Wed, 07 Jul 2021

Package RJcluster updated to version 3.0.0 with previous version 2.5.0 dated 2021-04-06

Title: A Fast Clustering Algorithm for High Dimensional Data Based on the Gram Matrix Decomposition
Description: Clustering algorithm for high dimensional data. Assuming that P feature measurements on N objects are arranged in an N×P matrix X, this package provides clustering based on the left Gram matrix XX^T. To simulate test data, type "help('simulate_HD_data')" and to learn how to use the clustering algorithm, type "help('RJclust')". To cite this package, type 'citation("RJcluster")'.
Author: Shahina Rahman [aut], Valen E. Johnson [aut], Suhasini Subba Rao [aut], Rachael Shudde [aut, cre, trl]
Maintainer: Rachael Shudde <rachael.shudde@gmail.com>

Diff between RJcluster versions 2.5.0 dated 2021-04-06 and 3.0.0 dated 2021-07-07

 DESCRIPTION                         |   37 +++++++++-------
 MD5                                 |   30 +++++++------
 NAMESPACE                           |    3 +
 R/AlgorithmImplementation.R         |   46 ++++++++------------
 R/FUNC_RJ_calls.R                   |   55 ++++++++++++++++++++++++-
 R/FUNC_RJmean.R                     |   79 ++++++++++++++++++++++++++++++++++++
 R/zzz.R                             |only
 README.md                           |    2 
 build/partial.rdb                   |binary
 cleanup                             |    2 
 inst/doc/RJclust_Vignette.R         |    9 +---
 inst/doc/RJclust_Vignette.Rmd       |   11 ++---
 inst/doc/RJclust_Vignette.pdf       |binary
 man/RJclust.Rd                      |   15 +++---
 man/RJcluster-package.Rd            |    4 -
 src/FUNC_dmvnrm_rcpp-52fc8e17.o.tmp |only
 vignettes/RJclust_Vignette.Rmd      |   11 ++---
 17 files changed, 216 insertions(+), 88 deletions(-)

More information about RJcluster at CRAN
Permanent link

Package movecost updated to version 1.2 with previous version 1.1 dated 2021-06-19

Title: Calculation of Slope-Dependant Accumulated Cost Surface, Least-Cost Paths, and Least-Cost Corridors Related to Human Movement Across the Landscape
Description: Provides the facility to calculate non-isotropic accumulated cost surface, least-cost paths, and least-cost corridors using a number of human-movement-related cost functions that can be selected by the user. It just requires a Digital Terrain Model, a start location and (optionally) destination locations. See Alberti (2019) <doi:10.1016/j.softx.2019.100331>.
Author: Gianmarco Alberti [aut, cre]
Maintainer: Gianmarco Alberti <gianmarcoalberti@gmail.com>

Diff between movecost versions 1.1 dated 2021-06-19 and 1.2 dated 2021-07-07

 DESCRIPTION      |   12 ++--
 MD5              |   18 +++----
 NAMESPACE        |    5 +
 NEWS.md          |   14 +++--
 R/movebound.R    |only
 R/movecorr.R     |   49 ++++++++++++-------
 R/movecost.R     |  141 ++++++++++++++++++++++++++++++++++++++++---------------
 README.md        |   13 ++++-
 man/movebound.Rd |only
 man/movecorr.Rd  |    7 +-
 man/movecost.Rd  |   43 ++++++++++------
 11 files changed, 211 insertions(+), 91 deletions(-)

More information about movecost at CRAN
Permanent link

Package JBrowseR updated to version 0.8.1 with previous version 0.8.0 dated 2021-05-21

Title: An R Interface to the JBrowse 2 Genome Browser
Description: Provides an R interface to the JBrowse 2 genome browser. Enables embedding a JB2 genome browser in a Shiny app or R Markdown document. The browser can also be launched from an interactive R console. The browser can be loaded with a variety of common genomics data types, and can be used with a custom theme.
Author: Elliot Hershberg [aut, cre] (<https://orcid.org/0000-0003-2068-3366>), the JBrowse 2 Team [aut]
Maintainer: Elliot Hershberg <eahershberg@gmail.com>

Diff between JBrowseR versions 0.8.0 dated 2021-05-21 and 0.8.1 dated 2021-07-07

 DESCRIPTION                  |    6 
 MD5                          |    8 -
 NEWS.md                      |   13 +
 README.md                    |   14 ++
 inst/htmlwidgets/JBrowseR.js |  301 +++----------------------------------------
 5 files changed, 58 insertions(+), 284 deletions(-)

More information about JBrowseR at CRAN
Permanent link

Package ggfortify updated to version 0.4.12 with previous version 0.4.11 dated 2020-10-02

Title: Data Visualization Tools for Statistical Analysis Results
Description: Unified plotting tools for statistics commonly used, such as GLM, time series, PCA families, clustering and survival analysis. The package offers a single plotting interface for these analysis results and plots in a unified style using 'ggplot2'.
Author: Masaaki Horikoshi [aut], Yuan Tang [aut, cre] (<https://orcid.org/0000-0001-5243-233X>), Austin Dickey [ctb], Matthias Grenié [ctb], Ryan Thompson [ctb], Luciano Selzer [ctb], Dario Strbenac [ctb], Kirill Voronin [ctb], Damir Pulatov [ctb]
Maintainer: Yuan Tang <terrytangyuan@gmail.com>

Diff between ggfortify versions 0.4.11 dated 2020-10-02 and 0.4.12 dated 2021-07-07

 ggfortify-0.4.11/ggfortify/tests/testthat/Rplots.pdf    |only
 ggfortify-0.4.11/ggfortify/tests/testthat/test_lint.R   |only
 ggfortify-0.4.12/ggfortify/DESCRIPTION                  |   10 +-
 ggfortify-0.4.12/ggfortify/MD5                          |   69 +++++++---------
 ggfortify-0.4.12/ggfortify/NAMESPACE                    |    2 
 ggfortify-0.4.12/ggfortify/NEWS.md                      |    6 +
 ggfortify-0.4.12/ggfortify/R/aaa.R                      |only
 ggfortify-0.4.12/ggfortify/R/base_fortify_ts.R          |    5 -
 ggfortify-0.4.12/ggfortify/R/fortify_basis.R            |    9 +-
 ggfortify-0.4.12/ggfortify/R/fortify_changepoint.R      |    4 
 ggfortify-0.4.12/ggfortify/R/fortify_cluster.R          |    3 
 ggfortify-0.4.12/ggfortify/R/fortify_forecast.R         |    4 
 ggfortify-0.4.12/ggfortify/R/fortify_spatial.R          |    2 
 ggfortify-0.4.12/ggfortify/R/fortify_stats.R            |    6 -
 ggfortify-0.4.12/ggfortify/R/fortify_stats_density.R    |   10 +-
 ggfortify-0.4.12/ggfortify/R/fortify_stats_lm.R         |    6 -
 ggfortify-0.4.12/ggfortify/R/fortify_surv.R             |   12 +-
 ggfortify-0.4.12/ggfortify/R/fortify_vars.R             |    4 
 ggfortify-0.4.12/ggfortify/R/ggfortify.R                |    2 
 ggfortify-0.4.12/ggfortify/R/plotlib.R                  |   32 +++++--
 ggfortify-0.4.12/ggfortify/R/tslib.R                    |    4 
 ggfortify-0.4.12/ggfortify/R/util.R                     |    2 
 ggfortify-0.4.12/ggfortify/build/vignette.rds           |binary
 ggfortify-0.4.12/ggfortify/inst/CITATION                |    6 -
 ggfortify-0.4.12/ggfortify/inst/doc/basics.html         |   26 +++---
 ggfortify-0.4.12/ggfortify/inst/doc/plot_dist.html      |   10 +-
 ggfortify-0.4.12/ggfortify/inst/doc/plot_map.html       |   14 +--
 ggfortify-0.4.12/ggfortify/inst/doc/plot_pca.html       |   47 +++++-----
 ggfortify-0.4.12/ggfortify/inst/doc/plot_surv.html      |   12 +-
 ggfortify-0.4.12/ggfortify/inst/doc/plot_ts.html        |   64 +++++++-------
 ggfortify-0.4.12/ggfortify/man/geom_factory.Rd          |    4 
 ggfortify-0.4.12/ggfortify/man/ggbiplot.Rd              |    6 +
 ggfortify-0.4.12/ggfortify/man/ggmultiplot-class.Rd     |    6 -
 ggfortify-0.4.12/ggfortify/man/plot_label.Rd            |    5 -
 ggfortify-0.4.12/ggfortify/tests/test-all.R             |    1 
 ggfortify-0.4.12/ggfortify/tests/testthat/test-glmnet.R |    4 
 ggfortify-0.4.12/ggfortify/tests/testthat/test-util.R   |    2 
 37 files changed, 224 insertions(+), 175 deletions(-)

More information about ggfortify at CRAN
Permanent link

Package evalITR updated to version 0.2.1 with previous version 0.2.0 dated 2020-10-14

Title: Evaluating Individualized Treatment Rules
Description: Provides various statistical methods for evaluating Individualized Treatment Rules under randomized data. The provided metrics include Population Average Value (PAV), Population Average Prescription Effect (PAPE), Area Under Prescription Effect Curve (AUPEC). It also provides the tools to analyze Individualized Treatment Rules under budget constraints. Detailed reference in Imai and Li (2019) <arXiv:1905.05389>.
Author: Michael Lingzhi Li [aut, cre], Kosuke Imai [aut]
Maintainer: Michael Lingzhi Li <mlli@mit.edu>

Diff between evalITR versions 0.2.0 dated 2020-10-14 and 0.2.1 dated 2021-07-07

 DESCRIPTION                         |    8 ++++----
 MD5                                 |   14 +++++++-------
 NEWS.md                             |    4 ++++
 R/AUPEC.R                           |    5 ++---
 R/AUPECcv.R                         |   10 ++++++++--
 R/PAPDcv.R                          |    4 ++--
 R/PAPEcv.R                          |    2 +-
 tests/testthat/test_functionality.R |    2 +-
 8 files changed, 29 insertions(+), 20 deletions(-)

More information about evalITR at CRAN
Permanent link

Package MIIVsem updated to version 0.5.7 with previous version 0.5.6 dated 2021-06-10

Title: Model Implied Instrumental Variable (MIIV) Estimation of Structural Equation Models
Description: Functions for estimating structural equation models using instrumental variables.
Author: Zachary Fisher [aut, cre], Kenneth Bollen [aut], Kathleen Gates [aut], Mikko Rönkkö [aut]
Maintainer: Zachary Fisher <fish.zachary@gmail.com>

Diff between MIIVsem versions 0.5.6 dated 2021-06-10 and 0.5.7 dated 2021-07-07

 DESCRIPTION     |    6 +++---
 MD5             |    4 ++--
 R/print.miivs.R |    4 ++--
 3 files changed, 7 insertions(+), 7 deletions(-)

More information about MIIVsem at CRAN
Permanent link

Package gsw updated to version 1.0-6 with previous version 1.0-5 dated 2017-08-09

Title: Gibbs Sea Water Functions
Description: Provides an interface to the Gibbs 'SeaWater' ('TEOS-10') C library, version 3.05 (commit 'f7bfebf44f686034636facb09852f1d5760c27f5', dated 2021-03-27, available at <https://github.com/TEOS-10/GSW-C>, which stems from 'Matlab' and other code written by members of Working Group 127 of 'SCOR'/'IAPSO' (Scientific Committee on Oceanic Research / International Association for the Physical Sciences of the Oceans).
Author: Dan Kelley [aut, cre, cph] (<https://orcid.org/0000-0001-7808-5911>), Clark Richards [aut, cph] (<https://orcid.org/0000-0002-7833-206X>), WG127 SCOR/IAPSO [aut, cph] (Original 'Matlab' and derived code)
Maintainer: Dan Kelley <dan.kelley@dal.ca>

