Title: Causal Inference and Prediction in Cohort-Based Analyses
Description: We propose numerous functions for cohort-based analyses, either for prediction or causal inference. For causal inference, it includes Inverse Probability Weighting and G-computation for marginal estimation of an exposure effect when confounders are expected. We deal with binary outcomes, times-to-events (Le Borgne, 2016, <doi:10.1002/sim.6777>), competing events (Trebern-Launay, 2018, <doi: 10.1007/s10654-017-0322-3>), and multi-state data (Gillaizeau, 2018, <doi: 10.1002/sim.7550>). For multistate data, semi-Markov model with interval censoring (Foucher, 2008, <doi: 10.1177/0962280208093889>) may be considered and we propose the possibility to consider the excess of mortality related to the disease compared to reference lifetime tables (Gillaizeau, 2017, <doi: 10.1177/0962280215586456>). For predictive studies, we propose a set of functions to estimate time-dependent receiver operating characteristic (ROC) curves with the possible consideration of right-censoring times-to-events or the presence of confounders (Le Borgne, 2018, <doi: 10.1177/0962280217702416>). Finally, several functions are available to assess time-dependent ROC curves (Combescure, 2017, <doi: 10.1177/0962280212464542>) or survival curves (Combescure, 2014, <doi: 10.1002/sim.6111>) from aggregated data.
Author: Yohann Foucher [aut, cre] (<https://orcid.org/0000-0003-0330-7457>),
Florent Le Borgne [aut],
Etienne Dantan [aut],
Florence Gillaizeau [aut],
Arthur Chatton [aut],
Christophe Combescure [aut]
Maintainer: Yohann Foucher <Yohann.Foucher@univ-nantes.fr>
Diff between RISCA versions 0.8 dated 2019-08-05 and 0.8.1 dated 2020-03-31
DESCRIPTION | 17 - MD5 | 82 ++++---- NAMESPACE | 12 - R/differentiation.r |only R/expect.utility1.R | 1 R/expect.utility2.R | 2 R/gc.logistic.R | 159 +++++++++++++--- R/gc.survival.R | 377 +++++++++++++++++++++++++++++---------- R/ipw.survival.R | 24 +- R/lines.roc.R | 2 R/plot.roc.R | 2 R/plot.survival.R |only R/rmst.r |only data/dataCSL.rda |binary data/dataDIVAT1.rda |binary data/dataDIVAT2.rda |binary data/dataDIVAT3.rda |binary data/dataDIVAT4.rda |binary data/dataDIVAT5.rda |binary data/dataHepatology.rda |binary data/dataKTFS.rda |binary data/dataKi67.rda |binary data/fr.ratetable.rda |binary data/rein.ratetable.rda |binary data/usa.ratetable.rda |binary man/auc.Rd | 2 man/dataDIVAT1.Rd | 29 +-- man/dataDIVAT2.Rd | 2 man/dataDIVAT3.Rd | 2 man/dataDIVAT4.Rd | 4 man/dataDIVAT5.Rd | 2 man/dataHepatology.Rd | 2 man/dataKTFS.Rd | 4 man/differentiation.Rd |only man/expect.utility1.Rd | 9 man/expect.utility2.Rd | 8 man/gc.logistic.Rd | 8 man/gc.survival.Rd | 17 + man/ipw.survival.Rd | 43 ---- man/lines.roc.Rd | 2 man/plot.roc.Rd | 2 man/plot.survival.Rd |only man/rmst.Rd |only man/roc.time.Rd | 2 man/semi.markov.3states.rsadd.Rd | 2 45 files changed, 551 insertions(+), 267 deletions(-)
Title: Zero Inflated Poisson Factor Analysis
Description: Estimation methods for zero-inflated Poisson factor analysis (ZIPFA) on sparse data.
It provides estimates of coefficients in a new type of zero-inflated regression.
It provides a cross-validation method to determine the potential rank of the data in the ZIPFA
and conducts zero-inflated Poisson factor analysis based on the determined rank.
Author: Tianchen Xu [aut, cre] (<https://orcid.org/0000-0002-0102-7630>),
Ryan T. Demmer [aut],
Gen Li [aut]
Maintainer: Tianchen Xu <tx2155@columbia.edu>
Diff between ZIPFA versions 0.8.0 dated 2019-10-25 and 0.8.1 dated 2020-03-31
DESCRIPTION | 15 ++++++++++----- MD5 | 5 +++-- R/ZIPFA.R | 10 ++++++++-- inst |only 4 files changed, 21 insertions(+), 9 deletions(-)
Title: Generates Expectations for 'testthat' Unit Testing
Description: Helps systematize and ease the process of
building unit tests with the 'testthat' package by providing
tools for generating expectations.
Author: Ludvig Renbo Olsen [aut, cre],
R. Mark Sharp [ctb]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>
Diff between xpectr versions 0.2.0 dated 2020-03-15 and 0.3.0 dated 2020-03-31
DESCRIPTION | 13 MD5 | 58 +- NAMESPACE | 1 NEWS.md | 14 R/addin_utils.R | 10 R/create_expectations.R | 70 ++- R/element_descriptors.R | 10 R/expectation_creators.R | 4 R/helpers.R | 6 R/initialize_gxs_function_addin.R | 6 R/navigateTestFileAddin.R |only R/side_effects.R | 4 README.md | 41 + build/xpectr.pdf |binary inst/doc/readme.R | 3 inst/doc/readme.Rmd | 17 inst/doc/readme.html | 26 - inst/rstudio/addins.dcf | 5 man/assertCollectionAddin.Rd | 1 man/dputSelectedAddin.Rd | 1 man/element_classes.Rd | 7 man/initializeGXSFunctionAddin.Rd | 1 man/initializeTestthatAddin.Rd | 1 man/insertExpectationsAddin.Rd | 1 man/navigateTestFileAddin.Rd |only man/wrapStringAddin.Rd | 3 tests/testthat/test_create_expectations.R | 32 - tests/testthat/test_gxs_function.R | 140 +++++- tests/testthat/test_gxs_selection.R | 418 +++++++++++++++++--- tests/testthat/test_initialize_gxs_function_addin.R |only tests/testthat/test_navigate_test_file_addin.R |only vignettes/readme.Rmd | 17 32 files changed, 722 insertions(+), 188 deletions(-)
Title: Summarizing OTU Table Regarding the Composition, Abundance and
Beta Diversity of Abundant and Rare Biospheres
Description: Summarizes the taxonomic composition, diversity contribution of the rare and abundant community by using OTU (operational taxonomic unit) table which was generated by analyzing pipeline of 'QIIME' or 'mothur'. The rare biosphere in this package is subset by the relative abundance threshold (for details about rare biosphere please see Lynch and Neufeld (2015) <doi:10.1038/nrmicro3400>).
Author: Sizhong Yang
Maintainer: Sizhong Yang <yanglzu@163.com>
Diff between otuSummary versions 0.1.0 dated 2018-06-19 and 0.1.1 dated 2020-03-31
otuSummary-0.1.0/otuSummary/R/bplot.R |only otuSummary-0.1.0/otuSummary/man/bplot.Rd |only otuSummary-0.1.1/otuSummary/DESCRIPTION | 16 ++++---- otuSummary-0.1.1/otuSummary/MD5 | 40 ++++++++++---------- otuSummary-0.1.1/otuSummary/NAMESPACE | 18 ++------- otuSummary-0.1.1/otuSummary/R/alphaDiversity.R | 24 +++++++----- otuSummary-0.1.1/otuSummary/R/chao2.R |only otuSummary-0.1.1/otuSummary/R/contrib.R | 4 +- otuSummary-0.1.1/otuSummary/R/gini.R |only otuSummary-0.1.1/otuSummary/R/ordination.R | 2 - otuSummary-0.1.1/otuSummary/R/otuCollap.R |only otuSummary-0.1.1/otuSummary/R/otuReport.R | 43 ++++++++++------------ otuSummary-0.1.1/otuSummary/R/rareBiosphere.R | 2 - otuSummary-0.1.1/otuSummary/R/subOTU.R | 26 +++++++------ otuSummary-0.1.1/otuSummary/data/otu4type.rda |binary otuSummary-0.1.1/otuSummary/data/otumothur.rda |binary otuSummary-0.1.1/otuSummary/data/otuqiime.rda |binary otuSummary-0.1.1/otuSummary/man/alphaDiversity.Rd | 12 +++--- otuSummary-0.1.1/otuSummary/man/contrib.Rd | 2 + otuSummary-0.1.1/otuSummary/man/matrixConvert.Rd | 2 - otuSummary-0.1.1/otuSummary/man/ordination.Rd | 2 - otuSummary-0.1.1/otuSummary/man/otuCollap.Rd |only otuSummary-0.1.1/otuSummary/man/otuReport.Rd | 17 +++++--- otuSummary-0.1.1/otuSummary/man/subOTU.Rd | 6 +-- 24 files changed, 112 insertions(+), 104 deletions(-)
Title: Feature-Based Landscape Analysis of Continuous and Constrained
Optimization Problems
Description: Tools and features for "Exploratory Landscape Analysis (ELA)" of
single-objective continuous optimization problems.
Those features are able to quantify rather complex properties, such as the
global structure, separability, etc., of the optimization problems.
Author: Pascal Kerschke [aut, cre],
Christian Hanster [ctb],
Jan Dagefoerde [ctb]
Maintainer: Pascal Kerschke <kerschke@uni-muenster.de>
Diff between flacco versions 1.7 dated 2017-06-14 and 1.8 dated 2020-03-31
flacco-1.7/flacco/man/plotFeatureImportance.Rd |only flacco-1.7/flacco/tests/testthat/test-ic-infocontent.R |only flacco-1.8/flacco/DESCRIPTION | 20 ++-- flacco-1.8/flacco/MD5 | 72 +++++++-------- flacco-1.8/flacco/NAMESPACE | 1 flacco-1.8/flacco/R/calculateFeatures.R | 16 ++- flacco-1.8/flacco/R/cm_computeGridCenters.R | 2 flacco-1.8/flacco/R/cm_convertInitDesignToGrid.R | 14 +- flacco-1.8/flacco/R/cm_findLinearNeighbours.R | 18 +-- flacco-1.8/flacco/R/cm_findNearestPrototype.R | 22 ++-- flacco-1.8/flacco/R/createFeatureObject.R | 14 +- flacco-1.8/flacco/R/feature_cm_gradhomo.R | 19 +-- flacco-1.8/flacco/R/feature_ela_curvature.R | 18 ++- flacco-1.8/flacco/R/feature_ela_levelset.R | 2 flacco-1.8/flacco/R/feature_ela_local_search.R | 2 flacco-1.8/flacco/R/feature_gcm.R | 9 - flacco-1.8/flacco/R/feature_gcm_barriertree.R | 16 +-- flacco-1.8/flacco/R/feature_ic_infocontent.R | 6 - flacco-1.8/flacco/R/feature_misc_nearest_better.R | 6 - flacco-1.8/flacco/R/ggplotFeatureImportance.R |only flacco-1.8/flacco/R/plotBarrierTree2D.R | 9 - flacco-1.8/flacco/R/plotBarrierTree3D.R | 9 - flacco-1.8/flacco/R/plotCellMapping.R | 19 +-- flacco-1.8/flacco/R/plotFeatureImportance.R | 25 ++++- flacco-1.8/flacco/R/plotInformationContent.R | 2 flacco-1.8/flacco/R/runApp.R | 15 +++ flacco-1.8/flacco/R/utilities.R | 44 +++++++++ flacco-1.8/flacco/build/vignette.rds |binary flacco-1.8/flacco/inst/CITATION |only flacco-1.8/flacco/inst/flaccogui/app.R | 1 flacco-1.8/flacco/man/FeatureObject.Rd | 14 ++ flacco-1.8/flacco/man/featureImportance.Rd |only flacco-1.8/flacco/man/features.Rd | 10 +- flacco-1.8/flacco/man/listAvailableFeatureSets.Rd | 8 + flacco-1.8/flacco/man/runFlaccoGUI.Rd | 15 +++ flacco-1.8/flacco/tests/testthat/Rplots.pdf |binary flacco-1.8/flacco/tests/testthat/test-ela-Curvature.R | 4 flacco-1.8/flacco/tests/testthat/test-ela-Levelset.R | 2 flacco-1.8/flacco/tests/testthat/test-gcm-BarrierTrees.R | 9 - flacco-1.8/flacco/tests/testthat/test-ic-InfoContent.R |only 40 files changed, 274 insertions(+), 169 deletions(-)
Title: General Resampling Infrastructure
Description: Classes and functions to create and summarize different types of resampling objects (e.g. bootstrap, cross-validation).
Author: Max Kuhn [aut, cre],
Fanny Chow [aut],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between rsample versions 0.0.5 dated 2019-07-12 and 0.0.6 dated 2020-03-31
DESCRIPTION | 17 - MD5 | 101 +++--- NAMESPACE | 14 NEWS.md | 20 - R/0_imports.R |only R/apparent.R | 3 R/boot.R | 4 R/bootci.R | 46 -- R/caret.R | 4 R/complement.R | 4 R/dplyr-compat.R | 30 - R/gather.R | 30 - R/groups.R | 6 R/initial_split.R | 36 +- R/lables.R | 22 + R/loo.R | 3 R/make_strata.R | 1 R/mc.R | 6 R/misc.R | 100 +++--- R/nest.R | 11 R/reexports.R | 5 R/rolling_origin.R | 26 + R/rsplit.R | 5 R/tidy.R | 25 - R/validation_split.R |only R/vfold.R | 5 build/vignette.rds |binary inst/doc/Basics.R | 8 inst/doc/Basics.html | 124 ++++--- inst/doc/Working_with_rsets.html | 411 ++++++++++++------------- man/add_resample_id.Rd | 1 man/as.data.frame.rsplit.Rd | 3 man/bootstraps.Rd | 3 man/gather.rset.Rd | 11 man/initial_split.Rd | 19 - man/int_pctl.Rd | 15 man/make_splits.Rd |only man/new_rset.Rd |only man/pretty.vfold_cv.Rd | 3 man/reexports.Rd | 3 man/rolling_origin.Rd | 16 man/rsample.Rd | 1 man/validation_split.Rd |only tests/testthat.R | 8 tests/testthat/test-print-groups.txt |only tests/testthat/test_bootci.R | 23 - tests/testthat/test_group.R | 5 tests/testthat/test_initial.R | 15 tests/testthat/test_rolling.R | 18 - tests/testthat/test_strata.R | 2 tests/testthat/test_tidy.R | 1 tests/testthat/test_validation.R |only vignettes/Applications/Intervals.Rmd | 1 vignettes/Applications/Recipes_and_rsample.Rmd | 2 vignettes/Applications/Time_Series.Rmd | 1 55 files changed, 687 insertions(+), 531 deletions(-)
Title: Network Meta-Analysis Using Bayesian Methods
Description: Network meta-analyses (mixed treatment comparisons) in the Bayesian
framework using JAGS. Includes methods to assess heterogeneity and
inconsistency, and a number of standard visualizations.
