Title: Interim Monitoring Using Adaptively Weighted Log-Rank Test in
Clinical Trials
Description: For any spending function specified by the user, this
package provides corresponding boundaries for interim testing using
the adaptively weighted log-rank test developed by Yang and Prentice
(2010 <doi:10.1111/j.1541-0420.2009.01243.x>).
The package uses a re-sampling method to obtain stopping boundaries
at the interim looks.The output consists of stopping boundaries
and observed values of the test statistics at the interim looks,
along with nominal p-values defined as the probability of the test
exceeding the specific observed test statistic value or critical
value, regardless of the test behavior at other looks.
The asymptotic validity of the stopping boundaries is established
in Yang (2018 <doi:10.1002/sim.7958>).
Author: Daewoo Pak and Song Yang
Maintainer: Daewoo Pak <heavyrain.pak@gmail.com>
Diff between YPInterimTesting versions 0.1.0 dated 2017-11-17 and 1.0.0 dated 2018-11-26
DESCRIPTION | 31 +-- MD5 | 27 +-- NAMESPACE | 2 NEWS.md | 19 ++ R/fun_estimate.R | 2 R/fun_interpol.R |only R/print.ypinterim.R | 72 ++++---- R/summary.ypinterim.R | 14 + R/ypinterim.default.R | 335 ++++++++++++++++++++++++--------------- README.md | 75 +++++++- data/virtual_data.rda |binary man/YPInterimTesting-internal.Rd | 1 man/YPInterimTesting-package.Rd | 10 - man/virtual_data.Rd | 4 man/ypinterim.Rd | 88 ++++++++-- 15 files changed, 457 insertions(+), 223 deletions(-)
More information about YPInterimTesting at CRAN
Permanent link
Title: CIE XYZ and some of Its Derived Color Spaces
Description: Functions for converting among CIE XYZ, xyY, Lab, and Luv.
The XYZs of some standard illuminants and some standard linear chromatic adaptation transforms (CATs) are included.
Compute CCT and the Planckian and daylight loci. Three different standard color difference metrics are included.
Author: Glenn Davis [aut,cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Diff between spacesXYZ versions 1.0-1 dated 2018-07-13 and 1.0-2 dated 2018-11-26
DESCRIPTION | 18 ++- MD5 | 44 +++++--- NAMESPACE | 19 +++ NEWS.md | 11 +- R/CCT.R |only R/DeltaE.R | 191 +++++++++++++++++++++++++++++++++---- R/basic.R | 79 ++++++++++++--- R/datasets.R | 22 +++- R/daylight.R |only R/hooks.R | 46 ++++++-- R/logging.R | 12 +- R/sysdata.rda |binary R/utils.R | 18 ++- build |only inst/doc |only inst/extdata/ciede2000testdata.txt |only inst/extdata/dataCCT.txt |only inst/extdata/illuminants.txt | 28 ++--- man/CCT.Rd |only man/DeltaE.Rd | 72 ++++++++++--- man/adaptation.Rd | 16 +-- man/daylight.Rd |only man/macros |only man/standardXYZ.Rd | 60 +++++++++-- man/uvfromXYZ.Rd | 32 ++++-- tests/test-CCT.R |only tests/test-DeltaE.R |only vignettes |only 28 files changed, 529 insertions(+), 139 deletions(-)
Title: Survival Analysis
Description: Contains the core survival analysis routines, including
definition of Surv objects,
Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models,
and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre],
Thomas Lumley [ctb, trl] (original S->R port and R maintainer until
2009)
Maintainer: Terry M Therneau <therneau.terry@mayo.edu>
Diff between survival versions 2.43-1 dated 2018-10-29 and 2.43-3 dated 2018-11-26
survival-2.43-1/survival/Changes |only survival-2.43-1/survival/R/survreg.S |only survival-2.43-1/survival/data/tobin.txt.gz |only survival-2.43-3/survival/DESCRIPTION | 7 survival-2.43-3/survival/MD5 | 77 survival-2.43-3/survival/NAMESPACE | 1 survival-2.43-3/survival/R/concordance.R | 22 survival-2.43-3/survival/R/coxph.R | 22 survival-2.43-3/survival/R/finegray.R | 3 survival-2.43-3/survival/R/model.matrix.coxph.R | 22 survival-2.43-3/survival/R/print.coxph.S | 14 survival-2.43-3/survival/R/survSplit.R | 7 survival-2.43-3/survival/R/survreg.R |only survival-2.43-3/survival/data/tobin.rda |only survival-2.43-3/survival/inst/NEWS.Rd | 26 survival-2.43-3/survival/inst/doc/adjcurve.pdf |binary survival-2.43-3/survival/inst/doc/compete.pdf |binary survival-2.43-3/survival/inst/doc/concordance.Rnw | 29 survival-2.43-3/survival/inst/doc/concordance.pdf |binary survival-2.43-3/survival/inst/doc/multi.pdf |binary survival-2.43-3/survival/inst/doc/population.pdf |binary survival-2.43-3/survival/inst/doc/splines.pdf |binary survival-2.43-3/survival/inst/doc/tests.pdf |binary survival-2.43-3/survival/inst/doc/tiedtimes.pdf |binary survival-2.43-3/survival/inst/doc/timedep.pdf |binary survival-2.43-3/survival/inst/doc/validate.pdf |binary survival-2.43-3/survival/man/coxph.Rd | 2 survival-2.43-3/survival/man/ridge.Rd | 12 survival-2.43-3/survival/man/strata.Rd | 5 survival-2.43-3/survival/man/survSplit.Rd | 9 survival-2.43-3/survival/man/survexp.us.Rd | 4 survival-2.43-3/survival/noweb/Makefile | 4 survival-2.43-3/survival/noweb/agreg.Rnw | 94 survival-2.43-3/survival/noweb/concordance.Rnw | 28 survival-2.43-3/survival/noweb/coxph.Rnw | 74 survival-2.43-3/survival/noweb/coxph2.Rnw |only survival-2.43-3/survival/noweb/finegray.Rnw | 17 survival-2.43-3/survival/noweb/parse.Rnw |only survival-2.43-3/survival/noweb/zph.Rnw | 5 survival-2.43-3/survival/src/norisk.c |only survival-2.43-3/survival/src/survproto.h | 3 survival-2.43-3/survival/tests/concordance3.Rout.save |only survival-2.43-3/survival/vignettes/concordance.Rnw | 29 survival-2.43-3/survival/vignettes/refer.bib | 2222 ++++++++++-------- 44 files changed, 1633 insertions(+), 1105 deletions(-)
Title: Functions for Set-Theoretic Multi-Method Research and Advanced
QCA
Description: Functions for performing set-theoretic multi-method research, QCA for clustered data, theory evaluation, Enhanced Standard Analysis, indirect calibration, radar visualisations. Additionally it includes data to replicate the examples in the book by C. Q. Schneider and C. Wagemann "Set Theoretic Methods for the Social Sciences", Cambridge University Press and in the online appendix.
Author: Ioana-Elena Oana [aut, cre],
Juraj Medzihorsky [aut],
Mario Quaranta [aut],
Carsten Q. Schneider [aut]
Maintainer: Ioana-Elena Oana <oana_ioana-elena@phd.ceu.edu>
Diff between SetMethods versions 2.3.1 dated 2018-04-25 and 2.4 dated 2018-11-26
DESCRIPTION | 15 +- MD5 | 76 +++++++----- NAMESPACE | 4 NEWS | 17 ++ R/LR.intersect.R |only R/QCAfit.R | 25 ++-- R/QCAradar.R | 2 R/ambig.cases.R |only R/cases.suf.typ.fct.R | 23 +++ R/cases.theory.evaluation.R | 206 +++++++++++++++++++++++++-------- R/intersectExp.R |only R/matches.suf.typiir.R | 23 +++ R/matches.suf.typtyp.R | 21 ++- R/mmr.R | 14 +- R/negateExp.R |only R/pimplot.R | 251 ++++++++++++++++++++++------------------- R/print.casestheoryeval.R | 5 R/print.theoryeval.R | 21 +-- R/print.thintersect.R |only R/property.cube.R |only R/skew.check.R |only R/theory.data.R | 35 ++++- R/theory.evaluation.R | 15 +- R/theory.fit.R | 2 R/theory.intersections.R |only R/xy.plot.R | 129 ++++++++++++--------- R/zzz.R | 9 - data/CUSFS.rda |only man/CUSFS.Rd |only man/LR.intersect.Rd |only man/QCAfit.Rd | 42 +++--- man/SetMethods-package.Rd | 6 man/ambig.cases.Rd |only man/cases.suf.typ.fct.Rd | 5 man/cases.theory.evaluation.Rd | 35 +++-- man/intersectExp.Rd |only man/matches.suf.typiir.Rd | 5 man/matches.suf.typtyp.Rd | 5 man/mmr.Rd | 5 man/negateExp.Rd |only man/pimplot.Rd | 61 +++++---- man/print.thintersect.Rd |only man/property.cube.Rd |only man/skew.check.Rd |only man/theory.data.Rd | 7 - man/theory.evaluation.Rd | 22 ++- man/theory.intersections.Rd |only man/xy.plot.Rd | 91 ++++---------- 48 files changed, 720 insertions(+), 457 deletions(-)
Title: Data Analysis of Liquid-Liquid Systems
Description: Analyses experimental data from liquid-liquid phase diagrams and
provide a simple way to obtain its parameters and a simplified report. Designed
initially to analyse Aqueous Two-Phases Systems, the package will include (every
other update) new functions in order to comprise useful tools in liquid-liquid
analysis.
Author: Diego F Coelho <diegofcoelho@gmail.com>
Maintainer: Diego F Coelho <diegofcoelho@gmail.com>
Diff between LLSR versions 0.0.2.2 dated 2018-11-06 and 0.0.2.3 dated 2018-11-26
LLSR-0.0.2.2/LLSR/R/LLSRxy.R |only LLSR-0.0.2.2/LLSR/data/sysdata.rda |only LLSR-0.0.2.2/LLSR/man/AQSys.crpt.Rd |only LLSR-0.0.2.2/LLSR/man/AQSysList.Rd |only LLSR-0.0.2.2/LLSR/man/LLSRxy.Rd |only LLSR-0.0.2.2/LLSR/man/llsr_cols.Rd |only LLSR-0.0.2.2/LLSR/man/scale_color_llsr.Rd |only LLSR-0.0.2.2/LLSR/man/scale_fill_llsr.Rd |only LLSR-0.0.2.3/LLSR/DESCRIPTION | 10 - LLSR-0.0.2.3/LLSR/MD5 | 45 ++++---- LLSR-0.0.2.3/LLSR/NAMESPACE | 5 LLSR-0.0.2.3/LLSR/R/AQSys.R | 7 - LLSR-0.0.2.3/LLSR/R/AQSys.err.R | 31 +++--- LLSR-0.0.2.3/LLSR/R/AQSys.mathDesc.R | 10 - LLSR-0.0.2.3/LLSR/R/AQSys.mrchk.R | 47 --------- LLSR-0.0.2.3/LLSR/R/AQSysDB.R | 6 - LLSR-0.0.2.3/LLSR/R/AQSysDOE.R |only LLSR-0.0.2.3/LLSR/R/AQSysEval.R | 63 +++++++----- LLSR-0.0.2.3/LLSR/R/AQSysUtils.R | 22 ++-- LLSR-0.0.2.3/LLSR/R/CorporateColours.R | 40 +++---- LLSR-0.0.2.3/LLSR/R/LLSRUtils.R | 126 ++++++++++++++++++++++++- LLSR-0.0.2.3/LLSR/R/datasets.R | 21 +++- LLSR-0.0.2.3/LLSR/data/llsr_data.rda |only LLSR-0.0.2.3/LLSR/data/temp_data.rda |only LLSR-0.0.2.3/LLSR/man/AQSys.Rd | 3 LLSR-0.0.2.3/LLSR/man/AQSys.plot.Rd | 2 LLSR-0.0.2.3/LLSR/man/AQSysDOE.Rd |only LLSR-0.0.2.3/LLSR/man/AQSysEval.Rd | 6 - LLSR-0.0.2.3/LLSR/man/llsr_data.Rd |only LLSR-0.0.2.3/LLSR/tests/testthat/testMainFns.R | 12 +- 30 files changed, 287 insertions(+), 169 deletions(-)
Title: Spatial Interpolation by Inverse Path Distance Weighting
Description: Functions are provided to interpolate geo-referenced point data via
Inverse Path Distance Weighting. Useful for coastal marine applications where
barriers in the landscape preclude interpolation with Euclidean distances.