Diff between gsw versions 1.0-5 dated 2017-08-09 and 1.0-6 dated 2021-07-07

 gsw-1.0-5/gsw/NEWS                                                        |only
 gsw-1.0-5/gsw/vignettes/SSS_2.png                                         |only
 gsw-1.0-5/gsw/vignettes/TS_gsw.png                                        |only
 gsw-1.0-5/gsw/vignettes/TS_unesco.png                                     |only
 gsw-1.0-5/gsw/vignettes/salinity_comparison.png                           |only
 gsw-1.0-5/gsw/vignettes/temperature_comparison.png                        |only
 gsw-1.0-6/gsw/DESCRIPTION                                                 |   50 
 gsw-1.0-6/gsw/MD5                                                         |  344 
 gsw-1.0-6/gsw/NAMESPACE                                                   |    2 
 gsw-1.0-6/gsw/NEWS.md                                                     |only
 gsw-1.0-6/gsw/R/gsw.R                                                     | 1071 
 gsw-1.0-6/gsw/README.md                                                   |    3 
 gsw-1.0-6/gsw/build/vignette.rds                                          |binary
 gsw-1.0-6/gsw/data/saar.rda                                               |binary
 gsw-1.0-6/gsw/inst/WORDLIST                                               |only
 gsw-1.0-6/gsw/inst/doc/gsw.R                                              |   42 
 gsw-1.0-6/gsw/inst/doc/gsw.Rmd                                            |  199 
 gsw-1.0-6/gsw/inst/doc/gsw.html                                           |  348 
 gsw-1.0-6/gsw/man/gsw.Rd                                                  |    7 
 gsw-1.0-6/gsw/man/gsw_CT_first_derivatives.Rd                             |   41 
 gsw-1.0-6/gsw/man/gsw_CT_first_derivatives_wrt_t_exact.Rd                 |   46 
 gsw-1.0-6/gsw/man/gsw_CT_freezing.Rd                                      |   35 
 gsw-1.0-6/gsw/man/gsw_CT_freezing_first_derivatives.Rd                    |   41 
 gsw-1.0-6/gsw/man/gsw_CT_freezing_first_derivatives_poly.Rd               |   41 
 gsw-1.0-6/gsw/man/gsw_CT_freezing_poly.Rd                                 |   35 
 gsw-1.0-6/gsw/man/gsw_CT_from_enthalpy.Rd                                 |   73 
 gsw-1.0-6/gsw/man/gsw_CT_from_entropy.Rd                                  |   47 
 gsw-1.0-6/gsw/man/gsw_CT_from_pt.Rd                                       |   35 
 gsw-1.0-6/gsw/man/gsw_CT_from_rho.Rd                                      |   83 
 gsw-1.0-6/gsw/man/gsw_CT_from_t.Rd                                        |   35 
 gsw-1.0-6/gsw/man/gsw_CT_maxdensity.Rd                                    |   83 
 gsw-1.0-6/gsw/man/gsw_CT_second_derivatives.Rd                            |   43 
 gsw-1.0-6/gsw/man/gsw_C_from_SP.Rd                                        |   65 
 gsw-1.0-6/gsw/man/gsw_Fdelta.Rd                                           |   37 
 gsw-1.0-6/gsw/man/gsw_Helmholtz_energy_ice.Rd                             |   36 
 gsw-1.0-6/gsw/man/gsw_IPV_vs_fNsquared_ratio.Rd                           |   38 
 gsw-1.0-6/gsw/man/gsw_Nsquared.Rd                                         |   37 
 gsw-1.0-6/gsw/man/gsw_SAAR.Rd                                             |   43 
 gsw-1.0-6/gsw/man/gsw_SA_freezing_from_CT.Rd                              |   35 
 gsw-1.0-6/gsw/man/gsw_SA_freezing_from_CT_poly.Rd                         |   35 
 gsw-1.0-6/gsw/man/gsw_SA_freezing_from_t.Rd                               |   35 
 gsw-1.0-6/gsw/man/gsw_SA_freezing_from_t_poly.Rd                          |   35 
 gsw-1.0-6/gsw/man/gsw_SA_from_SP.Rd                                       |   60 
 gsw-1.0-6/gsw/man/gsw_SA_from_SP_Baltic.Rd                                |   60 
 gsw-1.0-6/gsw/man/gsw_SA_from_Sstar.Rd                                    |   64 
 gsw-1.0-6/gsw/man/gsw_SA_from_rho.Rd                                      |   83 
 gsw-1.0-6/gsw/man/gsw_SP_from_C.Rd                                        |   65 
 gsw-1.0-6/gsw/man/gsw_SP_from_SA.Rd                                       |   60 
 gsw-1.0-6/gsw/man/gsw_SP_from_SK.Rd                                       |   30 
 gsw-1.0-6/gsw/man/gsw_SP_from_SR.Rd                                       |   61 
 gsw-1.0-6/gsw/man/gsw_SP_from_Sstar.Rd                                    |   61 
 gsw-1.0-6/gsw/man/gsw_SR_from_SP.Rd                                       |   61 
 gsw-1.0-6/gsw/man/gsw_Sstar_from_SA.Rd                                    |   60 
 gsw-1.0-6/gsw/man/gsw_Sstar_from_SP.Rd                                    |   60 
 gsw-1.0-6/gsw/man/gsw_Turner_Rsubrho.Rd                                   |   41 
 gsw-1.0-6/gsw/man/gsw_adiabatic_lapse_rate_from_CT.Rd                     |   36 
 gsw-1.0-6/gsw/man/gsw_adiabatic_lapse_rate_ice.Rd                         |   35 
 gsw-1.0-6/gsw/man/gsw_alpha.Rd                                            |   83 
 gsw-1.0-6/gsw/man/gsw_alpha_on_beta.Rd                                    |   83 
 gsw-1.0-6/gsw/man/gsw_alpha_wrt_t_exact.Rd                                |   84 
 gsw-1.0-6/gsw/man/gsw_alpha_wrt_t_ice.Rd                                  |   83 
 gsw-1.0-6/gsw/man/gsw_beta.Rd                                             |   83 
 gsw-1.0-6/gsw/man/gsw_beta_const_t_exact.Rd                               |   82 
 gsw-1.0-6/gsw/man/gsw_cabbeling.Rd                                        |   35 
 gsw-1.0-6/gsw/man/gsw_chem_potential_water_ice.Rd                         |   39 
 gsw-1.0-6/gsw/man/gsw_chem_potential_water_t_exact.Rd                     |   39 
 gsw-1.0-6/gsw/man/gsw_cp_ice.Rd                                           |   35 
 gsw-1.0-6/gsw/man/gsw_cp_t_exact.Rd                                       |   35 
 gsw-1.0-6/gsw/man/gsw_deltaSA_from_SP.Rd                                  |   61 
 gsw-1.0-6/gsw/man/gsw_dilution_coefficient_t_exact.Rd                     |   35 
 gsw-1.0-6/gsw/man/gsw_dynamic_enthalpy.Rd                                 |   73 
 gsw-1.0-6/gsw/man/gsw_enthalpy.Rd                                         |   73 
 gsw-1.0-6/gsw/man/gsw_enthalpy_CT_exact.Rd                                |   75 
 gsw-1.0-6/gsw/man/gsw_enthalpy_diff.Rd                                    |   73 
 gsw-1.0-6/gsw/man/gsw_enthalpy_first_derivatives.Rd                       |   77 
 gsw-1.0-6/gsw/man/gsw_enthalpy_first_derivatives_CT_exact.Rd              |   77 
 gsw-1.0-6/gsw/man/gsw_enthalpy_ice.Rd                                     |   73 
 gsw-1.0-6/gsw/man/gsw_enthalpy_second_derivatives.Rd                      |   43 
 gsw-1.0-6/gsw/man/gsw_enthalpy_second_derivatives_CT_exact.Rd             |   43 
 gsw-1.0-6/gsw/man/gsw_enthalpy_t_exact.Rd                                 |   73 
 gsw-1.0-6/gsw/man/gsw_entropy_first_derivatives.Rd                        |   51 
 gsw-1.0-6/gsw/man/gsw_entropy_from_pt.Rd                                  |   47 
 gsw-1.0-6/gsw/man/gsw_entropy_from_t.Rd                                   |   47 
 gsw-1.0-6/gsw/man/gsw_entropy_ice.Rd                                      |   47 
 gsw-1.0-6/gsw/man/gsw_entropy_second_derivatives.Rd                       |   50 
 gsw-1.0-6/gsw/man/gsw_frazil_properties.Rd                                |   43 
 gsw-1.0-6/gsw/man/gsw_frazil_properties_potential.Rd                      |   81 
 gsw-1.0-6/gsw/man/gsw_frazil_properties_potential_poly.Rd                 |   81 
 gsw-1.0-6/gsw/man/gsw_frazil_ratios_adiabatic.Rd                          |   46 
 gsw-1.0-6/gsw/man/gsw_frazil_ratios_adiabatic_poly.Rd                     |   46 
 gsw-1.0-6/gsw/man/gsw_geo_strf_dyn_height.Rd                              |   54 
 gsw-1.0-6/gsw/man/gsw_geo_strf_dyn_height_1.Rd                            |only
 gsw-1.0-6/gsw/man/gsw_geo_strf_dyn_height_pc.Rd                           |   41 
 gsw-1.0-6/gsw/man/gsw_gibbs.Rd                                            |   31 
 gsw-1.0-6/gsw/man/gsw_gibbs_ice.Rd                                        |   31 
 gsw-1.0-6/gsw/man/gsw_grav.Rd                                             |   35 
 gsw-1.0-6/gsw/man/gsw_ice_fraction_to_freeze_seawater.Rd                  |   43 
 gsw-1.0-6/gsw/man/gsw_internal_energy.Rd                                  |   35 
 gsw-1.0-6/gsw/man/gsw_internal_energy_ice.Rd                              |   35 
 gsw-1.0-6/gsw/man/gsw_kappa.Rd                                            |   43 
 gsw-1.0-6/gsw/man/gsw_kappa_const_t_ice.Rd                                |   42 
 gsw-1.0-6/gsw/man/gsw_kappa_ice.Rd                                        |   42 
 gsw-1.0-6/gsw/man/gsw_kappa_t_exact.Rd                                    |   43 
 gsw-1.0-6/gsw/man/gsw_latentheat_evap_CT.Rd                               |   41 
 gsw-1.0-6/gsw/man/gsw_latentheat_evap_t.Rd                                |   41 
 gsw-1.0-6/gsw/man/gsw_latentheat_melting.Rd                               |   41 
 gsw-1.0-6/gsw/man/gsw_melting_ice_SA_CT_ratio.Rd                          |   35 
 gsw-1.0-6/gsw/man/gsw_melting_ice_SA_CT_ratio_poly.Rd                     |   35 
 gsw-1.0-6/gsw/man/gsw_melting_ice_equilibrium_SA_CT_ratio.Rd              |   35 
 gsw-1.0-6/gsw/man/gsw_melting_ice_equilibrium_SA_CT_ratio_poly.Rd         |   35 
 gsw-1.0-6/gsw/man/gsw_melting_ice_into_seawater.Rd                        |   41 
 gsw-1.0-6/gsw/man/gsw_melting_seaice_into_seawater.Rd                     |   39 
 gsw-1.0-6/gsw/man/gsw_p_from_z.Rd                                         |   57 
 gsw-1.0-6/gsw/man/gsw_pot_enthalpy_from_pt_ice.Rd                         |   73 
 gsw-1.0-6/gsw/man/gsw_pot_enthalpy_from_pt_ice_poly.Rd                    |   73 
 gsw-1.0-6/gsw/man/gsw_pot_enthalpy_ice_freezing.Rd                        |   73 
 gsw-1.0-6/gsw/man/gsw_pot_enthalpy_ice_freezing_first_derivatives.Rd      |   39 
 gsw-1.0-6/gsw/man/gsw_pot_enthalpy_ice_freezing_first_derivatives_poly.Rd |   39 
 gsw-1.0-6/gsw/man/gsw_pot_enthalpy_ice_freezing_poly.Rd                   |   73 
 gsw-1.0-6/gsw/man/gsw_pot_rho_t_exact.Rd                                  |   82 
 gsw-1.0-6/gsw/man/gsw_pressure_coefficient_ice.Rd                         |   35 
 gsw-1.0-6/gsw/man/gsw_pressure_freezing_CT.Rd                             |   35 
 gsw-1.0-6/gsw/man/gsw_pt0_from_t.Rd                                       |   35 
 gsw-1.0-6/gsw/man/gsw_pt0_from_t_ice.Rd                                   |   35 
 gsw-1.0-6/gsw/man/gsw_pt_first_derivatives.Rd                             |   39 
 gsw-1.0-6/gsw/man/gsw_pt_from_CT.Rd                                       |   35 
 gsw-1.0-6/gsw/man/gsw_pt_from_entropy.Rd                                  |   47 
 gsw-1.0-6/gsw/man/gsw_pt_from_pot_enthalpy_ice.Rd                         |   73 
 gsw-1.0-6/gsw/man/gsw_pt_from_pot_enthalpy_ice_poly.Rd                    |   73 
 gsw-1.0-6/gsw/man/gsw_pt_from_t.Rd                                        |   35 
 gsw-1.0-6/gsw/man/gsw_pt_from_t_ice.Rd                                    |   35 
 gsw-1.0-6/gsw/man/gsw_pt_second_derivatives.Rd                            |   46 
 gsw-1.0-6/gsw/man/gsw_rho.Rd                                              |   84 
 gsw-1.0-6/gsw/man/gsw_rho_alpha_beta.Rd                                   |   91 
 gsw-1.0-6/gsw/man/gsw_rho_first_derivatives.Rd                            |   91 
 gsw-1.0-6/gsw/man/gsw_rho_first_derivatives_wrt_enthalpy.Rd               |   89 
 gsw-1.0-6/gsw/man/gsw_rho_ice.Rd                                          |   84 
 gsw-1.0-6/gsw/man/gsw_rho_second_derivatives.Rd                           |   51 
 gsw-1.0-6/gsw/man/gsw_rho_second_derivatives_wrt_enthalpy.Rd              |   55 
 gsw-1.0-6/gsw/man/gsw_rho_t_exact.Rd                                      |   84 
 gsw-1.0-6/gsw/man/gsw_seaice_fraction_to_freeze_seawater.Rd               |   43 
 gsw-1.0-6/gsw/man/gsw_sigma0.Rd                                           |   84 
 gsw-1.0-6/gsw/man/gsw_sigma1.Rd                                           |   84 
 gsw-1.0-6/gsw/man/gsw_sigma2.Rd                                           |   84 
 gsw-1.0-6/gsw/man/gsw_sigma3.Rd                                           |   84 
 gsw-1.0-6/gsw/man/gsw_sigma4.Rd                                           |   84 
 gsw-1.0-6/gsw/man/gsw_sound_speed.Rd                                      |   41 
 gsw-1.0-6/gsw/man/gsw_sound_speed_ice.Rd                                  |   41 
 gsw-1.0-6/gsw/man/gsw_sound_speed_t_exact.Rd                              |   41 
 gsw-1.0-6/gsw/man/gsw_specvol.Rd                                          |   84 
 gsw-1.0-6/gsw/man/gsw_specvol_alpha_beta.Rd                               |   91 
 gsw-1.0-6/gsw/man/gsw_specvol_anom_standard.Rd                            |   83 
 gsw-1.0-6/gsw/man/gsw_specvol_first_derivatives.Rd                        |   84 
 gsw-1.0-6/gsw/man/gsw_specvol_first_derivatives_wrt_enthalpy.Rd           |   79 
 gsw-1.0-6/gsw/man/gsw_specvol_ice.Rd                                      |   83 
 gsw-1.0-6/gsw/man/gsw_specvol_second_derivatives.Rd                       |   56 
 gsw-1.0-6/gsw/man/gsw_specvol_second_derivatives_wrt_enthalpy.Rd          |   53 
 gsw-1.0-6/gsw/man/gsw_specvol_t_exact.Rd                                  |   82 
 gsw-1.0-6/gsw/man/gsw_spiciness0.Rd                                       |   41 
 gsw-1.0-6/gsw/man/gsw_spiciness1.Rd                                       |   40 
 gsw-1.0-6/gsw/man/gsw_spiciness2.Rd                                       |   40 
 gsw-1.0-6/gsw/man/gsw_t_deriv_chem_potential_water_t_exact.Rd             |   35 
 gsw-1.0-6/gsw/man/gsw_t_freezing.Rd                                       |   35 
 gsw-1.0-6/gsw/man/gsw_t_freezing_first_derivatives.Rd                     |   41 
 gsw-1.0-6/gsw/man/gsw_t_freezing_first_derivatives_poly.Rd                |   48 
 gsw-1.0-6/gsw/man/gsw_t_from_CT.Rd                                        |   35 
 gsw-1.0-6/gsw/man/gsw_t_from_pt0_ice.Rd                                   |   35 
 gsw-1.0-6/gsw/man/gsw_thermobaric.Rd                                      |   35 
 gsw-1.0-6/gsw/man/gsw_z_from_p.Rd                                         |   57 
 gsw-1.0-6/gsw/src/gsw_internal_const.h                                    |  834 
 gsw-1.0-6/gsw/src/gsw_oceanographic_toolbox.c                             |12875 +++++-----
 gsw-1.0-6/gsw/src/gsw_saar.c                                              |  339 
 gsw-1.0-6/gsw/src/gswteos-10.h                                            |  193 
 gsw-1.0-6/gsw/src/wrappers.c                                              |   16 
 gsw-1.0-6/gsw/vignettes/fig01.png                                         |only
 gsw-1.0-6/gsw/vignettes/fig02.png                                         |only
 gsw-1.0-6/gsw/vignettes/fig03.png                                         |only
 gsw-1.0-6/gsw/vignettes/fig04.png                                         |only
 gsw-1.0-6/gsw/vignettes/gsw.Rmd                                           |  199 
 gsw-1.0-6/gsw/vignettes/gsw.bib                                           |only
 180 files changed, 13572 insertions(+), 11019 deletions(-)

More information about gsw at CRAN
Permanent link

Package FCPS updated to version 1.3.0 with previous version 1.2.7 dated 2021-01-15

Title: Fundamental Clustering Problems Suite
Description: Over sixty clustering algorithms are provided in this package with consistent input and output, which enables the user to try out algorithms swiftly. Additionally, 26 statistical approaches for the estimation of the number of clusters as well as the mirrored density plot (MD-plot) of clusterability are implemented. The packages is published in Thrun, M.C., Stier Q.: "Fundamental Clustering Algorithms Suite" (2021), SoftwareX, <DOI:10.1016/j.softx.2020.100642>. Moreover, the fundamental clustering problems suite (FCPS) offers a variety of clustering challenges any algorithm should handle when facing real world data, see Thrun, M.C., Ultsch A.: "Clustering Benchmark Datasets Exploiting the Fundamental Clustering Problems" (2020), Data in Brief, <DOI:10.1016/j.dib.2020.105501>.
Author: Michael Thrun [aut, cre, cph] (<https://orcid.org/0000-0001-9542-5543>), Peter Nahrgang [ctr, ctb], Felix Pape [ctr, ctb], Vasyl Pihur [ctb], Guy Brock [ctb], Susmita Datta [ctb], Somnath Datta [ctb], Luis Winckelmann [com], Alfred Ultsch [dtc, ctb], Quirin Stier [ctb, rev]
Maintainer: Michael Thrun <m.thrun@gmx.net>

Diff between FCPS versions 1.2.7 dated 2021-01-15 and 1.3.0 dated 2021-07-07

 FCPS-1.2.7/FCPS/R/CrossEntropyClustering.R                |only
 FCPS-1.2.7/FCPS/man/CrossEntropyClustering.Rd             |only
 FCPS-1.3.0/FCPS/DESCRIPTION                               |   16 
 FCPS-1.3.0/FCPS/MD5                                       |   54 
 FCPS-1.3.0/FCPS/NAMESPACE                                 |  188 
 FCPS-1.3.0/FCPS/R/ClusterCount.R                          |   99 
 FCPS-1.3.0/FCPS/R/ClusterDaviesBouldinIndex.R             |only
 FCPS-1.3.0/FCPS/R/ClusterDunnIndex.R                      |only
 FCPS-1.3.0/FCPS/R/ClusterShannonInfo.R                    |only
 FCPS-1.3.0/FCPS/R/HDDClustering.R                         |only
 FCPS-1.3.0/FCPS/R/HierarchicalClustering.R                |    5 
 FCPS-1.3.0/FCPS/R/MoGclustering.R                         |  121 
 FCPS-1.3.0/FCPS/R/ModelBasedVarSelClustering.R            |only
 FCPS-1.3.0/FCPS/R/SparseClustering.R                      |only
 FCPS-1.3.0/FCPS/R/kmeansClustering.R                      |   10 
 FCPS-1.3.0/FCPS/build/partial.rdb                         |binary
 FCPS-1.3.0/FCPS/build/vignette.rds                        |binary
 FCPS-1.3.0/FCPS/inst/doc/FCPS.R                           |  208 
 FCPS-1.3.0/FCPS/inst/doc/FCPS.html                        | 4814 +++++++-------
 FCPS-1.3.0/FCPS/man/AutomaticProjectionBasedClustering.Rd |  226 
 FCPS-1.3.0/FCPS/man/ClusterCount.Rd                       |   63 
 FCPS-1.3.0/FCPS/man/ClusterDaviesBouldinIndex.Rd          |only
 FCPS-1.3.0/FCPS/man/ClusterDistances.Rd                   |   10 
 FCPS-1.3.0/FCPS/man/ClusterDunnIndex.Rd                   |only
 FCPS-1.3.0/FCPS/man/ClusterInterDistances.Rd              |   11 
 FCPS-1.3.0/FCPS/man/ClusterShannonInfo.Rd                 |only
 FCPS-1.3.0/FCPS/man/FCPS-package.Rd                       |    3 
 FCPS-1.3.0/FCPS/man/HDDClustering.Rd                      |only
 FCPS-1.3.0/FCPS/man/HierarchicalClusterData.Rd            |   10 
 FCPS-1.3.0/FCPS/man/HierarchicalClusterDists.Rd           |   15 
 FCPS-1.3.0/FCPS/man/HierarchicalClustering.Rd             |  128 
 FCPS-1.3.0/FCPS/man/MoGclustering.Rd                      |  129 
 FCPS-1.3.0/FCPS/man/ModelBasedVarSelClustering.Rd         |only
 FCPS-1.3.0/FCPS/man/SparseClustering.Rd                   |only
 FCPS-1.3.0/FCPS/man/kmeansClustering.Rd                   |    8 
 35 files changed, 3153 insertions(+), 2965 deletions(-)

More information about FCPS at CRAN
Permanent link

Package dragon updated to version 1.2.0 with previous version 1.1.0 dated 2020-12-08

Title: Deep Time Redox Analysis of the Geobiology Ontology Network
Description: Create, visualize, manipulate, and analyze bipartite mineral-chemistry networks for set of focal element(s) across deep-time on Earth. The method is described in Spielman and Moore (2020) <doi:10.3389/feart.2020.585087>.
Author: Stephanie J. Spielman [aut, cre] (<https://orcid.org/0000-0002-9090-4788>)
Maintainer: Stephanie J. Spielman <spielman@rowan.edu>

Diff between dragon versions 1.1.0 dated 2020-12-08 and 1.2.0 dated 2021-07-07

 dragon-1.1.0/dragon/inst/testdata                             |only
 dragon-1.2.0/dragon/DESCRIPTION                               |   11 
 dragon-1.2.0/dragon/LICENSE                                   |only
 dragon-1.2.0/dragon/MD5                                       |   52 -
 dragon-1.2.0/dragon/NAMESPACE                                 |    1 
 dragon-1.2.0/dragon/R/app_server.R                            |   41 -
 dragon-1.2.0/dragon/R/app_ui.R                                |   11 
 dragon-1.2.0/dragon/R/fct_build-network.R                     |   58 -
 dragon-1.2.0/dragon/R/fct_build-shiny-tables.R                |   19 
 dragon-1.2.0/dragon/R/fct_timeline.R                          |    3 
 dragon-1.2.0/dragon/R/mod_choose-color-palette.R              |   25 
 dragon-1.2.0/dragon/R/mod_choose-custom-element-colors.R      |   22 
 dragon-1.2.0/dragon/R/sysdata.rda                             |binary
 dragon-1.2.0/dragon/R/utils_definitions.R                     |   77 --
 dragon-1.2.0/dragon/R/utils_globals.R                         |    2 
 dragon-1.2.0/dragon/R/utils_names.R                           |    8 
 dragon-1.2.0/dragon/R/utils_ui-choices.R                      |    9 
 dragon-1.2.0/dragon/README.md                                 |   20 
 dragon-1.2.0/dragon/build/vignette.rds                        |binary
 dragon-1.2.0/dragon/inst/doc/dragon.html                      |  353 +---------
 dragon-1.2.0/dragon/tests/testthat/edges_by_redox.csv.zip     |binary
 dragon-1.2.0/dragon/tests/testthat/locality_info.csv.zip      |binary
 dragon-1.2.0/dragon/tests/testthat/nodes_by_redox.csv.zip     |binary
 dragon-1.2.0/dragon/tests/testthat/styled_edges.csv.zip       |binary
 dragon-1.2.0/dragon/tests/testthat/styled_nodes.csv.zip       |binary
 dragon-1.2.0/dragon/tests/testthat/test_build-shiny-tables.R  |    2 
 dragon-1.2.0/dragon/tests/testthat/test_utils.R               |    6 
 dragon-1.2.0/dragon/tests/testthat/true_mineral_nodes.csv.zip |binary
 28 files changed, 239 insertions(+), 481 deletions(-)

More information about dragon at CRAN
Permanent link

Package weed updated to version 1.1.1 with previous version 1.0.6 dated 2021-03-22

Title: Wrangler for Emergency Events Database
Description: Makes research involving EMDAT and related datasets easier. These Datasets are manually filled and have several formatting and compatibility issues. Weed aims to resolve these with its functions.
Author: Ram Kripa [aut, cre]
Maintainer: Ram Kripa <ram.m.kripa@berkeley.edu>

Diff between weed versions 1.0.6 dated 2021-03-22 and 1.1.1 dated 2021-07-07

 DESCRIPTION                   |    7 +++----
 MD5                           |   26 ++++++++++++++------------
 NAMESPACE                     |    1 +
 R/geocode.R                   |    4 +---
 R/geocode_batches.R           |only
 R/percent_located_disasters.R |    3 ++-
 R/percent_located_locations.R |    3 ++-
 R/split_locations.R           |    8 ++++++--
 README.md                     |   20 ++++++++++----------
 man/figures/README-ex4-1.png  |binary
 man/figures/README-ex6-1.png  |binary
 man/figures/README-ex62-1.png |binary
 man/geocode.Rd                |    4 +---
 man/geocode_batches.Rd        |only
 man/split_locations.Rd        |    2 +-
 15 files changed, 41 insertions(+), 37 deletions(-)

