Title: Automatic Detection of Experimental Unit in Precision
Agriculture
Description: A part of precision agriculture is linked to the spectral image obtained from the cameras. With the image information of the agricultural experiment, the included functions facilitate the collection of spectral data associated with the experimental units. Some designs generated in R are linked to the images, which allows the use of the information of each pixel of the image in the experimental unit and the treatment. Tables and images are generated for the analysis of the precision agriculture experiment during the entire vegetative period of the crop.
Author: Felipe de Mendiburu [aut, cre],
David Mauricio [aut],
Rodrigo Morales [aut],
Roberto Quiroz [aut]
Maintainer: Felipe de Mendiburu <fmendiburu@lamolina.edu.pe>
Diff between rPAex versions 1.0.1 dated 2020-01-20 and 1.0.2 dated 2022-08-20
rPAex-1.0.1/rPAex/R/externalPoint.R |only rPAex-1.0.1/rPAex/R/imageField.R |only rPAex-1.0.1/rPAex/man/externalPoint.Rd |only rPAex-1.0.2/rPAex/DESCRIPTION | 8 +- rPAex-1.0.2/rPAex/MD5 | 36 ++++++------ rPAex-1.0.2/rPAex/NEWS | 10 +++ rPAex-1.0.2/rPAex/R/EUsPoint.R |only rPAex-1.0.2/rPAex/R/borderPoint.R | 64 +++++++++++++++++++--- rPAex-1.0.2/rPAex/R/designRaster.R | 2 rPAex-1.0.2/rPAex/R/fixedPoint.R | 40 ++++++-------- rPAex-1.0.2/rPAex/R/fourPoint.R | 3 + rPAex-1.0.2/rPAex/R/imagefield.R |only rPAex-1.0.2/rPAex/R/movePlot.R | 6 +- rPAex-1.0.2/rPAex/inst/NEWS.Rd | 92 +++++++++++++++++++++------------ rPAex-1.0.2/rPAex/man/EUsPoint.Rd |only rPAex-1.0.2/rPAex/man/borderPoint.Rd | 51 +++++++++++------- rPAex-1.0.2/rPAex/man/designRaster.Rd | 8 +- rPAex-1.0.2/rPAex/man/fixedPoint.Rd | 22 +++---- rPAex-1.0.2/rPAex/man/fourPoint.Rd | 8 +- rPAex-1.0.2/rPAex/man/imageField.Rd | 42 +++++++-------- rPAex-1.0.2/rPAex/man/movePlot.Rd | 1 rPAex-1.0.2/rPAex/man/rPAex.Rd | 22 ++----- 22 files changed, 248 insertions(+), 167 deletions(-)
Title: Mark-Recapture Distance Sampling
Description: Animal abundance estimation via conventional, multiple covariate
and mark-recapture distance sampling (CDS/MCDS/MRDS). Detection function
fitting is performed via maximum likelihood. Also included are diagnostics
and plotting for fitted detection functions. Abundance estimation is via a
Horvitz-Thompson-like estimator.
Author: Jeff Laake <jeff.laake@noaa.gov>, David Borchers
<dlb@st-and.ac.uk>, Len Thomas <len.thomas@st-and.ac.uk>, David
Miller <dave@ninepointeightone.net> and Jon Bishop
Maintainer: Laura Marshall <lhm@st-andrews.ac.uk>
Diff between mrds versions 2.2.6 dated 2022-03-17 and 2.2.7 dated 2022-08-20
DESCRIPTION | 9 +- MD5 | 72 +++++++++---------- NEWS | 10 ++ R/DeltaMethod.R | 45 ++---------- R/add.df.covar.line.R | 2 R/ddf.R | 1 R/ddf.ds.R | 12 +-- R/ddf.gof.R | 2 R/detfct.R | 4 - R/detfct.fit.R | 4 - R/detfct.fit.opt.R | 180 +++++++++++++++++++++++++++++++++++++------------ R/dht.R | 24 ++++-- R/dht.deriv.R | 15 ++-- R/flpt.lnl.r | 5 + R/flt.var.R | 28 ++----- R/mrds-package.R | 7 + R/nlminb_wrapper.R | 2 R/p.dist.table.R | 2 R/parse.optimx.R | 2 R/predict.io.fi.R | 4 - R/predict.rem.fi.R | 2 R/predict.trial.fi.R | 2 R/print.dht.R | 10 +- R/prob.deriv.R | 2 R/prob.se.R | 2 R/qqplot.ddf.R | 16 ++-- R/rescale_pars.R | 4 - R/sample_ddf.R | 2 R/solvecov.R | 2 build/partial.rdb |binary data/book.tee.data.rda |binary man/DeltaMethod.Rd | 7 - man/ddf.Rd | 1 man/detfct.fit.Rd | 2 man/detfct.fit.opt.Rd | 2 man/flt.var.Rd | 2 man/mrds-opt.Rd | 7 + 37 files changed, 294 insertions(+), 199 deletions(-)
Title: Distance Sampling Detection Function and Abundance Estimation
Description: A simple way of fitting detection functions to distance sampling
data for both line and point transects. Adjustment term selection, left and
right truncation as well as monotonicity constraints and binning are
supported. Abundance and density estimates can also be calculated (via a
Horvitz-Thompson-like estimator) if survey area information is provided. See
Miller et al. (2019) <doi:10.18637/jss.v089.i01> for more information on
methods and <https://examples.distancesampling.org/> for example analyses.
Author: David Lawrence Miller
Maintainer: Laura Marshall <lhm@st-andrews.ac.uk>
Diff between Distance versions 1.0.5 dated 2022-03-17 and 1.0.6 dated 2022-08-20
DESCRIPTION | 10 +++---- MD5 | 48 ++++++++++++++++++------------------ NAMESPACE | 3 ++ NEWS | 9 ++++++ R/ER_var_f.R | 18 ++++++++----- R/bootdht.R | 20 +++++++++------ R/bootdht_Dhat_summarize.R |only R/bootdht_Nhat_summarize.R | 6 +++- R/bootdht_bootit.R | 10 +++---- R/checkdata.R | 2 - R/create_bins.R | 12 ++++++--- R/dht2.R | 23 +++++++++-------- R/dht2_checkdata.R | 31 ++++++++++++----------- R/ds.R | 34 ++++++++++++++++--------- R/dsdata.R | 2 - R/safe_factorize.R | 3 -- R/varNhat.R | 53 ++++++++++++++++++---------------------- build/partial.rdb |binary man/bootdht.Rd | 3 +- man/bootdht_Dhat_summarize.Rd |only man/bootdht_Nhat_summarize.Rd | 6 +++- man/ds.Rd | 6 +++- man/golftees.Rd | 2 - tests/testthat/test_ds.R | 47 +++++++++++++++++++++++++++++------ tests/testthat/test_golftees.R | 18 ++++++++++++- tests/testthat/test_summarize.R | 21 ++++++++++++--- 26 files changed, 245 insertions(+), 142 deletions(-)
Title: Simple, Consistent Wrappers for Common String Operations
Description: A consistent, simple and easy to use set of
wrappers around the fantastic 'stringi' package. All function and
argument names (and positions) are consistent, all functions deal with
"NA"'s and zero length vectors in the same way, and the output from
one function is easy to feed into the input of another.
Author: Hadley Wickham [aut, cre, cph],
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between stringr versions 1.4.0 dated 2019-02-09 and 1.4.1 dated 2022-08-20
DESCRIPTION | 11 MD5 | 62 +-- NEWS.md | 8 README.md | 54 +-- build/vignette.rds |binary inst/doc/regular-expressions.R | 58 +-- inst/doc/regular-expressions.Rmd | 2 inst/doc/regular-expressions.html | 629 +++++++++++++++++++++++-------------- inst/doc/stringr.R | 50 +- inst/doc/stringr.html | 637 ++++++++++++++++++++++---------------- man/modifiers.Rd | 33 + man/str_count.Rd | 2 man/str_detect.Rd | 2 man/str_extract.Rd | 2 man/str_glue.Rd | 15 man/str_interp.Rd | 4 man/str_length.Rd | 2 man/str_locate.Rd | 2 man/str_match.Rd | 2 man/str_order.Rd | 20 - man/str_remove.Rd | 2 man/str_replace.Rd | 6 man/str_split.Rd | 2 man/str_starts.Rd | 2 man/str_subset.Rd | 2 man/str_trim.Rd | 8 man/str_trunc.Rd | 3 man/str_view.Rd | 2 man/str_wrap.Rd | 14 man/stringr-data.Rd | 10 man/stringr-package.Rd | 10 vignettes/regular-expressions.Rmd | 2 32 files changed, 992 insertions(+), 666 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>, and Choudhary and Satija (2022) <doi:10.1186/s13059-021-02584-9>
for more details.
Author: Christoph Hafemeister [aut] ,
Saket Choudhary [aut, cre] ,
Rahul Satija [ctb]
Maintainer: Saket Choudhary <schoudhary@nygenome.org>
Diff between sctransform versions 0.3.3 dated 2022-01-13 and 0.3.4 dated 2022-08-20
DESCRIPTION | 12 ++++++------ MD5 | 19 ++++++++++--------- NEWS.md | 14 +++++++++++--- R/denoise.R | 2 +- R/generate.R | 2 +- R/utils.R | 9 +++++++++ R/vst.R | 2 +- README.md | 13 ++++++------- build/partial.rdb |binary man/make.sparse.Rd |only src/utils.cpp | 52 ++++++++++++++++++++++++++-------------------------- 11 files changed, 71 insertions(+), 54 deletions(-)
Title: Database Interface Class
Description: 'R6' class interface for handling relational database connections using 'DBI' package as backend.
The class allows handling of connections to e.g. PostgreSQL, MariaDB and SQLite.
The purpose is having an intuitive object allowing straightforward handling of SQL databases.
Author: Nikolaus Pawlowski [aut, cre, cph]
Maintainer: Nikolaus Pawlowski <niko@fr33.net>
Diff between rocker versions 0.3.0 dated 2022-01-04 and 0.3.1 dated 2022-08-20
DESCRIPTION | 8 MD5 | 24 NEWS.md | 5 build/vignette.rds |binary inst/doc/DBI_objects_and_functions.html | 87 +- inst/doc/Database_connections.html | 20 inst/doc/Installation_and_Object.html | 30 inst/doc/Packages_and_databases.html | 36 inst/doc/Password_storage.html | 25 inst/doc/S3_and_R6_functions.html | 20 inst/doc/Transactions.html | 25 man/rocker-R6-class.Rd | 240 +++--- man/rocker-README.Rd | 1170 +++++++++++++++++++++++--------- 13 files changed, 1174 insertions(+), 516 deletions(-)
Title: Fast 2D Constrained Delaunay Triangulation
Description: Performs 2D Delaunay triangulation, constrained or
unconstrained, with the help of the C++ library 'CDT'. A function to
plot the triangulation is provided. The constrained Delaunay
triangulation has applications in geographic information systems.
Author: Stephane Laurent [aut, cre],
Artem Amirkhanov [cph]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between RCDT versions 1.2.0 dated 2022-08-07 and 1.2.1 dated 2022-08-20
DESCRIPTION | 6 +-- MD5 | 12 +++--- NEWS.md | 5 ++ R/RcppExports.R | 22 ++++++------ build/partial.rdb |binary inst/doc/the-RCDT-package.html | 2 - tests/testthat/test-delConstrained.R | 64 ++++++++++++++++++++++++++++------- 7 files changed, 78 insertions(+), 33 deletions(-)
Title: Estimating and Mapping Disaggregated Indicators
Description: Functions that support estimating, assessing and mapping regional
disaggregated indicators. So far, estimation methods comprise direct estimation,
the model-based unit-level approach Empirical Best Prediction (see "Small area
estimation of poverty indicators" by Molina and Rao (2010) <doi:10.1002/cjs.10051>),
the area-level model (see "Estimates of income for small places: An
application of James-Stein procedures to Census Data" by Fay and Herriot (1979)
<doi:10.1080/01621459.1979.10482505>) and various extensions of it (adjusted variance
estimation methods, log and arcsin transformation, spatial, robust and measurement
error models), as well as their precision estimates. The assessment of the used model
is supported by a summary and diagnostic plots. For a suitable presentation of
estimates, map plots can be easily created. Furthermore, results can easily be
exported to excel. For a detailed description of the package and the methods used
see "The R Package emdi for Estima [...truncated...]
