Title: Variational Merging
Description: A new mathematical formulation to merge observed data with gridded images of environmental variables using partial differential equations in a variational setting. The original method was created, developed and published by Ulloa, Samaniego, Campozano and Ballari (2018) <doi:10.1002/2017JD027982>.
Author: Jacinto Ulloa [aut],
Esteban Samaniego [aut],
Lenin Campozano [aut],
Daniela Ballari [aut],
Leandro Robaina [cre, com, trl],
Ronald Gualan [com]
Maintainer: Leandro Robaina <metclimaepn.libs@gmail.com>
Diff between VARMER versions 0.1.1 dated 2021-02-05 and 1.0.0 dated 2021-02-07
VARMER-0.1.1/VARMER/R/U.R |only VARMER-0.1.1/VARMER/R/coordinates.R |only VARMER-0.1.1/VARMER/R/elements.R |only VARMER-0.1.1/VARMER/R/img2varmer.R |only VARMER-0.1.1/VARMER/R/mesh_3.R |only VARMER-0.1.1/VARMER/R/plot_mesh.R |only VARMER-0.1.1/VARMER/R/pre_data.R |only VARMER-0.1.1/VARMER/R/uhat.R |only VARMER-0.1.1/VARMER/R/uhat_raster.R |only VARMER-0.1.1/VARMER/R/v.R |only VARMER-0.1.1/VARMER/R/v_raster.R |only VARMER-0.1.1/VARMER/R/var_merge.R |only VARMER-1.0.0/VARMER/DESCRIPTION | 31 VARMER-1.0.0/VARMER/MD5 | 68 +- VARMER-1.0.0/VARMER/NAMESPACE | 3 VARMER-1.0.0/VARMER/NEWS.md | 18 VARMER-1.0.0/VARMER/R/dataset_ecuador_tmax.R |only VARMER-1.0.0/VARMER/R/dataset_v-0.1.0.R |only VARMER-1.0.0/VARMER/R/varmer.R | 523 +++++++++++++--- VARMER-1.0.0/VARMER/R/varmer.ts.R |only VARMER-1.0.0/VARMER/README.md |only VARMER-1.0.0/VARMER/build |only VARMER-1.0.0/VARMER/data/ecuador.tmax.stations.df.RData |only VARMER-1.0.0/VARMER/data/ecuador.tmax.wrf.out.RData |only VARMER-1.0.0/VARMER/data/ecuador.tmax.zoo.RData |only VARMER-1.0.0/VARMER/inst |only VARMER-1.0.0/VARMER/man/U.Rd | 32 VARMER-1.0.0/VARMER/man/coordinates.Rd | 32 VARMER-1.0.0/VARMER/man/ecuador.tmax.stations.df.Rd |only VARMER-1.0.0/VARMER/man/ecuador.tmax.wrf.out.Rd |only VARMER-1.0.0/VARMER/man/ecuador.tmax.zoo.Rd |only VARMER-1.0.0/VARMER/man/elements.Rd | 32 VARMER-1.0.0/VARMER/man/fit.varmer.Rd |only VARMER-1.0.0/VARMER/man/idw.uhat.from.sf.Rd |only VARMER-1.0.0/VARMER/man/img2varmer.Rd | 64 - VARMER-1.0.0/VARMER/man/mesh_3.Rd | 80 +- VARMER-1.0.0/VARMER/man/plot_mesh.Rd | 84 +- VARMER-1.0.0/VARMER/man/pre_data.Rd | 52 - VARMER-1.0.0/VARMER/man/uhat.Rd | 32 VARMER-1.0.0/VARMER/man/uhat.raster.Rd | 32 VARMER-1.0.0/VARMER/man/v.Rd | 32 VARMER-1.0.0/VARMER/man/v.raster.Rd | 32 VARMER-1.0.0/VARMER/man/var_merge.Rd | 106 +-- VARMER-1.0.0/VARMER/man/varmer.Rd | 116 +-- VARMER-1.0.0/VARMER/man/varmer.ts.Rd |only VARMER-1.0.0/VARMER/vignettes |only 46 files changed, 892 insertions(+), 477 deletions(-)
Title: Hierarchical and Variation Partitioning for Canonical Analysis
Description: This function conducts variation partitioning and hierarchical partitioning to calculate the unique, shared (referred as to "common") and independent contributions of each predictor (or matrix) to explained variation (R-squared and adjusted R-squared) on canonical analysis (RDA,CCA and db-RDA), applying the hierarchy algorithm of Chevan, A. and Sutherland, M. 1991 Hierarchical Partitioning.The American Statistician, 90-96 <DOI:10.1080/00031305.1991.10475776>.
Author: Jiangshan Lai,Pedro Peres-neto
Maintainer: Jiangshan Lai <lai@ibcas.ac.cn>
Diff between rdacca.hp versions 0.5-3 dated 2021-02-06 and 0.5-4 dated 2021-02-07
DESCRIPTION | 7 +++---- MD5 | 2 +- 2 files changed, 4 insertions(+), 5 deletions(-)
Title: The Ranking Project: Visualizations for Comparing Populations
Description: Functions to generate plots and tables for comparing independently-
sampled populations. Companion package to "A Primer on Visualizations
for Comparing Populations, Including the Issue of Overlapping Confidence
Intervals" by Wright, Klein, and Wieczorek (2019)
<DOI:10.1080/00031305.2017.1392359> and "A Joint Confidence Region for an
Overall Ranking of Populations" by Klein, Wright, and Wieczorek (2020)
<DOI:10.1111/rssc.12402>.