More information about weed at CRAN
Permanent link

Package semTools updated to version 0.5-5 with previous version 0.5-4 dated 2021-01-11

Title: Useful Tools for Structural Equation Modeling
Description: Provides tools for structural equation modeling, many of which extend the 'lavaan' package; for example, to pool results from multiple imputations, probe latent interactions, or test measurement invariance.
Author: Terrence D. Jorgensen [aut, cre] (<https://orcid.org/0000-0001-5111-6773>), Sunthud Pornprasertmanit [aut], Alexander M. Schoemann [aut] (<https://orcid.org/0000-0002-8479-8798>), Yves Rosseel [aut] (<https://orcid.org/0000-0002-4129-4477>), Patrick Miller [ctb], Corbin Quick [ctb], Mauricio Garnier-Villarreal [ctb] (<https://orcid.org/0000-0002-2951-6647>), James Selig [ctb], Aaron Boulton [ctb], Kristopher Preacher [ctb], Donna Coffman [ctb], Mijke Rhemtulla [ctb] (<https://orcid.org/0000-0003-2572-2424>), Alexander Robitzsch [ctb] (<https://orcid.org/0000-0002-8226-3132>), Craig Enders [ctb], Ruben Arslan [ctb] (<https://orcid.org/0000-0002-6670-5658>), Bell Clinton [ctb], Pavel Panko [ctb], Edgar Merkle [ctb] (<https://orcid.org/0000-0001-7158-0653>), Steven Chesnut [ctb], Jarrett Byrnes [ctb], Jason D. Rights [ctb], Ylenio Longo [ctb], Maxwell Mansolf [ctb] (<https://orcid.org/0000-0001-6861-8657>), Mattan S. Ben-Shachar [ctb] (<https://orcid.org/0000-0002-4287-4801>), Mikko Rönkkö [ctb] (<https://orcid.org/0000-0001-7988-7609>), Andrew R. Johnson [ctb] (<https://orcid.org/0000-0001-7000-8065>)
Maintainer: Terrence D. Jorgensen <TJorgensen314@gmail.com>

Diff between semTools versions 0.5-4 dated 2021-01-11 and 0.5-5 dated 2021-07-07

 semTools-0.5-4/semTools/R/monteCarloMed.R              |only
 semTools-0.5-4/semTools/man/monteCarloMed.Rd           |only
 semTools-0.5-5/semTools/DESCRIPTION                    |   14 
 semTools-0.5-5/semTools/MD5                            |   68 +
 semTools-0.5-5/semTools/NAMESPACE                      |    6 
 semTools-0.5-5/semTools/NEWS.md                        |   29 
 semTools-0.5-5/semTools/R/compareFit.R                 |  204 ++++-
 semTools-0.5-5/semTools/R/dataDiagnosis.R              |   20 
 semTools-0.5-5/semTools/R/fitIndices.R                 |    4 
 semTools-0.5-5/semTools/R/measEq.R                     |   10 
 semTools-0.5-5/semTools/R/monteCarloCI.R               |only
 semTools-0.5-5/semTools/R/ordMoments.R                 |only
 semTools-0.5-5/semTools/R/permuteMeasEq.R              |   26 
 semTools-0.5-5/semTools/R/plausibleValues.R            |   44 +
 semTools-0.5-5/semTools/R/powerAnalysisRMSEA.R         |   11 
 semTools-0.5-5/semTools/R/powerAnalysisSS.R            |   99 +-
 semTools-0.5-5/semTools/R/probeInteraction.R           |  584 +++++++++--------
 semTools-0.5-5/semTools/R/reliability.R                |  495 +++++++++++---
 semTools-0.5-5/semTools/R/singleParamTest.R            |  166 ++--
 semTools-0.5-5/semTools/build/partial.rdb              |binary
 semTools-0.5-5/semTools/build/vignette.rds             |binary
 semTools-0.5-5/semTools/inst/doc/partialInvariance.pdf |binary
 semTools-0.5-5/semTools/man/FitDiff-class.Rd           |   30 
 semTools-0.5-5/semTools/man/SSpower.Rd                 |   87 +-
 semTools-0.5-5/semTools/man/compareFit.Rd              |   56 +
 semTools-0.5-5/semTools/man/findRMSEApower.Rd          |    9 
 semTools-0.5-5/semTools/man/kurtosis.Rd                |    7 
 semTools-0.5-5/semTools/man/lrv2ord.Rd                 |only
 semTools-0.5-5/semTools/man/monteCarloCI.Rd            |only
 semTools-0.5-5/semTools/man/plausibleValues.Rd         |   42 +
 semTools-0.5-5/semTools/man/plotProbe.Rd               |   14 
 semTools-0.5-5/semTools/man/probe2WayMC.Rd             |   43 -
 semTools-0.5-5/semTools/man/probe2WayRC.Rd             |   41 -
 semTools-0.5-5/semTools/man/probe3WayMC.Rd             |   54 -
 semTools-0.5-5/semTools/man/probe3WayRC.Rd             |   54 -
 semTools-0.5-5/semTools/man/reliability.Rd             |  127 ++-
 semTools-0.5-5/semTools/man/singleParamTest.Rd         |   14 
 semTools-0.5-5/semTools/man/skew.Rd                    |   13 
 38 files changed, 1530 insertions(+), 841 deletions(-)

More information about semTools at CRAN
Permanent link

Package incidence2 updated to version 1.2.0 with previous version 1.1 dated 2021-05-29

Title: Compute, Handle and Plot Incidence of Dated Events
Description: Provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class 'incidence2' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis (<https://www.reconverse.org>).
Author: Tim Taylor [aut, cre] (<https://orcid.org/0000-0002-8587-7113>), Thibaut Jombart [ctb], Zhian N. Kamvar [ctb] (<https://orcid.org/0000-0003-1458-7108>)
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>

Diff between incidence2 versions 1.1 dated 2021-05-29 and 1.2.0 dated 2021-07-07

 incidence2-1.1/incidence2/man/as.data.frame.incidence2.Rd             |only
 incidence2-1.1/incidence2/man/cumulate.Rd                             |only
 incidence2-1.1/incidence2/man/print.incidence2.Rd                     |only
 incidence2-1.1/incidence2/man/summary.incidence2.Rd                   |only
 incidence2-1.1/incidence2/tests/testthat/_snaps/period.new.md         |only
 incidence2-1.2.0/incidence2/DESCRIPTION                               |   14 
 incidence2-1.2.0/incidence2/MD5                                       |   92 +-
 incidence2-1.2.0/incidence2/NAMESPACE                                 |   52 +
 incidence2-1.2.0/incidence2/NEWS.md                                   |   24 
 incidence2-1.2.0/incidence2/R/accessors.R                             |   26 
 incidence2-1.2.0/incidence2/R/build_incidence.R                       |only
 incidence2-1.2.0/incidence2/R/complete_counts.R                       |    4 
 incidence2-1.2.0/incidence2/R/conversion.R                            |    6 
 incidence2-1.2.0/incidence2/R/cumulate.R                              |   65 --
 incidence2-1.2.0/incidence2/R/data.R                                  |only
 incidence2-1.2.0/incidence2/R/dplyr.R                                 |    8 
 incidence2-1.2.0/incidence2/R/incidence.R                             |  238 +------
 incidence2-1.2.0/incidence2/R/incidence2-package.R                    |   11 
 incidence2-1.2.0/incidence2/R/keep.R                                  |    4 
 incidence2-1.2.0/incidence2/R/make_grate.R                            |    5 
 incidence2-1.2.0/incidence2/R/new_incidence.R                         |only
 incidence2-1.2.0/incidence2/R/plot.R                                  |   79 +-
 incidence2-1.2.0/incidence2/R/print.R                                 |  105 +--
 incidence2-1.2.0/incidence2/R/regroup.R                               |   36 -
 incidence2-1.2.0/incidence2/R/summary.R                               |  112 +--
 incidence2-1.2.0/incidence2/R/zzz.R                                   |    4 
 incidence2-1.2.0/incidence2/build/vignette.rds                        |binary
 incidence2-1.2.0/incidence2/data                                      |only
 incidence2-1.2.0/incidence2/inst/doc/Introduction.Rmd                 |   28 
 incidence2-1.2.0/incidence2/inst/doc/Introduction.html                |   71 +-
 incidence2-1.2.0/incidence2/inst/doc/alternative_date_groupings.R     |only
 incidence2-1.2.0/incidence2/inst/doc/alternative_date_groupings.Rmd   |only
 incidence2-1.2.0/incidence2/inst/doc/alternative_date_groupings.html  |only
 incidence2-1.2.0/incidence2/inst/doc/customizing_incidence_plots.Rmd  |   22 
 incidence2-1.2.0/incidence2/inst/doc/customizing_incidence_plots.html |   25 
 incidence2-1.2.0/incidence2/inst/doc/handling_incidence_objects.Rmd   |    8 
 incidence2-1.2.0/incidence2/inst/doc/handling_incidence_objects.html  |  116 +--
 incidence2-1.2.0/incidence2/man/accessors.Rd                          |   24 
 incidence2-1.2.0/incidence2/man/as.data.frame.incidence_df.Rd         |only
 incidence2-1.2.0/incidence2/man/as_tibble.Rd                          |    8 
 incidence2-1.2.0/incidence2/man/build_incidence.Rd                    |only
 incidence2-1.2.0/incidence2/man/covidregionaldataUK.Rd                |only
 incidence2-1.2.0/incidence2/man/cumulate-deprecated.Rd                |only
 incidence2-1.2.0/incidence2/man/incidence.Rd                          |   12 
 incidence2-1.2.0/incidence2/man/keep.Rd                               |    8 
 incidence2-1.2.0/incidence2/man/new_incidence.Rd                      |only
 incidence2-1.2.0/incidence2/man/print_incidence.Rd                    |only
 incidence2-1.2.0/incidence2/man/summary.incidence_df.Rd               |only
 incidence2-1.2.0/incidence2/tests/testthat/_snaps/incidence.md        |  310 +++-------
 incidence2-1.2.0/incidence2/tests/testthat/_snaps/plots/day.png       |binary
 incidence2-1.2.0/incidence2/tests/testthat/test-cumulate.R            |   31 -
 incidence2-1.2.0/incidence2/tests/testthat/test-incidence.R           |   15 
 incidence2-1.2.0/incidence2/tests/testthat/test-regroup.R             |    2 
 incidence2-1.2.0/incidence2/vignettes/Introduction.Rmd                |   28 
 incidence2-1.2.0/incidence2/vignettes/alternative_date_groupings.Rmd  |only
 incidence2-1.2.0/incidence2/vignettes/customizing_incidence_plots.Rmd |   22 
 incidence2-1.2.0/incidence2/vignettes/handling_incidence_objects.Rmd  |    8 
 57 files changed, 668 insertions(+), 955 deletions(-)

More information about incidence2 at CRAN
Permanent link

New package emdi with initial version 2.1.0
Package: emdi
Title: Estimating and Mapping Disaggregated Indicators
Version: 2.1.0
Date: 2021-07-07
Authors@R: c(person("Sylvia", "Harmening", role="aut", email = "sylvia.harmening@fu-berlin.de"), person("Ann-Kristin", "Kreutzmann", role="aut", email="ann-kristin.kreutzmann@fu-berlin.de"), person("Soeren", "Pannier", role=c("aut", "cre"), email="soeren.pannier@fu-berlin.de"), person("Felix", "Skarke", role=("aut"), email="f.skarke@fu-berlin.de"), person("Natalia", "Rojas-Perilla", role="aut", email = "natalia.rojas@fu-berlin.de"), person("Nicola", "Salvati", role="aut", email = "nicola.salvati@unipi.it"), person("Timo", "Schmid", role="aut", email = "timo.schmid@fu-berlin.de"), person("Matthias", "Templ", role="aut", email = "templ@statistik.tuwien.ac.at"), person("Nikos", "Tzavidis", role="aut", email = "N.TZAVIDIS@soton.ac.uk"), person("Nora", "Würz", role="aut", email = "nora.wuerz@fu-berlin.de"))
Description: Functions that support estimating, assessing and mapping regional disaggregated indicators. So far, estimation methods comprise direct estimation, the model-based unit-level approach Empirical Best Prediction (see "Small area estimation of poverty indicators" by Molina and Rao (2010) <doi:10.1002/cjs.10051>), the area-level model (see "Estimates of income for small places: An application of James-Stein procedures to Census Data" by Fay and Herriot (1979) <doi:10.1080/01621459.1979.10482505>) and various extensions of it (adjusted variance estimation methods, log and arcsin transformation, spatial, robust and measurement error models), as well as their precision estimates. The assessment of the used model is supported by a summary and diagnostic plots. For a suitable presentation of estimates, map plots can be easily created. Furthermore, results can easily be exported to excel. For a detailed description of the package and the methods used see "The R Package emdi for Estimating and Mapping Regionally Disaggregated Indicators" by Kreutzmann et al. (2019) <doi:10.18637/jss.v091.i07> and the second package vignette "A Framework for Producing Small Area Estimates Based on Area-Level Models in {R}".
Depends: R (>= 3.5.0)
License: GPL-2
URL: https://github.com/SoerenPannier/emdi
LazyData: true
Encoding: UTF-8
Copyright: inst/COPYRIGHTS
Imports: nlme, moments, ggplot2, MuMIn, gridExtra, openxlsx, reshape2, stats, stringr, parallelMap, HLMdiag, parallel, boot, MASS, readODS, formula.tools, saeRobust, spdep
Suggests: testthat, R.rsp, simFrame, laeken, rgeos, maptools, graphics
VignetteBuilder: R.rsp
NeedsCompilation: no
Packaged: 2021-07-07 10:35:53 UTC; span
Author: Sylvia Harmening [aut], Ann-Kristin Kreutzmann [aut], Soeren Pannier [aut, cre], Felix Skarke [aut], Natalia Rojas-Perilla [aut], Nicola Salvati [aut], Timo Schmid [aut], Matthias Templ [aut], Nikos Tzavidis [aut], Nora Würz [aut]
Maintainer: Soeren Pannier <soeren.pannier@fu-berlin.de>
Repository: CRAN
Date/Publication: 2021-07-07 16:20:05 UTC

More information about emdi at CRAN
Permanent link

Package broom.mixed updated to version 0.2.7 with previous version 0.2.6 dated 2020-05-17

Title: Tidying Methods for Mixed Models
Description: Convert fitted objects from various R mixed-model packages into tidy data frames along the lines of the 'broom' package. The package provides three S3 generics for each model: tidy(), which summarizes a model's statistical findings such as coefficients of a regression; augment(), which adds columns to the original data such as predictions, residuals and cluster assignments; and glance(), which provides a one-row summary of model-level statistics.
Author: Ben Bolker [aut, cre] (<https://orcid.org/0000-0002-2127-0443>), David Robinson [aut], Dieter Menne [ctb], Jonah Gabry [ctb], Paul Buerkner [ctb], Christopher Hua [ctb], William Petry [ctb] (<https://orcid.org/0000-0002-5230-5987>), Joshua Wiley [ctb] (<https://orcid.org/0000-0002-0271-6702>), Patrick Kennedy [ctb], Eduard Szöcs [ctb] (<https://orcid.org/0000-0001-5376-1194>, BASF SE), Indrajeet Patil [ctb], Vincent Arel-Bundock [ctb] (<https://orcid.org/0000-0003-2042-7063>)
Maintainer: Ben Bolker <bolker@mcmaster.ca>

Diff between broom.mixed versions 0.2.6 dated 2020-05-17 and 0.2.7 dated 2021-07-07

 DESCRIPTION                       |   32 +--
 MD5                               |   79 ++++----
 NAMESPACE                         |   15 -
 R/MCMCglmm_prediction.R           |    8 
 R/TMB_tidiers.R                   |  116 +++++++----
 R/brms_tidiers.R                  |   43 +++-
 R/gamlss_tidiers.R                |   27 +-
 R/glmmADMB_tidiers.R              |    1 
 R/glmmTMB_tidiers.R               |   11 -
 R/lme4_tidiers.R                  |   41 ++--
 R/mcmc_tidiers.R                  |    9 
 R/nlme_tidiers.R                  |    1 
 R/rstanarm_tidiers.R              |    5 
 R/utilities.R                     |   54 ++++-
 build/vignette.rds                |binary
 inst/NEWS.Rd                      |   35 +++
 inst/doc/broom_mixed_intro.html   |  369 ++++++++++++++++++++++++++++++++------
 inst/extdata/MCMCglmm_example.rda |binary
 inst/extdata/R2jags_example.rds   |binary
 inst/extdata/brms_example.rda     |binary
 inst/extdata/example_helpers.R    |    3 
 inst/extdata/gamlss_example.rds   |binary
 inst/extdata/glmmADMB_example.rda |binary
 inst/extdata/glmmTMB_example.rda  |binary
 inst/extdata/lme4_example.rda     |binary
 inst/extdata/nlme_example.rda     |binary
 inst/extdata/rstanarm_example.rds |binary
 man/assert_dependency.Rd          |only
 man/brms_tidiers.Rd               |    7 
 man/glmmTMB_tidiers.Rd            |    2 
 man/reexports.Rd                  |    2 
 man/rstanarm_tidiers.Rd           |    6 
 man/tidy.TMB.Rd                   |   18 +
 tests/testthat/test-TMB.R         |only
 tests/testthat/test-alltibbles.R  |   33 ++-
 tests/testthat/test-brms.R        |    7 
 tests/testthat/test-gamlss.R      |only
 tests/testthat/test-glmmTMB.R     |    7 
 tests/testthat/test-lme4.R        |    6 
 tests/testthat/test-lmertest.R    |   15 +
 tests/testthat/test-nlme.R        |    4 
 tests/testthat/test-rstanarm.R    |    1 
 42 files changed, 700 insertions(+), 257 deletions(-)

More information about broom.mixed at CRAN
Permanent link

Package Rcpp updated to version 1.0.7 with previous version 1.0.6 dated 2021-01-15

Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about 'Rcpp' is provided by several vignettes included in this package, via the 'Rcpp Gallery' site at <https://gallery.rcpp.org>, the paper by Eddelbuettel and Francois (2011, <doi:10.18637/jss.v040.i08>), the book by Eddelbuettel (2013, <doi:10.1007/978-1-4614-6868-4>) and the paper by Eddelbuettel and Balamuta (2018, <doi:10.1080/00031305.2017.1375990>); see 'citation("Rcpp")' for details.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey, Qiang Kou, Nathan Russell, Inaki Ucar, Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between Rcpp versions 1.0.6 dated 2021-01-15 and 1.0.7 dated 2021-07-07

