Title: Bayesian Model Averaging for Multinomial Logit Models
Description: Provides a modified function bic.glm of the BMA package that can be applied to multinomial logit (MNL) data. The data is converted to binary logit using the Begg & Gray approximation. The package also contains functions for maximum likelihood estimation of MNL.
Author: Hana Sevcikova, Adrian Raftery
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between mlogitBMA versions 0.1-6 dated 2013-12-11 and 0.1-7 dated 2022-04-13
mlogitBMA-0.1-6/mlogitBMA/inst/doc/conversion.R |only mlogitBMA-0.1-7/mlogitBMA/ChangeLog | 4 ++++ mlogitBMA-0.1-7/mlogitBMA/DESCRIPTION | 8 ++++---- mlogitBMA-0.1-7/mlogitBMA/MD5 | 15 ++++++++------- mlogitBMA-0.1-7/mlogitBMA/NAMESPACE | 7 +++++++ mlogitBMA-0.1-7/mlogitBMA/R/bic.glm.bg.R | 8 ++++---- mlogitBMA-0.1-7/mlogitBMA/build |only mlogitBMA-0.1-7/mlogitBMA/inst/doc/conversion.pdf |binary mlogitBMA-0.1-7/mlogitBMA/man/mlogitBMA-package.Rd | 6 ------ mlogitBMA-0.1-7/mlogitBMA/src/mlogitBMA_init.c |only 10 files changed, 27 insertions(+), 21 deletions(-)
Title: Multivariate Response Generalized Linear Models
Description: Provides functions that (1) fit multivariate discrete distributions, (2) generate random numbers from multivariate discrete distributions, and (3) run regression and penalized regression on the multivariate categorical response data. Implemented models include: multinomial logit model, Dirichlet multinomial model, generalized Dirichlet multinomial model, and negative multinomial model. Making the best of the minorization-maximization (MM) algorithm and Newton-Raphson method, we derive and implement stable and efficient algorithms to find the maximum likelihood estimates. On a multi-core machine, multi-threading is supported.
Author: Yiwen Zhang <zhangyiwen1015@gmail.com> and Hua Zhou <huazhou@ucla.edu>
Maintainer: Juhyun Kim <juhkim111@ucla.edu>
Diff between MGLM versions 0.2.0 dated 2018-10-19 and 0.2.1 dated 2022-04-13
DESCRIPTION | 11 +++++------ MD5 | 42 +++++++++++++++++++++--------------------- R/DMD.NegMN.R | 4 ++-- R/MGLMsparsereg.R | 2 +- build/vignette.rds |binary inst/doc/mglm_vignette.R | 36 ++++++++++++++++++------------------ inst/doc/mglm_vignette.rmd | 2 +- man/AIC.Rd | 1 - man/BIC.Rd | 1 - man/MGLMfit.Rd | 41 +++++++++++++++++++++++++++++++++-------- man/MGLMreg-class.Rd | 4 ++-- man/MGLMreg.Rd | 38 ++++++++++++++++++++++++++++++++------ man/MGLMsparsereg.Rd | 38 ++++++++++++++++++++++++++++++++------ man/MGLMtune.Rd | 22 +++++++++++++++++++--- man/coef.Rd | 1 - man/dof.Rd | 1 - man/logLik.Rd | 1 - man/maxlambda.Rd | 1 - man/path.Rd | 1 - man/predict.Rd | 1 - man/rnaseq.Rd | 4 ++-- vignettes/mglm_vignette.rmd | 2 +- 22 files changed, 169 insertions(+), 85 deletions(-)
Title: Scale Functions for Visualization
Description: Graphical scales map data to aesthetics, and provide methods
for automatically determining breaks and labels for axes and legends.
Author: Hadley Wickham [aut, cre],
Dana Seidel [aut],
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between scales versions 1.1.1 dated 2020-05-11 and 1.2.0 dated 2022-04-13
scales-1.1.1/scales/build/scales.pdf |only scales-1.1.1/scales/man/figures/lifecycle-retired.svg |only scales-1.1.1/scales/man/figures/lifecycle-soft-deprecated.svg |only scales-1.1.1/scales/tests/testthat/test-breaks-extended.R |only scales-1.1.1/scales/tests/testthat/test-breaks-minor.r |only scales-1.1.1/scales/tests/testthat/test-discrete.R |only scales-1.1.1/scales/tests/testthat/test-label-date-short.txt |only scales-1.1.1/scales/tests/testthat/test-label-number-auto.txt |only scales-1.1.1/scales/tests/testthat/test-label-ordinal.txt |only scales-1.1.1/scales/tests/testthat/test-manual-pal.R |only scales-1.1.1/scales/tests/testthat/test-rescale.R |only scales-1.1.1/scales/tests/testthat/test-zero-range.r |only scales-1.2.0/scales/DESCRIPTION | 38 - scales-1.2.0/scales/MD5 | 250 ++++---- scales-1.2.0/scales/NAMESPACE | 11 scales-1.2.0/scales/NEWS.md | 73 ++ scales-1.2.0/scales/R/bounds.r | 50 + scales-1.2.0/scales/R/breaks-log.R | 14 scales-1.2.0/scales/R/breaks-retired.R | 22 scales-1.2.0/scales/R/breaks.r | 50 + scales-1.2.0/scales/R/colour-manip.r | 5 scales-1.2.0/scales/R/colour-mapping.r | 58 +- scales-1.2.0/scales/R/colour-ramp.R | 8 scales-1.2.0/scales/R/full-seq.r | 5 scales-1.2.0/scales/R/label-bytes.R | 58 +- scales-1.2.0/scales/R/label-date.R | 51 + scales-1.2.0/scales/R/label-dollar.R | 91 ++- scales-1.2.0/scales/R/label-expression.R | 42 - scales-1.2.0/scales/R/label-log.R |only scales-1.2.0/scales/R/label-number-auto.R | 17 scales-1.2.0/scales/R/label-number-si.R | 76 +- scales-1.2.0/scales/R/label-number.r | 285 ++++++++-- scales-1.2.0/scales/R/label-ordinal.R | 27 scales-1.2.0/scales/R/label-percent.R | 22 scales-1.2.0/scales/R/label-pvalue.R | 24 scales-1.2.0/scales/R/label-scientific.R | 26 scales-1.2.0/scales/R/label-wrap.R | 15 scales-1.2.0/scales/R/labels-retired.R | 25 scales-1.2.0/scales/R/minor_breaks.R | 5 scales-1.2.0/scales/R/offset-by.r |only scales-1.2.0/scales/R/pal-brewer.r | 9 scales-1.2.0/scales/R/pal-dichromat.r | 14 scales-1.2.0/scales/R/pal-gradient.r | 10 scales-1.2.0/scales/R/pal-hue.r | 4 scales-1.2.0/scales/R/pal-manual.r | 2 scales-1.2.0/scales/R/pal-viridis.r | 4 scales-1.2.0/scales/R/range.r | 4 scales-1.2.0/scales/R/scale-continuous.r | 13 scales-1.2.0/scales/R/scale-discrete.r | 14 scales-1.2.0/scales/R/scales-package.R | 2 scales-1.2.0/scales/R/trans-compose.R |only scales-1.2.0/scales/R/trans-date.r | 26 scales-1.2.0/scales/R/trans-numeric.r | 9 scales-1.2.0/scales/R/trans.r | 23 scales-1.2.0/scales/R/utils.r | 12 scales-1.2.0/scales/README.md | 23 scales-1.2.0/scales/build/partial.rdb |binary scales-1.2.0/scales/man/breaks_pretty.Rd | 4 scales-1.2.0/scales/man/breaks_width.Rd | 28 scales-1.2.0/scales/man/brewer_pal.Rd | 11 scales-1.2.0/scales/man/cbreaks.Rd | 9 scales-1.2.0/scales/man/col_numeric.Rd | 2 scales-1.2.0/scales/man/comma.Rd |only scales-1.2.0/scales/man/compose_trans.Rd |only scales-1.2.0/scales/man/cscale.Rd | 9 scales-1.2.0/scales/man/date_breaks.Rd | 3 scales-1.2.0/scales/man/date_format.Rd |only scales-1.2.0/scales/man/dichromat_pal.Rd | 10 scales-1.2.0/scales/man/div_gradient_pal.Rd | 4 scales-1.2.0/scales/man/dollar_format.Rd |only scales-1.2.0/scales/man/dscale.Rd | 6 scales-1.2.0/scales/man/figures/README-labels-1.png |binary scales-1.2.0/scales/man/figures/README-labels-2.png |binary scales-1.2.0/scales/man/figures/README-palettes-1.png |binary scales-1.2.0/scales/man/figures/README-transforms-1.png |binary scales-1.2.0/scales/man/figures/lifecycle-superseded.svg |only scales-1.2.0/scales/man/format_format.Rd | 3 scales-1.2.0/scales/man/fullseq.Rd | 3 scales-1.2.0/scales/man/hms_trans.Rd | 10 scales-1.2.0/scales/man/hue_pal.Rd | 2 scales-1.2.0/scales/man/label_bytes.Rd | 26 scales-1.2.0/scales/man/label_date.Rd | 27 scales-1.2.0/scales/man/label_dollar.Rd | 67 -- scales-1.2.0/scales/man/label_log.Rd |only scales-1.2.0/scales/man/label_number.Rd | 123 ++-- scales-1.2.0/scales/man/label_number_si.Rd | 36 - scales-1.2.0/scales/man/label_ordinal.Rd | 27 scales-1.2.0/scales/man/label_parse.Rd | 13 scales-1.2.0/scales/man/label_percent.Rd | 41 - scales-1.2.0/scales/man/label_pvalue.Rd | 19 scales-1.2.0/scales/man/label_scientific.Rd | 34 - scales-1.2.0/scales/man/label_wrap.Rd | 8 scales-1.2.0/scales/man/minor_breaks_width.Rd | 13 scales-1.2.0/scales/man/number.Rd | 54 + scales-1.2.0/scales/man/number_bytes_format.Rd | 3 scales-1.2.0/scales/man/ordinal_format.Rd |only scales-1.2.0/scales/man/parse_format.Rd |only scales-1.2.0/scales/man/percent_format.Rd |only scales-1.2.0/scales/man/pretty_breaks.Rd |only scales-1.2.0/scales/man/pvalue_format.Rd |only scales-1.2.0/scales/man/scales-package.Rd | 6 scales-1.2.0/scales/man/scientific_format.Rd |only scales-1.2.0/scales/man/time_trans.Rd | 2 scales-1.2.0/scales/man/trans_breaks.Rd | 7 scales-1.2.0/scales/man/trans_format.Rd | 4 scales-1.2.0/scales/man/trans_new.Rd | 2 scales-1.2.0/scales/man/unit_format.Rd | 11 scales-1.2.0/scales/man/viridis_pal.Rd | 25 scales-1.2.0/scales/man/wrap_format.Rd |only scales-1.2.0/scales/man/zero_range.Rd | 26 scales-1.2.0/scales/tests/testthat/_snaps |only scales-1.2.0/scales/tests/testthat/test-bounds.r | 90 ++- scales-1.2.0/scales/tests/testthat/test-breaks-log.r | 2 scales-1.2.0/scales/tests/testthat/test-breaks.r | 13 scales-1.2.0/scales/tests/testthat/test-colour-mapping.r | 23 scales-1.2.0/scales/tests/testthat/test-colour-ramp.R | 2 scales-1.2.0/scales/tests/testthat/test-label-bytes.R | 7 scales-1.2.0/scales/tests/testthat/test-label-date.R | 8 scales-1.2.0/scales/tests/testthat/test-label-dollar.R | 15 scales-1.2.0/scales/tests/testthat/test-label-expression.R | 4 scales-1.2.0/scales/tests/testthat/test-label-log.R |only scales-1.2.0/scales/tests/testthat/test-label-number-auto.R | 6 scales-1.2.0/scales/tests/testthat/test-label-number-si.R | 25 scales-1.2.0/scales/tests/testthat/test-label-number.r | 86 ++- scales-1.2.0/scales/tests/testthat/test-label-ordinal.R | 3 scales-1.2.0/scales/tests/testthat/test-label-percent.R | 4 scales-1.2.0/scales/tests/testthat/test-label-pvalue.R | 1 scales-1.2.0/scales/tests/testthat/test-labels-retired.R | 2 scales-1.2.0/scales/tests/testthat/test-minor_breaks.R |only scales-1.2.0/scales/tests/testthat/test-offset-by.R |only scales-1.2.0/scales/tests/testthat/test-pal-hue.r | 12 scales-1.2.0/scales/tests/testthat/test-pal-manual.R |only scales-1.2.0/scales/tests/testthat/test-range.r | 2 scales-1.2.0/scales/tests/testthat/test-round-any.R | 2 scales-1.2.0/scales/tests/testthat/test-scale-continuous.r | 8 scales-1.2.0/scales/tests/testthat/test-scale-discrete.r | 28 scales-1.2.0/scales/tests/testthat/test-trans-compose.R |only scales-1.2.0/scales/tests/testthat/test-trans-date.r | 20 scales-1.2.0/scales/tests/testthat/test-trans-numeric.r | 52 + scales-1.2.0/scales/tests/testthat/test-trans.r | 28 140 files changed, 1697 insertions(+), 941 deletions(-)
Title: Tools for Reading, Processing and Writing 'DSSAT' Files
Description: Provides methods for reading, displaying,
processing and writing files originally arranged for
the 'DSSAT-CSM' fixed width format. The 'DSSAT-CSM'
cropping system model is described at J.W. Jones,
G. Hoogenboomb, C.H. Porter, K.J. Boote, W.D. Batchelor,
L.A. Hunt, P.W. Wilkens, U. Singh, A.J. Gijsman,
J.T. Ritchie (2003) <doi:10.1016/S1161-0301(02)00107-7>.
Author: Homero Lozza [aut, cre]
Maintainer: Homero Lozza <homerolozza@gmail.com>
Diff between Dasst versions 0.3.3 dated 2017-11-13 and 0.3.4 dated 2022-04-13
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/Dasst-methods.R | 2 +- README.md | 1 + build/vignette.rds |binary data/plantGrowth.RData |binary inst/doc/aNoteOnDasst-knitr.pdf |binary inst/doc/aNoteOnDasst.pdf |binary 8 files changed, 13 insertions(+), 12 deletions(-)
Title: Universal Storage Engine for Sparse and Dense Multidimensional
Arrays
Description: The universal 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. [aut, cph],
Dirk Eddelbuettel [cre]
Maintainer: Dirk Eddelbuettel <dirk@tiledb.com>
Diff between tiledb versions 0.11.1 dated 2022-03-25 and 0.12.0 dated 2022-04-13
DESCRIPTION | 6 MD5 | 75 + NAMESPACE | 21 NEWS.md | 35 R/Group.R |only R/Object.R | 21 R/Query.R | 26 R/RcppExports.R | 112 ++ R/TileDBArray.R | 4 R/zzz.R | 12 inst/doc/data-ingestion-from-sql.html | 4 inst/doc/data-ingestion-from-sql.md | 2 inst/doc/introduction.html | 2 inst/doc/introduction.md | 1 inst/examples/ex_3.R | 10 inst/include/tiledb.h | 12 inst/tinytest/test_dim.R | 4 inst/tinytest/test_group.R |only inst/tinytest/test_query.R | 6 inst/tinytest/test_tiledbarray.R | 4 man/tiledb_group-class.Rd |only man/tiledb_group.Rd |only man/tiledb_group_add_member.Rd |only man/tiledb_group_close.Rd |only man/tiledb_group_create.Rd | 13 man/tiledb_group_delete_metadata.Rd |only man/tiledb_group_get_all_metadata.Rd |only man/tiledb_group_get_config.Rd |only man/tiledb_group_get_metadata.Rd |only man/tiledb_group_get_metadata_from_index.Rd |only man/tiledb_group_has_metadata.Rd |only man/tiledb_group_is_open.Rd |only man/tiledb_group_member.Rd |only man/tiledb_group_member_count.Rd |only man/tiledb_group_member_dump.Rd |only man/tiledb_group_metadata_num.Rd |only man/tiledb_group_open.Rd |only man/tiledb_group_put_metadata.Rd |only man/tiledb_group_query_type.Rd |only man/tiledb_group_remove_member.Rd |only man/tiledb_group_set_config.Rd |only man/tiledb_group_uri.Rd |only src/RcppExports.cpp | 324 ++++++- src/libtiledb.cpp | 1201 +++++++++++++++++++--------- src/libtiledb.h | 68 + src/shmem.cpp | 10 tools/ci/valgrind/buildTileDB.sh | 10 tools/tiledbVersion.txt | 4 vignettes/data-ingestion-from-sql.md | 2 vignettes/introduction.md | 1 50 files changed, 1475 insertions(+), 515 deletions(-)
Title: The Moving Epidemic Method
Description: The Moving Epidemic Method, created by T Vega and JE Lozano (2012, 2015) <doi:10.1111/j.1750-2659.2012.00422.x>, <doi:10.1111/irv.12330>, allows the weekly assessment of the epidemic and intensity status to help in routine respiratory infections surveillance in health systems. Allows the comparison of different epidemic indicators, timing and shape with past epidemics and across different regions or countries with different surveillance systems. Also, it gives a measure of the performance of the method in terms of sensitivity and specificity of the alert week.