Author: Jerzy Wieczorek [cre, aut],
Joel Beard [ctb],
Andy Liaw [ctb],
Robert Gentleman [ctb],
Martin Maechler [ctb]
Maintainer: Jerzy Wieczorek <jerzywieczorek@gmail.com>
Diff between RankingProject versions 0.3.0 dated 2021-02-07 and 0.3.1 dated 2021-02-07
RankingProject-0.3.0/RankingProject/inst/doc/joint.R |only RankingProject-0.3.0/RankingProject/inst/doc/joint.Rmd |only RankingProject-0.3.0/RankingProject/inst/doc/primer.R |only RankingProject-0.3.0/RankingProject/inst/doc/primer.Rmd |only RankingProject-0.3.1/RankingProject/DESCRIPTION | 10 ++-- RankingProject-0.3.1/RankingProject/MD5 | 25 +++++----- RankingProject-0.3.1/RankingProject/NEWS | 4 + RankingProject-0.3.1/RankingProject/NEWS.md | 4 + RankingProject-0.3.1/RankingProject/README | 14 ++++- RankingProject-0.3.1/RankingProject/build/vignette.rds |binary RankingProject-0.3.1/RankingProject/inst/doc/joint.pdf |binary RankingProject-0.3.1/RankingProject/inst/doc/joint.pdf.asis |only RankingProject-0.3.1/RankingProject/inst/doc/primer.pdf |binary RankingProject-0.3.1/RankingProject/inst/doc/primer.pdf.asis |only RankingProject-0.3.1/RankingProject/vignettes/joint.Rmd.orig |only RankingProject-0.3.1/RankingProject/vignettes/joint.pdf.asis |only RankingProject-0.3.1/RankingProject/vignettes/precompile.R |only RankingProject-0.3.1/RankingProject/vignettes/primer.Rmd.orig |only RankingProject-0.3.1/RankingProject/vignettes/primer.pdf.asis |only 19 files changed, 37 insertions(+), 20 deletions(-)
More information about RankingProject at CRAN
Permanent link
Title: Japanese Utility Functions and Data
Description: Some data treated by the Japanese R user require
unique operations and processing. These are caused by address, Kanji,
and traditional year representations. 'zipangu' transforms specific
to Japan into something more general one.
Author: Shinya Uryu [aut, cre] (<https://orcid.org/0000-0002-0493-6186>),
Hiroaki Yutani [ctb] (<https://orcid.org/0000-0002-3385-7233>),
Kazuhiro Maeda [ctb],
Mao Kobayashi [ctb]
Maintainer: Shinya Uryu <suika1127@gmail.com>
Diff between zipangu versions 0.2.2 dated 2021-02-01 and 0.2.3 dated 2021-02-07
DESCRIPTION | 6 +- MD5 | 37 +++++++------ NEWS.md | 6 ++ R/address.R | 2 R/convert-jyear.R | 14 ++++- R/jholiday.R | 22 ++++++-- R/kansuji.R | 11 +--- R/label-kansuji.R | 20 +++---- R/sysdata.rda |binary README.md | 17 ++++++ build/zipangu.pdf |binary man/convert_jdate.Rd | 7 +- man/convert_jyear.Rd | 19 ++++--- man/figures/readme_demo_label_kansuji.png |only man/figures/readme_demo_label_kansuji_suffix.png |only man/is_jholiday.Rd | 13 +++- man/jholiday.Rd | 62 +++++++++++++++++++++-- man/kansuji.Rd | 8 +- man/label_kansuji.Rd | 15 ++--- man/rmd |only man/separate_address.Rd | 2 21 files changed, 186 insertions(+), 75 deletions(-)
Title: Efficient Estimation of the Causal Effects of Stochastic
Interventions
Description: Efficient estimation of the population-level causal effects of
stochastic interventions on a continuous-valued exposure. Both one-step and
targeted minimum loss estimators are implemented for a causal parameter
defined as the counterfactual mean of an outcome of interest under a
stochastic intervention that may depend on the natural value of the
exposure (i.e., a modified treatment policy). To accommodate settings in
which two-phase sampling is employed, procedures for making use of inverse
probability of censoring weights are provided to facilitate construction of
inefficient and efficient one-step and targeted minimum loss estimators.
The causal parameter and its estimation were first described by Díaz and van
der Laan (2013) <doi:10.1111/j.1541-0420.2011.01685.x>, while the multiply
robust estimation procedure and its application to data arising in two-phase
sampling designs was detailed in NS Hejazi, MJ van der Laan, HE Janes, PB
Gilbert, and DC Benkeser (2020) <doi:10.1111/biom.13375>. Estimation of
nuisance parameters may be enhanced through the Super Learner ensemble model
in 'sl3', available for download from GitHub using
'remotes::install_github("tlverse/sl3")'.
Author: Nima Hejazi [aut, cre, cph] (<https://orcid.org/0000-0002-7127-2789>),
David Benkeser [aut] (<https://orcid.org/0000-0002-1019-8343>),
Iván Díaz [ctb] (<https://orcid.org/0000-0001-9056-2047>),
Jeremy Coyle [ctb] (<https://orcid.org/0000-0002-9874-6649>),
Mark van der Laan [ctb, ths] (<https://orcid.org/0000-0003-1432-5511>)
Maintainer: Nima Hejazi <nh@nimahejazi.org>
Diff between txshift versions 0.3.4 dated 2020-09-25 and 0.3.5 dated 2021-02-07
txshift-0.3.4/txshift/man/est_g.Rd |only txshift-0.3.4/txshift/man/est_ipcw.Rd |only txshift-0.3.4/txshift/man/summary.txshift.Rd |only txshift-0.3.5/txshift/DESCRIPTION | 19 txshift-0.3.5/txshift/LICENSE | 2 txshift-0.3.5/txshift/MD5 | 92 +- txshift-0.3.5/txshift/NAMESPACE | 6 txshift-0.3.5/txshift/NEWS.md | 34 + txshift-0.3.5/txshift/R/confint.R | 20 txshift-0.3.5/txshift/R/eifs.R | 153 ++-- txshift-0.3.5/txshift/R/fit_mechanisms.R | 391 +++++++----- txshift-0.3.5/txshift/R/msm.R | 200 +----- txshift-0.3.5/txshift/R/onestep_txshift.R | 99 +-- txshift-0.3.5/txshift/R/plots.R |only txshift-0.3.5/txshift/R/tmle_txshift.R | 109 +-- txshift-0.3.5/txshift/R/txshift.R | 311 +++++---- txshift-0.3.5/txshift/R/utils.R | 145 +--- txshift-0.3.5/txshift/README.md | 158 +++- txshift-0.3.5/txshift/build/vignette.rds |binary txshift-0.3.5/txshift/inst/CITATION | 25 txshift-0.3.5/txshift/inst/REFERENCES.bib | 27 txshift-0.3.5/txshift/inst/doc/intro_txshift.R | 84 +- txshift-0.3.5/txshift/inst/doc/intro_txshift.Rmd | 84 +- txshift-0.3.5/txshift/inst/doc/intro_txshift.html | 224 +++--- txshift-0.3.5/txshift/inst/doc/ipcw_txshift.R | 167 ++--- txshift-0.3.5/txshift/inst/doc/ipcw_txshift.Rmd | 169 ++--- txshift-0.3.5/txshift/inst/doc/ipcw_txshift.html | 310 ++++----- txshift-0.3.5/txshift/man/confint.txshift.Rd | 8 txshift-0.3.5/txshift/man/eif.Rd | 12 txshift-0.3.5/txshift/man/est_Hn.Rd | 16 txshift-0.3.5/txshift/man/est_Q.Rd | 29 txshift-0.3.5/txshift/man/est_g_cens.Rd |only txshift-0.3.5/txshift/man/est_g_exp.Rd |only txshift-0.3.5/txshift/man/est_samp.Rd |only txshift-0.3.5/txshift/man/fit_fluctuation.Rd | 2 txshift-0.3.5/txshift/man/ipcw_eif_update.Rd | 43 - txshift-0.3.5/txshift/man/msm_vimshift.Rd | 28 txshift-0.3.5/txshift/man/onestep_txshift.Rd | 33 - txshift-0.3.5/txshift/man/plot.txshift_msm.Rd | 6 txshift-0.3.5/txshift/man/print.txshift.Rd | 15 txshift-0.3.5/txshift/man/print.txshift_msm.Rd | 6 txshift-0.3.5/txshift/man/tmle_txshift.Rd | 44 - txshift-0.3.5/txshift/man/txshift.Rd | 163 +++-- txshift-0.3.5/txshift/tests/testthat/test-censoring_mech.R |only txshift-0.3.5/txshift/tests/testthat/test-estim_tmle_os.R | 34 - txshift-0.3.5/txshift/tests/testthat/test-matches_tmle_ID.R | 6 txshift-0.3.5/txshift/tests/testthat/test-msm_vim.R | 8 txshift-0.3.5/txshift/tests/testthat/test-nuisance_est.R | 114 +-- txshift-0.3.5/txshift/tests/testthat/test-tmle_comparison.R | 52 - txshift-0.3.5/txshift/vignettes/intro_txshift.Rmd | 84 +- txshift-0.3.5/txshift/vignettes/ipcw_txshift.Rmd | 169 ++--- 51 files changed, 1911 insertions(+), 1790 deletions(-)
Title: Utilities for Quantiles
Description: Functions for unconditional and conditional quantiles. These
include methods for transformation-based quantile regression,
quantile-based measures of location, scale and shape, methods for quantiles
of discrete variables, quantile-based multiple imputation, restricted
quantile regression, and directional quantile classification. A vignette
is given in Geraci (2016, The R Journal) <doi:10.32614/RJ-2016-037> and
included in the package.
Author: Marco Geraci [aut, cph, cre] (<https://orcid.org/0000-0002-6311-8685>),
Alessio Farcomeni [ctb] (Contributions to midrq code,
<https://orcid.org/0000-0002-7104-5826>),
Cinzia Viroli [ctb] (Contributions to dqc code,
<https://orcid.org/0000-0002-3278-5266>)
Maintainer: Marco Geraci <marco.geraci@uniroma1.it>
Diff between Qtools versions 1.5.3 dated 2020-11-27 and 1.5.4 dated 2021-02-07
DESCRIPTION | 13 ++++++------- MD5 | 12 ++++++------ NAMESPACE | 1 - NEWS | 5 +++++ R/Qtools.R | 44 ++++++++++++++++++++++++++++++++++++++++++++ man/Qtools-internal.Rd | 1 + man/Qtools-package.Rd | 4 ++-- 7 files changed, 64 insertions(+), 16 deletions(-)
Title: Genomic Breeding Tools: Genetic Variance Prediction and
Cross-Validation
Description: The main attribute of 'PopVar' is the prediction of genetic variance in bi-parental populations,
from which the package derives its name. 'PopVar' contains a set of functions that use phenotypic and genotypic
data from a set of candidate parents to 1) predict the mean, genetic variance, and superior progeny value of all,
or a defined set of pairwise bi-parental crosses, and 2) perform cross-validation to estimate genome-wide prediction
accuracy of multiple statistical models. More details are available in Mohammadi, Tiede, and Smith (2015, <doi:10.2135/cropsci2015.01.0030>).
A dataset 'think_barley.rda' is included for reference and examples.
Author: Tyler Tiede [aut],
Jeffrey Neyhart [aut, ctb, cre]
(<https://orcid.org/0000-0002-1991-5310>),
Mohsen Mohammadi [ctb] (<https://orcid.org/0000-0002-4536-1200>),
Kevin Smith [ctb] (<https://orcid.org/0000-0001-8253-3326>)
Maintainer: Jeffrey Neyhart <neyhartje@gmail.com>
Diff between PopVar versions 1.2.1 dated 2015-07-08 and 1.3.0 dated 2021-02-07
PopVar-1.2.1/PopVar/R/Internal_PopVar_functions_4.28.15.R |only PopVar-1.2.1/PopVar/R/XValidate.nonInd_function_4.28.15.R |only PopVar-1.2.1/PopVar/R/XValidate_Ind_function_4.28.15.R |only PopVar-1.2.1/PopVar/R/pop.predict_function_4.28.15.R |only PopVar-1.2.1/PopVar/R/x.val_function_4.28.15.R |only PopVar-1.3.0/PopVar/DESCRIPTION | 48 +- PopVar-1.3.0/PopVar/MD5 | 37 + PopVar-1.3.0/PopVar/NAMESPACE | 36 + PopVar-1.3.0/PopVar/NEWS.md |only PopVar-1.3.0/PopVar/R/cross_validation.R |only PopVar-1.3.0/PopVar/R/internal_functions.R |only PopVar-1.3.0/PopVar/R/mppop_predict.R |only PopVar-1.3.0/PopVar/R/pop_predict.R |only PopVar-1.3.0/PopVar/R/think_barley_dataset.R | 41 + PopVar-1.3.0/PopVar/README.md |only PopVar-1.3.0/PopVar/build |only PopVar-1.3.0/PopVar/data/think_barley.rda |binary PopVar-1.3.0/PopVar/inst |only PopVar-1.3.0/PopVar/man/PopVar-package.Rd | 48 +- PopVar-1.3.0/PopVar/man/figures |only PopVar-1.3.0/PopVar/man/internal.Rd |only PopVar-1.3.0/PopVar/man/mppop.predict.Rd |only PopVar-1.3.0/PopVar/man/pop.predict.Rd | 308 +++++++------- PopVar-1.3.0/PopVar/man/pop.predict2.Rd |only PopVar-1.3.0/PopVar/man/think_barley.rda.Rd | 55 +- PopVar-1.3.0/PopVar/man/x.val.Rd | 174 ++++--- PopVar-1.3.0/PopVar/vignettes |only 27 files changed, 421 insertions(+), 326 deletions(-)
Title: Tools for Easier Analysis of Meteorological Fields
Description: Many useful functions and extensions for dealing
with meteorological data in the tidy data framework. Extends 'ggplot2'
for better plotting of scalar and vector fields and provides commonly
used analysis methods in the atmospheric sciences.
