Title: Estimation and Inference in Random Attention Models
Description: It is widely documented in psychology, economics and other disciplines that socio-economic agent may not pay full attention to all available alternatives, rendering standard revealed preference theory invalid. This package implements the estimation and inference procedures of Cattaneo, Ma, Masatlioglu and Suleymanov (2019) <arXiv:1712.03448>, which utilizes standard choice data to partially identify and estimate a decision maker's preference. For inference, several simulation-based critical values are provided.
Author: Matias D. Cattaneo, Xinwei Ma, Yusufcan Masatlioglu, Elchin Suleymanov
Maintainer: Xinwei Ma <x1ma@ucsd.edu>
Diff between ramchoice versions 1.0 dated 2019-03-16 and 1.1 dated 2019-07-11
DESCRIPTION | 12 ++++++------ MD5 | 20 ++++++++++---------- R/rAtte.R | 16 +++++++++------- R/rAtte_fun.R | 26 +++++++++++++------------- R/ramchoice-package.R | 24 +++++++++++++----------- R/ramdata.R | 8 ++++---- man/genMat.Rd | 14 +++++++------- man/rAtte.Rd | 22 ++++++++++++---------- man/ramchoice-package.Rd | 24 +++++++++++++----------- man/ramdata.Rd | 8 ++++---- man/sumData.Rd | 12 ++++++------ 11 files changed, 97 insertions(+), 89 deletions(-)
Title: High-Throughput Toxicokinetics
Description: Functions and data tables for simulation and statistical analysis
of chemical toxicokinetics ("TK") as in Pearce et al. (2017)
<doi:10.18637/jss.v079.i04>. Chemical-specific in vitro
data have been obtained from relatively high throughput
experiments. Both physiologically-based ("PBTK") and empirical
(e.g., one compartment) "TK" models can be parameterized for
several hundred chemicals and multiple species. These models are
solved efficiently, often using compiled (C-based) code. A Monte
Carlo sampler is included for simulating biological variability
(Ring et al., 2017 <doi:10.1016/j.envint.2017.06.004>)
and measurement limitations. Calibrated methods are included for
predicting tissue:plasma partition coefficients and volume of
distribution
(Pearce et al., 2017 <doi:10.1007/s10928-017-9548-7>).
These functions and data provide a set of tools for
in vitro-in vivo extrapolation ("IVIVE") of high throughput
screening data (e.g., Tox21, ToxCast) to real-world exposures via
reverse dosimetry (also known as "RTK")
(Wetmore et al., 2015 <doi:10.1093/toxsci/kfv171>).
Author: John Wambaugh [aut, cre],
Robert Pearce [aut],
Caroline Ring [aut],
Greg Honda [aut],
Mark Sfeir [aut],
Jimena Davis [ctb],
James Sluka [ctb],
Nisha Sipes [ctb],
Barbara Wetmore [ctb],
Woodrow Setzer [ctb]
Maintainer: John Wambaugh <wambaugh.john@epa.gov>
Diff between httk versions 1.9.2 dated 2019-04-25 and 1.10.0 dated 2019-07-11
httk-1.10.0/httk/DESCRIPTION | 17 httk-1.10.0/httk/MD5 | 497 +++++----- httk-1.10.0/httk/NAMESPACE | 98 + httk-1.10.0/httk/NEWS |binary httk-1.10.0/httk/R/Calc_Hepatic_Clearance.r | 109 +- httk-1.10.0/httk/R/Calc_elimination_rate.R | 90 + httk-1.10.0/httk/R/Calc_ratioblood2plasma.R | 59 + httk-1.10.0/httk/R/Calc_total_clearance.R | 92 + httk-1.10.0/httk/R/Calc_volume_of_distribution.R | 84 + httk-1.10.0/httk/R/Export_PBTK_Jarnac.R | 30 httk-1.10.0/httk/R/Export_PBTK_SBML.R | 32 httk-1.10.0/httk/R/Get_invitroPK_param.r | 44 httk-1.10.0/httk/R/Get_physchem_param.r | 147 ++ httk-1.10.0/httk/R/Parameterize_3comp.r | 76 + httk-1.10.0/httk/R/Parameterize_PBTK.r | 196 +++ httk-1.10.0/httk/R/Parameterize_SteadyState.R | 200 +++- httk-1.10.0/httk/R/Predict_partitioning_Schmitt.R | 166 ++- httk-1.10.0/httk/R/add_chemtable.R | 81 + httk-1.10.0/httk/R/age_draw_smooth.R | 33 httk-1.10.0/httk/R/armitage.R | 226 ++-- httk-1.10.0/httk/R/available_rblood2plasma.R | 63 + httk-1.10.0/httk/R/calc_analytic_css.R | 411 ++------ httk-1.10.0/httk/R/calc_analytic_css_1comp.R |only httk-1.10.0/httk/R/calc_analytic_css_3comp.R |only httk-1.10.0/httk/R/calc_analytic_css_3compss.R |only httk-1.10.0/httk/R/calc_analytic_css_pbtk.R |only httk-1.10.0/httk/R/calc_css.R | 108 ++ httk-1.10.0/httk/R/calc_mc_css.R | 308 +++++- httk-1.10.0/httk/R/calc_mc_oral_equiv.R | 132 ++ httk-1.10.0/httk/R/calc_stats.R | 62 + httk-1.10.0/httk/R/ckd_epi_eq.R | 3 httk-1.10.0/httk/R/convert_httk.R | 62 - httk-1.10.0/httk/R/data.R | 407 +++++++- httk-1.10.0/httk/R/draw_fup_clint.R | 442 +++++--- httk-1.10.0/httk/R/estimate_gfr.R | 3 httk-1.10.0/httk/R/estimate_gfr_ped.R | 3 httk-1.10.0/httk/R/estimate_hematocrit.R | 8 httk-1.10.0/httk/R/gen_age_height_weight.R | 1 httk-1.10.0/httk/R/gen_height_weight.R | 35 httk-1.10.0/httk/R/get_Wetmore_Css.R | 58 + httk-1.10.0/httk/R/get_Wetmore_Oral_Equiv.R | 66 + httk-1.10.0/httk/R/get_Wetmore_cheminfo.R | 50 - httk-1.10.0/httk/R/get_cheminfo.R | 289 ++++- httk-1.10.0/httk/R/get_gfr_category.R | 3 httk-1.10.0/httk/R/get_httk_params.R | 168 +-- httk-1.10.0/httk/R/get_rblood2plasma.R | 31 httk-1.10.0/httk/R/get_weight_class.R | 5 httk-1.10.0/httk/R/hematocrit_infants.R | 2 httk-1.10.0/httk/R/honda.ivive.R | 108 +- httk-1.10.0/httk/R/httk-package.R |only httk-1.10.0/httk/R/httkpop.R | 1 httk-1.10.0/httk/R/httkpop_bio.R | 1 httk-1.10.0/httk/R/httkpop_direct_resample.R | 83 - httk-1.10.0/httk/R/httkpop_direct_resample_inner.R | 5 httk-1.10.0/httk/R/httkpop_generate.R | 124 +- httk-1.10.0/httk/R/httkpop_virtual_indiv.R | 2 httk-1.10.0/httk/R/in.list.R | 192 +++ httk-1.10.0/httk/R/ionization_functions.R | 118 +- httk-1.10.0/httk/R/load_sipes2017.R | 39 httk-1.10.0/httk/R/lump_tissues.R | 53 - httk-1.10.0/httk/R/modelinfo_1comp.R | 7 httk-1.10.0/httk/R/modelinfo_3comp.R | 13 httk-1.10.0/httk/R/modelinfo_3compss.R | 7 httk-1.10.0/httk/R/modelinfo_PBTK.R | 12 httk-1.10.0/httk/R/modelinfo_Schmitt.R | 4 httk-1.10.0/httk/R/monte_carlo.R | 145 ++ httk-1.10.0/httk/R/parameterize_1comp.R | 101 +- httk-1.10.0/httk/R/parameterize_schmitt.R | 96 + httk-1.10.0/httk/R/r_left_censored_norm.R | 9 httk-1.10.0/httk/R/solve_1comp.R | 118 ++ httk-1.10.0/httk/R/solve_3comp.R | 113 ++ httk-1.10.0/httk/R/solve_pbtk.R | 210 +++- httk-1.10.0/httk/R/sysdata.rda |binary httk-1.10.0/httk/R/tissue_mass_functions.R | 263 +++-- httk-1.10.0/httk/R/tissue_masses_flows.R | 5 httk-1.10.0/httk/R/tissue_scale.R | 3 httk-1.10.0/httk/R/utils.R | 68 - httk-1.10.0/httk/build/httk.pdf |only httk-1.10.0/httk/build/vignette.rds |binary httk-1.10.0/httk/data/Tables.RData |binary httk-1.10.0/httk/data/armitage_input.RData |binary httk-1.10.0/httk/data/datalist | 5 httk-1.10.0/httk/data/httkpop.RData |binary httk-1.10.0/httk/data/vignettes.RData |binary httk-1.10.0/httk/data/wambaugh2019.RData |only httk-1.10.0/httk/data/well_param.RData |binary httk-1.10.0/httk/inst/doc/Honda_2019_updated_armitage.R |only httk-1.10.0/httk/inst/doc/Honda_2019_updated_armitage.Rmd |only httk-1.10.0/httk/inst/doc/Honda_2019_updated_armitage.html |only httk-1.10.0/httk/inst/doc/Pearce_2017_partitioning_plots.Rmd | 2 httk-1.10.0/httk/inst/doc/Pearce_2017_partitioning_plots.html | 9 httk-1.10.0/httk/inst/doc/Ring_2017_supplemental_vignette_age_dist.Rmd | 2 httk-1.10.0/httk/inst/doc/Ring_2017_supplemental_vignette_age_dist.html | 9 httk-1.10.0/httk/inst/doc/Ring_2017_supplemental_vignette_globalsensitivityanalysis.R | 32 httk-1.10.0/httk/inst/doc/Ring_2017_supplemental_vignette_globalsensitivityanalysis.Rmd | 34 httk-1.10.0/httk/inst/doc/Ring_2017_supplemental_vignette_globalsensitivityanalysis.html | 41 httk-1.10.0/httk/inst/doc/Ring_2017_supplemental_vignette_globalsensitivityplot.R | 30 httk-1.10.0/httk/inst/doc/Ring_2017_supplemental_vignette_globalsensitivityplot.Rmd | 36 httk-1.10.0/httk/inst/doc/Ring_2017_supplemental_vignette_globalsensitivityplot.html | 43 httk-1.10.0/httk/inst/doc/Ring_2017_supplemental_vignette_heightweight_splines_kde.Rmd | 2 httk-1.10.0/httk/inst/doc/Ring_2017_supplemental_vignette_heightweight_splines_kde.html | 9 httk-1.10.0/httk/inst/doc/Ring_2017_supplemental_vignette_hematocrit_splines.Rmd | 2 httk-1.10.0/httk/inst/doc/Ring_2017_supplemental_vignette_hematocrit_splines.html | 9 httk-1.10.0/httk/inst/doc/Ring_2017_supplemental_vignette_plot_css95.R | 32 httk-1.10.0/httk/inst/doc/Ring_2017_supplemental_vignette_plot_css95.Rmd | 34 httk-1.10.0/httk/inst/doc/Ring_2017_supplemental_vignette_plot_css95.html | 41 httk-1.10.0/httk/inst/doc/Ring_2017_supplemental_vignette_serumcreat_splines_kde.Rmd | 2 httk-1.10.0/httk/inst/doc/Ring_2017_supplemental_vignette_serumcreat_splines_kde.html | 9 httk-1.10.0/httk/inst/doc/Ring_2017_vignette01_subpopulations.Rmd | 2 httk-1.10.0/httk/inst/doc/Ring_2017_vignette01_subpopulations.html | 9 httk-1.10.0/httk/inst/doc/Ring_2017_vignette02_evalmodelsubpop.R | 24 httk-1.10.0/httk/inst/doc/Ring_2017_vignette02_evalmodelsubpop.Rmd | 31 httk-1.10.0/httk/inst/doc/Ring_2017_vignette02_evalmodelsubpop.html | 35 httk-1.10.0/httk/inst/doc/Ring_2017_vignette03_paper_fig2.Rmd | 2 httk-1.10.0/httk/inst/doc/Ring_2017_vignette03_paper_fig2.html | 9 httk-1.10.0/httk/inst/doc/Ring_2017_vignette04_paper_fig3.R | 8 httk-1.10.0/httk/inst/doc/Ring_2017_vignette04_paper_fig3.Rmd | 10 httk-1.10.0/httk/inst/doc/Ring_2017_vignette04_paper_fig3.html | 17 httk-1.10.0/httk/inst/doc/Ring_2017_vignette05b_plothowgatejohnson.R | 32 httk-1.10.0/httk/inst/doc/Ring_2017_vignette05b_plothowgatejohnson.Rmd | 38 httk-1.10.0/httk/inst/doc/Ring_2017_vignette05b_plothowgatejohnson.html | 45 httk-1.10.0/httk/inst/doc/Ring_2017_vignette06_aerplotting.R | 30 httk-1.10.0/httk/inst/doc/Ring_2017_vignette06_aerplotting.Rmd | 32 httk-1.10.0/httk/inst/doc/Ring_2017_vignette06_aerplotting.html | 39 httk-1.10.0/httk/inst/doc/Ring_2017_vignette_05a_virtualstudypops.R | 20 httk-1.10.0/httk/inst/doc/Ring_2017_vignette_05a_virtualstudypops.Rmd | 22 httk-1.10.0/httk/inst/doc/Ring_2017_vignette_05a_virtualstudypops.html | 29 httk-1.10.0/httk/inst/doc/Wambaugh_2018_Figures.html | 9 httk-1.10.0/httk/inst/doc/Wambaugh_2019_figures.R |only httk-1.10.0/httk/inst/doc/Wambaugh_2019_figures.Rmd |only httk-1.10.0/httk/inst/doc/Wambaugh_2019_figures.html |only httk-1.10.0/httk/man/Obach2008.Rd | 20 httk-1.10.0/httk/man/Tables.Rdata.stamp.Rd |only httk-1.10.0/httk/man/ToxCast2015subset.Rd |only httk-1.10.0/httk/man/Wetmore.data.Rd | 46 httk-1.10.0/httk/man/Wetmore2012.Rd | 24 httk-1.10.0/httk/man/add_chemtable.Rd | 72 - httk-1.10.0/httk/man/age_dist_smooth.Rd | 30 httk-1.10.0/httk/man/age_draw_smooth.Rd | 15 httk-1.10.0/httk/man/armitage_estimate_sarea.Rd | 24 httk-1.10.0/httk/man/armitage_eval.Rd | 63 - httk-1.10.0/httk/man/armitage_input.Rd | 45 httk-1.10.0/httk/man/available_rblood2plasma.Rd |only httk-1.10.0/httk/man/blood_mass_correct.Rd | 8 httk-1.10.0/httk/man/blood_weight.Rd | 10 httk-1.10.0/httk/man/bmiage.Rd | 4 httk-1.10.0/httk/man/bone_mass_age.Rd | 7 httk-1.10.0/httk/man/calc_analytic_css.Rd | 63 - httk-1.10.0/httk/man/calc_analytic_css_1comp.Rd |only httk-1.10.0/httk/man/calc_analytic_css_3comp.Rd |only httk-1.10.0/httk/man/calc_analytic_css_3compss.Rd |only httk-1.10.0/httk/man/calc_analytic_css_pbtk.Rd |only httk-1.10.0/httk/man/calc_css.Rd | 141 +- httk-1.10.0/httk/man/calc_elimination_rate.Rd |only httk-1.10.0/httk/man/calc_hepatic_clearance.Rd | 87 - httk-1.10.0/httk/man/calc_ionization.Rd | 113 +- httk-1.10.0/httk/man/calc_mc_css.Rd | 389 ++++--- httk-1.10.0/httk/man/calc_mc_oral_equiv.Rd | 187 ++- httk-1.10.0/httk/man/calc_rblood2plasma.Rd |only httk-1.10.0/httk/man/calc_stats.Rd | 104 +- httk-1.10.0/httk/man/calc_total_clearance.Rd | 83 - httk-1.10.0/httk/man/calc_vdist.Rd |only httk-1.10.0/httk/man/chem.invivo.PK.aggregate.data.Rd | 30 httk-1.10.0/httk/man/chem.invivo.PK.data.Rd |only httk-1.10.0/httk/man/chem.invivo.PK.summary.data.Rd |only httk-1.10.0/httk/man/chem.lists.Rd | 58 - httk-1.10.0/httk/man/chem.physical_and_invitro.data.Rd |only httk-1.10.0/httk/man/convert_httk.Rd | 7 httk-1.10.0/httk/man/draw_fup_clint.Rd | 60 - httk-1.10.0/httk/man/export_pbtk_jarnac.Rd | 56 - httk-1.10.0/httk/man/export_pbtk_sbml.Rd | 54 - httk-1.10.0/httk/man/gen_height_weight.Rd | 16 httk-1.10.0/httk/man/get_cheminfo.Rd | 76 - httk-1.10.0/httk/man/get_httk_params.Rd | 134 +- httk-1.10.0/httk/man/get_lit_cheminfo.Rd | 72 - httk-1.10.0/httk/man/get_lit_css.Rd | 109 +- httk-1.10.0/httk/man/get_lit_oral_equiv.Rd | 125 +- httk-1.10.0/httk/man/get_physchem_param.Rd |only httk-1.10.0/httk/man/get_rblood2plasma.Rd | 64 - httk-1.10.0/httk/man/honda.ivive.Rd |only httk-1.10.0/httk/man/howgate.Rd | 9 httk-1.10.0/httk/man/httk-package.Rd | 57 - httk-1.10.0/httk/man/httkpop.Rd | 43 httk-1.10.0/httk/man/httkpop_direct_resample.Rd | 49 httk-1.10.0/httk/man/httkpop_generate.Rd | 72 - httk-1.10.0/httk/man/in.list.Rd |only httk-1.10.0/httk/man/is.httk.Rd |only httk-1.10.0/httk/man/is_in_inclusive.Rd | 31 httk-1.10.0/httk/man/johnson.Rd | 9 httk-1.10.0/httk/man/load_sipes2017.Rd | 60 - httk-1.10.0/httk/man/lump_tissues.Rd | 65 - httk-1.10.0/httk/man/mcnally_dt.Rd | 39 httk-1.10.0/httk/man/monte_carlo.Rd | 119 +- httk-1.10.0/httk/man/nhanes_mec_svy.Rd | 2 httk-1.10.0/httk/man/onlyp.Rd | 9 httk-1.10.0/httk/man/parameterize_1comp.Rd | 120 +- httk-1.10.0/httk/man/parameterize_3comp.Rd | 142 +- httk-1.10.0/httk/man/parameterize_pbtk.Rd |only httk-1.10.0/httk/man/parameterize_schmitt.Rd | 91 - httk-1.10.0/httk/man/parameterize_steadystate.Rd |only httk-1.10.0/httk/man/pc.data.Rd | 121 +- httk-1.10.0/httk/man/pharma.Rd |only httk-1.10.0/httk/man/physiology.data.Rd |only httk-1.10.0/httk/man/predict_partitioning_schmitt.Rd | 109 +- httk-1.10.0/httk/man/rfun.Rd | 6 httk-1.10.0/httk/man/sipes2017.Rd |only httk-1.10.0/httk/man/sipes2017.table.Rd | 159 ++- httk-1.10.0/httk/man/skeletal_muscle_mass.Rd | 7 httk-1.10.0/httk/man/skeletal_muscle_mass_children.Rd | 5 httk-1.10.0/httk/man/skin_mass_bosgra.Rd | 3 httk-1.10.0/httk/man/solve_1comp.Rd |only httk-1.10.0/httk/man/solve_3comp.Rd |only httk-1.10.0/httk/man/solve_pbtk.Rd | 186 ++- httk-1.10.0/httk/man/spline_heightweight.Rd | 12 httk-1.10.0/httk/man/spline_hematocrit.Rd | 11 httk-1.10.0/httk/man/spline_serumcreat.Rd | 11 httk-1.10.0/httk/man/tissue.data.Rd |only httk-1.10.0/httk/man/wambaugh2019.Rd |only httk-1.10.0/httk/man/wambaugh2019.nhanes.Rd |only httk-1.10.0/httk/man/wambaugh2019.raw.Rd |only httk-1.10.0/httk/man/wambaugh2019.seem3.Rd |only httk-1.10.0/httk/man/well_param.Rd | 19 httk-1.10.0/httk/man/wfl.Rd | 21 httk-1.10.0/httk/src/init.c | 32 httk-1.10.0/httk/src/model1comp.c |only httk-1.10.0/httk/src/model3comp.c |only httk-1.10.0/httk/src/modelPBTK.c |only httk-1.10.0/httk/tests/1comp_test.R | 4 httk-1.10.0/httk/tests/1comp_test.Rout.save | 315 ++---- httk-1.10.0/httk/tests/3comp_test.R | 4 httk-1.10.0/httk/tests/3comp_test.Rout.save | 326 ++---- httk-1.10.0/httk/tests/3compss_test.R | 4 httk-1.10.0/httk/tests/3compss_test.Rout.save | 145 +- httk-1.10.0/httk/tests/adddata_test.R | 3 httk-1.10.0/httk/tests/adddata_test.Rout.save | 132 -- httk-1.10.0/httk/tests/cheminfo_test.R | 12 httk-1.10.0/httk/tests/cheminfo_test.Rout.save | 46 httk-1.10.0/httk/tests/ivive_test.R | 4 httk-1.10.0/httk/tests/ivive_test.Rout.save | 96 - httk-1.10.0/httk/tests/other_tests.R | 4 httk-1.10.0/httk/tests/other_tests.Rout.save | 133 +- httk-1.10.0/httk/tests/pbtk_test.R | 26 httk-1.10.0/httk/tests/pbtk_test.Rout.save | 317 ++---- httk-1.10.0/httk/vignettes/Honda_2019_updated_armitage.Rmd |only httk-1.10.0/httk/vignettes/Pearce_2017_partitioning_plots.Rmd | 2 httk-1.10.0/httk/vignettes/Ring_2017_supplemental_vignette_age_dist.Rmd | 2 httk-1.10.0/httk/vignettes/Ring_2017_supplemental_vignette_globalsensitivityanalysis.Rmd | 34 httk-1.10.0/httk/vignettes/Ring_2017_supplemental_vignette_globalsensitivityplot.Rmd | 36 httk-1.10.0/httk/vignettes/Ring_2017_supplemental_vignette_heightweight_splines_kde.Rmd | 2 httk-1.10.0/httk/vignettes/Ring_2017_supplemental_vignette_hematocrit_splines.Rmd | 2 httk-1.10.0/httk/vignettes/Ring_2017_supplemental_vignette_plot_css95.Rmd | 34 httk-1.10.0/httk/vignettes/Ring_2017_supplemental_vignette_serumcreat_splines_kde.Rmd | 2 httk-1.10.0/httk/vignettes/Ring_2017_vignette01_subpopulations.Rmd | 2 httk-1.10.0/httk/vignettes/Ring_2017_vignette02_evalmodelsubpop.Rmd | 31 httk-1.10.0/httk/vignettes/Ring_2017_vignette03_paper_fig2.Rmd | 2 httk-1.10.0/httk/vignettes/Ring_2017_vignette04_paper_fig3.Rmd | 10 httk-1.10.0/httk/vignettes/Ring_2017_vignette05b_plothowgatejohnson.Rmd | 38 httk-1.10.0/httk/vignettes/Ring_2017_vignette06_aerplotting.Rmd | 32 httk-1.10.0/httk/vignettes/Ring_2017_vignette_05a_virtualstudypops.Rmd | 22 httk-1.10.0/httk/vignettes/Wambaugh_2019_figures.Rmd |only httk-1.9.2/httk/R/3compPBPKmodel_inits.R |only httk-1.9.2/httk/build/partial.rdb |only httk-1.9.2/httk/inst/CITATION |only httk-1.9.2/httk/inst/doc/Honda_2018_updated_armitage.R |only httk-1.9.2/httk/inst/doc/Honda_2018_updated_armitage.Rmd |only httk-1.9.2/httk/inst/doc/Honda_2018_updated_armitage.html |only httk-1.9.2/httk/man/Calc_elimination_rate.Rd |only httk-1.9.2/httk/man/Calc_ratioblood2plasma.Rd |only httk-1.9.2/httk/man/Calc_volume_of_distriution.Rd |only httk-1.9.2/httk/man/PK_physiology_data.Rd |only httk-1.9.2/httk/man/Parameterize_PBTK.Rd |only httk-1.9.2/httk/man/Parameterize_SteadyState.Rd |only httk-1.9.2/httk/man/Sipes2017.Rd |only httk-1.9.2/httk/man/available_ratioblood2plasma.Rd |only httk-1.9.2/httk/man/chem_invivo_PK_data.Rd |only httk-1.9.2/httk/man/chem_invivo_PK_summary_data.Rd |only httk-1.9.2/httk/man/chem_physical_and_invitro_data.Rd |only httk-1.9.2/httk/man/in_list.Rd |only httk-1.9.2/httk/man/solve_1comp_pk.Rd |only httk-1.9.2/httk/man/solve_3comp_pbpk.Rd |only httk-1.9.2/httk/man/tc.dt.Rd |only httk-1.9.2/httk/man/tissue_data.Rd |only httk-1.9.2/httk/src/3compPBPKmodel.c |only httk-1.9.2/httk/src/pbtk1comp.c |only httk-1.9.2/httk/src/vLiverPBPK.c |only httk-1.9.2/httk/vignettes/Honda_2018_updated_armitage.Rmd |only 286 files changed, 8725 insertions(+), 4835 deletions(-)
Title: Methods Used in the Economic Complexity Literature
Description: A wrapper of different indices and networks commonly used in Economic Complexity
to explore bipartite relations such as countries and their exported products. These methods
are also useful for different kind of relations such as countries and their spoken languages.
The functions within this package correspond to code implementations of the equations
described in Hausmann, et al. (2005) <doi:10.3386/w11905>, Hausmann, et al. (2014)
<doi:10.7551/mitpress/9647.001.0001>, and Mariani, et al. (2015) <doi:10.1140/epjb/e2015-60298-7>.
Author: Mauricio Vargas [aut, cre, cph]
(<https://orcid.org/0000-0003-1017-7574>),
Carlo Bottai [ctb] (improved the eigenvalues calculation),
Diego Kozlowski [ctb] (provided initial RCA and proximity functions he
used for his thesis),
Mark Padgham [rev] (compared PRODY equations from different articles),
Nico Pintar [rev] (suggested improvements to special cases in
eigenvalues calculation),
UN COMTRADE [dtc],
The World Bank [dtc]
Maintainer: Mauricio Vargas <mvargas@dcc.uchile.cl>
Diff between economiccomplexity versions 0.1.0 dated 2019-07-02 and 0.1.2 dated 2019-07-11
DESCRIPTION | 23 +++++---- MD5 | 10 +-- R/complexity_measures.R | 46 ++++++++++++++---- build/partial.rdb |binary inst/doc/basic-usage.html | 76 +++++++++++++++--------------- tests/testthat/test-complexity_measures.R | 5 + 6 files changed, 98 insertions(+), 62 deletions(-)
More information about economiccomplexity at CRAN
Permanent link
Title: 'DrugBank' Database XML Parser
Description: This tool is for parsing the 'DrugBank' XML database <http://drugbank.ca/>. The parsed
data are then returned in a proper 'R' dataframe with the ability to save
them in a given database.
