Title: A Flexible Color Scale for Ternary Compositions
Description: A flexible color scale for ternary compositions with options for
discretization, centering and scaling.
Author: Jonas Schöley, Ilya Kashnitsky
Maintainer: Jonas Schöley <jschoeley@gmail.com>
Diff between tricolore versions 1.0.3 dated 2018-05-27 and 1.2.0 dated 2018-09-13
tricolore-1.0.3/tricolore/data/euro_education.RData |only tricolore-1.0.3/tricolore/data/euro_geo_nuts2.RData |only tricolore-1.0.3/tricolore/data/euro_sectors.RData |only tricolore-1.0.3/tricolore/inst/doc/european_education.R |only tricolore-1.0.3/tricolore/inst/doc/european_education.Rmd |only tricolore-1.0.3/tricolore/inst/doc/european_education.html |only tricolore-1.0.3/tricolore/inst/shiny/rsconnect |only tricolore-1.0.3/tricolore/man/ColorKey.Rd |only tricolore-1.0.3/tricolore/man/ColorMap.Rd |only tricolore-1.0.3/tricolore/man/ValidateParameters.Rd |only tricolore-1.0.3/tricolore/man/euro_education.Rd |only tricolore-1.0.3/tricolore/man/euro_geo_nuts2.Rd |only tricolore-1.0.3/tricolore/man/euro_sectors.Rd |only tricolore-1.0.3/tricolore/vignettes/european_education.Rmd |only tricolore-1.2.0/tricolore/DESCRIPTION | 15 tricolore-1.2.0/tricolore/MD5 | 60 tricolore-1.2.0/tricolore/NAMESPACE | 3 tricolore-1.2.0/tricolore/NEWS.md | 43 tricolore-1.2.0/tricolore/R/tricolore.R | 838 +++++++--- tricolore-1.2.0/tricolore/build/vignette.rds |binary tricolore-1.2.0/tricolore/data/euro_basemap.RData |binary tricolore-1.2.0/tricolore/data/euro_example.RData |only tricolore-1.2.0/tricolore/inst/doc/choropleth_maps_with_tricolore.R |only tricolore-1.2.0/tricolore/inst/doc/choropleth_maps_with_tricolore.Rmd |only tricolore-1.2.0/tricolore/inst/doc/choropleth_maps_with_tricolore.html |only tricolore-1.2.0/tricolore/inst/shiny/app.R | 183 +- tricolore-1.2.0/tricolore/man/BasicKey.Rd |only tricolore-1.2.0/tricolore/man/BreaksAndLabels.Rd |only tricolore-1.2.0/tricolore/man/ColorKeySextant.Rd |only tricolore-1.2.0/tricolore/man/ColorKeyTricolore.Rd |only tricolore-1.2.0/tricolore/man/ColorMapSextant.Rd |only tricolore-1.2.0/tricolore/man/ColorMapTricolore.Rd |only tricolore-1.2.0/tricolore/man/PowerScale.Rd | 2 tricolore-1.2.0/tricolore/man/TernaryCenterGrid.Rd |only tricolore-1.2.0/tricolore/man/TernaryDistance.Rd | 3 tricolore-1.2.0/tricolore/man/TernaryLimits.Rd |only tricolore-1.2.0/tricolore/man/TernaryMeshCentroids.Rd | 3 tricolore-1.2.0/tricolore/man/TernaryMeshVertices.Rd | 4 tricolore-1.2.0/tricolore/man/TernarySextantVertices.Rd |only tricolore-1.2.0/tricolore/man/TernarySurroundingSextant.Rd |only tricolore-1.2.0/tricolore/man/Tricolore.Rd | 32 tricolore-1.2.0/tricolore/man/TricoloreSextant.Rd |only tricolore-1.2.0/tricolore/man/ValidateParametersShared.Rd |only tricolore-1.2.0/tricolore/man/ValidateParametersTricolore.Rd |only tricolore-1.2.0/tricolore/man/ValidateParametersTricoloreSextant.Rd |only tricolore-1.2.0/tricolore/man/euro_example.Rd |only tricolore-1.2.0/tricolore/tests/testthat/test-global.R | 18 tricolore-1.2.0/tricolore/vignettes/choropleth_maps_with_tricolore.Rmd |only 48 files changed, 907 insertions(+), 297 deletions(-)
Title: Easily Carry Out Latent Profile Analysis
Description: An interface to the 'mclust' package to easily carry out latent profile
analysis ("LPA"). Provides functionality to estimate commonly-specified models.
Follows a tidy approach, in that output is in the form of a data frame that can
subsequently be computed on. Also has functions to interface to the commercial
'MPlus' software via the 'MplusAutomation' package.
Author: Joshua M Rosenberg [aut, cre],
Jennifer A Schmidt [ctb],
Patrick N Beymer [ctb],
Daniel Anderson [ctb],
Caspar van Lissa [ctb]
Maintainer: Joshua M Rosenberg <jmichaelrosenberg@gmail.com>
Diff between tidyLPA versions 0.1.3 dated 2018-03-28 and 0.2.0 dated 2018-09-13
tidyLPA-0.1.3/tidyLPA/man/extract_mplus_summary.Rd |only tidyLPA-0.1.3/tidyLPA/man/reexports.Rd |only tidyLPA-0.1.3/tidyLPA/tests/testthat/test-create_profiles_mplus.R |only tidyLPA-0.2.0/tidyLPA/DESCRIPTION | 22 tidyLPA-0.2.0/tidyLPA/MD5 | 67 tidyLPA-0.2.0/tidyLPA/NAMESPACE | 80 - tidyLPA-0.2.0/tidyLPA/NEWS.md | 32 tidyLPA-0.2.0/tidyLPA/R/bootstrap_LRT.R | 29 tidyLPA-0.2.0/tidyLPA/R/compare_solutions.R | 91 - tidyLPA-0.2.0/tidyLPA/R/compare_solutions_mplus.R | 347 ++-- tidyLPA-0.2.0/tidyLPA/R/detect-outliers.R |only tidyLPA-0.2.0/tidyLPA/R/estimate_profiles.R | 210 +- tidyLPA-0.2.0/tidyLPA/R/estimate_profiles_mplus.R | 747 +++++----- tidyLPA-0.2.0/tidyLPA/R/helpers.R | 98 - tidyLPA-0.2.0/tidyLPA/R/plot_profiles.R | 296 +-- tidyLPA-0.2.0/tidyLPA/R/plot_profiles_mplus.R | 20 tidyLPA-0.2.0/tidyLPA/R/tidylpa.r |only tidyLPA-0.2.0/tidyLPA/README.md | 104 - tidyLPA-0.2.0/tidyLPA/build/vignette.rds |binary tidyLPA-0.2.0/tidyLPA/inst/doc/Introduction_to_tidyLPA.R | 24 tidyLPA-0.2.0/tidyLPA/inst/doc/Introduction_to_tidyLPA.Rmd | 83 - tidyLPA-0.2.0/tidyLPA/inst/doc/Introduction_to_tidyLPA.html | 162 +- tidyLPA-0.2.0/tidyLPA/man/bootstrap_lrt.Rd | 7 tidyLPA-0.2.0/tidyLPA/man/compare_solutions.Rd | 10 tidyLPA-0.2.0/tidyLPA/man/compare_solutions_mplus.Rd | 28 tidyLPA-0.2.0/tidyLPA/man/estimate_profiles.Rd | 10 tidyLPA-0.2.0/tidyLPA/man/estimate_profiles_mplus.Rd | 27 tidyLPA-0.2.0/tidyLPA/man/extract_LL_mplus.Rd | 1 tidyLPA-0.2.0/tidyLPA/man/figures/README-unnamed-chunk-5-1.png |binary tidyLPA-0.2.0/tidyLPA/man/plot_profiles.Rd | 14 tidyLPA-0.2.0/tidyLPA/man/plot_profiles_mplus.Rd | 6 tidyLPA-0.2.0/tidyLPA/man/tidyLPA.Rd |only tidyLPA-0.2.0/tidyLPA/tests/testthat/test-compare_solutions_mplus.R | 2 tidyLPA-0.2.0/tidyLPA/tests/testthat/test-estimate_profiles.R | 16 tidyLPA-0.2.0/tidyLPA/tests/testthat/test-estimate_profiles_mplus.R |only tidyLPA-0.2.0/tidyLPA/tests/testthat/test-plot_profiles.R | 2 tidyLPA-0.2.0/tidyLPA/tests/testthat/test-plot_profiles_mplus.R | 2 tidyLPA-0.2.0/tidyLPA/vignettes/Introduction_to_tidyLPA.Rmd | 83 - 38 files changed, 1533 insertions(+), 1087 deletions(-)
Title: Thermal Image Analysis
Description: A collection of functions and routines for inputting thermal
image video files, plotting and converting binary raw data into estimates of
temperature. First published 2015-03-26. Written primarily for research purposes
in biological applications of thermal images. v1 included the base calculations
for converting thermal image binary values to temperatures. v2 included additional
equations for providing heat transfer calculations and an import function for thermal
image files (v2.2.3 fixed error importing thermal image to windows OS). v3. Added numerous
functions for converting thermal image, videos, rewriting and exporting.