Author: Gert van Valkenhoef, Joel Kuiper
Maintainer: Gert van Valkenhoef <gert@gertvv.nl>
Diff between gemtc versions 0.8-2 dated 2016-12-23 and 0.8-4 dated 2020-03-31
DESCRIPTION | 10 +-- MD5 | 79 +++++++++++++------------ NAMESPACE | 5 - R/mtc.data.studyrow.R | 5 + R/mtc.network.R | 6 - R/nodesplit.R | 2 R/priors.R | 4 - R/rank.probability.R | 20 +++++- man/atrialFibrillation.Rd | 2 man/blocker.Rd | 4 - man/certolizumab.Rd | 2 man/depression.Rd | 2 man/dietfat.Rd | 4 - man/gemtc-package.Rd | 20 +++--- man/hfPrevention.Rd | 2 man/parkinson.Rd | 2 man/rank.probability.Rd | 23 ++++++- man/relative.effect.table.Rd | 2 man/smoking.Rd | 6 - man/thrombolytic.Rd | 4 - src/Makevars | 4 - src/gemtc-win.def |only src/gemtc.h |only src/init.c |only src/rank.c | 3 tests/data/studyrow/tsd2-1.out.txt | 37 ++++++----- tests/data/studyrow/tsd2-2.out.txt | 26 ++++---- tests/data/studyrow/tsd2-3.out.txt | 56 ++++++++--------- tests/data/studyrow/tsd2-5.out.txt | 14 ++-- tests/data/studyrow/tsd2-7.out.txt | 21 +++--- tests/data/studyrow/tsd2-8.out1.txt | 8 +- tests/data/studyrow/tsd2-8.out2.txt | 10 +-- tests/data/welton-cholesterol.gemtc | 2 tests/data/welton-systolic.gemtc | 2 tests/testthat/helper-regress.R | 2 tests/testthat/helper-validate.R | 12 +-- tests/testthat/test-regress-models.R | 16 +++-- tests/testthat/test-unit-allpairs.R | 20 ++++-- tests/testthat/test-unit-mtc.network_data.re.R | 62 +++++++++++++------ tests/testthat/test-unit-nodesplit.R | 61 ++++++++++++++----- tests/testthat/test-unit-rank.quantiles.R |only tests/testthat/test-unit-sucra.R |only tests/testthat/test-validate-riskratio.R | 2 43 files changed, 339 insertions(+), 223 deletions(-)
Title: Spatially Balanced Samples of Spatial Objects
Description: Routines for drawing samples from spatial objects, focused on spatially
balanced algorithms. Draws Halton Iterative Partition (HIP)
(Robertson et al., 2018; <doi:10.1007/s10651-018-0406-6>),
Balanced Acceptance Samples (BAS) (Robertson et al., 2013; <doi:10.1111/biom.12059>),
Generalized Random
Tessellation Stratified (GRTS) (Stevens and Olsen, 2004; <doi:10.1198/016214504000000250>),
Simple Systematic Samples (SSS) and
Simple Random Samples (SRS) from point, line, and polygon resources.
Frames are 'SpatialPoints', 'SpatialLines', or 'SpatialPolygons'
objects from package 'sp'.
Author: Trent McDonald [cre, aut],
Aidan McDonald [aut] (HIP sampling methods),
Michael Kleinsausser [ctb],
Stefan Emmons [ctb] (Auto testing and Travis)
Maintainer: Trent McDonald <tmcdonald@west-inc.com>
Diff between SDraw versions 2.1.8 dated 2019-03-07 and 2.1.11 dated 2020-03-31
DESCRIPTION | 18 +++++++----- MD5 | 65 +++++++++++++++++++++++++++------------------ NEWS.md | 27 ++++++++++++++++++ R/WY.r | 9 +++--- R/bas.point.r | 8 +++++ R/grts.line.r | 6 ++-- R/grts.point.r | 12 ++++---- R/grts.polygon.r | 7 +++- R/plot.sdrawSample.R | 2 - R/voronoi.polygons.r | 67 +++++++++++++++++++++++++++++++++++++++-------- R/zzz.r | 2 - build/vignette.rds |binary data/HI.coast.rda |binary data/WA.cities.rda |binary data/WA.rda |binary data/WY.rda |binary inst/doc/BASPoints.R | 14 ++++----- inst/doc/BASPoints.pdf |binary inst/doc/HIPPoints.R | 10 +++---- inst/doc/HIPPoints.pdf |binary inst/doc/HIPPolygons.R | 14 ++++----- inst/doc/HIPPolygons.pdf |binary man/WY.Rd | 8 +++-- man/grts.line.Rd | 6 ++-- man/grts.polygon.Rd | 7 +++- man/plotSample.Rd | 2 - man/voronoi.polygons.Rd | 45 +++++++++++++++++++++++++++---- tests |only 28 files changed, 236 insertions(+), 93 deletions(-)
Title: Adrian Dusa's Miscellaneous
Description: Contains functions used across packages 'QCA', 'DDIwR', and 'venn'.
Interprets and translates SOP - Sum of Products expressions, for both binary
and multi-value crisp sets, and extracts information (set names, set values)
from those expressions. Other functions perform various other checks if
possibly numeric (even if all numbers reside in a character vector) and coerce
to numeric, or check if the numbers are whole. It also offers, among others, a
highly flexible recoding routine.
Some functions need specific functionality from package QCA, but since that
package depends on this one, admisc cannot automatically load it due to
circular dependency.
Author: Adrian Dusa [aut, cre, cph]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between admisc versions 0.6 dated 2020-03-10 and 0.7 dated 2020-03-31
DESCRIPTION | 16 ++++++++-------- MD5 | 10 +++++----- R/simplify.R | 5 ++++- inst/ChangeLog | 4 ++++ man/SOPexpression.Rd | 8 ++++---- man/admisc.package.Rd | 4 ++-- 6 files changed, 27 insertions(+), 20 deletions(-)
Title: Simulation of Study Data
Description: Simulates data sets in order to explore modeling techniques or
better understand data generating processes. The user specifies a set of
relationships between covariates, and generates data based on these
specifications. The final data sets can represent data from randomized
control trials, repeated measure (longitudinal) designs, and cluster
randomized trials. Missingness can be generated using various
mechanisms (MCAR, MAR, NMAR).
Author: Keith Goldfeld [aut, cre]
Maintainer: Keith Goldfeld <Keith.Goldfeld@nyumc.org>
Diff between simstudy versions 0.1.15 dated 2019-10-16 and 0.1.16 dated 2020-03-31
DESCRIPTION | 10 +++--- MD5 | 75 ++++++++++++++++++++++++------------------------- NEWS.md | 8 ++++- R/defData.R | 3 + R/int_addStrataCode.R | 23 +++++++++++++-- R/int_evalDef.R | 29 ++++++++++++++++++ R/int_generate.R | 4 +- R/int_genmixture.R |only R/trimData.R | 2 - R/trtAssign.R | 67 ++++++++++++++++++++++--------------------- build/vignette.rds |binary inst/doc/simstudy.R | 18 +++++------ inst/doc/simstudy.html | 37 +++++++++++------------- man/addCorData.Rd | 12 ++++++- man/addCorFlex.Rd | 3 - man/addCorGen.Rd | 18 +++++++++-- man/addMarkov.Rd | 15 +++++++-- man/addMultiFac.Rd | 3 - man/addPeriods.Rd | 11 +++++-- man/defCondition.Rd | 10 +++++- man/defData.Rd | 14 +++++++-- man/defDataAdd.Rd | 10 +++++- man/defMiss.Rd | 10 +++++- man/genCorData.Rd | 12 ++++++- man/genCorFlex.Rd | 3 - man/genCorGen.Rd | 17 +++++++++-- man/genCorOrdCat.Rd | 12 ++++++- man/genFactor.Rd | 3 - man/genMarkov.Rd | 14 +++++++-- man/genMiss.Rd | 3 - man/genMultiFac.Rd | 10 +++++- man/genNthEvent.Rd | 3 - man/genSpline.Rd | 12 ++++++- man/iccRE.Rd | 3 - man/trimData.Rd | 2 - man/trtAssign.Rd | 16 +++++++++- man/trtStepWedge.Rd | 13 +++++++- man/updateDef.Rd | 11 +++++-- man/updateDefAdd.Rd | 11 +++++-- 39 files changed, 359 insertions(+), 168 deletions(-)
Title: Comprehensive and Easy to Use Quality Control of GWAS Results
Description: When evaluating the results of a genome-wide association study (GWAS), it is important to perform a quality control to ensure that the results are valid, complete, correctly formatted, and, in case of meta-analysis, consistent with other studies that have applied the same analysis. This package was developed to facilitate and streamline this process and provide the user with a comprehensive report.
Author: Alireza Ani [aut, cre],
Peter J. van der Most [aut],
Ahmad Vaez [aut],
Ilja M. Nolte [aut]
Maintainer: Alireza Ani <a.ani@umcg.nl>
Diff between GWASinspector versions 1.4.6 dated 2020-03-23 and 1.4.6.7 dated 2020-03-31
GWASinspector-1.4.6.7/GWASinspector/DESCRIPTION | 8 - GWASinspector-1.4.6.7/GWASinspector/MD5 | 66 ++++------ GWASinspector-1.4.6.7/GWASinspector/NAMESPACE | 1 GWASinspector-1.4.6.7/GWASinspector/R/GWASinspector.R | 22 +-- GWASinspector-1.4.6.7/GWASinspector/R/aaa.R | 2 GWASinspector-1.4.6.7/GWASinspector/R/alleleMatch.R | 62 +++++++-- GWASinspector-1.4.6.7/GWASinspector/R/compare_GWASs.R | 16 +- GWASinspector-1.4.6.7/GWASinspector/R/excelReportFunctions.R | 10 + GWASinspector-1.4.6.7/GWASinspector/R/getConfig.R | 9 - GWASinspector-1.4.6.7/GWASinspector/R/getHeaderTranslation.R | 8 - GWASinspector-1.4.6.7/GWASinspector/R/manhattanPlotFunction.R | 8 - GWASinspector-1.4.6.7/GWASinspector/R/multiStudyFunctions.R | 8 + GWASinspector-1.4.6.7/GWASinspector/R/processColumns.R | 7 - GWASinspector-1.4.6.7/GWASinspector/R/processInputFile.R | 2 GWASinspector-1.4.6.7/GWASinspector/R/rSQLiteFunctions.R | 3 GWASinspector-1.4.6.7/GWASinspector/R/reportRelatedFunctions.R | 4 GWASinspector-1.4.6.7/GWASinspector/R/result_inspector.R | 4 GWASinspector-1.4.6.7/GWASinspector/R/run_inspector.R | 8 - GWASinspector-1.4.6.7/GWASinspector/R/saveFilesFunctions.R | 2 GWASinspector-1.4.6.7/GWASinspector/R/setup_inspector.R | 6 GWASinspector-1.4.6.7/GWASinspector/R/studyFunctions.R | 8 - GWASinspector-1.4.6.7/GWASinspector/R/variantMatching.R | 2 GWASinspector-1.4.6.7/GWASinspector/R/variantModifierFunctions.R | 34 +++++ GWASinspector-1.4.6.7/GWASinspector/inst/doc/GWASinspector.html | 4 GWASinspector-1.4.6.7/GWASinspector/inst/rmd/multiFileReport_alone_extra.rmd | 14 +- GWASinspector-1.4.6.7/GWASinspector/inst/rmd/multiFileReport_extra.rmd | 12 + GWASinspector-1.4.6.7/GWASinspector/man/GWASinspector.Rd | 22 +-- GWASinspector-1.4.6.7/GWASinspector/man/compare.GWASs.Rd | 8 - GWASinspector-1.4.6.7/GWASinspector/man/get.config.Rd | 9 - GWASinspector-1.4.6.7/GWASinspector/man/get.headerTranslation.Rd | 8 - GWASinspector-1.4.6.7/GWASinspector/man/result.inspector.Rd | 4 GWASinspector-1.4.6.7/GWASinspector/man/run.inspector.Rd | 4 GWASinspector-1.4.6.7/GWASinspector/man/setup.inspector.Rd | 6 GWASinspector-1.4.6/GWASinspector/R/sqlite_db_check.R |only GWASinspector-1.4.6/GWASinspector/man/sqlite.db.check.Rd |only 35 files changed, 246 insertions(+), 145 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-18 1.0.1
2019-09-17 1.0.0
2019-03-27 0.7.6
2018-08-31 0.7.4
2018-04-13 0.7.3
2018-03-21 0.7.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-11-07 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-09 0.1.2
2018-10-15 0.1.1
2017-01-09 0.1.0
More information about impressionist.colors at CRAN
Permanent link
Title: MCMC for Spike and Slab Regression
Description: Spike and slab regression with a variety of residual error
distributions corresponding to Gaussian, Student T, probit, logit, SVM, and a
few others. Spike and slab regression is Bayesian regression with prior
distributions containing a point mass at zero. The posterior updates the
amount of mass on this point, leading to a posterior distribution that is
actually sparse, in the sense that if you sample from it many coefficients are
actually zeros. Sampling from this posterior distribution is an elegant way
to handle Bayesian variable selection and model averaging. See
<DOI:10.1504/IJMMNO.2014.059942> for an explanation of the Gaussian case.
Author: Steven L. Scott <steve.the.bayesian@gmail.com>
Maintainer: Steven L. Scott <steve.the.bayesian@gmail.com>
Diff between BoomSpikeSlab versions 1.2.1 dated 2019-09-04 and 1.2.2 dated 2020-03-31
BoomSpikeSlab-1.2.1/BoomSpikeSlab/inst/tests/tests |only BoomSpikeSlab-1.2.1/BoomSpikeSlab/tests |only BoomSpikeSlab-1.2.2/BoomSpikeSlab/DESCRIPTION | 15 +--- BoomSpikeSlab-1.2.2/BoomSpikeSlab/MD5 | 36 +--------- BoomSpikeSlab-1.2.2/BoomSpikeSlab/NAMESPACE | 2 BoomSpikeSlab-1.2.2/BoomSpikeSlab/R/nnet.R | 32 +++++--- BoomSpikeSlab-1.2.2/BoomSpikeSlab/inst/tests/testthat/test-nnet.R | 10 +- BoomSpikeSlab-1.2.2/BoomSpikeSlab/src/spike_slab_wrapper.cc | 36 ++++++---- 8 files changed, 64 insertions(+), 67 deletions(-)
Title: Long Term Water Quality Trend Analysis
Description: Enable users to evaluate long-term trends using a Generalized
Additive Modeling (GAM) approach. The model development includes selecting a
GAM structure to describe nonlinear seasonally-varying changes over time,
incorporation of hydrologic variability via either a river flow or salinity,
the use of an intervention to deal with method or laboratory changes
suspected to impact data values, and representation of left- and
interval-censored data. The approach has been applied to water quality data
in the Chesapeake Bay, a major estuary on the east coast of the United
States to provide insights to a range of management- and research-focused
questions.
