivariate factorial designs.
Author: Sarah Friedrich, Frank Konietschke, Markus Pauly
Maintainer: Sarah Friedrich <sarah.friedrich@uni-ulm.de>
Diff between MANOVA.RM versions 0.0.4 dated 2016-08-09 and 0.0.5 dated 2017-04-13
DESCRIPTION | 12 - MD5 | 48 +++---- NAMESPACE | 7 + R/Data.R | 2 R/GUI.R | 2 R/GUI_MANOVA.R | 2 R/MANOVA-function.R | 109 +++++++++++----- R/MANOVA.RM-package.R | 24 ++- R/MANOVA_Statistics.R | 64 ++++++--- R/RM-function.R | 36 +++-- R/RM_Statistics.R | 11 + R/RM_Statistics_oneway.R | 8 + R/RM_Statistics_subplot.R | 8 + R/confint_MANOVA.R |only R/utility_functions.R | 5 inst/doc/Introduction_to_MANOVA.RM.R | 22 ++- inst/doc/Introduction_to_MANOVA.RM.Rmd | 88 +++++++++++-- inst/doc/Introduction_to_MANOVA.RM.html | 209 +++++++++++++++++++++++++------- man/GUI.MANOVA.Rd | 2 man/GUI.RM.Rd | 2 man/MANOVA.RM-package.Rd | 24 ++- man/MANOVA.Rd | 44 ++++-- man/RM.Rd | 22 +-- man/conf.reg.Rd |only man/o2cons.Rd | 2 vignettes/Introduction_to_MANOVA.RM.Rmd | 88 +++++++++++-- 26 files changed, 612 insertions(+), 229 deletions(-)
Title: A Simple Web Framework for R
Description: jug is a web framework aimed at easily building APIs. It is mostly aimed at exposing R functions,
models and visualizations to third-parties by way of http requests.
Author: Bart Smeets [aut, cre]
Maintainer: Bart Smeets <bartsmeets86@gmail.com>
Diff between jug versions 0.1.6 dated 2017-02-23 and 0.1.7 dated 2017-04-13
DESCRIPTION | 11 ++- MD5 | 24 ++++---- NAMESPACE | 1 R/jug.R | 17 +++++ R/middleware_core.R | 5 + R/middleware_cors.R | 5 + build/vignette.rds |binary inst/doc/jug.R | 28 ++++++++- inst/doc/jug.Rmd | 130 +++++++++++++++++++++++++++++++++++---------- inst/doc/jug.html | 122 +++++++++++++++++++++++++++++++++--------- man/Jug.Rd | 18 +++++- tests/testthat/test_cors.R | 15 +++++ vignettes/jug.Rmd | 130 +++++++++++++++++++++++++++++++++++---------- 13 files changed, 404 insertions(+), 102 deletions(-)
Title: Case Influence in Structural Equation Models
Description: A set of tools for evaluating several measures of case influence for structural equation models.
Author: Massimiliano Pastore & Gianmarco Altoe'
Maintainer: Massimiliano Pastore <massimiliano.pastore@unipd.it>
Diff between influence.SEM versions 2.0 dated 2016-10-09 and 2.1 dated 2017-04-13
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++++---- NEWS | 5 +++++ R/lat.fitres.R |only R/obs.fitres.R |only R/sem.fitres.R |only man/explore.influence.Rd | 5 +++-- man/parinfluence.Rd | 2 +- man/sem.fitres.Rd |only 9 files changed, 22 insertions(+), 12 deletions(-)
Title: The Generalized DINA Model Framework
Description: A set of psychometric tools for cognitive diagnostic analyses for both dichotomous and polytomous responses. Various cognitive diagnosis models can be estimated, include the generalized deterministic inputs, noisy and gate (G-DINA) model by de la Torre (2011) <DOI:10.1007/s11336-011-9207-7>, the sequential G-DINA model by Ma and de la Torre (2016) <DOI:10.1111/bmsp.12070>, and many other models they subsume. Joint attribute distribution can be saturated, higher-order 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],
Jimmy de la Torre [aut]
Maintainer: Wenchao Ma <wenchao.ma@rutgers.edu>
Diff between GDINA versions 1.4.1 dated 2017-04-10 and 1.4.2 dated 2017-04-13
DESCRIPTION | 17 +++++------------ MD5 | 22 +++++++++++----------- NAMESPACE | 2 +- NEWS.md | 5 ++++- R/ExportedFuncs.R | 2 +- R/GDINA.R | 20 ++++++++------------ R/dif.R | 15 ++++++++++----- R/itemfit.R | 7 +++---- R/modelcomp.R | 22 +++++++++++++++------- R/print.GDINA.R | 6 +++--- inst/CITATION | 4 ++-- man/dif.Rd | 10 ++++++++-- 12 files changed, 71 insertions(+), 61 deletions(-)
Title: Dynamical Assembly of Islands by Speciation, Immigration and
Extinction
Description: Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction. See Valente et al. 2015. Ecology Letters 18: 844-852, <DOI:10.1111/ele.12461>.