Author: Mohammed Ali [aut, cre],
Ali Ezzat [aut]
Maintainer: Mohammed Ali <moh_fcis@yahoo.com>
Diff between dbparser versions 1.0.2 dated 2019-07-08 and 1.0.3 dated 2019-07-11
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS.md | 3 +++ inst/doc/dbparser.html | 4 ++-- tests/testthat/test_drug_all_nodes_parser.R | 3 --- 5 files changed, 14 insertions(+), 14 deletions(-)
Title: Methods for Joint Dimension Reduction and Clustering
Description: A class of methods that combine dimension reduction and clustering of continuous, categorical or mixed-type data. For continuous data, the package contains implementations of factorial K-means (Vichi and Kiers 2001; <DOI:10.1016/S0167-9473(00)00064-5>) and reduced K-means (De Soete and Carroll 1994; <DOI:10.1007/978-3-642-51175-2_24>); both methods that combine principal component analysis with K-means clustering. For categorical data, the package provides MCA K-means (Hwang, Dillon and Takane 2006; <DOI:10.1007/s11336-004-1173-x>), i-FCB (Iodice D'Enza and Palumbo 2013, <DOI:10.1007/s00180-012-0329-x>) and Cluster Correspondence Analysis (van de Velden, Iodice D'Enza and Palumbo 2017; <DOI:10.1007/s11336-016-9514-0>), which combine multiple correspondence analysis with K-means. For mixed-type data, it provides mixed Reduced K-means and mixed Factorial K-means (van de Velden, Iodice D'Enza and Markos 2019; <DOI:10.1002/wics.1456>), which combine PCA for mixed-type data with K-means.
Author: Angelos Markos [aut, cre], Alfonso Iodice D'Enza [aut], Michel van de Velden [ctb]
Maintainer: Angelos Markos <amarkos@gmail.com>
Diff between clustrd versions 1.3.1 dated 2019-05-08 and 1.3.2 dated 2019-07-11
DESCRIPTION | 8 +++--- MD5 | 16 ++++++------- R/cluspca.R | 4 +-- R/plot.clusmca.R | 62 +++++++++++++++++++++++++++++++++++++++++++++++++--- R/plot.cluspca.R | 8 +++--- R/plot.cluspcamix.R | 6 ++--- R/tune_clusmca.R | 2 - R/tune_cluspca.R | 6 ++--- R/tune_cluspcamix.R | 2 - 9 files changed, 85 insertions(+), 29 deletions(-)
Title: Chandler-Bate Sandwich Loglikelihood Adjustment
Description: Performs adjustments of a user-supplied independence loglikelihood
function using a robust sandwich estimator of the parameter covariance
matrix, based on the methodology in Chandler and Bate (2007)
<doi:10.1093/biomet/asm015>. This can be used for cluster correlated data
when interest lies in the parameters of the marginal distributions or for
performing inferences that are robust to certain types of model
misspecification. Functions for profiling the adjusted loglikelihoods are
also provided, as are functions for calculating and plotting confidence
intervals, for single model parameters, and confidence regions, for pairs
of model parameters. Nested models can be compared using an adjusted
likelihood ratio test.
Author: Paul J. Northrop [aut, cre, cph],
Richard E. Chandler [aut, cph]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Diff between chandwich versions 1.1.1 dated 2018-11-28 and 1.1.2 dated 2019-07-11
DESCRIPTION | 8 MD5 | 34 NEWS.md | 86 + R/adjust_loglik.R | 1624 +++++++++++++++++------------------ R/chandwich.R | 148 +-- R/confidence_intervals.R | 1781 +++++++++++++++++++-------------------- R/plot_summary_print.R | 1560 +++++++++++++++++----------------- build/vignette.rds |binary inst/doc/chandwich-vignette.html | 6 man/conf_intervals.Rd | 14 man/confint.chandwich.Rd | 4 man/owtemps.Rd | 4 man/plot.chandwich.Rd | 6 man/plot.confint.Rd | 4 man/plot.confreg.Rd | 4 man/print.summary.chandwich.Rd | 2 man/rats.Rd | 2 vignettes/chandwich.bib | 2 18 files changed, 2659 insertions(+), 2630 deletions(-)
Title: Bayesian Spectral Inference for Stationary Time Series
Description: Implementations of Bayesian parametric, nonparametric and semiparametric procedures for univariate and multivariate time series. The package is based on the methods presented in C. Kirch et al (2018) <doi:10.1214/18-BA1126> and A. Meier (2018) <https://opendata.uni-halle.de//handle/1981185920/13470>. It was supported by DFG grant KI 1443/3-1.
Author: Alexander Meier [aut, cre],
Claudia Kirch [aut],
Matthew C. Edwards [aut],
Renate Meyer [aut]
Maintainer: Alexander Meier <meier.alexander@posteo.de>
Diff between beyondWhittle versions 1.1 dated 2018-11-22 and 1.1.1 dated 2019-07-11
DESCRIPTION | 14 +++++++------- MD5 | 24 ++++++++++++------------ man/beyondWhittle-package.Rd | 2 +- man/gibbs_ar.Rd | 9 +++++---- man/gibbs_multivariate_nuisance_cpp.Rd | 4 ++-- man/gibbs_npc.Rd | 15 ++++++++------- man/gibbs_var.Rd | 8 ++++---- man/gibbs_vnp.Rd | 10 +++++----- man/llike.Rd | 4 ++-- man/lpost.Rd | 6 +++--- man/lpost_AR.Rd | 4 ++-- man/plotMPsd.Rd | 9 +++++---- man/psd_varma.Rd | 4 ++-- 13 files changed, 58 insertions(+), 55 deletions(-)
Title: Integrative Conditional Autoregressive Horseshoe Model
Description: Implements the integrative conditional autoregressive horseshoe model
discussed in Jendoubi, T., & Ebbels, T. (2018). "Integrative analysis of
time course metabolic data and biomarker discovery". arXiv preprint <arXiv:1801.07767>.
The model consists in three levels: Metabolic pathways level modeling interdependencies between
variables via a conditional auto-regressive (CAR) component , integrative analysis level to identify
potential associations between heterogeneous omic variables via a Horseshoe prior and experimental
design level to capture experimental design conditions through a mixed-effects model.
The package also provides functions to simulate data from the model, construct pathway matrices,
post process and plot model parameters.
Author: Takoua Jendoubi [aut, cre],
Timothy M.D. Ebbels [aut]
Maintainer: Takoua Jendoubi <t.jendoubi14@imperial.ac.uk>
Diff between iCARH versions 1.0.0 dated 2019-06-04 and 2.0.0 dated 2019-07-11
iCARH-1.0.0/iCARH/man/figures |only iCARH-2.0.0/iCARH/DESCRIPTION | 9 iCARH-2.0.0/iCARH/MD5 | 25 +- iCARH-2.0.0/iCARH/NAMESPACE | 9 iCARH-2.0.0/iCARH/R/iCARH.model.R | 140 +++++++----- iCARH-2.0.0/iCARH/R/iCARH.parameters.R |only iCARH-2.0.0/iCARH/R/postprocessing.R | 129 +++++++++-- iCARH-2.0.0/iCARH/R/summary-method.R |only iCARH-2.0.0/iCARH/inst/doc/example.R | 16 + iCARH-2.0.0/iCARH/inst/doc/example.Rmd | 20 + iCARH-2.0.0/iCARH/inst/doc/example.html | 348 ++++++++++++++++---------------- iCARH-2.0.0/iCARH/man/iCARH.getBeta.Rd |only iCARH-2.0.0/iCARH/man/iCARH.model.Rd | 8 iCARH-2.0.0/iCARH/man/iCARH.params.Rd |only iCARH-2.0.0/iCARH/man/iCARH.plotBeta.Rd | 24 +- iCARH-2.0.0/iCARH/vignettes/example.Rmd | 20 + 16 files changed, 466 insertions(+), 282 deletions(-)
Title: Hidden State Speciation and Extinction
Description: Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification. Beaulieu and O'Meara (2016) <doi:10.1093/sysbio/syw022>.
Author: Jeremy Beaulieu [aut, cre],
Brian O'Meara [aut],
Daniel Caetano [aut]
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>
Diff between hisse versions 1.9.4 dated 2019-05-10 and 1.9.5 dated 2019-07-11
DESCRIPTION | 8 ++-- MD5 | 30 ++++++++++------- R/fgeohisse.R | 32 ++++++++---------- R/geohisse.R | 20 ++++++----- R/hisse.R | 56 +++++++++++++++++++-------------- R/marginRecon.R | 2 - R/misse.R | 18 +++++----- R/muhisse.R | 45 +++++++++++++++++++++----- R/supportRegion.R | 6 +-- build/vignette.rds |binary inst/doc/Clade-specific-sampling.R |only inst/doc/Clade-specific-sampling.Rmd |only inst/doc/Clade-specific-sampling.pdf |only man/SimulateGeoHiSSE.Rd | 4 +- man/TranslateParsMakerGeoHiSSE.Rd | 4 +- vignettes/Clade-specific-sampling.Rmd |only vignettes/Clade-specific-sampling.html |only vignettes/GeoHiSSE-vignette.html | 19 ----------- vignettes/cladeSamplingVariables.Rsave |only 19 files changed, 138 insertions(+), 106 deletions(-)
Title: Detect Heatwaves and Cold-Spells
Description: The different methods of defining and detecting extreme events, known as heatwaves or cold-spells in both air and water temperature data are encompassed within this package. These detection algorithms may be used on non-temperature data as well however, this is not catered for explicitly here as no use of this technique in the literature currently exists.
