Title: Modeling Workflows
Description: Managing both a 'parsnip' model and a preprocessor, such as a
model formula or recipe from 'recipes', can often be challenging. The goal
of 'workflows' is to streamline this process by bundling the model alongside
the preprocessor, all within the same object.
Author: Davis Vaughan [aut, cre],
RStudio [cph]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between workflows versions 0.2.0 dated 2020-09-15 and 0.2.1 dated 2020-10-08
DESCRIPTION | 6 +- MD5 | 14 +++--- NAMESPACE | 1 NEWS.md | 4 + R/fit.R | 62 +++++++++++++++++++------- man/workflows-internals.Rd | 35 +++++++++++---- tests/testthat/test-fit.R | 67 ++++++++++++++++++++++------- tests/testthat/test-pre-action-variables.R | 12 +++++ 8 files changed, 151 insertions(+), 50 deletions(-)
Title: Bindings to the 'HarfBuzz' and 'Fribidi' Libraries for Text
Shaping
Description: Provides access to the text shaping functionality in the 'HarfBuzz'
library and the bidirectional algorithm in the 'Fribidi' library.
'textshaping' is a low-level utility package mainly for graphic devices that
expands upon the font tool-set provided by the 'systemfonts' package.
Author: Thomas Lin Pedersen [cre, aut]
(<https://orcid.org/0000-0002-5147-4711>),
RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@rstudio.com>
Diff between textshaping versions 0.1.1 dated 2020-09-29 and 0.1.2 dated 2020-10-08
DESCRIPTION | 6 +-- MD5 | 8 ++--- NEWS.md | 5 +++ inst/doc/c_interface.html | 71 ++++++++++++++++++++++++++++++++++++++++++++++ src/string_shape.cpp | 6 +-- 5 files changed, 86 insertions(+), 10 deletions(-)
Title: Fast R and C++ Access to NIfTI Images
Description: Provides very fast read and write access to images stored in the
NIfTI-1, NIfTI-2 and ANALYZE-7.5 formats, with seamless synchronisation
of in-memory image objects between compiled C and interpreted R code. Also
provides a simple image viewer, and a C/C++ API that can be used by other
packages. Not to be confused with 'RNiftyReg', which performs image
registration and applies spatial transformations.
Author: Jon Clayden [cre, aut] (<https://orcid.org/0000-0002-6608-0619>),
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 1.2.2 dated 2020-09-07 and 1.2.3 dated 2020-10-08
DESCRIPTION | 8 +-- MD5 | 6 +- NEWS | 6 ++ inst/include/RNiftiAPI.h | 110 +++++++++++++++++++++++++---------------------- 4 files changed, 73 insertions(+), 57 deletions(-)
Title: Call R from R
Description: It is sometimes useful to perform a computation in a
separate R process, without affecting the current R process at all.
This packages does exactly that.
Author: Gábor Csárdi [aut, cre, cph] (<https://orcid.org/0000-0001-7098-9676>),
Winston Chang [aut],
RStudio [cph, fnd],
Mango Solutions [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between callr versions 3.4.4 dated 2020-09-07 and 3.5.0 dated 2020-10-08
DESCRIPTION | 14 +++++----- MD5 | 45 ++++++++++++++++----------------- NEWS.md | 7 +++++ R/check.R | 4 ++ R/eval-bg.R | 3 +- R/eval.R | 10 +++++-- R/options.R | 3 +- R/package.R | 1 R/r-session.R | 28 ++++++++++++-------- R/setup.R | 23 +++++++++++++++- R/utils.R | 16 +++++++++++ README.md | 3 -- man/r.Rd | 13 ++++++++- man/r_bg.Rd | 12 ++++++++ man/r_copycat.Rd | 3 +- man/r_session.Rd | 30 +++++++++++++++++++--- man/r_vanilla.Rd | 3 +- tests/testthat.R | 22 ---------------- tests/testthat/helper.R | 11 +++++++- tests/testthat/test-clean-subprocess.R | 6 ++-- tests/testthat/test-function-env.R |only tests/testthat/test-libpath.R | 34 ++---------------------- tests/testthat/test-messages.R | 4 +- tests/testthat/test-r-session.R | 7 +++-- 24 files changed, 186 insertions(+), 116 deletions(-)
Title: A Tool Kit for Working with Time Series in R
Description: Easy visualization, wrangling, and feature engineering of time series data for
forecasting and machine learning prediction.
Methods discussed herein are commonplace in machine learning, and have been cited
in various literature. Refer to "Calendar Effects" in papers such as
Taieb, Souhaib Ben. "Machine learning strategies for multi-step-ahead time series
forecasting." Universit Libre de Bruxelles, Belgium (2014): 75-86.
<http://souhaib-bentaieb.com/pdf/2014_phd.pdf>.
Author: Matt Dancho [aut, cre],
Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between timetk versions 2.3.0 dated 2020-09-29 and 2.4.0 dated 2020-10-08
timetk-2.3.0/timetk/vignettes/temp_archive |only timetk-2.4.0/timetk/DESCRIPTION | 6 timetk-2.4.0/timetk/MD5 | 398 +- timetk-2.4.0/timetk/NAMESPACE | 716 +-- timetk-2.4.0/timetk/NEWS.md | 661 +-- timetk-2.4.0/timetk/R/00_global_vars.R | 22 timetk-2.4.0/timetk/R/augment-tk_augment_differences.R | 328 - timetk-2.4.0/timetk/R/augment-tk_augment_fourier.R | 328 - timetk-2.4.0/timetk/R/augment-tk_augment_holiday_signature.R | 342 - timetk-2.4.0/timetk/R/augment-tk_augment_lags.R | 270 - timetk-2.4.0/timetk/R/augment-tk_augment_slidify.R | 352 - timetk-2.4.0/timetk/R/augment-tk_augment_timeseries.R | 342 - timetk-2.4.0/timetk/R/coersion-tk_tbl.R | 558 +- timetk-2.4.0/timetk/R/coersion-tk_ts.R | 372 - timetk-2.4.0/timetk/R/coersion-tk_xts.R | 456 +- timetk-2.4.0/timetk/R/coersion-tk_zoo.R | 198 - timetk-2.4.0/timetk/R/coersion-tk_zooreg.R | 416 +- timetk-2.4.0/timetk/R/data-bike_sharing.R | 78 timetk-2.4.0/timetk/R/data-m4_daily.R | 44 timetk-2.4.0/timetk/R/data-m4_hourly.R | 44 timetk-2.4.0/timetk/R/data-m4_monthly.R | 44 timetk-2.4.0/timetk/R/data-m4_quarterly.R | 44 timetk-2.4.0/timetk/R/data-m4_weekly.R | 46 timetk-2.4.0/timetk/R/data-m4_yearly.R | 46 timetk-2.4.0/timetk/R/data-taylor_30_min.R | 40 timetk-2.4.0/timetk/R/data-walmart_sales_weekly.R | 98 timetk-2.4.0/timetk/R/data-wikipedia_traffic_daily.R | 54 timetk-2.4.0/timetk/R/diagnostics-tk_acf_diagnostics.R | 492 +- timetk-2.4.0/timetk/R/diagnostics-tk_anomaly_diagnostics.R | 618 +-- timetk-2.4.0/timetk/R/diagnostics-tk_seasonal_diagnostics.R | 488 +- timetk-2.4.0/timetk/R/diagnostics-tk_stl_diagnostics.R | 328 - 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timetk-2.4.0/timetk/R/recipes-step_box_cox.R | 470 +- timetk-2.4.0/timetk/R/recipes-step_diff.R | 422 +- timetk-2.4.0/timetk/R/recipes-step_fourier.R | 608 +-- timetk-2.4.0/timetk/R/recipes-step_holiday_signature.R | 620 +-- timetk-2.4.0/timetk/R/recipes-step_log_interval.R | 496 +- timetk-2.4.0/timetk/R/recipes-step_slidify.R | 607 +-- timetk-2.4.0/timetk/R/recipes-step_slidify_augment.R |only timetk-2.4.0/timetk/R/recipes-step_smooth.R | 642 +-- timetk-2.4.0/timetk/R/recipes-step_timeseries_signature.R | 504 +- timetk-2.4.0/timetk/R/recipes-step_ts_clean.R | 446 +- timetk-2.4.0/timetk/R/recipes-step_ts_impute.R | 454 +- timetk-2.4.0/timetk/R/recipes-step_ts_pad.R | 492 +- timetk-2.4.0/timetk/R/rsample-plot_time_series_cv_plan.R | 350 - timetk-2.4.0/timetk/R/rsample-time_series_cv.R | 696 +-- timetk-2.4.0/timetk/R/rsample-time_series_split.R | 248 - timetk-2.4.0/timetk/R/rsample-tk_time_series_cv_plan.R | 208 - timetk-2.4.0/timetk/R/tidyquant-theme-compat.R | 378 - timetk-2.4.0/timetk/R/timetk-internal.R | 20 timetk-2.4.0/timetk/R/timetk-package.R | 52 timetk-2.4.0/timetk/R/utils-dates.R | 272 - timetk-2.4.0/timetk/R/utils-parse-time.R | 580 +- timetk-2.4.0/timetk/R/utils-parse_period.R | 256 - timetk-2.4.0/timetk/R/utils-tidy-eval.R | 94 timetk-2.4.0/timetk/R/vec-box_cox.R | 226 - timetk-2.4.0/timetk/R/vec-diff.R | 370 - timetk-2.4.0/timetk/R/vec-fourier.R | 340 - timetk-2.4.0/timetk/R/vec-lag.R | 162 timetk-2.4.0/timetk/R/vec-log_interval.R | 264 - timetk-2.4.0/timetk/R/vec-normalize.R | 198 - timetk-2.4.0/timetk/R/vec-slidify.R | 400 +- timetk-2.4.0/timetk/R/vec-smooth.R | 236 - timetk-2.4.0/timetk/R/vec-standardize.R | 202 - timetk-2.4.0/timetk/R/vec-ts_clean.R | 176 timetk-2.4.0/timetk/R/vec-ts_impute.R | 208 - timetk-2.4.0/timetk/R/zzz.R | 224 - timetk-2.4.0/timetk/README.md | 460 +- timetk-2.4.0/timetk/build/vignette.rds |binary timetk-2.4.0/timetk/inst/doc/TK04_Plotting_Time_Series.R | 142 timetk-2.4.0/timetk/inst/doc/TK04_Plotting_Time_Series.Rmd | 354 - timetk-2.4.0/timetk/inst/doc/TK04_Plotting_Time_Series.html | 1034 ++--- timetk-2.4.0/timetk/inst/doc/TK05_Plotting_Seasonality_and_Correlation.R | 116 timetk-2.4.0/timetk/inst/doc/TK05_Plotting_Seasonality_and_Correlation.Rmd | 258 - timetk-2.4.0/timetk/inst/doc/TK05_Plotting_Seasonality_and_Correlation.html | 912 ++-- timetk-2.4.0/timetk/man/between_time.Rd | 214 - timetk-2.4.0/timetk/man/bike_sharing_daily.Rd | 104 timetk-2.4.0/timetk/man/box_cox_vec.Rd | 184 timetk-2.4.0/timetk/man/diff_vec.Rd | 254 - timetk-2.4.0/timetk/man/filter_by_time.Rd | 178 timetk-2.4.0/timetk/man/fourier_vec.Rd | 214 - timetk-2.4.0/timetk/man/future_frame.Rd | 262 - timetk-2.4.0/timetk/man/is_date_class.Rd | 52 timetk-2.4.0/timetk/man/lag_vec.Rd | 146 timetk-2.4.0/timetk/man/log_interval_vec.Rd | 172 timetk-2.4.0/timetk/man/m4_daily.Rd | 72 timetk-2.4.0/timetk/man/m4_hourly.Rd | 72 timetk-2.4.0/timetk/man/m4_monthly.Rd | 72 timetk-2.4.0/timetk/man/m4_quarterly.Rd | 72 timetk-2.4.0/timetk/man/m4_weekly.Rd | 72 timetk-2.4.0/timetk/man/m4_yearly.Rd | 74 timetk-2.4.0/timetk/man/mutate_by_time.Rd | 196 - timetk-2.4.0/timetk/man/normalize_vec.Rd | 128 timetk-2.4.0/timetk/man/pad_by_time.Rd | 272 - timetk-2.4.0/timetk/man/parse_date2.Rd | 126 timetk-2.4.0/timetk/man/plot_acf_diagnostics.Rd | 364 - 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timetk-2.4.0/timetk/man/step_ts_impute.Rd | 280 - timetk-2.4.0/timetk/man/step_ts_pad.Rd | 296 - timetk-2.4.0/timetk/man/summarise_by_time.Rd | 260 - timetk-2.4.0/timetk/man/taylor_30_min.Rd | 66 timetk-2.4.0/timetk/man/tidyeval.Rd | 104 timetk-2.4.0/timetk/man/time_arithmetic.Rd | 180 timetk-2.4.0/timetk/man/time_series_cv.Rd | 280 - timetk-2.4.0/timetk/man/time_series_split.Rd | 270 - timetk-2.4.0/timetk/man/timetk.Rd | 44 timetk-2.4.0/timetk/man/timetk_internal.Rd | 156 timetk-2.4.0/timetk/man/tk_acf_diagnostics.Rd | 202 - timetk-2.4.0/timetk/man/tk_anomaly_diagnostics.Rd | 254 - timetk-2.4.0/timetk/man/tk_augment_differences.Rd | 142 timetk-2.4.0/timetk/man/tk_augment_fourier.Rd | 124 timetk-2.4.0/timetk/man/tk_augment_holiday.Rd | 220 - timetk-2.4.0/timetk/man/tk_augment_lags.Rd | 118 timetk-2.4.0/timetk/man/tk_augment_slidify.Rd | 164 timetk-2.4.0/timetk/man/tk_augment_timeseries.Rd | 112 timetk-2.4.0/timetk/man/tk_get_frequency.Rd | 200 - timetk-2.4.0/timetk/man/tk_get_holiday.Rd | 218 - timetk-2.4.0/timetk/man/tk_get_timeseries.Rd | 148 timetk-2.4.0/timetk/man/tk_get_timeseries_unit_frequency.Rd | 42 timetk-2.4.0/timetk/man/tk_get_timeseries_variables.Rd | 64 timetk-2.4.0/timetk/man/tk_index.Rd | 164 timetk-2.4.0/timetk/man/tk_make_future_timeseries.Rd | 300 - timetk-2.4.0/timetk/man/tk_make_holiday_sequence.Rd | 266 - timetk-2.4.0/timetk/man/tk_make_timeseries.Rd | 360 - timetk-2.4.0/timetk/man/tk_seasonal_diagnostics.Rd | 180 timetk-2.4.0/timetk/man/tk_stl_diagnostics.Rd | 168 timetk-2.4.0/timetk/man/tk_summary_diagnostics.Rd | 98 timetk-2.4.0/timetk/man/tk_tbl.Rd | 226 - timetk-2.4.0/timetk/man/tk_time_scale_template.Rd | 90 timetk-2.4.0/timetk/man/tk_time_series_cv_plan.Rd | 102 timetk-2.4.0/timetk/man/tk_ts.Rd | 240 - timetk-2.4.0/timetk/man/tk_xts.Rd | 182 timetk-2.4.0/timetk/man/tk_zoo.Rd | 188 timetk-2.4.0/timetk/man/tk_zooreg.Rd | 258 - timetk-2.4.0/timetk/man/ts_clean_vec.Rd | 162 timetk-2.4.0/timetk/man/ts_impute_vec.Rd | 166 timetk-2.4.0/timetk/man/walmart_sales_weekly.Rd | 126 timetk-2.4.0/timetk/man/wikipedia_traffic_daily.Rd | 76 timetk-2.4.0/timetk/tests/testthat.R | 26 timetk-2.4.0/timetk/tests/testthat/test-recipes-step_timeseries_signature.R | 96 timetk-2.4.0/timetk/tests/testthat/test-tk_augment_timeseries.R | 120 timetk-2.4.0/timetk/tests/testthat/test-tk_get_timeseries.R | 316 - timetk-2.4.0/timetk/tests/testthat/test-tk_index.R | 666 +-- timetk-2.4.0/timetk/tests/testthat/test-tk_make_timeseries.R | 148 timetk-2.4.0/timetk/tests/testthat/test-tk_make_timeseries_future-OLD.R | 906 ++-- timetk-2.4.0/timetk/tests/testthat/test-tk_make_timeseries_future.R | 773 ++- timetk-2.4.0/timetk/tests/testthat/test-tk_tbl.R | 298 - timetk-2.4.0/timetk/tests/testthat/test-tk_ts.R | 156 timetk-2.4.0/timetk/tests/testthat/test-tk_xts.R | 164 timetk-2.4.0/timetk/tests/testthat/test-tk_zoo.R | 122 timetk-2.4.0/timetk/tests/testthat/test-tk_zooreg.R | 134 timetk-2.4.0/timetk/vignettes/TK04_Plotting_Time_Series.Rmd | 354 - timetk-2.4.0/timetk/vignettes/TK05_Plotting_Seasonality_and_Correlation.Rmd | 258 - timetk-2.4.0/timetk/vignettes/temp |only 196 files changed, 28532 insertions(+), 28448 deletions(-)
Title: A Framework to Smooth L1 Penalized Regression Operators using
Nesterov Smoothing
Description: We provide full functionality to smooth L1 penalized regression operators and to compute regression estimates thereof. For this, the objective function of a user-specified regression operator is first smoothed using Nesterov smoothing (see Y. Nesterov (2005) <doi:10.1007/s10107-004-0552-5>), resulting in a modified objective function with explicit gradients everywhere. The smoothed objective function and its gradient are minimized via BFGS, and the obtained minimizer is returned. Using Nesterov smoothing, the smoothed objective function can be made arbitrarily close to the original (unsmoothed) one. In particular, the Nesterov approach has the advantage that it comes with explicit accuracy bounds, both on the L1/L2 difference of the unsmoothed to the smoothed objective functions as well as on their respective minimizers (see G. Hahn, S.M. Lutz, N. Laha, C. Lange (2020) <doi:10.1101/2020.09.17.301788>). A progressive smoothing approach is provided which iteratively smoothes the objective function, resulting in more stable regression estimates.