Author: Joseph Stachelek [aut, cre] (<https://orcid.org/0000-0002-5924-2464>)
Maintainer: Joseph Stachelek <stachel2@msu.edu>
Diff between ipdw versions 0.2-6 dated 2017-05-19 and 0.2-7 dated 2018-11-26
ipdw-0.2-6/ipdw/R/pathdistGen_parallel.R |only ipdw-0.2-6/ipdw/tests/testthat/Rplots.pdf |only ipdw-0.2-7/ipdw/DESCRIPTION | 18 ipdw-0.2-7/ipdw/MD5 | 46 - ipdw-0.2-7/ipdw/NAMESPACE | 3 ipdw-0.2-7/ipdw/NEWS.md | 7 ipdw-0.2-7/ipdw/R/costrasterGen.R | 14 ipdw-0.2-7/ipdw/R/errorGen.R | 7 ipdw-0.2-7/ipdw/R/ipdw.R | 17 ipdw-0.2-7/ipdw/R/ipdwInterp.R | 98 ++-- ipdw-0.2-7/ipdw/R/pathdistGen.R | 15 ipdw-0.2-7/ipdw/README.md | 69 ++ ipdw-0.2-7/ipdw/build/vignette.rds |binary ipdw-0.2-7/ipdw/inst/doc/ipdw2.Rmd | 4 ipdw-0.2-7/ipdw/inst/doc/ipdw2.html | 485 ++++++++++++++------ ipdw-0.2-7/ipdw/man/costrasterGen.Rd | 4 ipdw-0.2-7/ipdw/man/ipdw.Rd | 21 ipdw-0.2-7/ipdw/man/ipdwInterp.Rd | 27 - ipdw-0.2-7/ipdw/man/pathdistGen.Rd | 5 ipdw-0.2-7/ipdw/tests/testthat/test-costrasterGen.R | 3 ipdw-0.2-7/ipdw/tests/testthat/test-errorGen.R | 3 ipdw-0.2-7/ipdw/tests/testthat/test-ipdwInterp.R | 33 - ipdw-0.2-7/ipdw/tests/testthat/test-pathdistGen.R | 4 ipdw-0.2-7/ipdw/vignettes/ipdw2.Rmd | 4 ipdw-0.2-7/ipdw/vignettes/ipdw2.bib | 15 25 files changed, 626 insertions(+), 276 deletions(-)
Title: Companion Animal Population Management
Description: Quantitative analysis to support companion animal population
management. Some functions assist survey sampling tasks (calculate sample
size for simple and complex designs, select sampling units and estimate
population parameters) while others assist the modelling of population
dynamics. For demographic characterizations and population management
evaluations see: "Baquero, et al." (2018),
<doi:10.1016/j.prevetmed.2018.07.006>. For modelling of
population dynamics see: "Baquero et al." (2016),
<doi:10.1016/j.prevetmed.2015.11.009>. For sampling methods
see: "Levy PS & Lemeshow S" (2013), "ISBN-10: 0470040076";
"Lumley" (2010), "ISBN: 978-0-470-28430-8".
Author: Oswaldo Santos Baquero [aut, cre],
Marcos Amaku [ctb],
Fernando Ferreira [ctb]
Maintainer: Oswaldo Santos Baquero <baquero@usp.br>
Diff between capm versions 0.13.8 dated 2018-11-22 and 0.13.9 dated 2018-11-26
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 5 +++++ R/MapkmlPSU.R | 10 +++++----- R/capm-package.R | 4 ++-- man/capm-package.Rd | 4 ++-- 6 files changed, 23 insertions(+), 18 deletions(-)
More information about coveffectsplot at CRAN
Permanent link
More information about changepoint.mv at CRAN
Permanent link
Title: Sample Size Estimation Functions for Studies of Interobserver
Agreement
Description: Contains basic tools for sample size estimation in studies of interobserver/interrater agreement (reliability). Includes functions for both the power-based and confidence interval-based methods, with binary or multinomial outcomes and two through six raters.
Author: Michael A Rotondi <mrotondi@yorku.ca>
Maintainer: Michael A Rotondi <mrotondi@yorku.ca>
Diff between kappaSize versions 1.1 dated 2013-03-12 and 1.2 dated 2018-11-26
DESCRIPTION | 15 +++++---------- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 34 +++++++++++++++++++++++++++++++++- man/CI3Cats.Rd | 6 ++++-- man/CI4Cats.Rd | 4 ++-- man/CI5Cats.Rd | 3 ++- man/CIBinary.Rd | 4 ++-- man/FixedN3Cats.Rd | 6 ++++-- man/FixedN4Cats.Rd | 6 ++++-- man/FixedN5Cats.Rd | 6 ++++-- man/FixedNBinary.Rd | 6 ++++-- man/power3Cats.Rd | 6 ++++-- man/power4Cats.Rd | 6 ++++-- man/power5Cats.Rd | 6 ++++-- man/powerBinary.Rd | 6 ++++-- 15 files changed, 94 insertions(+), 48 deletions(-)
Title: Analyse Audio Recordings and Automatically Extract Animal
Vocalizations
Description: Contains all the necessary tools to process audio recordings of
various formats (e.g., WAV, WAC, MP3, ZC), filter noisy files,
display audio signals, detect and extract automatically acoustic
features for further analysis such as classification.
Author: Jean Marchal [aut, cre],
Francois Fabianek [aut],
Christopher Scott [aut],
Chris Corben [ctb, cph] (Read ZC files, original C code),
Peter Wilson [ctb, cph] (Read ZC files, original R code),
Wildlife Acoustics, Inc. [ctb, cph] (Read WAC files, original C code),
WavX Inc. [cph]
Maintainer: Jean Marchal <jean.marchal@wavx.ca>
Diff between bioacoustics versions 0.1.5 dated 2018-08-15 and 0.1.6 dated 2018-11-26
DESCRIPTION | 8 ++--- MD5 | 50 +++++++++++++++---------------- NEWS.md | 72 +++++++++++++++++++++++++-------------------- R/BatBioacoustics.R | 4 +- R/BatClassify.R | 3 + R/RcppExports.R | 46 ++++++++++++++-------------- R/read_zc.R | 11 +++++- R/spectro.R | 4 +- R/tools.R | 11 +++++- build/vignette.rds |binary configure | 22 +++++++------ configure.ac | 6 ++- inst/doc/introduction.R | 2 - inst/doc/introduction.Rmd | 4 +- inst/doc/introduction.html | 4 +- inst/doc/tutorial.R | 31 ++++++++----------- inst/doc/tutorial.Rmd | 35 ++++++++++----------- inst/doc/tutorial.html | 31 ++++++++----------- man/to_dB.Rd | 2 - src/Makevars.in | 1 src/Makevars.win | 3 + src/fft.cpp | 2 - src/fft.h | 1 src/spectro.cpp | 4 +- vignettes/introduction.Rmd | 4 +- vignettes/tutorial.Rmd | 35 ++++++++++----------- 26 files changed, 208 insertions(+), 188 deletions(-)
Title: Select and Download Climate Data from 'DWD' (German Weather
Service)
Description: Handle climate data from the 'DWD' ('Deutscher Wetterdienst', see
<https://www.dwd.de/EN/climate_environment/cdc/cdc.html> for more information).
Choose files with 'selectDWD()', download and process data sets with 'dataDWD()' and 'readDWD()'.
Author: Berry Boessenkool
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between rdwd versions 0.10.2 dated 2018-05-29 and 0.11.0 dated 2018-11-26
rdwd-0.10.2/rdwd/inst/doc/mapDWD.R |only rdwd-0.10.2/rdwd/inst/doc/mapDWD.Rmd |only rdwd-0.10.2/rdwd/inst/doc/rdwd.R |only rdwd-0.10.2/rdwd/inst/doc/rdwd.Rmd |only rdwd-0.10.2/rdwd/tests |only rdwd-0.10.2/rdwd/vignettes/PackageSchematic.png |only rdwd-0.10.2/rdwd/vignettes/mapDWD.Rmd |only rdwd-0.10.2/rdwd/vignettes/rdwd.Rmd |only rdwd-0.11.0/rdwd/DESCRIPTION | 15 rdwd-0.11.0/rdwd/MD5 | 65 +- rdwd-0.11.0/rdwd/NAMESPACE | 2 rdwd-0.11.0/rdwd/NEWS | 21 rdwd-0.11.0/rdwd/R/createIndex.R | 20 rdwd-0.11.0/rdwd/R/dataDWD.R | 12 rdwd-0.11.0/rdwd/R/indexFTP.R | 308 ++++++----- rdwd-0.11.0/rdwd/R/rdwd-package.R | 124 ++++ rdwd-0.11.0/rdwd/R/readDWD.R | 9 rdwd-0.11.0/rdwd/R/readVars.R |only rdwd-0.11.0/rdwd/R/selectDWD.R | 627 ++++++++++++------------ rdwd-0.11.0/rdwd/README.md | 2 rdwd-0.11.0/rdwd/build/vignette.rds |binary rdwd-0.11.0/rdwd/data/DEU.rda |only rdwd-0.11.0/rdwd/data/fileIndex.rda |binary rdwd-0.11.0/rdwd/data/geoIndex.rda |binary rdwd-0.11.0/rdwd/data/metaIndex.rda |binary rdwd-0.11.0/rdwd/inst/doc/cases.html |only rdwd-0.11.0/rdwd/inst/doc/cases.html.asis |only rdwd-0.11.0/rdwd/inst/doc/mapDWD.html | 27 - rdwd-0.11.0/rdwd/inst/doc/mapDWD.html.asis |only rdwd-0.11.0/rdwd/inst/doc/rdwd.html | 88 +-- rdwd-0.11.0/rdwd/inst/doc/rdwd.html.asis |only rdwd-0.11.0/rdwd/man/DEU.Rd |only rdwd-0.11.0/rdwd/man/dataDWD.Rd | 9 rdwd-0.11.0/rdwd/man/index.Rd | 4 rdwd-0.11.0/rdwd/man/indexFTP.Rd | 10 rdwd-0.11.0/rdwd/man/parameter_abbreviations.Rd |only rdwd-0.11.0/rdwd/man/rdwd.Rd | 3 rdwd-0.11.0/rdwd/man/readDWD.Rd | 6 rdwd-0.11.0/rdwd/man/readVars.Rd |only rdwd-0.11.0/rdwd/man/selectDWD.Rd | 45 - rdwd-0.11.0/rdwd/vignettes/cases.html.asis |only rdwd-0.11.0/rdwd/vignettes/mapDWD.html.asis |only rdwd-0.11.0/rdwd/vignettes/rdwd.html.asis |only 43 files changed, 788 insertions(+), 609 deletions(-)
Title: Rename and Encode Data Frames Using External Crosswalk Files
Description: A pair of functions for renaming and encoding data frames
using external crosswalk files. It is especially useful when
constructing master data sets from multiple smaller data
sets that do not name or encode variables consistently
across files. Based on similar commands in 'Stata'.
Author: Benjamin Skinner [aut, cre] (<https://orcid.org/0000-0002-0337-7415>)
Maintainer: Benjamin Skinner <btskinner@virginia.edu>
Diff between crosswalkr versions 0.1.1 dated 2017-10-17 and 0.2.2 dated 2018-11-26
DESCRIPTION | 16 ++-- MD5 | 28 ++++---- NEWS.md |only R/encodefrom.R | 24 ++++--- R/renamefrom.R | 18 ++--- R/utility_functions.R | 3 build/vignette.rds |binary inst/doc/crosswalkr.R | 23 +++---- inst/doc/crosswalkr.Rmd | 53 ++++++++++------ inst/doc/crosswalkr.html | 126 ++++++++++++++++++++++++--------------- man/encodefrom.Rd | 17 ++--- man/figures |only man/renamefrom.Rd | 14 ++-- tests/testthat/test-encodefrom.R | 22 +++--- vignettes/crosswalkr.Rmd | 53 ++++++++++------ vignettes/vignette.css | 2 16 files changed, 238 insertions(+), 161 deletions(-)
Title: Some Algorithms for Mixed Models
Description: This program can be used to fit Gaussian linear mixed models (LMM). Univariate and multivariate response models, multiple variance components, as well as, certain correlation and covariance structures are supported. In many occasions, the user can pick one of the several mixed model fitting algorithms, which are explained further in the details section. Some algorithms are specific to certain types of models (univariate or multivariate, diagonal or non-diagonal residual, one or multiple variance components, etc,...).