Author: Elio Campitelli [cre, aut] (<https://orcid.org/0000-0002-7742-9230>)
Maintainer: Elio Campitelli <elio.campitelli@cima.fcen.uba.ar>
Diff between metR versions 0.9.0 dated 2020-11-25 and 0.9.1 dated 2021-02-07
metR-0.9.0/metR/R/circular-color.R |only metR-0.9.0/metR/R/circular.R |only metR-0.9.0/metR/R/circular_scale.R |only metR-0.9.0/metR/tests/figs/streamline/streamline-irregular.svg |only metR-0.9.0/metR/tests/figs/vis-arrow |only metR-0.9.0/metR/tests/testthat/needs_scale.nc |only metR-0.9.0/metR/tests/testthat/readnetcdf_default |only metR-0.9.0/metR/tests/testthat/readnetcdf_nc_open |only metR-0.9.0/metR/tests/testthat/readnetcdf_nc_open2 |only metR-0.9.0/metR/tests/testthat/readnetcdf_subset |only metR-0.9.0/metR/tests/testthat/readnetcdf_time_hours |only metR-0.9.0/metR/tests/testthat/test-vis-guide_vector.R |only metR-0.9.1/metR/DESCRIPTION | 8 metR-0.9.1/metR/MD5 | 172 metR-0.9.1/metR/NAMESPACE | 8 metR-0.9.1/metR/NEWS.md | 23 metR-0.9.1/metR/R/ConvertLongitude.R | 10 metR-0.9.1/metR/R/EOF.R | 2 metR-0.9.1/metR/R/EOF_methods.R | 4 metR-0.9.1/metR/R/FitWave.R | 2 metR-0.9.1/metR/R/GetTopography.R | 4 metR-0.9.1/metR/R/IdealGas.R | 16 metR-0.9.1/metR/R/ImputeEOF.R | 2 metR-0.9.1/metR/R/WaveFlux.R | 6 metR-0.9.1/metR/R/as-discretised-scale.R |only metR-0.9.1/metR/R/geom_arrow.R | 352 - 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Title: Missing Data Explorer
Description: Correct identification and handling of missing data is one of the most important steps in any analysis. To aid this process, 'mde' provides a very easy to use yet robust framework to quickly get an idea of where the missing data
lies and therefore find the most appropriate action to take.
Graham WJ (2009) <doi:10.1146/annurev.psych.58.110405.085530>.
Author: Nelson Gonzabato [aut, cre]
Maintainer: Nelson Gonzabato <gonzabato@hotmail.com>
Diff between mde versions 0.2.1 dated 2020-06-27 and 0.3.0 dated 2021-02-07
DESCRIPTION | 8 - MD5 | 94 +++++++++------- NAMESPACE | 13 ++ NEWS.md | 28 ++++- R/column_based_recode.R |only R/custom_na_recode.R | 13 -- R/drop_all_na.R | 9 - R/drop_na_at.R | 21 --- R/drop_na_if.R | 44 ++----- R/drop_row_if.R |only R/get_na_counts.R | 27 ++-- R/helpers.R | 166 ++++++++++++++++++++++++++---- R/na_summary.R | 58 +++++----- R/percent_missing.R | 33 ++--- R/recode_as_na.R | 8 - R/recode_as_na_for.R | 10 - R/recode_as_na_if.R |only R/recode_as_na_str.R |only R/recode_na_if.R | 5 R/sort_by_missingness.R | 34 ++---- build/vignette.rds |binary inst/doc/mde_vignette.R | 37 ++++++ inst/doc/mde_vignette.html | 158 +++++++++++++++++++++------- inst/doc/mde_vignette.rmd | 105 +++++++++++++++--- man/all_na.Rd |only man/column_based_recode.Rd |only man/custom_na_recode.Rd | 72 ++++++------- man/drop_all_na.Rd | 50 ++++----- man/drop_na_if.Rd | 74 ++++++------- man/drop_row_if.Rd |only man/get_na_counts.Rd | 61 +++++------ man/na_summary.Rd | 10 + man/percent_missing.Rd | 56 +++++----- man/recode_as_na_for.Rd | 56 +++++----- man/recode_as_na_if.Rd |only man/recode_as_na_str.Rd |only man/recode_helper.Rd |only man/recode_na_if.Rd | 56 +++++----- man/recode_selectors.Rd |only man/sort_by_missingness.Rd | 68 ++++++------ tests/testthat/test_column_based_recode.R |only tests/testthat/test_custom_na_recode.R | 2 tests/testthat/test_drop_all_na.R | 4 tests/testthat/test_drop_na_at.R | 8 - tests/testthat/test_drop_row_if.R |only tests/testthat/test_get_na_counts.R | 2 tests/testthat/test_helpers.R |only tests/testthat/test_na_summary.R | 18 +-- tests/testthat/test_percent_missing.R | 4 tests/testthat/test_recode_as_na.R | 6 - tests/testthat/test_recode_as_na_for.R | 8 - tests/testthat/test_recode_as_na_if.R |only tests/testthat/test_recode_as_na_str.R |only tests/testthat/test_recode_na_if.R | 2 tests/testthat/test_sorting_missingness.R | 23 ++-- vignettes/mde_vignette.rmd | 105 +++++++++++++++--- 56 files changed, 967 insertions(+), 589 deletions(-)
Title: Exact Variable-Subset Selection in Linear Regression
Description: Exact and approximation algorithms for variable-subset
selection in ordinary linear regression models. Either compute all
submodels with the lowest residual sum of squares, or determine the
single-best submodel according to a pre-determined statistical
criterion. Hofmann et al. (2020) <doi:10.18637/jss.v093.i03>.