Author: Georg Hahn [aut,cre], Sharon M. Lutz [ctb], Nilanjana Laha [ctb], Christoph Lange [ctb]
Maintainer: Georg Hahn <ghahn@hsph.harvard.edu>
Diff between smoothedLasso versions 1.4 dated 2020-09-22 and 1.5 dated 2020-10-08
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Search and Query CRAN R Packages
Description: Search CRAN metadata about packages by keyword, popularity,
recent activity, package name and more. Uses the 'R-hub' search server,
see <https://r-pkg.org> and the CRAN metadata database, that
contains information about CRAN packages. Note that this is _not_
a CRAN project.
Author: Gábor Csárdi [aut, cre],
Maëlle Salmon [aut] (<https://orcid.org/0000-0002-2815-0399>),
R Consortium [fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between pkgsearch versions 3.0.2 dated 2019-12-19 and 3.0.3 dated 2020-10-08
pkgsearch-3.0.2/pkgsearch/tests/manual |only pkgsearch-3.0.3/pkgsearch/DESCRIPTION | 12 ++++++------ pkgsearch-3.0.3/pkgsearch/MD5 | 18 +++++++++--------- pkgsearch-3.0.3/pkgsearch/NAMESPACE | 4 ---- pkgsearch-3.0.3/pkgsearch/NEWS.md | 7 +++++++ pkgsearch-3.0.3/pkgsearch/R/addin.R | 4 ++-- pkgsearch-3.0.3/pkgsearch/R/api.R | 13 ++++++------- pkgsearch-3.0.3/pkgsearch/R/crandb-public-api.R | 15 +++++++++------ pkgsearch-3.0.3/pkgsearch/R/http.R |only pkgsearch-3.0.3/pkgsearch/man/cran_packages.Rd | 2 +- pkgsearch-3.0.3/pkgsearch/man/pkgsearch-package.Rd | 2 +- 11 files changed, 41 insertions(+), 36 deletions(-)
Title: The Tidymodels Extension for Time Series Modeling
Description: The time series forecasting framework for use with the 'tidymodels' ecosystem.
Models include ARIMA, Exponential Smoothing, and additional time series models
from the 'forecast' and 'prophet' packages. Refer to "Forecasting Principles & Practice, Second edition"
(<https://otexts.com/fpp2/>).
Refer to "Prophet: forecasting at scale"
(<https://research.fb.com/blog/2017/02/prophet-forecasting-at-scale/>.).
Author: Matt Dancho [aut, cre],
Business Science [cph]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between modeltime versions 0.2.0 dated 2020-09-28 and 0.2.1 dated 2020-10-08
DESCRIPTION | 6 LICENSE | 4 MD5 | 254 - NAMESPACE | 400 - NEWS.md | 278 - R/data.R | 248 - R/dev-constructor.R | 178 R/dev-model_descriptions.R | 502 +- R/dev-parse_index.R | 216 R/dev-xregs.R | 664 +-- R/dials-arima_params.R | 206 R/dials-ets_params.R | 146 R/dials-nnetar_params.R | 74 R/dials-ts_params.R | 114 R/helpers-modeltime_residuals.R | 86 R/helpers-modeltime_table.R | 398 - R/modeltime-accuracy-table.R | 312 - R/modeltime-calibrate.R | 582 +- R/modeltime-forecast-plot.R | 398 - R/modeltime-forecast.R | 1512 +++--- R/modeltime-refit.R | 517 +- R/modeltime-residuals.R | 206 R/modeltime-table.R | 184 R/parsnip-arima_boost.R | 1548 +++---- R/parsnip-arima_boost_data.R | 738 +-- R/parsnip-arima_reg.R | 1070 ++-- R/parsnip-arima_reg_data.R | 490 +- R/parsnip-exp_smoothing.R | 798 +-- R/parsnip-exp_smoothing_data.R | 220 - R/parsnip-nnetar_reg.R | 774 +-- R/parsnip-nnetar_reg_data.R | 264 - R/parsnip-prophet_boost.R | 1338 +++--- R/parsnip-prophet_boost_data.R | 494 +- R/parsnip-prophet_reg.R | 1154 ++--- R/parsnip-seasonal_reg.R | 1336 +++--- R/parsnip-seasonal_reg_data.R | 504 +- R/tibble-type_sum.R | 24 R/utils-checks-validations.R | 581 +- R/utils-parsnip-helpers.R | 300 - R/utils-pipe.R | 22 R/utils-tidy-eval.R | 94 R/utils-xgboost.R | 106 R/zzz.R | 64 README.md | 244 - build/vignette.rds |binary inst/doc/extending-modeltime.R | 560 +- inst/doc/extending-modeltime.Rmd | 982 ++-- inst/doc/extending-modeltime.html | 1588 +++---- inst/doc/getting-started-with-modeltime.R | 280 - inst/doc/getting-started-with-modeltime.Rmd | 750 +-- inst/doc/getting-started-with-modeltime.html | 2174 ++++------ man/Arima_fit_impl.Rd | 88 man/Arima_predict_impl.Rd | 36 man/add_modeltime_model.Rd | 4 man/arima_boost.Rd | 608 +- man/arima_params.Rd | 112 man/arima_reg.Rd | 498 +- man/arima_workflow_tuned.Rd | 50 man/arima_xgboost_fit_impl.Rd | 238 - man/arima_xgboost_predict_impl.Rd | 36 man/auto_arima_fit_impl.Rd | 88 man/auto_arima_xgboost_fit_impl.Rd | 358 - man/combine_modeltime_tables.Rd | 126 man/create_xreg_recipe.Rd | 136 man/default_forecast_accuracy_metric_set.Rd | 94 man/ets_fit_impl.Rd | 78 man/ets_predict_impl.Rd | 36 man/exp_smoothing.Rd | 354 - man/exp_smoothing_params.Rd | 86 man/get_arima_description.Rd | 60 man/get_model_description.Rd | 84 man/get_tbats_description.Rd | 38 man/mdl_time_forecast.Rd | 84 man/mdl_time_refit.Rd | 51 man/modeltime_accuracy.Rd | 164 man/modeltime_calibrate.Rd | 192 man/modeltime_forecast.Rd | 374 - man/modeltime_refit.Rd | 177 man/modeltime_table.Rd | 142 man/new_modeltime_bridge.Rd | 102 man/nnetar_fit_impl.Rd | 100 man/nnetar_params.Rd | 80 man/nnetar_predict_impl.Rd | 36 man/nnetar_reg.Rd | 388 - man/parse_index.Rd | 88 man/pipe.Rd | 24 man/plot_modeltime_forecast.Rd | 198 man/pluck_modeltime_model.Rd | 56 man/prophet_boost.Rd | 648 +- man/prophet_fit_impl.Rd | 176 man/prophet_params.Rd | 172 man/prophet_predict_impl.Rd | 36 man/prophet_reg.Rd | 502 +- man/prophet_xgboost_fit_impl.Rd | 294 - man/prophet_xgboost_predict_impl.Rd | 36 man/recipe_helpers.Rd | 108 man/seasonal_reg.Rd | 390 - man/stlm_arima_fit_impl.Rd | 68 man/stlm_arima_predict_impl.Rd | 36 man/stlm_ets_fit_impl.Rd | 68 man/stlm_ets_predict_impl.Rd | 36 man/table_modeltime_accuracy.Rd | 240 - man/tbats_fit_impl.Rd | 74 man/tbats_predict_impl.Rd | 36 man/tidyeval.Rd | 102 man/time_series_params.Rd | 82 man/type_sum.mdl_time_tbl.Rd | 36 man/xgboost_impl.Rd | 114 man/xgboost_predict.Rd | 36 tests/testthat/test-algo-arima_boost-Arima.R | 580 +- tests/testthat/test-algo-arima_boost-auto_arima.R | 548 +- tests/testthat/test-algo-arima_reg-Arima.R | 416 - tests/testthat/test-algo-arima_reg-auto_arima.R | 384 - tests/testthat/test-algo-exp_smoothing-ets.R | 286 - tests/testthat/test-algo-nnetar_reg.R | 456 +- tests/testthat/test-algo-seasonal_decomp_arima.R | 318 - tests/testthat/test-algo-seasonal_decomp_ets.R | 302 - tests/testthat/test-algo-seasonal_reg_tbats.R | 308 - tests/testthat/test-developer-tools-constructor.R | 292 - tests/testthat/test-developer-tools-xregs.R | 124 tests/testthat/test-helpers-pull_parsnip_preprocessor.R | 132 tests/testthat/test-helpers-update-modeltime-tables.R | 248 - tests/testthat/test-modeltime_table-forecast-accuracy-refitting.R | 976 ++-- tests/testthat/test-results-forecast-plots.R | 268 - tests/testthat/test-tune_workflows.R | 146 vignettes/extending-modeltime.Rmd | 982 ++-- vignettes/getting-started-with-modeltime.Rmd | 750 +-- vignettes/temp/modeltime-model-list.Rmd | 472 +- 128 files changed, 21367 insertions(+), 21357 deletions(-)
Title: Discriminant Adaptive Nearest Neighbor Classification
Description: Discriminant Adaptive Nearest Neighbor Classification is a
variation of k nearest neighbors where the shape of the neighborhood is
data driven. This package implements dann and sub_dann from
Hastie (1995) <https://web.stanford.edu/~hastie/Papers/dann_IEEE.pdf>.
Author: Greg McMahan
Maintainer: Greg McMahan <gmcmacran@gmail.com>
Diff between dann versions 0.2.0 dated 2020-03-14 and 0.2.1 dated 2020-10-08
DESCRIPTION | 10 ++-- MD5 | 25 +++++----- NEWS.md |only R/dann.R | 21 +++++++- README.md | 93 ++++++++++---------------------------- inst/doc/dann.R | 42 +++++++---------- inst/doc/dann.Rmd | 55 +++++++++++----------- inst/doc/dann.html | 97 ++++++++++++++++++---------------------- inst/doc/sub_dann.R | 37 +++++++-------- inst/doc/sub_dann.Rmd | 58 ++++++++++++----------- inst/doc/sub_dann.html | 109 +++++++++++++++++++++------------------------ tests/testthat/test_dann.R | 20 ++++++++ vignettes/dann.Rmd | 55 +++++++++++----------- vignettes/sub_dann.Rmd | 58 ++++++++++++----------- 14 files changed, 338 insertions(+), 342 deletions(-)
Title: Highest Density Regions and Other Functions of Distributions
Description: Highest Density Regions are the smallest set in the support of a
probability distribution with the specified coverage probability. 'HDRs'
may contain disjoint intervals, but can be calculated efficiently using
iterative methods. One can similarly construct optimal (i.e., shortest)
confidence intervals for some basic inferential problems, including for
population means, variances, or proportion parameters.
Author: Ben O'Neill [aut, cph],
Neal Fultz [cre, ctb]
Maintainer: Neal Fultz <nfultz@gmail.com>
Diff between stat.extend versions 0.1.1 dated 2020-08-11 and 0.1.4 dated 2020-10-08
DESCRIPTION | 6 +- MD5 | 28 +++++++------ NAMESPACE | 3 + R/HDR.R | 4 - R/HDR.discrete.R |only R/conf.R | 107 +++++++++++++++++++++++++++++++-------------------- R/custom.R | 20 +-------- R/internals.R | 76 ------------------------------------ R/utils.R |only man/CONF.Rd | 24 ++++++++--- man/HDR.Rd | 4 - man/HDR.discrete.Rd |only man/checkIterArgs.Rd | 2 man/custom.Rd | 22 ++-------- man/reformat.Rd |only tests/test-CONF.R | 4 - tests/test-custom.R | 8 +-- 17 files changed, 126 insertions(+), 182 deletions(-)
Title: Datasets to Align Financial Markets with Climate Goals
Description: These datasets support the implementation in R of
the software 'PACTA' (Paris Agreement Capital Transition Assessment),
which is a free tool that calculates the alignment between financial
assets and climate scenarios (<https://2degrees-investing.org/>).
Financial institutions use 'PACTA' to study how their capital
allocation impacts the climate. Because both financial institutions
and market data providers keep their data private, this package
provides fake, public data to enable the development and use of
'PACTA' in R.
