Title: Fit Data to Any Conic Section
Description: Fit data to an ellipse, hyperbola, or parabola. Bootstrapping is available when needed. The conic curve can be rotated through an arbitrary angle and the fit will still succeed. Helper functions are provided to convert generator coefficients from one style to another, generate test data sets, rotate conic section parameters, and so on. References include Nikolai Chernov (2014) "Fitting ellipses, circles, and lines by least squares" <https://people.cas.uab.edu/~mosya/cl/>; A. W. Fitzgibbon, M. Pilu, R. B. Fisher (1999) "Direct Least Squares Fitting of Ellipses" IEEE Trans. PAMI, Vol. 21, pages 476-48; N. Chernov, Q. Huang, and H. Ma (2014) "Fitting quadratic curves to data points", British Journal of Mathematics & Computer Science, 4, 33-60; N. Chernov and H. Ma (2011) "Least squares fitting of quadratic curves and surfaces", Computer Vision, Editor S. R. Yoshida, Nova Science Publishers, pp. 285-302.
Author: Carl Witthoft [aut, cre],
Jose Gama [ctb],
Nikolai Chernov [ctb]
Maintainer: Carl Witthoft <carl@witthoft.com>
Diff between fitConic versions 1.1 dated 2020-06-25 and 1.2 dated 2022-01-11
ChangeLog | 1 + DESCRIPTION | 10 +++++----- MD5 | 18 ++++++++++-------- R/doWeights.R |only R/fitConic.R | 12 ++++++++++-- build/partial.rdb |binary man/bootEllipse.Rd | 2 +- man/doWeights.Rd |only man/fitConic-package.Rd | 4 ++-- man/fitConic.Rd | 7 +++++-- man/fitParabola.Rd | 2 +- 11 files changed, 35 insertions(+), 21 deletions(-)
Title: Filtering and Assessing the Sample Size of Tracking Data
Description: Functions to filter GPS/Argos locations, as well as assessing the sample size for the analysis of animal distributions. The filters remove temporal and spatial duplicates, fixes located at a given height from estimated high tide line, and locations with high error as described in Shimada et al. (2012) <doi:10.3354/meps09747> and Shimada et al. (2016) <doi:10.1007/s00227-015-2771-0>. Sample size for the analysis of animal distributions can be assessed by the conventional area-based approach or the alternative probability-based approach as described in Shimada et al. (2021) <doi:10.1111/2041-210X.13506>.
Author: Takahiro Shimada
Maintainer: Takahiro Shimada <taka.shimada@gmail.com>
Diff between SDLfilter versions 2.1.2 dated 2021-11-02 and 2.2.0 dated 2022-01-11
DESCRIPTION | 10 +- MD5 | 30 +++---- NAMESPACE | 5 + NEWS | 10 +- NEWS.md | 10 +- R/asymptote.R | 109 +++++++++++++++++++++++--- R/boot_area.R | 28 +++--- R/boot_overlap.R | 151 ++++++++++++++++++------------------- R/combn_overlap.R |only README.md | 36 ++++---- build/partial.rdb |binary inst/CITATION | 4 man/asymptote.Rd | 33 ++++++-- man/boot_area.Rd | 24 +++-- man/boot_overlap.Rd | 23 +++-- man/combn_overlap.Rd |only man/figures/unnamed-chunk-13-1.png |binary 17 files changed, 303 insertions(+), 170 deletions(-)
Title: Determining the Minimal Background Area for Species Distribution
Models
Description: A versatile tool that aims at (1) defining the minimum background extent necessary to fit Species Distribution Models reliable enough to extract ecologically relevant conclusions from them and (2) optimizing the modelling process in terms of computation demands. See Rotllan-Puig, X. & Traveset, A. (2021) <https://www.sciencedirect.com/science/article/pii/S0304380020304191>.
Author: Xavier Rotllan-Puig [aut, cre],
Anna Traveset [aut]
Maintainer: Xavier Rotllan-Puig <xavier.rotllan.puig@aster-projects.cat>
Diff between MinBAR versions 1.1.2 dated 2020-11-04 and 1.1.3 dated 2022-01-11
DESCRIPTION | 8 ++-- MD5 | 20 +++++------ R/minba.R | 10 ++--- README.md | 2 - build/vignette.rds |binary data/bioscrop.RData |binary data/sprecords.RData |binary inst/doc/Example_MinBAR_Balearics.html | 56 ++++++++++++++++++++++++++++----- man/bioscrop.Rd | 6 ++- man/minba-open-paren-close-paren.Rd | 18 ++++++++-- man/sprecords.Rd | 6 ++- 11 files changed, 90 insertions(+), 36 deletions(-)
Title: Isolation Forest-Based Presence-Only Species Distribution
Modeling
Description: Collection of R functions to do purely presence-only species
distribution modeling with isolation forest (iForest) and its
variations such as Extended isolation forest and SCiForest. See the
details of these methods in references: Liu, F.T., Ting, K.M. and
Zhou, Z.H. (2008) <doi:10.1109/ICDM.2008.17>, Hariri, S., Kind, M.C.
and Brunner, R.J. (2019) <doi:10.1109/TKDE.2019.2947676>, Liu, F.T.,
Ting, K.M. and Zhou, Z.H. (2010) <doi:10.1007/978-3-642-15883-4_18>,
Guha, S., Mishra, N., Roy, G. and Schrijvers, O. (2016)
<https://proceedings.mlr.press/v48/guha16.html>, Cortes, D. (2021)
<arXiv:2110.13402>. Additionally, Shapley values are used to explain
model inputs and outputs. See details in references: Shapley, L.S.
(1953) <doi:10.1515/9781400881970-018>, Lundberg, S.M. and Lee, S.I.
(2017) <https://dl.acm.org/doi/abs/10.5555/3295222.3295230>, Molnar,
C. (2020) <ISBN:978-0-244-76852-2>, Štrumbelj, E. and Kononenko, I.
(2014) <doi:10.1007/s10115-013-0679-x>. itsdm also provides functions
to diagnose variable response, analyze variable importance, draw
spatial dependence of variables and examine variable contribution. As
utilities, the package includes a few functions to download
bioclimatic variables including 'WorldClim' version 2.0 (see Fick,
S.E. and Hijmans, R.J. (2017) <doi:10.1002/joc.5086>) and
'CMCC-BioClimInd' (see Noce, S., Caporaso, L. and Santini, M. (2020)
<doi:10.1038/s41597-020-00726-5>.
Author: Lei Song [aut, cre] (<https://orcid.org/0000-0002-4371-1473>),
Lyndon Estes [ths]
Maintainer: Lei Song <lsong@clarku.edu>
Diff between itsdm versions 0.1.0 dated 2022-01-07 and 0.1.1 dated 2022-01-11
DESCRIPTION | 44 ++++++---- MD5 | 102 +++++++++++------------ NEWS.md | 8 + R/convert_to_pa.R | 2 R/evaluate_po.R | 7 + R/independent_response.R | 38 ++------ R/isotree_po.R | 29 +----- R/marginal_response.R | 2 R/plot.R | 18 ++-- R/print.R | 10 +- R/probability.R | 2 R/shap_dependence.R | 2 R/spatial_response.R | 38 ++------ R/variable_analysis.R | 84 +++++++------------ R/variable_contrib.R | 2 README.md | 6 + build/partial.rdb |binary inst/doc/introduction_of_itsdm.Rmd | 44 +++++----- inst/doc/introduction_of_itsdm.html | 52 ++++++------ inst/doc/itsdm_example.Rmd | 118 ++++++++++++++------------- inst/doc/itsdm_example.html | 120 ++++++++++++++-------------- man/convert_to_pa.Rd | 2 man/evaluate_po.Rd | 5 - man/independent_response.Rd | 2 man/isotree_po.Rd | 16 --- man/marginal_response.Rd | 2 man/plot.IndependentResponse.Rd | 2 man/plot.MarginalResponse.Rd | 2 man/plot.PAConversion.Rd | 2 man/plot.POEvaluation.Rd | 2 man/plot.ShapDependence.Rd | 2 man/plot.SpatialResponse.Rd | 2 man/plot.VariableAnalysis.Rd | 2 man/plot.VariableContribution.Rd | 2 man/print.PAConversion.Rd | 2 man/print.POEvaluation.Rd | 2 man/print.POIsotree.Rd | 2 man/print.VariableAnalysis.Rd | 2 man/probability.Rd | 2 man/shap_dependence.Rd | 2 man/spatial_response.Rd | 2 man/variable_analysis.Rd | 2 man/variable_contrib.Rd | 2 vignettes/intro-evaluation-1.png |binary vignettes/intro-independent_responses-1.png |binary vignettes/intro-spatial_response-1.png |binary vignettes/intro-variable_analysis-1.png |binary vignettes/introduction_of_itsdm.Rmd | 44 +++++----- vignettes/itsdm-eval-1.png |binary vignettes/itsdm-independent_responses-1.png |binary vignettes/itsdm_example.Rmd | 118 ++++++++++++++------------- vignettes/itsdm_example.Rmd.orig | 2 52 files changed, 453 insertions(+), 500 deletions(-)
Title: Semi-Parametric Joint Modeling of Longitudinal and Survival Data
Description: Maximum likelihood estimation for the semi-parametric joint modeling of competing risks and longitudinal data
applying customized linear scan algorithms, proposed by Li and colleagues (2021) <arXiv:2110.14822>. The time-to-event data is
modelled using a (cause-specific) Cox proportional hazards regression model with time-fixed covariates. The longitudinal
outcome is modelled using a linear mixed effects model. The association is captured by shared random effects. The model
is estimated using an Expectation Maximization algorithm.
Author: Shanpeng Li [aut, cre],
Ning Li [ctb],
Hong Wang [ctb],
Jin Zhou [ctb],
Hua Zhou [ctb],
Gang Li [ctb]
Maintainer: Shanpeng Li <lishanpeng0913@ucla.edu>
Diff between FastJM versions 1.0.0 dated 2022-01-06 and 1.0.1 dated 2022-01-11
DESCRIPTION | 14 +++++++------- MD5 | 23 ++++++++++++----------- NEWS.md |only README.md | 14 ++++++-------- src/getCov.cpp | 3 +-- src/getCovSF.cpp | 3 +-- src/getECpseudoSF.cpp | 2 +- src/getMC.cpp | 2 +- src/getMCSF.cpp | 2 +- src/getloglikeCpseudo.cpp | 2 +- src/getloglikeCpseudoSF.cpp | 2 +- src/getloglikeCstandard.cpp | 2 +- src/getloglikeCstandardSF.cpp | 2 +- 13 files changed, 34 insertions(+), 37 deletions(-)
Title: Dave Armstrong's Miscellaneous Functions
Description: Miscellaneous set of functions I use in my teaching either at the University of Western Ontario or the Inter-university Consortium for Political and Social Research (ICPSR) Summer Program in Quantitative Methods. Broadly, the functions help with presentation and interpretation of LMs and GLMs, but also implement some new tools like Alternating Least Squares Optimal Scaling for dependent variables, a Bayesian analog to the ALSOS algorithm. There are also tools to help understand interactions in both LMs and binary GLMs.
Author: Dave Armstrong [aut, cre]
Maintainer: Dave Armstrong <dave@quantoid.net>
Diff between DAMisc versions 1.6.2 dated 2020-11-12 and 1.7.2 dated 2022-01-11
DESCRIPTION | 19 MD5 | 44 - NAMESPACE | 23 R/DAMisc_functions.R | 1461 +++++++++++++++++++++++------------- R/damisc-package.R | 2 build/vignette.rds |binary inst/doc/alsos.html | 27 inst/doc/binaryDV_interactions.html | 35 man/DAintfun.Rd | 10 man/DAintfun2.Rd | 2 man/aveEffPlot.Rd | 18 man/balsos.Rd | 2 man/glmChange.Rd | 38 man/glmChange2.Rd | 47 + man/mnlChange.Rd | 3 man/mnlChange2.Rd | 4 man/ordChange.Rd | 3 man/ordChange2.Rd | 4 man/print.diffci.Rd | 27 man/probci.Rd | 5 man/scaleDataFrame.Rd | 8 man/sumStats.Rd | 13 man/tidy_boot_ci.Rd |only man/unformulate.Rd |only 24 files changed, 1219 insertions(+), 576 deletions(-)
Title: Flexible Tree Taper Curves Based on Semiparametric Mixed Models
Description: Implementation of functions for fitting taper curves (a semiparametric
linear mixed effects taper model) to diameter measurements along stems. Further
functions are provided to estimate the uncertainty around the predicted curves,
to calculate timber volume (also by sections) and marginal (e.g., upper) diameters.
For cases where tree heights are not measured, methods for estimating
additional variance in volume predictions resulting from uncertainties in
tree height models (tariffs) are provided. The example data include the taper
curve parameters for Norway spruce used in the 3rd German NFI fitted to 380 trees
and a subset of section-wise diameter measurements of these trees. The functions
implemented here are detailed in Kublin, E., Breidenbach, J., Kaendler, G. (2013)
<doi:10.1007/s10342-013-0715-0>.
