Title: Regularization Paths for SCAD and MCP Penalized Regression
Models
Description: Efficient algorithms for fitting regularization paths for linear or
logistic regression models penalized by MCP or SCAD, with optional additional
L2 penalty.
Author: Patrick Breheny [aut,cre]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between ncvreg versions 3.9-1 dated 2017-04-27 and 3.10-0 dated 2018-04-17
ncvreg-3.10-0/ncvreg/DESCRIPTION | 9 +- ncvreg-3.10-0/ncvreg/MD5 | 79 ++++++++++--------- ncvreg-3.10-0/ncvreg/NEWS | 12 ++ ncvreg-3.10-0/ncvreg/R/cv.ncvreg.R | 49 ++++++------ ncvreg-3.10-0/ncvreg/R/cv.ncvsurv.R | 74 +++++++++--------- ncvreg-3.10-0/ncvreg/R/local-mfdr.R |only ncvreg-3.10-0/ncvreg/R/loss.R | 8 + ncvreg-3.10-0/ncvreg/R/mfdr.R | 3 ncvreg-3.10-0/ncvreg/R/ncvreg.R | 13 ++- ncvreg-3.10-0/ncvreg/R/ncvsurv.R | 12 ++ ncvreg-3.10-0/ncvreg/R/plot.cv.ncvreg.R | 4 ncvreg-3.10-0/ncvreg/R/predict.R | 3 ncvreg-3.10-0/ncvreg/R/se-ncvsurv.R |only ncvreg-3.10-0/ncvreg/R/summary-ncvreg.R | 27 +++++- ncvreg-3.10-0/ncvreg/R/summary-ncvsurv.R | 7 + ncvreg-3.10-0/ncvreg/build/vignette.rds |binary ncvreg-3.10-0/ncvreg/data/Heart.rda |only ncvreg-3.10-0/ncvreg/data/Prostate.rda |only ncvreg-3.10-0/ncvreg/inst/doc/quick-start.R | 16 +-- ncvreg-3.10-0/ncvreg/inst/doc/quick-start.Rnw | 18 +--- ncvreg-3.10-0/ncvreg/inst/doc/quick-start.pdf |binary ncvreg-3.10-0/ncvreg/inst/tests/cv.ncvsurv.R | 20 +++- ncvreg-3.10-0/ncvreg/inst/tests/summary.R |only ncvreg-3.10-0/ncvreg/man/Heart.Rd |only ncvreg-3.10-0/ncvreg/man/Prostate.Rd |only ncvreg-3.10-0/ncvreg/man/cv.ncvreg.Rd | 18 ++-- ncvreg-3.10-0/ncvreg/man/cv.ncvsurv.Rd | 12 ++ ncvreg-3.10-0/ncvreg/man/mfdr.Rd | 31 ++----- ncvreg-3.10-0/ncvreg/man/ncvreg.Rd | 102 +++++++++++++------------ ncvreg-3.10-0/ncvreg/man/ncvsurv.Rd | 15 ++- ncvreg-3.10-0/ncvreg/man/perm.ncvreg.Rd | 23 ++--- ncvreg-3.10-0/ncvreg/man/permres.Rd | 6 - ncvreg-3.10-0/ncvreg/man/plot-mfdr.Rd | 11 -- ncvreg-3.10-0/ncvreg/man/plot.cv.ncvreg.Rd | 18 +--- ncvreg-3.10-0/ncvreg/man/plot.ncvreg.Rd | 12 -- ncvreg-3.10-0/ncvreg/man/predict-ncvsurv.Rd |only ncvreg-3.10-0/ncvreg/man/predict.Rd | 14 +-- ncvreg-3.10-0/ncvreg/man/summary-cv-ncvreg.Rd |only ncvreg-3.10-0/ncvreg/man/summary-ncvreg.Rd |only ncvreg-3.10-0/ncvreg/src/Makevars |only ncvreg-3.10-0/ncvreg/src/binomial.c | 2 ncvreg-3.10-0/ncvreg/src/gaussian.c | 2 ncvreg-3.10-0/ncvreg/src/poisson.c | 2 ncvreg-3.10-0/ncvreg/vignettes/quick-start.Rnw | 18 +--- ncvreg-3.9-1/ncvreg/man/heart.Rd |only ncvreg-3.9-1/ncvreg/man/predict.ncvsurv.Rd |only ncvreg-3.9-1/ncvreg/man/prostate.Rd |only ncvreg-3.9-1/ncvreg/man/summary.cv.ncvreg.Rd |only 48 files changed, 354 insertions(+), 286 deletions(-)
Title: Recurrent Event Regression
Description: A collection of regression models for recurrent event process and failure time.
Available methods include these from Xu et al. (2017) <doi:10.1080/01621459.2016.1173557>,
Lin et al. (2000) <doi:10.1111/1467-9868.00259>,
Wang et al. (2001) <doi:10.1198/016214501753209031>,
Ghosh and Lin (2003) <doi:10.1111/j.0006-341X.2003.00102.x>, and
Huang and Wang (2004) <doi:10.1198/016214504000001033>.
Author: Sy Han (Steven) Chiou
Maintainer: Sy Han (Steven) Chiou <schiou@utdallas.edu>
Diff between reReg versions 1.1-1 dated 2018-02-01 and 1.1-2 dated 2018-04-17
ChangeLog | 3 DESCRIPTION | 8 - MD5 | 16 +-- NAMESPACE | 7 - R/reReg.R | 313 ++++++++++++++++++++++++++++++++++++++---------------------- R/reSurv.R | 4 R/summary.R | 30 +++-- src/Ghosh.c | 3 src/reReg.c | 81 ++++++++------- 9 files changed, 279 insertions(+), 186 deletions(-)
Title: Format Output of Various Routines in a Suitable Way for Reports
and Publication
Description: A bunch of convenience functions that transform the results of some basic statistical analyses
into table format nearly ready for publication. This includes descriptive tables, tables of
logistic regression and Cox regression results as well as forest plots.
Author: Thomas A. Gerds [aut, cre],
Christian Torp-Pedersen [ctb],
Klaus K Holst [ctb],
Brice Ozenne [aut]
Maintainer: Thomas A. Gerds <tag@biostat.ku.dk>
Diff between Publish versions 2017.10.24 dated 2017-10-23 and 2018.04.17 dated 2018-04-17
DESCRIPTION | 12 - MD5 | 69 +++-- NAMESPACE | 14 + R/coxphSeries.R | 26 +- R/formatCI.R | 9 R/getFrequency.R | 22 + R/glmSeries.R | 31 +- R/labelUnits.R | 14 - R/parseFrequencyFormat.R | 2 R/plot.ci.R | 316 +------------------------- R/plot.regressionTable.R | 48 ++-- R/plotConfidence.R | 480 +++++++++++++++++++++++++++-------------- R/plotLabels.R | 4 R/prepareLabels.R | 7 R/print.table2x2.R | 8 R/publish-package.R | 15 + R/publish.MIresult.R | 7 R/publish.Score.R | 5 R/publish.glm.R | 1 R/regressionTable.R | 29 +- R/splinePlot.lrm.R |only R/summary.regressionTable.R | 5 R/summary.univariateTable.R | 4 R/table2x2.R | 2 R/univariateTable.R | 29 +- data/CiTable.csv | 56 ++-- man/CiTable.Rd | 6 man/Publish-package.Rd |only man/formatCI.Rd | 6 man/plot.ci.Rd | 94 +------- man/plot.regressionTable.Rd | 15 - man/plotConfidence.Rd | 201 +++++++++-------- man/publish.Score.Rd | 1 man/splinePlot.lrm.Rd |only man/summary.univariateTable.Rd | 2 man/univariateTable.Rd | 25 +- tests/test-glmSeries.R |only tests/test-publish-mi.R |only 38 files changed, 770 insertions(+), 795 deletions(-)
Title: Predict Gender from Brazilian First Names
Description: A method to predict and report gender from Brazilian first names
using the Brazilian Institute of Geography and Statistics' Census data.
Author: Fernando Meireles [aut, cre]
Maintainer: Fernando Meireles <fmeireles@ufmg.br>
Diff between genderBR versions 1.0.1 dated 2017-09-05 and 1.1.0 dated 2018-04-17
DESCRIPTION | 6 +- MD5 | 12 ++-- NEWS.md |only R/get_gender.R | 45 +++++++++++++--- R/sysdata.rda |only R/utils.R | 10 +-- README.md | 145 ++++++++++++++++++++++++++++++++++-------------------- man/get_gender.Rd | 15 +++-- 8 files changed, 153 insertions(+), 80 deletions(-)
Title: UNC Men's Basketball Match Results Since 1949-1950 Season
Description: Dataset contains select attributes for each match result since 1949-1950 season for UNC men's basketball team.
Author: Jay Lee [aut, cre]
Maintainer: Jay Lee <joongsup@gmail.com>
Diff between uncmbb versions 0.1.0 dated 2017-05-18 and 0.2.0 dated 2018-04-17
DESCRIPTION | 13 ++++---- MD5 | 20 ++++++++----- NAMESPACE | 10 ++++++ NEWS.md |only R/mbb_fns.R |only README.md | 72 +++++++++++++++++++++++++++++++++++++++++++---- data/duke.rda |binary data/unc.rda |binary man/duke.Rd | 1 man/mbb_champ_season.Rd |only man/mbb_season_result.Rd |only man/unc.Rd | 1 tests |only 13 files changed, 97 insertions(+), 20 deletions(-)
Title: Psychometric Meta-Analysis Toolkit
Description: Tools for computing bare-bones and psychometric meta-analyses and for generating psychometric data for use in meta-analysis simulations. Supports bare-bones, individual-correction, and artifact-distribution methods for meta-analyzing correlations and d values. Includes tools for converting effect sizes, computing sporadic artifact corrections, reshaping meta-analytic databases, computing multivariate corrections for range variation, and more.
