Title: Automated Deconvolution Augmentation of Profiles for Tissue
Specific Cells
Description: Augments existing or de-novo cell-type signature matrices to deconvolve bulk gene expression data.
Useful for building signature matrices from single cell RNAseq data, determine cell type deconvolution
spillover, and hierarchical deconvolution to use spillover to increase deconvolution accuracy. Please cite:
Danziger SA et al. (2019) ADAPTS: Automated Deconvolution Augmentation of Profiles for
Tissue Specific cells <doi:10.1101/633958>. This package expands on the techniques outlined in Newman AM,
Liu CL, Green MR, Gentles AJ, Feng W, Xu Y,
Hoang CD, Diehn M, Alizadeh, AA (2015) <doi:10.1038/nmeth.3337>'s Nature Methods paper:
'Robust enumeration of cell subsets from tissue expression profiles' to allow a user to easily add
their own cell types (e.g. a tumor specific cell type) to Newman's LM22 or other signature matrix.
Author: Samuel A Danziger
Maintainer: Samuel A Danziger <sam.danziger@gmail.com>
Diff between ADAPTS versions 0.9.14 dated 2019-05-17 and 0.9.20 dated 2019-06-17
ADAPTS-0.9.14/ADAPTS/man/heirarchicalClassify.Rd |only ADAPTS-0.9.14/ADAPTS/man/heirarchicalSplit.Rd |only ADAPTS-0.9.20/ADAPTS/DESCRIPTION | 15 - ADAPTS-0.9.20/ADAPTS/MD5 | 28 +- ADAPTS-0.9.20/ADAPTS/NAMESPACE | 5 ADAPTS-0.9.20/ADAPTS/R/MakeSigMatrix.R | 71 ++++-- ADAPTS-0.9.20/ADAPTS/R/onlyDeconAlgorithms.R | 160 +++++++++----- ADAPTS-0.9.20/ADAPTS/README.md | 2 ADAPTS-0.9.20/ADAPTS/build/vignette.rds |binary ADAPTS-0.9.20/ADAPTS/inst/doc/ADAPTS.vignette.html.asis | 2 ADAPTS-0.9.20/ADAPTS/inst/doc/ADAPTS2.vignette.html |only ADAPTS-0.9.20/ADAPTS/inst/doc/ADAPTS2.vignette.html.asis |only ADAPTS-0.9.20/ADAPTS/man/clustWspillOver.Rd | 7 ADAPTS-0.9.20/ADAPTS/man/estCellPercent.nnls.Rd |only ADAPTS-0.9.20/ADAPTS/man/hierarchicalClassify.Rd |only ADAPTS-0.9.20/ADAPTS/man/hierarchicalSplit.Rd |only ADAPTS-0.9.20/ADAPTS/man/rankByT.Rd | 9 ADAPTS-0.9.20/ADAPTS/vignettes/ADAPTS.vignette.html.asis | 2 ADAPTS-0.9.20/ADAPTS/vignettes/ADAPTS2.vignette.html.asis |only 19 files changed, 210 insertions(+), 91 deletions(-)
Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre],
Wendy Zeitlin [aut]
Maintainer: Charles Auerbach <auerbach@yu.edu>
Diff between SSDforR versions 1.5.4 dated 2019-04-05 and 1.5.5 dated 2019-06-17
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 5 ++++- R/ABma.R | 3 ++- R/Append.R | 4 ++-- R/Effectsize.R | 13 +++++++++---- R/diffchart.R | 4 +++- 7 files changed, 30 insertions(+), 19 deletions(-)
Title: Parallel Implementation of 'ETERNA 3.40' for Prediction and
Analysis of Earth Tides
Description: This is a port of 'Fortran ETERNA 3.4'
<http://igets.u-strasbg.fr/soft_and_tool.php> by H.G. Wenzel
for calculating synthetic Earth tides using the
Hartmann and Wenzel (1994) <doi:10.1029/95GL03324> or
Kudryavtsev (2004) <doi:10.1007/s00190-003-0361-2> tidal catalogs.
Author: Jonathan Kennel [aut, cre, trl],
Beth Parker [ths],
Wenzel Hans-Georg [ctb]
Maintainer: Jonathan Kennel <jkennel@uoguelph.ca>
Diff between earthtide versions 0.0.8 dated 2019-06-13 and 0.0.9 dated 2019-06-17
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ R/datasets.R | 18 +++++++++++------- R/sysdata.rda |binary build/partial.rdb |binary inst/doc/introduction.Rmd | 3 ++- inst/doc/introduction.html | 7 ++++--- man/get_iers.Rd | 5 +++-- tests/testthat/test-get_iers.R | 4 +++- vignettes/introduction.Rmd | 3 ++- 11 files changed, 42 insertions(+), 28 deletions(-)
Title: A 'dplyr' Back End for Databases
Description: A 'dplyr' back end for databases that allows you to
work with remote database tables as if they are in-memory data frames.
Basic features works with any database that has a 'DBI' back end; more
advanced features require 'SQL' translation to be provided by the
package author.
Author: Hadley Wickham [aut, cre],
Edgar Ruiz [aut],
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between dbplyr versions 1.4.1 dated 2019-06-05 and 1.4.2 dated 2019-06-17
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NAMESPACE | 1 + NEWS.md | 7 +++++++ R/escape.R | 14 ++++++++++++++ R/partial-eval.R | 2 +- R/translate-sql.R | 9 +++++---- R/verb-do.R | 21 ++++++++++++--------- R/verb-joins.R | 2 +- tests/testthat/test-tbl-sql.R | 8 ++++---- 10 files changed, 57 insertions(+), 31 deletions(-)
Title: Tidy, Type-Safe 'prediction()' Methods
Description: A one-function package containing 'prediction()', a type-safe alternative to 'predict()' that always returns a data frame. The 'summary()' method provides a data frame with average predictions, possibly over counterfactual versions of the data (a la the 'margins' command in 'Stata'). Marginal effect estimation is provided by the related package, 'margins' <https://cran.r-project.org/package=margins>. The package currently supports common model types (e.g., "lm", "glm") from the 'stats' package, as well as numerous other model classes from other add-on packages. See the README or main package documentation page for a complete listing.
Author: Thomas J. Leeper [aut, cre] (<https://orcid.org/0000-0003-4097-6326>),
Carl Ganz [ctb],
Vincent Arel-Bundock [ctb] (<https://orcid.org/0000-0003-2042-7063>)
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between prediction versions 0.3.6.2 dated 2019-01-31 and 0.3.14 dated 2019-06-17
DESCRIPTION | 20 +++-- MD5 | 150 ++++++++++++++++++++------------------- NAMESPACE | 8 -- NEWS.md | 27 +++++++ R/find_data.R | 2 R/margex.R |only R/mean_or_mode.R | 2 R/prediction.R | 35 ++++++--- R/prediction_Arima.R | 16 ++-- R/prediction_ar.R | 17 +++- R/prediction_betareg.R | 17 +++- R/prediction_bigFastLm.R |only R/prediction_bigglm.R | 15 ++- R/prediction_biglm.R | 15 ++- R/prediction_bruto.R | 15 ++- R/prediction_clm.R | 20 +++-- R/prediction_coxph.R | 17 +++- R/prediction_crch.R | 17 +++- R/prediction_earth.R | 19 +++- R/prediction_fda.R | 19 +++- R/prediction_gam.R | 17 +++- R/prediction_gausspr.R | 19 +++- R/prediction_gee.R | 17 +++- R/prediction_glimML.R | 15 ++- R/prediction_glimQL.R | 15 ++- R/prediction_glm.R | 59 +++++++++++++-- R/prediction_glmnet.R | 17 +++- R/prediction_glmx.R | 17 +++- R/prediction_gls.R | 19 +++- R/prediction_hetglm.R | 17 +++- R/prediction_hurdle.R | 17 +++- R/prediction_hxlr.R | 17 +++- R/prediction_ivreg.R | 18 +++- R/prediction_knnreg.R | 17 +++- R/prediction_kqr.R | 17 +++- R/prediction_lda.R | 17 +++- R/prediction_lm.R | 56 +++++++++++--- R/prediction_lme.R | 17 +++- R/prediction_loess.R | 19 +++- R/prediction_lqs.R | 17 +++- R/prediction_mars.R | 15 ++- R/prediction_mca.R | 17 +++- R/prediction_mclogit.R | 2 R/prediction_merMod.R | 17 +++- R/prediction_mlogit.R | 19 +++- R/prediction_mnlogit.R |only R/prediction_mnp.R | 19 +++- R/prediction_multinom.R | 19 +++- R/prediction_naiveBayes.R | 19 +++- R/prediction_nls.R | 17 +++- R/prediction_nnet.R | 19 +++- R/prediction_plm.R | 15 ++- R/prediction_polyreg.R | 15 ++- R/prediction_ppr.R | 15 ++- R/prediction_princomp.R | 17 +++- R/prediction_qda.R | 17 +++- R/prediction_rpart.R | 17 +++- R/prediction_rq.R | 17 +++- R/prediction_selection.R | 17 +++- R/prediction_speedglm.R | 17 +++- R/prediction_speedlm.R | 15 ++- R/prediction_survreg.R | 15 ++- R/prediction_svm.R | 20 +++-- R/prediction_svyglm.R | 17 +++- R/prediction_train.R | 15 ++- R/prediction_tree.R | 19 +++- R/prediction_truncreg.R | 17 +++- R/prediction_vgam.R | 19 +++- R/prediction_vglm.R | 15 ++- R/print.R | 110 +++++++++++++++++----------- R/summary.R |only README.md | 28 ++++--- data |only man/figures |only man/margex.Rd |only man/prediction.Rd | 37 ++++++--- tests/testthat/tests-core.R | 92 +++++++++++++++++++++-- tests/testthat/tests-find_data.R | 61 +++++++++++++++ tests/testthat/tests-methods.R | 39 ++-------- 79 files changed, 1185 insertions(+), 499 deletions(-)
Title: Management Strategy Evaluation Toolkit
Description: Simulation tools for management strategy evaluation are provided for the 'DLMtool' operating model to inform data-rich fisheries.
'MSEtool' provides complementary assessment models of varying complexity with standardized reporting, diagnostic tools for evaluating
assessment models within closed-loop simulation, and helper functions for building more complex operating models and management procedures.
