Title: Estimation Statistics with Confidence Intervals
Description: A collection of functions and 'jamovi' module for the estimation approach to inferential statistics, the approach which emphasizes effect sizes, interval estimates, and meta-analysis. Nearly all functions are based on 'statpsych' and 'metafor'. This package is still under active development, and breaking changes are likely, especially with the plot and hypothesis test functions. Data sets are included for all examples from Cumming & Calin-Jageman (2024) <ISBN:9780367531508>.
Author: Robert Calin-Jageman [aut, cre, cph]
Maintainer: Robert Calin-Jageman <rcalinjageman@dom.edu>
Diff between esci versions 1.0.6 dated 2024-12-21 and 1.0.7 dated 2025-02-21
DESCRIPTION | 6 MD5 | 140 NEWS.md | 8 R/CI_smd_ind_contrast.R | 10 R/estimate_pdiff_ind_contrast.R | 114 R/jamovicorrelation.b.R | 27 R/jamovidescribe.b.R | 33 R/jamovimagnitude.b.R | 35 R/jamovimdiff2x2.b.R | 40 R/jamovimdiffindcontrast.b.R | 14 R/jamovimdiffpaired.b.R | 28 R/jamovimdifftwo.b.R | 12 R/jamovipdifftwo.h.R | 3040 ++++++------ R/jamovirdifftwo.b.R | 26 R/jamovirdifftwo.h.R | 4590 +++++++++---------- README.md | 117 build/stage23.rdb |binary man/CI_smd_ind_contrast.Rd | 10 man/data_altruism_happiness.Rd | 76 man/data_anchor_estimate_ma.Rd | 86 man/data_basol_badnews.Rd | 96 man/data_bem_psychic.Rd | 96 man/data_bodywellf.Rd | 48 man/data_bodywellfm.Rd | 48 man/data_bodywellm.Rd | 48 man/data_campus_involvement.Rd | 66 man/data_chap_8_paired_ex_8.18.Rd | 54 man/data_clean_moral.Rd | 78 man/data_college_survey_1.Rd | 90 man/data_college_survey_2.Rd | 76 man/data_damischrcj.Rd | 52 man/data_emotion_heartrate.Rd | 64 man/data_exam_scores.Rd | 58 man/data_flag_priming_ma.Rd | 76 man/data_gender_math_iat.Rd | 78 man/data_gender_math_iat_ma.Rd | 84 man/data_halagappa.Rd | 82 man/data_home_prices.Rd | 66 man/data_kardas_expt_3.Rd | 86 man/data_kardas_expt_4.Rd | 94 man/data_labels_flavor.Rd | 78 man/data_latimier_3groups.Rd | 84 man/data_latimier_prequiz.Rd | 56 man/data_latimier_quiz.Rd | 56 man/data_latimier_quiz_prequiz.Rd | 56 man/data_latimier_reread.Rd | 56 man/data_latimier_reread_prequiz.Rd | 56 man/data_latimier_reread_quiz.Rd | 56 man/data_macnamara_r_ma.Rd | 86 man/data_mccabemichael_brain.Rd | 130 man/data_mccabemichael_brain2.Rd | 68 man/data_meditationbrain.Rd | 92 man/data_organicmoral.Rd | 92 man/data_penlaptop1.Rd | 52 man/data_powerperformance_ma.Rd | 94 man/data_rattanmotivation.Rd | 82 man/data_religionsharing.Rd | 72 man/data_religious_belief.Rd | 54 man/data_selfexplain.Rd | 78 man/data_simmonscredibility.Rd | 120 man/data_sleep_beauty.Rd | 58 man/data_smithrecall.Rd | 54 man/data_stickgold.Rd | 74 man/data_studystrategies.Rd | 82 man/data_thomason_1.Rd | 60 man/data_videogameaggression.Rd | 74 man/estimate_r.Rd | 312 - man/figures/plot_mdiff.png |binary man/jamovipdifftwo.Rd | 4 tests/testthat/_snaps/estimate_pdiff_ind_contrast.md | 16 tests/testthat/_snaps/estimate_pdiff_two.md | 8 71 files changed, 6195 insertions(+), 5917 deletions(-)
Title: Analysis of Short Tandem Repeat (STR) Massively Parallel
Sequencing (MPS) Data
Description: Loading, identifying, aggregating, manipulating, and analysing short tandem repeat regions of massively parallel sequencing data in forensic genetics. The analyses and framework implemented in this package relies on the papers of Vilsen et al. (2017) <doi:10.1016/j.fsigen.2017.01.017> and Vilsen et al. (2018) <doi:10.1016/j.fsigen.2018.04.003>. Note: that the parallelisation in the package relies on mclapply() and, thus, speed-ups will only be seen on UNIX based systems.