Author: Jeffrey A. Dahlke [aut, cre],
Brenton M. Wiernik [aut],
Michael T. Brannick [ctb],
Jack Kostal [ctb],
Sean Potter [ctb],
Yuejia (Mandy) Teng [ctb]
Maintainer: Jeffrey A. Dahlke <dahlk068@umn.edu>
Diff between psychmeta versions 0.2.4 dated 2018-03-21 and 1.0.0 dated 2018-04-17
psychmeta-0.2.4/psychmeta/R/data_wrangling.R |only psychmeta-0.2.4/psychmeta/R/matreg.R |only psychmeta-0.2.4/psychmeta/man/anova.summary_lm_mat.Rd |only psychmeta-0.2.4/psychmeta/man/confint.summary_lm_mat.Rd |only psychmeta-0.2.4/psychmeta/man/predict.summary_lm_mat.Rd |only psychmeta-0.2.4/psychmeta/man/print.summary_lm_mat.Rd |only psychmeta-1.0.0/psychmeta/DESCRIPTION | 15 psychmeta-1.0.0/psychmeta/MD5 | 362 +- psychmeta-1.0.0/psychmeta/NAMESPACE | 58 psychmeta-1.0.0/psychmeta/NEWS | 11 psychmeta-1.0.0/psychmeta/R/adjust_n.R | 2 psychmeta-1.0.0/psychmeta/R/bibliography.R |only psychmeta-1.0.0/psychmeta/R/composites.R | 16 psychmeta-1.0.0/psychmeta/R/compute_dmod.R | 46 psychmeta-1.0.0/psychmeta/R/convert_es.R | 36 psychmeta-1.0.0/psychmeta/R/convert_ma.R | 91 psychmeta-1.0.0/psychmeta/R/correct_d.R | 10 psychmeta-1.0.0/psychmeta/R/correct_mvrr.R | 10 psychmeta-1.0.0/psychmeta/R/correct_r.R | 38 psychmeta-1.0.0/psychmeta/R/correct_r_internal.R | 6 psychmeta-1.0.0/psychmeta/R/create_ad.R | 1223 +++++----- psychmeta-1.0.0/psychmeta/R/create_ad_wrappers.R | 1074 ++++---- psychmeta-1.0.0/psychmeta/R/data_doc.R | 17 psychmeta-1.0.0/psychmeta/R/estimate_artifacts.R | 2 psychmeta-1.0.0/psychmeta/R/estimate_mixture.R | 7 psychmeta-1.0.0/psychmeta/R/estimate_prods.R | 101 psychmeta-1.0.0/psychmeta/R/estimate_u.R | 24 psychmeta-1.0.0/psychmeta/R/estimate_var_artifacts.R | 2 psychmeta-1.0.0/psychmeta/R/estimate_var_rho_int.R | 2 psychmeta-1.0.0/psychmeta/R/estimate_var_rho_tsa.R | 6 psychmeta-1.0.0/psychmeta/R/estimate_var_tsa.R |only psychmeta-1.0.0/psychmeta/R/filter_ma.R |only psychmeta-1.0.0/psychmeta/R/filters.R | 66 psychmeta-1.0.0/psychmeta/R/get_stuff.R |only psychmeta-1.0.0/psychmeta/R/heterogeneity.R | 408 +-- psychmeta-1.0.0/psychmeta/R/intervals.R | 51 psychmeta-1.0.0/psychmeta/R/lm_mat.R |only psychmeta-1.0.0/psychmeta/R/ma_d.R | 60 psychmeta-1.0.0/psychmeta/R/ma_d_ad.R | 10 psychmeta-1.0.0/psychmeta/R/ma_d_bb.R | 39 psychmeta-1.0.0/psychmeta/R/ma_d_ic.R | 57 psychmeta-1.0.0/psychmeta/R/ma_d_order2.R | 69 psychmeta-1.0.0/psychmeta/R/ma_generic.R | 36 psychmeta-1.0.0/psychmeta/R/ma_r.R | 195 - psychmeta-1.0.0/psychmeta/R/ma_r_ad.R | 98 psychmeta-1.0.0/psychmeta/R/ma_r_ad_bvdrr.R | 126 - psychmeta-1.0.0/psychmeta/R/ma_r_ad_bvirr.R | 100 psychmeta-1.0.0/psychmeta/R/ma_r_ad_meas.R | 102 psychmeta-1.0.0/psychmeta/R/ma_r_ad_none.R | 12 psychmeta-1.0.0/psychmeta/R/ma_r_ad_rb_adj.R | 250 +- psychmeta-1.0.0/psychmeta/R/ma_r_ad_rb_orig.R | 251 +- psychmeta-1.0.0/psychmeta/R/ma_r_ad_uvdrr.R | 171 + psychmeta-1.0.0/psychmeta/R/ma_r_ad_uvirr.R | 169 + psychmeta-1.0.0/psychmeta/R/ma_r_bb.R | 39 psychmeta-1.0.0/psychmeta/R/ma_r_ic.R | 253 +- psychmeta-1.0.0/psychmeta/R/ma_r_order2.R | 125 - psychmeta-1.0.0/psychmeta/R/ma_wrappers.R | 15 psychmeta-1.0.0/psychmeta/R/metabulate.R | 26 psychmeta-1.0.0/psychmeta/R/metareg.R | 64 psychmeta-1.0.0/psychmeta/R/mix_matrix.R | 150 - psychmeta-1.0.0/psychmeta/R/plotting.R |only psychmeta-1.0.0/psychmeta/R/print_methods.R | 601 ++++ psychmeta-1.0.0/psychmeta/R/psychmeta.R | 3 psychmeta-1.0.0/psychmeta/R/remove_dependency.R | 46 psychmeta-1.0.0/psychmeta/R/reshape.R | 104 psychmeta-1.0.0/psychmeta/R/sensitivity.R | 7 psychmeta-1.0.0/psychmeta/R/sensitivity_bootstrap.R | 120 psychmeta-1.0.0/psychmeta/R/sensitivity_cumulative.R | 121 psychmeta-1.0.0/psychmeta/R/sensitivity_leave1out.R | 111 psychmeta-1.0.0/psychmeta/R/simulate.R | 2 psychmeta-1.0.0/psychmeta/R/simulate_d.R | 262 +- psychmeta-1.0.0/psychmeta/R/simulate_d_legacy.R | 16 psychmeta-1.0.0/psychmeta/R/simulate_psych.R | 2 psychmeta-1.0.0/psychmeta/R/simulate_r.R | 13 psychmeta-1.0.0/psychmeta/R/var_error.R | 14 psychmeta-1.0.0/psychmeta/R/var_error_tsa.R | 8 psychmeta-1.0.0/psychmeta/R/wrangle_ads.R |only psychmeta-1.0.0/psychmeta/R/wrangle_data.R |only psychmeta-1.0.0/psychmeta/R/zzz.R | 15 psychmeta-1.0.0/psychmeta/README.md | 10 psychmeta-1.0.0/psychmeta/build |only psychmeta-1.0.0/psychmeta/data/data_r_gonzalezmule_2014.RData |binary psychmeta-1.0.0/psychmeta/data/data_r_meas_multi.RData |binary psychmeta-1.0.0/psychmeta/inst |only psychmeta-1.0.0/psychmeta/man/adjust_n_r.Rd | 2 psychmeta-1.0.0/psychmeta/man/anova.lm_mat.Rd | 2 psychmeta-1.0.0/psychmeta/man/anova.summary.lm_mat.Rd |only psychmeta-1.0.0/psychmeta/man/composite_d_matrix.Rd | 2 psychmeta-1.0.0/psychmeta/man/composite_d_scalar.Rd | 2 psychmeta-1.0.0/psychmeta/man/composite_r_matrix.Rd | 8 psychmeta-1.0.0/psychmeta/man/composite_r_scalar.Rd | 2 psychmeta-1.0.0/psychmeta/man/composite_rel_matrix.Rd | 2 psychmeta-1.0.0/psychmeta/man/compute_dmod.Rd | 8 psychmeta-1.0.0/psychmeta/man/confidence.Rd | 17 psychmeta-1.0.0/psychmeta/man/confint.lm_mat.Rd | 2 psychmeta-1.0.0/psychmeta/man/confint.summary.lm_mat.Rd |only psychmeta-1.0.0/psychmeta/man/convert_es.Rd | 4 psychmeta-1.0.0/psychmeta/man/convert_ma.Rd | 3 psychmeta-1.0.0/psychmeta/man/correct_d.Rd | 10 psychmeta-1.0.0/psychmeta/man/correct_matrix_mvrr.Rd | 8 psychmeta-1.0.0/psychmeta/man/correct_means_mvrr.Rd | 2 psychmeta-1.0.0/psychmeta/man/correct_r.Rd | 6 psychmeta-1.0.0/psychmeta/man/correct_r_dich.Rd | 14 psychmeta-1.0.0/psychmeta/man/create_ad.Rd | 38 psychmeta-1.0.0/psychmeta/man/create_ad_int.Rd | 8 psychmeta-1.0.0/psychmeta/man/create_ad_list.Rd |only psychmeta-1.0.0/psychmeta/man/create_ad_tsa.Rd | 16 psychmeta-1.0.0/psychmeta/man/credibility.Rd | 2 psychmeta-1.0.0/psychmeta/man/data_d_meas_multi.Rd | 2 psychmeta-1.0.0/psychmeta/man/data_r_bvdrr.Rd | 4 psychmeta-1.0.0/psychmeta/man/data_r_bvirr.Rd | 2 psychmeta-1.0.0/psychmeta/man/data_r_gonzalezmule_2014.Rd | 1 psychmeta-1.0.0/psychmeta/man/data_r_meas.Rd | 2 psychmeta-1.0.0/psychmeta/man/data_r_meas_multi.Rd | 2 psychmeta-1.0.0/psychmeta/man/data_r_uvdrr.Rd | 2 psychmeta-1.0.0/psychmeta/man/data_r_uvirr.Rd | 2 psychmeta-1.0.0/psychmeta/man/estimate_matrix_prods.Rd |only psychmeta-1.0.0/psychmeta/man/estimate_rel_dist.Rd | 2 psychmeta-1.0.0/psychmeta/man/estimate_u.Rd | 2 psychmeta-1.0.0/psychmeta/man/estimate_var_artifacts.Rd | 2 psychmeta-1.0.0/psychmeta/man/estimate_var_rho_int.Rd | 2 psychmeta-1.0.0/psychmeta/man/estimate_var_rho_tsa.Rd | 6 psychmeta-1.0.0/psychmeta/man/estimate_var_tsa.Rd |only psychmeta-1.0.0/psychmeta/man/filter_listnonnull.Rd |only psychmeta-1.0.0/psychmeta/man/filter_ma.Rd |only psychmeta-1.0.0/psychmeta/man/generate_bib.Rd |only psychmeta-1.0.0/psychmeta/man/get_stuff.Rd |only psychmeta-1.0.0/psychmeta/man/heterogeneity.Rd | 4 psychmeta-1.0.0/psychmeta/man/ma_d.Rd | 57 psychmeta-1.0.0/psychmeta/man/ma_d_ad.Rd | 10 psychmeta-1.0.0/psychmeta/man/ma_d_bb.Rd | 16 psychmeta-1.0.0/psychmeta/man/ma_d_ic.Rd | 39 psychmeta-1.0.0/psychmeta/man/ma_d_order2.Rd | 20 psychmeta-1.0.0/psychmeta/man/ma_generic.Rd | 14 psychmeta-1.0.0/psychmeta/man/ma_r.Rd | 103 psychmeta-1.0.0/psychmeta/man/ma_r_ad.Rd | 8 psychmeta-1.0.0/psychmeta/man/ma_r_bb.Rd | 15 psychmeta-1.0.0/psychmeta/man/ma_r_ic.Rd | 25 psychmeta-1.0.0/psychmeta/man/ma_r_order2.Rd | 32 