Author: Marc Hofmann [aut, cre],
Cristian Gatu [aut],
Erricos J. Kontoghiorghes [aut],
Ana Colubi [aut],
Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>),
Martin Moene [cph] (for the GSL Lite library),
Microsoft Corporation [cph] (for the GSL Lite library),
Free Software Foundation, Inc. [cph] (for snippets from the GNU ISO C++
Library)
Maintainer: Marc Hofmann <marc.hofmann@gmail.com>
Diff between lmSubsets versions 0.5-1 dated 2020-05-23 and 0.5-2 dated 2021-02-07
lmSubsets-0.5-1/lmSubsets/man/image.Rd |only lmSubsets-0.5-1/lmSubsets/man/methods.Rd |only lmSubsets-0.5-2/lmSubsets/DESCRIPTION | 12 lmSubsets-0.5-2/lmSubsets/MD5 | 55 +++- lmSubsets-0.5-2/lmSubsets/build/partial.rdb |binary lmSubsets-0.5-2/lmSubsets/build/vignette.rds |binary lmSubsets-0.5-2/lmSubsets/inst/doc/lmSubsets.pdf |binary lmSubsets-0.5-2/lmSubsets/man/AIC.lmSubsets.Rd |only lmSubsets-0.5-2/lmSubsets/man/AirPollution.Rd | 98 +++++-- lmSubsets-0.5-2/lmSubsets/man/BIC.lmSubsets.Rd |only lmSubsets-0.5-2/lmSubsets/man/IbkTemperature.Rd | 180 +++++++++----- lmSubsets-0.5-2/lmSubsets/man/coef.lmSubsets.Rd |only lmSubsets-0.5-2/lmSubsets/man/deviance.lmSubsets.Rd |only lmSubsets-0.5-2/lmSubsets/man/fitted.lmSubsets.Rd |only lmSubsets-0.5-2/lmSubsets/man/formula.lmSubsets.Rd |only lmSubsets-0.5-2/lmSubsets/man/image.lmSubsets.Rd |only lmSubsets-0.5-2/lmSubsets/man/lmSelect.Rd | 118 +++------ lmSubsets-0.5-2/lmSubsets/man/lmSelect.lmSubsets.Rd |only lmSubsets-0.5-2/lmSubsets/man/lmSelect.matrix.Rd |only lmSubsets-0.5-2/lmSubsets/man/lmSelect_fit.Rd |only lmSubsets-0.5-2/lmSubsets/man/lmSubsets-package.Rd |only lmSubsets-0.5-2/lmSubsets/man/lmSubsets.Rd | 136 +++------- lmSubsets-0.5-2/lmSubsets/man/lmSubsets.matrix.Rd |only lmSubsets-0.5-2/lmSubsets/man/lmSubsets_fit.Rd |only lmSubsets-0.5-2/lmSubsets/man/logLik.lmSubsets.Rd |only lmSubsets-0.5-2/lmSubsets/man/model.frame.lmSubsets.Rd |only lmSubsets-0.5-2/lmSubsets/man/model.matrix.lmSubsets.Rd |only lmSubsets-0.5-2/lmSubsets/man/model_response.Rd |only lmSubsets-0.5-2/lmSubsets/man/model_response.lmSubsets.Rd |only lmSubsets-0.5-2/lmSubsets/man/plot.lmSubsets.Rd |only lmSubsets-0.5-2/lmSubsets/man/refit.Rd | 24 + lmSubsets-0.5-2/lmSubsets/man/refit.lmSubsets.Rd |only lmSubsets-0.5-2/lmSubsets/man/residuals.lmSubsets.Rd |only lmSubsets-0.5-2/lmSubsets/man/sigma.lmSubsets.Rd |only lmSubsets-0.5-2/lmSubsets/man/summary.lmSubsets.Rd |only lmSubsets-0.5-2/lmSubsets/man/variable.names.lmSubsets.Rd |only lmSubsets-0.5-2/lmSubsets/man/vcov.lmSubsets.Rd |only lmSubsets-0.5-2/lmSubsets/vignettes/bm-01.RData |binary lmSubsets-0.5-2/lmSubsets/vignettes/bm-02.RData |binary lmSubsets-0.5-2/lmSubsets/vignettes/bm-03.RData |binary lmSubsets-0.5-2/lmSubsets/vignettes/bm-04.RData |binary lmSubsets-0.5-2/lmSubsets/vignettes/bm-05.RData |binary 42 files changed, 342 insertions(+), 281 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-22 0.0.4
Title: Fitting Flexible Smooth-in-Time Hazards and Risk Functions via
Logistic and Multinomial Regression
Description: Fit flexible and fully parametric hazard regression models to survival data with single event type or multiple
competing causes via logistic and multinomial regression. Our formulation allows for arbitrary functional forms
of time and its interactions with other predictors for time-dependent hazards and hazard ratios. From the
fitted hazard model, we provide functions to readily calculate and plot cumulative incidence and survival
curves for a given covariate profile. This approach accommodates any log-linear hazard function of
prognostic time, treatment, and covariates, and readily allows for non-proportionality. We also provide
a plot method for visualizing incidence density via population time plots. Based on the case-base sampling
approach of Hanley and Miettinen (2009) <DOI:10.2202/1557-4679.1125>, Saarela and Arjas (2015) <DOI:10.1111/sjos.12125>,
and Saarela (2015) <DOI:10.1007/s10985-015-9352-x>.
