Title: Maximum Likelihood Analysis of Animal Movement Behavior Using
Multivariate Hidden Markov Models
Description: Extended tools for analyzing telemetry data using (multivariate) hidden Markov models. These include processing of tracking data, fitting HMMs to location and auxiliary biotelemetry or environmental data, multiple imputation for incorporating location measurement error and missing data, visualization of data and fitted model, decoding of the state process...
Author: Brett McClintock, Theo Michelot
Maintainer: Brett McClintock <brett.mcclintock@noaa.gov>
Diff between momentuHMM versions 1.1.0 dated 2017-08-15 and 1.1.1 dated 2017-09-20
DESCRIPTION | 13 +- MD5 | 118 ++++++++++++---------- NAMESPACE | 3 NEWS | 13 ++ R/RcppExports.R | 43 +++++++- R/allProbs.R | 1 R/fitHMM.R | 6 - R/momentuHMM_utils.R | 15 +- R/parDef.R | 41 ++++--- R/plot_momentuHMM.R | 6 - R/plot_momentuHMMData.R | 2 R/pseudoRes.R | 35 +++++- R/simData.R | 3 README.md | 7 - inst/doc/momentuHMM.R | 95 ++++++++++++++++++ inst/doc/momentuHMM.Rnw | 160 +++++++++++++++++++++++++++++-- inst/doc/momentuHMM.pdf |binary man/dbern_rcpp.Rd |only man/dnorm_rcpp.Rd |only man/fitHMM.Rd | 2 man/getDM_rcpp.Rd |only man/pseudoRes.Rd | 6 + man/simData.Rd | 2 src/RcppExports.cpp | 50 +++++++-- src/XBloop.cpp | 8 + src/densities.h | 48 +++++++++ src/getDM.cpp | 23 +++- src/momentuHMM_init.c | 34 +++--- src/nLogLike.cpp | 10 + tests/testthat/Rplots.pdf |binary tests/testthat/test_fitHMM.R | 67 ++++++++++++ tests/testthat/test_getDM.R |only tests/testthat/test_parDef.R | 2 vignettes/adjcalc.sty |only vignettes/harbourSealExample.R |only vignettes/momentuHMM-concordance.tex | 5 vignettes/momentuHMM.Rnw | 160 +++++++++++++++++++++++++++++-- vignettes/plot_elephantResults001.pdf |binary vignettes/plot_elephantResults002.pdf |binary vignettes/plot_elephantResults009.pdf |binary vignettes/plot_elephantResults010.pdf |binary vignettes/plot_elephantResults012.pdf |binary vignettes/plot_elephantResults013.pdf |binary vignettes/plot_elephantResults015.pdf |binary vignettes/plot_elephantResults016.pdf |binary vignettes/plot_elephantResults017.pdf |binary vignettes/plot_greySealResults002.pdf |binary vignettes/plot_greySealResults006.pdf |binary vignettes/plot_greySealResults009.pdf |binary vignettes/plot_greySealResults013.pdf |binary vignettes/plot_harbourSeal.png |only vignettes/plot_harbourSealResults021.pdf |only vignettes/plot_nfsResults.pdf |binary vignettes/plot_sesResults001.pdf | 4 vignettes/plot_sesResults003.pdf |binary vignettes/plot_sesResults007.pdf |binary vignettes/plot_sesResults009.pdf |binary vignettes/plot_sesResults2.pdf |binary vignettes/plot_turtleResults001.pdf |binary vignettes/plot_turtleResults002.pdf |binary vignettes/plot_turtleResults004.pdf |binary vignettes/plot_turtleResults2.pdf |binary vignettes/vignette_examples.R | 82 +++++++++++++++ vignettes/vignette_inputs.RData |binary 64 files changed, 899 insertions(+), 165 deletions(-)
Title: DataRobot Predictive Modeling API
Description: For working with the 'DataRobot' predictive modeling platform's API <https://www.datarobot.com/>.
Author: Ron Pearson [aut], Zachary Deane-Mayer [aut], David Chudzicki [aut], Dallin Akagi [aut], Sergey Yurgenson [aut], Thakur Raj Anand [aut]
Maintainer: Sergey Yurgenson <api-maintainer@datarobot.com>
Diff between datarobot versions 2.6.0 dated 2017-04-16 and 2.7.1 dated 2017-09-20
datarobot-2.6.0/datarobot/inst/doc/ComparingSubsetsRDSbuilder.R |only datarobot-2.6.0/datarobot/inst/doc/IntroductionToDataRobotRDSbuilder.R |only datarobot-2.6.0/datarobot/inst/doc/PartialDependenceRDSbuilder.R |only datarobot-2.6.0/datarobot/inst/doc/VariableImportanceRDSbuilder.R |only datarobot-2.7.1/datarobot/DESCRIPTION | 21 datarobot-2.7.1/datarobot/MD5 | 413 +++---- datarobot-2.7.1/datarobot/NAMESPACE | 10 datarobot-2.7.1/datarobot/NEWS | 33 datarobot-2.7.1/datarobot/R/ApplySchema.R | 17 datarobot-2.7.1/datarobot/R/Blenders.R | 253 ++-- datarobot-2.7.1/datarobot/R/Blueprints.R | 84 + datarobot-2.7.1/datarobot/R/ConnectToDataRobot.R | 46 datarobot-2.7.1/datarobot/R/CreateFeaturelist.R | 10 datarobot-2.7.1/datarobot/R/CreatePrimeCode.R | 11 datarobot-2.7.1/datarobot/R/DataRobotRequests.R | 19 datarobot-2.7.1/datarobot/R/DeleteModelJob.R | 13 datarobot-2.7.1/datarobot/R/DeletePredictJob.R | 9 datarobot-2.7.1/datarobot/R/DeleteProject.R | 11 datarobot-2.7.1/datarobot/R/DownloadPrimeCode.R | 25 datarobot-2.7.1/datarobot/R/Enums.R | 46 datarobot-2.7.1/datarobot/R/Exceptions.R | 2 datarobot-2.7.1/datarobot/R/FeatureImpact.R | 51 datarobot-2.7.1/datarobot/R/Features.R | 118 +- datarobot-2.7.1/datarobot/R/FormatMixedList.R | 14 datarobot-2.7.1/datarobot/R/GetFeaturelist.R | 21 datarobot-2.7.1/datarobot/R/GetModelJobs.R | 69 - datarobot-2.7.1/datarobot/R/GetPredictJobs.R | 70 - datarobot-2.7.1/datarobot/R/GetPredictions.R | 20 datarobot-2.7.1/datarobot/R/GetPrimeEligibility.R | 37 datarobot-2.7.1/datarobot/R/GetProject.R | 44 datarobot-2.7.1/datarobot/R/GetProjectList.R | 50 datarobot-2.7.1/datarobot/R/GetProjectStatus.R | 8 datarobot-2.7.1/datarobot/R/GetRulesets.R | 32 datarobot-2.7.1/datarobot/R/GetValidMetrics.R | 8 datarobot-2.7.1/datarobot/R/Jobs.R | 69 + datarobot-2.7.1/datarobot/R/LiftChart.R |only datarobot-2.7.1/datarobot/R/ListFeaturelists.R | 17 datarobot-2.7.1/datarobot/R/Models.R | 558 ++++++---- datarobot-2.7.1/datarobot/R/Partitions.R | 253 ++-- datarobot-2.7.1/datarobot/R/PauseQueue.R | 6 datarobot-2.7.1/datarobot/R/PredictionDatasets.R | 56 - datarobot-2.7.1/datarobot/R/PrimeFiles.R | 53 datarobot-2.7.1/datarobot/R/PrimeModels.R | 38 datarobot-2.7.1/datarobot/R/ReasonCodes.R | 441 +++++-- datarobot-2.7.1/datarobot/R/ReformatMetrics.R | 8 datarobot-2.7.1/datarobot/R/RequestApproximation.R | 16 datarobot-2.7.1/datarobot/R/RequestPredictions.R | 13 datarobot-2.7.1/datarobot/R/RequestPrimeModel.R | 14 datarobot-2.7.1/datarobot/R/RequestSampleSizeUpdate.R | 8 datarobot-2.7.1/datarobot/R/RocCurve.R |only datarobot-2.7.1/datarobot/R/SetupProject.R | 207 ++- datarobot-2.7.1/datarobot/R/StartAutopilot.R | 109 + datarobot-2.7.1/datarobot/R/StartRetryWaiter.R | 27 datarobot-2.7.1/datarobot/R/Stringify.R | 8 datarobot-2.7.1/datarobot/R/TransferrableModels.R | 256 ++-- datarobot-2.7.1/datarobot/R/UnpauseQueue.R | 6 datarobot-2.7.1/datarobot/R/UpdateProject.R | 8 datarobot-2.7.1/datarobot/R/ValidateProject.R | 7 datarobot-2.7.1/datarobot/R/ViewWebModel.R | 8 datarobot-2.7.1/datarobot/R/ViewWebProject.R | 6 datarobot-2.7.1/datarobot/R/WaitForAutopilot.R | 18 datarobot-2.7.1/datarobot/R/WaitForJobToComplete.R | 9 datarobot-2.7.1/datarobot/R/asDataFrame.R | 34 datarobot-2.7.1/datarobot/R/plot.listOfModels.R | 85 - datarobot-2.7.1/datarobot/R/summaryMethods.R | 57 - datarobot-2.7.1/datarobot/R/zzz.R | 2 datarobot-2.7.1/datarobot/build/vignette.rds |binary datarobot-2.7.1/datarobot/inst/doc/AdvancedVignette.R |only datarobot-2.7.1/datarobot/inst/doc/AdvancedVignette.Rmd |only datarobot-2.7.1/datarobot/inst/doc/AdvancedVignette.html |only datarobot-2.7.1/datarobot/inst/doc/ComparingSubsets.html | 48 datarobot-2.7.1/datarobot/inst/doc/DatetimePartitionedProjects.html | 12 datarobot-2.7.1/datarobot/inst/doc/IntroductionToDataRobot.R | 4 datarobot-2.7.1/datarobot/inst/doc/IntroductionToDataRobot.Rmd | 16 datarobot-2.7.1/datarobot/inst/doc/IntroductionToDataRobot.html | 32 datarobot-2.7.1/datarobot/inst/doc/PartialDependence.html | 68 - datarobot-2.7.1/datarobot/inst/doc/ReasonCodeVignette.R | 6 datarobot-2.7.1/datarobot/inst/doc/ReasonCodeVignette.Rmd | 16 datarobot-2.7.1/datarobot/inst/doc/ReasonCodeVignette.html | 48 