Author: Robert W. Schlegel [aut, cre, ctb]
(<https://orcid.org/0000-0002-0705-1287>),
Albertus J. Smit [aut, ctb] (<https://orcid.org/0000-0002-3799-6126>)
Maintainer: Robert W. Schlegel <robwschlegel@gmail.com>
Diff between heatwaveR versions 0.3.6 dated 2019-01-16 and 0.4.0 dated 2019-07-11
DESCRIPTION | 13 + MD5 | 102 ++++++++------- NAMESPACE | 5 NEWS.md | 39 +++++ R/Algiers.R |only R/clim_calc.R | 3 R/clim_spread.R | 3 R/detect_event.R | 6 R/geom2plotly.R |only R/geoms.R | 38 +++++ R/graph_functions.R | 54 +++++++- R/sst_med.R | 6 R/sst_nw_atl.R | 6 R/sst_wa.R | 8 - R/ts2clm.R | 18 ++ README.md | 12 + build/vignette.rds |binary data/Algiers.rda |only data/sst_Med.rda |binary data/sst_NW_Atl.rda |binary data/sst_WA.rda |binary inst/doc/OISST_preparation.html | 9 - inst/doc/complex_clims.R | 56 +++----- inst/doc/complex_clims.Rmd | 85 +++++------- inst/doc/complex_clims.html | 171 ++++++++++++------------- inst/doc/detection_and_visualisation.R | 46 ++++++ inst/doc/detection_and_visualisation.Rmd | 58 ++++++++ inst/doc/detection_and_visualisation.html | 198 ++++++++++++++++++------------ inst/doc/event_categories.R | 2 inst/doc/event_categories.Rmd | 2 inst/doc/event_categories.html | 39 +++-- inst/doc/exceedance.R | 2 inst/doc/exceedance.Rmd | 2 inst/doc/exceedance.html | 31 ++-- inst/doc/gridded_event_detection.html | 9 - man/Algiers.Rd |only man/event_line.Rd | 14 +- man/geom_flame.Rd | 16 ++ man/plotly_helpers.Rd |only man/sst_Med.Rd | 6 man/sst_NW_Atl.Rd | 6 man/sst_WA.Rd | 8 - man/ts2clm.Rd | 7 - tests/testthat/test-category.R | 23 +-- tests/testthat/test-detect_event.R | 10 - tests/testthat/test-exceedance.R | 13 + tests/testthat/test-geom2plotly.R |only tests/testthat/test-geoms.R | 10 + tests/testthat/test-graph_functions.R | 26 +++ tests/testthat/test-proto_event.R | 6 tests/testthat/test-ts2clm.R | 25 +++ vignettes/complex_clims.Rmd | 85 +++++------- vignettes/detection_and_visualisation.Rmd | 58 ++++++++ vignettes/event_categories.Rmd | 2 vignettes/exceedance.Rmd | 2 55 files changed, 853 insertions(+), 487 deletions(-)
Title: Authoring Books and Technical Documents with R Markdown
Description: Output formats and utilities for authoring books and technical documents with R Markdown.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
JJ Allaire [ctb],
Albert Kim [ctb],
Alessandro Samuel-Rosa [ctb],
Andrzej Oles [ctb],
Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>),
Aust Frederik [ctb] (<https://orcid.org/0000-0003-4900-788X>),
Bastiaan Quast [ctb],
Ben Marwick [ctb],
Chester Ismay [ctb],
Christophe Dervieux [ctb],
Clifton Franklund [ctb],
Daniel Emaasit [ctb],
David Shuman [ctb],
Dean Attali [ctb],
Drew Tyre [ctb],
Ellis Valentiner [ctb],
Frans van Dunne [ctb],
Hadley Wickham [ctb],
Jeff Allen [ctb],
Jennifer Bryan [ctb],
Jonathan McPhers [ctb],
Junwen Huang [ctb],
Kevin Cheung [ctb],
Kevin Ushey [ctb],
Kim Seonghyun [ctb],
Kirill Muller [ctb],
Luciano Selzer [ctb],
Matthew Lincoln [ctb],
Maximilian Held [ctb],
Michael Sachs [ctb],
Michal Bojanowski [ctb],
Noam Ross [ctb],
Peter Hickey [ctb],
Sahir Bhatnagar [ctb],
Steve Simpson [ctb],
Thierry Onkelinx [ctb] (<https://orcid.org/0000-0001-8804-4216>),
Vincent Fulco [ctb],
Yixuan Qiu [ctb],
Zhuoer Dong [ctb],
RStudio Inc [cph],
Bartek Szopka [ctb] (The jQuery Highlight plugin),
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/resources/AUTHORS),
MathQuill contributors [ctb] (The MathQuill library; authors listed in
inst/resources/AUTHORS),
FriendCode Inc [cph, ctb] (The gitbook style, with modifications)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between bookdown versions 0.11 dated 2019-05-28 and 0.12 dated 2019-07-11
DESCRIPTION | 8 +++++--- MD5 | 8 ++++---- R/gitbook.R | 7 +++++++ R/html.R | 16 +--------------- man/html_document2.Rd | 5 +---- 5 files changed, 18 insertions(+), 26 deletions(-)
Title: Tidy Output from Regular Expression Matching
Description: Wrappers on 'regexpr' and 'gregexpr' to return the match
results in tidy data frames.
Author: Gábor Csárdi [aut, cre],
Matthew Lincoln [ctb]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between rematch2 versions 2.0.1 dated 2017-06-20 and 2.1.0 dated 2019-07-11
rematch2-2.0.1/rematch2/inst |only rematch2-2.1.0/rematch2/DESCRIPTION | 14 +++++++++----- rematch2-2.1.0/rematch2/MD5 | 12 +++++++----- rematch2-2.1.0/rematch2/NAMESPACE | 2 ++ rematch2-2.1.0/rematch2/NEWS.md |only rematch2-2.1.0/rematch2/R/bind_re_match.R |only rematch2-2.1.0/rematch2/README.md |only rematch2-2.1.0/rematch2/man/bind_re_match.Rd |only rematch2-2.1.0/rematch2/tests/testthat/test-bind.R |only 9 files changed, 18 insertions(+), 10 deletions(-)
Title: Computation and Visualization of Package Download Counts and
Percentiles
Description: Compute and visualize the cross-sectional and longitudinal number
and rank percentile of package downloads from RStudio's CRAN mirror.
Author: Peter Li [aut, cre]
Maintainer: Peter Li <lindbrook@gmail.com>
Diff between packageRank versions 0.1.0 dated 2019-05-16 and 0.2.0 dated 2019-07-11
DESCRIPTION | 10 - MD5 | 44 ++--- NEWS | 56 ------- R/cran_downloads2.R | 25 ++- R/multiCore.R | 45 +++-- R/packageRank.R | 223 +++++++++++++++-------------- R/packageRankTime.R | 72 +++++---- README.md | 271 +++++++++++++++++++----------------- build/vignette.rds |binary inst/doc/introduction.Rmd | 6 inst/doc/introduction.html | 8 - man/cran_downloads2.Rd | 1 man/figures/README-cranlogsB2-1.png |binary man/figures/README-cranlogsB3-1.png |binary man/figures/README-plot2-1.png |binary man/figures/README-plot_ts-1.png |binary man/figures/README-plot_ts2-1.png |binary man/packageRank.Rd | 3 man/packageRankTime.Rd | 13 - man/plot.cranlogs.Rd | 9 - man/plot.package_rank.Rd | 6 man/plot.package_rank_time.Rd | 12 - vignettes/introduction.Rmd | 6 23 files changed, 408 insertions(+), 402 deletions(-)
Title: Sensitivity Analysis of Neural Networks
Description: Analysis functions to quantify inputs importance in neural network models.
Functions are available for calculating and plotting the inputs importance and obtaining
the activation function of each neuron layer and its derivatives. The importance of a given
input is defined as the distribution of the derivatives of the output with respect to that
input in each training data point.
Author: José Portela González [aut],
Antonio Muñoz San Roque [aut],
Jaime Pizarroso Gonzalo [ctb, cre]
Maintainer: Jaime Pizarroso Gonzalo <jpizarroso@alu.comillas.edu>
Diff between NeuralSens versions 0.0.3 dated 2019-06-08 and 0.0.5 dated 2019-07-11
DESCRIPTION | 11 +- MD5 | 6 - R/SensAnalysisMLP.R | 255 ++++++++++++++++++++++++++++--------------------- man/SensAnalysisMLP.Rd | 77 +++++++++----- 4 files changed, 205 insertions(+), 144 deletions(-)
Title: Searching for Footprints of Selection using 'Extended Haplotype
Homozygosity' Based Tests
Description: Population genetic data such as 'Single Nucleotide
Polymorphisms' (SNPs) is often used to identify genomic regions
that have been under recent natural or artificial selection
and might provide clues about the molecular mechanisms of adaptation.