Author: Rebecca Murphy, Elgin Perry, Jennifer Keisman, Jon Harcum, Erik W Leppo
Maintainer: Erik Leppo <Erik.Leppo@tetratech.com>
Diff between baytrends versions 1.1.0 dated 2019-03-14 and 1.2.1 dated 2020-03-31
baytrends-1.1.0/baytrends/vignettes/data/dataCensored_TEST.csv |only baytrends-1.2.1/baytrends/DESCRIPTION | 48 - baytrends-1.2.1/baytrends/MD5 | 427 +++++----- baytrends-1.2.1/baytrends/NAMESPACE | 12 baytrends-1.2.1/baytrends/NEWS | 349 +++++--- baytrends-1.2.1/baytrends/NEWS.md |only baytrends-1.2.1/baytrends/R/analysisOrganizeData.R | 218 ++++- baytrends-1.2.1/baytrends/R/closeOut.R | 13 baytrends-1.2.1/baytrends/R/createResiduals.R | 10 baytrends-1.2.1/baytrends/R/data.R | 145 +++ baytrends-1.2.1/baytrends/R/expectMaxFunctions.r | 1 baytrends-1.2.1/baytrends/R/findFile.R | 5 baytrends-1.2.1/baytrends/R/gamPlotCalc.r | 2 baytrends-1.2.1/baytrends/R/gamPlotDisp.R | 4 baytrends-1.2.1/baytrends/R/gamPlotDispSeason.R |only baytrends-1.2.1/baytrends/R/gamTest.r | 243 ++++- baytrends-1.2.1/baytrends/R/gamTestSeason.r |only baytrends-1.2.1/baytrends/R/layerAggregation.R | 16 baytrends-1.2.1/baytrends/R/loadModels.R | 19 baytrends-1.2.1/baytrends/R/qw.export.R | 4 baytrends-1.2.1/baytrends/R/qw.import.R | 8 baytrends-1.2.1/baytrends/R/saveDF.R | 32 baytrends-1.2.1/baytrends/R/selectData.R | 30 baytrends-1.2.1/baytrends/R/smwrBase_group2row.R | 2 baytrends-1.2.1/baytrends/R/smwrBase_importRDB.R | 4 baytrends-1.2.1/baytrends/R/smwrBase_isLike.R | 37 baytrends-1.2.1/baytrends/R/smwrGraphs_addCaption.R | 4 baytrends-1.2.1/baytrends/R/smwrGraphs_colorPlot.R | 4 baytrends-1.2.1/baytrends/R/smwrGraphs_colors.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_logPretty.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_month.USGS.R | 2 baytrends-1.2.1/baytrends/R/smwrGraphs_refLine.R | 4 baytrends-1.2.1/baytrends/R/smwrGraphs_setAxis.R |only baytrends-1.2.1/baytrends/R/smwrGraphs_setColor.R | 4 baytrends-1.2.1/baytrends/R/smwrGraphs_setPage.R | 38 baytrends-1.2.1/baytrends/R/smwrGraphs_timePlot.R | 12 baytrends-1.2.1/baytrends/R/smwrGraphs_xyPlot.R | 12 baytrends-1.2.1/baytrends/R/smwrQW_x_dlimit.R | 2 baytrends-1.2.1/baytrends/R/smwrQW_x_importQW.R | 2 baytrends-1.2.1/baytrends/R/smwrQW_x_readNWQLdl.R | 3 baytrends-1.2.1/baytrends/R/sysdata.rda |binary baytrends-1.2.1/baytrends/R/zzz.R | 2 baytrends-1.2.1/baytrends/README.md | 46 + baytrends-1.2.1/baytrends/build/vignette.rds |binary baytrends-1.2.1/baytrends/data/Q05078470.rda |only baytrends-1.2.1/baytrends/data/QW05078470.rda |only baytrends-1.2.1/baytrends/data/QWstacked.rda |only baytrends-1.2.1/baytrends/data/parameterList.rda |binary baytrends-1.2.1/baytrends/data/pcodeColData.rda |only baytrends-1.2.1/baytrends/inst/doc/create_Seasonally_Detrended_Flow_and_Salinity_Data_Sets.R | 14 baytrends-1.2.1/baytrends/inst/doc/create_Seasonally_Detrended_Flow_and_Salinity_Data_Sets.html | 185 ++-- baytrends-1.2.1/baytrends/inst/doc/statgam_and_statchng_output_fields.pdf |only baytrends-1.2.1/baytrends/inst/doc/vignette_qw.R | 22 baytrends-1.2.1/baytrends/inst/doc/vignette_qw.Rmd | 16 baytrends-1.2.1/baytrends/inst/doc/vignette_qw.html | 142 +-- baytrends-1.2.1/baytrends/man/Arith-censored.Rd | 113 +- baytrends-1.2.1/baytrends/man/Math-censored.Rd | 59 - baytrends-1.2.1/baytrends/man/Q05078470.Rd |only baytrends-1.2.1/baytrends/man/QW05078470.Rd |only baytrends-1.2.1/baytrends/man/QWstacked.Rd |only baytrends-1.2.1/baytrends/man/View.Rd | 44 - baytrends-1.2.1/baytrends/man/add.Rd | 68 - baytrends-1.2.1/baytrends/man/addCaption.Rd | 76 - baytrends-1.2.1/baytrends/man/analysisOrganizeData.Rd | 381 ++++---- baytrends-1.2.1/baytrends/man/appendDateFeatures.Rd | 24 baytrends-1.2.1/baytrends/man/as.character.lcens.Rd | 58 - baytrends-1.2.1/baytrends/man/as.data.frame.Rd | 104 +- baytrends-1.2.1/baytrends/man/as.double.Rd | 86 +- baytrends-1.2.1/baytrends/man/as.lcens.Rd | 178 ++-- baytrends-1.2.1/baytrends/man/as.mcens.Rd | 169 +-- baytrends-1.2.1/baytrends/man/as.qw.Rd | 219 ++--- baytrends-1.2.1/baytrends/man/baseDay.Rd | 84 - baytrends-1.2.1/baytrends/man/baseDay2decimal.Rd | 72 - baytrends-1.2.1/baytrends/man/baytrends.Rd | 39 baytrends-1.2.1/baytrends/man/c.Rd | 66 - baytrends-1.2.1/baytrends/man/censorLevels.Rd | 100 +- baytrends-1.2.1/baytrends/man/censoring.Rd | 92 +- baytrends-1.2.1/baytrends/man/censpp.Rd | 124 +- baytrends-1.2.1/baytrends/man/closeOut.Rd | 48 - baytrends-1.2.1/baytrends/man/colorPlot.Rd | 316 ++++--- baytrends-1.2.1/baytrends/man/convert2qw.Rd | 112 +- baytrends-1.2.1/baytrends/man/convertFqw.Rd | 96 +- baytrends-1.2.1/baytrends/man/createResiduals.Rd | 94 +- baytrends-1.2.1/baytrends/man/dataCensored.Rd | 72 - baytrends-1.2.1/baytrends/man/datePretty.Rd | 112 +- baytrends-1.2.1/baytrends/man/dectime.Rd | 108 +- baytrends-1.2.1/baytrends/man/dectime2Date.Rd | 76 - baytrends-1.2.1/baytrends/man/detrended.flow.Rd | 286 +++--- baytrends-1.2.1/baytrends/man/detrended.salinity.Rd | 251 ++--- baytrends-1.2.1/baytrends/man/dlimit.Rd | 161 +-- baytrends-1.2.1/baytrends/man/dot-ExpLNiCens.Rd | 46 - baytrends-1.2.1/baytrends/man/dot-ExpLNlCens.Rd | 46 - baytrends-1.2.1/baytrends/man/dot-ExpLNmCens.Rd | 42 baytrends-1.2.1/baytrends/man/dot-ExpLNrCens.Rd | 46 - baytrends-1.2.1/baytrends/man/dot-ExpNiCens.Rd | 46 - baytrends-1.2.1/baytrends/man/dot-ExpNlCens.Rd | 46 - baytrends-1.2.1/baytrends/man/dot-ExpNmCens.Rd | 42 baytrends-1.2.1/baytrends/man/dot-ExpNrCens.Rd | 46 - baytrends-1.2.1/baytrends/man/dot-F.Rd | 64 - baytrends-1.2.1/baytrends/man/dot-H.Rd | 52 - baytrends-1.2.1/baytrends/man/dot-H1.Rd | 50 - baytrends-1.2.1/baytrends/man/dot-H2.Rd | 50 - baytrends-1.2.1/baytrends/man/dot-H3.Rd | 50 - baytrends-1.2.1/baytrends/man/dot-H4.Rd | 50 - baytrends-1.2.1/baytrends/man/dot-H5.Rd | 50 - baytrends-1.2.1/baytrends/man/dot-P.Rd | 48 - baytrends-1.2.1/baytrends/man/dot-T.Rd | 64 - baytrends-1.2.1/baytrends/man/dot-V.Rd | 58 - baytrends-1.2.1/baytrends/man/dot-appendDateFeatures.Rd | 56 - baytrends-1.2.1/baytrends/man/dot-checkRange.Rd | 121 +- baytrends-1.2.1/baytrends/man/dot-chkParameter.Rd | 50 - baytrends-1.2.1/baytrends/man/dot-findFile.Rd | 109 +- baytrends-1.2.1/baytrends/man/dot-fmtPval.Rd | 30 baytrends-1.2.1/baytrends/man/dot-gamANOVA.Rd | 30 baytrends-1.2.1/baytrends/man/dot-gamCoeff.Rd | 34 baytrends-1.2.1/baytrends/man/dot-gamDiffPORtbl.Rd | 34 baytrends-1.2.1/baytrends/man/dot-gamPlotCalc.Rd | 90 +- baytrends-1.2.1/baytrends/man/dot-initializeResults.Rd | 28 baytrends-1.2.1/baytrends/man/dot-layerAggregation.Rd | 79 - baytrends-1.2.1/baytrends/man/dot-mergeFlow.Rd | 53 - baytrends-1.2.1/baytrends/man/dot-mergeSalinity.Rd | 43 - baytrends-1.2.1/baytrends/man/dot-reAttDF.Rd | 70 - baytrends-1.2.1/baytrends/man/dot-simCensored.Rd | 56 - baytrends-1.2.1/baytrends/man/dot-vTable.Rd | 34 baytrends-1.2.1/baytrends/man/eventProcessing.Rd | 128 +- baytrends-1.2.1/baytrends/man/fillMissing.Rd | 190 ++-- baytrends-1.2.1/baytrends/man/filterWgts.Rd | 60 - baytrends-1.2.1/baytrends/man/flwAveragePred.Rd | 44 - baytrends-1.2.1/baytrends/man/format.Rd | 109 +- baytrends-1.2.1/baytrends/man/gamDiff.Rd | 204 ++-- baytrends-1.2.1/baytrends/man/gamPlotDisp.Rd | 105 +- baytrends-1.2.1/baytrends/man/gamPlotDispSeason.Rd |only baytrends-1.2.1/baytrends/man/gamTest.Rd | 211 +++- baytrends-1.2.1/baytrends/man/gamTestSeason.Rd |only baytrends-1.2.1/baytrends/man/getUSGSflow.Rd | 110 +- baytrends-1.2.1/baytrends/man/group2row.Rd | 120 +- baytrends-1.2.1/baytrends/man/importNWISqw.Rd | 190 ++-- baytrends-1.2.1/baytrends/man/importQW.Rd | 203 ++-- baytrends-1.2.1/baytrends/man/importRDB.Rd | 179 ++-- baytrends-1.2.1/baytrends/man/impute.Rd | 70 - baytrends-1.2.1/baytrends/man/imputeLessThans.Rd | 108 +- baytrends-1.2.1/baytrends/man/is.na.Rd | 62 - baytrends-1.2.1/baytrends/man/isLike.Rd | 121 +- baytrends-1.2.1/baytrends/man/layerLukup.Rd | 42 baytrends-1.2.1/baytrends/man/lcens-class.Rd | 76 - baytrends-1.2.1/baytrends/man/length.Rd | 68 - baytrends-1.2.1/baytrends/man/lineWt.Rd | 60 - baytrends-1.2.1/baytrends/man/linearPretty.Rd | 104 +- baytrends-1.2.1/baytrends/man/loadData.Rd | 175 ++-- baytrends-1.2.1/baytrends/man/loadExcel.Rd | 160 +-- baytrends-1.2.1/baytrends/man/loadModels.Rd | 54 - baytrends-1.2.1/baytrends/man/loadModelsResid.Rd | 36 baytrends-1.2.1/baytrends/man/logPretty.Rd |only baytrends-1.2.1/baytrends/man/makeColNames.Rd | 64 - baytrends-1.2.1/baytrends/man/mcenKM.Rd | 46 - baytrends-1.2.1/baytrends/man/mcenMLE.Rd | 70 - baytrends-1.2.1/baytrends/man/mcenROS.Rd | 72 - baytrends-1.2.1/baytrends/man/mcens-class.Rd | 92 +- baytrends-1.2.1/baytrends/man/mdlKM.Rd | 48 - baytrends-1.2.1/baytrends/man/mdlKMstats.Rd | 44 - baytrends-1.2.1/baytrends/man/mdlMLE.Rd | 70 - baytrends-1.2.1/baytrends/man/mdlROS.Rd | 82 - baytrends-1.2.1/baytrends/man/mean.qw.Rd | 72 - baytrends-1.2.1/baytrends/man/meanStats.Rd | 62 - baytrends-1.2.1/baytrends/man/medianStats.Rd | 84 - baytrends-1.2.1/baytrends/man/month.USGS.Rd | 58 - baytrends-1.2.1/baytrends/man/na2miss.Rd | 82 - baytrends-1.2.1/baytrends/man/namePretty.Rd | 98 +- baytrends-1.2.1/baytrends/man/numericData.Rd | 50 - baytrends-1.2.1/baytrends/man/parameterList.Rd | 68 - baytrends-1.2.1/baytrends/man/pcodeColData.Rd |only baytrends-1.2.1/baytrends/man/pcodeNWISqw.Rd | 119 +- baytrends-1.2.1/baytrends/man/print.censMCT.Rd | 66 - baytrends-1.2.1/baytrends/man/print.censQuantile.Rd | 54 - baytrends-1.2.1/baytrends/man/print.censReg.Rd | 56 - baytrends-1.2.1/baytrends/man/print.censStats.Rd | 56 - baytrends-1.2.1/baytrends/man/print.summary.censReg.Rd | 56 - baytrends-1.2.1/baytrends/man/printData.Rd | 58 - baytrends-1.2.1/baytrends/man/quantile.Rd | 176 ++-- baytrends-1.2.1/baytrends/man/qw-class.Rd | 128 +- baytrends-1.2.1/baytrends/man/qw.export.Rd | 94 +- baytrends-1.2.1/baytrends/man/qw.import.Rd | 140 +-- baytrends-1.2.1/baytrends/man/qw2mcens.Rd | 46 - baytrends-1.2.1/baytrends/man/qwCoalesce.Rd | 88 +- baytrends-1.2.1/baytrends/man/ratio.Rd | 58 - baytrends-1.2.1/baytrends/man/rbindQW.Rd | 48 - baytrends-1.2.1/baytrends/man/readNWQLdl.Rd | 77 - baytrends-1.2.1/baytrends/man/refLine.Rd | 124 +- baytrends-1.2.1/baytrends/man/renderPretty.Rd | 125 +- baytrends-1.2.1/baytrends/man/residuals.censReg.Rd | 89 +- baytrends-1.2.1/baytrends/man/rmse.Rd | 150 +-- baytrends-1.2.1/baytrends/man/sal.Rd | 42 baytrends-1.2.1/baytrends/man/saveDF.Rd | 98 +- baytrends-1.2.1/baytrends/man/sdlFill.Rd | 70 - baytrends-1.2.1/baytrends/man/seasAdjflow.Rd | 118 +- baytrends-1.2.1/baytrends/man/selectData.Rd | 297 +++--- baytrends-1.2.1/baytrends/man/setAxis.Rd |only baytrends-1.2.1/baytrends/man/setColor.Rd | 60 - baytrends-1.2.1/baytrends/man/setExplan.Rd | 94 +- baytrends-1.2.1/baytrends/man/setMargin.Rd | 62 - baytrends-1.2.1/baytrends/man/setMultiPlot.Rd | 154 +-- baytrends-1.2.1/baytrends/man/setPage.Rd | 275 +++--- baytrends-1.2.1/baytrends/man/setPlot.Rd | 156 +-- baytrends-1.2.1/baytrends/man/show-censored.Rd | 55 - baytrends-1.2.1/baytrends/man/smwr.colors.Rd |only baytrends-1.2.1/baytrends/man/sort.censored.Rd | 82 - baytrends-1.2.1/baytrends/man/splitQual.Rd | 50 - baytrends-1.2.1/baytrends/man/stationMasterList.Rd | 98 +- baytrends-1.2.1/baytrends/man/str.Rd | 72 - baytrends-1.2.1/baytrends/man/strip.blanks.Rd | 56 - baytrends-1.2.1/baytrends/man/subset.Rd | 112 +- baytrends-1.2.1/baytrends/man/summary.Rd | 88 +- baytrends-1.2.1/baytrends/man/summary.censReg.Rd | 82 - baytrends-1.2.1/baytrends/man/timePlot.Rd | 395 +++++---- baytrends-1.2.1/baytrends/man/timePretty.Rd | 56 - baytrends-1.2.1/baytrends/man/transData.Rd | 61 - baytrends-1.2.1/baytrends/man/usgsGages.Rd | 38 baytrends-1.2.1/baytrends/man/vcov.censReg.Rd | 48 - baytrends-1.2.1/baytrends/man/vif.Rd | 70 - baytrends-1.2.1/baytrends/man/xyPlot.Rd | 318 ++++--- baytrends-1.2.1/baytrends/man/zcn.Rd | 62 - baytrends-1.2.1/baytrends/man/zeq.Rd | 68 - baytrends-1.2.1/baytrends/vignettes/data/data_censored_test.csv |only baytrends-1.2.1/baytrends/vignettes/dataCensored.test.rda |only baytrends-1.2.1/baytrends/vignettes/dataCensored_TEST.csv |only baytrends-1.2.1/baytrends/vignettes/statgam_and_statchng_output_fields.pdf |only baytrends-1.2.1/baytrends/vignettes/vignette_qw.Rmd | 16 227 files changed, 9175 insertions(+), 7881 deletions(-)
Title: Record 'HTTP' Calls to Disk
Description: Record test suite 'HTTP' requests and replays them during
future runs. A port of the Ruby gem of the same name
(<https://github.com/vcr/vcr/>). Works by hooking into the 'webmockr'
R package for matching 'HTTP' requests by various rules ('HTTP' method,
'URL', query parameters, headers, body, etc.), and then caching
real 'HTTP' responses on disk in 'cassettes'. Subsequent 'HTTP' requests
matching any previous requests in the same 'cassette' use a cached
'HTTP' response.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Aaron Wolen [ctb] (<https://orcid.org/0000-0003-2542-2202>)
Maintainer: Scott Chamberlain <sckott@protonmail.com>
Diff between vcr versions 0.5.0 dated 2020-03-03 and 0.5.4 dated 2020-03-31
DESCRIPTION | 10 +- MD5 | 62 +++++++------- NAMESPACE | 1 NEWS.md | 13 +++ R/cassette_class.R | 1 R/configuration.R | 44 +++++++++- R/errors.R | 78 ++++++++++++++---- R/zzz.R | 5 + README.md | 11 +- inst/doc/configuration.html | 4 inst/doc/request_matching.html | 4 inst/doc/vcr.html | 4 man/Cassette.Rd | 29 ++++++ man/FileSystem.Rd | 5 + man/HTTPInteraction.Rd | 4 man/HTTPInteractionList.Rd | 7 + man/Hooks.Rd | 4 man/Persisters.Rd | 2 man/Request.Rd | 4 man/RequestHandler.Rd | 3 man/RequestHandlerCrul.Rd | 1 man/RequestHandlerHttr.Rd | 2 man/RequestIgnorer.Rd | 7 + man/RequestMatcherRegistry.Rd | 5 + man/Serializers.Rd | 2 man/UnhandledHTTPRequestError.Rd | 42 +++++++++ man/VcrResponse.Rd | 10 ++ man/YAML.Rd | 5 + man/crul_request.Rd | 4 man/vcr_configure.Rd | 22 ++++- tests/testthat/test-ause_cassette_record_modes.R | 4 tests/testthat/test-vcr_last_error.R |only tests/testthat/test-write_disk_path_package_context.R |only 33 files changed, 327 insertions(+), 72 deletions(-)
More information about statnipokladna at CRAN
Permanent link
Title: Phylogenetic Ridge Regression Methods for Comparative Studies
Description: Functions for phylogenetic analysis (Castiglione et al, 2018 <doi:10.1111/2041-210X.12954>). The functions perform the estimation of phenotypic evolutionary rates, identification of phenotypic evolutionary rate shifts, quantification of direction and size of evolutionary change in multivariate traits, the computation of ontogenetic shape vectors and test for morphological convergence.