psychmeta-1.0.0/psychmeta/man/matreg.Rd | 2 psychmeta-1.0.0/psychmeta/man/metabulate.Rd | 20 psychmeta-1.0.0/psychmeta/man/metareg.Rd | 12 psychmeta-1.0.0/psychmeta/man/mix_matrix.Rd | 13 psychmeta-1.0.0/psychmeta/man/mix_r_2group.Rd | 2 psychmeta-1.0.0/psychmeta/man/organize_database.Rd | 12 psychmeta-1.0.0/psychmeta/man/plot_forest.Rd |only psychmeta-1.0.0/psychmeta/man/plot_funnel.Rd |only psychmeta-1.0.0/psychmeta/man/predict.lm_mat.Rd | 2 psychmeta-1.0.0/psychmeta/man/predict.summary.lm_mat.Rd |only psychmeta-1.0.0/psychmeta/man/print.lm_mat.Rd | 17 psychmeta-1.0.0/psychmeta/man/print.psychmeta.Rd | 4 psychmeta-1.0.0/psychmeta/man/print.psychmeta.get_bootstrap.Rd |only psychmeta-1.0.0/psychmeta/man/print.psychmeta.get_cumulative.Rd |only psychmeta-1.0.0/psychmeta/man/print.psychmeta.get_escalc.Rd |only psychmeta-1.0.0/psychmeta/man/print.psychmeta.get_followup.Rd |only psychmeta-1.0.0/psychmeta/man/print.psychmeta.get_heterogeneity.Rd |only psychmeta-1.0.0/psychmeta/man/print.psychmeta.get_leave1out.Rd |only psychmeta-1.0.0/psychmeta/man/print.psychmeta.get_matrix.Rd |only psychmeta-1.0.0/psychmeta/man/print.psychmeta.get_metareg.Rd |only psychmeta-1.0.0/psychmeta/man/print.psychmeta.get_metatab.Rd |only psychmeta-1.0.0/psychmeta/man/print.psychmeta.get_plots.Rd |only psychmeta-1.0.0/psychmeta/man/print.psychmeta.ma_bootstrap.Rd |only psychmeta-1.0.0/psychmeta/man/print.psychmeta.ma_cumulative.Rd |only psychmeta-1.0.0/psychmeta/man/print.psychmeta.ma_d.ad.Rd | 4 psychmeta-1.0.0/psychmeta/man/print.psychmeta.ma_d.ad.master.Rd | 5 psychmeta-1.0.0/psychmeta/man/print.psychmeta.ma_d.barebones.Rd | 5 psychmeta-1.0.0/psychmeta/man/print.psychmeta.ma_d.barebones.master.Rd | 5 psychmeta-1.0.0/psychmeta/man/print.psychmeta.ma_d.ic.Rd | 4 psychmeta-1.0.0/psychmeta/man/print.psychmeta.ma_d.ic.master.Rd | 5 psychmeta-1.0.0/psychmeta/man/print.psychmeta.ma_d.order2.Rd | 4 psychmeta-1.0.0/psychmeta/man/print.psychmeta.ma_generic.Rd | 4 psychmeta-1.0.0/psychmeta/man/print.psychmeta.ma_leave1out.Rd |only psychmeta-1.0.0/psychmeta/man/print.psychmeta.ma_r.ad.Rd | 4 psychmeta-1.0.0/psychmeta/man/print.psychmeta.ma_r.ad.master.Rd | 5 psychmeta-1.0.0/psychmeta/man/print.psychmeta.ma_r.barebones.Rd | 5 psychmeta-1.0.0/psychmeta/man/print.psychmeta.ma_r.barebones.master.Rd | 5 psychmeta-1.0.0/psychmeta/man/print.psychmeta.ma_r.ic.Rd | 4 psychmeta-1.0.0/psychmeta/man/print.psychmeta.ma_r.ic.master.Rd | 5 psychmeta-1.0.0/psychmeta/man/print.psychmeta.ma_r.order2.Rd | 4 psychmeta-1.0.0/psychmeta/man/print.summary.lm_mat.Rd |only psychmeta-1.0.0/psychmeta/man/psychmeta-package.Rd | 3 psychmeta-1.0.0/psychmeta/man/reshape_mat2dat.Rd | 2 psychmeta-1.0.0/psychmeta/man/reshape_vec2mat.Rd | 15 psychmeta-1.0.0/psychmeta/man/reshape_wide2long.Rd | 8 psychmeta-1.0.0/psychmeta/man/sensitivity.Rd | 2 psychmeta-1.0.0/psychmeta/man/simulate_alpha.Rd | 2 psychmeta-1.0.0/psychmeta/man/simulate_d_database.Rd | 4 psychmeta-1.0.0/psychmeta/man/simulate_psych.Rd | 2 psychmeta-1.0.0/psychmeta/man/simulate_r_database.Rd | 4 psychmeta-1.0.0/psychmeta/man/simulate_r_sample.Rd | 2 psychmeta-1.0.0/psychmeta/man/sparsify_simdat_d.Rd | 2 psychmeta-1.0.0/psychmeta/man/sparsify_simdat_r.Rd | 2 psychmeta-1.0.0/psychmeta/man/summary.lm_mat.Rd | 2 psychmeta-1.0.0/psychmeta/man/unmix_matrix.Rd | 23 psychmeta-1.0.0/psychmeta/man/unmix_r_2group.Rd | 5 psychmeta-1.0.0/psychmeta/man/var_error_A.Rd | 2 psychmeta-1.0.0/psychmeta/man/var_error_alpha.Rd | 2 psychmeta-1.0.0/psychmeta/man/var_error_q.Rd | 2 psychmeta-1.0.0/psychmeta/man/var_error_r_bvirr.Rd | 8 psychmeta-1.0.0/psychmeta/man/var_error_u.Rd | 8 psychmeta-1.0.0/psychmeta/vignettes |only 201 files changed, 5526 insertions(+), 2814 deletions(-)
Title: Power Analysis for Longitudinal Multilevel Models
Description: Calculate power for the 'time x treatment' effect
in two- and three-level multilevel longitudinal studies with missing data.
Both the third-level factor (e.g. therapists, schools, or physicians),
and the second-level factor (e.g. subjects), can be assigned random slopes.
Studies with partially nested designs, unequal cluster sizes,
unequal allocation to treatment arms, and different dropout patterns
per treatment are supported. For all designs power can be
calculated both analytically and via simulations. The analytical
calculations extends the method described in Galbraith et al. (2002)
<doi:10.1016/S0197-2456(02)00205-2>, to three-level models.
Additionally, the simulation tools provides flexible ways to investigate
bias, Type I errors and the consequences of model misspecification.
Author: Kristoffer Magnusson [aut, cre]
Maintainer: Kristoffer Magnusson <hello@kristoffer.email>
Diff between powerlmm versions 0.2.0 dated 2018-03-20 and 0.3.0 dated 2018-04-17
DESCRIPTION | 19 +- MD5 | 73 ++++---- NAMESPACE | 6 NEWS.md | 13 + R/DEFT.R | 4 R/VPC.r | 20 +- R/helpers.R | 9 - R/power.R | 6 R/powerlmm-package.R | 7 R/setup.R | 337 ++++++++++++++++++++++++++++++++++---- R/simulate.R | 58 ++++-- README.md | 39 ++-- inst/doc/simulations.R | 8 inst/doc/simulations.Rmd | 10 - inst/doc/simulations.html | 14 - inst/doc/technical.pdf |binary inst/doc/three-level.R | 45 +++-- inst/doc/three-level.Rmd | 90 ++++++---- inst/doc/three-level.html | 159 +++++++++-------- inst/doc/two-level.R | 21 +- inst/doc/two-level.Rmd | 66 ++++--- inst/doc/two-level.html | 94 +++++----- man/cohend.Rd |only man/get_DEFT.Rd | 4 man/get_VPC.Rd | 3 man/get_power.Rd | 2 man/get_sds.Rd | 6 man/get_slope_diff.Rd |only man/powerlmm.Rd | 9 - man/simulate.plcp.Rd | 21 +- man/simulate_data.Rd | 3 man/study_parameters.Rd | 43 ++-- tests/testthat/tests.cohend.R |only tests/testthat/tests.helpers.R | 11 + tests/testthat/tests.simulation.R | 46 +++-- vignettes/citations.bib | 10 + vignettes/simulations.Rmd | 10 - vignettes/three-level.Rmd | 90 ++++++---- vignettes/two-level.Rmd | 66 ++++--- 39 files changed, 985 insertions(+), 437 deletions(-)
Title: Convert a Matrix of Raw Values into Nice and Tidy Data
Description: Functions to help dealing with raw data from measurements, like
reading and transforming raw values organized in matrices, calculating and
converting concentrations and calculating precision of duplicates /
triplicates / ... . It is compatible with and building on top of some
'tidyverse'-packages.
Author: Eike Christian Kühn [aut, cre]
Maintainer: Eike Christian Kühn <eike.kuehn@pixelwoelkchen.de>
Diff between bioset versions 0.2.1 dated 2018-04-04 and 0.2.2 dated 2018-04-17
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/helper.R | 3 ++- R/set.R | 1 + R/sets.R | 2 +- inst/doc/introduction.html | 4 ++-- 7 files changed, 19 insertions(+), 13 deletions(-)
Title: Manipulate and Visualize VCF Data
Description: Facilitates easy manipulation of variant call format (VCF) data.
Functions are provided to rapidly read from and write to VCF files. Once
VCF data is read into R a parser function extracts matrices of data. This
information can then be used for quality control or other purposes. Additional
functions provide visualization of genomic data. Once processing is complete
data may be written to a VCF file (*.vcf.gz). It also may be converted into
other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between
VCF data and familiar R software.