One approach, the concept of an 'Extended Haplotype Homozygosity' (EHH),
introduced by (Sabeti 2002) <doi:10.1038/nature01140>, has given rise to
several statistics designed for whole genome scans.
The package provides functions to compute three of these,
namely: 'iHS' (Voight 2006) <doi:10.1371/journal.pbio.0040072> for
detecting positive or 'Darwinian' selection within a single population as well as
'Rsb' (Tang 2007) <doi:10.1371/journal.pbio.0050171> and
'XP-EHH' (Sabeti 2007) <doi:10.1038/nature06250>, targeted
at differential selection between two populations.
Various plotting functions are also included to facilitate
visualization and interpretation of these statistics.
Due to changes in the API, albeit mostly minor,
this version is not compatible with versions 2.0.X.
Author: Mathieu Gautier, Alexander Klassmann and Renaud Vitalis
Maintainer: Alexander Klassmann <rehh@oneoverx.eu>
Diff between rehh versions 3.0.0 dated 2019-07-09 and 3.0.1 dated 2019-07-11
DESCRIPTION | 6 ++-- MD5 | 14 +++++------ NEWS.md | 4 +++ inst/doc/rehh.html | 4 +-- src/CALL_ASNEWICK.c | 20 ++++++---------- src/calc_furcation.c | 63 +++++++++++++++++++++++++++++++-------------------- src/haplotypes.c | 15 +++++++++--- src/init.c | 2 - 8 files changed, 76 insertions(+), 52 deletions(-)
Title: Tools for the IUCN Red List of Ecosystems and Species
Description: A toolbox created by members of the International Union for
Conservation of Nature (IUCN) Red List of Ecosystems Committee for
Scientific Standards. Primarily, it is a set of tools suitable
for calculating the metrics required for making assessments of species and
ecosystems against the IUCN Red List of Threatened Species and the IUCN Red
List of Ecosystems categories and criteria. See the IUCN website for
detailed guidelines, the criteria, publications and other information.
Author: Calvin Lee [cre, aut] (<https://orcid.org/0000-0001-8277-8614>),
Nicholas Murray [aut] (<https://orcid.org/0000-0002-4008-3053>)
Maintainer: Calvin Lee <calvinkflee@gmail.com>
Diff between redlistr versions 1.0.2 dated 2018-11-02 and 1.0.3 dated 2019-07-11
DESCRIPTION | 8 ++--- MD5 | 50 ++++++++++++++++++------------------- NEWS.md | 14 ++++++++++ R/gridUncertainty_functions.R | 16 +++++------ README.md | 4 ++ build/vignette.rds |binary inst/doc/iteration-vignette.html | 31 ++++++++++++++++++++-- inst/doc/redlistr-vignette.html | 44 ++++++++++++++++++++++++++------ man/createGrid.Rd | 1 man/extrapolateEstimate.Rd | 4 ++ man/futureAreaEstimate.Rd | 4 ++ man/getAOO.Rd | 1 man/getAOOSilent.Rd | 1 man/getArea.Rd | 1 man/getAreaEOO.Rd | 1 man/getAreaLoss.Rd | 1 man/getDeclineStats.Rd | 1 man/gridUncertainty.Rd | 1 man/gridUncertaintyBase.Rd | 6 ++-- man/gridUncertaintyRandom.Rd | 1 man/gridUncertaintyRandomManual.Rd | 1 man/gridUncertaintyRestricted.Rd | 1 man/gridUncertaintySimulation.Rd | 1 man/makeAOOGrid.Rd | 4 ++ man/makeEOO.Rd | 1 man/sequentialExtrapolate.Rd | 4 ++ 26 files changed, 147 insertions(+), 55 deletions(-)
Title: Create and Visualize Hillshaded Maps from Elevation Matrices
Description: Uses a combination of raytracing, spherical texture mapping, lambertian reflectance, and ambient occlusion to produce 2D and 3D data visualizations and maps. Includes water detection and layering functions, programmable color palette generation, several built-in textures for hill shading, 2D and 3D plotting options, and the ability to export 3D visualizations to a 3D printable format.
Author: Tyler Morgan-Wall
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between rayshader versions 0.11.4 dated 2019-07-10 and 0.11.5 dated 2019-07-11
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- R/render_movie.R | 3 +++ 3 files changed, 11 insertions(+), 8 deletions(-)
Title: Geographic Data Analysis and Modeling
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported. There is a also support for vector data operations such as intersections. See the manual and tutorials on <https://rspatial.org/> to get started.
Author: Robert J. Hijmans [cre, aut] (<https://orcid.org/0000-0001-5872-2872>),
Jacob van Etten [ctb],
Michael Sumner [ctb],
Joe Cheng [ctb],
Andrew Bevan [ctb],
Roger Bivand [ctb],
Lorenzo Busetto [ctb],
Mort Canty [ctb],
David Forrest [ctb],
Aniruddha Ghosh [ctb],
Duncan Golicher [ctb],
Josh Gray [ctb],
Jonathan A. Greenberg [ctb],
Paul Hiemstra [ctb],
Institute for Mathematics Applied Geosciences [cph],
Charles Karney [ctb],
Matteo Mattiuzzi [ctb],
Steven Mosher [ctb],
Jakub Nowosad [ctb],
Edzer Pebesma [ctb],
Oscar Perpinan Lamigueiro [ctb],
Etienne B. Racine [ctb],
Barry Rowlingson [ctb],
Ashton Shortridge [ctb],
Bill Venables [ctb],
Rafael Wueest [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between raster versions 2.9-22 dated 2019-07-10 and 2.9-23 dated 2019-07-11
DESCRIPTION | 8 ++--- MD5 | 36 +++++++++++++------------- NAMESPACE | 2 - R/AAgeneric_functions.R | 40 ++++++++--------------------- R/contour.R | 4 -- R/density.R | 4 -- R/pairs.R | 4 -- R/persp.R | 4 -- R/text.R | 4 -- inst/doc/Raster.pdf |binary inst/doc/functions.pdf |binary inst/doc/rasterfile.pdf |binary man/persp.Rd | 2 - man/slopeAspect.Rd | 17 +++++------- src/focal_fun.cpp | 8 ++--- src/focal_get.cpp | 8 ++--- src/focal_sum.cpp | 8 ++--- src/raster_aggregate.cpp | 23 ++++++++-------- src/raster_distance.cpp | 64 +++++++++++++++++++++++------------------------ 19 files changed, 99 insertions(+), 137 deletions(-)
Title: Basic Biological Sequence Handling
Description: Basic functions for microbial sequence data analysis. The idea is to use the basic R data structures as much as possible, without building complex data types.
Author: Lars Snipen, Kristian Hovde Liland
Maintainer: Lars Snipen <lars.snipen@nmbu.no>
Diff between microseq versions 1.2.2 dated 2018-02-12 and 1.2.3 dated 2019-07-11
microseq-1.2.2/microseq/inst/doc |only microseq-1.2.2/microseq/vignettes |only microseq-1.2.3/microseq/DESCRIPTION | 12 - microseq-1.2.3/microseq/MD5 | 38 ++--- microseq-1.2.3/microseq/R/RcppExports.R | 4 microseq-1.2.3/microseq/R/dnaManipulate.R | 34 ++--- microseq-1.2.3/microseq/R/fasta.R | 46 +++---- microseq-1.2.3/microseq/R/fastq.R | 46 +++---- microseq-1.2.3/microseq/R/multialign.R | 122 +++++++++--------- microseq-1.2.3/microseq/R/utilityfun.R | 15 +- microseq-1.2.3/microseq/man/gregexpr.Rd | 8 - microseq-1.2.3/microseq/man/iupac2regex.Rd | 9 - microseq-1.2.3/microseq/man/msalign.Rd | 4 microseq-1.2.3/microseq/man/muscle.Rd | 3 microseq-1.2.3/microseq/man/plot.Fasta.Rd | 1 microseq-1.2.3/microseq/man/plot.Fastq.Rd | 1 microseq-1.2.3/microseq/man/readFasta.Rd | 1 microseq-1.2.3/microseq/man/translate.Rd | 15 +- microseq-1.2.3/microseq/src/RcppExports.cpp | 7 - microseq-1.2.3/microseq/src/init.c | 4 microseq-1.2.3/microseq/src/translate.cpp | 181 ++++++++-------------------- 21 files changed, 244 insertions(+), 307 deletions(-)
Title: Kernel Density Estimation with Parametric Starts and Asymmetric
Kernels
Description: Handles univariate non-parametric density estimation with
parametric starts and asymmetric kernels in a simple and flexible way.
Kernel density estimation with parametric starts involves fitting a
parametric density to the data before making a correction with kernel
density estimation, see Hjort & Glad (1995) <doi:10.1214/aos/1176324627>.
Asymmetric kernels make kernel density estimation more efficient on bounded
intervals such as (0, 1) and the positive half-line. Supported asymmetric
kernels are the gamma kernel of Chen (2000) <doi:10.1023/A:1004165218295>,
the beta kernel of Chen (1999) <doi:10.1016/S0167-9473(99)00010-9>, and the
copula kernel of Jones & Henderson (2007) <doi:10.1093/biomet/asm068>.
User-supplied kernels, parametric starts, and bandwidths are supported.