Author: Quang Huynh [aut],
Tom Carruthers [aut, cre],
Adrian Hordyk [aut],
Chris Grandin [ctb] (iSCAM functions)
Maintainer: Tom Carruthers <t.carruthers@oceans.ubc.ca>
Diff between MSEtool versions 1.1.0 dated 2018-10-17 and 1.2.0 dated 2019-06-17
MSEtool-1.1.0/MSEtool/NEWS |only MSEtool-1.1.0/MSEtool/R/define_S4_class.R |only MSEtool-1.1.0/MSEtool/R/report_DD_SS.R |only MSEtool-1.1.0/MSEtool/R/report_SCA2.R |only MSEtool-1.1.0/MSEtool/R/report_SP_SS.R |only MSEtool-1.1.0/MSEtool/R/report_core.R |only MSEtool-1.1.0/MSEtool/R/report_html.R |only MSEtool-1.1.0/MSEtool/inst/doc/Assessment.R |only MSEtool-1.1.0/MSEtool/inst/doc/Assessment.Rmd |only MSEtool-1.1.0/MSEtool/inst/doc/Assessment.html |only MSEtool-1.1.0/MSEtool/man/LinInterp.Rd |only MSEtool-1.1.0/MSEtool/man/SRopt.Rd |only MSEtool-1.1.0/MSEtool/man/calculate_TAC.Rd |only MSEtool-1.1.0/MSEtool/man/getGpars.Rd |only MSEtool-1.1.0/MSEtool/man/getSR.Rd |only MSEtool-1.1.0/MSEtool/man/movdistil.Rd |only MSEtool-1.1.0/MSEtool/man/negcorlogspace.Rd |only MSEtool-1.1.0/MSEtool/man/optSR.Rd |only MSEtool-1.1.0/MSEtool/man/plot-Assessment.Rd |only MSEtool-1.1.0/MSEtool/man/profile_likelihood.Rd |only MSEtool-1.1.0/MSEtool/man/summary-Assessment.Rd |only MSEtool-1.1.0/MSEtool/vignettes/Assessment.Rmd |only MSEtool-1.1.0/MSEtool/vignettes/DD_TAC.png |only MSEtool-1.1.0/MSEtool/vignettes/DD_Tplot2.png |only MSEtool-1.1.0/MSEtool/vignettes/DD_diagnostic_AM.png |only MSEtool-1.1.0/MSEtool/vignettes/DD_profile.png |only MSEtool-1.1.0/MSEtool/vignettes/DD_retrospective_AM.png |only MSEtool-1.1.0/MSEtool/vignettes/DLMtool_design.png |only MSEtool-1.1.0/MSEtool/vignettes/DLMtool_process.jpg |only MSEtool-1.1.0/MSEtool/vignettes/MSEtool_design.png |only MSEtool-1.2.0/MSEtool/DESCRIPTION | 18 MSEtool-1.2.0/MSEtool/MD5 | 258 ++-- MSEtool-1.2.0/MSEtool/NAMESPACE | 58 MSEtool-1.2.0/MSEtool/NEWS.md |only MSEtool-1.2.0/MSEtool/R/Ancillary_Indicators.R | 26 MSEtool-1.2.0/MSEtool/R/CASAL2OM.R |only MSEtool-1.2.0/MSEtool/R/DD.R | 17 MSEtool-1.2.0/MSEtool/R/HCRs.R | 130 +- MSEtool-1.2.0/MSEtool/R/MMSE_Object.R |only MSEtool-1.2.0/MSEtool/R/MMSE_plots.R |only MSEtool-1.2.0/MSEtool/R/MOM_functions.R |only MSEtool-1.2.0/MSEtool/R/MOM_object.R |only MSEtool-1.2.0/MSEtool/R/MOM_plots.R |only MSEtool-1.2.0/MSEtool/R/MPs.R | 17 MSEtool-1.2.0/MSEtool/R/MSEtool-package.R | 24 MSEtool-1.2.0/MSEtool/R/Misc_exported.R | 15 MSEtool-1.2.0/MSEtool/R/Misc_fun.R | 30 MSEtool-1.2.0/MSEtool/R/Movement_calcs.R | 4 MSEtool-1.2.0/MSEtool/R/SCA.R | 330 ++--- MSEtool-1.2.0/MSEtool/R/SCA2.R | 162 -- MSEtool-1.2.0/MSEtool/R/SCA_Pope.R |only MSEtool-1.2.0/MSEtool/R/SP.R | 164 +- MSEtool-1.2.0/MSEtool/R/SRA_scope.R |only MSEtool-1.2.0/MSEtool/R/SS2Data.R | 194 ++- MSEtool-1.2.0/MSEtool/R/SS2OM.R | 604 ++++++---- MSEtool-1.2.0/MSEtool/R/Single_stock_multi_q_REDUNDANT.R |only MSEtool-1.2.0/MSEtool/R/VPA.R |only MSEtool-1.2.0/MSEtool/R/applyMMP.R |only MSEtool-1.2.0/MSEtool/R/cDD.R |only MSEtool-1.2.0/MSEtool/R/define_S4_class_assess.R |only MSEtool-1.2.0/MSEtool/R/define_S4_class_profile.R |only MSEtool-1.2.0/MSEtool/R/define_S4_class_retro.R |only MSEtool-1.2.0/MSEtool/R/diagnostic_AM.R | 28 MSEtool-1.2.0/MSEtool/R/document_data.R | 28 MSEtool-1.2.0/MSEtool/R/multiMSE.R |only MSEtool-1.2.0/MSEtool/R/multiMSE_internal.R |only MSEtool-1.2.0/MSEtool/R/multi_q_estimation.R |only MSEtool-1.2.0/MSEtool/R/popdyn_MICE.R |only MSEtool-1.2.0/MSEtool/R/report_DD_TMB.R | 689 +++-------- MSEtool-1.2.0/MSEtool/R/report_SCA.R | 871 +++------------ MSEtool-1.2.0/MSEtool/R/report_SCA_Pope.R |only MSEtool-1.2.0/MSEtool/R/report_SP.R | 641 +++-------- MSEtool-1.2.0/MSEtool/R/report_VPA.R |only MSEtool-1.2.0/MSEtool/R/report_auxiliary.R | 274 +++- MSEtool-1.2.0/MSEtool/R/report_cDD.R |only MSEtool-1.2.0/MSEtool/R/report_spict.R |only MSEtool-1.2.0/MSEtool/R/retrospective_AM.R | 37 MSEtool-1.2.0/MSEtool/R/rmd_report.R |only MSEtool-1.2.0/MSEtool/README.md | 2 MSEtool-1.2.0/MSEtool/build/vignette.rds |binary MSEtool-1.2.0/MSEtool/data/Albacore_TwoFleet.rda |only MSEtool-1.2.0/MSEtool/data/swordfish.rda |binary MSEtool-1.2.0/MSEtool/inst/doc/Delay_difference.R |only MSEtool-1.2.0/MSEtool/inst/doc/Delay_difference.Rmd |only MSEtool-1.2.0/MSEtool/inst/doc/Delay_difference.html |only MSEtool-1.2.0/MSEtool/inst/doc/MSEtool.R | 4 MSEtool-1.2.0/MSEtool/inst/doc/MSEtool.Rmd | 73 - 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Title: Import and Manipulate ForestGEO Data
Description: To help you access, transform, analyze, and
visualize ForestGEO data, we developed a collection of R packages
(<https://forestgeo.github.io/fgeo/>). This package, in particular,
helps you to easily import, filter, and modify ForestGEO data. To
learn more about ForestGEO visit <http://www.forestgeo.si.edu/>.
Author: Mauro Lepore [aut, ctr, cre] (<https://orcid.org/0000-0002-1986-7988>),
Richard Condit [aut],
Suzanne Lao [aut],
Anudeep Singh [aut],
CTFS-ForestGEO [cph, fnd]
Maintainer: Mauro Lepore <maurolepore@gmail.com>
Diff between fgeo.tool versions 1.2.4 dated 2019-05-13 and 1.2.5 dated 2019-06-17
DESCRIPTION | 10 MD5 | 184 ++-- NAMESPACE | 266 ++--- NEWS.md | 57 - R/aaa-imports-reeports.R | 162 +-- R/aaa-utils-pipe.R | 22 R/aaa-utils-tidy-eval.R | 94 +- R/aaa-utils.R | 114 +- R/add_status_tree.R | 148 +-- R/add_subquad.R | 364 +++---- R/add_var.R | 668 +++++++------- R/assert_is_installed.R | 38 R/check_crucial_names.R | 66 - R/cut_number.R | 186 ++-- R/detect_if.R | 52 - R/drop_if_na.R | 82 - R/extract_from_habitat.R | 146 +-- R/fgeo.tool-package.R | 4 R/fgeo_elevation.R | 208 ++-- R/flag_if.R | 166 +-- R/flag_if_group.R | 110 +- R/from_var_to_var.R | 394 ++++---- R/guess_plotdim.R | 166 +-- R/is_duplicated.R | 66 - R/nms_manipulate_names.R | 650 +++++++------- R/pick_drop_var_cond.R | 284 +++--- R/pick_main_stem.R | 250 ++--- R/read_fgeo.R | 398 ++++---- R/rename_matches.R | 146 +-- R/sanitize.R | 132 +- R/type_ensure.R | 92 +- R/warn_na.R | 48 - README.md | 372 ++++---- inst/WORDLIST | 90 - inst/buildignore/issues/iss59/TianTong_Elev.txt | 1094 ++++++++++++------------ man/add_status_tree.Rd | 122 +- man/add_subquad.Rd | 142 +-- man/add_var.Rd | 328 +++---- man/assert_is_installed.Rd | 48 - man/check_crucial_names.Rd | 80 - man/drop_if_na.Rd | 58 - man/extract_from_habitat.Rd | 64 - man/extract_insensitive.Rd | 92 +- man/fgeo.tool-package.Rd | 78 - man/fgeo_elevation.Rd | 112 +- man/flag_if.Rd | 134 +- man/flag_if_group.Rd | 110 +- man/from_var_to_var.Rd | 214 ++-- man/guess_plotdim.Rd | 94 +- man/is_multiple.Rd | 96 +- man/nms_try_rename.Rd | 84 - man/pick_drop.Rd | 260 ++--- man/pick_main_stem.Rd | 164 +-- man/pipe.Rd | 24 man/read_vft.Rd | 114 +- man/recode_subquad.Rd | 74 - man/reexports.Rd | 86 - man/rename_matches.Rd | 72 - man/sanitize_vft.Rd | 146 +-- man/tidyeval.Rd | 102 +- man/type_ensure.Rd | 94 +- man/type_vft.Rd | 144 +-- tests/spelling.R | 12 tests/testthat.R | 8 tests/testthat/ref-cluster_elevation | 28 tests/testthat/ref-fgeo_topography_bci_head | 18 tests/testthat/ref-fgeo_topography_bci_tail | 18 tests/testthat/ref-fgeo_topography_luq_head | 18 tests/testthat/ref-fgeo_topography_luq_tail | 18 tests/testthat/test-add_status_tree.R | 258 ++--- tests/testthat/test-add_subquad.R | 172 +-- tests/testthat/test-add_var.R | 426 ++++----- tests/testthat/test-assert_is_installed.R | 20 tests/testthat/test-check_crucial_names.R | 16 tests/testthat/test-detect_if.R | 104 +- tests/testthat/test-drop_if_na.R | 36 tests/testthat/test-extract_from_habitat.R | 112 +- tests/testthat/test-fgeo_elevation.R | 60 - tests/testthat/test-flag_if.R | 112 +- tests/testthat/test-flag_if_group.R | 108 +- tests/testthat/test-from_var_to_var.R | 78 - tests/testthat/test-guess_plotdim.R | 80 - tests/testthat/test-is_duplicated.R | 34 tests/testthat/test-nms_manipulate_names.R | 250 ++--- tests/testthat/test-pick_drop_var_cond.R | 128 +- tests/testthat/test-pick_main_stem.R | 390 ++++---- tests/testthat/test-read_fgeo.R | 154 +-- tests/testthat/test-rename_matches.R | 254 ++--- tests/testthat/test-sanitize.R | 94 +- tests/testthat/test-status_tree.R | 58 - tests/testthat/test-type_ensure.R | 42 tests/testthat/test-utils.R | 24 tests/testthat/test-warn_na.R | 12 93 files changed, 6792 insertions(+), 6815 deletions(-)
Title: Read Large Text Files
Description: Read large text files by splitting them in smaller files.