Author: Sylvia Harmening [aut],
Ann-Kristin Kreutzmann [aut],
Soeren Pannier [aut, cre],
Felix Skarke [aut],
Natalia Rojas-Perilla [aut],
Nicola Salvati [aut],
Timo Schmid [aut],
Matthias Templ [aut],
Nikos Tzavidis [aut],
Nora Wuerz [aut]
Maintainer: Soeren Pannier <soeren.pannier@fu-berlin.de>
Diff between emdi versions 2.1.1 dated 2022-01-04 and 2.1.2 dated 2022-08-20
emdi-2.1.1/emdi/tests/testthat/Direct/arpr_all.csv |only emdi-2.1.1/emdi/tests/testthat/Direct/arpr_all_cali.csv |only emdi-2.1.1/emdi/tests/testthat/Direct/arpr_all_naive.csv |only emdi-2.1.1/emdi/tests/testthat/Direct/gini_all.csv |only emdi-2.1.1/emdi/tests/testthat/Direct/gini_all_cali.csv |only emdi-2.1.1/emdi/tests/testthat/Direct/gini_all_naive.csv |only emdi-2.1.1/emdi/tests/testthat/Direct/qsr_all.csv |only emdi-2.1.1/emdi/tests/testthat/Direct/qsr_all_cali.csv |only emdi-2.1.1/emdi/tests/testthat/Direct/qsr_all_naive.csv |only emdi-2.1.2/emdi/DESCRIPTION | 10 emdi-2.1.2/emdi/MD5 | 221 - emdi-2.1.2/emdi/NEWS.md | 9 emdi-2.1.2/emdi/R/FH.R | 1088 +++--- emdi-2.1.2/emdi/R/auxiliary_functions.R | 21 emdi-2.1.2/emdi/R/back_transformation.R | 429 +- emdi-2.1.2/emdi/R/benchmark.R | 195 - emdi-2.1.2/emdi/R/check_compare_arguments.R | 102 emdi-2.1.2/emdi/R/check_direct_arguments.R | 262 - emdi-2.1.2/emdi/R/check_ebp_arguments.R | 396 +- emdi-2.1.2/emdi/R/check_estimators_arguments.R | 58 emdi-2.1.2/emdi/R/check_fh_arguments.R | 765 ++-- emdi-2.1.2/emdi/R/check_mapplot_arguments.R | 54 emdi-2.1.2/emdi/R/check_plot_arguments.R | 36 emdi-2.1.2/emdi/R/check_writeexcel_arguments.R | 28 emdi-2.1.2/emdi/R/combine_data.R | 26 emdi-2.1.2/emdi/R/compare.R | 449 +- emdi-2.1.2/emdi/R/compare_plot.R | 758 ++-- emdi-2.1.2/emdi/R/compare_plot.direct.R | 49 emdi-2.1.2/emdi/R/compare_plot.ebp.R | 150 emdi-2.1.2/emdi/R/compare_plot.fh.R | 175 emdi-2.1.2/emdi/R/direct_estimation.R | 363 +- emdi-2.1.2/emdi/R/direct_variance.R | 221 - emdi-2.1.2/emdi/R/drop1.add1.fh.R | 120 emdi-2.1.2/emdi/R/eblup.R | 325 - emdi-2.1.2/emdi/R/eblup_robust.R | 144 emdi-2.1.2/emdi/R/ebp.R | 425 +- emdi-2.1.2/emdi/R/emdi.R | 52 emdi-2.1.2/emdi/R/emdiObject.R | 110 emdi-2.1.2/emdi/R/estim_sigmau2.R | 493 +- emdi-2.1.2/emdi/R/estimators.emdi.R | 137 emdi-2.1.2/emdi/R/eusilcA_pop.R | 16 emdi-2.1.2/emdi/R/eusilcA_popAgg.R | 20 emdi-2.1.2/emdi/R/eusilcA_prox.R | 24 emdi-2.1.2/emdi/R/eusilcA_smp.R | 15 emdi-2.1.2/emdi/R/eusilcA_smpAgg.R | 21 emdi-2.1.2/emdi/R/framework_direct.R | 268 - emdi-2.1.2/emdi/R/framework_ebp.R | 184 - emdi-2.1.2/emdi/R/framework_fh.R | 84 emdi-2.1.2/emdi/R/load_shape.R | 9 emdi-2.1.2/emdi/R/map_plot.R | 328 + emdi-2.1.2/emdi/R/mse.R | 1973 +++++------ emdi-2.1.2/emdi/R/mse_emdi.R | 74 emdi-2.1.2/emdi/R/mse_estimation.R | 468 +- emdi-2.1.2/emdi/R/nlme_methods.R | 664 ++- emdi-2.1.2/emdi/R/optimal_parameter.R | 127 emdi-2.1.2/emdi/R/plot.ebp.R | 123 emdi-2.1.2/emdi/R/plot.emdi.R | 733 ++-- emdi-2.1.2/emdi/R/plot.fh.R | 32 emdi-2.1.2/emdi/R/point_emdi.R | 89 emdi-2.1.2/emdi/R/point_estimation.R | 433 +- emdi-2.1.2/emdi/R/point_estimation_direct.R | 72 emdi-2.1.2/emdi/R/print.emdi.R | 82 emdi-2.1.2/emdi/R/qqnorm.R | 105 emdi-2.1.2/emdi/R/spatialcor.R | 113 emdi-2.1.2/emdi/R/stats_methods.R | 119 emdi-2.1.2/emdi/R/step.R | 425 +- emdi-2.1.2/emdi/R/summary.direct.R | 47 emdi-2.1.2/emdi/R/summary.ebp.R | 165 emdi-2.1.2/emdi/R/summary.emdi.R | 77 emdi-2.1.2/emdi/R/summary.fh.R | 100 emdi-2.1.2/emdi/R/transformation_functions.R | 152 emdi-2.1.2/emdi/R/variable_selection.R | 308 - emdi-2.1.2/emdi/R/write.excel.emdi.R | 986 +++-- emdi-2.1.2/emdi/R/write.ods.emdi.R | 285 - emdi-2.1.2/emdi/README.md | 4 emdi-2.1.2/emdi/build/vignette.rds |binary emdi-2.1.2/emdi/inst/COPYRIGHTS | 43 emdi-2.1.2/emdi/inst/doc/vignette_fh.pdf |binary emdi-2.1.2/emdi/man/benchmark.Rd | 74 emdi-2.1.2/emdi/man/combine_data.Rd | 8 emdi-2.1.2/emdi/man/compare.Rd | 34 emdi-2.1.2/emdi/man/compare_plot.Rd | 159 emdi-2.1.2/emdi/man/compare_pred.Rd | 42 emdi-2.1.2/emdi/man/data_transformation.Rd | 36 emdi-2.1.2/emdi/man/direct.Rd | 129 emdi-2.1.2/emdi/man/ebp.Rd | 228 - emdi-2.1.2/emdi/man/emdi.Rd | 50 emdi-2.1.2/emdi/man/emdiObject.Rd | 106 emdi-2.1.2/emdi/man/emdi_summaries.Rd | 69 emdi-2.1.2/emdi/man/estimators.Rd | 66 emdi-2.1.2/emdi/man/eusilcA_pop.Rd | 12 emdi-2.1.2/emdi/man/eusilcA_popAgg.Rd | 16 emdi-2.1.2/emdi/man/eusilcA_prox.Rd | 12 emdi-2.1.2/emdi/man/eusilcA_smp.Rd | 13 emdi-2.1.2/emdi/man/eusilcA_smpAgg.Rd | 19 emdi-2.1.2/emdi/man/fh.Rd | 396 +- emdi-2.1.2/emdi/man/fixef.Rd | 32 emdi-2.1.2/emdi/man/getData.Rd | 31 emdi-2.1.2/emdi/man/getGroups.Rd | 26 emdi-2.1.2/emdi/man/getGroupsFormula.Rd | 28 emdi-2.1.2/emdi/man/getResponse.Rd | 31 emdi-2.1.2/emdi/man/getVarCov.Rd | 63 emdi-2.1.2/emdi/man/intervals.Rd | 40 emdi-2.1.2/emdi/man/load_shapeaustria.Rd | 2 emdi-2.1.2/emdi/man/map_plot.Rd | 94 emdi-2.1.2/emdi/man/plot.emdi.Rd | 123 emdi-2.1.2/emdi/man/predict.emdi.Rd | 24 emdi-2.1.2/emdi/man/qqnorm.emdi.Rd | 39 emdi-2.1.2/emdi/man/ranef.Rd | 33 emdi-2.1.2/emdi/man/spatialcor.tests.Rd | 36 emdi-2.1.2/emdi/man/step.Rd | 95 emdi-2.1.2/emdi/man/write.excel.Rd | 103 emdi-2.1.2/emdi/tests/testthat/Direct/arpr_naive_value.csv |only emdi-2.1.2/emdi/tests/testthat/Direct/arpr_naive_var.csv |only emdi-2.1.2/emdi/tests/testthat/Direct/gini_cali_value.csv |only emdi-2.1.2/emdi/tests/testthat/Direct/gini_cali_var.csv |only emdi-2.1.2/emdi/tests/testthat/FH/fh_backtransform_mse.csv |only emdi-2.1.2/emdi/tests/testthat/FH/fh_backtransform_point.csv |only emdi-2.1.2/emdi/tests/testthat/test_direct_estimation.R | 139 119 files changed, 10428 insertions(+), 8419 deletions(-)
Title: Density Surface Modelling of Distance Sampling Data
Description: Density surface modelling of line transect data. A Generalized
Additive Model-based approach is used to calculate spatially-explicit estimates
of animal abundance from distance sampling (also presence/absence and strip
transect) data. Several utility functions are provided for model checking,
plotting and variance estimation.
Author: David L. Miller, Eric Rexstad, Louise Burt, Mark V. Bravington,
Sharon Hedley, Megan Ferguson, Natalie Kelly.
Maintainer: Laura Marshall <lhm@st-andrews.ac.uk>
Diff between dsm versions 2.3.2 dated 2022-03-17 and 2.3.3 dated 2022-08-20
dsm-2.3.2/dsm/R/dsm.cor.R |only dsm-2.3.2/dsm/R/dsm.var.gam.R |only dsm-2.3.2/dsm/R/dsm.var.movblk.R |only dsm-2.3.2/dsm/R/dsm.var.prop.R |only dsm-2.3.2/dsm/R/rqgam.check.R |only dsm-2.3.2/dsm/R/vis.concurvity.R |only dsm-2.3.3/dsm/DESCRIPTION | 9 + dsm-2.3.3/dsm/MD5 | 65 +++++++------ dsm-2.3.3/dsm/NAMESPACE | 6 + dsm-2.3.3/dsm/NEWS | 13 ++ dsm-2.3.3/dsm/R/dead_functions.R |only dsm-2.3.3/dsm/R/dsm_cor.R |only dsm-2.3.3/dsm/R/dsm_var_gam.R |only dsm-2.3.3/dsm/R/dsm_var_movblk.R |only dsm-2.3.3/dsm/R/dsm_var_prop.R |only dsm-2.3.3/dsm/R/dsm_varprop.R | 23 +++- dsm-2.3.3/dsm/R/dummy_ddf.R | 2 dsm-2.3.3/dsm/R/plot.dsm.var.R | 12 +- dsm-2.3.3/dsm/R/plot_pred_by_term.R | 13 ++ dsm-2.3.3/dsm/R/predict.dsm.R | 4 dsm-2.3.3/dsm/R/rqgam_check.R |only dsm-2.3.3/dsm/R/summary.dsm.var.R | 4 dsm-2.3.3/dsm/R/vis_concurvity.R |only dsm-2.3.3/dsm/man/dsm.cor.Rd | 49 ---------- dsm-2.3.3/dsm/man/dsm.var.gam.Rd | 41 -------- dsm-2.3.3/dsm/man/dsm.var.movblk.Rd | 47 ---------- dsm-2.3.3/dsm/man/dsm.var.prop.Rd | 78 ---------------- dsm-2.3.3/dsm/man/dsm_cor.Rd |only dsm-2.3.3/dsm/man/dsm_var_gam.Rd |only dsm-2.3.3/dsm/man/dsm_var_movblk.Rd |only dsm-2.3.3/dsm/man/dsm_var_prop.Rd |only dsm-2.3.3/dsm/man/dsm_varprop.Rd | 14 ++ dsm-2.3.3/dsm/man/plot.dsm.var.Rd | 10 +- dsm-2.3.3/dsm/man/plot_pred_by_term.Rd | 5 - dsm-2.3.3/dsm/man/predict.dsm.Rd | 4 dsm-2.3.3/dsm/man/predict.fake_ddf.Rd | 2 dsm-2.3.3/dsm/man/rqgam.check.Rd | 43 --------- dsm-2.3.3/dsm/man/rqgam_check.Rd |only dsm-2.3.3/dsm/man/vis.concurvity.Rd | 34 ------- dsm-2.3.3/dsm/man/vis_concurvity.Rd |only dsm-2.3.3/dsm/tests/testthat/test_mex.R | 2 dsm-2.3.3/dsm/tests/testthat/test_movblk.R | 136 ++++++++++++++--------------- dsm-2.3.3/dsm/tests/testthat/test_vargam.R | 6 - 43 files changed, 201 insertions(+), 421 deletions(-)
Title: High Dimensional Numerical and Symbolic Calculus
Description: Efficient C++ optimized functions for numerical and symbolic calculus as described in Guidotti (2020) <arXiv:2101.00086>. It includes basic arithmetic, tensor calculus, Einstein summing convention, fast computation of the Levi-Civita symbol and generalized Kronecker delta, Taylor series expansion, multivariate Hermite polynomials, high-order derivatives, ordinary differential equations, differential operators (Gradient, Jacobian, Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary orthogonal coordinate systems: cartesian, polar, spherical, cylindrical, parabolic or user defined by custom scale factors.
