Title: Prioritize Variables with Joint Variable Importance Plot in
Observational Study Design
Description: In the observational study design stage, matching/weighting methods are
conducted. However, when many background variables are present, the decision as to
which variables to prioritize for matching/weighting is not trivial. Thus, the
joint treatment-outcome variable importance plots are created to guide variable
selection. The joint variable importance plots enhance variable comparisons via
unadjusted bias curves derived under the omitted variable bias framework. The
plots translate variable importance into recommended values for tuning parameters
in existing methods. Post-matching and/or weighting plots can also be used to
visualize and assess the quality of the observational study design. The method
motivation and derivation is presented in "Prioritizing Variables for Observational
Study Design using the Joint Variable Importance Plot" by Liao et al. (2024)
<doi:10.1080/00031305.2024.2303419>. See the package paper by Liao and Pimentel
(2024) <doi:10.21105/joss.06093> for [...truncated...]
Author: Lauren D. Liao [aut, cre] ,
Samuel D. Pimentel [aut]
Maintainer: Lauren D. Liao <ldliao@berkeley.edu>
Diff between jointVIP versions 0.1.2 dated 2023-03-08 and 1.0.0 dated 2024-11-21
jointVIP-0.1.2/jointVIP/R/general.R |only jointVIP-0.1.2/jointVIP/R/measures.R |only jointVIP-1.0.0/jointVIP/DESCRIPTION | 26 jointVIP-1.0.0/jointVIP/LICENSE | 2 jointVIP-1.0.0/jointVIP/MD5 | 92 +- jointVIP-1.0.0/jointVIP/NEWS.md | 16 jointVIP-1.0.0/jointVIP/R/check_measures.R |only jointVIP-1.0.0/jointVIP/R/create_jointVIP.R |only jointVIP-1.0.0/jointVIP/R/create_post_jointVIP.R |only jointVIP-1.0.0/jointVIP/R/data.R |only jointVIP-1.0.0/jointVIP/R/get_boot_measures.R |only jointVIP-1.0.0/jointVIP/R/get_measures.R |only jointVIP-1.0.0/jointVIP/R/get_post_measures.R |only jointVIP-1.0.0/jointVIP/R/plot.R |only jointVIP-1.0.0/jointVIP/R/print.R |only jointVIP-1.0.0/jointVIP/R/summary.R |only jointVIP-1.0.0/jointVIP/R/support.R |only jointVIP-1.0.0/jointVIP/README.md | 51 + jointVIP-1.0.0/jointVIP/build/vignette.rds |binary jointVIP-1.0.0/jointVIP/data |only jointVIP-1.0.0/jointVIP/inst/CITATION | 21 jointVIP-1.0.0/jointVIP/inst/doc/additional_options.R | 2 jointVIP-1.0.0/jointVIP/inst/doc/additional_options.Rmd | 1 jointVIP-1.0.0/jointVIP/inst/doc/additional_options.html | 305 ++++---- jointVIP-1.0.0/jointVIP/inst/doc/jointVIP.R | 2 jointVIP-1.0.0/jointVIP/inst/doc/jointVIP.html | 380 +++++----- jointVIP-1.0.0/jointVIP/man/add_bias_curves.Rd | 2 jointVIP-1.0.0/jointVIP/man/add_variable_labels.Rd | 2 jointVIP-1.0.0/jointVIP/man/bootstrap.plot.Rd | 4 jointVIP-1.0.0/jointVIP/man/brfss.Rd |only jointVIP-1.0.0/jointVIP/man/ceiling_dec.Rd | 2 jointVIP-1.0.0/jointVIP/man/check_measures.Rd | 2 jointVIP-1.0.0/jointVIP/man/create_jointVIP.Rd | 12 jointVIP-1.0.0/jointVIP/man/create_post_jointVIP.Rd | 8 jointVIP-1.0.0/jointVIP/man/figures/README-plot-1.png |binary jointVIP-1.0.0/jointVIP/man/floor_dec.Rd | 2 jointVIP-1.0.0/jointVIP/man/get_boot_measures.Rd | 2 jointVIP-1.0.0/jointVIP/man/get_measures.Rd | 2 jointVIP-1.0.0/jointVIP/man/get_post_measures.Rd | 2 jointVIP-1.0.0/jointVIP/man/one_hot.Rd |only jointVIP-1.0.0/jointVIP/man/plot.jointVIP.Rd | 4 jointVIP-1.0.0/jointVIP/man/plot.post_jointVIP.Rd | 6 jointVIP-1.0.0/jointVIP/man/print.jointVIP.Rd | 4 jointVIP-1.0.0/jointVIP/man/print.post_jointVIP.Rd | 6 jointVIP-1.0.0/jointVIP/man/summary.jointVIP.Rd | 4 jointVIP-1.0.0/jointVIP/man/summary.post_jointVIP.Rd | 6 jointVIP-1.0.0/jointVIP/tests/testthat.R | 5 jointVIP-1.0.0/jointVIP/tests/testthat/test-create_jointVIP.R | 118 +++ jointVIP-1.0.0/jointVIP/tests/testthat/test-create_post_jointVIP.R |only jointVIP-1.0.0/jointVIP/tests/testthat/test-get_measures.R |only jointVIP-1.0.0/jointVIP/tests/testthat/test-plot.R | 311 +++++++- jointVIP-1.0.0/jointVIP/tests/testthat/test-post.R | 21 jointVIP-1.0.0/jointVIP/tests/testthat/test-print.R | 52 + jointVIP-1.0.0/jointVIP/tests/testthat/test-summary.R | 57 + jointVIP-1.0.0/jointVIP/vignettes/additional_options.Rmd | 1 jointVIP-1.0.0/jointVIP/vignettes/ref.bib | 2 56 files changed, 1059 insertions(+), 476 deletions(-)
Title: Allelic Series Test
Description: Implementation of gene-level rare variant association tests targeting allelic series: genes where increasingly deleterious mutations have increasingly large phenotypic effects. The COding-variant Allelic Series Test (COAST) operates on the benign missense variants (BMVs), deleterious missense variants (DMVs), and protein truncating variants (PTVs) within a gene. COAST uses a set of adjustable weights that tailor the test towards rejecting the null hypothesis for genes where the average magnitude of effect increases monotonically from BMVs to DMVs to PTVs. See McCaw ZR, O’Dushlaine C, Somineni H, Bereket M, Klein C, Karaletsos T, Casale FP, Koller D, Soare TW. (2023) "An allelic series rare variant association test for candidate gene discovery" <doi:10.1016/j.ajhg.2023.07.001>.
Author: Zachary McCaw [aut, cre] ,
Christoph Klein [ctb] ,
Thomas Soare [ctb] ,
Jianhui Gao [ctb] ,
insitro [cph]
Maintainer: Zachary McCaw <zmccaw@insitro.com>
Diff between AllelicSeries versions 0.1.0.2 dated 2024-10-22 and 0.1.1.1 dated 2024-11-21
AllelicSeries-0.1.0.2/AllelicSeries/R/allelic_series_test.R |only AllelicSeries-0.1.1.1/AllelicSeries/DESCRIPTION | 13 AllelicSeries-0.1.1.1/AllelicSeries/MD5 | 100 +-- AllelicSeries-0.1.1.1/AllelicSeries/NEWS.md | 13 AllelicSeries-0.1.1.1/AllelicSeries/R/RcppExports.R | 46 + AllelicSeries-0.1.1.1/AllelicSeries/R/allelic_series.R |only AllelicSeries-0.1.1.1/AllelicSeries/R/allelic_series_sumstats.R | 149 +++-- AllelicSeries-0.1.1.1/AllelicSeries/R/class.R | 15 AllelicSeries-0.1.1.1/AllelicSeries/R/generate_data.R | 125 ++-- AllelicSeries-0.1.1.1/AllelicSeries/R/generate_sumstats.R | 33 - AllelicSeries-0.1.1.1/AllelicSeries/R/input_checks.R | 60 +- AllelicSeries-0.1.1.1/AllelicSeries/R/utilities.R | 54 + AllelicSeries-0.1.1.1/AllelicSeries/build/vignette.rds |binary AllelicSeries-0.1.1.1/AllelicSeries/inst/doc/coast.R | 27 AllelicSeries-0.1.1.1/AllelicSeries/inst/doc/coast.Rmd | 43 + AllelicSeries-0.1.1.1/AllelicSeries/inst/doc/coast.html | 284 ++++++---- AllelicSeries-0.1.1.1/AllelicSeries/inst/doc/coast_ss.R |only AllelicSeries-0.1.1.1/AllelicSeries/inst/doc/coast_ss.Rmd |only AllelicSeries-0.1.1.1/AllelicSeries/inst/doc/coast_ss.html |only AllelicSeries-0.1.1.1/AllelicSeries/inst/doc/data_generation.R |only AllelicSeries-0.1.1.1/AllelicSeries/inst/doc/data_generation.Rmd |only AllelicSeries-0.1.1.1/AllelicSeries/inst/doc/data_generation.html |only AllelicSeries-0.1.1.1/AllelicSeries/man/ASBT.Rd | 17 AllelicSeries-0.1.1.1/AllelicSeries/man/ASBTSS.Rd | 29 - AllelicSeries-0.1.1.1/AllelicSeries/man/ASKAT.Rd | 10 AllelicSeries-0.1.1.1/AllelicSeries/man/ASKATSS.Rd | 23 AllelicSeries-0.1.1.1/AllelicSeries/man/Aggregator.Rd | 22 AllelicSeries-0.1.1.1/AllelicSeries/man/AllelicSeries-package.Rd | 8 AllelicSeries-0.1.1.1/AllelicSeries/man/BaselineSS.Rd | 13 AllelicSeries-0.1.1.1/AllelicSeries/man/COAST-class.Rd | 2 AllelicSeries-0.1.1.1/AllelicSeries/man/COAST.Rd | 17 AllelicSeries-0.1.1.1/AllelicSeries/man/COASTSS.Rd | 28 AllelicSeries-0.1.1.1/AllelicSeries/man/CalcRegParam.Rd | 4 AllelicSeries-0.1.1.1/AllelicSeries/man/CalcSumstats.Rd | 16 AllelicSeries-0.1.1.1/AllelicSeries/man/CheckInputs.Rd | 2 AllelicSeries-0.1.1.1/AllelicSeries/man/CheckInputsSS.Rd | 6 AllelicSeries-0.1.1.1/AllelicSeries/man/Counts.Rd | 7 AllelicSeries-0.1.1.1/AllelicSeries/man/DGP.Rd | 40 - AllelicSeries-0.1.1.1/AllelicSeries/man/GenAnno.Rd | 12 AllelicSeries-0.1.1.1/AllelicSeries/man/GenGeno.Rd | 10 AllelicSeries-0.1.1.1/AllelicSeries/man/GenGenoMat.Rd | 5 AllelicSeries-0.1.1.1/AllelicSeries/man/GenPheno.Rd | 26 AllelicSeries-0.1.1.1/AllelicSeries/man/SumCountSS.Rd | 14 AllelicSeries-0.1.1.1/AllelicSeries/src/RcppExports.cpp | 37 - AllelicSeries-0.1.1.1/AllelicSeries/src/counting.cpp | 17 AllelicSeries-0.1.1.1/AllelicSeries/src/skat.cpp | 13 AllelicSeries-0.1.1.1/AllelicSeries/src/sumstats.cpp | 73 ++ AllelicSeries-0.1.1.1/AllelicSeries/tests/testthat/test-allelic_series.R | 219 +++++++ AllelicSeries-0.1.1.1/AllelicSeries/tests/testthat/test-allelic_series_sumstats.R | 217 ++++++- AllelicSeries-0.1.1.1/AllelicSeries/tests/testthat/test-binary.R | 40 - AllelicSeries-0.1.1.1/AllelicSeries/tests/testthat/test-counts.R | 45 + AllelicSeries-0.1.1.1/AllelicSeries/tests/testthat/test-data_generation.R | 220 ++++++- AllelicSeries-0.1.1.1/AllelicSeries/tests/testthat/test-score_test.R | 6 AllelicSeries-0.1.1.1/AllelicSeries/vignettes/coast.Rmd | 43 + AllelicSeries-0.1.1.1/AllelicSeries/vignettes/coast_ss.Rmd |only AllelicSeries-0.1.1.1/AllelicSeries/vignettes/data_generation.Rmd |only 56 files changed, 1653 insertions(+), 550 deletions(-)
Title: VPC Percentiles and Prediction Intervals
Description: Perform a Visual Predictive Check (VPC), while accounting for
stratification, censoring, and prediction correction. Using piping from
'magrittr', the intuitive syntax gives users a flexible and powerful method
to generate VPCs using both traditional binning and a new binless approach
Jamsen et al. (2018) <doi:10.1002/psp4.12319> with Additive Quantile
Regression (AQR) and Locally Estimated Scatterplot Smoothing (LOESS)
prediction correction.