Author: Mauro Lepore [aut, cre, ctr] (<https://orcid.org/0000-0002-1986-7988>),
Jackson Hoffart [aut, dtc] (<https://orcid.org/0000-0002-8600-5042>),
Klaus Hagedorn [aut],
2 Degrees Investing Initiative [cph, fnd]
Maintainer: Mauro Lepore <maurolepore@gmail.com>
Diff between r2dii.data versions 0.1.3 dated 2020-09-12 and 0.1.4 dated 2020-10-08
r2dii.data-0.1.3/r2dii.data/LICENSE |only r2dii.data-0.1.4/r2dii.data/DESCRIPTION | 8 - r2dii.data-0.1.4/r2dii.data/MD5 | 33 ++--- r2dii.data-0.1.4/r2dii.data/NEWS.md | 6 + r2dii.data-0.1.4/r2dii.data/R/classification_bridge.R | 17 ++ r2dii.data-0.1.4/r2dii.data/README.md | 60 ++-------- r2dii.data-0.1.4/r2dii.data/data/data_dictionary.rda |binary r2dii.data-0.1.4/r2dii.data/data/gics_classification.rda |only r2dii.data-0.1.4/r2dii.data/data/sector_classifications.rda |binary r2dii.data-0.1.4/r2dii.data/man/data_dictionary.Rd | 2 r2dii.data-0.1.4/r2dii.data/man/gics_classification.Rd |only r2dii.data-0.1.4/r2dii.data/man/isic_classification.Rd | 5 r2dii.data-0.1.4/r2dii.data/man/nace_classification.Rd | 5 r2dii.data-0.1.4/r2dii.data/man/naics_classification.Rd | 5 r2dii.data-0.1.4/r2dii.data/man/sector_classifications.Rd | 5 r2dii.data-0.1.4/r2dii.data/man/sic_classification.Rd | 5 r2dii.data-0.1.4/r2dii.data/tests/testthat/ref-data_dictionary |binary r2dii.data-0.1.4/r2dii.data/tests/testthat/ref-sector_classifications |binary r2dii.data-0.1.4/r2dii.data/tests/testthat/test-data_dictionary.R | 1 19 files changed, 76 insertions(+), 76 deletions(-)
Title: Biodiversity Information Review and Decision Support
Description: It helps making the evaluation and preparation of biodiversity data
easy, systematic and reproducible. It also helps the users to overlay the
point observations into a custom grid that is useful for further analysis.
The review summarise statistics that helps evaluate whether a set of species
observations is fit-for-use and take decisions upon its use of on further
analyses. It does so by quantifying the sampling effort (amount of effort
expended during an event) and data completeness (data gaps) to help judge
whether the data is representative, valid and fit for any intended purpose.
The 'BIRDS' package is most useful when working with heterogeneous data sets
with variation in the sampling process, i.e. where data have been collected
and reported in various ways and therefore varying in sampling effort
and data completeness (i.e. how well the reported observations describe the
true state). Primary biodiversity data (PBD) combining data from different
data sets, like e.g. Global Biodiversity Information Facility (GBIF) mediated
data, commonly vary in the ways data has been generated - containing
opportunistically collected presence-only data together with and data from
systematic monitoring programs. The set of tools provided is aimed at
understanding the process that generated the data (i.e. observing, recording
and reporting species into databases). There is a non-vital function on this
package (makeDggrid()) that depends the package 'dggridR' that is no longer on CRAN.
You can find it here <https://github.com/r-barnes/dggridR>. References:
Ruete (2015) <doi:10.3897/BDJ.3.e5361>; Szabo, Vesk, Baxter & Possingham (2010)
<doi:10.1890/09-0877.1>; Telfer, Preston 6 Rothery (2002) <doi:10.1016/S0006-3207(02)00050-2>.
Author: Debora Arlt [aut] (<https://orcid.org/0000-0003-0874-4250>),
Alejandro Ruete [aut, cre] (<https://orcid.org/0000-0001-7681-2812>),
Anton Hammarström [aut]
Maintainer: Alejandro Ruete <aleruete@gmail.com>
Diff between BIRDS versions 0.1 dated 2020-03-20 and 0.1.2 dated 2020-10-08
BIRDS-0.1.2/BIRDS/DESCRIPTION | 23 - BIRDS-0.1.2/BIRDS/MD5 | 73 +-- BIRDS-0.1.2/BIRDS/NAMESPACE | 18 BIRDS-0.1.2/BIRDS/R/biodiversityFunctions.R |only BIRDS-0.1.2/BIRDS/R/exploreVisits.r | 118 +++-- BIRDS-0.1.2/BIRDS/R/exportBirds.R | 58 +- BIRDS-0.1.2/BIRDS/R/focalSpecies.R | 160 ++++--- BIRDS-0.1.2/BIRDS/R/makeGrid.r | 40 + BIRDS-0.1.2/BIRDS/R/organizeBirds.R | 71 ++- BIRDS-0.1.2/BIRDS/R/overlayBirds.R | 74 +++ BIRDS-0.1.2/BIRDS/R/removeObservations.R | 82 +++- BIRDS-0.1.2/BIRDS/R/summarizeBirds.R | 39 + BIRDS-0.1.2/BIRDS/README.md | 13 BIRDS-0.1.2/BIRDS/build/vignette.rds |binary BIRDS-0.1.2/BIRDS/inst/doc/BIRDS.html | 181 +++++++- BIRDS-0.1.2/BIRDS/inst/doc/technical_details.html | 117 +++++ BIRDS-0.1.2/BIRDS/inst/doc/working_with_xts_timeseries.R | 2 BIRDS-0.1.2/BIRDS/inst/doc/working_with_xts_timeseries.Rmd | 2 BIRDS-0.1.2/BIRDS/inst/doc/working_with_xts_timeseries.html | 138 +++++- BIRDS-0.1.2/BIRDS/man/BIRDS.Rd | 98 ++-- BIRDS-0.1.2/BIRDS/man/communityMatrix.Rd | 66 +-- BIRDS-0.1.2/BIRDS/man/communityMatrixGrid.Rd |only BIRDS-0.1.2/BIRDS/man/exploreVisits.Rd | 133 +++--- BIRDS-0.1.2/BIRDS/man/extractPresence.Rd | 36 - BIRDS-0.1.2/BIRDS/man/focalSpReport.Rd | 104 ++--- BIRDS-0.1.2/BIRDS/man/focalSpSummary.Rd | 66 +-- BIRDS-0.1.2/BIRDS/man/getSpatial.Rd | 42 +- BIRDS-0.1.2/BIRDS/man/getSpatioTemporal.Rd | 42 +- BIRDS-0.1.2/BIRDS/man/getTemporal.Rd | 42 +- BIRDS-0.1.2/BIRDS/man/listSpecies.Rd | 48 +- BIRDS-0.1.2/BIRDS/man/makeDggrid.Rd | 137 +++--- BIRDS-0.1.2/BIRDS/man/normalize.Rd | 36 - BIRDS-0.1.2/BIRDS/man/organizeBirds.Rd | 246 ++++++------ BIRDS-0.1.2/BIRDS/man/recBySpp.Rd |only BIRDS-0.1.2/BIRDS/man/removeObs.Rd | 140 +++--- BIRDS-0.1.2/BIRDS/man/simplifySpp.Rd | 39 - BIRDS-0.1.2/BIRDS/man/summarizeBirds.Rd | 2 BIRDS-0.1.2/BIRDS/man/whichNonEmpty.Rd |only BIRDS-0.1.2/BIRDS/vignettes/working_with_xts_timeseries.Rmd | 2 BIRDS-0.1/BIRDS/data/datalist |only 40 files changed, 1532 insertions(+), 956 deletions(-)
Title: Interface to 'Digital Ocean'
Description: Provides a set of functions for interacting with the 'Digital
Ocean' API <https://www.digitalocean.com/>, including
creating images, destroying them, rebooting, getting details on regions, and
available images.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Hadley Wickham [aut],
Winston Chang [aut],
Bob Rudis [ctb],
Bryce Mecum [ctb] (<https://orcid.org/0000-0002-0381-3766>),
RStudio [cph]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between analogsea versions 0.8.0 dated 2020-01-30 and 0.9.0 dated 2020-10-08
analogsea-0.8.0/analogsea/build |only analogsea-0.8.0/analogsea/inst/doc |only analogsea-0.8.0/analogsea/vignettes |only analogsea-0.9.0/analogsea/DESCRIPTION | 14 +-- analogsea-0.9.0/analogsea/LICENSE | 2 analogsea-0.9.0/analogsea/MD5 | 42 +++++------ analogsea-0.9.0/analogsea/NAMESPACE | 1 analogsea-0.9.0/analogsea/NEWS.md | 22 +++++- analogsea-0.9.0/analogsea/R/analogsea-package.R | 18 ++-- analogsea-0.9.0/analogsea/R/debian.R | 62 ++++++++++++++--- analogsea-0.9.0/analogsea/R/deprecated_defunct.R | 8 -- analogsea-0.9.0/analogsea/R/droplet-actions.R | 11 +-- analogsea-0.9.0/analogsea/R/droplet-ssh.R | 58 ++++++++++----- analogsea-0.9.0/analogsea/R/droplet_execute.R | 4 - analogsea-0.9.0/analogsea/R/info.R | 8 +- analogsea-0.9.0/analogsea/README.md | 6 + analogsea-0.9.0/analogsea/man/adjectives.Rd | 2 analogsea-0.9.0/analogsea/man/analogsea-defunct.Rd | 6 - analogsea-0.9.0/analogsea/man/analogsea-package.Rd | 14 +-- analogsea-0.9.0/analogsea/man/debian.Rd | 9 ++ analogsea-0.9.0/analogsea/man/droplet_functions.Rd | 8 +- analogsea-0.9.0/analogsea/man/nouns.Rd | 2 analogsea-0.9.0/analogsea/tests/testthat/test-images.R | 4 - 23 files changed, 189 insertions(+), 112 deletions(-)
Title: Fitting Finite Mixture of Scale Mixture of Skew-Normal
Distributions
Description: Functions to fit finite mixture of scale mixture of skew-normal (FM-SMSN) distributions, details in Prates, Lachos and Cabral (2013) <doi: 10.18637/jss.v054.i12>, Cabral, Lachos and Prates (2012) <doi:10.1016/j.csda.2011.06.026> and Basso, Lachos, Cabral and Ghosh (2010) <doi:10.1016/j.csda.2009.09.031>.
Author: Marcos Prates [aut, cre, trl],
Victor Lachos [aut],
Celso Cabral [aut]
Maintainer: Marcos Prates <marcosop@est.ufmg.br>
Diff between mixsmsn versions 1.1-7 dated 2020-04-17 and 1.1-8 dated 2020-10-08
ChangeLog | 8 + DESCRIPTION | 8 - MD5 | 14 +- R/mixsmsn.R | 136 +++++++++++++++++++++++++++- R/smsn.mmix.R | 173 ++++++++++++++++++++++++++++++++++++ inst/CITATION | 4 man/smsn.mix.Rd | 238 +++++++++++++++++++++++++------------------------- man/smsn.mmix.Rd | 258 +++++++++++++++++++++++++++---------------------------- 8 files changed, 566 insertions(+), 273 deletions(-)
Title: Bayesian Regression Models using 'Stan'
Description: Fit Bayesian generalized (non-)linear multivariate multilevel models
using 'Stan' for full Bayesian inference. A wide range of distributions
and link functions are supported, allowing users to fit -- among others --
linear, robust linear, count data, survival, response times, ordinal,
zero-inflated, hurdle, and even self-defined mixture models all in a
multilevel context. Further modeling options include non-linear and
smooth terms, auto-correlation structures, censored data, meta-analytic
standard errors, and quite a few more. In addition, all parameters of the
response distribution can be predicted in order to perform distributional
regression. Prior specifications are flexible and explicitly encourage
users to apply prior distributions that actually reflect their beliefs.
Model fit can easily be assessed and compared with posterior predictive
checks and leave-one-out cross-validation. References: Bürkner (2017)
<doi:10.18637/jss.v080.i01>; Bürkner (2018) <doi:10.32614/RJ-2018-017>;
Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>.
Author: Paul-Christian Bürkner [aut, cre],
Jonah Gabry [ctb],
Sebastian Weber [ctb]
Maintainer: Paul-Christian Bürkner <paul.buerkner@gmail.com>
Diff between brms versions 2.13.5 dated 2020-07-31 and 2.14.0 dated 2020-10-08
brms-2.13.5/brms/inst/chunks/fun_kronecker.stan |only brms-2.14.0/brms/DESCRIPTION | 25 brms-2.14.0/brms/MD5 | 257 brms-2.14.0/brms/NAMESPACE | 16 brms-2.14.0/brms/NEWS.md | 45 brms-2.14.0/brms/R/autocor.R | 1268 +- brms-2.14.0/brms/R/backends.R | 544 - brms-2.14.0/brms/R/bridgesampling.R | 3 brms-2.14.0/brms/R/brm.R | 1004 +- brms-2.14.0/brms/R/brms-package.R | 168 brms-2.14.0/brms/R/brmsfit-class.R | 186 brms-2.14.0/brms/R/brmsfit-helpers.R | 1491 +-- brms-2.14.0/brms/R/brmsfit-methods.R | 1 brms-2.14.0/brms/R/brmsformula.R | 3359 +++---- brms-2.14.0/brms/R/brmsterms.R | 2131 ++-- brms-2.14.0/brms/R/conditional_effects.R | 2425 ++--- brms-2.14.0/brms/R/conditional_smooths.R | 482 - brms-2.14.0/brms/R/data-helpers.R | 1087 +- brms-2.14.0/brms/R/data-predictor.R | 4 brms-2.14.0/brms/R/data-response.R | 1196 +- brms-2.14.0/brms/R/datasets.R | 336 brms-2.14.0/brms/R/distributions.R | 4274 +++++----- brms-2.14.0/brms/R/emmeans.R | 72 brms-2.14.0/brms/R/exclude_pars.R | 334 brms-2.14.0/brms/R/families.R | 3380 +++---- brms-2.14.0/brms/R/family-lists.R | 929 +- brms-2.14.0/brms/R/formula-ac.R | 1344 +-- brms-2.14.0/brms/R/formula-ad.R | 2 brms-2.14.0/brms/R/kfold.R | 692 - 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brms-2.14.0/brms/tests/testthat/tests.priors.R | 224 brms-2.14.0/brms/tests/testthat/tests.rename_pars.R | 18 brms-2.14.0/brms/tests/testthat/tests.restructure.R | 381 brms-2.14.0/brms/tests/testthat/tests.stan_functions.R | 428 - brms-2.14.0/brms/vignettes/brms_customfamilies.Rmd | 3 brms-2.14.0/brms/vignettes/brms_families.Rmd | 664 - brms-2.14.0/brms/vignettes/brms_nonlinear.Rmd | 656 - brms-2.14.0/brms/vignettes/brms_threading.Rmd |only 137 files changed, 24952 insertions(+), 23182 deletions(-)
Title: Find Differences Between R Objects
Description: Compare complex R objects and reveal the key
differences. Designed particularly for use in testing packages where
being able to quickly isolate key differences makes understanding test
failures much easier.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between waldo versions 0.2.0 dated 2020-07-13 and 0.2.1 dated 2020-10-08
DESCRIPTION | 7 +- MD5 | 73 ++++++++++++++-------------- NEWS.md | 23 ++++++++ R/compare-class.R | 7 +- R/compare-value.R | 49 +++++++++++------- R/compare.R | 25 +++++---- R/diff.R | 6 +- R/utils.R | 8 +-- README.md | 7 +- man/compare.Rd | 18 ++++-- man/figures/README/unnamed-chunk-10.svg | 2 man/figures/README/unnamed-chunk-11.svg | 2 man/figures/README/unnamed-chunk-12.svg | 2 man/figures/README/unnamed-chunk-2.svg | 2 man/figures/README/unnamed-chunk-3.svg | 2 man/figures/README/unnamed-chunk-4.svg | 2 man/figures/README/unnamed-chunk-5.svg | 2 man/figures/README/unnamed-chunk-6.svg | 2 man/figures/README/unnamed-chunk-7.svg | 2 man/figures/README/unnamed-chunk-8.svg | 2 tests/testthat/test-compare-atomic.txt | 8 +-- tests/testthat/test-compare-attr-1.txt |only tests/testthat/test-compare-chr.txt | 4 - tests/testthat/test-compare-fun.txt | 56 ++++++++++----------- tests/testthat/test-compare-lang.txt | 14 ++--- tests/testthat/test-compare-list.txt | 52 +++++++++---------- tests/testthat/test-compare-r6.txt | 32 ++++++------ tests/testthat/test-compare-s3-weird.txt | 16 +++--- tests/testthat/test-compare-s3.txt | 16 +++--- tests/testthat/test-compare-s4.txt | 20 +++---- tests/testthat/test-compare-value-chr.txt | 4 - tests/testthat/test-compare-value-lines.txt | 4 - tests/testthat/test-compare-value-num.txt | 33 +++++++----- tests/testthat/test-compare-value.R | 10 +-- tests/testthat/test-compare.R | 18 ++++++ tests/testthat/test-diff-element-wise.txt | 4 - tests/testthat/test-diff-paired.txt | 9 +++ tests/testthat/test-diff.R | 4 + 38 files changed, 316 insertions(+), 231 deletions(-)
Title: Numerical Calibration of Proxy-Climate Relationships
Description: Bootstrapped response and correlation functions,
seasonal correlations and evaluation of reconstruction
skills for use in dendroclimatology and dendroecology,
see Zang and Biondi (2015) <doi:10.1111/ecog.01335>.