Author: Edgar Kublin [aut],
Johannes Breidenbach [ctb],
Christian Vonderach [ctb, cre]
Maintainer: Christian Vonderach <christian.vonderach@forst.bwl.de>
Diff between TapeR versions 0.3.3 dated 2015-08-10 and 0.5.0 dated 2022-01-11
DESCRIPTION | 35 ++- MD5 | 96 +++++--- NAMESPACE | 41 ++- R/BSplines.R | 27 +- R/CdN_DHxHt.f.R | 46 ++-- R/EYx_ssp.f.R | 12 + R/E_DHx_HmDm_HT.f.R | 166 +++++++++++++- R/E_DHx_HmDm_HT_CIdHt.f.R | 430 ++++++++++++++++++++++---------------- R/E_HDx_HmDm_HT.f.R | 82 ++++++- R/E_VOL_AB_HmDm_Ht.f.R | 80 +++++-- R/Hx_root.f.R | 30 ++ R/Int_CdN_DHx_dHt.f.R | 31 ++ R/Int_E_VOL_AB_HmDm_HT_dHt.f.R | 45 +++ R/ResVar.R |only R/SK_EBLUP_LME.f.R | 75 +++++- R/SK_VOLab_EBLUP_LME.f.R | 45 ++- R/TapeR_FIT_LME.f.R | 190 ++++++++++++---- R/TransKnots.R | 10 R/XZ_BSPLINE.f.R | 37 +-- R/dN.f.R | 10 R/e_vol_ab_hmdm_ht.f_1.R | 220 +++++++++++++++++-- R/qD.rout.f.R | 28 ++ R/xy0_SK_EBLUP_LME.f.R | 28 ++ R/xy0_root.f.R | 24 +- R/y2x_isp.f.R | 14 + R/y2x_ssp.f.R | 18 + R/yx_isp.f.R | 14 + R/yx_ssp.f.R | 18 + README.md |only build/vignette.rds |binary inst/CITATION | 34 +-- inst/NEWS.rd |only inst/doc/TapeR.R | 137 ++++++++++++ inst/doc/TapeR.Rnw | 139 ++++++++++++ inst/doc/TapeR.pdf |binary man/BSplines.Rd |only man/CdN_DHxHt.f.Rd |only man/EYx_ssp.f.Rd |only man/E_DHx_HmDm_HT.f.Rd | 375 ++++++++++----------------------- man/E_DHx_HmDm_HT_CIdHt.f.Rd |only man/E_HDx_HmDm_HT.f.Rd |only man/E_VOL_AB_HmDm_HT.f.Rd |only man/Hx_root.f.Rd |only man/Int_CdN_DHx_dHt.f.Rd |only man/Int_E_VOL_AB_HmDm_HT_dHt.f.Rd |only man/SK_EBLUP_LME.f.Rd |only man/SK_VOLab_EBLUP_LME.f.Rd |only man/TapeR_FIT_LME.f.Rd | 248 ++++++++++----------- man/TransKnots.Rd |only man/XZ_BSPLINE.f.Rd |only man/dN.f.Rd |only man/qD.rout.f.Rd |only man/resVar.Rd |only man/xy0_SK_EBLUP_LME.f.Rd |only man/xy0_root.f.Rd |only man/y2x_isp.f.Rd |only man/y2x_ssp.f.Rd |only man/yx_isp.f.Rd |only man/yx_ssp.f.Rd | 255 ++-------------------- tests |only vignettes/TapeR.Rnw | 139 ++++++++++++ 61 files changed, 2116 insertions(+), 1063 deletions(-)
Title: Robust Calibration of Imperfect Mathematical Models
Description: Implements full Bayesian analysis for calibrating mathematical models with new methodology for modeling the discrepancy function. It allows for emulation, calibration and prediction using complex mathematical model outputs and experimental data. See the reference: Mengyang Gu and Long Wang (2018) <arXiv:1707.08215>, Mengyang Gu, Fangzheng Xie and Long Wang (2021) <arXiv:1807.03829>, Mengyang Gu, Kyle Anderson and Erika McPhillips (2021) <arXiv:1810.11664>.
Author: Mengyang Gu [aut, cre]
Maintainer: Mengyang Gu <mengyang@pstat.ucsb.edu>
Diff between RobustCalibration versions 0.5.1 dated 2018-05-14 and 0.5.2 dated 2022-01-11
RobustCalibration-0.5.1/RobustCalibration/man/predict_discrepancy_separable_2dim.Rd |only RobustCalibration-0.5.2/RobustCalibration/CHANGELOG | 6 RobustCalibration-0.5.2/RobustCalibration/DESCRIPTION | 16 RobustCalibration-0.5.2/RobustCalibration/MD5 | 61 RobustCalibration-0.5.2/RobustCalibration/NAMESPACE | 13 RobustCalibration-0.5.2/RobustCalibration/R/RcppExports.R | 44 RobustCalibration-0.5.2/RobustCalibration/R/functions.R | 1236 ++++++++-- RobustCalibration-0.5.2/RobustCalibration/R/predict.R | 903 ++++--- RobustCalibration-0.5.2/RobustCalibration/R/predict_MS.R | 746 +++++- RobustCalibration-0.5.2/RobustCalibration/R/rcalibration.R | 505 +++- RobustCalibration-0.5.2/RobustCalibration/R/rcalibration_MS.R | 586 ++++ RobustCalibration-0.5.2/RobustCalibration/R/structure.R | 116 RobustCalibration-0.5.2/RobustCalibration/build/partial.rdb |binary RobustCalibration-0.5.2/RobustCalibration/man/Get_R_z_new.Rd | 4 RobustCalibration-0.5.2/RobustCalibration/man/Log_marginal_post.Rd | 11 RobustCalibration-0.5.2/RobustCalibration/man/Log_marginal_post_no_discrepancy.Rd | 9 RobustCalibration-0.5.2/RobustCalibration/man/Sample_sigma_2_theta_m.Rd | 10 RobustCalibration-0.5.2/RobustCalibration/man/Sample_sigma_2_theta_m_no_discrepancy.Rd | 11 RobustCalibration-0.5.2/RobustCalibration/man/Update_R_inv_y.Rd | 4 RobustCalibration-0.5.2/RobustCalibration/man/mathematical_model_eval.Rd | 13 RobustCalibration-0.5.2/RobustCalibration/man/post_sample.Rd | 26 RobustCalibration-0.5.2/RobustCalibration/man/post_sample_no_discrepancy.Rd | 27 RobustCalibration-0.5.2/RobustCalibration/man/post_sample_with_discrepancy.Rd | 34 RobustCalibration-0.5.2/RobustCalibration/man/predict.rcalibration.Rd | 32 RobustCalibration-0.5.2/RobustCalibration/man/predict_MS.rcalibration_MS.Rd | 5 RobustCalibration-0.5.2/RobustCalibration/man/predict_separable_2dim.Rd |only RobustCalibration-0.5.2/RobustCalibration/man/rcalibration-class.Rd | 21 RobustCalibration-0.5.2/RobustCalibration/man/rcalibration.Rd | 39 RobustCalibration-0.5.2/RobustCalibration/man/rcalibration_MS-class.Rd | 16 RobustCalibration-0.5.2/RobustCalibration/man/rcalibration_MS.Rd | 47 RobustCalibration-0.5.2/RobustCalibration/src/RcppExports.cpp | 165 + RobustCalibration-0.5.2/RobustCalibration/src/functions.cpp | 358 ++ RobustCalibration-0.5.2/RobustCalibration/src/init.c |only 33 files changed, 4147 insertions(+), 917 deletions(-)
More information about RobustCalibration at CRAN
Permanent link
Title: Latent Environmental & Genetic InTeraction (LEGIT) Model
Description: Constructs genotype x environment interaction (GxE) models where
G is a weighted sum of genetic variants (genetic score) and E is a weighted
sum of environments (environmental score) using the alternating optimization algorithm
by Jolicoeur-Martineau et al. (2017) <arXiv:1703.08111>. This approach has greatly
enhanced predictive power over traditional GxE models which include only a single
genetic variant and a single environmental exposure. Although this approach was
originally made for GxE modelling, it is flexible and does not require the use of
genetic and environmental variables. It can also handle more than 2 latent variables
(rather than just G and E) and 3-way interactions or more. The LEGIT model produces
highly interpretable results and is very parameter-efficient thus it can even be
used with small sample sizes (n < 250). Tools to determine the type of interaction
(vantage sensitivity, diathesis-stress or differential susceptibility), with any
number of genetic variants or environments, are available <arXiv:1712.04058>. The
software can now produce mixed-effects LEGIT models through the lme4 package.
Author: Alexia Jolicoeur-Martineau <alexia.jolicoeur-martineau@mail.mcgill.ca>
Maintainer: Alexia Jolicoeur-Martineau <alexia.jolicoeur-martineau@mail.mcgill.ca>
Diff between LEGIT versions 1.3.1 dated 2019-08-29 and 1.4.0 dated 2022-01-11
DESCRIPTION | 15 MD5 | 75 - NAMESPACE | 1 NEWS | 10 R/LEGIT.R | 2548 ++++++++++++++++++++++-------------------- R/rGE.R | 31 build/vignette.rds |binary inst/doc/ElasticNet.R | 19 inst/doc/ElasticNet.html | 804 +++++++------ inst/doc/GxE_testing.R | 22 inst/doc/GxE_testing.html | 724 ++++++----- inst/doc/LEGIT.R | 36 inst/doc/LEGIT.Rmd | 2 inst/doc/LEGIT.html | 853 +++++++------- man/GxE_interaction_RoS.Rd | 17 man/GxE_interaction_test.Rd | 38 man/IMLEGIT.Rd | 14 man/IMLEGIT_cv.Rd | 24 man/IMLEGIT_net.Rd | 31 man/IMLEGIT_to_LEGIT.Rd | 14 man/LEGIT.Rd | 27 man/LEGIT_cv.Rd | 35 man/LEGIT_to_IMLEGIT.Rd | 14 man/backward_step.Rd | 17 man/backward_step_IM.Rd | 17 man/bootstrap_var_select.Rd | 36 man/elastic_net_var_select.Rd | 34 man/example_2way_lme4.Rd |only man/example_with_crossover.Rd | 14 man/forward_step.Rd | 14 man/forward_step_IM.Rd | 13 man/genetic_var_select.Rd | 35 man/longitudinal_folds.Rd | 11 man/nes_var_select.Rd | 35 man/plot.LEGIT.Rd | 29 man/r1nes_var_select.Rd | 35 man/stepwise_search.Rd | 43 man/stepwise_search_IM.Rd | 39 vignettes/LEGIT.Rmd | 2 39 files changed, 3224 insertions(+), 2504 deletions(-)
Title: Download Crypto Currency Data from 'CoinMarketCap' without 'API'
Description: Retrieves crypto currency information and historical prices as well as information on the exchanges they are listed on. Historical data contains daily open, high, low and close values for all crypto currencies. All data is scraped from <https://coinmarketcap.com> via their 'web-api'.
Author: Sebastian Stoeckl [aut, cre] (<https://orcid.org/0000-0002-4196-6093>,
Package commissioner and maintainer.),
Jesse Vent [ctb] (Creator of the crypto package that provided the idea
and basis for this package.)
Maintainer: Sebastian Stoeckl <sebastian.stoeckl@uni.li>
Diff between crypto2 versions 1.4.0 dated 2022-01-10 and 1.4.2 dated 2022-01-11
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 8 ++++++++ R/crypto_history.R | 10 +++++----- R/crypto_list.R | 10 ---------- man/crypto_history.Rd | 3 --- 6 files changed, 21 insertions(+), 26 deletions(-)
Title: Get Executing Script's Path, from 'RStudio', 'Rgui', 'Rscript'
(Command-Line / / Terminal), and 'source'
Description: Determine the full path of the executing script. Works when running
a line or selection from a script in 'RStudio' and 'Rgui', when using
'source', 'sys.source', 'debugSource' ('RStudio' exclusive), and
'testthat::source_file', and when running R from the Windows command-line /
/ Unix terminal.
Author: Andrew Simmons
Maintainer: Andrew Simmons <akwsimmo@gmail.com>
Diff between this.path versions 0.4.4 dated 2021-03-21 and 0.5.0 dated 2022-01-11
this.path-0.4.4/this.path/man/Running.R.from.the.command-line.Rd |only this.path-0.5.0/this.path/DESCRIPTION | 28 this.path-0.5.0/this.path/MD5 | 54 this.path-0.5.0/this.path/NAMESPACE | 121 this.path-0.5.0/this.path/R/ArgumentParser-class.R |only this.path-0.5.0/this.path/R/Check_This.R | 25 this.path-0.5.0/this.path/R/Hooks_for_Namespace_Events.R |only this.path-0.5.0/this.path/R/R.R |only this.path-0.5.0/this.path/R/all.char.R |only this.path-0.5.0/this.path/R/check.path.R |only this.path-0.5.0/this.path/R/commandArgs.R |only this.path-0.5.0/this.path/R/commandPrompt.R |only this.path-0.5.0/this.path/R/commandQuote.R |only this.path-0.5.0/this.path/R/dedent.R |only this.path-0.5.0/this.path/R/delayedAssign2.R |only this.path-0.5.0/this.path/R/error.R |only this.path-0.5.0/this.path/R/file.open.R |only this.path-0.5.0/this.path/R/help.R |only this.path-0.5.0/this.path/R/here.R |only this.path-0.5.0/this.path/R/list.files2.R |only this.path-0.5.0/this.path/R/normalizeAgainst.R |only this.path-0.5.0/this.path/R/normalizeURL.R |only this.path-0.5.0/this.path/R/path.contract.R |only this.path-0.5.0/this.path/R/path.exists.R |only this.path-0.5.0/this.path/R/pseudoglobalenv.R |only this.path-0.5.0/this.path/R/readArgs.R |only this.path-0.5.0/this.path/R/supports.8.bit.color.R |only this.path-0.5.0/this.path/R/this.path.R | 1436 ++++++---- this.path-0.5.0/this.path/R/withArgs.R |only this.path-0.5.0/this.path/R/write.code.R |only this.path-0.5.0/this.path/README |only this.path-0.5.0/this.path/build/partial.rdb |binary this.path-0.5.0/this.path/inst |only this.path-0.5.0/this.path/man/check.path.Rd |only this.path-0.5.0/this.path/man/here.Rd |only this.path-0.5.0/this.path/man/running.R.from.command-line.Rd |only this.path-0.5.0/this.path/man/this.path-defunct.Rd |only this.path-0.5.0/this.path/man/this.path-package.Rd | 77 this.path-0.5.0/this.path/man/this.path.Rd | 913 +++--- this.path-0.5.0/this.path/man/this.path2.Rd |only this.path-0.5.0/this.path/tests/faster_subsequent_times.R |only this.path-0.5.0/this.path/tests/main.R | 146 - this.path-0.5.0/this.path/tests/test.R | 10 this.path-0.5.0/this.path/tests/this.path_w_URLs.R |only 44 files changed, 1758 insertions(+), 1052 deletions(-)
Title: Helpful Functions from Oliver Wyman Actuarial Consulting
Description: Makes difficult operations easy. Includes these types of functions:
shorthand, type conversion, data wrangling, and work flow.