v3.1. Added new functions to convert files.
Author: Glenn J. Tattersall
Maintainer: Glenn J. Tattersall <gtatters@brocku.ca>
Diff between Thermimage versions 3.1.0 dated 2017-11-29 and 3.1.1 dated 2018-09-13
DESCRIPTION | 20 +++++------ MD5 | 37 +++++++++++---------- R/convertflirJPG.R | 13 ++++--- R/convertflirVID.R | 66 +++++++++++++++++++++++++++----------- R/ffmpegcall.R | 12 +++++-- R/readflirJPG.R | 5 ++ inst/CITATION |only inst/exiftool |only man/Te.Rd | 3 + man/Teq.Rd | 4 ++ man/Tground.Rd | 5 ++ man/convertflirJPG.Rd | 5 ++ man/convertflirVID.Rd | 5 ++ man/flirsettings.Rd | 38 +++++++++++++++++++++- man/qabs.Rd | 2 + man/qconv.Rd | 3 + man/qrad.Rd | 4 +- man/raw2temp.Rd | 3 + man/readflirJPG.Rd | 85 ++++++++++++++++++++++++++++++++++++++++++++++++-- man/temp2raw.Rd | 3 + 20 files changed, 250 insertions(+), 63 deletions(-)
Title: Dose Response Data Analysis using the 4 Parameter Logistic (4pl)
Model
Description: Models the relationship between dose levels and responses in a pharmacological experiment using the 4 Parameter Logistic model. Traditional packages on dose-response modelling such as 'drc' and 'nplr' often draw errors due to convergence failure especially when data have outliers or non-logistic shapes. This package provides robust estimation methods that are less affected by outliers and other initialization methods that work well for data lacking logistic shapes. We provide the bounds on the parameters of the 4PL model that prevent parameter estimates from diverging or converging to zero and base their justification in a statistical principle. These methods are used as remedies to convergence failure problems. Gadagkar, S. R. and Call, G. B. (2015) <doi:10.1016/j.vascn.2014.08.006> Ritz, C. and Baty, F. and Streibig, J. C. and Gerhard, D. (2015) <doi:10.1371/journal.pone.0146021>.
Author: Justin T. Landis [aut, cre],
Hyowon An [aut],
Aubrey G. Bailey [aut]
Maintainer: Justin T. Landis <jtlandis314@gmail.com>
Diff between dr4pl versions 1.1.6 dated 2018-08-24 and 1.1.7.1 dated 2018-09-13
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 8 ++++++-- R/auxiliary.R | 14 ++++++-------- R/main.R | 2 +- README.md | 2 +- build/partial.rdb |binary inst/doc/usageExamples.html | 10 +++++----- inst/doc/usage_examples_HA.html | 14 +++++++------- man/summary.dr4pl.Rd | 2 +- tests/testthat/test_error_cases.R | 4 ++-- 11 files changed, 43 insertions(+), 41 deletions(-)
Title: Composite Kernel Machine Regression Based on Likelihood Ratio
Test
Description: Composite Kernel Machine Regression based on Likelihood Ratio Test (CKLRT): in this package, we develop a kernel machine regression framework to model the overall genetic effect of a SNP-set, considering the possible GE interaction. Specifically, we use a composite kernel to specify the overall genetic effect via a nonparametric function and we model additional covariates parametrically within the regression framework. The composite kernel is constructed as a weighted average of two kernels, one corresponding to the genetic main effect and one corresponding to the GE interaction effect. We propose a likelihood ratio test (LRT) and a restricted likelihood ratio test (RLRT) for statistical significance. We derive a Monte Carlo approach for the finite sample distributions of LRT and RLRT statistics. (N. Zhao, H. Zhang, J. Clark, A. Maity, M. Wu. Composite Kernel Machine Regression based on Likelihood Ratio Test with Application for Combined Genetic and Gene-environment Interaction Effect (Submitted).)
Author: Ni Zhao [aut], Haoyu Zhang [aut, cre]
Maintainer: Haoyu Zhang <andrew.haoyu@gmail.com>
Diff between CKLRT versions 0.2.2 dated 2018-07-19 and 0.2.3 dated 2018-09-13
DESCRIPTION | 8 ++--- MD5 | 6 ++-- R/omniLRT_fast.R | 77 ++++++++++++++++++++++++++-------------------------- man/omniLRT_fast.Rd | 4 +- 4 files changed, 48 insertions(+), 47 deletions(-)
Title: Regularization Paths for SCAD and MCP Penalized Regression
Models
Description: Fits regularization paths for linear regression, GLM, and Cox regression models using lasso or nonconvex penalties, in particular the minimax concave penalty (MCP) and smoothly clipped absolute deviation (SCAD) penalty, with options for additional L2 penalties (the "elastic net" idea). Utilities for carrying out cross-validation as well as post-fitting visualization, summarization, inference, and prediction are also provided.