Author: Christian Zang [aut, cre, cph, trl],
Franco Biondi [ctb, cph]
Maintainer: Christian Zang <christian.zang@wzw.tum.de>
Diff between treeclim versions 2.0.3 dated 2019-03-22 and 2.0.5.1 dated 2020-10-08
DESCRIPTION | 17 ++++++---- MD5 | 52 ++++++++++++++++----------------- R/abbrev_name.R | 2 - R/as_tcclimate.R | 2 - README.md | 6 +-- man/abbrev_name.Rd | 2 - man/as_tcclimate.Rd | 2 - man/dcc.Rd | 20 ++++++++++-- man/dlm.Rd | 12 ++++++- man/muc_clim.Rd | 6 ++- man/muc_fake.Rd | 6 ++- man/muc_spruce.Rd | 6 ++- man/norw015.Rd | 6 ++- man/norway_prec.Rd | 6 ++- man/norway_temp.Rd | 6 ++- man/rt_prec.Rd | 6 ++- man/rt_spruce.Rd | 6 ++- man/rt_temp.Rd | 6 ++- man/seascorr.Rd | 14 ++++++-- man/skills.Rd | 9 ++++- man/spai020.Rd | 6 ++- man/spain_prec.Rd | 6 ++- man/spain_temp.Rd | 6 ++- man/tc_mfunc.Rd | 13 ++++++-- man/truncate_input.Rd | 10 +++++- tests/testthat/test_eval_selection.R | 8 ++--- tests/testthat/test_month_processing.R | 28 ++++++++--------- 27 files changed, 172 insertions(+), 97 deletions(-)
Title: Patient Rule Induction Method (PRIM)
Description: Patient Rule Induction Method (PRIM) for bump hunting in high-dimensional data.
Author: Tarn Duong <tarn.duong@gmail.com>
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between prim versions 1.0.18 dated 2020-10-05 and 1.0.19 dated 2020-10-08
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- inst/doc/prim-2d.R | 2 -- inst/doc/prim-2d.Rmd | 6 ++---- inst/doc/prim-2d.html | 16 +++++++--------- inst/doc/prim-3d.R | 1 - inst/doc/prim-3d.Rmd | 5 ++--- inst/doc/prim-3d.html | 11 +++++------ vignettes/prim-2d.Rmd | 6 ++---- vignettes/prim-3d.Rmd | 5 ++--- 10 files changed, 33 insertions(+), 45 deletions(-)
Title: Generating Time Series with Diverse and Controllable
Characteristics
Description: Generates time series based on mixture autoregressive models. Kang,Y.,Hyndman,R.,Li,F.(2020)<doi:10.1002/sam.11461>.
Author: Yanfei Kang [aut, cre] (<https://orcid.org/0000-0001-8769-6650>),
Feng Li [aut] (<https://orcid.org/0000-0002-4248-9778>),
Rob Hyndman [ctb] (<https://orcid.org/0000-0002-2140-5352>),
Mitchell O'Hara-Wild [ctb] (<https://orcid.org/0000-0001-6729-7695>),
Bocong Zhao [ctb] (<https://orcid.org/0000-0001-8434-9047>)
Maintainer: Yanfei Kang <yanfeikang@buaa.edu.cn>
Diff between gratis versions 0.2.0 dated 2020-08-03 and 0.2.1 dated 2020-10-08
gratis-0.2.0/gratis/R/tsgeneration.R |only gratis-0.2.1/gratis/DESCRIPTION | 18 +- gratis-0.2.1/gratis/MD5 | 45 +++--- gratis-0.2.1/gratis/NAMESPACE | 1 gratis-0.2.1/gratis/NEWS.md | 14 + gratis-0.2.1/gratis/R/generate_ts.R | 31 +++- gratis-0.2.1/gratis/R/generate_ts_with_target.R | 11 + gratis-0.2.1/gratis/R/generate_ts_with_target_ts.R | 12 + gratis-0.2.1/gratis/R/gratis.R |only gratis-0.2.1/gratis/R/lnorm2.R | 6 gratis-0.2.1/gratis/R/rmixmorm.R | 8 - gratis-0.2.1/gratis/README.md | 9 + gratis-0.2.1/gratis/build/vignette.rds |binary gratis-0.2.1/gratis/inst/CITATION |only gratis-0.2.1/gratis/inst/doc/QuickStart.R | 33 ++-- gratis-0.2.1/gratis/inst/doc/QuickStart.Rmd | 57 +++++-- gratis-0.2.1/gratis/inst/doc/QuickStart.html | 150 +++++++++++++++++---- gratis-0.2.1/gratis/man/figures/logo.PNG |binary gratis-0.2.1/gratis/man/generate_msts.Rd | 11 + gratis-0.2.1/gratis/man/generate_ts.Rd | 9 - gratis-0.2.1/gratis/man/generate_ts_with_target.Rd | 5 gratis-0.2.1/gratis/man/rlnorm2.Rd | 6 gratis-0.2.1/gratis/man/rmixnorm_ts.Rd | 6 gratis-0.2.1/gratis/man/tsgeneration.Rd | 2 gratis-0.2.1/gratis/vignettes/QuickStart.Rmd | 57 +++++-- 25 files changed, 352 insertions(+), 139 deletions(-)
Title: Read and Write from the System Clipboard
Description: Simple utility functions to read from and write to
the Windows, OS X, and X11 clipboards.
Author: Matthew Lincoln [aut, cre] (<https://orcid.org/0000-0002-4387-3384>),
Louis Maddox [ctb],
Steve Simpson [ctb],
Jennifer Bryan [ctb]
Maintainer: Matthew Lincoln <matthew.d.lincoln@gmail.com>
Diff between clipr versions 0.7.0 dated 2019-07-23 and 0.7.1 dated 2020-10-08
clipr-0.7.0/clipr/tests/testthat/test_render.R |only clipr-0.7.1/clipr/DESCRIPTION | 8 - clipr-0.7.1/clipr/MD5 | 24 ++--- clipr-0.7.1/clipr/NEWS.md | 4 clipr-0.7.1/clipr/R/linux_clipboard.R | 6 - clipr-0.7.1/clipr/README.md | 83 ++++++++---------- clipr-0.7.1/clipr/build/vignette.rds |binary clipr-0.7.1/clipr/inst/doc/developing-with-clipr.R | 2 clipr-0.7.1/clipr/inst/doc/developing-with-clipr.html | 41 ++++++-- clipr-0.7.1/clipr/man/clipr.Rd | 1 clipr-0.7.1/clipr/man/read_clip.Rd | 3 clipr-0.7.1/clipr/man/read_clip_tbl.Rd | 2 clipr-0.7.1/clipr/man/write_clip.Rd | 14 ++- clipr-0.7.1/clipr/tests/testthat/test-render.R |only 14 files changed, 106 insertions(+), 82 deletions(-)
Title: Cell-Type-Specific Association Testing in Bulk Omics Experiments
Description: In bulk epigenome/transcriptome experiments, molecular expression
is measured in a tissue, which is a mixture of multiple types of cells.
This package tests association of a disease/phenotype with a molecular marker
for each cell type.
The proportion of cell types in each sample needs to be given as input.
The package is applicable to epigenome-wide association study (EWAS) and
differential gene expression analysis.
Takeuchi and Kato (submitted)
"omicwas: cell-type-specific epigenome-wide and transcriptome association study".
Author: Fumihiko Takeuchi [aut, cre] (<https://orcid.org/0000-0003-3185-5661>)
Maintainer: Fumihiko Takeuchi <fumihiko@takeuchi.name>
Diff between omicwas versions 0.7.0 dated 2020-06-02 and 0.8.0 dated 2020-10-08
omicwas-0.7.0/omicwas/man/ctRUV.Rd |only omicwas-0.8.0/omicwas/DESCRIPTION | 10 omicwas-0.8.0/omicwas/MD5 | 19 - omicwas-0.8.0/omicwas/NAMESPACE | 3 omicwas-0.8.0/omicwas/R/omicwas.R | 229 +++++++++-------- omicwas-0.8.0/omicwas/R/supplement.estimators.R |only omicwas-0.8.0/omicwas/README.md | 2 omicwas-0.8.0/omicwas/build/vignette.rds |binary omicwas-0.8.0/omicwas/inst/doc/intro.html | 89 ++++++ omicwas-0.8.0/omicwas/man/ctassoc.Rd | 25 + omicwas-0.8.0/omicwas/tests/GSE42861smallresult3.RData |only omicwas-0.8.0/omicwas/tests/testthat/testomicwas.R | 14 - 12 files changed, 263 insertions(+), 128 deletions(-)
Title: Genomic Annotation in Livestock for Positional Candidate LOci
Description: The accurate annotation of genes and Quantitative Trait Loci (QTLs) located within candidate markers and/or regions (haplotypes, windows, CNVs, etc) is a crucial step the most common genomic analyses performed in livestock, such as Genome-Wide Association Studies or transcriptomics. The Genomic Annotation in Livestock for positional candidate LOci (GALLO) is an R package designed to provide an intuitive and straightforward environment to annotate positional candidate genes and QTLs from high-throughput genetic studies in livestock. Moreover, GALLO allows the graphical visualization of gene and QTL annotation results, data comparison among different grouping factors (e.g., methods, breeds, tissues, statistical models, studies, etc.), and QTL enrichment in different livestock species including cattle, pigs, sheep, and chicken, among others.
Author: Pablo Fonseca [aut, cre],
Aroa Suarez-Vega [aut],
Gabriele Marras [aut],
Angela Cánovas [aut]
Maintainer: Pablo Fonseca <pfonseca@uoguelph.ca>
Diff between GALLO versions 0.99.0 dated 2020-09-01 and 1.0 dated 2020-10-08
DESCRIPTION | 10 ++-- MD5 | 10 ++-- inst/doc/GALLO.R | 6 -- inst/doc/GALLO.Rmd | 7 -- inst/doc/GALLO.html | 126 +++++++++++++++++++++++----------------------------- vignettes/GALLO.Rmd | 7 -- 6 files changed, 66 insertions(+), 100 deletions(-)
Title: Variance Stabilizing Transformations for Single Cell UMI Data
Description: A normalization method for single-cell UMI count data using a
variance stabilizing transformation. The transformation is based on a
negative binomial regression model with regularized parameters. As part of the
same regression framework, this package also provides functions for
batch correction, and data correction. See Hafemeister and Satija 2019
<doi:10.1186/s13059-019-1874-1> for more details.
Author: Christoph Hafemeister [aut, cre]
(<https://orcid.org/0000-0001-6365-8254>)
Maintainer: Christoph Hafemeister <christoph.hafemeister@nyu.edu>
Diff between sctransform versions 0.3 dated 2020-09-20 and 0.3.1 dated 2020-10-08
DESCRIPTION | 16 ++++++---- MD5 | 46 ++++++++++++++++--------------- NAMESPACE | 1 NEWS.md | 16 ++++++++++ R/RcppExports.R | 8 +---- R/denoise.R | 22 ++++++-------- R/differential_expression.R | 19 +++--------- R/fit.R | 31 ++++++++------------ R/plotting.R | 17 +++++------ R/utils.R | 55 +++++++++++++++++-------------------- R/vst.R | 48 ++++++++++++++------------------ README.md | 18 ++++++++---- man/compare_expression.Rd | 13 +------- man/correct.Rd | 4 +- man/correct_counts.Rd | 4 +- man/get_model_var.Rd | 8 ++--- man/get_residual_var.Rd | 10 +++--- man/get_residuals.Rd | 10 +++--- man/plot_model.Rd | 4 +- man/plot_model_pars.Rd | 6 ++-- man/vst.Rd | 19 ++++++------ src/Makevars |only src/Makevars.win |only src/RcppExports.cpp | 31 ++++++++------------ src/utils.cpp | 65 +++++++++++++++++++++++++++++--------------- 25 files changed, 237 insertions(+), 234 deletions(-)
Title: Delineating Temporal Dataset Shifts in Electronic Health Records
Description: Functions to delineate temporal dataset shifts in Electronic Health
Records through the projection and visualization of dissimilarities
among data temporal batches. This is done through the estimation of
data statistical distributions over time and their projection in
non-parametric statistical manifolds, uncovering the patterns of the
data latent temporal variability. 'EHRtemporalVariability' is
particularly suitable for multi-modal data and categorical variables
with a high number of values, common features of biomedical data where
traditional statistical process control or time-series methods may not
be appropriate. 'EHRtemporalVariability' allows you to explore and
identify dataset shifts through visual analytics formats such as
Data Temporal heatmaps and Information Geometric Temporal (IGT) plots.