Author: Emanuele Guidotti [aut, cre]
Maintainer: Emanuele Guidotti <emanuele.guidotti@unine.ch>
Diff between calculus versions 0.3.3 dated 2022-01-22 and 0.3.4 dated 2022-08-20
DESCRIPTION | 8 MD5 | 162 +- NAMESPACE | 100 - NEWS.md | 76 - R/RcppExports.R | 78 - R/contraction.R | 190 +- R/delta.R | 64 R/derivative.R | 616 ++++---- R/einstein.R | 316 ++-- R/epsilon.R | 62 R/evaluate.R | 158 +- R/hermite.R | 226 +- R/integral.R | 508 +++--- R/mxdet.R | 100 - R/mxinv.R | 118 - R/mxtr.R | 70 R/ode.R | 494 +++--- R/operators.R | 2652 +++++++++++++++++------------------ R/package.R | 14 R/partitions.R | 108 - R/taylor.R | 274 +-- R/utils.R | 626 ++++---- README.md | 122 - build/vignette.rds |binary inst/CITATION | 24 inst/doc/derivatives.R | 102 - inst/doc/derivatives.Rmd | 248 +-- inst/doc/derivatives.html | 695 ++++++--- inst/doc/differential-operators.R | 172 +- inst/doc/differential-operators.Rmd | 516 +++--- inst/doc/differential-operators.html | 1052 +++++++++---- inst/doc/einstein.R | 54 inst/doc/einstein.Rmd | 146 - inst/doc/einstein.html | 631 +++++--- inst/doc/hermite.R | 36 inst/doc/hermite.Rmd | 150 - inst/doc/hermite.html | 1030 ++++++++----- inst/doc/integrals.R | 98 - inst/doc/integrals.Rmd | 242 +-- inst/doc/integrals.html | 680 +++++--- inst/doc/ode.R | 100 - inst/doc/ode.Rmd | 342 ++-- inst/doc/ode.html | 807 ++++++---- inst/doc/taylor.R | 38 inst/doc/taylor.Rmd | 154 +- inst/doc/taylor.html | 670 +++++--- man/calculus-package.Rd | 4 man/cross.Rd | 4 man/curl.Rd | 4 man/diagonal.Rd | 4 man/divergence.Rd | 4 man/gradient.Rd | 4 man/hessian.Rd | 4 man/index.Rd | 4 man/jacobian.Rd | 4 man/laplacian.Rd | 4 man/mx.Rd | 4 src/calculus.cpp | 2 tests/testthat.R | 8 tests/testthat/test-basics.R | 278 +-- tests/testthat/test-curl.R | 246 +-- tests/testthat/test-derivative.R | 334 ++-- tests/testthat/test-divergence.R | 250 +-- tests/testthat/test-evaluate.R | 56 tests/testthat/test-gradient.R | 218 +- tests/testthat/test-hessian.R | 232 +-- tests/testthat/test-integral.R | 694 ++++----- tests/testthat/test-laplacian.R | 116 - tests/testthat/test-mx.R | 118 - tests/testthat/test-mxdet.R | 86 - tests/testthat/test-mxinv.R | 86 - tests/testthat/test-mxtr.R | 38 tests/testthat/test-ode.R | 640 ++++---- tests/testthat/test-taylor.R | 82 - tests/testthat/test-utils.R | 12 vignettes/derivatives.Rmd | 248 +-- vignettes/differential-operators.Rmd | 516 +++--- vignettes/einstein.Rmd | 146 - vignettes/hermite.Rmd | 150 - vignettes/integrals.Rmd | 242 +-- vignettes/ode.Rmd | 342 ++-- vignettes/taylor.Rmd | 154 +- 82 files changed, 11043 insertions(+), 9424 deletions(-)
Title: Time Series with Matrix Profile
Description: A toolkit implementing the Matrix Profile concept
that was created by CS-UCR
<http://www.cs.ucr.edu/~eamonn/MatrixProfile.html>.
Author: Francisco Bischoff [aut, cre] ,
Michael Yeh [res, ccp, ctb] ,
Diego Silva [res, ccp, ctb] ,
Yan Zhu [res, ccp, ctb] ,
Hoang Dau [res, ccp, ctb] ,
Michele Linardi [res, ccp, ctb]
Maintainer: Francisco Bischoff <fbischoff@med.up.pt>
Diff between tsmp versions 0.4.14 dated 2020-04-06 and 0.4.15 dated 2022-08-20
DESCRIPTION | 10 MD5 | 124 +-- NAMESPACE | 10 NEWS | 261 +++--- NEWS.md |only R/RcppExports.R | 142 +-- R/analyze.R | 146 +-- R/compute.R | 288 +++---- R/find-snippet.R | 284 +++---- R/mp-toy-data.R | 34 R/mstomp.R | 640 ++++++++-------- R/pmp.R | 2 R/salient.R | 958 ++++++++++++------------ R/scrimp.R | 680 ++++++++--------- R/sdts-predict.R | 374 ++++----- R/sdts-train.R | 710 +++++++++--------- R/serialize.R | 7 R/stamp.R | 460 +++++------ R/stomp.R | 460 +++++------ R/subset.R | 43 + R/tsmp.R | 564 +++++++------- R/valmod.R | 1404 ++++++++++++++++++------------------ R/zzz.R | 44 - README.md | 325 ++++---- build/vignette.rds |binary data/motifs_discords_small.rda |binary data/mp_fluss_data.rda |binary data/mp_gait_data.rda |binary data/mp_meat_data.rda |binary data/mp_test_data.rda |binary data/mp_toy_data.rda |binary inst/API-v0.4.13 | 266 +++--- inst/API-v0.4.14 | 266 +++--- inst/API-v0.4.15 |only inst/WORDLIST | 150 +-- inst/doc/press.R | 50 - inst/doc/press.Rmd | 4 inst/doc/press.html | 939 +++++++++++++----------- inst/schemaorg.json |only man/as.matrixprofile.Rd | 24 man/figures/dependency_plot-1.png |binary man/mstomp.Rd | 6 man/read.Rd | 6 man/salient_subsequences.Rd | 2 man/stamp.Rd | 6 man/stomp.Rd | 6 src/RcppExports.cpp | 5 src/mpx.cpp | 12 tests/fontconfig-helper.R | 12 tests/prints/cac-print | 22 tests/prints/fluss-print | 32 tests/prints/mmp-print | 18 tests/prints/mp-print | 12 tests/prints/smp-print | 14 tests/prints/valmod-print | 12 tests/testthat/_snaps |only tests/testthat/test-stress-stamps.R | 130 +-- vignettes/press.Rmd | 4 58 files changed, 5066 insertions(+), 4902 deletions(-)
Title: SNPs-Based Whole Genome Association Studies
Description: Functions to perform most of the common analysis in genome association studies are implemented. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented. Max-statistic and genetic risk-allele score exact distributions are also possible to be estimated. The methods are described in Gonzalez JR et al., 2007 <doi: 10.1093/bioinformatics/btm025>.
Author: Victor Moreno [aut],
Juan R Gonzalez [aut],
Dolors Pelegri [aut, cre]
Maintainer: Dolors Pelegri <dolors.pelegri@isglobal.org>
Diff between SNPassoc versions 2.0-11 dated 2021-12-03 and 2.0-12 dated 2022-08-20
DESCRIPTION | 18 MD5 | 220 +- R/GenotypeRate.R | 16 R/Table.N.Per.R | 38 R/Table.mean.se.R | 24 R/WGassociation.R | 186 - R/WGstats.R | 32 R/additive.R | 6 R/additive.WGassociation.R | 12 R/additive.default.R | 14 R/additive.snp.R | 42 R/as.snp.R | 12 R/assoc.R | 98 R/association.R | 364 +-- R/association.fit.R | 630 +++--- R/c.WGassociation.r | 68 R/codominant.R | 6 R/codominant.WGassociation.R | 12 R/codominant.default.R | 16 R/codominant.snp.R | 16 R/crea.lab.R | 32 R/dominant.R | 6 R/dominant.WGassociation.R | 12 R/dominant.default.R | 24 R/dominant.snp.R | 12 R/dscore.R | 32 R/dscore.default.R | 22 R/dscore.setupSNP.R | 16 R/extractPval.R | 44 R/extractPval.i.R | 74 R/getNiceTable.R | 92 R/getSignificantSNPs.R | 80 R/int.R | 12 R/interactionPval.R | 330 +-- R/interleave.R | 74 R/intervals.R | 8 R/intervals.dif.R | 110 - R/intervals.haplo.glm.R | 136 - R/intervals.or.R | 84 R/is.Monomorphic.R | 28 R/is.quantitative.R | 24 R/is.snp.R | 12 R/labels.WGassociation.R | 6 R/labels.setupSNP.R | 6 R/maxstat.R | 4 R/maxstat.default.R | 32 R/maxstat.matrix.R | 438 ++-- R/maxstat.setupSNP.R | 28 R/maxstat.table.R | 12 R/modelTest.R | 80 R/odds.r | 102 R/orderChromosome.R | 30 R/overdominant.R | 6 R/overdominant.WGassociation.R | 12 R/overdominant.default.R | 26 R/overdominant.snp.R | 46 R/plot.permTest.R | 42 R/plot.setupSNP.R | 6 R/plotWGassociation.R | 60 R/print.SNPinteraction.R | 12 R/print.WGassociation.R | 48 R/print.haploOut.R | 68 R/print.intervals.R | 94 R/print.maxstat.R | 6 R/print.permTest.R | 62 R/print.snp.r | 92 R/print.snpOut.R | 128 - R/print.summary.snp.R | 20 R/print.tableHWE.R | 26 R/pvalTest.R | 18 R/pvalues.R | 6 R/pvalues.WGassociation.R | 6 R/qqpval.r | 14 R/recessive.R | 6 R/recessive.WGassociation.R | 12 R/recessive.default.R | 44 R/recessive.snp.R | 16 R/scanWGassociation.R | 22 R/setupSNP.R | 88 R/snp.R | 248 +- R/summary.snp.R | 108 - R/table.corner.R | 344 +-- R/table.interaction.R | 370 +-- R/togeno.R | 22 R/trim.R | 10 R/z$.setupSNP.R | 8 R/z[.WGassociation.R | 72 R/z[.setupSNP.R | 40 R/z[.snp.r | 24 R/z[[_-.setupSNP.R | 64 R/z[_-.setupSNP.R | 10 README.md | 6 build/vignette.rds |binary inst/doc/SNPassoc.R | 418 ++-- inst/doc/SNPassoc.html | 4040 +++++++++++++++++++++++++++------------ inst/docs/changelog.txt | 416 ++-- man/BonferroniSig.Rd | 92 man/GenomicControl.Rd | 98 man/LD.Rd | 144 - man/association.Rd | 266 +- man/asthma.Rd | 40 man/interactionPval.Rd | 168 - man/makegeno.Rd | 78 man/maxstat.Rd | 128 - man/odds.Rd | 80 man/related.Rd | 44 man/setupSNP.Rd | 134 - man/snp.Rd | 288 +- man/sortSNPs.Rd | 88 man/tableHWE.Rd | 114 - vignettes/multiomic.bib | 4232 ++++++++++++++++++++--------------------- 111 files changed, 9326 insertions(+), 7686 deletions(-)
Title: Calculate and Visualize 'SNOTEL' Snow Data and Seasonality
Description: Programmatic interface to the 'SNOTEL' snow data
(<https://www.nrcs.usda.gov/wps/portal/wcc/home>). Provides easy downloads of snow
data into your R work space or a local directory. Additional post-processing
routines to extract snow season indexes are provided.
Author: Koen Hufkens [aut, cre] ,
BlueGreen Labs [cph, fnd]
Maintainer: Koen Hufkens <koen.hufkens@gmail.com>
Diff between snotelr versions 1.0.4 dated 2020-05-08 and 1.1 dated 2022-08-20
DESCRIPTION | 35 ++-- MD5 | 27 +-- NAMESPACE | 7 R/snotel_explorer.r | 26 ++- R/snotel_info.r | 79 +++------ R/snotel_phenology.r | 2 build/vignette.rds |binary inst/CITATION |only inst/doc/snotelr-vignette.Rmd | 2 inst/doc/snotelr-vignette.html | 288 +++++++++++++++++++++--------------- inst/shiny/snotel_explorer/help.r | 8 - inst/shiny/snotel_explorer/server.R | 1 inst/shiny/snotel_explorer/ui.R | 31 +++ man/snotel_info.Rd | 4 vignettes/snotelr-vignette.Rmd | 2 15 files changed, 290 insertions(+), 222 deletions(-)
Title: Mosquito Gene Drive Explorer 2
Description: A simulation modeling framework which significantly extends capabilities from the
'MGDrivE' simulation package via a new mathematical and computational framework based on stochastic Petri nets.
For more information about 'MGDrivE', see our publication: <https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.13318>.
Some of the notable capabilities of 'MGDrivE2' include: incorporation of human populations,
epidemiological dynamics, time-varying parameters, and a continuous-time simulation
framework with various sampling algorithms for both deterministic and stochastic interpretations.
'MGDrivE2' relies on the genetic inheritance structures provided in package 'MGDrivE', so we
suggest installing that package initially.