Also includes some helpful data objects: NA strings, U.S. state list, color blind charting colors.
Built and shared by Oliver Wyman Actuarial Consulting. Accepting proposed contributions through GitHub.
Author: Oliver Wyman Actuarial Consulting [aut, cph],
Bryce Chamberlain [aut, cre],
Rajesh Sahasrabuddhe [ctb]
Maintainer: Bryce Chamberlain <bryce.chamberlain@oliverwyman.com>
Diff between easyr versions 0.5-4 dated 2021-06-02 and 0.5-8 dated 2022-01-11
easyr-0.5-4/easyr/data/cblind.R |only easyr-0.5-4/easyr/data/nastrings.R |only easyr-0.5-8/easyr/DESCRIPTION | 6 +- easyr-0.5-8/easyr/MD5 | 38 ++++++++-------- easyr-0.5-8/easyr/R/cache.R | 59 +++++++++++++++---------- easyr-0.5-8/easyr/R/eq.R | 6 ++ easyr-0.5-8/easyr/R/fmat.R | 15 +++--- easyr-0.5-8/easyr/R/hashfiles.R | 40 +++++++++++----- easyr-0.5-8/easyr/R/spl.R | 2 easyr-0.5-8/easyr/R/todate.R | 2 easyr-0.5-8/easyr/data/cblind.rda |only easyr-0.5-8/easyr/data/nastrings.rda |only easyr-0.5-8/easyr/man/cache.init.Rd | 24 +++++----- easyr-0.5-8/easyr/man/cache.ok.Rd | 11 ++-- easyr-0.5-8/easyr/man/checkeq.Rd | 8 ++- easyr-0.5-8/easyr/man/clear.cache.Rd | 4 + easyr-0.5-8/easyr/man/hashfiles.Rd | 3 - easyr-0.5-8/easyr/man/save.cache.Rd | 18 ++++--- easyr-0.5-8/easyr/tests/testthat/test_ecopy.R | 18 ++++--- easyr-0.5-8/easyr/tests/testthat/test_eq.R | 3 + easyr-0.5-8/easyr/tests/testthat/test_fmat.R | 10 +++- easyr-0.5-8/easyr/tests/testthat/test_todate.R | 15 +++++- 22 files changed, 180 insertions(+), 102 deletions(-)
Title: Polychoric and Polyserial Correlations
Description: Computes polychoric and polyserial correlations by quick "two-step" methods or ML,
optionally with standard errors; tetrachoric and biserial correlations are special cases.
Author: John Fox [aut, cre],
Adrian Dusa [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between polycor versions 0.8-0 dated 2021-12-01 and 0.8-1 dated 2022-01-11
DESCRIPTION | 21 +- MD5 | 27 +-- NAMESPACE | 10 - NEWS | 10 + R/hetcor.R | 5 R/hetcor.data.frame.R | 444 +++++++++++++++++++++++--------------------------- R/hetcor.default.R | 8 R/polychor.R | 39 +++- R/polyserial.R | 34 +++ R/print.polycor.R | 135 +++++++++------ R/standard-methods.R |only man/hetcor.Rd | 16 + man/polychor.Rd | 9 - man/polyserial.Rd | 5 man/print.polycor.Rd | 27 ++- 15 files changed, 447 insertions(+), 343 deletions(-)
Title: Standard Schedules Information Parser
Description: Parse Standard Schedules Information file (types 2 and 3) into a Data Frame.
Can also expand schedules into flights.
Author: Sebastien Thonnard
Maintainer: Sebastien Thonnard <sebastien.thonnard@icloud.com>
Diff between ssimparser versions 0.1.0 dated 2021-05-11 and 0.1.1 dated 2022-01-11
DESCRIPTION | 9 ++++----- LICENSE | 2 +- MD5 | 6 +++--- R/ssimparser.R | 6 ++++-- 4 files changed, 12 insertions(+), 11 deletions(-)
Title: Statistical Quantification of Individual Differences
Description: A simulation-based tool made to help researchers to become familiar with
multilevel variations, and to build up sampling designs for their study.
This tool has two main objectives: First, it provides an educational tool useful for students,
teachers and researchers who want to learn to use mixed-effects models.
Users can experience how the mixed-effects model framework can be used to understand
distinct biological phenomena by interactively exploring simulated multilevel data.
Second, it offers research opportunities to those who are already familiar with
mixed-effects models, as it enables the generation of data sets that users may download
and use for a range of simulation-based statistical analyses such as power
and sensitivity analysis of multilevel and multivariate data [Allegue, H., Araya-Ajoy, Y.G., Dingemanse,
N.J., Dochtermann N.A., Garamszegi, L.Z., Nakagawa, S., Reale, D., Schielzeth, H. and Westneat, D.F. (2016)
<doi: 10.1111/2041-210X.12659>].
Author: Hassen Allegue [aut, cre],
Yimen G. Araya-Ajoy [aut],
Niels J. Dingemanse [aut],
Ned A. Dochtermann [aut],
Laszlo Z. Garamszegi [aut],
Shinichi Nakagawa [aut],
Denis Reale [aut],
Holger Schielzeth [aut],
David F. Westneat [aut]
Maintainer: Hassen Allegue <h.all@disroot.org>
Diff between squid versions 0.1.2 dated 2019-08-06 and 0.2.0 dated 2022-01-11
squid-0.1.2/squid/R/Cor2CovMatrix.R |only squid-0.1.2/squid/R/check_matrix.R |only squid-0.1.2/squid/R/check_one_boolean.R |only squid-0.1.2/squid/R/check_one_integer.R |only squid-0.1.2/squid/R/check_one_numeric.R |only squid-0.1.2/squid/R/createEnvironment.R |only squid-0.1.2/squid/R/decayRate.R |only squid-0.1.2/squid/R/error_management.R |only squid-0.1.2/squid/R/getEnvironment.R |only squid-0.1.2/squid/R/getIndMatrix.R |only squid-0.1.2/squid/R/getNRI.R |only squid-0.1.2/squid/R/getTxUniform.R |only squid-0.1.2/squid/R/multiplot.R |only squid-0.1.2/squid/R/plotEnvironment.R |only squid-0.1.2/squid/R/repmat.R |only squid-0.1.2/squid/R/reshapeMat.R |only squid-0.1.2/squid/R/setEnvironments.R |only squid-0.1.2/squid/inst/shiny-squid/source/SVRsource.R |only squid-0.1.2/squid/inst/shiny-squid/source/UIsource.R |only squid-0.1.2/squid/inst/shiny-squid/source/inputs/getCheckboxInput.R |only squid-0.1.2/squid/inst/shiny-squid/source/inputs/getEnvironmentInput.R |only squid-0.1.2/squid/inst/shiny-squid/source/inputs/getNumericInput.R |only squid-0.1.2/squid/inst/shiny-squid/source/inputs/getSelectInput.R |only squid-0.1.2/squid/inst/shiny-squid/source/inputs/getSliderInput.R |only squid-0.1.2/squid/inst/shiny-squid/source/pages/Rcode |only squid-0.1.2/squid/inst/shiny-squid/source/pages/fullModel |only squid-0.1.2/squid/inst/shiny-squid/source/pages/fullModelSbyS |only squid-0.1.2/squid/inst/shiny-squid/source/pages/modules/UImodules.R |only squid-0.1.2/squid/inst/shiny-squid/source/pages/modules/module1/UIMod1Step1.R |only squid-0.1.2/squid/inst/shiny-squid/source/pages/modules/module1/UIMod1Step2.R |only squid-0.1.2/squid/inst/shiny-squid/source/pages/modules/module1/UIMod1Step3.R |only squid-0.1.2/squid/inst/shiny-squid/source/pages/modules/module1/UIMod1Step4.R |only squid-0.1.2/squid/inst/shiny-squid/source/pages/modules/module3/UIMod3Step1.R |only squid-0.1.2/squid/inst/shiny-squid/source/pages/modules/module3/UIMod3Step2.R |only squid-0.1.2/squid/inst/shiny-squid/source/pages/modules/module3/UIMod3Step3.R |only squid-0.1.2/squid/inst/shiny-squid/source/pages/modules/module6/UIMod6Step1.R |only squid-0.1.2/squid/inst/shiny-squid/source/pages/modules/module6/UIMod6Step2.R |only squid-0.1.2/squid/inst/shiny-squid/source/pages/modules/module6/UIMod6Step3.R |only squid-0.1.2/squid/inst/shiny-squid/source/pages/portal/UIportal.R |only squid-0.1.2/squid/inst/shiny-squid/source/server/fullmodel/SVRDispayModelEquation.R |only squid-0.1.2/squid/inst/shiny-squid/source/server/fullmodel/SVRFullModel.R |only squid-0.1.2/squid/inst/shiny-squid/source/server/fullmodel/SVRGetBMatrix.R |only squid-0.1.2/squid/inst/shiny-squid/source/server/fullmodel/SVRGetModelEquation.R |only squid-0.1.2/squid/inst/shiny-squid/source/server/fullmodel/SVRGetSummaryVariances.R |only squid-0.1.2/squid/inst/shiny-squid/source/server/fullmodel/SVRGetVindMatrix.R |only squid-0.1.2/squid/inst/shiny-squid/source/server/fullmodel/SVRcreateRcode.R |only squid-0.1.2/squid/inst/shiny-squid/source/server/modules/SVRmodules.R |only squid-0.1.2/squid/inst/shiny-squid/source/server/modules/module1/SVRMod1Step1.R |only squid-0.1.2/squid/inst/shiny-squid/source/server/modules/module1/SVRMod1Step2.R |only squid-0.1.2/squid/inst/shiny-squid/source/server/modules/module1/SVRMod1Step3.R |only squid-0.1.2/squid/inst/shiny-squid/source/server/modules/module1/SVRMod1Step4.R |only squid-0.1.2/squid/inst/shiny-squid/source/server/modules/module3/SVRMod3Step1.R |only squid-0.1.2/squid/inst/shiny-squid/source/server/modules/module3/SVRMod3Step2.R |only squid-0.1.2/squid/inst/shiny-squid/source/server/modules/module3/SVRMod3Step3.R |only squid-0.1.2/squid/inst/shiny-squid/source/server/modules/module6/SVRMod6Step1.R |only squid-0.1.2/squid/inst/shiny-squid/source/server/modules/module6/SVRMod6Step2.R |only squid-0.1.2/squid/inst/shiny-squid/source/server/modules/module6/SVRMod6Step3.R |only squid-0.1.2/squid/inst/shiny-squid/source/text/fullmodel/TXTfullmodel.R |only squid-0.1.2/squid/inst/shiny-squid/source/text/modules/TXTmodule1.R |only squid-0.1.2/squid/inst/shiny-squid/source/text/modules/TXTmodule3.R |only squid-0.1.2/squid/inst/shiny-squid/source/text/modules/TXTmodule6.R |only squid-0.1.2/squid/inst/shiny-squid/source/text/portal/TXTportal.R |only squid-0.1.2/squid/inst/shiny-squid/source/utilities/Cor2CovMatrix.R |only squid-0.1.2/squid/inst/shiny-squid/source/utilities/disableActionButton.R |only squid-0.1.2/squid/inst/shiny-squid/source/utilities/displayRCode.R |only squid-0.1.2/squid/inst/shiny-squid/source/utilities/error_msg.R |only squid-0.1.2/squid/inst/shiny-squid/source/utilities/getIcon.R |only squid-0.1.2/squid/inst/shiny-squid/source/utilities/getLabel.R |only squid-0.1.2/squid/inst/shiny-squid/source/utilities/getTable.R |only squid-0.1.2/squid/inst/shiny-squid/source/utilities/info_msg.R |only squid-0.1.2/squid/inst/shiny-squid/source/utilities/matrixInput2.R |only squid-0.1.2/squid/inst/shiny-squid/source/utilities/matrixInputB.R |only squid-0.1.2/squid/inst/shiny-squid/source/utilities/matrixInputVind.R |only squid-0.1.2/squid/inst/shiny-squid/source/utilities/runPowerAnalysis.R |only squid-0.1.2/squid/inst/shiny-squid/source/utilities/runningIndicator.R |only squid-0.1.2/squid/inst/shiny-squid/source/utilities/testInput.R |only squid-0.1.2/squid/inst/shiny-squid/source/utilities/testInputBMatrix.R |only squid-0.1.2/squid/inst/shiny-squid/source/utilities/testInputVindMatrix.R |only squid-0.1.2/squid/inst/shiny-squid/source/utilities/testInteger.R |only squid-0.1.2/squid/inst/shiny-squid/source/utilities/warning_msg.R |only squid-0.1.2/squid/inst/shiny-squid/source/variables/fullmodel/VARfullmodel.R |only squid-0.1.2/squid/inst/shiny-squid/source/variables/general/VARgeneral.R |only squid-0.1.2/squid/inst/shiny-squid/source/variables/modules/VARmodules.R |only squid-0.2.0/squid/DESCRIPTION | 25 squid-0.2.0/squid/MD5 | 247 +++---- squid-0.2.0/squid/NEWS.md | 25 squid-0.2.0/squid/R/displayResults.R | 129 +++ squid-0.2.0/squid/R/environment.R |only squid-0.2.0/squid/R/errorManagement.R |only squid-0.2.0/squid/R/getFullData.R | 60 + squid-0.2.0/squid/R/getSampledData.R | 156 ++++ squid-0.2.0/squid/R/setVariables.R | 134 ++-- squid-0.2.0/squid/R/squidApp.R | 9 squid-0.2.0/squid/R/squidR.R | 4 squid-0.2.0/squid/R/utilities.R |only squid-0.2.0/squid/README.md | 15 