An additional 'EHRtemporalVariability' Shiny app can be used to load
and explore the package results and even to allow the use of these
functions to those users non-experienced in R coding. (Sáez et al. 2020)
<doi:10.1093/gigascience/giaa079>.
Author: Carlos Sáez [aut, cre],
Alba Gutiérrez-Sacristán [aut],
Isaac Kohane [aut],
Juan M García-Gómez [aut],
Paul Avillach [aut],
Biomedical Data Science Lab, Universitat Politècnica de València
(Spain) [cph],
Department of Biomedical Informatics, Harvard Medical School [cph]
Maintainer: Carlos Sáez <carsaesi@upv.es>
Diff between EHRtemporalVariability versions 1.1.1 dated 2020-05-25 and 1.1.2 dated 2020-10-08
DESCRIPTION | 18 MD5 | 21 NEWS.md | 4 README.md | 8 build/vignette.rds |binary inst/doc/EHRtemporalVariability.R | 38 inst/doc/EHRtemporalVariability.Rmd | 52 - inst/doc/EHRtemporalVariability.html | 1283 +++++++++++-------------------- vignettes/EHRtemporalVariability.Rmd | 52 - vignettes/EHRtemporalVariability.md |only vignettes/EHRtemporalVariabilityHelp.pdf |binary vignettes/general-overview.bib | 17 12 files changed, 615 insertions(+), 878 deletions(-)
More information about EHRtemporalVariability at CRAN
Permanent link
Title: Dynamic Bayesian Network Learning and Inference
Description: Learning and inference over dynamic Bayesian networks of arbitrary
Markovian order. Extends some of the functionality offered by the 'bnlearn'
package to learn the networks from data and perform exact inference.
It offers two structure learning algorithms for dynamic Bayesian networks
and the possibility to perform forecasts of arbitrary length. A tool for
visualizing the structure of the net is also provided via the 'visNetwork'
package.
Author: David Quesada [aut, cre],
Gabriel Valverde [ctb]
Maintainer: David Quesada <dkesada@gmail.com>
Diff between dbnR versions 0.4.5 dated 2020-06-11 and 0.5.2 dated 2020-10-08
dbnR-0.4.5/dbnR/data/motor.rda |only dbnR-0.5.2/dbnR/DESCRIPTION | 20 +- dbnR-0.5.2/dbnR/MD5 | 75 +++++--- dbnR-0.5.2/dbnR/NEWS.md | 20 ++ dbnR-0.5.2/dbnR/R/RcppExports.R | 100 +++++++++++ dbnR-0.5.2/dbnR/R/dbn_inference.R | 6 dbnR-0.5.2/dbnR/R/dbn_learn.R | 86 --------- dbnR-0.5.2/dbnR/R/dbn_visualization.R | 3 dbnR-0.5.2/dbnR/R/motor_data.R | 2 dbnR-0.5.2/dbnR/R/mvn_exact_inference.R | 2 dbnR-0.5.2/dbnR/R/security_checks.R | 81 +++++++++ dbnR-0.5.2/dbnR/R/structure_learning_dmmhc.R |only dbnR-0.5.2/dbnR/R/structure_learning_psoho.R |only dbnR-0.5.2/dbnR/README.md | 49 +++-- dbnR-0.5.2/dbnR/data/motor.RData |only dbnR-0.5.2/dbnR/man/Causlist.Rd |only dbnR-0.5.2/dbnR/man/Particle.Rd |only dbnR-0.5.2/dbnR/man/Position.Rd |only dbnR-0.5.2/dbnR/man/PsoCtrl.Rd |only dbnR-0.5.2/dbnR/man/Velocity.Rd |only dbnR-0.5.2/dbnR/man/cl_to_arc_matrix_cpp.Rd |only dbnR-0.5.2/dbnR/man/create_blacklist.Rd | 2 dbnR-0.5.2/dbnR/man/create_causlist_cpp.Rd |only dbnR-0.5.2/dbnR/man/cte_times_vel_cpp.Rd |only dbnR-0.5.2/dbnR/man/dmmhc.Rd |only dbnR-0.5.2/dbnR/man/fold_dt.Rd | 52 +++--- dbnR-0.5.2/dbnR/man/fold_dt_rec.Rd | 54 +++--- dbnR-0.5.2/dbnR/man/forecast_ts.Rd | 2 dbnR-0.5.2/dbnR/man/init_list_cpp.Rd |only dbnR-0.5.2/dbnR/man/initialize_cl_cpp.Rd |only dbnR-0.5.2/dbnR/man/learn_dbn_struc.Rd | 7 dbnR-0.5.2/dbnR/man/merge_nets.Rd | 2 dbnR-0.5.2/dbnR/man/motor.Rd | 4 dbnR-0.5.2/dbnR/man/mvn_inference.Rd | 2 dbnR-0.5.2/dbnR/man/plot_network.Rd | 1 dbnR-0.5.2/dbnR/man/pos_minus_pos_cpp.Rd |only dbnR-0.5.2/dbnR/man/pos_plus_vel_cpp.Rd |only dbnR-0.5.2/dbnR/man/predict_dt.Rd | 4 dbnR-0.5.2/dbnR/man/psoho.Rd |only dbnR-0.5.2/dbnR/man/randomize_vl_cpp.Rd |only dbnR-0.5.2/dbnR/man/rename_nodes_cpp.Rd |only dbnR-0.5.2/dbnR/man/time_rename.Rd | 48 ++--- dbnR-0.5.2/dbnR/man/vel_plus_vel_cpp.Rd |only dbnR-0.5.2/dbnR/src/Makevars | 1 dbnR-0.5.2/dbnR/src/RcppExports.cpp | 147 ++++++++++++++++- dbnR-0.5.2/dbnR/src/gauss_transform.cpp | 53 +++--- dbnR-0.5.2/dbnR/src/include/gauss_transform.h | 10 + dbnR-0.5.2/dbnR/src/include/psoho_structure_learning.h |only dbnR-0.5.2/dbnR/src/structure_learning_psoho.cpp |only dbnR-0.5.2/dbnR/tests/testthat/test-position.R |only dbnR-0.5.2/dbnR/tests/testthat/test-velocity.R |only 51 files changed, 573 insertions(+), 260 deletions(-)
Title: Functions for Base Types and Core R and 'Tidyverse' Features
Description: A toolbox for working with base types, core R features
like the condition system, and core 'Tidyverse' features like tidy
evaluation.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between rlang versions 0.4.7 dated 2020-07-09 and 0.4.8 dated 2020-10-08
rlang-0.4.7/rlang/tools |only rlang-0.4.8/rlang/DESCRIPTION | 9 rlang-0.4.8/rlang/MD5 | 141 +++++----- rlang-0.4.8/rlang/NEWS.md | 22 + rlang-0.4.8/rlang/R/attr.R | 2 rlang-0.4.8/rlang/R/cnd-abort.R | 99 ++++--- rlang-0.4.8/rlang/R/cnd-entrace.R | 4 rlang-0.4.8/rlang/R/cnd-error.R | 12 rlang-0.4.8/rlang/R/env.R | 6 rlang-0.4.8/rlang/R/lifecycle-retired.R | 8 rlang-0.4.8/rlang/R/node.R | 2 rlang-0.4.8/rlang/R/state.R | 7 rlang-0.4.8/rlang/R/trace.R | 94 ++++-- rlang-0.4.8/rlang/build/rlang.pdf |binary rlang-0.4.8/rlang/man/env.Rd | 4 rlang-0.4.8/rlang/man/is_interactive.Rd | 4 rlang-0.4.8/rlang/src/export/exported-tests.c | 2 rlang-0.4.8/rlang/src/export/exported.c | 6 rlang-0.4.8/rlang/src/export/init.c | 11 rlang-0.4.8/rlang/src/internal/arg.c | 6 rlang-0.4.8/rlang/src/internal/attr.c | 19 - rlang-0.4.8/rlang/src/internal/call.c | 2 rlang-0.4.8/rlang/src/internal/dots.c | 18 - rlang-0.4.8/rlang/src/internal/env-binding.c | 6 rlang-0.4.8/rlang/src/internal/eval-tidy.c | 26 - rlang-0.4.8/rlang/src/internal/expr-interp.c | 2 rlang-0.4.8/rlang/src/internal/quo.c | 4 rlang-0.4.8/rlang/src/lib/attrs.c | 49 +-- rlang-0.4.8/rlang/src/lib/attrs.h | 60 ++-- rlang-0.4.8/rlang/src/lib/cnd.c | 2 rlang-0.4.8/rlang/src/lib/env-binding.c | 2 rlang-0.4.8/rlang/src/lib/env.c | 4 rlang-0.4.8/rlang/src/lib/env.h | 4 rlang-0.4.8/rlang/src/lib/eval.c | 44 +-- rlang-0.4.8/rlang/src/lib/fn.c | 2 rlang-0.4.8/rlang/src/lib/formula.c | 6 rlang-0.4.8/rlang/src/lib/node.c | 15 - rlang-0.4.8/rlang/src/lib/node.h | 95 +++--- rlang-0.4.8/rlang/src/lib/sym.c | 52 +-- rlang-0.4.8/rlang/src/lib/sym.h | 42 +- rlang-0.4.8/rlang/src/lib/vec-chr.c | 4 rlang-0.4.8/rlang/src/lib/vec.h | 3 rlang-0.4.8/rlang/src/version.c | 2 rlang-0.4.8/rlang/tests/testthat/fixtures/error-entrace.R |only rlang-0.4.8/rlang/tests/testthat/output-cnd-abort-parent-trace.txt | 16 + rlang-0.4.8/rlang/tests/testthat/test-c-api.R | 12 rlang-0.4.8/rlang/tests/testthat/test-cnd-abort.R | 25 + rlang-0.4.8/rlang/tests/testthat/test-cnd-entrace.R | 19 + rlang-0.4.8/rlang/tests/testthat/test-cnd-error-empty.txt | 2 rlang-0.4.8/rlang/tests/testthat/test-cnd-error-parent-default.txt | 2 rlang-0.4.8/rlang/tests/testthat/test-cnd-error-parent.txt | 21 - rlang-0.4.8/rlang/tests/testthat/test-cnd-error.R | 3 rlang-0.4.8/rlang/tests/testthat/test-cnd-error.txt | 1 rlang-0.4.8/rlang/tests/testthat/test-entrace.txt |only rlang-0.4.8/rlang/tests/testthat/test-env.R | 4 rlang-0.4.8/rlang/tests/testthat/test-trace-collapse-magrittr-before-after1.txt | 27 - rlang-0.4.8/rlang/tests/testthat/test-trace-collapse-magrittr-before-after2.txt | 28 - rlang-0.4.8/rlang/tests/testthat/test-trace-collapse-magrittr-before-after3.txt | 33 -- rlang-0.4.8/rlang/tests/testthat/test-trace-collapse-magrittr-children.txt | 36 -- rlang-0.4.8/rlang/tests/testthat/test-trace-collapse-magrittr-complete-leading1.txt | 19 - rlang-0.4.8/rlang/tests/testthat/test-trace-collapse-magrittr-complete-leading2.txt | 20 - rlang-0.4.8/rlang/tests/testthat/test-trace-collapse-magrittr-complete1.txt | 18 - rlang-0.4.8/rlang/tests/testthat/test-trace-collapse-magrittr-complete2.txt | 19 - rlang-0.4.8/rlang/tests/testthat/test-trace-collapse-magrittr-incomplete-leading1.txt | 11 rlang-0.4.8/rlang/tests/testthat/test-trace-collapse-magrittr-incomplete-leading2.txt | 23 - rlang-0.4.8/rlang/tests/testthat/test-trace-collapse-magrittr-incomplete.txt | 22 - rlang-0.4.8/rlang/tests/testthat/test-trace-collapse-magrittr.txt | 20 - rlang-0.4.8/rlang/tests/testthat/test-trace-collapse-magrittr2.txt | 20 - rlang-0.4.8/rlang/tests/testthat/test-trace-collapse-magrittr3.txt | 28 - rlang-0.4.8/rlang/tests/testthat/test-trace-collapsed1.txt | 18 - rlang-0.4.8/rlang/tests/testthat/test-trace-collapsed2.txt | 8 rlang-0.4.8/rlang/tests/testthat/test-trace-print.txt | 8 rlang-0.4.8/rlang/tests/testthat/test-trace.R | 30 +- 73 files changed, 719 insertions(+), 676 deletions(-)
Title: Multi-Locus Random-SNP-Effect Mixed Linear Model Tools for
Genome-Wide Association Study with Graphical User Interface
Description: Conduct multi-locus genome-wide association study under the framework of multi-locus random-SNP-effect mixed linear model (mrMLM). First, each marker on the genome is scanned. Bonferroni correction is replaced by a less stringent selection criterion for significant test. Then, all the markers that are potentially associated with the trait are included in a multi-locus genetic model, their effects are estimated by empirical Bayes and all the nonzero effects were further identified by likelihood ratio test for true QTL. Wen YJ, Zhang H, Ni YL, Huang B, Zhang J, Feng JY, Wang SB, Dunwell JM, Zhang YM, Wu R (2018) <doi:10.1093/bib/bbw145>.
Author: Zhang Ya-Wen, Li Pei, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Diff between mrMLM.GUI versions 4.0.1 dated 2020-09-29 and 4.0.2 dated 2020-10-08
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- R/RcppExports.R | 2 +- R/mrMLM.GUI.R | 2 +- inst/doc/Instruction.pdf |binary man/mrMLM.GUI-package.Rd | 4 ++-- src/RcppExports.cpp | 4 +--- src/multiplication_speed.cpp | 5 +---- 8 files changed, 19 insertions(+), 24 deletions(-)
Title: Multi-Locus Random-SNP-Effect Mixed Linear Model Tools for
Genome-Wide Association Study
Description: Conduct multi-locus genome-wide association study under the framework of multi-locus random-SNP-effect mixed linear model (mrMLM). First, each marker on the genome is scanned. Bonferroni correction is replaced by a less stringent selection criterion for significant test. Then, all the markers that are potentially associated with the trait are included in a multi-locus genetic model, their effects are estimated by empirical Bayes and all the nonzero effects were further identified by likelihood ratio test for true QTL. Wen YJ, Zhang H, Ni YL, Huang B, Zhang J, Feng JY, Wang SB, Dunwell JM, Zhang YM, Wu R (2018) <doi:10.1093/bib/bbw145>.
Author: Zhang Ya-Wen, Li Pei, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Diff between mrMLM versions 4.0.1 dated 2020-09-29 and 4.0.2 dated 2020-10-08
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ R/RcppExports.R | 3 ++- inst/doc/Instruction.pdf |binary man/mrMLM.Rd | 6 +++--- src/RcppExports.cpp | 4 +--- src/multiplication_speed.cpp | 5 +---- 7 files changed, 19 insertions(+), 23 deletions(-)
Title: An Extended Mixed-Effects Framework for Meta-Analysis
Description: A collection of functions to perform various meta-analytical models
through a unified mixed-effects framework, including standard univariate
fixed and random-effects meta-analysis and meta-regression, and non-standard
extensions such as multivariate, multilevel, longitudinal, and dose-response
models.