Author: Pasquale Raia, Silvia Castiglione, Carmela Serio, Alessandro Mondanaro, Marina Melchionna, Mirko Di Febbraro, Antonio Profico, Francesco Carotenuto
Maintainer: Pasquale Raia <pasquale.raia@unina.it>
Diff between RRphylo versions 2.4.0 dated 2020-01-16 and 2.4.4 dated 2020-03-31
DESCRIPTION | 19 - MD5 | 103 +++---- NAMESPACE | 265 +++++++++--------- R/PGLS_fossil.R | 15 - R/RRphylo.R | 24 - R/StableTraitsR.R | 13 R/angle.matrix.R | 30 +- R/auxilliary.functions.R |only R/cutPhylo.R |only R/distNodes.R | 11 R/evo.dir.R | 668 +++++++++++++++++++++++------------------------ R/getMommy.R | 5 R/makeL.R | 133 ++++----- R/overfitRR.R | 42 +- R/phyloclust.R | 1 R/plotRates.R | 5 R/retrieve.angles.R | 7 R/scaleTree.R | 16 - R/search.conv.R | 204 +------------- R/search.shift.R | 30 -- R/search.trend.R | 40 +- R/swap.phylo.R | 27 + R/swapONE.R | 223 ++++++++------- inst/CITATION | 23 - man/DataApes.Rd | 56 ++- man/DataCetaceans.Rd | 54 +-- man/DataFelids.Rd | 50 +-- man/DataOrnithodirans.Rd | 52 +-- man/DataUng.Rd | 52 +-- man/PGLS_fossil.Rd | 111 +++---- man/RRphylo-package.Rd | 36 +- man/RRphylo.Rd | 192 ++++++------- man/StableTraitsR.Rd | 134 ++++----- man/angle.matrix.Rd | 155 +++++----- man/cutPhylo.Rd |only man/distNodes.Rd | 73 ++--- man/evo.dir.Rd | 260 +++++++++--------- man/getMommy.Rd | 72 ++--- man/getSis.Rd | 60 ++-- man/makeFossil.Rd | 60 ++-- man/makeL.Rd | 52 +-- man/makeL1.Rd | 52 +-- man/overfitRR.Rd | 287 ++++++++++---------- man/phyloclust.Rd | 72 ++--- man/plotRates.Rd | 69 ++-- man/retrieve.angles.Rd | 323 +++++++++++----------- man/scaleTree.Rd | 164 +++++------ man/search.conv.Rd | 204 +++++++------- man/search.shift.Rd | 185 ++++++------- man/search.trend.Rd | 239 ++++++++-------- man/setBM.Rd | 102 +++---- man/sizedsubtree.Rd | 66 ++-- man/swap.phylo.Rd | 120 ++++---- man/swapONE.Rd | 90 +++--- 54 files changed, 2614 insertions(+), 2732 deletions(-)
Title: Quantitative Financial Modelling Framework
Description: Specify, build, trade, and analyse quantitative financial trading strategies.
Author: Jeffrey A. Ryan [aut, cph],
Joshua M. Ulrich [cre, aut],
Wouter Thielen [ctb],
Paul Teetor [ctb],
Steve Bronder [ctb]
Maintainer: Joshua M. Ulrich <josh.m.ulrich@gmail.com>
Diff between quantmod versions 0.4-16 dated 2020-03-08 and 0.4.17 dated 2020-03-31
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/chartSeries.R | 2 +- build/partial.rdb |binary 5 files changed, 13 insertions(+), 8 deletions(-)
Title: Analysis & Measurement of Promotion Effectiveness
Description: Analysis and measurement of promotion effectiveness on a given target variable (e.g. daily sales). After converting promotion schedule into dummy or smoothed predictor variables, the package estimates the effects of these variables controlled for trend/periodicity/structural change using prophet by Taylor and Letham (2017) <doi:10.7287/peerj.preprints.3190v2> and some prespecified variables (e.g. start of a month).
Author: Nahyun Kim [cre, aut],
Hyemin Um [aut],
Eunjo Lee [aut],
NCSOFT Corporation [cph]
Maintainer: Nahyun Kim <nhkim1302@ncsoft.com>
Diff between promotionImpact versions 0.1.2 dated 2019-06-05 and 0.1.3 dated 2020-03-31
DESCRIPTION | 10 +- MD5 | 28 ++++---- NAMESPACE | 2 R/promotion_impact.R | 4 - man/compareModels.Rd | 136 +++++++++++++++++++++------------------- man/create.dummy.vars.Rd | 22 +++--- man/create.smooth.vars.Rd | 33 +++++---- man/detectOutliers.Rd | 87 +++++++++++++------------ man/format_time.Rd | 22 +++--- man/promotion.model.Rd | 39 +++++++---- man/promotionImpact.Rd | 151 ++++++++++++++++++++++++--------------------- man/sim.data.Rd | 38 +++++------ man/sim.promotion.Rd | 42 ++++++------ man/sim.promotion.sales.Rd | 46 ++++++------- man/value_fit_plot.Rd | 22 +++--- 15 files changed, 362 insertions(+), 320 deletions(-)
More information about promotionImpact at CRAN
Permanent link
Title: Amazon Web Services Software Development Kit
Description: Interface to Amazon Web Services <https://aws.amazon.com>,
including storage, database, and compute services, such as 'Simple
Storage Service' ('S3'), 'DynamoDB' 'NoSQL' database, and 'Lambda'
functions-as-a-service.
Author: David Kretch [aut, cre],
Adam Banker [aut],
Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>
Diff between paws versions 0.1.6 dated 2020-01-15 and 0.1.7 dated 2020-03-31
DESCRIPTION | 20 - MD5 | 269 +++++++++++------------ NEWS.md |only R/paws.R | 385 ++++++++++++++++----------------- man/acm.Rd | 2 man/acmpca.Rd | 2 man/apigateway.Rd | 2 man/apigatewaymanagementapi.Rd | 2 man/apigatewayv2.Rd | 2 man/applicationautoscaling.Rd | 2 man/applicationinsights.Rd | 2 man/appmesh.Rd | 2 man/athena.Rd | 2 man/autoscaling.Rd | 2 man/autoscalingplans.Rd | 2 man/backup.Rd | 2 man/batch.Rd | 2 man/budgets.Rd | 2 man/clouddirectory.Rd | 2 man/cloudformation.Rd | 2 man/cloudfront.Rd | 2 man/cloudhsm.Rd | 2 man/cloudhsmv2.Rd | 2 man/cloudsearch.Rd | 2 man/cloudsearchdomain.Rd | 2 man/cloudtrail.Rd | 2 man/cloudwatch.Rd | 2 man/cloudwatchevents.Rd | 2 man/cloudwatchlogs.Rd | 2 man/cognitoidentity.Rd | 2 man/cognitoidentityprovider.Rd | 2 man/cognitosync.Rd | 2 man/comprehend.Rd | 2 man/comprehendmedical.Rd | 2 man/configservice.Rd | 2 man/connect.Rd | 2 man/costandusagereportservice.Rd | 2 man/costexplorer.Rd | 2 man/datapipeline.Rd | 2 man/dax.Rd | 2 man/directconnect.Rd | 2 man/directoryservice.Rd | 2 man/dlm.Rd | 2 man/docdb.Rd | 2 man/dynamodb.Rd | 2 man/dynamodbstreams.Rd | 2 man/ec2.Rd | 2 man/ec2instanceconnect.Rd | 2 man/ecr.Rd | 2 man/ecs.Rd | 2 man/efs.Rd | 2 man/eks.Rd | 2 man/elasticache.Rd | 2 man/elasticbeanstalk.Rd | 2 man/elasticsearchservice.Rd | 2 man/elb.Rd | 2 man/elbv2.Rd | 2 man/emr.Rd | 2 man/eventbridge.Rd | 2 man/firehose.Rd | 2 man/fms.Rd | 2 man/fsx.Rd | 2 man/glacier.Rd | 2 man/globalaccelerator.Rd | 110 ++++----- man/glue.Rd | 2 man/guardduty.Rd | 2 man/health.Rd | 2 man/iam.Rd | 2 man/inspector.Rd | 2 man/kafka.Rd | 2 man/kinesis.Rd | 2 man/kinesisanalytics.Rd | 2 man/kinesisanalyticsv2.Rd | 2 man/kms.Rd | 2 man/lambda.Rd | 2 man/lexmodelbuildingservice.Rd | 2 man/lexruntimeservice.Rd | 2 man/licensemanager.Rd | 2 man/lightsail.Rd | 2 man/machinelearning.Rd | 2 man/macie.Rd | 2 man/marketplacecommerceanalytics.Rd | 2 man/marketplaceentitlementservice.Rd | 2 man/marketplacemetering.Rd | 2 man/mq.Rd | 2 man/mturk.Rd | 2 man/neptune.Rd | 2 man/opsworks.Rd | 2 man/opsworkscm.Rd | 2 man/organizations.Rd | 2 man/personalize.Rd | 2 man/personalizeevents.Rd | 2 man/personalizeruntime.Rd | 2 man/pi.Rd | 2 man/pinpoint.Rd | 2 man/pinpointemail.Rd | 2 man/pinpointsmsvoice.Rd | 2 man/polly.Rd | 2 man/pricing.Rd | 2 man/quicksight.Rd | 2 man/ram.Rd | 2 man/rds.Rd | 2 man/rdsdataservice.Rd | 2 man/redshift.Rd | 2 man/rekognition.Rd | 2 man/resourcegroups.Rd | 2 man/resourcegroupstaggingapi.Rd | 2 man/route53.Rd | 2 man/route53domains.Rd | 2 man/route53resolver.Rd | 2 man/s3.Rd | 2 man/s3control.Rd | 2 man/sagemaker.Rd | 2 man/sagemakerruntime.Rd | 2 man/secretsmanager.Rd | 2 man/securityhub.Rd | 2 man/serverlessapplicationrepository.Rd | 2 man/servicecatalog.Rd | 2 man/servicediscovery.Rd | 2 man/servicequotas.Rd | 2 man/ses.Rd | 2 man/sfn.Rd | 2 man/shield.Rd | 2 man/simpledb.Rd | 2 man/sns.Rd | 2 man/sqs.Rd | 2 man/ssm.Rd | 2 man/storagegateway.Rd | 2 man/sts.Rd | 4 man/support.Rd | 2 man/swf.Rd | 2 man/textract.Rd | 2 man/transcribeservice.Rd | 2 man/translate.Rd | 2 man/waf.Rd | 2 man/wafregional.Rd | 2 136 files changed, 524 insertions(+), 524 deletions(-)
Title: Comfortable Search for R Packages on CRAN Directly from the R
Console
Description: Search for R packages on CRAN directly from the R console, based on the packages' titles, short and long descriptions, or other fields. Combine multiple keywords with logical operators ('and', 'or'), view detailed information on any package and keep track of the latest package contributions to CRAN.
Author: Joachim Zuckarelli [aut, cre] (<https://orcid.org/0000-0002-9280-3016>)
Maintainer: Joachim Zuckarelli <joachim@zuckarelli.de>
Diff between packagefinder versions 0.2.0 dated 2020-03-16 and 0.2.1 dated 2020-03-31
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 9 +++++++++ R/packagefinder.r | 19 +++++++++++-------- README.md | 12 ++---------- man/findPackage.Rd | 5 +++-- 6 files changed, 33 insertions(+), 28 deletions(-)
Title: Mixtures of Exponential-Distance Models with Covariates
Description: Implements a model-based clustering method for categorical life-course sequences relying on mixtures of exponential-distance models introduced by Murphy et al. (2019) <arXiv:1908.07963>. A range of flexible precision parameter settings corresponding to weighted generalisations of the Hamming distance metric are considered, along with the potential inclusion of a noise component. Gating covariates can be supplied in order to relate sequences to baseline characteristics. Sampling weights are also accommodated. The models are fitted using the EM algorithm and tools for visualising the results are also provided.
Author: Keefe Murphy [aut, cre] (<https://orcid.org/0000-0002-7709-3159>),
Thomas Brendan Murphy [ctb] (<https://orcid.org/0000-0002-5668-7046>),
Raffaella Piccarreta [ctb],
Isobel Claire Gormley [ctb]
Maintainer: Keefe Murphy <keefe.murphy@ucd.ie>
Diff between MEDseq versions 1.0.1 dated 2019-12-10 and 1.1.0 dated 2020-03-31
DESCRIPTION | 18 +- MD5 | 51 +++--- NAMESPACE | 4 R/Functions.R | 343 ++++++++++++++++++++++++++++++++------------ R/Hidden_Functions.R | 45 +++-- R/MEDseq.R | 12 - R/data.R | 2 README.md | 6 build/vignette.rds |binary inst/NEWS.md | 17 ++ inst/doc/MEDseq.R | 14 + inst/doc/MEDseq.Rmd | 24 ++- inst/doc/MEDseq.html | 62 +++---- man/MEDseq-package.Rd | 186 ++++++++++++----------- man/MEDseq_compare.Rd | 22 +- man/MEDseq_control.Rd | 15 + man/MEDseq_fit.Rd | 18 +- man/MEDseq_meantime.Rd | 89 +++++------ man/MEDseq_news.Rd | 34 ++-- man/MEDseq_stderr.Rd |only man/biofam.Rd | 6 man/dbs.Rd | 1 man/get_MEDseq_results.Rd | 5 man/mvad.Rd | 4 man/plot.MEDseq.Rd | 30 +-- vignettes/MEDseq.Rmd | 24 ++- vignettes/MVAD_Clusters.png |only vignettes/MVAD_Mean.png |only 28 files changed, 631 insertions(+), 401 deletions(-)
Title: A Class of Mixture Models for Ordinal Data
Description: For ordinal rating data, estimate and test models within the family of
CUB models and their extensions (where CUB stands for Combination of a
discrete Uniform and a shifted Binomial distributions). Simulation routines, plotting facilities
and fitting measures are also provided.