Author: Brian J. Knaus [cre, aut] (<https://orcid.org/0000-0003-1665-4343>),
Niklaus J. Grunwald [aut] (<https://orcid.org/0000-0003-1656-7602>),
Eric C. Anderson [ctb],
David J. Winter [ctb],
Zhian N. Kamvar [ctb] (<https://orcid.org/0000-0003-1458-7108>),
Javier F. Tabima [ctb] (<https://orcid.org/0000-0002-3603-2691>)
Maintainer: Brian J. Knaus <briank.lists@gmail.com>
Diff between vcfR versions 1.7.0 dated 2018-02-07 and 1.8.0 dated 2018-04-17
DESCRIPTION | 10 +- MD5 | 78 +++++++++-------- NAMESPACE | 1 R/check_keys.R |only R/freq_peak_plot.R | 35 ++++++-- R/genetic_diff.R | 2 R/gt_to_popsum.R |only R/io_vcfR.R | 27 +++++- R/pairwise_genetic_diff.R | 16 +++ R/proc_chromR.R | 139 -------------------------------- R/rePOS.R | 9 +- R/vcfR-method.R | 2 R/vcfR2migrate.R | 9 +- R/vcfR_conversion.R | 4 R/vcfR_to_tidy_functions.R | 35 ++++++-- README.md | 2 build/vignette.rds |binary inst/doc/converting_data.Rmd | 2 inst/doc/converting_data.html | 11 +- inst/doc/intro_to_vcfR.html | 16 +-- inst/doc/vcf_data.html | 4 inst/doc/workflow.html | 4 man/check_keys.Rd |only man/freq_peak_plot.Rd | 17 ++- man/genetic_diff.Rd | 2 man/io_vcfR.Rd | 6 - man/pairwise_genetic_diff.Rd | 3 man/pop_gen_sum.Rd |only man/proc_chromR.Rd | 6 - man/vcfR2migrate.Rd | 7 + man/vcfR_conversion.Rd | 5 + src/gt_to_popsum.cpp | 44 ++++++---- src/read_vcfR.cpp | 24 +++-- tests/testthat/test_013_read_vcfR_cpp.R | 8 - tests/testthat/test_014_read_vcfR.R | 2 tests/testthat/test_015_write_vcfR.R | 16 +-- tests/testthat/test_020_chromR.R | 3 tests/testthat/test_chromR_method.R | 10 +- tests/testthat/test_rePOS.R | 7 + tests/testthat/test_vcfR2DNAbin.R | 9 -- tests/testthat/test_vcfRtidy.R | 15 +-- vignettes/converting_data.Rmd | 2 42 files changed, 291 insertions(+), 301 deletions(-)
Title: Variable Metric Nonlinear Function Minimization
Description: Variable metric nonlinear function minimization with bounds constraints.
Author: John C. Nash [aut, cre]
Maintainer: John C. Nash <nashjc@uottawa.ca>
Diff between Rvmmin versions 2017-7.18 dated 2017-07-18 and 2018-4.17 dated 2018-04-17
DESCRIPTION | 8 - MD5 | 25 ++--- NAMESPACE | 1 NEWS | 5 - R/Rvmminb.R | 43 +++++--- R/Rvmminu.R | 25 ++--- build/vignette.rds |binary inst/doc/Rvmmin.R | 42 ++++++++ inst/doc/Rvmmin.Rmd | 100 +++++++++++++++++--- inst/doc/Rvmmin.pdf |binary tests/BTbad.R | 10 +- tests/groseRvmmin.R |only vignettes/Rvmmin.Rmd | 100 +++++++++++++++++--- vignettes/Rvmmin.html | 240 +++++++++++++++++++++++++++++++++++--------------- 14 files changed, 447 insertions(+), 152 deletions(-)
Title: Search 'Vertnet', a 'Database' of Vertebrate Specimen Records
Description: Retrieve, map and summarize data from the 'VertNet.org'
archives (<http://vertnet.org/>). Functions allow searching by many
parameters, including 'taxonomic' names, places, and dates. In addition,
there is an interface for conducting spatially delimited searches, and
another for requesting large 'datasets' via email.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Chris Ray [ctb],
Vijay Barve [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rvertnet versions 0.6.2 dated 2017-10-11 and 0.7.0 dated 2018-04-17
DESCRIPTION | 37 +- LICENSE | 2 MD5 | 44 +-- NEWS.md | 8 R/bigsearch.R | 59 +--- R/searchbyterm.R | 84 +++-- R/spatialsearch.R | 31 +- R/traitsearch.R | 44 +-- R/zzz.R | 66 ++-- README.md | 155 +++++----- build/vignette.rds |binary inst/doc/rvertnet_vignette.Rmd | 466 +++++++++++++++---------------- inst/doc/rvertnet_vignette.html | 468 +++++++++++++++----------------- inst/vign/figure/unnamed-chunk-13-1.png |binary inst/vign/rvertnet_vignette.Rmd | 12 inst/vign/rvertnet_vignette.md | 466 +++++++++++++++---------------- man/bigsearch.Rd | 43 +- man/searchbyterm.Rd | 65 ++-- man/spatialsearch.Rd | 21 - man/traitsearch.Rd | 17 - tests/testthat/test-searchbyterm.R | 3 tests/testthat/test-vert_id.R | 16 - vignettes/rvertnet_vignette.Rmd | 466 +++++++++++++++---------------- 23 files changed, 1287 insertions(+), 1286 deletions(-)
Title: Quick Wraps 2
Description: A collection of (wrapper) functions the creator found useful
for quickly placing data summaries and formatted regression results into
'.Rnw' or '.Rmd' files. Functions for generating commonly used graphics,
such as receiver operating curves or Bland-Altman plots, are also provided
by 'qwraps2'. 'qwraps2' is a updated version of a package 'qwraps'. The
original version 'qwraps' was never submitted to CRAN but can be found at
<https://github.com/dewittpe/qwraps/>. The implementation and limited scope
of the functions within 'qwraps2' <https://github.com/dewittpe/qwraps2/> is
fundamentally different from 'qwraps'.
Author: Peter DeWitt [aut, cre],
Tell Bennett [ctb]
Maintainer: Peter DeWitt <dewittpe@gmail.com>
Diff between qwraps2 versions 0.2.4 dated 2016-12-19 and 0.3.0 dated 2018-04-17
qwraps2-0.2.4/qwraps2/README.md |only qwraps2-0.3.0/qwraps2/DESCRIPTION | 15 qwraps2-0.3.0/qwraps2/MD5 | 106 - qwraps2-0.3.0/qwraps2/NAMESPACE | 21 qwraps2-0.3.0/qwraps2/R/RcppExports.R | 52 qwraps2-0.3.0/qwraps2/R/confusion_matrix.R | 67 qwraps2-0.3.0/qwraps2/R/create_pkg.R |only qwraps2-0.3.0/qwraps2/R/file-check.R |only qwraps2-0.3.0/qwraps2/R/geometric_mean_sd.R |only qwraps2-0.3.0/qwraps2/R/lazyload_cache.R |only qwraps2-0.3.0/qwraps2/R/mean_sd.R | 15 qwraps2-0.3.0/qwraps2/R/package_checks.R |only qwraps2-0.3.0/qwraps2/R/qable.R | 4 qwraps2-0.3.0/qwraps2/R/qacf.R | 8 qwraps2-0.3.0/qwraps2/R/qblandaltman.R | 63 qwraps2-0.3.0/qwraps2/R/qkmplot.R | 41 qwraps2-0.3.0/qwraps2/R/qwraps2.R | 7 qwraps2-0.3.0/qwraps2/R/stat-stepribbon.R |only qwraps2-0.3.0/qwraps2/R/summary_table.R | 188 - qwraps2-0.3.0/qwraps2/R/zzz.R |only qwraps2-0.3.0/qwraps2/build/vignette.rds |binary qwraps2-0.3.0/qwraps2/inst/doc/create_pkg.R |only qwraps2-0.3.0/qwraps2/inst/doc/create_pkg.Rmd |only qwraps2-0.3.0/qwraps2/inst/doc/create_pkg.html |only qwraps2-0.3.0/qwraps2/inst/doc/summary-statistics.R | 138 + qwraps2-0.3.0/qwraps2/inst/doc/summary-statistics.Rmd | 375 ++- qwraps2-0.3.0/qwraps2/inst/doc/summary-statistics.html | 1088 ++++++++--- qwraps2-0.3.0/qwraps2/inst/templates |only qwraps2-0.3.0/qwraps2/man/StatStepribbon.Rd |only qwraps2-0.3.0/qwraps2/man/confusion_matrix.Rd | 42 qwraps2-0.3.0/qwraps2/man/create_pkg.Rd |only qwraps2-0.3.0/qwraps2/man/extract.Rd | 3 qwraps2-0.3.0/qwraps2/man/file_check.Rd |only qwraps2-0.3.0/qwraps2/man/frmt.Rd | 3 qwraps2-0.3.0/qwraps2/man/geometric_mean_var_sd.Rd |only qwraps2-0.3.0/qwraps2/man/ggplot2_tools.Rd | 1 qwraps2-0.3.0/qwraps2/man/lazyload_cache.Rd |only qwraps2-0.3.0/qwraps2/man/ll.Rd | 1 qwraps2-0.3.0/qwraps2/man/logit.Rd | 32 qwraps2-0.3.0/qwraps2/man/mean_ci.Rd | 1 qwraps2-0.3.0/qwraps2/man/mean_sd.Rd | 12 qwraps2-0.3.0/qwraps2/man/median_iqr.Rd | 1 qwraps2-0.3.0/qwraps2/man/n_perc.Rd | 3 qwraps2-0.3.0/qwraps2/man/pkg_check.Rd |only qwraps2-0.3.0/qwraps2/man/qable.Rd | 5 qwraps2-0.3.0/qwraps2/man/qacf.Rd | 1 qwraps2-0.3.0/qwraps2/man/qblandaltman.Rd | 14 qwraps2-0.3.0/qwraps2/man/qkmplot.Rd | 7 qwraps2-0.3.0/qwraps2/man/qroc.Rd | 3 qwraps2-0.3.0/qwraps2/man/stat_stepribbon.Rd |only qwraps2-0.3.0/qwraps2/man/summary_table.Rd | 42 qwraps2-0.3.0/qwraps2/man/tab_summary.Rd |only qwraps2-0.3.0/qwraps2/man/traprule.Rd |only qwraps2-0.3.0/qwraps2/src/RcppExports.cpp | 29 qwraps2-0.3.0/qwraps2/src/logit.cpp | 38 qwraps2-0.3.0/qwraps2/src/traprule.cpp |only qwraps2-0.3.0/qwraps2/tests/testthat/test-confusion_matrix.R | 17 qwraps2-0.3.0/qwraps2/tests/testthat/test-summary_table.R | 2 qwraps2-0.3.0/qwraps2/vignettes/create_pkg.Rmd |only qwraps2-0.3.0/qwraps2/vignettes/summary-statistics.Rmd | 375 ++- 60 files changed, 1981 insertions(+), 839 deletions(-)
Title: Simulation of Synthetic Populations for Survey Data Considering
Auxiliary Information
Description: Tools and methods to simulate populations for surveys based
on auxiliary data. The tools include model-based methods, calibration and
combinatorial optimization algorithms. The package was developed with support of
the International Household Survey Network, DFID Trust Fund TF011722 and funds
from the World bank.