Author: Patrick Breheny [aut, cre] (<https://orcid.org/000-0002-0650-1119>)
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between ncvreg versions 3.10-0 dated 2018-04-17 and 3.11-0 dated 2018-09-13
ncvreg-3.10-0/ncvreg/NEWS |only ncvreg-3.10-0/ncvreg/R/summary-cv-ncvsurv.R |only ncvreg-3.10-0/ncvreg/R/summary-ncvsurv.R |only ncvreg-3.10-0/ncvreg/inst/doc/quick-start.R |only ncvreg-3.10-0/ncvreg/inst/doc/quick-start.Rnw |only ncvreg-3.10-0/ncvreg/inst/doc/quick-start.pdf |only ncvreg-3.10-0/ncvreg/man/cv.ncvreg.Rd |only ncvreg-3.10-0/ncvreg/man/cv.ncvsurv.Rd |only ncvreg-3.10-0/ncvreg/man/perm.ncvreg.Rd |only ncvreg-3.10-0/ncvreg/man/plot.cv.ncvreg.Rd |only ncvreg-3.10-0/ncvreg/man/plot.ncvreg.Rd |only ncvreg-3.10-0/ncvreg/man/plot.ncvsurv.func.Rd |only ncvreg-3.10-0/ncvreg/vignettes/quick-start.Rnw |only ncvreg-3.11-0/ncvreg/DESCRIPTION | 21 +- ncvreg-3.11-0/ncvreg/MD5 | 75 +++++----- ncvreg-3.11-0/ncvreg/NAMESPACE | 15 +- ncvreg-3.11-0/ncvreg/NEWS.md |only ncvreg-3.11-0/ncvreg/R/cv.ncvreg.R | 2 ncvreg-3.11-0/ncvreg/R/cv.ncvsurv.R | 12 - ncvreg-3.11-0/ncvreg/R/local-mfdr.R | 4 ncvreg-3.11-0/ncvreg/R/loss.R | 4 ncvreg-3.11-0/ncvreg/R/ncvreg.R | 4 ncvreg-3.11-0/ncvreg/R/ncvsurv.R | 4 ncvreg-3.11-0/ncvreg/R/plot.cv.ncvreg.R | 35 +++- ncvreg-3.11-0/ncvreg/R/summary-cv-ncvreg.R | 18 +- ncvreg-3.11-0/ncvreg/R/summary-ncvreg.R | 40 ++--- ncvreg-3.11-0/ncvreg/README.md | 89 +++++++++++- ncvreg-3.11-0/ncvreg/build/vignette.rds |binary ncvreg-3.11-0/ncvreg/inst/doc/getting-started.R |only ncvreg-3.11-0/ncvreg/inst/doc/getting-started.html |only ncvreg-3.11-0/ncvreg/inst/doc/getting-started.rmd |only ncvreg-3.11-0/ncvreg/inst/tests/rsq.R |only ncvreg-3.11-0/ncvreg/man/auc.Rd | 16 +- ncvreg-3.11-0/ncvreg/man/cv-ncvreg.Rd |only ncvreg-3.11-0/ncvreg/man/mfdr.Rd | 12 + ncvreg-3.11-0/ncvreg/man/ncvreg-package.Rd | 7 ncvreg-3.11-0/ncvreg/man/ncvreg.Rd | 149 +++++++++++---------- ncvreg-3.11-0/ncvreg/man/ncvsurv.Rd | 113 ++++++++------- ncvreg-3.11-0/ncvreg/man/perm-ncvreg.Rd |only ncvreg-3.11-0/ncvreg/man/permres.Rd | 35 ++-- ncvreg-3.11-0/ncvreg/man/plot-cv-ncvreg.Rd |only ncvreg-3.11-0/ncvreg/man/plot-mfdr.Rd | 12 + ncvreg-3.11-0/ncvreg/man/plot-ncvreg.Rd |only ncvreg-3.11-0/ncvreg/man/plot-ncvsurv-func.Rd |only ncvreg-3.11-0/ncvreg/man/predict.Rd | 8 - ncvreg-3.11-0/ncvreg/man/summary-cv-ncvreg.Rd | 51 ++++--- ncvreg-3.11-0/ncvreg/man/summary-ncvreg.Rd | 3 ncvreg-3.11-0/ncvreg/vignettes/getting-started.rmd |only ncvreg-3.11-0/ncvreg/vignettes/vignette.css |only ncvreg-3.11-0/ncvreg/vignettes/web |only 50 files changed, 442 insertions(+), 287 deletions(-)
Title: High Dimensional Hypothesis Testing for Mean Vectors, Covariance
Matrices, and White Noise of Vector Time Series
Description: High dimensional testing procedures on mean, covariance and white noises.
Author: Meng Cao, Tong He, Wen Zhou
Maintainer: Wen Zhou <riczw@stat.colostate.edu>
Diff between HDtest versions 0.1 dated 2016-12-30 and 2.1 dated 2018-09-13
HDtest-0.1/HDtest/man/aeS.Rd |only HDtest-0.1/HDtest/man/autocovm.Rd |only HDtest-0.1/HDtest/man/opbw.Rd |only HDtest-0.1/HDtest/man/segment.Rd |only HDtest-2.1/HDtest/DESCRIPTION | 14 +- HDtest-2.1/HDtest/MD5 | 44 +++---- HDtest-2.1/HDtest/NAMESPACE | 6 - HDtest-2.1/HDtest/R/HDtest_data.R | 48 ++++---- HDtest-2.1/HDtest/R/aeS.R | 28 ----- HDtest-2.1/HDtest/R/autocovm.R | 14 -- HDtest-2.1/HDtest/R/cv_fastclime.R |only HDtest-2.1/HDtest/R/opbw.R | 14 -- HDtest-2.1/HDtest/R/segment.R | 18 --- HDtest-2.1/HDtest/R/sgTs_thre.R | 82 +++++++++----- HDtest-2.1/HDtest/R/wntest.R | 173 ++++++++++++++++++++++++++----- HDtest-2.1/HDtest/man/CLX.Rd | 7 - HDtest-2.1/HDtest/man/CQ2.Rd | 7 - HDtest-2.1/HDtest/man/GO26.Rd | 1 HDtest-2.1/HDtest/man/GO54.Rd | 1 HDtest-2.1/HDtest/man/equalCovs.Rd | 7 - HDtest-2.1/HDtest/man/oneMean.Rd | 7 - HDtest-2.1/HDtest/man/testCov.Rd | 1 HDtest-2.1/HDtest/man/testMean.Rd | 1 HDtest-2.1/HDtest/man/twoMeans.Rd | 7 - HDtest-2.1/HDtest/man/wntest.Rd | 135 ++++++++++++++++++++---- HDtest-2.1/HDtest/src/packagename_init.c |only 26 files changed, 393 insertions(+), 222 deletions(-)
Title: Data and Variable Transformation Functions
Description: Collection of miscellaneous utility functions, supporting data
transformation tasks like recoding, dichotomizing or grouping variables,
setting and replacing missing values. The data transformation functions
also support labelled data, and all integrate seamlessly into a
'tidyverse'-workflow.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjmisc versions 2.7.4 dated 2018-08-04 and 2.7.5 dated 2018-09-13
DESCRIPTION | 12 MD5 | 150 +++++---- NAMESPACE | 20 - NEWS.md | 213 +------------ R/S3-methods.R | 13 R/add_cases.R |only R/add_columns.R | 7 R/all_na.R | 3 R/big_mark.R | 7 R/count_na.R | 4 R/de_mean.R |only R/descr.R | 130 ++++++-- R/dicho.R | 10 R/find_var.R | 13 R/frq.R | 147 ++++----- R/group_str.R | 12 R/has_na.R | 10 R/helpfunctions.R | 12 R/is_empty.R | 21 - R/is_num_fac.R | 23 + R/move_column.R |only R/rec.R | 17 - R/recode_to.R | 11 R/ref_lvl.R | 5 R/remove_vars.R | 3 R/replace_na.R | 10 R/rotate_df.R | 6 R/round_num.R | 10 R/row_count.R | 30 - R/row_sums.R | 28 + R/select_helpers.R |only R/seq_col.R |only R/set_na.R | 4 R/spread_coef.R | 12 R/std.R | 2 R/str_start_end.R | 153 ++++----- R/to_dummy.R | 6 R/to_factor.R | 15 R/to_label.R | 12 R/to_long.R | 4 R/to_value.R | 4 R/trim.R | 4 R/var_labels.R | 4 R/var_type.R | 27 + build/partial.rdb |binary inst/doc/design_philosophy.R | 30 + inst/doc/design_philosophy.Rmd | 30 + inst/doc/design_philosophy.html | 635 ++++++++++++++++++++++++++-------------- inst/doc/exploringdatasets.html | 540 +++++++++++++++++++++++----------- man/add_variables.Rd |only man/count_na.Rd | 3 man/de_mean.Rd |only man/descr.Rd | 10 man/dicho.Rd | 2 man/find_var.Rd | 6 man/frq.Rd | 51 +-- man/group_str.Rd | 5 man/group_var.Rd | 2 man/is_empty.Rd | 21 - man/is_num_fac.Rd | 18 - man/move_columns.Rd |only man/rec.Rd | 2 man/recode_to.Rd | 2 man/reexports.Rd | 3 man/replace_na.Rd | 6 man/rotate_df.Rd | 3 man/row_count.Rd | 21 - man/row_sums.Rd | 7 man/seq_col.Rd |only man/split_var.Rd | 2 man/std.Rd | 4 man/to_factor.Rd | 4 man/var_rename.Rd | 4 tests/testthat/test-add_case.R |only tests/testthat/test-colcnt.R | 14 tests/testthat/test-countna.R | 3 tests/testthat/test-demean.R |only tests/testthat/test-frq.R | 21 + tests/testthat/test-rowcnt.R | 15 tests/testthat/test-rowmeans.R | 4 tests/testthat/test-rowsums.R |only vignettes/design_philosophy.Rmd | 30 + 82 files changed, 1530 insertions(+), 1142 deletions(-)
Title: Joint Estimation in Linear Quantile Regression
Description: Joint estimation of quantile specific intercept and slope parameters in a linear regression setting.
Author: Surya Tokdar <surya.tokdar@duke.edu> and Erika Cunningham <erika.ball@duke.edu>
Maintainer: Surya Tokdar <surya.tokdar@duke.edu>
Diff between qrjoint versions 2.0-1 dated 2018-09-12 and 2.0-2 dated 2018-09-13
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/qrjoint.c | 17 +++++++++-------- 3 files changed, 15 insertions(+), 14 deletions(-)
Title: Measuring Multivariate Dependence Using Distance Multivariance
Description: Distance multivariance is a measure of dependence which can be used to detect
and quantify dependence. The necessary functions are implemented in this packages,
and examples are given. For the theoretic background we refer to the papers:
B. Böttcher, M. Keller-Ressel, R.L. Schilling, Detecting independence of random vectors I. Generalized distance covariance and Gaussian covariance. Preprint 2017, <arXiv:1711.07778>.
B. Böttcher, M. Keller-Ressel, R.L. Schilling, Detecting independence of random vectors II. Distance multivariance and Gaussian multivariance. Preprint 2017, <arXiv:1711.07775>.
B. Böttcher, Dependence Structures - Estimation and Visualization Using Distance Multivariance. Preprint 2017, <arXiv:1712.06532>.
G. Berschneider, B. Böttcher, On complex Gaussian random fields, Gaussian quadratic forms and sample distance multivariance. Preprint 2018, <arXiv:1808.07280>.
Author: Björn Böttcher [aut, cre],
Martin Keller-Ressel [ctb]
Maintainer: Björn Böttcher <bjoern.boettcher@tu-dresden.de>
Diff between multivariance versions 1.1.0 dated 2018-01-10 and 1.2.0 dated 2018-09-13
DESCRIPTION | 16 - MD5 | 42 ++- NAMESPACE | 6 R/RcppExports.R |only R/multivariance-functions.R | 480 ++++++++++++++++++++++++++++++++---- inst/NEWS | 14 + man/N.coefficients.Rd |only man/cdm.Rd | 6 man/cdm.mu.bcd.Rd |only man/cdm.product.Rd | 4 man/cdms.mu.bcd.Rd |only man/d2.Rd |only man/dep_struct_ring_15_100.Rd | 2 man/fastdist.Rd |only man/find.cluster.Rd | 10 man/independence.test.Rd | 12 man/m.multivariance.Rd | 2 man/moments.for.pearson.Rd |only man/mu3.unbiased.Rd |only man/multivariance-package.Rd | 14 - man/pearson.pvalue.Rd |only man/pearson.qf.Rd |only man/resample.multivariance.Rd | 8 man/resample.pvalue.Rd | 2 man/sample.cdms.Rd |only man/sums.of.products.Rd |only src |only tests/testthat/testmultivariances.R | 2 28 files changed, 532 insertions(+), 88 deletions(-)
Title: Tools for Statistical Content Analysis
Description: A framework for statistical analysis in content analysis. In addition to a pipeline for preprocessing text corpora and linking to the latent Dirichlet allocation from the 'lda' package, plots are offered for the descriptive analysis of text corpora and topic models. In addition, an implementation of Chang's intruder words and intruder topics is provided.
Author: Lars Koppers [aut, cre] (<https://orcid.org/0000-0002-1642-9616>),
Jonas Rieger [aut],
Karin Boczek [ctb] (<https://orcid.org/0000-0003-1516-4094>),
Gerret von Nordheim [ctb] (<https://orcid.org/0000-0001-7553-3838>)
Maintainer: Lars Koppers <koppers@statistik.tu-dortmund.de>
Diff between tosca versions 0.1-1 dated 2018-09-03 and 0.1-2 dated 2018-09-13
DESCRIPTION | 8 MD5 | 44 R/readTextmeta.R | 2 inst/doc/Vignette.Rmd | 6 inst/doc/Vignette.pdf | 871 +++++------ tests/testthat/test_LDAgen.R | 10 tests/testthat/test_mergeLDA.R | 4 tests/testthat/test_readTextmeta.R | 10 vignettes/Vignette.Rmd | 6 vignettes/Vignette_files/figure-latex/unnamed-chunk-15-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-16-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-17-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-17-2.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-18-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-42-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-43-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-44-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-46-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-47-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-49-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-51-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-52-1.pdf |binary vignettes/Vignette_files/figure-latex/unnamed-chunk-53-1.pdf |binary 23 files changed, 475 insertions(+), 486 deletions(-)
Title: Tools to Simulate Phenotype(s) with Epistatic Interaction
Description: Provides functions to simulate single or multiple, independent or correlated phenotype(s) with additive, dominance effects and their interactions. Also includes functions to generate phenotype(s) with specific heritability. Flexible and user-friendly options for simulation.