 ChangeLog                                   |  154 +++++++++++++++++++
 DESCRIPTION                                 |   10 -
 MD5                                         |  112 +++++++-------
 R/Attributes.R                              |   15 +
 R/Module.R                                  |   14 -
 R/Rcpp.package.skeleton.R                   |   24 +--
 R/RcppClass.R                               |   23 +-
 R/RcppLdpath.R                              |   10 -
 README.md                                   |   35 ++++
 build/vignette.rds                          |binary
 inst/NEWS.Rd                                |   37 ++++
 inst/bib/Rcpp.bib                           |    2 
 inst/doc/Rcpp-FAQ.pdf                       |binary
 inst/doc/Rcpp-attributes.pdf                |binary
 inst/doc/Rcpp-extending.pdf                 |binary
 inst/doc/Rcpp-introduction.pdf              |binary
 inst/doc/Rcpp-jss-2011.pdf                  |binary
 inst/doc/Rcpp-libraries.pdf                 |binary
 inst/doc/Rcpp-modules.pdf                   |binary
 inst/doc/Rcpp-package.pdf                   |binary
 inst/doc/Rcpp-quickref.pdf                  |binary
 inst/doc/Rcpp-sugar.pdf                     |binary
 inst/include/Rcpp/DataFrame.h               |    5 
 inst/include/Rcpp/String.h                  |  221 +++++++++++++++++++++-------
 inst/include/Rcpp/api/meat/meat.h           |    2 
 inst/include/Rcpp/api/meat/message.h        |only
 inst/include/Rcpp/config.h                  |   10 -
 inst/include/Rcpp/exceptions.h              |    1 
 inst/include/Rcpp/hash/IndexHash.h          |   38 ++--
 inst/include/Rcpp/iostream/Rstreambuf.h     |   12 +
 inst/include/Rcpp/r/headers.h               |    5 
 inst/include/Rcpp/routines.h                |   50 +++++-
 inst/include/Rcpp/storage/PreserveStorage.h |   35 ++++
 inst/include/Rcpp/traits/named_object.h     |   20 +-
 inst/include/Rcpp/unwindProtect.h           |    4 
 inst/include/RcppCommon.h                   |   33 ++--
 inst/tinytest/cpp/misc.cpp                  |    5 
 inst/tinytest/cpp/rcppversion.cpp           |    3 
 inst/tinytest/test_global_rostream.R        |only
 inst/tinytest/test_misc.R                   |   15 +
 inst/tinytest/test_packageversion.R         |    5 
 man/cppFunction.Rd                          |   27 +--
 man/sourceCpp.Rd                            |   51 +++---
 src/api.cpp                                 |   14 +
 src/attributes.cpp                          |   39 ++++
 src/barrier.cpp                             |   46 +++++
 src/rcpp_init.cpp                           |   29 ++-
 tests/tinytest.R                            |   20 +-
 vignettes/pdf/Rcpp-FAQ.pdf                  |binary
 vignettes/pdf/Rcpp-attributes.pdf           |binary
 vignettes/pdf/Rcpp-extending.pdf            |binary
 vignettes/pdf/Rcpp-introduction.pdf         |binary
 vignettes/pdf/Rcpp-jss-2011.pdf             |binary
 vignettes/pdf/Rcpp-libraries.pdf            |binary
 vignettes/pdf/Rcpp-modules.pdf              |binary
 vignettes/pdf/Rcpp-package.pdf              |binary
 vignettes/pdf/Rcpp-quickref.pdf             |binary
 vignettes/pdf/Rcpp-sugar.pdf                |binary
 58 files changed, 836 insertions(+), 290 deletions(-)

More information about Rcpp at CRAN
Permanent link

Package nzilbb.labbcat updated to version 1.0-1 with previous version 0.7-1 dated 2021-05-27

Title: Accessing Data Stored in 'LaBB-CAT' Instances
Description: 'LaBB-CAT' is a web-based language corpus management system developed by the New Zealand Institute of Language, Brain and Behaviour (NZILBB) - see <https://labbcat.canterbury.ac.nz>. This package defines functions for accessing corpus data in a 'LaBB-CAT' instance. You must have at least version 20210601.1528 of 'LaBB-CAT' to use this package. For more information about 'LaBB-CAT', see Robert Fromont and Jennifer Hay (2008) <doi:10.3366/E1749503208000142> or Robert Fromont (2017) <doi:10.1016/j.csl.2017.01.004>.
Author: Robert Fromont [aut, cre] (<https://orcid.org/0000-0001-5271-5487>)
Maintainer: Robert Fromont <robert.fromont@canterbury.ac.nz>

Diff between nzilbb.labbcat versions 0.7-1 dated 2021-05-27 and 1.0-1 dated 2021-07-07

 DESCRIPTION                                     |   10 -
 MD5                                             |   95 ++++++++--------
 NAMESPACE                                       |    1 
 NEWS.md                                         |   39 ++++++
 R/countAnnotations.R                            |    6 -
 R/getAllUtterances.R                            |    9 +
 R/getAnchors.R                                  |   11 +
 R/getAnnotations.R                              |   14 +-
 R/getDictionaryEntries.R                        |   11 +
 R/getFragments.R                                |   12 +-
 R/getMatchAlignments.R                          |  104 +++++++++++------
 R/getMatchLabels.R                              |   93 ++++++++++-----
 R/getMatches.R                                  |  141 ++++++++++++++++++------
 R/getMatchingGraphIds.R                         |   51 ++++++--
 R/getMatchingParticipantIds.R                   |only
 R/getMatchingTranscriptIds.R                    |   55 ++++++---
 R/getMedia.R                                    |    8 -
 R/getParticipantAttributes.R                    |   18 +--
 R/getSoundFragments.R                           |   18 +--
 R/getTranscriptAttributes.R                     |   22 +--
 R/newTranscript.R                               |    9 +
 R/nzilbb.labbcat.R                              |    8 -
 R/processWithPraat.R                            |   29 ++--
 R/updateTranscript.R                            |    9 +
 build/partial.rdb                               |binary
 man/countAnnotations.Rd                         |    4 
 man/getAllUtterances.Rd                         |    6 -
 man/getAnchors.Rd                               |    9 +
 man/getAnnotations.Rd                           |   14 +-
 man/getDictionaryEntries.Rd                     |    6 -
 man/getFragments.Rd                             |   10 -
 man/getMatchAlignments.Rd                       |   34 ++++-
 man/getMatchLabels.Rd                           |   30 +++--
 man/getMatches.Rd                               |   21 ++-
 man/getMatchingGraphIds.Rd                      |   51 ++++++--
 man/getMatchingParticipantIds.Rd                |only
 man/getMatchingTranscriptIds.Rd                 |   53 ++++++---
 man/getMedia.Rd                                 |    6 -
 man/getParticipantAttributes.Rd                 |    6 -
 man/getSoundFragments.Rd                        |   18 +--
 man/getTranscriptAttributes.Rd                  |    8 -
 man/newTranscript.Rd                            |    6 -
 man/nzilbb.labbcat.Rd                           |    2 
 man/processWithPraat.Rd                         |   18 +--
 man/updateTranscript.Rd                         |    5 
 tests/testthat/test-getMatchAlignments.R        |    3 
 tests/testthat/test-getMatchLabels.R            |    2 
 tests/testthat/test-getMatches.R                |    4 
 tests/testthat/test-getMatchingParticipantIds.R |only
 tests/testthat/test-getMatchingTrancriptIds.R   |    4 
 50 files changed, 723 insertions(+), 370 deletions(-)

More information about nzilbb.labbcat at CRAN
Permanent link

Package image.textlinedetector updated to version 0.1.4 with previous version 0.1.3 dated 2021-01-25

Title: Segment Images in Text Lines and Words
Description: Find text lines in scanned images and segment the lines into words. Includes implementations of the paper 'Novel A* Path Planning Algorithm for Line Segmentation of Handwritten Documents' by Surinta O. et al (2014) <doi:10.1109/ICFHR.2014.37> available at <https://github.com/smeucci/LineSegm>, an implementation of 'A Statistical approach to line segmentation in handwritten documents' by Arivazhagan M. et al (2007) <doi:10.1117/12.704538>, and a wrapper for an image segmentation technique to detect words in text lines as described in the paper 'Scale Space Technique for Word Segmentation in Handwritten Documents' by Manmatha R. and Srimal N. (1999) paper at <doi:10.1007/3-540-48236-9_3>, wrapper for code available at <https://github.com/arthurflor23/text-segmentation>.
Author: Jan Wijffels [aut, cre, cph] (R wrapper), Vrije Universiteit Brussel - DIGI: Brussels Platform for Digital Humanities [cph] (R wrapper), Jeroen Ooms [ctb, cph] (More details in LICENSE.note file), Arthur Flôr [ctb, cph] (More details in LICENSE.note file), Saverio Meucci [ctb, cph] (More details in LICENSE.note file), Yeara Kozlov [ctb, cph] (More details in LICENSE.note file), Tino Weinkauf [ctb, cph] (More details in LICENSE.note file)
Maintainer: Jan Wijffels <jan.wijffels@vub.be>

Diff between image.textlinedetector versions 0.1.3 dated 2021-01-25 and 0.1.4 dated 2021-07-07

 DESCRIPTION                  |    7 
 LICENSE                      |    2 
 LICENSE.note                 |  176 ++++++++---------
 MD5                          |   24 +-
 NAMESPACE                    |   24 +-
 NEWS.md                      |   45 ++--
 R/RcppExports.R              |  110 +++++-----
 R/pkg.R                      |   10 
 R/textlinedetector.R         |  444 +++++++++++++++++++++----------------------
 README.md                    |  178 ++++++++---------
 man/image_textlines_astar.Rd |  118 +++++------
 src/LineSegmentation.cpp     |   10 
 tools/winlibs.R              |   20 -
 13 files changed, 589 insertions(+), 579 deletions(-)

More information about image.textlinedetector at CRAN
Permanent link

Package pense updated to version 2.1.0 with previous version 2.0.3 dated 2021-04-14

Title: Penalized Elastic Net S/MM-Estimator of Regression
Description: Robust penalized (adaptive) elastic net S and M estimators for linear regression. The methods are proposed in Cohen Freue, G. V., Kepplinger, D., Salibián-Barrera, M., and Smucler, E. (2019) <https://projecteuclid.org/euclid.aoas/1574910036>. The package implements the extensions and algorithms described in Kepplinger, D. (2020) <doi:10.14288/1.0392915>.
Author: David Kepplinger [aut, cre], Matías Salibián-Barrera [aut], Gabriela Cohen Freue [aut]
Maintainer: David Kepplinger <david.kepplinger@gmail.com>

Diff between pense versions 2.0.3 dated 2021-04-14 and 2.1.0 dated 2021-07-07

 pense-2.0.3/pense/vignettes/migration_guide_cache/html/unnamed-chunk-4_157feaabf1df04e255ebc73ea452985c.RData |only
 pense-2.0.3/pense/vignettes/migration_guide_cache/html/unnamed-chunk-4_157feaabf1df04e255ebc73ea452985c.rdb   |only
 pense-2.0.3/pense/vignettes/migration_guide_cache/html/unnamed-chunk-4_157feaabf1df04e255ebc73ea452985c.rdx   |only
 pense-2.0.3/pense/vignettes/migration_guide_cache/html/unnamed-chunk-5_0ca31a39d247ac109db72b262777fa3d.RData |only
 pense-2.0.3/pense/vignettes/migration_guide_cache/html/unnamed-chunk-5_0ca31a39d247ac109db72b262777fa3d.rdb   |only
 pense-2.0.3/pense/vignettes/migration_guide_cache/html/unnamed-chunk-5_0ca31a39d247ac109db72b262777fa3d.rdx   |only
 pense-2.0.3/pense/vignettes/migration_guide_cache/html/unnamed-chunk-6_d370271aeb4e78cb6f40f286cf70f150.RData |only
 pense-2.0.3/pense/vignettes/migration_guide_cache/html/unnamed-chunk-6_d370271aeb4e78cb6f40f286cf70f150.rdb   |only
 pense-2.0.3/pense/vignettes/migration_guide_cache/html/unnamed-chunk-6_d370271aeb4e78cb6f40f286cf70f150.rdx   |only
 pense-2.1.0/pense/DESCRIPTION                                                                                 |   11 
 pense-2.1.0/pense/MD5                                                                                         |  184 +--
 pense-2.1.0/pense/NEWS.md                                                                                     |   12 
 pense-2.1.0/pense/R/coef-methods.R                                                                            |  250 ++--
 pense-2.1.0/pense/R/control_options.R                                                                         |   26 
 pense-2.1.0/pense/R/elnet.R                                                                                   |  296 +++--
 pense-2.1.0/pense/R/enpy.R                                                                                    |   11 
 pense-2.1.0/pense/R/pense_regression.R                                                                        |  588 ++++++----
 pense-2.1.0/pense/R/plot-methods.R                                                                            |  186 ++-
 pense-2.1.0/pense/R/print-methods.R                                                                           |  127 +-
 pense-2.1.0/pense/R/regmest_regression.R                                                                      |  395 ++++--
 pense-2.1.0/pense/R/residuals-methods.R                                                                       |   78 -
 pense-2.1.0/pense/R/utilities-internal.R                                                                      |  152 ++
 pense-2.1.0/pense/R/utilities.R                                                                               |  195 ++-
 pense-2.1.0/pense/build/partial.rdb                                                                           |binary
 pense-2.1.0/pense/build/pense.pdf                                                                             |binary
 pense-2.1.0/pense/build/vignette.rds                                                                          |binary
 pense-2.1.0/pense/configure                                                                                   |   12 
 pense-2.1.0/pense/configure.ac                                                                                |   12 
 pense-2.1.0/pense/inst/doc/computing_adapense.R                                                               |   31 
 pense-2.1.0/pense/inst/doc/computing_adapense.Rmd                                                             |   64 -
 pense-2.1.0/pense/inst/doc/computing_adapense.html                                                            |  184 +--
 pense-2.1.0/pense/inst/doc/computing_adapense_fits.RData                                                      |binary
 pense-2.1.0/pense/inst/doc/lambda_grids.R                                                                     |    7 
 pense-2.1.0/pense/inst/doc/lambda_grids.Rmd                                                                   |   13 
 pense-2.1.0/pense/inst/doc/lambda_grids.html                                                                  |   13 
 pense-2.1.0/pense/inst/doc/migration_guide.html                                                               |   54 
 pense-2.1.0/pense/man/coef.pense_cvfit.Rd                                                                     |   65 -
 pense-2.1.0/pense/man/coef.pense_fit.Rd                                                                       |   42 
 pense-2.1.0/pense/man/elnet.Rd                                                                                |   56 
 pense-2.1.0/pense/man/elnet_cv.Rd                                                                             |   87 -
 pense-2.1.0/pense/man/enpy_initial_estimates.Rd                                                               |   30 
 pense-2.1.0/pense/man/mlocscale.Rd                                                                            |    8 
 pense-2.1.0/pense/man/mm_algorithm_options.Rd                                                                 |    2 
 pense-2.1.0/pense/man/mscale.Rd                                                                               |   11 
 pense-2.1.0/pense/man/pense.Rd                                                                                |  138 +-
 pense-2.1.0/pense/man/pense_cv.Rd                                                                             |  138 +-
 pense-2.1.0/pense/man/pensem_cv.Rd                                                                            |   91 -
 pense-2.1.0/pense/man/plot.pense_cvfit.Rd                                                                     |   20 
 pense-2.1.0/pense/man/plot.pense_fit.Rd                                                                       |   14 
 pense-2.1.0/pense/man/predict.pense_cvfit.Rd                                                                  |   59 -
 pense-2.1.0/pense/man/predict.pense_fit.Rd                                                                    |   31 
 pense-2.1.0/pense/man/prediction_performance.Rd                                                               |   11 
 pense-2.1.0/pense/man/prinsens.Rd                                                                             |   17 
 pense-2.1.0/pense/man/regmest.Rd                                                                              |   67 -
 pense-2.1.0/pense/man/regmest_cv.Rd                                                                           |  128 +-
 pense-2.1.0/pense/man/residuals.pense_cvfit.Rd                                                                |   51 
 pense-2.1.0/pense/man/residuals.pense_fit.Rd                                                                  |   36 
 pense-2.1.0/pense/man/starting_point.Rd                                                                       |   59 -
 pense-2.1.0/pense/man/summary.pense_cvfit.Rd                                                                  |   14 
 pense-2.1.0/pense/src/Makevars.in                                                                             |    2 
 pense-2.1.0/pense/src/Makevars.win                                                                            |    2 
 pense-2.1.0/pense/src/enpy_psc.hpp                                                                            |    8 
 pense-2.1.0/pense/src/m_loss.hpp                                                                              |   49 
 pense-2.1.0/pense/src/nsoptim/container/data.hpp                                                              |   31 
 pense-2.1.0/pense/src/nsoptim/container/regression_coefficients.hpp                                           |    2 
 pense-2.1.0/pense/src/nsoptim/objective/adaptive_en_penalty.hpp                                               |    4 
 pense-2.1.0/pense/src/nsoptim/objective/ls_regression_loss.hpp                                                |   65 +
 pense-2.1.0/pense/src/nsoptim/optimizer/admm.hpp                                                              |   91 -
 pense-2.1.0/pense/src/nsoptim/optimizer/auglars.hpp                                                           |  115 -
 pense-2.1.0/pense/src/nsoptim/optimizer/dal.hpp                                                               |  168 ++
 pense-2.1.0/pense/src/nsoptim/optimizer/dal_helper.hpp                                                        |  113 -
 pense-2.1.0/pense/src/nsoptim/optimizer/linear_algebra_utilities.hpp                                          |   93 +
 pense-2.1.0/pense/src/nsoptim/optimizer/mm.hpp                                                                |   46 
 pense-2.1.0/pense/src/nsoptim/optimizer/optimum.hpp                                                           |   74 -
 pense-2.1.0/pense/src/nsoptim/utilities.hpp                                                                   |only
 pense-2.1.0/pense/src/r_interface_utils.cc                                                                    |    9 
 pense-2.1.0/pense/src/r_mesten_regression.cc                                                                  |    4 
 pense-2.1.0/pense/src/r_pense_regression.cc                                                                   |    4 
 pense-2.1.0/pense/src/regularization_path.hpp                                                                 |   49 
 pense-2.1.0/pense/src/s_loss.hpp                                                                              |   60 -
 pense-2.1.0/pense/tests/testthat.R                                                                            |   10 
 pense-2.1.0/pense/tests/testthat/Rplots.pdf                                                                   |only
 pense-2.1.0/pense/tests/testthat/snap                                                                         |only
 pense-2.1.0/pense/tests/testthat/test_elnet_algorithms.R                                                      |   19 
 pense-2.1.0/pense/tests/testthat/test_multiple_alpha.R                                                        |only
 pense-2.1.0/pense/tests/testthat/test_pense_algorithm.R                                                       |only
 pense-2.1.0/pense/tests/testthat/testthat-problems.rds                                                        |only
 pense-2.1.0/pense/vignettes/computing_adapense.Rmd                                                            |   64 -
 pense-2.1.0/pense/vignettes/computing_adapense_files/figure-html/unnamed-chunk-10-1.png                       |binary
 pense-2.1.0/pense/vignettes/computing_adapense_files/figure-html/unnamed-chunk-6-1.png                        |binary
 pense-2.1.0/pense/vignettes/computing_adapense_files/figure-html/unnamed-chunk-7-1.png                        |binary
 pense-2.1.0/pense/vignettes/computing_adapense_files/figure-html/unnamed-chunk-8-1.png                        |only
 pense-2.1.0/pense/vignettes/computing_adapense_files/figure-html/unnamed-chunk-9-1.png                        |binary
 pense-2.1.0/pense/vignettes/computing_adapense_fits.RData                                                     |binary
 pense-2.1.0/pense/vignettes/lambda_grids.Rmd                                                                  |   13 
 pense-2.1.0/pense/vignettes/lambda_grids_fits.RData                                                           |binary
 pense-2.1.0/pense/vignettes/migration_guide_cache/html/unnamed-chunk-4_48807d83cc5fb6cf2463ef80d5d7ddd7.RData |only
 pense-2.1.0/pense/vignettes/migration_guide_cache/html/unnamed-chunk-4_48807d83cc5fb6cf2463ef80d5d7ddd7.rdb   |only
 pense-2.1.0/pense/vignettes/migration_guide_cache/html/unnamed-chunk-4_48807d83cc5fb6cf2463ef80d5d7ddd7.rdx   |only
 pense-2.1.0/pense/vignettes/migration_guide_cache/html/unnamed-chunk-5_22951aa6abea8973c9e5ba08064a8e38.RData |only
 pense-2.1.0/pense/vignettes/migration_guide_cache/html/unnamed-chunk-5_22951aa6abea8973c9e5ba08064a8e38.rdb   |only
 pense-2.1.0/pense/vignettes/migration_guide_cache/html/unnamed-chunk-5_22951aa6abea8973c9e5ba08064a8e38.rdx   |only
 pense-2.1.0/pense/vignettes/migration_guide_cache/html/unnamed-chunk-6_fa3f2d0727238f3562e13501679913fe.RData |only
 pense-2.1.0/pense/vignettes/migration_guide_cache/html/unnamed-chunk-6_fa3f2d0727238f3562e13501679913fe.rdb   |only
 pense-2.1.0/pense/vignettes/migration_guide_cache/html/unnamed-chunk-6_fa3f2d0727238f3562e13501679913fe.rdx   |only
 105 files changed, 3290 insertions(+), 1881 deletions(-)