Author: Olivier Barriere [aut],
Benjamin Rich [aut],
James Craig [aut, cre] ,
Samer Mouksassi [aut],
Bill Denney [ctb] ,
Michael Tomashevskiy [ctb],
Kris Jamsen [ctb],
Certara USA, Inc. [cph, fnd]
Maintainer: James Craig <james.craig@certara.com>
Diff between tidyvpc versions 1.5.1 dated 2024-01-18 and 1.5.2 dated 2024-11-21
tidyvpc-1.5.1/tidyvpc/inst/doc/tidyvpc_cat.R |only tidyvpc-1.5.1/tidyvpc/inst/doc/tidyvpc_cat.Rmd |only tidyvpc-1.5.1/tidyvpc/inst/doc/tidyvpc_cat.html |only tidyvpc-1.5.1/tidyvpc/inst/doc/tidyvpc_cont.R |only tidyvpc-1.5.1/tidyvpc/inst/doc/tidyvpc_cont.Rmd |only tidyvpc-1.5.1/tidyvpc/inst/doc/tidyvpc_cont.html |only tidyvpc-1.5.1/tidyvpc/inst/doc/tidyvpc_nlmixr2.R |only tidyvpc-1.5.1/tidyvpc/inst/doc/tidyvpc_nlmixr2.Rmd |only tidyvpc-1.5.1/tidyvpc/inst/doc/tidyvpc_nlmixr2.html |only tidyvpc-1.5.2/tidyvpc/DESCRIPTION | 17 tidyvpc-1.5.2/tidyvpc/LICENSE | 2 tidyvpc-1.5.2/tidyvpc/MD5 | 64 tidyvpc-1.5.2/tidyvpc/NEWS.md | 11 tidyvpc-1.5.2/tidyvpc/R/binless.R | 15 tidyvpc-1.5.2/tidyvpc/R/npde.R | 117 - tidyvpc-1.5.2/tidyvpc/R/plot.R | 22 tidyvpc-1.5.2/tidyvpc/R/vpcstats.R | 179 + tidyvpc-1.5.2/tidyvpc/R/vpcstats_fun.R | 27 tidyvpc-1.5.2/tidyvpc/README.md | 2 tidyvpc-1.5.2/tidyvpc/build/vignette.rds |binary tidyvpc-1.5.2/tidyvpc/inst/doc/tidyvpc_cat.pdf |only tidyvpc-1.5.2/tidyvpc/inst/doc/tidyvpc_cat.pdf.asis |only tidyvpc-1.5.2/tidyvpc/inst/doc/tidyvpc_cont.pdf |only tidyvpc-1.5.2/tidyvpc/inst/doc/tidyvpc_cont.pdf.asis |only tidyvpc-1.5.2/tidyvpc/inst/doc/tidyvpc_nlmixr2.pdf |only tidyvpc-1.5.2/tidyvpc/inst/doc/tidyvpc_nlmixr2.pdf.asis |only tidyvpc-1.5.2/tidyvpc/inst/extdata/NPDE/npdeobs.csv | 1102 +++++----- tidyvpc-1.5.2/tidyvpc/man/npde.Rd | 2 tidyvpc-1.5.2/tidyvpc/man/observed.Rd | 16 tidyvpc-1.5.2/tidyvpc/man/predcorrect.Rd | 38 tidyvpc-1.5.2/tidyvpc/man/simulated.Rd | 7 tidyvpc-1.5.2/tidyvpc/tests/testthat/_snaps/plot/censored-plot-with-aql.svg | 212 + tidyvpc-1.5.2/tidyvpc/tests/testthat/_snaps/plot/censored-plot-with-bql-aql.svg | 286 +- tidyvpc-1.5.2/tidyvpc/tests/testthat/_snaps/plot/censored-plot-with-bql.svg | 214 + tidyvpc-1.5.2/tidyvpc/tests/testthat/_snaps/plot/one-sided-strat-formula-with-facet-wrap.svg | 52 tidyvpc-1.5.2/tidyvpc/tests/testthat/_snaps/plot/single-value-group.svg | 52 tidyvpc-1.5.2/tidyvpc/tests/testthat/_snaps/plot/two-sided-strat-formula-with-facet-grid.svg | 52 tidyvpc-1.5.2/tidyvpc/tests/testthat/test-vpcstats.R | 92 tidyvpc-1.5.2/tidyvpc/tests/testthat/test_npde.R | 56 tidyvpc-1.5.2/tidyvpc/vignettes/tidyvpc_cat.pdf.asis |only tidyvpc-1.5.2/tidyvpc/vignettes/tidyvpc_cont.pdf.asis |only tidyvpc-1.5.2/tidyvpc/vignettes/tidyvpc_nlmixr2.pdf.asis |only 42 files changed, 1514 insertions(+), 1123 deletions(-)
Title: Assessing and Visualizing Fragility of Clinical Results with
Binary Outcomes
Description: A collection of user-friendly functions for assessing and visualizing fragility of individual studies (Walsh et al., 2014 <doi:10.1016/j.jclinepi.2013.10.019>; Lin, 2021 <doi:10.1111/jep.13428>), conventional pairwise meta-analyses (Atal et al., 2019 <doi:10.1016/j.jclinepi.2019.03.012>), and network meta-analyses of multiple treatments with binary outcomes (Xing et al., 2020 <doi:10.1016/j.jclinepi.2020.07.003>). The included functions are designed to: 1) calculate the fragility index (i.e., the minimal event status modifications that can alter the significance or non-significance of the original result) and fragility quotient (i.e., fragility index divided by sample size) at a specific significance level; 2) give the cases of event status modifications for altering the result's significance or non-significance and visualize these cases; 3) visualize the trend of statistical significance as event status is modified; 4) efficiently derive fragility indexes and f [...truncated...]
Author: Lifeng Lin [aut, cre] ,
Haitao Chu [aut]
Maintainer: Lifeng Lin <lifenglin@arizona.edu>
Diff between fragility versions 1.5 dated 2024-08-18 and 1.6 dated 2024-11-21
DESCRIPTION | 13 +++++++------ MD5 | 10 +++++----- NAMESPACE | 4 +++- R/frag.nma.R | 8 ++++---- R/frag.nma.alpha.R | 8 ++++---- build/partial.rdb |binary 6 files changed, 23 insertions(+), 20 deletions(-)
Title: Log-Likelihood Functions for 'rxode2'
Description: Provides the log-likelihoods with gradients from 'stan'
(Carpenter et al (2015), <doi:10.48550/arXiv.1509.07164>) needed
for generalized log-likelihood estimation in 'nlmixr2'
(Fidler et al (2019) <doi:10.1002/psp4.12445>). This is
split of to reduce computational burden of recompiling 'rxode2'
(Wang, Hallow and James (2016) <doi:10.1002/psp4.12052>) which runs
the 'nlmixr2' models during estimation.
Author: Matthew L. Fidler [aut, cre]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2ll versions 2.0.11 dated 2023-03-17 and 2.0.12 dated 2024-11-21
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 5 +++++ inst/CITATION | 3 +-- inst/tools/workaround.R | 26 ++++++++++++++++---------- 5 files changed, 30 insertions(+), 20 deletions(-)
Title: Optimal Adaptive Allocation Using Deep Reinforcement Learning
Description: An implementation to compute an optimal adaptive allocation rule
using deep reinforcement learning in a dose-response study
(Matsuura et al. (2022) <doi:10.1002/sim.9247>).
The adaptive allocation rule can directly optimize a performance metric,
such as power, accuracy of the estimated target dose, or mean absolute error
over the estimated dose-response curve.