Author: Jose E. Lozano [aut, cre]
Maintainer: Jose E. Lozano <lozalojo@gmail.com>
Diff between mem versions 2.16 dated 2020-09-13 and 2.17 dated 2022-04-13
DESCRIPTION | 12 MD5 | 66 +-- NAMESPACE | 1 R/memmodel.R | 576 ++++++++++++++++------------------ R/memtiming.R | 3 README.md | 3 man/calcular.indicadores.2.timings.Rd | 46 +- man/calcular.indicadores.Rd | 52 +-- man/create.calendar.Rd | 30 - man/epimem.Rd | 80 ++-- man/epitiming.Rd | 50 +- man/flucyl.Rd | 106 +++--- man/flucylraw.Rd | 94 ++--- man/full.series.graph.Rd | 224 ++++++------- man/get.dates.Rd | 24 - man/get.epiweek.Rd | 24 - man/mem-package.Rd | 46 +- man/memevolution.Rd | 180 +++++----- man/memgoodness.Rd | 368 ++++++++++----------- man/memintensity.Rd | 174 +++++----- man/memmodel.Rd | 432 ++++++++++++------------- man/memstability.Rd | 122 +++---- man/memsurveillance.Rd | 330 +++++++++---------- man/memsurveillance.animated.Rd | 192 +++++------ man/memtiming.Rd | 226 ++++++------- man/memtrend.Rd | 184 +++++----- man/optimal.tickmarks.Rd | 44 +- man/optimum.by.inspection.Rd | 158 ++++----- man/processPlots.Rd | 112 +++--- man/roc.analysis.Rd | 182 +++++----- man/transformdata.Rd | 134 +++---- man/transformdata.back.Rd | 128 +++---- man/transformseries.Rd | 152 ++++---- man/transformseries.multiple.Rd | 48 +- 34 files changed, 2300 insertions(+), 2303 deletions(-)
Title: Least Angle Regression, Lasso and Forward Stagewise
Description: Efficient procedures for fitting an entire lasso
sequence with the cost of a single least squares
fit. Least angle regression and infinitesimal forward
stagewise regression are related to the lasso, as
described in the paper below.
Author: Trevor Hastie <hastie@stanford.edu> and Brad Efron
<brad@stat.stanford.edu>
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between lars versions 1.2 dated 2013-04-24 and 1.3 dated 2022-04-13
lars-1.2/lars/INDEX |only lars-1.3/lars/DESCRIPTION | 23 ++++++++++++----------- lars-1.3/lars/MD5 | 21 +++++++++++---------- lars-1.3/lars/NAMESPACE | 3 +++ lars-1.3/lars/R/lars.R | 4 ++-- lars-1.3/lars/build |only lars-1.3/lars/man/cv.lars.Rd | 8 ++++---- lars-1.3/lars/man/diabetes.Rd | 2 +- lars-1.3/lars/man/lars.Rd | 12 ++++++++---- lars-1.3/lars/man/plot.lars.Rd | 6 +++--- lars-1.3/lars/man/predict.lars.Rd | 2 +- lars-1.3/lars/man/summary.lars.Rd | 2 +- lars-1.3/lars/src/lars_init.c |only 13 files changed, 46 insertions(+), 37 deletions(-)
Title: Algorithms for Helping Build Dynamic TOPMODEL Implementations
from Spatial Data
Description: A set of algorithms based on Quinn et al. (1991) <doi:10.1002/hyp.3360050106> for processing river network and digital elevation data to build implementations of Dynamic TOPMODEL, a semi-distributed hydrological model proposed in Beven and Freer (2001) <doi:10.1002/hyp.252>. The 'dynatop' package implements simulation code for Dynamic TOPMODEL based on the output of 'dynatopGIS'.
Author: Paul Smith [aut, cre]
Maintainer: Paul Smith <paul@waternumbers.co.uk>
Diff between dynatopGIS versions 0.2.1 dated 2022-01-07 and 0.2.2 dated 2022-04-13
DESCRIPTION | 7 - MD5 | 25 ++-- NEWS.md | 18 +- R/dygis.R | 118 +++++-------------- R/dynatopGIS-package.R | 2 build/vignette.rds |binary inst/WORDLIST |only inst/doc/Banding.Rmd | 4 inst/doc/Banding.html | 5 inst/doc/dynatopGIS.Rmd | 16 +- inst/doc/dynatopGIS.html | 290 +++++++++++------------------------------------ man/dynatopGIS.Rd | 182 +++-------------------------- vignettes/Banding.Rmd | 4 vignettes/dynatopGIS.Rmd | 16 +- 14 files changed, 177 insertions(+), 510 deletions(-)
Title: An Implementation of Dynamic TOPMODEL Hydrological Model in R
Description: An R implementation and enhancement of the Dynamic TOPMODEL semi-distributed hydrological model originally proposed by Beven and Freer (2001) <doi:10.1002/hyp.252>. The 'dynatop' package implements code for simulating models which can be created using the 'dynatopGIS' package.
Author: Paul Smith [aut, cre] ,
Peter Metcalfe [aut]
Maintainer: Paul Smith <paul@waternumbers.co.uk>
Diff between dynatop versions 0.2.1 dated 2022-01-18 and 0.2.2 dated 2022-04-13
DESCRIPTION | 8 MD5 | 79 - NEWS.md | 57 - R/RcppExports.R | 4 R/dynatop-package.R | 2 R/dynatop.R | 170 +-- R/evap.R | 6 R/xts_utilities.R | 6 README.md | 1 build/vignette.rds |binary data/Swindale.rda |binary inst/WORDLIST |only inst/doc/Channel_HRU.Rmd | 26 inst/doc/Channel_HRU.html | 44 inst/doc/Hillslope_HRU.Rmd | 520 ++++++---- inst/doc/Hillslope_HRU.html | 498 ++++++--- inst/doc/Notes_on_the_implementation_of_Dynamic_TOPMODEL.Rmd | 2 inst/doc/Notes_on_the_implementation_of_Dynamic_TOPMODEL.html | 16 inst/doc/Selected_References.Rmd | 4 inst/doc/Selected_References.html | 7 inst/doc/The_Model_Object.Rmd | 4 inst/doc/The_Model_Object.html | 32 inst/doc/dynatop.Rmd | 4 inst/doc/dynatop.html | 19 man/dynatop-package.Rd | 2 man/dynatop.Rd | 26 man/evap_est.Rd | 6 man/resample_xts.Rd | 6 src/RcppExports.cpp | 9 src/dt_courant.cpp | 3 src/dt_implicit_sim.cpp | 30 src/dt_init.cpp | 23 src/hillslope_hru.cpp | 116 +- src/hillslope_hru.h | 5 tests/testthat/test-dynatop.R | 19 vignettes/Channel_HRU.Rmd | 26 vignettes/Hillslope_HRU.Rmd | 520 ++++++---- vignettes/Notes_on_the_implementation_of_Dynamic_TOPMODEL.Rmd | 2 vignettes/Selected_References.Rmd | 4 vignettes/The_Model_Object.Rmd | 4 vignettes/dynatop.Rmd | 4 41 files changed, 1466 insertions(+), 848 deletions(-)
Title: Estimation of Caribou Abundance Based on Radio Telemetry Data
Description: Estimation of population size of migratory caribou herds based on large scale
aggregations monitored by radio telemetry. It implements the methodology found
in the article by Rivest et al. (1998) about caribou abundance estimation. It
also includes a function based on the Lincoln-Petersen Index as applied to
radio telemetry data by White and Garrott (1990).
Author: Louis-Paul Rivest [aut, cre],
Helene Crepeau [aut],
Serge Couturier [ctb],
Sophie Baillargeon [aut]
Maintainer: Louis-Paul Rivest <Louis-Paul.Rivest@mat.ulaval.ca>
Diff between caribou versions 1.1 dated 2012-06-11 and 1.1-1 dated 2022-04-13
DESCRIPTION | 41 +++++++++++++++++++++++------------------ MD5 | 28 ++++++++++++++-------------- NAMESPACE | 2 +- R/abundance.R | 4 ++-- R/petersen.R | 4 ++-- inst/NEWS.Rd | 8 +++++++- man/BEH00.Rd | 1 - man/GRH01.Rd | 1 - man/GRH10.Rd | 1 - man/GRH93.Rd | 1 - man/LRH01.Rd | 1 - man/WAH11.Rd | 1 - man/abundance.Rd | 6 ++++-- man/caribou.package.Rd | 14 ++++++++------ man/petersen.Rd | 6 ++++-- 15 files changed, 65 insertions(+), 54 deletions(-)
Title: Extra Recipes Steps for Dealing with Unbalanced Data
Description: A dataset with an uneven number of cases in each class is
said to be unbalanced. Many models produce a subpar performance on
unbalanced datasets. A dataset can be balanced by increasing the
number of minority cases using SMOTE 2011 <arXiv:1106.1813>,
BorderlineSMOTE 2005 <doi:10.1007/11538059_91> and ADASYN 2008
<https://ieeexplore.ieee.org/document/4633969>. Or by decreasing the
number of majority cases using NearMiss 2003
<https://www.site.uottawa.ca/~nat/Workshop2003/jzhang.pdf> or Tomek
link removal 1976 <https://ieeexplore.ieee.org/document/4309452>.
Author: Emil Hvitfeldt [aut, cre]
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
Diff between themis versions 0.2.0 dated 2022-03-30 and 0.2.1 dated 2022-04-13
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/step_downsample.R | 2 +- R/step_upsample.R | 2 +- 5 files changed, 13 insertions(+), 9 deletions(-)
Title: Determine and Evaluate Optimal Cutpoints in Binary
Classification Tasks
Description: Estimate cutpoints that optimize a specified metric in binary classification tasks
and validate performance using bootstrapping. Some methods for more robust cutpoint
estimation are supported, e.g. a parametric method assuming normal distributions,
bootstrapped cutpoints, and smoothing of the metric values per cutpoint using
Generalized Additive Models. Various plotting functions are included. For an overview
of the package see Thiele and Hirschfeld (2021) <doi:10.18637/jss.v098.i11>.
Author: Christian Thiele [cre, aut]
Maintainer: Christian Thiele <c.thiele@gmx-topmail.de>
Diff between cutpointr versions 1.1.1 dated 2021-06-29 and 1.1.2 dated 2022-04-13
DESCRIPTION | 10 MD5 | 54 NEWS.md | 13 R/boot_ci.R | 172 +-- R/cutpointr.R | 39 R/optimize_metric.R | 4 build/vignette.rds |binary inst/doc/cutpointr.R | 455 -------- inst/doc/cutpointr.Rmd | 1786 +++++++++------------------------ inst/doc/cutpointr.html | 614 +---------- inst/doc/cutpointr_benchmarks.R |only inst/doc/cutpointr_benchmarks.Rmd |only inst/doc/cutpointr_benchmarks.html |only inst/doc/cutpointr_bootstrapping.R |only inst/doc/cutpointr_bootstrapping.Rmd |only inst/doc/cutpointr_bootstrapping.html |only inst/doc/cutpointr_estimation.R |only inst/doc/cutpointr_estimation.Rmd |only inst/doc/cutpointr_estimation.html |only inst/doc/cutpointr_plotting.R |only inst/doc/cutpointr_plotting.Rmd |only inst/doc/cutpointr_plotting.html |only inst/doc/cutpointr_roc.R |only inst/doc/cutpointr_roc.Rmd |only inst/doc/cutpointr_roc.html |only inst/doc/cutpointr_user_functions.R |only inst/doc/cutpointr_user_functions.Rmd |only inst/doc/cutpointr_user_functions.html |only man/boot_ci.Rd | 2 man/multi_cutpointr.Rd | 3 src/RcppExports.cpp | 5 tests/testthat/Rplots.pdf |binary tests/testthat/test-cutpointr.R | 21 vignettes/cutpointr.Rmd | 1786 +++++++++------------------------ vignettes/cutpointr_benchmarks.Rmd |only vignettes/cutpointr_bootstrapping.Rmd |only vignettes/cutpointr_estimation.Rmd |only vignettes/cutpointr_plotting.Rmd |only vignettes/cutpointr_roc.Rmd |only vignettes/cutpointr_user_functions.Rmd |only 40 files changed, 1341 insertions(+), 3623 deletions(-)
Title: Miscellaneous R Functions and Aliases
Description: Provides utility functions for, and drawing on, the 'data.table' package. The package also collates useful miscellaneous functions extending base R not available elsewhere. The name is a portmanteau of 'utils' and the author.
Author: Hugh Parsonage [aut, cre],
Michael Frasco [ctb],
Ben Hamner [ctb]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between hutils versions 1.7.1 dated 2021-07-22 and 1.8.1 dated 2022-04-13
DESCRIPTION | 16 - MD5 | 34 +- NAMESPACE | 3 NEWS.md | 26 ++ R/drop_empty_cols.R | 36 ++ R/fst_columns.R |only R/if_else.R | 8 R/longest_affix.R | 350 ++++++++++++++-------------- R/select_which.R | 79 +++--- R/seq_nrow.R |only inst/doc/hutils.html | 38 +-- man/fst_columns.Rd |only man/select_which.Rd | 5 man/seq_nrow.Rd |only tests/testthat/test-if_else-raw.R |only tests/testthat/test_1-3-0_longest_affix.R | 140 +++++------ tests/testthat/test_1-8-0_drop_empty_cols.R |only tests/testthat/test_1-8-0_longest_affix.R |only tests/testthat/test_drop_empty_cols.R |only tests/testthat/test_find_pattern_in.R | 10 tests/testthat/test_fst_columns.R |only tests/testthat/test_provide-file.R | 41 +-- tests/testthat/test_select_which.R |only 23 files changed, 437 insertions(+), 349 deletions(-)
Title: An Implementation of the EcoTroph Ecosystem Modelling Approach
Description: An approach and software for modelling marine and freshwater ecosystems. It is articulated entirely around trophic levels. EcoTroph's key displays are bivariate plots, with trophic levels as the abscissa, and biomass flows or related quantities as ordinates. Thus, trophic ecosystem functioning can be modelled as a continuous flow of biomass surging up the food web, from lower to higher trophic levels, due to predation and ontogenic processes. Such an approach, wherein species as such disappear, may be viewed as the ultimate stage in the use of the trophic level metric for ecosystem modelling, providing a simplified but potentially useful caricature of ecosystem functioning and impacts of fishing. This version contains catch trophic spectrum analysis (CTSA) function and corrected versions of the mf.diagnosis and create.ETmain functions.
Author: J. Guitton, M. Colleter, P. Gatti, and D. Gascuel
Maintainer: Jerome Guitton <jerome.guitton@agrocampus-ouest.fr>
Diff between EcoTroph versions 1.6 dated 2013-09-13 and 1.6.1 dated 2022-04-13
EcoTroph-1.6.1/EcoTroph/DESCRIPTION | 16 EcoTroph-1.6.1/EcoTroph/MD5 | 83 + EcoTroph-1.6.1/EcoTroph/NAMESPACE | 46 - EcoTroph-1.6.1/EcoTroph/R/CTSA.catch.input.R | 33 EcoTroph-1.6.1/EcoTroph/R/E0.1.R |only EcoTroph-1.6.1/EcoTroph/R/E_MSY_0.1.R | 117 +- EcoTroph-1.6.1/EcoTroph/R/Emsy.R |only EcoTroph-1.6.1/EcoTroph/R/Transpose.R | 58 - EcoTroph-1.6.1/EcoTroph/R/a13.eq.R |only EcoTroph-1.6.1/EcoTroph/R/a13.eq.ac.R |only EcoTroph-1.6.1/EcoTroph/R/check.table.R | 93 +- EcoTroph-1.6.1/EcoTroph/R/convert.list2tab.R | 623 +++++++-------- EcoTroph-1.6.1/EcoTroph/R/create.ETdiagnosis.R | 315 ++++--- EcoTroph-1.6.1/EcoTroph/R/create.ETmain.R | 92 +- EcoTroph-1.6.1/EcoTroph/R/create.smooth.R | 163 ++- EcoTroph-1.6.1/EcoTroph/R/mf.diagnosis.R | 342 ++++---- EcoTroph-1.6.1/EcoTroph/R/plot.ETdiagnosis.R | 448 +++++----- EcoTroph-1.6.1/EcoTroph/R/plot.ETmain.R | 174 ++-- EcoTroph-1.6.1/EcoTroph/R/plot.Transpose.R | 155 ++- EcoTroph-1.6.1/EcoTroph/R/plot.smooth.R | 30 EcoTroph-1.6.1/EcoTroph/R/plot_ETdiagnosis_isopleth.R | 279 +++--- EcoTroph-1.6.1/EcoTroph/R/read.ecopath.model.R | 101 +- EcoTroph-1.6.1/EcoTroph/R/regPB.R |only EcoTroph-1.6.1/EcoTroph/R/regPB.ac.R |only EcoTroph-1.6.1/EcoTroph/R/saturation.R | 41 EcoTroph-1.6.1/EcoTroph/README.md |only EcoTroph-1.6.1/EcoTroph/man/CTSA.catch.input.Rd | 94 -- EcoTroph-1.6.1/EcoTroph/man/E0.1.Rd |only EcoTroph-1.6.1/EcoTroph/man/E_MSY_0.1.Rd | 95 -- EcoTroph-1.6.1/EcoTroph/man/Emsy.Rd |only EcoTroph-1.6.1/EcoTroph/man/Transpose.Rd | 71 - EcoTroph-1.6.1/EcoTroph/man/a13.eq.Rd |only EcoTroph-1.6.1/EcoTroph/man/a13.eq.ac.Rd |only EcoTroph-1.6.1/EcoTroph/man/check.table.Rd | 53 - EcoTroph-1.6.1/EcoTroph/man/convert.list2tab.Rd | 58 - EcoTroph-1.6.1/EcoTroph/man/create.ETdiagnosis.Rd | 146 +-- EcoTroph-1.6.1/EcoTroph/man/create.ETmain.Rd | 95 -- EcoTroph-1.6.1/EcoTroph/man/create.smooth.Rd | 101 -- EcoTroph-1.6.1/EcoTroph/man/mf.diagnosis.Rd |only EcoTroph-1.6.1/EcoTroph/man/plot.ETdiagnosis.Rd | 91 -- EcoTroph-1.6.1/EcoTroph/man/plot.ETmain.Rd | 102 +- EcoTroph-1.6.1/EcoTroph/man/plot.Transpose.Rd | 83 - EcoTroph-1.6.1/EcoTroph/man/plot.smooth.Rd | 65 - EcoTroph-1.6.1/EcoTroph/man/plot_ETdiagnosis_isopleth.Rd | 122 +- EcoTroph-1.6.1/EcoTroph/man/read.ecopath.model.Rd | 53 - EcoTroph-1.6.1/EcoTroph/man/regPB.Rd |only EcoTroph-1.6.1/EcoTroph/man/regPB.ac.Rd |only EcoTroph-1.6.1/EcoTroph/man/saturation.Rd | 84 -- EcoTroph-1.6/EcoTroph/R/CTSA.forward.R |only EcoTroph-1.6/EcoTroph/R/sub.mf.R |only EcoTroph-1.6/EcoTroph/man/CTSA.forward.Rd |only 51 files changed, 2280 insertions(+), 2242 deletions(-)
Title: B Cell Receptor Phylogenetics Toolkit
Description: Provides a set of functions for inferring, visualizing, and analyzing B cell phylogenetic trees.