Author: Maria Iannario <maria.iannario@unina.it>, Domenico Piccolo
<domenico.piccolo@unina.it>, Rosaria Simone <rosaria.simone@unina.it>
Maintainer: Rosaria Simone <rosaria.simone@unina.it>
Diff between CUB versions 1.1.3 dated 2018-11-27 and 1.1.4 dated 2020-03-31
DESCRIPTION | 6 MD5 | 274 ++++++++++----------- R/CUB.R | 384 +++++++++++++---------------- R/CUBE.R | 287 ++++++++++------------ R/CUB_package.R | 102 +++---- R/GEM.R | 525 ++++++++++++++++++----------------------- R/IHG.R | 182 ++++++-------- R/cub00.R | 21 - R/cub0q.R | 36 -- R/cube000.R | 28 -- R/cubecsi.R | 36 -- R/loglikCUB.R | 11 R/varmatCUBE.R | 3 build/vignette.rds |binary inst/doc/CUBvignette-knitr.R | 110 ++++---- inst/doc/CUBvignette-knitr.pdf |binary man/BIC.GEM.Rd | 46 +-- man/CUB.Rd | 159 ++++-------- man/CUBE.Rd | 147 ++++------- man/CUB_package.Rd | 122 ++++----- man/CUSH.Rd | 90 +++---- man/GEM.Rd | 328 +++++++++++-------------- man/Hadprod.Rd | 56 ++-- man/IHG.Rd | 121 +++------ man/Q2gecub.Rd | 36 +- man/Qdue.Rd | 56 ++-- man/Quno.Rd | 50 +-- man/Qunogecub.Rd | 40 +-- man/auxmat.Rd | 70 ++--- man/betabinomial.Rd | 118 ++++----- man/betabinomialcsi.Rd | 104 ++++---- man/betar.Rd | 74 ++--- man/bitcsi.Rd | 74 ++--- man/bitgama.Rd | 78 +++--- man/chi2cub.Rd | 100 +++---- man/chi2cub1cov.Rd | 72 ++--- man/chi2cub2cov.Rd | 72 ++--- man/coef.GEM.Rd | 52 ++-- man/cormat.Rd | 48 +-- man/cub00.Rd | 76 ++--- man/cub0q.Rd | 110 ++------ man/cube000.Rd | 101 ++----- man/cubecov.Rd | 80 +++--- man/cubecsi.Rd | 111 ++------ man/cubevisual.Rd | 76 ++--- man/cubp0.Rd | 68 ++--- man/cubpq.Rd | 80 +++--- man/cubshe.Rd | 72 ++--- man/cubshevisual.Rd | 84 +++--- man/cubvisual.Rd | 72 ++--- man/cush00.Rd | 44 +-- man/cushcov.Rd | 50 +-- man/deltaprob.Rd | 46 +-- man/dissim.Rd | 52 ++-- man/effe01.Rd | 48 +-- man/effe10.Rd | 50 +-- man/effecube.Rd | 56 ++-- man/effecubecsi.Rd | 46 +-- man/effecush.Rd | 54 ++-- man/effeihg.Rd | 46 +-- man/effeihgcov.Rd | 54 ++-- man/ellecub.Rd | 84 +++--- man/ellegecub.Rd | 58 ++-- man/expcub00.Rd | 64 ++-- man/expcube.Rd | 74 ++--- man/fitted.GEM.Rd | 56 ++-- man/gecubpqs.Rd | 86 +++--- man/gini.Rd | 46 +-- man/ihg00.Rd | 52 ++-- man/ihgcov.Rd | 58 ++-- man/inibest.Rd | 78 +++--- man/inibestcube.Rd | 62 ++-- man/inibestcubecov.Rd | 106 ++++---- man/inibestcubecsi.Rd | 108 ++++---- man/inibestgama.Rd | 84 +++--- man/inigrid.Rd | 78 +++--- man/iniihg.Rd | 70 ++--- man/kkk.Rd | 38 +- man/laakso.Rd | 54 ++-- man/logLik.GEM.Rd | 48 +-- man/logis.Rd | 56 ++-- man/loglikCUB.Rd | 205 +++++++--------- man/loglikCUSH.Rd | 102 +++---- man/loglikcub00.Rd | 44 +-- man/loglikcub0q.Rd | 50 +-- man/loglikcube.Rd | 128 ++++----- man/loglikcubecov.Rd | 66 ++--- man/loglikcubecsi.Rd | 60 ++-- man/loglikcuben.Rd | 94 +++---- man/loglikcubp0.Rd | 50 +-- man/loglikcubpq.Rd | 56 ++-- man/loglikcubshe.Rd | 52 ++-- man/loglikcush00.Rd | 50 +-- man/loglikcushcov.Rd | 50 +-- man/loglikihg.Rd | 94 +++---- man/loglikihgcov.Rd | 52 ++-- man/logscore.Rd | 100 +++---- man/makeplot.Rd | 56 ++-- man/multicub.Rd | 92 +++---- man/multicube.Rd | 86 +++--- man/parnames.Rd | 48 +-- man/plotloglikihg.Rd | 50 +-- man/print.GEM.Rd | 42 +-- man/probbit.Rd | 60 ++-- man/probcub00.Rd | 74 ++--- man/probcub0q.Rd | 110 ++++---- man/probcube.Rd | 80 +++--- man/probcubp0.Rd | 106 ++++---- man/probcubpq.Rd | 112 ++++---- man/probcubshe1.Rd | 100 +++---- man/probcubshe2.Rd | 104 ++++---- man/probcubshe3.Rd | 110 ++++---- man/probcush.Rd | 74 ++--- man/probgecub.Rd | 84 +++--- man/probihg.Rd | 62 ++-- man/probihgcovn.Rd | 82 +++--- man/relgoods.Rd | 212 ++++++++-------- man/simcub.Rd | 64 ++-- man/simcube.Rd | 72 ++--- man/simcubshe.Rd | 78 +++--- man/simcush.Rd | 66 ++--- man/simihg.Rd | 58 ++-- man/summary.GEM.Rd | 60 ++-- man/univer.Rd | 102 ++++--- man/varcovcub00.Rd | 80 +++--- man/varcovcub0q.Rd | 84 +++--- man/varcovcubecov.Rd | 82 +++--- man/varcovcubeexp.Rd | 70 ++--- man/varcovcubeobs.Rd | 70 ++--- man/varcovcubp0.Rd | 70 ++--- man/varcovcubpq.Rd | 76 ++--- man/varcovcubshe.Rd | 72 ++--- man/varcovgecub.Rd | 78 +++--- man/varcub00.Rd | 64 ++-- man/varcube.Rd | 72 ++--- man/varmatCUB.Rd | 190 +++++++------- man/varmatCUBE.Rd | 138 +++++----- man/vcov.GEM.Rd | 48 +-- 138 files changed, 5553 insertions(+), 6092 deletions(-)
Title: Spatially Balanced Sampling
Description: Selection of spatially balanced samples. In particular, the implemented sampling designs allow to select probability samples well spread over the population of interest, in any dimension and using any distance function (e.g. Euclidean distance, Manhattan distance). For more details, Benedetti R and Piersimoni F (2017) <doi:10.1002/bimj.201600194> and Benedetti R and Piersimoni F (2017) <arXiv:1710.09116>. The implementation has been done in C++ through the use of 'Rcpp' and 'RcppArmadillo'.
Author: Francesco Pantalone [aut, cre],
Roberto Benedetti [aut],
Federica Piersimoni [aut]
Maintainer: Francesco Pantalone <pantalone.fra@gmail.com>
Diff between Spbsampling versions 1.3.2 dated 2020-03-04 and 1.3.3 dated 2020-03-31
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/RcppExports.R | 8 ++++---- man/sbi.Rd | 4 ++-- man/swd.Rd | 4 ++-- src/sbi.cpp | 4 ++-- src/swd.cpp | 4 ++-- 8 files changed, 26 insertions(+), 22 deletions(-)
Title: Extract, Analyze and Visualize Signatures for Genomic Variations
Description: Genomic alterations including single nucleotide substitution,
copy number alteration, etc. are the major force for cancer
initialization and development. Due to the specificity of molecular
lesions caused by genomic alterations, we can generate characteristic
alteration spectra, called 'signature' (Alexandrov, Ludmil B., et al. (2020) <DOI:10.1038/s41586-020-1943-3>
& Macintyre, Geoff, et al. (2018) <DOI:10.1038/s41588-018-0179-8>).
This package helps users to extract, analyze and visualize signatures from genomic alteration records,
thus providing new insight into cancer study.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Xue-Song Liu [aut, ctb] (<https://orcid.org/0000-0002-7736-0077>),
Geoffrey Macintyre [ctb],
Anand Mayakonda [ctb]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between sigminer versions 0.1.11 dated 2019-05-07 and 1.0.0 dated 2020-03-31
sigminer-0.1.11/sigminer/R/cnv_helper.R |only sigminer-0.1.11/sigminer/R/draw_series.R |only sigminer-0.1.11/sigminer/R/get_series.R |only sigminer-0.1.11/sigminer/R/prepare_series.R |only sigminer-0.1.11/sigminer/R/read_series.R |only sigminer-0.1.11/sigminer/R/signature_series.R |only sigminer-0.1.11/sigminer/R/test.R |only sigminer-0.1.11/sigminer/build/partial.rdb |only sigminer-0.1.11/sigminer/inst/doc/sigminer.R |only sigminer-0.1.11/sigminer/inst/extdata/blood_normal.segtab.txt |only sigminer-0.1.11/sigminer/inst/extdata/example_cn_list.RData |only sigminer-0.1.11/sigminer/inst/extdata/solid_tumor.segtab.txt |only sigminer-0.1.11/sigminer/inst/extdata/toy_cn_components.RData |only sigminer-0.1.11/sigminer/inst/extdata/toy_cn_features.RData |only sigminer-0.1.11/sigminer/inst/extdata/toy_copynumber_prepare.RData |only sigminer-0.1.11/sigminer/inst/extdata/toy_copynumber_signature.RData |only sigminer-0.1.11/sigminer/inst/test |only sigminer-0.1.11/sigminer/man/GenomicVariation-class.Rd |only sigminer-0.1.11/sigminer/man/draw_cn_components.Rd |only sigminer-0.1.11/sigminer/man/draw_cn_distribution.Rd |only sigminer-0.1.11/sigminer/man/draw_cn_features.Rd |only sigminer-0.1.11/sigminer/man/draw_sig_activity.Rd |only sigminer-0.1.11/sigminer/man/draw_sig_corrplot.Rd |only sigminer-0.1.11/sigminer/man/draw_sig_profile.Rd |only sigminer-0.1.11/sigminer/man/draw_subtypes_comparison.Rd |only sigminer-0.1.11/sigminer/man/get_ArmLocation.Rd |only sigminer-0.1.11/sigminer/man/get_LengthFraction.Rd |only sigminer-0.1.11/sigminer/man/get_cnlist.Rd |only sigminer-0.1.11/sigminer/man/get_cnsummary_sample.Rd |only sigminer-0.1.11/sigminer/man/get_components.Rd |only sigminer-0.1.11/sigminer/man/get_features.Rd |only sigminer-0.1.11/sigminer/man/get_matrix.Rd |only sigminer-0.1.11/sigminer/man/prepare_copynumber.Rd |only sigminer-0.1.11/sigminer/man/prepare_maf.Rd |only sigminer-0.1.11/sigminer/man/read_variation.Rd |only sigminer-0.1.11/sigminer/man/sig_assign_samples.Rd |only sigminer-0.1.11/sigminer/man/sig_get_activity.Rd |only sigminer-0.1.11/sigminer/man/sig_get_correlation.Rd |only sigminer-0.1.11/sigminer/man/sig_get_similarity.Rd |only sigminer-0.1.11/sigminer/man/sig_prepare.Rd |only sigminer-0.1.11/sigminer/man/sig_summarize_subtypes.Rd |only sigminer-0.1.11/sigminer/man/test_run_components.Rd |only sigminer-0.1.11/sigminer/tests |only sigminer-1.0.0/sigminer/DESCRIPTION | 67 - sigminer-1.0.0/sigminer/LICENSE | 4 sigminer-1.0.0/sigminer/MD5 | 215 ++-- sigminer-1.0.0/sigminer/NAMESPACE | 159 ++- sigminer-1.0.0/sigminer/NEWS.md | 83 - sigminer-1.0.0/sigminer/R/add_h_arrow.R |only sigminer-1.0.0/sigminer/R/add_labels.R |only sigminer-1.0.0/sigminer/R/assert.R |only sigminer-1.0.0/sigminer/R/bayesianNMF.R |only sigminer-1.0.0/sigminer/R/class.R | 272 ++--- sigminer-1.0.0/sigminer/R/data.R | 103 +- sigminer-1.0.0/sigminer/R/find_enriched_signature.R |only sigminer-1.0.0/sigminer/R/get.R |only sigminer-1.0.0/sigminer/R/get_adj_p.R |only sigminer-1.0.0/sigminer/R/get_bayesian_result.R |only sigminer-1.0.0/sigminer/R/get_cn_ploidy.R |only sigminer-1.0.0/sigminer/R/get_genome_annotation.R |only sigminer-1.0.0/sigminer/R/get_group_comparison.R |only sigminer-1.0.0/sigminer/R/get_groups.R |only sigminer-1.0.0/sigminer/R/get_sig_exposure.R |only sigminer-1.0.0/sigminer/R/get_sig_feature_association.R |only sigminer-1.0.0/sigminer/R/get_sig_optimal_exposure.R |only sigminer-1.0.0/sigminer/R/get_sig_similarity.R |only sigminer-1.0.0/sigminer/R/get_tidy_association.R |only sigminer-1.0.0/sigminer/R/get_tidy_parameter.R |only sigminer-1.0.0/sigminer/R/handle_hyper_mutation.R |only sigminer-1.0.0/sigminer/R/hello.R | 55 - sigminer-1.0.0/sigminer/R/helper_calc_sum_of_events.R |only sigminer-1.0.0/sigminer/R/helper_create_colormap.R |only sigminer-1.0.0/sigminer/R/helper_derive_cn_features.R |only sigminer-1.0.0/sigminer/R/helper_fit_cn_components.R |only sigminer-1.0.0/sigminer/R/helper_join_segments.R |only sigminer-1.0.0/sigminer/R/helper_normalize_by_feature.R |only sigminer-1.0.0/sigminer/R/helper_scale_nmf_matrix.R |only sigminer-1.0.0/sigminer/R/helper_sort_signature.R |only sigminer-1.0.0/sigminer/R/read_copynumber.R |only sigminer-1.0.0/sigminer/R/read_maf.R |only sigminer-1.0.0/sigminer/R/scoring.R |only sigminer-1.0.0/sigminer/R/show_catalogue.R |only sigminer-1.0.0/sigminer/R/show_cn_circos.R |only sigminer-1.0.0/sigminer/R/show_cn_components.R |only sigminer-1.0.0/sigminer/R/show_cn_distribution.R |only sigminer-1.0.0/sigminer/R/show_cn_features.R |only sigminer-1.0.0/sigminer/R/show_cn_group_profile.R |only sigminer-1.0.0/sigminer/R/show_cn_profile.R |only sigminer-1.0.0/sigminer/R/show_cosmic_signatures.R |only sigminer-1.0.0/sigminer/R/show_group_comparison.R |only sigminer-1.0.0/sigminer/R/show_group_mapping.R |only sigminer-1.0.0/sigminer/R/show_sig_consensusmap.R |only sigminer-1.0.0/sigminer/R/show_sig_exposure.R |only sigminer-1.0.0/sigminer/R/show_sig_feature_corrplot.R |only sigminer-1.0.0/sigminer/R/show_sig_number_survey.R |only sigminer-1.0.0/sigminer/R/show_sig_number_survey2.R |only sigminer-1.0.0/sigminer/R/show_sig_profile.R |only sigminer-1.0.0/sigminer/R/sig_auto_extract.R |only sigminer-1.0.0/sigminer/R/sig_convert.R |only sigminer-1.0.0/sigminer/R/sig_estimate.R |only sigminer-1.0.0/sigminer/R/sig_extract.R |only sigminer-1.0.0/sigminer/R/sig_fit.R |only sigminer-1.0.0/sigminer/R/sig_tally.R |only sigminer-1.0.0/sigminer/R/sigminer.R | 77 - 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Title: Full Pattern Summation of X-Ray Powder Diffraction Data
Description: Full pattern summation of X-ray powder diffraction data as
described in Chipera and Bish (2002) <doi:10.1107/S0021889802017405>.