Author: Deniz Akdemir
Maintainer: Deniz Akdemir <deniz.akdemir.work@gmail.com>
Diff between SAMM versions 0.0.1 dated 2016-07-10 and 1.1 dated 2018-11-26
DESCRIPTION | 10 MD5 | 23 NAMESPACE | 3 R/RcppExports.R | 92 +- build/partial.rdb |binary man/SAMM-package.Rd | 10 man/SAMM.Rd | 212 +++-- man/loglikfuncmmmkmv.Rd |only man/sigcovfuncs_cppforR.Rd | 4 src/Makevars | 15 src/Makevars.win | 12 src/RcppExports.cpp | 503 +++++++----- src/SAMM.cpp | 1811 ++++++++++++++++++++++++--------------------- 13 files changed, 1501 insertions(+), 1194 deletions(-)
Title: Child Anthropometry z-Score Calculator
Description: A tool for calculating z-scores and centiles for weight-for-age,
length/height-for-age, weight-for-length/height, BMI-for-age,
head circumference-for-age, age circumference-for-age,
subscapular skinfold-for-age, triceps skinfold-for-age based on the
WHO Child Growth Standards.
Author: Mark Myatt [aut],
Ernest Guevarra [aut, cre] (<https://orcid.org/0000-0002-4887-4415>)
Maintainer: Ernest Guevarra <ernestgmd@gmail.com>
Diff between zscorer versions 0.1.0 dated 2018-02-05 and 0.2.0 dated 2018-11-26
DESCRIPTION | 26 +- MD5 | 52 ++-- NAMESPACE | 6 NEWS.md | 18 + R/addWGSR.R |only R/getWGS.R | 13 - R/zscorer.R | 70 +++++ README.md | 515 ++++++++++++++++++++++++++--------------- build/vignette.rds |binary data/anthro1.rda |binary data/anthro2.rda |binary data/anthro3.rda |only data/wgsData.rda |binary data/wgsrData.rda |only inst/doc/anthropometry.Rmd | 4 inst/doc/anthropometry.html | 8 inst/doc/calculate_zscore.R |only inst/doc/calculate_zscore.Rmd |only inst/doc/calculate_zscore.html |only inst/zscorer/server.R | 368 ++++++++++++++++++++++++++--- inst/zscorer/ui.R | 113 ++++---- man/addWGSR.Rd |only man/anthro1.Rd | 2 man/anthro2.Rd | 2 man/anthro3.Rd |only man/getCohortWGS.Rd | 3 man/getWGS.Rd | 25 + man/getWGSR.Rd |only man/wgsData.Rd | 2 man/wgsrData.Rd |only tests/testthat/test_getWGSR.R |only vignettes/anthropometry.Rmd | 4 vignettes/calculate_zscore.Rmd |only 33 files changed, 897 insertions(+), 334 deletions(-)
Title: Functions to Make Surveys Processing Easier
Description: Set of functions to make the processing and analysis of
surveys easier : interactive shiny apps and addins for data recoding,
contingency tables, dataset metadata handling, and several convenience
functions.
Author: Julien Barnier [aut, cre],
François Briatte [aut],
Joseph Larmarange [aut]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>
Diff between questionr versions 0.6.3 dated 2018-07-17 and 0.7.0 dated 2018-11-26
DESCRIPTION | 12 - MD5 | 46 +++--- NAMESPACE | 2 NEWS.md | 6 R/describe.R | 12 - R/lookfor.R | 2 R/recode.R | 2 R/table.multi.R | 2 build/vignette.rds |binary data/fecondite.RData |binary data/fertility.RData |binary data/happy.RData |binary data/hdv2003.RData |binary data/rp2012.RData |binary data/rp99.RData |binary inst/doc/recoding_addins.html | 303 ++++++++++++++---------------------------- man/clipcopy.Rd | 2 man/cprop.Rd | 8 - man/cross.multi.table.Rd | 4 man/describe.Rd | 16 +- man/lookfor.Rd | 3 man/prop.Rd | 8 - man/quant.cut.Rd | 4 man/rprop.Rd | 8 - 24 files changed, 175 insertions(+), 265 deletions(-)
Title: Nonparametric Tests for Equality of Location Against Ordered
Alternatives
Description: Performs nonparametric tests for equality of location against ordered alternatives.
Author: Bulent Altunkaynak [aut, cre], Hamza Gamgam [aut]
Maintainer: Bulent Altunkaynak <bulenta@gazi.edu.tr>
Diff between npordtests versions 1.0 dated 2018-11-19 and 1.1 dated 2018-11-26
DESCRIPTION | 6 +++--- MD5 | 30 +++++++++++++++--------------- R/AtTest.R | 14 +++++++------- R/FtmTest.R | 14 +++++++------- R/GcTest.R | 18 +++++++++--------- R/JtTest.R | 14 +++++++------- R/KtpTest.R | 14 +++++++------- R/LsTest.R | 14 +++++++------- R/LtTest.R | 14 +++++++------- R/MjtTest.R | 14 +++++++------- R/RsTest.R | 14 +++++++------- R/SsTest.R | 14 +++++++------- R/StTest.R | 14 +++++++------- R/TmTest.R | 21 +++++++++++---------- R/WsTest.R | 14 +++++++------- man/MjtTest.rd | 2 ++ 16 files changed, 117 insertions(+), 114 deletions(-)
Title: Archetypoid Algorithms and Anomaly Detection
Description: Collection of several algorithms to obtain archetypoids with small and large databases and with both classical
multivariate data and functional data (univariate and multivariate). Some of these algorithms also allow to detect
anomalies (outliers).
Author: Guillermo Vinue, Irene Epifanio
Maintainer: Guillermo Vinue <Guillermo.Vinue@uv.es>
Diff between adamethods versions 1.0 dated 2018-11-14 and 1.1 dated 2018-11-26
DESCRIPTION | 14 - MD5 | 178 ++++++++--------- NAMESPACE | 2 NEWS | 8 R/adalara.R | 62 ++--- R/adalara_no_paral.R | 64 ++---- R/archetypoids_funct.R | 7 R/archetypoids_funct_internal.R | 7 R/archetypoids_funct_multiv.R | 7 R/archetypoids_funct_multiv_internal.R | 7 R/archetypoids_funct_multiv_robust.R | 7 R/archetypoids_funct_multiv_robust_internal.R | 7 R/archetypoids_funct_robust.R | 7 R/archetypoids_funct_robust_internal.R | 7 R/archetypoids_norm_frob.R | 31 +- R/archetypoids_norm_frob_internal.R | 32 +-- R/archetypoids_robust.R | 39 +-- R/archetypoids_robust_internal.R | 7 R/bisquare_function.R | 7 R/do_ada.R | 16 + R/do_ada_robust.R | 65 +----- R/do_clean.R | 2 R/do_clean_multiv.R | 2 R/do_fada.R | 7 R/do_fada_multiv.R | 7 R/do_fada_multiv_robust.R | 7 R/do_fada_robust.R | 7 R/fadalara.R | 41 +++ R/fadalara_no_paral.R | 43 +++- R/frame_in_r.R |only R/frobenius_norm.R | 16 + R/frobenius_norm_funct.R | 7 R/frobenius_norm_funct_multiv.R | 7 R/frobenius_norm_funct_multiv_robust.R | 7 R/frobenius_norm_funct_robust.R | 7 R/frobenius_norm_robust.R | 7 R/int_prod_mat.R | 7 R/int_prod_mat_funct.R | 7 R/int_prod_mat_sq.R | 7 R/int_prod_mat_sq_funct.R | 7 R/memento.R | 12 - R/outl_toler.R | 5 R/stepArchetypesRawData_funct.R | 14 + R/stepArchetypesRawData_funct_internal.R | 13 - R/stepArchetypesRawData_funct_multiv.R | 14 + R/stepArchetypesRawData_funct_multiv_internal.R | 13 - R/stepArchetypesRawData_funct_multiv_robust.R | 18 + R/stepArchetypesRawData_funct_multiv_robust_internal.R | 17 + R/stepArchetypesRawData_funct_robust.R | 18 + R/stepArchetypesRawData_funct_robust_internal.R | 17 + R/stepArchetypesRawData_norm_frob.R | 31 +- R/stepArchetypesRawData_norm_frob_internal.R | 19 + R/stepArchetypesRawData_robust.R | 7 R/stepArchetypesRawData_robust_internal.R | 6 man/adalara.Rd | 31 +- man/adalara_no_paral.Rd | 33 +-- man/archetypoids_funct.Rd | 7 man/archetypoids_funct_multiv.Rd | 7 man/archetypoids_funct_multiv_robust.Rd | 7 man/archetypoids_funct_robust.Rd | 7 man/archetypoids_norm_frob.Rd | 23 +- man/archetypoids_robust.Rd | 26 -- man/bisquare_function.Rd | 7 man/do_ada.Rd | 16 + man/do_ada_robust.Rd | 55 ----- man/do_clean.Rd | 2 man/do_clean_multiv.Rd | 2 man/do_fada.Rd | 7 man/do_fada_multiv.Rd | 7 man/do_fada_multiv_robust.Rd | 7 man/do_fada_robust.Rd | 7 man/fadalara.Rd | 25 ++ man/fadalara_no_paral.Rd | 26 ++ man/frame_in_r.Rd |only man/frobenius_norm.Rd | 16 + man/frobenius_norm_funct.Rd | 7 man/frobenius_norm_funct_multiv.Rd | 7 man/frobenius_norm_funct_multiv_robust.Rd | 7 man/frobenius_norm_funct_robust.Rd | 7 man/frobenius_norm_robust.Rd | 7 man/int_prod_mat.Rd | 7 man/int_prod_mat_funct.Rd | 7 man/int_prod_mat_sq.Rd | 7 man/int_prod_mat_sq_funct.Rd | 7 man/outl_toler.Rd | 5 man/stepArchetypesRawData_funct.Rd | 14 + man/stepArchetypesRawData_funct_multiv.Rd | 14 + man/stepArchetypesRawData_funct_multiv_robust.Rd | 18 + man/stepArchetypesRawData_funct_robust.Rd | 18 + man/stepArchetypesRawData_norm_frob.Rd | 23 +- man/stepArchetypesRawData_robust.Rd | 7 91 files changed, 966 insertions(+), 494 deletions(-)
Title: The Variance Gamma Distribution
Description: Provides functions for the variance gamma
distribution. Density, distribution and quantile functions.
Functions for random number generation and fitting of the
variance gamma to data. Also, functions for computing moments
of the variance gamma distribution of any order about any
location. In addition, there are functions for checking the
validity of parameters and to interchange different sets of
parameterizations for the variance gamma distribution.
Author: David Scott <d.scott@auckland.ac.nz> and
Christine Yang Dong <c.dong@auckland.ac.nz>
Maintainer: David Scott <d.scott@auckland.ac.nz>
Diff between VarianceGamma versions 0.3-1 dated 2012-04-13 and 0.4-0 dated 2018-11-26
VarianceGamma-0.3-1/VarianceGamma/Todo |only VarianceGamma-0.3-1/VarianceGamma/VarianceGamma-Ex.R |only VarianceGamma-0.4-0/VarianceGamma/ChangeLog | 4 VarianceGamma-0.4-0/VarianceGamma/DESCRIPTION | 25 ++-- VarianceGamma-0.4-0/VarianceGamma/MD5 | 23 +--- VarianceGamma-0.4-0/VarianceGamma/NAMESPACE | 33 ++++- VarianceGamma-0.4-0/VarianceGamma/R/dvg.R | 54 ++++----- VarianceGamma-0.4-0/VarianceGamma/R/vgCalcRange.R | 2 VarianceGamma-0.4-0/VarianceGamma/R/vgChangePars.R | 2 VarianceGamma-0.4-0/VarianceGamma/R/vgFit.R | 5 VarianceGamma-0.4-0/VarianceGamma/TODO |only VarianceGamma-0.4-0/VarianceGamma/data/vgParam.rda |binary VarianceGamma-0.4-0/VarianceGamma/inst/unitTests/Makefile | 44 +++---- VarianceGamma-0.4-0/VarianceGamma/man/VarianceGamma.Rd | 78 ++++++-------- 14 files changed, 141 insertions(+), 129 deletions(-)
Title: Representative and Adequate Prioritization Toolkit in R
Description: Biodiversity is in crisis. The overarching aim of conservation
is to preserve biodiversity patterns and processes. To this end, protected
areas are established to buffer species and preserve biodiversity processes.