Provides methods to 1) reconstruct unmutated ancestral sequences,
2) build B cell phylogenetic trees using multiple methods,
3) visualize trees with metadata at the tips,
4) reconstruct intermediate sequences,
5) detect biased ancestor-descendant relationships among metadata types
Workflow examples available at documentation site (see URL).
Citations:
Hoehn et al (2020) <doi:10.1101/2020.05.30.124446>,
Hoehn et al (2021) <doi:10.1101/2021.01.06.425648>.
Author: Kenneth Hoehn [aut, cre],
Susanna Marquez [ctb],
Jason Vander Heiden [ctb],
Steven Kleinstein [aut, cph]
Maintainer: Kenneth Hoehn <kenneth.hoehn@yale.edu>
Diff between dowser versions 0.1.0 dated 2021-07-22 and 1.0.0 dated 2022-04-13
DESCRIPTION | 12 MD5 | 107 ++++--- NAMESPACE | 3 NEWS.md | 17 + R/Clones.R | 138 ++++++--- R/Dowser.R | 8 R/Germlines.R | 213 ++++++++------- R/Plotting.R | 40 +- R/Statistics.R | 106 ++++--- R/TreeFunctions.R | 482 +++++++++++++++++++++++----------- README.md | 20 + build/vignette.rds |binary data/ExampleAirr.rda |binary data/ExampleClones.rda |binary inst/doc/Building-Trees-Vignette.Rmd | 2 inst/doc/Building-Trees-Vignette.pdf |binary inst/doc/Discrete-Trait-Vignette.R |only inst/doc/Discrete-Trait-Vignette.Rmd |only inst/doc/Discrete-Trait-Vignette.pdf |only inst/doc/Germlines-Vignette.Rmd | 4 inst/doc/Germlines-Vignette.pdf |binary inst/doc/Measurable-Evolution.R |only inst/doc/Measurable-Evolution.Rmd |only inst/doc/Measurable-Evolution.pdf |only inst/doc/Plotting-Trees-Vignette.Rmd | 2 inst/doc/Plotting-Trees-Vignette.pdf |binary inst/doc/Quickstart-Vignette.R | 48 +-- inst/doc/Quickstart-Vignette.Rmd | 2 inst/doc/Quickstart-Vignette.pdf |binary inst/doc/Sequences-Vignette.R | 2 inst/doc/Sequences-Vignette.Rmd | 6 inst/doc/Sequences-Vignette.pdf |binary man/bootstrapTrees.Rd | 44 --- man/buildPML.Rd | 3 man/correlationTest.Rd | 6 man/createGermlines.Rd | 8 man/dowser.Rd | 5 man/findSwitches.Rd |only man/formatClones.Rd | 2 man/getDivergence.Rd | 9 man/getNodeSeq.Rd |only man/getSeq.Rd | 6 man/getSubclones.Rd | 4 man/getTrees.Rd | 2 man/makeModelFile.Rd | 2 man/plotTrees.Rd | 10 man/readModelFile.Rd | 2 man/reconIgPhyML.Rd |only man/rerootTree.Rd | 2 man/testPS.Rd | 6 man/testSC.Rd | 6 man/testSP.Rd | 8 man/treesToPDF.Rd | 2 vignettes/Building-Trees-Vignette.Rmd | 2 vignettes/Discrete-Trait-Vignette.Rmd |only vignettes/Germlines-Vignette.Rmd | 4 vignettes/Measurable-Evolution.Rmd |only vignettes/Plotting-Trees-Vignette.Rmd | 2 vignettes/Quickstart-Vignette.Rmd | 2 vignettes/Sequences-Vignette.Rmd | 6 60 files changed, 843 insertions(+), 512 deletions(-)
Title: Broadly Useful Convenient and Efficient R Functions
Description: Broadly useful convenient and efficient R functions
that bring users concise and elegant R data analyses.
This package includes easy-to-use functions for
(1) basic R programming
(e.g., set working directory to the path of currently opened file,
import/export data from/to files with any format,
print strings with rich formats and colors);
(2) multivariate computation
(e.g., compute scale sums/means/... with reverse scoring);
(3) reliability analyses and factor analyses;
(4) descriptive statistics and correlation analyses;
(5) t-test, multi-factor analysis of variance (ANOVA),
simple-effect analysis, and post-hoc multiple comparison;
(6) tidy report of statistical models
(to R Console and Microsoft Word);
(7) mediation and moderation analyses (PROCESS);
and (8) additional toolbox for statistics and graphics.
Author: Han-Wu-Shuang Bao [aut, cre]
Maintainer: Han-Wu-Shuang Bao <baohws@foxmail.com>
Diff between bruceR versions 0.8.5 dated 2022-03-02 and 0.8.6 dated 2022-04-13
DESCRIPTION | 10 MD5 | 94 - NEWS.md | 88 - R/bruceR.R | 94 + R/bruceR_basic.R | 529 +++++---- R/bruceR_stats_01_basic.R | 645 +++++------- R/bruceR_stats_02_scale.R | 586 +++++------ R/bruceR_stats_03_manova.R | 424 +++---- R/bruceR_stats_04_regress.R | 704 ++++++------- R/bruceR_stats_05_advance.R | 1542 ++++++++++++++--------------- R/bruceR_stats_06_plot.R | 60 - R/deprecated.R | 3 README.md | 33 man/Alpha.Rd | 2 man/CFA.Rd | 18 man/Corr.Rd | 16 man/Describe.Rd | 16 man/EFA.Rd | 2 man/EMMEANS.Rd | 4 man/Freq.Rd | 2 man/GLM_summary.Rd | 6 man/HLM_ICC_rWG.Rd | 4 man/HLM_summary.Rd | 14 man/LOOKUP.Rd | 14 man/MANOVA.Rd | 6 man/PROCESS.Rd | 29 man/Print.Rd | 2 man/RECODE.Rd | 4 man/RESCALE.Rd | 6 man/TTEST.Rd | 14 man/bruceR-package.Rd | 15 man/cc.Rd | 11 man/ccf_plot.Rd | 10 man/dtime.Rd | 55 - man/export.Rd | 6 man/figures |only man/grand_mean_center.Rd | 6 man/granger_causality.Rd | 2 man/grapes-grapes-COMPUTE-grapes-grapes.Rd | 36 man/grapes-notin-grapes.Rd | 2 man/group_mean_center.Rd | 6 man/import.Rd | 6 man/lavaan_summary.Rd | 12 man/med_summary.Rd | 20 man/model_summary.Rd | 32 man/print_table.Rd | 2 man/regress.Rd | 2 man/theme_bruce.Rd | 14 48 files changed, 2667 insertions(+), 2541 deletions(-)
Title: Convert Statistical Objects into Tidy Tibbles
Description: Summarizes key information about statistical
objects in tidy tibbles. This makes it easy to report results, create
plots and consistently work with large numbers of models at once.
Broom provides three verbs that each provide different types of
information about a model. tidy() summarizes information about model
components such as coefficients of a regression. glance() reports
information about an entire model, such as goodness of fit measures
like AIC and BIC. augment() adds information about individual
observations to a dataset, such as fitted values or influence
measures.
Author: David Robinson [aut],
Alex Hayes [aut] ,
Simon Couch [aut, cre] ,
RStudio [cph, fnd],
Indrajeet Patil [ctb] ,
Derek Chiu [ctb],
Matthieu Gomez [ctb],
Boris Demeshev [ctb],
Dieter Menne [ctb],
Benjamin Nutter [ctb],
Luke Johnston [ctb],
Ben Bolker [ct [...truncated...]
Maintainer: Simon Couch <simonpatrickcouch@gmail.com>
Diff between broom versions 0.7.12 dated 2022-01-28 and 0.8.0 dated 2022-04-13
broom-0.7.12/broom/R/leaps.R |only broom-0.7.12/broom/R/mediate-tidiers.R |only broom-0.7.12/broom/R/pam-tidiers.R |only broom-0.7.12/broom/R/rma-tidiers.R |only broom-0.7.12/broom/tests/testthat/test-mediate.R |only broom-0.7.12/broom/tests/testthat/test-pam.R |only broom-0.7.12/broom/tests/testthat/test-rma.R |only broom-0.8.0/broom/DESCRIPTION | 80 +- broom-0.8.0/broom/MD5 | 633 ++++++++++----------- broom-0.8.0/broom/NEWS.md | 27 broom-0.8.0/broom/R/aer-tidiers.R | 8 broom-0.8.0/broom/R/auc-tidiers.R | 9 broom-0.8.0/broom/R/base-tidiers.R | 6 broom-0.8.0/broom/R/bbmle-tidiers.R | 6 broom-0.8.0/broom/R/betareg-tidiers.R | 8 broom-0.8.0/broom/R/biglm-tidiers.R | 15 broom-0.8.0/broom/R/bingroup-tidiers.R | 12 broom-0.8.0/broom/R/boot-tidiers.R | 12 broom-0.8.0/broom/R/btergm-tidiers.R | 39 + broom-0.8.0/broom/R/car-tidiers.R | 20 broom-0.8.0/broom/R/caret-tidiers.R | 11 broom-0.8.0/broom/R/cluster-tidiers.R |only broom-0.8.0/broom/R/cmprsk-tidiers.R | 10 broom-0.8.0/broom/R/deprecated-0-7-0.R | 12 broom-0.8.0/broom/R/drc-tidiers.R | 5 broom-0.8.0/broom/R/emmeans-tidiers.R | 9 broom-0.8.0/broom/R/epiR-tidiers.R | 6 broom-0.8.0/broom/R/ergm-tidiers.R | 15 broom-0.8.0/broom/R/fixest-tidiers.R | 29 broom-0.8.0/broom/R/gam-tidiers.R | 6 broom-0.8.0/broom/R/geepack-tidiers.R | 8 broom-0.8.0/broom/R/glmnet-cv-glmnet-tidiers.R | 7 broom-0.8.0/broom/R/glmnet-glmnet-tidiers.R | 5 broom-0.8.0/broom/R/gmm-tidiers.R | 7 broom-0.8.0/broom/R/hmisc-tidiers.R | 9 broom-0.8.0/broom/R/joinerml-tidiers.R | 27 broom-0.8.0/broom/R/kendall-tidiers.R | 4 broom-0.8.0/broom/R/ks-tidiers.R | 5 broom-0.8.0/broom/R/lavaan-tidiers.R | 16 broom-0.8.0/broom/R/leaps-tidiers.R |only broom-0.8.0/broom/R/lfe-tidiers.R | 19 broom-0.8.0/broom/R/list-svd-tidiers.R | 2 broom-0.8.0/broom/R/lm-beta-tidiers.R | 11 broom-0.8.0/broom/R/lmodel2-tidiers.R | 5 broom-0.8.0/broom/R/lmtest-tidiers.R | 21 broom-0.8.0/broom/R/maps-tidiers.R | 6 broom-0.8.0/broom/R/margins-tidiers.R | 53 + broom-0.8.0/broom/R/mass-fitdistr-tidiers.R | 9 broom-0.8.0/broom/R/mass-negbin-tidiers.R | 7 broom-0.8.0/broom/R/mass-polr-tidiers.R | 8 broom-0.8.0/broom/R/mass-ridgelm-tidiers.R | 10 broom-0.8.0/broom/R/mass-rlm-tidiers.R | 5 broom-0.8.0/broom/R/mclust-tidiers.R | 34 - broom-0.8.0/broom/R/mediation-tidiers.R |only broom-0.8.0/broom/R/metafor-tidiers.R |only broom-0.8.0/broom/R/mfx-tidiers.R | 44 - broom-0.8.0/broom/R/mgcv-tidiers.R | 9 broom-0.8.0/broom/R/mlogit-tidiers.R | 9 broom-0.8.0/broom/R/muhaz-tidiers.R | 6 broom-0.8.0/broom/R/multcomp-tidiers.R | 6 broom-0.8.0/broom/R/nnet-tidiers.R | 12 broom-0.8.0/broom/R/orcutt-tidiers.R | 7 broom-0.8.0/broom/R/ordinal-clm-tidiers.R | 7 broom-0.8.0/broom/R/ordinal-clmm-tidiers.R | 7 broom-0.8.0/broom/R/plm-tidiers.R | 9 broom-0.8.0/broom/R/polca-tidiers.R | 22 broom-0.8.0/broom/R/psych-tidiers.R | 8 broom-0.8.0/broom/R/quantreg-nlrq-tidiers.R | 27 broom-0.8.0/broom/R/quantreg-rq-tidiers.R | 38 + broom-0.8.0/broom/R/quantreg-rqs-tidiers.R | 2 broom-0.8.0/broom/R/robust-glmrob-tidiers.R | 15 broom-0.8.0/broom/R/robust-lmrob-tidiers.R | 17 broom-0.8.0/broom/R/robustbase-glmrob-tidiers.R | 2 broom-0.8.0/broom/R/robustbase-lmrob-tidiers.R | 14 broom-0.8.0/broom/R/spdep-tidiers.R | 22 broom-0.8.0/broom/R/speedglm-speedglm-tidiers.R | 6 broom-0.8.0/broom/R/speedglm-speedlm-tidiers.R | 11 broom-0.8.0/broom/R/stats-anova-tidiers.R | 8 broom-0.8.0/broom/R/stats-arima-tidiers.R | 3 broom-0.8.0/broom/R/stats-decompose-tidiers.R | 25 broom-0.8.0/broom/R/stats-factanal-tidiers.R | 14 broom-0.8.0/broom/R/stats-glm-tidiers.R | 6 broom-0.8.0/broom/R/stats-htest-tidiers.R | 17 broom-0.8.0/broom/R/stats-kmeans-tidiers.R | 12 broom-0.8.0/broom/R/stats-lm-tidiers.R | 18 broom-0.8.0/broom/R/stats-loess-tidiers.R | 1 broom-0.8.0/broom/R/stats-mlm-tidiers.R | 4 broom-0.8.0/broom/R/stats-nls-tidiers.R | 7 broom-0.8.0/broom/R/stats-prcomp-tidiers.R | 23 broom-0.8.0/broom/R/stats-smooth.spline-tidiers.R | 8 broom-0.8.0/broom/R/stats-summary-lm-tidiers.R | 16 broom-0.8.0/broom/R/stats-time-series-tidiers.R | 1 broom-0.8.0/broom/R/survey-tidiers.R | 9 broom-0.8.0/broom/R/survival-aareg-tidiers.R | 5 broom-0.8.0/broom/R/survival-cch-tidiers.R | 14 broom-0.8.0/broom/R/survival-coxph-tidiers.R | 6 broom-0.8.0/broom/R/survival-pyears-tidiers.R | 7 broom-0.8.0/broom/R/survival-survdiff-tidiers.R | 6 broom-0.8.0/broom/R/survival-survexp-tidiers.R | 6 broom-0.8.0/broom/R/survival-survfit-tidiers.R | 9 broom-0.8.0/broom/R/survival-survreg-tidiers.R | 7 broom-0.8.0/broom/R/systemfit-tidiers.R | 8 broom-0.8.0/broom/R/tseries-tidiers.R | 7 broom-0.8.0/broom/R/utilities.R | 20 broom-0.8.0/broom/R/vars-tidiers.R | 7 broom-0.8.0/broom/R/zoo-tidiers.R | 6 broom-0.8.0/broom/inst/WORDLIST | 2 broom-0.8.0/broom/inst/doc/adding-tidiers.html | 5 broom-0.8.0/broom/inst/doc/available-methods.html | 5 broom-0.8.0/broom/inst/doc/bootstrapping.html | 5 broom-0.8.0/broom/inst/doc/broom.html | 5 broom-0.8.0/broom/inst/doc/broom_and_dplyr.html | 5 broom-0.8.0/broom/inst/doc/kmeans.html | 1 broom-0.8.0/broom/man/augment.Mclust.Rd | 34 - 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Title: Analyze Experimental High-Throughput (Omics) Data
Description: The efficient treatment and convenient analysis of experimental high-throughput (omics) data gets facilitated through this collection of diverse functions.