datarobot-2.7.1/datarobot/inst/doc/VariableImportance.html | 60 - datarobot-2.7.1/datarobot/man/ApplySchema.Rd |only datarobot-2.7.1/datarobot/man/AutopilotMode.Rd | 2 datarobot-2.7.1/datarobot/man/BlendMethods.Rd | 2 datarobot-2.7.1/datarobot/man/BlueprintChartToGraphviz.Rd | 12 datarobot-2.7.1/datarobot/man/ConnectToDataRobot.Rd | 23 datarobot-2.7.1/datarobot/man/ConstructDurationString.Rd | 19 datarobot-2.7.1/datarobot/man/CreateBacktestSpecification.Rd | 22 datarobot-2.7.1/datarobot/man/CreateDatetimePartitionSpecification.Rd | 33 datarobot-2.7.1/datarobot/man/CreateDerivedFeatures.Rd | 5 datarobot-2.7.1/datarobot/man/CreateFeaturelist.Rd | 15 datarobot-2.7.1/datarobot/man/CreateGroupPartition.Rd | 6 datarobot-2.7.1/datarobot/man/CreatePrimeCode.Rd | 16 datarobot-2.7.1/datarobot/man/CreateRandomPartition.Rd | 7 datarobot-2.7.1/datarobot/man/CreateStratifiedPartition.Rd | 7 datarobot-2.7.1/datarobot/man/CreateUserPartition.Rd | 13 datarobot-2.7.1/datarobot/man/DataPartition.Rd |only datarobot-2.7.1/datarobot/man/DeleteJob.Rd | 11 datarobot-2.7.1/datarobot/man/DeleteModel.Rd | 8 datarobot-2.7.1/datarobot/man/DeleteModelJob.Rd | 13 datarobot-2.7.1/datarobot/man/DeletePredictJob.Rd | 16 datarobot-2.7.1/datarobot/man/DeletePredictionDataset.Rd | 14 datarobot-2.7.1/datarobot/man/DeleteProject.Rd | 11 datarobot-2.7.1/datarobot/man/DeleteReasonCodes.Rd | 20 datarobot-2.7.1/datarobot/man/DeleteReasonCodesInitialization.Rd | 8 datarobot-2.7.1/datarobot/man/DeleteTransferrableModel.Rd | 8 datarobot-2.7.1/datarobot/man/DownloadPrimeCode.Rd | 23 datarobot-2.7.1/datarobot/man/DownloadReasonCodes.Rd | 28 datarobot-2.7.1/datarobot/man/DownloadScoringCode.Rd |only datarobot-2.7.1/datarobot/man/DownloadTransferrableModel.Rd | 22 datarobot-2.7.1/datarobot/man/FormatMixedList.Rd |only datarobot-2.7.1/datarobot/man/GenerateDatetimePartition.Rd | 113 +- datarobot-2.7.1/datarobot/man/GetAllLiftCharts.Rd |only datarobot-2.7.1/datarobot/man/GetAllModels.Rd | 11 datarobot-2.7.1/datarobot/man/GetAllReasonCodesRowsAsDataFrame.Rd | 88 - 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datarobot-2.7.1/datarobot/man/SetupProject.Rd | 15 datarobot-2.7.1/datarobot/man/SetupProjectFromHDFS.Rd | 22 datarobot-2.7.1/datarobot/man/SetupProjectFromMySQL.Rd | 46 datarobot-2.7.1/datarobot/man/SetupProjectFromOracle.Rd | 36 datarobot-2.7.1/datarobot/man/SetupProjectFromPostgreSQL.Rd | 50 datarobot-2.7.1/datarobot/man/StartNewAutoPilot.Rd | 19 datarobot-2.7.1/datarobot/man/StartRetryWaiter.Rd |only datarobot-2.7.1/datarobot/man/Stringify.Rd |only datarobot-2.7.1/datarobot/man/UnpauseQueue.Rd | 11 datarobot-2.7.1/datarobot/man/UpdateProject.Rd | 13 datarobot-2.7.1/datarobot/man/UpdateTransferrableModel.Rd | 51 datarobot-2.7.1/datarobot/man/UploadPredictionDataset.Rd | 15 datarobot-2.7.1/datarobot/man/UploadTransferrableModel.Rd | 48 datarobot-2.7.1/datarobot/man/ValidateModel.Rd |only datarobot-2.7.1/datarobot/man/ValidateProject.Rd |only datarobot-2.7.1/datarobot/man/ViewWebModel.Rd | 8 datarobot-2.7.1/datarobot/man/ViewWebProject.Rd | 11 datarobot-2.7.1/datarobot/man/WaitForAutopilot.Rd | 18 datarobot-2.7.1/datarobot/man/WaitForJobToComplete.Rd | 14 datarobot-2.7.1/datarobot/man/as.data.frame.Rd | 12 datarobot-2.7.1/datarobot/man/datarobot-package.Rd | 2 datarobot-2.7.1/datarobot/man/plot.listOfModels.Rd | 35 datarobot-2.7.1/datarobot/man/summary.dataRobotModel.Rd | 48 datarobot-2.7.1/datarobot/tests/testthat/test-StartAutopilot.R | 5 datarobot-2.7.1/datarobot/vignettes/AdvancedVignette.Rmd |only datarobot-2.7.1/datarobot/vignettes/CrossValidationRocPoints.rds |only datarobot-2.7.1/datarobot/vignettes/IntroductionToDataRobot.Rmd | 16 datarobot-2.7.1/datarobot/vignettes/LiftChartDataCV.rds |only datarobot-2.7.1/datarobot/vignettes/LiftChartDataVal.rds |only datarobot-2.7.1/datarobot/vignettes/OptimalThresholdCV.rds |only datarobot-2.7.1/datarobot/vignettes/OptimalThresholdVal.rds |only datarobot-2.7.1/datarobot/vignettes/ROCCurveModelInsights.rds |only datarobot-2.7.1/datarobot/vignettes/ReasonCodeVignette.Rmd | 16 datarobot-2.7.1/datarobot/vignettes/StatisticsAtOptimalThresholdCV.rds |only datarobot-2.7.1/datarobot/vignettes/StatisticsAtOptimalThresholdVal.rds |only datarobot-2.7.1/datarobot/vignettes/ValidationRocPoints.rds |only datarobot-2.7.1/datarobot/vignettes/liftChartModelInsights.rds |only datarobot-2.7.1/datarobot/vignettes/modelsModelInsights.rds |only datarobot-2.7.1/datarobot/vignettes/resultsModelInsights.rds |only datarobot-2.7.1/datarobot/vignettes/wordCloudModelInsights.rds |only 228 files changed, 4486 insertions(+), 2618 deletions(-)
Title: An Arsenal of 'R' Functions for Large-Scale Statistical
Summaries
Description: An Arsenal of 'R' functions for large-scale statistical summaries,
which are streamlined to work within the latest reporting tools in 'R' and
'RStudio' and which use formulas and versatile summary statistics for summary
tables and models. The primary functions include tableby(), a Table-1-like
summary of multiple variable types 'by' the levels of a categorical
variable; modelsum(), which performs simple model fits on the same endpoint
for many variables (univariate or adjusted for standard covariates);
freqlist(), a powerful frequency table across many categorical variables;
compare.data.frame(), the S3 method for comparing data.frames; and
write2(), a function to output tables to a document.
Author: Ethan Heinzen [aut, cre],
Jason Sinnwell [aut],
Elizabeth Atkinson [aut],
Tina Gunderson [aut],
Gregory Dougherty [aut],
Patrick Votruba [ctb],
Ryan Lennon [ctb],
Andrew Hanson [ctb],
Krista Goergen [ctb],
Emily Lundt [ctb],
Brendan Broderick [ctb]
Maintainer: Ethan Heinzen <heinzen.ethan@mayo.edu>
Diff between arsenal versions 0.5.0 dated 2017-08-14 and 0.6.0 dated 2017-09-20
DESCRIPTION | 16 ++- MD5 | 75 +++++++++--------- NAMESPACE | 7 + NEWS.md | 26 ++++++ R/formulize.R | 2 R/freqlist.R | 65 +++++++-------- R/freqlist.internal.R | 13 ++- R/internal.functions.R | 4 R/labels.R | 2 R/modelsum.R | 3 R/summary.compare.R | 2 R/tableby.R | 143 ++++++++++++++++------------------- R/tableby.control.R | 16 +-- R/tableby.internal.R | 39 ++++++--- R/write2.R | 91 ++++++++++------------ R/yaml.R |only README.md | 6 - inst/doc/compare.html | 2 inst/doc/freqlist.html | 2 inst/doc/labels.html | 2 inst/doc/modelsum.html | 6 - inst/doc/tableby.html | 12 +- inst/doc/write2.R | 32 +++++++ inst/doc/write2.Rmd | 52 ++++++++++++ inst/doc/write2.html | 44 ++++++++++ man/freqlist.Rd | 5 - man/labels.Rd | 2 man/summary.compare.data.frame.Rd | 2 man/tableby.internal.Rd | 4 man/write2.Rd | 16 +++ man/yaml.Rd |only tests/testthat/test_formulize.R | 11 ++ tests/testthat/test_freqlist.R | 91 +++++++++++----------- tests/testthat/test_tableby.R | 88 +++++++++++++++------ tests/testthat/test_write2.R | 38 ++++++++- tests/testthat/write2.mylist.pdf.md | 6 - tests/testthat/write2.mylist2.doc.md | 6 - tests/testthat/write2.mylists.pdf.md | 12 +- tests/testthat/write2.yaml.pdf.md |only vignettes/write2.Rmd | 52 ++++++++++++ 40 files changed, 643 insertions(+), 352 deletions(-)
Title: A Statistically Sound 'data.frame' Processor/Conditioner
Description: A 'data.frame' processor/conditioner that prepares real-world data for predictive modeling in a statistically sound manner.
'vtreat' prepares variables so that data has fewer exceptional cases, making
it easier to safely use models in production. Common problems 'vtreat' defends
against: 'Inf', 'NA', too many categorical levels, rare categorical levels, and new
categorical levels (levels seen during application, but not during training).