But resources are limited and so protected areas must be cost-effective.
This package contains tools to generate plans for protected areas
(prioritizations), using spatially explicit targets for biodiversity
patterns and processes. To obtain solutions in a feasible amount of time,
this package uses the commercial 'Gurobi' software package (obtained from
<http://www.gurobi.com/>). For more information on using
this package, see Hanson et al. (2017) <doi:10.1111/2041-210X.12862>.
Author: Jeffrey O Hanson [aut, cre],
Jonathan R Rhodes [aut],
Hugh P Possingham [aut],
Richard A Fuller [aut]
Maintainer: Jeffrey O Hanson <jeffrey.hanson@uqconnect.edu.au>
Diff between raptr versions 0.1.2 dated 2018-06-28 and 0.1.3 dated 2018-11-26
DESCRIPTION | 8 MD5 | 60 - NEWS.md | 10 R/DemandPoints.R | 7 R/RcppExports.R | 8 build/vignette.rds |binary inst/CITATION | 7 inst/doc/raptr.html | 1890 ++++++++++++++-------------------- man/SpatialPolygons2PolySet.Rd | 3 man/basemap.Rd | 3 man/cache.Rd | 4 man/calcSpeciesAverageInPus.Rd | 4 man/casestudy_data.Rd | 3 man/is.cached.Rd | 2 man/is.comparable.Rd | 4 man/make.RapData.Rd | 3 man/plot.Rd | 3 man/show.Rd | 8 man/sim.space.Rd | 4 man/sim.species.Rd | 5 man/simulated_data.Rd | 2 man/solve.Rd | 5 man/space.held.Rd | 3 man/space.plot.Rd | 12 man/space.target.Rd | 3 man/spp.plot.Rd | 7 man/update.Rd | 4 src/RcppExports.cpp | 24 src/rcpp_extract_model_object.cpp | 50 tests/testthat/test-07-DemandPoints.R | 10 tests/testthat/test-11-RapUnsolved.R | 44 31 files changed, 971 insertions(+), 1229 deletions(-)
Title: The Normal Laplace Distribution
Description: Functions for the normal Laplace distribution. The package is
under development and provides only limited functionality.
Density, distribution and quantile functions, random number generation,
and moments are provided.
Author: David Scott <d.scott@auckland.ac.nz>, Jason Shicong Fu and
Simon Potter
Maintainer: David Scott <d.scott@auckland.ac.nz>
Diff between NormalLaplace versions 0.2-0 dated 2014-04-23 and 0.3-0 dated 2018-11-26
ChangeLog | 4 ++++ DESCRIPTION | 19 ++++++++++--------- MD5 | 8 ++++---- NAMESPACE | 21 +++++++++++++++++++-- inst/unitTests/Makefile | 44 ++++++++++++++++++++++---------------------- 5 files changed, 59 insertions(+), 37 deletions(-)
Title: Open Population Capture-Recapture
Description: Functions for non-spatial and spatial open-population capture-recapture analysis.
Author: Murray Efford [aut, cre] (<https://orcid.org/0000-0001-5231-5184>)
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between openCR versions 1.2.0 dated 2018-05-25 and 1.3.0 dated 2018-11-26
openCR-1.2.0/openCR/vignettes/openCR-vignette_cache |only openCR-1.2.0/openCR/vignettes/openCR-vignette_files |only openCR-1.3.0/openCR/DESCRIPTION | 8 openCR-1.3.0/openCR/MD5 | 93 ++++---- openCR-1.3.0/openCR/NAMESPACE | 7 openCR-1.3.0/openCR/NEWS | 42 +++ openCR-1.3.0/openCR/R/AIC.R | 24 +- openCR-1.3.0/openCR/R/PCH1.R | 4 openCR-1.3.0/openCR/R/RcppExports.R | 16 - openCR-1.3.0/openCR/R/derived.r | 50 ++-- openCR-1.3.0/openCR/R/getfn.R | 12 - openCR-1.3.0/openCR/R/geth.R |only openCR-1.3.0/openCR/R/loglik.R | 68 ++---- openCR-1.3.0/openCR/R/openCR.design.R | 222 +++++++++++++++----- openCR-1.3.0/openCR/R/openCR.fit.R | 43 ++- openCR-1.3.0/openCR/R/openCR.make.newdata.R | 22 + openCR-1.3.0/openCR/R/par.openCR.fit.R | 2 openCR-1.3.0/openCR/R/posterior.R | 25 -- openCR-1.3.0/openCR/R/posterior2.R |only openCR-1.3.0/openCR/R/predict.openCR.R | 7 openCR-1.3.0/openCR/R/prwisecr.R | 3 openCR-1.3.0/openCR/R/rev.capthist.R |only openCR-1.3.0/openCR/R/simulate.R | 57 +++-- openCR-1.3.0/openCR/R/summary.R |only openCR-1.3.0/openCR/R/utility.R | 37 ++- openCR-1.3.0/openCR/build/vignette.rds |binary openCR-1.3.0/openCR/data/dipper.RData |binary openCR-1.3.0/openCR/inst/doc/openCR-manual.pdf |binary openCR-1.3.0/openCR/inst/doc/openCR-vignette.R | 24 +- openCR-1.3.0/openCR/inst/doc/openCR-vignette.Rmd | 110 ++++++--- openCR-1.3.0/openCR/inst/doc/openCR-vignette.pdf |binary openCR-1.3.0/openCR/man/AIC.openCR.Rd | 10 openCR-1.3.0/openCR/man/classMembership.Rd |only openCR-1.3.0/openCR/man/dipper.Rd | 5 openCR-1.3.0/openCR/man/gonodontis.Rd | 14 - openCR-1.3.0/openCR/man/openCR-package.Rd | 4 openCR-1.3.0/openCR/man/openCR.design.Rd | 31 +- openCR-1.3.0/openCR/man/openCR.fit.Rd | 72 ++++-- openCR-1.3.0/openCR/man/par.openCR.fit.Rd | 2 openCR-1.3.0/openCR/man/print.openCR.Rd | 36 ++- openCR-1.3.0/openCR/man/rev.capthist.Rd |only openCR-1.3.0/openCR/man/simulate.Rd | 18 + openCR-1.3.0/openCR/src/RcppExports.cpp | 43 ++- openCR-1.3.0/openCR/src/geth.cpp | 135 ++++-------- openCR-1.3.0/openCR/src/makelookup.cpp |only openCR-1.3.0/openCR/src/prwi.cpp | 4 openCR-1.3.0/openCR/src/prwiparallel.cpp | 13 - openCR-1.3.0/openCR/src/prwisecrparallel.cpp | 29 +- openCR-1.3.0/openCR/src/utils.h | 3 openCR-1.3.0/openCR/vignettes/openCR-vignette.Rmd | 110 ++++++--- 50 files changed, 876 insertions(+), 529 deletions(-)
Title: Omics Data Integration Using Kernel Methods
Description: Kernel-based methods are powerful methods for integrating
heterogeneous types of data. mixKernel aims at providing methods to combine
kernel for unsupervised exploratory analysis. Different solutions are
provided to compute a meta-kernel, in a consensus way or in a way that
best preserves the original topology of the data. mixKernel also integrates
kernel PCA to visualize similarities between samples in a non linear space
and from the multiple source point of view. Functions to assess and display
important variables are also provided in the package. Jerome Mariette and
Nathalie Villa-Vialaneix (2017) <doi:10.1093/bioinformatics/btx682>.
Author: Jerome Mariette [aut, cre],
Nathalie Villa-Vialaneix [aut]
Maintainer: Jerome Mariette <jerome.mariette@inra.fr>
Diff between mixKernel versions 0.2 dated 2018-09-11 and 0.3 dated 2018-11-26
DESCRIPTION | 20 +++++++++++--------- MD5 | 6 +++--- NEWS | 5 +++++ R/kernel.pca.permute.R | 8 -------- 4 files changed, 19 insertions(+), 20 deletions(-)
Title: Group Sequential Enrichment Design
Description: Provides function to apply "Group sequential enrichment design incorporating subgroup selection" (GSED) method proposed by Magnusson and Turnbull (2013) <doi:10.1002/sim.5738>.
Author: Marie-Karelle Riviere
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between GSED versions 1.10 dated 2018-10-13 and 2.0 dated 2018-11-26
DESCRIPTION | 8 MD5 | 10 - NAMESPACE | 2 R/GSED.R | 357 ++++++++++++++++++++---------------------- man/GSED-package.Rd | 4 man/sim_magnusson_turnbull.Rd | 11 - 6 files changed, 189 insertions(+), 203 deletions(-)
More information about FlexParamCurve at CRAN
Permanent link
Title: Tools for 'CRAN'-Like Repositories
Description: A set of functions to manage 'CRAN'-like repositories
efficiently.
Author: Gábor Csárdi
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between cranlike versions 1.0.1 dated 2017-08-03 and 1.0.2 dated 2018-11-26
DESCRIPTION | 8 +-- MD5 | 30 ++++++----- NAMESPACE | 2 NEWS.md | 5 + R/cranlike.R | 30 ++++------- R/db.R | 98 +++++++++++++++++++++++++++------------ R/parse.R | 7 ++ R/utils.R | 4 + man/add_PACKAGES.Rd | 1 man/remove_PACKAGES.Rd | 1 man/update_PACKAGES.Rd | 1 man/with_db.Rd |only man/with_db_lock.Rd |only tests/testthat/test-cranlike.R | 8 +-- tests/testthat/test-db.R | 7 +- tests/testthat/test-edge-cases.R | 2 tests/testthat/test-old.R | 5 + 17 files changed, 132 insertions(+), 77 deletions(-)
Title: General Frailty Models: Shared, Joint and Nested Frailty Models
with Prediction; Evaluation of Failure-Time Surrogate Endpoints
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package:
1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied.
2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope).
3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects.
4) Joint frailty models in the context of the joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed.
5) Joint general frailty models in the context of the joint modelling for recurrent events with terminal event data with two independent frailty terms.
6) Joint Nested frailty models in the context of the joint modelling for recurrent events with terminal event, for hierarchically clustered data (with two levels of clustering) by including two iid gamma random effects.
7) Multivariate joint frailty models for two types of recurrent events and a terminal event.
8) Joint models for longitudinal data and a terminal event.
9) Trivariate joint models for longitudinal data, recurrent events and a terminal event.