Author: Soeren B. Vilsen [aut, cre]
Maintainer: Soeren B. Vilsen <svilsen@math.aau.dk>
Diff between STRMPS versions 0.5.8 dated 2018-07-02 and 0.6.8 dated 2025-02-21
DESCRIPTION | 24 MD5 | 110 +- NAMESPACE | 52 + R/STR_Region_Identification.R | 224 +++-- R/all_in_one_workflow_fun.R | 248 +++-- R/allele_genotype_functions.R | 427 ++++++++-- R/auxiliary_functions.R | 49 - R/quality_functions.R | 11 R/stutter_functions.R | 214 +++-- README.md |only build |only data/flankingRegions.rda |binary inst/doc |only inst/examples/blmm.R | 6 inst/examples/identify.R | 17 inst/examples/stringCoverageAggregated.R | 20 inst/examples/workFlow.R | 11 inst/extdata/flankingRegions10plexSTRsShifted.RData |binary inst/extdata/flankingRegionsForenSeqSTRsShifted.RData |binary inst/extdata/flankingRegionsS5STRsShifted.RData |only man/BLMM.Rd | 6 man/STRMPSWorkflow.Rd | 19 man/STRMPSWorkflowBatch.Rd | 9 man/findNeighbours-stringCoverageGenotypeList-method.Rd | 9 man/findNeighbours.Rd | 7 man/findStutter-stringCoverageGenotypeList-method.Rd | 5 man/flankingRegions.Rd | 4 man/genotypeList.Rd | 4 man/getGenotype-stringCoverageList-method.Rd | 11 man/getGenotype.Rd | 10 man/identifiedSTRs.Rd | 4 man/identifyNoise-stringCoverageList-method.Rd | 8 man/identifyNoise.Rd | 7 man/identifySTRRegions-ShortReadQ-method.Rd | 34 man/identifySTRRegions-character-method.Rd | 34 man/identifySTRRegions.Rd | 17 man/identifySTRRegions.control.Rd | 18 man/mergeGenotypeStringCoverage-genotypeIdentifiedList-method.Rd | 8 man/mergeGenotypeStringCoverage.Rd | 6 man/mergeNoiseStringCoverage-noiseIdentifiedList-method.Rd | 8 man/mergeNoiseStringCoverage.Rd | 6 man/noiseList.Rd | 4 man/probabilityOfError.Rd | 1 man/qualityScore.Rd | 1 man/stringCoverage-extractedReadsList-method.Rd | 30 man/stringCoverage-extractedReadsListCombined-method.Rd | 30 man/stringCoverage-extractedReadsListNonCombined-method.Rd | 31 man/stringCoverage-extractedReadsListReverseComplement-method.Rd | 31 man/stringCoverage.Rd | 30 man/stringCoverage.control.Rd | 28 man/stringCoverageGenotypeList.Rd | 4 man/stringCoverageList.Rd | 4 man/workflow.control.Rd | 33 vignettes |only 54 files changed, 1260 insertions(+), 614 deletions(-)
Title: 'SAS' Interface
Description: Provides a 'SAS' interface, through
'SASPy'(<https://sassoftware.github.io/saspy/>) and
'reticulate'(<https://rstudio.github.io/reticulate/>). This package
helps you create 'SAS' sessions, execute 'SAS' code in remote 'SAS'
servers, retrieve execution results and log, and exchange datasets
between 'SAS' and 'R'. It also helps you to install 'SASPy' and
create a configuration file for the connection. Please review the
'SASPy' license file as instructed so that you comply with its
separate and independent license.
Author: Liming Li [aut, cre],
Daniel Sabanes Bove [aut],
Isaac Gravestock [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Liming Li <clark.liming@gmail.com>
Diff between sasr versions 0.1.2 dated 2023-05-24 and 0.1.3 dated 2025-02-21
sasr-0.1.2/sasr/man/validate_ssh_with_tunnel.Rd |only sasr-0.1.3/sasr/DESCRIPTION | 37 +++++++------ sasr-0.1.3/sasr/MD5 | 43 ++++++++------- sasr-0.1.3/sasr/NAMESPACE | 3 - sasr-0.1.3/sasr/NEWS.md | 5 + sasr-0.1.3/sasr/R/run_sas.R | 2 sasr-0.1.3/sasr/R/sas_engine.R |only sasr-0.1.3/sasr/R/sascfg.R | 4 - sasr-0.1.3/sasr/R/sasr-package.R | 1 sasr-0.1.3/sasr/R/utils.R | 51 ++++++++---------- sasr-0.1.3/sasr/R/zzz.R | 3 + sasr-0.1.3/sasr/build/vignette.rds |binary sasr-0.1.3/sasr/inst/WORDLIST | 3 - sasr-0.1.3/sasr/inst/doc/introduction.Rmd | 6 +- sasr-0.1.3/sasr/inst/doc/introduction.html | 19 ++---- sasr-0.1.3/sasr/inst/example.Rmd |only sasr-0.1.3/sasr/man/sas_engine.Rd |only sasr-0.1.3/sasr/man/sas_session.Rd |only sasr-0.1.3/sasr/man/sas_session_ssh.Rd | 12 ++-- sasr-0.1.3/sasr/man/sascfg.Rd | 3 - sasr-0.1.3/sasr/man/sasr-package.Rd | 7 +- sasr-0.1.3/sasr/tests/testthat/_snaps/rmarkdown.md |only sasr-0.1.3/sasr/tests/testthat/helper-dummy_session.R | 2 sasr-0.1.3/sasr/tests/testthat/test-rmarkdown.R |only sasr-0.1.3/sasr/tests/testthat/test-utils.R | 27 ++------- sasr-0.1.3/sasr/vignettes/introduction.Rmd | 6 +- 26 files changed, 118 insertions(+), 116 deletions(-)
Title: Fast R and C++ Access to NIfTI Images
Description: Provides very fast read and write access to images stored in the
NIfTI-1, NIfTI-2 and ANALYZE-7.5 formats, with seamless synchronisation
of in-memory image objects between compiled C and interpreted R code. Also
provides a simple image viewer, and a C/C++ API that can be used by other
packages. Not to be confused with 'RNiftyReg', which performs image
registration and applies spatial transformations.