squid-0.2.0/squid/inst/shiny-squid/global.R |only squid-0.2.0/squid/inst/shiny-squid/server.R | 116 ++- squid-0.2.0/squid/inst/shiny-squid/source/inputs/get_checkbox_input.R |only squid-0.2.0/squid/inst/shiny-squid/source/inputs/get_environment_input.R |only squid-0.2.0/squid/inst/shiny-squid/source/inputs/get_numeric_input.R |only squid-0.2.0/squid/inst/shiny-squid/source/inputs/get_select_input.R |only squid-0.2.0/squid/inst/shiny-squid/source/inputs/get_slider_input.R |only squid-0.2.0/squid/inst/shiny-squid/source/pages/full_model |only squid-0.2.0/squid/inst/shiny-squid/source/pages/full_model_sbys |only squid-0.2.0/squid/inst/shiny-squid/source/pages/modules/module1/ui_mod1_step1.R |only squid-0.2.0/squid/inst/shiny-squid/source/pages/modules/module1/ui_mod1_step2.R |only squid-0.2.0/squid/inst/shiny-squid/source/pages/modules/module1/ui_mod1_step3.R |only squid-0.2.0/squid/inst/shiny-squid/source/pages/modules/module1/ui_mod1_step4.R |only squid-0.2.0/squid/inst/shiny-squid/source/pages/modules/module2 |only squid-0.2.0/squid/inst/shiny-squid/source/pages/modules/module3/ui_mod3_step1.R |only squid-0.2.0/squid/inst/shiny-squid/source/pages/modules/module3/ui_mod3_step2.R |only squid-0.2.0/squid/inst/shiny-squid/source/pages/modules/module3/ui_mod3_step3.R |only squid-0.2.0/squid/inst/shiny-squid/source/pages/modules/module4 |only squid-0.2.0/squid/inst/shiny-squid/source/pages/modules/module5 |only squid-0.2.0/squid/inst/shiny-squid/source/pages/modules/module6/ui_mod6_step1.R |only squid-0.2.0/squid/inst/shiny-squid/source/pages/modules/module6/ui_mod6_step2.R |only squid-0.2.0/squid/inst/shiny-squid/source/pages/modules/module6/ui_mod6_step3.R |only squid-0.2.0/squid/inst/shiny-squid/source/pages/modules/module8 |only squid-0.2.0/squid/inst/shiny-squid/source/pages/modules/ui_modules.R |only squid-0.2.0/squid/inst/shiny-squid/source/pages/portal/ui_portal.R |only squid-0.2.0/squid/inst/shiny-squid/source/pages/squidR |only squid-0.2.0/squid/inst/shiny-squid/source/server/fullmodel/svr_create_rcode.R |only squid-0.2.0/squid/inst/shiny-squid/source/server/fullmodel/svr_dispay_model_equation.R |only squid-0.2.0/squid/inst/shiny-squid/source/server/fullmodel/svr_full_model.R |only squid-0.2.0/squid/inst/shiny-squid/source/server/fullmodel/svr_get_b_matrix.R |only squid-0.2.0/squid/inst/shiny-squid/source/server/fullmodel/svr_get_model_equation.R |only squid-0.2.0/squid/inst/shiny-squid/source/server/fullmodel/svr_get_summary_variances.R |only squid-0.2.0/squid/inst/shiny-squid/source/server/fullmodel/svr_get_vind_matrix.R |only squid-0.2.0/squid/inst/shiny-squid/source/server/modules/module1/svr_mod1_step_1.R |only squid-0.2.0/squid/inst/shiny-squid/source/server/modules/module1/svr_mod1_step_2.R |only squid-0.2.0/squid/inst/shiny-squid/source/server/modules/module1/svr_mod1_step_3.R |only squid-0.2.0/squid/inst/shiny-squid/source/server/modules/module1/svr_mod1_step_4.R |only squid-0.2.0/squid/inst/shiny-squid/source/server/modules/module2 |only squid-0.2.0/squid/inst/shiny-squid/source/server/modules/module3/svr_mod3_step_1.R |only squid-0.2.0/squid/inst/shiny-squid/source/server/modules/module3/svr_mod3_step_2.R |only squid-0.2.0/squid/inst/shiny-squid/source/server/modules/module3/svr_mod3_step_3.R |only squid-0.2.0/squid/inst/shiny-squid/source/server/modules/module4 |only squid-0.2.0/squid/inst/shiny-squid/source/server/modules/module5 |only squid-0.2.0/squid/inst/shiny-squid/source/server/modules/module6/svr_mod6_step_1.R |only squid-0.2.0/squid/inst/shiny-squid/source/server/modules/module6/svr_mod6_step_2.R |only squid-0.2.0/squid/inst/shiny-squid/source/server/modules/module6/svr_mod6_step_3.R |only squid-0.2.0/squid/inst/shiny-squid/source/server/modules/module8 |only squid-0.2.0/squid/inst/shiny-squid/source/server/modules/svr_modules.R |only squid-0.2.0/squid/inst/shiny-squid/source/svr_source.R |only squid-0.2.0/squid/inst/shiny-squid/source/text/fullmodel/txt_full_model.R |only squid-0.2.0/squid/inst/shiny-squid/source/text/modules/txt_module1.R |only squid-0.2.0/squid/inst/shiny-squid/source/text/modules/txt_module3.R |only squid-0.2.0/squid/inst/shiny-squid/source/text/modules/txt_module6.R |only squid-0.2.0/squid/inst/shiny-squid/source/text/portal/txt_portal.R |only squid-0.2.0/squid/inst/shiny-squid/source/ui_source.R |only squid-0.2.0/squid/inst/shiny-squid/source/utilities/all_msg.R |only squid-0.2.0/squid/inst/shiny-squid/source/utilities/citations.R |only squid-0.2.0/squid/inst/shiny-squid/source/utilities/cor2cov_matrix.R |only squid-0.2.0/squid/inst/shiny-squid/source/utilities/disable_action_button.R |only squid-0.2.0/squid/inst/shiny-squid/source/utilities/display_rcode.R |only squid-0.2.0/squid/inst/shiny-squid/source/utilities/get_icon.R |only squid-0.2.0/squid/inst/shiny-squid/source/utilities/get_label.R |only squid-0.2.0/squid/inst/shiny-squid/source/utilities/get_table.R |only squid-0.2.0/squid/inst/shiny-squid/source/utilities/matrix_input_2.R |only squid-0.2.0/squid/inst/shiny-squid/source/utilities/matrix_input_b.R |only squid-0.2.0/squid/inst/shiny-squid/source/utilities/matrix_input_vind.R |only squid-0.2.0/squid/inst/shiny-squid/source/utilities/plot_design.R |only squid-0.2.0/squid/inst/shiny-squid/source/utilities/powerAnalysis.R | 4 squid-0.2.0/squid/inst/shiny-squid/source/utilities/run_power_analysis.R |only squid-0.2.0/squid/inst/shiny-squid/source/utilities/running_indicator.R |only squid-0.2.0/squid/inst/shiny-squid/source/utilities/showEnvironment.R | 6 squid-0.2.0/squid/inst/shiny-squid/source/utilities/test_input.R |only squid-0.2.0/squid/inst/shiny-squid/source/utilities/test_input_b_matrix.R |only squid-0.2.0/squid/inst/shiny-squid/source/utilities/test_input_vind_matrix.R |only squid-0.2.0/squid/inst/shiny-squid/source/utilities/test_integer.R |only squid-0.2.0/squid/inst/shiny-squid/source/variables/fullmodel/var_fullmodel.R |only squid-0.2.0/squid/inst/shiny-squid/source/variables/general/var_general.R |only squid-0.2.0/squid/inst/shiny-squid/source/variables/modules/var_modules.R |only squid-0.2.0/squid/inst/shiny-squid/test.R | 331 ++++------ squid-0.2.0/squid/inst/shiny-squid/ui.R | 235 +++---- squid-0.2.0/squid/inst/shiny-squid/www/css/stylesheet.css | 11 squid-0.2.0/squid/inst/shiny-squid/www/pictures/Alligator_mississippiensis.jpg |only squid-0.2.0/squid/inst/shiny-squid/www/pictures/Environment_examples.jpg |binary squid-0.2.0/squid/inst/shiny-squid/www/pictures/Vit_examples.jpg |binary squid-0.2.0/squid/inst/shiny-squid/www/pictures/shared_vs_unshared_examples.jpg |binary squid-0.2.0/squid/man/package-squid.Rd | 4 squid-0.2.0/squid/man/pictures |only squid-0.2.0/squid/man/squidApp.Rd | 10 squid-0.2.0/squid/man/squidR.Rd | 4 185 files changed, 941 insertions(+), 584 deletions(-)
Title: Bottom-Up Proteomics and LiP-MS Quality Control and Data
Analysis Tools
Description: Useful functions and workflows for proteomics quality control and data analysis of both limited proteolysis-coupled mass spectrometry (LiP-MS) (Feng et. al. (2014) <doi:10.1038/nbt.2999>) and regular bottom-up proteomics experiments. Data generated with search tools such as 'Spectronaut', 'MaxQuant' and 'Proteome Discover' can be easily used due to flexibility of functions.
Author: Jan-Philipp Quast [aut, cre] (<https://orcid.org/0000-0003-2713-778X>),
Dina Schuster [aut] (<https://orcid.org/0000-0001-6611-8237>),
ETH Zurich [cph, fnd]
Maintainer: Jan-Philipp Quast <quast@imsb.biol.ethz.ch>
Diff between protti versions 0.2.0 dated 2021-09-17 and 0.2.1 dated 2022-01-11
DESCRIPTION | 22 MD5 | 86 +-- NAMESPACE | 4 NEWS.md | 19 R/calculate_diff_abundance.R | 5 R/create_structure_contact_map.R | 295 ++++++++---- R/data.R | 8 R/fetch_alphafold_prediction.R | 44 + R/fetch_pdb.R | 3 R/fetch_pdb_structure.R | 39 + R/find_peptide_in_structure.R | 85 ++- R/map_peptides_on_structure.R | 85 +-- R/parallel_create_structure_contact_map.R |only R/parallel_fit_drc_4p.R | 5 R/qc_cvs.R | 6 R/qc_ids.R | 8 R/qc_intensity_distribution.R | 7 R/qc_sample_correlation.R | 11 R/try_query.R | 12 README.md | 15 build/vignette.rds |binary data/viridis_colours.rda |only inst/doc/data_analysis_dose_response_workflow.R | 148 +++--- inst/doc/data_analysis_dose_response_workflow.Rmd | 2 inst/doc/data_analysis_dose_response_workflow.html | 206 --------- inst/doc/data_analysis_single_dose_treatment_workflow.R | 296 ++++++------- inst/doc/data_analysis_single_dose_treatment_workflow.Rmd | 10 inst/doc/data_analysis_single_dose_treatment_workflow.html | 217 ++++----- inst/doc/input_preparation_workflow.Rmd | 2 inst/doc/input_preparation_workflow.html | 6 inst/doc/quality_control_workflow.R | 254 +++++------ inst/doc/quality_control_workflow.html | 215 ++++----- man/create_structure_contact_map.Rd | 52 +- man/fetch_alphafold_prediction.Rd | 2 man/fetch_pdb_structure.Rd | 2 man/find_peptide_in_structure.Rd | 12 man/map_peptides_on_structure.Rd | 32 - man/parallel_create_structure_contact_map.Rd |only man/parallel_fit_drc_4p.Rd | 2 man/qc_ids.Rd | 2 man/qc_intensity_distribution.Rd | 5 man/viridis_colours.Rd |only tests/testthat/test-structure_functions.R | 14 vignettes/data_analysis_dose_response_workflow.Rmd | 2 vignettes/data_analysis_single_dose_treatment_workflow.Rmd | 10 vignettes/input_preparation_workflow.Rmd | 2 46 files changed, 1111 insertions(+), 1141 deletions(-)
Title: Maximum Likelihood Conjoint Measurement
Description: Conjoint measurement is a psychophysical procedure in which stimulus pairs are presented that vary along 2 or more dimensions and the observer is required to compare the stimuli along one of them. This package contains functions to estimate the contribution of the n scales to the judgment by a maximum likelihood method under several hypotheses of how the perceptual dimensions interact. Reference: Knoblauch & Maloney (2012) "Modeling Psychophysical Data in R". <doi:10.1007/978-1-4614-4475-6>.
Author: Ken Knoblauch [aut],
Laurence T. Maloney [aut],
Guillermo Aguilar [aut, cre]
Maintainer: Guillermo Aguilar <guillermo.aguilar@mail.tu-berlin.de>
Diff between MLCM versions 0.4.2 dated 2019-03-28 and 0.4.3 dated 2022-01-11
DESCRIPTION | 10 +++++----- MD5 | 13 ++++++++----- README.md | 4 ---- build |only data/Texture.rda |only inst/NEWS | 11 ++++++++++- man/MLCM-package.Rd | 47 ++++++++++++++++++++++++----------------------- man/Texture.Rd |only man/mlcm.Rd | 34 +++++++++++++++++++++++++++++++++- 9 files changed, 80 insertions(+), 39 deletions(-)
Title: Get Images Out of DICOM Format Quickly
Description: Provides tools to sort DICOM-format medical image files, and
convert them to NIfTI-1 format.