Author: Beibei Jiang <beibei_jiang@psych.mpg.de> and Benno Pütz
Maintainer: Beibei Jiang <beibei_jiang@psych.mpg.de>
Diff between SimPhe versions 0.1.1 dated 2017-01-04 and 0.2.0 dated 2018-09-13
DESCRIPTION | 10 MD5 | 77 R/getgenotype.R | 2 R/readpars.R | 3 R/simPheno.R | 345 +-- README.md |only build/vignette.rds |binary inst/doc/SimPhe.R | 4 inst/doc/SimPhe.Rmd | 46 inst/doc/SimPhe.html | 734 +++--- inst/extdata/10SNP.txt | 4649 ------------------------------------------ inst/extdata/bdemo.bed |binary inst/extdata/bdemo.fam | 4649 ------------------------------------------ inst/extdata/demo.ped | 4649 ------------------------------------------ inst/extdata/sep_simupars.txt | 12 man/allele.freq.Rd | 1 man/build.cor.phe.Rd | 1 man/build.sd.matrix.Rd | 1 man/calc.gene.var.Rd | 1 man/calc.herit.Rd | 1 man/check.snp.par.Rd | 1 man/count.allele.Rd | 1 man/epistasis.pars.Rd | 1 man/gene.coefficients.Rd | 1 man/gene.effect.Rd | 1 man/genepars.Rd | 1 man/genetic.scale.Rd | 1 man/get.freq.Rd | 1 man/get.gene.coef.Rd | 1 man/get.noise.var.Rd | 1 man/list2frame.Rd | 1 man/maineff.pars.Rd | 1 man/pars.writer.Rd | 1 man/phe.writer.Rd | 1 man/read.geno.Rd | 3 man/read.simu.pars.Rd | 4 man/regextract.Rd | 1 man/sim.phe.Rd | 36 man/specify.pars.Rd | 1 vignettes/SimPhe.Rmd | 46 40 files changed, 727 insertions(+), 14563 deletions(-)
Title: Numerical Standard Errors Computation in R
Description: Collection of functions designed to calculate numerical standard error (NSE) of univariate time series as described in Ardia et al. (2018) <doi:10.2139/ssrn.2741587> and Ardia and Bluteau (2017) <doi:10.21105/joss.00172>.
Author: David Ardia [aut],
Keven Bluteau [aut, cre]
Maintainer: Keven Bluteau <Keven.Bluteau@unine.ch>
Diff between nse versions 1-00.17 dated 2017-02-08 and 1.19 dated 2018-09-13
DESCRIPTION | 18 - MD5 | 41 +- NAMESPACE | 4 NEWS | 4 R/RcppExports.R | 2 R/cos.basis.R |only R/kernel_addon.R |only R/nse.R | 616 +++++++++++++++++++++++------------------ R/optimal_spectral_bandwidth.R |only R/prewhitening.R | 14 R/welch.R |only build/partial.rdb |binary inst/CITATION | 19 - inst/COPYRIGHTS | 2 man/nse.Rd | 89 +++-- man/nse.andrews.Rd | 46 +-- man/nse.boot.Rd | 34 -- man/nse.cos.Rd |only man/nse.geyer.Rd | 19 - man/nse.hiruk.Rd | 27 - man/nse.nw.Rd | 19 - man/nse.spec0.Rd | 80 +++-- src/RcppExports.cpp | 12 tests/testthat/test.R | 55 ++- 24 files changed, 613 insertions(+), 488 deletions(-)
Title: Detection of Structural Changes in Climate and Environment Time
Series
Description: Tools for automatic model selection and diagnostics for Climate and Environmental data. In particular the envcpt() function does automatic model selection between a variety of trend, changepoint and autocorrelation models. The envcpt() function should be your first port of call.
Author: Rebecca Killick [aut, cre],
Claudie Beaulieu [aut],
Simon Taylor [aut],
Harjit Hullait [aut]
Maintainer: Rebecca Killick <r.killick@lancs.ac.uk>
Diff between EnvCpt versions 1.1 dated 2018-09-11 and 1.1.1 dated 2018-09-13
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 6 ++++++ R/envcpt.R | 25 ++++++++++++++++++++----- man/envcpt-package.Rd | 4 ++-- man/envcpt.Rd | 4 ++-- 6 files changed, 39 insertions(+), 18 deletions(-)
Title: Local Polynomial Regression of State Dependent Covariates in
State-Space Models
Description: Facilitates local polynomial regression for state dependent covariates in state-space models. The functionality can also be used from 'C++' based model builder tools such as 'Rcpp'/'inline', 'TMB', or 'JAGS'.
Author: Christoffer Moesgaard Albertsen [aut, cre]
(<https://orcid.org/0000-0003-0088-4363>)
Maintainer: Christoffer Moesgaard Albertsen <cmoe@aqua.dtu.dk>
Diff between covafillr versions 0.4.2 dated 2017-11-20 and 0.4.3 dated 2018-09-13
DESCRIPTION | 18 +- MD5 | 46 +++--- NAMESPACE | 4 NEWS | 8 + R/kde.R | 6 R/statcovafill.R | 68 ++++----- R/utils.R | 1 inst/include/covafill/TMB | 3 inst/include/covafill/Tree | 2 inst/include/covafill/dox/Doxyfile | 2 inst/include/covafill/src/Core/covafill_operators.hpp | 4 inst/include/covafill/src/Core/covafill_privateFunctions.hpp | 17 +- inst/include/covafill/src/Interpolate/bicubicInterpolation.hpp | 6 inst/include/covafill/src/Interpolate/cubicInterpolation.hpp | 19 ++ inst/include/covafill/src/Interpolate/ncubicInterpolation.hpp | 9 - inst/include/covafill/src/Interpolate/tricubicInterpolation.hpp | 4 inst/include/covafill/src/Interpolate/unicubicInterpolation.hpp | 8 - inst/include/covafill/src/Tree/covanode_constructors.hpp | 3 inst/include/covafill/src/Tree/covatree_constructors.hpp | 3 man/suggestBandwith.Rd | 2 src/headers/fill.hpp | 75 +++++----- src/headers/tree.hpp | 40 +++-- src/main.cpp | 18 ++ src/utils/convert.hpp | 22 +- 24 files changed, 231 insertions(+), 157 deletions(-)
Title: Calculate and Analyze Blau Status for (Covert) Organizations
Description: An integrated set of tools to calculate and analyze Blau statuses quantifying social distance between individuals belonging to (covert) organizations. Relational (network) data can be incorporated for additional analyses. This project is supported by Defense Threat Reduction Agency (DTRA) Grant HDTRA-10-1-0043.
Author: Cheng Wang*, Michael Genkin*, George Berry, Liyuan Chen, Matthew Brashears *Both authors contributed equally to this work and their names are randomly ordered
Maintainer: Cheng Wang <cwang3@nd.edu>
Diff between Blaunet versions 2.0.7 dated 2017-10-06 and 2.0.8 dated 2018-09-13
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ inst/scripts/blaunetgui.R | 15 +++++++++------ inst/scripts/command.pdf |binary inst/scripts/graphic.pdf |binary inst/scripts/open.R | 2 +- man/Blaunet-package.Rd | 8 ++++---- 7 files changed, 23 insertions(+), 20 deletions(-)
Title: Download and Aggregate Data from Public Hire Bicycle Systems
Description: Download and aggregate data from all public hire bicycle systems
which provide open data, currently including 'Santander' Cycles in London,
U.K., and from the U.S.A., 'citibike' in New York City NY, 'Divvy' in
Chicago IL, 'Capital Bikeshare' in Washington DC, 'Hubway' in Boston MA,
'Metro' in Los Angeles LA, and 'Indego' in Philadelphia PA.