Author: Jon Clayden [cre, aut] ,
Bob Cox [aut],
Mark Jenkinson [aut],
Matt Hall [ctb],
Rick Reynolds [ctb],
Kate Fissell [ctb],
Jean-loup Gailly [cph],
Mark Adler [cph]
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNifti versions 1.7.0 dated 2024-06-19 and 1.8.0 dated 2025-02-21
DESCRIPTION | 12 ++++----- MD5 | 28 +++++++++++++--------- NAMESPACE | 4 +++ NEWS | 17 +++++++++++++ R/attribs.R |only R/nifti.R | 49 +++++++++++++++++++++++++++++++++++----- R/viewer.R | 12 +++++++-- README.md | 2 - build |only inst/extdata/example.json |only inst/tinytest/test-35-viewer.R | 3 ++ inst/tinytest/test-50-attribs.R |only man/bidsJson.Rd |only man/imageAttributes.Rd |only man/readNifti.Rd | 11 ++++++++ man/view.Rd | 4 ++- man/writeNifti.Rd | 7 ++++- src/main.cpp | 12 ++++++++- 18 files changed, 129 insertions(+), 32 deletions(-)
Title: Connect to an OMOP Common Data Model
Description: Provides tools for working with observational health data in the
Observational Medical Outcomes Partnership (OMOP) Common Data Model format with a pipe friendly syntax.
Common data model database table references are stored in a single compound object along with metadata.
Author: Adam Black [aut, cre] ,
Artem Gorbachev [aut],
Edward Burn [aut],
Marti Catala Sabate [aut]
Maintainer: Adam Black <black@ohdsi.org>
Diff between CDMConnector versions 1.7.0 dated 2024-12-19 and 2.0.0 dated 2025-02-21
CDMConnector-1.7.0/CDMConnector/R/cdm_from_environment.R |only CDMConnector-1.7.0/CDMConnector/R/cohortTransformations.R |only CDMConnector-1.7.0/CDMConnector/R/copy_cdm_to.R |only CDMConnector-1.7.0/CDMConnector/R/validate.R |only CDMConnector-1.7.0/CDMConnector/R/zzz-deprecated.R |only CDMConnector-1.7.0/CDMConnector/inst/doc/a05_cdm_reference_backends.R |only CDMConnector-1.7.0/CDMConnector/inst/doc/a05_cdm_reference_backends.Rmd |only CDMConnector-1.7.0/CDMConnector/inst/doc/a05_cdm_reference_backends.html |only CDMConnector-1.7.0/CDMConnector/man/assertTables.Rd |only CDMConnector-1.7.0/CDMConnector/man/assert_write_schema.Rd |only CDMConnector-1.7.0/CDMConnector/man/cdmDisconnect.Rd |only CDMConnector-1.7.0/CDMConnector/man/cdmFromEnvironment.Rd |only CDMConnector-1.7.0/CDMConnector/man/cdmFromFiles.Rd |only CDMConnector-1.7.0/CDMConnector/man/cdmSelectTbl.Rd |only CDMConnector-1.7.0/CDMConnector/man/cdm_from_tables.Rd |only CDMConnector-1.7.0/CDMConnector/man/cdm_name.Rd |only CDMConnector-1.7.0/CDMConnector/man/cohortAttrition.Rd |only CDMConnector-1.7.0/CDMConnector/man/cohortErafy.Rd |only CDMConnector-1.7.0/CDMConnector/man/cohortSet.Rd |only CDMConnector-1.7.0/CDMConnector/man/cohortUnion.Rd |only CDMConnector-1.7.0/CDMConnector/man/cohort_count.Rd |only CDMConnector-1.7.0/CDMConnector/man/intersectCohorts.Rd |only CDMConnector-1.7.0/CDMConnector/man/new_generated_cohort_set.Rd |only CDMConnector-1.7.0/CDMConnector/man/record_cohort_attrition.Rd |only CDMConnector-1.7.0/CDMConnector/man/stow.Rd |only CDMConnector-1.7.0/CDMConnector/man/unionCohorts.Rd |only CDMConnector-1.7.0/CDMConnector/man/unique_table_name.Rd |only CDMConnector-1.7.0/CDMConnector/man/validateCdm.Rd |only CDMConnector-1.7.0/CDMConnector/tests/testthat/test-db-sample.R |only CDMConnector-1.7.0/CDMConnector/vignettes/a05_cdm_reference_backends.Rmd |only CDMConnector-2.0.0/CDMConnector/DESCRIPTION | 17 CDMConnector-2.0.0/CDMConnector/MD5 | 189 +--- CDMConnector-2.0.0/CDMConnector/NAMESPACE | 63 - CDMConnector-2.0.0/CDMConnector/NEWS.md | 10 CDMConnector-2.0.0/CDMConnector/R/CDMConnector-package.R | 2 CDMConnector-2.0.0/CDMConnector/R/Eunomia.R | 73 - CDMConnector-2.0.0/CDMConnector/R/cdm.R | 430 +-------- CDMConnector-2.0.0/CDMConnector/R/cdmSubset.R | 140 --- CDMConnector-2.0.0/CDMConnector/R/compute.R | 41 CDMConnector-2.0.0/CDMConnector/R/copyCdmTo.R |only CDMConnector-2.0.0/CDMConnector/R/dateadd.R | 8 CDMConnector-2.0.0/CDMConnector/R/dbSource.R | 94 ++ CDMConnector-2.0.0/CDMConnector/R/generateCohortSet.R | 311 ------ CDMConnector-2.0.0/CDMConnector/R/generateConceptCohortSet.R | 129 ++ CDMConnector-2.0.0/CDMConnector/R/reexports-omopgenerics.R | 55 - CDMConnector-2.0.0/CDMConnector/R/summariseQuantile.R | 31 CDMConnector-2.0.0/CDMConnector/R/utils.R | 45 CDMConnector-2.0.0/CDMConnector/README.md | 2 CDMConnector-2.0.0/CDMConnector/build/vignette.rds |binary CDMConnector-2.0.0/CDMConnector/inst/cohorts5 |only CDMConnector-2.0.0/CDMConnector/inst/doc/a01_getting-started.R | 61 - CDMConnector-2.0.0/CDMConnector/inst/doc/a01_getting-started.Rmd | 81 - CDMConnector-2.0.0/CDMConnector/inst/doc/a01_getting-started.html | 454 ++++------ CDMConnector-2.0.0/CDMConnector/inst/doc/a02_cohorts.R | 66 - CDMConnector-2.0.0/CDMConnector/inst/doc/a02_cohorts.Rmd | 66 - CDMConnector-2.0.0/CDMConnector/inst/doc/a02_cohorts.html | 388 +++----- CDMConnector-2.0.0/CDMConnector/inst/doc/a03_dbplyr.R | 6 CDMConnector-2.0.0/CDMConnector/inst/doc/a03_dbplyr.Rmd | 6 CDMConnector-2.0.0/CDMConnector/inst/doc/a03_dbplyr.html | 10 CDMConnector-2.0.0/CDMConnector/inst/doc/a06_using_cdm_attributes.R | 22 CDMConnector-2.0.0/CDMConnector/inst/doc/a06_using_cdm_attributes.Rmd | 24 CDMConnector-2.0.0/CDMConnector/inst/doc/a06_using_cdm_attributes.html | 50 - CDMConnector-2.0.0/CDMConnector/man/appendPermanent.Rd | 5 CDMConnector-2.0.0/CDMConnector/man/asDate.Rd | 3 CDMConnector-2.0.0/CDMConnector/man/cdmDisconnect.db_cdm.Rd |only CDMConnector-2.0.0/CDMConnector/man/cdmFlatten.Rd | 20 CDMConnector-2.0.0/CDMConnector/man/cdmFromCon.Rd | 31 CDMConnector-2.0.0/CDMConnector/man/cdmSample.Rd | 6 CDMConnector-2.0.0/CDMConnector/man/cdmSubset.Rd | 8 CDMConnector-2.0.0/CDMConnector/man/cdmSubsetCohort.Rd | 15 CDMConnector-2.0.0/CDMConnector/man/computeQuery.Rd | 10 CDMConnector-2.0.0/CDMConnector/man/copyCdmTo.Rd | 5 CDMConnector-2.0.0/CDMConnector/man/downloadEunomiaData.Rd | 18 CDMConnector-2.0.0/CDMConnector/man/dropTable.db_cdm.Rd |only CDMConnector-2.0.0/CDMConnector/man/eunomiaDir.Rd | 13 CDMConnector-2.0.0/CDMConnector/man/eunomiaIsAvailable.Rd | 9 CDMConnector-2.0.0/CDMConnector/man/exampleDatasets.Rd | 5 CDMConnector-2.0.0/CDMConnector/man/generateCohortSet.Rd | 17 CDMConnector-2.0.0/CDMConnector/man/generateConceptCohortSet.Rd | 21 CDMConnector-2.0.0/CDMConnector/man/inSchema.Rd | 3 CDMConnector-2.0.0/CDMConnector/man/listTables.Rd | 3 CDMConnector-2.0.0/CDMConnector/man/readCohortSet.Rd | 3 CDMConnector-2.0.0/CDMConnector/man/reexports.Rd | 4 CDMConnector-2.0.0/CDMConnector/man/requireEunomia.Rd | 9 CDMConnector-2.0.0/CDMConnector/man/summariseQuantile.Rd | 11 CDMConnector-2.0.0/CDMConnector/man/tblGroup.Rd | 3 CDMConnector-2.0.0/CDMConnector/tests/testthat/old_tests/test-cdm.R | 22 CDMConnector-2.0.0/CDMConnector/tests/testthat/old_tests/test-cdmSubset.R | 4 CDMConnector-2.0.0/CDMConnector/tests/testthat/old_tests/test-intersect.R | 14 CDMConnector-2.0.0/CDMConnector/tests/testthat/setup.R | 17 CDMConnector-2.0.0/CDMConnector/tests/testthat/test-02-db-cdm.R | 17 CDMConnector-2.0.0/CDMConnector/tests/testthat/test-03-db-generateCohortSet.R | 49 - CDMConnector-2.0.0/CDMConnector/tests/testthat/test-04-db-generateConceptCohortSet.R | 18 CDMConnector-2.0.0/CDMConnector/tests/testthat/test-06-db-compute.R | 2 CDMConnector-2.0.0/CDMConnector/tests/testthat/test-07-db-dateadd.R | 10 CDMConnector-2.0.0/CDMConnector/tests/testthat/test-12-db-dplyr.R | 4 CDMConnector-2.0.0/CDMConnector/tests/testthat/test-13-db-custom_cohort_creation.R | 4 CDMConnector-2.0.0/CDMConnector/tests/testthat/test-14-db-cohortTransformations.R | 46 - CDMConnector-2.0.0/CDMConnector/tests/testthat/test-16-db-dbSource.R | 22 CDMConnector-2.0.0/CDMConnector/tests/testthat/test-17-db-generic-bind.R | 2 CDMConnector-2.0.0/CDMConnector/tests/testthat/test-18-db-newGeneratedCohortSet.R | 4 CDMConnector-2.0.0/CDMConnector/tests/testthat/test-db-cdmSubset.R |only CDMConnector-2.0.0/CDMConnector/tests/testthat/test-db-dplyr.R | 4 CDMConnector-2.0.0/CDMConnector/tests/testthat/test-db-example-analysis.R | 2 CDMConnector-2.0.0/CDMConnector/tests/testthat/test-db-utils.R | 118 ++ CDMConnector-2.0.0/CDMConnector/tests/testthat/test-local_cdm.R | 37 CDMConnector-2.0.0/CDMConnector/tests/testthat/test-writePrefixDropUseCase.R | 10 CDMConnector-2.0.0/CDMConnector/tests/testthat/test-write_prefix_cohort_generation_snowflake.R | 2 CDMConnector-2.0.0/CDMConnector/tests/testthat/test-zzz-dplyr.R | 4 CDMConnector-2.0.0/CDMConnector/vignettes/a01_getting-started.Rmd | 81 - CDMConnector-2.0.0/CDMConnector/vignettes/a02_cohorts.Rmd | 66 - CDMConnector-2.0.0/CDMConnector/vignettes/a03_dbplyr.Rmd | 6 CDMConnector-2.0.0/CDMConnector/vignettes/a06_using_cdm_attributes.Rmd | 24 113 files changed, 1384 insertions(+), 2301 deletions(-)
Title: Probabilistic Population Projection
Description: Generating population projections for all countries of the world using several probabilistic components, such as total fertility rate and life expectancy (Raftery et al., 2012 <doi:10.1073/pnas.1211452109>).