'vtreat::prepare' should be used as you would use 'model.matrix'.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between vtreat versions 0.5.32 dated 2017-06-13 and 0.6.0 dated 2017-09-20
DESCRIPTION | 24 +++- MD5 | 74 +++++++------- NEWS.md |only R/customCoder.R |only R/effectTreatmentC.R | 3 R/effectTreatmentN.R | 3 R/outOfSample.R | 28 +++-- R/utils.R | 29 ++++- R/vtreat.R | 85 ++++++++++++++--- R/vtreatImpl.R | 123 +++++++++++++++++------- README.md | 55 +++++------ build/vignette.rds |binary inst/doc/SavingTreamentPlans.html | 12 ++ inst/doc/vtreat.html | 70 +++++++------- inst/doc/vtreatCrossFrames.Rmd | 2 inst/doc/vtreatCrossFrames.html | 54 +++++----- inst/doc/vtreatGrouping.html | 4 inst/doc/vtreatOverfit.html | 36 +++---- inst/doc/vtreatRareLevels.html | 4 inst/doc/vtreatScaleMode.html | 16 +-- inst/doc/vtreatSignificance.html | 22 ++-- inst/doc/vtreatSplitting.R | 2 inst/doc/vtreatSplitting.Rmd | 8 - inst/doc/vtreatSplitting.html | 60 +++--------- inst/doc/vtreatVariableTypes.R | 40 +++++++- inst/doc/vtreatVariableTypes.Rmd | 52 +++++++++- inst/doc/vtreatVariableTypes.html | 189 +++++++++++++++++++++++--------------- man/designTreatmentsC.Rd | 12 ++ man/designTreatmentsN.Rd | 9 + man/designTreatmentsZ.Rd | 7 + man/getSplitPlanAppLabels.Rd | 2 man/mkCrossFrameCExperiment.Rd | 13 ++ man/mkCrossFrameNExperiment.Rd | 11 +- man/oneWayHoldout.Rd | 8 - man/prepare.Rd | 2 man/problemAppPlan.Rd | 2 vignettes/vtreatCrossFrames.Rmd | 2 vignettes/vtreatSplitting.Rmd | 8 - vignettes/vtreatVariableTypes.Rmd | 52 +++++++++- 39 files changed, 726 insertions(+), 397 deletions(-)
Title: Sparsity Oriented Importance Learning
Description: Sparsity Oriented Importance Learning (SOIL) provides a new variable importance measure for high dimensional linear regression and logistic regression from a sparse penalization perspective, by taking into account the variable selection uncertainty via the use of a sensible model weighting. The package is an implementation of Ye, C., Yang, Y., and Yang, Y. (2017+).
Author: Chenglong Ye <yexxx323@umn.edu>, Yi Yang <yi.yang6@mcgill.ca>, Yuhong Yang <yyang@stat.umn.edu>
Maintainer: Yi Yang <yi.yang6@mcgill.ca>
Diff between SOIL versions 1.0 dated 2016-07-07 and 1.1 dated 2017-09-20
ChangeLog | 7 ++++++- DESCRIPTION | 12 ++++++------ MD5 | 16 +++++++++------- NAMESPACE | 2 +- R/SOIL.R | 10 ++++++++-- R/binomialfit_lasso.R |only R/gaussianfit_lasso.R |only R/logitARM.R | 4 ++-- R/logitIC.R | 6 +++--- man/SOIL.Rd | 25 +++++++++++-------------- 10 files changed, 46 insertions(+), 36 deletions(-)
Title: Generalized Survival Models
Description: R implementation of generalized survival models, where g(S(t|x))=eta(t,x) for a link function g, survival S at time t with covariates x and a linear predictor eta(t,x). The main assumption is that the time effect(s) are smooth. For fully parametric models with natural splines, this re-implements Stata's 'stpm2' function, which are flexible parametric survival models developed by Royston and colleagues. We have extended the parametric models to include any smooth parametric smoothers for time. We have also extended the model to include any smooth penalized smoothers from the 'mgcv' package, using penalized likelihood. These models include left truncation, right censoring, interval censoring, gamma frailties and normal random effects. This also includes a smooth implementation of accelerated failure time models.
Author: Mark Clements [aut, cre], Xing-Rong Liu [aut], Paul Lambert [ctb]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between rstpm2 versions 1.4.0 dated 2017-08-31 and 1.4.1 dated 2017-09-20
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/pm2-3.R | 3 ++- inst/doc/Introduction.pdf |binary inst/working_code.R | 10 ++++++++++ 5 files changed, 20 insertions(+), 9 deletions(-)
Title: Airborne LiDAR Data Manipulation and Visualization for Forestry
Applications
Description: Airborne LiDAR (Light Detection and Ranging) interface for data
manipulation and visualization. Read/write 'las' and 'laz' files, computation
of metrics in area based approach, point filtering, artificial point reduction,
classification from geographic data, normalization, individual tree segmentation
and other manipulations.
Author: Jean-Romain Roussel [aut, cre, cph],
David Auty [aut, ctb] (Reviews the documentation),
Florian De Boissieu [ctb] (Fixed bugs and improved catalog features),
Andrew Sánchez Meador [ctb] (Helped to review the documentation)
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>
Diff between lidR versions 1.3.0 dated 2017-09-16 and 1.3.1 dated 2017-09-20
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ R/grid_tincanopy.r | 10 +++++++--- R/utils_interpolations.r | 2 +- README.md | 2 +- src/QuadTree.cpp | 26 +++++++++++++------------- 7 files changed, 38 insertions(+), 28 deletions(-)
Title: Genomic Data Retrieval
Description: Perform metagenomic data retrieval and functional annotation
retrieval. In detail, this package aims to provide users with a standardized
way to automate genome, proteome, coding sequence ('CDS'), 'GFF', and metagenome
retrieval from 'NCBI' and 'ENSEMBL' databases. Furthermore, an interface to the 'BioMart' database
(Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve
functional annotation for genomic loci. Users can download entire databases such
as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr',
'NCBI nt' and 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>) as
well as 'ENSEMBL' and 'ENSEMBLGENOMES' with only one command.
Author: Hajk-Georg Drost
Maintainer: Hajk-Georg Drost <hgd23@cam.ac.uk>
Diff between biomartr versions 0.5.1 dated 2017-05-28 and 0.5.2 dated 2017-09-20
DESCRIPTION | 10 - MD5 | 38 +++--- NEWS.md | 10 + R/getAssemblyStats.R | 2 R/getCDS.R | 2 R/getGFF.R | 2 R/getGenome.R | 2 R/getProteome.R | 2 R/getRNA.R | 2 R/getRepeatMasker.R | 2 R/read_rm.R | 3 README.md | 5 build/vignette.rds |binary inst/doc/BioMart_Examples.html | 4 inst/doc/Database_Retrieval.html | 22 ++- inst/doc/Functional_Annotation.html | 173 +++++++++++++++---------------- inst/doc/Introduction.html | 4 inst/doc/MetaGenome_Retrieval.html | 4 inst/doc/Sequence_Retrieval.html | 4 tests/testthat/test-organismAttributes.R | 4 20 files changed, 151 insertions(+), 144 deletions(-)
Title: Create and Navigate Large Multi-Panel Visual Displays
Description: An extension of Trellis Display that enables creation,
organization, and interactive viewing of multi-panel displays created
against potentially very large data sets. The dynamic viewer tiles
panels of a display across the screen in a web browser and allows the
user to interactively page through the panels and sort and filter them
based on "cognostic" metrics computed for each panel. Panels can be
created using many of R's plotting capabilities, including base R
graphics, 'lattice', 'ggplot2', and many 'htmlwidgets'. Conditioning is
handled through the 'datadr' package, which enables 'Trelliscope' displays
with potentially millions of panels to be created against terabytes of
data on systems like 'Hadoop'. While designed to scale, 'Trelliscope'
displays can also be very useful for small data sets.
Author: Ryan Hafen [aut, cre],
Jeremiah Rounds [ctb],
Barret Schloerke [ctb],
Landon Sego [ctb]
Maintainer: Ryan Hafen <rhafen@gmail.com>
Diff between trelliscope versions 0.9.7 dated 2016-10-03 and 0.9.8 dated 2017-09-20
DESCRIPTION | 10 +- MD5 | 115 +++++++++++++++++----------------- NEWS.md | 1 R/zzz.R |only inst/trelliscopeViewer/www/index.html | 10 +- man/applyCogFn.Rd | 1 man/batting.Rd | 1 man/cleanupDisplays.Rd | 1 man/cog.Rd | 1 man/cogConn-methods.Rd | 3 man/cogDisplayHref.Rd | 1 man/cogHref.Rd | 1 man/cogLoessRMSE.Rd | 1 man/cogMean.Rd | 1 man/cogRange.Rd | 1 man/cogScagnostics.Rd | 1 man/cogSlope.Rd | 1 man/deployVDB.Rd | 1 man/dfCogConn.Rd | 1 man/encodePNG.Rd | 1 man/getDisplay.Rd | 1 man/getVdbPath.Rd | 1 man/hash-methods.Rd | 3 man/listDisplays.Rd | 1 man/makeDisplay.Rd | 1 man/makePNG.Rd | 1 man/makeSplodData.Rd | 1 man/makeStateHash.Rd | 1 man/mr-methods.Rd | 5 - man/noMargins.Rd | 1 man/phantomInstall.Rd | 1 man/plot.trsPre.Rd | 1 man/prepanel.Rd | 1 man/print.cog.Rd | 1 man/print.dfCogConn.Rd | 1 man/print.displayObj.Rd | 1 man/print.qtrellis.Rd | 1 man/print.vdbConn.Rd | 1 man/qtrellis.Rd | 1 man/removeDisplay.Rd | 1 man/restoreDisplay.Rd | 1 man/setLims.Rd | 1 man/splod.Rd | 1 man/splodCogFn.Rd | 1 man/splodPanelFn.Rd | 1 man/stateSpec.Rd | 1 man/syncLocalData.Rd | 1 man/trelliscope-package.Rd | 3 man/updateDisplay.Rd | 1 man/validateState.Rd | 1 man/vdbConn.Rd | 1 man/vdbConvert.Rd | 1 man/vdbCopyRSource.Rd | 1 man/vdbGlobalsExist.Rd | 1 man/vdbGlobalsFile.Rd | 1 man/view.Rd | 1 man/webConn.Rd | 1 man/webSync.Rd | 1 man/widgetThumbnail.Rd | 1 59 files changed, 74 insertions(+), 126 deletions(-)
Title: Selected ISO Codes
Description: ISO language, territory, currency, script and character codes.
Provides ISO 639 language codes, ISO 3166 territory codes, ISO 4217
currency codes, ISO 15924 script codes, and the ISO 8859 character codes
as well as the UN M.49 area codes.
Author: Christian Buchta [aut],
Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between ISOcodes versions 2016.12.09 dated 2016-12-09 and 2017.09.20 dated 2017-09-20
DESCRIPTION | 9 +++++---- MD5 | 40 ++++++++++++++++++++-------------------- data/ISO_15924.rda |binary data/ISO_3166_1.rda |binary data/ISO_3166_2.rda |binary data/ISO_3166_3.rda |binary data/ISO_4217.rda |binary data/ISO_4217_Historic.rda |binary data/ISO_639_2.rda |binary data/ISO_639_3.rda |binary data/ISO_639_3_Retirements.rda |binary data/ISO_639_5.rda |binary data/ISO_8859.rda |binary data/UN_M.49_Countries.rda |binary data/UN_M.49_Regions.rda |binary man/ISO_15924.Rd | 2 +- man/ISO_3166.Rd | 14 +++++++------- man/ISO_4217.Rd | 4 ++-- man/ISO_639.Rd | 8 ++++---- man/ISO_8859.Rd | 2 +- man/UN_M.49.Rd | 4 ++-- 21 files changed, 42 insertions(+), 41 deletions(-)
Title: Estimation and Fit Assessment of Frailty Exponential Random
Graph Models
Description: Frailty Exponential Random Graph Models estimated through pseudo likelihood with frailty terms estimated using 'Stan' as per Box-Steffensmeier et. al (2017) <doi:10.7910/DVN/K3D1M2>.