Author: Mark Padgham [aut, cre] (<https://orcid.org/0000-0003-2172-5265>),
Richard Ellison [aut],
Tom Buckley [aut],
Bea Hernández [rev] (Bea reviewed the package for ropensci, see
https://github.com/ropensci/onboarding/issues/116),
Elaine McVey [rev] (Elaine reviewed the package for ropensci, see
https://github.com/ropensci/onboarding/issues/116),
SQLite Consortium [ctb] (Authors of included SQLite code)
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between bikedata versions 0.2.0 dated 2018-04-27 and 0.2.1 dated 2018-09-13
DESCRIPTION | 8 MD5 | 65 - NAMESPACE | 1 R/bikedata-files.R | 8 R/database-stats.R | 6 R/distmat.R | 2 R/dl-bikedata.R | 6 R/stations.R | 4 R/store-bikedata.R | 1 R/utils.R | 50 + R/write-test-data.R | 4 inst/CITATION |only inst/doc/bikedata.R | 92 -- inst/doc/bikedata.Rmd | 99 +- inst/doc/bikedata.html | 1520 +++++++++++++++++++++++++++++++++++---- man/bike_cities.Rd |only man/bike_datelimits.Rd | 2 man/bike_latest_files.Rd | 2 man/bike_rm_test_data.Rd | 2 man/bike_summary_stats.Rd | 2 man/bike_write_test_data.Rd | 2 src/read-city-files.cpp | 112 +- src/read-city-files.h | 4 src/read-station-files.cpp | 12 src/read-station-files.h | 3 src/sqlite3db-add-data.cpp | 38 src/sqlite3db-add-data.h | 4 src/sqlite3db-utils.cpp | 6 src/sqlite3db-utils.h | 4 src/utils.cpp | 109 ++ src/utils.h | 6 tests/testthat/test-stations.R | 1 tests/testthat/test-store-data.R | 68 - vignettes/bikedata.Rmd | 99 +- vignettes/la_map_simple.png |only 35 files changed, 1864 insertions(+), 478 deletions(-)
Title: Evaluation of the Proportional Hazards Assumption with a
Standardized Score Process
Description: Provides tools for the evaluation of the goodness of fit and the predictive capacity of the proportional hazards model.
Author: Cecile Chauvel
Maintainer: Cecile Chauvel <chauvel.cecile@gmail.com>
Diff between PHeval versions 0.5.3 dated 2015-12-16 and 0.5.4 dated 2018-09-13
DESCRIPTION | 13 +++++++------ MD5 | 10 +++++----- NAMESPACE | 4 ++-- man/PHeval-package.Rd | 6 ++++-- man/plotscore.Rd | 2 +- man/standscore.Rd | 7 ++++--- 6 files changed, 23 insertions(+), 19 deletions(-)
Title: Automated Method for Verbal Autopsy
Description: Implements multiple existing open-source algorithms for coding cause of death from verbal autopsies. It also provides tools for data manipulation tasks commonly used in Verbal Autopsy analysis and implements easy graphical visualization of individual and population level statistics.
Author: Zehang Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Li <lizehang@gmail.com>
Diff between openVA versions 1.0.6 dated 2018-08-30 and 1.0.7 dated 2018-09-13
DESCRIPTION | 12 +++++++----- MD5 | 6 +++--- R/CSMF.r | 4 ++++ inst/NEWS.Rd | 5 +++++ 4 files changed, 19 insertions(+), 8 deletions(-)
Title: Performing Continuous-Time Microsimulation
Description: This entry-level toolkit allows performing continuous-time microsimulation for a wide range of demographic applications. Individual life-courses are specified by a continuous-time multi-state model.
Author: Sabine Zinn
Maintainer: Sabine Zinn <sabine.zinn@lifbi.de>
Diff between MicSim versions 1.0.12 dated 2016-06-13 and 1.0.13 dated 2018-09-13
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/micSim.r | 2 +- inst/NEWS.Rd | 5 +++++ man/MicSim-package.Rd | 4 ++-- man/buildTransitionMatrix.Rd | 3 ++- man/micSim.Rd | 2 ++ man/micSimParallel.Rd | 2 ++ 8 files changed, 25 insertions(+), 15 deletions(-)
Title: Obtain and Visualize Regulome-Gene Expression Correlations in
Cancer
Description: Builds a 'SQLite' database file of pre-calculated transcription
factor/microRNA-gene correlations (co-expression) in cancer from the
Cistrome Cancer Liu et al. (2011) <doi:10.1186/gb-2011-12-8-r83> and
'miRCancerdb' databases (in press). Provides custom classes and functions
to query, tidy and plot the correlation data.
Author: Mahmoud Ahmed [aut, cre]
Maintainer: Mahmoud Ahmed <mahmoud.s.fahmy@students.kasralainy.edu.eg>
Diff between cRegulome versions 0.1.1 dated 2018-03-17 and 0.2.0 dated 2018-09-13
cRegulome-0.1.1/cRegulome/R/methods.R |only cRegulome-0.1.1/cRegulome/tests/testthat/test_generics.R |only cRegulome-0.1.1/cRegulome/tests/testthat/test_methods.R |only cRegulome-0.1.1/cRegulome/tests/testthat/test_plots.R |only cRegulome-0.2.0/cRegulome/DESCRIPTION | 18 cRegulome-0.2.0/cRegulome/MD5 | 70 - cRegulome-0.2.0/cRegulome/NAMESPACE | 18 cRegulome-0.2.0/cRegulome/NEWS.md | 5 cRegulome-0.2.0/cRegulome/R/cRegulome.R | 35 cRegulome-0.2.0/cRegulome/R/get_data.R | 439 ++++++---- cRegulome-0.2.0/cRegulome/R/methods.plots.R |only cRegulome-0.2.0/cRegulome/R/methods.tidy.R |only cRegulome-0.2.0/cRegulome/R/objects.R | 106 +- cRegulome-0.2.0/cRegulome/build/vignette.rds |binary cRegulome-0.2.0/cRegulome/inst/doc/case_study.R | 4 cRegulome-0.2.0/cRegulome/inst/doc/case_study.Rmd | 4 cRegulome-0.2.0/cRegulome/inst/doc/case_study.html | 13 cRegulome-0.2.0/cRegulome/inst/doc/using_cRegulome.R | 2 cRegulome-0.2.0/cRegulome/inst/doc/using_cRegulome.Rmd | 2 cRegulome-0.2.0/cRegulome/inst/doc/using_cRegulome.html | 75 - cRegulome-0.2.0/cRegulome/inst/extdata/make_testset.R |only cRegulome-0.2.0/cRegulome/man/cRegulome.Rd | 28 cRegulome-0.2.0/cRegulome/man/cTF.Rd | 8 cRegulome-0.2.0/cRegulome/man/cmicroRNA.Rd | 6 cRegulome-0.2.0/cRegulome/man/cor_hist.Rd | 10 cRegulome-0.2.0/cRegulome/man/cor_igraph.Rd | 2 cRegulome-0.2.0/cRegulome/man/cor_joy.Rd | 10 cRegulome-0.2.0/cRegulome/man/cor_plot.Rd | 10 cRegulome-0.2.0/cRegulome/man/cor_prep.Rd |only cRegulome-0.2.0/cRegulome/man/cor_tidy.Rd | 8 cRegulome-0.2.0/cRegulome/man/cor_upset.Rd | 11 cRegulome-0.2.0/cRegulome/man/cor_venn_diagram.Rd | 12 cRegulome-0.2.0/cRegulome/man/get_db.Rd | 1 cRegulome-0.2.0/cRegulome/man/get_mir.Rd | 14 cRegulome-0.2.0/cRegulome/man/get_tf.Rd | 31 cRegulome-0.2.0/cRegulome/man/stat_collect.Rd |only cRegulome-0.2.0/cRegulome/man/stat_make.Rd |only cRegulome-0.2.0/cRegulome/tests/testthat/test-get_data.R |only cRegulome-0.2.0/cRegulome/tests/testthat/test-methods.plots.R |only cRegulome-0.2.0/cRegulome/tests/testthat/test-methods.tidy.R |only cRegulome-0.2.0/cRegulome/tests/testthat/test-objects.R |only cRegulome-0.2.0/cRegulome/vignettes/case_study.Rmd | 4 cRegulome-0.2.0/cRegulome/vignettes/using_cRegulome.Rmd | 2 43 files changed, 543 insertions(+), 405 deletions(-)
Title: Efficient and Publishing-Oriented Workflow for Psychological
Science
Description: The main goal of the psycho package is to provide tools for psychologists, neuropsychologists and neuroscientists,
to facilitate and speed up the time spent on data analysis. It aims at supporting best practices and tools to format the output
of statistical methods to directly paste them into a manuscript, ensuring statistical reporting standardization and conformity.