Derives quantitative estimates of crystalline and amorphous phase
concentrations in complex mixtures.
Author: Benjamin Butler [aut, cre],
Stephen Hillier [aut],
Dylan Beaudette [ctb],
Dennis Eberl [ctb]
Maintainer: Benjamin Butler <benjamin.butler@hutton.ac.uk>
Diff between powdR versions 1.1.0 dated 2020-01-10 and 1.2.0 dated 2020-03-31
powdR-1.1.0/powdR/inst/shiny/Global.R |only powdR-1.2.0/powdR/DESCRIPTION | 14 powdR-1.2.0/powdR/MD5 | 80 powdR-1.2.0/powdR/NEWS.md | 10 powdR-1.2.0/powdR/R/afps.R | 234 +- powdR-1.2.0/powdR/R/alignment.R | 50 powdR-1.2.0/powdR/R/create_library.R | 15 powdR-1.2.0/powdR/R/data.R | 8 powdR-1.2.0/powdR/R/fps.R | 224 +- powdR-1.2.0/powdR/R/fullpat_shift.R |only powdR-1.2.0/powdR/R/harmonise.R | 14 powdR-1.2.0/powdR/R/plotting.R | 5 powdR-1.2.0/powdR/R/run_powdR.R | 9 powdR-1.2.0/powdR/R/shift.R | 286 +-- powdR-1.2.0/powdR/R/summarise_mineralogy.R | 2 powdR-1.2.0/powdR/README.md | 28 powdR-1.2.0/powdR/build/vignette.rds |binary powdR-1.2.0/powdR/inst/doc/powdR_vignette.Rmd | 12 powdR-1.2.0/powdR/inst/doc/powdR_vignette.html | 111 - powdR-1.2.0/powdR/inst/shiny/server.R | 1793 +++++++-------------- powdR-1.2.0/powdR/inst/shiny/ui.R | 1031 ++++-------- powdR-1.2.0/powdR/man/afps.Rd | 2 powdR-1.2.0/powdR/man/afps.powdRlib.Rd | 36 powdR-1.2.0/powdR/man/bkg.Rd | 2 powdR-1.2.0/powdR/man/figures/README-example-1.png |binary powdR-1.2.0/powdR/man/fps.Rd | 2 powdR-1.2.0/powdR/man/fps.powdRlib.Rd | 38 powdR-1.2.0/powdR/man/minerals.Rd | 2 powdR-1.2.0/powdR/man/minerals_phases.Rd | 2 powdR-1.2.0/powdR/man/minerals_xrd.Rd | 2 powdR-1.2.0/powdR/man/plot.powdRafps.Rd | 3 powdR-1.2.0/powdR/man/plot.powdRbkg.Rd | 2 powdR-1.2.0/powdR/man/plot.powdRfps.Rd | 3 powdR-1.2.0/powdR/man/plot.powdRlib.Rd | 5 powdR-1.2.0/powdR/man/powdR.Rd | 2 powdR-1.2.0/powdR/man/powdRlib.Rd | 19 powdR-1.2.0/powdR/man/rockjock.Rd | 5 powdR-1.2.0/powdR/man/rockjock_mixtures.Rd | 5 powdR-1.2.0/powdR/man/soils.Rd | 2 powdR-1.2.0/powdR/man/subset.powdRlib.Rd | 2 powdR-1.2.0/powdR/man/summarise_mineralogy.Rd | 4 powdR-1.2.0/powdR/vignettes/powdR_vignette.Rmd | 12 42 files changed, 1760 insertions(+), 2316 deletions(-)
Title: SPRE Statistics for Exploring Heterogeneity in Meta-Analysis
Description: An implementation of SPRE (standardised predicted random-effects)
statistics in R to explore heterogeneity in genetic association meta-
analyses, as described by Magosi et al. (2019)
<doi:10.1093/bioinformatics/btz590>. SPRE statistics are precision
weighted residuals that indicate the direction and extent with which
individual study-effects in a meta-analysis deviate from the average
genetic effect. Overly influential positive outliers have the potential
to inflate average genetic effects in a meta-analysis whilst negative
outliers might lower or change the direction of effect. See the 'getspres'
website for documentation and examples
<https://magosil86.github.io/getspres/>.
Author: Lerato E Magosi [aut],
Jemma C Hopewell [aut],
Martin Farrall [aut],
Lerato E Magosi [cre]
Maintainer: Lerato E Magosi <magosil86@gmail.com>
Diff between getspres versions 0.1.0 dated 2019-08-28 and 0.1.1 dated 2020-03-31
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 8 ++++++++ R/compute_spre_statistics.R | 8 ++++---- R/driver_generate_forestplot_incl_spres.R | 2 +- R/generate_forestplot_incl_spres.R | 10 +++++----- man/plotspres.Rd | 2 +- 7 files changed, 29 insertions(+), 21 deletions(-)
Title: Cross-Platform File System Operations Based on 'libuv'
Description: A cross-platform interface to file system operations, built on
top of the 'libuv' C library.
Author: Jim Hester [aut, cre],
Hadley Wickham [aut],
libuv project contributors [cph] (libuv library),
Joyent, Inc. and other Node contributors [cph] (libuv library),
RStudio [cph, fnd]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between fs versions 1.3.2 dated 2020-03-05 and 1.4.0 dated 2020-03-31
fs-1.3.2/fs/R/RcppExports.R |only fs-1.3.2/fs/src/RcppExports.cpp |only fs-1.3.2/fs/src/libuv/Dockerfile |only fs-1.4.0/fs/DESCRIPTION | 9 -- fs-1.4.0/fs/MD5 | 81 ++++++++---------- fs-1.4.0/fs/NAMESPACE | 4 fs-1.4.0/fs/NEWS.md | 10 ++ fs-1.4.0/fs/R/access.R | 2 fs-1.4.0/fs/R/copy.R | 2 fs-1.4.0/fs/R/create.R | 12 +- fs-1.4.0/fs/R/delete.R | 8 - fs-1.4.0/fs/R/file.R | 16 +-- fs-1.4.0/fs/R/fs_bytes.R | 5 + fs-1.4.0/fs/R/fs_path.R | 7 + fs-1.4.0/fs/R/fs_perms.R | 11 +- fs-1.4.0/fs/R/id.R | 4 fs-1.4.0/fs/R/link.R | 2 fs-1.4.0/fs/R/list.R | 2 fs-1.4.0/fs/R/package.R | 3 fs-1.4.0/fs/R/path.R | 47 +++++++--- fs-1.4.0/fs/R/stat.R | 2 fs-1.4.0/fs/inst/WORDLIST | 1 fs-1.4.0/fs/src/CollectorList.h | 15 ++- fs-1.4.0/fs/src/Makevars | 4 fs-1.4.0/fs/src/Makevars.win | 2 fs-1.4.0/fs/src/dir.cc | 61 ++++++++----- fs-1.4.0/fs/src/error.h | 3 fs-1.4.0/fs/src/file.cc | 130 +++++++++++++++++++---------- fs-1.4.0/fs/src/fs.cc | 8 + fs-1.4.0/fs/src/getmode.cc |only fs-1.4.0/fs/src/getmode.h | 18 ++-- fs-1.4.0/fs/src/id.cc | 119 ++++++++++++++++++++------ fs-1.4.0/fs/src/init.cc |only fs-1.4.0/fs/src/link.cc | 24 +++-- fs-1.4.0/fs/src/path.cc | 67 ++++++++++---- fs-1.4.0/fs/src/unix/getmode.cc | 11 +- fs-1.4.0/fs/src/utils.cc | 6 - fs-1.4.0/fs/src/utils.h | 19 +++- fs-1.4.0/fs/src/windows/getmode.cc | 8 - fs-1.4.0/fs/tests/testthat/test-file.R | 4 fs-1.4.0/fs/tests/testthat/test-fs_bytes.R | 7 + fs-1.4.0/fs/tests/testthat/test-fs_path.R | 5 + fs-1.4.0/fs/tests/testthat/test-fs_perms.R | 4 fs-1.4.0/fs/tests/testthat/test-path.R | 28 ++++-- 44 files changed, 517 insertions(+), 254 deletions(-)
Title: Forecasting Functions for Time Series and Linear Models
Description: Methods and tools for displaying and analysing
univariate time series forecasts including exponential smoothing
via state space models and automatic ARIMA modelling.
Author: Rob Hyndman [aut, cre, cph] (<https://orcid.org/0000-0002-2140-5352>),
George Athanasopoulos [aut],
Christoph Bergmeir [aut] (<https://orcid.org/0000-0002-3665-9021>),
Gabriel Caceres [aut],
Leanne Chhay [aut],
Mitchell O'Hara-Wild [aut] (<https://orcid.org/0000-0001-6729-7695>),
Fotios Petropoulos [aut] (<https://orcid.org/0000-0003-3039-4955>),
Slava Razbash [aut],
Earo Wang [aut],
Farah Yasmeen [aut] (<https://orcid.org/0000-0002-1479-5401>),
R Core Team [ctb, cph],
Ross Ihaka [ctb, cph],
Daniel Reid [ctb],
David Shaub [ctb],
Yuan Tang [ctb] (<https://orcid.org/0000-0001-5243-233X>),
Zhenyu Zhou [ctb]
Maintainer: Rob Hyndman <Rob.Hyndman@monash.edu>
Diff between forecast versions 8.11 dated 2020-02-09 and 8.12 dated 2020-03-31
DESCRIPTION | 8 +-- MD5 | 86 ++++++++++++++++----------------- NEWS.md | 9 ++- R/HoltWintersNew.R | 6 +- R/arima.R | 4 - R/armaroots.R | 20 +++---- R/bats.R | 25 +++++---- R/calendar.R | 18 +++--- R/clean.R | 2 R/errors.R | 64 +++++++++++++----------- R/ets.R | 12 ++-- R/etsforecast.R | 2 R/forecastTBATS.R | 6 +- R/ggplot.R | 2 R/msts.R | 2 R/simulate.R | 6 +- R/theta.R | 26 +++++----- README.md | 2 build/vignette.rds |binary inst/doc/JSS2008.pdf |binary man/accuracy.Rd | 22 ++++---- man/bats.Rd | 3 - man/bizdays.Rd | 5 - man/easter.Rd | 3 - man/gas.Rd | 4 + man/geom_forecast.Rd | 6 +- man/gold.Rd | 4 + man/msts.Rd | 2 man/plot.Arima.Rd | 5 - man/taylor.Rd | 4 + man/thetaf.Rd | 1 man/wineind.Rd | 4 + man/woolyrnq.Rd | 4 + tests/testthat/test-bats.R | 2 tests/testthat/test-clean.R | 4 - tests/testthat/test-forecast2.R | 6 +- tests/testthat/test-ggplot.R | 4 - tests/testthat/test-graph.R | 2 tests/testthat/test-modelAR.R | 103 ++++++++++++++++++++-------------------- tests/testthat/test-newarima2.R | 14 ++--- tests/testthat/test-refit.R | 4 - tests/testthat/test-season.R | 26 +++++----- tests/testthat/test-subset.R | 2 tests/testthat/test-thetaf.R | 4 - 44 files changed, 283 insertions(+), 255 deletions(-)
Title: N-Gram Analysis of Biological Sequences
Description: Tools for extraction and analysis of various
n-grams (k-mers) derived from biological sequences (proteins
or nucleic acids). Contains QuiPT (quick permutation test) for fast
feature-filtering of the n-gram data.
Author: Michal Burdukiewicz [cre, aut]
(<https://orcid.org/0000-0001-8926-582X>),
Piotr Sobczyk [aut],
Chris Lauber [aut],
Dominik Rafacz [aut],
Katarzyna Sidorczuk [ctb] (<https://orcid.org/0000-0001-6576-9054>)
Maintainer: Michal Burdukiewicz <michalburdukiewicz@gmail.com>
Diff between biogram versions 1.6.1 dated 2020-01-08 and 1.6.3 dated 2020-03-31
CHANGELOG | 4 ++ DESCRIPTION | 20 ++++++++------ MD5 | 54 ++++++++++++++++++++------------------- NAMESPACE | 3 +- R/biogram.R | 1 R/chi_square.R | 7 ++--- R/create_encoding.R | 2 - R/criterions.R | 36 +++++++++++++------------- R/degenerate.R | 38 +++++++++++++++++++++++++++ R/distr_crit.R | 22 ++++++++++++--- R/indices_and_positions.R | 2 - R/information_gain.R | 11 +++---- R/kl_divergence.R | 7 ++--- R/position_ngrams.R | 4 +- R/table_ngrams.R | 2 - R/test_features.R | 9 +----- R/utilities.R | 18 +++++-------- build/vignette.rds |binary inst/doc/overview.html | 8 ++--- man/aaprop.Rd | 4 ++ man/calc_cs.Rd | 7 ++--- man/calc_ig.Rd | 9 ++---- man/calc_kl.Rd | 7 ++--- man/check_criterion.Rd |only man/degenerate_ngrams.Rd |only man/distr_crit.Rd | 5 ++- man/fast_crosstable.Rd | 13 ++++----- man/human_cleave.Rd | 6 ++-- tests/testthat/test_crosstable.R | 4 +- 29 files changed, 176 insertions(+), 127 deletions(-)
Title: Mixed Effect Model with the Box-Cox Transformation
Description: Inference on the marginal model of the mixed effect model with
the Box-Cox transformation and on the model median differences between
treatment groups for longitudinal randomized clinical trials. These
statistical methods are proposed by Maruo et al. (2017)
<doi:10.1002/sim.7279>.
Author: Kazushi Maruo [aut, cre],
Ryota Ishii [aut],
Yusuke Yamaguchi [ctb],
Masahiko Gosho [ctb]
Maintainer: Kazushi Maruo <kazushi.maruo@gmail.com>
Diff between bcmixed versions 0.1.3 dated 2020-03-02 and 0.1.4 dated 2020-03-31
DESCRIPTION | 8 +++---- MD5 | 24 +++++++++++----------- NAMESPACE | 4 +++ NEWS.md | 2 + R/bcmarg.R | 41 +++++++++++++++++++++++++++++++++++++-- R/bcmixed.R | 4 +-- R/bcmmrm.R | 32 +++++++++++++++++++++++++++--- R/bcreg.R | 9 +++----- R/bct.R | 2 - README.md | 7 ------ man/bcmixed.Rd | 4 +-- man/bcmmrm.Rd | 3 -- man/figures/README-example-1.png |binary 13 files changed, 101 insertions(+), 39 deletions(-)
Title: Data Access Tools for the Soil and Landscape Grid of Australia
Description: Provides access to soil and landscape grid of Australia raster datasets via existing open geospatial consortium web coverage services. See <https://www.csiro.au/soil-and-landscape-grid>.