Goodness of fit for Frailty Exponential Random Graph Models is also available, with easy visualizations for comparison to fit Exponential Random Graph Models.
Author: Jason W. Morgan [aut], Benjamin W. Campbell [aut, cre], Dino P. Christenson [aut], Janet M. Box-Steffensmeier [aut]
Maintainer: Benjamin W. Campbell <campbell.1721@osu.edu>
Diff between fergm versions 0.2.0 dated 2017-08-14 and 0.2.1 dated 2017-09-20
DESCRIPTION | 14 +++++----- MD5 | 53 ++++++++++++++++++++------------------- NEWS.md |only R/clean_summary.R | 22 +++++----------- R/coef_plot.R | 17 ++++++++---- R/coef_posterior_density.R | 13 ++++++--- R/compare_predictions.R | 20 +++++++------- R/compare_predictions_plot.R | 10 +++---- R/compare_predictions_test.R | 12 +++++--- R/ergm.fit.R | 2 - R/fergm.R | 4 +- R/fergm_beta_traceplot.R | 36 ++++++++++++-------------- R/mesa.R | 2 - data/fergm.fit.rda |binary inst/doc/mesaHighVignette.R | 20 +++++++++++--- inst/doc/mesaHighVignette.Rmd | 48 +++++++++++++++++++++-------------- inst/doc/mesaHighVignette.html | 54 +++++++++++++++++++++++----------------- man/clean_summary.Rd | 20 +++++--------- man/coef_plot.Rd | 12 ++++---- man/coef_posterior_density.Rd | 8 ++--- man/compare_predictions.Rd | 12 ++++---- man/compare_predictions_plot.Rd | 12 ++++---- man/compare_predictions_test.Rd | 10 +++---- man/ergm.fit.Rd | 2 - man/fergm.Rd | 2 - man/fergm_beta_traceplot.Rd | 14 +++------- man/mesa.Rd | 2 - vignettes/mesaHighVignette.Rmd | 48 +++++++++++++++++++++-------------- 28 files changed, 252 insertions(+), 217 deletions(-)
Title: Dental Surface Complexity Measurement Tools
Description: Surface topography calculations of Dirichlet's normal energy,
relief index, surface slope, and orientation patch count for teeth using scans of
enamel caps.
Importantly, for the relief index and orientation patch count calculations to
work, the scanned tooth files must be oriented with the occlusal plane parallel
to the x and y axes, and perpendicular to the z axis. The files should also be
simplified, and smoothed in some other software prior to uploading into R.
Author: James D. Pampush [aut, cre, cph],
Julia M. Winchester [aut, cph],
Paul E. Morse [aut, cph],
Alexander Q. Vining [aut, cph]
Maintainer: James D. Pampush <jdpampush@gmail.com>
Diff between molaR versions 4.2 dated 2016-08-30 and 4.3 dated 2017-09-20
molaR-4.2/molaR/R/plyZClip.R |only molaR-4.2/molaR/build/molaR.pdf |only molaR-4.2/molaR/man/plyZClip.Rd |only molaR-4.3/molaR/DESCRIPTION | 8 molaR-4.3/molaR/MD5 | 91 +- molaR-4.3/molaR/NAMESPACE | 4 molaR-4.3/molaR/R/Check2D.R |only molaR-4.3/molaR/R/RFI.R | 259 +++--- molaR-4.3/molaR/R/molaR_Batch.R | 604 +++++++++------ molaR-4.3/molaR/R/plyClip.R |only molaR-4.3/molaR/build/vignette.rds |binary molaR-4.3/molaR/inst/doc/molaR_vignette.R | 90 +- molaR-4.3/molaR/inst/doc/molaR_vignette.Rmd | 22 molaR-4.3/molaR/inst/doc/molaR_vignette.html | 793 ++++++++++----------- molaR-4.3/molaR/man/Check2D.Rd |only molaR-4.3/molaR/man/DNE.Rd | 1 molaR-4.3/molaR/man/DNE3d.Rd | 1 molaR-4.3/molaR/man/DNE_Legend.Rd | 1 molaR-4.3/molaR/man/Directional_Bins.Rd | 1 molaR-4.3/molaR/man/Equal_Vertex_Normals.Rd | 1 molaR-4.3/molaR/man/Face_Normals.Rd | 1 molaR-4.3/molaR/man/OPC.Rd | 1 molaR-4.3/molaR/man/OPC3d.Rd | 1 molaR-4.3/molaR/man/OPC_Legend.Rd | 1 molaR-4.3/molaR/man/OPCr.Rd | 1 molaR-4.3/molaR/man/RFI.Rd | 1 molaR-4.3/molaR/man/RFI3d.Rd | 1 molaR-4.3/molaR/man/RFI_Legend.Rd | 1 molaR-4.3/molaR/man/Slope.Rd | 1 molaR-4.3/molaR/man/Slope3d.Rd | 1 molaR-4.3/molaR/man/Slope_Legend.Rd | 1 molaR-4.3/molaR/man/cSize.Rd | 1 molaR-4.3/molaR/man/clustered_patches.Rd | 1 molaR-4.3/molaR/man/compute_energy_per_face.Rd | 1 molaR-4.3/molaR/man/edge_vertices.Rd | 1 molaR-4.3/molaR/man/face_areas.Rd | 1 molaR-4.3/molaR/man/index_paired_directed_faces.Rd | 1 molaR-4.3/molaR/man/molaR_Batch.Rd | 17 molaR-4.3/molaR/man/molaR_Clean.Rd | 1 molaR-4.3/molaR/man/molaR_bgplot.Rd | 1 molaR-4.3/molaR/man/patch_details.Rd | 1 molaR-4.3/molaR/man/patches_for_each_direction.Rd | 1 molaR-4.3/molaR/man/patches_per.Rd | 1 molaR-4.3/molaR/man/plyClip.Rd |only molaR-4.3/molaR/man/read.AVIZO.ply.Rd | 1 molaR-4.3/molaR/man/remove_boundary_faces.Rd | 1 molaR-4.3/molaR/man/remove_outliers.Rd | 1 molaR-4.3/molaR/man/tr.Rd | 1 molaR-4.3/molaR/man/vertex_to_face_list.Rd | 1 molaR-4.3/molaR/vignettes/molaR_vignette.Rmd | 13 50 files changed, 1007 insertions(+), 926 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 0.1.3 dated 2017-07-03 and 0.1.4 dated 2017-09-20
DESCRIPTION | 8 +- MD5 | 42 ++++++---- NAMESPACE | 5 + NEWS.md | 45 ++++++----- R/RcppExports.R | 2 R/addCondition.R |only R/defCondition.R |only R/defData.R | 4 - R/defMiss.R | 2 R/defReadCond.R |only R/genDummy.R |only R/genFactor.R |only R/genMiss.R | 5 - R/int_gencat.R | 2 R/int_generate.R | 4 + R/trtObserve.R | 2 inst/doc/simstudy.R | 6 - inst/doc/simstudy.Rmd | 6 - inst/doc/simstudy.html | 190 ++++++++++++++++++++++++------------------------- man/addCondition.Rd |only man/defCondition.Rd |only man/defMiss.Rd | 2 man/defReadCond.Rd |only man/genDummy.Rd |only man/genFactor.Rd |only src/RcppExports.cpp | 4 - vignettes/simstudy.Rmd | 6 - 27 files changed, 182 insertions(+), 153 deletions(-)
Title: Random Walk Covariance Models
Description: Code to facilitate simulation and inference when connectivity is defined by underlying random walks. Methods for spatially-correlated pairwise distance data are especially considered. This provides core code to conduct analyses similar to that in Hanks and Hooten (2013) <doi:10.1080/01621459.2012.724647>.
Author: Ephraim M. Hanks
Maintainer: Ephraim M. Hanks <hanks@psu.edu>
Diff between rwc versions 1.0 dated 2017-09-07 and 1.1 dated 2017-09-20
DESCRIPTION | 10 +++++----- MD5 | 10 ++++++---- NAMESPACE | 6 +++++- R/get.Q.R | 2 +- R/mcmc.wish.icar.R |only man/mcmc.wish.icar.Rd |only man/rwc-package.Rd | 4 ++-- 7 files changed, 19 insertions(+), 13 deletions(-)
Title: Smoothed Bootstrap and Random Generation from Kernel Densities
Description: Smoothed bootstrap and functions for random generation from
univariate and multivariate kernel densities. It does not
estimate kernel densities.
Author: Tymoteusz Wolodzko
Maintainer: Tymoteusz Wolodzko <twolodzko+kernelboot@gmail.com>
Diff between kernelboot versions 0.1.1 dated 2017-06-05 and 0.1.2 dated 2017-09-20
kernelboot-0.1.1/kernelboot/src/registerRoutines.c |only kernelboot-0.1.2/kernelboot/DESCRIPTION | 8 kernelboot-0.1.2/kernelboot/MD5 | 56 kernelboot-0.1.2/kernelboot/NAMESPACE | 54 kernelboot-0.1.2/kernelboot/R/RcppExports.R | 22 kernelboot-0.1.2/kernelboot/R/bandwidth.R | 182 +-- kernelboot-0.1.2/kernelboot/R/kernelboot-methods.R | 184 +-- kernelboot-0.1.2/kernelboot/R/kernelboot.R | 38 kernelboot-0.1.2/kernelboot/R/multivar-gaussian-kd.R | 8 kernelboot-0.1.2/kernelboot/R/multivar-kd.R | 13 kernelboot-0.1.2/kernelboot/R/onUnload.R | 8 kernelboot-0.1.2/kernelboot/R/other.R | 84 - kernelboot-0.1.2/kernelboot/R/univar-kd.R | 12 kernelboot-0.1.2/kernelboot/man/bw.silv.Rd | 124 +- kernelboot-0.1.2/kernelboot/man/kernelboot-class.Rd | 90 - kernelboot-0.1.2/kernelboot/man/kernelboot.Rd | 570 +++++----- kernelboot-0.1.2/kernelboot/man/rmvg.Rd | 202 +-- kernelboot-0.1.2/kernelboot/man/rmvk.Rd | 191 +-- kernelboot-0.1.2/kernelboot/man/ruvk.Rd | 182 +-- kernelboot-0.1.2/kernelboot/man/summary.kernelboot.Rd | 44 kernelboot-0.1.2/kernelboot/src/RcppExports.cpp | 15 kernelboot-0.1.2/kernelboot/tests/test_parallel.R | 38 kernelboot-0.1.2/kernelboot/tests/testthat.R | 8 kernelboot-0.1.2/kernelboot/tests/testthat/test_bandwidth.R | 46 kernelboot-0.1.2/kernelboot/tests/testthat/test_kernelboot.R | 476 ++++---- kernelboot-0.1.2/kernelboot/tests/testthat/test_misc.R |only kernelboot-0.1.2/kernelboot/tests/testthat/test_multivar-gaussian.R | 146 +- kernelboot-0.1.2/kernelboot/tests/testthat/test_multivar-kd.R | 120 +- kernelboot-0.1.2/kernelboot/tests/testthat/test_univar-kd.R | 82 - kernelboot-0.1.2/kernelboot/tests/testthat/test_univar_vs_multivar.R | 158 +- 30 files changed, 1589 insertions(+), 1572 deletions(-)
Title: Convert Strings into any Case
Description: A consistent, flexible and easy to use tool to parse and convert strings into cases like snake or camel among others.
