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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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 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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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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
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
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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(-)
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(-)
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(-)
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
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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(-)
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
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
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(-)
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(-)
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(-)
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(-)
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(-)