Author: Kentaro Matsuura [aut, cre, cph]
,
Koji Makiyama [aut, ctb]
Maintainer: Kentaro Matsuura <matsuurakentaro55@gmail.com>
Diff between RLoptimal versions 1.1.0 dated 2024-11-03 and 1.1.1 dated 2024-11-21
DESCRIPTION | 8 ++++---- MD5 | 17 ++++++++++------- NAMESPACE | 1 + NEWS.md | 4 ++++ R/allocation_rule.R | 9 +-------- R/utils.R | 29 ++++++++++++++++++++++++++--- README.md | 2 +- inst/doc/RLoptimal.html | 4 ++-- inst/extdata |only tests/testthat/test-allocation_rule.R |only 10 files changed, 49 insertions(+), 25 deletions(-)
Title: Realistic Quantitative Structure Models
Description: Real Twig is a method to correct branch overestimation in quantitative structure models. Overestimated cylinders are correctly tapered using measured twig diameters of corresponding tree species. Supported quantitative structure modeling software includes 'TreeQSM', 'SimpleForest', 'Treegraph', and 'aRchi'. Also included is a novel database of twig diameters and tools for fractal analysis of point clouds.
Author: Aidan Morales [aut, cre, cph] ,
David W. MacFarlane [aut, cph]
Maintainer: Aidan Morales <moral169@msu.edu>
Diff between rTwig versions 1.2.0 dated 2024-11-08 and 1.3.0 dated 2024-11-21
DESCRIPTION | 6 MD5 | 73 +- NAMESPACE | 2 NEWS.md | 340 ++++++------ R/cluster_cloud.R | 2 R/correct_radii.R | 7 R/export_mat.R | 2 R/export_mesh.R | 4 R/plot_qsm.R | 36 - R/qsm_summary.R | 157 ++++- R/rTwig-package.R | 23 R/standardize_qsm.R | 4 R/tools.R | 31 + R/tree_metrics.R | 229 +++++++- R/update_cylinders.R | 9 README.md | 2 build/partial.rdb |binary inst/doc/Box-Dimension.R | 8 inst/doc/Box-Dimension.Rmd | 2 inst/doc/Box-Dimension.html | 14 inst/doc/Metrics.R | 850 ++++++++++++++++---------------- inst/doc/Metrics.html | 4 inst/doc/Overview.R | 118 ++-- inst/doc/Twigs.R | 8 inst/doc/Validation.R | 88 +++ inst/doc/Validation.Rmd | 106 +++- inst/doc/Validation.html | 1128 +++++++++++++++++++++++++++++-------------- inst/extdata/validation2.csv |only man/cluster_cloud.Rd | 2 man/correct_radii.Rd | 7 man/export_mat.Rd | 2 man/export_mesh.Rd | 4 man/plot_qsm.Rd | 8 man/standardize_qsm.Rd | 4 man/tree_metrics.Rd | 16 src/colors.cpp | 2 vignettes/Box-Dimension.Rmd | 2 vignettes/Validation.Rmd | 106 +++- 38 files changed, 2203 insertions(+), 1203 deletions(-)
Title: Calculates the Percentage CV for Mass Spectrometry-Based
Proteomics Data
Description: Calculates the percentage coefficient of variation (CV) for mass spectrometry-based proteomic data. The CV can be calculated with the traditional formula for raw (non log transformed) intensity data, or log transformed data.
Author: Alejandro Brenes [aut, cre]
Maintainer: Alejandro Brenes <abrenes@ed.ac.uk>
Diff between proteomicsCV versions 0.3.0 dated 2024-08-16 and 0.4.0 dated 2024-11-21
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/proteomicsCV.R | 2 +- man/proteomicsCV.Rd | 7 ++++--- 4 files changed, 12 insertions(+), 11 deletions(-)
Title: Flexible Bayesian Optimization
Description: A modern and flexible approach to Bayesian Optimization / Model
Based Optimization building on the 'bbotk' package. 'mlr3mbo' is a toolbox
providing both ready-to-use optimization algorithms as well as their fundamental
building blocks allowing for straightforward implementation of custom
algorithms. Single- and multi-objective optimization is supported as well as
mixed continuous, categorical and conditional search spaces. Moreover, using
'mlr3mbo' for hyperparameter optimization of machine learning models within the
'mlr3' ecosystem is straightforward via 'mlr3tuning'. Examples of ready-to-use
optimization algorithms include Efficient Global Optimization by Jones et al.
(1998) <doi:10.1023/A:1008306431147>, ParEGO by Knowles (2006)
<doi:10.1109/TEVC.2005.851274> and SMS-EGO by Ponweiser et al. (2008)
<doi:10.1007/978-3-540-87700-4_78>.
Author: Lennart Schneider [cre, aut] ,
Jakob Richter [aut] ,
Marc Becker [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Florian Pfisterer [aut] ,
Martin Binder [aut],
Sebastian Fischer [aut] ,
Michael H. Buselli [cph],
Wessel Dankers [cph],
Carlos Fonseca [...truncated...]
Maintainer: Lennart Schneider <lennart.sch@web.de>
Diff between mlr3mbo versions 0.2.7 dated 2024-11-15 and 0.2.8 dated 2024-11-21
DESCRIPTION | 6 +-- MD5 | 37 +++++++++++----------- NAMESPACE | 1 NEWS.md | 7 +++- R/OptimizerADBO.R | 41 +++++++++++++----------- R/OptimizerAsyncMbo.R | 43 ++++++++++++++------------ R/TunerADBO.R | 35 ++++++++++++--------- R/TunerAsyncMbo.R | 37 ++++++++++++---------- R/helper.R | 27 ++++++++++++++++ man/mlr_optimizers_adbo.Rd | 41 +++++++++++++----------- man/mlr_optimizers_async_mbo.Rd | 43 ++++++++++++++------------ man/mlr_tuners_adbo.Rd | 34 +++++++++++--------- man/mlr_tuners_async_mbo.Rd | 37 ++++++++++++---------- man/redis_available.Rd |only tests/testthat/test_AcqFunctionStochasticCB.R | 5 +++ tests/testthat/test_AcqFunctionStochasticEI.R | 3 + tests/testthat/test_OptimizerADBO.R | 1 tests/testthat/test_OptimizerAsyncMbo.R | 2 + tests/testthat/test_TunerADBO.R | 1 tests/testthat/test_TunerAsyncMbo.R | 1 20 files changed, 244 insertions(+), 158 deletions(-)
Title: Discontinuous Regression and Image Processing
Description: A collection of functions that perform jump regression
and image analysis such as denoising, deblurring and
jump detection. The implemented methods are based on
the following research: Qiu, P. (1998) <doi:10.1214/aos/1024691468>,
Qiu, P. and Yandell, B. (1997) <doi: 10.1080/10618600.1997.10474746>,
Qiu, P. (2009) <doi: 10.1007/s10463-007-0166-9>,
Kang, Y. and Qiu, P. (2014) <doi: 10.1080/00401706.2013.844732>,
Qiu, P. and Kang, Y. (2015) <doi: 10.5705/ss.2014.054>,
Kang, Y., Mukherjee, P.S. and Qiu, P. (2018) <doi: 10.1080/00401706.2017.1415975>,
Kang, Y. (2020) <doi: 10.1080/10618600.2019.1665536>.
Author: Yicheng Kang [aut, cre],
Peihua Qiu [aut, ctb]
Maintainer: Yicheng Kang <kangyicheng0527@gmail.com>
Diff between DRIP versions 2.2 dated 2024-11-18 and 2.3 dated 2024-11-21
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/JPLLK_surface.R | 5 +++++ tests/testthat/test-JPLLK_surface.R | 6 +++++- 4 files changed, 16 insertions(+), 7 deletions(-)
Title: Parametrized Active Bindings
Description: Provides a simple interface for creating active bindings where the
bound function accepts additional arguments.
Author: Kirill Mueller [aut, cre] ,
RStudio [cph, fnd]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between bindr versions 0.1.1 dated 2018-03-13 and 0.1.2 dated 2024-11-21
DESCRIPTION | 17 +++----- MD5 | 12 ++--- NEWS.md | 12 +++++ R/populate.R | 4 - README.md | 106 ++++++++++++++++++++++++++++++++++++++------------- man/bindr-package.Rd | 9 +--- man/create_env.Rd | 3 - 7 files changed, 112 insertions(+), 51 deletions(-)
Title: Annual Regional Database of the European Commission (ARDECO)
Description: A set of functions to access the 'ARDECO' (Annual Regional Database
of the European Commission) data directly from the official ARDECO public
repository through the exploitation of the 'ARDECO' APIs.
The APIs are completely transparent to the user and the provided functions
provide a direct access to the 'ARDECO' data.
The 'ARDECO' database is a collection of variables related to demography,
employment, labour market, domestic product, capital formation.
Each variable can be exposed in one or more units of measure as well as
refers to total values plus additional dimensions like economic sectors, gender,
age classes. Data can be also aggregated at country level according
to the tercet classes as defined by EUROSTAT.
The description of the 'ARDECO' database can be found at the following URL
<https://urban.jrc.ec.europa.eu/ardeco>.
Author: Carmelo Attardo [cre],
Giuseppe Bucciarelli [aut],
European Commission, JRC [cph]
Maintainer: Carmelo Attardo <carmelo.attardo@ec.europa.eu>
Diff between ARDECO versions 2.0.0 dated 2024-08-27 and 2.1.0 dated 2024-11-21
DESCRIPTION | 12 ++++---- MD5 | 21 ++++++++------ NAMESPACE | 2 - NEWS | 2 + R/get_dataset_data.R | 71 +++++++++++++++++++++++++++++++++++++++++++----- R/get_dataset_list.R | 3 -- R/get_tercet_list.R |only R/get_variable_list.R | 31 +------------------- R/get_variable_props.R |only README.md | 7 +--- man/ardeco.Rd | 7 ++++ man/get_dataset_data.Rd | 15 ++++++++-- man/get_tercet_list.Rd |only 13 files changed, 110 insertions(+), 61 deletions(-)
Title: Merge and Download International Large-Scale Assessments (ILSA)
Data
Description: Merges and downloads 'SPSS' data from different International Large-Scale Assessments (ILSA), including: Trends in International Mathematics and Science Study (TIMSS), Progress in International Reading Literacy Study (PIRLS), Programme for International Student Assessment (PISA), and others.