10) Joint frailty models for the validation of surrogate endpoints in multiple randomized clinical trials with failure-time endpoints
Prediction values are available (for a terminal event or for a new recurrent event). Left-truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata are allowed. In each model, the random effects have the gamma or normal distribution. Now, you can also consider time-varying covariates effects in Cox, shared and joint frailty models (1-5). The package includes concordance measures for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey
Mauguen, Amadou Diakite, Alexandre Laurent, Myriam Lopez,
Agnieszka Krol and Casimir L. Sofeu
Maintainer: Virginie Rondeau <Virginie.Rondeau@inserm.fr>
Diff between frailtypack versions 2.13.2 dated 2018-09-25 and 3.0.1 dated 2018-11-26
frailtypack-2.13.2/frailtypack/man/plotAdditive.Rd |only frailtypack-2.13.2/frailtypack/man/plotFrailtyPenal.Rd |only frailtypack-2.13.2/frailtypack/man/plotJointNestedPenal.Rd |only frailtypack-2.13.2/frailtypack/man/plotJointPenal.Rd |only frailtypack-2.13.2/frailtypack/man/plotLongiPenal.Rd |only frailtypack-2.13.2/frailtypack/man/plotNestedPenal.Rd |only frailtypack-2.13.2/frailtypack/man/plotTrivPenal.Rd |only frailtypack-2.13.2/frailtypack/man/plotTrivPenalNL.Rd |only frailtypack-2.13.2/frailtypack/man/printAdditive.Rd |only frailtypack-2.13.2/frailtypack/man/printFrailtyPenal.Rd |only frailtypack-2.13.2/frailtypack/man/printJointNestedPenal.Rd |only frailtypack-2.13.2/frailtypack/man/printJointPenal.Rd |only frailtypack-2.13.2/frailtypack/man/printLongiPenal.Rd |only frailtypack-2.13.2/frailtypack/man/printNestedPenal.Rd |only frailtypack-2.13.2/frailtypack/man/printTrivPenal.Rd |only frailtypack-2.13.2/frailtypack/man/printTrivPenalNL.Rd |only frailtypack-2.13.2/frailtypack/man/summaryAdditive.Rd |only frailtypack-2.13.2/frailtypack/man/summaryFrailtyPenal.Rd |only frailtypack-2.13.2/frailtypack/man/summaryJointNestedPenal.Rd |only frailtypack-2.13.2/frailtypack/man/summaryJointPenal.Rd |only frailtypack-2.13.2/frailtypack/man/summaryLongiPenal.Rd |only frailtypack-2.13.2/frailtypack/man/summaryNestedPenal.Rd |only frailtypack-2.13.2/frailtypack/man/summaryTrivPenal.Rd |only frailtypack-2.13.2/frailtypack/man/summaryTrivPenalNL.Rd |only frailtypack-3.0.1/frailtypack/DESCRIPTION | 19 frailtypack-3.0.1/frailtypack/MD5 | 480 frailtypack-3.0.1/frailtypack/NAMESPACE | 172 frailtypack-3.0.1/frailtypack/NEWS | 704 frailtypack-3.0.1/frailtypack/R/Cmeasures.R | 134 frailtypack-3.0.1/frailtypack/R/Diffepoce.R | 122 frailtypack-3.0.1/frailtypack/R/SurvIC.R | 49 frailtypack-3.0.1/frailtypack/R/additivePenal.R | 219 frailtypack-3.0.1/frailtypack/R/cluster.R | 31 frailtypack-3.0.1/frailtypack/R/dataHelp.R |only frailtypack-3.0.1/frailtypack/R/epoce.R | 180 frailtypack-3.0.1/frailtypack/R/evalOpenMPFortran.R |only frailtypack-3.0.1/frailtypack/R/event2.R | 19 frailtypack-3.0.1/frailtypack/R/frailtyPenal.R | 799 + frailtypack-3.0.1/frailtypack/R/frailtypack-package.R |only frailtypack-3.0.1/frailtypack/R/hazard.R | 27 frailtypack-3.0.1/frailtypack/R/integrant.R |only frailtypack-3.0.1/frailtypack/R/jointSurrSimul.R |only frailtypack-3.0.1/frailtypack/R/jointSurroKendall.R |only frailtypack-3.0.1/frailtypack/R/jointSurroPenal.R |only frailtypack-3.0.1/frailtypack/R/jointSurroPenalSimul.R |only frailtypack-3.0.1/frailtypack/R/jointSurroTKendall.R |only frailtypack-3.0.1/frailtypack/R/kappa_val_croisee.r |only frailtypack-3.0.1/frailtypack/R/kendall_bootstrap.r |only frailtypack-3.0.1/frailtypack/R/lines.frailtyPenal.R | 2 frailtypack-3.0.1/frailtypack/R/longiPenal.R | 318 frailtypack-3.0.1/frailtypack/R/multivPenal.R | 299 frailtypack-3.0.1/frailtypack/R/num.id.R | 42 frailtypack-3.0.1/frailtypack/R/plot.Diffepoce.R | 20 frailtypack-3.0.1/frailtypack/R/plot.epoce.R | 27 frailtypack-3.0.1/frailtypack/R/plot.frailtyPenal.R | 152 frailtypack-3.0.1/frailtypack/R/plot.jointNestedPenal.R | 64 frailtypack-3.0.1/frailtypack/R/plot.jointPenal.R | 66 frailtypack-3.0.1/frailtypack/R/plot.jointSurroPenal.R |only frailtypack-3.0.1/frailtypack/R/plot.longiPenal.R | 66 frailtypack-3.0.1/frailtypack/R/plot.multivPenal.R | 45 frailtypack-3.0.1/frailtypack/R/plot.nestedPenal.additivePenal.R | 66 frailtypack-3.0.1/frailtypack/R/plot.predFrailty.R | 24 frailtypack-3.0.1/frailtypack/R/plot.predJoint.R | 28 frailtypack-3.0.1/frailtypack/R/plot.predJointNested.R | 1 frailtypack-3.0.1/frailtypack/R/plot.predLongi.R | 98 frailtypack-3.0.1/frailtypack/R/plot.trivPenal.R | 376 frailtypack-3.0.1/frailtypack/R/plot.trivPenalNL.R | 62 frailtypack-3.0.1/frailtypack/R/prediction.R | 755 frailtypack-3.0.1/frailtypack/R/print.Cmeasures.R | 16 frailtypack-3.0.1/frailtypack/R/print.Diffepoce.R | 2 frailtypack-3.0.1/frailtypack/R/print.additivePenal.R | 488 frailtypack-3.0.1/frailtypack/R/print.epoce.R | 2 frailtypack-3.0.1/frailtypack/R/print.frailtyPenal.R | 41 frailtypack-3.0.1/frailtypack/R/print.jointNestedPenal.R | 50 frailtypack-3.0.1/frailtypack/R/print.jointPenal.R | 58 frailtypack-3.0.1/frailtypack/R/print.longiPenal.R | 41 frailtypack-3.0.1/frailtypack/R/print.multivPenal.R | 45 frailtypack-3.0.1/frailtypack/R/print.nestedPenal.R | 458 frailtypack-3.0.1/frailtypack/R/print.predFrailty.R | 2 frailtypack-3.0.1/frailtypack/R/print.predJoint.R | 2 frailtypack-3.0.1/frailtypack/R/print.predJointNested.R | 1 frailtypack-3.0.1/frailtypack/R/print.predLongi.R | 2 frailtypack-3.0.1/frailtypack/R/print.trivPenal.R | 72 frailtypack-3.0.1/frailtypack/R/print.trivPenalNL.R | 97 frailtypack-3.0.1/frailtypack/R/slope.R | 51 frailtypack-3.0.1/frailtypack/R/subcluster.R | 44 frailtypack-3.0.1/frailtypack/R/summary.additivePenal.R | 37 frailtypack-3.0.1/frailtypack/R/summary.frailtyPenal.R | 50 frailtypack-3.0.1/frailtypack/R/summary.jointNestedPenal.R | 51 frailtypack-3.0.1/frailtypack/R/summary.jointPenal.R | 49 frailtypack-3.0.1/frailtypack/R/summary.jointSurroPenal.R |only frailtypack-3.0.1/frailtypack/R/summary.jointSurroPenalSimul.R |only frailtypack-3.0.1/frailtypack/R/summary.longiPenal.R | 220 frailtypack-3.0.1/frailtypack/R/summary.multivPenal.R | 20 frailtypack-3.0.1/frailtypack/R/summary.nestedPenal.R | 39 frailtypack-3.0.1/frailtypack/R/summary.trivPenal.R | 242 frailtypack-3.0.1/frailtypack/R/summary.trivPenalNL.R | 53 frailtypack-3.0.1/frailtypack/R/survival.R | 28 frailtypack-3.0.1/frailtypack/R/synthese_result_modele_reduit.r |only frailtypack-3.0.1/frailtypack/R/terminal.R | 18 frailtypack-3.0.1/frailtypack/R/test.R |only frailtypack-3.0.1/frailtypack/R/testOpenMPFortran.R |only frailtypack-3.0.1/frailtypack/R/timedep.R | 90 frailtypack-3.0.1/frailtypack/R/timedep.names.R | 14 frailtypack-3.0.1/frailtypack/R/trivPenal.R | 418 frailtypack-3.0.1/frailtypack/R/trivPenalNL.R | 425 frailtypack-3.0.1/frailtypack/R/wts.R | 33 frailtypack-3.0.1/frailtypack/README | 2 frailtypack-3.0.1/frailtypack/data/dataOvarian.rda |only frailtypack-3.0.1/frailtypack/data/gastadj.rda |only frailtypack-3.0.1/frailtypack/demo/00Index | 2 frailtypack-3.0.1/frailtypack/demo/frailtypack_jointSurroPenal.R |only frailtypack-3.0.1/frailtypack/demo/frailtypack_jointSurroPenalSimul.R |only frailtypack-3.0.1/frailtypack/inst/doc/Package_summary.Rmd | 50 frailtypack-3.0.1/frailtypack/inst/doc/Package_summary.html | 1055 - frailtypack-3.0.1/frailtypack/man/Cmeasures.Rd | 185 frailtypack-3.0.1/frailtypack/man/Diffepoce.Rd | 252 frailtypack-3.0.1/frailtypack/man/SurvIC.Rd | 50 frailtypack-3.0.1/frailtypack/man/additivePenal.Rd | 386 frailtypack-3.0.1/frailtypack/man/bcos.Rd | 44 frailtypack-3.0.1/frailtypack/man/cluster.Rd | 33 frailtypack-3.0.1/frailtypack/man/colorectal.Rd | 83 frailtypack-3.0.1/frailtypack/man/colorectalLongi.Rd | 83 frailtypack-3.0.1/frailtypack/man/dataAdditive.Rd | 55 frailtypack-3.0.1/frailtypack/man/dataMultiv.Rd | 47 frailtypack-3.0.1/frailtypack/man/dataNCC.Rd | 45 frailtypack-3.0.1/frailtypack/man/dataNested.Rd | 56 frailtypack-3.0.1/frailtypack/man/dataOvarian.Rd |only frailtypack-3.0.1/frailtypack/man/epoce.Rd | 359 frailtypack-3.0.1/frailtypack/man/event2.Rd | 63 frailtypack-3.0.1/frailtypack/man/frailtyPenal.Rd | 1010 - frailtypack-3.0.1/frailtypack/man/frailtypack-package.Rd | 147 frailtypack-3.0.1/frailtypack/man/gastadj.Rd |only frailtypack-3.0.1/frailtypack/man/hazard.Rd | 30 frailtypack-3.0.1/frailtypack/man/jointSurrSimul.Rd |only frailtypack-3.0.1/frailtypack/man/jointSurroPenal.Rd |only frailtypack-3.0.1/frailtypack/man/jointSurroPenalSimul.Rd |only frailtypack-3.0.1/frailtypack/man/jointSurroTKendall.Rd |only frailtypack-3.0.1/frailtypack/man/longiPenal.Rd | 597 frailtypack-3.0.1/frailtypack/man/multivPenal.Rd | 462 frailtypack-3.0.1/frailtypack/man/num.id.Rd | 48 frailtypack-3.0.1/frailtypack/man/plot.Diffepoce.Rd | 39 frailtypack-3.0.1/frailtypack/man/plot.epoce.Rd | 52 frailtypack-3.0.1/frailtypack/man/plot.frailtyPenal.Rd |only frailtypack-3.0.1/frailtypack/man/plot.jointNestedPenal.Rd |only frailtypack-3.0.1/frailtypack/man/plot.jointPenal.Rd |only frailtypack-3.0.1/frailtypack/man/plot.jointSurroPenal.Rd |only frailtypack-3.0.1/frailtypack/man/plot.longiPenal.Rd |only frailtypack-3.0.1/frailtypack/man/plot.multivPenal.Rd | 127 frailtypack-3.0.1/frailtypack/man/plot.nestedPenal.Rd |only frailtypack-3.0.1/frailtypack/man/plot.predFrailty.Rd | 50 frailtypack-3.0.1/frailtypack/man/plot.predJoint.Rd | 57 frailtypack-3.0.1/frailtypack/man/plot.predLongi.Rd | 72 frailtypack-3.0.1/frailtypack/man/plot.trivPenal.Rd |only frailtypack-3.0.1/frailtypack/man/plot.trivPenalNL.Rd |only frailtypack-3.0.1/frailtypack/man/prediction.Rd | 1416 - frailtypack-3.0.1/frailtypack/man/print.Cmeasures.Rd | 28 frailtypack-3.0.1/frailtypack/man/print.additivePenal.Rd |only frailtypack-3.0.1/frailtypack/man/print.frailtyPenal.Rd |only frailtypack-3.0.1/frailtypack/man/print.jointNestedPenal.Rd |only frailtypack-3.0.1/frailtypack/man/print.jointPenal.Rd |only frailtypack-3.0.1/frailtypack/man/print.longiPenal.Rd |only frailtypack-3.0.1/frailtypack/man/print.multivPenal.Rd | 62 frailtypack-3.0.1/frailtypack/man/print.nestedPenal.Rd |only frailtypack-3.0.1/frailtypack/man/print.prediction.Rd | 67 frailtypack-3.0.1/frailtypack/man/print.trivPenal.Rd |only frailtypack-3.0.1/frailtypack/man/print.trivPenalNL.Rd |only frailtypack-3.0.1/frailtypack/man/readmission.Rd | 53 frailtypack-3.0.1/frailtypack/man/slope.Rd | 41 frailtypack-3.0.1/frailtypack/man/subcluster.Rd | 39 frailtypack-3.0.1/frailtypack/man/summary.additivePenal.Rd |only frailtypack-3.0.1/frailtypack/man/summary.frailtyPenal.Rd |only frailtypack-3.0.1/frailtypack/man/summary.jointNestedPenal.Rd |only frailtypack-3.0.1/frailtypack/man/summary.jointPenal.Rd |only frailtypack-3.0.1/frailtypack/man/summary.jointSurroPenal.Rd |only frailtypack-3.0.1/frailtypack/man/summary.jointSurroPenalSimul.Rd |only frailtypack-3.0.1/frailtypack/man/summary.longiPenal.Rd |only frailtypack-3.0.1/frailtypack/man/summary.multivPenal.Rd | 69 frailtypack-3.0.1/frailtypack/man/summary.nestedPenal.Rd |only frailtypack-3.0.1/frailtypack/man/summary.trivPenal.Rd |only frailtypack-3.0.1/frailtypack/man/summary.trivPenalNL.Rd |only frailtypack-3.0.1/frailtypack/man/survival.Rd | 28 frailtypack-3.0.1/frailtypack/man/terminal.Rd | 40 frailtypack-3.0.1/frailtypack/man/timedep.Rd | 84 frailtypack-3.0.1/frailtypack/man/trivPenal.Rd | 780 - frailtypack-3.0.1/frailtypack/man/trivPenalNL.Rd | 801 - frailtypack-3.0.1/frailtypack/man/wts.Rd | 32 frailtypack-3.0.1/frailtypack/src/Adonnees.f90 | 308 frailtypack-3.0.1/frailtypack/src/AparamMultive.f90 | 284 frailtypack-3.0.1/frailtypack/src/Aparameters.f90 | 698 frailtypack-3.0.1/frailtypack/src/Integrale_mult_scl.f90 |only frailtypack-3.0.1/frailtypack/src/Integrant_scl.f90 |only frailtypack-3.0.1/frailtypack/src/Makevars | 23 frailtypack-3.0.1/frailtypack/src/Pour_Adaptative.f90 |only frailtypack-3.0.1/frailtypack/src/aGhermite.f90 | 518 frailtypack-3.0.1/frailtypack/src/aaOptim.f90 | 4352 ++--- frailtypack-3.0.1/frailtypack/src/aaOptim_New_scl.f90 |only frailtypack-3.0.1/frailtypack/src/aaOptim_New_scl2.f90 |only frailtypack-3.0.1/frailtypack/src/aaOptim_SCL_0.f90 |only frailtypack-3.0.1/frailtypack/src/aaOptimres.f90 | 1676 +- frailtypack-3.0.1/frailtypack/src/aaUseFunction.f90 | 2388 +-- frailtypack-3.0.1/frailtypack/src/aaUseFunctionG.f90 | 766 frailtypack-3.0.1/frailtypack/src/aamarq98o.f90 | 930 - frailtypack-3.0.1/frailtypack/src/additive.f90 | 4856 +++--- frailtypack-3.0.1/frailtypack/src/afuncpasres.f90 | 2806 +-- frailtypack-3.0.1/frailtypack/src/ahrmsym.f90 | 2994 +-- frailtypack-3.0.1/frailtypack/src/aresidusMartingale.f90 | 2876 +-- frailtypack-3.0.1/frailtypack/src/autres_fonctions.f90 |only frailtypack-3.0.1/frailtypack/src/distance.f90 | 6912 ++++---- frailtypack-3.0.1/frailtypack/src/epoce.f90 | 1498 - frailtypack-3.0.1/frailtypack/src/epoce_log.f90 | 1538 - frailtypack-3.0.1/frailtypack/src/epoce_long.f90 | 5868 +++---- frailtypack-3.0.1/frailtypack/src/epoce_long_nl.f90 | 2658 +-- frailtypack-3.0.1/frailtypack/src/frailtypack.f90 | 5478 +++---- frailtypack-3.0.1/frailtypack/src/frailtypack.h | 37 frailtypack-3.0.1/frailtypack/src/funcpaG_tps.f90 | 706 frailtypack-3.0.1/frailtypack/src/funcpaGcpm.f90 | 908 - frailtypack-3.0.1/frailtypack/src/funcpaGcpm_intcens.f90 | 996 - frailtypack-3.0.1/frailtypack/src/funcpaGcpm_log.f90 | 856 - frailtypack-3.0.1/frailtypack/src/funcpaGsplines.f90 | 860 - frailtypack-3.0.1/frailtypack/src/funcpaGsplines_intcens.f90 | 854 - frailtypack-3.0.1/frailtypack/src/funcpaGsplines_log.f90 | 874 - frailtypack-3.0.1/frailtypack/src/funcpaGweib.f90 | 662 frailtypack-3.0.1/frailtypack/src/funcpaGweib_intcens.f90 | 670 frailtypack-3.0.1/frailtypack/src/funcpaGweib_log.f90 | 666 frailtypack-3.0.1/frailtypack/src/funcpaMultivCpm.f90 | 690 frailtypack-3.0.1/frailtypack/src/funcpaMultivSplines.f90 | 1150 - frailtypack-3.0.1/frailtypack/src/funcpaMultivWeib.f90 | 498 frailtypack-3.0.1/frailtypack/src/funcpa_adaptative.f90 |only frailtypack-3.0.1/frailtypack/src/funcpa_laplace.f90 |only frailtypack-3.0.1/frailtypack/src/funcpaacpm.f90 | 1374 - frailtypack-3.0.1/frailtypack/src/funcpaasplines.f90 | 1348 - frailtypack-3.0.1/frailtypack/src/funcpaaweib.f90 | 1122 - frailtypack-3.0.1/frailtypack/src/funcpaj_tps.f90 | 882 - frailtypack-3.0.1/frailtypack/src/funcpajcpm.f90 | 546 frailtypack-3.0.1/frailtypack/src/funcpajcpm_log.f90 | 548 frailtypack-3.0.1/frailtypack/src/funcpajgeneral.f90 | 676 frailtypack-3.0.1/frailtypack/src/funcpajlongisplines.f90 | 1718 +- frailtypack-3.0.1/frailtypack/src/funcpajlongisplines_nl.f90 | 1902 +- frailtypack-3.0.1/frailtypack/src/funcpajlongiweib.f90 | 1442 - frailtypack-3.0.1/frailtypack/src/funcpajlongiweib_nl.f90 | 1282 - frailtypack-3.0.1/frailtypack/src/funcpajsplines.f90 | 738 frailtypack-3.0.1/frailtypack/src/funcpajsplinesIndiv.f90 | 660 frailtypack-3.0.1/frailtypack/src/funcpajsplines_fam.f90 | 888 - frailtypack-3.0.1/frailtypack/src/funcpajsplines_intcens.f90 | 662 frailtypack-3.0.1/frailtypack/src/funcpajsplines_log.f90 | 732 frailtypack-3.0.1/frailtypack/src/funcpajsplines_logIndiv.f90 | 666 frailtypack-3.0.1/frailtypack/src/funcpajsplines_surrogate_scl_1.f90 |only frailtypack-3.0.1/frailtypack/src/funcpajsplines_surrogate_scl_2.f90 |only frailtypack-3.0.1/frailtypack/src/funcpajweib.f90 | 460 frailtypack-3.0.1/frailtypack/src/funcpajweib_fam.f90 | 436 frailtypack-3.0.1/frailtypack/src/funcpajweib_intcens.f90 | 458 frailtypack-3.0.1/frailtypack/src/funcpajweib_log.f90 | 466 frailtypack-3.0.1/frailtypack/src/funcpancpm.f90 | 1164 - frailtypack-3.0.1/frailtypack/src/funcpansplines.f90 | 1244 - frailtypack-3.0.1/frailtypack/src/funcpanweib.f90 | 814 - frailtypack-3.0.1/frailtypack/src/funcpas_tps.f90 | 850 - frailtypack-3.0.1/frailtypack/src/funcpascpm.f90 | 660 frailtypack-3.0.1/frailtypack/src/funcpascpm_intcens.f90 | 654 frailtypack-3.0.1/frailtypack/src/funcpascpm_log.f90 | 616 frailtypack-3.0.1/frailtypack/src/funcpassplines.f90 | 622 frailtypack-3.0.1/frailtypack/src/funcpassplines_intcens.f90 | 744 frailtypack-3.0.1/frailtypack/src/funcpassplines_log.f90 | 638 frailtypack-3.0.1/frailtypack/src/funcpasweib.f90 | 468 frailtypack-3.0.1/frailtypack/src/funcpasweib_intcens.f90 | 562 frailtypack-3.0.1/frailtypack/src/funcpasweib_log.f90 | 508 frailtypack-3.0.1/frailtypack/src/init.c | 7 frailtypack-3.0.1/frailtypack/src/joint.f90 | 6990 ++++----- frailtypack-3.0.1/frailtypack/src/jointSurrogate.f90 |only frailtypack-3.0.1/frailtypack/src/joint_longi.f90 | 7750 +++++----- frailtypack-3.0.1/frailtypack/src/joint_longi_nl.f90 | 7710 ++++----- frailtypack-3.0.1/frailtypack/src/joint_surrogate.f90 |only frailtypack-3.0.1/frailtypack/src/jointsurrokendall.f90 |only frailtypack-3.0.1/frailtypack/src/multiveJoint.f90 | 4678 +++--- frailtypack-3.0.1/frailtypack/src/nested.f90 | 5328 +++--- frailtypack-3.0.1/frailtypack/src/prediction.f90 | 2522 +-- frailtypack-3.0.1/frailtypack/src/prediction_Recurr_Sha.f90 | 428 frailtypack-3.0.1/frailtypack/src/prediction_biv.f90 | 2544 +-- frailtypack-3.0.1/frailtypack/src/prediction_sha_logn.f90 | 452 frailtypack-3.0.1/frailtypack/src/prediction_tri.f90 | 2828 +-- frailtypack-3.0.1/frailtypack/src/prediction_tri_nl.f90 | 7746 ++++----- frailtypack-3.0.1/frailtypack/src/predictionfam.f90 | 1160 - frailtypack-3.0.1/frailtypack/src/risque.f90 | 260 frailtypack-3.0.1/frailtypack/src/somme.f90 |only frailtypack-3.0.1/frailtypack/src/surrosim.f90 |only frailtypack-3.0.1/frailtypack/src/survival.f90 | 1070 - frailtypack-3.0.1/frailtypack/src/test.f90 |only frailtypack-3.0.1/frailtypack/vignettes/Package_summary.Rmd | 50 288 files changed, 82062 insertions(+), 75671 deletions(-)
Title: Markov Random Fields with Additional Covariates
Description: Approximate node interaction parameters of Markov Random Fields
graphical networks. Models can incorporate additional covariates, allowing users to estimate
how interactions between nodes in the graph are predicted to change across
covariate gradients. The general methods implemented in this package are described
in Clark et al. (2018) <doi:10.1002/ecy.2221>.
Author: Nicholas J Clark [aut, cre],
Konstans Wells [aut],
Oscar Lindberg [aut]
Maintainer: Nicholas J Clark <nicholas.j.clark1214@gmail.com>
Diff between MRFcov versions 1.0.35 dated 2018-08-24 and 1.0.36 dated 2018-11-26
DESCRIPTION | 6 - MD5 | 44 +++++----- NEWS.md | 6 + R/MRFcov.R | 65 ++++++++------- R/MRFcov_spatial.R | 44 +++++----- R/bootstrap_MRF.R | 149 ++++++++++++++++-------------------- R/plotMRF_hm.R | 5 - R/predict_MRF.R | 7 - R/predict_MRFnetworks.R | 27 +++--- inst/doc/Bird_Parasite_CRF.R | 6 + inst/doc/Bird_Parasite_CRF.Rmd | 20 ++-- inst/doc/Bird_Parasite_CRF.html | 122 +++++++++++------------------ inst/doc/Gaussian_Poisson_CRFs.R | 2 inst/doc/Gaussian_Poisson_CRFs.Rmd | 2 inst/doc/Gaussian_Poisson_CRFs.html | 22 ++--- man/MRFcov.Rd | 65 ++++++++------- man/MRFcov_spatial.Rd | 20 ++-- man/bootstrap_MRF.Rd | 10 +- man/plotMRF_hm.Rd | 2 man/predict_MRF.Rd | 7 - man/predict_MRFnetworks.Rd | 19 ++-- vignettes/Bird_Parasite_CRF.Rmd | 20 ++-- vignettes/Gaussian_Poisson_CRFs.Rmd | 2 23 files changed, 340 insertions(+), 332 deletions(-)
Title: A Swiss-Army Knife for Data I/O
Description: Streamlined data import and export by making assumptions that
the user is probably willing to make: 'import()' and 'export()' determine
the data structure from the file extension, reasonable defaults are used for
data import and export (e.g., 'stringsAsFactors=FALSE'), web-based import is
natively supported (including from SSL/HTTPS), compressed files can be read
directly without explicit decompression, and fast import packages are used where
appropriate. An additional convenience function, 'convert()', provides a simple
method for converting between file types.