Author: Jon Clayden [aut, cre] (<https://orcid.org/0000-0002-6608-0619>),
Chris Rorden [aut],
Martin J Fiedler [cph],
Cong Xu [cph],
Pascal Gloor [cph]
Maintainer: Jon Clayden <code@clayden.org>
Diff between divest versions 0.10.1 dated 2021-04-02 and 0.10.2 dated 2022-01-11
DESCRIPTION | 8 MD5 | 26 NEWS | 6 src/dcm2niix/jpg_0XC3.cpp | 998 +-- src/dcm2niix/nifti1_io_core.cpp | 13 src/dcm2niix/nifti1_io_core.h | 10 src/dcm2niix/nii_dicom.cpp |12458 +++++++++++++++++++-------------------- src/dcm2niix/nii_dicom.h | 65 src/dcm2niix/nii_dicom_batch.cpp |10295 +++++++++++++++++--------------- src/dcm2niix/nii_dicom_batch.h | 29 src/dcm2niix/nii_foreign.cpp | 615 - src/dcm2niix/nii_ortho.cpp | 631 + src/dcm2niix/nii_ortho.h | 4 src/ujpeg/ujpeg.cpp | 2 14 files changed, 13140 insertions(+), 12020 deletions(-)
Title: Helper Functions for 'mlr3'
Description: Frequently used helper functions and assertions
used in 'mlr3' and its companion packages. Comes with helper functions
for functional programming, for printing, to work with 'data.table',
as well as some generally useful 'R6' classes. This package also
supersedes the package 'BBmisc'.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3misc versions 0.9.5 dated 2021-11-16 and 0.10.0 dated 2022-01-11
DESCRIPTION | 6 - MD5 | 17 +++-- NAMESPACE | 7 ++ NEWS.md | 7 ++ R/get_private.R |only R/purrr_map.R | 112 ++++++++++++++++++++++++++-------- R/recycle_vector.R |only man/compat-map.Rd | 25 ++++++- man/get_private.Rd |only man/recycle_vectors.Rd |only tests/testthat/test_map.R | 32 +++++++++ tests/testthat/test_recycle_vectors.R |only 12 files changed, 168 insertions(+), 38 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-09-02 0.0.1.5
2021-04-27 0.0.1.4
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@cnrs.fr>
Diff between questionr versions 0.7.5 dated 2021-10-06 and 0.7.6 dated 2022-01-11
questionr-0.7.5/questionr/data/rp99.RData |only questionr-0.7.5/questionr/man/ifunc_get_css.Rd |only questionr-0.7.5/questionr/man/ifunc_run_as_addin.Rd |only questionr-0.7.5/questionr/man/ifunc_show_alert.Rd |only questionr-0.7.5/questionr/man/rp99.Rd |only questionr-0.7.6/questionr/DESCRIPTION | 10 questionr-0.7.6/questionr/MD5 | 37 questionr-0.7.6/questionr/NEWS.md | 90 - questionr-0.7.6/questionr/R/datasets.R | 98 +- questionr-0.7.6/questionr/R/icut.R | 770 ++++++++-------- questionr-0.7.6/questionr/R/iorder.R | 318 +++--- questionr-0.7.6/questionr/R/irec.R | 430 +++++--- questionr-0.7.6/questionr/R/odds.ratio.R | 4 questionr-0.7.6/questionr/R/shiny-utils.R | 3 questionr-0.7.6/questionr/build/vignette.rds |binary questionr-0.7.6/questionr/data/datalist | 2 questionr-0.7.6/questionr/data/rp2018.RData |only questionr-0.7.6/questionr/inst/doc/recoding_addins.html | 4 questionr-0.7.6/questionr/man/icut.Rd | 6 questionr-0.7.6/questionr/man/iorder.Rd | 10 questionr-0.7.6/questionr/man/irec.Rd | 8 questionr-0.7.6/questionr/man/odds.ratio.Rd | 2 questionr-0.7.6/questionr/man/rp2018.Rd |only 23 files changed, 978 insertions(+), 814 deletions(-)
Title: Functions to Declare Missing Values
Description: A set of functions that offer an alternative to package 'haven', to deal with
labelled objects with existing values declared as missing.
Author: Adrian Dusa [aut, cre, cph] (<https://orcid.org/0000-0002-3525-9253>)
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between declared versions 0.7 dated 2021-09-02 and 0.8 dated 2022-01-11
DESCRIPTION | 10 +- MD5 | 26 ++++--- NAMESPACE | 4 + R/declared.R | 166 +++++++++++++++++++++++++++++++++++++----------- R/frtable.R |only R/haven.R | 4 - R/internals.R | 21 +++--- R/onLoad.R | 110 ------------------------------- R/pillar.R | 2 build/vignette.rds |binary inst/ChangeLog | 14 ++-- inst/doc/declared.pdf |binary man/declared-package.Rd | 4 - man/declared.Rd | 82 ++++++++++++++++------- man/frtable.Rd |only 15 files changed, 236 insertions(+), 207 deletions(-)
Title: Statistical Methods for Phenology Analysis in Temperate Fruit
Trees
Description: The phenology of plants (i.e. the timing of their annual life
phases) depends on climatic cues. For temperate trees and many other plants,
spring phases, such as leaf emergence and flowering, have been found to result
from the effects of both cool (chilling) conditions and heat. Fruit tree
scientists (pomologists) have developed some metrics to quantify chilling
and heat (e.g. see Luedeling (2012) <doi:10.1016/j.scienta.2012.07.011>).
'chillR' contains functions for processing temperature records into
chilling (Chilling Hours, Utah Chill Units and Chill Portions) and heat units
(Growing Degree Hours). Regarding chilling metrics, Chill Portions are often
considered the most promising, but they are difficult to calculate. This package
makes it easy. 'chillR' also contains procedures for conducting a PLS analysis
relating phenological dates (e.g. bloom dates) to either mean temperatures or
mean chill and heat accumulation rates, based on long-term weather and phenology
records (Luedeling and Gassner (2012) <doi:10.1016/j.agrformet.2011.10.020>).
As of version 0.65, it also includes functions for generating weather
scenarios with a weather generator, for conducting climate change analyses
for temperature-based climatic metrics and for plotting results from such
analyses. Since version 0.70, 'chillR' contains a function for interpolating
hourly temperature records.
Author: Eike Luedeling [aut, cre] (<https://orcid.org/0000-0002-7316-3631>),
Eduardo Fernandez [aut] (<https://orcid.org/0000-0002-6949-9685>)
Maintainer: Eike Luedeling <eike@eikeluedeling.com>
Diff between chillR versions 0.72.6 dated 2021-12-05 and 0.72.7 dated 2022-01-11
DESCRIPTION | 8 +- MD5 | 16 ++--- NAMESPACE | 2 R/extract_temperatures_from_grids.R | 6 -- R/make_hourly_temps.R | 3 - R/plot_climate_scenarios.R | 1 build/partial.rdb |binary inst/doc/PhenoFlex.html | 60 ++++++++++----------- inst/doc/hourly_temperatures.html | 100 ++++++++++++++++++------------------ 9 files changed, 95 insertions(+), 101 deletions(-)
Title: Tidy IP Addresses
Description: Classes and functions for working with IP (Internet Protocol)
addresses and networks, inspired by the Python 'ipaddress' module.
Offers full support for both IPv4 and IPv6 (Internet Protocol versions
4 and 6) address spaces. It is specifically designed to work well with
the 'tidyverse'.
Author: David Hall [aut, cre] (<https://orcid.org/0000-0002-2193-0480>)
Maintainer: David Hall <david.hall.physics@gmail.com>
Diff between ipaddress versions 0.5.3 dated 2021-07-27 and 0.5.4 dated 2022-01-11
DESCRIPTION | 8 ++++---- MD5 | 17 +++++++++-------- NEWS.md | 4 ++++ README.md | 6 +++--- build/vignette.rds |binary inst/doc/ipaddress-examples.html | 34 +++++++++++++++++----------------- inst/include/ipaddress/IpAddress.h | 1 + man/ipaddress-package.Rd | 6 +----- src/Makevars.ucrt |only src/RcppExports.cpp | 5 +++++ 10 files changed, 44 insertions(+), 37 deletions(-)
Title: Improving MrP with Ensemble Learning
Description: A tool that improves the prediction performance of multilevel
regression with post-stratification (MrP) by combining a number of machine
learning methods. For information on the method, please refer to Broniecki,
Wüest, Leemann (2020) ''Improving Multilevel Regression with
Post-Stratification Through Machine Learning (autoMrP)'' forthcoming in
'Journal of Politics'. Final pre-print version:
<https://lucasleemann.files.wordpress.com/2020/07/automrp-r2pa.pdf>.
Author: Reto Wüest [aut] (<https://orcid.org/0000-0002-7502-6489>),
Lucas Leemann [aut] (<https://orcid.org/0000-0001-5201-869X>),
Philipp Broniecki [aut, cre] (<https://orcid.org/0000-0001-9214-4404>),
Hadley Wickham [ctb]
Maintainer: Philipp Broniecki <philippbroniecki@gmail.com>
Diff between autoMrP versions 0.99 dated 2021-12-15 and 1.0.0 dated 2022-01-11
DESCRIPTION | 10 +++---- MD5 | 18 ++++++------- R/auto_mrp.R | 24 ++++++++--------- R/boot_auto_mrp.R | 14 +++++----- R/ebma.R | 67 ++++++++++++++++++++++++++++++++++++++++--------- R/globals.R | 1 R/run_classifiers.R | 17 ++++++------ R/utils.R | 21 +++++++++------ man/boot_auto_mrp.Rd | 14 ++++++++++ man/run_classifiers.Rd | 14 ++++++++++ 10 files changed, 140 insertions(+), 60 deletions(-)
Title: Generative Mechanism Estimation in Temporal Complex Networks
Description: Statistical methods for estimating preferential attachment and node fitness generative mechanisms in temporal complex networks are provided. Thong Pham et al. (2015) <doi:10.1371/journal.pone.0137796>. Thong Pham et al. (2016) <doi:10.1038/srep32558>. Thong Pham et al. (2020) <doi:10.18637/jss.v092.i03>. Thong Pham et al. (2021) <doi:10.1093/comnet/cnab024>.
Author: Thong Pham, Paul Sheridan, Hidetoshi Shimodaira
Maintainer: Thong Pham <thongphamthe@gmail.com>
Diff between PAFit versions 1.2.4 dated 2021-12-22 and 1.2.5 dated 2022-01-11
DESCRIPTION | 10 MD5 | 25 - NAMESPACE | 8 R/RcppExports.R | 126 +++--- R/generate_simulation.R |only R/plot_contribution.R |only build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 17 man/PAFit-package.Rd | 206 +++++------ man/generate_simulated_data_from_estimated_model.rd |only man/get_statistics.Rd | 6 man/joint_estimate.rd | 366 ++++++++++---------- man/plot_contribution.rd |only tests/test_joint_estimate.R | 66 +-- tests/test_re_generate.R |only 16 files changed, 429 insertions(+), 401 deletions(-)
Title: Big Quadratic Inverse Covariance Estimation
Description: Use Newton's method, coordinate descent, and METIS clustering
to solve the L1 regularized Gaussian MLE inverse covariance
matrix estimation problem.
Author: Khalid B. Kunji [aut, cre],
Cho-Jui Hsieh [ctb],
Matyas A. Sustik [ctb],
Inderjit S. Dhillon [ctb],
Pradeep Ravikumar [ctb],
Tuo Zhao [ctb],
Xingguo Li [ctb],
Han Liu [ctb],
Kathryn Roeder [ctb],
John Lafferty [ctb],
Larry Wasserman [ctb],
George Karypis [ctb],
Melissa O'Neill [ctb],
Richard Henderson [ctb]
Maintainer: Khalid B. Kunji <kkunji@hbku.edu.qa>
Diff between BigQuic versions 1.1-9.1 dated 2021-03-01 and 1.1-10 dated 2022-01-11
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/BigQuic.select.R | 4 ++-- build/partial.rdb |binary man/BigQuic-package.Rd | 6 +++--- 5 files changed, 13 insertions(+), 13 deletions(-)
Title: Routines for Descriptive and Model-Based APC Analysis
Description: Age-Period-Cohort (APC) analyses are used to differentiate relevant drivers for long-term developments.
The 'APCtools' package offers visualization techniques and general routines to simplify the workflow of an APC analysis.
Sophisticated functions are available both for descriptive and regression model-based analyses.
For the former, we use density (or ridgeline) matrices and (hexagonally binned) heatmaps as innovative visualization
techniques building on the concept of Lexis diagrams.
Model-based analyses build on the separation of the temporal dimensions based on generalized additive models,
where a tensor product interaction surface (usually between age and period) is utilized
to represent the third dimension (usually cohort) on its diagonal.
Such tensor product surfaces can also be estimated while accounting for
further covariates in the regression model.
See Weigert et al. (2021) <doi:10.1177/1354816620987198> for methodological details.
Author: Alexander Bauer [aut, cre] (<https://orcid.org/0000-0003-3495-5131>),
Maximilian Weigert [aut] (<https://orcid.org/0000-0003-4400-134X>),
Hawre Jalal [aut] (<https://orcid.org/0000-0002-8224-6834>),
Pauline Hohenemser [ctb]
Maintainer: Alexander Bauer <alexander.bauer@stat.uni-muenchen.de>
Diff between APCtools versions 1.0.0 dated 2022-01-05 and 1.0.1 dated 2022-01-11
DESCRIPTION | 10 ++++--- LICENSE |only MD5 | 32 ++++++++++++----------- NEWS.md |only R/plot_APCheatmap.R | 11 +++---- R/plot_APChexamap.R | 11 +++---- R/plot_linearEffects.R | 28 ++++++++++++++++++-- R/plot_smoothEffects.R | 43 ++++++++++++++++--------------- README.md | 10 +++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/main_functionality.Rmd | 2 - inst/doc/main_functionality.html | 10 ++----- man/plot_1Dsmooth.Rd | 12 +++++++- man/plot_linearEffects.Rd | 11 +++++++ tests/testthat/test-plots_APCsurface.R | 4 +- tests/testthat/test-plots_covarEffects.R | 16 ++++++++++- vignettes/main_functionality.Rmd | 2 - 18 files changed, 130 insertions(+), 72 deletions(-)
Title: Data Sets, Etc. for the Text "Using R for Introductory
Statistics", Second Edition
Description: A collection of data sets to accompany the
textbook "Using R for Introductory Statistics," second
edition.