Author: Antonio Gasparrini [aut, cre],
Francesco Sera [aut]
Maintainer: Antonio Gasparrini <antonio.gasparrini@lshtm.ac.uk>
Diff between mixmeta versions 1.0.8 dated 2020-03-09 and 1.1.0 dated 2020-10-08
DESCRIPTION | 8 - MD5 | 23 ++--- NAMESPACE | 201 ++++++++++++++++++++++++------------------------- NEWS.md | 17 ++++ R/extractAIC.mixmeta.R | 2 R/formula.mixmeta.R |only R/getContrXlev.R | 4 R/getFixTerms.R | 6 - R/getFullFormula.R | 7 - R/mixmeta.R | 10 +- R/terms.mixmeta.R | 41 ++++----- inst/NEWS | 17 ++++ man/mixmeta.control.Rd | 2 13 files changed, 184 insertions(+), 154 deletions(-)
Title: Sequential and Batch Change Detection Using Parametric and
Nonparametric Methods
Description: Sequential and batch change detection for univariate data streams, using the change point model framework. Functions are provided to allow nonparametric distribution-free change detection in the mean, variance, or general distribution of a given sequence of observations. Parametric change detection methods are also provided for Gaussian, Bernoulli and Exponential sequences. Both the batch (Phase I) and sequential (Phase II) settings are supported, and the sequences may contain either a single or multiple change points. A full description of this package is available in Ross, G.J (2015) - "Parametric and nonparametric sequential change detection in R" available at <https://www.jstatsoft.org/article/view/v066i03>.
Author: Gordon J. Ross
Maintainer: Gordon J. Ross <gordon@gordonjross.co.uk>
Diff between cpm versions 2.2 dated 2015-07-27 and 2.3 dated 2020-10-08
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/detectChangePoint.R | 2 +- R/detectChangePointBatch.R | 4 ++-- R/makeChangePointModel.R | 2 +- R/processStream.R | 2 +- inst/CITATION | 2 +- 7 files changed, 17 insertions(+), 17 deletions(-)
Title: Black-Box Optimization Toolkit
Description: Provides a common framework for optimization of
black-box functions for other packages, e.g. 'mlr3'. It offers various
optimization methods e.g. grid search, random search and generalized
simulated annealing.
Author: Marc Becker [cre, aut] (<https://orcid.org/0000-0002-8115-0400>),
Jakob Richter [aut] (<https://orcid.org/0000-0003-4481-5554>),
Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>),
Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>),
Martin Binder [aut],
Olaf Mersmann [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between bbotk versions 0.2.1 dated 2020-09-05 and 0.2.2 dated 2020-10-08
bbotk-0.2.1/bbotk/inst/references.bib |only bbotk-0.2.2/bbotk/DESCRIPTION | 17 bbotk-0.2.2/bbotk/MD5 | 48 +- bbotk-0.2.2/bbotk/NAMESPACE | 3 bbotk-0.2.2/bbotk/NEWS.md | 6 bbotk-0.2.2/bbotk/R/Archive.R | 7 bbotk-0.2.2/bbotk/R/ObjectiveRFun.R | 26 + bbotk-0.2.2/bbotk/R/OptimInstance.R | 4 bbotk-0.2.2/bbotk/R/OptimizerCmaes.R |only bbotk-0.2.2/bbotk/R/OptimizerGenSA.R | 4 bbotk-0.2.2/bbotk/R/OptimizerNLoptr.R | 2 bbotk-0.2.2/bbotk/R/OptimizerRandomSearch.R | 2 bbotk-0.2.2/bbotk/R/TerminatorStagnationBatch.R | 2 bbotk-0.2.2/bbotk/R/bibentries.R |only bbotk-0.2.2/bbotk/R/helper.R | 15 bbotk-0.2.2/bbotk/build/partial.rdb |binary bbotk-0.2.2/bbotk/build/vignette.rds |binary bbotk-0.2.2/bbotk/inst/doc/bbotk.html | 314 ++++++++------ bbotk-0.2.2/bbotk/man/ObjectiveRFun.Rd | 27 + bbotk-0.2.2/bbotk/man/OptimizerNLoptr.Rd | 4 bbotk-0.2.2/bbotk/man/mlr_optimizers_cmaes.Rd |only bbotk-0.2.2/bbotk/man/mlr_optimizers_gensa.Rd | 11 bbotk-0.2.2/bbotk/man/mlr_optimizers_random_search.Rd | 5 bbotk-0.2.2/bbotk/man/mlr_terminators_stagnation_batch.Rd | 4 bbotk-0.2.2/bbotk/man/mult_max_to_min.Rd |only bbotk-0.2.2/bbotk/tests/testthat/helper.R | 6 bbotk-0.2.2/bbotk/tests/testthat/test_Optimizer.R | 2 bbotk-0.2.2/bbotk/tests/testthat/test_OptimizerCmaes.R |only 28 files changed, 335 insertions(+), 174 deletions(-)
Title: 'Rcpp' Implementation of 'FSelector' Entropy-Based Feature
Selection Algorithms with a Sparse Matrix Support
Description: 'Rcpp' (free of 'Java'/'Weka') implementation of 'FSelector' entropy-based feature selection
algorithms based on an MDL discretization (Fayyad U. M., Irani K. B.: Multi-Interval Discretization of Continuous-Valued Attributes for Classification Learning.
In 13'th International Joint Conference on Uncertainly in Artificial Intelligence (IJCAI93), pages 1022-1029, Chambery, France, 1993.) <https://www.ijcai.org/Proceedings/93-2/Papers/022.pdf>
with a sparse matrix support.
Author: Zygmunt Zawadzki [aut, cre],
Marcin Kosinski [aut],
Krzysztof Slomczynski [ctb],
Damian Skrzypiec [ctb],
Patrick Schratz [ctb] (<https://orcid.org/0000-0003-0748-6624>)
Maintainer: Zygmunt Zawadzki <zygmunt@zstat.pl>
Diff between FSelectorRcpp versions 0.3.3 dated 2020-01-24 and 0.3.7 dated 2020-10-08
DESCRIPTION | 19 +- MD5 | 31 ++- NAMESPACE | 1 R/information_gain.R | 22 +- R/relief.R |only build/vignette.rds |binary inst/doc/benchmarks_discretize.R | 64 ++++---- inst/doc/benchmarks_discretize.Rmd | 16 +- inst/doc/benchmarks_discretize.html | 288 +++++++++++++++++++----------------- inst/doc/get_started.Rmd | 6 inst/doc/get_started.html | 170 +++++++++++---------- inst/doc/integer-variables.html | 230 +++++++++++++++------------- man/information_gain.Rd | 5 man/relief.Rd |only tests/testthat/test-relief.R |only vignettes/RJreferences.bib | 32 ++-- vignettes/benchmarks_discretize.Rmd | 16 +- vignettes/get_started.Rmd | 6 18 files changed, 485 insertions(+), 421 deletions(-)
Title: Neat and Painless Statistical Reporting
Description: User-friendly, clear and simple statistics, primarily for
publication in psychological science. The main functions are wrappers for
other packages, but there are various additions as well. Every relevant step
from data aggregation to reportable printed statistics is covered for basic
experimental designs.
Author: Gáspár Lukács [aut, cre] (<https://orcid.org/0000-0001-9401-4830>),
Bennett Kleinberg [ctb] (<https://orcid.org/0000-0003-1658-9086>),
Johnny van Doorn [ctb] (<https://orcid.org/0000-0003-0270-096X>)
Maintainer: Gáspár Lukács <lkcsgaspar@gmail.com>
Diff between neatStats versions 1.4.2 dated 2020-07-11 and 1.5.1 dated 2020-10-08
DESCRIPTION | 12 - MD5 | 68 ++++-- NAMESPACE | 7 R/aggr_neat.R | 32 ++- R/anova_neat.R | 364 ++++++++++++++++++++++++++----------- R/ci_from_p.R |only R/corr_neat.R | 8 R/dems_neat.R | 106 ++++++---- R/enum.R |only R/excl_neat.R | 27 +- R/internal.R | 290 ++++++++++++++++++++--------- R/mean_ci.R | 2 R/norm_tests.R |only R/peek_neat.R |only R/plot_neat.R | 529 ++++++++++++++++++++++++++++++++++++++++++++---------- R/props_neat.R | 37 +-- R/rbind_loop.R |only R/read_dir.R |only R/ro.R | 36 +++ R/roc_neat.R | 71 ++++++- R/se.R | 2 R/t_neat.R | 259 ++++++++++++++++++++------ R/var_tests.R |only README.md | 112 +++++++---- build/partial.rdb |binary man/aggr_neat.Rd | 6 man/anova_neat.Rd | 146 ++++++++++++-- man/ci_from_p.Rd |only man/corr_neat.Rd | 8 man/dems_neat.Rd | 72 +++++-- man/enum.Rd |only man/excl_neat.Rd | 3 man/norm_tests.Rd |only man/peek_neat.Rd |only man/plot_neat.Rd | 124 +++++++++--- man/props_neat.Rd | 35 +-- man/rbind_loop.Rd |only man/read_dir.Rd |only man/ro.Rd | 24 ++ man/roc_neat.Rd | 12 - man/t_neat.Rd | 91 +++++++-- man/var_tests.Rd |only 42 files changed, 1845 insertions(+), 638 deletions(-)
Title: Kinetic Evaluation of Chemical Degradation Data
Description: Calculation routines based on the FOCUS Kinetics Report (2006,
2014). Includes a function for conveniently defining differential equation
models, model solution based on eigenvalues if possible or using numerical
solvers. If a C compiler (on windows: 'Rtools') is installed, differential
equation models are solved using automatically generated C functions. Please
note that no warranty is implied for correctness of results or fitness for a
particular purpose.
Author: Johannes Ranke [aut, cre, cph]
(<https://orcid.org/0000-0003-4371-6538>),
Katrin Lindenberger [ctb],
René Lehmann [ctb],
Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Diff between mkin versions 0.9.50.2 dated 2020-05-12 and 0.9.50.3 dated 2020-10-08
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Title: Vehicular Emissions by Top-Down Methods
Description: Creates emissions for use in air quality models. Vehicular emissions
are estimated by a top-down approach, total emissions are calculated using the
statistical description of the fleet of vehicles, the emission is spatially
distributed according to satellite images or openstreetmap data
<https://www.openstreetmap.org> and then distributed temporarily
(Vara-Vela et al., 2016, <doi:10.5194/acp-16-777-2016>).
Author: Daniel Schuch [aut, cre] (<https://orcid.org/0000-0001-5977-4519>),
Sergio Ibarra-Espinosa [aut] (<https://orcid.org/0000-0002-3162-1905>)
Maintainer: Daniel Schuch <schuch@usp.br>
Diff between EmissV versions 0.665.2.1 dated 2020-04-01 and 0.665.3.0 dated 2020-10-08
EmissV-0.665.2.1/EmissV/inst/extdata/dmsp_hi-res.tiff |only EmissV-0.665.3.0/EmissV/DESCRIPTION | 12 ++-- EmissV-0.665.3.0/EmissV/MD5 | 35 ++++++------ EmissV-0.665.3.0/EmissV/NAMESPACE | 2 EmissV-0.665.3.0/EmissV/NEWS.md | 3 + EmissV-0.665.3.0/EmissV/R/areaSouce.R | 2 EmissV-0.665.3.0/EmissV/R/rasterSource.R | 2 EmissV-0.665.3.0/EmissV/R/read.R | 50 ++++++++++++------ EmissV-0.665.3.0/EmissV/inst/CITATION | 2 EmissV-0.665.3.0/EmissV/man/areaSource.Rd | 6 +- EmissV-0.665.3.0/EmissV/man/emission.Rd | 4 + EmissV-0.665.3.0/EmissV/man/emissionFactor.Rd | 4 + EmissV-0.665.3.0/EmissV/man/perfil.Rd | 4 + EmissV-0.665.3.0/EmissV/man/plumeRise.Rd | 4 + EmissV-0.665.3.0/EmissV/man/rasterSource.Rd | 2 EmissV-0.665.3.0/EmissV/man/read.Rd | 20 ++++--- EmissV-0.665.3.0/EmissV/man/species.Rd | 4 + EmissV-0.665.3.0/EmissV/man/totalEmission.Rd | 4 + EmissV-0.665.3.0/EmissV/man/totalVOC.Rd | 4 + 19 files changed, 105 insertions(+), 59 deletions(-)
Title: Antimicrobial Resistance Analysis
Description: Functions to simplify the analysis and prediction of Antimicrobial
Resistance (AMR) and to work with microbial and antimicrobial properties by
using evidence-based methods, like those defined by Leclercq et al. (2013)
<doi:10.1111/j.1469-0691.2011.03703.x> and the Clinical and Laboratory
Standards Institute (2014) <isbn: 1-56238-899-1>.
Author: Matthijs S. Berends [aut, cre]
(<https://orcid.org/0000-0001-7620-1800>),
Christian F. Luz [aut, ctb] (<https://orcid.org/0000-0001-5809-5995>),
Alexander W. Friedrich [aut, ths]
(<https://orcid.org/0000-0003-4881-038X>),
Bhanu N. M. Sinha [aut, ths] (<https://orcid.org/0000-0003-1634-0010>),
Casper J. Albers [aut, ths] (<https://orcid.org/0000-0002-9213-6743>),
Corinna Glasner [aut, ths] (<https://orcid.org/0000-0003-1241-1328>),
Judith M. Fonville [ctb],
Erwin E. A. Hassing [ctb],
Eric H. L. C. M. Hazenberg [ctb],
Gwen Knight [ctb],
Annick Lenglet [ctb],
Bart C. Meijer [ctb],
Sofia Ny [ctb],
Dennis Souverein [ctb],
Anthony Underwood [ctb]
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>
Diff between AMR versions 1.3.0 dated 2020-07-31 and 1.4.0 dated 2020-10-08
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Title: Bindings for the 'Geospatial' Data Abstraction Library
Description: Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4) and access to projection/transformation operations from the 'PROJ' library. Use is made of classes defined in the 'sp' package. Raster and vector map data can be imported into R, and raster and vector 'sp' objects exported. The 'GDAL' and 'PROJ' libraries are external to the package, and, when installing the package from source, must be correctly installed first; it is important that 'GDAL' < 3 be matched with 'PROJ' < 6. From 'rgdal' 1.5-8, installed with to 'GDAL' >=3, 'PROJ' >=6 and 'sp' >= 1.4, coordinate reference systems use 'WKT2_2019' strings, not 'PROJ' strings. 'Windows' and 'macOS' binaries (including 'GDAL', 'PROJ' and their dependencies) are provided on 'CRAN'.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>),
Tim Keitt [aut],
Barry Rowlingson [aut, ctb],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Even Rouault [cph, ctb],
Frank Warmerdam [cph, ctb],
Jeroen Ooms [ctb],
Colin Rundel [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 1.5-16 dated 2020-08-07 and 1.5-17 dated 2020-10-08
ChangeLog | 91 ++++++ DESCRIPTION | 8 MD5 | 67 ++-- NAMESPACE | 4 R/AAA.R | 1 R/Class-CRSx.R | 50 ++- R/list_coordOps.R | 13 R/ogr_sp.R | 37 ++ R/project.R | 12 configure | 23 + configure.ac | 5 inst/ChangeLog | 91 ++++++ inst/SVN_VERSION | 2 inst/doc/CRS_projections_transformations.R | 49 ++- inst/doc/CRS_projections_transformations.Rmd | 86 +++++- inst/doc/CRS_projections_transformations.html | 357 +++++++++++++++++++------- inst/doc/OGR_shape_encoding.pdf |binary inst/doc/PROJ6_GDAL3.R | 2 inst/doc/PROJ6_GDAL3.Rmd | 2 inst/doc/PROJ6_GDAL3.html | 173 ++++++------ inst/misc/GGHB.IG_CRS.rda |only man/CRS-class.Rd | 10 man/list_coordOps.Rd | 12 man/showWKT.Rd | 26 + man/spTransform-methods.Rd | 8 src/init.c | 5 src/ogr_proj.cpp | 26 + src/proj6.cpp | 119 ++++++++ src/projectit.cpp | 14 - src/rgdal.h | 5 tests/srs_rendering.Rout.save | 18 - tests/test_enforce_xy.R |only tests/test_enforce_xy.Rout.save |only tests/test_proj.Rout.save | 4 vignettes/CRS_projections_transformations.Rmd | 86 +++++- vignettes/PROJ6_GDAL3.Rmd | 2 36 files changed, 1098 insertions(+), 310 deletions(-)
Title: Zebra-Striped Tables in LaTeX and HTML Formats
Description: Makes zebra-striped tables (tables with alternating row colors)
in LaTeX and HTML formats easily from a data.frame, matrix, lm, aov, anova,
glm, coxph, nls, fitdistr, mytable and cbind.mytable objects.