Author: Malte Grosser [aut, cre]
Maintainer: Malte Grosser <malte.grosser@gmail.com>
Diff between snakecase versions 0.5.0 dated 2017-08-08 and 0.5.1 dated 2017-09-20
DESCRIPTION | 10 - MD5 | 32 ++--- NEWS.md | 10 + R/caseconverters.R | 37 +++++- R/to_any_case.R | 8 + inst/doc/caseconverters.html | 4 man/to_any_case.Rd | 2 tests/testthat.R | 1 tests/testthat/test-to_any_case.R | 150 ++++++++++++++++++++++++++ tests/testthat/test-to_big_camel_case.R | 8 + tests/testthat/test-to_lower_upper_case.R | 10 + tests/testthat/test-to_mixed_case.R | 10 + tests/testthat/test-to_parsed_case.R | 10 + tests/testthat/test-to_screaming_snake_case.R | 10 + tests/testthat/test-to_small_camel_case.R | 10 + tests/testthat/test-to_snake_case.R | 10 + tests/testthat/test-to_upper_lower_case.R | 10 + 17 files changed, 303 insertions(+), 29 deletions(-)
Title: Supplementary Item Response Theory Models
Description: Supplementary item response theory models to complement existing
functions in R, including multidimensional compensatory and
noncompensatory IRT models, MCMC for hierarchical IRT models and
testlet models, NOHARM, Rasch copula model, faceted and
hierarchical rater models, ordinal IRT model (ISOP),
DETECT statistic, local structural equation modeling (LSEM).
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between sirt versions 2.1-24 dated 2017-08-09 and 2.2-14 dated 2017-09-20
DESCRIPTION | 8 MD5 | 956 ++++++++++----------- NAMESPACE | 3 R/IRT.expectedCounts_sirt.R | 3 R/IRT.factor.scores.sirt.R | 3 R/IRT.factor.scores.xxirt.R | 3 R/IRT.irfprob.sirt.R | 3 R/IRT.likelihood_sirt.R | 3 R/IRT.mle.R | 3 R/IRT.modelfit.sirt.R | 3 R/IRT.posterior_sirt.R | 3 R/Probtrace_sirt.R | 5 R/Q3.R | 3 R/Q3.testlet.R | 3 R/R2conquest.R | 3 R/R2noharm-utility.R | 3 R/R2noharm.EAP.R | 3 R/R2noharm.R | 3 R/R2noharm.jackknife.R | 3 R/RcppExports.R | 89 + R/Rhat_sirt.R | 3 R/amh_plot.R | 3 R/anova_sirt.R | 3 R/attach.environment.sirt.R | 3 R/automatic.recode.R | 3 R/bounds_parameters.R | 3 R/brm.irf.R | 3 R/brm.sim.R | 3 R/btm.R | 3 R/btm_fit.R | 3 R/btm_fit_combine_tables.R | 5 R/categorize.R | 3 R/ccov.np.R | 3 R/class.accuracy.rasch.R | 3 R/conf.detect.R | 3 R/confint.xxirt.R | 3 R/create.ccov.R | 3 R/data.prep.R | 3 R/data.wide2long.R | 3 R/decategorize.R | 3 R/detect.index.R | 3 R/diag2.R | 3 R/dif.logisticregression.R | 3 R/dif.variance.R | 3 R/dimproper.R | 3 R/dirichlet.R | 3 R/eigenvalues.manymatrices.R | 3 R/eigenvalues.sirt.R | 3 R/equating.rasch.R | 3 R/expl.detect.R | 3 R/f1d.irt.R | 3 R/fit.adisop.R | 3 R/fit.gradedresponse.R | 3 R/fit.gradedresponse_alg.R | 3 R/fit.isop.R | 3 R/fit.logistic.R | 3 R/fit.logistic_alg.R | 3 R/fuzcluster.R | 3 R/fuzcluster_alg.R | 24 R/fuzdiscr.R | 3 R/ginverse_sym.R | 3 R/gom.em.R | 3 R/gom.em.alg.R | 3 R/gom.jml.R | 3 R/gom.jml_alg.R | 3 R/greenyang.reliability.R | 3 R/hard_thresholding.R | 3 R/invariance.alignment.R | 3 R/invariance.alignment.aux.R | 3 R/invariance.alignment2.R | 3 R/invariance.alignment2.aux.R | 3 R/invgamma2.R | 5 R/isop.dich.R | 3 R/isop.poly.R | 3 R/isop.scoring.R | 3 R/isop.test.R | 40 R/isop_tests_cpp.R |only R/latent.regression.em.normal.R | 3 R/latent.regression.em.raschtype.R | 3 R/lavaan2mirt.R | 3 R/lavaanify.sirt.R | 3 R/lc.2raters.R | 3 R/lc.2raters.aux.R | 3 R/likelihood_adjustment.R | 3 R/likelihood_adjustment_aux.R | 3 R/likelihood_moments.R | 3 R/linking.haberman.R | 91 - R/linking.robust.R | 3 R/linking_haberman_als.R | 14 R/linking_haberman_als_residual_weights.R | 8 R/linking_haberman_als_vcov.R | 3 R/linking_haberman_vcov_transformation.R | 3 R/logLik_sirt.R | 3 R/lsdm.R | 3 R/lsdm_aux.R | 3 R/lsem.MGM.stepfunctions.R | 3 R/lsem.estimate.R | 3 R/lsem.permutationTest.R | 3 R/lsem_fitsem.R | 3 R/lsem_group_moderator.R | 3 R/lsem_parameter_summary.R | 3 R/lsem_residualize.R | 5 R/lsem_weighted_cov.R | 5 R/lsem_weighted_mean.R | 5 R/lsem_wtdSD.R | 3 R/marginal.truescore.reliability.R | 3 R/matrix_functions.R | 3 R/matrixfunctions_sirt.R | 3 R/mcmc.2pno.R | 3 R/mcmc.2pno.ml.R | 3 R/mcmc.2pno.ml_alg.R | 3 R/mcmc.2pno.ml_output.R | 3 R/mcmc.2pno_alg.R | 7 R/mcmc.2pnoh.R | 3 R/mcmc.2pnoh_alg.R | 3 R/mcmc.3pno.testlet.R | 75 - R/mcmc.3pno.testlet_alg.R | 116 -- R/mcmc.3pno.testlet_output.R | 3 R/mcmc.aux.R | 3 R/mcmc.list.descriptives.R | 3 R/mcmc_3pno_testlet_draw_itempars.R |only R/mcmc_Rhat.R | 3 R/mcmc_WaldTest.R | 3 R/mcmc_coef.R | 3 R/mcmc_confint.R | 3 R/mcmc_derivedPars.R | 3 R/mcmc_plot.R | 3 R/mcmc_summary.R | 3 R/mcmc_summary_print_information_criteria.R |only R/mcmc_vcov.R | 3 R/mcmclist2coda.R | 3 R/md.pattern.sirt.R | 3 R/mirt.IRT.functions.R | 3 R/mirt.model.vars.R | 3 R/mirt.specify.partable.R | 3 R/mirt.wrapper.calc.counts.R | 3 R/mirt.wrapper.coef.R | 3 R/mirt.wrapper.fscores.R | 3 R/mirt.wrapper.itemplot.R | 3 R/mirt.wrapper.posterior.R | 3 R/mirt_prodterms.R | 3 R/mle.pcm.group.R | 3 R/mle.reliability.R | 3 R/modelfit.cor.R | 3 R/modelfit.cor.poly.R | 3 R/monoreg.rowwise.R | 3 R/nedelsky.irf.R | 3 R/nedelsky.latresp.R | 3 R/nedelsky.sim.R | 3 R/noharm.sirt.R | 3 R/noharm.sirt.est.aux.R | 3 R/noharm.sirt.preprocess.R | 3 R/normal2.cw.R | 3 R/np.dich.R | 3 R/nr.numdiff.R | 3 R/package_version_date.R | 5 R/parmsummary_extend.R | 3 R/pbivnorm2.R | 3 R/pcm.conversion.R | 3 R/pcm.fit.R | 3 R/personfit.R | 3 R/personfit.stat.R | 3 R/pgenlogis.R | 3 R/plausible.values.raschtype.R | 11 R/plot.invariance.alignment.R | 3 R/plot.isop.R | 3 R/plot.lsem.R | 3 R/plot.lsem.permutationTest.R | 3 R/plot.mcmc.sirt.R | 3 R/plot.rasch.mml.R | 3 R/plot.rm.sdt.R | 3 R/polychoric2.R | 3 R/pow.R | 3 R/print.xxirt.R | 3 R/prior_extract_density.R | 3 R/prior_model_pars_CleanString.R | 3 R/prior_model_parse.R | 3 R/prmse.subscores.R | 3 R/prob.guttman.R | 3 R/prob_genlogis_4pl.R | 5 R/qmc.nodes.R | 3 R/rasch.conquest.R | 3 R/rasch.copula.R | 3 R/rasch.copula2.R | 3 R/rasch.copula2_aux.R | 3 R/rasch.copula3.R | 3 R/rasch.copula3.covariance.R | 3 R/rasch.copula3_aux.R | 3 R/rasch.evm.pcm.R | 3 R/rasch.evm.pcm.methods.R | 3 R/rasch.evm.pcm_aux.R | 3 R/rasch.jml.R | 3 R/rasch.jml.biascorr.R | 3 R/rasch.mirtlc.R | 3 R/rasch.mirtlc_aux.R | 3 R/rasch.mml.R | 3 R/rasch.mml.npirt.R | 3 R/rasch.mml.ramsay.R | 3 R/rasch.mml.raschtype.R | 3 R/rasch.mml2.R | 3 R/rasch.mml2.missing1.R | 3 R/rasch.pairwise.R | 3 R/rasch.pairwise.itemcluster.R | 3 R/rasch.pml.R | 3 R/rasch.pml2.R | 3 R/rasch.pml2_aux.R | 3 R/rasch.pml3.R | 3 R/rasch.pml3_aux.R | 3 R/rasch.pml_aux.R | 3 R/rasch.prox.R | 3 R/rasch.va.R | 3 R/rasch_mml2_calc_prob.R | 5 R/rasch_mml2_difference_quotient.R | 5 R/rasch_mml2_modify_list_element.R | 5 R/rasch_mml2_mstep_calc_likelihood.R | 5 R/read.fwf2.R | 3 R/reliability.nonlinear.sem.R | 3 R/rm.facets.R | 3 R/rm.facets_IC.R | 3 R/rm.facets_PP.R | 3 R/rm.facets_alg.R | 3 R/rm.hrm.calcprobs.R | 3 R/rm.hrm.est.tau.item.R | 3 R/rm.sdt.R | 3 R/rm.sdt_alg.R | 3 R/rm.smooth.distribution.R | 3 R/rm_proc.R | 3 R/sia.sirt.R | 3 R/sim.rasch.dep.R | 5 R/sim.raschtype.R | 3 R/sirt_antifisherz.R | 5 R/sirt_csink.R |only R/sirt_fisherz.R | 5 R/sirt_matrix2.R | 5 R/sirt_osink.R |only R/sirt_rbind_fill.R | 5 R/sirt_rmvnorm.R |only R/sirt_round_vector.R |only R/sirt_summary_print_call.R |only R/sirt_summary_print_computation_time.R |only R/sirt_summary_print_objects.R |only R/sirt_summary_print_package.R |only R/sirt_summary_print_package_rsession.R |only R/sirt_summary_print_packages.R |only R/sirt_vector_with_names.R |only R/sirtcat.R | 3 R/smirt.R | 3 R/smirt_alg_comp.R | 3 R/smirt_alg_noncomp.R | 3 R/smirt_alg_partcomp.R | 3 R/smirt_postproc.R | 3 R/smirt_preproc.R | 3 R/smirt_squeeze.R | 3 R/soft_thresholding.R | 3 R/stratified.cronbach.alpha.R | 3 R/sum0.R |only R/summary.R2noharm.R | 3 R/summary.R2noharm.jackknife.R | 3 R/summary.btm.R | 3 R/summary.conf.detect.R | 7 R/summary.fuzcluster.R | 3 R/summary.gom.em.R | 3 R/summary.invariance.alignment.R | 