Author: Bernhard Meindl, Matthias Templ, Andreas Alfons, Alexander Kowarik and
with contributions from Mathieu Ribatet, Johannes Gussenbauer and Gregor De Cillia
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between simPop versions 1.0.0 dated 2017-08-08 and 1.1.0 dated 2018-04-17
simPop-1.0.0/simPop/tests/debug_ipu.r |only simPop-1.0.0/simPop/tests/dontruns.R |only simPop-1.0.0/simPop/tests/reproducTest.R |only simPop-1.0.0/simPop/tests/simInitSpatialTest.R |only simPop-1.0.0/simPop/tests/test_sprague.R |only simPop-1.1.0/simPop/DESCRIPTION | 37 - simPop-1.1.0/simPop/MD5 | 113 ++- simPop-1.1.0/simPop/NAMESPACE | 11 simPop-1.1.0/simPop/R/0classes.R | 5 simPop-1.1.0/simPop/R/RcppExports.R |only simPop-1.1.0/simPop/R/addKnownMargins.R | 2 simPop-1.1.0/simPop/R/calibPop.R | 177 ++++-- simPop-1.1.0/simPop/R/correctHeap.R | 187 ++++-- simPop-1.1.0/simPop/R/ipu2.r | 724 ++++++++++++++----------- simPop-1.1.0/simPop/R/numericalWeighting.R |only simPop-1.1.0/simPop/R/sampHH.R | 2 simPop-1.1.0/simPop/R/simAnnealingDT.R |only simPop-1.1.0/simPop/R/simCategorical.R | 5 simPop-1.1.0/simPop/R/simComponents.R | 6 simPop-1.1.0/simPop/R/simContinuous.R | 17 simPop-1.1.0/simPop/R/simInitSpatial.R | 2 simPop-1.1.0/simPop/R/simPop-package.R | 6 simPop-1.1.0/simPop/R/simStructure.R | 2 simPop-1.1.0/simPop/R/spBwplot.R | 3 simPop-1.1.0/simPop/R/spCdf.R | 3 simPop-1.1.0/simPop/R/spMosaic.R | 5 simPop-1.1.0/simPop/R/specifyInput.R | 8 simPop-1.1.0/simPop/R/sprague.R | 2 simPop-1.1.0/simPop/README.md | 1 simPop-1.1.0/simPop/build |only simPop-1.1.0/simPop/data/eusilc13puf.rda |binary simPop-1.1.0/simPop/data/eusilcP.RData |binary simPop-1.1.0/simPop/data/eusilcS.RData |binary simPop-1.1.0/simPop/data/ghanaS.RData |binary simPop-1.1.0/simPop/data/totalsRG.rda |binary simPop-1.1.0/simPop/data/totalsRGtab.rda |binary simPop-1.1.0/simPop/man/addKnownMargins.Rd | 2 simPop-1.1.0/simPop/man/calibPop.Rd | 32 - simPop-1.1.0/simPop/man/computeFrac.Rd |only simPop-1.1.0/simPop/man/correctHeaps.Rd | 10 simPop-1.1.0/simPop/man/correctSingleHeap.Rd | 12 simPop-1.1.0/simPop/man/cpp_mean.Rd |only simPop-1.1.0/simPop/man/ipu2.Rd | 133 ++-- simPop-1.1.0/simPop/man/ipu_step.Rd |only simPop-1.1.0/simPop/man/simCategorical.Rd | 5 simPop-1.1.0/simPop/man/simComponents.Rd | 7 simPop-1.1.0/simPop/man/simContinuous.Rd | 7 simPop-1.1.0/simPop/man/simInitSpatial.Rd | 2 simPop-1.1.0/simPop/man/simPop-package.Rd | 6 simPop-1.1.0/simPop/man/simStructure.Rd | 2 simPop-1.1.0/simPop/man/spBwplot.Rd | 3 simPop-1.1.0/simPop/man/spCdf.Rd | 3 simPop-1.1.0/simPop/man/spMosaic.Rd | 5 simPop-1.1.0/simPop/man/specifyInput.Rd | 2 simPop-1.1.0/simPop/man/sprague.Rd | 2 simPop-1.1.0/simPop/src/RcppExports.cpp |only simPop-1.1.0/simPop/src/combine_factors.cpp |only simPop-1.1.0/simPop/src/compute_linear.cpp |only simPop-1.1.0/simPop/src/gm_mean.cpp |only simPop-1.1.0/simPop/src/ipu_step.cpp |only simPop-1.1.0/simPop/src/updateMat.cpp |only simPop-1.1.0/simPop/src/updateVec.cpp |only simPop-1.1.0/simPop/tests/testthat |only simPop-1.1.0/simPop/tests/testthat.R |only 64 files changed, 972 insertions(+), 579 deletions(-)
Title: Tools for Model Specification in the Latent Variable Framework
Description: Tools for model specification in the latent variable framework
(add-on to the 'lava' package). The package contains three main functionalities:
Wald tests/F-tests with improved control of the type 1 error in small samples,
adjustment for multiple comparisons when searching for local dependencies,
and adjustment for multiple comparisons when doing inference for multiple latent variable models.
Author: Brice Ozenne [aut, cre]
Maintainer: Brice Ozenne <brice.ozenne@orange.fr>
Diff between lavaSearch2 versions 1.2.0 dated 2018-03-16 and 1.3.3 dated 2018-04-17
lavaSearch2-1.2.0/lavaSearch2/R/Utils-nlme.R |only lavaSearch2-1.2.0/lavaSearch2/R/adjustEstimate.R |only lavaSearch2-1.2.0/lavaSearch2/man/adjustEstimate.Rd |only lavaSearch2-1.2.0/lavaSearch2/man/lavaSearch.Rd |only lavaSearch2-1.2.0/lavaSearch2/tests/testthat/test1-sCorrect-clubSandwich.R |only lavaSearch2-1.3.3/lavaSearch2/DESCRIPTION | 9 lavaSearch2-1.3.3/lavaSearch2/MD5 | 136 - lavaSearch2-1.3.3/lavaSearch2/NAMESPACE | 12 lavaSearch2-1.3.3/lavaSearch2/NEWS | 52 lavaSearch2-1.3.3/lavaSearch2/R/autoplot.calibrateType1.R |only lavaSearch2-1.3.3/lavaSearch2/R/calcDistMax.R | 9 lavaSearch2-1.3.3/lavaSearch2/R/calibrateType1.R |only lavaSearch2-1.3.3/lavaSearch2/R/checkData.R | 12 lavaSearch2-1.3.3/lavaSearch2/R/coefByType.R | 10 lavaSearch2-1.3.3/lavaSearch2/R/coefType.R | 12 lavaSearch2-1.3.3/lavaSearch2/R/compare2.R | 74 lavaSearch2-1.3.3/lavaSearch2/R/compareSearch.R | 41 lavaSearch2-1.3.3/lavaSearch2/R/conditionalMoment.R | 446 +++-- lavaSearch2-1.3.3/lavaSearch2/R/createContrast.R | 6 lavaSearch2-1.3.3/lavaSearch2/R/estimate2.R |only lavaSearch2-1.3.3/lavaSearch2/R/getVarCov2.R |only lavaSearch2-1.3.3/lavaSearch2/R/information2.R | 7 lavaSearch2-1.3.3/lavaSearch2/R/lavaSearch2-package.R | 17 lavaSearch2-1.3.3/lavaSearch2/R/leverage.R | 6 lavaSearch2-1.3.3/lavaSearch2/R/methods-modelsearch2.R | 7 lavaSearch2-1.3.3/lavaSearch2/R/modelsearch2.R | 9 lavaSearch2-1.3.3/lavaSearch2/R/modelsearchMax.R | 9 lavaSearch2-1.3.3/lavaSearch2/R/multcomp.R | 8 lavaSearch2-1.3.3/lavaSearch2/R/residuals2.R | 49 lavaSearch2-1.3.3/lavaSearch2/R/sCorrect.R | 567 +++---- lavaSearch2-1.3.3/lavaSearch2/R/score2.R | 11 lavaSearch2-1.3.3/lavaSearch2/R/skeleton.R | 777 +++++++--- lavaSearch2-1.3.3/lavaSearch2/R/summary2.R | 59 lavaSearch2-1.3.3/lavaSearch2/R/utils-nlme.R |only lavaSearch2-1.3.3/lavaSearch2/R/vcov2.R | 6 lavaSearch2-1.3.3/lavaSearch2/inst/implementationScheme.png |binary lavaSearch2-1.3.3/lavaSearch2/inst/implementationScheme.svg | 162 +- lavaSearch2-1.3.3/lavaSearch2/man/autoplot_calibrateType1.Rd |only lavaSearch2-1.3.3/lavaSearch2/man/calibrateType1.Rd |only lavaSearch2-1.3.3/lavaSearch2/man/checkData.Rd | 8 lavaSearch2-1.3.3/lavaSearch2/man/coef2-internal.Rd | 2 lavaSearch2-1.3.3/lavaSearch2/man/coefByType.Rd | 6 lavaSearch2-1.3.3/lavaSearch2/man/coefType.Rd | 8 lavaSearch2-1.3.3/lavaSearch2/man/compare2.Rd | 17 lavaSearch2-1.3.3/lavaSearch2/man/conditionalMoment.Rd | 42 lavaSearch2-1.3.3/lavaSearch2/man/createContrast.Rd | 2 lavaSearch2-1.3.3/lavaSearch2/man/estfun.lvmfit.Rd | 2 lavaSearch2-1.3.3/lavaSearch2/man/estimate2.Rd |only lavaSearch2-1.3.3/lavaSearch2/man/getCluster2-internal.Rd | 2 lavaSearch2-1.3.3/lavaSearch2/man/getIndexOmega2-internal.Rd | 2 lavaSearch2-1.3.3/lavaSearch2/man/getVarCov2-internal.Rd | 2 lavaSearch2-1.3.3/lavaSearch2/man/getVarCov2.Rd | 19 lavaSearch2-1.3.3/lavaSearch2/man/glht2.Rd | 2 lavaSearch2-1.3.3/lavaSearch2/man/lavaSearch2.Rd |only lavaSearch2-1.3.3/lavaSearch2/man/leverage2.Rd | 2 lavaSearch2-1.3.3/lavaSearch2/man/merge.Rd | 3 lavaSearch2-1.3.3/lavaSearch2/man/residuals2.Rd | 38 lavaSearch2-1.3.3/lavaSearch2/man/sCorrect.Rd | 32 lavaSearch2-1.3.3/lavaSearch2/man/score2.Rd | 2 lavaSearch2-1.3.3/lavaSearch2/man/skeleton.Rd | 42 lavaSearch2-1.3.3/lavaSearch2/man/summary2.Rd | 18 lavaSearch2-1.3.3/lavaSearch2/man/vcov2.Rd | 2 lavaSearch2-1.3.3/lavaSearch2/tests/testthat/test-coefType.R | 16 lavaSearch2-1.3.3/lavaSearch2/tests/testthat/test-initVar.R | 2 lavaSearch2-1.3.3/lavaSearch2/tests/testthat/test1-Utils-nlme.R | 23 lavaSearch2-1.3.3/lavaSearch2/tests/testthat/test1-adjustMoment.R |only lavaSearch2-1.3.3/lavaSearch2/tests/testthat/test1-calibrateType1.R |only lavaSearch2-1.3.3/lavaSearch2/tests/testthat/test1-compare2.R | 92 - lavaSearch2-1.3.3/lavaSearch2/tests/testthat/test1-sCorrect-adjustedResiduals.R | 118 + lavaSearch2-1.3.3/lavaSearch2/tests/testthat/test1-sCorrect-dVcov.R | 102 - lavaSearch2-1.3.3/lavaSearch2/tests/testthat/test1-sCorrect-lava.R | 69 lavaSearch2-1.3.3/lavaSearch2/tests/testthat/test1-sCorrect-missingValues.R | 26 lavaSearch2-1.3.3/lavaSearch2/tests/testthat/test1-sCorrect-smallSampleCorrection.R |only lavaSearch2-1.3.3/lavaSearch2/tests/testthat/test1-sCorrect-summary2.R |only lavaSearch2-1.3.3/lavaSearch2/tests/testthat/test1-sCorrect-validObjects.R | 40 lavaSearch2-1.3.3/lavaSearch2/tests/testthat/test2-compareSearch.R | 6 lavaSearch2-1.3.3/lavaSearch2/tests/testthat/test2-modelsearch2.R | 6 lavaSearch2-1.3.3/lavaSearch2/tests/testthat/test3-multcomp.R | 6 78 files changed, 2081 insertions(+), 1191 deletions(-)
Title: Weighted Estimation in Cox Regression
Description: Implements weighted estimation in Cox regression as proposed by
Schemper, Wakounig and Heinze (Statistics in Medicine, 2009,
<doi:10.1002/sim.3623>) and as described in Dunkler, Ploner, Schemper and
Heinze (Journal of Statistical Software, 2018, <doi:10.18637/jss.v084.i02>).