Author: Lauren O'Brien [aut, cre] (<https://orcid.org/0000-0002-7336-2171>),
Ross Searle [ant] (<https://orcid.org/0000-0003-0256-1496>)
Maintainer: Lauren O'Brien <obrlsoilau@gmail.com>
Diff between slga versions 1.1.0 dated 2019-08-05 and 1.1.1 dated 2020-03-31
DESCRIPTION | 22 ++-- MD5 | 86 ++++++++--------- NEWS.md | 7 + R/aoi_processing.R | 27 ++--- R/data.R | 4 R/raster_processing.R | 6 - R/slga.R | 2 R/url_generate.R | 6 - README.md | 18 ++- build/vignette.rds |binary inst/doc/slga.R | 23 ++-- inst/doc/slga.Rmd | 7 - inst/doc/slga.html | 23 +--- man/aoi_align.Rd | 44 ++++---- man/aoi_convert.Rd | 74 +++++++------- man/aoi_overlaps.Rd | 48 ++++----- man/aoi_tile.Rd | 44 ++++---- man/aoi_transform.Rd | 62 ++++++------ man/bne_surface_clay.Rd | 62 ++++++------ man/check_avail.Rd | 52 +++++----- man/figures/README-dplot-1.png |binary man/get_lscape_data.Rd | 105 ++++++++++----------- man/get_lscape_point.Rd | 107 +++++++++++---------- man/get_slga_data.Rd | 46 ++++----- man/get_soils_data.Rd | 175 ++++++++++++++++++----------------- man/get_soils_point.Rd | 161 ++++++++++++++++---------------- man/get_soils_raster.Rd | 92 +++++++++--------- man/make_circ_mask.Rd | 106 ++++++++++----------- man/make_lscape_url.Rd | 52 +++++----- man/make_point_url.Rd | 50 +++++----- man/make_soils_url.Rd | 72 +++++++------- man/metadata_lscape.Rd | 66 ++++++------- man/metadata_soils.Rd | 98 ++++++++++--------- man/slga-package.Rd | 58 +++++------ man/slga_attribute_info.Rd | 60 ++++++------ man/slga_filenamer.Rd | 60 ++++++------ man/slga_product_info.Rd | 82 ++++++++-------- man/tidy_lscape_data.Rd | 53 +++++----- man/tidy_soils_data.Rd | 42 ++++---- man/validate_aoi.Rd | 46 ++++----- man/validate_poi.Rd | 80 ++++++++-------- tests/testthat/test_aoi_processing.R | 2 tests/testthat/test_url_generator.R | 24 ++-- vignettes/slga.Rmd | 7 - 44 files changed, 1151 insertions(+), 1110 deletions(-)
Title: Iterated Racing for Automatic Algorithm Configuration
Description: Iterated race is an extension of the Iterated F-race method for
the automatic configuration of optimization algorithms, that is,
(offline) tuning their parameters by finding the most appropriate
settings given a set of instances of an optimization problem.
M. López-Ibáñez, J. Dubois-Lacoste, L. Pérez Cáceres, T. Stützle,
and M. Birattari (2016) <doi:10.1016/j.orp.2016.09.002>.
Author: Manuel López-Ibáñez [aut, cre]
(<https://orcid.org/0000-0001-9974-1295>),
Jérémie Dubois-Lacoste [aut],
Leslie Pérez Cáceres [aut],
Thomas Stützle [aut],
Mauro Birattari [aut],
Eric Yuan [ctb],
Prasanna Balaprakash [ctb],
Nguyen Dang [ctb]
Maintainer: Manuel López-Ibáñez <manuel.lopez-ibanez@manchester.ac.uk>
Diff between irace versions 3.4 dated 2020-03-30 and 3.4.1 dated 2020-03-31
irace-3.4.1/irace/DESCRIPTION | 11 irace-3.4.1/irace/MD5 | 30 - irace-3.4.1/irace/NEWS.md |only irace-3.4.1/irace/R/main.R | 4 irace-3.4.1/irace/R/parameterAnalysis.R | 2 irace-3.4.1/irace/R/version.R | 2 irace-3.4.1/irace/README.md | 26 - irace-3.4.1/irace/build/partial.rdb |binary irace-3.4.1/irace/inst/doc/irace-package.pdf |binary irace-3.4.1/irace/src/Makevars | 4 irace-3.4.1/irace/src/Makevars.win | 4 irace-3.4.1/irace/tests/testthat/saved_maxim_bug.rds |binary irace-3.4.1/irace/tests/testthat/saved_maxim_bug2.rds |binary irace-3.4.1/irace/tests/testthat/test-GenericWrapper4AC.R | 5 irace-3.4.1/irace/tests/testthat/test-bugs.R | 66 +-- irace-3.4.1/irace/vignettes/NEWS.txt | 250 +++++++------- irace-3.4/irace/NEWS |only 17 files changed, 210 insertions(+), 194 deletions(-)
Title: Various R Programming Tools
Description: Functions to assist in R programming, including:
- assist in developing, updating, and maintaining R and R packages ('ask', 'checkRVersion',
'getDependencies', 'keywords', 'scat'),
- calculate the logit and inverse logit transformations ('logit', 'inv.logit'),
- test if a value is missing, empty or contains only NA and NULL values ('invalid'),
- manipulate R's .Last function ('addLast'),
- define macros ('defmacro'),
- detect odd and even integers ('odd', 'even'),
- convert strings containing non-ASCII characters (like single quotes) to plain ASCII ('ASCIIfy'),
- perform a binary search ('binsearch'),
- sort strings containing both numeric and character components ('mixedsort'),
- create a factor variable from the quantiles of a continuous variable ('quantcut'),
- enumerate permutations and combinations ('combinations', 'permutation'),
- calculate and convert between fold-change and log-ratio ('foldchange',
'logratio2foldchange', 'foldchange2logratio'),
- calculate probabilities and generate random numbers from Dirichlet distributions
('rdirichlet', 'ddirichlet'),
- apply a function over adjacent subsets of a vector ('running'),
- modify the TCP\_NODELAY ('de-Nagle') flag for socket objects,
- efficient 'rbind' of data frames, even if the column names don't match ('smartbind'),
- generate significance stars from p-values ('stars.pval'),
- convert characters to/from ASCII codes ('asc', 'chr'),
- convert character vector to ASCII representation ('ASCIIfy').
Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley
Maintainer: Gregory R. Warnes <greg@warnes.net>
Diff between gtools versions 3.8.1 dated 2018-06-26 and 3.8.2 dated 2020-03-31
gtools-3.8.1/gtools/R/RSCompat.S |only gtools-3.8.1/gtools/R/newVersionAvailable.R |only gtools-3.8.2/gtools/DESCRIPTION | 11 + gtools-3.8.2/gtools/MD5 | 86 ++++++------- gtools-3.8.2/gtools/NEWS | 5 gtools-3.8.2/gtools/R/combinations.R | 29 ++-- gtools-3.8.2/gtools/R/defmacro.R | 8 - gtools-3.8.2/gtools/R/dirichlet.R | 2 gtools-3.8.2/gtools/R/foldchange.R | 2 gtools-3.8.2/gtools/R/invalid.R | 2 gtools-3.8.2/gtools/R/logit.R | 4 gtools-3.8.2/gtools/R/oddeven.R | 4 gtools-3.8.2/gtools/R/permute.R | 2 gtools-3.8.2/gtools/R/quantcut.R | 12 - gtools-3.8.2/gtools/R/running.R | 2 gtools-3.8.2/gtools/R/scat.R | 3 gtools-3.8.2/gtools/inst |only gtools-3.8.2/gtools/man/ELISA.Rd | 6 gtools-3.8.2/gtools/man/asc.Rd | 2 gtools-3.8.2/gtools/man/ask.Rd | 6 gtools-3.8.2/gtools/man/badDend.Rd | 6 gtools-3.8.2/gtools/man/baseOf.Rd | 2 gtools-3.8.2/gtools/man/checkRVersion.Rd | 2 gtools-3.8.2/gtools/man/combinations.Rd | 2 gtools-3.8.2/gtools/man/defmacro.Rd | 2 gtools-3.8.2/gtools/man/dirichlet.Rd | 5 gtools-3.8.2/gtools/man/foldchange.Rd | 4 gtools-3.8.2/gtools/man/getDependencies.Rd | 162 ++++++++++++------------- gtools-3.8.2/gtools/man/gtools-defunct.Rd | 2 gtools-3.8.2/gtools/man/invalid.Rd | 4 gtools-3.8.2/gtools/man/lastAdd.Rd | 2 gtools-3.8.2/gtools/man/logit.Rd | 12 - gtools-3.8.2/gtools/man/mixedsort.Rd | 4 gtools-3.8.2/gtools/man/na.replace.Rd | 4 gtools-3.8.2/gtools/man/oddeven.Rd | 2 gtools-3.8.2/gtools/man/permute.Rd | 2 gtools-3.8.2/gtools/man/quantcut.Rd | 6 gtools-3.8.2/gtools/man/roman2int.Rd | 2 gtools-3.8.2/gtools/man/running.Rd | 4 gtools-3.8.2/gtools/man/scat.Rd | 4 gtools-3.8.2/gtools/man/setTCPNoDelay.Rd | 4 gtools-3.8.2/gtools/man/split_path.Rd | 4 gtools-3.8.2/gtools/man/unByteCode.Rd | 4 gtools-3.8.2/gtools/tests/test_mixedorder.R | 2 gtools-3.8.2/gtools/tests/test_setTCPNoDelay.R | 7 - 45 files changed, 209 insertions(+), 231 deletions(-)
More information about changepoint.geo at CRAN
Permanent link
Title: Kinetic Evaluation of Chemical Degradation Data
Description: Calculation routines based on the FOCUS Kinetics Report (2006,
2014). Includes a function for conveniently defining differential equation
models, model solution based on eigenvalues if possible or using numerical
solvers. If a C compiler (on windows: 'Rtools') is installed, differential
equation models are solved using automatically generated C functions. Please
note that no warranty is implied for correctness of results or fitness for a
particular purpose.
Author: Johannes Ranke [aut, cre, cph]
(<https://orcid.org/0000-0003-4371-6538>),
Katrin Lindenberger [ctb],
René Lehmann [ctb],
Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Diff between mkin versions 0.9.49.8 dated 2020-01-09 and 0.9.49.9 dated 2020-03-31
DESCRIPTION | 21 - MD5 | 68 +++--- NAMESPACE | 1 NEWS.md | 8 R/lrtest.mkinfit.R | 2 R/mkinds.R | 53 ++-- R/mkinmod.R | 135 ++++++------ R/mmkin.R | 22 +- build/vignette.rds |binary inst/doc/FOCUS_D.R | 14 - inst/doc/FOCUS_D.html | 46 ++-- inst/doc/FOCUS_L.R | 32 +- inst/doc/FOCUS_L.html | 182 ++++++++--------- inst/doc/mkin.R | 2 inst/doc/mkin.html | 14 - inst/doc/twa.html | 15 - man/CAKE_export.Rd | 21 + man/add_err.Rd | 12 - man/confint.mkinfit.Rd | 17 + man/lrtest.mkinfit.Rd | 2 man/mkinds.Rd | 84 ++++++- man/mkinerrplot.Rd | 19 + man/mkinfit.Rd | 33 ++- man/mkinmod.Rd | 9 man/mkinpredict.Rd | 53 +++- man/mkinresplot.Rd | 18 + man/mmkin.Rd | 11 - man/plot.mkinfit.Rd | 51 +++- man/plot.mmkin.Rd | 17 + man/print.mkinds.Rd | 2 man/summary.mkinfit.Rd | 6 man/transform_odeparms.Rd | 16 + tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg | 6 tests/testthat/DFOP_FOCUS_C_messages.txt | 4 tests/testthat/FOCUS_2006_D.csf | 2 35 files changed, 600 insertions(+), 398 deletions(-)
Title: Create Interactive Chart with the JavaScript 'ApexCharts'
Library
Description: Provides an 'htmlwidgets' interface to 'apexcharts.js'.
'Apexcharts' is a modern JavaScript charting library to build interactive charts and visualizations with simple API.
'Apexcharts' examples and documentation are available here: <https://apexcharts.com/>.
Author: Victor Perrier [aut, cre],
Fanny Meyer [aut],
Juned Chhipa [cph] (apexcharts.js library),
Mike Bostock [cph] (d3.format library)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between apexcharter versions 0.1.3 dated 2019-11-27 and 0.1.4 dated 2020-03-31
apexcharter-0.1.3/apexcharter/inst/doc/advanced-configuration.R |only apexcharter-0.1.3/apexcharter/inst/doc/advanced-configuration.Rmd |only apexcharter-0.1.3/apexcharter/inst/doc/advanced-configuration.html |only apexcharter-0.1.3/apexcharter/inst/doc/starting-with-apexcharts.R |only apexcharter-0.1.3/apexcharter/inst/doc/starting-with-apexcharts.Rmd |only apexcharter-0.1.3/apexcharter/inst/doc/starting-with-apexcharts.html |only apexcharter-0.1.3/apexcharter/inst/htmlwidgets/lib/apexcharts-3.10 |only apexcharter-0.1.3/apexcharter/inst/htmlwidgets/lib/apexcharts-3.8 |only apexcharter-0.1.3/apexcharter/tests/testthat/test-parse_df.R |only apexcharter-0.1.3/apexcharter/vignettes/advanced-configuration.Rmd |only apexcharter-0.1.3/apexcharter/vignettes/starting-with-apexcharts.Rmd |only apexcharter-0.1.4/apexcharter/DESCRIPTION | 15 apexcharter-0.1.4/apexcharter/MD5 | 154 ++-- apexcharter-0.1.4/apexcharter/NAMESPACE | 11 apexcharter-0.1.4/apexcharter/NEWS.md | 11 apexcharter-0.1.4/apexcharter/R/apex-options.R | 2 apexcharter-0.1.4/apexcharter/R/apex-utils.R | 24 apexcharter-0.1.4/apexcharter/R/apex.R | 155 +++- apexcharter-0.1.4/apexcharter/R/apexcharter.R | 92 +- apexcharter-0.1.4/apexcharter/R/format.R | 28 apexcharter-0.1.4/apexcharter/R/labs.R | 6 apexcharter-0.1.4/apexcharter/R/onLoad.R |only apexcharter-0.1.4/apexcharter/R/parse-data.R | 49 + apexcharter-0.1.4/apexcharter/R/proxy.R | 2 apexcharter-0.1.4/apexcharter/R/shiny-input.R |only apexcharter-0.1.4/apexcharter/R/utils.R | 34 apexcharter-0.1.4/apexcharter/README.md | 6 apexcharter-0.1.4/apexcharter/build/vignette.rds |binary apexcharter-0.1.4/apexcharter/data/unhcr_popstats_2017.rda |binary apexcharter-0.1.4/apexcharter/data/unhcr_ts.rda |binary apexcharter-0.1.4/apexcharter/inst/doc/apexcharter.R |only apexcharter-0.1.4/apexcharter/inst/doc/apexcharter.Rmd |only apexcharter-0.1.4/apexcharter/inst/doc/apexcharter.html |only apexcharter-0.1.4/apexcharter/inst/doc/labs.html | 348 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apexcharter-0.1.4/apexcharter/inst/htmlwidgets/lib/apexcharts-locales/de.json | 75 +- apexcharter-0.1.4/apexcharter/inst/htmlwidgets/lib/apexcharts-locales/el.json | 75 +- apexcharter-0.1.4/apexcharter/inst/htmlwidgets/lib/apexcharts-locales/en.json | 75 +- apexcharter-0.1.4/apexcharter/inst/htmlwidgets/lib/apexcharts-locales/es.json | 75 +- apexcharter-0.1.4/apexcharter/inst/htmlwidgets/lib/apexcharts-locales/fi.json |only apexcharter-0.1.4/apexcharter/inst/htmlwidgets/lib/apexcharts-locales/fr.json | 75 +- apexcharter-0.1.4/apexcharter/inst/htmlwidgets/lib/apexcharts-locales/hi.json | 75 +- apexcharter-0.1.4/apexcharter/inst/htmlwidgets/lib/apexcharts-locales/hr.json | 75 +- apexcharter-0.1.4/apexcharter/inst/htmlwidgets/lib/apexcharts-locales/hy.json | 75 +- apexcharter-0.1.4/apexcharter/inst/htmlwidgets/lib/apexcharts-locales/id.json | 67 + apexcharter-0.1.4/apexcharter/inst/htmlwidgets/lib/apexcharts-locales/it.json | 75 +- apexcharter-0.1.4/apexcharter/inst/htmlwidgets/lib/apexcharts-locales/ko.json | 75 +- apexcharter-0.1.4/apexcharter/inst/htmlwidgets/lib/apexcharts-locales/nl.json |only apexcharter-0.1.4/apexcharter/inst/htmlwidgets/lib/apexcharts-locales/pt-br.json | 75 +- apexcharter-0.1.4/apexcharter/inst/htmlwidgets/lib/apexcharts-locales/ru.json | 75 +- apexcharter-0.1.4/apexcharter/inst/htmlwidgets/lib/apexcharts-locales/se.json |only apexcharter-0.1.4/apexcharter/inst/htmlwidgets/lib/apexcharts-locales/tr.json | 75 +- apexcharter-0.1.4/apexcharter/inst/htmlwidgets/lib/apexcharts-locales/ua.json | 75 +- apexcharter-0.1.4/apexcharter/man/apex.Rd | 21 apexcharter-0.1.4/apexcharter/man/apexchart.Rd | 8 apexcharter-0.1.4/apexcharter/man/apexcharter-exports.Rd | 24 apexcharter-0.1.4/apexcharter/man/apexcharter-package.Rd | 26 apexcharter-0.1.4/apexcharter/man/ax_chart.Rd | 65 + apexcharter-0.1.4/apexcharter/man/ax_colors.Rd | 2 apexcharter-0.1.4/apexcharter/man/ax_dataLabels.Rd | 2 apexcharter-0.1.4/apexcharter/man/ax_labs.Rd | 6 apexcharter-0.1.4/apexcharter/man/ax_legend.Rd | 6 apexcharter-0.1.4/apexcharter/man/ax_stroke.Rd | 6 apexcharter-0.1.4/apexcharter/man/ax_tooltip.Rd | 2 apexcharter-0.1.4/apexcharter/man/ax_yaxis.Rd | 2 apexcharter-0.1.4/apexcharter/man/config_update.Rd |only apexcharter-0.1.4/apexcharter/man/events_opts.Rd | 2 apexcharter-0.1.4/apexcharter/man/format_date.Rd |only apexcharter-0.1.4/apexcharter/man/run_input_demo.Rd |only apexcharter-0.1.4/apexcharter/man/set_input_click.Rd |only apexcharter-0.1.4/apexcharter/man/set_input_selection.Rd |only apexcharter-0.1.4/apexcharter/man/set_input_zoom.Rd |only apexcharter-0.1.4/apexcharter/man/unhcr_popstats_2017.Rd | 22 apexcharter-0.1.4/apexcharter/man/unhcr_ts.Rd | 18 apexcharter-0.1.4/apexcharter/tests/testthat/test-apex-config.R | 24 apexcharter-0.1.4/apexcharter/tests/testthat/test-apex-utils.R | 65 - apexcharter-0.1.4/apexcharter/tests/testthat/test-apex.R | 45 + apexcharter-0.1.4/apexcharter/tests/testthat/test-apexcharter.R |only apexcharter-0.1.4/apexcharter/tests/testthat/test-labs.R | 2 apexcharter-0.1.4/apexcharter/tests/testthat/test-parse-data.R |only apexcharter-0.1.4/apexcharter/tests/testthat/test-shiny-input.R |only apexcharter-0.1.4/apexcharter/vignettes/apexcharter.Rmd |only apexcharter-0.1.4/apexcharter/vignettes/articles |only apexcharter-0.1.4/apexcharter/vignettes/shiny-integration.Rmd |only apexcharter-0.1.4/apexcharter/vignettes/sync-charts.Rmd |only 98 files changed, 2254 insertions(+), 824 deletions(-)
Title: Landscape Meteorology Tools
Description: Functions to estimate weather variables at any position of a landscape [De Caceres et al. (2018) <doi:10.1016/j.envsoft.2018.08.003>].