Author: Rampal S. Etienne, Luis M. Valente, Albert B. Phillimore & Bart Haegeman
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Diff between DAISIE versions 1.2 dated 2016-11-14 and 1.4 dated 2017-04-13
DAISIE-1.2/DAISIE/R/DAISIE_format_sim.R |only DAISIE-1.2/DAISIE/man/DAISIE_format_sim.Rd |only DAISIE-1.4/DAISIE/DESCRIPTION | 11 DAISIE-1.4/DAISIE/MD5 | 46 - DAISIE-1.4/DAISIE/NAMESPACE | 4 DAISIE-1.4/DAISIE/R/DAISIE_ML.R | 233 ------- DAISIE-1.4/DAISIE/R/DAISIE_ML1.R |only DAISIE-1.4/DAISIE/R/DAISIE_ML2.R |only DAISIE-1.4/DAISIE/R/DAISIE_dataprep.R | 4 DAISIE-1.4/DAISIE/R/DAISIE_format_CS.R |only DAISIE-1.4/DAISIE/R/DAISIE_format_IW.R |only DAISIE-1.4/DAISIE/R/DAISIE_loglik_all.R | 227 ++++--- DAISIE-1.4/DAISIE/R/DAISIE_plot_age_diversity.R |only DAISIE-1.4/DAISIE/R/DAISIE_plot_island.R |only DAISIE-1.4/DAISIE/R/DAISIE_plot_sims.R | 250 ++++---- DAISIE-1.4/DAISIE/R/DAISIE_sim.R | 184 +++--- DAISIE-1.4/DAISIE/R/DAISIE_sim_core.R | 632 +++++++++++---------- DAISIE-1.4/DAISIE/R/DAISIE_sim_min_type2.R | 9 DAISIE-1.4/DAISIE/R/DAISIE_test.R |only DAISIE-1.4/DAISIE/data/Macaronesia_datalist.RData |only DAISIE-1.4/DAISIE/man/DAISIE-internal.Rd | 8 DAISIE-1.4/DAISIE/man/DAISIE-package.Rd | 12 DAISIE-1.4/DAISIE/man/DAISIE_ML.Rd | 52 + DAISIE-1.4/DAISIE/man/DAISIE_dataprep.Rd | 8 DAISIE-1.4/DAISIE/man/DAISIE_loglik_all.Rd | 174 ++--- DAISIE-1.4/DAISIE/man/DAISIE_plot_age_diversity.Rd |only DAISIE-1.4/DAISIE/man/DAISIE_plot_island.Rd |only DAISIE-1.4/DAISIE/man/DAISIE_plot_sims.Rd | 2 DAISIE-1.4/DAISIE/man/DAISIE_sim.Rd | 53 - DAISIE-1.4/DAISIE/man/Macaronesia_datalist.Rd |only DAISIE-1.4/DAISIE/tests |only 31 files changed, 927 insertions(+), 982 deletions(-)
Title: Cytobank API Wrapper for R
Description: Tools to interface with Cytobank's API via R, organized by various
endpoints that represent various areas of Cytobank functionality. Learn more
about Cytobank at <https://www.cytobank.org>.