Author: Sahir Bhatnagar [aut, cre] (http://sahirbhatnagar.com/),
Maxime Turgeon [aut] (<https://orcid.org/0000-0003-4863-6035>),
Jesse Islam [aut] (https://www.jesseislam.com/),
Olli Saarela [aut] (http://individual.utoronto.ca/osaarela/),
James Hanley [aut] (http://www.medicine.mcgill.ca/epidemiology/hanley/)
Maintainer: Sahir Bhatnagar <sahir.bhatnagar@gmail.com>
Diff between casebase versions 0.9.0 dated 2020-07-05 and 0.9.1 dated 2021-02-07
DESCRIPTION | 10 MD5 | 71 +-- NAMESPACE | 2 NEWS.md | 6 R/data.R | 6 R/fitting.R | 31 + R/plot_methods.R | 15 R/utils.R | 13 README.md | 49 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/competingRisk.html | 118 ++--- inst/doc/customizingpopTime.html | 95 ++-- inst/doc/plotabsRisk.html | 60 +- inst/doc/plotsmoothHazard.html | 696 ++++++++++++++++--------------- inst/doc/popTime.html | 131 +++-- inst/doc/smoothHazard.html | 282 ++++++------ man/absoluteRisk.Rd | 2 man/bmtcrr.Rd | 4 man/figures/README-plot-mason-1.png |binary man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/hazardPlot.Rd | 8 man/plot.singleEventCB.Rd | 4 man/popTime.Rd | 2 man/support.Rd | 2 tests/testthat/Rplots.pdf |only tests/testthat/test-fitting.R | 16 tests/testthat/test-gam.R | 11 tests/testthat/test-gbm.R | 22 tests/testthat/test-plotSingleEventCB.R | 1 tests/testthat/test-popTime.R | 2 tests/testthat/test-sampling.R | 12 vignettes/competingRisk.Rmd | 4 vignettes/plotsmoothHazard.Rmd | 6 vignettes/smoothHazard.Rmd | 2 37 files changed, 959 insertions(+), 724 deletions(-)
Title: Geographically-Weighted Models
Description: Techniques from a particular branch of spatial statistics,termed geographically-weighted (GW) models. GW models suit situations when data are not described well by some global model, but where there are spatial regions where a suitably localised calibration provides a better description. 'GWmodel' includes functions to calibrate: GW summary statistics (Brunsdon et al., 2002)<doi: 10.1016/s0198-9715(01)00009-6>, GW principal components analysis (Harris et al., 2011)<doi: 10.1080/13658816.2011.554838>, GW discriminant analysis (Brunsdon et al., 2007)<doi: 10.1111/j.1538-4632.2007.00709.x> and various forms of GW regression (Brunsdon et al., 1996)<doi: 10.1111/j.1538-4632.1996.tb00936.x>; some of which are provided in basic and robust (outlier resistant) forms.
Author: Binbin Lu[aut], Paul Harris[aut], Martin Charlton[aut], Chris Brunsdon[aut], Tomoki Nakaya[aut], Daisuke Murakami[aut],Isabella Gollini[ctb], Yigong Hu[ctb], Fiona H Evans[ctb]
Maintainer: Binbin Lu <binbinlu@whu.edu.cn>
Diff between GWmodel versions 2.2-2 dated 2020-11-22 and 2.2-3 dated 2021-02-07
DESCRIPTION | 8 MD5 | 56 +- NAMESPACE | 64 +- R/BootstrapGWR.r | 95 +--- R/Model.selection.r | 14 R/MontCarlo.r | 6 R/RcppExports.R | 144 +----- R/bw.gtwr.R | 5 R/bw.sel.r | 110 ++++ R/gtwr.R | 1 R/gw.dist.r | 97 ---- R/gw.weight.r | 304 ------------ R/gwda.r | 2 R/gwr.basic.r | 28 - R/gwr.mixed.r | 43 - R/gwr.multiscale.R | 183 ++++--- R/gwr.predict.r | 13 R/gwr.robust.r | 3 R/zzz.r | 2 man/GWmodel-package.Rd | 4 man/bw.gwr.Rd | 6 man/gw.dist.Rd | 14 man/gw.weight.Rd | 19 man/gwr.basic.rd | 10 man/gwr.bootstrap.rd | 18 man/gwr.multiscale.rd | 25 - src/GWmodel.cpp | 1160 ++++++++++++++++++++++++++----------------------- src/RcppExports.cpp | 568 +++++------------------ src/init.c | 121 +---- 29 files changed, 1281 insertions(+), 1842 deletions(-)
Title: Chemical Information from the Web
Description: Chemical information from around the web. This package interacts
with a suite of web services for chemical information. Sources include: Alan
Wood's Compendium of Pesticide Common Names, Chemical Identifier Resolver,
ChEBI, Chemical Translation Service, ChemIDplus, ChemSpider, ETOX,
Flavornet, NIST Chemistry WebBook, OPSIN, PAN Pesticide Database, PubChem,
SRS, Wikidata.
Author: Eduard Szöcs [aut],
Robert Allaway [ctb],
Daniel Muench [ctb],
Johannes Ranke [ctb],
Andreas Scharmüller [ctb],
Eric R Scott [ctb],
Jan Stanstrup [ctb],
João Vitor F Cavalcante [ctb],
Gordon Getzinger [ctb],
Tamás Stirling [ctb, cre]
Maintainer: Tamás Stirling <stirling.tamas@gmail.com>
Diff between webchem versions 1.1.0 dated 2020-10-02 and 1.1.1 dated 2021-02-07
webchem-1.1.0/webchem/R/zzz.R |only webchem-1.1.1/webchem/DESCRIPTION | 12 webchem-1.1.1/webchem/MD5 | 102 +- webchem-1.1.1/webchem/NAMESPACE | 13 webchem-1.1.1/webchem/NEWS.md | 10 webchem-1.1.1/webchem/R/alanwood.R | 7 webchem-1.1.1/webchem/R/chebi.R | 23 webchem-1.1.1/webchem/R/chemid.R | 7 webchem-1.1.1/webchem/R/chemspider.R | 679 +++++------------ webchem-1.1.1/webchem/R/cir.R | 6 webchem-1.1.1/webchem/R/cts.R | 14 webchem-1.1.1/webchem/R/etox.R | 28 webchem-1.1.1/webchem/R/extractors.R | 2 webchem-1.1.1/webchem/R/flavornet.R | 5 webchem-1.1.1/webchem/R/integration.R | 2 webchem-1.1.1/webchem/R/nist.R | 8 webchem-1.1.1/webchem/R/opsin.R | 4 webchem-1.1.1/webchem/R/pan.R | 22 webchem-1.1.1/webchem/R/pubchem.R | 26 webchem-1.1.1/webchem/R/srs.R | 1 webchem-1.1.1/webchem/R/utils.R | 38 webchem-1.1.1/webchem/R/wikidata.R | 22 webchem-1.1.1/webchem/build/partial.rdb |only