Author: Jason Becker [ctb],
Chung-hong Chan [aut],
Geoffrey CH Chan [ctb],
Thomas J. Leeper [aut, cre] (<https://orcid.org/0000-0003-4097-6326>),
Christopher Gandrud [ctb],
Andrew MacDonald [ctb],
Ista Zahn [ctb],
Stanislaus Stadlmann [ctb],
Ruaridh Williamson [ctb],
Patrick Kennedy [ctb],
Ryan Price [ctb],
Trevor L Davis [ctb]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between rio versions 0.5.15 dated 2018-11-25 and 0.5.16 dated 2018-11-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ R/standardize_attributes.R | 2 +- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Read and Write ODS Files
Description: Import ODS (OpenDocument Spreadsheet) into R as a data frame. Also support writing data frame into ODS file.
Author: Gerrit-Jan Schutten, Chung-hong Chan, Thomas J. Leeper and other contributors
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between readODS versions 1.6.4 dated 2016-11-27 and 1.6.7 dated 2018-11-26
DESCRIPTION | 14 +++--- MD5 | 25 +++++++---- NAMESPACE | 1 R/readODS.R | 61 ++++++++++++++++++----------- man/get_num_sheet_in_ods.Rd | 9 +--- man/ods_sheets.Rd | 1 man/read_ods.Rd | 16 +++---- man/write_ods.Rd | 1 tests/testdata/decimal_comma.ods |only tests/testdata/megairis.ods |only tests/testdata/na_test.ods |only tests/testdata/wild_character_encoding.ods |only tests/testthat/test.ods |binary tests/testthat/test_col_types.R | 20 +++++++++ tests/testthat/test_na.R |only tests/testthat/test_read_ods.R | 14 ++++++ 16 files changed, 107 insertions(+), 55 deletions(-)
Title: Phasing, Pedigree Reconstruction, Sire Imputation and
Recombination Events Identification of Half-sib Families Using
SNP Data
Description: Identification of recombination events, haplotype reconstruction, sire imputation and pedigree reconstruction using half-sib family SNP data.
Author: Mohammad Ferdosi <mferdosi@myune.edu.au>, Cedric Gondro <gondroce@msu.edu>
Maintainer: Mohammad Ferdosi <mferdosi@myune.edu.au>
Diff between hsphase versions 2.0.1 dated 2015-01-10 and 2.0.2 dated 2018-11-26
DESCRIPTION | 14 +++++----- MD5 | 14 +++++----- NAMESPACE | 5 ++- build/vignette.rds |binary data/genotypes.rda |binary inst/doc/hsphase.Rnw | 68 +++++++++++++++++++++++++++------------------------ inst/doc/hsphase.pdf |binary src/Makevars | 2 - 8 files changed, 54 insertions(+), 49 deletions(-)
Title: An HR Analytics Toolkit
Description: Toolkit for leveraging people data.
Author: Dale Kube [aut, cre]
Maintainer: Dale Kube <dkube@uwalumni.com>
Diff between hR versions 0.1.3 dated 2018-04-11 and 0.1.4 dated 2018-11-26
DESCRIPTION | 14 ++++------ MD5 | 12 ++++---- NAMESPACE | 2 - R/hierarchyLong.R | 58 ++++++++++++++++++++++-------------------- R/hierarchyWide.R | 69 ++++++++++++++++++++++++++++++--------------------- man/hierarchyLong.Rd | 8 ++--- man/hierarchyWide.Rd | 8 ++--- 7 files changed, 90 insertions(+), 81 deletions(-)
Title: Hidden Markov Models with Discrete Non-Parametric Observation
Distributions
Description: Fits hidden Markov models with discrete non-parametric
observation distributions to data sets. The observations may
be univariate or bivariate. Simulates data from such models.
Finds most probable underlying hidden states, the most
probable sequences of such states, and the log likelihood
of a collection of observations given the parameters of
the model. Auxiliary predictors are accommodated in the
univariate setting.
Author: Rolf Turner
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>
Diff between hmm.discnp versions 2.1-3 dated 2018-11-11 and 2.1-5 dated 2018-11-26
ChangeLog | 37 ++++++++++++++++++++---- DESCRIPTION | 8 ++--- MD5 | 58 +++++++++++++++++++-------------------- R/derivf.R | 4 ++ R/derivp.R | 5 ++- R/hmmUV.R | 22 ++++++++++++++ R/revise.rho.R | 14 ++++++++- data/Bovine.rda |binary data/Cryptosporidiosis.rda |binary data/Downloads.rda |binary data/EricssonB_Jul2.rda |binary data/FattyLiver.rda |binary data/FattyLiver2.rda |binary data/Hanta.rda |binary data/IPs.rda |binary data/InfantEEGsleepstates.rda |binary data/LegionnairesDisease.rda |binary data/OffshoreRigcountsAlaska.rda |binary data/PriceStability.rda |binary data/Strikes.rda |binary data/SydColDisc.rda |binary data/WoodPeweeSong.rda |binary data/ccprSim.rda |binary data/ftLiardFlows.rda |binary data/goldparticle380.rda |binary data/lesionCount.rda |binary data/linLandFlows.rda |binary data/portMannFlows.rda |binary data/portMannSedCon.rda |binary data/portMannSedLoads.rda |binary 30 files changed, 104 insertions(+), 44 deletions(-)
Title: Change Point Analysis in Functional Data
Description: Change point estimation and detection methods for functional data are implemented using dimension reduction via functional principal component analysis and a fully-functional (norm-based) method. Detecting and dating structural breaks for both dependent and independent functional samples is illustrated along with some basic functional data generating processes.
Author: Ozan Sonmez, Alexander Aue, Gregory Rice
Maintainer: Ozan Sonmez <osonmez@ucdavis.edu>
Diff between fChange versions 0.1.0 dated 2017-07-29 and 0.2.0 dated 2018-11-26
DESCRIPTION | 9 ++--- MD5 | 28 ++++++++++++---- NAMESPACE | 6 +++ NEWS.md |only R/Australian_Temp.R | 35 +++++++++++--------- R/Cov_test.R |only R/LongRunCovMatrix.R |only R/eval_component.R |only R/eval_joint.R |only R/insert_change.R | 84 ++++++++++++++++++++++++++---------------------- R/partial_cov.R |only R/trace_change.R |only README.md |only man/Australian_Temp.Rd | 31 ++++++++++------- man/Cov_test.Rd |only man/LongRunCovMatrix.Rd |only man/eval_component.Rd |only man/eval_joint.Rd |only man/fun_IID.Rd | 3 + man/fun_heavy_tailed.Rd | 3 + man/partial_cov.Rd |only man/trace_change.Rd |only 22 files changed, 119 insertions(+), 80 deletions(-)
Title: Importing and Analysing SNP and Silicodart Data Generated by
Genome-Wide Restriction Fragment Analysis
Description: Functions are provided that facilitate the import and analysis of
SNP (single nucleotide polymorphism) and silicodart (presence/absence) data. The main focus is on data generated
by DarT (Diversity Arrays Technology). However, once SNP or related fragment
presence/absence data from any source is imported into a genlight object many
of the functions can be used. Functions are available for input and output of
SNP and silicodart data, for reporting on and filtering on various criteria
(e.g. CallRate, Heterozygosity, Reproducibility, maximum allele frequency).
Advanced filtering is based on Linkage Disequilibrium and HWE (Hardy-Weinberg equilibrium). Other functions
are available for visualization after PCoA (Principle Coordinate Analysis), or to facilitate transfer of data
between genlight/genind objects and newhybrids, related, phylip, structure, faststructure packages.
Author: Bernd Gruber [aut, cre],
Arthur Georges [aut],
Peter J. Unmack [ctb],
Lindsay V. Clark [ctb],
Oliver Berry [ctb]
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Diff between dartR versions 1.0.5 dated 2018-05-11 and 1.1.6 dated 2018-11-26