Author: Andres Christiansen [aut, cre]
Maintainer: Andres Christiansen <andres.christiansen@iea-hamburg.de>
Diff between ILSAmerge versions 1.0.0 dated 2024-11-08 and 1.2.5 dated 2024-11-21
DESCRIPTION | 13 + MD5 | 88 +++++++++++-- NAMESPACE | 4 NEWS.md | 29 +++- R/ILSAdownload.R | 9 - R/ILSAfile.info.R | 27 +--- R/ILSAmerge.R | 246 +++++++++++++++++++++++++++---------- R/ILSArename.R |only R/addSchools.R |only R/availableILSA.R |only R/combineStudents.R |only R/justload.R | 84 ++++++++++-- R/readILSA.R |only R/spss.syntax.R | 36 ++--- R/uID.R |only README.md | 325 +++---------------------------------------------- build |only inst |only man/ILSAdownload.Rd | 5 man/ILSAfile.info.Rd | 9 - man/ILSAmerge.Rd | 25 ++- man/ILSArename.Rd |only man/addSchools.Rd |only man/availableILSA.Rd |only man/combineStudents.Rd |only man/justload.Rd | 30 +++- man/spss.syntax.Rd | 19 +- vignettes |only 28 files changed, 466 insertions(+), 483 deletions(-)
Title: Quickly Get Datetime Data Ready for Analysis
Description: Transforms datetime data into a format ready for analysis.
It offers two core functionalities; aggregating data to a higher level interval
(thicken) and imputing records where observations were absent (pad).
Author: Edwin Thoen [aut, cre]
Maintainer: Edwin Thoen <edwinthoen@gmail.com>
Diff between padr versions 0.6.2 dated 2022-11-23 and 0.6.3 dated 2024-11-21
DESCRIPTION | 18 ++-- MD5 | 18 ++-- NEWS.md | 4 + R/create_emrgency.R | 1 README.md | 10 +- inst/doc/padr.html | 142 +++++++++++++++++++------------------- inst/doc/padr_custom.html | 72 +++++++++---------- inst/doc/padr_implementation.html | 28 +++---- man/emergency.Rd | 3 tests/testthat/test_thicken.R | 3 10 files changed, 150 insertions(+), 149 deletions(-)
Title: Orchestration of Data Pipelines
Description: Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.
Author: Will Hipson [cre, aut, cph] ,
Ryan Garnett [aut, ctb, cph]
Maintainer: Will Hipson <will.e.hipson@gmail.com>
Diff between maestro versions 0.3.0 dated 2024-09-23 and 0.4.0 dated 2024-11-21
maestro-0.3.0/maestro/tests/testthat/test_pipelines/test_pipeline_inputs.R |only maestro-0.4.0/maestro/DESCRIPTION | 10 maestro-0.4.0/maestro/MD5 | 107 +++--- maestro-0.4.0/maestro/NAMESPACE | 14 maestro-0.4.0/maestro/NEWS.md | 22 + maestro-0.4.0/maestro/R/MaestroPipeline.R | 114 ++++-- maestro-0.4.0/maestro/R/MaestroPipelineList.R | 161 +++++++++ maestro-0.4.0/maestro/R/MaestroSchedule.R | 49 ++ maestro-0.4.0/maestro/R/build_schedule.R | 3 maestro-0.4.0/maestro/R/build_schedule_entry.R | 40 ++ maestro-0.4.0/maestro/R/create_pipeline.R | 26 + maestro-0.4.0/maestro/R/maestro_tags.R | 3 maestro-0.4.0/maestro/R/roxy_maestro.R | 122 +++---- maestro-0.4.0/maestro/R/show_network.R |only maestro-0.4.0/maestro/R/suggest_orch_frequency.R | 5 maestro-0.4.0/maestro/R/utils.R | 51 ++ maestro-0.4.0/maestro/README.md | 17 maestro-0.4.0/maestro/build/vignette.rds |binary maestro-0.4.0/maestro/inst/doc/maestro-1-quick-start.R | 32 - maestro-0.4.0/maestro/inst/doc/maestro-1-quick-start.html | 2 maestro-0.4.0/maestro/inst/doc/maestro-2-motivation-concepts.R | 44 +- maestro-0.4.0/maestro/inst/doc/maestro-2-motivation-concepts.Rmd | 4 maestro-0.4.0/maestro/inst/doc/maestro-2-motivation-concepts.html | 19 - maestro-0.4.0/maestro/inst/doc/maestro-3-use-cases.R | 172 +++++----- maestro-0.4.0/maestro/inst/doc/maestro-3-use-cases.html | 2 maestro-0.4.0/maestro/inst/doc/maestro-4-advanced-scheduling.R | 102 ++--- maestro-0.4.0/maestro/inst/doc/maestro-4-advanced-scheduling.html | 14 maestro-0.4.0/maestro/inst/doc/maestro-5-directed-acyclic-graphs.R |only maestro-0.4.0/maestro/inst/doc/maestro-5-directed-acyclic-graphs.Rmd |only maestro-0.4.0/maestro/inst/doc/maestro-5-directed-acyclic-graphs.html |only maestro-0.4.0/maestro/inst/pipeline_template | 3 maestro-0.4.0/maestro/man/MaestroPipeline.Rd | 55 +++ maestro-0.4.0/maestro/man/MaestroPipelineList.Rd | 63 +++ maestro-0.4.0/maestro/man/MaestroSchedule.Rd | 37 +- maestro-0.4.0/maestro/man/create_pipeline.Rd | 11 maestro-0.4.0/maestro/man/figures/README-/unnamed-chunk-3-dark.svg | 2 maestro-0.4.0/maestro/man/figures/README-/unnamed-chunk-3.svg | 2 maestro-0.4.0/maestro/man/is_valid_dag.Rd |only maestro-0.4.0/maestro/man/maestro_tags.Rd | 3 maestro-0.4.0/maestro/man/show_network.Rd |only maestro-0.4.0/maestro/tests/testthat/_snaps/MaestroSchedule.md |only maestro-0.4.0/maestro/tests/testthat/_snaps/dags.md |only maestro-0.4.0/maestro/tests/testthat/_snaps/get_schedule.md | 21 + maestro-0.4.0/maestro/tests/testthat/test-MaestroPipeline.R | 2 maestro-0.4.0/maestro/tests/testthat/test-MaestroPipelineList.R | 5 maestro-0.4.0/maestro/tests/testthat/test-MaestroSchedule.R | 1 maestro-0.4.0/maestro/tests/testthat/test-build_schedule_entry.R | 21 + maestro-0.4.0/maestro/tests/testthat/test-dags.R |only maestro-0.4.0/maestro/tests/testthat/test-get_schedule.R | 6 maestro-0.4.0/maestro/tests/testthat/test-roclets.R | 40 ++ maestro-0.4.0/maestro/tests/testthat/test-show_network.R |only maestro-0.4.0/maestro/tests/testthat/test-suggest_orch_frequency.R | 5 maestro-0.4.0/maestro/tests/testthat/test_pipelines/test_pipeline_inputs_bad.R |only maestro-0.4.0/maestro/tests/testthat/test_pipelines/test_pipeline_inputs_good.R |only maestro-0.4.0/maestro/tests/testthat/test_pipelines/test_pipeline_maestro.R |only maestro-0.4.0/maestro/tests/testthat/test_pipelines/test_pipeline_outputs_bad.R |only maestro-0.4.0/maestro/tests/testthat/test_pipelines/test_pipeline_outputs_good.R |only maestro-0.4.0/maestro/tests/testthat/test_pipelines_dags_good/dags.R | 60 +++ maestro-0.4.0/maestro/tests/testthat/test_pipelines_dags_run_bad |only maestro-0.4.0/maestro/tests/testthat/test_pipelines_parse_all_bad/dags.R | 3 maestro-0.4.0/maestro/tests/testthat/test_pipelines_parse_all_bad/dags_self_reference_inputs.R |only maestro-0.4.0/maestro/tests/testthat/test_pipelines_parse_all_bad/dags_self_reference_outputs.R |only maestro-0.4.0/maestro/tests/testthat/test_pipelines_parse_all_good/dags.R |only maestro-0.4.0/maestro/vignettes/maestro-2-motivation-concepts.Rmd | 4 maestro-0.4.0/maestro/vignettes/maestro-5-directed-acyclic-graphs.Rmd |only 65 files changed, 1064 insertions(+), 415 deletions(-)
Title: Bayesian Latent Gaussian Modelling using INLA and Extensions
Description: Facilitates spatial and general latent Gaussian modeling using
integrated nested Laplace approximation via the INLA package (<https://www.r-inla.org>).
Additionally, extends the GAM-like model class to more general nonlinear predictor
expressions, and implements a log Gaussian Cox process likelihood for
modeling univariate and spatial point processes based on ecological survey data.
Model components are specified with general inputs and mapping methods to the
latent variables, and the predictors are specified via general R expressions,
with separate expressions for each observation likelihood model in
multi-likelihood models. A prediction method based on fast Monte Carlo sampling
allows posterior prediction of general expressions of the latent variables.
Ecology-focused introduction in Bachl, Lindgren, Borchers, and Illian (2019)
<doi:10.1111/2041-210X.13168>.
Author: Finn Lindgren [aut, cre, cph] ,
Fabian E. Bachl [aut, cph] ,
David L. Borchers [ctb, dtc, cph] ,
Daniel Simpson [ctb, cph] ,
Lindesay Scott-Howard [ctb, dtc, cph] ,
Seaton Andy [ctb] ,
Suen Man Ho [ctb, cph] ,
Roudier Pierre [ctb, cph] ,
Meehan Tim [ [...truncated...]