Weighted Cox regression provides unbiased average hazard ratio
estimates also in case of non-proportional hazards.
Approximated generalized concordance probability an effect size measure for clear-cut
decisions can be obtained.
The package provides options to estimate time-dependent effects conveniently by
including interactions of covariates with arbitrary functions of time, with or without
making use of the weighting option.
Author: Georg Heinze [aut, cre],
Meinhard Ploner [aut],
Daniela Dunkler [aut]
Maintainer: Georg Heinze <georg.heinze@meduniwien.ac.at>
Diff between coxphw versions 4.0.0 dated 2017-01-02 and 4.0.1 dated 2018-04-17
coxphw-4.0.0/coxphw/data/biofeedback.txt.gz |only coxphw-4.0.0/coxphw/data/gastric.txt.gz |only coxphw-4.0.0/coxphw/inst/doc/JSS_2015_example_code.R |only coxphw-4.0.0/coxphw/inst/doc/JSS_2015_example_code.Rmd |only coxphw-4.0.0/coxphw/inst/doc/JSS_2015_example_code.html |only coxphw-4.0.0/coxphw/vignettes/JSS_2015_example_code.Rmd |only coxphw-4.0.1/coxphw/DESCRIPTION | 15 ++++-- coxphw-4.0.1/coxphw/MD5 | 33 +++++++------- coxphw-4.0.1/coxphw/NAMESPACE | 2 coxphw-4.0.1/coxphw/README.md | 5 +- coxphw-4.0.1/coxphw/build/partial.rdb |binary coxphw-4.0.1/coxphw/build/vignette.rds |binary coxphw-4.0.1/coxphw/data/biofeedback.txt |only coxphw-4.0.1/coxphw/data/gastric.txt |only coxphw-4.0.1/coxphw/inst/CITATION | 36 ++++++++-------- coxphw-4.0.1/coxphw/inst/NEWS.Rd | 9 +++- coxphw-4.0.1/coxphw/inst/doc/jss_2018_example_code.R |only coxphw-4.0.1/coxphw/inst/doc/jss_2018_example_code.Rmd |only coxphw-4.0.1/coxphw/inst/doc/jss_2018_example_code.html |only coxphw-4.0.1/coxphw/man/coxphw-package.Rd | 11 +++- coxphw-4.0.1/coxphw/man/coxphw.Rd | 8 ++- coxphw-4.0.1/coxphw/man/predict.coxphw.Rd | 8 +-- coxphw-4.0.1/coxphw/src/init.c |only coxphw-4.0.1/coxphw/vignettes/jss_2018_example_code.Rmd |only 24 files changed, 73 insertions(+), 54 deletions(-)
Title: Sensitivity Analysis and Optimum Experiment Design for Microbial
Inactivation
Description: Extends the bioinactivation package with functions for Sensitivity
Analysis and Optimum Experiment Design.
Author: Alberto Garre [aut, cre],
Jose Lucas Penalver [aut],
Pablo S. Fernandez [aut],
Jose A. Egea [aut]
Maintainer: Alberto Garre <garre.alberto@gmail.com>
Diff between bioOED versions 0.1.1 dated 2017-03-13 and 0.1.4 dated 2018-04-17
DESCRIPTION | 14 - MD5 | 52 +++--- NEWS.md |only R/OED_penalty.R | 31 ++- R/methods_S3.R | 4 R/optimize_ref_temp.R | 6 build/vignette.rds |binary inst/CITATION |only inst/doc/vignette_bioOED.Rmd | 2 inst/doc/vignette_bioOED.html | 312 +++++++++++++++++++++++--------------- man/calculate_FIM.Rd | 1 man/calculate_pars_correlation.Rd | 1 man/criterium_D.Rd | 1 man/criterium_modE.Rd | 1 man/inactivation_OED.Rd | 1 man/inactivation_OED_penalty.Rd | 7 man/inactivation_sens_handler.Rd | 1 man/objective_D.Rd | 1 man/objective_D_penalty.Rd | 5 man/objective_Emod.Rd | 1 man/objective_Emod_penalty.Rd | 5 man/optimize_refTemp.Rd | 9 - man/penalty_function.Rd | 8 man/plot.OEDinactivation.Rd | 1 man/plot.parCorrelation.Rd | 1 man/refTemp_optim_handler.Rd | 1 man/sensitivity_inactivation.Rd | 1 vignettes/vignette_bioOED.Rmd | 2 28 files changed, 262 insertions(+), 207 deletions(-)
Title: Wrapper to the 'spaCy' 'NLP' Library
Description: An R wrapper to the 'Python' 'spaCy' 'NLP' library,
from <http://spacy.io>.
Author: Kenneth Benoit [aut, cre, cph],
Akitaka Matsuo [aut]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between spacyr versions 0.9.6 dated 2018-02-18 and 0.9.9 dated 2018-04-17
DESCRIPTION | 8 MD5 | 55 +++-- NAMESPACE | 7 NEWS.md | 5 R/data.R | 7 R/entity-functions.R | 48 ++-- R/parse-extractor-functions.R | 55 ++--- R/python-functions.R | 1 R/spacy_initialize.R | 308 +++++++++++++++++++------------ R/spacy_install.R |only R/spacy_langmodel_functions.R |only R/spacy_parse.R | 27 +- R/utils.R |only README.md | 178 +++++++---------- inst/python/spacyr_class.py | 31 ++- man/data_char_paragraph.Rd | 2 man/data_char_sentences.Rd | 2 man/entity_extract.Rd | 2 man/find_spacy.Rd | 6 man/find_spacy_env.Rd |only man/get-functions.Rd | 4 man/process_document.Rd | 12 - man/spacy_download_langmodel.Rd |only man/spacy_finalize.Rd | 8 man/spacy_initialize.Rd | 57 +++-- man/spacy_install.Rd |only man/spacy_parse.Rd | 13 - man/spacy_uninstall.Rd |only man/spacy_upgrade.Rd |only man/spacyr-package.Rd | 5 tests/testthat/test-1-spacy_initialize.R | 2 tests/testthat/test-5-spacy-install.R |only tests/testthat/utils.R | 7 33 files changed, 470 insertions(+), 380 deletions(-)
Title: Distance Measure Based Judgment and Learning
Description: Implements various decision support tools related to the new product development.
Subroutines include correlation reliability test, Mahalanobis distance measure for outlier detection, combinatorial search (all possible subset regression), non-parametric efficiency analysis measures: DDF (directional distance function), DEA (data envelopment analysis), HDF (hyperbolic distance function), SBM (slack-based measure), and SF (shortage function), benchmarking, risk analysis, technology adoption model, new product target setting, etc.
Author: Dong-Joon Lim, PhD
Maintainer: Dong-Joon Lim <tgno3.com@gmail.com>
Diff between DJL versions 2.6 dated 2016-09-28 and 2.7 dated 2018-04-17
DESCRIPTION | 10 +- MD5 | 12 +- NAMESPACE | 1 NEWS | 16 ++- R/DJL-internal.R | 250 +++++++++++++++++++++++++-------------------------- R/dm.hdf.R | 2 R/roc.malmquist.R |only man/roc.malmquist.Rd |only 8 files changed, 153 insertions(+), 138 deletions(-)
Title: Visualization Package for CanvasXpress in R
Description: Enables creation of visualizations using the CanvasXpress framework
in R. CanvasXpress is a standalone JavaScript library for reproducible research
with complete tracking of data and end-user modifications stored in a single
PNG image that can be played back. See <http://canvasxpress.org> for more
information.
Author: Isaac Neuhaus [aut],
Connie Brett [aut, cre]
Maintainer: Connie Brett <connie@aggregate-genius.com>
Diff between canvasXpress versions 1.18.8 dated 2018-03-15 and 1.19.0 dated 2018-04-17
DESCRIPTION | 16 MD5 | 28 - NEWS.md | 2 inst/doc/additional_examples.html | 4 inst/doc/getting_started.html | 4 inst/extdata/cX-networkbasic-edges.txt | 4 inst/extdata/cX-networkbasic-nodes.txt | 18 inst/extdata/cX-wpapoptosis-edges.txt | 134 +++---- inst/extdata/cX-wpapoptosis-nodes.txt | 34 - inst/htmlwidgets/canvasXpress.yaml | 2 inst/htmlwidgets/lib/canvasXpress/canvasXpress.css | 334 ++++++++++-------- inst/htmlwidgets/lib/canvasXpress/canvasXpress.min.js | 6 man/canvasXpress-package.Rd | 9 tests/testthat/test-network.R | 4 tests/testthat/test-scatter2D.R | 8 15 files changed, 344 insertions(+), 263 deletions(-)
Title: Nonlinear Cointegrating Autoregressive Distributed Lag Model
Description: Computes the nonlinear cointegrating autoregressive distributed lag model with p lags of the dependent variables and q lags of independent variables proposed by (Shin, Yu & Greenwood-Nimmo, 2014 <doi:10.1007/978-1-4899-8008-3_9>).