dartR-1.0.5/dartR/R/gl.dist.r |only dartR-1.0.5/dartR/man/gl.dist.Rd |only dartR-1.1.6/dartR/DESCRIPTION | 23 - dartR-1.1.6/dartR/MD5 | 363 +++++++++++--------- dartR-1.1.6/dartR/NAMESPACE | 68 +++ dartR-1.1.6/dartR/R/datasets.r | 30 + dartR-1.1.6/dartR/R/gi2gl.R | 2 dartR-1.1.6/dartR/R/gl.Ho.r |only dartR-1.1.6/dartR/R/gl.Hs.r |only dartR-1.1.6/dartR/R/gl.alf.r |only dartR-1.1.6/dartR/R/gl.amova.r |only dartR-1.1.6/dartR/R/gl.assign.r | 60 ++- dartR-1.1.6/dartR/R/gl.basic.stats.r |only dartR-1.1.6/dartR/R/gl.collapse.pval.r | 2 dartR-1.1.6/dartR/R/gl.collapse.r | 2 dartR-1.1.6/dartR/R/gl.collapse.recursive.r | 2 dartR-1.1.6/dartR/R/gl.costdistances.r |only dartR-1.1.6/dartR/R/gl.define.pop.r |only dartR-1.1.6/dartR/R/gl.dist.heatmap.r |only dartR-1.1.6/dartR/R/gl.dist.pop.r |only dartR-1.1.6/dartR/R/gl.diversity.r |only dartR-1.1.6/dartR/R/gl.drop.ind.r | 74 ++-- dartR-1.1.6/dartR/R/gl.drop.loc.r |only dartR-1.1.6/dartR/R/gl.drop.pop.r | 66 ++- dartR-1.1.6/dartR/R/gl.edit.recode.ind.r | 2 dartR-1.1.6/dartR/R/gl.edit.recode.pop.r | 2 dartR-1.1.6/dartR/R/gl.filter.callrate.r | 143 +++++-- dartR-1.1.6/dartR/R/gl.filter.hamming.r | 36 + dartR-1.1.6/dartR/R/gl.filter.hwe.r | 68 ++- dartR-1.1.6/dartR/R/gl.filter.maf.r |only dartR-1.1.6/dartR/R/gl.filter.monomorphs.r | 17 dartR-1.1.6/dartR/R/gl.filter.repavg.r | 57 +-- dartR-1.1.6/dartR/R/gl.filter.secondaries.r | 29 + dartR-1.1.6/dartR/R/gl.fixed.diff.r | 2 dartR-1.1.6/dartR/R/gl.fst.pop.r |only dartR-1.1.6/dartR/R/gl.gene.freq.r | 4 dartR-1.1.6/dartR/R/gl.genleastcost.r |only dartR-1.1.6/dartR/R/gl.grm.network.r |only dartR-1.1.6/dartR/R/gl.grm.r |only dartR-1.1.6/dartR/R/gl.ibd.r | 2 dartR-1.1.6/dartR/R/gl.keep.ind.r | 78 ++-- dartR-1.1.6/dartR/R/gl.keep.pop.r | 67 ++- dartR-1.1.6/dartR/R/gl.make.recode.ind.r | 4 dartR-1.1.6/dartR/R/gl.make.recode.pop.r | 2 dartR-1.1.6/dartR/R/gl.map.interactive.r |only dartR-1.1.6/dartR/R/gl.merge.pop.r | 2 dartR-1.1.6/dartR/R/gl.nhybrids.r | 2 dartR-1.1.6/dartR/R/gl.pcoa.plot.3d.r | 3 dartR-1.1.6/dartR/R/gl.pcoa.plot.r | 3 dartR-1.1.6/dartR/R/gl.pcoa.r | 2 dartR-1.1.6/dartR/R/gl.pcoa.scree.r | 2 dartR-1.1.6/dartR/R/gl.percent.freq.r | 15 dartR-1.1.6/dartR/R/gl.plot.r |only dartR-1.1.6/dartR/R/gl.read.dart.2row.r | 2 dartR-1.1.6/dartR/R/gl.read.silicodart.r | 2 dartR-1.1.6/dartR/R/gl.recalc.metrics.r | 20 - dartR-1.1.6/dartR/R/gl.recode.ind.r | 38 +- dartR-1.1.6/dartR/R/gl.recode.pop.r | 2 dartR-1.1.6/dartR/R/gl.report.bases.r | 2 dartR-1.1.6/dartR/R/gl.report.callrate.r | 91 ++++- dartR-1.1.6/dartR/R/gl.report.hamming.r | 2 dartR-1.1.6/dartR/R/gl.report.heterozygosity.r | 2 dartR-1.1.6/dartR/R/gl.report.hwe.r | 2 dartR-1.1.6/dartR/R/gl.report.ld.r | 2 dartR-1.1.6/dartR/R/gl.report.maf.r | 179 ++++++++- dartR-1.1.6/dartR/R/gl.report.monomorphs.r | 2 dartR-1.1.6/dartR/R/gl.report.pa.pop.r |only dartR-1.1.6/dartR/R/gl.report.pa.r | 141 +++++-- dartR-1.1.6/dartR/R/gl.report.repavg.r | 2 dartR-1.1.6/dartR/R/gl.report.secondaries.r | 2 dartR-1.1.6/dartR/R/gl.sexlinkage.r | 8 dartR-1.1.6/dartR/R/gl.sim.ind.r |only dartR-1.1.6/dartR/R/gl.sim.offspring.r |only dartR-1.1.6/dartR/R/gl.subsample.loci.r | 2 dartR-1.1.6/dartR/R/gl.tree.nj.r | 2 dartR-1.1.6/dartR/R/gl.utils.fdsim.r | 2 dartR-1.1.6/dartR/R/gl.write.csv.r | 2 dartR-1.1.6/dartR/R/gl2demerelate.r | 2 dartR-1.1.6/dartR/R/gl2fasta.r | 2 dartR-1.1.6/dartR/R/gl2faststructure.r | 2 dartR-1.1.6/dartR/R/gl2gds.r | 2 dartR-1.1.6/dartR/R/gl2gi.r | 19 - dartR-1.1.6/dartR/R/gl2phylip.r | 2 dartR-1.1.6/dartR/R/gl2plink.r |only dartR-1.1.6/dartR/R/gl2sa.r |only dartR-1.1.6/dartR/R/gl2shp.R | 14 dartR-1.1.6/dartR/R/gl2snapp.r |only dartR-1.1.6/dartR/R/gl2svdquartets.r | 18 dartR-1.1.6/dartR/R/gl2treemix.r |only dartR-1.1.6/dartR/R/imports.r | 2 dartR-1.1.6/dartR/R/is.fixed.r | 2 dartR-1.1.6/dartR/R/prob.hwe.r | 2 dartR-1.1.6/dartR/R/util.outflank.r | 2 dartR-1.1.6/dartR/R/utils.hamming.r | 2 dartR-1.1.6/dartR/R/utils.hwe.r | 2 dartR-1.1.6/dartR/R/utils.recalc.avgpic.r | 41 ++ dartR-1.1.6/dartR/R/utils.recalc.callrate.r | 11 dartR-1.1.6/dartR/R/utils.recalc.freqhets.r | 10 dartR-1.1.6/dartR/R/utils.recalc.freqhomref.r | 11 dartR-1.1.6/dartR/R/utils.recalc.freqhomsnp.r | 10 dartR-1.1.6/dartR/R/utils.recalc.maf.r |only dartR-1.1.6/dartR/build/vignette.rds |binary dartR-1.1.6/dartR/data/foxes.gl.rda |only dartR-1.1.6/dartR/data/possums.gl.rda |only dartR-1.1.6/dartR/inst/doc/IntroTutorial_dartR.R | 22 - dartR-1.1.6/dartR/inst/doc/IntroTutorial_dartR.Rmd | 28 - dartR-1.1.6/dartR/inst/doc/IntroTutorial_dartR.pdf |binary dartR-1.1.6/dartR/inst/extdata/landscape.sim.rdata |only dartR-1.1.6/dartR/man/foxes.gl.Rd |only dartR-1.1.6/dartR/man/gi2gl.Rd | 2 dartR-1.1.6/dartR/man/gl.Ho.Rd |only dartR-1.1.6/dartR/man/gl.Hs.Rd |only dartR-1.1.6/dartR/man/gl.alf.Rd |only dartR-1.1.6/dartR/man/gl.amova.Rd |only dartR-1.1.6/dartR/man/gl.assign.Rd | 12 dartR-1.1.6/dartR/man/gl.basic.stats.Rd |only dartR-1.1.6/dartR/man/gl.collapse.Rd | 5 dartR-1.1.6/dartR/man/gl.collapse.pval.Rd | 2 dartR-1.1.6/dartR/man/gl.collapse.recursive.Rd | 2 dartR-1.1.6/dartR/man/gl.costdistances.Rd |only dartR-1.1.6/dartR/man/gl.define.pop.Rd |only dartR-1.1.6/dartR/man/gl.dist.heatmap.Rd |only dartR-1.1.6/dartR/man/gl.dist.pop.Rd |only dartR-1.1.6/dartR/man/gl.diversity.Rd |only dartR-1.1.6/dartR/man/gl.drop.ind.Rd | 6 dartR-1.1.6/dartR/man/gl.drop.loc.Rd |only dartR-1.1.6/dartR/man/gl.drop.pop.Rd | 8 dartR-1.1.6/dartR/man/gl.edit.recode.ind.Rd | 6 dartR-1.1.6/dartR/man/gl.edit.recode.pop.Rd | 6 dartR-1.1.6/dartR/man/gl.filter.callrate.Rd | 22 - dartR-1.1.6/dartR/man/gl.filter.hamming.Rd | 9 dartR-1.1.6/dartR/man/gl.filter.hwe.Rd | 12 dartR-1.1.6/dartR/man/gl.filter.maf.Rd |only dartR-1.1.6/dartR/man/gl.filter.monomorphs.Rd | 2 dartR-1.1.6/dartR/man/gl.filter.repavg.Rd | 12 dartR-1.1.6/dartR/man/gl.filter.secondaries.Rd | 4 dartR-1.1.6/dartR/man/gl.fixed.diff.Rd | 2 dartR-1.1.6/dartR/man/gl.fst.pop.Rd |only dartR-1.1.6/dartR/man/gl.gene.freq.Rd | 4 dartR-1.1.6/dartR/man/gl.genleastcost.Rd |only dartR-1.1.6/dartR/man/gl.grm.Rd |only dartR-1.1.6/dartR/man/gl.grm.network.Rd |only dartR-1.1.6/dartR/man/gl.ibd.Rd | 2 dartR-1.1.6/dartR/man/gl.keep.ind.Rd | 6 dartR-1.1.6/dartR/man/gl.keep.pop.Rd | 6 dartR-1.1.6/dartR/man/gl.make.recode.ind.Rd | 2 dartR-1.1.6/dartR/man/gl.make.recode.pop.Rd | 5 dartR-1.1.6/dartR/man/gl.map.interactive.Rd |only dartR-1.1.6/dartR/man/gl.merge.pop.Rd | 2 dartR-1.1.6/dartR/man/gl.nhybrids.Rd | 2 dartR-1.1.6/dartR/man/gl.pcoa.Rd | 2 dartR-1.1.6/dartR/man/gl.pcoa.plot.3d.Rd | 7 dartR-1.1.6/dartR/man/gl.pcoa.plot.Rd | 6 dartR-1.1.6/dartR/man/gl.pcoa.scree.Rd | 2 dartR-1.1.6/dartR/man/gl.percent.freq.Rd | 2 dartR-1.1.6/dartR/man/gl.plot.Rd |only dartR-1.1.6/dartR/man/gl.read.dart.2row.Rd | 2 dartR-1.1.6/dartR/man/gl.read.dart.Rd | 4 dartR-1.1.6/dartR/man/gl.read.silicodart.Rd | 2 dartR-1.1.6/dartR/man/gl.recalc.metrics.Rd | 6 dartR-1.1.6/dartR/man/gl.recode.ind.Rd | 8 dartR-1.1.6/dartR/man/gl.recode.pop.Rd | 2 dartR-1.1.6/dartR/man/gl.report.bases.Rd | 2 dartR-1.1.6/dartR/man/gl.report.callrate.Rd | 10 dartR-1.1.6/dartR/man/gl.report.hamming.Rd | 2 dartR-1.1.6/dartR/man/gl.report.heterozygosity.Rd | 2 dartR-1.1.6/dartR/man/gl.report.hwe.Rd | 2 dartR-1.1.6/dartR/man/gl.report.ld.Rd | 2 dartR-1.1.6/dartR/man/gl.report.maf.Rd | 26 - dartR-1.1.6/dartR/man/gl.report.monomorphs.Rd | 2 dartR-1.1.6/dartR/man/gl.report.pa.Rd | 16 dartR-1.1.6/dartR/man/gl.report.pa.pop.Rd |only dartR-1.1.6/dartR/man/gl.report.repavg.Rd | 2 dartR-1.1.6/dartR/man/gl.report.secondaries.Rd | 2 dartR-1.1.6/dartR/man/gl.sexlinkage.Rd | 2 dartR-1.1.6/dartR/man/gl.sim.ind.Rd |only dartR-1.1.6/dartR/man/gl.sim.offspring.Rd |only dartR-1.1.6/dartR/man/gl.subsample.loci.Rd | 2 dartR-1.1.6/dartR/man/gl.tree.nj.Rd | 2 dartR-1.1.6/dartR/man/gl.utils.fdsim.Rd | 2 dartR-1.1.6/dartR/man/gl.write.csv.Rd | 2 dartR-1.1.6/dartR/man/gl2demerelate.Rd | 2 dartR-1.1.6/dartR/man/gl2fasta.Rd | 5 dartR-1.1.6/dartR/man/gl2faststructure.Rd | 2 dartR-1.1.6/dartR/man/gl2gds.Rd | 2 dartR-1.1.6/dartR/man/gl2gi.Rd | 2 dartR-1.1.6/dartR/man/gl2phylip.Rd | 5 dartR-1.1.6/dartR/man/gl2plink.Rd |only dartR-1.1.6/dartR/man/gl2sa.Rd |only dartR-1.1.6/dartR/man/gl2shp.Rd | 9 dartR-1.1.6/dartR/man/gl2snapp.Rd |only dartR-1.1.6/dartR/man/gl2svdquartets.Rd | 8 dartR-1.1.6/dartR/man/gl2treemix.Rd |only dartR-1.1.6/dartR/man/is.fixed.Rd | 2 dartR-1.1.6/dartR/man/platy.Rd | 2 dartR-1.1.6/dartR/man/possums.gl.Rd |only dartR-1.1.6/dartR/man/prob.hwe.Rd | 2 dartR-1.1.6/dartR/man/testset.gl.Rd | 2 dartR-1.1.6/dartR/man/testset_SNPs_2Row.Rd | 2 dartR-1.1.6/dartR/man/testset_metadata.Rd | 2 dartR-1.1.6/dartR/man/testset_pop_recode.Rd | 2 dartR-1.1.6/dartR/man/util.outflank.Rd | 2 dartR-1.1.6/dartR/man/util.outflank.plotter.Rd | 4 dartR-1.1.6/dartR/man/utils.hamming.Rd | 2 dartR-1.1.6/dartR/man/utils.hwe.Rd | 2 dartR-1.1.6/dartR/man/utils.recalc.avgpic.Rd | 8 dartR-1.1.6/dartR/man/utils.recalc.callrate.Rd | 4 dartR-1.1.6/dartR/man/utils.recalc.freqhets.Rd | 4 dartR-1.1.6/dartR/man/utils.recalc.freqhomref.Rd | 4 dartR-1.1.6/dartR/man/utils.recalc.freqhomsnp.Rd | 4 dartR-1.1.6/dartR/man/utils.recalc.maf.Rd |only dartR-1.1.6/dartR/vignettes/IntroTutorial_dartR.Rmd | 28 - 212 files changed, 1526 insertions(+), 794 deletions(-)