More information about pense at CRAN
Permanent link

New package topologyGSA with initial version 1.4.7
Package: topologyGSA
Version: 1.4.7
Date: 2021-07-07
Title: Gene Set Analysis Exploiting Pathway Topology
Author: Sofia Massa, Gabriele Sales
Maintainer: Gabriele Sales <gabriele.sales@unipd.it>
Description: Using Gaussian graphical models we propose a novel approach to perform pathway analysis using gene expression. Given the structure of a graph (a pathway) we introduce two statistical tests to compare the mean and the concentration matrices between two groups. Specifically, these tests can be performed on the graph and on its connected components (cliques).
Imports: graph, gRbase (>= 1.7), qpgraph, fields, methods
Suggests: Rgraphviz
License: GPL-3
LazyLoad: yes
NeedsCompilation: no
Packaged: 2021-07-07 11:34:04 UTC; sales
Repository: CRAN
Date/Publication: 2021-07-07 12:20:02 UTC

More information about topologyGSA at CRAN
Permanent link

Package FLAME updated to version 2.1.0 with previous version 2.0.0 dated 2020-04-14

Title: Interpretable Matching for Causal Inference
Description: Efficient implementations of the algorithms in the Almost-Matching-Exactly framework for interpretable matching in causal inference. These algorithms match units via a learned, weighted Hamming distance that determines which covariates are more important to match on. For more information and examples, see the Almost-Matching-Exactly website.
Author: Vittorio Orlandi [aut, cre], Sudeepa Roy [aut], Cynthia Rudin [aut], Alexander Volfovsky [aut]
Maintainer: Vittorio Orlandi <almost.matching.exactly@gmail.com>

Diff between FLAME versions 2.0.0 dated 2020-04-14 and 2.1.0 dated 2021-07-07

 FLAME-2.0.0/FLAME/R/FLAME_bit.R                             |only
 FLAME-2.0.0/FLAME/inst/doc/FLAME_overview.R                 |only
 FLAME-2.0.0/FLAME/inst/doc/FLAME_overview.Rmd               |only
 FLAME-2.0.0/FLAME/inst/doc/FLAME_overview.html              |only
 FLAME-2.0.0/FLAME/man/ATT.Rd                                |only
 FLAME-2.0.0/FLAME/man/FLAME.Rd                              |only
 FLAME-2.0.0/FLAME/tests/testthat/test_FLAME_output.R        |only
 FLAME-2.0.0/FLAME/tests/testthat/test_additional_features.R |only
 FLAME-2.0.0/FLAME/tests/testthat/test_basic_functionality.R |only
 FLAME-2.0.0/FLAME/vignettes/FLAME_overview.Rmd              |only
 FLAME-2.1.0/FLAME/DESCRIPTION                               |   16 
 FLAME-2.1.0/FLAME/MD5                                       |   68 -
 FLAME-2.1.0/FLAME/NAMESPACE                                 |   21 
 FLAME-2.1.0/FLAME/R/BF.R                                    |only
 FLAME-2.1.0/FLAME/R/GenerateNewActiveSets.R                 |only
 FLAME-2.1.0/FLAME/R/PE_functions.R                          |  225 ++++-
 FLAME-2.1.0/FLAME/R/algos.R                                 |only
 FLAME-2.1.0/FLAME/R/arg_checker.R                           |  293 ++++--
 FLAME-2.1.0/FLAME/R/class_funs.R                            |only
 FLAME-2.1.0/FLAME/R/data_read.R                             |   18 
 FLAME-2.1.0/FLAME/R/gen_data.R                              |   83 +
 FLAME-2.1.0/FLAME/R/get_cov_set.R                           |only
 FLAME-2.1.0/FLAME/R/helpers.R                               |  310 +++++--
 FLAME-2.1.0/FLAME/R/loop.R                                  |only
 FLAME-2.1.0/FLAME/R/missing.R                               |  273 ++----
 FLAME-2.1.0/FLAME/R/post_matching.R                         |  520 +++++-------
 FLAME-2.1.0/FLAME/R/postprocess.R                           |only
 FLAME-2.1.0/FLAME/R/preprocess.R                            |only
 FLAME-2.1.0/FLAME/R/remap_covariates.R                      |only
 FLAME-2.1.0/FLAME/R/stopping.R                              |   92 +-
 FLAME-2.1.0/FLAME/build/vignette.rds                        |binary
 FLAME-2.1.0/FLAME/inst/doc/intro_to_AME.R                   |only
 FLAME-2.1.0/FLAME/inst/doc/intro_to_AME.Rmd                 |only
 FLAME-2.1.0/FLAME/inst/doc/intro_to_AME.html                |only
 FLAME-2.1.0/FLAME/man/AME.Rd                                |only
 FLAME-2.1.0/FLAME/man/ATE.Rd                                |   25 
 FLAME-2.1.0/FLAME/man/CATE.Rd                               |   87 +-
 FLAME-2.1.0/FLAME/man/MG.Rd                                 |   98 +-
 FLAME-2.1.0/FLAME/man/gen_data.Rd                           |   26 
 FLAME-2.1.0/FLAME/man/plot.ame.Rd                           |only
 FLAME-2.1.0/FLAME/man/summary.ame.Rd                        |only
 FLAME-2.1.0/FLAME/tests/testthat/test_PE.R                  |only
 FLAME-2.1.0/FLAME/tests/testthat/test_columns.R             |only
 FLAME-2.1.0/FLAME/tests/testthat/test_data_splitting.R      |only
 FLAME-2.1.0/FLAME/tests/testthat/test_factors.R             |only
 FLAME-2.1.0/FLAME/tests/testthat/test_inputs.R              |only
 FLAME-2.1.0/FLAME/tests/testthat/test_missingness.R         |  136 ++-
 FLAME-2.1.0/FLAME/tests/testthat/test_one_covariate.R       |only
 FLAME-2.1.0/FLAME/tests/testthat/test_output.R              |only
 FLAME-2.1.0/FLAME/tests/testthat/test_user_PE.R             |only
 FLAME-2.1.0/FLAME/tests/testthat/test_warnings.R            |only
 FLAME-2.1.0/FLAME/vignettes/biblio.bibtex                   |only
 FLAME-2.1.0/FLAME/vignettes/intro_to_AME.Rmd                |only
 53 files changed, 1424 insertions(+), 867 deletions(-)

More information about FLAME at CRAN
Permanent link

Package DHARMa updated to version 0.4.3 with previous version 0.4.2 dated 2021-07-05

Title: Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models
Description: The 'DHARMa' package uses a simulation-based approach to create readily interpretable scaled (quantile) residuals for fitted (generalized) linear mixed models. Currently supported are linear and generalized linear (mixed) models from 'lme4' (classes 'lmerMod', 'glmerMod'), 'glmmTMB' 'GLMMadaptive' and 'spaMM', generalized additive models ('gam' from 'mgcv'), 'glm' (including 'negbin' from 'MASS', but excluding quasi-distributions) and 'lm' model classes. Moreover, externally created simulations, e.g. posterior predictive simulations from Bayesian software such as 'JAGS', 'STAN', or 'BUGS' can be processed as well. The resulting residuals are standardized to values between 0 and 1 and can be interpreted as intuitively as residuals from a linear regression. The package also provides a number of plot and test functions for typical model misspecification problems, such as over/underdispersion, zero-inflation, and residual spatial and temporal autocorrelation.
Author: Florian Hartig [aut, cre] (<https://orcid.org/0000-0002-6255-9059>), Lukas Lohse [ctb]
Maintainer: Florian Hartig <florian.hartig@biologie.uni-regensburg.de>

Diff between DHARMa versions 0.4.2 dated 2021-07-05 and 0.4.3 dated 2021-07-07

 DHARMa-0.4.2/DHARMa/tests/testthat/testModelTypes.R  |only
 DHARMa-0.4.3/DHARMa/DESCRIPTION                      |   11 
 DHARMa-0.4.3/DHARMa/MD5                              |   21 
 DHARMa-0.4.3/DHARMa/NEWS                             |    8 
 DHARMa-0.4.3/DHARMa/R/compatibility.R                |    4 
 DHARMa-0.4.3/DHARMa/inst/doc/DHARMa.R                |   84 +--
 DHARMa-0.4.3/DHARMa/inst/doc/DHARMa.Rmd              |   18 
 DHARMa-0.4.3/DHARMa/inst/doc/DHARMa.html             |  424 +++++++------------
 DHARMa-0.4.3/DHARMa/inst/doc/DHARMaForBayesians.html |    4 
 DHARMa-0.4.3/DHARMa/inst/examples/hurricanes.R       |    6 
 DHARMa-0.4.3/DHARMa/man/hurricanes.Rd                |    4 
 DHARMa-0.4.3/DHARMa/vignettes/DHARMa.Rmd             |   18 
 12 files changed, 264 insertions(+), 338 deletions(-)

More information about DHARMa at CRAN
Permanent link

Package academictwitteR updated to version 0.2.1 with previous version 0.2.0 dated 2021-06-29

Title: Access the Twitter Academic Research Product Track V2 API Endpoint
Description: Package to query the Twitter Academic Research Product Track, providing access to full-archive search and other v2 API endpoints. Functions are written with academic research in mind. They provide flexibility in how the user wishes to store collected data, and encourage regular storage of data to mitigate loss when collecting large volumes of tweets. They also provide workarounds to manage and reshape the format in which data is provided on the client side.
Author: Christopher Barrie [aut, cre] (<https://orcid.org/0000-0002-9156-990X>), Justin Chun-ting Ho [aut] (<https://orcid.org/0000-0002-7884-1059>), Chung-hong Chan [ctb] (<https://orcid.org/0000-0002-6232-7530>)
Maintainer: Christopher Barrie <christopher.barrie@ed.ac.uk>

Diff between academictwitteR versions 0.2.0 dated 2021-06-29 and 0.2.1 dated 2021-07-07

 academictwitteR-0.2.0/academictwitteR/tests/testdata/commtwitter/data_1399005777138962433.json  |only
 academictwitteR-0.2.0/academictwitteR/tests/testdata/commtwitter/users_1399005777138962433.json |only
 academictwitteR-0.2.1/academictwitteR/DESCRIPTION                                               |    6 +--
 academictwitteR-0.2.1/academictwitteR/MD5                                                       |   16 +++++-----
 academictwitteR-0.2.1/academictwitteR/NEWS.md                                                   |    3 +
 academictwitteR-0.2.1/academictwitteR/R/get_all_tweets.R                                        |    8 ++++-
 academictwitteR-0.2.1/academictwitteR/R/utils.R                                                 |    9 +++++
 academictwitteR-0.2.1/academictwitteR/man/get_all_tweets.Rd                                     |    3 +
 academictwitteR-0.2.1/academictwitteR/tests/testdata/commtwitter/data_1399765322509557763.json  |only
 academictwitteR-0.2.1/academictwitteR/tests/testdata/commtwitter/query                          |    4 +-
 academictwitteR-0.2.1/academictwitteR/tests/testdata/commtwitter/users_1399765322509557763.json |only
 11 files changed, 35 insertions(+), 14 deletions(-)

More information about academictwitteR at CRAN
Permanent link

Package SteppedPower updated to version 0.2.0 with previous version 0.1.0 dated 2021-02-04

Title: Power Calculation for Stepped Wedge Designs
Description: Tools for power and sample size calculation as well as design diagnostics for longitudinal mixed model settings, with a focus on stepped wedge designs. All calculations are oracle estimates i.e. assume random effect variances to be known (or guessed) in advance. The method is introduced in Hussey and Hughes (2007) <doi:10.1016/j.cct.2006.05.007>, extensions are discussed in Li et al. (2020) <doi:10.1177/0962280220932962>.
Author: Philipp Mildenberger [aut, cre] (<https://orcid.org/0000-0002-7367-1708>), Federico Marini [ctb] (<https://orcid.org/0000-0003-3252-7758>)
Maintainer: Philipp Mildenberger <pmildenb@uni-mainz.de>

Diff between SteppedPower versions 0.1.0 dated 2021-02-04 and 0.2.0 dated 2021-07-07

 SteppedPower-0.1.0/SteppedPower/man/construct_timeadjust.Rd   |only
 SteppedPower-0.2.0/SteppedPower/DESCRIPTION                   |    9 
 SteppedPower-0.2.0/SteppedPower/LICENSE                       |    4 
 SteppedPower-0.2.0/SteppedPower/MD5                           |   72 -
 SteppedPower-0.2.0/SteppedPower/NAMESPACE                     |   82 -
 SteppedPower-0.2.0/SteppedPower/NEWS.md                       |   13 
 SteppedPower-0.2.0/SteppedPower/R/SteppedPower-pkg.R          |   40 
 SteppedPower-0.2.0/SteppedPower/R/closed_formulae.R           |only
 SteppedPower-0.2.0/SteppedPower/R/construct_CovMat.R          |  173 +--
 SteppedPower-0.2.0/SteppedPower/R/construct_DesMat.R          |   93 +
 SteppedPower-0.2.0/SteppedPower/R/helper_functions.R          |  204 +++-
 SteppedPower-0.2.0/SteppedPower/R/wlsPower.R                  |  455 +++++----
 SteppedPower-0.2.0/SteppedPower/README.md                     |   16 
 SteppedPower-0.2.0/SteppedPower/build/vignette.rds            |binary
 SteppedPower-0.2.0/SteppedPower/inst/doc/Getting_Started.R    |   97 +
 SteppedPower-0.2.0/SteppedPower/inst/doc/Getting_Started.Rmd  |  283 ++++-
 SteppedPower-0.2.0/SteppedPower/inst/doc/Getting_Started.html |  340 ++++--
 SteppedPower-0.2.0/SteppedPower/man/RandEff_to_alpha012.Rd    |only
 SteppedPower-0.2.0/SteppedPower/man/SteppedPower-pkg.Rd       |   32 
 SteppedPower-0.2.0/SteppedPower/man/VarClosed_Kasza.Rd        |only
 SteppedPower-0.2.0/SteppedPower/man/VarClosed_Li.Rd           |only
 SteppedPower-0.2.0/SteppedPower/man/alpha012_to_RandEff.Rd    |only
 SteppedPower-0.2.0/SteppedPower/man/compute_wlsPower.Rd       |  173 +--
 SteppedPower-0.2.0/SteppedPower/man/construct_CovBlk.Rd       |   30 
 SteppedPower-0.2.0/SteppedPower/man/construct_CovMat.Rd       |  194 +--
 SteppedPower-0.2.0/SteppedPower/man/construct_CovSubMat.Rd    |   17 
 SteppedPower-0.2.0/SteppedPower/man/construct_DesMat.Rd       |   36 
 SteppedPower-0.2.0/SteppedPower/man/construct_timeAdjust.Rd   |only
 SteppedPower-0.2.0/SteppedPower/man/construct_trtMat.Rd       |   72 -
 SteppedPower-0.2.0/SteppedPower/man/plot.DesMat.Rd            |    9 
 SteppedPower-0.2.0/SteppedPower/man/plot.wlsPower.Rd          |   14 
 SteppedPower-0.2.0/SteppedPower/man/plot_CovMat.Rd            |only
 SteppedPower-0.2.0/SteppedPower/man/print.DesMat.Rd           |   38 
 SteppedPower-0.2.0/SteppedPower/man/print.wlsPower.Rd         |   40 
 SteppedPower-0.2.0/SteppedPower/man/tTestPwr.Rd               |   65 -
 SteppedPower-0.2.0/SteppedPower/man/wlsPower.Rd               |  503 +++++-----
 SteppedPower-0.2.0/SteppedPower/tests/testthat.R              |    8 
 SteppedPower-0.2.0/SteppedPower/tests/testthat/test_CovMat.R  |   44 
 SteppedPower-0.2.0/SteppedPower/tests/testthat/test_DesMat.R  |    2 
 SteppedPower-0.2.0/SteppedPower/vignettes/Getting_Started.Rmd |  283 ++++-
 SteppedPower-0.2.0/SteppedPower/vignettes/references.bib      |  127 ++
 41 files changed, 2255 insertions(+), 1313 deletions(-)

More information about SteppedPower at CRAN
Permanent link

Package JMbayes2 updated to version 0.1-7 with previous version 0.1-6 dated 2021-05-12

Title: Extended Joint Models for Longitudinal and Time-to-Event Data
Description: Fit joint models for longitudinal and time-to-event data under the Bayesian approach. Multiple longitudinal outcomes of mixed type (continuous/categorical) and multiple event times (competing risks and multi-state processes) are accommodated. Rizopoulos (2012, ISBN:9781439872864).
Author: Dimitris Rizopoulos [aut, cre] (<https://orcid.org/0000-0001-9397-0900>), Grigorios Papageorgiou [aut], Pedro Miranda Afonso [aut]
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>

Diff between JMbayes2 versions 0.1-6 dated 2021-05-12 and 0.1-7 dated 2021-07-07

 DESCRIPTION            |    8 -
 MD5                    |   32 +++----
 NAMESPACE              |   14 +--
 NEWS.md                |   14 +++
 R/accuracy_measures.R  |  214 ++++++++++++++++++++++++++++++++++++++++++++++++-
 R/basic_methods.R      |  117 +++++++++++++++++---------
 R/help_functions.R     |   73 +++++++++++-----
 R/jm.R                 |   15 ++-
 R/jm_fit.R             |   30 ++----
 R/predict_funs.R       |   11 ++
 man/JMbayes2.Rd        |    4 
 man/accuracy.Rd        |   26 +++++
 man/jm.Rd              |    1 
 man/predict.Rd         |   21 ++--
 src/JMbayes2_Funs.h    |   34 +++++++
 src/JMbayes2_LogDens.h |   16 ++-
 src/mcmc_fit.cpp       |   22 +++--
 17 files changed, 507 insertions(+), 145 deletions(-)