Author: Miquel De Cáceres [aut, cre],
Nicolas Martin [aut],
Víctor Granda [aut],
Antoine Cabon [aut]
Maintainer: Miquel De Cáceres <miquelcaceres@gmail.com>
Diff between meteoland versions 0.8.3 dated 2019-11-05 and 0.9.2 dated 2020-03-31
meteoland-0.8.3/meteoland/R/extractpointdates.R |only meteoland-0.8.3/meteoland/R/readmeteorologypixels.R |only meteoland-0.8.3/meteoland/R/summarygrid.R |only meteoland-0.8.3/meteoland/R/summarypixels.R |only meteoland-0.8.3/meteoland/R/writemeteorologypixels.R |only meteoland-0.8.3/meteoland/man/extractSpatialData.Rd |only meteoland-0.8.3/meteoland/man/extractpointdates.Rd |only meteoland-0.8.3/meteoland/man/writemeteorologypixels.Rd |only meteoland-0.9.2/meteoland/DESCRIPTION | 10 meteoland-0.9.2/meteoland/MD5 | 211 - meteoland-0.9.2/meteoland/NAMESPACE | 149 meteoland-0.9.2/meteoland/NEWS.md | 262 - meteoland-0.9.2/meteoland/R/DefineProcedureClasses.R | 306 - meteoland-0.9.2/meteoland/R/DefineSpatialDataClasses.R | 12 meteoland-0.9.2/meteoland/R/MeteorologyInterpolationData.R | 286 - meteoland-0.9.2/meteoland/R/MeteorologyUncorrectedData.R | 34 meteoland-0.9.2/meteoland/R/RcppExports.R | 454 +- meteoland-0.9.2/meteoland/R/SpatialGridMeteorology-methods.R | 234 - meteoland-0.9.2/meteoland/R/SpatialGridTopography-methods.R | 246 - meteoland-0.9.2/meteoland/R/SpatialPixelsMeteorology-methods.R | 238 - meteoland-0.9.2/meteoland/R/SpatialPixelsTopography-methods.R | 256 - meteoland-0.9.2/meteoland/R/SpatialPointsMeteorology-methods.R | 227 - meteoland-0.9.2/meteoland/R/SpatialPointsTopography-methods.R | 214 - meteoland-0.9.2/meteoland/R/averagearea.R |only meteoland-0.9.2/meteoland/R/bias_correction_internals.R |only meteoland-0.9.2/meteoland/R/correctionpoints.R | 684 --- meteoland-0.9.2/meteoland/R/correctionpoints.errors.R | 560 +- meteoland-0.9.2/meteoland/R/defaultCorrectionParams.R | 32 meteoland-0.9.2/meteoland/R/defaultGenerationParams.R |only meteoland-0.9.2/meteoland/R/defaultInterpolationParams.R | 48 meteoland-0.9.2/meteoland/R/download_currentday.R | 510 +- meteoland-0.9.2/meteoland/R/download_historical.R | 797 ++- meteoland-0.9.2/meteoland/R/download_historicalstationlist.R | 200 meteoland-0.9.2/meteoland/R/extractNetCDF.R | 487 +- meteoland-0.9.2/meteoland/R/extractdates.R |only meteoland-0.9.2/meteoland/R/extractgridpoints.R | 151 meteoland-0.9.2/meteoland/R/interpolation.calibration.R | 584 +- meteoland-0.9.2/meteoland/R/interpolation.coverage.R | 54 meteoland-0.9.2/meteoland/R/interpolation.cv.R | 524 +- meteoland-0.9.2/meteoland/R/interpolationgrid.R | 384 - meteoland-0.9.2/meteoland/R/interpolationpixels.R | 384 - meteoland-0.9.2/meteoland/R/interpolationpoints.R | 436 +- meteoland-0.9.2/meteoland/R/mergegrids.R |only meteoland-0.9.2/meteoland/R/meteocomplete.R | 172 meteoland-0.9.2/meteoland/R/meteoplot.R | 146 meteoland-0.9.2/meteoland/R/ncdf_internals.R |only meteoland-0.9.2/meteoland/R/precipitationconcentration.R | 127 meteoland-0.9.2/meteoland/R/readmeteorologygrid.R | 310 - meteoland-0.9.2/meteoland/R/readmeteorologypoints.R | 142 meteoland-0.9.2/meteoland/R/reshapeweathercan.R | 306 - meteoland-0.9.2/meteoland/R/reshapeworldmet.R | 203 meteoland-0.9.2/meteoland/R/summary.interpolation.cv.R | 228 - meteoland-0.9.2/meteoland/R/summarygridpixels.R |only meteoland-0.9.2/meteoland/R/summaryinterpolationdata.R | 92 meteoland-0.9.2/meteoland/R/summarypoints.R | 201 meteoland-0.9.2/meteoland/R/sysdata.rda |binary meteoland-0.9.2/meteoland/R/utils.R | 228 - meteoland-0.9.2/meteoland/R/weathergeneration.R |only meteoland-0.9.2/meteoland/R/writemeteorologygrid.R | 123 meteoland-0.9.2/meteoland/R/writemeteorologypoints.R | 118 meteoland-0.9.2/meteoland/build/vignette.rds |binary meteoland-0.9.2/meteoland/data/examplecorrectiondata.rda |binary meteoland-0.9.2/meteoland/data/examplegridtopography.rda |binary meteoland-0.9.2/meteoland/data/exampleinterpolationdata.rda |binary meteoland-0.9.2/meteoland/inst/CITATION | 36 meteoland-0.9.2/meteoland/inst/doc/UserGuide.R | 470 +- meteoland-0.9.2/meteoland/inst/doc/UserGuide.Rmd | 905 ++-- meteoland-0.9.2/meteoland/inst/doc/UserGuide.html | 2074 ++++------ meteoland-0.9.2/meteoland/man/MeteorologyInterpolationData-class.Rd | 114 meteoland-0.9.2/meteoland/man/MeteorologyInterpolationData.Rd | 118 meteoland-0.9.2/meteoland/man/MeteorologyProcedureData-class.Rd | 76 meteoland-0.9.2/meteoland/man/MeteorologyUncorrectedData-class.Rd | 88 meteoland-0.9.2/meteoland/man/MeteorologyUncorrectedData.Rd | 68 meteoland-0.9.2/meteoland/man/SpatialGridMeteorology-class.Rd | 96 meteoland-0.9.2/meteoland/man/SpatialGridTopography-class.Rd | 96 meteoland-0.9.2/meteoland/man/SpatialGridTopography.Rd | 140 meteoland-0.9.2/meteoland/man/SpatialPixelsMeteorology-class.Rd | 104 meteoland-0.9.2/meteoland/man/SpatialPixelsMeteorology.Rd | 68 meteoland-0.9.2/meteoland/man/SpatialPixelsTopography-class.Rd | 108 meteoland-0.9.2/meteoland/man/SpatialPixelsTopography.Rd | 108 meteoland-0.9.2/meteoland/man/SpatialPointsMeteorology-class.Rd | 92 meteoland-0.9.2/meteoland/man/SpatialPointsMeteorology.Rd | 62 meteoland-0.9.2/meteoland/man/SpatialPointsTopography-class.Rd | 90 meteoland-0.9.2/meteoland/man/SpatialPointsTopography.Rd | 92 meteoland-0.9.2/meteoland/man/averagearea.Rd |only meteoland-0.9.2/meteoland/man/correction_lowlevel.Rd | 68 meteoland-0.9.2/meteoland/man/correctionpoints.Rd | 248 - meteoland-0.9.2/meteoland/man/defaultCorrectionParams.Rd | 80 meteoland-0.9.2/meteoland/man/defaultGenerationParams.Rd |only meteoland-0.9.2/meteoland/man/defaultInterpolationParams.Rd | 92 meteoland-0.9.2/meteoland/man/downloadAEMET.Rd | 112 meteoland-0.9.2/meteoland/man/downloadMG.Rd |only meteoland-0.9.2/meteoland/man/downloadSMC.Rd | 122 meteoland-0.9.2/meteoland/man/examplecorrectiondata.Rd | 42 meteoland-0.9.2/meteoland/man/extractNetCDF.Rd | 106 meteoland-0.9.2/meteoland/man/extractdates.Rd |only meteoland-0.9.2/meteoland/man/humidity.Rd |only meteoland-0.9.2/meteoland/man/interpolation.coverage.Rd | 78 meteoland-0.9.2/meteoland/man/interpolation.cv.Rd | 264 - meteoland-0.9.2/meteoland/man/interpolation_lowlevel.Rd | 156 meteoland-0.9.2/meteoland/man/interpolationpoints.Rd | 198 meteoland-0.9.2/meteoland/man/mergegrids.Rd |only meteoland-0.9.2/meteoland/man/meteocomplete.Rd | 116 meteoland-0.9.2/meteoland/man/meteoplot.Rd | 120 meteoland-0.9.2/meteoland/man/penman.Rd | 112 meteoland-0.9.2/meteoland/man/precipitationconcentration.Rd | 63 meteoland-0.9.2/meteoland/man/radiation.Rd | 220 - meteoland-0.9.2/meteoland/man/readmeteorologygrid.Rd | 93 meteoland-0.9.2/meteoland/man/readmeteorologypoint.Rd | 80 meteoland-0.9.2/meteoland/man/reshapeworldmet.Rd | 82 meteoland-0.9.2/meteoland/man/spplot.Rd | 80 meteoland-0.9.2/meteoland/man/subsample.Rd | 76 meteoland-0.9.2/meteoland/man/summarypoints.Rd | 149 meteoland-0.9.2/meteoland/man/utils.Rd | 122 meteoland-0.9.2/meteoland/man/weathergeneration.Rd |only meteoland-0.9.2/meteoland/man/writemeteorologygrid.Rd | 40 meteoland-0.9.2/meteoland/man/writemeteorologypoint.Rd | 78 meteoland-0.9.2/meteoland/vignettes/UserGuide.Rmd | 905 ++-- 118 files changed, 10257 insertions(+), 10020 deletions(-)
Title: Presentation Ninja
Description: Create HTML5 slides with R Markdown and the JavaScript library
'remark.js' (<https://remarkjs.com>).
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Alessandro Gasparini [ctb] (<https://orcid.org/0000-0002-8319-7624>),
Benjie Gillam [ctb],
Claus Thorn Ekstrøm [ctb],
Daniel Anderson [ctb],
Dawei Lang [ctb],
Emi Tanaka [ctb],
Garrick Aden-Buie [ctb] (<https://orcid.org/0000-0002-7111-0077>),
Iñaki Ucar [ctb] (<https://orcid.org/0000-0001-6403-5550>),
John Little [ctb],
Joseph Casillas [ctb],
Lucy D'Agostino McGowan [ctb] (<https://orcid.org/0000-0001-7297-9359>),
Malcolm Barrett [ctb] (<https://orcid.org/0000-0003-0299-5825>),
Matthew Mark Strasiotto [ctb] (mstr3336),
Michael Wayne Kearney [ctb],
Nan-Hung Hsieh [ctb],
Ole Petter Bang [ctb] (CSS in
rmarkdown/templates/xaringan/resources/default.css),
Patrick Schratz [ctb],
Paul Klemm [ctb] (<https://orcid.org/0000-0002-5985-1737>),
Paul Lemmens [ctb],
Sean Lopp [ctb],
Yongfu Liao [ctb],
Yue Jiang [ctb] (<https://orcid.org/0000-0002-9798-5517>)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xaringan versions 0.15 dated 2020-03-04 and 0.16 dated 2020-03-31
xaringan-0.15/xaringan/tests/testit/parameterized.Rmd |only xaringan-0.15/xaringan/tests/testit/test-render.R |only xaringan-0.16/xaringan/DESCRIPTION | 6 +- xaringan-0.16/xaringan/MD5 | 12 ++--- xaringan-0.16/xaringan/build/vignette.rds |binary xaringan-0.16/xaringan/inst/rmarkdown/templates/xaringan/resources/js/script-tags.js | 22 ++-------- xaringan-0.16/xaringan/tests/test-all.R | 1 xaringan-0.16/xaringan/tests/test2 |only 8 files changed, 16 insertions(+), 25 deletions(-)
Title: Helper Functions to Install and Maintain 'TeX Live', and Compile
'LaTeX' Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>),
RStudio, PBC [cph],
Fernando Cagua [ctb],
Ethan Heinzen [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.20 dated 2020-02-25 and 0.21 dated 2020-03-31
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/install.R | 16 +++++++++++++--- R/latex.R | 3 +++ R/tlmgr.R | 3 +++ 5 files changed, 27 insertions(+), 11 deletions(-)