Author: John Verzani <verzani@math.csi.cuny.edu>
Maintainer: John Verzani <verzani@math.csi.cuny.edu>
Diff between UsingR versions 2.0-6 dated 2018-05-01 and 2.0-7 dated 2022-01-11
UsingR-2.0-6/UsingR/data/datalist |only UsingR-2.0-7/UsingR/DESCRIPTION | 8 UsingR-2.0-7/UsingR/MD5 | 323 ++++++++++------------ UsingR-2.0-7/UsingR/R/datasets.R | 45 +-- UsingR-2.0-7/UsingR/R/yahoo.get.hist.quote.R | 45 +-- UsingR-2.0-7/UsingR/data/BushApproval.rda |binary UsingR-2.0-7/UsingR/data/HUMMER.rda |binary UsingR-2.0-7/UsingR/data/KSI.rda |binary UsingR-2.0-7/UsingR/data/MLBattend.rda |binary UsingR-2.0-7/UsingR/data/Medicare.rda |binary UsingR-2.0-7/UsingR/data/OBP.rda |binary UsingR-2.0-7/UsingR/data/ObamaApproval.rda |binary UsingR-2.0-7/UsingR/data/age.universe.rda |binary UsingR-2.0-7/UsingR/data/aid.rda |binary UsingR-2.0-7/UsingR/data/alaska.pipeline.rda |binary UsingR-2.0-7/UsingR/data/alltime.movies.rda |binary UsingR-2.0-7/UsingR/data/aosat.rda |binary UsingR-2.0-7/UsingR/data/arctic.oscillations.rda |binary UsingR-2.0-7/UsingR/data/babies.rda |binary UsingR-2.0-7/UsingR/data/babyboom.rda |binary UsingR-2.0-7/UsingR/data/batting.rda |binary UsingR-2.0-7/UsingR/data/baycheck.rda |binary UsingR-2.0-7/UsingR/data/best.times.rda |binary UsingR-2.0-7/UsingR/data/blood.rda |binary UsingR-2.0-7/UsingR/data/breakdown.rda |binary UsingR-2.0-7/UsingR/data/bright.stars.rda |binary UsingR-2.0-7/UsingR/data/brightness.rda |binary UsingR-2.0-7/UsingR/data/bumpers.rda |binary UsingR-2.0-7/UsingR/data/bycatch.rda |binary UsingR-2.0-7/UsingR/data/cabinet.rda |binary UsingR-2.0-7/UsingR/data/camp.rda |binary UsingR-2.0-7/UsingR/data/cancer.rda |binary UsingR-2.0-7/UsingR/data/carbon.rda |binary UsingR-2.0-7/UsingR/data/carsafety.rda |binary UsingR-2.0-7/UsingR/data/central.park.cloud.rda |binary UsingR-2.0-7/UsingR/data/central.park.rda |binary UsingR-2.0-7/UsingR/data/ceo2013.rda |binary UsingR-2.0-7/UsingR/data/cfb.rda |binary UsingR-2.0-7/UsingR/data/chicken.rda |binary UsingR-2.0-7/UsingR/data/chips.rda |binary UsingR-2.0-7/UsingR/data/co2emiss.rda |binary UsingR-2.0-7/UsingR/data/coins.rda |binary UsingR-2.0-7/UsingR/data/coldvermont.rda |binary UsingR-2.0-7/UsingR/data/corn.rda |binary UsingR-2.0-7/UsingR/data/crime.rda |binary UsingR-2.0-7/UsingR/data/deflection.rda |binary UsingR-2.0-7/UsingR/data/diamond.rda |binary UsingR-2.0-7/UsingR/data/divorce.rda |binary UsingR-2.0-7/UsingR/data/dottodot.rda |binary UsingR-2.0-7/UsingR/data/dowdata.rda |binary UsingR-2.0-7/UsingR/data/dvdsales.rda |binary UsingR-2.0-7/UsingR/data/emissions.rda |binary UsingR-2.0-7/UsingR/data/ewr.rda |binary UsingR-2.0-7/UsingR/data/exec.pay.rda |binary UsingR-2.0-7/UsingR/data/fat.rda |binary UsingR-2.0-7/UsingR/data/father.son.rda |binary UsingR-2.0-7/UsingR/data/female.inc.rda |binary UsingR-2.0-7/UsingR/data/firstchi.rda |binary UsingR-2.0-7/UsingR/data/five.yr.temperature.rda |binary UsingR-2.0-7/UsingR/data/florida.rda |binary UsingR-2.0-7/UsingR/data/galileo.rda |binary UsingR-2.0-7/UsingR/data/galton.rda |binary UsingR-2.0-7/UsingR/data/gap.rda |binary UsingR-2.0-7/UsingR/data/gasprices.rda |binary UsingR-2.0-7/UsingR/data/goalspergame.rda |binary UsingR-2.0-7/UsingR/data/google.rda |binary UsingR-2.0-7/UsingR/data/grades.rda |binary UsingR-2.0-7/UsingR/data/grip.rda |binary UsingR-2.0-7/UsingR/data/hall.fame.rda |binary UsingR-2.0-7/UsingR/data/heartrate.rda |binary UsingR-2.0-7/UsingR/data/home.rda |binary UsingR-2.0-7/UsingR/data/homedata.rda |binary UsingR-2.0-7/UsingR/data/homeprice.rda |binary UsingR-2.0-7/UsingR/data/homework.rda |binary UsingR-2.0-7/UsingR/data/income_percentiles.RData |binary UsingR-2.0-7/UsingR/data/iq.rda |binary UsingR-2.0-7/UsingR/data/kid.weights.rda |binary UsingR-2.0-7/UsingR/data/last.tie.rda |binary UsingR-2.0-7/UsingR/data/lawsuits.rda |binary UsingR-2.0-7/UsingR/data/malpract.rda |binary UsingR-2.0-7/UsingR/data/mandms.rda |binary UsingR-2.0-7/UsingR/data/math.rda |binary UsingR-2.0-7/UsingR/data/maydow.rda |binary UsingR-2.0-7/UsingR/data/movie_data_2011.rda |binary UsingR-2.0-7/UsingR/data/movies.rda |binary UsingR-2.0-7/UsingR/data/mw.ages.rda |binary UsingR-2.0-7/UsingR/data/nba.draft.rda |binary UsingR-2.0-7/UsingR/data/nisdc.rda |binary UsingR-2.0-7/UsingR/data/normtemp.rda |binary UsingR-2.0-7/UsingR/data/nym.2002.rda |binary UsingR-2.0-7/UsingR/data/oral.lesion.rda |binary UsingR-2.0-7/UsingR/data/ozonemonthly.rda |binary UsingR-2.0-7/UsingR/data/paradise.rda |binary UsingR-2.0-7/UsingR/data/pi2000.rda |binary UsingR-2.0-7/UsingR/data/primes.rda |binary UsingR-2.0-7/UsingR/data/puerto.rda |binary UsingR-2.0-7/UsingR/data/rat.rda |binary UsingR-2.0-7/UsingR/data/reaction.time.rda |binary UsingR-2.0-7/UsingR/data/reddrum.rda |binary UsingR-2.0-7/UsingR/data/salmon.rate.rda |binary UsingR-2.0-7/UsingR/data/salmonharvest.rda |binary UsingR-2.0-7/UsingR/data/samhda.rda |binary UsingR-2.0-7/UsingR/data/scrabble.rda |binary UsingR-2.0-7/UsingR/data/slc.rda |binary UsingR-2.0-7/UsingR/data/smokyph.rda |binary UsingR-2.0-7/UsingR/data/snacks.rda |binary UsingR-2.0-7/UsingR/data/south.rda |binary UsingR-2.0-7/UsingR/data/southernosc.rda |binary UsingR-2.0-7/UsingR/data/sp500.excess.rda |binary UsingR-2.0-7/UsingR/data/stud.recs.rda |binary UsingR-2.0-7/UsingR/data/student.expenses.rda |binary UsingR-2.0-7/UsingR/data/tcm1y.rda |binary UsingR-2.0-7/UsingR/data/tempsalinity.rda |binary UsingR-2.0-7/UsingR/data/too.young.rda |binary UsingR-2.0-7/UsingR/data/twins.rda |binary UsingR-2.0-7/UsingR/data/u2.rda |binary UsingR-2.0-7/UsingR/data/urchin.growth.rda |binary UsingR-2.0-7/UsingR/data/vacation.rda |binary UsingR-2.0-7/UsingR/data/watertemp.rda |binary UsingR-2.0-7/UsingR/data/wchomes.rda |binary UsingR-2.0-7/UsingR/data/wellbeing.rda |binary UsingR-2.0-7/UsingR/data/yellowfin.rda |binary UsingR-2.0-7/UsingR/inst/errata/errata.html | 8 UsingR-2.0-7/UsingR/inst/errata/errata.md | 8 UsingR-2.0-7/UsingR/man/MLBattend.Rd | 4 UsingR-2.0-7/UsingR/man/Medicare.Rd | 2 UsingR-2.0-7/UsingR/man/OBP.Rd | 4 UsingR-2.0-7/UsingR/man/ObamaApproval.Rd | 2 UsingR-2.0-7/UsingR/man/age.universe.Rd | 14 UsingR-2.0-7/UsingR/man/babies.Rd | 10 UsingR-2.0-7/UsingR/man/babyboom.Rd | 4 UsingR-2.0-7/UsingR/man/batting.Rd | 8 UsingR-2.0-7/UsingR/man/carsafety.Rd | 2 UsingR-2.0-7/UsingR/man/central.park.cloud.Rd | 2 UsingR-2.0-7/UsingR/man/ceo2013.Rd | 2 UsingR-2.0-7/UsingR/man/cfb.Rd | 6 UsingR-2.0-7/UsingR/man/co2emiss.Rd | 12 UsingR-2.0-7/UsingR/man/diamond.Rd | 4 UsingR-2.0-7/UsingR/man/exec.pay.Rd | 2 UsingR-2.0-7/UsingR/man/fat.Rd | 16 - UsingR-2.0-7/UsingR/man/hall.fame.Rd | 18 - UsingR-2.0-7/UsingR/man/kid.weights.Rd | 6 UsingR-2.0-7/UsingR/man/lorem.Rd | 4 UsingR-2.0-7/UsingR/man/mandms.Rd | 4 UsingR-2.0-7/UsingR/man/maydow.Rd | 4 UsingR-2.0-7/UsingR/man/midsize.Rd | 2 UsingR-2.0-7/UsingR/man/movie_data_2011.Rd | 2 UsingR-2.0-7/UsingR/man/nba.draft.Rd | 2 UsingR-2.0-7/UsingR/man/nisdc.Rd | 9 UsingR-2.0-7/UsingR/man/normtemp.Rd | 6 UsingR-2.0-7/UsingR/man/npdb.Rd | 10 UsingR-2.0-7/UsingR/man/ozonemonthly.Rd | 6 UsingR-2.0-7/UsingR/man/reaction.time.Rd | 4 UsingR-2.0-7/UsingR/man/reddrum.Rd | 4 UsingR-2.0-7/UsingR/man/salmon.rate.Rd | 2 UsingR-2.0-7/UsingR/man/samhda.Rd | 2 UsingR-2.0-7/UsingR/man/sp500.excess.Rd | 4 UsingR-2.0-7/UsingR/man/squareplot.Rd | 2 UsingR-2.0-7/UsingR/man/tcm1y.Rd | 2 UsingR-2.0-7/UsingR/man/tempsalinity.Rd | 2 UsingR-2.0-7/UsingR/man/wchomes.Rd | 6 UsingR-2.0-7/UsingR/man/wellbeing.Rd | 4 UsingR-2.0-7/UsingR/man/yellowfin.Rd | 2 163 files changed, 314 insertions(+), 324 deletions(-)
Title: Multiscale Fisher's Independence Test for Multivariate
Dependence
Description: Test for independence of two random vectors, learn and report the dependency structure. For more information, see Gorsky, Shai and Li Ma, Multiscale Fisher's Independence Test for Multivariate Dependence, Biometrika, accepted, January 2022.
Author: S. Gorsky, L. Ma
Maintainer: S. Gorsky <sgorsky@umass.edu>
Diff between MultiFit versions 1.0.1 dated 2020-01-10 and 1.1.0 dated 2022-01-11
MultiFit-1.0.1/MultiFit/R/multiFit.R |only MultiFit-1.0.1/MultiFit/inst/doc/multiFit.R |only MultiFit-1.0.1/MultiFit/inst/doc/multiFit.Rmd |only MultiFit-1.0.1/MultiFit/inst/doc/multiFit.html |only MultiFit-1.0.1/MultiFit/man/multiFit.Rd |only MultiFit-1.0.1/MultiFit/man/multiSummary.Rd |only MultiFit-1.0.1/MultiFit/man/multiTree.Rd |only MultiFit-1.0.1/MultiFit/man/permNullTest.Rd |only MultiFit-1.0.1/MultiFit/man/uvApproxNull.Rd |only MultiFit-1.0.1/MultiFit/man/uvExactNull.Rd |only MultiFit-1.0.1/MultiFit/src/makeCDF.cpp |only MultiFit-1.0.1/MultiFit/src/stepFunRcpp.cpp |only MultiFit-1.0.1/MultiFit/vignettes/multiFit.Rmd |only MultiFit-1.1.0/MultiFit/DESCRIPTION | 10 ++--- MultiFit-1.1.0/MultiFit/MD5 | 36 ++++++++---------- MultiFit-1.1.0/MultiFit/NAMESPACE | 2 - MultiFit-1.1.0/MultiFit/NEWS.md | 4 ++ MultiFit-1.1.0/MultiFit/R/MultiFIT.R |only MultiFit-1.1.0/MultiFit/R/RcppExports.R | 8 ---- MultiFit-1.1.0/MultiFit/R/multiple_testing.R |only MultiFit-1.1.0/MultiFit/R/utilities.R | 50 +++++++++++++++++-------- MultiFit-1.1.0/MultiFit/build/vignette.rds |binary MultiFit-1.1.0/MultiFit/inst/doc/MultiFIT.R |only MultiFit-1.1.0/MultiFit/inst/doc/MultiFIT.Rmd |only MultiFit-1.1.0/MultiFit/inst/doc/MultiFIT.html |only MultiFit-1.1.0/MultiFit/man/MultiFIT.Rd |only MultiFit-1.1.0/MultiFit/man/MultiSummary.Rd |only MultiFit-1.1.0/MultiFit/man/MultiTree.Rd |only MultiFit-1.1.0/MultiFit/src/RcppExports.cpp | 38 ++----------------- MultiFit-1.1.0/MultiFit/vignettes/MultiFIT.Rmd |only 30 files changed, 66 insertions(+), 82 deletions(-)
Title: Genetic Linkage Maps in Autopolyploids
Description: Construction of genetic maps in autopolyploid full-sib populations.