Author: Dominique Makowski [aut, cre, cph]
(<https://orcid.org/0000-0001-5375-9967>),
Hugo Najberg [ctb],
Viliam Simko [ctb],
Sasha Epskamp [rev] (Sasha reviewed the package for JOSS, see
https://github.com/openjournals/joss-reviews/issues/470)
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between psycho versions 0.3.6 dated 2018-08-30 and 0.3.7 dated 2018-09-13
DESCRIPTION | 8 - MD5 | 12 - R/dprime.R | 9 - inst/doc/bayesian.html | 314 +++++++++++++++++++++---------------------- inst/doc/overview.html | 8 - man/dprime.Rd | 4 tests/testthat/test-dprime.R | 3 7 files changed, 180 insertions(+), 178 deletions(-)
Title: Optimal Bayesian Experimental Design using the ACE Algorithm
Description: Optimal Bayesian experimental design using the approximate coordinate exchange (ACE) algorithm.
Author: Antony M. Overstall, David C. Woods & Maria Adamou
Maintainer: Antony M. Overstall <A.M.Overstall@soton.ac.uk>
Diff between acebayes versions 1.5 dated 2018-06-22 and 1.5.1 dated 2018-09-13
DESCRIPTION | 8 - MD5 | 26 ++--- R/acebayes.R | 243 ++++++++++++++++++++++++++++++++---------------- R/sysdata.rda |binary build/vignette.rds |binary inst/doc/acebayes.pdf |binary man/ace.Rd | 2 man/acebayes-package.Rd | 4 man/aceglm.Rd | 18 +-- man/acenlm.Rd | 4 man/utilities.Rd | 2 src/Makevars | 2 src/Makevars.win | 2 src/acebayes.cpp | 166 ++++++++++++++++---------------- 14 files changed, 281 insertions(+), 196 deletions(-)
Title: Probabilistic Verbal Autopsy Coding with 'InSilicoVA' Algorithm
Description: Computes individual causes of death and population cause-specific mortality fractions using the 'InSilicoVA' algorithm from McCormick et al. (2016) <DOI:10.1080/01621459.2016.1152191>. It uses data derived from verbal autopsy (VA) interviews, in a format similar to the input of the widely used 'InterVA4' method. This package provides general model fitting and customization for 'InSilicoVA' algorithm and basic graphical visualization of the output.
Author: Zehang Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Li <lizehang@gmail.com>
Diff between InSilicoVA versions 1.2.3 dated 2018-08-30 and 1.2.4 dated 2018-09-13
DESCRIPTION | 12 +++++---- MD5 | 14 +++++----- R/insilico_core.r | 65 +++++++++++++++++++++++++++++++++++-------------- R/insilico_standard.r | 14 +++++++++- inst/NEWS.rd | 16 ++++++++++++ inst/java/Insilico.jar |binary man/insilico.Rd | 7 +++-- man/insilico.fit.Rd | 3 +- 8 files changed, 95 insertions(+), 36 deletions(-)
Title: Run 'roxygen2' on (Chunks of) Single Code Files
Description: Have you ever been tempted to create 'roxygen2'-style documentation
comments for one of your functions that was not part of one of your
packages (yet)?
This is exactly what this package is about: running 'roxygen2' on
(chunks of) a single code file.
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <adc-r@arcor.de>
Diff between document versions 3.0.1 dated 2018-03-20 and 3.0.2 dated 2018-09-13
DESCRIPTION | 8 +-- MD5 | 26 ++++++------ NEWS.md | 5 +- R/package_functions.R | 29 ++++++------- build/vignette.rds |binary inst/doc/Introduction_to_document.R | 18 -------- inst/doc/Introduction_to_document.html | 70 +++++++++++++++++++++------------ man/document.Rd | 11 ++--- man/fake_package.Rd | 3 - man/write_the_docs.Rd | 4 - tests/testthat.R | 16 +++++++ tests/testthat/test_basic.R | 9 ++-- tests/testthat/test_check.R | 36 +++++++++------- tests/testthat/test_parse.R | 2 14 files changed, 133 insertions(+), 104 deletions(-)
Title: Disease-Gene-Variant Relations Mining from the Public Databases
and Literature
Description: Captures and compiles the genes and variants related to a disease, a phenotype or a clinical feature from the public databases including HPO (Human Phenotype Ontology, <http://human-phenotype-ontology.github.io/about.html>), Orphanet <http://www.orpha.net/consor/cgi-bin/index.php>, OMIM (Online Mendelian Inheritance in Man, <http://www.omim.org>), ClinVar <http://www.ncbi.nlm.nih.gov/clinvar>, and UniProt (Universal Protein Resource, <http://www.uniprot.org>) and PubMed abstracts. HPO provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. HPO currently contains approximately 11,000 terms and over 115,000 annotations to hereditary diseases. Orphanet is the reference portal for information on rare diseases and orphan drugs, whose aim is to help improve the diagnosis, care and treatment of patients with rare diseases. OMIM is a continuously updated catalog of human genes and genetic disorders and traits, with particular focus on the molecular relationship between genetic variation and phenotypic expression. ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. UniProt focuses on amino acid altering variants imported from Ensembl Variation databases. For Homo sapiens, the variants including human polymorphisms and disease mutations in the UniProt are manually curated from UniProtKB/Swiss-Prot. Additionally, PubMed provides the primary and latest source of the information. Text mining was employed to capture the information from PubMed abstracts.