More information about JMbayes2 at CRAN
Permanent link

Package ggVennDiagram updated to version 1.1.4 with previous version 1.1.0 dated 2021-05-07

Title: A 'ggplot2' Implement of Venn Diagram
Description: Easy-to-use functions to generate 2-7 sets Venn plot in publication quality. 'ggVennDiagram' plot Venn using well-defined geometry dataset and 'ggplot2'. The shapes of 2-4 sets Venn use circles and ellipses, while the shapes of 4-7 sets Venn use irregular polygons (4 has both forms), which are developed and imported from another package 'venn', authored by Adrian Dusa. We provided internal functions to integrate shape data with user provided sets data, and calculated the geometry of every regions/intersections of them, then separately plot Venn in three components: set edges, set labels, and regions. From version 1.0, it is possible to customize these components as you demand in ordinary 'ggplot2' grammar.
Author: Chun-Hui Gao [aut, cre] (<https://orcid.org/0000-0002-1445-7939>), Guangchuang Yu [ctb] (<https://orcid.org/0000-0002-6485-8781>), Adrian Dusa [ctb]
Maintainer: Chun-Hui Gao <gaospecial@gmail.com>

Diff between ggVennDiagram versions 1.1.0 dated 2021-05-07 and 1.1.4 dated 2021-07-07

 DESCRIPTION                  |   12 ++++---
 MD5                          |   51 ++++++++++++++++++++++---------
 NAMESPACE                    |   11 ++++++
 NEWS.md                      |   21 ++++++++++++
 R/build_shape.R              |    1 
 R/process_data.R             |    6 +++
 R/shape_generator.R          |   37 +++++++++++++++++++---
 README.md                    |   69 ++++++++++++++++++++++--------------------
 build                        |only
 inst                         |only
 man/Polygon-class.Rd         |   38 +++++++++++------------
 man/Venn-class.Rd            |   40 ++++++++++++------------
 man/fancy_2d_circle.Rd       |only
 man/fancy_3d_circle.Rd       |only
 man/fancy_6d_triangle.Rd     |only
 man/ggVennDiagram-package.Rd |   30 +++++++++---------
 man/label_position.Rd        |   27 +++++++++++++++-
 man/plotData_add_venn.Rd     |only
 man/plot_shapes.Rd           |   44 +++++++++++++--------------
 man/polygon-methods.Rd       |   36 +++++++++++-----------
 man/process_data.Rd          |   52 +++++++++++++++----------------
 man/vennplot-shapes.Rd       |   70 +++++++++++++++++++++----------------------
 vignettes                    |only
 23 files changed, 330 insertions(+), 215 deletions(-)

More information about ggVennDiagram at CRAN
Permanent link

Package AnnoProbe updated to version 0.1.5 with previous version 0.1.4 dated 2021-06-21

Title: Annotate the Gene Symbols for Probes in Expression Array
Description: We curated 147 of expression array, from 3 species(human,mouse,rat), 3 companies('Affymetrix','Illumina','Agilent'), by aligning the 'Fasta' sequences of all probes of each platform to their corresponding reference genome, and then annotate them to genes.
Author: Jianming Zeng [aut], Yujia Xiang [aut], Yonghe Xia [ctb, cre]
Maintainer: Yonghe Xia <xiayh17@gmail.com>

Diff between AnnoProbe versions 0.1.4 dated 2021-06-21 and 0.1.5 dated 2021-07-07

 DESCRIPTION  |   16 ++++++++--------
 MD5          |    4 ++--
 R/annoGene.R |    2 +-
 3 files changed, 11 insertions(+), 11 deletions(-)

More information about AnnoProbe at CRAN
Permanent link

Package odin updated to version 1.2.0 with previous version 1.0.8 dated 2020-10-28

Title: ODE Generation and Integration
Description: Generate systems of ordinary differential equations (ODE) and integrate them, using a domain specific language (DSL). The DSL uses R's syntax, but compiles to C in order to efficiently solve the system. A solver is not provided, but instead interfaces to the packages 'deSolve' and 'dde' are generated. With these, while solving the differential equations, no allocations are done and the calculations remain entirely in compiled code. Alternatively, a model can be transpiled to R for use in contexts where a C compiler is not present. After compilation, models can be inspected to return information about parameters and outputs, or intermediate values after calculations. 'odin' is not targeted at any particular domain and is suitable for any system that can be expressed primarily as mathematical expressions. Additional support is provided for working with delays (delay differential equations, DDE), using interpolated functions during interpolation, and for integrating quantities that represent arrays.
Author: Rich FitzJohn [aut, cre], Thibaut Jombart [ctb], Imperial College of Science, Technology and Medicine [cph]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>

Diff between odin versions 1.0.8 dated 2020-10-28 and 1.2.0 dated 2021-07-07

 odin-1.0.8/odin/R/compile.R                                |only
 odin-1.0.8/odin/R/generate_c_class.R                       |only
 odin-1.0.8/odin/tests/testthat/run                         |only
 odin-1.0.8/odin/tests/testthat/setup-odin.R                |only
 odin-1.0.8/odin/tests/testthat/test-compile.R              |only
 odin-1.2.0/odin/DESCRIPTION                                |   17 
 odin-1.2.0/odin/MD5                                        |  163 -
 odin-1.2.0/odin/NAMESPACE                                  |    6 
 odin-1.2.0/odin/NEWS.md                                    |   40 
 odin-1.2.0/odin/R/can_compile.R                            |   48 
 odin-1.2.0/odin/R/common.R                                 |   14 
 odin-1.2.0/odin/R/compat.R                                 |only
 odin-1.2.0/odin/R/dependencies.R                           |    1 
 odin-1.2.0/odin/R/generate_c.R                             |  106 
 odin-1.2.0/odin/R/generate_c_compiled.R                    |  111 
 odin-1.2.0/odin/R/generate_c_sexp.R                        |    2 
 odin-1.2.0/odin/R/generate_r.R                             |   18 
 odin-1.2.0/odin/R/generate_r_class.R                       |   58 
 odin-1.2.0/odin/R/generate_r_support.R                     |    3 
 odin-1.2.0/odin/R/generate_r_utils.R                       |    6 
 odin-1.2.0/odin/R/interface.R                              |   38 
 odin-1.2.0/odin/R/ir_deserialise.R                         |   17 
 odin-1.2.0/odin/R/ir_parse.R                               |  342 ++
 odin-1.2.0/odin/R/ir_parse_arrays.R                        |  108 
 odin-1.2.0/odin/R/ir_parse_config.R                        |  115 -
 odin-1.2.0/odin/R/ir_serialise.R                           |   18 
 odin-1.2.0/odin/R/misc.R                                   |   60 
 odin-1.2.0/odin/R/odin.R                                   |  117 -
 odin-1.2.0/odin/R/odin_build.R                             |   28 
 odin-1.2.0/odin/R/odin_options.R                           |   93 
 odin-1.2.0/odin/R/odin_package.R                           |   62 
 odin-1.2.0/odin/R/odin_parse.R                             |   19 
 odin-1.2.0/odin/R/odin_preprocess.R                        |    2 
 odin-1.2.0/odin/R/odin_validate.R                          |   12 
 odin-1.2.0/odin/R/opt.R                                    |only
 odin-1.2.0/odin/R/utils.R                                  |   70 
 odin-1.2.0/odin/R/wrapper.R                                |only
 odin-1.2.0/odin/README.md                                  |    2 
 odin-1.2.0/odin/build/vignette.rds                         |binary
 odin-1.2.0/odin/inst/WORDLIST                              |    5 
 odin-1.2.0/odin/inst/doc/discrete.R                        |    8 
 odin-1.2.0/odin/inst/doc/discrete.Rmd                      |   10 
 odin-1.2.0/odin/inst/doc/discrete.html                     | 1493 ++++++-------
 odin-1.2.0/odin/inst/doc/functions.html                    |  814 +++----
 odin-1.2.0/odin/inst/doc/odin.R                            |   18 
 odin-1.2.0/odin/inst/doc/odin.Rmd                          |   22 
 odin-1.2.0/odin/inst/doc/odin.html                         | 1315 +++++------
 odin-1.2.0/odin/inst/library.c                             |   36 
 odin-1.2.0/odin/inst/schema.json                           |   33 
 odin-1.2.0/odin/inst/template                              |only
 odin-1.2.0/odin/man/can_compile.Rd                         |   20 
 odin-1.2.0/odin/man/odin.Rd                                |   68 
 odin-1.2.0/odin/man/odin_build.Rd                          |   28 
 odin-1.2.0/odin/man/odin_ir.Rd                             |    6 
 odin-1.2.0/odin/man/odin_ir_deserialise.Rd                 |    2 
 odin-1.2.0/odin/man/odin_options.Rd                        |   65 
 odin-1.2.0/odin/man/odin_package.Rd                        |   27 
 odin-1.2.0/odin/man/odin_parse.Rd                          |    8 
 odin-1.2.0/odin/man/odin_validate.Rd                       |    6 
 odin-1.2.0/odin/tests/testthat/helper-odin.R               |   56 
 odin-1.2.0/odin/tests/testthat/identity.c                  |only
 odin-1.2.0/odin/tests/testthat/test-interface.R            |   89 
 odin-1.2.0/odin/tests/testthat/test-ir.R                   |    9 
 odin-1.2.0/odin/tests/testthat/test-odin-options.R         |only
 odin-1.2.0/odin/tests/testthat/test-odin-validate.R        |    3 
 odin-1.2.0/odin/tests/testthat/test-opt.R                  |only
 odin-1.2.0/odin/tests/testthat/test-package.R              |   33 
 odin-1.2.0/odin/tests/testthat/test-parse2-config.R        |   66 
 odin-1.2.0/odin/tests/testthat/test-parse2-general.R       |  187 -
 odin-1.2.0/odin/tests/testthat/test-parse2-rewrite.R       |  138 +
 odin-1.2.0/odin/tests/testthat/test-parse2-unused.R        |   38 
 odin-1.2.0/odin/tests/testthat/test-preprocess.R           |   19 
 odin-1.2.0/odin/tests/testthat/test-ring-cache.R           |   17 
 odin-1.2.0/odin/tests/testthat/test-run-basic.R            |only
 odin-1.2.0/odin/tests/testthat/test-run-delay-continuous.R |only
 odin-1.2.0/odin/tests/testthat/test-run-delay-discrete.R   |only
 odin-1.2.0/odin/tests/testthat/test-run-discrete.R         |only
 odin-1.2.0/odin/tests/testthat/test-run-examples.R         |only
 odin-1.2.0/odin/tests/testthat/test-run-general.R          |only
 odin-1.2.0/odin/tests/testthat/test-run-interpolation.R    |only
 odin-1.2.0/odin/tests/testthat/test-run-library.R          |only
 odin-1.2.0/odin/tests/testthat/test-run-regression.R       |only
 odin-1.2.0/odin/tests/testthat/test-run-stochastic.R       |only
 odin-1.2.0/odin/tests/testthat/test-support.R              |   24 
 odin-1.2.0/odin/tests/testthat/test-util.R                 |  119 +
 odin-1.2.0/odin/tests/testthat/user_fns.R                  |only
 odin-1.2.0/odin/tests/testthat/user_fns4.c                 |only
 odin-1.2.0/odin/vignettes/discrete.Rmd                     |   10 
 odin-1.2.0/odin/vignettes/odin.Rmd                         |   22 
 89 files changed, 3596 insertions(+), 2914 deletions(-)

More information about odin at CRAN
Permanent link

Package naspaclust updated to version 0.2.1 with previous version 0.1.0 dated 2021-03-12

Title: Nature-Inspired Spatial Clustering
Description: Implement and enhance the performance of spatial fuzzy clustering using Fuzzy Geographically Weighted Clustering with various optimization algorithms, mainly from Xin She Yang (2014) <ISBN:9780124167438> with book entitled Nature-Inspired Optimization Algorithms. The optimization algorithm is useful to tackle the disadvantages of clustering inconsistency when using the traditional approach. The distance measurements option is also provided in order to increase the quality of clustering results. The Fuzzy Geographically Weighted Clustering with nature inspired optimisation algorithm was firstly developed by Arie Wahyu Wijayanto and Ayu Purwarianti (2014) <doi:10.1109/CITSM.2014.7042178> using Artificial Bee Colony algorithm.
Author: Bahrul Ilmi Nasution [aut, cre], Robert Kurniawan [aut], Rezzy Eko Caraka [aut]
Maintainer: Bahrul Ilmi Nasution <bahrulnst@gmail.com>

Diff between naspaclust versions 0.1.0 dated 2021-03-12 and 0.2.1 dated 2021-07-07

 DESCRIPTION       |    6 ++---
 MD5               |   18 ++++++++---------
 R/ei.R            |   57 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 R/fpafgwc.R       |    1 
 R/ifafgwc.R       |   10 ++++-----
 R/mainfunction.R  |   48 ++++++++++++++++++++++-----------------------
 R/psofgwc.R       |    4 +--
 build/partial.rdb |binary
 man/ifafgwc.Rd    |   10 ++++-----
 man/psofgwc.Rd    |    4 +--
 10 files changed, 108 insertions(+), 50 deletions(-)

More information about naspaclust at CRAN
Permanent link

New package tscopula with initial version 0.2.1
Package: tscopula
Title: Time Series Copula Models
Version: 0.2.1
Date: 2021-07-03
Authors@R: c(person(given = "Alexander", family = "McNeil", email = "alexanderjmcneil@gmail.com", role = c("aut", "cre")), person(given = "Martin", family = "Bladt", email = "martinbladt@gmail.com", role = "aut"))
Maintainer: Alexander McNeil <alexanderjmcneil@gmail.com>
Description: Functions for the analysis of time series using copula models. The package is based on methodology described in the following references. McNeil, A.J. (2021) <doi:10.3390/risks9010014>, Bladt, M., & McNeil, A.J. (2020) <arXiv:2006.11088>.
Depends: R (>= 3.5.0)
License: GPL-3
LazyData: true
Encoding: UTF-8
Imports: methods, stats, graphics, utils, zoo, xts, FKF, ltsa, rvinecopulib, FitAR, arfima, Matrix
Collate: 'basic_objects.R' 'armacopula.R' 'dvinecopula.R' 'dvinecopula2.R' 'fitting_basic.R' 'margins.R' 'full_models.R' 'vtransforms.R' 'fitting_vtscopula.R' 'helper_vtarma.R' 'data.R'
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-07-06 13:04:26 UTC; alexanderjmcneil
Author: Alexander McNeil [aut, cre], Martin Bladt [aut]
Repository: CRAN
Date/Publication: 2021-07-07 08:20:02 UTC

More information about tscopula at CRAN
Permanent link

Package tidyBdE updated to version 0.1.2 with previous version 0.1.1 dated 2021-06-05

Title: Download Data from Bank of Spain
Description: Tools to download data series from 'Banco de España' ('BdE') on 'tibble' format. 'Banco de España' is the national central bank and, within the framework of the Single Supervisory Mechanism ('SSM'), the supervisor of the Spanish banking system along with the European Central Bank. This package is in no way sponsored endorsed or administered by 'Banco de España'.
Author: Diego H. Herrero [aut, cre, cph] (<https://orcid.org/0000-0001-8457-4658>), Banco de España [cph] (for the data.)
Maintainer: Diego H. Herrero <dev.dieghernan@gmail.com>

Diff between tidyBdE versions 0.1.1 dated 2021-06-05 and 0.1.2 dated 2021-07-07

 DESCRIPTION                          |    6 +-
 MD5                                  |   35 +++++++-----
 NEWS.md                              |    6 ++
 R/catalogs.R                         |   44 ++++++++--------
 R/series.R                           |   15 +++++
 R/utils.R                            |    5 +
 README.md                            |    2 
 inst/doc/tidyBdE.R                   |   26 ++++-----
 inst/doc/tidyBdE.Rmd                 |   61 +++++++---------------
 inst/doc/tidyBdE.html                |   95 ++---------------------------------
 inst/schemaorg.json                  |    2 
 inst/tinytest/test_series.R          |    2 
 man/bde_catalog_search.Rd            |   21 +------
 man/figures/README-chart-1.png       |binary
 man/figures/README-gdp-1.png         |binary
 man/figures/README-macroseries-1.png |binary
 vignettes/chart-1.png                |only
 vignettes/gdp-1.png                  |only
 vignettes/macroseries-1.png          |only
 vignettes/tidyBdE.Rmd                |   61 +++++++---------------
 20 files changed, 133 insertions(+), 248 deletions(-)

More information about tidyBdE at CRAN
Permanent link

New package squeezy with initial version 1.0
Package: squeezy
Title: Group-Adaptive Elastic Net Penalised Generalised Linear Models
Version: 1.0
Date: 2021-06-07
Authors@R: c(person(c("Mirrelijn","M."), "van Nee", role = c("aut", "cre"), email = "m.vannee@amsterdamumc.nl"), person("Tim", "van de Brug", role = "aut"), person(c("Mark","A."), "van de Wiel", role = "aut"))
Author: Mirrelijn M. van Nee [aut, cre], Tim van de Brug [aut], Mark A. van de Wiel [aut]
Maintainer: Mirrelijn M. van Nee <m.vannee@amsterdamumc.nl>
Depends: R (>= 3.5.0)
Imports: glmnet, stats, Matrix, multiridge (>= 1.5), mvtnorm
Suggests: ggplot2, ecpc
Description: Fit linear and logistic regression models penalised with group-adaptive elastic net penalties. The group penalties correspond to groups of covariates defined by a co-data group set. The method accommodates inclusion of unpenalised covariates and overlapping groups. See Van Nee et al. (2021) <arXiv:2101.03875>.
License: GPL (>= 3)
URL: https://arxiv.org/abs/2101.03875
NeedsCompilation: no
Packaged: 2021-07-06 13:04:08 UTC; VNOB-0728
Repository: CRAN
Date/Publication: 2021-07-07 08:20:06 UTC