Author: Jonas Moss, Martin Tveten
Maintainer: Jonas Moss <jonas.gjertsen@gmail.com>
Diff between kdensity versions 1.0.0 dated 2018-02-27 and 1.0.1 dated 2019-07-11
DESCRIPTION | 13 +- MD5 | 23 ++-- NEWS.md |only R/builtin_starts_estimation.R | 11 ++ R/builtin_starts_list.R | 8 + R/kdensity.R | 22 +++- README.md | 31 +++-- build/vignette.rds |binary inst/doc/tutorial.html | 221 ++++++++++++++++++++++------------------- man/kdensity.Rd | 5 man/mlgumbel.Rd | 3 tests/testthat/test_kdensity.R | 8 + tests/testthat/test_ml.R | 14 ++ 13 files changed, 221 insertions(+), 138 deletions(-)
Title: Streamlined Plot Theme and Plot Annotations for 'ggplot2'
Description: Provides various features that help with creating publication-quality figures
with 'ggplot2', such as a set of themes, functions to align plots and arrange
them into complex compound figures, and functions that make it easy to annotate
plots and or mix plots with images. The package was originally written for
internal use in the Wilke lab, hence the name (Claus O. Wilke's plot package).
It has also been used extensively in the book Fundamentals of Data
Visualization.
Author: Claus O. Wilke [aut, cre] (<https://orcid.org/0000-0002-7470-9261>)
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>
Diff between cowplot versions 0.9.4 dated 2019-01-08 and 1.0.0 dated 2019-07-11
cowplot-0.9.4/cowplot/NEWS |only cowplot-0.9.4/cowplot/R/plot_to_gtable.R |only cowplot-0.9.4/cowplot/R/switch_axis.R |only cowplot-0.9.4/cowplot/inst/doc/axis_position.R |only cowplot-0.9.4/cowplot/inst/doc/axis_position.Rmd |only cowplot-0.9.4/cowplot/inst/doc/axis_position.html |only cowplot-0.9.4/cowplot/inst/doc/plot_annotations.R |only cowplot-0.9.4/cowplot/inst/doc/plot_annotations.Rmd |only cowplot-0.9.4/cowplot/inst/doc/plot_annotations.html |only cowplot-0.9.4/cowplot/inst/doc/plot_grid.R |only cowplot-0.9.4/cowplot/inst/doc/plot_grid.Rmd |only cowplot-0.9.4/cowplot/inst/doc/plot_grid.html |only cowplot-0.9.4/cowplot/inst/doc/shared_legends.R |only cowplot-0.9.4/cowplot/inst/doc/shared_legends.Rmd |only cowplot-0.9.4/cowplot/inst/doc/shared_legends.html |only cowplot-0.9.4/cowplot/man/ggsave.Rd |only cowplot-0.9.4/cowplot/man/plot_to_gtable.Rd |only cowplot-0.9.4/cowplot/vignettes/axis_position.Rmd |only cowplot-0.9.4/cowplot/vignettes/plot_annotations.Rmd |only cowplot-0.9.4/cowplot/vignettes/plot_grid.Rmd |only cowplot-0.9.4/cowplot/vignettes/shared_legends.Rmd |only cowplot-1.0.0/cowplot/DESCRIPTION | 60 cowplot-1.0.0/cowplot/MD5 | 181 +- cowplot-1.0.0/cowplot/NAMESPACE | 40 cowplot-1.0.0/cowplot/NEWS.md |only cowplot-1.0.0/cowplot/R/add_sub.R | 15 cowplot-1.0.0/cowplot/R/align_plots.R |only cowplot-1.0.0/cowplot/R/as_grob.R |only cowplot-1.0.0/cowplot/R/as_gtable.R |only cowplot-1.0.0/cowplot/R/axis_canvas.R | 9 cowplot-1.0.0/cowplot/R/cowplot.R | 2 cowplot-1.0.0/cowplot/R/draw.R | 207 ++- cowplot-1.0.0/cowplot/R/get_axes.R |only cowplot-1.0.0/cowplot/R/get_legend.R | 19 cowplot-1.0.0/cowplot/R/get_panel.R | 62 cowplot-1.0.0/cowplot/R/get_plot_component.R |only cowplot-1.0.0/cowplot/R/get_titles.R |only cowplot-1.0.0/cowplot/R/key_glyph.R |only cowplot-1.0.0/cowplot/R/plot_grid.R | 302 +--- cowplot-1.0.0/cowplot/R/save.R | 221 +-- cowplot-1.0.0/cowplot/R/set_null_device.R |only cowplot-1.0.0/cowplot/R/setup.R | 7 cowplot-1.0.0/cowplot/R/stamp.R |only cowplot-1.0.0/cowplot/R/themes.R | 502 ++++++-- cowplot-1.0.0/cowplot/README.md | 20 cowplot-1.0.0/cowplot/build/vignette.rds |binary cowplot-1.0.0/cowplot/inst/doc/introduction.R | 164 -- cowplot-1.0.0/cowplot/inst/doc/introduction.Rmd | 212 --- cowplot-1.0.0/cowplot/inst/doc/introduction.html | 753 ++++++------ cowplot-1.0.0/cowplot/inst/extdata |only cowplot-1.0.0/cowplot/man/add_sub.Rd | 8 cowplot-1.0.0/cowplot/man/align_margin.Rd | 37 cowplot-1.0.0/cowplot/man/align_plots.Rd | 24 cowplot-1.0.0/cowplot/man/as_grob.Rd |only cowplot-1.0.0/cowplot/man/as_gtable.Rd |only cowplot-1.0.0/cowplot/man/axis_canvas.Rd | 2 cowplot-1.0.0/cowplot/man/background_grid.Rd | 27 cowplot-1.0.0/cowplot/man/draw_figure_label.Rd | 12 cowplot-1.0.0/cowplot/man/draw_grob.Rd | 13 cowplot-1.0.0/cowplot/man/draw_image.Rd | 41 cowplot-1.0.0/cowplot/man/draw_label.Rd | 42 cowplot-1.0.0/cowplot/man/draw_line.Rd | 9 cowplot-1.0.0/cowplot/man/draw_plot.Rd | 18 cowplot-1.0.0/cowplot/man/draw_plot_label.Rd | 5 cowplot-1.0.0/cowplot/man/draw_text.Rd | 8 cowplot-1.0.0/cowplot/man/figures |only cowplot-1.0.0/cowplot/man/get_legend.Rd | 5 cowplot-1.0.0/cowplot/man/get_panel.Rd | 32 cowplot-1.0.0/cowplot/man/get_plot_component.Rd |only cowplot-1.0.0/cowplot/man/get_title.Rd |only cowplot-1.0.0/cowplot/man/get_y_axis.Rd |only cowplot-1.0.0/cowplot/man/ggdraw.Rd | 14 cowplot-1.0.0/cowplot/man/ggsave2.Rd |only cowplot-1.0.0/cowplot/man/insert_xaxis_grob.Rd | 1 cowplot-1.0.0/cowplot/man/panel_border.Rd | 9 cowplot-1.0.0/cowplot/man/plot_grid.Rd | 91 + cowplot-1.0.0/cowplot/man/png_null_device.Rd |only cowplot-1.0.0/cowplot/man/rectangle_key_glyph.Rd |only cowplot-1.0.0/cowplot/man/save_plot.Rd | 76 - cowplot-1.0.0/cowplot/man/set_null_device.Rd |only cowplot-1.0.0/cowplot/man/stamp.Rd |only cowplot-1.0.0/cowplot/man/theme_cowplot.Rd | 33 cowplot-1.0.0/cowplot/man/theme_map.Rd | 25 cowplot-1.0.0/cowplot/man/theme_minimal_grid.Rd |only cowplot-1.0.0/cowplot/man/theme_nothing.Rd | 14 cowplot-1.0.0/cowplot/tests/figs |only cowplot-1.0.0/cowplot/tests/testthat/Rplots.pdf |binary cowplot-1.0.0/cowplot/tests/testthat/helper-vdiffr.R |only cowplot-1.0.0/cowplot/tests/testthat/test_align_plots.R | 60 cowplot-1.0.0/cowplot/tests/testthat/test_draw_.R |only cowplot-1.0.0/cowplot/tests/testthat/test_get_axes.R |only cowplot-1.0.0/cowplot/tests/testthat/test_get_legend.R | 7 cowplot-1.0.0/cowplot/tests/testthat/test_get_panel.R | 9 cowplot-1.0.0/cowplot/tests/testthat/test_get_titles.R |only cowplot-1.0.0/cowplot/tests/testthat/test_ggdraw.R | 7 cowplot-1.0.0/cowplot/tests/testthat/test_key_glyph.R |only cowplot-1.0.0/cowplot/tests/testthat/test_plot_components.R |only cowplot-1.0.0/cowplot/tests/testthat/test_plot_grid.R |only cowplot-1.0.0/cowplot/tests/testthat/test_themes.R |only cowplot-1.0.0/cowplot/vignettes/introduction.Rmd | 212 --- 100 files changed, 1937 insertions(+), 1680 deletions(-)
More information about readwritesqlite at CRAN
Permanent link
Title: Ferguson-Klass Type Algorithm for Posterior Normalized Random
Measures
Description: Bayesian nonparametric density estimation modeling mixtures by a Ferguson-Klass type algorithm for posterior normalized random measures.