Author: Florian Privé [aut, cre]
Maintainer: Florian Privé <florian.prive.21@gmail.com>
Diff between bigreadr versions 0.1.3 dated 2018-08-13 and 0.1.5 dated 2019-06-17
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/read.R | 28 +++++++++++++++++++++------- R/utils.R | 2 +- README.md | 11 ++++++++++- man/big_fread1.Rd | 2 +- man/fread2.Rd | 3 ++- tests/testthat/test-read.R | 28 ++++++++++++++++++++++++++++ 8 files changed, 75 insertions(+), 23 deletions(-)
Title: Regression Models with Break-Points / Change-Points Estimation
Description: Given a regression model, segmented `updates' it by adding one or more segmented (i.e., piece-wise linear) relationships. Several variables with multiple breakpoints are allowed. The estimation method is discussed in Muggeo (2003, <doi:10.1002/sim.1545>) and illustrated in Muggeo (2008, <https://www.r-project.org/doc/Rnews/Rnews_2008-1.pdf>). An approach for hypothesis testing is presented in Muggeo (2016, <doi:10.1080/00949655.2016.1149855>), and interval estimation for the breakpoint is discussed in Muggeo (2017, <doi:10.1111/anzs.12200>).
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>
Diff between segmented versions 0.5-4.0 dated 2019-05-13 and 1.0-0 dated 2019-06-17
segmented-0.5-4.0/segmented/R/pscore.test.r |only segmented-1.0-0/segmented/DESCRIPTION | 10 segmented-1.0-0/segmented/MD5 | 96 - segmented-1.0-0/segmented/NAMESPACE | 7 segmented-1.0-0/segmented/NEWS | 572 ++++---- segmented-1.0-0/segmented/R/aapc.r | 43 segmented-1.0-0/segmented/R/broken.line.r | 43 segmented-1.0-0/segmented/R/confint.segmented.R | 1246 +++++++++--------- segmented-1.0-0/segmented/R/davies.test.r | 2 segmented-1.0-0/segmented/R/draw.history.R | 103 - segmented-1.0-0/segmented/R/plot.segmented.R | 80 - segmented-1.0-0/segmented/R/predict.segmented.r | 41 segmented-1.0-0/segmented/R/print.segmented.R | 80 - segmented-1.0-0/segmented/R/print.summary.segmented.R | 6 segmented-1.0-0/segmented/R/pscore.test.R |only segmented-1.0-0/segmented/R/seg.Ar.fit.boot.r | 77 - segmented-1.0-0/segmented/R/seg.Ar.fit.r | 369 +++-- segmented-1.0-0/segmented/R/seg.control.R | 11 segmented-1.0-0/segmented/R/seg.def.fit.boot.r | 28 segmented-1.0-0/segmented/R/seg.def.fit.r | 420 ++++-- segmented-1.0-0/segmented/R/seg.glm.fit.boot.r | 142 +- segmented-1.0-0/segmented/R/seg.glm.fit.r | 354 +++-- segmented-1.0-0/segmented/R/seg.lm.fit.boot.r | 56 segmented-1.0-0/segmented/R/seg.lm.fit.r | 438 ++++-- segmented-1.0-0/segmented/R/segmented.Arima.r | 363 ++--- segmented-1.0-0/segmented/R/segmented.R | 2 segmented-1.0-0/segmented/R/segmented.default.r | 255 +-- segmented-1.0-0/segmented/R/segmented.glm.R | 269 ++- segmented-1.0-0/segmented/R/segmented.lm.R | 170 +- segmented-1.0-0/segmented/R/slope.R | 25 segmented-1.0-0/segmented/R/summary.segmented.R | 129 - segmented-1.0-0/segmented/R/vcov.segmented.R | 61 segmented-1.0-0/segmented/data/down.rda |binary segmented-1.0-0/segmented/data/plant.rda |binary segmented-1.0-0/segmented/data/stagnant.rda |binary segmented-1.0-0/segmented/inst/CITATION | 30 segmented-1.0-0/segmented/man/aapc.Rd | 7 segmented-1.0-0/segmented/man/broken.line.Rd | 23 segmented-1.0-0/segmented/man/confint.segmented.Rd | 13 segmented-1.0-0/segmented/man/draw.history.Rd | 4 segmented-1.0-0/segmented/man/intercept.Rd | 132 - segmented-1.0-0/segmented/man/plot.segmented.Rd | 20 segmented-1.0-0/segmented/man/predict.segmented.Rd | 2 segmented-1.0-0/segmented/man/pscore.test.rd | 163 +- segmented-1.0-0/segmented/man/seg.control.Rd | 70 - segmented-1.0-0/segmented/man/segmented-package.Rd | 151 +- segmented-1.0-0/segmented/man/segmented.Rd | 101 - segmented-1.0-0/segmented/man/slope.Rd | 9 segmented-1.0-0/segmented/man/summary.segmented.Rd | 25 segmented-1.0-0/segmented/man/vcov.segmented.Rd | 80 - 50 files changed, 3527 insertions(+), 2801 deletions(-)
Title: Library of Research Designs
Description: A simple interface to build designs using the package 'DeclareDesign'.
In one line of code, users can specify the parameters of individual
designs and diagnose their properties. The designers can also be used
to compare performance of a given design across a range of combinations
of parameters, such as effect size, sample size, and assignment probabilities.
Author: Graeme Blair [aut],
Jasper Cooper [aut, cre],
Alexander Coppock [aut],
Macartan Humphreys [aut],
Clara Bicalho [aut],
Neal Fultz [aut],
Lily Medina [aut]
Maintainer: Jasper Cooper <jjc2247@columbia.edu>
Diff between DesignLibrary versions 0.1.3 dated 2019-05-02 and 0.1.4 dated 2019-06-17
DESCRIPTION | 6 ++-- MD5 | 18 ++++++------- NEWS.md | 6 ++++ R/binary_iv_designer.R | 8 +++--- R/factorial_designer.R | 6 ++-- R/helpers.R | 24 ++++++++++-------- R/process_tracing_designer.R | 2 - R/two_by_two_designer.R | 4 +-- tests/testthat/test_designers.R | 53 ++++++++++++++++++---------------------- tests/testthat/test_helpers.R | 16 ++++++++---- 10 files changed, 78 insertions(+), 65 deletions(-)
Title: Core Methods and Classes Used by 'aroma.*' Packages Part of the
Aroma Framework
Description: Core methods and classes used by higher-level 'aroma.*' packages
part of the Aroma Project, e.g. 'aroma.affymetrix' and 'aroma.cn'.
Author: Henrik Bengtsson [aut, cre, cph],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.core versions 3.1.3 dated 2018-05-06 and 3.2.0 dated 2019-06-17
DESCRIPTION | 13 MD5 | 57 - NEWS | 1139 ++++++++++----------- R/AromaMicroarrayTabularBinaryFile.R | 2 R/AromaRepository.R | 10 R/BinnedScatter.R | 2 R/ChromosomeExplorer.R | 2 R/CopyNumberSegmentationModel.R | 2 R/RawGenomicSignals.R | 2 R/TextUnitNamesFile.R | 2 R/simpleXml.R | 2 inst/WORDLIST |only man/AbstractCNData.Rd | 2 man/AbstractPSCNData.Rd | 2 man/AromaRepository.Rd | 4 man/BinnedScatter.Rd | 4 man/ChromosomeExplorer.Rd | 2 man/NonPairedPSCNData.Rd | 2 man/PairedPSCNData.Rd | 2 man/RawAlleleBFractions.Rd | 2 man/RawCopyNumbers.Rd | 2 man/RawGenomicSignals.Rd | 2 man/RawMirroredAlleleBFractions.Rd | 2 man/RawSequenceReads.Rd | 2 man/SegmentedAlleleBFractions.Rd | 2 man/SegmentedCopyNumbers.Rd | 2 man/downloadChipTypeFile.AromaRepository.Rd | 2 man/downloadFile.AromaRepository.Rd | 4 man/estimateStandardDeviation.RawGenomicSignals.Rd | 2 man/listFiles.AromaRepository.Rd | 2 30 files changed, 642 insertions(+), 633 deletions(-)
Title: Create Summary Tables for Statistical Reports
Description: Contains functions for creating various types of summary tables, e.g. comparing characteristics across levels of a categorical variable and summarizing fitted generalized linear models, generalized estimating equations, and Cox proportional hazards models. Functions are available to handle data from simple random samples as well as complex surveys.
Author: Dane R. Van Domelen
Maintainer: Dane R. Van Domelen <vandomed@gmail.com>
Diff between tab versions 3.1.2 dated 2016-09-20 and 4.1.1 dated 2019-06-17
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Title: Fast R and C++ Access to NIfTI Images
Description: Provides very fast read and write access to images stored in the
NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
compiled C and interpreted R code. Also provides a C/C++ API that can be
used by other packages. Not to be confused with 'RNiftyReg', which performs
image registration.