More information about squeezy at CRAN
Permanent link

New package sdmApp with initial version 0.0.2
Package: sdmApp
Title: A User-Friendly Application for Species Distribution Modeling
Version: 0.0.2
Authors@R: c(person(given = "Aboubacar", family = "HEMA", role = c("aut", "cre"), email = "aboubacarhema94@gmail.com"), person(given = "Babacar", family = "NDAO", role = "aut", email = "babacar.ndao@cse.sn"), person(given = "Louise", family = "LEROUX", role = "aut", email = "louise.leroux@cirad.fr"), person(given = "Abdoul Aziz", family = "DIOUF", role = "aut", email = "aziz.diouf@cse.sn"))
Author: Aboubacar HEMA [aut, cre], Babacar NDAO [aut], Louise LEROUX [aut], Abdoul Aziz DIOUF [aut]
Maintainer: Aboubacar HEMA <aboubacarhema94@gmail.com>
Description: A 'shiny' application that allows non-expert 'R' users to easily model species distribution. It offers a reproducible work flow for species distribution modeling into a single and user friendly environment. 'sdmApp' takes 'raster' data (in format supported by the 'raster package') and species occurrence data (several format supported) as input argument. It provides an interactive graphical user interface (GUI).
License: GPL-3
URL: https://github.com/Abson-dev/sdmApp
BugReports: https://github.com/Abson-dev/sdmApp/issues
Depends: R (>= 3.5.0)
Imports: raster (>= 2.6.7), sp (>= 1.2.0), shiny (>= 0.12.2)
Suggests: covr, grDevices, knitr, rmarkdown, stats, testthat, utils, rgdal (>= 1.5-8), automap (>= 1.0-14), future.apply, blockCV (>= 2.1.1), dismo (>= 1.0.12), DT, kernlab (>= 0.9-29), randomForest (>= 4.6.10), readxl (>= 1.3.1), rhandsontable (>= 0.3.7), sf, shinyBS (>= 0.61), shinyFiles (>= 0.7.0), SSDM (>= 0.2.8), ggcorrplot (>= 0.1.3), ggplot2 (>= 3.1.1), cowplot (>= 1.1.1), haven (>= 2.3.1), dplyr (>= 1.0.3), tidyr (>= 1.1.2), data.table, rgeos (>= 0.3-8), rJava (>= 0.9-13)
VignetteBuilder: knitr, rmarkdown
Encoding: UTF-8
Language: en-US
LazyLoad: yes
LazyData: no
ZipData: no
BuildResaveData: no
SystemRequirements: Java (>= 8)
NeedsCompilation: no
Packaged: 2021-07-06 15:07:43 UTC; DELLDRAMOMO
Repository: CRAN
Date/Publication: 2021-07-07 08:30:02 UTC

More information about sdmApp at CRAN
Permanent link

New package revpref with initial version 0.1.0
Package: revpref
Title: Tools for Computational Revealed Preference Analysis
Version: 0.1.0
Authors@R: person(given = "Khushboo", family = "Surana", role = c("aut", "cre"), email = "khushboo.surana@york.ac.uk", comment = c(ORCID = "0000-0002-0453-6182"))
Maintainer: Khushboo Surana <khushboo.surana@york.ac.uk>
Description: Tools to (i) check consistency of a finite set of consumer demand observations with a number of revealed preference axioms at a given efficiency level, (ii) compute goodness-of-fit indices when the data do not obey the axioms, and (iii) compute power against uniformly random behavior.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/ksurana21/revpref
BugReports: https://github.com/ksurana21/revpref/issues
Imports: gtools
Suggests: rmarkdown, knitr
NeedsCompilation: no
Packaged: 2021-07-05 11:03:31 UTC; ks1779
Author: Khushboo Surana [aut, cre] (<https://orcid.org/0000-0002-0453-6182>)
Repository: CRAN
Date/Publication: 2021-07-07 08:10:02 UTC

More information about revpref at CRAN
Permanent link

New package katex with initial version 1.0.0
Package: katex
Title: Rendering Math to HTML, 'MathML', or R-Documentation Format
Version: 1.0.0
Authors@R: person("Jeroen", "Ooms", role = c("aut", "cre"), email = "jeroen@berkeley.edu", comment = c(ORCID = "0000-0002-4035-0289"))
Description: Convert latex math expressions to HTML and 'MathML' for use in markdown documents or package manual pages. The rendering is done in R using the V8 engine (i.e. server-side), which eliminates the need for embedding the 'MathJax' library into your web pages. In addition a 'math-to-rd' wrapper is provided to automatically render beautiful math in R documentation files.
License: MIT + file LICENSE
URL: https://docs.ropensci.org/katex/, https://github.com/ropensci/katex https://katex.org/docs/options.html (upstream)
BugReports: https://github.com/ropensci/katex/issues
Encoding: UTF-8
Imports: V8
NeedsCompilation: no
Packaged: 2021-07-06 09:09:35 UTC; jeroen
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Repository: CRAN
Date/Publication: 2021-07-07 08:10:05 UTC

More information about katex at CRAN
Permanent link

New package immunarch with initial version 0.6.6
Package: immunarch
Title: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires
Version: 0.6.6
Authors@R: c( person("Vadim I.", "Nazarov", , "vdm.nazarov@gmail.com", c("aut", "cre")), person("Vasily O.", "Tsvetkov", , role = "aut"), person("Eugene", "Rumynskiy", , role = "aut"), person("Anna", "Lorenc", , role = "ctb"), person("Daniel J.", "Moore", , role = "ctb"), person("Victor", "Greiff", , role = "ctb"), person("ImmunoMind", role = c("cph", "fnd")) )
Contact: support@immunomind.io
Description: A comprehensive framework for bioinformatics exploratory analysis of bulk and single-cell T-cell receptor and antibody repertoires. It provides seamless data loading, analysis and visualisation for AIRR (Adaptive Immune Receptor Repertoire) data, both bulk immunosequencing (RepSeq) and single-cell sequencing (scRNAseq). It implements most of the widely used AIRR analysis methods, such as: clonality analysis, estimation of repertoire similarities in distribution of clonotypes and gene segments, repertoire diversity analysis, annotation of clonotypes using external immune receptor databases and clonotype tracking in vaccination and cancer studies. A successor to our previously published 'tcR' immunoinformatics package (Nazarov 2015) <doi:10.1186/s12859-015-0613-1>.
License: AGPL-3
URL: https://immunarch.com/, https://github.com/immunomind/immunarch
BugReports: https://github.com/immunomind/immunarch/issues
Imports: factoextra (>= 1.0.4), fpc, UpSetR (>= 1.4.0), pheatmap (>= 1.0.12), ggrepel (>= 0.8.0), reshape2 (>= 1.4.2), circlize, MASS (>= 7.3), Rtsne (>= 0.15), readr (>= 1.3.1), readxl (>= 1.3.1), shiny (>= 1.4.0), shinythemes, airr, ggseqlogo, stringr (>= 1.4.0), ggalluvial (>= 0.10.0), Rcpp (>= 1.0), magrittr, tibble (>= 2.0), methods, scales, ggpubr (>= 0.2), rlang (>= 0.4), plyr, dbplyr (>= 1.4.0)
Depends: R (>= 3.5.0), ggplot2 (>= 3.1.0), dplyr (>= 0.8.0), dtplyr (>= 1.0.0), data.table (>= 1.12.6), patchwork
LinkingTo: Rcpp
Suggests: knitr (>= 1.8), roxygen2 (>= 3.0.0), testthat (>= 2.1.0), pkgdown (>= 0.1.0), assertthat, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
Packaged: 2021-07-06 14:16:36 UTC; user
Author: Vadim I. Nazarov [aut, cre], Vasily O. Tsvetkov [aut], Eugene Rumynskiy [aut], Anna Lorenc [ctb], Daniel J. Moore [ctb], Victor Greiff [ctb], ImmunoMind [cph, fnd]
Maintainer: Vadim I. Nazarov <vdm.nazarov@gmail.com>
Repository: CRAN
Date/Publication: 2021-07-07 08:20:09 UTC

More information about immunarch at CRAN
Permanent link

New package ctf with initial version 0.1.0
Package: ctf
Title: Read and Write Column Text Format (CTF)
Version: 0.1.0
Date: 2021-06-21
Authors@R: person("Clark", "Fitzgerald", role = c("aut", "cre"), email = "fitzgerald@csus.edu", comment = c(ORCID = "0000-0003-3446-6389"))
Maintainer: Clark Fitzgerald <fitzgerald@csus.edu>
Depends: R (>= 3.1.0)
Imports: jsonlite, iotools
Suggests: roxygen2, knitr, rmarkdown, testthat
Description: Column Text Format (CTF) is a new tabular data format designed for simplicity and performance. CTF is the simplest column store you can imagine: plain text files for each column in a table, and a metadata file. The underlying plain text means the data is human readable and familiar to programmers, unlike specialized binary formats. CTF is faster than row oriented formats like CSV when loading a subset of the columns in a table. This package provides functions to read and write CTF data from R.
License: MIT + file LICENSE
URL: https://github.com/julianofhernandez/ctf
BugReports: https://github.com/julianofhernandez/ctf
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-07-06 23:21:57 UTC; fitzgerald
Author: Clark Fitzgerald [aut, cre] (<https://orcid.org/0000-0003-3446-6389>)
Repository: CRAN
Date/Publication: 2021-07-07 09:00:05 UTC

More information about ctf at CRAN
Permanent link

New package CALANGO with initial version 1.0.2
Package: CALANGO
Title: Comparative Analysis with Annotation-Based Genomic Components
Version: 1.0.2
Date: 2021-07-05
Language: en-US
Authors@R: c(person("Francisco", "Lobo", email = "franciscolobo@gmail.com", role = c("aut")), person("Felipe", "Campelo", email = "fcampelo@gmail.com", role = c("aut", "cre")), person("Jorge Augusto", "Hongo", email = "jorgeahongo@gmail.com", role = "aut"), person("Giovanni", "Marques de Castro", email = "giomcastro@gmail.com", role = "aut"), person("Gabriel", "Almeida", email = "gabriel.magno@gmail.com", role = c("sad", "dnc")))
Maintainer: Felipe Campelo <fcampelo@gmail.com>
Description: A first-principle, phylogeny-aware comparative genomics tool for investigating associations between terms used to annotate genomic components (e.g., Pfam IDs, Gene Ontology terms,) with quantitative or rank variables such as number of cell types, genome size, or density of specific genomic elements. See the project website for more information, documentation and examples.
License: GPL-2
Depends: R (>= 3.6.0)
Imports: assertthat (>= 0.2.1), pbmcapply (>= 1.5.0), ape (>= 5.3.0), rmarkdown (>= 2.1.0), nlme (>= 3.1.0), BiocManager (>= 1.30.10), taxize (>= 0.9.92), dendextend (>= 1.13.4), heatmaply (>= 1.1.0), ggplot2 (>= 2.3.2), plotly (>= 4.9.2), DT (>= 0.13), htmltools (>= 0.5.0), htmlwidgets (>= 1.5.1), pkgdown (>= 1.5.1), knitr (>= 1.28)
Suggests: AnnotationDbi, KEGGREST, GO.db
Encoding: UTF-8
URL: https://fcampelo.github.io/CALANGO/
BugReports: https://github.com/fcampelo/CALANGO/issues/
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-07-05 12:46:29 UTC; campelof
Author: Francisco Lobo [aut], Felipe Campelo [aut, cre], Jorge Augusto Hongo [aut], Giovanni Marques de Castro [aut], Gabriel Almeida [sad, dnc]
Repository: CRAN
Date/Publication: 2021-07-07 08:10:08 UTC

More information about CALANGO at CRAN
Permanent link

Package gpindex updated to version 0.3.1 with previous version 0.2.5 dated 2021-02-02

Title: Generalized Price and Quantity Indexes
Description: A small package for calculating lots of different price indexes, and by extension quantity indexes. Provides tools to build and work with any type of bilateral generalized-mean index (of which most price indexes are), along with a few important indexes that don't belong to the generalized-mean family. Implements and extends many of the methods in Balk (2008, ISBN:978-1-107-40496-0) and ILO, IMF, OECD, Eurostat, UN, and World Bank (2020, ISBN:978-1-51354-298-0) for bilateral price indexes.
Author: Steve Martin [aut, cre, cph]
Maintainer: Steve Martin <stevemartin041@gmail.com>

Diff between gpindex versions 0.2.5 dated 2021-02-02 and 0.3.1 dated 2021-07-07

 gpindex-0.2.5/gpindex/build                               |only
 gpindex-0.2.5/gpindex/inst                                |only
 gpindex-0.2.5/gpindex/man/nested_contributions.Rd         |only
 gpindex-0.2.5/gpindex/tests/vignette_gpindex.R            |only
 gpindex-0.2.5/gpindex/tests/vignette_gpindex.Rout.save    |only
 gpindex-0.2.5/gpindex/vignettes                           |only
 gpindex-0.3.1/gpindex/DESCRIPTION                         |   10 
 gpindex-0.3.1/gpindex/MD5                                 |   60 -
 gpindex-0.3.1/gpindex/NAMESPACE                           |   24 
 gpindex-0.3.1/gpindex/NEWS                                |   48 -
 gpindex-0.3.1/gpindex/R/1_means.R                         |   62 -
 gpindex-0.3.1/gpindex/R/2_weights.R                       |   94 +-
 gpindex-0.3.1/gpindex/R/3_price_indexes.R                 |  105 +-
 gpindex-0.3.1/gpindex/R/5_utilities.R                     |   73 +
 gpindex-0.3.1/gpindex/README.md                           |   43 
 gpindex-0.3.1/gpindex/man/contributions.Rd                |only
 gpindex-0.3.1/gpindex/man/generalized_mean.Rd             |  152 +--
 gpindex-0.3.1/gpindex/man/gpindex.Rd                      |   26 
 gpindex-0.3.1/gpindex/man/lehmer_mean.Rd                  |   84 -
 gpindex-0.3.1/gpindex/man/logarithmic_means.Rd            |   81 -
 gpindex-0.3.1/gpindex/man/nested_mean.Rd                  |only
 gpindex-0.3.1/gpindex/man/offset_prices.Rd                |   12 
 gpindex-0.3.1/gpindex/man/outlier.Rd                      |only
 gpindex-0.3.1/gpindex/man/pq6.Rd                          |   19 
 gpindex-0.3.1/gpindex/man/price_indexes.Rd                |  169 +--
 gpindex-0.3.1/gpindex/man/quantity_index.Rd               |   10 
 gpindex-0.3.1/gpindex/man/transform_weights.Rd            |  164 +--
 gpindex-0.3.1/gpindex/tests/Examples/gpindex-Ex.Rout.save |  656 ++++++++------
 gpindex-0.3.1/gpindex/tests/test_means.R                  |  342 ++-----
 gpindex-0.3.1/gpindex/tests/test_means.Rout.save          |only
 gpindex-0.3.1/gpindex/tests/test_price_indexes.R          |  232 +---
 gpindex-0.3.1/gpindex/tests/test_price_indexes.Rout.save  |only
 gpindex-0.3.1/gpindex/tests/test_utilities.R              |   65 -
 gpindex-0.3.1/gpindex/tests/test_utilities.Rout.save      |only
 gpindex-0.3.1/gpindex/tests/test_weights.R                |  156 +--
 gpindex-0.3.1/gpindex/tests/test_weights.Rout.save        |only
 36 files changed, 1328 insertions(+), 1359 deletions(-)

More information about gpindex at CRAN
Permanent link

Package LipidMS updated to version 3.0.1 with previous version 3.0.0 dated 2021-05-25

Title: Lipid Annotation for LC-MS/MS DDA or DIA Data
Description: Lipid annotation in untargeted LC-MS lipidomics based on fragmentation rules. Alcoriza-Balaguer MI, Garcia-Canaveras JC, Lopez A, Conde I, Juan O, Carretero J, Lahoz A (2019) <doi:10.1021/acs.analchem.8b03409>.
Author: M Isabel Alcoriza-Balaguer
Maintainer: M Isabel Alcoriza-Balaguer <maribel_alcoriza@iislafe.es>

Diff between LipidMS versions 3.0.0 dated 2021-05-25 and 3.0.1 dated 2021-07-07

 DESCRIPTION                    |    6 
 MD5                            |   44 ++--
 R/LipidMSapp.R                 |    2 
 R/additionalFunctions.R        |   84 --------
 R/dataProcessing.R             |   28 --
 R/idFunctionsPos.R             |  420 ++++++++++++++++++++---------------------
 R/internalProcessing.R         |   34 ++-
 R/subfunctionsIdentification.R |  224 ---------------------
 man/LipidMSapp.Rd              |    2 
 man/chainFrags.Rd              |   29 --
 man/checkClass.Rd              |   25 --
 man/checkIntensityRules.Rd     |   32 ---
 man/coelutingFrags.Rd          |   21 --
 man/combineChains.Rd           |   30 --
 man/crossTables.Rd             |    9 
 man/dataProcessing.Rd          |    2 
 man/ddaFrags.Rd                |   22 --
 man/findCandidates.Rd          |   30 --
 man/getInclusionList.Rd        |   10 
 man/organizeResults.Rd         |   35 ---
 man/plotLipids.Rd              |   56 -----
 man/readMSfile.Rd              |    4 
 man/searchIsotopes.Rd          |    7 
 23 files changed, 281 insertions(+), 875 deletions(-)

More information about LipidMS at CRAN
Permanent link

Package jmvcore updated to version 1.8 with previous version 1.2.23 dated 2020-06-02

Title: Dependencies for the 'jamovi' Framework
Description: A framework for creating rich interactive analyses for the jamovi platform (see <https://www.jamovi.org> for more information).
Author: Jonathon Love
Maintainer: Jonathon Love <jon@thon.cc>

Diff between jmvcore versions 1.2.23 dated 2020-06-02 and 1.8 dated 2021-07-07

 DESCRIPTION       |   11 ++++-----
 MD5               |   35 ++++++++++++++--------------
 NAMESPACE         |    4 +++
 R/analysis.R      |   46 +++++++++++++++++++++++++++----------
 R/array.R         |   24 +++++++++++++------
 R/cell.R          |    2 +
 R/create.R        |   12 ++++++---
 R/group.R         |    4 ---
 R/html.R          |    2 -
 R/image.R         |   32 +++++++++++++++++++-------
 R/options.R       |   66 +++++++++++++++++++++++++++++++++++-------------------
 R/output.R        |only
 R/preformatted.R  |    2 -
 R/results.R       |    8 +-----
 R/table.R         |    4 +--
 R/utils.R         |   11 +++++++--
 inst/jamovi.proto |   34 +++++++++++++++++++++++++++
 man/Analysis.Rd   |    5 +++-
 man/Options.Rd    |    6 ++++
 19 files changed, 214 insertions(+), 94 deletions(-)

More information about jmvcore at CRAN
Permanent link

Package VancouvR (with last version 0.1.4) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-06-07 0.1.4
2021-05-10 0.1.3
2021-01-13 0.1.2

Permanent link
Package gfilinreg (with last version 2.0.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-03-16 2.0.1
2021-01-04 2.0.0
2020-12-04 1.0.0

Permanent link
Package tidyHeatmap updated to version 1.3.1 with previous version 1.2.2 dated 2021-03-22

Title: A Tidy Implementation of Heatmap
Description: This is a tidy implementation for heatmap. At the moment it is based on the (great) package 'ComplexHeatmap'. The goal of this package is to interface a tidy data frame with this powerful tool. Some of the advantages are: Row and/or columns colour annotations are easy to integrate just specifying one parameter (column names). Custom grouping of rows is easy to specify providing a grouped tbl. For example: df %>% group_by(...). Labels size adjusted by row and column total number. Default use of Brewer and Viridis palettes.
Author: Stefano Mangiola [aut, cre], Anthony Papenfuss [ctb]
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>