Author: Sean L. Wu [aut, cre],
Jared B. Bennett [aut],
Hector Manuel Sanchez Castellanos [ctb],
Tomas M. Leon [ctb],
Andrew J. Dolgert [ctb],
John M. Marshall [aut],
Agastya Mondal [aut]
Maintainer: Sean L. Wu <slwood89@gmail.com>
Diff between MGDrivE2 versions 1.1.0 dated 2021-01-13 and 2.0.0 dated 2022-08-20
MGDrivE2-1.1.0/MGDrivE2/inst/doc/output-storage.R |only MGDrivE2-1.1.0/MGDrivE2/inst/doc/output-storage.Rmd |only MGDrivE2-1.1.0/MGDrivE2/inst/doc/output-storage.html |only MGDrivE2-1.1.0/MGDrivE2/vignettes/output-storage.Rmd |only MGDrivE2-2.0.0/MGDrivE2/DESCRIPTION | 20 MGDrivE2-2.0.0/MGDrivE2/MD5 | 101 MGDrivE2-2.0.0/MGDrivE2/NAMESPACE | 19 MGDrivE2-2.0.0/MGDrivE2/NEWS.md | 48 MGDrivE2-2.0.0/MGDrivE2/R/Imperial-model-params.R |only MGDrivE2-2.0.0/MGDrivE2/R/Imperial-ode.R |only MGDrivE2-2.0.0/MGDrivE2/R/PN-epi-node-decoupled-P.R |only MGDrivE2-2.0.0/MGDrivE2/R/PN-epi-node-decoupled-T.R |only MGDrivE2-2.0.0/MGDrivE2/R/PN-matrix.R | 116 MGDrivE2-2.0.0/MGDrivE2/R/auxiliary-analysis.R | 488 +++ MGDrivE2-2.0.0/MGDrivE2/R/auxiliary-batch.R | 50 MGDrivE2-2.0.0/MGDrivE2/R/auxiliary-internal.R | 55 MGDrivE2-2.0.0/MGDrivE2/R/auxiliary-plot.R | 48 MGDrivE2-2.0.0/MGDrivE2/R/equilibrium-epi-decoupled.R |only MGDrivE2-2.0.0/MGDrivE2/R/equilibrium-epiImperial.R |only MGDrivE2-2.0.0/MGDrivE2/R/equilibrium-epiSIS.R | 4 MGDrivE2-2.0.0/MGDrivE2/R/hazard-functions-mosy.R | 222 + MGDrivE2-2.0.0/MGDrivE2/R/hazard-main-decoupled.R |only MGDrivE2-2.0.0/MGDrivE2/R/human-SIS-ode-decoupled.R |only MGDrivE2-2.0.0/MGDrivE2/R/interventions.R |only MGDrivE2-2.0.0/MGDrivE2/R/sampling-ODE.R | 206 + MGDrivE2-2.0.0/MGDrivE2/R/sampling-PTS-decoupled.R |only MGDrivE2-2.0.0/MGDrivE2/R/sampling-trajectory-CSV.R | 4 MGDrivE2-2.0.0/MGDrivE2/R/sampling-trajectory-R-decoupled.R |only MGDrivE2-2.0.0/MGDrivE2/R/sampling-trajectory-R.R | 8 MGDrivE2-2.0.0/MGDrivE2/R/sampling-trajectory-decoupled-CSV.R |only MGDrivE2-2.0.0/MGDrivE2/R/zzz.R | 4 MGDrivE2-2.0.0/MGDrivE2/build/vignette.rds |binary MGDrivE2-2.0.0/MGDrivE2/inst/doc/advanced_topics.html | 411 +- MGDrivE2-2.0.0/MGDrivE2/inst/doc/epi-SEIR.html | 971 ++++-- MGDrivE2-2.0.0/MGDrivE2/inst/doc/epi-network.html | 656 ++-- MGDrivE2-2.0.0/MGDrivE2/inst/doc/epi-node-Imperial-decoupled.R |only MGDrivE2-2.0.0/MGDrivE2/inst/doc/epi-node-Imperial-decoupled.Rmd |only MGDrivE2-2.0.0/MGDrivE2/inst/doc/epi-node-Imperial-decoupled.html |only MGDrivE2-2.0.0/MGDrivE2/inst/doc/epi-node-SIS-decoupled.R |only MGDrivE2-2.0.0/MGDrivE2/inst/doc/epi-node-SIS-decoupled.Rmd |only MGDrivE2-2.0.0/MGDrivE2/inst/doc/epi-node-SIS-decoupled.html |only MGDrivE2-2.0.0/MGDrivE2/inst/doc/epi-node.R | 2 MGDrivE2-2.0.0/MGDrivE2/inst/doc/epi-node.Rmd | 43 MGDrivE2-2.0.0/MGDrivE2/inst/doc/epi-node.html | 466 ++- MGDrivE2-2.0.0/MGDrivE2/inst/doc/inhomogeneous.html | 1390 +++++----- MGDrivE2-2.0.0/MGDrivE2/inst/doc/lifecycle-network.html | 420 +-- MGDrivE2-2.0.0/MGDrivE2/inst/doc/lifecycle-node.html | 716 +++-- MGDrivE2-2.0.0/MGDrivE2/man/add_interventions.Rd |only MGDrivE2-2.0.0/MGDrivE2/man/batch_migration.Rd | 5 MGDrivE2-2.0.0/MGDrivE2/man/convert_prevalence_to_eir.Rd |only MGDrivE2-2.0.0/MGDrivE2/man/equilibrium_Imperial_decoupled.Rd |only MGDrivE2-2.0.0/MGDrivE2/man/equilibrium_Imperial_decoupled_human.Rd |only MGDrivE2-2.0.0/MGDrivE2/man/equilibrium_SEI_Imperial.Rd |only MGDrivE2-2.0.0/MGDrivE2/man/equilibrium_SEI_decoupled_human.Rd |only MGDrivE2-2.0.0/MGDrivE2/man/equilibrium_SEI_decoupled_mosy.Rd |only MGDrivE2-2.0.0/MGDrivE2/man/human_Imperial_ODE.Rd |only MGDrivE2-2.0.0/MGDrivE2/man/imperial_model_param_list_create.Rd |only MGDrivE2-2.0.0/MGDrivE2/man/make_Q_Imperial.Rd |only MGDrivE2-2.0.0/MGDrivE2/man/sim_trajectory_CSV.Rd | 2 MGDrivE2-2.0.0/MGDrivE2/man/sim_trajectory_CSV_decoupled.Rd |only MGDrivE2-2.0.0/MGDrivE2/man/sim_trajectory_R_decoupled.Rd |only MGDrivE2-2.0.0/MGDrivE2/man/sim_trajectory_base_CSV_decoupled.Rd |only MGDrivE2-2.0.0/MGDrivE2/man/sim_trajectory_base_R_decoupled_Imperial.Rd |only MGDrivE2-2.0.0/MGDrivE2/man/sim_trajectory_base_R_decoupled_SIS.Rd |only MGDrivE2-2.0.0/MGDrivE2/man/split_aggregate_CSV_decoupled.Rd |only MGDrivE2-2.0.0/MGDrivE2/man/spn_P_epi_decoupled_node.Rd |only MGDrivE2-2.0.0/MGDrivE2/man/spn_T_epi_decoupled_node.Rd |only MGDrivE2-2.0.0/MGDrivE2/man/spn_hazards_decoupled.Rd |only MGDrivE2-2.0.0/MGDrivE2/man/step_ODE_decoupled.Rd |only MGDrivE2-2.0.0/MGDrivE2/man/step_PTS_decoupled.Rd |only MGDrivE2-2.0.0/MGDrivE2/man/summarize_humans_epiImperial.Rd |only MGDrivE2-2.0.0/MGDrivE2/man/summarize_stats_CSV_decoupled.Rd |only MGDrivE2-2.0.0/MGDrivE2/vignettes/epi-node-Imperial-decoupled.Rmd |only MGDrivE2-2.0.0/MGDrivE2/vignettes/epi-node-SIS-decoupled.Rmd |only MGDrivE2-2.0.0/MGDrivE2/vignettes/epi-node.Rmd | 43 75 files changed, 4184 insertions(+), 2334 deletions(-)
Title: Unbiased Thematic Map Accuracy and Area
Description: Unbiased estimators of overall and per-class thematic map accuracy and area published in Olofsson et al. (2014) <doi:10.1016/j.rse.2014.02.015> and Stehman (2014) <doi:10.1080/01431161.2014.930207>.
Author: Hugo Costa [aut, cre]
Maintainer: Hugo Costa <hugoagcosta@gmail.com>
Diff between mapaccuracy versions 0.1.0 dated 2021-02-18 and 0.1.1 dated 2022-08-20
DESCRIPTION | 18 +++++++++++------- MD5 | 10 +++++----- NEWS.md | 7 ++++++- R/olofsson.R | 2 +- R/stehman2014.R | 4 ++-- man/olofsson.Rd | 2 +- 6 files changed, 26 insertions(+), 17 deletions(-)
Title: Knowledge Discovery by Accuracy Maximization
Description: An unsupervised and semi-supervised learning algorithm that performs feature extraction
from noisy and high-dimensional data. It facilitates identification of patterns representing underlying
groups on all samples in a data set. Based on Cacciatore S, Tenori L, Luchinat C, Bennett PR, MacIntyre DA.
(2017) Bioinformatics <doi:10.1093/bioinformatics/btw705> and Cacciatore S, Luchinat C, Tenori L. (2014)
Proc Natl Acad Sci USA <doi:10.1073/pnas.1220873111>.
Author: Stefano Cacciatore [aut, trl, cre]
,
Leonardo Tenori [aut]
Maintainer: Stefano Cacciatore <tkcaccia@gmail.com>
Diff between KODAMA versions 2.0 dated 2022-07-04 and 2.1 dated 2022-08-20
DESCRIPTION | 8 +- MD5 | 14 ++--- NAMESPACE | 4 - R/KOD.R | 83 ++++++++++++++++------------- build/vignette.rds |binary inst/doc/KODAMA.pdf |binary man/KODAMA.Rd | 2 man/core_cpp.Rd | 144 ++++++++++++++++++++++++++-------------------------- 8 files changed, 133 insertions(+), 122 deletions(-)
Title: The Hyperdirichlet Distribution, Mark 2
Description: A suite of routines for the hyperdirichlet distribution;
supersedes the 'hyperdirichlet' package. Uses 'disordR' discipline.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between hyper2 versions 2.0-3 dated 2022-03-22 and 3.0-0 dated 2022-08-20
hyper2-2.0-3/hyper2/NEWS.md |only hyper2-2.0-3/hyper2/inst/surfing_jsa_rebuttal.tex |only hyper2-2.0-3/hyper2/man/zermelo.Rd |only hyper2-3.0-0/hyper2/DESCRIPTION | 13 - hyper2-3.0-0/hyper2/MD5 | 148 +++++++++------- hyper2-3.0-0/hyper2/NAMESPACE | 15 + hyper2-3.0-0/hyper2/R/RcppExports.R | 32 +++ hyper2-3.0-0/hyper2/R/cheering.R |only hyper2-3.0-0/hyper2/R/hyper2.R | 124 +++++++++++-- hyper2-3.0-0/hyper2/R/hyper3.R |only hyper2-3.0-0/hyper2/R/listsuplist.R |only hyper2-3.0-0/hyper2/R/suplist.R | 32 +++ hyper2-3.0-0/hyper2/build/hyper2.pdf |binary hyper2-3.0-0/hyper2/build/partial.rdb |binary hyper2-3.0-0/hyper2/build/vignette.rds |binary hyper2-3.0-0/hyper2/data/NBA.rda |binary hyper2-3.0-0/hyper2/data/T20.rda |binary hyper2-3.0-0/hyper2/data/baseball.rda |only hyper2-3.0-0/hyper2/data/carcinoma.rda |only hyper2-3.0-0/hyper2/data/chess.rda |binary hyper2-3.0-0/hyper2/data/constructor.rda |only hyper2-3.0-0/hyper2/data/counterstrike.rda |binary hyper2-3.0-0/hyper2/data/curling.rda |binary hyper2-3.0-0/hyper2/data/eurodance.rda |binary hyper2-3.0-0/hyper2/data/eurovision.rda |binary hyper2-3.0-0/hyper2/data/formula1.rda |binary hyper2-3.0-0/hyper2/data/handover.rda |binary hyper2-3.0-0/hyper2/data/hepatitis.rda |only hyper2-3.0-0/hyper2/data/icons.rda |binary hyper2-3.0-0/hyper2/data/interzonal.rda |binary hyper2-3.0-0/hyper2/data/javelin.rda |only hyper2-3.0-0/hyper2/data/jester.rda |binary hyper2-3.0-0/hyper2/data/karate.rda |binary hyper2-3.0-0/hyper2/data/kka.rda |binary hyper2-3.0-0/hyper2/data/masterchef.rda |binary hyper2-3.0-0/hyper2/data/moto.rda |binary hyper2-3.0-0/hyper2/data/pentathlon.rda |binary hyper2-3.0-0/hyper2/data/powerboat.rda |binary hyper2-3.0-0/hyper2/data/rowing.rda |binary hyper2-3.0-0/hyper2/data/skating.rda |binary hyper2-3.0-0/hyper2/data/soling.rda |binary hyper2-3.0-0/hyper2/data/surfing.rda |binary hyper2-3.0-0/hyper2/data/table_tennis.rda |binary hyper2-3.0-0/hyper2/data/tennis.rda |binary hyper2-3.0-0/hyper2/data/universities.rda |binary hyper2-3.0-0/hyper2/data/volleyball.rda |binary hyper2-3.0-0/hyper2/data/volvo.rda |binary hyper2-3.0-0/hyper2/inst/carcinoma.Rmd |only hyper2-3.0-0/hyper2/inst/doc/hyper2.Rnw | 2 hyper2-3.0-0/hyper2/inst/doc/hyper2.pdf |binary hyper2-3.0-0/hyper2/inst/doc/hyper3.R |only hyper2-3.0-0/hyper2/inst/doc/hyper3.Rmd |only hyper2-3.0-0/hyper2/inst/doc/hyper3.html |only hyper2-3.0-0/hyper2/inst/doc/icons.html | 43 +++- hyper2-3.0-0/hyper2/inst/doc/integration.pdf |binary hyper2-3.0-0/hyper2/inst/elastic.R |only hyper2-3.0-0/hyper2/inst/fisher_inf_PL3.Rmd |only hyper2-3.0-0/hyper2/inst/global_liveability_ranking.Rmd |only hyper2-3.0-0/hyper2/inst/grad_weight.Rmd |only hyper2-3.0-0/hyper2/inst/hepatitis.Rmd |only hyper2-3.0-0/hyper2/inst/javelin.Rmd |only hyper2-3.0-0/hyper2/inst/loadlibrary.R |only hyper2-3.0-0/hyper2/inst/mann_whitney_wilcoxon.Rmd |only hyper2-3.0-0/hyper2/inst/multiset_hyper2.Rmd |only hyper2-3.0-0/hyper2/inst/plackett_luce_monster.Rmd |only hyper2-3.0-0/hyper2/inst/race3.Rmd |only hyper2-3.0-0/hyper2/man/Ops.hyper3.Rd |only hyper2-3.0-0/hyper2/man/Print.Rd | 19 +- hyper2-3.0-0/hyper2/man/attemptstable2supp3.Rd |only hyper2-3.0-0/hyper2/man/baseball.Rd |only hyper2-3.0-0/hyper2/man/carcinoma.Rd |only hyper2-3.0-0/hyper2/man/constructor.Rd |only hyper2-3.0-0/hyper2/man/cplusplus.Rd | 8 hyper2-3.0-0/hyper2/man/formula1.Rd | 6 hyper2-3.0-0/hyper2/man/ggrl.Rd | 21 +- hyper2-3.0-0/hyper2/man/hepatitis.Rd |only hyper2-3.0-0/hyper2/man/hyper3.Rd |only hyper2-3.0-0/hyper2/man/increment.Rd | 5 hyper2-3.0-0/hyper2/man/javelin.Rd |only hyper2-3.0-0/hyper2/man/jester.Rd | 8 hyper2-3.0-0/hyper2/man/kka.Rd | 89 +++++---- hyper2-3.0-0/hyper2/man/loglik.Rd | 42 +++- hyper2-3.0-0/hyper2/man/maxp.Rd | 11 - hyper2-3.0-0/hyper2/man/ordertrans.Rd | 29 ++- hyper2-3.0-0/hyper2/man/ordervec2supp3.Rd |only hyper2-3.0-0/hyper2/man/pairwise.Rd |only hyper2-3.0-0/hyper2/man/rhyper3.Rd |only hyper2-3.0-0/hyper2/man/suplist.Rd | 21 +- hyper2-3.0-0/hyper2/man/tests.Rd | 5 hyper2-3.0-0/hyper2/src/RcppExports.cpp | 136 ++++++++++++++ hyper2-3.0-0/hyper2/src/hyperdirichlet2.cpp | 20 -- hyper2-3.0-0/hyper2/src/hyperdirichlet2.h |only hyper2-3.0-0/hyper2/src/hyperdirichlet3.cpp |only hyper2-3.0-0/hyper2/vignettes/hyper2.Rnw | 2 hyper2-3.0-0/hyper2/vignettes/hyper3.Rmd |only 95 files changed, 626 insertions(+), 205 deletions(-)
Title: Retrieve and Analyze Clinical Trials in Public Registers
Description: A system for querying, retrieving and analyzing
protocol- and results-related information on clinical trials from
three public registers, the 'European Union Clinical Trials Register'
('EUCTR', <https://www.clinicaltrialsregister.eu/>),
'ClinicalTrials.gov' ('CTGOV', <https://clinicaltrials.gov/>) and
the 'ISRCTN' (<http://www.isrctn.com/>).