Author: Jon Clayden [cre, aut],
Bob Cox [aut],
Mark Jenkinson [aut],
Matt Hall [ctb],
Rick Reynolds [ctb],
Kate Fissell [ctb],
Jean-loup Gailly [cph],
Mark Adler [cph]
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNifti versions 0.10.0 dated 2018-10-19 and 0.11.0 dated 2019-06-17
RNifti-0.10.0/RNifti/inst/doxygen/html/class_nifti_image-members.html |only RNifti-0.10.0/RNifti/inst/doxygen/html/class_nifti_image.html |only RNifti-0.10.0/RNifti/inst/doxygen/html/struct_nifti_image_1_1_block-members.html |only RNifti-0.10.0/RNifti/inst/doxygen/html/struct_nifti_image_1_1_block.html |only RNifti-0.10.0/RNifti/inst/include/lib/NiftiImage_internal.h |only RNifti-0.10.0/RNifti/inst/include/lib/print.h |only RNifti-0.11.0/RNifti/DESCRIPTION | 10 RNifti-0.11.0/RNifti/MD5 | 302 - RNifti-0.11.0/RNifti/NAMESPACE | 2 RNifti-0.11.0/RNifti/NEWS | 27 RNifti-0.11.0/RNifti/R/image.R | 79 RNifti-0.11.0/RNifti/README.md | 9 RNifti-0.11.0/RNifti/inst/doxygen/html/_nifti_image_8h_source.html | 157 RNifti-0.11.0/RNifti/inst/doxygen/html/annotated.html | 19 RNifti-0.11.0/RNifti/inst/doxygen/html/class_r_nifti_1_1_nifti_image-members.html | 93 RNifti-0.11.0/RNifti/inst/doxygen/html/class_r_nifti_1_1_nifti_image.html | 709 ++- 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Title: Integrated Text Mining Solution
Description: An integrated solution to perform
a series of text mining tasks such as importing and cleaning a corpus, and
analyses like terms and documents counts, lexical summary, terms
co-occurrences and documents similarity measures, graphs of terms,
correspondence analysis and hierarchical clustering. Corpora can be imported
from spreadsheet-like files, directories of raw text files,
as well as from 'Dow Jones Factiva', 'LexisNexis', 'Europresse' and 'Alceste' files.
Author: Milan Bouchet-Valat [aut, cre],
Gilles Bastin [aut],
Antoine Chollet [aut]
Maintainer: Milan Bouchet-Valat <nalimilan@club.fr>
Diff between R.temis versions 0.1.1 dated 2019-01-07 and 0.1.2 dated 2019-06-17
DESCRIPTION | 8 ++- MD5 | 18 ++++---- NAMESPACE | 1 NEWS |only R/corpus.R | 91 +++++++++++++++++++++++++++++++++++++++++++++ R/matrix.R | 10 ++-- R/terms.R | 2 man/build_dtm.Rd | 8 ++- man/characteristic_docs.Rd |only man/frequent_terms.Rd | 1 man/specific_terms.Rd | 1 11 files changed, 122 insertions(+), 18 deletions(-)
Title: Fast Creation of Dummy (Binary) Columns and Rows from
Categorical Variables
Description: Creates dummy columns from columns that have categorical variables (character or factor types). You can also specify which columns to make dummies out of, or which columns to ignore. Also creates dummy rows from character, factor, and Date columns. This package provides a significant speed increase from creating dummy variables through model.matrix().
Author: Jacob Kaplan [aut, cre] (<https://orcid.org/0000-0002-0601-0387>),
Benjamin Schlegel [ctb]
Maintainer: Jacob Kaplan <jkkaplan6@gmail.com>
Diff between fastDummies versions 1.3.0 dated 2019-04-22 and 1.4.0 dated 2019-06-17
DESCRIPTION | 13 ++++----- LICENSE |only MD5 | 30 +++++++++++---------- NEWS.md | 9 +++++- R/dummy_cols.R | 37 +++++++++++++++++++++++--- R/dummy_rows.R | 2 - build/vignette.rds |binary inst/doc/making-dummy-rows.html | 4 +- inst/doc/making-dummy-variables.html | 4 +- man/dummy_cols.Rd | 19 ++++++++++--- man/dummy_columns.Rd | 13 ++++++++- tests/testthat/test-columns-sort-order.R | 12 ++++++-- tests/testthat/test-columns-value-order.R | 9 +++++- tests/testthat/test-columns-warnings-errors.R | 13 ++++++++- tests/testthat/test-ignore_na.R |only tests/testthat/test-return-type.R | 24 ++++++++-------- tests/testthat/test-rows-warnings-errors.R | 13 +++++++++ 17 files changed, 150 insertions(+), 52 deletions(-)
Title: CUSUM Charts for Monitoring of Hospital Performance
Description: Provides functions for constructing and evaluating
CUSUM charts and RA-CUSUM charts with focus on false signal probability.
Author: Lena Hubig [aut, cre] (<https://orcid.org/0000-0002-9454-1232>)
Maintainer: Lena Hubig <cs@lenahubig.de>
Diff between cusum versions 0.2.1 dated 2019-03-19 and 0.3.0 dated 2019-06-17
DESCRIPTION | 8 - MD5 | 56 +++---- NAMESPACE | 3 NEWS.md | 9 + R/cusum.R | 38 +++- R/cusum_alpha_sim.R | 19 +- R/cusum_limit_exact.R |only R/cusum_limit_sim.R | 18 +- R/data.R | 18 +- R/plot_cusum.R | 66 +++++--- R/print_cusum.R | 18 +- R/racusum.R | 65 +++++--- R/racusum_alpha_sim.R | 16 +- R/racusum_limit_dpcl.R |only R/racusum_limit_sim.R | 14 - README.md | 8 - build/vignette.rds |binary inst/doc/cusum.html | 248 ++++++++++++++++---------------- man/cusum.Rd | 16 +- man/cusum_alpha_sim.Rd | 15 + man/cusum_example_data.Rd | 2 man/cusum_limit_exact.Rd |only man/cusum_limit_sim.Rd | 14 + man/figures/README-example-1.png |binary man/racusum.Rd | 30 ++- man/racusum_alpha_sim.Rd | 11 - man/racusum_example_data.Rd | 2 man/racusum_limit_dpcl.Rd |only man/racusum_limit_sim.Rd | 11 - tests/testthat/test-cusum.R | 2 tests/testthat/test-racusum_alpha_sim.R | 2 31 files changed, 401 insertions(+), 308 deletions(-)
Title: Mixture Hidden Markov Models for Social Sequence Data and Other
Multivariate, Multichannel Categorical Time Series
Description: Designed for fitting hidden (latent) Markov models and mixture
hidden Markov models for social sequence data and other categorical time series.
Also some more restricted versions of these type of models are available: Markov
models, mixture Markov models, and latent class models. The package supports
models for one or multiple subjects with one or multiple parallel sequences
(channels). External covariates can be added to explain cluster membership in
mixture models. The package provides functions for evaluating and comparing
models, as well as functions for visualizing of multichannel sequence data and
hidden Markov models. Models are estimated using maximum likelihood via the EM
algorithm and/or direct numerical maximization with analytical gradients. All
main algorithms are written in C++ with support for parallel computation.
Documentation is available via several vignettes in this page, and the
paper by Helske and Helske (2019, <doi:10.18637/jss.v088.i03>).
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>),
Satu Helske [aut] (<https://orcid.org/0000-0003-0532-0153>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between seqHMM versions 1.0.12 dated 2019-04-11 and 1.0.13 dated 2019-06-17
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 5 +++++ R/biofam3c.R | 2 +- R/plot.mhmm.R | 1 + inst/doc/seqHMM.pdf | 38 +++++++++++++++++++------------------- inst/doc/seqHMM_algorithms.pdf |binary inst/doc/seqHMM_estimation.pdf |binary inst/doc/seqHMM_visualization.pdf |binary man/biofam3c.Rd | 2 +- 10 files changed, 40 insertions(+), 34 deletions(-)
Title: Quantitative Financial Modelling Framework
Description: Specify, build, trade, and analyse quantitative financial trading strategies.
Author: Jeffrey A. Ryan [aut, cph],
Joshua M. Ulrich [cre, aut],
Wouter Thielen [ctb],
Paul Teetor [ctb],
Steve Bronder [ctb]
Maintainer: Joshua M. Ulrich <josh.m.ulrich@gmail.com>
Diff between quantmod versions 0.4-14 dated 2019-03-24 and 0.4-15 dated 2019-06-17
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NEWS.md | 10 ++++++++++ R/quantmod.R | 17 +++++++++++++++++ R/zzz.R | 12 +++++++++--- build/partial.rdb |binary man/getFX.Rd | 2 +- man/getMetals.Rd | 2 +- man/getSymbols.MySQL.Rd | 9 +++++---- man/getSymbols.oanda.Rd | 4 ++-- man/setSymbolLookup.Rd | 2 ++ tests/test_getDividends.R | 12 ++++++++---- tests/test_getSplits.R | 10 +++++++--- 13 files changed, 77 insertions(+), 33 deletions(-)
Title: Data and Variable Transformation Functions
Description: Collection of miscellaneous utility functions, supporting data
transformation tasks like recoding, dichotomizing or grouping variables,
setting and replacing missing values. The data transformation functions
also support labelled data, and all integrate seamlessly into a
'tidyverse'-workflow.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjmisc versions 2.8.0 dated 2019-06-11 and 2.8.1 dated 2019-06-17
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- NAMESPACE | 4 ++++ NEWS.md | 11 +++++++++++ R/de_mean.R | 16 +++------------- R/find_var.R | 5 +++++ R/shorten_string.R | 7 ++++++- README.md | 7 +------ build/partial.rdb |binary inst/doc/design_philosophy.html | 4 ++-- inst/doc/exploringdatasets.html | 4 ++-- inst/doc/recodingvariables.html | 4 ++-- man/find_var.Rd | 6 ++++++ man/shorten_string.Rd | 8 +++++++- tests/testthat/test-demean.R | 5 ----- tests/testthat/test-frq.R | 2 ++ 16 files changed, 70 insertions(+), 51 deletions(-)
Title: Analysis of Oceanographic Data
Description: Supports the analysis of Oceanographic data, including 'ADCP'
measurements, measurements made with 'argo' floats, 'CTD' measurements,
sectional data, sea-level time series, coastline and topographic data, etc.
Provides specialized functions for calculating seawater properties such as
potential temperature in either the 'UNESCO' or 'TEOS-10' equation of state.
Produces graphical displays that conform to the conventions of the
Oceanographic literature. This package is discussed extensively in
Dan Kelley's book Oceanographic Analysis with R, published
in 2018 by 'Springer-Verlag' with ISBN 978-1-4939-8842-6.