webchem-1.1.1/webchem/build/vignette.rds |binary webchem-1.1.1/webchem/inst/doc/webchem.html | 268 ++---- webchem-1.1.1/webchem/man/aw_query.Rd | 2 webchem-1.1.1/webchem/man/chebi_comp_entity.Rd | 2 webchem-1.1.1/webchem/man/cs_compinfo.Rd | 4 webchem-1.1.1/webchem/man/cs_control.Rd | 8 webchem-1.1.1/webchem/man/cs_convert.Rd | 6 webchem-1.1.1/webchem/man/cs_datasources.Rd | 4 webchem-1.1.1/webchem/man/etox_basic.Rd | 2 webchem-1.1.1/webchem/man/etox_targets.Rd | 2 webchem-1.1.1/webchem/man/extractors.Rd | 2 webchem-1.1.1/webchem/man/get_chebiid.Rd | 2 webchem-1.1.1/webchem/man/get_cid.Rd | 4 webchem-1.1.1/webchem/man/get_csid.Rd | 2 webchem-1.1.1/webchem/man/get_etoxid.Rd | 2 webchem-1.1.1/webchem/man/is.cas.Rd | 2 webchem-1.1.1/webchem/man/is.inchikey.Rd | 2 webchem-1.1.1/webchem/man/nist_ri.Rd | 2 webchem-1.1.1/webchem/man/opsin_query.Rd | 2 webchem-1.1.1/webchem/man/pan_query.Rd | 7 webchem-1.1.1/webchem/man/parse_mol.Rd | 2 webchem-1.1.1/webchem/man/pc_prop.Rd | 2 webchem-1.1.1/webchem/man/pc_sect.Rd | 2 webchem-1.1.1/webchem/man/wd_ident.Rd | 8 webchem-1.1.1/webchem/tests/testthat/test-chemspider.R | 67 - webchem-1.1.1/webchem/tests/testthat/test-etox.R | 4 webchem-1.1.1/webchem/tests/testthat/test-extractors.R | 1 webchem-1.1.1/webchem/tests/testthat/test-pan.R | 1 webchem-1.1.1/webchem/tests/testthat/test-pubchem.R | 8 webchem-1.1.1/webchem/tests/testthat/test-wikidata.R | 18 53 files changed, 608 insertions(+), 861 deletions(-)
Title: The Ranking Project: Visualizations for Comparing Populations
Description: Functions to generate plots and tables for comparing independently-
sampled populations. Companion package to "A Primer on Visualizations
for Comparing Populations, Including the Issue of Overlapping Confidence
Intervals" by Wright, Klein, and Wieczorek (2019)
<DOI:10.1080/00031305.2017.1392359> and "A Joint Confidence Region for an
Overall Ranking of Populations" by Klein, Wright, and Wieczorek (2020)
<DOI:10.1111/rssc.12402>.
Author: Jerzy Wieczorek [cre, aut],
Joel Beard [ctb],
Andy Liaw [ctb],
Robert Gentleman [ctb],
Martin Maechler [ctb]
Maintainer: Jerzy Wieczorek <jerzywieczorek@gmail.com>
Diff between RankingProject versions 0.2.0 dated 2020-01-29 and 0.3.0 dated 2021-02-07
RankingProject-0.2.0/RankingProject/vignettes/joint.Rmd |only RankingProject-0.2.0/RankingProject/vignettes/primer.Rmd |only RankingProject-0.3.0/RankingProject/DESCRIPTION | 18 RankingProject-0.3.0/RankingProject/MD5 | 42 - RankingProject-0.3.0/RankingProject/NAMESPACE | 2 RankingProject-0.3.0/RankingProject/NEWS | 12 RankingProject-0.3.0/RankingProject/NEWS.md | 12 RankingProject-0.3.0/RankingProject/R/RankPlot.R | 79 +- RankingProject-0.3.0/RankingProject/R/RankingProject.R | 25 RankingProject-0.3.0/RankingProject/R/Utils.R | 21 RankingProject-0.3.0/RankingProject/README | 4 RankingProject-0.3.0/RankingProject/build/vignette.rds |binary RankingProject-0.3.0/RankingProject/inst/doc/intro.Rmd | 4 RankingProject-0.3.0/RankingProject/inst/doc/intro.html | 8 RankingProject-0.3.0/RankingProject/inst/doc/joint.Rmd | 2 RankingProject-0.3.0/RankingProject/inst/doc/joint.pdf |binary RankingProject-0.3.0/RankingProject/inst/doc/primer.Rmd | 2 RankingProject-0.3.0/RankingProject/inst/doc/primer.pdf |binary RankingProject-0.3.0/RankingProject/man/RankPlot.Rd | 389 +++++----- RankingProject-0.3.0/RankingProject/man/RankingProject.Rd | 27 RankingProject-0.3.0/RankingProject/man/TravelTime2011.1dec.Rd | 6 RankingProject-0.3.0/RankingProject/man/TravelTime2011.Rd | 6 RankingProject-0.3.0/RankingProject/vignettes/intro.Rmd | 4 23 files changed, 387 insertions(+), 276 deletions(-)
More information about RankingProject at CRAN
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Title: The Pareto, Piecewise Pareto and Generalized Pareto Distribution
Description: Utilities for the Pareto, piecewise Pareto and generalized Pareto distribution
that are useful for reinsurance pricing. In particular, the package provides
a non-trivial algorithm that can be used to match the expected losses of a
tower of reinsurance layers with a layer-independent collective risk model.
The theoretical background of the matching algorithm and most other methods
are described in Ulrich Riegel (2018) <doi:10.1007/s13385-018-0177-3>.
Author: Ulrich Riegel [aut, cre]
Maintainer: Ulrich Riegel <ulrich.riegel@gmx.de>
Diff between Pareto versions 2.2.2 dated 2021-01-27 and 2.3.0 dated 2021-02-07
DESCRIPTION | 8 MD5 | 18 NEWS.md | 23 + R/Functions.R | 336 +++++++++++++---- build/vignette.rds |binary inst/doc/Pareto.html | 456 ++++++------------------ man/Local_Pareto_Alpha.Rd | 2 tests/testthat/test_functions_GenPareto.R | 15 tests/testthat/test_functions_Pareto.R | 37 + tests/testthat/test_functions_PiecewisePareto.R | 32 + 10 files changed, 504 insertions(+), 423 deletions(-)
Title: Kernel Smoothing
Description: Kernel smoothers for univariate and multivariate data, including densities, density derivatives, cumulative distributions, clustering, classification, density ridges, significant modal regions, and two-sample hypothesis tests. Chacon & Duong (2018) <doi:10.1201/9780429485572>.