Maintainer: Finn Lindgren <finn.lindgren@gmail.com>
Diff between inlabru versions 2.11.1 dated 2024-07-01 and 2.12.0 dated 2024-11-21
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inlabru-2.12.0/inlabru/man/bru_mapper_const.Rd | 2 inlabru-2.12.0/inlabru/man/bru_mapper_factor.Rd | 2 inlabru-2.12.0/inlabru/man/bru_mapper_fm_mesh_1d.Rd | 36 inlabru-2.12.0/inlabru/man/bru_mapper_fm_mesh_2d.Rd | 17 inlabru-2.12.0/inlabru/man/bru_mapper_fmesher.Rd |only inlabru-2.12.0/inlabru/man/bru_mapper_generics.Rd | 22 inlabru-2.12.0/inlabru/man/bru_mapper_harmonics.Rd | 12 inlabru-2.12.0/inlabru/man/bru_mapper_index.Rd | 2 inlabru-2.12.0/inlabru/man/bru_mapper_linear.Rd | 2 inlabru-2.12.0/inlabru/man/bru_mapper_logsumexp.Rd | 49 inlabru-2.12.0/inlabru/man/bru_mapper_marginal.Rd | 23 inlabru-2.12.0/inlabru/man/bru_mapper_matrix.Rd | 7 inlabru-2.12.0/inlabru/man/bru_mapper_mesh_B.Rd | 2 inlabru-2.12.0/inlabru/man/bru_mapper_multi.Rd | 19 inlabru-2.12.0/inlabru/man/bru_mapper_pipe.Rd | 14 inlabru-2.12.0/inlabru/man/bru_mapper_repeat.Rd |only inlabru-2.12.0/inlabru/man/bru_mapper_scale.Rd | 10 inlabru-2.12.0/inlabru/man/bru_mapper_shift.Rd | 10 inlabru-2.12.0/inlabru/man/bru_mapper_summary.Rd | 19 inlabru-2.12.0/inlabru/man/bru_mapper_taylor.Rd | 13 inlabru-2.12.0/inlabru/man/bru_model.Rd | 33 inlabru-2.12.0/inlabru/man/bru_obs.Rd |only inlabru-2.12.0/inlabru/man/bru_options.Rd | 33 inlabru-2.12.0/inlabru/man/bru_response_size.Rd |only inlabru-2.12.0/inlabru/man/bru_safe_inla.Rd | 6 inlabru-2.12.0/inlabru/man/bru_safe_sp.Rd | 11 inlabru-2.12.0/inlabru/man/bru_standardise_names.Rd | 1 inlabru-2.12.0/inlabru/man/bru_summarise.Rd | 15 inlabru-2.12.0/inlabru/man/bru_transformation.Rd | 16 inlabru-2.12.0/inlabru/man/bru_used.Rd | 12 inlabru-2.12.0/inlabru/man/bru_used_update.Rd | 2 inlabru-2.12.0/inlabru/man/bru_used_vars.Rd | 2 inlabru-2.12.0/inlabru/man/comp_lin_eval.Rd | 7 inlabru-2.12.0/inlabru/man/deltaIC.Rd | 9 inlabru-2.12.0/inlabru/man/devel.cvmeasure.Rd | 22 inlabru-2.12.0/inlabru/man/evaluate_comp_lin.Rd | 12 inlabru-2.12.0/inlabru/man/evaluate_comp_simple.Rd | 27 inlabru-2.12.0/inlabru/man/evaluate_effect.Rd | 10 inlabru-2.12.0/inlabru/man/evaluate_index.Rd | 1 inlabru-2.12.0/inlabru/man/evaluate_inputs.Rd | 1 inlabru-2.12.0/inlabru/man/evaluate_model.Rd | 4 inlabru-2.12.0/inlabru/man/evaluate_predictor.Rd | 10 inlabru-2.12.0/inlabru/man/expand_labels.Rd | 1 inlabru-2.12.0/inlabru/man/figures/README-example-1.png |binary inlabru-2.12.0/inlabru/man/figures/README-plot-1.png |only inlabru-2.12.0/inlabru/man/generate.Rd | 4 inlabru-2.12.0/inlabru/man/gg.RasterLayer.Rd | 8 inlabru-2.12.0/inlabru/man/gg.Rd | 28 inlabru-2.12.0/inlabru/man/gg.SpatRaster.Rd | 16 inlabru-2.12.0/inlabru/man/gg.SpatialGridDataFrame.Rd | 23 inlabru-2.12.0/inlabru/man/gg.SpatialLines.Rd | 36 inlabru-2.12.0/inlabru/man/gg.SpatialPixels.Rd | 12 inlabru-2.12.0/inlabru/man/gg.SpatialPixelsDataFrame.Rd | 41 inlabru-2.12.0/inlabru/man/gg.SpatialPoints.Rd | 37 inlabru-2.12.0/inlabru/man/gg.SpatialPolygons.Rd | 40 inlabru-2.12.0/inlabru/man/gg.bru_prediction.Rd | 39 inlabru-2.12.0/inlabru/man/gg.data.frame.Rd | 9 inlabru-2.12.0/inlabru/man/gg.fm_mesh_1d.Rd | 11 inlabru-2.12.0/inlabru/man/gg.fm_mesh_2d.Rd | 37 inlabru-2.12.0/inlabru/man/gg.matrix.Rd | 6 inlabru-2.12.0/inlabru/man/gg.sf.Rd | 58 inlabru-2.12.0/inlabru/man/globe.Rd | 2 inlabru-2.12.0/inlabru/man/glplot.Rd | 26 inlabru-2.12.0/inlabru/man/gorillas.Rd | 86 inlabru-2.12.0/inlabru/man/gorillas_sf.Rd | 71 inlabru-2.12.0/inlabru/man/iinla.Rd | 2 inlabru-2.12.0/inlabru/man/inlabru-deprecated.Rd | 205 - inlabru-2.12.0/inlabru/man/inlabru-package.Rd | 17 inlabru-2.12.0/inlabru/man/input_eval.Rd | 84 inlabru-2.12.0/inlabru/man/lgcp.Rd | 61 inlabru-2.12.0/inlabru/man/local_testthat.Rd | 17 inlabru-2.12.0/inlabru/man/materncov.bands.Rd | 15 inlabru-2.12.0/inlabru/man/mexdolphin.Rd | 77 inlabru-2.12.0/inlabru/man/mexdolphin_sf.Rd | 76 inlabru-2.12.0/inlabru/man/mrsea.Rd | 21 inlabru-2.12.0/inlabru/man/multiplot.Rd | 26 inlabru-2.12.0/inlabru/man/plot.bru_prediction.Rd | 6 inlabru-2.12.0/inlabru/man/plotsample.Rd | 40 inlabru-2.12.0/inlabru/man/point2count.Rd | 18 inlabru-2.12.0/inlabru/man/predict.bru.Rd | 14 inlabru-2.12.0/inlabru/man/reexports.Rd | 62 inlabru-2.12.0/inlabru/man/robins_subset.Rd | 9 inlabru-2.12.0/inlabru/man/sample.lgcp.Rd | 84 inlabru-2.12.0/inlabru/man/shrimp.Rd | 22 inlabru-2.12.0/inlabru/man/sline.Rd | 48 inlabru-2.12.0/inlabru/man/spatial.to.ppp.Rd | 20 inlabru-2.12.0/inlabru/man/spde.posterior.Rd | 17 inlabru-2.12.0/inlabru/man/spoly.Rd | 42 inlabru-2.12.0/inlabru/man/summary.bru.Rd | 30 inlabru-2.12.0/inlabru/man/summary.component.Rd | 39 inlabru-2.12.0/inlabru/man/toygroups.Rd | 9 inlabru-2.12.0/inlabru/man/toypoints.Rd | 3 inlabru-2.12.0/inlabru/tests/testthat/_snaps/01_lgcp_2d.md | 4 inlabru-2.12.0/inlabru/tests/testthat/_snaps/lgcp_2d_plotsample.md | 2 inlabru-2.12.0/inlabru/tests/testthat/test-01_lgcp_2d.R | 10 inlabru-2.12.0/inlabru/tests/testthat/test-aggregate.R | 22 inlabru-2.12.0/inlabru/tests/testthat/test-bru_sf.R | 52 inlabru-2.12.0/inlabru/tests/testthat/test-component.R | 98 inlabru-2.12.0/inlabru/tests/testthat/test-copy.R | 38 inlabru-2.12.0/inlabru/tests/testthat/test-data.R | 62 inlabru-2.12.0/inlabru/tests/testthat/test-eval_spatial.R | 39 inlabru-2.12.0/inlabru/tests/testthat/test-fmesher_pixels.R | 3 inlabru-2.12.0/inlabru/tests/testthat/test-globe_mesh.R | 21 inlabru-2.12.0/inlabru/tests/testthat/test-latent_fixed_effects.R | 10 inlabru-2.12.0/inlabru/tests/testthat/test-latent_rw2.R | 5 inlabru-2.12.0/inlabru/tests/testthat/test-latent_spde_2d.R | 13 inlabru-2.12.0/inlabru/tests/testthat/test-lgcp_1d.R | 32 inlabru-2.12.0/inlabru/tests/testthat/test-lgcp_1d_nonlinear.R | 34 inlabru-2.12.0/inlabru/tests/testthat/test-lgcp_2d_covars.R | 5 inlabru-2.12.0/inlabru/tests/testthat/test-lgcp_2d_plotsample.R | 7 inlabru-2.12.0/inlabru/tests/testthat/test-linearisation.R | 17 inlabru-2.12.0/inlabru/tests/testthat/test-mapper.R | 125 inlabru-2.12.0/inlabru/tests/testthat/test-mdata.R | 38 inlabru-2.12.0/inlabru/tests/testthat/test-multi_like.R | 53 inlabru-2.12.0/inlabru/tests/testthat/test-offset.R | 22 inlabru-2.12.0/inlabru/tests/testthat/test-response_size.R |only inlabru-2.12.0/inlabru/tests/testthat/test-utils.R | 8 inlabru-2.12.0/inlabru/vignettes/bru_mapper.Rmd | 33 inlabru-2.12.0/inlabru/vignettes/component.Rmd | 4 inlabru-2.12.0/inlabru/vignettes/linearapprox.Rmd | 28 241 files changed, 5950 insertions(+), 4366 deletions(-)
Title: DBI Package for the DuckDB Database Management System
Description: The DuckDB project is an embedded analytical data management
system with support for the Structured Query Language (SQL). This
package includes all of DuckDB and an R Database Interface (DBI)
connector.