Author: Hana Sevcikova [aut, cre],
Adrian Raftery [aut],
Thomas Buettner [aut]
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between bayesPop versions 10.0-1 dated 2023-08-09 and 11.0-2 dated 2025-02-21
bayesPop-10.0-1/bayesPop/R/sysdata.rda |only bayesPop-11.0-2/bayesPop/ChangeLog | 45 bayesPop-11.0-2/bayesPop/DESCRIPTION | 22 bayesPop-11.0-2/bayesPop/MD5 | 52 bayesPop-11.0-2/bayesPop/NAMESPACE | 1 bayesPop-11.0-2/bayesPop/R/adjustments.R | 26 bayesPop-11.0-2/bayesPop/R/aggregate.R | 18 bayesPop-11.0-2/bayesPop/R/get_outputs.R | 118 + bayesPop-11.0-2/bayesPop/R/plot_functions.R | 33 bayesPop-11.0-2/bayesPop/R/predict.pop.R | 1485 ++++++++++------- bayesPop-11.0-2/bayesPop/R/predict_subnat.R | 229 ++ bayesPop-11.0-2/bayesPop/build/partial.rdb |binary bayesPop-11.0-2/bayesPop/data/pasfr_global_norms.rda |binary bayesPop-11.0-2/bayesPop/data/rc1FDM.rda |only bayesPop-11.0-2/bayesPop/data/rc5FDM.rda |only bayesPop-11.0-2/bayesPop/data/vwBaseYear2024.rda |only bayesPop-11.0-2/bayesPop/man/age.specific.migration.Rd | 45 bayesPop-11.0-2/bayesPop/man/bayesPop-internal.Rd | 3 bayesPop-11.0-2/bayesPop/man/bayesPop-package.Rd | 5 bayesPop-11.0-2/bayesPop/man/peak.probability.Rd |only bayesPop-11.0-2/bayesPop/man/pop.aggregate.Rd | 10 bayesPop-11.0-2/bayesPop/man/pop.predict.subnat.Rd | 18 bayesPop-11.0-2/bayesPop/man/predict.pop.Rd | 52 bayesPop-11.0-2/bayesPop/man/project.pasfr.Rd | 5 bayesPop-11.0-2/bayesPop/man/rcFDM.Rd |only bayesPop-11.0-2/bayesPop/man/vwBaseYear.Rd | 25 bayesPop-11.0-2/bayesPop/src/bayesPop_init.c | 5 bayesPop-11.0-2/bayesPop/src/projection_functions.c | 225 ++ bayesPop-11.0-2/bayesPop/tests/run_tests.R | 25 bayesPop-11.0-2/bayesPop/tests/test_functions.R | 190 ++ 30 files changed, 1898 insertions(+), 739 deletions(-)
Title: Run Interruptible Code Asynchronously
Description: Takes an R expression and returns a Job object with a $stop() method
which can be called to terminate the background job. Also provides timeouts
and other mechanisms for automatically terminating a background job. The
result of the expression is available synchronously via $result or
asynchronously with callbacks or through the 'promises' package framework.
Author: Daniel P. Smith [aut, cre] ,
Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Diff between jobqueue versions 1.3.1 dated 2025-02-14 and 1.4.1 dated 2025-02-21
DESCRIPTION | 8 - MD5 | 50 +++++------ NAMESPACE | 4 NEWS.md | 2 R/job.r | 27 ++---- R/process.r | 15 ++- R/queue.r | 180 +++++++++++++++++++++-------------------- R/utils.r | 30 ++++-- R/validate.r | 19 +++- R/worker.r | 125 ++++++++++++++++------------ README.md | 3 inst/doc/hooks.Rmd | 3 inst/doc/hooks.html | 8 - inst/doc/results.Rmd | 22 +---- inst/doc/results.html | 22 +---- man/Job.Rd | 2 man/Queue.Rd | 23 ++--- man/Worker.Rd | 51 +++++++++-- tests/testthat.r | 8 - tests/testthat/test-job.r | 20 +++- tests/testthat/test-process.r | 9 +- tests/testthat/test-queue.r | 108 +++++++++++++++++------- tests/testthat/test-validate.r | 7 + tests/testthat/test-worker.r | 65 +++++++++----- vignettes/hooks.Rmd | 3 vignettes/results.Rmd | 22 +---- 26 files changed, 475 insertions(+), 361 deletions(-)
Title: Easily Install and Load the 'Tidymodels' Packages
Description: The tidy modeling "verse" is a collection of packages for
modeling and statistical analysis that share the underlying design
philosophy, grammar, and data structures of the tidyverse.