Author: Preston Ng
Maintainer: Preston Ng <preston@cytobank.org>
Diff between CytobankAPI versions 1.0.0 dated 2017-01-12 and 1.0.1 dated 2017-04-13
DESCRIPTION | 6 +-- MD5 | 54 +++++++++++++++---------------- NAMESPACE | 1 R/CITRUS-class.R | 4 +- R/SPADE-class.R | 2 - R/citrus.R | 5 ++ R/fcs_files.R | 2 - R/gates.R | 9 ++++- R/populations.R | 2 - R/sample_tags.R | 2 - R/spade.R | 35 +++++++++++++++++++- R/viSNE-class.R | 16 ++++----- R/visne.R | 9 ++++- inst/doc/cytobank-advanced-analyses.Rmd | 3 + inst/doc/cytobank-advanced-analyses.html | 21 ++++++------ inst/doc/cytobank-quickstart.Rmd | 2 + inst/doc/cytobank-quickstart.html | 5 ++ man/CITRUS-class.Rd | 4 +- man/SPADE-class.Rd | 2 - man/citrus.Rd | 5 ++ man/fcs_files.Rd | 2 - man/populations.Rd | 2 - man/sample_tags.Rd | 2 - man/spade.Rd | 14 +++++++- man/viSNE-class.Rd | 2 - man/visne.Rd | 5 ++ vignettes/cytobank-advanced-analyses.Rmd | 3 + vignettes/cytobank-quickstart.Rmd | 2 + 28 files changed, 150 insertions(+), 71 deletions(-)
Title: Bayesian Additive Regression Trees
Description: Bayesian Additive Regression Trees (BART) provide flexible nonparametric modeling of covariates for continuous, binary and time-to-event outcomes. For more information on BART, see Chipman, George and McCulloch (2010) <doi:10.1214/09-AOAS285> and Sparapani, Logan, McCulloch and Laud (2016) <doi:10.1002/sim.6893>.
Author: Robert McCulloch <robert.e.mcculloch@gmail.com> and Rodney Sparapani <rsparapa@mcw.edu>
Maintainer: Rodney Sparapani <rsparapa@mcw.edu>
Diff between BART versions 1.0 dated 2017-04-07 and 1.1 dated 2017-04-13
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/BART-package.Rd | 23 +++++++++-------------- src/cpbart.cpp | 2 +- 4 files changed, 17 insertions(+), 22 deletions(-)
Title: Extended Structural Equation Modelling
Description: Facilitates treatment of statistical model specifications
as things that can be generated and manipulated programmatically.
Structural equation models may be specified with reticular action model matrices or paths,
linear structural relations matrices or paths, or
directly in matrix algebra.
Fit functions include full information maximum likelihood,
maximum likelihood, and weighted least squares.
Example models include confirmatory factor, multiple group, mixture
distribution, categorical threshold, modern test theory, differential
equations, state space, and many others.
Author: Steven M. Boker [aut],
Michael C. Neale [aut],
Hermine H. Maes [aut],
Michael J. Wilde [ctb],
Michael Spiegel [aut],
Timothy R. Brick [aut],
Ryne Estabrook [aut],
Timothy C. Bates [aut],
Paras Mehta [ctb],
Timo von Oertzen [ctb],
Ross J. Gore [aut],
Michael D. Hunter [aut],
Daniel C. Hackett [ctb],
Julian Karch [ctb],
Andreas M. Brandmaier [ctb],
Joshua N. Pritikin [aut, cre],
Mahsa Zahery [aut],
Robert M. Kirkpatrick [aut],
Yang Wang [ctb],
Charles Driver [ctb],
Massachusetts Institute of Technology [cph],
S. G. Johnson [cph],
Association for Computing Machinery [cph],
Dieter Kraft [cph],
Stefan Wilhelm [cph],
Manjunath B G [cph]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between OpenMx versions 2.7.9 dated 2017-03-22 and 2.7.9-1 dated 2017-04-13
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/ComputeNM.cpp | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: ODBC Database Access
Description: An ODBC database interface.
Author: Brian Ripley [aut, cre],
Michael Lapsley [aut] (1999 to Oct 2002)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between RODBC versions 1.3-14 dated 2016-09-26 and 1.3-15 dated 2017-04-13
ChangeLog | 4 ++++ DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/RODBC.pdf |binary src/RODBC.c | 6 +++--- 6 files changed, 17 insertions(+), 13 deletions(-)