Author: Zongfu Cao <caozongfu@gmail.com>; Lei Wang <isan.wong@gmail.com>
Maintainer: Zongfu Cao <caozongfu@gmail.com>
Diff between VarfromPDB versions 2.2.7 dated 2017-05-06 and 2.2.10 dated 2018-09-13
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- R/extract_clinvar.R | 31 ++++++++++++++++++------------- R/extract_omim.R | 9 +++++---- R/extract_pubmed.R | 12 ++++++------ R/extract_uniprot.R | 12 ++++++++---- R/genes_add_pubmed.R | 4 ++-- R/genes_compile.R | 12 ++++++------ R/localPDB.R | 6 +++--- R/pheno_extract_HPO.R | 18 ++++++++++-------- R/variants_compile.R | 16 +++++++++++++--- inst/doc/VarfromPDB.R | 2 +- inst/doc/VarfromPDB.Rmd | 4 ++-- inst/doc/VarfromPDB.html | 10 +++++----- vignettes/VarfromPDB.Rmd | 4 ++-- 15 files changed, 99 insertions(+), 77 deletions(-)
Title: Interactive Interfaces for Results Exploration
Description: Shiny interfaces and graphical functions for multivariate analysis results exploration.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>
Diff between explor versions 0.3.3 dated 2017-10-10 and 0.3.4 dated 2018-09-13
DESCRIPTION | 18 ++-- MD5 | 24 +++--- NEWS | 7 + R/prepare_results_PCA.R | 11 ++ R/prepare_results_dudi_coa.R | 4 - R/prepare_results_dudi_mca.R | 4 - R/prepare_results_dudi_pca.R | 4 - build/vignette.rds |binary inst/doc/introduction_en.html | 158 +++++++++++++++++++++--------------------- inst/doc/introduction_fr.html | 158 +++++++++++++++++++++--------------------- man/CA_var_plot.Rd | 9 +- man/MCA_ind_plot.Rd | 3 man/PCA_var_plot.Rd | 4 - 13 files changed, 210 insertions(+), 194 deletions(-)
Title: Non-Uniform Memory Access ('NUMA') Optimized, Parallel K-Means
Description: The k-means 'NUMA' Optimized Routine library or 'knor' is a highly optimized and fast library for computing k-means in parallel with accelerations for Non-Uniform Memory Access ('NUMA') architectures.
Author: Disa Mhembere [aut, cre],
Neurodata (https://neurodata.io) [cph]
Maintainer: Disa Mhembere <disa@jhu.edu>
Diff between knor versions 0.0-5.1 dated 2018-08-05 and 0.0-6 dated 2018-09-13
DESCRIPTION | 8 ++-- MD5 | 18 +++++------ configure | 14 -------- src/Makevars.in | 14 -------- src/Makevars.win | 2 - src/cknor/binding/knori.hpp | 17 +++++----- src/cknor/libauto/kmeans.cpp | 14 ++++---- src/cknor/libauto/min-tri-kmeans.cpp | 12 ++++--- src/cknor/libkcommon/unit-test/test_thd_safe_bool_vector.cpp | 2 - src/cknor/libkcommon/util.cpp | 6 --- 10 files changed, 40 insertions(+), 67 deletions(-)
Title: Tumor Clones Percentage Estimations
Description: Includes R functions for the estimation of tumor clones percentages for both snp data and (whole) genome sequencing data. See Cheng, Y., Dai, J. Y., Paulson, T. G., Wang, X., Li, X., Reid, B. J., & Kooperberg, C. (2017). Quantification of multiple tumor clones using gene array and sequencing data. The Annals of Applied Statistics, 11(2), 967-991, <doi:10.1214/17-AOAS1026> for more details.
Author: Xuan You <youxuan90@gmail.com>, Yichen Cheng <ycheng11@gsu.edu>
Maintainer: Xuan You <youxuan90@gmail.com>
Diff between EstMix versions 1.0 dated 2018-08-31 and 1.0.1 dated 2018-09-13
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- src/calcll_baf.cpp | 2 +- src/calcll_cpp.cpp | 2 +- src/calcll_p3.cpp | 4 ++-- 5 files changed, 11 insertions(+), 11 deletions(-)
Title: Conditional Visualization for Statistical Models
Description: Exploring fitted models by interactively taking 2-D and 3-D
sections in data space.
Author: Mark O'Connell [aut, cre],
Catherine Hurley [aut],
Katarina Domijan [aut],
Achim Zeileis [ctb] (spineplot, see copied.R),
R Core Team [ctb] (barplot, see copied.R)
Maintainer: Mark O'Connell <mark_ajoc@yahoo.ie>
Diff between condvis versions 0.4-2 dated 2017-10-11 and 0.5-1 dated 2018-09-13
DESCRIPTION | 8 +++---- MD5 | 25 ++++++++++++---------- NAMESPACE | 8 +++++-- NEWS | 22 +++++++++++++++++++- R/arrangeC.R | 7 ++++-- R/ceplot.shiny.R | 4 +-- R/interpolate.R |only R/makepath.R | 29 +++----------------------- R/similarityweight.R | 26 ++++++++++++++--------- man/condvis-package.Rd | 4 +-- man/crab.Rd | 36 ++++++++++++++++----------------- man/interpolate.Rd |only tests/testthat/test.interpolate.R |only tests/testthat/test.makepath.R | 2 - tests/testthat/test.similarityweight.R | 18 ++++++++++++++++ 15 files changed, 111 insertions(+), 78 deletions(-)
Title: Solving 1D Advection Bi-Flux Diffusion Equation
Description: This software solves an Advection Bi-Flux Diffusive Problem using the Finite Difference Method FDM. Vasconcellos, J.F.V., Marinho, G.M., Zanni, J.H., 2016, Numerical analysis of an anomalous diffusion with a bimodal flux distribution. <doi:10.1016/j.rimni.2016.05.001>. Silva, L.G., Knupp, D.C., Bevilacqua, L., Galeao, A.C.N.R., Silva Neto, A.J., 2014, Formulation and solution of an Inverse Anomalous Diffusion Problem with Stochastic Techniques. <doi:10.5902/2179460X13184>. In this version, it is possible to include a source as a function depending on space and time, that is, s(x,t).
Author: Jader Lugon Junior, Pedro Paulo Gomes Watts Rodrigues, Luiz Bevilacqua, Diego Campos Knupp, Joao Flavio Vieira Vasconcellos and Antonio Jose da Silva Neto.
Maintainer: Jader Lugon Junior <jlugonjr@gmail.com>
Diff between AdvDif4 versions 0.2.18 dated 2018-06-07 and 0.3.18 dated 2018-09-13
DESCRIPTION | 6 ++--- MD5 | 20 ++++++++++++++--- R/AdvDif4.R | 56 +++++++++++++++++++++++++------------------------- inst/doc/ENMC_1_Pdf.R |only inst/doc/ENMC_2_Pdf.R |only inst/doc/ENMC_3_Pdf.R |only inst/doc/ENMC_4_Pdf.R |only inst/doc/ENMC_5_Pdf.R |only inst/doc/ENMC_6_Pdf.R |only inst/doc/MAI_1_Pdf.R |only inst/doc/MAI_2_Pdf.R |only inst/doc/MAI_3_Pdf.R |only inst/doc/MAI_4_Pdf.R |only inst/doc/MAI_5_Pdf.R |only inst/doc/MAI_6_Pdf.R |only inst/doc/News.md | 7 +++++- man/AdvDif4.Rd | 2 - 17 files changed, 54 insertions(+), 37 deletions(-)