3 R/summary.isop.R | 3 R/summary.isop.test.R |only R/summary.latent.regression.R | 3 R/summary.linking.haberman.R | 7 R/summary.lsem.R | 20 R/summary.lsem.permutationTest.R | 18 R/summary.mcmc.sirt.R | 83 - R/summary.noharm.sirt.R | 3 R/summary.rasch.copula.R | 3 R/summary.rasch.evm.pcm.R | 3 R/summary.rasch.mirtlc.R | 3 R/summary.rasch.mml2.R | 3 R/summary.rasch.pml.R | 3 R/summary.rm.facets.R | 3 R/summary.rm.sdt.R | 3 R/summary.smirt.R | 3 R/summary.xxirt.R | 9 R/summary_round_helper.R | 3 R/tam2mirt.R | 3 R/tam2mirt.aux.R | 3 R/testlet.marginalized.R | 3 R/testlet.yen.q3.R | 3 R/tetrachoric2.R | 3 R/tracemat.R | 3 R/truescore.irt.R | 3 R/unidim.csn.R | 3 R/weighted_colMeans.R | 3 R/weighted_colSums.R | 3 R/weighted_rowMeans.R | 3 R/weighted_rowSums.R | 3 R/weighted_stats_extend_wgt.R | 3 R/wle.rasch.R | 3 R/write.format2.R | 3 R/write.fwf2.R | 3 R/xxirt.R | 3 R/xxirt_EAP.R | 3 R/xxirt_IRT.se.R | 3 R/xxirt_ThetaDistribution_extract_freeParameters.R | 3 R/xxirt_coef.R | 3 R/xxirt_compute_itemprobs.R | 3 R/xxirt_compute_likelihood.R | 3 R/xxirt_compute_posterior.R | 3 R/xxirt_compute_priorDistribution.R | 3 R/xxirt_createDiscItem.R | 3 R/xxirt_createItemList.R | 3 R/xxirt_createParTable.R | 3 R/xxirt_createThetaDistribution.R | 3 R/xxirt_data_proc.R | 3 R/xxirt_hessian.R | 3 R/xxirt_ic.R | 3 R/xxirt_modifyParTable.R | 3 R/xxirt_mstep_ThetaParameters.R | 3 R/xxirt_mstep_itemParameters.R | 3 R/xxirt_mstep_itemParameters_evalPrior.R | 3 R/xxirt_parTheta_extract_freeParameters.R | 3 R/xxirt_partable_extract_freeParameters.R | 3 R/xxirt_partable_include_freeParameters.R | 3 R/xxirt_postproc_parameters.R | 3 R/xxirt_prepare_response_data.R | 5 R/xxirt_proc_ParTable.R | 3 R/xxirt_vcov.R | 3 R/yen.q3.R | 3 R/zzz.R | 3 inst/CITATION | 20 inst/NEWS | 17 man/IRT.mle.Rd | 4 man/Q3.Rd | 4 man/Q3.testlet.Rd | 4 man/R2conquest.Rd | 4 man/R2noharm.EAP.Rd | 4 man/R2noharm.Rd | 4 man/R2noharm.jackknife.Rd | 4 man/automatic.recode.Rd | 4 man/brm.sim.Rd | 4 man/btm.Rd | 4 man/categorize.Rd | 4 man/ccov.np.Rd | 4 man/class.accuracy.rasch.Rd | 4 man/conf.detect.Rd | 4 man/data.activity.itempars.Rd | 4 man/data.big5.Rd | 4 man/data.bs.Rd | 4 man/data.eid.Rd | 4 man/data.ess2005.Rd | 4 man/data.g308.Rd | 4 man/data.inv4gr.Rd | 4 man/data.liking.science.Rd | 4 man/data.long.Rd | 4 man/data.lsem.Rd | 4 man/data.math.Rd | 4 man/data.mcdonald.Rd | 4 man/data.mixed1.Rd | 4 man/data.ml.Rd | 4 man/data.noharm.Rd | 4 man/data.pars1.rasch.Rd | 4 man/data.pirlsmissing.Rd | 4 man/data.pisaMath.Rd | 4 man/data.pisaPars.Rd | 4 man/data.pisaRead.Rd | 4 man/data.pw01.Rd | 4 man/data.ratings1.Rd | 4 man/data.raw1.Rd | 4 man/data.read.Rd | 4 man/data.reck.Rd | 4 man/data.si.Rd | 4 man/data.timss.Rd | 4 man/data.timss07.G8.RUS.Rd | 4 man/data.wide2long.Rd | 4 man/detect.index.Rd | 4 man/dif.logistic.regression.Rd | 4 man/dif.strata.variance.Rd | 4 man/dif.variance.Rd | 4 man/dirichlet.mle.Rd | 4 man/dirichlet.simul.Rd | 4 man/eigenvalues.manymatrices.Rd | 4 man/eigenvalues.sirt.Rd | 4 man/equating.rasch.Rd | 4 man/equating.rasch.jackknife.Rd | 4 man/expl.detect.Rd | 4 man/f1d.irt.Rd | 4 man/fit.isop.Rd | 4 man/fuzcluster.Rd | 4 man/fuzdiscr.Rd | 4 man/gom.em.Rd | 4 man/gom.jml.Rd | 4 man/greenyang.reliability.Rd | 4 man/invariance.alignment.Rd | 4 man/isop.Rd | 4 man/isop.scoring.Rd | 4 man/isop.test.Rd | 4 man/latent.regression.em.raschtype.Rd | 4 man/lavaan2mirt.Rd | 4 man/lc.2raters.Rd | 4 man/likelihood.adjustment.Rd | 4 man/linking.haberman.Rd | 28 man/linking.robust.Rd | 4 man/lsdm.Rd | 4 man/lsem.estimate.Rd | 4 man/lsem.permutationTest.Rd | 4 man/marginal.truescore.reliability.Rd | 4 man/matrixfunctions.sirt.Rd | 4 man/mcmc.2pno.Rd | 4 man/mcmc.2pno.ml.Rd | 4 man/mcmc.2pnoh.Rd | 4 man/mcmc.3pno.testlet.Rd | 4 man/mcmc.list.descriptives.Rd | 4 man/mcmc_Rhat.Rd | 4 man/mcmc_coef.Rd | 4 man/mcmclist2coda.Rd | 4 man/md.pattern.sirt.Rd | 4 man/mirt.specify.partable.Rd | 4 man/mirt.wrapper.Rd | 4 man/mle.pcm.group.Rd | 4 man/modelfit.sirt.Rd | 4 man/monoreg.rowwise.Rd | 4 man/nedelsky.sim.Rd | 4 man/noharm.sirt.Rd | 4 man/np.dich.Rd | 4 man/parmsummary_extend.Rd | 4 man/pbivnorm2.Rd | 4 man/pcm.conversion.Rd | 4 man/pcm.fit.Rd | 4 man/person.parameter.rasch.copula.Rd | 4 man/personfit.stat.Rd | 4 man/pgenlogis.Rd | 4 man/plausible.value.imputation.raschtype.Rd | 4 man/plot.mcmc.sirt.Rd | 4 man/plot.np.dich.Rd | 4 man/polychoric2.Rd | 4 man/prior_model_parse.Rd | 4 man/prmse.subscores.scales.Rd | 12 man/prob.guttman.Rd | 4 man/qmc.nodes.Rd | 4 man/rasch.copula.Rd | 4 man/rasch.evm.pcm.Rd | 4 man/rasch.jml.Rd | 4 man/rasch.jml.biascorr.Rd | 4 man/rasch.jml.jackknife1.Rd | 4 man/rasch.mirtlc.Rd | 4 man/rasch.mml.Rd | 4 man/rasch.pairwise.Rd | 4 man/rasch.pairwise.itemcluster.Rd | 4 man/rasch.pml3.Rd | 4 man/rasch.prox.Rd | 4 man/rasch.va.Rd | 4 man/reliability.nonlinearSEM.Rd | 4 man/rinvgamma2.Rd | 4 man/rm.facets.Rd | 4 man/rm.sdt.Rd | 4 man/sia.sirt.Rd | 4 man/sim.qm.ramsay.Rd | 4 man/sim.rasch.dep.Rd | 4 man/sim.raschtype.Rd | 4 man/sirt-defunct.Rd | 92 +- man/sirt-package.Rd | 4 man/sirt-utilities.Rd | 4 man/smirt.Rd | 4 man/stratified.cronbach.alpha.Rd | 4 man/summary.mcmc.sirt.Rd | 7 man/tam2mirt.Rd | 4 man/testlet.marginalized.Rd | 4 man/tetrachoric2.Rd | 4 man/truescore.irt.Rd | 4 man/unidim.test.csn.Rd | 4 man/wle.rasch.Rd | 4 man/wle.rasch.jackknife.Rd | 4 man/xxirt.Rd | 4 man/xxirt_createParTable.Rd | 4 man/xxirt_createThetaDistribution.Rd | 4 src/RcppExports.cpp | 172 +-- src/eigenvaluessirt.cpp | 3 src/evm_comp_matrix_poly.cpp | 3 src/first_eigenvalue_sirt.h | 3 src/gooijer_isop.cpp | 3 src/gooijercsntableaux.h | 3 src/invariance_alignment.cpp | 3 src/matrixfunctions_sirt.cpp | 3 src/mle_pcm_group_c.cpp | 3 src/noharm_sirt_auxfunctions.cpp | 3 src/pbivnorm_rcpp_aux.h | 3 src/polychoric2_tetrachoric2_rcpp_aux.cpp | 3 src/probs_multcat_items_counts_csirt.cpp | 3 src/rm_smirt_mml2_code.cpp | 3 src/xxirt_functions.cpp | 3 487 files changed, 2436 insertions(+), 1009 deletions(-)
Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 3.0.1 dated 2017-05-03 and 3.1.0 dated 2017-09-20
DESCRIPTION | 12 - MD5 | 102 ++++++------ NAMESPACE | 8 NEWS | 36 ++++ R/DENSITY.R | 98 +++++++----- R/addCovariates.R | 2 R/make.grid.R | 9 - R/methods.R | 111 ------------- R/onAttach.R | 5 R/par.secr.fit.R | 48 +++++ R/plot.secr.R | 27 ++- R/randomHabitat.R | 25 ++- R/rbind.capthist.R | 346 ++++++++----------------------------------- R/rbind.mask.R |only R/rbind.popn.R |only R/read.traps.R | 320 +++++++++++++++++++++------------------ R/secr.design.MS.R | 15 + R/secr.fit.R | 14 + R/secr.test.R | 10 - R/sim.capthist.R | 94 ++++++++--- R/sim.popn.R | 27 ++- R/sim.secr.R | 4 R/utility.R | 3 inst/doc/index.html | 132 +++------------- inst/doc/secr-datainput.R | 9 + inst/doc/secr-datainput.Rmd | 45 ++++- inst/doc/secr-datainput.pdf |binary inst/doc/secr-manual.pdf |binary inst/doc/secr-overview.Rmd | 32 ++- inst/doc/secr-overview.pdf |binary inst/extdata/stoat.xlsx |only man/DENSITY.Rd | 4 man/contour.Rd | 4 man/ip.secr.Rd | 2 man/make.traps.Rd | 5 man/par.secr.fit.Rd | 12 + man/pdot.Rd | 2 man/plot.secr.Rd | 3 man/randomHabitat.Rd | 12 - man/rbind.capthist.Rd | 11 - man/rbind.popn.Rd | 17 +- man/read.telemetry.Rd | 2 man/read.traps.Rd | 12 - man/secr-package.Rd | 10 - man/secr.fit.Rd | 10 - man/secr.test.Rd | 2 man/secrRNG.Rd |only man/sim.capthist.Rd | 3 man/sim.popn.Rd | 3 man/sim.secr.Rd | 2 man/smooths.Rd | 6 src/secr.c | 5 vignettes/secr-datainput.Rmd | 45 ++++- vignettes/secr-overview.Rmd | 32 ++- 54 files changed, 859 insertions(+), 879 deletions(-)
Title: 'pinp' is not 'PNAS'
Description: A 'PNAS'-alike style for 'rmarkdown', derived from the
'Proceedings of the National Academy of Sciences of the United States
of America' (PNAS, see <https://www.pnas.org>) LaTeX style, and
adapted for use with 'markdown' and 'pandoc'.