Uses pairwise recombination fraction estimation as the first
source of information to sequentially position allelic variants
in specific homologues. For situations where pairwise analysis has
limited power, the algorithm relies on the multilocus likelihood
obtained through a hidden Markov model (HMM). For more detail,
please see Mollinari and Garcia (2019) <doi:10.1534/g3.119.400378>
and Mollinari et al. (2020) <doi:10.1534/g3.119.400620>.
Author: Marcelo Mollinari [aut, cre] (<https://orcid.org/0000-0002-7001-8498>),
Gabriel Gesteira [aut] (<https://orcid.org/0000-0002-4106-7346>),
Guilhereme Pereira [ctb] (<https://orcid.org/0000-0002-7106-8630>),
Augusto Garcia [ctb] (<https://orcid.org/0000-0003-0634-3277>),
Zhao-Bang Zeng [ctb] (<https://orcid.org/0000-0002-3115-1149>),
Katharine Preedy [ctb, cph] (MDS ordering algorithm),
Robert Gentleman [cph] (C code for MLE optimization in
src/pairwise_estimation.cpp),
Ross Ihaka [cph] (C code for MLE optimization in
src/pairwise_estimation.cpp),
R Foundation [cph] (C code for MLE optimization in
src/pairwise_estimation.cpp),
R-core [cph] (C code for MLE optimization in
src/pairwise_estimation.cpp)
Maintainer: Marcelo Mollinari <mmollin@ncsu.edu>
Diff between mappoly versions 0.2.3 dated 2021-04-20 and 0.3.0 dated 2022-01-11
mappoly-0.2.3/mappoly/data/hexafake.geno.dist.rda |only mappoly-0.2.3/mappoly/data/hexafake.rda |only mappoly-0.2.3/mappoly/data/maps.hexafake.rda |only mappoly-0.2.3/mappoly/data/solcap.dose.map.rda |only mappoly-0.2.3/mappoly/data/solcap.error.map.rda |only mappoly-0.2.3/mappoly/data/solcap.mds.map.rda |only mappoly-0.2.3/mappoly/data/solcap.prior.map.rda |only mappoly-0.2.3/mappoly/data/tetra.solcap.geno.dist.rda |only mappoly-0.2.3/mappoly/data/tetra.solcap.rda |only mappoly-0.2.3/mappoly/man/calc_homoprob.Rd |only mappoly-0.2.3/mappoly/man/pos_twopt_est.Rd |only mappoly-0.3.0/mappoly/DESCRIPTION | 27 mappoly-0.3.0/mappoly/MD5 | 326 ++-- mappoly-0.3.0/mappoly/NAMESPACE | 21 mappoly-0.3.0/mappoly/NEWS.md | 9 mappoly-0.3.0/mappoly/R/RcppExports.R | 4 mappoly-0.3.0/mappoly/R/cache_twopts.R | 40 mappoly-0.3.0/mappoly/R/calc_genoprob.R | 89 - mappoly-0.3.0/mappoly/R/calc_genoprob_dist.R | 46 mappoly-0.3.0/mappoly/R/calc_genoprob_error.R | 86 - mappoly-0.3.0/mappoly/R/calc_genoprob_one_parent.R |only mappoly-0.3.0/mappoly/R/check_phase_configurations.R | 132 - mappoly-0.3.0/mappoly/R/data.R | 42 mappoly-0.3.0/mappoly/R/eliminate_redundant.R | 34 mappoly-0.3.0/mappoly/R/est_map_hmm.R | 378 ++-- mappoly-0.3.0/mappoly/R/export_map_list.R | 26 mappoly-0.3.0/mappoly/R/export_qtlpoly.R |only mappoly-0.3.0/mappoly/R/filters.R | 269 ++- mappoly-0.3.0/mappoly/R/get_counts.R | 62 mappoly-0.3.0/mappoly/R/get_counts_from_web.R | 16 mappoly-0.3.0/mappoly/R/get_submap.R | 38 mappoly-0.3.0/mappoly/R/group.R | 67 mappoly-0.3.0/mappoly/R/haplotype_map_utils.R | 98 - mappoly-0.3.0/mappoly/R/homolog_probs.R | 72 mappoly-0.3.0/mappoly/R/import_from_polymapR.R | 80 - mappoly-0.3.0/mappoly/R/import_from_updog.R | 80 - mappoly-0.3.0/mappoly/R/loglike_hmm.R | 20 mappoly-0.3.0/mappoly/R/make_mat.R | 18 mappoly-0.3.0/mappoly/R/make_pairs.R | 56 mappoly-0.3.0/mappoly/R/make_seq.R | 166 +- mappoly-0.3.0/mappoly/R/marker_info.R | 114 - mappoly-0.3.0/mappoly/R/mds.R | 91 - mappoly-0.3.0/mappoly/R/merge_maps.R | 138 - mappoly-0.3.0/mappoly/R/one_paprent_single_map_hmm.R |only mappoly-0.3.0/mappoly/R/pairwise_rf.R | 505 +++--- mappoly-0.3.0/mappoly/R/plot_genome_vs_map.R | 25 mappoly-0.3.0/mappoly/R/plot_map_list.R | 34 mappoly-0.3.0/mappoly/R/poly_cross_simulate.R | 54 mappoly-0.3.0/mappoly/R/preferential_pairing.R | 214 +- mappoly-0.3.0/mappoly/R/prior_dist_hmm.R | 10 mappoly-0.3.0/mappoly/R/read_fitpoly.R | 88 - mappoly-0.3.0/mappoly/R/read_mappoly.R | 188 +- mappoly-0.3.0/mappoly/R/read_mappoly_csv.R | 129 - mappoly-0.3.0/mappoly/R/read_mappoly_prob.R | 122 - mappoly-0.3.0/mappoly/R/read_mappoly_vcf.R | 142 - mappoly-0.3.0/mappoly/R/reestimate_map.R | 48 mappoly-0.3.0/mappoly/R/reestimate_map_with_global_genotypic_error.R | 138 - mappoly-0.3.0/mappoly/R/reestimate_map_with_prior_genotypic_probability.R | 50 mappoly-0.3.0/mappoly/R/rf_list_to_matrix.R | 281 +-- mappoly-0.3.0/mappoly/R/rf_snp_filter.R | 67 mappoly-0.3.0/mappoly/R/segreg_poly.R | 20 mappoly-0.3.0/mappoly/R/sim_homologous.R | 74 mappoly-0.3.0/mappoly/R/simulation_utils.R | 132 - mappoly-0.3.0/mappoly/R/single_map_hmm.R | 44 mappoly-0.3.0/mappoly/R/split_and_rephase.R | 121 - mappoly-0.3.0/mappoly/R/sysdata.rda |binary mappoly-0.3.0/mappoly/R/utils.R | 789 +++++----- mappoly-0.3.0/mappoly/R/zzz.R | 6 mappoly-0.3.0/mappoly/README.md | 59 mappoly-0.3.0/mappoly/build/partial.rdb |binary mappoly-0.3.0/mappoly/build/vignette.rds |only mappoly-0.3.0/mappoly/data/example_data.rda |only mappoly-0.3.0/mappoly/inst/doc |only mappoly-0.3.0/mappoly/inst/extdata |only mappoly-0.3.0/mappoly/man/add_marker.Rd | 28 mappoly-0.3.0/mappoly/man/cache_counts_twopt.Rd | 6 mappoly-0.3.0/mappoly/man/calc_genoprob.Rd | 2 mappoly-0.3.0/mappoly/man/calc_genoprob_dist.Rd | 2 mappoly-0.3.0/mappoly/man/calc_genoprob_error.Rd | 2 mappoly-0.3.0/mappoly/man/calc_genoprob_haplo.Rd | 4 mappoly-0.3.0/mappoly/man/calc_genoprob_one_parent.Rd |only mappoly-0.3.0/mappoly/man/calc_homologprob.Rd |only mappoly-0.3.0/mappoly/man/check_if_rf_is_possible.Rd |only mappoly-0.3.0/mappoly/man/check_pairwise.Rd | 2 mappoly-0.3.0/mappoly/man/compare_haplotypes.Rd | 6 mappoly-0.3.0/mappoly/man/compare_maps.Rd |only mappoly-0.3.0/mappoly/man/concatenate_new_marker.Rd | 4 mappoly-0.3.0/mappoly/man/draw_cross.Rd | 2 mappoly-0.3.0/mappoly/man/draw_phases.Rd | 4 mappoly-0.3.0/mappoly/man/drop_marker.Rd | 2 mappoly-0.3.0/mappoly/man/elim_conf_using_two_pts.Rd | 2 mappoly-0.3.0/mappoly/man/elim_redundant.Rd | 6 mappoly-0.3.0/mappoly/man/est_full_hmm_with_global_error.Rd | 16 mappoly-0.3.0/mappoly/man/est_full_hmm_with_prior_prob.Rd | 18 mappoly-0.3.0/mappoly/man/est_haplo_hmm.Rd | 2 mappoly-0.3.0/mappoly/man/est_pairwise_rf.Rd | 14 mappoly-0.3.0/mappoly/man/est_pairwise_rf2.Rd |only mappoly-0.3.0/mappoly/man/est_rf_hmm.Rd | 24 mappoly-0.3.0/mappoly/man/est_rf_hmm_sequential.Rd | 28 mappoly-0.3.0/mappoly/man/est_rf_hmm_single.Rd | 8 mappoly-0.3.0/mappoly/man/est_rf_hmm_single_one_parent.Rd |only mappoly-0.3.0/mappoly/man/export_qtlpoly.Rd |only mappoly-0.3.0/mappoly/man/extract_map.Rd | 2 mappoly-0.3.0/mappoly/man/filter_individuals.Rd |only mappoly-0.3.0/mappoly/man/filter_missing.Rd | 2 mappoly-0.3.0/mappoly/man/filter_missing_ind.Rd | 2 mappoly-0.3.0/mappoly/man/filter_missing_mrk.Rd | 2 mappoly-0.3.0/mappoly/man/filter_segregation.Rd | 2 mappoly-0.3.0/mappoly/man/generate_all_link_phase_elim_equivalent.Rd | 4 mappoly-0.3.0/mappoly/man/generate_all_link_phases_elim_equivalent_haplo.Rd | 4 mappoly-0.3.0/mappoly/man/genotyping_global_error.Rd | 8 mappoly-0.3.0/mappoly/man/get_cache_two_pts_from_web.Rd | 2 mappoly-0.3.0/mappoly/man/get_counts.Rd | 2 mappoly-0.3.0/mappoly/man/get_counts_all_phases.Rd | 2 mappoly-0.3.0/mappoly/man/get_genomic_order.Rd | 4 mappoly-0.3.0/mappoly/man/get_rf_from_list.Rd | 6 mappoly-0.3.0/mappoly/man/get_states_and_emission_one_parent.Rd |only mappoly-0.3.0/mappoly/man/get_submap.Rd | 4 mappoly-0.3.0/mappoly/man/get_w_m.Rd | 2 mappoly-0.3.0/mappoly/man/group_mappoly.Rd | 6 mappoly-0.3.0/mappoly/man/hexafake.Rd | 12 mappoly-0.3.0/mappoly/man/hexafake.geno.dist.Rd | 10 mappoly-0.3.0/mappoly/man/import_from_updog.Rd | 14 mappoly-0.3.0/mappoly/man/loglike_hmm.Rd | 2 mappoly-0.3.0/mappoly/man/ls_linkage_phases.Rd | 8 mappoly-0.3.0/mappoly/man/make_mat_mappoly.Rd | 10 mappoly-0.3.0/mappoly/man/make_pairs_mappoly.Rd | 18 mappoly-0.3.0/mappoly/man/make_seq_mappoly.Rd | 10 mappoly-0.3.0/mappoly/man/mds_mappoly.Rd | 5 mappoly-0.3.0/mappoly/man/merge_datasets.Rd | 14 mappoly-0.3.0/mappoly/man/merge_maps.Rd | 32 mappoly-0.3.0/mappoly/man/mrk_chisq_test.Rd | 2 mappoly-0.3.0/mappoly/man/paralell_pairwise_discrete_rcpp.Rd |only mappoly-0.3.0/mappoly/man/ph_list_to_matrix.Rd | 4 mappoly-0.3.0/mappoly/man/plot.mappoly.prefpair.profiles.Rd | 8 mappoly-0.3.0/mappoly/man/plot_GIC.Rd | 2 mappoly-0.3.0/mappoly/man/plot_compare_haplotypes.Rd | 2 mappoly-0.3.0/mappoly/man/plot_genome_vs_map.Rd | 1 mappoly-0.3.0/mappoly/man/poly_cross_simulate.Rd | 10 mappoly-0.3.0/mappoly/man/poly_hmm_est.Rd | 14 mappoly-0.3.0/mappoly/man/read_fitpoly.Rd | 14 mappoly-0.3.0/mappoly/man/read_geno.Rd | 20 mappoly-0.3.0/mappoly/man/read_geno_csv.Rd | 20 mappoly-0.3.0/mappoly/man/read_geno_prob.Rd | 22 mappoly-0.3.0/mappoly/man/read_vcf.Rd | 14 mappoly-0.3.0/mappoly/man/rf_list_to_matrix.Rd | 16 mappoly-0.3.0/mappoly/man/rf_snp_filter.Rd | 25 mappoly-0.3.0/mappoly/man/sample_data.Rd | 2 mappoly-0.3.0/mappoly/man/segreg_poly.Rd | 8 mappoly-0.3.0/mappoly/man/sim_cross_one_informative_parent.Rd | 2 mappoly-0.3.0/mappoly/man/sim_cross_two_informative_parents.Rd | 2 mappoly-0.3.0/mappoly/man/sim_homologous.Rd | 12 mappoly-0.3.0/mappoly/man/split_and_rephase.Rd | 17 mappoly-0.3.0/mappoly/man/table_to_mappoly.Rd |only mappoly-0.3.0/mappoly/man/tetra.solcap.Rd | 10 mappoly-0.3.0/mappoly/man/tetra.solcap.geno.dist.Rd | 10 mappoly-0.3.0/mappoly/man/v_2_m.Rd |only mappoly-0.3.0/mappoly/src/Makevars.win | 5 mappoly-0.3.0/mappoly/src/RcppExports.cpp | 56 mappoly-0.3.0/mappoly/src/combinatorial.cpp | 8 mappoly-0.3.0/mappoly/src/hmm_elements.cpp | 64 mappoly-0.3.0/mappoly/src/hmm_elements.h | 15 mappoly-0.3.0/mappoly/src/hmm_one_parent.cpp |only mappoly-0.3.0/mappoly/src/pairwise_estimation_rcppparallel.cpp |only mappoly-0.3.0/mappoly/src/read_mappoly_vcf.cpp | 3 mappoly-0.3.0/mappoly/tests/testthat/test-2pt.R | 6 mappoly-0.3.0/mappoly/tests/testthat/test-cahe_twopts.R | 2 mappoly-0.3.0/mappoly/tests/testthat/test-est_hmm_map.R | 10 mappoly-0.3.0/mappoly/tests/testthat/test-get_submap.R | 2 mappoly-0.3.0/mappoly/tests/testthat/test-homolog_prob.R | 2 mappoly-0.3.0/mappoly/tests/testthat/test-merge_maps.R | 4 mappoly-0.3.0/mappoly/tests/testthat/test-simulation.R | 4 mappoly-0.3.0/mappoly/tests/testthat/test-utility_func.R | 8 mappoly-0.3.0/mappoly/vignettes |only 174 files changed, 3674 insertions(+), 3108 deletions(-)
Title: Isolation-Based Outlier Detection
Description: Fast and multi-threaded implementation of
isolation forest (Liu, Ting, Zhou (2008) <doi:10.1109/ICDM.2008.17>),
extended isolation forest (Hariri, Kind, Brunner (2018) <arXiv:1811.02141>),
SCiForest (Liu, Ting, Zhou (2010) <doi:10.1007/978-3-642-15883-4_18>),
fair-cut forest (Cortes (2021) <arXiv:2110:13402>),
robust random-cut forest (Guha, Mishra, Roy, Schrijvers (2016) <http://proceedings.mlr.press/v48/guha16.html>),
and customizable variations of them, for isolation-based outlier detection, clustered outlier detection,
distance or similarity approximation (Cortes (2019) <arXiv:1910.12362>),
and imputation of missing values (Cortes (2019) <arXiv:1911.06646>),
based on random or guided decision tree splitting, and providing different metrics for
scoring anomalies based on isolation depth or density (Cortes (2021) <arXiv:2111.11639>).