Diff between tidyHeatmap versions 1.2.2 dated 2021-03-22 and 1.3.1 dated 2021-07-07

 tidyHeatmap-1.2.2/tidyHeatmap/man/layer_symbol-methods.Rd        |only
 tidyHeatmap-1.2.2/tidyHeatmap/man/layer_symbol.Rd                |only
 tidyHeatmap-1.2.2/tidyHeatmap/tests/figs                         |only
 tidyHeatmap-1.3.1/tidyHeatmap/DESCRIPTION                        |    8 
 tidyHeatmap-1.3.1/tidyHeatmap/MD5                                |   97 -
 tidyHeatmap-1.3.1/tidyHeatmap/NAMESPACE                          |   11 
 tidyHeatmap-1.3.1/tidyHeatmap/R/functions.R                      |   34 
 tidyHeatmap-1.3.1/tidyHeatmap/R/methods.R                        |  546 +++++++++-
 tidyHeatmap-1.3.1/tidyHeatmap/R/utilities.R                      |    9 
 tidyHeatmap-1.3.1/tidyHeatmap/README.md                          |  164 ++-
 tidyHeatmap-1.3.1/tidyHeatmap/build/tidyHeatmap.pdf              |binary
 tidyHeatmap-1.3.1/tidyHeatmap/build/vignette.rds                 |binary
 tidyHeatmap-1.3.1/tidyHeatmap/inst/doc/introduction.R            |   90 +
 tidyHeatmap-1.3.1/tidyHeatmap/inst/doc/introduction.Rmd          |  504 +++++----
 tidyHeatmap-1.3.1/tidyHeatmap/inst/doc/introduction.html         |  532 ++++-----
 tidyHeatmap-1.3.1/tidyHeatmap/man/add_bar-methods.Rd             |    2 
 tidyHeatmap-1.3.1/tidyHeatmap/man/add_line-methods.Rd            |    2 
 tidyHeatmap-1.3.1/tidyHeatmap/man/add_point-methods.Rd           |    2 
 tidyHeatmap-1.3.1/tidyHeatmap/man/add_tile-methods.Rd            |    2 
 tidyHeatmap-1.3.1/tidyHeatmap/man/figures/unnamed-chunk-10-1.png |binary
 tidyHeatmap-1.3.1/tidyHeatmap/man/figures/unnamed-chunk-11-1.png |binary
 tidyHeatmap-1.3.1/tidyHeatmap/man/figures/unnamed-chunk-12-1.png |binary
 tidyHeatmap-1.3.1/tidyHeatmap/man/figures/unnamed-chunk-13-1.png |binary
 tidyHeatmap-1.3.1/tidyHeatmap/man/figures/unnamed-chunk-14-1.png |only
 tidyHeatmap-1.3.1/tidyHeatmap/man/figures/unnamed-chunk-15-1.png |only
 tidyHeatmap-1.3.1/tidyHeatmap/man/figures/unnamed-chunk-16-1.png |only
 tidyHeatmap-1.3.1/tidyHeatmap/man/figures/unnamed-chunk-17-1.png |only
 tidyHeatmap-1.3.1/tidyHeatmap/man/figures/unnamed-chunk-18-1.png |only
 tidyHeatmap-1.3.1/tidyHeatmap/man/figures/unnamed-chunk-19-1.png |only
 tidyHeatmap-1.3.1/tidyHeatmap/man/figures/unnamed-chunk-8-1.png  |binary
 tidyHeatmap-1.3.1/tidyHeatmap/man/figures/unnamed-chunk-9-1.png  |binary
 tidyHeatmap-1.3.1/tidyHeatmap/man/layer-methods.Rd               |only
 tidyHeatmap-1.3.1/tidyHeatmap/man/split-methods.Rd               |only
 tidyHeatmap-1.3.1/tidyHeatmap/tests/testthat/_snaps              |only
 tidyHeatmap-1.3.1/tidyHeatmap/tests/testthat/tests.R             |   28 
 tidyHeatmap-1.3.1/tidyHeatmap/vignettes/introduction.Rmd         |  504 +++++----
 36 files changed, 1667 insertions(+), 868 deletions(-)

More information about tidyHeatmap at CRAN
Permanent link

Package Qapprox updated to version 0.2.0 with previous version 0.1.0 dated 2020-09-29

Title: Approximation to the Survival Functions of Quadratic Forms of Gaussian Variables
Description: Calculates the right-tail probability of quadratic forms of Gaussian variables using the skewness-kurtosis ratio matching method, modified Liu-Tang-Zhang method and Satterthwaite-Welch method. The technical details can be found in Hong Zhang, Judong Shen and Zheyang Wu (2020) <arXiv:2005.00905>.
Author: Hong Zhang
Maintainer: Hong Zhang <hzhang@wpi.edu>

Diff between Qapprox versions 0.1.0 dated 2020-09-29 and 0.2.0 dated 2021-07-07

 DESCRIPTION       |    7 ++--
 MD5               |   10 +++----
 R/Qapprox.R       |   58 +++++++++++++++++++++-------------------
 R/Qapprox_nc.R    |   77 +++++++++++++++++++++++++++++-------------------------
 man/Qapprox.Rd    |    6 ++--
 man/Qapprox_nc.Rd |    8 ++---
 6 files changed, 88 insertions(+), 78 deletions(-)

More information about Qapprox at CRAN
Permanent link

Package policytree updated to version 1.1.1 with previous version 1.1.0 dated 2021-06-24

Title: Policy Learning via Doubly Robust Empirical Welfare Maximization over Trees
Description: Learn optimal policies via doubly robust empirical welfare maximization over trees. This package implements the multi-action doubly robust approach of Zhou, Athey and Wager (2018) <arXiv:1810.04778> in the case where we want to learn policies that belong to the class of depth k decision trees.
Author: Erik Sverdrup [aut, cre], Ayush Kanodia [aut], Zhengyuan Zhou [aut], Susan Athey [aut], Stefan Wager [aut]
Maintainer: Erik Sverdrup <erikcs@stanford.edu>

Diff between policytree versions 1.1.0 dated 2021-06-24 and 1.1.1 dated 2021-07-07

 DESCRIPTION                           |    6 ++---
 MD5                                   |    4 +--
 tests/testthat/test_cran_smoke_test.R |   38 ----------------------------------
 3 files changed, 6 insertions(+), 42 deletions(-)

More information about policytree at CRAN
Permanent link

Package NEONiso updated to version 0.5.0 with previous version 0.4.0 dated 2021-03-19

Title: Tools to Calibrate and Work with NEON Atmospheric Isotope Data
Description: Functions for downloading, calibrating, and analyzing atmospheric isotope data bundled into the eddy covariance data products of the National Ecological Observatory Network (NEON) <https://www.neonscience.org>. In this version, calibration tools are provided for only the carbon isotope products. Tools for calibrating water isotope products are under development. More details are found in Fiorella et al. (2021) <doi:10.1029/2020JG005862>, and the readme file at <https://github.com/SPATIAL-Lab/NEONiso>.
Author: Rich Fiorella [aut, cre] (<https://orcid.org/0000-0002-0824-4777>), Gabriel J. Bowen [rth]
Maintainer: Rich Fiorella <rich.fiorella@utah.edu>

Diff between NEONiso versions 0.4.0 dated 2021-03-19 and 0.5.0 dated 2021-07-07

 NEONiso-0.4.0/NEONiso/inst/extdata/NEON.D15.ONAQ.DP4.00200.001.nsae.2019-05.basic.20201020T211037Z.packed.h5 |only
 NEONiso-0.5.0/NEONiso/DESCRIPTION                                                                            |   13 
 NEONiso-0.5.0/NEONiso/MD5                                                                                    |  132 +-
 NEONiso-0.5.0/NEONiso/NAMESPACE                                                                              |    5 
 NEONiso-0.5.0/NEONiso/NEWS.md                                                                                |    8 
 NEONiso-0.5.0/NEONiso/R/NEONiso.R                                                                            |    2 
 NEONiso-0.5.0/NEONiso/R/calibrate_ambient_carbon_Bowling2003.R                                               |   16 
 NEONiso-0.5.0/NEONiso/R/calibrate_ambient_carbon_linreg.R                                                    |   10 
 NEONiso-0.5.0/NEONiso/R/calibrate_ambient_water_isotopes.R                                                   |only
 NEONiso-0.5.0/NEONiso/R/calibrate_carbon.R                                                                   |only
 NEONiso-0.5.0/NEONiso/R/calibrate_carbon_bymonth.R                                                           |    7 
 NEONiso-0.5.0/NEONiso/R/calibrate_standards_carbon.R                                                         |  288 ++--
 NEONiso-0.5.0/NEONiso/R/calibrate_standards_water.R                                                          |only
 NEONiso-0.5.0/NEONiso/R/calibrate_water.R                                                                    |only
 NEONiso-0.5.0/NEONiso/R/calibrate_water_linreg_bymonth.R                                                     |only
 NEONiso-0.5.0/NEONiso/R/filtering_functions.R                                                                |    2 
 NEONiso-0.5.0/NEONiso/R/output_functions.R                                                                   |  581 +++++++---
 NEONiso-0.5.0/NEONiso/R/reference_data_extraction.R                                                          |    5 
 NEONiso-0.5.0/NEONiso/R/reference_data_regression.R                                                          |  217 +++
 NEONiso-0.5.0/NEONiso/R/reference_data_selection.R                                                           |   18 
 NEONiso-0.5.0/NEONiso/R/restructure_data.R                                                                   |only
 NEONiso-0.5.0/NEONiso/R/standard_corrections.R                                                               |    5 
 NEONiso-0.5.0/NEONiso/R/time_functions.R                                                                     |    6 
 NEONiso-0.5.0/NEONiso/R/utility_functions.R                                                                  |   15 
 NEONiso-0.5.0/NEONiso/README.md                                                                              |   44 
 NEONiso-0.5.0/NEONiso/build/vignette.rds                                                                     |binary
 NEONiso-0.5.0/NEONiso/inst/doc/example_workflow.html                                                         |    1 
 NEONiso-0.5.0/NEONiso/inst/extdata/NEON.D15.ONAQ.DP4.00200.001.nsae.2019-05.basic.packed.h5                  |only
 NEONiso-0.5.0/NEONiso/man/R_to_delta.Rd                                                                      |    2 
 NEONiso-0.5.0/NEONiso/man/calibrate_ambient_carbon_Bowling2003.Rd                                            |   10 
 NEONiso-0.5.0/NEONiso/man/calibrate_ambient_carbon_linreg.Rd                                                 |    8 
 NEONiso-0.5.0/NEONiso/man/calibrate_ambient_water_linreg.Rd                                                  |only
 NEONiso-0.5.0/NEONiso/man/calibrate_carbon.Rd                                                                |only
 NEONiso-0.5.0/NEONiso/man/calibrate_carbon_bymonth.Rd                                                        |   21 
 NEONiso-0.5.0/NEONiso/man/calibrate_carbon_reference_data.Rd                                                 |    3 
 NEONiso-0.5.0/NEONiso/man/calibrate_carbon_reference_data2.Rd                                                |only
 NEONiso-0.5.0/NEONiso/man/calibrate_standards_carbon.Rd                                                      |    4 
 NEONiso-0.5.0/NEONiso/man/calibrate_standards_water.Rd                                                       |only
 NEONiso-0.5.0/NEONiso/man/calibrate_water.Rd                                                                 |only
 NEONiso-0.5.0/NEONiso/man/calibrate_water_linreg_bymonth.Rd                                                  |only
 NEONiso-0.5.0/NEONiso/man/calibrate_water_reference_data.Rd                                                  |only
 NEONiso-0.5.0/NEONiso/man/convert_NEONhdf5_to_POSIXct_time.Rd                                                |    1 
 NEONiso-0.5.0/NEONiso/man/convert_POSIXct_to_NEONhdf5_time.Rd                                                |    5 
 NEONiso-0.5.0/NEONiso/man/copy_qfqm_group.Rd                                                                 |    3 
 NEONiso-0.5.0/NEONiso/man/copy_ucrt_group.Rd                                                                 |    3 
 NEONiso-0.5.0/NEONiso/man/correct_carbon_ref_cval.Rd                                                         |    4 
 NEONiso-0.5.0/NEONiso/man/delta_to_R.Rd                                                                      |    2 
 NEONiso-0.5.0/NEONiso/man/extract_carbon_calibration_data.Rd                                                 |    1 
 NEONiso-0.5.0/NEONiso/man/extract_water_calibration_data.Rd                                                  |    1 
 NEONiso-0.5.0/NEONiso/man/figures                                                                            |only
 NEONiso-0.5.0/NEONiso/man/fit_carbon_regression.Rd                                                           |   12 
 NEONiso-0.5.0/NEONiso/man/fit_water_regression.Rd                                                            |only
 NEONiso-0.5.0/NEONiso/man/get_Rstd.Rd                                                                        |    6 
 NEONiso-0.5.0/NEONiso/man/ingest_data.Rd                                                                     |only
 NEONiso-0.5.0/NEONiso/man/manage_local_EC_archive.Rd                                                         |   12 
 NEONiso-0.5.0/NEONiso/man/restructure_ambient_data.Rd                                                        |only
 NEONiso-0.5.0/NEONiso/man/restructure_ambient_data2.Rd                                                       |only
 NEONiso-0.5.0/NEONiso/man/restructure_carbon_variables.Rd                                                    |only
 NEONiso-0.5.0/NEONiso/man/restructure_water_variables.Rd                                                     |only
 NEONiso-0.5.0/NEONiso/man/select_daily_reference_data.Rd                                                     |    2 
 NEONiso-0.5.0/NEONiso/man/setup_output_file.Rd                                                               |    5 
 NEONiso-0.5.0/NEONiso/man/swap_standard_isotoperatios.Rd                                                     |    9 
 NEONiso-0.5.0/NEONiso/man/terrestrial_core_sites.Rd                                                          |    1 
 NEONiso-0.5.0/NEONiso/man/validate_analyte.Rd                                                                |    4 
 NEONiso-0.5.0/NEONiso/man/water_isotope_sites.Rd                                                             |    4 
 NEONiso-0.5.0/NEONiso/man/write_carbon_ambient_data.Rd                                                       |    1 
 NEONiso-0.5.0/NEONiso/man/write_carbon_calibration_data.Rd                                                   |    9 
 NEONiso-0.5.0/NEONiso/man/write_carbon_reference_data.Rd                                                     |    3 
 NEONiso-0.5.0/NEONiso/man/write_carbon_reference_data2.Rd                                                    |only
 NEONiso-0.5.0/NEONiso/man/write_qfqm.Rd                                                                      |    3 
 NEONiso-0.5.0/NEONiso/man/write_ucrt.Rd                                                                      |    3 
 NEONiso-0.5.0/NEONiso/man/write_water_calibration_data.Rd                                                    |only
 NEONiso-0.5.0/NEONiso/man/write_water_reference_data.Rd                                                      |only
 NEONiso-0.5.0/NEONiso/tests/testthat/test-data_extraction.R                                                  |only
 NEONiso-0.5.0/NEONiso/tests/testthat/test-data_ingestion.R                                                   |only
 NEONiso-0.5.0/NEONiso/tests/testthat/test-data_regression.R                                                  |only
 NEONiso-0.5.0/NEONiso/tests/testthat/test-high_level_functions.R                                             |only
 NEONiso-0.5.0/NEONiso/tests/testthat/test-reference_extractions.R                                            |  198 +--
 78 files changed, 1126 insertions(+), 589 deletions(-)

More information about NEONiso at CRAN
Permanent link

Package momentuHMM updated to version 1.5.3 with previous version 1.5.2 dated 2021-01-08

Title: Maximum Likelihood Analysis of Animal Movement Behavior Using Multivariate Hidden Markov Models
Description: Extended tools for analyzing telemetry data using generalized hidden Markov models. Features of momentuHMM (pronounced ``momentum'') include data pre-processing and visualization, fitting HMMs to location and auxiliary biotelemetry or environmental data, biased and correlated random walk movement models, hierarchical HMMs, multiple imputation for incorporating location measurement error and missing data, user-specified design matrices and constraints for covariate modelling of parameters, random effects, decoding of the state process, visualization of fitted models, model checking and selection, and simulation. See McClintock and Michelot (2018) <doi:10.1111/2041-210X.12995>.
Author: Brett McClintock, Theo Michelot
Maintainer: Brett McClintock <brett.mcclintock@noaa.gov>

Diff between momentuHMM versions 1.5.2 dated 2021-01-08 and 1.5.3 dated 2021-07-07

 DESCRIPTION                                |   19 +--
 MD5                                        |  129 ++++++++++----------
 NAMESPACE                                  |   21 ---
 NEWS                                       |   27 ++++
 R/CIbeta.R                                 |    4 
 R/CIreal.R                                 |   20 +--
 R/MIfitHMM.R                               |  180 +++++++++++++++++++----------
 R/MIpool.R                                 |  113 ++++++++++++------
 R/allProbs.R                               |   19 ++-
 R/checkInputs.R                            |   27 ++++
 R/checkPar0.R                              |   30 ++--
 R/crawlWrap.R                              |   81 ++++++++-----
 R/fitHMM.R                                 |   40 ++++--
 R/formatHierFormula.R                      |   14 +-
 R/formatHierHMM.R                          |   36 +++--
 R/formatmiSum.R                            |    2 
 R/getCovNames.R                            |    2 
 R/getDM.R                                  |   27 +++-
 R/getPar.R                                 |   16 +-
 R/getPar0.R                                |   30 ++--
 R/getParDM.R                               |   19 ++-
 R/getSplineDM.R                            |   10 +
 R/getTrProbs.R                             |   11 +
 R/getWorkBounds.R                          |   14 +-
 R/get_fixParIndex.R                        |   72 +++++------
 R/get_retrySD.R                            |   18 +-
 R/mixtureProbs.R                           |    8 -
 R/momentuHMM_utils.R                       |   30 ++++
 R/n2w.R                                    |    2 
 R/nLogLike.R                               |    2 
 R/parDef.R                                 |    4 
 R/plotPR.R                                 |   31 +++-
 R/plotStates.R                             |    6 
 R/plotStationary.R                         |   42 ++++--
 R/plot_miSum.R                             |    2 
 R/plot_momentuHMM.R                        |   25 ++--
 R/prepData.R                               |   20 +++
 R/print_momentuHMM.R                       |   14 +-
 R/pseudoRes.R                              |   52 ++++++--
 R/randomEffects.R                          |   33 ++++-
 R/simData.R                                |  129 +++++++++++++++-----
 R/simHierData.R                            |  133 +++++++++++++++------
 R/simObsData.R                             |   26 ++--
 R/stateFormulas.R                          |   36 +++++
 R/stateProbs.R                             |    7 -
 R/stationary.R                             |    6 
 R/timeInStates.R                           |   41 ++++--
 R/turnAngle.R                              |    8 -
 R/viterbi.R                                |    3 
 R/w2n.R                                    |   11 +
 README.md                                  |    6 
 build/partial.rdb                          |only
 inst/doc/momentuHMM.pdf                    |binary
 man/MIfitHMM.Rd                            |    2 
 man/MIpool.Rd                              |    8 -
 man/crawlWrap.Rd                           |    2 
 man/fitHMM.Rd                              |    7 -
 man/plotStationary.Rd                      |    3 
 man/pseudoRes.Rd                           |    4 
 man/randomEffects.Rd                       |    2 
 man/simData.Rd                             |    5 
 man/turnAngle.Rd                           |    2 
 src/densities.h                            |    7 -
 vignettes/examples/codExample.R            |   25 ++--
 vignettes/examples/garterSnakeExample.R    |   22 +--
 vignettes/examples/harborPorpoiseExample.R |   20 +--
 66 files changed, 1188 insertions(+), 579 deletions(-)

More information about momentuHMM at CRAN
Permanent link


Built and running on Debian GNU/Linux using R, littler and blosxom. Styled with Bootstrap.