Author: Dan Kelley [aut, cre] (<https://orcid.org/0000-0001-7808-5911>),
Clark Richards [aut] (<https://orcid.org/0000-0002-7833-206X>),
Chantelle Layton [ctb] (<https://orcid.org/0000-0002-3199-5763>, curl()
coauthor),
British Geological Survey [ctb, cph] (magnetic-field subroutine)
Maintainer: Dan Kelley <Dan.Kelley@Dal.Ca>
Diff between oce versions 1.0-1 dated 2018-10-04 and 1.1-1 dated 2019-06-17
oce-1.0-1/oce/man/read.ad2cp.Rd |only oce-1.0-1/oce/tests/testthat/test_deprecation.R |only oce-1.1-1/oce/DESCRIPTION | 19 oce-1.1-1/oce/MD5 | 893 +++---- oce-1.1-1/oce/NAMESPACE | 43 oce-1.1-1/oce/NEWS.md | 1297 +++++----- oce-1.1-1/oce/R/AllClass.R | 377 ++- oce-1.1-1/oce/R/RcppExports.R | 4 oce-1.1-1/oce/R/accessors.R | 20 oce-1.1-1/oce/R/ad.R | 28 oce-1.1-1/oce/R/adp.R | 1642 +++++++++---- oce-1.1-1/oce/R/adp.nortek.R | 1837 ++++++++++++++- oce-1.1-1/oce/R/adp.rdi.R | 89 oce-1.1-1/oce/R/adp.sontek.R | 6 oce-1.1-1/oce/R/adv.R | 36 oce-1.1-1/oce/R/air.R | 2 oce-1.1-1/oce/R/amsr.R | 38 oce-1.1-1/oce/R/argo.R | 501 +++- oce-1.1-1/oce/R/bremen.R | 18 oce-1.1-1/oce/R/cm.R | 38 oce-1.1-1/oce/R/coastline.R | 232 + oce-1.1-1/oce/R/colors.R | 20 oce-1.1-1/oce/R/ctd.R | 659 +++-- oce-1.1-1/oce/R/ctd.itp.R | 8 oce-1.1-1/oce/R/ctd.odf.R | 12 oce-1.1-1/oce/R/ctd.sbe.R | 201 - oce-1.1-1/oce/R/ctd.woce.R | 37 oce-1.1-1/oce/R/echosounder.R | 34 oce-1.1-1/oce/R/g1sst.R | 18 oce-1.1-1/oce/R/geod.R | 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oce-1.1-1/oce/man/read.gps.Rd | 4 oce-1.1-1/oce/man/read.landsat.Rd | 4 oce-1.1-1/oce/man/read.lisst.Rd | 4 oce-1.1-1/oce/man/read.lobo.Rd | 9 oce-1.1-1/oce/man/read.met.Rd | 4 oce-1.1-1/oce/man/read.odf.Rd | 14 oce-1.1-1/oce/man/read.rsk.Rd | 4 oce-1.1-1/oce/man/read.sealevel.Rd | 4 oce-1.1-1/oce/man/read.section.Rd | 4 oce-1.1-1/oce/man/read.topo.Rd | 4 oce-1.1-1/oce/man/rotateAboutZ.Rd | 20 oce-1.1-1/oce/man/rsk-class.Rd | 8 oce-1.1-1/oce/man/rsk.Rd | 8 oce-1.1-1/oce/man/rskPatm.Rd | 4 oce-1.1-1/oce/man/rskToc.Rd | 4 oce-1.1-1/oce/man/sealevel-class.Rd | 8 oce-1.1-1/oce/man/sealevel.Rd | 8 oce-1.1-1/oce/man/sealevelTuktoyaktuk.Rd | 10 oce-1.1-1/oce/man/section-class.Rd | 8 oce-1.1-1/oce/man/section.Rd | 8 oce-1.1-1/oce/man/sectionAddStation.Rd | 4 oce-1.1-1/oce/man/sectionGrid.Rd | 52 oce-1.1-1/oce/man/sectionSmooth.Rd | 173 + oce-1.1-1/oce/man/sectionSort.Rd | 4 oce-1.1-1/oce/man/setFlags-adp-method.Rd | 14 oce-1.1-1/oce/man/setFlags-ctd-method.Rd | 6 oce-1.1-1/oce/man/setFlags-oce-method.Rd | 2 oce-1.1-1/oce/man/setFlags.Rd | 2 oce-1.1-1/oce/man/standardDepths.Rd | 41 oce-1.1-1/oce/man/sub-sub-adp-method.Rd | 87 oce-1.1-1/oce/man/sub-sub-adv-method.Rd | 80 oce-1.1-1/oce/man/sub-sub-amsr-method.Rd | 87 oce-1.1-1/oce/man/sub-sub-argo-method.Rd | 127 - oce-1.1-1/oce/man/sub-sub-bremen-method.Rd | 78 oce-1.1-1/oce/man/sub-sub-cm-method.Rd | 78 oce-1.1-1/oce/man/sub-sub-coastline-method.Rd | 78 oce-1.1-1/oce/man/sub-sub-ctd-method.Rd | 103 oce-1.1-1/oce/man/sub-sub-echosounder-method.Rd | 80 oce-1.1-1/oce/man/sub-sub-g1sst-method.Rd | 78 oce-1.1-1/oce/man/sub-sub-gps-method.Rd | 78 oce-1.1-1/oce/man/sub-sub-ladp-method.Rd | 80 oce-1.1-1/oce/man/sub-sub-landsat-method.Rd | 80 oce-1.1-1/oce/man/sub-sub-lisst-method.Rd | 78 oce-1.1-1/oce/man/sub-sub-lobo-method.Rd | 79 oce-1.1-1/oce/man/sub-sub-met-method.Rd | 77 oce-1.1-1/oce/man/sub-sub-oce-method.Rd | 130 - oce-1.1-1/oce/man/sub-sub-odf-method.Rd | 77 oce-1.1-1/oce/man/sub-sub-rsk-method.Rd | 77 oce-1.1-1/oce/man/sub-sub-sealevel-method.Rd | 78 oce-1.1-1/oce/man/sub-sub-section-method.Rd | 80 oce-1.1-1/oce/man/sub-sub-tidem-method.Rd | 82 oce-1.1-1/oce/man/sub-sub-topo-method.Rd | 80 oce-1.1-1/oce/man/sub-sub-windrose-method.Rd | 78 oce-1.1-1/oce/man/sub-subset-adp-method.Rd | 15 oce-1.1-1/oce/man/sub-subset-adv-method.Rd | 78 oce-1.1-1/oce/man/sub-subset-amsr-method.Rd | 9 oce-1.1-1/oce/man/sub-subset-argo-method.Rd | 8 oce-1.1-1/oce/man/sub-subset-bremen-method.Rd | 8 oce-1.1-1/oce/man/sub-subset-cm-method.Rd | 8 oce-1.1-1/oce/man/sub-subset-coastline-method.Rd | 8 oce-1.1-1/oce/man/sub-subset-ctd-method.Rd | 8 oce-1.1-1/oce/man/sub-subset-echosounder-method.Rd | 8 oce-1.1-1/oce/man/sub-subset-g1sst-method.Rd | 8 oce-1.1-1/oce/man/sub-subset-gps-method.Rd | 8 oce-1.1-1/oce/man/sub-subset-ladp-method.Rd | 8 oce-1.1-1/oce/man/sub-subset-landsat-method.Rd | 8 oce-1.1-1/oce/man/sub-subset-lisst-method.Rd | 8 oce-1.1-1/oce/man/sub-subset-lobo-method.Rd | 9 oce-1.1-1/oce/man/sub-subset-met-method.Rd | 8 oce-1.1-1/oce/man/sub-subset-oce-method.Rd | 4 oce-1.1-1/oce/man/sub-subset-odf-method.Rd | 8 oce-1.1-1/oce/man/sub-subset-rsk-method.Rd | 8 oce-1.1-1/oce/man/sub-subset-sealevel-method.Rd | 8 oce-1.1-1/oce/man/sub-subset-section-method.Rd | 30 oce-1.1-1/oce/man/sub-subset-tidem-method.Rd | 12 oce-1.1-1/oce/man/sub-subset-topo-method.Rd | 8 oce-1.1-1/oce/man/sub-subset-windrose-method.Rd | 8 oce-1.1-1/oce/man/subset-adp-method.Rd | 27 oce-1.1-1/oce/man/subset-adv-method.Rd | 8 oce-1.1-1/oce/man/subset-amsr-method.Rd | 10 oce-1.1-1/oce/man/subset-argo-method.Rd | 8 oce-1.1-1/oce/man/subset-cm-method.Rd | 8 oce-1.1-1/oce/man/subset-coastline-method.Rd | 47 oce-1.1-1/oce/man/subset-ctd-method.Rd | 8 oce-1.1-1/oce/man/subset-echosounder-method.Rd | 8 oce-1.1-1/oce/man/subset-lobo-method.Rd | 10 oce-1.1-1/oce/man/subset-met-method.Rd | 8 oce-1.1-1/oce/man/subset-oce-method.Rd | 4 oce-1.1-1/oce/man/subset-odf-method.Rd | 8 oce-1.1-1/oce/man/subset-rsk-method.Rd | 8 oce-1.1-1/oce/man/subset-sealevel-method.Rd | 8 oce-1.1-1/oce/man/subset-section-method.Rd | 8 oce-1.1-1/oce/man/subset-topo-method.Rd | 8 oce-1.1-1/oce/man/summary-adp-method.Rd | 12 oce-1.1-1/oce/man/summary-adv-method.Rd | 4 oce-1.1-1/oce/man/summary-amsr-method.Rd | 6 oce-1.1-1/oce/man/summary-argo-method.Rd | 4 oce-1.1-1/oce/man/summary-bremen-method.Rd | 4 oce-1.1-1/oce/man/summary-cm-method.Rd | 4 oce-1.1-1/oce/man/summary-coastline-method.Rd | 4 oce-1.1-1/oce/man/summary-ctd-method.Rd | 4 oce-1.1-1/oce/man/summary-echosounder-method.Rd | 4 oce-1.1-1/oce/man/summary-gps-method.Rd | 4 oce-1.1-1/oce/man/summary-ladp-method.Rd | 4 oce-1.1-1/oce/man/summary-landsat-method.Rd | 4 oce-1.1-1/oce/man/summary-lisst-method.Rd | 4 oce-1.1-1/oce/man/summary-lobo-method.Rd | 6 oce-1.1-1/oce/man/summary-met-method.Rd | 4 oce-1.1-1/oce/man/summary-odf-method.Rd | 4 oce-1.1-1/oce/man/summary-rsk-method.Rd | 4 oce-1.1-1/oce/man/summary-sealevel-method.Rd | 4 oce-1.1-1/oce/man/summary-section-method.Rd | 4 oce-1.1-1/oce/man/summary-tidem-method.Rd | 9 oce-1.1-1/oce/man/summary-topo-method.Rd | 4 oce-1.1-1/oce/man/summary-windrose-method.Rd | 4 oce-1.1-1/oce/man/sunAngle.Rd | 2 oce-1.1-1/oce/man/swN2.Rd | 51 oce-1.1-1/oce/man/swSCTp.Rd | 46 oce-1.1-1/oce/man/swSpice.Rd | 66 oce-1.1-1/oce/man/swTFreeze.Rd | 70 oce-1.1-1/oce/man/tidedata.Rd | 9 oce-1.1-1/oce/man/tidem-class.Rd | 13 oce-1.1-1/oce/man/tidem.Rd | 9 oce-1.1-1/oce/man/tidemAstron.Rd | 10 oce-1.1-1/oce/man/tidemVuf.Rd | 10 oce-1.1-1/oce/man/toEnu.Rd | 16 oce-1.1-1/oce/man/toEnuAdp.Rd | 12 oce-1.1-1/oce/man/toEnuAdv.Rd | 4 oce-1.1-1/oce/man/topo-class.Rd | 8 oce-1.1-1/oce/man/topoInterpolate.Rd | 4 oce-1.1-1/oce/man/topoWorld.Rd | 49 oce-1.1-1/oce/man/utm2lonlat.Rd | 5 oce-1.1-1/oce/man/velocityStatistics.Rd | 19 oce-1.1-1/oce/man/webtide.Rd | 24 oce-1.1-1/oce/man/wind.Rd | 4 oce-1.1-1/oce/man/windrose-class.Rd | 8 oce-1.1-1/oce/man/woceNames2oceNames.Rd | 4 oce-1.1-1/oce/man/woceUnit2oceUnit.Rd | 4 oce-1.1-1/oce/man/write.ctd.Rd | 4 oce-1.1-1/oce/man/xyzToEnu.Rd | 24 oce-1.1-1/oce/man/xyzToEnuAdp.Rd | 27 oce-1.1-1/oce/man/xyzToEnuAdpAD2CP.Rd |only oce-1.1-1/oce/man/xyzToEnuAdv.Rd | 4 oce-1.1-1/oce/src/RcppExports.cpp | 12 oce-1.1-1/oce/src/ad2cp_ahrs.cpp |only oce-1.1-1/oce/src/curl.cpp | 2 oce-1.1-1/oce/src/interp_barnes.cpp | 2 oce-1.1-1/oce/src/ldc_ad2cp_in_file.cpp | 62 oce-1.1-1/oce/src/ldc_rdi_in_file.cpp | 12 oce-1.1-1/oce/src/magdec.f | 888 +++---- oce-1.1-1/oce/src/registerDynamicSymbol.c | 6 oce-1.1-1/oce/src/time.cpp | 4 oce-1.1-1/oce/tests/testthat/test_accessors.R | 23 oce-1.1-1/oce/tests/testthat/test_ad2cp.R | 511 ++++ oce-1.1-1/oce/tests/testthat/test_adp.R | 97 oce-1.1-1/oce/tests/testthat/test_allclass.R | 22 oce-1.1-1/oce/tests/testthat/test_argo.R | 41 oce-1.1-1/oce/tests/testthat/test_astronomical.R | 11 oce-1.1-1/oce/tests/testthat/test_ctd.R | 14 oce-1.1-1/oce/tests/testthat/test_datasets.R | 8 oce-1.1-1/oce/tests/testthat/test_flags.R | 8 oce-1.1-1/oce/tests/testthat/test_map.R | 18 oce-1.1-1/oce/tests/testthat/test_misc.R | 16 oce-1.1-1/oce/tests/testthat/test_oce.R | 44 oce-1.1-1/oce/tests/testthat/test_odf.R | 30 oce-1.1-1/oce/tests/testthat/test_rsk.R | 24 oce-1.1-1/oce/tests/testthat/test_section.R | 58 oce-1.1-1/oce/tests/testthat/test_sw.R | 71 oce-1.1-1/oce/tests/testthat/test_topo.R | 7 oce-1.1-1/oce/vignettes/adp.Rmd | 9 oce-1.1-1/oce/vignettes/flags.Rmd | 46 oce-1.1-1/oce/vignettes/map_projections.Rmd |only oce-1.1-1/oce/vignettes/oce.Rmd | 26 oce-1.1-1/oce/vignettes/subclassing.Rmd |only 459 files changed, 14666 insertions(+), 7273 deletions(-)