Provides simple heuristics for fitting the model to categorical columns and handling missing data,
and offers options for varying between random and guided splits, and for using different splitting criteria.
Author: David Cortes [aut, cre, cph],
Thibaut Goetghebuer-Planchon [cph] (Copyright holder of included
robinmap library),
David Blackman [cph] (Copyright holder of original xoshiro code),
Sebastiano Vigna [cph] (Copyright holder of original xoshiro code)
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between isotree versions 0.3.9 dated 2021-10-23 and 0.5.5 dated 2022-01-11
isotree-0.3.9/isotree/src/instantiate_model.h |only isotree-0.3.9/isotree/src/model_joined.h |only isotree-0.5.5/isotree/DESCRIPTION | 28 isotree-0.5.5/isotree/LICENSE | 2 isotree-0.5.5/isotree/MD5 | 70 isotree-0.5.5/isotree/R/RcppExports.R | 8 isotree-0.5.5/isotree/R/helpers.R | 60 isotree-0.5.5/isotree/R/isoforest.R | 696 ++++-- isotree-0.5.5/isotree/configure | 75 isotree-0.5.5/isotree/configure.ac | 24 isotree-0.5.5/isotree/inst |only isotree-0.5.5/isotree/man/isolation.forest.Rd | 450 +++- isotree-0.5.5/isotree/man/isotree.add.tree.Rd | 10 isotree-0.5.5/isotree/man/isotree.to.sql.Rd | 3 isotree-0.5.5/isotree/man/predict.isolation_forest.Rd | 51 isotree-0.5.5/isotree/src/Makevars.in | 2 isotree-0.5.5/isotree/src/Makevars.win | 2 isotree-0.5.5/isotree/src/RcppExports.cpp | 33 isotree-0.5.5/isotree/src/Rwrapper.cpp | 79 isotree-0.5.5/isotree/src/crit.h | 1247 +++++++++-- isotree-0.5.5/isotree/src/dist.h | 30 isotree-0.5.5/isotree/src/extended.h | 562 ++++- isotree-0.5.5/isotree/src/fit_model.h | 856 ++++++- isotree-0.5.5/isotree/src/headers_joined.h |only isotree-0.5.5/isotree/src/helpers_iforest.h | 474 ++++ isotree-0.5.5/isotree/src/impute.h | 22 isotree-0.5.5/isotree/src/instantiate_template_headers.h |only isotree-0.5.5/isotree/src/isoforest.h | 1205 ++++++++-- isotree-0.5.5/isotree/src/isotree.h | 572 +++-- isotree-0.5.5/isotree/src/merge_models.cpp | 20 isotree-0.5.5/isotree/src/mult.h | 173 - isotree-0.5.5/isotree/src/other_helpers.h | 20 isotree-0.5.5/isotree/src/predict.h | 190 + isotree-0.5.5/isotree/src/robinmap/LICENSE |only isotree-0.5.5/isotree/src/serialize.cpp | 185 + isotree-0.5.5/isotree/src/sql.cpp | 71 isotree-0.5.5/isotree/src/subset_models.cpp | 20 isotree-0.5.5/isotree/src/utils.h | 1678 ++++++++++++++- isotree-0.5.5/isotree/src/xoshiro.h | 32 39 files changed, 7374 insertions(+), 1576 deletions(-)
Title: Draw with 'grid' in 'ggplot2'
Description: An extension of 'ggplot2' that makes it easy to add
raw 'grid' output, such as customised annotations, to a
'ggplot2' plot.
Author: Paul Murrell [aut, cre]
Maintainer: Paul Murrell <paul@stat.auckland.ac.nz>
Diff between gggrid versions 0.1-1 dated 2021-11-22 and 0.2-0 dated 2022-01-11
DESCRIPTION | 6 +- MD5 | 23 +++++---- NAMESPACE | 2 R/grid_group.R | 28 ++++++++---- R/grid_panel.R | 27 ++++++++--- build/vignette.rds |binary inst/NEWS.Rd |only inst/doc/gggrid.R | 15 ++++++ inst/doc/gggrid.Rmd | 37 ++++++++++++++- inst/doc/gggrid.html | 25 +++++++++- man/grid_panel.Rd | 19 +++++++- vignettes/gggrid.Rmd | 37 ++++++++++++++- vignettes/minard-troops.txt | 102 ++++++++++++++++++++++---------------------- 13 files changed, 230 insertions(+), 91 deletions(-)
More information about freqdistributionNogives at CRAN
Permanent link
Title: Extended HOF (Huisman-Olff-Fresco) Models
Description: Extended and enhanced hierarchical logistic regression models (called Huisman-Olff-Fresco in biology, see Huisman et al. 1993 Journal of Vegetation Science <doi:10.1111/jvs.12050>) models. Response curves along one-dimensional gradients including no response, monotone, plateau, unimodal and bimodal models.
Author: Florian Jansen, Jari Oksanen
Maintainer: Florian Jansen <florian.jansen@uni-rostock.de>
Diff between eHOF versions 1.9 dated 2020-05-22 and 1.10 dated 2022-01-11
eHOF-1.10/eHOF/DESCRIPTION | 7 +++---- eHOF-1.10/eHOF/MD5 | 13 ++++++------- eHOF-1.10/eHOF/R/plot.HOF.r | 2 +- eHOF-1.10/eHOF/inst/doc/eHOF.R | 18 +++++++++--------- eHOF-1.10/eHOF/inst/doc/eHOF.Rnw | 20 ++++++++++---------- eHOF-1.10/eHOF/inst/doc/eHOF.pdf |binary eHOF-1.10/eHOF/vignettes/eHOF.Rnw | 20 ++++++++++---------- eHOF-1.9/eHOF/vignettes/taxonnames.csv |only 8 files changed, 39 insertions(+), 41 deletions(-)
Title: Generalized Pairwise Comparisons
Description: Implementation of the Generalized Pairwise Comparisons (GPC)
as defined in Buyse (2010) <doi:10.1002/sim.3923> for complete observations,
and extended in Peron (2018) <doi:10.1177/0962280216658320> to deal with right-censoring.
GPC compare two groups of observations (intervention vs. control group)
regarding several prioritized endpoints to estimate the probability that a random observation drawn from
one group performs better than a random observation drawn from the other group (Mann-Whitney parameter).
The net benefit and win ratio statistics,
i.e. the difference and ratio between the probabilities relative to the intervention and control groups,
can then also be estimated. Confidence intervals and p-values are obtained based on asymptotic results (Ozenne 2021 <doi:10.1177/09622802211037067>),
non-parametric bootstrap, or permutations.
The software enables the use of thresholds of minimal importance difference,
stratification, non-prioritized endpoints (O Brien test), and can handle right-censoring and competing-risks.
Author: Brice Ozenne [aut, cre] (<https://orcid.org/0000-0001-9694-2956>),
Julien Peron [ctb],
Eva Cantagallo [aut]
Maintainer: Brice Ozenne <brice.mh.ozenne@gmail.com>
Diff between BuyseTest versions 2.3.9 dated 2022-01-03 and 2.3.10 dated 2022-01-11
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/doc/overview.pdf |binary src/FCT_calcOnePair.h | 46 ++++++++++++++++++++++++++++------------------ 4 files changed, 35 insertions(+), 25 deletions(-)
Title: Load WARC Files into Apache Spark
Description: Load WARC (Web ARChive) files into Apache Spark using 'sparklyr'. This
allows to read files from the Common Crawl project <http://commoncrawl.org/>.
Author: Javier Luraschi [aut],
Yitao Li [aut] (<https://orcid.org/0000-0002-1261-905X>),
Edgar Ruiz [aut, cre]
Maintainer: Edgar Ruiz <edgar@rstudio.com>
Diff between sparkwarc versions 0.1.5 dated 2020-12-15 and 0.1.6 dated 2022-01-11
DESCRIPTION | 24 +++++------ MD5 | 24 ++++++----- R/RcppExports.R | 4 - R/dependencies.R | 4 + R/sparkwarc.R | 11 ++--- inst/java/sparkwarc-1.5-2.10.jar |binary inst/java/sparkwarc-1.6-2.10.jar |binary inst/java/sparkwarc-2.0-2.11.jar |binary inst/java/sparkwarc-2.3-2.11.jar |only inst/java/sparkwarc-2.4-2.11.jar |only inst/java/sparkwarc-2.4-2.12.jar |only inst/java/sparkwarc-3.0-2.12.jar |only man/spark_read_warc.Rd | 9 ++-- src/RcppExports.cpp | 19 +------- src/warc.cpp | 85 ++++++++++++++++++--------------------- 15 files changed, 86 insertions(+), 94 deletions(-)
Title: Sparklyr Extension for 'Flint'
Description: This sparklyr extension makes 'Flint' time series
library functionalities (<https://github.com/twosigma/flint>) easily
accessible through R.
Author: Yitao Li [aut] (<https://orcid.org/0000-0002-1261-905X>),
Edgar Ruiz [aut, cre]
Maintainer: Edgar Ruiz <edgar@rstudio.com>
Diff between sparklyr.flint versions 0.2.1 dated 2021-03-01 and 0.2.2 dated 2022-01-11
DESCRIPTION | 22 +- MD5 | 12 - NEWS.md | 18 + build/vignette.rds |binary inst/doc/importing-time-series-data.html | 242 +++---------------------- inst/doc/overview.html | 183 ------------------- inst/doc/working-with-time-series-rdd.html | 270 +++++------------------------ 7 files changed, 122 insertions(+), 625 deletions(-)
More information about sparklyr.flint at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-09 0.2.2
2021-03-12 0.2.1
Title: Generation of Different Animated Christmas Cards
Description: Generation of different Christmas cards, most of them being
animated. Most of the cards can be generated in three languages (English,
Catalan and Spanish). The collection started in 2009.
Author: Jose Barrera-Gomez
Maintainer: Jose Barrera-Gomez <jose.barrera@isglobal.org>
Diff between christmas versions 1.1.0 dated 2021-12-14 and 1.1.1 dated 2022-01-11
DESCRIPTION | 6 - MD5 | 10 +- NEWS | 14 ++- R/auxiliarFunctions.R | 216 +++++++++++++++++++++++++------------------------- R/xmasgalton.R | 2 R/xmastreeshape.R | 15 +-- 6 files changed, 135 insertions(+), 128 deletions(-)