Author: Hannes Muehleisen [aut] ,
Mark Raasveldt [aut] ,
Kirill Mueller [cre] ,
Stichting DuckDB Foundation [cph],
Apache Software Foundation [cph],
PostgreSQL Global Development Group [cph],
The Regents of the University of California [cph],
Cameron Desrocher [...truncated...]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between duckdb versions 1.1.2 dated 2024-10-30 and 1.1.3 dated 2024-11-21
duckdb-1.1.2/duckdb/src/Makevars.duckdb |only duckdb-1.1.2/duckdb/src/duckdb |only duckdb-1.1.3/duckdb/DESCRIPTION | 6 duckdb-1.1.3/duckdb/MD5 | 3071 ---------------- duckdb-1.1.3/duckdb/NEWS.md | 23 duckdb-1.1.3/duckdb/R/cpp11.R | 20 duckdb-1.1.3/duckdb/R/relational.R | 46 duckdb-1.1.3/duckdb/R/rethrow-gen.R | 26 duckdb-1.1.3/duckdb/cleanup |only duckdb-1.1.3/duckdb/cleanup.win |only duckdb-1.1.3/duckdb/src/cpp11.cpp | 38 duckdb-1.1.3/duckdb/src/duckdb.tar.xz |only duckdb-1.1.3/duckdb/src/include/rapi.hpp | 3 duckdb-1.1.3/duckdb/src/relational.cpp | 25 duckdb-1.1.3/duckdb/src/reltoaltrep.cpp | 51 duckdb-1.1.3/duckdb/src/utils.cpp | 6 duckdb-1.1.3/duckdb/tests/testthat/_snaps/relational.md |only duckdb-1.1.3/duckdb/tests/testthat/test-DBItest.R | 19 duckdb-1.1.3/duckdb/tests/testthat/test-list.R | 1 duckdb-1.1.3/duckdb/tests/testthat/test-register.R | 2 duckdb-1.1.3/duckdb/tests/testthat/test-rel_api.R | 8 duckdb-1.1.3/duckdb/tests/testthat/test-relational.R | 119 22 files changed, 294 insertions(+), 3170 deletions(-)
Title: Diversity Dynamics using Fossil Sampling Data
Description: Functions to describe sampling and diversity dynamics of fossil occurrence datasets (e.g. from the Paleobiology Database). The package includes methods to calculate range- and occurrence-based metrics of taxonomic richness, extinction and origination rates, along with traditional sampling measures. A powerful subsampling tool is also included that implements frequently used sampling standardization methods in a multiple bin-framework. The plotting of time series and the occurrence data can be simplified by the functions incorporated in the package, as well as other calculations, such as environmental affinities and extinction selectivity testing. Details can be found in: Kocsis, A.T.; Reddin, C.J.; Alroy, J. and Kiessling, W. (2019) <doi:10.1101/423780>.
Author: Adam T. Kocsis [cre, aut] ,
John Alroy [aut] ,
Carl J. Reddin [aut] ,
Wolfgang Kiessling [aut] ,
Deutsche Forschungsgemeinschaft [fnd],
FAU GeoZentrum Nordbayern [fnd]
Maintainer: Adam T. Kocsis <adam.t.kocsis@gmail.com>
Diff between divDyn versions 0.8.2 dated 2022-09-05 and 0.8.3 dated 2024-11-21
divDyn-0.8.2/divDyn/inst/NEWS |only divDyn-0.8.2/divDyn/inst/doc/handout.R |only divDyn-0.8.2/divDyn/inst/doc/handout.Rmd |only divDyn-0.8.2/divDyn/inst/doc/handout.pdf |only divDyn-0.8.2/divDyn/vignettes/handout.Rmd |only divDyn-0.8.3/divDyn/DESCRIPTION | 26 + divDyn-0.8.3/divDyn/MD5 | 79 +++-- divDyn-0.8.3/divDyn/NEWS.md |only divDyn-0.8.3/divDyn/R/RcppExports.R | 4 divDyn-0.8.3/divDyn/R/affinity.R | 95 +++++-- divDyn-0.8.3/divDyn/R/data.R | 15 - divDyn-0.8.3/divDyn/R/diversityDynamics.r | 10 divDyn-0.8.3/divDyn/R/fadLad.R | 2 divDyn-0.8.3/divDyn/R/georange.R | 2 divDyn-0.8.3/divDyn/R/slice.R | 2 divDyn-0.8.3/divDyn/R/subsample.R | 19 + divDyn-0.8.3/divDyn/R/subtrials.R | 20 + divDyn-0.8.3/divDyn/R/tabinate.R | 2 divDyn-0.8.3/divDyn/R/zzz.R | 2 divDyn-0.8.3/divDyn/README.md | 343 -------------------------- divDyn-0.8.3/divDyn/build/vignette.rds |binary divDyn-0.8.3/divDyn/data/corals.RData |binary divDyn-0.8.3/divDyn/data/keys.RData |binary divDyn-0.8.3/divDyn/data/stages.RData |binary divDyn-0.8.3/divDyn/data/stages2018.RData |binary divDyn-0.8.3/divDyn/data/stratkeys.RData |binary divDyn-0.8.3/divDyn/data/tens.RData |binary divDyn-0.8.3/divDyn/inst/CITATION | 7 divDyn-0.8.3/divDyn/inst/doc/handout_pdf.R |only divDyn-0.8.3/divDyn/inst/doc/handout_pdf.Rmd |only divDyn-0.8.3/divDyn/inst/doc/handout_pdf.pdf |only divDyn-0.8.3/divDyn/man/affinity.Rd | 12 divDyn-0.8.3/divDyn/man/corals.Rd | 2 divDyn-0.8.3/divDyn/man/divDyn.Rd | 8 divDyn-0.8.3/divDyn/man/fadlad.Rd | 2 divDyn-0.8.3/divDyn/man/figures |only divDyn-0.8.3/divDyn/man/keys.Rd | 4 divDyn-0.8.3/divDyn/man/slice.Rd | 2 divDyn-0.8.3/divDyn/man/stratkeys.Rd | 4 divDyn-0.8.3/divDyn/man/subsample.Rd | 2 divDyn-0.8.3/divDyn/man/tabinate.Rd | 2 divDyn-0.8.3/divDyn/man/tens.Rd | 5 divDyn-0.8.3/divDyn/src/Engine.cpp | 9 divDyn-0.8.3/divDyn/src/RcppExports.cpp | 7 divDyn-0.8.3/divDyn/src/init.c | 4 divDyn-0.8.3/divDyn/vignettes/handout_pdf.Rmd |only 46 files changed, 233 insertions(+), 458 deletions(-)
More information about roxy.shinylive at CRAN
Permanent link
Title: Estimate Brain Networks and Connectivity with ICA and Empirical
Priors
Description: Implements the template ICA (independent components analysis) model
proposed in Mejia et al. (2020) <doi:10.1080/01621459.2019.1679638> and the
spatial template ICA model proposed in proposed in Mejia et al. (2022)
<doi:10.1080/10618600.2022.2104289>. Both models estimate subject-level
brain as deviations from known population-level networks, which are
estimated using standard ICA algorithms. Both models employ an
expectation-maximization algorithm for estimation of the latent brain
networks and unknown model parameters. Includes direct support for 'CIFTI',
'GIFTI', and 'NIFTI' neuroimaging file formats.
Author: Amanda Mejia [aut, cre],
Damon Pham [aut] ,
Daniel Spencer [ctb] ,
Mary Beth Nebel [ctb]
Maintainer: Amanda Mejia <mandy.mejia@gmail.com>
Diff between templateICAr versions 0.8.8 dated 2024-10-14 and 0.9.1 dated 2024-11-21
templateICAr-0.8.8/templateICAr/R/EM_FCtemplateICA.R |only templateICAr-0.8.8/templateICAr/R/RcppExports.R |only templateICAr-0.8.8/templateICAr/R/templateICAr-package.R |only templateICAr-0.8.8/templateICAr/build |only templateICAr-0.8.8/templateICAr/man/EM_FCtemplateICA.Rd |only templateICAr-0.8.8/templateICAr/man/Gibbs_AS_posteriorCPP.Rd |only templateICAr-0.8.8/templateICAr/man/UpdateTheta_FCtemplateICA.Rd |only templateICAr-0.8.8/templateICAr/man/UpdateTheta_FCtemplateICAcpp.Rd |only templateICAr-0.8.8/templateICAr/man/compute_LL_FC.Rd |only templateICAr-0.8.8/templateICAr/man/templateICAr-package.Rd |only templateICAr-0.8.8/templateICAr/src |only templateICAr-0.9.1/templateICAr/DESCRIPTION | 18 +++--- templateICAr-0.9.1/templateICAr/MD5 | 26 ++-------- templateICAr-0.9.1/templateICAr/NAMESPACE | 8 --- templateICAr-0.9.1/templateICAr/NEWS.md | 5 + templateICAr-0.9.1/templateICAr/R/VB_FCtemplateICA.R | 3 - templateICAr-0.9.1/templateICAr/R/activations.R | 12 +++- templateICAr-0.9.1/templateICAr/R/dual_reg2.R | 2 templateICAr-0.9.1/templateICAr/R/make_mesh.R | 9 +-- 19 files changed, 38 insertions(+), 45 deletions(-)
Title: A 'shiny' App to Compare Two Data Frames
Description: A tool developed with the 'Golem' framework which provides
an easier way to check cells differences between two data
frames. The user provides two data frames for comparison,
selects IDs variables identifying each row of input data,
then clicks a button to perform the comparison. Several
'R' package functions are used to describe the data
and perform the comparison in the server of the
application. The main ones are comparedf() from 'arsenal'
and skim() from 'skimr'. For more details see the
description of comparedf() from the 'arsenal' package and
that of skim() from the 'skimr' package.
Author: Sergio Ewane Ebouele [aut, cre]
Maintainer: Sergio Ewane Ebouele <info@dataforknow.com>
Diff between dataCompare versions 1.0.3 dated 2024-11-14 and 1.0.4 dated 2024-11-21
DESCRIPTION | 14 +++--- MD5 | 35 ++++++++------- NAMESPACE | 9 ++-- NEWS.md | 11 ++++ R/apex_libraries.R | 6 -- R/app_server.R | 2 R/dataCompare-package.R | 8 +-- R/mod_comp_desc.R | 24 ++++++++-- R/mod_comp_details.R | 8 ++- R/mod_comp_report.R | 6 ++ R/mod_comp_report_fct_display.R | 47 +++++++++++++++++++++ R/mod_intro.R | 3 - R/mod_load_data.R | 43 +++++++++++++------ README.md | 9 +++- inst/doc/dataCompare.R | 10 ++++ inst/doc/dataCompare.Rmd | 13 +++++ inst/doc/dataCompare.html | 71 ++++++++++++++++++-------------- man/compare_data_frame_object_report.Rd |only vignettes/dataCompare.Rmd | 13 +++++ 19 files changed, 242 insertions(+), 90 deletions(-)
Title: Graphics in the Context of Analyzing High-Throughput Data
Description: Additional options for making graphics in the context of analyzing high-throughput data are available here.