Trial information is downloaded, converted and stored in a database
('PostgreSQL', 'SQLite' or 'MongoDB'; via package 'nodbi').
Functions are included to identify deduplicated records,
to easily find and extract variables (fields) of interest even
from complex nesting as used by the registers, and
to update previous queries.
The package can be used for meta-analysis and trend-analysis of
the design and conduct as well as for results of clinical trials.
Author: Ralf Herold [aut, cre]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between ctrdata versions 1.10.1 dated 2022-07-24 and 1.10.2 dated 2022-08-20
DESCRIPTION | 8 MD5 | 72 +-- NAMESPACE | 1 NEWS.md | 12 R/ctrdata-registers.R | 4 R/main.R | 43 +- R/utils.R | 316 ++++++++-------- README.md | 253 ++++++------ inst/extdata |only inst/tinytest/ctrdata_isrctn.R | 27 + inst/tinytest/more_test_ctrdata_mongo_remote_rw_ctgov.R | 4 inst/tinytest/more_test_ctrdata_mongo_remote_rw_euctr.R | 5 inst/tinytest/more_test_ctrdata_postgres_ctgov.R | 4 inst/tinytest/more_test_ctrdata_postgres_euctr.R | 2 inst/tinytest/more_test_ctrdata_postgres_isrctn.R | 4 inst/tinytest/setup_ctrdata.R | 2 inst/tinytest/test_ctrdata_mongo_local_ctgov.R | 4 inst/tinytest/test_ctrdata_mongo_local_euctr.R | 5 inst/tinytest/test_ctrdata_mongo_local_isrctn.R | 4 inst/tinytest/test_ctrdata_other_functions.R | 30 + inst/tinytest/test_ctrdata_sqlite_ctgov.R | 4 inst/tinytest/test_ctrdata_sqlite_euctr.R | 2 inst/tinytest/test_ctrdata_sqlite_isrctn.R | 4 man/ctrFindActiveSubstanceSynonyms.Rd | 4 man/ctrGetQueryUrl.Rd | 24 - man/ctrLoadQueryIntoDb.Rd | 10 man/ctrOpenSearchPagesInBrowser.Rd | 14 man/ctrdata-registers.Rd | 4 man/dbFindFields.Rd | 8 man/dbFindIdsUniqueTrials.Rd | 14 man/dbGetFieldsIntoDf.Rd | 25 - man/dbQueryHistory.Rd | 8 man/dfListExtractKey.Rd | 26 - man/dfMergeTwoVariablesRelevel.Rd | 14 man/dfName2Value.Rd | 81 ++-- man/dfTrials2Long.Rd | 16 man/figures/README-ctrdata_json_postgresql.jpg |only man/installCygwinWindowsDoInstall.Rd | 5 38 files changed, 607 insertions(+), 456 deletions(-)
Title: A Compilation of Applicability Domain Methods
Description: A modeling package compiling applicability domain methods in
R. It combines different methods to measure the amount of
extrapolation new samples can have from the training set. See Gadaleta et
al (2016) <doi:10.4018/IJQSPR.2016010102> for an overview of
applicability domains.
Author: Marly Gotti [aut, cre],
Max Kuhn [aut],
RStudio [cph]
Maintainer: Marly Gotti <marlygotti@gmail.com>
Diff between applicable versions 0.0.1.2 dated 2020-07-12 and 0.1.0 dated 2022-08-20
applicable-0.0.1.2/applicable/tests/testthat/out |only applicable-0.1.0/applicable/DESCRIPTION | 42 - applicable-0.1.0/applicable/MD5 | 112 +-- applicable-0.1.0/applicable/NAMESPACE | 8 applicable-0.1.0/applicable/R/data.R | 10 applicable-0.1.0/applicable/R/hat_values-fit.R | 9 applicable-0.1.0/applicable/R/hat_values-score.R | 11 applicable-0.1.0/applicable/R/helpers.R | 14 applicable-0.1.0/applicable/R/isolation-fit.R |only applicable-0.1.0/applicable/R/isolation-score.R |only applicable-0.1.0/applicable/R/misc.R | 2 applicable-0.1.0/applicable/R/pca-fit.R | 9 applicable-0.1.0/applicable/R/pca-score.R | 13 applicable-0.1.0/applicable/R/plot.R | 30 applicable-0.1.0/applicable/R/print.R | 31 applicable-0.1.0/applicable/R/score.R | 2 applicable-0.1.0/applicable/R/similarity.R | 48 - applicable-0.1.0/applicable/R/zzz.R | 2 applicable-0.1.0/applicable/README.md | 27 applicable-0.1.0/applicable/build/partial.rdb |only applicable-0.1.0/applicable/build/vignette.rds |binary applicable-0.1.0/applicable/data/ames_new.rda |binary applicable-0.1.0/applicable/inst/WORDLIST | 34 - applicable-0.1.0/applicable/inst/doc/binary-data.Rmd | 2 applicable-0.1.0/applicable/inst/doc/binary-data.html | 122 ++- applicable-0.1.0/applicable/inst/doc/continuous-data.R | 18 applicable-0.1.0/applicable/inst/doc/continuous-data.Rmd | 26 applicable-0.1.0/applicable/inst/doc/continuous-data.html | 315 ++++++---- applicable-0.1.0/applicable/man/ames_new.Rd | 6 applicable-0.1.0/applicable/man/apd_hat_values.Rd | 1 applicable-0.1.0/applicable/man/apd_isolation.Rd |only applicable-0.1.0/applicable/man/apd_pca.Rd | 1 applicable-0.1.0/applicable/man/apd_similarity.Rd | 8 applicable-0.1.0/applicable/man/applicable-package.Rd | 7 applicable-0.1.0/applicable/man/autoplot.apd_pca.Rd | 5 applicable-0.1.0/applicable/man/autoplot.apd_similarity.Rd | 7 applicable-0.1.0/applicable/man/okc_binary.Rd | 2 applicable-0.1.0/applicable/man/print.apd_hat_values.Rd | 1 applicable-0.1.0/applicable/man/print.apd_pca.Rd | 1 applicable-0.1.0/applicable/man/print.apd_similarity.Rd | 7 applicable-0.1.0/applicable/man/score.apd_hat_values.Rd | 5 applicable-0.1.0/applicable/man/score.apd_isolation.Rd |only applicable-0.1.0/applicable/man/score.apd_pca.Rd | 3 applicable-0.1.0/applicable/tests/spelling.R | 8 applicable-0.1.0/applicable/tests/testthat/_snaps |only applicable-0.1.0/applicable/tests/testthat/test-hat_values-fit.R | 48 - applicable-0.1.0/applicable/tests/testthat/test-hat_values-score.R | 30 applicable-0.1.0/applicable/tests/testthat/test-isolation-fit.R |only applicable-0.1.0/applicable/tests/testthat/test-isolation-score.R |only applicable-0.1.0/applicable/tests/testthat/test-misc.R | 10 applicable-0.1.0/applicable/tests/testthat/test-pca-fit.R | 29 applicable-0.1.0/applicable/tests/testthat/test-pca-score.R | 40 - applicable-0.1.0/applicable/tests/testthat/test-plot.R | 2 applicable-0.1.0/applicable/tests/testthat/test-print.R | 29 applicable-0.1.0/applicable/tests/testthat/test-similarity.R | 102 +-- applicable-0.1.0/applicable/vignettes/binary-data.Rmd | 2 applicable-0.1.0/applicable/vignettes/continuous-data.Rmd | 26 57 files changed, 671 insertions(+), 596 deletions(-)
Title: Custom 'xaringan' CSS Themes
Description: Create beautifully color-coordinated and customized themes
for your 'xaringan' slides, without writing any CSS. Complete your
slide theme with 'ggplot2' themes that match the font and colors used
in your slides. Customized styles can be created directly in your
slides' 'R Markdown' source file or in a separate external script.
Author: Garrick Aden-Buie [aut, cre]
Maintainer: Garrick Aden-Buie <garrick@adenbuie.com>
Diff between xaringanthemer versions 0.4.1 dated 2021-11-21 and 0.4.2 dated 2022-08-20
DESCRIPTION | 10 MD5 | 86 ++-- NEWS.md | 11 R/style_duo.R | 6 R/style_duo_accent.R | 15 R/style_duo_accent_inverse.R | 15 R/style_mono_accent.R | 15 R/style_mono_accent_inverse.R | 15 R/style_mono_dark.R | 15 R/style_mono_light.R | 15 R/sysdata.rda |binary build/vignette.rds |binary inst/doc/ggplot2-themes.html | 427 +++++++++++++++++++++--- inst/doc/template-variables.html | 282 ++++++++++++++- inst/doc/xaringanthemer.html | 413 ++++++++++++++++++++--- inst/resources/template.css | 4 inst/scripts/generate_theme_functions.R | 4 man/figures/index-theme_xaringan_demo-1.png |binary man/style_duo.Rd | 11 man/style_duo_accent.Rd | 25 - man/style_duo_accent_inverse.Rd | 25 - man/style_mono_accent.Rd | 19 - man/style_mono_accent_inverse.Rd | 19 - man/style_mono_dark.Rd | 19 - man/style_mono_light.Rd | 19 - man/style_solarized_dark.Rd | 7 man/style_solarized_light.Rd | 7 man/style_xaringan.Rd | 11 man/theme_xaringan_set_defaults.Rd | 4 man/xaringanthemer-package.Rd | 2 tests/testthat/css/duo-header_bg.css | 4 tests/testthat/css/duo.css | 4 tests/testthat/css/duo_accent.css | 4 tests/testthat/css/duo_accent_inverse.css | 4 tests/testthat/css/google_fonts.css | 4 tests/testthat/css/mono_accent.css | 4 tests/testthat/css/mono_accent_inverse.css | 4 tests/testthat/css/mono_dark.css | 4 tests/testthat/css/mono_light-header_bg.css | 4 tests/testthat/css/mono_light.css | 4 tests/testthat/css/solarized_dark-header_bg.css | 4 tests/testthat/css/solarized_dark.css | 4 tests/testthat/css/solarized_light.css | 4 tests/testthat/css/xaringan.css | 4 44 files changed, 1250 insertions(+), 307 deletions(-)
More information about xaringanthemer at CRAN
Permanent link
Title: Integrated Toolkit for Psychological Analysis and Modeling in R
Description: A beginner-friendly R package for modeling in psychology or
related field. It allows fitting models, plotting, checking goodness
of fit, and model assumption violations all in one place. It also
produces beautiful and easy-to-read output.