Author: Taha Zaghdoudi
Maintainer: Taha Zaghdoudi <zedtaha@gmail.com>
Diff between nardl versions 0.1.3 dated 2018-03-04 and 0.1.4 dated 2018-04-17
DESCRIPTION | 9 + MD5 | 22 ++- NAMESPACE | 3 R/fod.R |only R/helperfunctions_nardl.R |only R/nardl.R | 254 +++---------------------------------------- R/pssbounds.r | 268 ++++++++++++++++++++++++++-------------------- R/summary.nardl.R |only man/ArchTest.Rd |only man/Nardl-package.Rd | 4 man/bp2.Rd |only man/fod.Rd | 10 + man/nardl.Rd | 2 man/pssbounds.Rd |only man/summary.nardl.Rd | 10 + 15 files changed, 215 insertions(+), 367 deletions(-)
Title: Bayesian Structure Learning in Graphical Models using
Birth-Death MCMC
Description: Provides statistical tools for Bayesian structure learning in undirected graphical models for continuous, discrete, and mixed data. The package is implemented the recent improvements in the Bayesian graphical models literature, including Mohammadi and Wit (2015) <doi:10.1214/14-BA889> and Mohammadi et al. (2017) <doi:10.1111/rssc.12171>. To speed up the computations, the BDMCMC sampling algorithms are implemented in parallel using OpenMP in C++.
Author: Reza Mohammadi (<https://orcid.org/0000-0001-9538-0648>) and Ernst Wit
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between BDgraph versions 2.45 dated 2018-03-29 and 2.46 dated 2018-04-17
DESCRIPTION | 17 +++----- MD5 | 30 +++++++------- NAMESPACE | 107 ++++++++++++++++++++++++++--------------------------- NEWS | 3 + R/bdgraph.sim.R | 8 +-- R/compare.R | 55 ++++++++++++++++++++------- R/rgcwish.R | 15 +++++-- R/rgwish.R | 18 ++++++-- R/rmvnorm.R |only R/rwish.R | 17 +++++--- inst/CITATION | 4 - man/bdgraph.mpl.Rd | 2 man/plinks.Rd | 4 - man/plotcoda.Rd | 4 - man/rgwish.Rd | 2 man/rmvnorm.Rd |only man/rwish.Rd | 104 +++++++++++++++++++++++++-------------------------- 17 files changed, 222 insertions(+), 168 deletions(-)
Title: Tidy Anomaly Detection
Description: The 'anomalize' package enables a "tidy" workflow for detecting anomalies in data.
The main functions are time_decompose(), anomalize(), and time_recompose().
When combined, it's quite simple to decompose time series, detect anomalies,
and create bands separating the "normal" data from the anomalous data at scale (i.e. for multiple time series).
Time series decomposition is used to remove trend and seasonal components via the time_decompose() function
and methods include seasonal decomposition of time series by Loess ("stl") and
seasonal decomposition by piecewise medians ("twitter"). The anomalize() function implements
two methods for anomaly detection of residuals including using an inner quartile range ("iqr")
and generalized extreme studentized deviation ("gesd"). These methods are based on
those used in the 'forecast' package and the Twitter 'AnomalyDetection' package.
Refer to the associated functions for specific references for these methods.
Author: Matt Dancho [aut, cre],
Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between anomalize versions 0.1.0 dated 2018-04-06 and 0.1.1 dated 2018-04-17
DESCRIPTION | 6 ++--- MD5 | 20 ++++++++--------- NEWS.md | 6 +++++ R/plot_anomalies.R | 5 ++-- R/plot_anomaly_decomposition.R | 2 - README.md | 34 +++++++++++------------------- inst/doc/anomalize_methods.html | 4 +-- inst/doc/anomalize_quick_start_guide.Rmd | 8 +++++++ inst/doc/anomalize_quick_start_guide.html | 11 +++++++-- tests/testthat/test-time_frequency.R | 5 ++-- vignettes/anomalize_quick_start_guide.Rmd | 8 +++++++ 11 files changed, 66 insertions(+), 43 deletions(-)
Title: Joint Modeling of Longitudinal and Time-to-Event Data under a
Bayesian Approach
Description: Shared parameter models for the joint modeling of longitudinal and time-to-event data using MCMC; Dimitris Rizopoulos (2016) <doi:10.18637/jss.v072.i07>.
Author: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between JMbayes versions 0.8-70 dated 2017-10-30 and 0.8-71 dated 2018-04-17
DESCRIPTION | 8 - MD5 | 28 +-- R/aucJM.mvJMbayes.R | 28 ++- R/dynPred_lme.R | 37 +++-- R/methods_mvJointModelBayes.R | 6 R/mvJointModelBayes.R | 2 R/prederrJM.mvJMbayes.R | 28 ++- R/rocJM.mvJMbayes.R | 3 R/supportFuns_mvJointModelBayes.R | 4 R/survfitJM.mvJMbayes.R | 4 R/td_effect.R | 2 inst/doc/Dynamic_Predictions.html | 97 ++++++------- inst/doc/Multivariate_Joint_Models.html | 226 ++++++++++++++++---------------- man/IndvPred.Rd | 6 man/JMbayes.Rd | 4 15 files changed, 263 insertions(+), 220 deletions(-)
Title: Bindings for the 'HaveIBeenPwned.com' Data Breach API
Description: Utilising the 'Have I been pwned?' API (see <https://haveibeenpwned.com/API/v2>
for more information), check whether email addresses and/or user names have been present
in a publicly disclosed data breach.
Author: Steph Locke [aut, cre],
Troy Hunt [aut] (HaveIBeenPwned.com),
Locke Data [fnd],
Maëlle Salmon [ctb]
Maintainer: Steph Locke <stephanie.g.locke@gmail.com>
Diff between HIBPwned versions 0.1.6 dated 2017-05-30 and 0.1.7 dated 2018-04-17
HIBPwned-0.1.6/HIBPwned/README.md |only HIBPwned-0.1.6/HIBPwned/man/GETcontent.Rd |only HIBPwned-0.1.7/HIBPwned/DESCRIPTION | 26 HIBPwned-0.1.7/HIBPwned/MD5 | 53 - HIBPwned-0.1.7/HIBPwned/NEWS.md | 41 - HIBPwned-0.1.7/HIBPwned/R/HIBP_headers.R | 40 HIBPwned-0.1.7/HIBPwned/R/account_breaches.R | 104 +- HIBPwned-0.1.7/HIBPwned/R/breached_site.R | 62 - HIBPwned-0.1.7/HIBPwned/R/breached_sites.R | 57 - HIBPwned-0.1.7/HIBPwned/R/data_classes.R | 36 HIBPwned-0.1.7/HIBPwned/R/pastes.R | 63 - HIBPwned-0.1.7/HIBPwned/R/utils.R | 85 +- HIBPwned-0.1.7/HIBPwned/build/vignette.rds |binary HIBPwned-0.1.7/HIBPwned/inst/doc/HIBP.Rmd | 72 - HIBPwned-0.1.7/HIBPwned/inst/doc/HIBP.html | 405 +++++++--- HIBPwned-0.1.7/HIBPwned/man/account_breaches.Rd | 19 HIBPwned-0.1.7/HIBPwned/man/breached_site.Rd | 12 HIBPwned-0.1.7/HIBPwned/man/breached_sites.Rd | 12 HIBPwned-0.1.7/HIBPwned/man/data_classes.Rd | 12 HIBPwned-0.1.7/HIBPwned/man/dot-GETcontent.Rd |only HIBPwned-0.1.7/HIBPwned/man/pastes.Rd | 12 HIBPwned-0.1.7/HIBPwned/tests/testthat/test-HIBP_headers.R | 69 - HIBPwned-0.1.7/HIBPwned/tests/testthat/test-account_breaches.R | 263 +++--- HIBPwned-0.1.7/HIBPwned/tests/testthat/test-breached_site.R | 62 - HIBPwned-0.1.7/HIBPwned/tests/testthat/test-breached_sites.R | 76 - HIBPwned-0.1.7/HIBPwned/tests/testthat/test-data_classes.R | 20 HIBPwned-0.1.7/HIBPwned/tests/testthat/test-http-errors-handling.R |only HIBPwned-0.1.7/HIBPwned/tests/testthat/test-lintr.R |only HIBPwned-0.1.7/HIBPwned/tests/testthat/test-pastes.R | 93 +- HIBPwned-0.1.7/HIBPwned/vignettes/HIBP.Rmd | 72 - 30 files changed, 1081 insertions(+), 685 deletions(-)
Title: Linear and Nonlinear Methods for Analyzing Dendroclimatological
Data
Description: Provides novel dendroclimatological methods, primarily used by the
Tree-ring research community. There are two core functions. The first one is
daily_response(), which finds the optimal sequence of days that are related
to one or more tree-ring proxy records. The second one is compare_methods(),
which effectively compares several linear and nonlinear regression algorithms.
Author: Jernej Jevsenak [aut, cre], Tom Levanic [ctb]
Maintainer: Jernej Jevsenak <jernej.jevsenak@gmail.com>
Diff between dendroTools versions 0.0.6 dated 2018-02-08 and 0.0.7 dated 2018-04-17
DESCRIPTION | 13 MD5 | 44 - NAMESPACE | 9 NEWS.md | 18 R/compare_methods.R | 1438 ++++++++++++++++++++++++++++++--- R/daily_response.R | 36 R/dataset_MVA.R |only R/dataset_MVA_individual.R |only R/dataset_TRW.R |only R/dataset_TRW_complete.R |only R/plot_specific.R | 2 build/vignette.rds |binary data/dataset_MVA.rda |only data/dataset_MVA_individual.rda |only data/dataset_TRW.rda |only data/dataset_TRW_complete.rda |only inst/CITATION | 7 inst/doc/Examples_daily_response.Rmd | 2 inst/doc/Examples_daily_response.html | 40 inst/doc/compare_methods_vignette.R |only inst/doc/compare_methods_vignette.Rmd |only inst/doc/compare_methods_vignette.html |only man/compare_methods.Rd | 129 ++ man/daily_response.Rd | 36 man/dataset_MVA.Rd |only man/dataset_MVA_individual.Rd |only man/dataset_TRW.Rd |only man/dataset_TRW_complete.Rd |only man/plot_specific.Rd | 25 vignettes/Examples_daily_response.Rmd | 2 vignettes/compare_methods_vignette.Rmd |only 31 files changed, 1540 insertions(+), 261 deletions(-)
Title: Comparative Analyses of Phylogenetics and Evolution in R
Description: Functions for performing phylogenetic comparative analyses.