This includes automatic segmenting of the current device (eg window) to accommodate multiple new plots,
automatic checking for optimal location of legends in plots, small histograms to insert as legends,
histograms re-transforming axis labels to linear when plotting log2-transformed data,
a violin-plot <doi:10.1080/00031305.1998.10480559> function for a wide variety of input-formats,
principal components analysis (PCA) <doi:10.1080/14786440109462720> with bag-plots <doi:10.1080/00031305.1999.10474494> to highlight and compare the center areas for groups of samples,
generic MA-plots (differential- versus average-value plots) <doi:10.1093/nar/30.4.e15>,
staggered count plots and generation of mouse-over interactive html pages.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrGraph versions 1.3.7 dated 2024-01-22 and 1.3.8 dated 2024-11-21
DESCRIPTION | 11 MD5 | 24 R/VolcanoPlotW.R | 38 - R/imageW.R | 166 ++++-- R/plotPCAw.R | 8 R/vioplotW.R | 72 +- build/vignette.rds |binary inst/doc/wrGraphVignette1.R | 45 + inst/doc/wrGraphVignette1.Rmd | 109 ++-- inst/doc/wrGraphVignette1.html | 999 ++++++++++++++--------------------------- man/imageW.Rd | 38 - man/vioplotW.Rd | 5 vignettes/wrGraphVignette1.Rmd | 109 ++-- 13 files changed, 744 insertions(+), 880 deletions(-)
Title: R Interface to 'Redatam' Library
Description: Provides an API to work with 'Redatam' (see <https://redatam.org>)
databases in both formats: 'RXDB' (new format) and 'DICX' (old format) and running
'Redatam' programs written in 'SPC' language. It's a wrapper around 'Redatam'
core and provides functions to open/close a database (redatam_open()/redatam_close()),
list entities and variables from the database (redatam_entities(), redatam_variables())
and execute a 'SPC' program and gets the results as data frames
(redatam_query(), redatam_run()).
Author: Jaime Salvador [aut, cre] ,
CELADE [cph]
Maintainer: Jaime Salvador <jaime.salvador@ideasybits.com>
Diff between redatamx versions 1.0.0 dated 2024-10-29 and 1.0.1 dated 2024-11-21
redatamx-1.0.0/redatamx/src/dependencies.txt |only redatamx-1.0.1/redatamx/DESCRIPTION | 11 redatamx-1.0.1/redatamx/MD5 | 43 +-- redatamx-1.0.1/redatamx/NAMESPACE | 4 redatamx-1.0.1/redatamx/NEWS.md | 13 - redatamx-1.0.1/redatamx/R/output-env.R | 8 redatamx-1.0.1/redatamx/R/redatam-api.R | 33 +- redatamx-1.0.1/redatamx/R/redatam-query.R | 205 +++++++++--------- redatamx-1.0.1/redatamx/R/redatam-run.R | 1 redatamx-1.0.1/redatamx/README.md | 52 ++++ redatamx-1.0.1/redatamx/man/outputs.Rd | 6 redatamx-1.0.1/redatamx/man/redatam_close.Rd | 5 redatamx-1.0.1/redatamx/man/redatam_destroy_.Rd | 1 redatamx-1.0.1/redatamx/man/redatam_entities.Rd | 2 redatamx-1.0.1/redatamx/man/redatam_init_.Rd | 3 redatamx-1.0.1/redatamx/man/redatam_internal_query.Rd | 3 redatamx-1.0.1/redatamx/man/redatam_internal_run.Rd | 7 redatamx-1.0.1/redatamx/man/redatam_open.Rd | 2 redatamx-1.0.1/redatamx/man/redatam_query.Rd | 1 redatamx-1.0.1/redatamx/man/redatam_run.Rd | 1 redatamx-1.0.1/redatamx/man/redatam_save.Rd | 4 redatamx-1.0.1/redatamx/man/redatam_variables.Rd | 2 redatamx-1.0.1/redatamx/man/redatamx-package.Rd | 9 23 files changed, 237 insertions(+), 179 deletions(-)
Title: R Bayesian Evidence Synthesis Tools
Description: Tool-set to support Bayesian evidence synthesis. This
includes meta-analysis, (robust) prior derivation from historical
data, operating characteristics and analysis (1 and 2 sample
cases). Please refer to Weber et al. (2021) <doi:10.18637/jss.v100.i19>
for details on applying this package while Neuenschwander et al. (2010)
<doi:10.1177/1740774509356002> and Schmidli et al. (2014)
<doi:10.1111/biom.12242> explain details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Beat Neuenschwander [ctb],
Heinz Schmidli [ctb],
Baldur Magnusson [ctb],
Yue Li [ctb],
Satrajit Roychoudhury [ctb],
Trustees of Columbia University [cph]
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between RBesT versions 1.7-3 dated 2024-01-08 and 1.7-4 dated 2024-11-21
DESCRIPTION | 17 MD5 | 125 - NAMESPACE | 1 NEWS.md | 23 R/RBesT-package.R | 1 R/dlink.R | 1 R/integrate_logit_log.R | 32 R/mix.R | 40 R/mixcombine.R | 10 R/mixess.R | 62 R/mixplot.R | 4 R/mixstanvar.R | 35 R/plot_gMAP.R | 2 R/predict_gMAP.R | 36 R/sysdata.rda |binary R/zzz.R | 1 build/vignette.rds |binary configure | 1 data/AS.rda |binary data/colitis.rda |binary data/crohn.rda |binary data/transplant.rda |binary demo/robustMAP.R | 24 inst/doc/RBesT.pdf |binary inst/doc/introduction.R | 20 inst/doc/introduction.Rmd | 16 inst/doc/introduction.html | 394 ++--- inst/examples |only inst/sbc/calibration.md5 | 6 inst/sbc/make_reference_rankhist.R | 17 inst/sbc/sbc_report.html | 976 ++++++------- inst/sbc/sbc_tools.R | 75 - inst/stan/gMAP.stan | 32 man/RBesT-package.Rd | 1 man/ess.Rd | 8 man/integrate_density_log.Rd | 2 man/mixbeta.Rd | 4 man/mixcombine.Rd | 5 man/mixgamma.Rd | 4 man/mixmvnorm.Rd | 4 man/mixnorm.Rd | 4 man/mixplot.Rd | 6 man/oc1S.Rd | 2 man/oc2S.Rd | 2 man/plot.gMAP.Rd | 2 man/pos1S.Rd | 2 man/pos2S.Rd | 2 man/predict.gMAP.Rd | 1 src/stanExports_gMAP.h | 2770 ++++++++++++++++++------------------- tests/testthat/helper-utils.R |only tests/testthat/test-EM.R | 36 tests/testthat/test-gMAP.R | 47 tests/testthat/test-mixdiff.R | 29 tests/testthat/test-mixdist.R | 65 tests/testthat/test-mixstanvar.R | 73 tests/testthat/test-oc1S.R | 39 tests/testthat/test-oc2S.R | 52 tests/testthat/test-pos1S.R | 11 tests/testthat/test-pos2S.R | 38 tests/testthat/test-postmix.R | 1 tests/testthat/test-preddist.R | 13 tests/testthat/test-utils.R | 74 vignettes/introduction.Rmd | 16 63 files changed, 2665 insertions(+), 2599 deletions(-)
Title: Grab Longitudinal Employer-Household Dynamics (LEHD) Flat Files
Description: Designed to query Longitudinal Employer-Household Dynamics (LEHD)
workplace/residential association and origin-destination flat files and
optionally aggregate Census block-level data to block group, tract, county,
or state. Data comes from the LODES FTP server <https://lehd.ces.census.gov/data/lodes/LODES8/>.
Author: Jamaal Green [cre, aut],
Liming Wang [aut],
Dillon Mahmoudi [aut],
Matthew Rogers [ctb],
Kyle Walker [ctb]
Maintainer: Jamaal Green <jamaal.green@gmail.com>
Diff between lehdr versions 1.1.3 dated 2023-11-27 and 1.1.4 dated 2024-11-21
DESCRIPTION | 8 LICENSE | 2 MD5 | 30 - NAMESPACE | 32 - R/grab_crosswalk.R | 212 ++++---- R/lehdr.R | 568 +++++++++++----------- README.md | 274 +++++----- build/vignette.rds |binary inst/doc/getting_started.R | 224 ++++---- inst/doc/getting_started.Rmd | 342 ++++++------- inst/doc/getting_started.html | 1066 +++++++++++++++++++++--------------------- man/grab_crosswalk.Rd | 66 +- man/grab_lodes.Rd | 196 +++---- tests/testthat.R | 10 tests/testthat/test-lehdr.R | 268 +++++----- vignettes/getting_started.Rmd | 342 ++++++------- 16 files changed, 1820 insertions(+), 1820 deletions(-)
Title: Stratigraphic Paleobiology Modeling Pipelines
Description: The fossil record is a joint expression of ecological, taphonomic,
evolutionary, and stratigraphic processes (Holland and Patzkowsky, 2012, ISBN:978-0226649382).
This package allowing to simulate biological processes in the time domain
(e.g., trait evolution, fossil abundance), and examine how their expression
in the rock record (stratigraphic domain) is influenced based on
age-depth models, ecological niche models, and taphonomic effects.
Functions simulating common processes used in modeling trait evolution or
event type data such as first/last occurrences are provided and can be used
standalone or as part of a pipeline. The package comes with example
data sets and tutorials in several vignettes, which can be used as a
template to set up one's own simulation.