Author: Julyan Arbel [ctb],
Ernesto Barrios [aut],
Guillaume Kon Kam King [aut, cre],
Antonio Lijoi [aut],
Luis E. Nieto-Barajas [aut],
Igor Prünster [aut]
Maintainer: Guillaume Kon Kam King <guillaume.konkamking.work@gmail.com>
Diff between BNPdensity versions 2017.03 dated 2017-03-02 and 2019.7.9 dated 2019-07-11
CHANGES | 13 DESCRIPTION | 35 + MD5 | 203 ++++++----- NAMESPACE | 25 + R/GOF_plots.R |only R/MixNRMI1.R | 165 +++++---- R/MixNRMI1cens.R | 181 +++++---- R/MixNRMI2.R | 180 +++++---- R/MixNRMI2cens.R | 198 +++++----- R/Mv.R | 11 R/MvInv.R | 94 ++++- R/MvInv_old.R |only R/cens_data_check.R | 17 R/censor_code_rl.R | 27 - R/comp1.R | 25 - R/comp2.R | 36 + R/convert_fit_to_MCMC_chain.R |only R/cpo.R | 7 R/dhalfcauchy.R | 11 R/dhalfnorm.R | 11 R/dhalft.R | 11 R/dk.R | 80 ++-- R/dkcens2.R | 37 +- R/dkcens2_1val.R | 25 - R/dt_.R | 7 R/dtnorm.R | 31 - R/expected_number_of_clusters_stable_process.R |only R/fcondXA.R | 9 R/fcondXA2.R | 9 R/fcondXA2cens2.R | 15 R/fcondYXA.R | 9 R/fcondYXAcens2.R | 13 R/fcondYZXA.R | 26 - R/fcondYZXAcens2.R | 30 - R/gs3.R | 23 - R/gs4.R | 30 - R/gs4cens2.R | 40 +- R/gs5.R | 24 - R/gs5cens2.R | 35 + R/gsHP.R | 63 +-- R/gsYZstar.R | 87 ++-- R/gsYZstarcens2.R | 93 ++--- R/helper_functions.R |only R/mixture_density_functions.R |only R/multMixNRMI.R |only R/p0.R | 40 +- R/phalfcauchy.R | 11 R/phalfnorm.R | 11 R/phalft.R | 11 R/pk.R | 80 ++-- R/posterior_clustering_analysis.R |only R/pt_.R | 7 R/ptnorm.R | 43 +- R/qgeneric.R | 79 ++-- R/qhalfcauchy.R | 11 R/qhalfnorm.R | 11 R/qhalft.R | 11 R/qt_.R | 5 R/qtnorm.R | 15 R/rfystar.R | 17 R/rfystarcens2.R | 28 - R/rfyzstar.R | 24 - R/rfyzstarcens2.R | 33 + R/rhalfcauchy.R | 5 R/rhalfnorm.R | 5 R/rhalft.R | 5 R/rk.R | 78 ++-- R/rt_.R | 5 R/rtnorm.R | 81 ++-- R/sysdata.rda |only R/thresholdGG.R |only R/traceplot.R |only README.md |only man/Enzyme1.out.Rd | 4 man/Enzyme2.out.Rd | 4 man/Galaxy1.out.Rd | 4 man/Galaxy2.out.Rd | 6 man/MixNRMI1.Rd | 454 ++++++++++++------------- man/MixNRMI1cens.Rd | 332 +++++++++--------- man/MixNRMI2.Rd | 430 +++++++++++------------ man/MixNRMI2cens.Rd | 322 ++++++++--------- man/Mv.Rd | 62 +-- man/acidity.Rd | 51 +- man/comp1.Rd | 84 ++-- man/comp2.Rd | 94 ++--- man/compute_optimal_clustering.Rd |only man/compute_thinning_grid.Rd |only man/convert_to_mcmc.Rd |only man/enzyme.Rd | 55 +-- man/expected_number_of_components_Dirichlet.Rd |only man/expected_number_of_components_stable.Rd |only man/figures |only man/fill_sigmas.Rd |only man/galaxy.Rd | 51 +- man/grid_from_data.Rd |only man/grid_from_data_censored.Rd |only man/grid_from_data_noncensored.Rd |only man/gs4.Rd | 74 ++-- man/gs4cens2.Rd | 86 ++-- man/is_censored.Rd |only man/is_semiparametric.Rd |only man/multMixNRMI1.Rd |only man/multMixNRMI1cens.Rd |only man/multMixNRMI2.Rd |only man/multMixNRMI2cens.Rd |only man/plotCDF_censored.Rd |only man/plotCDF_noncensored.Rd |only man/plotGOF.Rd |only man/plotGOF_censored.Rd |only man/plotGOF_noncensored.Rd |only man/plotPDF_censored.Rd |only man/plotPDF_noncensored.Rd |only man/plot_clustering_and_CDF.Rd |only man/plot_prior_number_of_components.Rd |only man/pp_plot_censored.Rd |only man/pp_plot_noncensored.Rd |only man/qq_plot_censored.Rd |only man/qq_plot_noncensored.Rd |only man/salinity.Rd | 4 man/traceplot.Rd |only 120 files changed, 2498 insertions(+), 2171 deletions(-)
Title: Unconstrained Numerical Optimization Algorithms
Description: Optimization algorithms implemented in R, including
conjugate gradient (CG), Broyden-Fletcher-Goldfarb-Shanno (BFGS) and the
limited memory BFGS (L-BFGS) methods. Most internal parameters can be set
through the call interface. The solvers hold up quite well for
higher-dimensional problems.
Author: James Melville [aut, cre]
Maintainer: James Melville <jlmelville@gmail.com>
Diff between mize versions 0.2.1 dated 2019-04-14 and 0.2.2 dated 2019-07-11
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 12 ++++++++++++ R/schmidt.R | 7 +++++-- build/vignette.rds |binary inst/doc/convergence.html | 22 +++++++++++----------- inst/doc/mize.Rmd | 6 +++--- inst/doc/mize.html | 40 ++++++++++++++++++++-------------------- inst/doc/mmds.html | 28 ++++++++++++++-------------- inst/doc/stateful.html | 4 ++-- tests/testthat/test_api.R | 16 ++++++++++++++++ vignettes/mize.Rmd | 6 +++--- 12 files changed, 100 insertions(+), 69 deletions(-)
Title: Create Visuals for Publication
Description: A small set of functions for making visuals for publication in 'ggplot2'. Key functions include geom_stepconfint() for drawing a step confidence interval on a Kaplan-Meier curve and theme_white()/theme_black() which are minimalist 'ggplot2' themes with transparent backgrounds.
Author: Eric Finnesgard [aut, cre]
Maintainer: Eric Finnesgard <finnesgard.eric@mayo.edu>
Diff between utile.visuals versions 0.1.1 dated 2019-06-14 and 0.2.0 dated 2019-07-11
DESCRIPTION | 14 +++--- MD5 | 24 ++++++---- NAMESPACE | 4 + NEWS.md | 7 +++ R/append.R |only R/geoms.R | 2 R/gg.R |only R/themes.R | 110 ++++++++++++++++++++++++++++++++++++++++++++---- README.md | 19 +++++--- man/append_table.Rd |only man/geom_stepconfint.Rd | 2 man/ggrisktable.Rd |only man/theme_black.Rd | 4 - man/theme_risk_black.Rd |only man/theme_risk_white.Rd |only man/theme_white.Rd | 4 - 16 files changed, 153 insertions(+), 37 deletions(-)
Title: JAR Files of the Apache Commons Mathematics Library
Description: Java JAR files for the Apache Commons Mathematics Library for use by users and other packages.
Author: David B. Dahl [cre],
The Apache Software Foundation [aut, cph]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between commonsMath versions 1.2.3 dated 2019-07-02 and 1.2.4 dated 2019-07-11
commonsMath-1.2.3/commonsMath/inst/java/commons-math3-3.6.1.jar |only commonsMath-1.2.3/commonsMath/inst/java/scala-2.13/scala-parallel-collections_2.13-0.2.0.jar |only commonsMath-1.2.4/commonsMath/DESCRIPTION | 11 ++-- commonsMath-1.2.4/commonsMath/LICENSE | 25 --------- commonsMath-1.2.4/commonsMath/MD5 | 26 +++++----- commonsMath-1.2.4/commonsMath/NAMESPACE | 1 commonsMath-1.2.4/commonsMath/NEWS | 7 ++ commonsMath-1.2.4/commonsMath/R/scalaDevelDownloadJARs.R |only commonsMath-1.2.4/commonsMath/R/zzz.R |only commonsMath-1.2.4/commonsMath/build/partial.rdb |binary commonsMath-1.2.4/commonsMath/inst/java/scala-2.11/commonsMath.jar |binary commonsMath-1.2.4/commonsMath/inst/java/scala-2.12/commonsMath.jar |binary commonsMath-1.2.4/commonsMath/inst/java/scala-2.13/commonsMath.jar |binary commonsMath-1.2.4/commonsMath/java/README | 10 +-- commonsMath-1.2.4/commonsMath/java/commonsMath-source.jar |binary commonsMath-1.2.4/commonsMath/tests/testthat/tests-transcompile.R | 24 ++++----- 16 files changed, 44 insertions(+), 60 deletions(-)