Author: Jason Moy [aut, cre]
Maintainer: Jason Moy <jasonmoy28@gmail.com>
Diff between psycModel versions 0.3.2 dated 2021-09-05 and 0.3.3 dated 2022-08-20
psycModel-0.3.2/psycModel/R/integrated_model_summary.R |only psycModel-0.3.2/psycModel/R/integrated_multilevel_model_summary.R |only psycModel-0.3.2/psycModel/man/integrated_model_summary.Rd |only psycModel-0.3.2/psycModel/man/integrated_multilevel_model_summary.Rd |only psycModel-0.3.3/psycModel/DESCRIPTION | 13 psycModel-0.3.3/psycModel/MD5 | 86 - psycModel-0.3.3/psycModel/NAMESPACE | 5 psycModel-0.3.3/psycModel/NEWS.md | 4 psycModel-0.3.3/psycModel/R/cfa_groupwise.R | 1 psycModel-0.3.3/psycModel/R/cfa_summary.R | 2 psycModel-0.3.3/psycModel/R/compare_fit.R | 2 psycModel-0.3.3/psycModel/R/glme_model.R | 11 psycModel-0.3.3/psycModel/R/lm_model.R | 1 psycModel-0.3.3/psycModel/R/lm_model_summary.R |only psycModel-0.3.3/psycModel/R/lme_model.R | 2 psycModel-0.3.3/psycModel/R/lme_model_summary.R |only psycModel-0.3.3/psycModel/R/mediation_summary.R | 22 psycModel-0.3.3/psycModel/R/model_summary.R | 70 - psycModel-0.3.3/psycModel/R/simple_slope.R | 121 +- psycModel-0.3.3/psycModel/R/three_way_interaction_plot.R | 132 -- psycModel-0.3.3/psycModel/R/two_way_interaction_plot.R | 225 ++-- psycModel-0.3.3/psycModel/R/utils-get-interaction-term.R |only psycModel-0.3.3/psycModel/R/utils-get-predict-df.R |only psycModel-0.3.3/psycModel/R/utils-interaction-check.R |only psycModel-0.3.3/psycModel/R/utils-label-name.R |only psycModel-0.3.3/psycModel/R/utils-tidy-eval.R | 2 psycModel-0.3.3/psycModel/README.md | 5 psycModel-0.3.3/psycModel/build/vignette.rds |binary psycModel-0.3.3/psycModel/inst/doc/brief-introduction-to-select-syntax.html | 289 +++++ psycModel-0.3.3/psycModel/inst/doc/quick-introduction.R | 4 psycModel-0.3.3/psycModel/inst/doc/quick-introduction.Rmd | 4 psycModel-0.3.3/psycModel/inst/doc/quick-introduction.html | 489 +++++++--- psycModel-0.3.3/psycModel/man/cfa_summary.Rd | 2 psycModel-0.3.3/psycModel/man/get_interaction_term.Rd |only psycModel-0.3.3/psycModel/man/get_predict_df.Rd |only psycModel-0.3.3/psycModel/man/glme_model.Rd | 9 psycModel-0.3.3/psycModel/man/interaction_check.Rd |only psycModel-0.3.3/psycModel/man/label_name.Rd |only psycModel-0.3.3/psycModel/man/lm_model_summary.Rd |only psycModel-0.3.3/psycModel/man/lme_multilevel_model_summary.Rd |only psycModel-0.3.3/psycModel/man/mediation_summary.Rd | 3 psycModel-0.3.3/psycModel/man/model_summary.Rd | 7 psycModel-0.3.3/psycModel/man/simple_slope.Rd | 15 psycModel-0.3.3/psycModel/man/three_way_interaction_plot.Rd | 13 psycModel-0.3.3/psycModel/man/tidyeval.Rd | 2 psycModel-0.3.3/psycModel/man/two_way_interaction_plot.Rd | 29 psycModel-0.3.3/psycModel/tests/testthat/test-integrated-model-summary.R | 10 psycModel-0.3.3/psycModel/tests/testthat/test-integrated-multilevel-model-summary.R | 32 psycModel-0.3.3/psycModel/tests/testthat/test-lme-model.R | 6 psycModel-0.3.3/psycModel/tests/testthat/test-model-summary.R | 112 +- psycModel-0.3.3/psycModel/tests/testthat/test-simple-slope.R | 11 psycModel-0.3.3/psycModel/vignettes/quick-introduction.Rmd | 4 52 files changed, 1076 insertions(+), 669 deletions(-)
Title: EM Algorithm for Model-Based Clustering of Finite Mixture
Gaussian Distribution
Description: EM algorithms and several efficient
initialization methods for model-based clustering of finite
mixture Gaussian distribution with unstructured dispersion
in both of unsupervised and semi-supervised learning.
Author: Wei-Chen Chen [aut, cre],
Ranjan Maitra [aut],
Volodymyr Melnykov [ctb],
Dan Nettleton [ctb],
David Faden [ctb],
Rouben Rostamian [ctb],
R Core team [ctb]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between EMCluster versions 0.2-13 dated 2021-03-16 and 0.2-14 dated 2022-08-20
ChangeLog | 8 ++++++++ DESCRIPTION | 14 +++++++------- MD5 | 18 +++++++++--------- NAMESPACE | 2 +- R/fcn_dlmvnorm.r | 29 ++++++++++++++++++++++------- R/fcn_init_EM.r | 1 + R/fcn_mytool.r | 2 +- R/lmt_main.r | 2 +- R/lmt_project_to_2d.r | 12 ++++++++---- man/a0_project.on.2d.Rd | 2 +- 10 files changed, 59 insertions(+), 31 deletions(-)
Title: Methods for Partial Linear Single Index Model
Description: Estimation, hypothesis tests, and variable selection in partially linear single-index models. Please see H. (2010) at <doi:10.1214/10-AOS835> for more details.
Author: Shunyao Wu, Qi Zhang, Zhiruo Li, Hua Liang
Maintainer: Shunyao Wu <wushunyao@qdu.edu.cn>
Diff between PLSiMCpp versions 1.0.2 dated 2022-05-10 and 1.0.3 dated 2022-08-20
DESCRIPTION | 12 ++++++------ MD5 | 30 +++++++++++++++--------------- R/plsim.MAVE.r | 8 ++++---- R/plsim.bw.r | 4 ++-- R/plsim.est.r | 8 ++++---- R/plsim.ini.r | 4 ++-- R/plsim.lam.r | 4 ++-- R/plsim.vs.hard.r | 4 ++-- R/plsim.vs.soft.r | 8 ++++---- man/plsim.MAVE.Rd | 8 ++++---- man/plsim.bw.Rd | 4 ++-- man/plsim.est.Rd | 8 ++++---- man/plsim.ini.Rd | 4 ++-- man/plsim.lam.Rd | 4 ++-- man/plsim.vs.hard.Rd | 4 ++-- man/plsim.vs.soft.Rd | 8 ++++---- 16 files changed, 61 insertions(+), 61 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-18 0.2.4
2021-07-25 0.2.3
2021-07-16 0.2.2
2021-02-17 0.2.1
2020-11-06 0.2.0
2020-07-27 0.1.8
2020-07-18 0.1.7
2020-07-17 0.1.6
2020-07-01 0.1.5
2020-05-18 0.1.4
2020-03-16 0.1.3
2020-02-19 0.1.2
2020-02-04 0.1.1
2019-12-23 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-14 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-15 0.2.4
2021-10-05 0.2.3
2021-09-22 0.2.2
2021-07-29 0.2.1
2021-07-26 0.2.0
2021-03-17 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-03-27 1.6.9
2022-03-22 1.6.8
2022-02-21 1.6.7
2022-02-15 1.6.6
2022-01-17 1.6.4
2021-10-05 1.6.2
2021-09-06 1.6.0
2021-07-17 1.5.6
2021-07-14 1.5.4
2021-04-17 1.5.2
2021-02-16 1.5.0
2020-12-12 1.4.8
2020-11-07 1.4.7
2020-11-02 1.4.6
2020-10-30 1.4.5
2020-09-27 1.4.4
2020-08-26 1.4.3
2020-07-22 1.4.1
2020-07-22 1.4.2
2020-07-20 1.4.0
2020-05-20 1.3.7
2020-04-16 1.3.6
2020-03-19 1.3.5
2020-02-19 1.3.4
2020-01-29 1.3.3
2020-01-12 1.3.2
2019-11-25 1.3.1
2019-10-31 1.3.0
2019-10-02 1.2.0
2019-08-27 1.1.0
2019-07-25 1.0.1
2019-07-19 1.0.0
Title: Versatile Curation of Table Metadata
Description: A YAML-based
mechanism for working with table metadata. Supports
compact syntax for creating, modifying, viewing, exporting,
importing, displaying, and plotting metadata coded as column
attributes. The 'yamlet' dialect is valid 'YAML' with
defaults and conventions chosen to improve readability.
See ?yamlet, ?decorate.data.frame and ?modify.default.
See ?read_yamlet ?write_yamlet, ?io_csv, and ?ggplot.decorated.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between yamlet versions 0.9.2 dated 2022-07-13 and 0.9.3 dated 2022-08-20
DESCRIPTION | 6 +-- MD5 | 25 ++++++++------- R/io_csv.R | 60 +++++++++++++++++++++++++++++--------- R/io_res.R | 2 - R/io_table.R | 10 +++--- inst/doc/yamlet-introduction.html | 36 ++++++++++++---------- inst/extdata/xanomeline.R | 10 +----- man/io_csv.character.Rd | 12 ++++++- man/io_csv.data.frame.Rd | 17 ++++++++-- man/io_res.Rd | 2 - man/io_table.data.frame.Rd | 4 +- tests/testthat/Rplots.pdf |binary tests/testthat/test-gz.R |only tests/testthat/test-yamlet.R | 8 +++++ 14 files changed, 126 insertions(+), 66 deletions(-)
Title: Data Table Back-End for 'dplyr'
Description: Provides a data.table backend for 'dplyr'. The goal of
'dtplyr' is to allow you to write 'dplyr' code that is automatically
translated to the equivalent, but usually much faster, data.table
code.
Author: Hadley Wickham [cre, aut],
Maximilian Girlich [aut],
Mark Fairbanks [aut],
Ryan Dickerson [aut],
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between dtplyr versions 1.2.1 dated 2022-01-19 and 1.2.2 dated 2022-08-20
DESCRIPTION | 8 - MD5 | 22 ++-- NEWS.md | 4 build/dtplyr.pdf |binary inst/doc/translation.html | 134 ++++++++++++++++++------- man/drop_na.dtplyr_step.Rd | 2 man/dtplyr-package.Rd | 2 man/nest.dtplyr_step.Rd | 12 +- man/pivot_longer.dtplyr_step.Rd | 39 ++----- man/pivot_wider.dtplyr_step.Rd | 14 -- man/relocate.dtplyr_step.Rd | 6 - tests/testthat/_snaps/step-call-pivot_wider.md | 6 - 12 files changed, 149 insertions(+), 100 deletions(-)
Title: Bayesian Inference with Laplace Approximations and P-Splines
Description: Laplace approximations and penalized B-splines are combined
for fast Bayesian inference in latent Gaussian models. The routines can be
used to fit survival models, especially proportional hazards and promotion
time cure models (Gressani, O. and Lambert, P. (2018)
<doi:10.1016/j.csda.2018.02.007>). The Laplace-P-spline methodology can also
be implemented for inference in (generalized) additive models
(Gressani, O. and Lambert, P. (2021) <doi:10.1016/j.csda.2020.107088>).
See the associated website for more information and examples.
Author: Oswaldo Gressani [aut, cre] ,
Philippe Lambert [aut, ths]
Maintainer: Oswaldo Gressani <oswaldo_gressani@hotmail.fr>
Diff between blapsr versions 0.5.5 dated 2020-10-19 and 0.6.1 dated 2022-08-20
DESCRIPTION | 8 - MD5 | 114 +++++++++++++------------- NEWS.md | 4 R/S3_amlps_plot.R | 2 R/S3_amlps_print.R | 2 R/S3_coxlps_plot.R | 2 R/S3_coxlps_print.R | 2 R/S3_curelps_plot.R | 2 R/S3_curelps_print.R | 2 R/S3_gamlps_plot.R | 2 R/S3_gamlps_print.R | 2 R/amlps.R | 8 - R/amlps_object.R | 4 R/coxlps.R | 16 +-- R/coxlps_baseline.R | 22 ++--- R/coxlps_object.R | 4 R/cubicbs.R | 16 +-- R/curelps.R | 34 ++++--- R/curelps_extract.R | 2 R/curelps_object.R | 4 R/ecog1684.R | 1 R/gamlps.R | 6 - R/gamlps_object.R | 4 R/penaltyplot.R | 8 - R/simcuredata.R | 6 - R/simgamdata.R | 4 R/simsurvdata.R | 25 ++--- R/snmatch.R | 14 +-- README.md | 4 build/vignette.rds |binary inst/CITATION | 4 inst/COPYRIGHTS | 2 inst/doc/blapsr-vignette.html | 101 +++-------------------- man/amlps.Rd | 5 - man/amlps.object.Rd | 4 man/coxlps.Rd | 16 +-- man/coxlps.baseline.Rd | 23 ++--- man/coxlps.object.Rd | 4 man/cubicbs.Rd | 16 +-- man/curelps.Rd | 14 +-- man/curelps.extract.Rd | 2 man/curelps.object.Rd | 4 man/ecog1684.Rd | 1 man/gamlps.Rd | 4 man/gamlps.object.Rd | 4 man/penaltyplot.Rd | 2 man/plot.amlps.Rd | 2 man/plot.coxlps.Rd | 2 man/plot.curelps.Rd | 2 man/plot.gamlps.Rd | 2 man/print.amlps.Rd | 2 man/print.coxlps.Rd | 2 man/print.curelps.Rd | 2 man/print.gamlps.Rd | 2 man/simcuredata.Rd | 6 - man/simgamdata.Rd | 4 man/simsurvdata.Rd | 23 ++--- man/snmatch.Rd | 180 +++++++++++++++++++++--------------------- 58 files changed, 343 insertions(+), 416 deletions(-)
Title: Spatial Seemingly Unrelated Regression Models
Description: A collection of functions to test and estimate Seemingly
Unrelated Regression (usually called SUR) models, with spatial structure, by maximum
likelihood and three-stage least squares. The package estimates the
most common spatial specifications, that is, SUR with Spatial Lag of
X regressors (called SUR-SLX), SUR with Spatial Lag Model (called SUR-SLM),
SUR with Spatial Error Model (called SUR-SEM), SUR with Spatial Durbin Model (called SUR-SDM),
SUR with Spatial Durbin Error Model (called SUR-SDEM),
SUR with Spatial Autoregressive terms and Spatial Autoregressive
Disturbances (called SUR-SARAR), SUR-SARAR with Spatial Lag of X
regressors (called SUR-GNM) and SUR with Spatially Independent Model (called SUR-SIM).