Author: David Orme, Rob Freckleton, Gavin Thomas, Thomas Petzoldt, Susanne Fritz, Nick Isaac, Will Pearse
Maintainer: David Orme <d.orme@imperial.ac.uk>
Diff between caper versions 0.5.2.1 dated 2018-04-16 and 1.0.1 dated 2018-04-17
CHANGES | 38 ++++++++++++++------ DESCRIPTION | 14 ++++--- MD5 | 21 ++++++----- NAMESPACE | 21 +++++------ R/pgls.R | 2 - R/phylo.d.R | 6 +-- README | 77 +----------------------------------------- build/vignette.rds |binary inst/doc/caper-benchmarks.pdf |binary inst/doc/caper.R |only inst/doc/caper.pdf |binary man/pgls-methods.Rd | 4 ++ 12 files changed, 67 insertions(+), 116 deletions(-)
Title: The Breakdown of Genomic Ancestry Blocks in Hybrid Lineages
Description: Individual based simulations of hybridizing populations, where the accumulation of junctions is tracked. Furthermore, mathematical equations are provided to verify simulation outcomes. Both simulations and mathematical equations are based on Janzen (2018) <doi:10.1101/058107>.
Author: Thijs Janzen [aut, cre]
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Diff between junctions versions 1.0 dated 2018-01-17 and 1.0.1 dated 2018-04-17
junctions-1.0.1/junctions/DESCRIPTION | 14 ++---- junctions-1.0.1/junctions/MD5 | 28 ++++++------- junctions-1.0.1/junctions/R/sim_fin_chrom.R | 1 junctions-1.0.1/junctions/R/sim_inf_chrom.R | 1 junctions-1.0.1/junctions/README.md | 7 ++- junctions-1.0.1/junctions/inst/doc/junctions_vignette.html | 12 ++--- junctions-1.0.1/junctions/man/calculate_J.Rd | 2 junctions-1.0.1/junctions/man/calculate_MAT.Rd | 2 junctions-1.0.1/junctions/man/calculate_error.Rd | 2 junctions-1.0.1/junctions/man/calculate_time.Rd | 2 junctions-1.0.1/junctions/man/junctions-package.Rd | 2 junctions-1.0.1/junctions/src/Fish.cpp | 27 ------------ junctions-1.0.1/junctions/src/main_functions.cpp | 5 -- junctions-1.0.1/junctions/src/random_functions.cpp |only junctions-1.0.1/junctions/src/random_functions.h |only junctions-1.0/junctions/src/mersenne.cpp |only junctions-1.0/junctions/src/randomc.h |only 17 files changed, 42 insertions(+), 63 deletions(-)
Title: Spatio-Temporal Generalised Linear Mixed Models for Areal Unit
Data
Description: Implements a class of spatio-temporal generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (MCMC) simulation. The response variable can be binomial, Gaussian or Poisson, but for some models only the binomial and Poisson data likelihoods are available. The spatio-temporal autocorrelation is modelled by random effects, which are assigned conditional autoregressive (CAR) style prior distributions. A number of different random effects structures are available, including Bernardinelli et al. (1995) <doi:10.1002/sim.4780142112>, Rushworth et al. (2014) <doi:10.1016/j.sste.2014.05.001> and Lee et al. (2016) <doi:10.1214/16-AOAS941>. Full details are given in the vignette accompanying this package. The creation of this package was supported by the Engineering and Physical Sciences Research Council (EPSRC) grant EP/J017442/1 and the Medical Research Council (MRC) grant MR/L022184/1.
Author: Duncan Lee, Alastair Rushworth and Gary Napier
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>
Diff between CARBayesST versions 2.5.1 dated 2017-08-14 and 2.5.2 dated 2018-04-17
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- build/vignette.rds |binary inst/CITATION |only inst/doc/CARBayesST.pdf |binary man/CARBayesST-package.Rd | 8 ++++++-- 6 files changed, 15 insertions(+), 10 deletions(-)
Title: Weibull Analysis for Reliability Engineering
Description: Life data analysis in the graphical tradition of Waloddi Weibull. Methods derived from Robert B. Abernethy (2008, ISBN 0-965306-3-2), Wayne Nelson (1982, ISBN: 9780471094586) <DOI:10.1002/0471725234>, William Q. Meeker and Lois A. Escobar (1998, ISBN: 1-471-14328-6), John I. McCool, (2012, ISBN: 9781118217986) <DOI:10.1002/9781118351994>.
Author: David Silkworth [aut],
Jurgen Symynck [aut],
Jacob Ormerod [cre],
OpenReliability.org [cph]
Maintainer: Jacob Ormerod <jake@openreliability.org>
Diff between WeibullR versions 1.0.5 dated 2018-04-12 and 1.0.6 dated 2018-04-17
DESCRIPTION | 13 +++++-------- MD5 | 7 ++++--- README.md |only man/WeibullR-package.Rd | 2 +- src/CallgetCCC2.cpp | 4 +++- 5 files changed, 13 insertions(+), 13 deletions(-)
Title: Latent Trait Models under IRT
Description: Analysis of multivariate dichotomous and polytomous data using latent trait models under the Item Response Theory approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's Three-Parameter, the Graded Response, and the Generalized Partial Credit Models.
Author: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between ltm versions 1.1-0 dated 2017-09-11 and 1.1-1 dated 2018-04-17
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/biserial.cor.R | 3 ++- R/descript.R | 2 +- inst/NEWS | 7 +++++++ man/ltm-package.Rd | 4 ++-- 6 files changed, 22 insertions(+), 14 deletions(-)
More information about germinationmetrics at CRAN
Permanent link
Title: Tools for Developing R Packages Interfacing with 'Stan'
Description: Provides various tools for developers of R packages interfacing
with 'Stan' <http://mc-stan.org>, including functions to set up the required
package structure, S3 generics and default methods to unify function naming
across 'Stan'-based R packages, and vignettes with recommendations for
developers.
Author: Jonah Gabry [aut, cre],
Ben Goodrich [aut],
Stefan Siegert [ctb],
Trustees of Columbia University [cph]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between rstantools versions 1.4.0 dated 2017-12-21 and 1.5.0 dated 2018-04-17
rstantools-1.4.0/rstantools/inst/doc/developer-guidelines.R |only rstantools-1.5.0/rstantools/DESCRIPTION | 21 rstantools-1.5.0/rstantools/MD5 | 53 - rstantools-1.5.0/rstantools/NAMESPACE | 1 rstantools-1.5.0/rstantools/NEWS.md | 33 rstantools-1.5.0/rstantools/R/posterior_interval.R | 4 rstantools-1.5.0/rstantools/R/predictive_error.R | 4 rstantools-1.5.0/rstantools/R/rstan_package_skeleton.R | 391 ++++++---- rstantools-1.5.0/rstantools/R/rstantools-package.r | 1 rstantools-1.5.0/rstantools/build/vignette.rds |binary rstantools-1.5.0/rstantools/inst/doc/developer-guidelines.Rmd | 61 - rstantools-1.5.0/rstantools/inst/doc/developer-guidelines.html | 61 - rstantools-1.5.0/rstantools/inst/doc/minimal-rstan-package.R |only rstantools-1.5.0/rstantools/inst/doc/minimal-rstan-package.Rmd |only rstantools-1.5.0/rstantools/inst/doc/minimal-rstan-package.html |only rstantools-1.5.0/rstantools/man/bayes_R2.Rd | 11 rstantools-1.5.0/rstantools/man/figures/stanlogo.png |binary rstantools-1.5.0/rstantools/man/log_lik.Rd | 11 rstantools-1.5.0/rstantools/man/loo-prediction.Rd | 11 rstantools-1.5.0/rstantools/man/posterior_interval.Rd | 15 rstantools-1.5.0/rstantools/man/posterior_linpred.Rd | 11 rstantools-1.5.0/rstantools/man/posterior_predict.Rd | 11 rstantools-1.5.0/rstantools/man/predictive_error.Rd | 15 rstantools-1.5.0/rstantools/man/predictive_interval.Rd | 11 rstantools-1.5.0/rstantools/man/prior_summary.Rd | 11 rstantools-1.5.0/rstantools/man/rstan_package_skeleton.Rd | 87 +- rstantools-1.5.0/rstantools/man/rstantools-package.Rd | 23 rstantools-1.5.0/rstantools/tests/testthat/test-rstan_package_skeleton.R | 65 + rstantools-1.5.0/rstantools/vignettes/developer-guidelines.Rmd | 61 - rstantools-1.5.0/rstantools/vignettes/minimal-rstan-package.Rmd |only 30 files changed, 529 insertions(+), 444 deletions(-)
Title: Nonlinear Conditional Independence Tests
Description: Code for a variety of nonlinear conditional independence tests:
Kernel conditional independence test (Zhang et al., UAI 2011, <arXiv:1202.3775>),
Residual Prediction test (based on Shah and Buehlmann, <arXiv:1511.03334>),
Invariant environment prediction,
Invariant target prediction,
Invariant residual distribution test,
Invariant conditional quantile prediction (all from Heinze-Deml et al., <arXiv:1706.08576>).
Author: Christina Heinze-Deml <heinzedeml@stat.math.ethz.ch>, Jonas Peters <jonas.peters@math.ku.dk>
Maintainer: Christina Heinze-Deml <heinzedeml@stat.math.ethz.ch>
Diff between CondIndTests versions 0.1.1 dated 2017-06-29 and 0.1.3 dated 2018-04-17
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/InvariantEnvironmentPrediction.R | 8 +++++--- R/InvariantTargetPrediction.R | 8 +++++--- R/KCI.R | 13 ++++++++----- man/KCI.Rd | 3 ++- 6 files changed, 29 insertions(+), 21 deletions(-)
Title: Various Utilities for Microbial Genomics and Metagenomics
Description: A collection of functions for microbial ecology and other
applications of genomics and metagenomics. Companion package for the
Enveomics Collection (Rodriguez-R, L.M. and Konstantinidis, K.T., 2016
<DOI:10.7287/peerj.preprints.1900v1>).
Author: Luis M. Rodriguez-R [aut, cre]
Maintainer: Luis M. Rodriguez-R <lmrodriguezr@gmail.com>
Diff between enveomics.R versions 1.2.1 dated 2018-03-29 and 1.3 dated 2018-04-17
DESCRIPTION | 6 MD5 | 27 ++- NAMESPACE | 1 R/recplot2.R | 238 +++++++++++++++++++++++++-------- README.md | 44 +++--- man/enve.RecPlot2-class.Rd | 2 man/enve.recplot2.ANIr.Rd |only man/enve.recplot2.compareIdentities.Rd | 7 man/enve.recplot2.coordinates.Rd |only man/enve.recplot2.extractWindows.Rd | 17 +- man/enve.recplot2.findPeaks.Rd | 3 man/enve.recplot2.findPeaks.em.Rd | 14 + man/enve.recplot2.findPeaks.emauto.Rd | 6 man/enve.recplot2.findPeaks.mower.Rd | 5 man/enve.recplot2.seqdepth.Rd |only man/plot.enve.RecPlot2.Rd | 34 ++-- 16 files changed, 285 insertions(+), 119 deletions(-)