Author: Keon-Woong Moon [aut, cre]
Maintainer: Keon-Woong Moon <cardiomoon@gmail.com>
Diff between ztable versions 0.2.0 dated 2018-07-22 and 0.2.2 dated 2020-10-08
DESCRIPTION | 17 MD5 | 71 - NAMESPACE | 3 NEWS | 14 R/makeHeatmap.R | 4 R/print.ztable.html.R | 19 R/ztable.R | 4 R/ztable.mytable.R | 4 R/ztable2.R | 11 R/ztable2flextable.R | 4 R/zzz.R | 4 README.md | 2 build/vignette.rds |binary inst/doc/heatmapTable.R | 28 inst/doc/heatmapTable.Rmd | 6 inst/doc/heatmapTable.html | 732 +++++++++----- inst/doc/ztable.R | 88 - inst/doc/ztable.Rmd | 12 inst/doc/ztable.html | 2182 ++++++++++++++++++-------------------------- inst/doc/ztable_update.R | 36 inst/doc/ztable_update.Rmd | 4 inst/doc/ztable_update.html | 856 +++++++++++------ man/addCellColor.Rd | 14 man/addrgroup.Rd | 10 man/dot-onAttach.Rd |only man/gradientColor.Rd | 3 man/make.cell.color.Rd | 11 man/makeHeatmap.Rd | 16 man/totalLeft.Rd | 4 man/update_ztable.Rd | 62 - man/zcolors.Rd | 6 man/ztable2flextable.Rd | 4 man/ztable2viewer.Rd | 4 man/ztable_sub.Rd | 55 - vignettes/heatmapTable.Rmd | 6 vignettes/ztable.Rmd | 12 vignettes/ztable_update.Rmd | 4 37 files changed, 2288 insertions(+), 2024 deletions(-)
Title: Sparse and Dense Multidimensional Array Storage Engine for Data
Science
Description: The data science storage engine 'TileDB' introduces a
powerful on-disk format for multi-dimensional arrays. It supports
dense and sparse arrays, dataframes and key-values stores, cloud
storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression,
encryption and checksum filters, uses a fully multi-threaded
implementation, supports parallel I/O, data versioning ('time
travel'), metadata and groups. It is implemented as an embeddable
cross-platform C++ library with APIs from several languages, and
integrations.
Author: TileDB, Inc.
Maintainer: Dirk Eddelbuettel <dirk@tiledb.com>
Diff between tiledb versions 0.8.0 dated 2020-09-03 and 0.8.1 dated 2020-10-08
DESCRIPTION | 11 ++++++--- MD5 | 48 +++++++++++++++++++++--------------------- R/Config.R | 2 - R/Ctx.R | 2 - R/Metadata.R | 32 +++++++++++++++------------- R/Query.R | 2 - R/VFS.R | 4 +-- README.md | 24 +++++++++++++-------- configure | 22 +++++++++++-------- configure.ac | 22 +++++++++++-------- inst/NEWS.md | 20 +++++++++++++++++ inst/doc/introduction.Rmd | 3 -- inst/doc/introduction.html | 16 ++++++++++---- inst/tinytest/test_attr.R | 5 +++- inst/tinytest/test_ctx.R | 3 ++ inst/tinytest/test_metadata.R | 36 +++++++++++++++---------------- man/tiledb_config.Rd | 2 - man/tiledb_ctx.Rd | 2 - man/tiledb_query.Rd | 2 - man/tiledb_vfs.Rd | 4 +-- src/Makevars.win | 2 - tools/fetchTileDBLib.R | 7 ++++-- tools/fetchTileDBSrc.R | 2 - tools/winlibs.R | 4 +-- vignettes/introduction.Rmd | 3 -- 25 files changed, 168 insertions(+), 112 deletions(-)
Title: Extract and Tidy Canadian 'Hydrometric' Data
Description: Provides functions to access historical and real-time national 'hydrometric'
data from Water Survey of Canada data sources (<https://dd.weather.gc.ca/hydrometric/csv/> and
<https://collaboration.cmc.ec.gc.ca/cmc/hydrometrics/www/>) and then applies tidy data principles.
Author: Sam Albers [aut, cre] (<https://orcid.org/0000-0002-9270-7884>),
David Hutchinson [ctb],
Dewey Dunnington [ctb],
Ryan Whaley [ctb],
Province of British Columbia [cph],
Luke Winslow [rev] (Reviewed for rOpenSci),
Laura DeCicco [rev] (Reviewed for rOpenSci)
Maintainer: Sam Albers <sam.albers@gov.bc.ca>
Diff between tidyhydat versions 0.5.0 dated 2019-12-02 and 0.5.1 dated 2020-10-08
DESCRIPTION | 14 - MD5 | 120 +++++----- NAMESPACE | 2 NEWS.md | 8 R/download.R | 2 R/hy_daily.R | 10 R/realtime-classes.R | 4 R/tidyhydat-package.R | 8 R/utils-realtime.R | 2 R/utils.R | 2 README.md | 48 +--- build/vignette.rds |binary data/allstations.rda |binary data/hy_data_symbols.rda |binary data/hy_data_types.rda |binary inst/doc/tidyhydat_an_introduction.Rmd | 2 inst/doc/tidyhydat_an_introduction.html | 253 +++++++++++++++------- inst/doc/tidyhydat_example_analysis.R | 4 inst/doc/tidyhydat_example_analysis.Rmd | 20 - inst/doc/tidyhydat_example_analysis.html | 343 +++++++++++++++++++------------ inst/doc/tidyhydat_hydat_db.Rmd | 4 inst/doc/tidyhydat_hydat_db.html | 227 ++++++++++++++------ inst/test_db/tinyhydat.sqlite3 |binary man/allstations.Rd | 62 ++--- man/figures/README-unnamed-chunk-7-1.png |binary man/hy_annual_stats.Rd | 180 ++++++++-------- man/hy_daily.Rd | 156 +++++++------- man/hy_daily_flows.Rd | 182 ++++++++-------- man/hy_daily_levels.Rd | 180 ++++++++-------- man/hy_data_symbols.Rd | 100 ++++----- man/hy_data_types.Rd | 100 ++++----- man/hy_dir.Rd | 38 +-- man/hy_monthly_flows.Rd | 180 ++++++++-------- man/hy_monthly_levels.Rd | 178 ++++++++-------- man/hy_sed_daily_loads.Rd | 164 +++++++------- man/hy_sed_daily_suscon.Rd | 174 +++++++-------- man/hy_sed_monthly_loads.Rd | 174 +++++++-------- man/hy_sed_monthly_suscon.Rd | 172 +++++++-------- man/hy_sed_samples.Rd | 190 ++++++++--------- man/hy_sed_samples_psd.Rd | 166 +++++++-------- man/hy_src.Rd | 104 ++++----- man/hy_stations.Rd | 200 +++++++++--------- man/hy_stn_data_coll.Rd | 156 +++++++------- man/hy_stn_data_range.Rd | 152 ++++++------- man/hy_stn_datum_conv.Rd | 88 ++++--- man/hy_stn_datum_unrelated.Rd | 88 ++++--- man/hy_stn_op_schedule.Rd | 150 ++++++------- man/hy_stn_regulation.Rd | 160 +++++++------- man/hy_stn_remarks.Rd | 88 ++++--- man/pull_station_number.Rd | 56 ++--- man/realtime_add_local_datetime.Rd | 60 ++--- man/realtime_daily_mean.Rd | 46 ++-- man/realtime_dd.Rd | 106 ++++----- man/realtime_stations.Rd | 80 +++---- man/reexports.Rd | 30 +- man/tidyhydat-package.Rd | 12 - tests/testthat/test_download_realtime.R | 7 tests/testthat/test_station_choice.R | 2 vignettes/tidyhydat_an_introduction.Rmd | 2 vignettes/tidyhydat_example_analysis.Rmd | 20 - vignettes/tidyhydat_hydat_db.Rmd | 4 61 files changed, 2702 insertions(+), 2378 deletions(-)
Title: Sunburst 'Htmlwidget'
Description: Make interactive 'd3.js' sequence sunburst diagrams in R with the
convenience and infrastructure of an 'htmlwidget'.
Author: Mike Bostock [aut, cph] (d3.js library, http://d3js.org),
Kerry Rodden [aut, cph] (sequences library in htmlwidgets/lib,
https://gist.github.com/kerryrodden/7090426),
Kevin Warne [aut, cph] (d2b sunburst library in htmlwidgets/lib,
https://github.com/d2bjs/d2b),
Kent Russell [aut, cre] (R interface),
Florian Breitwieser [ctb] (R interface),
CJ Yetman [ctb] (R interface, <https://orcid.org/0000-0001-5099-9500>)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>
Diff between sunburstR versions 2.1.4 dated 2020-07-06 and 2.1.5 dated 2020-10-08
DESCRIPTION | 8 ++++---- MD5 | 15 ++++++++------- NEWS.md | 4 ++++ R/converters.R | 12 ++++++++++-- README.md | 4 ++-- inst/doc/sunburst-2-0-0.R | 12 ++++++------ inst/doc/sunburst-2-0-0.html | 22 +++++++++++++--------- inst/htmlwidgets/sund2b.js | 4 ++++ tests/testthat/test-conversion.R |only 9 files changed, 51 insertions(+), 30 deletions(-)
Title: Class and Methods for Hyperspectral Data
Description: Input/Output, processing and visualization of spectra taken with different spectrometers, including SVC (Spectra Vista), ASD and PSR (Spectral Evolution). Implements an S3 class 'spectra' that other packages can build on. Provides methods to access, plot, manipulate, splice sensor overlap, vector normalize and smooth spectra.