Author: Max Kuhn [aut, cre] ,
Hadley Wickham [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between tidymodels versions 1.2.0 dated 2024-03-25 and 1.3.0 dated 2025-02-21
DESCRIPTION | 22 +- MD5 | 14 - NEWS.md | 8 + R/conflicts.R | 61 ++++---- R/tidymodels_prefer.R | 2 README.md | 19 +- build/vignette.rds |binary inst/doc/Tags.html | 380 ++------------------------------------------------ 8 files changed, 92 insertions(+), 414 deletions(-)
Title: Calibration Curves for Clinical Prediction Models
Description: Fit calibrations curves for clinical prediction models and calculate several associated
metrics (Eavg, E50, E90, Emax). Ideally predicted probabilities from a prediction model
should align with observed probabilities. Calibration curves relate predicted probabilities
(or a transformation thereof) to observed outcomes via a flexible non-linear smoothing function.
'pmcalibration' allows users to choose between several smoothers (regression splines, generalized
additive models/GAMs, lowess, loess). Both binary and time-to-event outcomes are supported.
See Van Calster et al. (2016) <doi:10.1016/j.jclinepi.2015.12.005>;
Austin and Steyerberg (2019) <doi:10.1002/sim.8281>;
Austin et al. (2020) <doi:10.1002/sim.8570>.
Author: Stephen Rhodes [aut, cre, cph]
Maintainer: Stephen Rhodes <steverho89@gmail.com>
Diff between pmcalibration versions 0.1.0 dated 2023-09-06 and 0.2.0 dated 2025-02-21
pmcalibration-0.1.0/pmcalibration/build/vignette.rds |only pmcalibration-0.1.0/pmcalibration/inst/doc |only pmcalibration-0.1.0/pmcalibration/man/get_cc.Rd |only pmcalibration-0.1.0/pmcalibration/vignettes |only pmcalibration-0.2.0/pmcalibration/DESCRIPTION | 15 pmcalibration-0.2.0/pmcalibration/MD5 | 57 - pmcalibration-0.2.0/pmcalibration/NAMESPACE | 14 pmcalibration-0.2.0/pmcalibration/NEWS.md | 14 pmcalibration-0.2.0/pmcalibration/R/glm_cal.R | 39 - pmcalibration-0.2.0/pmcalibration/R/logistic_cal.R |only pmcalibration-0.2.0/pmcalibration/R/pmcalibration-package.R | 11 pmcalibration-0.2.0/pmcalibration/R/pmcalibration.R | 25 pmcalibration-0.2.0/pmcalibration/R/reg_spline_X.R | 8 pmcalibration-0.2.0/pmcalibration/R/utils.R | 210 ++--- pmcalibration-0.2.0/pmcalibration/README.md | 370 +++++++++- pmcalibration-0.2.0/pmcalibration/build/partial.rdb |binary pmcalibration-0.2.0/pmcalibration/inst/CITATION | 4 pmcalibration-0.2.0/pmcalibration/man/figures |only pmcalibration-0.2.0/pmcalibration/man/get_curve.Rd |only pmcalibration-0.2.0/pmcalibration/man/logistic_cal.Rd | 11 pmcalibration-0.2.0/pmcalibration/man/plot.pmcalibration.Rd | 33 pmcalibration-0.2.0/pmcalibration/man/pmcalibration-package.Rd | 1 pmcalibration-0.2.0/pmcalibration/man/pmcalibration.Rd | 8 pmcalibration-0.2.0/pmcalibration/man/print.logistic_cal.Rd | 2 pmcalibration-0.2.0/pmcalibration/man/print.logistic_calsummary.Rd | 2 pmcalibration-0.2.0/pmcalibration/man/riskdist.Rd |only pmcalibration-0.2.0/pmcalibration/man/summary.logistic_cal.Rd | 15 27 files changed, 625 insertions(+), 214 deletions(-)
More information about runExamplesWrapper at CRAN
Permanent link
Title: Repeatable Analysis in R
Description: Set of utilities to facilitate the reproduction of analysis in R.
It allow to make_structure(), clean_structure(), and run and log programs in a
predefined order to allow secondary files, analysis and reports be constructed in
an ordered and reproducible form.
Author: John J. Aponte [aut, cre]
Maintainer: John J. Aponte <john.j.aponte@gmail.com>
Diff between repana versions 2.2.0 dated 2024-05-03 and 2.2.1 dated 2025-02-21
DESCRIPTION | 7 +++-- MD5 | 12 ++++----- NEWS.md | 7 ++++- build/vignette.rds |binary inst/doc/targets.html | 2 - man/repana-package.Rd | 1 tests/testthat/test_master.R | 57 +++++++++++++++++++++---------------------- 7 files changed, 47 insertions(+), 39 deletions(-)
Title: Vertical Profiles of Biological Signals in Weather Radar Data
Description: 'R' implementation of the 'vol2bird' software for generating vertical profiles
of birds and other biological signals in weather radar data. See Dokter et al.