Several functions address advanced object-conversions, like manipulating lists of lists or lists of arrays, reorganizing lists to arrays or into separate vectors, merging of multiple entries, etc.
Another set of functions provides speed-optimized calculation of standard deviation (sd), coefficient of variance (CV) or standard error of the mean (SEM)
for data in matrixes or means per line with respect to additional grouping (eg n groups of replicates).
Other functions facilitate dealing with non-redundant information, by indexing unique, adding counters to redundant or eliminating lines with respect redundancy in a given reference-column, etc.
Help is provided to identify very closely matching numeric values to generate (partial) distance matrixes for very big data in a memory efficient manner or to reduce the complexity of large data-sets by combining very close values.
Many times large experimental datasets need some additional filtering, adequate functions are provided.
Batch reading (or writing) of sets of files and combining data to arrays is supported, too.
Convenient data normalization is supported in various different modes, parameter estimation via permutations or boot-strap as well as flexible testing of multiple pair-wise combinations using the framework of 'limma' is provided, too.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrMisc versions 1.9.0 dated 2022-03-25 and 1.9.1 dated 2022-04-13
DESCRIPTION | 6 MD5 | 53 ++-- NAMESPACE | 1 R/asSepList.R | 19 + R/buildTree.R | 51 ++-- R/keepCommonText.R |only R/packageDownloadStat.R | 10 R/pairsAsPropensMatr.R | 26 +- R/randIndFx.R | 2 R/readTabulatedBatch.R | 11 - R/readXlsxBatch.R | 6 R/replicateStructure.R | 2 R/sampNoDeMArrayLM.R | 21 + R/trimRedundText.R | 32 +- inst/doc/doc |only inst/doc/wrMiscVignette1.R | 16 + inst/doc/wrMiscVignette1.Rmd | 36 +++ inst/doc/wrMiscVignette1.html | 455 +++++++++++++++++++++--------------------- man/asSepList.Rd | 15 - man/keepCommonText.Rd |only man/packageDownloadStat.Rd | 10 man/pairsAsPropensMatr.Rd | 28 +- man/randIndFx.Rd | 2 man/readTabulatedBatch.Rd | 14 - man/readXlsxBatch.Rd | 6 man/sampNoDeMArrayLM.Rd | 11 - man/trimRedundText.Rd | 11 - vignettes/wrMiscVignette1.Rmd | 36 +++ 28 files changed, 500 insertions(+), 380 deletions(-)
Title: Optimum Sample Allocation in Stratified Sampling Schemes
Description: Functions in this package provide solution to classical problem in
survey methodology - an optimum sample allocation in stratified sampling
schemes. In this context, the optimal allocation is in the classical
Tschuprov-Neyman's sense and it satisfies additional either lower or upper
bounds restrictions imposed on sample sizes in strata. There are few different
algorithms available to use, and one them is based on popular sample
allocation method that applies Neyman allocation to recursively reduced set of
strata.
This package also provides the function that computes a solution to the minimum
sample size allocation problem, which is a minor modification of the classical
optimium sample allocation. This problems lies in the determination
of a vector of strata sample sizes that minimizes total sample size, under
assumed fixed level of the pi-estimator's variance. As in the case of the
classical optimal allocation, the problem of minimum sample size allocation
can be complemented by imposing upper bounds constraints on sample sizes in
strata.
Author: Wojciech Wojciak [aut, cre],
Jacek Wesolowski [sad],
Robert Wieczorkowski [ctb]
Maintainer: Wojciech Wojciak <wojciech.wojciak@gmail.com>
Diff between stratallo versions 2.0.0 dated 2022-04-12 and 2.0.1 dated 2022-04-13
DESCRIPTION | 26 +++++++++++++------------- MD5 | 24 ++++++++++++------------ NEWS.md | 4 ++++ R/opt.R | 4 ++-- R/stratallo-package.R | 2 +- README.md | 34 +++++++++++++++++++++------------- build/partial.rdb |binary inst/WORDLIST | 1 + inst/doc/stratallo.Rmd | 8 ++++---- inst/doc/stratallo.html | 2 +- man/nopt.Rd | 4 ++-- man/stratallo-package.Rd | 2 +- vignettes/stratallo.Rmd | 8 ++++---- 13 files changed, 66 insertions(+), 53 deletions(-)
Title: Interface for 'MicroStrategy' REST API
Description: Interface for creating data sets and extracting data through the
'MicroStrategy' REST API. Access the demo API at
<https://demo.microstrategy.com/MicroStrategyLibrary/api-docs/index.html>.
Author: Piotr Kowal [aut, cre]
Maintainer: Piotr Kowal <pkowal@microstrategy.com>
Diff between mstrio versions 11.3.0.1 dated 2020-12-21 and 11.3.5.101 dated 2022-04-13
mstrio-11.3.0.1/mstrio/inst/www/precache-manifest.369bfcec07b8cf600bfeddb01603729c.js |only mstrio-11.3.0.1/mstrio/inst/www/static/css/2.ef729b12.chunk.css |only mstrio-11.3.0.1/mstrio/inst/www/static/css/main.3c78b4f0.chunk.css |only mstrio-11.3.0.1/mstrio/inst/www/static/js/2.eea63ad5.chunk.js |only mstrio-11.3.0.1/mstrio/inst/www/static/js/2.eea63ad5.chunk.js.LICENSE.txt |only mstrio-11.3.0.1/mstrio/inst/www/static/js/main.0e3fc029.chunk.js |only mstrio-11.3.5.101/mstrio/DESCRIPTION | 42 ++-------- mstrio-11.3.5.101/mstrio/MD5 | 36 ++++---- mstrio-11.3.5.101/mstrio/NEWS.md | 15 +++ mstrio-11.3.5.101/mstrio/R/cube.R | 29 ++++++ mstrio-11.3.5.101/mstrio/R/utils-errors.R | 6 - mstrio-11.3.5.101/mstrio/README.md | 39 ++++----- mstrio-11.3.5.101/mstrio/inst/doc/mstrio.Rmd | 4 mstrio-11.3.5.101/mstrio/inst/doc/mstrio.html | 2 mstrio-11.3.5.101/mstrio/inst/www/asset-manifest.json | 20 ++-- mstrio-11.3.5.101/mstrio/inst/www/index.html | 2 mstrio-11.3.5.101/mstrio/inst/www/precache-manifest.f557778d7eba9aabbdcb31427717dff5.js |only mstrio-11.3.5.101/mstrio/inst/www/service-worker.js | 2 mstrio-11.3.5.101/mstrio/inst/www/static/css/2.103a785d.chunk.css |only mstrio-11.3.5.101/mstrio/inst/www/static/css/main.d166975e.chunk.css |only mstrio-11.3.5.101/mstrio/inst/www/static/js/2.a97c3f93.chunk.js |only mstrio-11.3.5.101/mstrio/inst/www/static/js/2.a97c3f93.chunk.js.LICENSE.txt |only mstrio-11.3.5.101/mstrio/inst/www/static/js/main.a171ef35.chunk.js |only mstrio-11.3.5.101/mstrio/man/Cube.Rd | 7 - mstrio-11.3.5.101/mstrio/vignettes/mstrio.Rmd | 4 25 files changed, 113 insertions(+), 95 deletions(-)
Title: Generalized Linear Models with Clustering
Description: Binomial and Poisson regression for clustered data, fixed
and random effects with bootstrapping.
Author: Goeran Brostroem [aut, cre],
Jianming Jin [ctb],
Henrik Holmberg [ctb]
Maintainer: Goeran Brostroem <goran.brostrom@umu.se>
Diff between glmmML versions 1.1.1 dated 2020-05-28 and 1.1.2 dated 2022-04-13
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/glmmML.pdf |binary src/fun.c | 11 ++++++++--- 6 files changed, 20 insertions(+), 12 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>;
Bürkner (2021) <doi:10.18637/jss.v100.i05>; Carpenter et al. (2017)
<doi:10.18637/jss.v076.i01>.
Author: Paul-Christian Buerkner [aut, cre],
Jonah Gabry [ctb],
Sebastian Weber [ctb],
Andrew Johnson [ctb],
Martin Modrak [ctb],
Hamada S. Badr [ctb],
Frank Weber [ctb],
Mattan S. Ben-Shachar [ctb],
Hayden Rabel [ctb]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Diff between brms versions 2.16.3 dated 2021-11-22 and 2.17.0 dated 2022-04-13
DESCRIPTION | 43 MD5 | 751 +-- NAMESPACE | 1308 +++-- NEWS.md | 403 + R/autocor.R | 1268 ++--- R/backends.R | 153 R/bayes_R2.R | 188 R/bridgesampling.R | 496 +- R/brm.R | 164 R/brm_multiple.R | 68 R/brms-package.R | 168 R/brmsfit-class.R | 204 R/brmsfit-helpers.R | 374 - R/brmsfit-methods.R | 1128 ++--- R/brmsformula.R | 3406 +++++++-------- R/brmsterms.R | 2287 +++++----- R/conditional_effects.R | 2461 +++++------ R/conditional_smooths.R | 60 R/data-helpers.R | 1266 ++--- R/data-predictor.R | 1966 ++++----- R/data-response.R | 1213 ++--- R/datasets.R | 388 - R/diagnostics.R | 202 R/distributions.R | 5015 +++++++++++------------ R/emmeans.R | 420 - R/exclude_pars.R | 436 - R/exclude_terms.R | 114 R/families.R | 3679 ++++++++-------- R/family-lists.R | 1107 ++--- R/formula-ac.R | 192 R/formula-ad.R | 856 +-- R/formula-cs.R | 70 R/formula-gp.R | 642 +- R/formula-re.R | 1761 ++++---- R/formula-sm.R | 202 R/formula-sp.R | 1245 ++--- R/ggplot-themes.R | 182 R/hypothesis.R | 1172 ++--- R/kfold.R | 151 R/launch_shinystan.R | 116 R/log_lik.R | 2054 ++++----- R/loo.R | 1874 ++++---- R/loo_moment_match.R | 410 - R/loo_predict.R | 448 +- R/loo_subsample.R | 180 R/lsp.R | 88 R/make_stancode.R | 161 R/make_standata.R | 607 +- R/misc.R | 2231 +++++----- R/model_weights.R | 690 +-- R/numeric-helpers.R | 429 + R/plot.R | 568 +- R/posterior.R | 624 +- R/posterior_epred.R | 1701 +++---- R/posterior_predict.R | 2076 ++++----- R/posterior_samples.R | 496 +- R/posterior_smooths.R | 230 - R/pp_check.R | 418 + R/pp_mixture.R | 228 - R/predictive_error.R | 318 - R/predictor.R | 1048 ++-- R/prepare_predictions.R | 2433 +++++------ R/prior_draws.R | 304 - R/priors.R | 1245 +++-- R/projpred.R | 210 R/reloo.R | 57 R/rename_pars.R | 70 R/restructure.R | 1467 +++--- R/stan-helpers.R | 522 +- R/stan-likelihood.R | 153 R/stan-predictor.R | 740 +-- R/stan-prior.R | 209 R/stan-response.R | 117 R/stanvars.R | 514 +- R/summary.R | 1171 ++--- R/update.R | 103 README.md | 22 build/vignette.rds |binary inst/CITATION | 2 inst/chunks/fun_asym_laplace.stan | 116 inst/chunks/fun_cauchit.stan | 36 inst/chunks/fun_cholesky_cor_ar1.stan | 40 inst/chunks/fun_cholesky_cor_arma1.stan | 44 inst/chunks/fun_cholesky_cor_cosy.stan | 36 inst/chunks/fun_cholesky_cor_ma1.stan | 40 inst/chunks/fun_cloglog.stan | 18 inst/chunks/fun_com_poisson.stan | 236 - inst/chunks/fun_cox.stan | 74 inst/chunks/fun_dirichlet_logit.stan | 22 inst/chunks/fun_discrete_weibull.stan | 38 inst/chunks/fun_gaussian_process.stan | 58 inst/chunks/fun_gaussian_process_approx.stan | 62 inst/chunks/fun_gen_extreme_value.stan | 96 inst/chunks/fun_horseshoe.stan | 32 inst/chunks/fun_hurdle_gamma.stan | 86 inst/chunks/fun_hurdle_lognormal.stan | 84 inst/chunks/fun_hurdle_negbinomial.stan | 168 inst/chunks/fun_hurdle_poisson.stan | 160 inst/chunks/fun_inv_gaussian.stan | 100 inst/chunks/fun_logistic_normal.stan |only inst/chunks/fun_logm1.stan | 36 inst/chunks/fun_monotonic.stan | 28 inst/chunks/fun_multinomial_logit.stan | 20 inst/chunks/fun_normal_errorsar.stan | 46 inst/chunks/fun_normal_fcor.stan | 52 inst/chunks/fun_normal_lagsar.stan | 46 inst/chunks/fun_normal_time.stan | 142 inst/chunks/fun_r2d2.stan | 22 inst/chunks/fun_scale_r_cor.stan | 24 inst/chunks/fun_scale_r_cor_by.stan | 42 inst/chunks/fun_scale_r_cor_by_cov.stan | 86 inst/chunks/fun_scale_r_cor_cov.stan | 72 inst/chunks/fun_scale_time_err.stan | 40 inst/chunks/fun_scale_xi.stan | 68 inst/chunks/fun_sequence.stan | 12 inst/chunks/fun_softit.stan |only inst/chunks/fun_softplus.stan | 18 inst/chunks/fun_sparse_car_lpdf.stan | 74 inst/chunks/fun_sparse_icar_lpdf.stan | 64 inst/chunks/fun_squareplus.stan | 36 inst/chunks/fun_student_t_errorsar.stan | 52 inst/chunks/fun_student_t_fcor.stan | 70 inst/chunks/fun_student_t_lagsar.stan | 52 inst/chunks/fun_student_t_time.stan | 142 inst/chunks/fun_tan_half.stan | 36 inst/chunks/fun_von_mises.stan | 68 inst/chunks/fun_which_range.stan | 96 inst/chunks/fun_wiener_diffusion.stan | 38 inst/chunks/fun_zero_inflated_asym_laplace.stan | 124 inst/chunks/fun_zero_inflated_beta.stan | 90 inst/chunks/fun_zero_inflated_beta_binomial.stan |only inst/chunks/fun_zero_inflated_binomial.stan | 182 inst/chunks/fun_zero_inflated_negbinomial.stan | 182 inst/chunks/fun_zero_inflated_poisson.stan | 166 inst/chunks/fun_zero_one_inflated_beta.stan | 42 inst/doc/brms_customfamilies.R | 197 inst/doc/brms_customfamilies.Rmd | 683 +-- inst/doc/brms_customfamilies.html | 785 +-- inst/doc/brms_distreg.R | 162 inst/doc/brms_distreg.Rmd | 508 +- inst/doc/brms_distreg.html | 716 +-- inst/doc/brms_families.Rmd | 681 +-- inst/doc/brms_families.html | 481 +- inst/doc/brms_missings.R | 122 inst/doc/brms_missings.Rmd | 474 +- inst/doc/brms_missings.html | 604 +- inst/doc/brms_monotonic.R | 172 inst/doc/brms_monotonic.Rmd | 468 +- inst/doc/brms_monotonic.html | 913 ++-- inst/doc/brms_multilevel.ltx | 1358 +++--- inst/doc/brms_multilevel.pdf |binary inst/doc/brms_multivariate.R | 148 inst/doc/brms_multivariate.Rmd | 388 - inst/doc/brms_multivariate.html | 890 ++-- inst/doc/brms_nonlinear.R | 256 - inst/doc/brms_nonlinear.Rmd | 662 +-- inst/doc/brms_nonlinear.html | 981 ++-- inst/doc/brms_overview.ltx | 1044 ++-- inst/doc/brms_overview.pdf |binary inst/doc/brms_phylogenetics.R | 354 - inst/doc/brms_phylogenetics.Rmd | 730 +-- inst/doc/brms_phylogenetics.html | 1192 ++--- inst/doc/brms_threading.R | 894 ++-- inst/doc/brms_threading.Rmd | 1158 ++--- inst/doc/brms_threading.html | 1515 +++--- man/AsymLaplace.Rd | 124 man/BetaBinomial.Rd |only man/Dirichlet.Rd | 60 man/ExGaussian.Rd | 88 man/Frechet.Rd | 94 man/GenExtremeValue.Rd | 98 man/Hurdle.Rd | 120 man/InvGaussian.Rd | 80 man/LogisticNormal.Rd |only man/MultiNormal.Rd | 72 man/MultiStudentT.Rd | 78 man/R2D2.Rd | 80 man/Shifted_Lognormal.Rd | 122 man/SkewNormal.Rd | 166 man/StudentT.Rd | 96 man/VarCorr.brmsfit.Rd | 114 man/VonMises.Rd | 82 man/Wiener.Rd | 148 man/ZeroInflated.Rd | 138 man/add_criterion.Rd | 144 man/add_ic.Rd | 84 man/add_rstan_model.Rd | 46 man/addition-terms.Rd | 313 - man/ar.Rd | 102 man/arma.Rd | 108 man/as.data.frame.brmsfit.Rd | 114 man/as.mcmc.brmsfit.Rd | 84 man/autocor-terms.Rd | 72 man/autocor.brmsfit.Rd | 52 man/bayes_R2.brmsfit.Rd | 140 man/bayes_factor.brmsfit.Rd | 144 man/bridge_sampler.brmsfit.Rd | 142 man/brm.Rd | 1022 ++-- man/brm_multiple.Rd | 434 - man/brms-package.Rd | 168 man/brmsfamily.Rd | 713 +-- man/brmsfit-class.Rd | 152 man/brmsfit_needs_refit.Rd | 100 man/brmsformula-helpers.Rd | 268 - man/brmsformula.Rd | 1366 +++--- man/brmshypothesis.Rd | 144 man/brmsterms.Rd | 116 man/car.Rd | 152 man/coef.brmsfit.Rd | 106 man/combine_models.Rd | 60 man/compare_ic.Rd | 114 man/conditional_effects.brmsfit.Rd | 644 +- man/conditional_smooths.brmsfit.Rd | 240 - man/control_params.Rd | 54 man/cor_ar.Rd | 104 man/cor_arma.Rd | 106 man/cor_arr.Rd | 50 man/cor_brms.Rd | 58 man/cor_bsts.Rd | 46 man/cor_car.Rd | 148 man/cor_cosy.Rd | 66 man/cor_fixed.Rd | 60 man/cor_ma.Rd | 94 man/cor_sar.Rd | 120 man/cosy.Rd | 78 man/cs.Rd | 75 man/custom_family.Rd | 364 - man/data_predictor.Rd | 2 man/data_response.Rd | 42 man/density_ratio.Rd | 88 man/diagnostic-quantities.Rd | 118 man/do_call.Rd | 60 man/draws-brms.Rd | 152 man/draws-index-brms.Rd | 82 man/emmeans-brms-helpers.Rd | 178 man/epilepsy.Rd | 124 man/expose_functions.brmsfit.Rd | 58 man/expp1.Rd | 28 man/family.brmsfit.Rd | 46 man/fcor.Rd | 74 man/fitted.brmsfit.Rd | 244 - man/fixef.brmsfit.Rd | 112 man/get_dpar.Rd | 98 man/get_prior.Rd | 186 man/get_refmodel.brmsfit.Rd | 146 man/get_y.Rd | 62 man/gp.Rd | 286 - man/gr.Rd | 118 man/horseshoe.Rd | 238 - man/hypothesis.brmsfit.Rd | 332 - man/inhaler.Rd | 108 man/is.brmsfit.Rd | 28 man/is.brmsfit_multiple.Rd | 28 man/is.brmsformula.Rd | 28 man/is.brmsprior.Rd | 28 man/is.brmsterms.Rd | 34 man/is.cor_brms.Rd | 60 man/is.mvbrmsformula.Rd | 28 man/is.mvbrmsterms.Rd | 34 man/kfold.brmsfit.Rd | 285 - man/kfold_predict.Rd | 110 man/kidney.Rd | 116 man/lasso.Rd | 10 man/launch_shinystan.brmsfit.Rd | 74 man/log_lik.brmsfit.Rd | 188 man/logit_scaled.Rd | 42 man/logm1.Rd | 34 man/loo.brmsfit.Rd | 236 - man/loo_R2.brmsfit.Rd | 122 man/loo_compare.brmsfit.Rd | 96 man/loo_model_weights.brmsfit.Rd | 82 man/loo_moment_match.brmsfit.Rd | 154 man/loo_predict.brmsfit.Rd | 188 man/loo_subsample.brmsfit.Rd | 104 man/loss.Rd | 118 man/ma.Rd | 102 man/make_conditions.Rd | 72 man/make_stancode.Rd | 288 - man/make_standata.Rd | 242 - man/mcmc_plot.brmsfit.Rd | 184 man/me.Rd | 108 man/mi.Rd | 152 man/mixture.Rd | 38 man/mm.Rd | 170 man/mmc.Rd | 82 man/mo.Rd | 129 man/model_weights.brmsfit.Rd | 116 man/mvbrmsformula.Rd | 10 man/ngrps.brmsfit.Rd | 46 man/nsamples.brmsfit.Rd | 50 man/opencl.Rd | 78 man/pairs.brmsfit.Rd | 96 man/parnames.Rd | 40 man/plot.brmsfit.Rd | 172 man/post_prob.brmsfit.Rd | 168 man/posterior_average.brmsfit.Rd | 196 man/posterior_epred.brmsfit.Rd | 212 man/posterior_interval.brmsfit.Rd | 78 man/posterior_linpred.brmsfit.Rd | 186 man/posterior_predict.brmsfit.Rd | 278 - man/posterior_samples.brmsfit.Rd | 152 man/posterior_smooths.brmsfit.Rd | 140 man/posterior_summary.Rd | 132 man/posterior_table.Rd | 68 man/pp_average.brmsfit.Rd | 220 - man/pp_check.brmsfit.Rd | 199 man/pp_mixture.brmsfit.Rd | 242 - man/predict.brmsfit.Rd | 264 - man/predictive_error.brmsfit.Rd | 146 man/predictive_interval.brmsfit.Rd | 62 man/prepare_predictions.Rd | 246 - man/print.brmsfit.Rd | 48 man/print.brmsprior.Rd | 40 man/prior_draws.brmsfit.Rd | 118 man/prior_summary.brmsfit.Rd | 74 man/ranef.brmsfit.Rd | 126 man/reloo.brmsfit.Rd | 177 man/rename_pars.Rd | 70 man/residuals.brmsfit.Rd | 210 man/restructure.Rd | 50 man/rows2labels.Rd | 64 man/s.Rd | 94 man/sar.Rd | 116 man/save_pars.Rd | 102 man/set_prior.Rd | 788 +-- man/stancode.brmsfit.Rd | 79 man/standata.brmsfit.Rd | 102 man/stanvar.Rd | 164 man/summary.brmsfit.Rd | 96 man/theme_black.Rd | 90 man/theme_default.Rd | 36 man/threading.Rd | 114 man/update.brmsfit.Rd | 102 man/update.brmsfit_multiple.Rd | 76 man/validate_newdata.Rd | 128 man/validate_prior.Rd | 166 man/vcov.brmsfit.Rd | 76 man/waic.brmsfit.Rd | 176 tests/testthat.R | 8 tests/testthat/helpers/insert_refcat_ch.R | 76 tests/testthat/helpers/inv_link_categorical_ch.R | 89 tests/testthat/helpers/inv_link_ordinal_ch.R | 184 tests/testthat/helpers/link_categorical_ch.R | 46 tests/testthat/helpers/link_ordinal_ch.R | 164 tests/testthat/helpers/simopts_catlike.R | 8 tests/testthat/helpers/simopts_catlike_oneobs.R | 8 tests/testthat/tests.brm.R | 62 tests/testthat/tests.brmsfit-helpers.R | 414 - tests/testthat/tests.brmsfit-methods.R | 1957 ++++---- tests/testthat/tests.brmsformula.R | 122 tests/testthat/tests.brmsterms.R | 180 tests/testthat/tests.data-helpers.R | 4 tests/testthat/tests.distributions.R | 1170 ++--- tests/testthat/tests.emmeans.R | 102 tests/testthat/tests.exclude_pars.R | 96 tests/testthat/tests.families.R | 35 tests/testthat/tests.log_lik.R | 1017 ++-- tests/testthat/tests.make_stancode.R | 1339 +++--- tests/testthat/tests.make_standata.R | 401 - tests/testthat/tests.misc.R | 18 tests/testthat/tests.posterior_epred.R | 436 + tests/testthat/tests.posterior_predict.R | 800 +-- tests/testthat/tests.priors.R | 260 - tests/testthat/tests.rename_pars.R | 4 tests/testthat/tests.restructure.R | 382 - tests/testthat/tests.stan_functions.R | 100 vignettes/brms_customfamilies.Rmd | 683 +-- vignettes/brms_distreg.Rmd | 508 +- vignettes/brms_families.Rmd | 681 +-- vignettes/brms_missings.Rmd | 474 +- vignettes/brms_monotonic.Rmd | 468 +- vignettes/brms_multilevel.ltx | 1358 +++--- vignettes/brms_multivariate.Rmd | 388 - vignettes/brms_nonlinear.Rmd | 662 +-- vignettes/brms_overview.ltx | 1044 ++-- vignettes/brms_phylogenetics.Rmd | 730 +-- vignettes/brms_threading.Rmd | 1158 ++--- vignettes/citations_multilevel.bib | 702 +-- vignettes/citations_overview.bib | 1694 +++---- 379 files changed, 65799 insertions(+), 64508 deletions(-)
Title: 'Drat' R Archive Template
Description: Creation and use of R Repositories via helper functions
to insert packages into a repository, and to add repository information
to the current R session. Two primary types of repositories are support:
gh-pages at GitHub, as well as local repositories on either the same machine
or a local network. Drat is a recursive acronym: Drat R Archive Template.
Author: Dirk Eddelbuettel with contributions by Carl Boettiger, Neal Fultz,
Sebastian Gibb, Colin Gillespie, Jan Gorecki, Matt Jones, Thomas Leeper,
Steven Pav, Jan Schulz, Christoph Stepper, Felix G.M. Ernst and Patrick
Schratz.
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between drat versions 0.2.2 dated 2021-12-02 and 0.2.3 dated 2022-04-13
ChangeLog | 29 +++++++++++++++ DESCRIPTION | 8 ++-- MD5 | 47 ++++++++++++++----------- R/archivePackages.R | 2 - R/insertPackage.R | 27 ++++++++++---- R/pruneRepo.R | 6 +-- README.md | 6 +-- build/vignette.rds |binary inst/NEWS.Rd | 9 ++++ inst/doc/CombiningDratAndTravis.html | 65 ++++++++++++++++++----------------- inst/doc/DratFAQ.html | 11 ++++- inst/doc/DratForPackageAuthors.html | 19 ++++++---- inst/doc/DratForPackageAuthors.md | 3 - inst/doc/DratForPackageUsers.html | 13 ++++--- inst/doc/DratForPackageUsers.md | 2 - inst/doc/DratStepByStep.html | 33 ++++++++++------- inst/doc/WhyDrat.html | 11 ++++- inst/extdata/4.1 |only inst/extdata/big-sur-arm64 |only inst/extdata/src/bar_1.0.tar.gz |only inst/extdata/src/foo_1.3.tar.gz |only man/pruneRepo.Rd | 4 +- tests/simpleTests.R | 2 - tests/skeleton_git2r.R | 29 +++++++++------ tests/testArmBinary.R |only vignettes/DratForPackageAuthors.md | 3 - vignettes/DratForPackageUsers.md | 2 - 27 files changed, 209 insertions(+), 122 deletions(-)
Title: Functions to Declare Missing Values
Description: A set of functions to declare labels and missing values, coupled with
associated functions to create (weighted) tables of frequencies and various
other summary measures.
Various base functions are rewritten to make use of the specific information
about the missing values, most importantly to distinguish between empty and
declared missing values.
Many functions have a similar functionality with the corresponding functions
from packages "haven" and "labelled". A lot of effort was spent to ensure as
much compatibility as possible with these packages, with the intention to
offer a complementary alternative for the objects of class "declared".
Author: Adrian Dusa [aut, cre, cph]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between declared versions 0.13 dated 2022-04-03 and 0.15 dated 2022-04-13
declared-0.13/declared/man/declared-internal.Rd |only declared-0.13/declared/man/declared-package.Rd |only declared-0.15/declared/DESCRIPTION | 24 declared-0.15/declared/MD5 | 53 declared-0.15/declared/NAMESPACE | 92 - declared-0.15/declared/R/declared.R | 779 ++++++---- declared-0.15/declared/R/haven.R | 63 declared-0.15/declared/R/internals.R | 492 +++++- declared-0.15/declared/R/is_empty.R |only declared-0.15/declared/R/labelled.R | 2 declared-0.15/declared/R/labels.R | 2 declared-0.15/declared/R/onLoad.R | 36 declared-0.15/declared/R/print.R |only declared-0.15/declared/R/w_mean.R | 10 declared-0.15/declared/R/w_median.R | 2 declared-0.15/declared/R/w_mode.R | 8 declared-0.15/declared/R/w_quantile.R | 16 declared-0.15/declared/R/w_standardize.R | 4 declared-0.15/declared/R/w_summary.R | 4 declared-0.15/declared/R/w_table.R | 257 --- declared-0.15/declared/R/w_var.R | 12 declared-0.15/declared/inst/ChangeLog | 12 declared-0.15/declared/inst/doc/declared.pdf |binary declared-0.15/declared/inst/doc/why_the_package_declared.pdf |binary declared-0.15/declared/man/declared.Rd | 55 declared-0.15/declared/man/declared_internal.Rd |only declared-0.15/declared/man/declared_package.Rd |only declared-0.15/declared/man/is.empty.Rd |only declared-0.15/declared/man/weighted.Rd | 23 declared-0.15/declared/src |only declared-0.15/declared/vignettes/why_the_package_declared.pdf |binary 31 files changed, 1151 insertions(+), 795 deletions(-)
Title: Create Custom Taxonomies Based on the NCBI Taxonomy and GBIF
Backbone Taxonomy
Description: The NCBI taxonomy is a popular resource for taxonomic studies but it only contains
data on species with sequence data whereas the GBIF has a more extensive coverage of
extinct species. Taxonbridge is useful for the creation and analysis of custom taxonomies
based on the NCBI taxonomy and GBIF backbone taxonomy.
Author: Werner Veldsman [aut, cre]
Maintainer: Werner Veldsman <wernerpieter.veldsman@unil.ch>
Diff between taxonbridge versions 1.1.0 dated 2022-04-08 and 1.2.0 dated 2022-04-13
DESCRIPTION | 6 +- MD5 | 30 +++++++------- NEWS.md | 5 ++ R/get_methods.R | 15 +++++-- R/helper_methods.R | 2 R/load_methods.R | 28 +++++++++---- README.md | 44 ++++++++++++++++++--- inst/doc/Examples.R | 1 inst/doc/Examples.Rmd | 1 inst/doc/Examples.html | 93 ++++++++++++++++++++++----------------------- inst/extdata/sample.tsv.gz |binary man/download_ncbi.Rd | 2 man/fuzzy_search.Rd | 2 man/get_taxa.Rd | 10 +++- man/get_validity.Rd | 7 +-- vignettes/Examples.Rmd | 1 16 files changed, 152 insertions(+), 95 deletions(-)
Title: Helper Package for Installing OpenCV with R
Description: Installs 'OpenCV' for use by other packages. 'OpenCV' <https://opencv.org/>
is library of programming functions mainly aimed at real-time computer
vision. This 'Lite' version contains the stable base version of 'OpenCV' and
does not contain any of its externally contributed modules.
Author: Simon Garnier [aut, cre] ,
Muschelli John [ctb]
Maintainer: Simon Garnier <garnier@njit.edu>
Diff between ROpenCVLite versions 4.52.1 dated 2022-02-17 and 4.55.0 dated 2022-04-13
ROpenCVLite-4.52.1/ROpenCVLite/inst/OpenCVModule.4.5.1.cmake |only ROpenCVLite-4.52.1/ROpenCVLite/inst/OpenCVModule.4.5.2.cmake |only ROpenCVLite-4.55.0/ROpenCVLite/DESCRIPTION | 8 ROpenCVLite-4.55.0/ROpenCVLite/MD5 | 15 ROpenCVLite-4.55.0/ROpenCVLite/NEWS.md | 12 ROpenCVLite-4.55.0/ROpenCVLite/R/opencv.R | 22 ROpenCVLite-4.55.0/ROpenCVLite/build/vignette.rds |binary ROpenCVLite-4.55.0/ROpenCVLite/inst/OpenCVModule.4.5.5.cmake |only ROpenCVLite-4.55.0/ROpenCVLite/inst/doc/install.html | 286 +++++++++-- ROpenCVLite-4.55.0/ROpenCVLite/inst/doc/usage.html | 223 ++++++++ 10 files changed, 508 insertions(+), 58 deletions(-)
Title: Access the City of Toronto Open Data Portal
Description: Access data from the "City of Toronto
Open Data Portal" (<https://open.toronto.ca>) directly from R.
Author: Sharla Gelfand [aut, cre],
City of Toronto [cph, fnd]
Maintainer: Sharla Gelfand <sharla.gelfand@gmail.com>
Diff between opendatatoronto versions 0.1.4 dated 2020-10-14 and 0.1.5 dated 2022-04-13
DESCRIPTION | 12 +- MD5 | 24 ++-- R/get_resource.R | 1 R/opendatatoronto.R | 1 R/utils.R | 2 README.md | 152 +++++++++++++------------- build/vignette.rds |binary inst/doc/intro-opendatatoronto.html | 209 ++---------------------------------- man/get_resource.Rd | 1 man/opendatatoronto-package.Rd | 1 tests/testthat/test-browse.R | 2 tests/testthat/test-get_resource.R | 4 vignettes/articles/spatial_data.Rmd | 128 ++++++++++++++++++++-- 13 files changed, 232 insertions(+), 305 deletions(-)
More information about opendatatoronto at CRAN
Permanent link
Title: Markov Chain Monte Carlo (MCMC) Package
Description: Contains functions to perform Bayesian
inference using posterior simulation for a number of
statistical models. Most simulation is done in compiled C++
written in the Scythe Statistical Library Version 1.0.3. All
models return 'coda' mcmc objects that can then be summarized
using the 'coda' package. Some useful
utility functions such as density functions,
pseudo-random number generators for statistical
distributions, a general purpose Metropolis sampling algorithm,
and tools for visualization are provided.
Author: Andrew D. Martin [aut], Kevin M. Quinn [aut], Jong Hee Park [aut,cre], Ghislain Vieilledent [ctb], Michael Malecki[ctb], Matthew Blackwell [ctb], Keith Poole [ctb], Craig Reed [ctb], Ben Goodrich [ctb], Qiushi Yu [ctb], Ross Ihaka [cph], The R Develo [...truncated...]