The methodology of these models can be found in next references
Mur, J., Lopez, F., and Herrera, M. (2010) <doi:10.1080/17421772.2010.516443>
Lopez, F.A., Mur, J., and Angulo, A. (2014) <doi:10.1007/s00168-014-0624-2>.
Author: Ana Angulo [aut],
Fernando A Lopez [aut],
Roman Minguez [aut, cre],
Jesus Mur [aut]
Maintainer: Roman Minguez <roman.minguez@uclm.es>
Diff between spsur versions 1.0.2.1 dated 2022-04-22 and 1.0.2.2 dated 2022-08-20
spsur-1.0.2.1/spsur/R/lrtestspsur.R |only spsur-1.0.2.1/spsur/R/package-spsur.R |only spsur-1.0.2.1/spsur/R/spsurgs3sls.R |only spsur-1.0.2.1/spsur/demo/demo_lrtestspsur.R |only spsur-1.0.2.1/spsur/man/lrtestspsur.Rd |only spsur-1.0.2.1/spsur/man/spsur.Rd |only spsur-1.0.2.1/spsur/man/spsurgs3sls.Rd |only spsur-1.0.2.1/spsur/vignettes/Vignette_User_Guide.Rmd.orig |only spsur-1.0.2.1/spsur/vignettes/montecarlo_spsur_spse.Rmd.orig |only spsur-1.0.2.1/spsur/vignettes/plotgeom-1-vignette1.png |only spsur-1.0.2.1/spsur/vignettes/quantilemap-1-vignette1.png |only spsur-1.0.2.1/spsur/vignettes/residualquantilemap-1-vignette1.png |only spsur-1.0.2.1/spsur/vignettes/residualsurquantilemap-1-vignette1.png |only spsur-1.0.2.1/spsur/vignettes/spsur-vs-spatialreg.Rmd.orig |only spsur-1.0.2.1/spsur/vignettes/spsur-vs-spse.Rmd.orig |only spsur-1.0.2.1/spsur/vignettes/spsur_pysal.Rmd.orig |only spsur-1.0.2.1/spsur/vignettes/unnamed-chunk-2-1-vignette1.png |only spsur-1.0.2.1/spsur/vignettes/unnamed-chunk-2-2-vignette1.png |only spsur-1.0.2.1/spsur/vignettes/unnamed-chunk-2-3-vignette1.png |only spsur-1.0.2.1/spsur/vignettes/unnamed-chunk-4-1-vignette1.png |only spsur-1.0.2.1/spsur/vignettes/unnamed-chunk-5-1-vignette1.png |only spsur-1.0.2.1/spsur/vignettes/unnamed-chunk-6-1-vignette1.png |only spsur-1.0.2.1/spsur/vignettes/unnamed-chunk-7-1-vignette1.png |only spsur-1.0.2.1/spsur/vignettes/unnamed-chunk-8-1-vignette1.png |only spsur-1.0.2.2/spsur/DESCRIPTION | 35 spsur-1.0.2.2/spsur/MD5 | 130 spsur-1.0.2.2/spsur/NAMESPACE | 173 spsur-1.0.2.2/spsur/R/cov_spsur_f.R | 55 spsur-1.0.2.2/spsur/R/datasets.R | 33 spsur-1.0.2.2/spsur/R/f_surGRT_beta.R | 34 spsur-1.0.2.2/spsur/R/fit_spsur.R | 18 spsur-1.0.2.2/spsur/R/fit_spsur_3sls.R | 198 spsur-1.0.2.2/spsur/R/impactspsur.R | 2 spsur-1.0.2.2/spsur/R/llikspsur.R | 18 spsur-1.0.2.2/spsur/R/spSUR-package.R |only spsur-1.0.2.2/spsur/R/spsur3sls.R | 12 spsur-1.0.2.2/spsur/R/spsurml.R | 16 spsur-1.0.2.2/spsur/R/spsurtime.R | 2 spsur-1.0.2.2/spsur/R/sur3_spdiag.R | 22 spsur-1.0.2.2/spsur/R/wald_betas.R | 4 spsur-1.0.2.2/spsur/build/vignette.rds |binary spsur-1.0.2.2/spsur/data/spc.RData |binary spsur-1.0.2.2/spsur/demo/00Index | 1 spsur-1.0.2.2/spsur/inst/CITATION | 62 spsur-1.0.2.2/spsur/inst/doc/Vignette_User_Guide.Rmd | 2055 +++------ spsur-1.0.2.2/spsur/inst/doc/Vignette_User_Guide.html | 2089 +++------- spsur-1.0.2.2/spsur/inst/doc/montecarlo_spsur_spse.Rmd | 2 spsur-1.0.2.2/spsur/inst/doc/montecarlo_spsur_spse.html | 23 spsur-1.0.2.2/spsur/inst/doc/spsur-vs-spatialreg.Rmd | 495 -- spsur-1.0.2.2/spsur/inst/doc/spsur-vs-spatialreg.html | 526 +- spsur-1.0.2.2/spsur/inst/doc/spsur_pysal.Rmd | 10 spsur-1.0.2.2/spsur/inst/doc/spsur_pysal.html | 23 spsur-1.0.2.2/spsur/man/NCOVR.sf.Rd | 108 spsur-1.0.2.2/spsur/man/Wspc.Rd | 58 spsur-1.0.2.2/spsur/man/dgp_spsur.Rd | 696 +-- spsur-1.0.2.2/spsur/man/impactspsur.Rd | 604 +- spsur-1.0.2.2/spsur/man/lmtestspsur.Rd | 548 +- spsur-1.0.2.2/spsur/man/lr_betas.Rd | 302 - spsur-1.0.2.2/spsur/man/methods_spsur.Rd | 206 spsur-1.0.2.2/spsur/man/print.summary.spsur.Rd | 66 spsur-1.0.2.2/spsur/man/spain.covid.Rd | 242 - spsur-1.0.2.2/spsur/man/spain.covid.sf.Rd | 42 spsur-1.0.2.2/spsur/man/spc.Rd | 81 spsur-1.0.2.2/spsur/man/spsur-package.Rd |only spsur-1.0.2.2/spsur/man/spsur3sls.Rd | 638 +-- spsur-1.0.2.2/spsur/man/spsurml.Rd | 1122 ++--- spsur-1.0.2.2/spsur/man/spsurtime.Rd | 528 +- spsur-1.0.2.2/spsur/man/summary.spsur.Rd | 78 spsur-1.0.2.2/spsur/man/wald_betas.Rd | 297 - spsur-1.0.2.2/spsur/man/wald_deltas.Rd | 288 - spsur-1.0.2.2/spsur/vignettes/Vignette_User_Guide.Rmd | 2055 +++------ spsur-1.0.2.2/spsur/vignettes/bibliosure.bib | 32 spsur-1.0.2.2/spsur/vignettes/montecarlo_spsur_spse.Rmd | 2 spsur-1.0.2.2/spsur/vignettes/quantilemap-1.png |only spsur-1.0.2.2/spsur/vignettes/residualquantilemap-1.png |only spsur-1.0.2.2/spsur/vignettes/residualsurquantilemap-1.png |only spsur-1.0.2.2/spsur/vignettes/spsur-vs-spatialreg.Rmd | 495 -- spsur-1.0.2.2/spsur/vignettes/spsur_pysal.Rmd | 10 spsur-1.0.2.2/spsur/vignettes/unnamed-chunk-2-2.png |only spsur-1.0.2.2/spsur/vignettes/unnamed-chunk-2-3.png |only spsur-1.0.2.2/spsur/vignettes/unnamed-chunk-4-1.png |only spsur-1.0.2.2/spsur/vignettes/unnamed-chunk-7-1.png |only spsur-1.0.2.2/spsur/vignettes/unnamed-chunk-8-1.png |only 83 files changed, 6453 insertions(+), 8083 deletions(-)
Title: Base Class and Methods for 'gson' Format
Description: Proposes a new file format ('gson') for storing gene set and related information, and provides read, write and other utilities to process this file format.
Author: Guangchuang Yu [aut, cre, cph]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between gson versions 0.0.7 dated 2022-08-09 and 0.0.8 dated 2022-08-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/IO.R | 8 +++++--- 4 files changed, 15 insertions(+), 9 deletions(-)
Title: Working with Audio and Video in R
Description: Bindings to 'FFmpeg' <http://www.ffmpeg.org/> AV library for working with
audio and video in R. Generates high quality video from images or R graphics with
custom audio. Also offers high performance tools for reading raw audio, creating
'spectrograms', and converting between countless audio / video formats. This package
interfaces directly to the C API and does not require any command line utilities.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between av versions 0.8.0 dated 2022-08-13 and 0.8.1 dated 2022-08-20
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- NEWS | 5 ++++- src/avcompat.h |only src/fft.c | 5 +---- src/info.c | 4 +--- src/video.c | 5 +---- 7 files changed, 16 insertions(+), 20 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-09-08 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-02-16 1.1.1
2021-02-09 1.1.0
2020-08-03 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-22 0.2.0
2019-07-01 0.1.0
Title: Rigorous - Positron Emission Tomography
Description: Image analysis techniques for positron emission tomography
(PET) that form part of the Rigorous Analytics bundle.