Author: Dirk Eddelbuettel and James Balamuta
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between pinp versions 0.0.1 dated 2017-09-16 and 0.0.2 dated 2017-09-20
ChangeLog | 80 ++++++++++++++++++++ DESCRIPTION | 9 +- MD5 | 25 ++++-- R/pinp.R | 34 +++++--- README.md | 24 +++--- build |only cleanup |only inst/NEWS.Rd | 19 ++++ inst/doc |only inst/rmarkdown/templates/pdf/resources/template.tex | 38 +++------ inst/rmarkdown/templates/pdf/skeleton/jss.bst |only inst/rmarkdown/templates/pdf/skeleton/pinp.bib | 58 ++++++++------ inst/rmarkdown/templates/pdf/skeleton/pinp.cls | 34 ++------ inst/rmarkdown/templates/pdf/skeleton/skeleton.Rmd | 44 ++++++++--- vignettes |only 15 files changed, 245 insertions(+), 120 deletions(-)
Title: Text Corpus Analysis
Description: Text corpus data analysis, with full support for international text (Unicode). Functions for reading data from newline-delimited JSON files, for normalizing and tokenizing text, for searching for term occurrences, and for computing term occurrence frequencies, including n-grams.
Author: Patrick O. Perry [aut, cph, cre],
Finn Årup Nielsen [cph, dtc] (AFINN Sentiment Lexicon),
Martin Porter and Richard Boulton [ctb, cph, dtc] (Snowball Stemmer and
Stopword Lists),
Carlo Strapparava and Alessandro Valitutti [cph, dtc] (WordNet-Affect
Lexicon),
Unicode, Inc. [cph, dtc] (Unicode Character Database)
Maintainer: Patrick O. Perry <pperry@stern.nyu.edu>
Diff between corpus versions 0.9.1 dated 2017-08-20 and 0.9.2 dated 2017-09-20
corpus-0.9.1/corpus/R/corpus.R |only corpus-0.9.1/corpus/man/as_text.Rd |only corpus-0.9.1/corpus/man/corpus.Rd |only corpus-0.9.1/corpus/vignettes/.install_extras |only corpus-0.9.1/corpus/vignettes/corpus-witch-occurences-1.png |only corpus-0.9.2/corpus/DESCRIPTION | 44 corpus-0.9.2/corpus/MD5 | 208 - corpus-0.9.2/corpus/NAMESPACE | 83 corpus-0.9.2/corpus/NEWS | 496 +- corpus-0.9.2/corpus/R/coerce.R | 210 - corpus-0.9.2/corpus/R/corpus_frame.R |only corpus-0.9.2/corpus/R/deprecated.R | 50 corpus-0.9.2/corpus/R/frame-stats.R |only corpus-0.9.2/corpus/R/frame.R | 29 corpus-0.9.2/corpus/R/gutenberg.R |only corpus-0.9.2/corpus/R/json.R | 20 corpus-0.9.2/corpus/R/sentence.R | 4 corpus-0.9.2/corpus/R/term.R | 70 corpus-0.9.2/corpus/R/text-base.R | 139 corpus-0.9.2/corpus/R/text-primitive.R | 24 corpus-0.9.2/corpus/R/text-stats.R |only corpus-0.9.2/corpus/R/text.R | 116 corpus-0.9.2/corpus/R/text_filter.R | 37 corpus-0.9.2/corpus/R/text_locate.R | 104 corpus-0.9.2/corpus/R/text_split.R | 5 corpus-0.9.2/corpus/R/text_stats.R | 4 corpus-0.9.2/corpus/R/text_types.R | 8 corpus-0.9.2/corpus/R/token.R | 16 corpus-0.9.2/corpus/R/utf8.R | 2 corpus-0.9.2/corpus/R/util.R | 17 corpus-0.9.2/corpus/R/wordlist.R | 2 corpus-0.9.2/corpus/README | 292 - 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Title: Tools to Work with the 'Dark Sky' 'API'
Description: Provides programmatic access to the 'Dark Sky' 'API'
<https://darksky.net/dev/docs>, which provides current or historical global
weather conditions.
Author: Bob Rudis [aut, cre],
Lasse Vilhelmsen [ctb],
David Severski [ctb]
Maintainer: Bob Rudis <bob@rud.is>
Diff between darksky versions 1.0.0 dated 2016-09-22 and 1.3.0 dated 2017-09-20
darksky-1.0.0/darksky/README.md |only darksky-1.3.0/darksky/DESCRIPTION | 26 ++++++------ darksky-1.3.0/darksky/MD5 | 31 ++++++-------- darksky-1.3.0/darksky/NAMESPACE | 3 - darksky-1.3.0/darksky/NEWS.md | 9 ++++ darksky-1.3.0/darksky/R/aaa.r | 9 +++- darksky-1.3.0/darksky/R/darksky-package.r | 3 - darksky-1.3.0/darksky/R/ds-print.r | 2 darksky-1.3.0/darksky/R/get-current-forecast.r | 36 +++++++++++----- darksky-1.3.0/darksky/R/get-forecast-for.r | 43 +++++++++++++------- darksky-1.3.0/darksky/man/darksky.Rd | 1 darksky-1.3.0/darksky/man/darksky_api_key.Rd | 1 darksky-1.3.0/darksky/man/get_current_forecast.Rd | 1 darksky-1.3.0/darksky/man/get_forecast_for.Rd | 10 ++-- darksky-1.3.0/darksky/man/plot.darksky.Rd | 5 -- darksky-1.3.0/darksky/man/print.darksky.Rd | 1 darksky-1.3.0/darksky/tests/testthat/test-darksky.R | 2 17 files changed, 112 insertions(+), 71 deletions(-)
Title: Quasi-Periodic Time Series Characteristics
Description: Calculate Characteristics of Quasi-Periodic Time Series, e.g. Estuarine Water Levels.
Author: Tom Cox <tom.cox@uantwerp.be>, Lennert Schepers <lennert.schepers@uantwerp.be>
Maintainer: Tom Cox <tom.cox@uantwerp.be>
Diff between Tides versions 1.2 dated 2016-09-15 and 2.0 dated 2017-09-20
Tides-1.2/Tides/data/data.rda |only Tides-2.0/Tides/ChangeLog | 6 Tides-2.0/Tides/DESCRIPTION | 9 - Tides-2.0/Tides/MD5 | 39 ++-- Tides-2.0/Tides/NAMESPACE | 3 Tides-2.0/Tides/R/RemoveGaps.R |only Tides-2.0/Tides/R/Summary.R |only Tides-2.0/Tides/R/Tides.R | 239 ++++++++++++++++++++-------- Tides-2.0/Tides/R/gapstsExt.R | 92 +++++----- Tides-2.0/Tides/build/vignette.rds |binary Tides-2.0/Tides/data/example.RData |binary Tides-2.0/Tides/inst/doc/Tides.R | 10 - Tides-2.0/Tides/inst/doc/Tides.Rnw | 61 +++++-- Tides-2.0/Tides/inst/doc/Tides.pdf |binary Tides-2.0/Tides/man/IT.Rd | 37 ++-- Tides-2.0/Tides/man/RemoveGaps.Rd |only Tides-2.0/Tides/man/TidalCharacteristics.Rd | 79 +++++---- Tides-2.0/Tides/man/Tides.Rd | 79 ++++----- Tides-2.0/Tides/man/gapsts.Rd | 2 Tides-2.0/Tides/man/print.Tides.Rd | 2 Tides-2.0/Tides/man/summary.Tides.Rd |only Tides-2.0/Tides/vignettes/Tides.Rnw | 61 +++++-- Tides-2.0/Tides/vignettes/Tides.bib | 2 23 files changed, 462 insertions(+), 259 deletions(-)
Title: Scale Bar, North Arrow, and Pretty Margins in R
Description: Automates the process of creating a scale bar and north arrow in
any package that uses base graphics to plot in R. Bounding box tools help find
and manipulate extents. Finally, there is a function to automate the process
of setting margins, plotting the map, scale bar, and north arrow, and resetting
graphic parameters upon completion.