Author: Tarn Duong [aut, cre],
Matt Wand [ctb],
Jose Chacon [ctb],
Artur Gramacki [ctb]
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between ks versions 1.11.7 dated 2020-02-11 and 1.12.0 dated 2021-02-07
CHANGELOG | 17 ++++ DESCRIPTION | 12 +-- MD5 | 110 ++++++++++++++--------------- NAMESPACE | 7 - R/integrate-kde.R | 2 R/kcde.R | 65 ++++++++++++----- R/kda.R | 134 +++++++++++++++++++++++------------ R/kdde.R | 30 +++---- R/kde-boundary.R | 2 R/kde-test.R | 20 +++-- R/kde.R | 182 ++++++++++++++++++++++++++++++------------------ R/kfs.R | 113 +++++++++++++++-------------- R/kms.R | 21 ++--- build/vignette.rds |binary data/plate.RData |binary inst/doc/kde.pdf |binary man/Hlscv.Rd | 5 - man/Hpi.Rd | 2 man/Hscv.Rd | 7 - man/air.Rd | 4 - man/binning.Rd | 2 man/cardio.Rd | 2 man/contour.Rd | 31 +++++--- man/grevillea.Rd | 4 - man/histde.Rd | 2 man/hsct.Rd | 2 man/ise.mixt.Rd | 2 man/kcde.Rd | 8 -- man/kcopula.Rd | 3 man/kda.Rd | 12 +-- man/kdcde.Rd | 4 - man/kdde.Rd | 6 - man/kde.Rd | 18 +--- man/kde.boundary.Rd | 3 man/kde.local.test.Rd | 4 - man/kde.test.Rd | 8 +- man/kde.truncate.Rd | 7 - man/kdr.Rd | 8 +- man/kfs.Rd | 11 ++ man/kms.Rd | 8 +- man/kroc.Rd | 2 man/ks-package.Rd | 13 ++- man/plot.histde.Rd | 5 - man/plot.kcde.Rd | 15 ++- man/plot.kda.Rd | 11 +- man/plot.kdde.Rd | 15 ++- man/plot.kde.Rd | 45 ++++++----- man/plot.kde.loctest.Rd | 30 ++++--- man/plot.kde.part.Rd | 15 ++- man/plot.kfs.Rd | 11 +- man/plot.kroc.Rd | 4 - man/plotmixt.Rd | 12 +-- man/rkde.Rd | 8 +- man/tempb.Rd | 4 - man/vector.Rd | 4 - man/vkde.Rd | 5 - 56 files changed, 618 insertions(+), 459 deletions(-)
Title: Immunoglobulin Clonal Lineage and Diversity Analysis
Description: Provides methods for high-throughput adaptive immune
receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In
particular, immunoglobulin (Ig) sequence lineage reconstruction,
lineage topology analysis, diversity profiling, amino acid property
analysis and gene usage.
Citations:
Gupta and Vander Heiden, et al (2017) <doi:10.1093/bioinformatics/btv359>,
Stern, Yaari and Vander Heiden, et al (2014) <doi:10.1126/scitranslmed.3008879>.
Author: Namita Gupta [aut],
Susanna Marquez [aut],
Nima Nouri [aut],
Ruoyi Jiang [aut],
Julian Zhou [aut],
Kenneth Hoehn [aut],
Daniel Gadala-Maria [ctb],
Edel Aron [ctb],
Jason Vander Heiden [cre, aut],
Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@gmail.com>
Diff between alakazam versions 1.0.2 dated 2020-07-18 and 1.1.0 dated 2021-02-07
DESCRIPTION | 26 ++-- MD5 | 103 ++++++++++------ NAMESPACE | 14 ++ NEWS.md | 61 +++++++++- R/Alakazam.R | 8 - R/AminoAcids.R | 20 +-- R/Data.R | 50 ++++++++ R/Diversity.R | 24 +++ R/Fastq.R |only R/Gene.R | 95 ++++++++++++--- R/Lineage.R | 231 ++++++++++++++++++++++++++++---------- R/Sequence.R | 14 +- README.md | 2 build/vignette.rds |binary data/Example10x.rda |only data/ExampleDb.rda |binary data/ExampleDbChangeo.rda |binary data/ExampleTrees.rda |binary inst/doc/AminoAcids-Vignette.R | 8 - inst/doc/AminoAcids-Vignette.Rmd | 12 - inst/doc/AminoAcids-Vignette.pdf |binary inst/doc/Diversity-Vignette.Rmd | 4 inst/doc/Diversity-Vignette.pdf |binary inst/doc/Fastq-Vignette.R |only inst/doc/Fastq-Vignette.Rmd |only inst/doc/Fastq-Vignette.pdf |only inst/doc/Files-Vignette.R |only inst/doc/Files-Vignette.Rmd |only inst/doc/Files-Vignette.pdf |only inst/doc/GeneUsage-Vignette.Rmd | 9 - inst/doc/GeneUsage-Vignette.pdf |binary inst/doc/Lineage-Vignette.Rmd | 3 inst/doc/Lineage-Vignette.pdf |binary inst/doc/Topology-Vignette.Rmd | 2 inst/doc/Topology-Vignette.pdf |binary inst/extdata |only man/Example10x.Rd |only man/IUPAC_CODES.Rd | 6 man/aminoAcidProperties.Rd | 10 - man/buildPhylipLineage.Rd | 23 +++ man/countClones.Rd | 14 +- man/countGenes.Rd | 15 +- man/countPatterns.Rd | 4 man/getPositionQuality.Rd |only man/getSegment.Rd | 27 ++++ man/groupGenes.Rd | 2 man/maskPositionsByQuality.Rd |only man/padSeqEnds.Rd | 4 man/phyloToGraph.Rd | 2 man/readFastqDb.Rd |only man/readIgphyml.Rd | 2 vignettes/AminoAcids-Vignette.Rmd | 12 - vignettes/Diversity-Vignette.Rmd | 4 vignettes/Fastq-Vignette.Rmd |only vignettes/Files-Vignette.Rmd |only vignettes/Files-Vignette.html |only vignettes/GeneUsage-Vignette.Rmd | 9 - vignettes/Lineage-Vignette.Rmd | 3 vignettes/Topology-Vignette.Rmd | 2 59 files changed, 616 insertions(+), 209 deletions(-)