Author: Jose Eduardo Meireles [aut, cre],
Anna K. Schweiger [aut],
Jeannine Cavender-Bares [aut]
Maintainer: Jose Eduardo Meireles <jemeireles@gmail.com>
Diff between spectrolab versions 0.0.9 dated 2020-06-09 and 0.0.10 dated 2020-10-08
spectrolab-0.0.10/spectrolab/DESCRIPTION | 13 spectrolab-0.0.10/spectrolab/MD5 | 170 ++++------ spectrolab-0.0.10/spectrolab/NAMESPACE | 11 spectrolab-0.0.10/spectrolab/NEWS.md | 12 spectrolab-0.0.10/spectrolab/R/conversion.R | 18 - spectrolab-0.0.10/spectrolab/R/data.R | 2 spectrolab-0.0.10/spectrolab/R/descrip_summary_overloads.R | 36 -- spectrolab-0.0.10/spectrolab/R/getters_and_setters.R | 65 --- spectrolab-0.0.10/spectrolab/R/graveyard.R |only spectrolab-0.0.10/spectrolab/R/internal_utils.R | 47 -- spectrolab-0.0.10/spectrolab/R/match_sensors.R | 49 -- spectrolab-0.0.10/spectrolab/R/math_operator_overloads.R | 4 spectrolab-0.0.10/spectrolab/R/plotting_functions.R | 12 spectrolab-0.0.10/spectrolab/R/query.R | 2 spectrolab-0.0.10/spectrolab/R/read_spectra.R | 6 spectrolab-0.0.10/spectrolab/R/spectrolab.R | 3 spectrolab-0.0.10/spectrolab/R/stats_function_overloads.R | 20 - spectrolab-0.0.10/spectrolab/R/transform_spectra.R | 148 ++------ spectrolab-0.0.10/spectrolab/R/utils.R | 48 -- spectrolab-0.0.10/spectrolab/README.md | 12 spectrolab-0.0.10/spectrolab/build/vignette.rds |binary spectrolab-0.0.10/spectrolab/inst/CITATION | 14 spectrolab-0.0.10/spectrolab/inst/doc/introduction_to_spectrolab.R | 4 spectrolab-0.0.10/spectrolab/inst/doc/introduction_to_spectrolab.Rmd | 11 spectrolab-0.0.10/spectrolab/inst/doc/introduction_to_spectrolab.pdf |binary spectrolab-0.0.10/spectrolab/man/Ops.spectra.Rd | 2 spectrolab-0.0.10/spectrolab/man/aggregate.spectra.Rd | 2 spectrolab-0.0.10/spectrolab/man/apply_by_band.Rd | 4 spectrolab-0.0.10/spectrolab/man/as.data.frame.spectra.Rd | 4 spectrolab-0.0.10/spectrolab/man/as.matrix.spectra.Rd | 2 spectrolab-0.0.10/spectrolab/man/as_spectra.Rd |only spectrolab-0.0.10/spectrolab/man/as_spectra.data.frame.Rd |only spectrolab-0.0.10/spectrolab/man/as_spectra.matrix.Rd |only spectrolab-0.0.10/spectrolab/man/bands-set.Rd | 6 spectrolab-0.0.10/spectrolab/man/bands.Rd | 2 spectrolab-0.0.10/spectrolab/man/combine.Rd | 6 spectrolab-0.0.10/spectrolab/man/dim.spectra.Rd | 2 spectrolab-0.0.10/spectrolab/man/i_is_increasing.Rd | 12 spectrolab-0.0.10/spectrolab/man/i_read_ascii_spectra.Rd | 2 spectrolab-0.0.10/spectrolab/man/i_read_asd_spectra.Rd | 2 spectrolab-0.0.10/spectrolab/man/is_spectra.Rd | 2 spectrolab-0.0.10/spectrolab/man/match_sensors.Rd | 4 spectrolab-0.0.10/spectrolab/man/max.spectra.Rd | 4 spectrolab-0.0.10/spectrolab/man/mean.spectra.Rd | 2 spectrolab-0.0.10/spectrolab/man/median.spectra.Rd | 2 spectrolab-0.0.10/spectrolab/man/meta-set.Rd | 2 spectrolab-0.0.10/spectrolab/man/meta.Rd | 2 spectrolab-0.0.10/spectrolab/man/min.spectra.Rd | 4 spectrolab-0.0.10/spectrolab/man/names-set-.spectra.Rd | 2 spectrolab-0.0.10/spectrolab/man/names.spectra.Rd | 2 spectrolab-0.0.10/spectrolab/man/normalize.Rd | 5 spectrolab-0.0.10/spectrolab/man/plot.spectra.Rd | 2 spectrolab-0.0.10/spectrolab/man/plot_interactive.Rd | 2 spectrolab-0.0.10/spectrolab/man/plot_quantile.Rd | 2 spectrolab-0.0.10/spectrolab/man/plot_regions.Rd | 2 spectrolab-0.0.10/spectrolab/man/print.spectra.Rd | 2 spectrolab-0.0.10/spectrolab/man/quantile.spectra.Rd | 7 spectrolab-0.0.10/spectrolab/man/range.spectra.Rd | 6 spectrolab-0.0.10/spectrolab/man/resample.Rd | 10 spectrolab-0.0.10/spectrolab/man/sd.spectra.Rd | 2 spectrolab-0.0.10/spectrolab/man/smooth.spectra.Rd | 2 spectrolab-0.0.10/spectrolab/man/smooth_moving_avg.Rd |only spectrolab-0.0.10/spectrolab/man/smooth_spline.Rd |only spectrolab-0.0.10/spectrolab/man/spec_matrix_example.Rd | 2 spectrolab-0.0.10/spectrolab/man/split.spectra.Rd | 2 spectrolab-0.0.10/spectrolab/man/str.spectra.Rd | 2 spectrolab-0.0.10/spectrolab/man/sub-.spectra.Rd | 4 spectrolab-0.0.10/spectrolab/man/subset-.spectra.Rd | 4 spectrolab-0.0.10/spectrolab/man/subset_by.Rd | 2 spectrolab-0.0.10/spectrolab/man/summary.spectra.Rd | 2 spectrolab-0.0.10/spectrolab/man/t.spectra.Rd | 2 spectrolab-0.0.10/spectrolab/man/value-set.Rd | 2 spectrolab-0.0.10/spectrolab/man/value.Rd | 2 spectrolab-0.0.10/spectrolab/man/var.spectra.Rd | 2 spectrolab-0.0.10/spectrolab/tests/testthat/test_combine.R | 2 spectrolab-0.0.10/spectrolab/tests/testthat/test_conversion.R | 6 spectrolab-0.0.10/spectrolab/tests/testthat/test_quantile_name.R | 2 spectrolab-0.0.10/spectrolab/tests/testthat/test_simple_stats_functions.R | 2 spectrolab-0.0.10/spectrolab/tests/testthat/test_spec_setter.R | 2 spectrolab-0.0.10/spectrolab/tests/testthat/test_spectra_matrix_operations.R | 2 spectrolab-0.0.10/spectrolab/tests/testthat/test_spectra_subset.R | 2 spectrolab-0.0.10/spectrolab/tests/testthat/test_stats_overloads.R | 2 spectrolab-0.0.10/spectrolab/tests/testthat/test_subset_by.R | 2 spectrolab-0.0.10/spectrolab/tests/testthat/test_transpose.R | 2 spectrolab-0.0.10/spectrolab/vignettes/introduction_to_spectrolab.Rmd | 11 spectrolab-0.0.9/spectrolab/man/as.spectra.Rd |only spectrolab-0.0.9/spectrolab/man/as.spectra.data.frame.Rd |only spectrolab-0.0.9/spectrolab/man/as.spectra.matrix.Rd |only spectrolab-0.0.9/spectrolab/man/i_index_pairwise_combn.Rd |only spectrolab-0.0.9/spectrolab/man/i_remove_duplicated_band.Rd |only spectrolab-0.0.9/spectrolab/man/i_smooth_mav_spectra.Rd |only spectrolab-0.0.9/spectrolab/man/i_smooth_spline_spectra.Rd |only spectrolab-0.0.9/spectrolab/man/ratio.Rd |only 93 files changed, 328 insertions(+), 554 deletions(-)
Title: Process Performance Qualification (PPQ) Plans in Chemistry,
Manufacturing and Controls (CMC) Statistical Analysis
Description: Assessment for statistically-based PPQ sampling plan, including calculating the passing probability, optimizing the baseline and high performance cutoff points, visualizing the PPQ plan and power dynamically. The analytical idea is based on the simulation methods from the textbook Burdick, R. K., LeBlond, D. J., Pfahler, L. B., Quiroz, J., Sidor, L., Vukovinsky, K., & Zhang, L. (2017). Statistical Methods for CMC Applications. In Statistical Applications for Chemistry, Manufacturing and Controls (CMC) in the Pharmaceutical Industry (pp. 227-250). Springer, Cham.
Author: Yalin Zhu [aut, cre] (<https://orcid.org/0000-0003-3830-8660>),
Merck & Co., Inc. [cph]
Maintainer: Yalin Zhu <yalin.zhu@merck.com>
Diff between PPQplan versions 1.0.0 dated 2019-09-03 and 1.1.0 dated 2020-10-08
PPQplan-1.0.0/PPQplan/LICENSE |only PPQplan-1.0.0/PPQplan/R/PIfun.R |only PPQplan-1.0.0/PPQplan/R/TIfun.R |only PPQplan-1.0.0/PPQplan/R/functions.R |only PPQplan-1.0.0/PPQplan/inst/doc/PPQnote.pdf |only PPQplan-1.0.0/PPQplan/man/PPQ.ctplot.Rd |only PPQplan-1.0.0/PPQplan/man/PPQ.ggplot.Rd |only PPQplan-1.0.0/PPQplan/man/PPQ.occurve.Rd |only PPQplan-1.0.0/PPQplan/man/PPQ.pp.Rd |only PPQplan-1.0.0/PPQplan/man/pi.ctplot.Rd |only PPQplan-1.0.0/PPQplan/man/pi.occurve.Rd |only PPQplan-1.0.0/PPQplan/man/pi.pp.Rd |only PPQplan-1.0.0/PPQplan/man/rl.pp.Rd |only PPQplan-1.0.0/PPQplan/man/ti.ctplot.Rd |only PPQplan-1.0.0/PPQplan/man/ti.occurve.Rd |only PPQplan-1.0.0/PPQplan/man/ti.pp.Rd |only PPQplan-1.1.0/PPQplan/DESCRIPTION | 22 - PPQplan-1.1.0/PPQplan/MD5 | 69 ++-- PPQplan-1.1.0/PPQplan/NAMESPACE | 24 - PPQplan-1.1.0/PPQplan/NEWS.md |only PPQplan-1.1.0/PPQplan/R/PPQ_ctplot.R |only PPQplan-1.1.0/PPQplan/R/PPQ_ggplot.R |only PPQplan-1.1.0/PPQplan/R/PPQ_occurve.R |only PPQplan-1.1.0/PPQplan/R/PPQ_pp.R |only PPQplan-1.1.0/PPQplan/R/global_var.R |only PPQplan-1.1.0/PPQplan/R/heatmap_ly.R |only PPQplan-1.1.0/PPQplan/R/k_factor.R |only PPQplan-1.1.0/PPQplan/R/pi_ctplot.R |only PPQplan-1.1.0/PPQplan/R/pi_occurve.R |only PPQplan-1.1.0/PPQplan/R/pi_pp.R |only PPQplan-1.1.0/PPQplan/R/pp.R |only PPQplan-1.1.0/PPQplan/R/rl_pp.R |only PPQplan-1.1.0/PPQplan/R/ti_ctplot.R |only PPQplan-1.1.0/PPQplan/R/ti_occurve.R |only PPQplan-1.1.0/PPQplan/R/ti_pp.R |only PPQplan-1.1.0/PPQplan/README.md | 2 PPQplan-1.1.0/PPQplan/build/vignette.rds |binary PPQplan-1.1.0/PPQplan/inst/doc/PPQnote.Rmd | 8 PPQplan-1.1.0/PPQplan/inst/doc/PPQnote.html |only PPQplan-1.1.0/PPQplan/inst/doc/PPQplan-vignette.R | 127 +++---- PPQplan-1.1.0/PPQplan/inst/doc/PPQplan-vignette.Rmd | 137 +++----- PPQplan-1.1.0/PPQplan/inst/doc/PPQplan-vignette.html | 315 ++++++++++--------- PPQplan-1.1.0/PPQplan/man/PPQ_ctplot.Rd |only PPQplan-1.1.0/PPQplan/man/PPQ_ggplot.Rd |only PPQplan-1.1.0/PPQplan/man/PPQ_occurve.Rd |only PPQplan-1.1.0/PPQplan/man/PPQ_pp.Rd |only PPQplan-1.1.0/PPQplan/man/heatmap_ly.Rd | 6 PPQplan-1.1.0/PPQplan/man/k_factor.Rd |only PPQplan-1.1.0/PPQplan/man/pi_ctplot.Rd |only PPQplan-1.1.0/PPQplan/man/pi_occurve.Rd |only PPQplan-1.1.0/PPQplan/man/pi_pp.Rd |only PPQplan-1.1.0/PPQplan/man/pp.Rd | 4 PPQplan-1.1.0/PPQplan/man/rl_pp.Rd |only PPQplan-1.1.0/PPQplan/man/ti_ctplot.Rd |only PPQplan-1.1.0/PPQplan/man/ti_occurve.Rd |only PPQplan-1.1.0/PPQplan/man/ti_pp.Rd |only PPQplan-1.1.0/PPQplan/vignettes/PPQnote.Rmd | 8 PPQplan-1.1.0/PPQplan/vignettes/PPQplan-vignette.Rmd | 137 +++----- 58 files changed, 440 insertions(+), 419 deletions(-)
Title: A Test Environment for Database Requests
Description: Testing and documenting code that communicates with remote
databases can be painful. Although the interaction with R is usually relatively
simple (e.g. data(frames) passed to and from a database), because they rely on
a separate service and the data there, testing them can be difficult to set up,
unsustainable in a continuous integration environment, or impossible without
replicating an entire production cluster. This package addresses that by
allowing you to make recordings from your database interactions and then play
them back while testing (or in other contexts) all without needing to spin up
or have access to the database your code would typically connect to.
Author: Jonathan Keane [aut, cre] (<https://orcid.org/0000-0001-7087-9776>),
Mauricio Vargas [aut] (<https://orcid.org/0000-0003-1017-7574>),
Helen Miller [rev] (reviewed the package for rOpenSci, see
https://github.com/ropensci/software-review/issues/366),
Etienne Racine [rev] (reviewed the package for rOpenSci, see
https://github.com/ropensci/software-review/issues/366)
Maintainer: Jonathan Keane <jkeane@gmail.com>
Diff between dittodb versions 0.1.1 dated 2020-07-29 and 0.1.2 dated 2020-10-08
dittodb-0.1.1/dittodb/vignettes/travelling/conInfo-.R |only dittodb-0.1.1/dittodb/vignettes/travelling/resultInfo-6f7e1a.R |only dittodb-0.1.1/dittodb/vignettes/travelling/resultInfo-cb2164.R |only dittodb-0.1.1/dittodb/vignettes/travelling/resultInfo-e0d545.R |only dittodb-0.1.2/dittodb/DESCRIPTION | 14 dittodb-0.1.2/dittodb/MD5 | 92 ++- dittodb-0.1.2/dittodb/NAMESPACE | 2 dittodb-0.1.2/dittodb/NEWS.md | 16 dittodb-0.1.2/dittodb/R/dbQueries-Results.R | 59 +- dittodb-0.1.2/dittodb/R/expect-sql.R |only dittodb-0.1.2/dittodb/R/mock-db.R | 17 dittodb-0.1.2/dittodb/R/paths.R | 8 dittodb-0.1.2/dittodb/R/utils.R | 15 dittodb-0.1.2/dittodb/README.md | 6 dittodb-0.1.2/dittodb/build/vignette.rds |binary dittodb-0.1.2/dittodb/inst/REFERENCES.bib |only dittodb-0.1.2/dittodb/inst/WORDLIST | 3 dittodb-0.1.2/dittodb/inst/doc/developing-dittodb.html | 13 dittodb-0.1.2/dittodb/inst/doc/dittodb.html | 83 +++ dittodb-0.1.2/dittodb/inst/doc/nycflights.html | 13 dittodb-0.1.2/dittodb/inst/doc/travelling.R | 22 dittodb-0.1.2/dittodb/inst/doc/travelling.Rmd | 22 dittodb-0.1.2/dittodb/inst/doc/travelling.html | 89 +++ dittodb-0.1.2/dittodb/inst/paper.md |only dittodb-0.1.2/dittodb/man/expect_sql.Rd |only dittodb-0.1.2/dittodb/man/figures |only dittodb-0.1.2/dittodb/man/mock-db-methods.Rd | 2 dittodb-0.1.2/dittodb/man/mockdb.Rd | 7 dittodb-0.1.2/dittodb/tests/testthat/helper.R | 9 dittodb-0.1.2/dittodb/tests/testthat/test-a-recording.R | 5 dittodb-0.1.2/dittodb/tests/testthat/test-capture-requests.R | 7 dittodb-0.1.2/dittodb/tests/testthat/test-connection.R | 4 dittodb-0.1.2/dittodb/tests/testthat/test-dbi-generic-integration.R | 10 dittodb-0.1.2/dittodb/tests/testthat/test-dbi-sqlite-integration.R | 6 dittodb-0.1.2/dittodb/tests/testthat/test-dbplyr-integration.R | 15 dittodb-0.1.2/dittodb/tests/testthat/test-expect-sql.R |only dittodb-0.1.2/dittodb/tests/testthat/test-mock-paths.R | 2 dittodb-0.1.2/dittodb/tests/testthat/test-nycflights13.R | 6 dittodb-0.1.2/dittodb/tests/testthat/test-onLoad.R | 4 dittodb-0.1.2/dittodb/tests/testthat/test-paths.R | 2 dittodb-0.1.2/dittodb/tests/testthat/test-redact.R | 3 dittodb-0.1.2/dittodb/tests/testthat/test-start-stop-mocks.R | 1 dittodb-0.1.2/dittodb/tests/testthat/test-use-dittodb.R | 10 dittodb-0.1.2/dittodb/tests/testthat/test-utils.R | 15 dittodb-0.1.2/dittodb/tests/testthat/test-verbosity.R | 63 +- dittodb-0.1.2/dittodb/vignettes/travelling.Rmd | 22 dittodb-0.1.2/dittodb/vignettes/travelling/SELECT-526b8c.R |only dittodb-0.1.2/dittodb/vignettes/travelling/SELECT-90cd6a.R |only dittodb-0.1.2/dittodb/vignettes/travelling/SELECT-cb2164.R | 239 +++++----- 49 files changed, 577 insertions(+), 329 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-24 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-04-14 1.0.2
2014-01-20 1.0.1
2013-07-06 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-02-25 1.2.2
2016-01-04 1.2.1
2015-09-01 1.1.5
2015-06-16 1.0.5