Title: Tidy Model Visualisation for Generalised Additive Models
Description: Provides functions for visualising generalised
additive models and getting predicted values using tidy tools from the 'tidyverse' packages.
Author: Stefano Coretta [aut, cre]
Maintainer: Stefano Coretta <stefano.coretta@gmail.com>
Diff between tidymv versions 2.1.0 dated 2019-04-25 and 2.2.0 dated 2019-06-17
tidymv-2.1.0/tidymv/R/functions.R |only tidymv-2.2.0/tidymv/DESCRIPTION | 12 tidymv-2.2.0/tidymv/MD5 | 46 +-- tidymv-2.2.0/tidymv/NEWS.md | 21 + tidymv-2.2.0/tidymv/R/data.R |only tidymv-2.2.0/tidymv/R/plotting.R |only tidymv-2.2.0/tidymv/R/utils.R |only tidymv-2.2.0/tidymv/README.md | 2 tidymv-2.2.0/tidymv/data |only tidymv-2.2.0/tidymv/inst/doc/plot-smooths.R | 125 +++++---- tidymv-2.2.0/tidymv/inst/doc/plot-smooths.Rmd | 154 ++++++----- tidymv-2.2.0/tidymv/inst/doc/plot-smooths.html | 208 ++++++++------- tidymv-2.2.0/tidymv/inst/doc/predict-gam.R | 12 tidymv-2.2.0/tidymv/inst/doc/predict-gam.Rmd | 22 + tidymv-2.2.0/tidymv/inst/doc/predict-gam.html | 339 ++++++++++++------------- tidymv-2.2.0/tidymv/man/create_start_event.Rd | 2 tidymv-2.2.0/tidymv/man/geom_smooth_ci.Rd | 2 tidymv-2.2.0/tidymv/man/get_gam_predictions.Rd | 11 tidymv-2.2.0/tidymv/man/inter_df.Rd |only tidymv-2.2.0/tidymv/man/plot_difference.Rd | 8 tidymv-2.2.0/tidymv/man/plot_gamsd-defunct.Rd | 2 tidymv-2.2.0/tidymv/man/plot_smooths.Rd | 15 - tidymv-2.2.0/tidymv/man/pois_df.Rd |only tidymv-2.2.0/tidymv/man/predict_gam.Rd | 10 tidymv-2.2.0/tidymv/man/tidymv-defunct.Rd | 2 tidymv-2.2.0/tidymv/vignettes/plot-smooths.Rmd | 154 ++++++----- tidymv-2.2.0/tidymv/vignettes/predict-gam.Rmd | 22 + 27 files changed, 689 insertions(+), 480 deletions(-)
Title: A Graphical User Interface for Network Modeling with 'Statnet'
Description: A graphical user interface for network modeling with the 'statnet'
software <https://github.com/statnet>.
Author: Martina Morris [cre, aut],
Emily Beylerian [aut],
Kirk Li [ctb],
Samuel Jenness [ctb]
Maintainer: Martina Morris <morrism@uw.edu>
Diff between statnetWeb versions 0.5.4 dated 2019-06-15 and 0.5.5 dated 2019-06-17
DESCRIPTION | 6 ++-- MD5 | 6 ++-- inst/shiny/statnetWeb/server.R | 58 +++++++++++++++++++++-------------------- inst/shiny/statnetWeb/ui.R | 5 ++- 4 files changed, 40 insertions(+), 35 deletions(-)
Title: Pandoc Filters for R
Description: The document converter 'pandoc' <http://pandoc.org/> is widely used
in the R community. One feature of 'pandoc' is that it can produce and consume
JSON-formatted abstract syntax trees (AST). This allows to transform a given
source document into JSON-formatted AST, alter it by so called filters and pass
the altered JSON-formatted AST back to 'pandoc'. This package provides functions
which allow to write such filters in native R code.
Although this package is inspired by the Python package 'pandocfilters'
<https://github.com/jgm/pandocfilters/>, it provides additional convenience functions which make it simple to use the 'pandocfilters' package as a
report generator. Since 'pandocfilters' inherits most of it's functionality
from 'pandoc' it can create documents in many formats
(for more information see <http://pandoc.org/>) but is also bound to the same
limitations as 'pandoc'.
Author: Florian Schwendinger [aut, cre],
Kurt Hornik [aut],
Andrie de Vries [ctb]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between pandocfilters versions 0.1-1 dated 2016-04-27 and 0.1-3 dated 2019-06-17
pandocfilters-0.1-1/pandocfilters/README.md |only pandocfilters-0.1-1/pandocfilters/man/pandocfilters_writer.Rd |only pandocfilters-0.1-1/pandocfilters/man/set_pandoc_version.Rd |only pandocfilters-0.1-3/pandocfilters/DESCRIPTION | 20 pandocfilters-0.1-3/pandocfilters/MD5 | 148 +++-- pandocfilters-0.1-3/pandocfilters/NAMESPACE | 12 pandocfilters-0.1-3/pandocfilters/R/pandocfilters.R | 278 +++++----- pandocfilters-0.1-3/pandocfilters/R/utility.R | 197 +++++-- pandocfilters-0.1-3/pandocfilters/R/zzz.R | 18 pandocfilters-0.1-3/pandocfilters/build |only pandocfilters-0.1-3/pandocfilters/inst/doc |only pandocfilters-0.1-3/pandocfilters/man/Attr.Rd | 1 pandocfilters-0.1-3/pandocfilters/man/BlockQuote.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/BulletList.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/Citation.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/Cite.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/Code.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/CodeBlock.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/Definition.Rd | 4 pandocfilters-0.1-3/pandocfilters/man/DefinitionList.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/Div.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/Emph.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/Header.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/HorizontalRule.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/Image.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/LineBreak.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/Link.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/ListAttributes.Rd | 1 pandocfilters-0.1-3/pandocfilters/man/Math.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/Note.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/Null.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/OrderedList.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/Para.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/Plain.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/Quoted.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/RawInline.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/SmallCaps.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/SoftBreak.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/Space.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/Span.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/Str.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/Strikeout.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/Strong.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/Subscript.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/Superscript.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/Table.Rd | 3 pandocfilters-0.1-3/pandocfilters/man/TableCell.Rd | 1 pandocfilters-0.1-3/pandocfilters/man/as.block.Rd | 1 pandocfilters-0.1-3/pandocfilters/man/as.inline.Rd | 1 pandocfilters-0.1-3/pandocfilters/man/astrapply.Rd | 1 pandocfilters-0.1-3/pandocfilters/man/c.block.Rd | 1 pandocfilters-0.1-3/pandocfilters/man/c.inline.Rd | 1 pandocfilters-0.1-3/pandocfilters/man/document.Rd | 110 ++- pandocfilters-0.1-3/pandocfilters/man/filter.Rd | 7 pandocfilters-0.1-3/pandocfilters/man/get_pandoc_path.Rd |only pandocfilters-0.1-3/pandocfilters/man/get_pandoc_types_version.Rd |only pandocfilters-0.1-3/pandocfilters/man/get_pandoc_version.Rd | 9 pandocfilters-0.1-3/pandocfilters/man/is.block.Rd | 1 pandocfilters-0.1-3/pandocfilters/man/is.inline.Rd | 1 pandocfilters-0.1-3/pandocfilters/man/set_pandoc_path.Rd |only pandocfilters-0.1-3/pandocfilters/man/utility_functions.Rd |only pandocfilters-0.1-3/pandocfilters/man/write.pandoc.Rd |only pandocfilters-0.1-3/pandocfilters/tests |only pandocfilters-0.1-3/pandocfilters/vignettes |only 64 files changed, 543 insertions(+), 366 deletions(-)
Title: Bayesian Additive Regression Trees
Description: Bayesian Additive Regression Trees (BART) provide flexible nonparametric modeling of covariates for continuous, binary, categorical and time-to-event outcomes. For more information on BART, see Chipman, George and McCulloch (2010) <doi:10.1214/09-AOAS285> and Sparapani, Logan, McCulloch and Laud (2016) <doi:10.1002/sim.6893>.