Maintainer: Jong Hee Park <jongheepark@snu.ac.kr>
Diff between MCMCpack versions 1.6-2 dated 2022-03-30 and 1.6-3 dated 2022-04-13
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/MCMCmnl.R | 2 +- build/partial.rdb |binary inst/HISTORY.txt | 4 ++++ man/MCMCmnl.Rd | 2 +- 6 files changed, 15 insertions(+), 11 deletions(-)
Title: Statistical Analysis in Epidemiology
Description: Functions for demographic and epidemiological analysis in
the Lexis diagram, i.e. register and cohort follow-up data. In
particular representation, manipulation, rate estimation and
simulation for multistate data - the Lexis suite of functions, which
includes interfaces to 'mstate', 'etm' and 'cmprsk' packages.
Contains functions for Age-Period-Cohort and Lee-Carter modeling and
a function for interval censored data and some useful functions for
tabulation and plotting, as well as a number of epidemiological data
sets.
Author: Bendix Carstensen [aut, cre],
Martyn Plummer [aut],
Esa Laara [ctb],
Michael Hills [ctb]
Maintainer: Bendix Carstensen <b@bxc.dk>
Diff between Epi versions 2.44 dated 2021-02-27 and 2.46 dated 2022-04-13
Epi-2.44/Epi/R/list.lex.R |only Epi-2.44/Epi/man/list.lex.Rd |only Epi-2.44/Epi/vignettes/crisk.R |only Epi-2.44/Epi/vignettes/flup.R |only Epi-2.44/Epi/vignettes/sL.tex |only Epi-2.44/Epi/vignettes/simLexis.R |only Epi-2.44/Epi/vignettes/yl.tex |only Epi-2.44/Epi/vignettes/yll.R |only Epi-2.46/Epi/CHANGES | 47 + Epi-2.46/Epi/DESCRIPTION | 32 Epi-2.46/Epi/MD5 | 108 +- Epi-2.46/Epi/NAMESPACE | 32 Epi-2.46/Epi/R/AaJ.Lexis.R |only Epi-2.46/Epi/R/Relevel.Lexis.R | 11 Epi-2.46/Epi/R/addCov.Lexis.R | 29 Epi-2.46/Epi/R/addDrug.Lexis.R | 232 +++--- Epi-2.46/Epi/R/apc.fit.R | 46 - Epi-2.46/Epi/R/cal.yr.R | 65 - Epi-2.46/Epi/R/ci.Crisk.R | 95 +- Epi-2.46/Epi/R/ci.cum.R | 64 - Epi-2.46/Epi/R/ci.lin.R | 86 +- Epi-2.46/Epi/R/coarse.Lexis.R |only Epi-2.46/Epi/R/cutLexis.R | 34 Epi-2.46/Epi/R/lexis.R | 84 +- Epi-2.46/Epi/R/mod.Lexis.R | 43 - Epi-2.46/Epi/R/rcutLexis.R | 20 Epi-2.46/Epi/R/summary.Lexis.r | 24 Epi-2.46/Epi/inst/doc/addLexis.R |only Epi-2.46/Epi/inst/doc/addLexis.pdf |only Epi-2.46/Epi/inst/doc/crisk.R | 272 +++++-- Epi-2.46/Epi/inst/doc/crisk.pdf |binary Epi-2.46/Epi/inst/doc/flup.R | 150 +-- Epi-2.46/Epi/inst/doc/flup.pdf |binary Epi-2.46/Epi/inst/doc/index.html | 33 Epi-2.46/Epi/inst/doc/simLexis.R | 79 -- Epi-2.46/Epi/inst/doc/simLexis.pdf |binary Epi-2.46/Epi/inst/doc/yll.R | 239 ++---- Epi-2.46/Epi/inst/doc/yll.pdf |binary Epi-2.46/Epi/man/AaJ.Lexis.Rd |only Epi-2.46/Epi/man/LCa.fit.Rd | 5 Epi-2.46/Epi/man/Lexis.Rd | 127 ++- Epi-2.46/Epi/man/addCov.Lexis.Rd | 42 - Epi-2.46/Epi/man/addDrug.Lexis.Rd | 119 ++- Epi-2.46/Epi/man/ci.Crisk.Rd | 133 +-- Epi-2.46/Epi/man/ci.cum.Rd | 148 ++- Epi-2.46/Epi/man/start.Lexis.Rd | 2 Epi-2.46/Epi/man/summary.Lexis.Rd | 37 Epi-2.46/Epi/man/transform.Lexis.Rd | 3 Epi-2.46/Epi/vignettes/2Bappended2adLexisrnw.txt |only Epi-2.46/Epi/vignettes/addLexis.rnw |only Epi-2.46/Epi/vignettes/addLexis.rwl |only Epi-2.46/Epi/vignettes/addLexis.tex |only Epi-2.46/Epi/vignettes/cpall |only Epi-2.46/Epi/vignettes/crisk.rnw | 651 ++++++++++++---- Epi-2.46/Epi/vignettes/crisk.rwl |only Epi-2.46/Epi/vignettes/crisk.tex | 884 +++++++++++++++++------ Epi-2.46/Epi/vignettes/fixall | 37 Epi-2.46/Epi/vignettes/flup.rnw | 173 ++-- Epi-2.46/Epi/vignettes/flup.rwl |only Epi-2.46/Epi/vignettes/flup.tex | 501 +++++++------ Epi-2.46/Epi/vignettes/simLexis.rnw | 179 ---- Epi-2.46/Epi/vignettes/simLexis.rwl |only Epi-2.46/Epi/vignettes/simLexis.tex | 485 ------------ Epi-2.46/Epi/vignettes/yll.rnw | 285 ++----- Epi-2.46/Epi/vignettes/yll.rwl |only Epi-2.46/Epi/vignettes/yll.tex | 390 ++-------- 66 files changed, 3148 insertions(+), 2878 deletions(-)
Title: Extra Recipes for Encoding Predictors
Description: Predictors can be converted to one or more numeric
representations using a variety of methods. Effect encodings using
simple generalized linear models <arXiv:1611.09477> or nonlinear
models <arXiv:1604.06737> can be used. There are also functions for
dimension reduction and other approaches.
Author: Emil Hvitfeldt [aut, cre] ,
Max Kuhn [aut] ,
RStudio [cph]
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
Diff between embed versions 0.1.5 dated 2021-11-24 and 0.2.0 dated 2022-04-13
DESCRIPTION | 28 +- MD5 | 116 ++++++----- NAMESPACE | 7 NEWS.md | 12 + R/0_imports.R | 20 - R/bayes.R | 167 ++++++---------- R/discretize_cart.R | 126 ++++++------ R/discretize_xgb.R | 204 ++++++++++--------- R/embed-package.R |only R/glm.R | 71 +++--- R/hash.R | 98 +++++---- R/lme.R | 105 +++++----- R/pca_sparse.R | 99 ++++----- R/pca_sparse_bayes.R | 115 +++++------ R/solubility.R | 6 R/tf.R | 276 ++++++++++++++------------ R/tidy.R |only R/tunable.R | 5 R/umap.R | 116 +++++------ R/woe.R | 135 +++++++----- man/add_woe.Rd | 1 man/dictionary.Rd | 2 man/embed-package.Rd |only man/figures/lifecycle-archived.svg |only man/figures/lifecycle-defunct.svg |only man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-maturing.svg |only man/figures/lifecycle-questioning.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/step_discretize_cart.Rd | 20 - man/step_discretize_xgb.Rd | 20 - man/step_embed.Rd | 32 +-- man/step_feature_hash.Rd | 27 +- man/step_lencode_bayes.Rd | 26 +- man/step_lencode_glm.Rd | 18 - man/step_lencode_mixed.Rd | 18 - man/step_pca_sparse.Rd | 47 ++-- man/step_pca_sparse_bayes.Rd | 47 ++-- man/step_umap.Rd | 34 +-- man/step_woe.Rd | 33 +-- man/tidy.recipe.Rd |only tests/testthat/_snaps/discretize_cart.md | 75 ++++++- tests/testthat/_snaps/discretize_xgb.md | 189 +++++++++++++++++- tests/testthat/_snaps/hash.md |only tests/testthat/_snaps/hash.new.md |only tests/testthat/_snaps/mixed.md | 31 ++ tests/testthat/_snaps/no_pooling.md | 36 +++ tests/testthat/_snaps/pooling.md |only tests/testthat/_snaps/sparse_pca.md | 4 tests/testthat/_snaps/tf.md | 31 ++ tests/testthat/_snaps/umap.md |only tests/testthat/_snaps/woe.md | 89 ++++++++ tests/testthat/make_binned_data.R | 32 +-- tests/testthat/make_example_data.R | 4 tests/testthat/test-s3-methods.R | 29 +- tests/testthat/test_discretize_cart.R | 147 ++++++-------- tests/testthat/test_discretize_xgb.R | 209 ++++++++------------ tests/testthat/test_hash.R | 123 ++++++----- tests/testthat/test_mixed.R | 180 ++++++++--------- tests/testthat/test_no_pooling.R | 185 ++++++++--------- tests/testthat/test_pooling.R | 322 +++++++++++++++++++------------ tests/testthat/test_sparse_pca.R | 57 ++--- tests/testthat/test_tf.R | 203 +++++++++---------- tests/testthat/test_umap.R | 103 ++++----- tests/testthat/test_woe.R | 135 ++++++++---- 67 files changed, 2405 insertions(+), 1810 deletions(-)
Title: Continuous Cartogram
Description: Procedures for making continuous cartogram. Procedures available are:
flow based cartogram (Gastner & Newman (2004) <doi:10.1073/pnas.0400280101>),
fast flow based cartogram (Gastner, Seguy & More (2018) <doi:10.1073/pnas.1712674115>),
rubber band based cartogram (Dougenik et al. (1985)
<doi:10.1111/j.0033-0124.1985.00075.x>).
Author: Pierre-Andre Cornillon [aut, cre],
Florent Demoraes [aut],
Flow-Based-Cartograms [cph]
Maintainer: Pierre-Andre Cornillon <pierre-andre.cornillon@univ-rennes2.fr>
Diff between cartogramR versions 1.0-6 dated 2022-03-22 and 1.0-7 dated 2022-04-13
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/cartogramR_options.R | 18 +++++++++--------- man/cartogramR_options.Rd | 4 ++-- 4 files changed, 18 insertions(+), 18 deletions(-)
Title: Vector Helpers
Description: Defines new notions of prototype and size that are
used to provide tools for consistent and well-founded type-coercion
and size-recycling, and are in turn connected to ideas of type- and
size-stability useful for analysing function interfaces.
Author: Hadley Wickham [aut],
Lionel Henry [aut, cre],
Davis Vaughan [aut],
data.table team [cph] and
their contribution to R's order),
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between vctrs versions 0.4.0 dated 2022-03-30 and 0.4.1 dated 2022-04-13
DESCRIPTION | 6 - MD5 | 28 +++--- NEWS.md | 9 + R/subscript-loc.R | 5 - inst/doc/stability.html | 4 src/arg-counter.c | 154 +++++++++++++++------------------ src/arg-counter.h | 16 ++- src/type-data-frame.c | 6 + src/version.c | 2 tests/testthat/_snaps/bind.md | 12 +- tests/testthat/_snaps/c.md | 18 +-- tests/testthat/_snaps/conditions.md | 6 - tests/testthat/_snaps/slice-assign.md | 2 tests/testthat/_snaps/slice.md | 6 - tests/testthat/_snaps/subscript-loc.md | 10 +- 15 files changed, 148 insertions(+), 136 deletions(-)
Title: MLOps Metadata Store - Experiment Tracking and Model Registry
for Production Teams
Description: An interface to Neptune. A metadata store for MLOps, built for teams that run a lot of experiments.
It gives you a single place to log, store, display, organize, compare, and query all your model-building metadata.
Neptune is used for:
• Experiment tracking: Log, display, organize, and compare ML experiments in a single place.
• Model registry: Version, store, manage, and query trained models, and model building metadata.
• Monitoring ML runs live: Record and monitor model training, evaluation, or production runs live
For more information see <https://neptune.ai/>.
Author: Mateusz Dominiak [aut],
Rafal Jankowski [aut, cre]
Maintainer: Rafal Jankowski <rafal.jankowski@neptune.ai>
Diff between neptune versions 0.2.2 dated 2022-04-06 and 0.2.3 dated 2022-04-13
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/neptune_install.R | 2 +- man/neptune_install.Rd | 2 +- 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Download Stats of R Packages
Description: Monthly download stats of 'CRAN' and 'Bioconductor' packages.
Download stats of 'CRAN' packages is from the 'RStudio' 'CRAN mirror', see <https://cranlogs.r-pkg.org:443>.
'Bioconductor' package download stats is at <https://bioconductor.org/packages/stats/>.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between dlstats versions 0.1.4 dated 2021-04-23 and 0.1.5 dated 2022-04-13
DESCRIPTION | 6 +-- MD5 | 12 +++---- build/vignette.rds |binary inst/doc/dlstats.R | 6 ++- inst/doc/dlstats.Rmd | 6 ++- inst/doc/dlstats.html | 82 ++++++++++++++++++++++++++++++++++---------------- vignettes/dlstats.Rmd | 6 ++- 7 files changed, 77 insertions(+), 41 deletions(-)
Title: Entropy Based Method for the Detection of Significant Variation
in Gene Expression Data
Description: An implementation of a method based on information theory devised
for the identification of genes showing a significant variation of expression
across multiple conditions. Given expression estimates from any number of
RNA-Seq samples and conditions it identifies genes or transcripts with a
significant variation of expression across all the conditions studied,
together with the samples in which they are over- or under-expressed.
Zambelli et al. (2018) <doi:10.1093/nar/gky055>.
Author: Federico Zambelli [cre] ,
Giulio Pavesi [aut]
Maintainer: Federico Zambelli <federico.zambelli@unimi.it>
Diff between RNentropy versions 1.2.2 dated 2018-06-01 and 1.2.3 dated 2022-04-13
DESCRIPTION | 12 - MD5 | 24 +-- NEWS.md |only R/RNentropy-internal.R | 254 +++++++++++++++++++-------------------- README.md |only build/partial.rdb |binary data/RN_BarresLab_FPKM.rda |binary data/RN_BarresLab_design.rda |binary data/RN_Brain_Example_design.rda |binary data/RN_Brain_Example_tpm.rda |binary man/RN_BarresLab_FPMK.Rd | 2 man/RN_pmi.Rd | 2 man/RNentropy-package.Rd | 1 man/RNentropy.Rd | 2 14 files changed, 150 insertions(+), 147 deletions(-)
Title: Relational Data Modeler
Description: The aim of this package is to manipulate relational
data models in R.
It provides functions to create, modify and export data models
in json format.
It also allows importing models created
with 'MySQL Workbench' (<https://www.mysql.com/products/workbench/>).
These functions are accessible through a graphical user
interface made with 'shiny'.
Constraints such as types, keys, uniqueness and mandatory fields are
automatically checked and corrected when editing a model.
Finally, real data can be confronted to a model to check their compatibility.
Author: Patrice Godard [aut, cre, cph]
Maintainer: Patrice Godard <patrice.godard@gmail.com>
Diff between ReDaMoR versions 0.5.2 dated 2022-01-13 and 0.6.3 dated 2022-04-13
DESCRIPTION | 11 MD5 | 26 NAMESPACE | 5 R/RelDataModel.R | 219 - R/RelTableModel.R | 19 R/df_to_model.R | 10 R/model_relational_data.R | 290 + R/named_MM.R |only R/namespace.R | 3 inst/doc/ReDaMoR.R | 35 inst/doc/ReDaMoR.Rmd | 59 inst/doc/ReDaMoR.html | 7039 ++++++++++++++++++++++++++++++++++++++++++-- man/is_MM.Rd |only man/read_named_MM.Rd |only man/read_named_MM_header.Rd |only vignettes/ReDaMoR.Rmd | 59 16 files changed, 7199 insertions(+), 576 deletions(-)
Title: Translation Layer from MATLAB to R
Description: Allows users familiar with MATLAB to use MATLAB-named functions in
R. Several basic MATLAB functions are written in this package to mimic the
behavior of their original counterparts, with more to come as this package
grows.
Author: Waldir Leoncio [aut, cre]
Maintainer: Waldir Leoncio <w.l.netto@medisin.uio.no>
Diff between matlab2r versions 1.0.0 dated 2022-01-28 and 1.1.0 dated 2022-04-13
DESCRIPTION | 9 ++-- MD5 | 22 ++++++----- NAMESPACE | 2 + R/gammaln.R |only R/isfield.R | 6 ++- R/matlab2r.R | 51 ++++++++++++++++++--------- R/min_max.R | 12 +++++- R/setdiff.R | 1 R/strcmp.R | 4 +- man/gammaln.Rd |only man/matlab2r.Rd | 6 ++- tests/testthat.R | 5 -- tests/testthat/test-convertedBaseFunctions.R | 14 ++++++- 13 files changed, 89 insertions(+), 43 deletions(-)
Title: Single-Species, Multi-Species, and Integrated Spatial Occupancy
Models
Description: Fits single-species, multi-species, and integrated non-spatial and spatial occupancy models using Markov Chain Monte Carlo (MCMC). Models are fit using Polya-Gamma data augmentation detailed in Polson, Scott, and Windle (2013) <doi:10.1080/01621459.2013.829001>. Spatial models are fit using either Gaussian processes or Nearest Neighbor Gaussian Processes (NNGP) for large spatial datasets. Details on NNGP models are given in Datta, Banerjee, Finley, and Gelfand (2016) <doi:10.1080/01621459.2015.1044091> and Finley, Datta, and Banerjee (2020) <arXiv:2001.09111>. Provides functionality for data integration of multiple single-species occupancy data sets using a joint likelihood framework. Details on data integration are given in Miller, Pacifici, Sanderlin, and Reich (2019) <doi:10.1111/2041-210X.13110>. Details on single-species and multi-species models are found in MacKenzie, Nichols, Lachman, Droege, Royle, and Langtimm (2002) <doi:10.1890/0012-9658(2002)083[2248:ESORWD]2.0.CO;2> and Dorazio and Royle <doi:10.1198/016214505000000015>, respectively.