Author: Brandon Whitcher
Maintainer: Brandon Whitcher <bwhitcher@gmail.com>
Diff between oro.pet versions 0.2.6 dated 2017-10-06 and 0.2.7 dated 2022-08-20
oro.pet-0.2.6/oro.pet/NEWS.md |only oro.pet-0.2.7/oro.pet/DESCRIPTION | 15 +-- oro.pet-0.2.7/oro.pet/MD5 | 35 +++----- oro.pet-0.2.7/oro.pet/R/hill.R | 6 - oro.pet-0.2.7/oro.pet/R/model.R | 2 oro.pet-0.2.7/oro.pet/R/occupancy.R | 4 oro.pet-0.2.7/oro.pet/R/plot.R | 2 oro.pet-0.2.7/oro.pet/R/qiba.R | 4 oro.pet-0.2.7/oro.pet/R/reference.R | 6 - oro.pet-0.2.7/oro.pet/R/suv.R | 4 oro.pet-0.2.7/oro.pet/README.md | 7 + oro.pet-0.2.7/oro.pet/man/compartmentalModel.Rd | 2 oro.pet-0.2.7/oro.pet/man/hillEquation.Rd | 14 ++- oro.pet-0.2.7/oro.pet/man/multilinearReferenceTissueModel.Rd | 12 ++ oro.pet-0.2.7/oro.pet/man/occupancy.Rd | 4 oro.pet-0.2.7/oro.pet/man/plotBindingPotential.Rd | 28 +++++- oro.pet-0.2.7/oro.pet/man/qiba.Rd | 48 +++++++---- oro.pet-0.2.7/oro.pet/man/simplifiedReferenceTissueModel.Rd | 15 ++- oro.pet-0.2.7/oro.pet/man/suv.Rd | 5 - 19 files changed, 135 insertions(+), 78 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] ,
David Hutchinson [ctb],
Dewey Dunnington [ctb],
Ryan Whaley [ctb],
Province of British Columbia [cph],
Government of Canada [dtc],
Luke Winslow [rev] ,
Laura DeCicco [rev]
Maintainer: Sam Albers <sam.albers@gmail.com>
Diff between tidyhydat versions 0.5.5 dated 2022-03-18 and 0.5.6 dated 2022-08-20
tidyhydat-0.5.5/tidyhydat/tests/testthat/test-onattach.R |only tidyhydat-0.5.6/tidyhydat/DESCRIPTION | 8 tidyhydat-0.5.6/tidyhydat/LICENSE | 402 +-- tidyhydat-0.5.6/tidyhydat/MD5 | 271 +- tidyhydat-0.5.6/tidyhydat/NAMESPACE | 148 - tidyhydat-0.5.6/tidyhydat/NEWS.md | 666 +++--- tidyhydat-0.5.6/tidyhydat/R/cli_style.R | 80 tidyhydat-0.5.6/tidyhydat/R/data.R | 128 - tidyhydat-0.5.6/tidyhydat/R/download.R | 301 +- tidyhydat-0.5.6/tidyhydat/R/hy-classes.R | 162 - tidyhydat-0.5.6/tidyhydat/R/hy.R | 926 ++++---- tidyhydat-0.5.6/tidyhydat/R/hy_annual_instant_peaks.R | 208 +- tidyhydat-0.5.6/tidyhydat/R/hy_annual_stats.R | 270 +- tidyhydat-0.5.6/tidyhydat/R/hy_daily.R | 192 - tidyhydat-0.5.6/tidyhydat/R/hy_daily_flows.R | 276 +- tidyhydat-0.5.6/tidyhydat/R/hy_daily_levels.R | 262 +- tidyhydat-0.5.6/tidyhydat/R/hy_db.R | 332 +-- tidyhydat-0.5.6/tidyhydat/R/hy_monthly_flows.R | 244 +- tidyhydat-0.5.6/tidyhydat/R/hy_monthly_levels.R | 240 +- tidyhydat-0.5.6/tidyhydat/R/hy_plot.R | 414 ++-- tidyhydat-0.5.6/tidyhydat/R/hy_sed_daily_loads.R | 228 +- tidyhydat-0.5.6/tidyhydat/R/hy_sed_daily_suscon.R | 256 +- tidyhydat-0.5.6/tidyhydat/R/hy_sed_monthly_loads.R | 236 +- tidyhydat-0.5.6/tidyhydat/R/hy_sed_monthly_suscon.R | 236 +- tidyhydat-0.5.6/tidyhydat/R/hy_sed_samples.R | 226 +- tidyhydat-0.5.6/tidyhydat/R/hy_sed_samples_psd.R | 180 - 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tidyhydat-0.5.6/tidyhydat/tests/testthat/test_utils.R | 114 - tidyhydat-0.5.6/tidyhydat/vignettes/precompile.R | 108 - tidyhydat-0.5.6/tidyhydat/vignettes/tidyhydat_an_introduction.Rmd | 549 ++--- tidyhydat-0.5.6/tidyhydat/vignettes/tidyhydat_an_introduction.Rmd.orig | 300 +- tidyhydat-0.5.6/tidyhydat/vignettes/tidyhydat_example_analysis.Rmd | 605 ++--- tidyhydat-0.5.6/tidyhydat/vignettes/tidyhydat_example_analysis.Rmd.orig | 392 +-- tidyhydat-0.5.6/tidyhydat/vignettes/tidyhydat_hydat_db.Rmd | 212 +- tidyhydat-0.5.6/tidyhydat/vignettes/tidyhydat_hydat_db.Rmd.orig | 152 - tidyhydat-0.5.6/tidyhydat/vignettes/vignette-fig-old_rec-1.png |binary tidyhydat-0.5.6/tidyhydat/vignettes/vignette-fig-old_rec_yr-1.png |binary tidyhydat-0.5.6/tidyhydat/vignettes/vignette-fig-pcrtile_plt-1.png |binary tidyhydat-0.5.6/tidyhydat/vignettes/vignette-fig-tile_plt-1.png |binary tidyhydat-0.5.6/tidyhydat/vignettes/vignette-fig-unnamed-chunk-8-1.png |binary 137 files changed, 12576 insertions(+), 11778 deletions(-)
Title: Sum of Single Effects Linear Regression
Description: Implements methods for variable selection in linear
regression based on the "Sum of Single Effects" (SuSiE) model, as
described in Wang et al (2020) <DOI:10.1101/501114> and Zou et al
(2021) <DOI:10.1101/2021.11.03.467167>. These methods provide
simple summaries, called "Credible Sets", for accurately
quantifying uncertainty in which variables should be selected.
The methods are motivated by genetic fine-mapping applications,
and are particularly well-suited to settings where variables are
highly correlated and detectable effects are sparse. The fitting
algorithm, a Bayesian analogue of stepwise selection methods
called "Iterative Bayesian Stepwise Selection" (IBSS), is simple
and fast, allowing the SuSiE model be fit to large data sets
(thousands of samples and hundreds of thousands of variables).
Author: Gao Wang [aut],
Yuxin Zou [aut],
Kaiqian Zhang [aut],
Peter Carbonetto [aut, cre],
Matthew Stephens [aut]
Maintainer: Peter Carbonetto <peter.carbonetto@gmail.com>
Diff between susieR versions 0.12.16 dated 2022-06-27 and 0.12.19 dated 2022-08-20
DESCRIPTION | 10 ++-- MD5 | 36 +++++++-------- R/susie_ss.R | 10 +++- R/susie_utils.R | 1 build/partial.rdb |binary inst/doc/finemapping.html | 10 ++-- inst/doc/finemapping_summary_statistics.html | 10 ++-- inst/doc/l0_initialization.html | 4 - inst/doc/mwe.html | 10 ++-- inst/doc/sparse_susie_eval.html | 4 - inst/doc/susie_refine.html | 10 ++-- inst/doc/susie_rss.html | 4 - inst/doc/susierss_diagnostic.html | 10 ++-- inst/doc/trend_filtering.R | 53 ++++++++++------------ inst/doc/trend_filtering.Rmd | 47 ++++++++++--------- inst/doc/trend_filtering.html | 64 ++++++++------------------- inst/doc/trendfiltering_derivations.pdf |binary man/susie.Rd | 6 ++ vignettes/trend_filtering.Rmd | 47 ++++++++++--------- 19 files changed, 164 insertions(+), 172 deletions(-)
Title: 'C++' Header Files for Color Conversion and Color Mappings
Description: Provides 'C++' header files to deal with color conversion
from some color spaces to hexadecimal with 'Rcpp', and exports some
color mapping functions for usage in R. Also exports functions to
convert colors from the 'HSLuv' color space for usage in R. 'HSLuv' is
a human-friendly alternative to HSL.
Author: Stephane Laurent [cre, aut],
Scott Spencer [aut]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between RcppColors versions 0.1.0 dated 2022-07-01 and 0.1.1 dated 2022-08-20
DESCRIPTION | 8 MD5 | 18 - NAMESPACE | 16 - NEWS.md | 11 - R/RcppExports.R | 46 ++-- R/colorMaps.R | 216 ++++++++++----------- R/hsluv.R | 116 +++++------ README.md | 464 +++++++++++++++++++++++----------------------- man/RcppColors-package.Rd | 44 ++-- man/colorMaps.Rd | 2 10 files changed, 473 insertions(+), 468 deletions(-)
Title: Hyperbolic Geometry
Description: Hyperbolic geometry in the Minkowski model and the Poincaré
model. The methods are based on the gyrovector space theory developed
by A. A. Ungar that can be found in the book 'Analytic Hyperbolic
Geometry: Mathematical Foundations And Applications'
<doi:10.1142/5914>. The package provides functions to plot
three-dimensional hyperbolic polyhedra and to plot hyperbolic tilings
of the Poincaré disk.
Author: Stephane Laurent
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between gyro versions 1.1.0 dated 2022-07-20 and 1.1.1 dated 2022-08-20
DESCRIPTION | 8 MD5 | 56 ++-- NEWS.md | 63 ++--- R/RcppExports.R | 38 +-- R/aaa.R | 10 R/examples.R | 106 ++++---- R/gyro_operations.R | 74 +++--- R/gyrocentroid.R | 52 ++-- R/gyromidpoint.R | 40 +-- R/gyrosegment.R | 24 - R/gyrosubdiv.R | 46 +-- R/hdelaunay.R | 512 +++++++++++++++++++++--------------------- R/isomorphisms.R | 42 +-- R/misc.R | 72 ++--- R/plot.R | 468 +++++++++++++++++++------------------- R/tiling.R | 340 +++++++++++++-------------- build/vignette.rds |binary inst/approx_sqrt.R | 122 +++++----- inst/doc/getstarted.R | 18 - inst/doc/getstarted.html | 416 +++++++++++++++++----------------- inst/hdelaunay/DESCRIPTION | 44 +-- inst/hdelaunay/Makevars | 20 - inst/hdelaunay/Makevars.win | 22 - inst/hdelaunay/NEWS.md | 44 +-- inst/hdelaunay/getstarted.Rmd | 122 +++++----- inst/hdelaunay/gyro.h | 16 - inst/hdelaunay/hdelaunay.R | 478 +++++++++++++++++++-------------------- inst/hdelaunay/hdelaunay.cpp | 318 +++++++++++++------------- man/gyrodemos.Rd | 2 29 files changed, 1789 insertions(+), 1784 deletions(-)
Title: Linked Micromap Plots for U. S. and Other Geographic Areas
Description: Provides the users with the ability to quickly create
linked micromap plots for a collection of geographic areas.
Linked micromap plots are visualizations of geo-referenced data
that link statistical graphics to an organized series of small
maps or graphic images. The Help description contains examples
of how to use the 'micromapST' function. Contained in this
package are border group datasets to support creating linked
micromap plots for the 50 U.S. states and District of Columbia
(51 areas), the U. S. 20 Seer Registries, the 105 counties in
the state of Kansas, the 62 counties of New York, the 24
counties of Maryland, the 29 counties of Utah, the 32
administrative areas in China, the 218 administrative areas in
the UK and Ireland (for testing only), the 25 districts in the
city of Seoul South Korea, and the 52 counties on the Africa
continent.
A border group dataset contains the boundaries related to the
data level areas, a second layer boundaries, a top or third
layer boundary, a pa [...truncated...]
Author: Jim Pearson [aut, cre, cph],
Dan Carr [aut, cph],
Linda Pickle [ctb, cph]
Maintainer: Jim Pearson <jbpearson353@gmail.com>
Diff between micromapST versions 1.1.3 dated 2022-04-29 and 2.0.0 dated 2022-08-20
micromapST-1.1.3/micromapST/man/messages.Rd |only micromapST-2.0.0/micromapST/DESCRIPTION | 15 micromapST-2.0.0/micromapST/MD5 | 97 - micromapST-2.0.0/micromapST/NAMESPACE | 47 micromapST-2.0.0/micromapST/R/BuildBorderGroup.r |only micromapST-2.0.0/micromapST/R/globals.r |only micromapST-2.0.0/micromapST/R/micromapDefSets.r | 158 + micromapST-2.0.0/micromapST/R/micromapST.r | 824 +++------- micromapST-2.0.0/micromapST/build/vignette.rds |binary micromapST-2.0.0/micromapST/data/AfricaBG.rda |binary micromapST-2.0.0/micromapST/data/AfricaPopData.rda |binary micromapST-2.0.0/micromapST/data/ChinaBG.rda |binary micromapST-2.0.0/micromapST/data/Educ8thData.rda |binary micromapST-2.0.0/micromapST/data/KY_ADD.rda |only micromapST-2.0.0/micromapST/data/KY_ADD_BG.rda |only micromapST-2.0.0/micromapST/data/KansPopInc.rda |binary micromapST-2.0.0/micromapST/data/KansasBG.rda |binary micromapST-2.0.0/micromapST/data/Ky_ADD_LungCancer_2006_2010.rda |only micromapST-2.0.0/micromapST/data/MarylandBG.rda |binary micromapST-2.0.0/micromapST/data/NewYorkBG.rda |binary micromapST-2.0.0/micromapST/data/Seer18Area.rda |binary micromapST-2.0.0/micromapST/data/SeoulPopData.rda |binary micromapST-2.0.0/micromapST/data/SeoulSKoreaBG.rda |binary micromapST-2.0.0/micromapST/data/TSdata.rda |binary micromapST-2.0.0/micromapST/data/UKIrelandBG.rda |binary micromapST-2.0.0/micromapST/data/UKIrelandPopData.rda |binary micromapST-2.0.0/micromapST/data/UKIrelandPopData2.rda |binary micromapST-2.0.0/micromapST/data/USSeerBG.rda |binary micromapST-2.0.0/micromapST/data/USStatesBG.rda |binary micromapST-2.0.0/micromapST/data/UtahBG.rda |binary micromapST-2.0.0/micromapST/data/UtahPopData.rda |binary micromapST-2.0.0/micromapST/data/cnPopData.rda |binary micromapST-2.0.0/micromapST/data/detailsVariables.rda |binary micromapST-2.0.0/micromapST/data/mdPopData.rda |binary micromapST-2.0.0/micromapST/data/nyPopData.rda |binary micromapST-2.0.0/micromapST/data/statePop2010.rda |binary micromapST-2.0.0/micromapST/data/wflung00and95.rda |binary micromapST-2.0.0/micromapST/data/wflung00and95US.rda |binary micromapST-2.0.0/micromapST/data/wflung00cnty.rda |binary micromapST-2.0.0/micromapST/data/wmlung5070.rda |binary micromapST-2.0.0/micromapST/data/wmlung5070US.rda |binary micromapST-2.0.0/micromapST/inst/CITATION | 8 micromapST-2.0.0/micromapST/inst/doc/NEWS |only micromapST-2.0.0/micromapST/man/BuildBorderGroup.Rd |only micromapST-2.0.0/micromapST/man/KY_ADD.Rd |only micromapST-2.0.0/micromapST/man/KY_ADD_BG.Rd |only micromapST-2.0.0/micromapST/man/KansasBG.Rd | 2 micromapST-2.0.0/micromapST/man/Ky_ADD_LungCancer_2006_2010.Rd |only micromapST-2.0.0/micromapST/man/TSdata.Rd | 3 micromapST-2.0.0/micromapST/man/bordGrp.Rd | 20 micromapST-2.0.0/micromapST/man/detailsVariables.Rd | 11 micromapST-2.0.0/micromapST/man/messages-BG.Rd |only micromapST-2.0.0/micromapST/man/messages-MM.Rd |only micromapST-2.0.0/micromapST/man/micromapGDefaults.Rd | 10 micromapST-2.0.0/micromapST/man/micromapST-package.Rd | 15 micromapST-2.0.0/micromapST/man/micromapST.Rd | 13 56 files changed, 561 insertions(+), 662 deletions(-)