Author: Robert McCulloch [aut],
Rodney Sparapani [aut, cre],
Robert Gramacy [aut],
Charles Spanbauer [aut],
Matthew Pratola [aut],
Martyn Plummer [ctb],
Nicky Best [ctb],
Kate Cowles [ctb],
Karen Vines [ctb]
Maintainer: Rodney Sparapani <rsparapa@mcw.edu>
Diff between BART versions 2.4 dated 2019-04-16 and 2.5 dated 2019-06-17
DESCRIPTION | 8 +- MD5 | 49 +++++++----- NAMESPACE | 1 NEWS | 13 +++ R/bartModelMatrix.R | 28 ++++--- R/gbart.R | 2 R/mc.pbart.R | 6 + R/stratrs.R | 32 ++++++-- cleanup | 9 +- cleanup.win | 9 +- demo/00Index | 1 demo/lung.surv.ice.R |only demo/nox.R | 20 +++-- inst/cxx-ex/cdpmbart.cpp |only inst/cxx-ex/cdpmwbart.cpp |only inst/cxx-ex/common.h | 6 + inst/cxx-ex/dp.cpp |only inst/cxx-ex/dp.h |only inst/cxx-ex/dpm.cpp |only inst/cxx-ex/dpm.h |only inst/cxx-ex/dpmain.cpp |only inst/cxx-ex/dpmwmain.cpp |only inst/cxx-ex/dps.cpp |only inst/cxx-ex/dps.h |only inst/doc/the-BART-R-package.Rnw | 154 +++++++++++++++++++-------------------- inst/doc/the-BART-R-package.pdf |binary man/stratrs.Rd | 10 +- src/common.h | 6 + src/init.c | 8 +- vignettes/references.bib | 2 vignettes/the-BART-R-package.Rnw | 154 +++++++++++++++++++-------------------- 31 files changed, 301 insertions(+), 217 deletions(-)
Title: Log Rotation and Conditional Backups
Description: Conditionally rotate or back-up files based on
their size or the date of the last backup; inspired by the 'Linux'
utility 'logrotate'.
Author: Stefan Fleck [aut, cre] (<https://orcid.org/0000-0003-3344-9851>)
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>
Diff between rotor versions 0.2.2 dated 2019-05-28 and 0.2.3 dated 2019-06-17
rotor-0.2.2/rotor/man/list_backups.Rd |only rotor-0.2.3/rotor/DESCRIPTION | 8 + rotor-0.2.3/rotor/MD5 | 32 +++---- rotor-0.2.3/rotor/NAMESPACE | 1 rotor-0.2.3/rotor/NEWS.md | 16 +++ rotor-0.2.3/rotor/R/BackupQueue.R | 63 +++++++++++--- rotor-0.2.3/rotor/R/list_backups.R | 38 ++++++-- rotor-0.2.3/rotor/R/rotate.R | 2 rotor-0.2.3/rotor/R/rotate_date.R | 2 rotor-0.2.3/rotor/R/rotate_time.R | 2 rotor-0.2.3/rotor/R/utils-predicates.R | 30 +++++- rotor-0.2.3/rotor/README.md | 87 +++++++++++++++----- rotor-0.2.3/rotor/man/BackupQueue.Rd | 4 rotor-0.2.3/rotor/man/backup_info.Rd |only rotor-0.2.3/rotor/man/rotor-package.Rd | 8 + rotor-0.2.3/rotor/tests/testthat/test_BackupQueue.R | 85 ++++++++++++++++++- rotor-0.2.3/rotor/tests/testthat/test_rotate_date.R | 34 +++---- rotor-0.2.3/rotor/tests/testthat/test_rotate_time.R | 2 18 files changed, 319 insertions(+), 95 deletions(-)
Title: Nonparametric Estimation in Mixture Cure Models
Description: Performs nonparametric estimation in mixture cure models, and significance tests for the cure probability. For details, see López-Cheda et al. (2017a) <doi:10.1016/j.csda.2016.08.002> and López-Cheda et al. (2017b) <doi:10.1007/s11749-016-0515-1>.
Author: Ignacio López-de-Ullibarri [aut, cre],
Ana López-Cheda [aut],
Maria Amalia Jácome [aut]
Maintainer: Ignacio López-de-Ullibarri <ignacio.lopezdeullibarri@udc.es>
Diff between npcure versions 0.1-2 dated 2019-05-08 and 0.1-4 dated 2019-06-17
ChangeLog |only DESCRIPTION | 8 ++-- MD5 | 49 ++++++++++++------------- R/beran.R | 10 ++--- R/hselect.R | 12 +++--- R/latency.R | 10 ++--- R/print.R | 98 +++++++++++++++++++++++++++++++++++++++++++------- R/probcure.R | 8 ++-- R/tests.R | 2 - build/partial.rdb |binary man/beran.Rd | 59 +++++++++++++++--------------- man/berancv.Rd | 43 +++++++++++---------- man/controlpars.Rd | 49 ++++++++++++------------- man/hpilot.Rd | 5 +- man/latency.Rd | 55 ++++++++++++++-------------- man/latencyhboot.Rd | 46 +++++++++++------------ man/print.npcure.Rd | 25 +++++++++--- man/probcure.Rd | 67 +++++++++++++++++----------------- man/probcurehboot.Rd | 33 ++++++++-------- man/summary.npcure.Rd | 12 ++++-- man/testcov.Rd | 49 ++++++++++++------------- man/testmz.Rd | 11 +++-- src/beran.c | 10 ++++- src/boot.c | 20 +++++----- src/latency.c | 6 ++- src/probcure.c | 34 +++++++++-------- 26 files changed, 415 insertions(+), 306 deletions(-)
Title: Nonparametric Change Detection in Multivariate Linear
Relationships
Description: Contains implementation of the Nonparametric Splitting Algorithm (NSA), which estimates a set of structural change points (change dates) within a multivariate time-wise linear regression. Additionally, it contains utility functions to estimate corresponding changing linear model, moving energy distance and a change-detection test. For more information, see Malo et. al (2019) <arXiv:1805.08512v2>.
Author: Olga Gorskikh, Pekka Malo, Pauliina Ilmonen, Lauri Viitasaari, Joni Virta
Maintainer: Olga Gorskikh <olga.a.gorskikh@gmail.com>
Diff between changedetection versions 0.1.0 dated 2019-04-04 and 0.2.0 dated 2019-06-17
changedetection-0.1.0/changedetection/man/eDistance.Rd |only changedetection-0.1.0/changedetection/man/movingEDistance.Rd |only changedetection-0.2.0/changedetection/DESCRIPTION | 10 changedetection-0.2.0/changedetection/MD5 | 33 +-- changedetection-0.2.0/changedetection/NAMESPACE | 4 changedetection-0.2.0/changedetection/R/change_detection.R | 59 ++--- changedetection-0.2.0/changedetection/R/first_step_estimation.R | 56 +---- changedetection-0.2.0/changedetection/R/regression_functions.R | 110 ++++++---- changedetection-0.2.0/changedetection/R/sample_dataset.R | 37 +-- changedetection-0.2.0/changedetection/R/second_step_estimation.R | 75 +++--- changedetection-0.2.0/changedetection/R/statistics_calculation.R | 49 ++-- changedetection-0.2.0/changedetection/R/utility_functions.R | 23 +- changedetection-0.2.0/changedetection/build/partial.rdb |binary changedetection-0.2.0/changedetection/data/sampledataset.RData |only changedetection-0.2.0/changedetection/inst/REFERENCES.bib | 4 changedetection-0.2.0/changedetection/man/changeTest.Rd | 14 - changedetection-0.2.0/changedetection/man/changes.Rd | 18 - changedetection-0.2.0/changedetection/man/energyDistance.Rd |only changedetection-0.2.0/changedetection/man/movingEnergyDistance.Rd |only changedetection-0.2.0/changedetection/man/sampledataset.Rd | 27 -- 20 files changed, 254 insertions(+), 265 deletions(-)
More information about changedetection at CRAN
Permanent link
Title: Functions for the Book "An Introduction to the Bootstrap"
Description: Software (bootstrap, cross-validation, jackknife) and data
for the book "An Introduction to the Bootstrap" by B. Efron and
R. Tibshirani, 1993, Chapman and Hall. This package is
primarily provided for projects already based on it, and for
support of the book. New projects should preferentially use the
recommended package "boot".
Author: S original, from StatLib, by Rob Tibshirani. R port by
Friedrich Leisch.
Maintainer: Scott Kostyshak <scott.kostyshak@gmail.com>
Diff between bootstrap versions 2017.2 dated 2017-02-27 and 2019.6 dated 2019-06-17
DESCRIPTION | 10 ++++++---- MD5 | 11 ++++++----- NEWS | 5 +++++ R/ctsub1.R | 2 +- R/xinter1.R | 2 +- R/yinter1.R | 2 +- src/bootstrap_init.c |only 7 files changed, 20 insertions(+), 12 deletions(-)
Title: Bayesian Exponential Random Graph Models
Description: Bayesian analysis for exponential random graph models using advanced computational algorithms. More information can be found at: <https://acaimo.github.io/Bergm>.