Author: Jeffrey Doser [aut, cre],
Andrew Finley [aut]
Maintainer: Jeffrey Doser <doserjef@msu.edu>
Diff between spOccupancy versions 0.3.0 dated 2022-03-29 and 0.3.1 dated 2022-04-13
DESCRIPTION | 6 +- MD5 | 62 +++++++++++------------ NEWS.md | 5 + R/generics.R | 31 +++++++++-- R/intPGOcc.R | 55 +++++++++------------ R/ppcOcc.R | 8 +-- R/spIntPGOcc.R | 71 ++++++++++----------------- README.md | 6 +- build/partial.rdb |binary inst/CITATION | 24 ++++++++- man/intPGOcc.Rd | 3 - man/spIntPGOcc.Rd | 3 - src/PGOcc.cpp | 40 ++++++++------- src/intPGOcc.cpp | 57 +++++++++------------ src/lfJSDM.cpp | 66 +++++++++++++------------ src/lfMsPGOcc.cpp | 104 ++++++++++++++++++++------------------- src/msPGOcc.cpp | 80 ++++++++++++++++-------------- src/nn.cpp | 6 +- src/sfJSDMNNGP.cpp | 74 ++++++++++++++-------------- src/sfMsPGOccNNGP.cpp | 112 ++++++++++++++++++++++--------------------- src/sfMsPGOccNNGPPredict.cpp | 12 +++- src/spIntPGOcc.cpp | 94 +++++++++++++++++------------------- src/spIntPGOccNNGP.cpp | 76 +++++++++++++---------------- src/spMsPGOcc.cpp | 107 +++++++++++++++++++++-------------------- src/spMsPGOccNNGP.cpp | 87 +++++++++++++++++---------------- src/spMsPGOccNNGPPredict.cpp | 10 ++- src/spMsPGOccPredict.cpp | 16 +++--- src/spPGOcc.cpp | 65 +++++++++++++----------- src/spPGOccNNGP.cpp | 47 +++++++++--------- src/spPGOccNNGPPredict.cpp | 10 ++- src/spPGOccPredict.cpp | 16 +++--- src/util.cpp | 6 +- 32 files changed, 717 insertions(+), 642 deletions(-)
Title: R Interface to the Levenberg-Marquardt Nonlinear Least-Squares
Algorithm Found in MINPACK, Plus Support for Bounds
Description: The nls.lm function provides an R interface to lmder and lmdif from the MINPACK library, for solving nonlinear least-squares problems by a modification of the Levenberg-Marquardt algorithm, with support for lower and upper parameter bounds. The implementation can be used via nls-like calls using the nlsLM function.
Author: Timur V. Elzhov, Katharine M. Mullen, Andrej-Nikolai Spiess, Ben Bolker
Maintainer: Katharine M. Mullen <mullenkate@gmail.com>
Diff between minpack.lm versions 1.2-1 dated 2016-11-20 and 1.2-2 dated 2022-04-13
DESCRIPTION | 7 ++++--- MD5 | 8 +++++--- NEWS | 6 ++++++ inst |only src/init.c |only src/prod.c | 25 +++++++++++++++++++++++-- 6 files changed, 38 insertions(+), 8 deletions(-)
Title: Interactive Analysis of UCSC Xena Data
Description: Provides functions and a Shiny application for downloading,
analyzing and visualizing datasets from UCSC Xena
(<http://xena.ucsc.edu/>), which is a collection of UCSC-hosted public
databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
Author: Shixiang Wang [aut, cre] ,
Yi Xiong [aut] ,
Longfei Zhao [aut] ,
Kai Gu [aut] ,
Yin Li [aut],
Fei Zhao [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between UCSCXenaShiny versions 1.1.5 dated 2022-01-15 and 1.1.7 dated 2022-04-13
UCSCXenaShiny-1.1.5/UCSCXenaShiny/inst/extdata/ccle_drug_response_extend.rda |only UCSCXenaShiny-1.1.7/UCSCXenaShiny/DESCRIPTION | 6 UCSCXenaShiny-1.1.7/UCSCXenaShiny/MD5 | 290 UCSCXenaShiny-1.1.7/UCSCXenaShiny/NAMESPACE | 152 UCSCXenaShiny-1.1.7/UCSCXenaShiny/NEWS.md | 106 UCSCXenaShiny-1.1.7/UCSCXenaShiny/R/GeomSplitViolin.R | 110 UCSCXenaShiny-1.1.7/UCSCXenaShiny/R/analyze_gene_drug_response.R | 908 UCSCXenaShiny-1.1.7/UCSCXenaShiny/R/ccle.R | 288 UCSCXenaShiny-1.1.7/UCSCXenaShiny/R/data.R | 244 UCSCXenaShiny-1.1.7/UCSCXenaShiny/R/ezcor.R | 870 UCSCXenaShiny-1.1.7/UCSCXenaShiny/R/get_pancan_value.R | 758 UCSCXenaShiny-1.1.7/UCSCXenaShiny/R/get_pcawg_value.R | 254 UCSCXenaShiny-1.1.7/UCSCXenaShiny/R/globalVariables.R | 34 UCSCXenaShiny-1.1.7/UCSCXenaShiny/R/load_data.R | 204 UCSCXenaShiny-1.1.7/UCSCXenaShiny/R/ope_pancan_value.R | 122 UCSCXenaShiny-1.1.7/UCSCXenaShiny/R/query_custom_value.R | 20 UCSCXenaShiny-1.1.7/UCSCXenaShiny/R/query_toil_value_df.R | 122 UCSCXenaShiny-1.1.7/UCSCXenaShiny/R/query_value.R | 400 UCSCXenaShiny-1.1.7/UCSCXenaShiny/R/run.R | 50 UCSCXenaShiny-1.1.7/UCSCXenaShiny/R/tcga_surv.R | 412 UCSCXenaShiny-1.1.7/UCSCXenaShiny/R/utils-pipe.R | 36 UCSCXenaShiny-1.1.7/UCSCXenaShiny/R/utils.R | 116 UCSCXenaShiny-1.1.7/UCSCXenaShiny/R/vis_analyze_gene_drug_response.R | 224 UCSCXenaShiny-1.1.7/UCSCXenaShiny/R/vis_ccle_value.R | 332 UCSCXenaShiny-1.1.7/UCSCXenaShiny/R/vis_identifier.R | 748 UCSCXenaShiny-1.1.7/UCSCXenaShiny/R/vis_pancan_value.R | 2619 - UCSCXenaShiny-1.1.7/UCSCXenaShiny/R/vis_pcawg_value.R | 928 UCSCXenaShiny-1.1.7/UCSCXenaShiny/R/xenashiny.R | 18 UCSCXenaShiny-1.1.7/UCSCXenaShiny/R/zzz.R | 32 UCSCXenaShiny-1.1.7/UCSCXenaShiny/README.md | 575 UCSCXenaShiny-1.1.7/UCSCXenaShiny/build/vignette.rds |binary UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/doc/api.R | 108 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/doc/api.Rmd | 254 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/doc/api.html | 914 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/modules_apps/app.R | 38 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/modules_apps/simple_module_from_rstudio.R | 66 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/modules_apps/xx_modules.R | 98 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/App.R | 674 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/modules/combo-single-gene-pan-cancer-analysis.R | 125 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/modules/home-pancan-search.R | 178 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/modules/modules-ccle-gene-drug-respose-df.R | 352 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/modules/modules-ccle-gene-drug-target.R | 358 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/modules/modules-ccle-genecor.R | 516 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/modules/modules-ccle-search.R | 328 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/modules/modules-file-upload.R | 238 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/modules/modules-ga-group-comparison.R | 1496 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/modules/modules-ga-matrix-correlation.R | 778 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/modules/modules-ga-scatter-correlation.R | 764 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/modules/modules-ga-surv-analysis.R | 1440 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/modules/modules-pancan-anatomy.R | 340 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/modules/modules-pancan-genecor.R | 498 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/modules/modules-pancan-immune.R | 352 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/modules/modules-pancan-radar.R | 402 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/modules/modules-pancan-search-cancer.R | 380 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/modules/modules-pancan-search.R | 380 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/modules/modules-pancan-til.R | 376 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/modules/modules-pancan-unicox.R | 350 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/modules/modules-pcawg-genecor.R | 590 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/modules/modules-pcawg-search.R | 432 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/modules/modules-pcawg-survival-analysis.R | 736 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/modules/modules-pcawg-unicox.R | 398 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/modules/modules-survival-analysis.R | 842 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/server/general-analysis.R | 384 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/server/global.R | 32 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/server/home.R | 170 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/server/modules.R | 36 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/server/repository.R | 832 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/shiny-doc/citation.md | 108 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/shiny-doc/datasets.md |only UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/shiny-doc/terms.md | 324 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/shiny-doc/usage.md | 324 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/ui/chooser.R | 94 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/ui/developers.R | 244 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/ui/footer.R | 32 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/ui/general-analysis.R | 188 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/ui/global.R | 22 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/ui/help.R | 70 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/ui/home.R | 284 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/ui/pancan-analysis.R | 156 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/ui/repository.R | 238 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/www/bootstrap4.css | 704 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/www/chooser-binding.js | 168 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/www/css/bootstrap-grid.css | 4098 +- UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/www/css/bootstrap-grid.min.css | 12 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/www/css/bootstrap-reboot.css | 658 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/www/css/bootstrap-reboot.min.css | 14 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/www/css/bootstrap.css |17948 +++++----- UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/www/css/bootstrap.min.css | 12 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/www/js/bootstrap.bundle.js |12656 +++---- UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/www/js/bootstrap.bundle.min.js | 12 UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/www/js/bootstrap.js | 7788 ++-- UCSCXenaShiny-1.1.7/UCSCXenaShiny/inst/shinyapp/www/js/bootstrap.min.js | 12 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/TCGA.organ.Rd | 30 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/UCSCXenaShiny.Rd | 18 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/analyze_gene_drug_response_asso.Rd | 74 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/analyze_gene_drug_response_diff.Rd | 130 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/app_run.Rd | 54 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/available_hosts.Rd | 34 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/ccle_absolute.Rd | 36 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/ccle_info.Rd | 36 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/ezcor.Rd | 98 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/ezcor_batch.Rd | 104 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/ezcor_partial_cor.Rd | 98 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/get_pancan_value.Rd | 298 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/keep_cat_cols.Rd | 44 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/load_data.Rd | 122 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/pcawg_info.Rd | 36 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/pcawg_purity.Rd | 36 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/pipe.Rd | 24 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/query_molecule_value.Rd | 76 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/query_pancan_value.Rd | 120 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/query_toil_value_df.Rd | 68 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/tcga_clinical.Rd | 36 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/tcga_genome_instability.Rd | 36 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/tcga_gtex.Rd | 30 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/tcga_purity.Rd | 36 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/tcga_subtypes.Rd | 36 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/tcga_surv.Rd | 36 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/tcga_surv_analysis.Rd | 154 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/tcga_tmb.Rd | 36 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/toil_info.Rd | 36 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/vis_ccle_gene_cor.Rd | 108 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/vis_ccle_tpm.Rd | 44 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/vis_gene_TIL_cor.Rd | 74 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/vis_gene_cor.Rd | 84 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/vis_gene_cor_cancer.Rd | 96 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/vis_gene_drug_response_asso.Rd | 52 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/vis_gene_drug_response_diff.Rd | 70 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/vis_gene_immune_cor.Rd | 72 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/vis_gene_msi_cor.Rd | 66 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/vis_gene_stemness_cor.Rd | 88 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/vis_gene_tmb_cor.Rd | 66 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/vis_identifier_cor.Rd | 136 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/vis_identifier_grp_comparison.Rd | 210 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/vis_identifier_grp_surv.Rd | 144 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/vis_identifier_multi_cor.Rd | 146 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/vis_pancan_anatomy.Rd | 62 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/vis_pcawg_dist.Rd | 102 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/vis_pcawg_gene_cor.Rd | 120 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/vis_pcawg_unicox_tree.Rd | 74 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/vis_toil_TvsN.Rd | 114 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/vis_toil_TvsN_cancer.Rd | 92 UCSCXenaShiny-1.1.7/UCSCXenaShiny/man/vis_unicox_tree.Rd | 74 UCSCXenaShiny-1.1.7/UCSCXenaShiny/tests/testthat.R | 8 UCSCXenaShiny-1.1.7/UCSCXenaShiny/tests/testthat/test-run_app.R | 2 UCSCXenaShiny-1.1.7/UCSCXenaShiny/tests/testthat/test-vis_pancan_value.R | 10 UCSCXenaShiny-1.1.7/UCSCXenaShiny/vignettes/api.Rmd | 254 147 files changed, 38912 insertions(+), 38827 deletions(-)
Title: Alt String Implementation
Description: Provides an extendable, performant and multithreaded 'alt-string' implementation backed by 'C++' vectors and strings.
Author: Travers Ching [aut, cre, cph],
Phillip Hazel [ctb] ,
Zoltan Herczeg [ctb, cph] ,
University of Cambridge [cph] ,
Tilera Corporation [cph] ,
Yann Collet [ctb, cph]
Maintainer: Travers Ching <traversc@gmail.com>
Diff between stringfish versions 0.15.5 dated 2021-12-01 and 0.15.7 dated 2022-04-13
stringfish-0.15.5/stringfish/R/RcppExportsCustom.R |only stringfish-0.15.7/stringfish/ChangeLog | 11 + stringfish-0.15.7/stringfish/DESCRIPTION | 10 - stringfish-0.15.7/stringfish/MD5 | 26 +-- stringfish-0.15.7/stringfish/R/RcppExports.R |only stringfish-0.15.7/stringfish/R/sf_functions.r | 12 - stringfish-0.15.7/stringfish/build/vignette.rds |binary stringfish-0.15.7/stringfish/configure | 6 stringfish-0.15.7/stringfish/configure.ac | 6 stringfish-0.15.7/stringfish/inst/doc/vignette.html | 2 stringfish-0.15.7/stringfish/inst/extra_tests/benchmark_test.r | 56 +++---- stringfish-0.15.7/stringfish/src/Makevars.in | 2 stringfish-0.15.7/stringfish/src/Makevars.win | 2 stringfish-0.15.7/stringfish/src/sf_functions.cpp | 78 +++++----- stringfish-0.15.7/stringfish/tests/tests.r | 71 ++++----- 15 files changed, 150 insertions(+), 132 deletions(-)
Title: Time Feature Extrapolation Using Spectral Analysis and
Jack-Knife Resampling
Description: Proposes application of spectral analysis and jack-knife resampling for multivariate sequence forecasting. The application allows for a fast random search in a compact space of hyper-parameters composed by Sequence Length and Jack-Knife Leave-N-Out.
Author: Giancarlo Vercellino
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>
Diff between spooky versions 1.0.0 dated 2022-04-12 and 1.1.0 dated 2022-04-13
DESCRIPTION | 6 ++--- MD5 | 10 ++++----- NEWS.md | 4 +++ R/hood.R | 64 +++++++++++++++++++++++++++++++--------------------------- R/main.R | 7 +++++- man/spooky.Rd | 3 ++ 6 files changed, 56 insertions(+), 38 deletions(-)
Title: Mass Spectrometry Metabolomics Feature Clustering and
Interpretation
Description: A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. This method is compatible with gas and liquid chromatography coupled mass spectrometry, including indiscriminant tandem mass spectrometry <DOI: 10.1021/ac501530d> data.
Author: Corey D. Broeckling [aut] ,
Fayyaz Afsar [aut],
Steffen Neumann [aut],
Asa Ben-Hur [aut],
Jessica Prenni [aut],
Helge Hecht [cre]
Maintainer: Helge Hecht <helge.hecht@recetox.muni.cz>
Diff between RAMClustR versions 1.2.3 dated 2022-03-30 and 1.2.4 dated 2022-04-13
ChangeLog | 7 +++++-- DESCRIPTION | 42 ++++++++++++++++++++++++++++++------------ MD5 | 20 +++++++++++--------- NAMESPACE | 2 -- R/do.findmain.R | 4 ++++ R/ramclustR.R | 23 ++++++++++++++++++++++- R/rc.ramclustr.R | 3 +-- inst/doc/RAMClustR.html | 4 ++-- inst/extdata |only man/ramclustR.Rd | 23 +++++++++++++++++++++++ tests/testthat/helper.R |only tests/testthat/test.R | 8 +++++++- 12 files changed, 105 insertions(+), 31 deletions(-)
Title: Mixed Model Association Test for GEne-Environment Interaction
Description: Use a 'glmmkin' class object (GMMAT package) from the null model to perform generalized linear mixed model-based single-variant and variant set main effect tests, gene-environment interaction tests, and joint tests for association, as proposed in Wang et al. (2020) <DOI:10.1002/gepi.22351>.