(2011) <doi:10.1098/rsif.2010.0116> for a paper describing the methodology.
Author: Anders Henja [aut] ,
Adriaan M. Dokter [aut, cre] ,
Alexander Tedeschi [ctb] ,
Tsung-Yu Lin [ctb] ,
Subranshu Maji [ctb] ,
Daniel Sheldon [ctb] ,
Bart Kranstauber [ctb] ,
Jurriaan H. Spaaks [ctb] ,
Lourens Veen [ctb] ,
Iwan Holleman [ctb] ,
Hidde Lei [...truncated...]
Maintainer: Adriaan M. Dokter <vol2birdr@cornell.edu>
Diff between vol2birdR versions 1.0.6 dated 2025-02-07 and 1.0.7 dated 2025-02-21
DESCRIPTION | 9 +++-- MD5 | 24 +++++++------- NEWS.md | 5 +++ R/install.R | 6 +-- R/vol2bird_config.R | 2 - README.md | 69 +++++++++++++++++++++++-------------------- configure.win | 30 ++++++++++++++++++ inst/COPYRIGHTS | 22 +++++++++++++ man/install_mistnet.Rd | 2 - man/install_mistnet_model.Rd | 2 - src/Makevars.win | 2 - src/RaveIO.cpp | 1 src/libvol2bird/librender.c | 2 - 13 files changed, 119 insertions(+), 57 deletions(-)
Title: Tidy Tuning Tools
Description: The ability to tune models is important. 'tune' contains
functions and classes to be used in conjunction with other
'tidymodels' packages for finding reasonable values of
hyper-parameters in models, pre-processing methods, and
post-processing steps.
Author: Max Kuhn [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between tune versions 1.2.1 dated 2024-04-18 and 1.3.0 dated 2025-02-21
DESCRIPTION | 16 +++--- MD5 | 69 ++++++++++++++-------------- NEWS.md | 6 ++ R/checks.R | 2 R/int_pctl.R | 4 + R/parallel.R | 61 ++++++++++++++++++++++++ R/tune_bayes.R | 4 - R/tune_grid.R | 5 -- R/zzz.R | 1 inst/WORDLIST | 3 - man/parallelism.Rd |only man/tune_grid.Rd | 5 -- tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/bayes.md | 32 ++++++------ tests/testthat/_snaps/fit_best.md | 12 ++-- tests/testthat/_snaps/grid.md | 28 +++++------ tests/testthat/_snaps/resample.md | 4 - tests/testthat/_snaps/select_best.md | 6 +- tests/testthat/data/knn_gp.rds |binary tests/testthat/data/knn_grid.rds |binary tests/testthat/data/knn_results.rds |binary tests/testthat/data/knn_set.rds |binary tests/testthat/data/lm_bayes.rds |binary tests/testthat/data/lm_resamples.rds |binary tests/testthat/data/rcv_results.rds |binary tests/testthat/data/surv_boost_tree_res.rds |binary tests/testthat/data/svm_reg_results.rds |binary tests/testthat/data/svm_results.rds |binary tests/testthat/data/test_objects.RData |binary tests/testthat/test-GP.R | 4 - tests/testthat/test-autoplot.R | 17 +++++- tests/testthat/test-extract.R | 2 tests/testthat/test-int_pctl.R | 8 +-- tests/testthat/test-notes.R | 1 tests/testthat/test-resample.R | 3 - tests/testthat/test-select_best.R | 7 ++ 36 files changed, 191 insertions(+), 109 deletions(-)
Title: Statistical Tools for Bivariate Spatial Dependence Analysis
Description: A collection of functions to test spatial autocorrelation between variables, including Moran I, Geary C and Getis G together with scatter plots, functions for mapping and identifying clusters and outliers, functions associated with the moments of the previous statistics that will allow testing whether there is bivariate spatial autocorrelation, and a function that allows identifying (visualizing neighbours) on the map, the neighbors of any region once the scheme of the spatial weights matrix has been established.
Author: Carlos Melo [aut, cre] ,
Oscar Melo [ctb] ,
Sandra Melo [ctb]
Maintainer: Carlos Melo <cmelo@udistrital.edu.co>
Diff between bispdep versions 1.0-1 dated 2024-08-21 and 1.0-2 dated 2025-02-21
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/connectivity.map.R | 1 + R/moran.cluster.R | 19 ++++++++----------- R/moranbi.cluster.R | 15 ++++++--------- build/partial.rdb |binary inst/CITATION | 6 +++--- 7 files changed, 28 insertions(+), 33 deletions(-)
Title: Generate Samples with a Variety of Probability Distributions
Description: Simplifies the process of generating samples from a variety of probability distributions, allowing users to quickly create data frames for demonstrations, troubleshooting, or teaching purposes. Data is available in multiple sizes—small, medium, and large. For more information, refer to the package documentation.
Author: Nicholas Vietto [aut, cre, cph]
Maintainer: Nicholas Vietto <nicholasvietto@gmail.com>
Diff between samplezoo versions 1.2.0 dated 2025-01-31 and 1.2.1 dated 2025-02-21
DESCRIPTION | 6 - MD5 | 20 ++--- NEWS.md | 14 ++-- R/distributions.R | 14 ++-- R/samplezoo.R | 2 README.md | 33 ++++----- inst/doc/Example.R | 10 ++ inst/doc/Example.Rmd | 16 ++++ inst/doc/Example.html | 172 ++++++++++++++++++++++++++++++-------------------- man/samplezoo.Rd | 2 vignettes/Example.Rmd | 16 ++++ 11 files changed, 193 insertions(+), 112 deletions(-)
Title: Execute and Control System Processes
Description: Tools to run system processes in the background. It can
check if a background process is running; wait on a background process
to finish; get the exit status of finished processes; kill background
processes. It can read the standard output and error of the processes,
using non-blocking connections. 'processx' can poll a process for
standard output or error, with a timeout. It can also poll several
processes at once.