Author: Niklas Hohmann [aut, cre]
Maintainer: Niklas Hohmann <N.H.Hohmann@uu.nl>
Diff between StratPal versions 0.2.0 dated 2024-10-04 and 0.3.0 dated 2024-11-21
DESCRIPTION | 6 MD5 | 48 +- NAMESPACE | 1 NEWS.md | 64 +- R/StratPal-package.R | 12 R/apply_niche.R | 174 ++++---- R/apply_taphonomy.R | 112 ++--- R/ornstein_uhlenbeck_sl.R | 2 R/plot.pre_paleoTS.R |only R/random_walk_sl.R | 104 ++-- README.md | 206 ++++----- inst/CITATION | 16 inst/WORDLIST | 5 inst/doc/event_data.Rmd | 672 +++++++++++++++---------------- inst/doc/paleoTS_functionality.R | 4 inst/doc/paleoTS_functionality.Rmd | 6 inst/doc/paleoTS_functionality.html | 16 inst/doc/phenotypic_evolution.html | 8 man/ornstein_uhlenbeck_sl.Rd | 2 man/plot.pre_paleoTS.Rd |only man/random_walk_sl.Rd | 2 tests/testthat/test_ornstein_uhlenbeck.R | 34 - tests/testthat/test_p3.R | 42 - tests/testthat/test_p3_var_rate.R | 42 - vignettes/event_data.Rmd | 672 +++++++++++++++---------------- vignettes/paleoTS_functionality.Rmd | 6 26 files changed, 1134 insertions(+), 1122 deletions(-)
Title: Ceteris Paribus Profiles
Description: Ceteris Paribus Profiles (What-If Plots) are designed to present model
responses around selected points in a feature space.
For example around a single prediction for an interesting observation.
Plots are designed to work in a model-agnostic fashion, they are working
for any predictive Machine Learning model and allow for model comparisons.
Ceteris Paribus Plots supplement the Break Down Plots from 'breakDown' package.
Author: Przemyslaw Biecek [aut, cre]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between ceterisParibus versions 0.4.2 dated 2020-03-27 and 0.6 dated 2024-11-21
ceterisParibus-0.4.2/ceterisParibus/R/plot_interactive_what_if.R |only ceterisParibus-0.4.2/ceterisParibus/README.md |only ceterisParibus-0.4.2/ceterisParibus/man/plot_interactive.Rd |only ceterisParibus-0.4.2/ceterisParibus/tests/testthat/test_plot_interactive_what_if.R |only ceterisParibus-0.6/ceterisParibus/DESCRIPTION | 11 +-- ceterisParibus-0.6/ceterisParibus/MD5 | 36 ++++------ ceterisParibus-0.6/ceterisParibus/NAMESPACE | 4 - ceterisParibus-0.6/ceterisParibus/NEWS.md | 23 +++--- ceterisParibus-0.6/ceterisParibus/R/calculate_profiles.R | 12 ++- ceterisParibus-0.6/ceterisParibus/R/calculate_profiles_lce.R | 1 ceterisParibus-0.6/ceterisParibus/R/ceteris_paribus.R | 5 - ceterisParibus-0.6/ceterisParibus/R/coral_plots.R | 4 - ceterisParibus-0.6/ceterisParibus/R/plot_ceteris_paribus.R | 2 ceterisParibus-0.6/ceterisParibus/R/plot_coral_plots.R | 2 ceterisParibus-0.6/ceterisParibus/R/select_neighbours.R | 4 - ceterisParibus-0.6/ceterisParibus/R/select_samples.R | 2 ceterisParibus-0.6/ceterisParibus/man/calculate_variable_splits.Rd | 9 ++ ceterisParibus-0.6/ceterisParibus/man/ceteris_paribus.Rd | 3 ceterisParibus-0.6/ceterisParibus/man/local_fit.Rd | 4 - ceterisParibus-0.6/ceterisParibus/man/select_neighbours.Rd | 4 - ceterisParibus-0.6/ceterisParibus/man/select_sample.Rd | 2 21 files changed, 72 insertions(+), 56 deletions(-)
More information about ceterisParibus at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-19 0.2.0
2023-03-31 0.1.0
Title: Read and Write '.gltf' and '.glb' Files
Description: The 'glTF' file format is used to describe 3D models. This package
provides read and write functions to work with it.
Author: Duncan Murdoch [aut, cre],
Morten S. Mikkelsen [cph]
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between rgl2gltf versions 1.0.5 dated 2024-09-24 and 1.0.7 dated 2024-11-21
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/gltfWidget.R | 19 +++++++++---------- inst/doc/shininess.html | 12 ++++++------ 5 files changed, 26 insertions(+), 23 deletions(-)
Title: Power and Sample Size Tools
Description: Power and sample size calculations for a variety of study designs and
outcomes. Methods include t tests, ANOVA (including tests for interactions,
simple effects and contrasts), proportions, categorical data (chi-square tests
and proportional odds), linear, logistic and Poisson regression, alternative
and coprimary endpoints, power for confidence intervals, correlation
coefficient tests, cluster randomized trials, individually randomized group
treatment trials, multisite trials, treatment-by-covariate interaction effects
and nonparametric tests of location. Utilities are provided for
computing various effect sizes. Companion package to the book
"Power and Sample Size in R", Crespi (2025, ISBN:9781138591622).
Author: Catherine M. Crespi [aut, cre],
Zichen Liu [aut],
Kristen M. McGreevy [ctb]
Maintainer: Catherine M. Crespi <ccrespi@ucla.edu>
Diff between powertools versions 0.1.0 dated 2024-11-14 and 0.1.2 dated 2024-11-21
DESCRIPTION | 6 +- MD5 | 20 ++++---- R/check.param.R | 2 R/chisq.gof.R | 2 man/chisq.gof.Rd | 2 man/ttest.1samp.Rd | 88 ++++++++++++++++++------------------ man/ttest.2samp.Rd | 126 ++++++++++++++++++++++++++-------------------------- man/ttest.paired.Rd | 94 +++++++++++++++++++------------------- man/ztest.1samp.Rd | 90 ++++++++++++++++++------------------- man/ztest.2samp.Rd | 114 +++++++++++++++++++++++------------------------ man/ztest.paired.Rd | 98 ++++++++++++++++++++-------------------- 11 files changed, 321 insertions(+), 321 deletions(-)
Title: Circle Packing
Description: Algorithms to find arrangements of non-overlapping circles.
Author: Michael Bedward [aut, cre],
David Eppstein [aut] ,
Peter Menzel [aut]
Maintainer: Michael Bedward <michael.bedward@gmail.com>
Diff between packcircles versions 0.3.6 dated 2023-09-08 and 0.3.7 dated 2024-11-21
DESCRIPTION | 12 +- MD5 | 44 ++++----- NEWS.md | 7 + R/circleGraphLayout.R | 5 + R/circleRemoveOverlaps.R | 19 +++- R/circleRepelLayout.R | 56 ++++++++---- R/circleVertices.R | 112 ++++++++++++++++++------- README.md | 9 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/graph_packing.R | 78 ++++++++--------- inst/doc/graph_packing.html | 10 +- inst/doc/intro.R | 6 - inst/doc/intro.html | 14 +-- inst/doc/progressive_packing.R | 2 inst/doc/progressive_packing.Rmd | 2 inst/doc/progressive_packing.html | 53 ++++++++--- man/circleLayoutVertices.Rd | 170 +++++++++++++++++++------------------- man/circlePlotData.Rd | 64 +++++++------- man/circleRemoveOverlaps.Rd | 156 +++++++++++++++++----------------- man/circleRepelLayout.Rd | 161 +++++++++++++++++------------------ man/circleVertices.Rd | 58 ++++++------ vignettes/progressive_packing.Rmd | 2 23 files changed, 582 insertions(+), 458 deletions(-)
Title: Estimating Length-Based Indicators for Fish Stock
Description: Provides tools for estimating length-based indicators from length frequency data to assess fish stock status and manage fisheries sustainably. Implements methods from Cope and Punt (2009) <doi:10.1577/C08-025.1> for data-limited stock assessment and Froese (2004) <doi:10.1111/j.1467-2979.2004.00144.x> for detecting overfishing using simple indicators. Key functions include:
FrequencyTable(): Calculate the frequency table from the collected and also the extract the length frequency data from the frequency table with the upper length_range. A numeric value specifying the bin width for class intervals. If not provided, the bin width is automatically calculated using Sturges (1926) <doi:10.1080/01621459.1926.10502161> formula.
CalPar(): Calculates various lengths used in fish stock assessment as biological length indicators such as asymptotic length (Linf), maximum length (Lmax), length at sexual maturity (Lm), and optimal length (Lopt).
FishPar(): Calculates length-based [...truncated...]
Author: Ataher Ali [aut, cre],
Mohammed Shahidul Alam [aut]
Maintainer: Ataher Ali <ataher.cu.ms@gmail.com>
Diff between aLBI versions 0.1.6 dated 2024-11-13 and 0.1.7 dated 2024-11-21
DESCRIPTION | 6 - MD5 | 18 +-- NAMESPACE | 7 - R/FishPar.R | 204 +++++++++++++++++++++++++++++---------------- R/FrequencyTable.R | 73 +++++++++------- inst/doc/Introduction.R | 2 inst/doc/Introduction.Rmd | 14 +-- inst/doc/Introduction.html | 132 +++++++++++++++-------------- man/FrequencyTable.Rd | 26 ++--- vignettes/Introduction.Rmd | 14 +-- 10 files changed, 287 insertions(+), 209 deletions(-)
More information about OutcomeWeights at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-16 1.0.0
2019-02-04 0.1.1
Title: Synthetic Microdata Generator
Description: This tool fits a non-parametric Bayesian model called a "hierarchically coupled mixture model with local dependence (HCMM-LD)" to the original microdata in order to generate synthetic microdata for privacy protection. The non-parametric feature of the adopted model is useful for capturing the joint distribution of the original input data in a highly flexible manner, leading to the generation of synthetic data whose distributional features are similar to that of the input data. The package allows the original input data to have missing values and impute them with the posterior predictive distribution, so no missing values exist in the synthetic data output. The method builds on the work of Murray and Reiter (2016) <doi:10.1080/01621459.2016.1174132>.
Author: Hang J. Kim [aut, cre],
Juhee Lee [aut],
Young-Min Kim [aut],
Jared Murray [aut]
Maintainer: Hang J. Kim <hangkim0@gmail.com>
Diff between synMicrodata versions 2.0.0 dated 2024-04-07 and 2.1.0 dated 2024-11-21
DESCRIPTION | 8 +- MD5 | 13 +-- NAMESPACE | 2 R/R_functions.R | 163 ++++++++++++++++++++++++++++++++--------- man/Rcpp_modelobject-class.Rd | 6 + man/plot.synMicro_object.Rd | 9 ++ man/readData.Rd | 9 ++ man/summary.synMicro_object.Rd |only 8 files changed, 165 insertions(+), 45 deletions(-)