Author: Dewey Dunnington <dewey@fishandwhistle.net>
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between prettymapr versions 0.2.1 dated 2017-04-07 and 0.2.2 dated 2017-09-20
prettymapr-0.2.1/prettymapr/README.md |only prettymapr-0.2.2/prettymapr/DESCRIPTION | 8 ++++---- prettymapr-0.2.2/prettymapr/MD5 | 7 +++---- prettymapr-0.2.2/prettymapr/R/geocode.R | 10 ++++++---- prettymapr-0.2.2/prettymapr/man/geocode.Rd | 2 +- 5 files changed, 14 insertions(+), 13 deletions(-)
Title: Perceptual Analysis, Visualization and Organization of Spectral
Color Data in R
Description: A cohesive framework for parsing, analyzing and organizing color from spectral data.
Author: Rafael Maia [aut, cre],
Thomas White [aut],
Chad Eliason [aut],
Pierre-Paul Bitton [aut]
Maintainer: Rafael Maia <rm72@zips.uakron.edu>
Diff between pavo versions 1.1.0 dated 2017-05-05 and 1.3.0 dated 2017-09-20
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Title: Interpreting High Resolution Mass Spectra
Description: Annotate and interpret deconvoluted mass spectra (mass*intensity pairs) from high resolution mass spectrometry devices.
Author: Jan Lisec [aut, cre]
Maintainer: Jan Lisec <jan.lisec@charite.de>
Diff between InterpretMSSpectrum versions 1.0 dated 2017-05-10 and 1.1 dated 2017-09-20
DESCRIPTION | 8 +- MD5 | 28 ++++--- NAMESPACE | 7 + R/InterpretMSSpectrum.R | 19 ++--- R/PlotSpec.R | 168 +++++++++++++++++++++++---------------------- R/findMAIN.r | 142 ++++++-------------------------------- R/plot.findMAIN.R |only R/print.findMAIN.R |only R/sendToMSF.r | 39 ++++++---- R/summary.findMAIN.R |only R/tmp.R |only R/writeMSF.r | 17 ++-- man/InterpretMSSpectrum.Rd | 3 man/PlotSpec.Rd | 2 man/findMAIN.Rd | 2 man/sendToMSF.Rd | 12 ++- man/writeMSF.Rd | 2 17 files changed, 203 insertions(+), 246 deletions(-)
More information about InterpretMSSpectrum at CRAN
Permanent link
Title: Bradley-Terry Models
Description: Specify and fit the Bradley-Terry model, including structured versions in which the parameters are related to explanatory variables through a linear predictor and versions with contest-specific effects, such as a home advantage.
Author: Heather Turner [aut, cre],
David Firth [aut]
Maintainer: Heather Turner <ht@heatherturner.net>
Diff between BradleyTerry2 versions 1.0-7 dated 2017-08-26 and 1.0-8 dated 2017-09-20
BradleyTerry2-1.0-7/BradleyTerry2/inst/NEWS |only BradleyTerry2-1.0-8/BradleyTerry2/DESCRIPTION | 14 - BradleyTerry2-1.0-8/BradleyTerry2/MD5 | 25 - BradleyTerry2-1.0-8/BradleyTerry2/NAMESPACE | 1 BradleyTerry2-1.0-8/BradleyTerry2/NEWS.md |only BradleyTerry2-1.0-8/BradleyTerry2/R/BTabilities.R | 2 BradleyTerry2-1.0-8/BradleyTerry2/R/citations.R | 2 BradleyTerry2-1.0-8/BradleyTerry2/R/qvcalc.BTabilities.R | 73 ++++- BradleyTerry2-1.0-8/BradleyTerry2/README.md | 7 BradleyTerry2-1.0-8/BradleyTerry2/inst/doc/BradleyTerry.Rnw | 153 ++++++++++- BradleyTerry2-1.0-8/BradleyTerry2/inst/doc/BradleyTerry.pdf |binary BradleyTerry2-1.0-8/BradleyTerry2/man/GenDavidson.Rd | 2 BradleyTerry2-1.0-8/BradleyTerry2/man/citations.Rd | 2 BradleyTerry2-1.0-8/BradleyTerry2/man/qvcalc.BTabilities.Rd |only BradleyTerry2-1.0-8/BradleyTerry2/vignettes/BradleyTerry.Rnw | 153 ++++++++++- 15 files changed, 405 insertions(+), 29 deletions(-)
Title: SOM Bound to Realize Euclidean and Relational Outputs
Description: The stochastic (also called on-line) version of the Self-Organising
Map (SOM) algorithm is provided. Different versions of the
algorithm are implemented, for numeric and relational data and for
contingency tables as described, respectively, in Kohonen (2001)
<isbn:3-540-67921-9>, Olteanu & Villa-Vialaneix (2005)
<doi:10.1016/j.neucom.2013.11.047> and Cottrell et al (2004)
<doi:10.1016/j.neunet.2004.07.010>. The package also contains many
plotting features (to help the user interpret the results) and a
graphical user interface based on 'shiny'.
Author: Nathalie Villa-Vialaneix [aut, cre],
Jerome Mariette [aut],
Madalina Olteanu [aut],
Fabrice Rossi [aut],
Laura Bendhaiba [ctb],
Julien Boelaert [ctb]
Maintainer: Nathalie Villa-Vialaneix <nathalie.villa-vialaneix@inra.fr>
Diff between SOMbrero versions 1.2 dated 2016-09-02 and 1.2-2 dated 2017-09-20
SOMbrero-1.2-2/SOMbrero/DESCRIPTION | 34 ++++---- SOMbrero-1.2-2/SOMbrero/MD5 | 54 ++++++------- SOMbrero-1.2-2/SOMbrero/NEWS | 17 ++++ SOMbrero-1.2-2/SOMbrero/R/grids.R | 7 + SOMbrero-1.2-2/SOMbrero/R/plots.R | 6 + SOMbrero-1.2-2/SOMbrero/R/superclasses.R | 64 ++++++++++++---- SOMbrero-1.2-2/SOMbrero/TODO |only SOMbrero-1.2-2/SOMbrero/build/vignette.rds |binary SOMbrero-1.2-2/SOMbrero/inst/CITATION | 21 +++-- SOMbrero-1.2-2/SOMbrero/inst/doc/doc-korrespSOM.html | 6 - SOMbrero-1.2-2/SOMbrero/inst/doc/doc-numericSOM.html | 10 +- SOMbrero-1.2-2/SOMbrero/inst/doc/doc-relationalSOM.html | 22 ++--- SOMbrero-1.2-2/SOMbrero/inst/shiny/server.R | 24 +++++- SOMbrero-1.2-2/SOMbrero/inst/shiny/ui.R | 21 ++--- SOMbrero-1.2-2/SOMbrero/man/SOMbrero-package.Rd | 64 ++++++++-------- SOMbrero-1.2-2/SOMbrero/man/initGrid.Rd | 9 +- SOMbrero-1.2-2/SOMbrero/man/initSOM.Rd | 12 +-- SOMbrero-1.2-2/SOMbrero/man/lesmis.Rd | 4 - SOMbrero-1.2-2/SOMbrero/man/plot.myGrid.Rd | 12 ++- SOMbrero-1.2-2/SOMbrero/man/plot.somRes.Rd | 5 - SOMbrero-1.2-2/SOMbrero/man/predict.somRes.Rd | 6 - SOMbrero-1.2-2/SOMbrero/man/projectIGraph.somRes.Rd | 11 ++ SOMbrero-1.2-2/SOMbrero/man/protoDist.somRes.Rd | 6 - SOMbrero-1.2-2/SOMbrero/man/quality.Rd | 8 -- SOMbrero-1.2-2/SOMbrero/man/somRes.plotting.Rd | 5 - SOMbrero-1.2-2/SOMbrero/man/sombreroGUI.Rd | 14 +-- SOMbrero-1.2-2/SOMbrero/man/superClass.Rd | 33 +++++--- SOMbrero-1.2-2/SOMbrero/man/trainSOM.Rd | 35 ++++---- SOMbrero-1.2/SOMbrero/inst/shiny/LICENSE |only 29 files changed, 303 insertions(+), 207 deletions(-)
Title: FDR-Control in Multiscale Change-Point Segmentation
Description: Estimate step functions via multiscale inference with controlled false discovery rate (FDR). For details see H. Li, A. Munk and H. Sieling (2016) <doi:10.1214/16-EJS1131>.
Author: Housen Li [aut],
Hannes Sieling [aut],
Timo Aspelmeier [cre]
Maintainer: Timo Aspelmeier <timo.aspelmeier@mathematik.uni-goettingen.de>
Diff between FDRSeg versions 1.0-2 dated 2017-09-07 and 1.0-3 dated 2017-09-20
DESCRIPTION | 20 +++++++++++--------- MD5 | 6 +++--- build/partial.rdb |binary man/FDRSeg-package.Rd | 4 ++-- 4 files changed, 16 insertions(+), 14 deletions(-)
Title: 'Clp (Coin-or linear programming)' Plugin for the 'R'
Optimization Interface
Description: Enhances the R Optimization Infrastructure (ROI) package by registering
the COIN-OR Clp open-source solver from the COIN-OR suite <https://projects.coin-or.org/>.
It allows for solving linear programming with continuous objective variables
keeping sparse constraints definition.
Author: Benoit Thieurmel [aut, cre]
Maintainer: Benoit Thieurmel <benoit.thieurmel@datastorm.fr>
Diff between ROI.plugin.clp versions 0.3 dated 2017-05-21 and 0.4 dated 2017-09-20
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/plugin.R | 3 +-- tests/testthat/test_LP.R | 18 ++++++++++++++++++ 4 files changed, 26 insertions(+), 9 deletions(-)
More information about ROI.plugin.clp at CRAN
Permanent link
Title: Functions and Datasets to Accompany Hollander, Wolfe, and
Chicken - Nonparametric Statistical Methods, Third Edition
Description: Designed to replace the tables which were in the back of the first two editions of Hollander and Wolfe - Nonparametric Statistical Methods. Exact procedures are performed when computationally possible. Monte Carlo and Asymptotic procedures are performed otherwise. For those procedures included in the base packages, our code simply provides a wrapper to standardize the output with the other procedures in the package.
Author: Grant Schneider, Eric Chicken, Rachel Becvarik
Maintainer: Grant Schneider <schneider.393@osu.edu>
Diff between NSM3 versions 1.8 dated 2016-10-10 and 1.10 dated 2017-09-20
DESCRIPTION | 8 ++-- MD5 | 9 ++--- NAMESPACE | 78 ++++++++++++++++++++++---------------------- R/pRangeNor.R | 36 ++++++++++---------- R/theil.R | 4 +- src/registerDynamicSymbol.c |only 6 files changed, 68 insertions(+), 67 deletions(-)