Author: Alberto Caimo [aut, cre],
Lampros Bouranis [aut],
Robert Krause [aut]
Nial Friel [ctb]
Maintainer: Alberto Caimo <acaimo.stats@gmail.com>
Diff between Bergm versions 4.2.0 dated 2018-09-25 and 5.0.0 dated 2019-06-17
Bergm-4.2.0/Bergm/R/adjustPL.R |only Bergm-4.2.0/Bergm/R/bergm.output.R |only Bergm-4.2.0/Bergm/R/calibrate.bergm.R |only Bergm-4.2.0/Bergm/R/evidence_CJ.R |only Bergm-4.2.0/Bergm/R/evidence_PP.R |only Bergm-4.2.0/Bergm/R/missBergm.R |only Bergm-4.2.0/Bergm/man/adjustPL.Rd |only Bergm-4.2.0/Bergm/man/bergm.output.Rd |only Bergm-4.2.0/Bergm/man/calibrate.bergm.Rd |only Bergm-4.2.0/Bergm/man/evidence_CJ.Rd |only Bergm-4.2.0/Bergm/man/evidence_PP.Rd |only Bergm-4.2.0/Bergm/man/missBergm.Rd |only Bergm-5.0.0/Bergm/DESCRIPTION | 16 - Bergm-5.0.0/Bergm/MD5 | 42 ++- Bergm-5.0.0/Bergm/NAMESPACE | 14 - Bergm-5.0.0/Bergm/R/Bergm-package.R | 3 Bergm-5.0.0/Bergm/R/bergm.R | 258 +++++++++++------------ Bergm-5.0.0/Bergm/R/bergmC.R |only Bergm-5.0.0/Bergm/R/bergmM.R |only Bergm-5.0.0/Bergm/R/bgof.R | 341 +++++++++++++++---------------- Bergm-5.0.0/Bergm/R/ergmAPL.R |only Bergm-5.0.0/Bergm/R/evidenceCJ.R |only Bergm-5.0.0/Bergm/R/evidencePP.R |only Bergm-5.0.0/Bergm/R/plot.bergm.R |only Bergm-5.0.0/Bergm/R/summary.bergm.R |only Bergm-5.0.0/Bergm/man/Bergm-package.Rd | 2 Bergm-5.0.0/Bergm/man/bergm.Rd | 82 +++---- Bergm-5.0.0/Bergm/man/bergmC.Rd |only Bergm-5.0.0/Bergm/man/bergmM.Rd |only Bergm-5.0.0/Bergm/man/bgof.Rd | 32 ++ Bergm-5.0.0/Bergm/man/ergmAPL.Rd |only Bergm-5.0.0/Bergm/man/evidenceCJ.Rd |only Bergm-5.0.0/Bergm/man/evidencePP.Rd |only Bergm-5.0.0/Bergm/man/plot.bergm.Rd |only Bergm-5.0.0/Bergm/man/summary.bergm.Rd |only 35 files changed, 403 insertions(+), 387 deletions(-)
Title: Packed Bar Charts with 'plotly'
Description: Packed bar charts are a variation of treemaps for visualizing skewed data. The concept was introduced by Xan Gregg at 'JMP'.
Author: Adam Spannbauer [aut, cre]
Maintainer: Adam Spannbauer <spannbaueradam@gmail.com>
Diff between rPackedBar versions 0.2.1 dated 2019-03-18 and 0.2.2 dated 2019-06-17
DESCRIPTION | 7 +- MD5 | 34 +++++++------ R/gen_color_bars.R | 36 +++++++------- R/gen_gray_bars.R | 36 +++++++------- R/gen_plotly_packed_bar.R | 82 ++++++++++++++++---------------- R/gen_xaxis_labels.R | 6 +- R/guess_bar_count.R | 55 +++++++++------------ R/plotly_packed_bar.R | 33 ++++++------ R/renderPackedBar.R | 23 ++++---- R/sysdata.rda |only build/vignette.rds |binary man/guess_bar_count.Rd | 2 man/plotly_packed_bar.Rd | 12 ++-- tests/testthat.R | 2 tests/testthat/test-gen_color_bars.R | 15 +++-- tests/testthat/test-gen_gray_bars.R | 17 +++--- tests/testthat/test-gen_xaxis_labels.R | 4 - tests/testthat/test-guess_bar_count.R |only tests/testthat/test-plotly_packed_bar.R | 6 +- 19 files changed, 184 insertions(+), 186 deletions(-)
Title: Tools for Acquiring and Analyzing Political Data
Description: Provides useful functions for obtaining commonly-used data
in political analysis and political science, including from sources
such as the Comparative Agendas Project <https://www.comparativeagendas.net>,
which provides data on politics and policy from 20+ countries, the
MIT Election and Data Science Lab <https://www.electionlab.mit.edu>,
and FiveThirtyEight <https://www.FiveThirtyEight.com>.
Author: G. Elliott Morris [aut, cre],
Comparative Agendas Project [cph],
MIT Election and Data Science Lab [cph],
FiveThirtyEight.com [cph]
Maintainer: G. Elliott Morris <elliott@thecrosstab.com>
Diff between politicaldata versions 0.1.2 dated 2019-03-13 and 0.1.3 dated 2019-06-17
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 6 +++++- data/house_results.RData |binary man/house_results.Rd | 2 +- 5 files changed, 13 insertions(+), 9 deletions(-)
Title: Number and Brightness Image Analysis
Description: Calculation of molecular number and brightness from
fluorescence microscopy image series. The software was published in a 2016
paper <doi:10.1093/bioinformatics/btx434>. The seminal paper for the
technique is Digman et al. 2008 <doi:10.1529/biophysj.107.114645>. A review
of the technique was published in 2017 <doi:10.1016/j.ymeth.2017.12.001>.
Author: Rory Nolan [aut, cre, cph] (<https://orcid.org/0000-0002-5239-4043>),
Luis Alvarez [ctb, cph] (<https://orcid.org/0000-0003-1316-1906>),
Sergi Padilla-Parra [ctb, ths, cph]
(<https://orcid.org/0000-0002-8010-9481>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between nandb versions 2.0.1 dated 2019-05-31 and 2.0.2 dated 2019-06-17
DESCRIPTION | 20 +-- MD5 | 80 ++++++------- NEWS.md | 38 +++--- R/brightness.R | 76 ++++++------- R/cc_brightness.R | 80 +++++++------ R/cc_number.R | 80 +++++++------ R/class_constructors.R | 46 ++++--- R/cross_var.R | 1 R/graphics.R | 66 +++++++---- R/number.R | 107 ++++++++++-------- R/utils.R | 82 +++++++++----- build/partial.rdb |binary inst/doc/batch-mode.html | 4 inst/doc/brightness-timeseries.html | 4 inst/doc/single-images.html | 12 +- man/brightness.Rd | 2 man/brightness_folder.Rd | 6 - man/brightness_timeseries.Rd | 2 man/brightness_timeseries_folder.Rd | 6 - man/cc_brightness.Rd | 3 man/cc_brightness_folder.Rd | 4 man/cc_brightness_timeseries.Rd | 11 + man/cc_brightness_timeseries_folder.Rd | 4 man/cc_number.Rd | 3 man/cc_number_folder.Rd | 4 man/cc_number_timeseries.Rd | 12 +- man/cc_number_timeseries_folder.Rd | 4 man/cross_var.Rd | 1 man/matrix_raster_plot.Rd | 61 ++++++---- man/nb-img-classes.Rd | 4 man/number.Rd | 2 man/number_folder.Rd | 4 man/number_timeseries.Rd | 2 man/number_timeseries_folder.Rd | 6 - tests/spelling.R | 9 + tests/testthat/test-brightness.R | 4 tests/testthat/test-cc_brightness.R | 181 +++++++++++++++++-------------- tests/testthat/test-cc_number.R | 175 +++++++++++++++++------------ tests/testthat/test-class_constructors.R | 11 + tests/testthat/test-number.R | 93 ++++++++------- tests/testthat/test-utils.R | 90 ++++++++------- 41 files changed, 797 insertions(+), 603 deletions(-)
Title: Simplifies Exploratory Data Analysis
Description: Interactive data exploration with one line of code or use an easy to remember set of tidy functions for exploratory data analysis. Introduces two main verbs. describe() to describe a variable or table, explore() to graphically explore a variable or table.
Author: Roland Krasser
Maintainer: Roland Krasser <roland.krasser@gmail.com>
Diff between explore versions 0.4.2 dated 2019-05-22 and 0.4.3 dated 2019-06-17
explore-0.4.2/explore/inst/extdata/template_report_attribute.Rmd |only explore-0.4.3/explore/DESCRIPTION | 8 explore-0.4.3/explore/MD5 | 30 - explore-0.4.3/explore/R/explore.R | 217 +++++----- explore-0.4.3/explore/inst/doc/explore.R | 2 explore-0.4.3/explore/inst/doc/explore.Rmd | 4 explore-0.4.3/explore/inst/doc/explore.html | 28 - explore-0.4.3/explore/inst/extdata/template_report_target_den.Rmd | 2 explore-0.4.3/explore/inst/extdata/template_report_target_pct.Rmd | 2 explore-0.4.3/explore/inst/extdata/template_report_variable.Rmd |only explore-0.4.3/explore/man/explore_cat.Rd | 11 explore-0.4.3/explore/man/explore_cor.Rd | 8 explore-0.4.3/explore/man/explore_num.Rd | 4 explore-0.4.3/explore/man/format_target.Rd | 4 explore-0.4.3/explore/man/replace_na_with.Rd | 2 explore-0.4.3/explore/man/report.Rd | 4 explore-0.4.3/explore/vignettes/explore.Rmd | 4 17 files changed, 183 insertions(+), 147 deletions(-)
Title: List Comprehensions
Description: Provides 'Python'-style list comprehensions.
List comprehension expressions use usual loops (for(), while() and repeat()) and
usual if() as list producers. In many cases it gives more concise notation than
standard "*apply + filter" strategy.
Author: Gregory Demin [aut, cre]
Maintainer: Gregory Demin <gdemin@gmail.com>
Diff between comprehenr versions 0.6.6 dated 2019-06-07 and 0.6.7 dated 2019-06-17
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS | 7 ++++++- R/numerate.R | 2 +- R/to_list.R | 15 ++++++++++++--- tests/testthat/test_to_list.R | 31 +++++++++++++++++++++++++++++++ 6 files changed, 58 insertions(+), 13 deletions(-)