Author: Xinyu Wang [aut],
Han Chen [aut, cre],
Duy Pham [aut],
Kenneth Westerman [aut],
Cong Pan [aut]
Maintainer: Han Chen <han.chen.2@uth.tmc.edu>
Diff between MAGEE versions 1.1.0 dated 2022-03-31 and 1.1.1 dated 2022-04-13
DESCRIPTION | 8 ++--- MD5 | 16 +++++------ R/MAGEE.R | 2 - README.md | 2 - inst/doc/MAGEE.Rnw | 4 +- inst/doc/MAGEE.pdf |binary src/fitglmm.cpp | 59 ++++++++++++++++++++++++++++++++++------- tests/testthat/test_glmm.gei.R | 5 ++- vignettes/MAGEE.Rnw | 4 +- 9 files changed, 70 insertions(+), 30 deletions(-)
Title: The Kernel Method of Test Equating
Description: Implements the kernel method of test equating as defined in von Davier, A. A., Holland, P. W. and Thayer, D. T. (2004) <doi:10.1007/b97446> and Andersson, B. and Wiberg, M. (2017) <doi:10.1007/s11336-016-9528-7> using the CB, EG, SG, NEAT CE/PSE and NEC designs, supporting Gaussian, logistic and uniform kernels and unsmoothed and pre-smoothed input data.
Author: Bjoern Andersson [aut, cre] ,
Kenny Braenberg [aut],
Marie Wiberg [aut]
Maintainer: Bjoern Andersson <bjoern.h.andersson@gmail.com>
Diff between kequate versions 1.6.3 dated 2020-02-07 and 1.6.4 dated 2022-04-13
DESCRIPTION | 16 +- MD5 | 34 ++--- NEWS | 5 R/kernel.R | 310 ++++++++++++++++++++++++------------------------- build/vignette.rds |binary inst/CITATION | 4 inst/doc/irtguide.R | 1 inst/doc/irtguide.pdf |binary inst/doc/kequate.R | 1 inst/doc/kequate.pdf |binary man/FTres.Rd | 2 man/PREp.Rd | 2 man/genseed.Rd | 2 man/irtose.Rd | 18 +- man/kefreq.Rd | 2 man/kequate-package.Rd | 14 +- man/kequate.Rd | 2 man/simeq.Rd | 2 18 files changed, 206 insertions(+), 209 deletions(-)
Title: Item Response Models for Multiple Ratings
Description: Implements some item response models for multiple
ratings, including the hierarchical rater model,
conditional maximum likelihood estimation of linear
logistic partial credit model and a wrapper function
to the commercial FACETS program. See Robitzsch and
Steinfeld (2018) for a description of the functionality
of the package.
See Wang, Su and Qiu (2014; <doi:10.1111/jedm.12045>)
for an overview of modeling alternatives.
Author: Alexander Robitzsch [aut, cre], Jan Steinfeld [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between immer versions 1.1-35 dated 2018-12-10 and 1.2-19 dated 2022-04-13
DESCRIPTION | 17 +-- MD5 | 103 +++++++++++----------- NAMESPACE | 8 + R/RcppExports.R | 2 R/immer_FACETS.R | 137 ++++++++++++++++++------------ R/immer_ccml.R | 6 - R/immer_create_design_matrix_A.R | 4 R/immer_ginv.R |only R/immer_install.R | 125 +++++++++++++++++---------- R/immer_jml.R | 54 +++++++---- R/immer_jml_calc_item_intercepts.R | 2 R/immer_jml_update_item_R.R | 6 - R/immer_jml_update_item_Rcpp.R | 10 +- R/immer_latent_regression.R | 6 - R/immer_proc_data.R | 5 - R/summary.immer_hrm.R | 6 - R/summary.immer_jml.R | 34 +++---- README.md | 4 build/partial.rdb |binary data/data.immer01a.rda |binary data/data.immer01b.rda |binary data/data.immer02.rda |binary data/data.immer03.rda |binary data/data.immer04a.rda |binary data/data.immer04b.rda |binary data/data.immer05.rda |binary data/data.immer06.rda |binary data/data.immer07.rda |binary data/data.immer08.rda |binary data/data.immer09.rda |binary data/data.immer10.rda |binary data/data.immer11.rda |binary data/data.immer12.rda |binary data/data.ptam1.rda |binary data/data.ptam2.rda |binary data/data.ptam3.rda |binary data/data.ptam4.rda |binary data/data.ptam4long.rda |binary data/data.ptam4wide.rda |binary inst/NEWS | 24 +++++ man/data.immer.Rd | 4 man/data.ptam.Rd | 4 man/immer_cml.Rd | 17 +-- man/immer_hrm.Rd | 8 - man/immer_install.Rd | 4 man/immer_jml.Rd | 33 ++++++- man/immer_opcat.Rd | 6 - man/immer_reshape_wideformat.Rd | 4 src/RcppExports.cpp | 7 + src/immer_rcpp_ccml.cpp | 4 src/immer_rcpp_cmml.cpp | 6 - src/immer_rcpp_dnorm_pbivnorm_drezner.cpp | 12 +- src/immer_rcpp_dnorm_pbivnorm_drezner.h | 2 53 files changed, 409 insertions(+), 255 deletions(-)
Title: Robust Inference for Absolute Abundance in Microbiome Analysis
Description: IFAA is a robust approach to make inference on the association of covariates with the absolute abundance (AA) of microbiome in an ecosystem. It can be also directly applied to relative abundance (RA) data to make inference on AA because the ratio of two RA is equal ratio of their AA. This algorithm can estimate and test the associations of interest while adjusting for potential confounders. High-dimensional covariates are handled with regularization. The estimates of this method have easy interpretation like a typical regression analysis. High-dimensional covariates are handled with regularization and it is implemented by parallel computing. False discovery rate is automatically controlled by this approach. Zeros do not need to be imputed by a positive value for the analysis. The IFAA package also offers the 'MZILN' function for estimating and testing associations of abundance ratios with covariates.
Author: Quran Wu [aut],
Zhigang Li [aut, cre]
Maintainer: Zhigang Li <zhigang.li@ufl.edu>
Diff between IFAA versions 1.0.5 dated 2022-03-10 and 1.0.6 dated 2022-04-13
IFAA-1.0.5/IFAA/vignettes/vignettes.html |only IFAA-1.0.5/IFAA/vignettes/vignettes.pdf |only IFAA-1.0.6/IFAA/DESCRIPTION | 14 IFAA-1.0.6/IFAA/MD5 | 48 - IFAA-1.0.6/IFAA/NAMESPACE | 1 IFAA-1.0.6/IFAA/NEWS.md | 4 IFAA-1.0.6/IFAA/R/IFAAfunc.R | 447 ++++++------ IFAA-1.0.6/IFAA/R/MZILN.R | 342 ++++----- IFAA-1.0.6/IFAA/R/Regulariz_MZILN.R | 265 ++++--- IFAA-1.0.6/IFAA/R/bootResuHDCI.R | 528 +++++++-------- IFAA-1.0.6/IFAA/R/getScrResu.R | 180 ++--- IFAA-1.0.6/IFAA/R/metaData.R | 535 +++++++-------- IFAA-1.0.6/IFAA/R/originDataScreen.R | 609 ++++++++--------- IFAA-1.0.6/IFAA/R/regulariz.R | 596 ++++++++--------- IFAA-1.0.6/IFAA/R/runBootLassHDCI.R | 187 ++--- IFAA-1.0.6/IFAA/R/runGlmnet.R | 143 +--- IFAA-1.0.6/IFAA/R/runScrParal.R | 236 +++--- IFAA-1.0.6/IFAA/R/runlinear.R | 99 +- IFAA-1.0.6/IFAA/build/IFAA.pdf |binary IFAA-1.0.6/IFAA/build/vignette.rds |binary IFAA-1.0.6/IFAA/inst/doc/IFAA.R | 134 +-- IFAA-1.0.6/IFAA/inst/doc/IFAA.Rmd | 26 IFAA-1.0.6/IFAA/inst/doc/IFAA.html | 1083 ++++++++++++------------------- IFAA-1.0.6/IFAA/man/IFAA.Rd | 9 IFAA-1.0.6/IFAA/man/MZILN.Rd | 9 IFAA-1.0.6/IFAA/vignettes/IFAA.Rmd | 26 26 files changed, 2681 insertions(+), 2840 deletions(-)
Title: Joint Distribution of Number of Crossings and Longest Run
Description: Joint distribution of number of crossings and the
longest run in a series of independent Bernoulli trials. The
computations uses an iterative procedure where computations
are based on results from shorter series. The procedure
conditions on the start value and partitions by further
conditioning on the position of the first crossing (or none).
Author: Tore Wentzel-Larsen [aut, cre],
Jacob Anhoej [aut]
Maintainer: Tore Wentzel-Larsen <tore.wentzellarsen@gmail.com>
Diff between crossrun versions 0.1.0 dated 2018-10-08 and 0.1.1 dated 2022-04-13
crossrun-0.1.0/crossrun/data/joint15.6.rda |only crossrun-0.1.0/crossrun/data/joint15symm.rda |only crossrun-0.1.0/crossrun/man/joint15.6.Rd |only crossrun-0.1.0/crossrun/man/joint15symm.Rd |only crossrun-0.1.1/crossrun/DESCRIPTION | 10 crossrun-0.1.1/crossrun/MD5 | 71 crossrun-0.1.1/crossrun/NAMESPACE | 27 crossrun-0.1.1/crossrun/R/auxiliary.r | 132 crossrun-0.1.1/crossrun/R/crossrunauto.r |only crossrun-0.1.1/crossrun/R/crossrunbin.r | 176 - crossrun-0.1.1/crossrun/R/crossrunchange.r | 210 - crossrun-0.1.1/crossrun/R/crossrunem.r |only crossrun-0.1.1/crossrun/R/crossrunsymm.r | 90 crossrun-0.1.1/crossrun/R/data.R | 83 crossrun-0.1.1/crossrun/README.md |only crossrun-0.1.1/crossrun/build/vignette.rds |binary crossrun-0.1.1/crossrun/data/joint14.6.rda |only crossrun-0.1.1/crossrun/data/joint14em.rda |only crossrun-0.1.1/crossrun/data/joint14symm.rda |only crossrun-0.1.1/crossrun/data/joint60em.rda |only crossrun-0.1.1/crossrun/inst/doc/vignettecrossrun.R | 392 +- crossrun-0.1.1/crossrun/inst/doc/vignettecrossrun.Rmd | 684 ++-- crossrun-0.1.1/crossrun/inst/doc/vignettecrossrun.html | 2599 ++++++++++------- crossrun-0.1.1/crossrun/man/boxprobt.Rd | 62 crossrun-0.1.1/crossrun/man/clshift.Rd | 50 crossrun-0.1.1/crossrun/man/crossrunauto.Rd |only crossrun-0.1.1/crossrun/man/crossrunbin.Rd | 67 crossrun-0.1.1/crossrun/man/crossrunchange.Rd | 83 crossrun-0.1.1/crossrun/man/crossrunem.Rd |only crossrun-0.1.1/crossrun/man/crossrunemcont.Rd |only crossrun-0.1.1/crossrun/man/crossrunshift.Rd | 67 crossrun-0.1.1/crossrun/man/crossrunsymm.Rd | 66 crossrun-0.1.1/crossrun/man/cumsumm.Rd | 54 crossrun-0.1.1/crossrun/man/cumsummcol.Rd | 56 crossrun-0.1.1/crossrun/man/exactbin.Rd | 58 crossrun-0.1.1/crossrun/man/joint100.6.Rd | 54 crossrun-0.1.1/crossrun/man/joint100symm.Rd | 56 crossrun-0.1.1/crossrun/man/joint14.6.Rd |only crossrun-0.1.1/crossrun/man/joint14em.Rd |only crossrun-0.1.1/crossrun/man/joint14symm.Rd |only crossrun-0.1.1/crossrun/man/joint60.6.Rd | 54 crossrun-0.1.1/crossrun/man/joint60em.Rd |only crossrun-0.1.1/crossrun/man/joint60symm.Rd | 56 crossrun-0.1.1/crossrun/man/simclbin.Rd | 69 crossrun-0.1.1/crossrun/man/simclem.Rd |only crossrun-0.1.1/crossrun/vignettes/vignettecrossrun.Rmd | 684 ++-- 46 files changed, 3573 insertions(+), 2437 deletions(-)
Title: Bayesian Inference for Directed Acyclic Graphs
Description: Implementation of a collection of MCMC methods for Bayesian structure learning
of directed acyclic graphs (DAGs), both from continuous and discrete data. For efficient
inference on larger DAGs, the space of DAGs is pruned according to the data. To filter
the search space, the algorithm employs a hybrid approach, combining constraint-based
learning with search and score. A reduced search space is initially defined on the basis
of a skeleton obtained by means of the PC-algorithm, and then iteratively improved with
search and score. Search and score is then performed following two approaches:
Order MCMC, or Partition MCMC.
The BGe score is implemented for continuous data and the BDe score is implemented
for binary data or categorical data. The algorithms may provide the maximum a posteriori
(MAP) graph or a sample (a collection of DAGs) from the posterior distribution given the data.
All algorithms are also applicable for structure learning and sampling for dynamic Bayesian networks.
References:
J. Kuipers, P. Suter, G. Moffa (2022) <doi:10.1080/10618600.2021.2020127>,
N. Friedman and D. Koller (2003) <doi:10.1023/A:1020249912095>,
D. Geiger and D. Heckerman (2002) <doi:10.1214/aos/1035844981>,
J. Kuipers and G. Moffa (2017) <doi:10.1080/01621459.2015.1133426>,
M. Kalisch et al. (2012) <doi:10.18637/jss.v047.i11>.
Author: Polina Suter [aut, cre], Jack Kuipers [aut]
Maintainer: Polina Suter <polina.suter@bsse.ethz.ch>
Diff between BiDAG versions 2.0.4 dated 2021-11-30 and 2.0.5 dated 2022-04-13
DESCRIPTION | 14 +++++----- MD5 | 50 ++++++++++++++++++------------------ NAMESPACE | 2 + R/DBNfns.R | 6 ++-- R/graphhelpfns.R | 31 ++++++++++++++++------ R/initpar.R | 4 ++ R/iterativeMCMC.R | 23 +++++++++------- R/main.R | 65 +++++++++++++++++++++++++++++------------------- R/orderMCMCbase.R | 25 +++++++++++++----- R/orderMCMCbasemax.R | 24 +++++++++++++---- R/orderMCMCmain.R | 11 ++++---- R/orderMCMCplus1.R | 25 ++++++++++++++---- R/orderMCMCplus1max.R | 26 +++++++++++++------ R/other.R | 6 ++-- R/partitionMCMC.R | 24 +++++++++++++---- R/partitionMCMCmain.R | 4 +- R/performanceassess.R | 14 +++++----- R/plotusingrgraphviz.R | 8 +++-- R/scoreagainstDBN.R | 4 +- R/spacefns.R | 31 +++++++++++----------- man/iterativeMCMC.Rd | 8 +++++ man/orderMCMC.Rd | 3 ++ man/partitionMCMC.Rd | 3 ++ man/scoreagainstDBN.Rd | 2 - man/scoreagainstDBN3.Rd | 2 - man/scoreparameters.Rd | 2 - 26 files changed, 263 insertions(+), 154 deletions(-)
Title: Analyze Cricket Performances Based on Data from Cricsheet
Description: Analyzing performances of cricketers and cricket teams
based on 'yaml' match data from Cricsheet <https://cricsheet.org/>.
Author: Tinniam V Ganesh
Maintainer: Tinniam V Ganesh <tvganesh.85@gmail.com>
Diff between yorkr versions 0.0.32 dated 2022-04-01 and 0.0.33 dated 2022-04-13
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/batsmanVsBowlerPerf.R | 4 ---- R/bowlerVsBatsmanPerf.R | 15 +++++++++++++-- R/convertAllYaml2RDataframesT20.R | 2 +- R/convertYaml2RDataframeT20.R | 2 +- R/parseYamlOver.R | 2 +- 7 files changed, 26 insertions(+), 19 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-14 0.5.7.1
2018-03-18 0.5.7
2017-09-19 0.5.6
2017-05-19 0.5.5
2017-02-26 0.5.4
2016-12-09 0.5.3
2016-12-08 0.5.2
2016-11-13 0.5.1
2016-10-13 0.5.0
Title: RNA-Seq Profile Classifier
Description: We developed a lightweight machine learning tool for RNA profiling of acute lymphoblastic leukemia (ALL), however, it can be used for any problem where multiple classes need to be identified from multi-dimensional data. The methodology is described in Makinen V-P, Rehn J, Breen J, Yeung D, White DL (2022) Multi-cohort transcriptomic subtyping of B-cell acute lymphoblastic leukemia, medRxiv, <doi:10.1101/2022.02.17.22270919>. The classifier contains optimized mean profiles of the classes (centroids) as observed in the training data, and new samples are matched to these centroids using the shortest Euclidean distance. Centroids derived from a dataset of 1,598 ALL patients are included, but users can train the models with their own data as well. The output includes both numerical and visual presentations of the classification results. Samples with mixed features from multiple classes or atypical values are also identified.
Author: Ville-Petteri Makinen [aut, cre]
Maintainer: Ville-Petteri Makinen <vpmakine@gmail.com>
Diff between Allspice versions 1.0.3 dated 2022-02-22 and 1.0.4 dated 2022-04-13
DESCRIPTION | 8 +- MD5 | 10 +-- build/vignette.rds |binary inst/doc/intro.html | 122 +++++++++++++++++++++---------------------- inst/drivers/categories.txt | 42 +++++++------- inst/subtypes/categories.txt | 6 +- 6 files changed, 94 insertions(+), 94 deletions(-)