Author: Gabor Csardi [aut, cre, cph] ,
Winston Chang [aut],
Posit Software, PBC [cph, fnd],
Ascent Digital Services [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between processx versions 3.8.5 dated 2025-01-08 and 3.8.6 dated 2025-02-21
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 7 +++++++ R/process.R | 1 - src/win/stdio.c | 11 ++++++----- 5 files changed, 20 insertions(+), 13 deletions(-)
Title: Continuous Time Mediation
Description: Calculates standard errors and confidence intervals for effects in continuous-time mediation models. This package extends the work of
Deboeck and Preacher (2015) <doi:10.1080/10705511.2014.973960> and
Ryan and Hamaker (2021) <doi:10.1007/s11336-021-09767-0>
by providing methods to generate standard errors and confidence intervals for the total, direct, and indirect effects in these models.
Author: Ivan Jacob Agaloos Pesigan [aut, cre, cph]
Maintainer: Ivan Jacob Agaloos Pesigan <r.jeksterslab@gmail.com>
Diff between cTMed versions 1.0.5 dated 2025-01-23 and 1.0.6 dated 2025-02-21
cTMed-1.0.5/cTMed/R/cTMed-exp-cov.R |only cTMed-1.0.5/cTMed/R/cTMed-exp-mean.R |only cTMed-1.0.5/cTMed/man/ExpCov.Rd |only cTMed-1.0.5/cTMed/man/ExpMean.Rd |only cTMed-1.0.6/cTMed/DESCRIPTION | 8 cTMed-1.0.6/cTMed/MD5 | 140 ++--- cTMed-1.0.6/cTMed/NAMESPACE | 2 cTMed-1.0.6/cTMed/NEWS.md | 6 cTMed-1.0.6/cTMed/R/RcppExports.R | 8 cTMed-1.0.6/cTMed/R/cTMed-boot-beta-std.R | 2 cTMed-1.0.6/cTMed/R/cTMed-boot-beta.R | 2 cTMed-1.0.6/cTMed/R/cTMed-boot-indirect-central.R | 2 cTMed-1.0.6/cTMed/R/cTMed-boot-med-std.R | 2 cTMed-1.0.6/cTMed/R/cTMed-boot-med.R | 2 cTMed-1.0.6/cTMed/R/cTMed-boot-total-central.R | 2 cTMed-1.0.6/cTMed/R/cTMed-direct-std.R | 22 cTMed-1.0.6/cTMed/R/cTMed-indirect-std.R | 4 cTMed-1.0.6/cTMed/R/cTMed-total-std.R | 16 cTMed-1.0.6/cTMed/R/linearAlgebra-vec-dot.R | 2 cTMed-1.0.6/cTMed/R/linearAlgebra-vech-dot.R | 14 cTMed-1.0.6/cTMed/R/nBootstrap-bc-ci-dot.R | 12 cTMed-1.0.6/cTMed/R/nBootstrap-bc-probs-dot.R | 6 cTMed-1.0.6/cTMed/R/nBootstrap-ci-format-dot.R | 2 cTMed-1.0.6/cTMed/R/nBootstrap-pc-ci-dot.R | 12 cTMed-1.0.6/cTMed/R/nBootstrap-pc-probs-dot.R | 8 cTMed-1.0.6/cTMed/R/nBootstrap-z0-dot.R | 10 cTMed-1.0.6/cTMed/R/nBootstrap-z1-dot.R | 4 cTMed-1.0.6/cTMed/man/BootBeta.Rd | 4 cTMed-1.0.6/cTMed/man/BootBetaStd.Rd | 4 cTMed-1.0.6/cTMed/man/BootIndirectCentral.Rd | 4 cTMed-1.0.6/cTMed/man/BootMed.Rd | 4 cTMed-1.0.6/cTMed/man/BootMedStd.Rd | 4 cTMed-1.0.6/cTMed/man/BootTotalCentral.Rd | 4 cTMed-1.0.6/cTMed/man/DeltaBeta.Rd | 2 cTMed-1.0.6/cTMed/man/DeltaBetaStd.Rd | 2 cTMed-1.0.6/cTMed/man/DeltaIndirectCentral.Rd | 2 cTMed-1.0.6/cTMed/man/DeltaMed.Rd | 2 cTMed-1.0.6/cTMed/man/DeltaMedStd.Rd | 2 cTMed-1.0.6/cTMed/man/DeltaTotalCentral.Rd | 2 cTMed-1.0.6/cTMed/man/Direct.Rd | 2 cTMed-1.0.6/cTMed/man/DirectStd.Rd | 24 cTMed-1.0.6/cTMed/man/Indirect.Rd | 2 cTMed-1.0.6/cTMed/man/IndirectCentral.Rd | 2 cTMed-1.0.6/cTMed/man/IndirectStd.Rd | 6 cTMed-1.0.6/cTMed/man/MCBeta.Rd | 2 cTMed-1.0.6/cTMed/man/MCBetaStd.Rd | 2 cTMed-1.0.6/cTMed/man/MCIndirectCentral.Rd | 2 cTMed-1.0.6/cTMed/man/MCMed.Rd | 2 cTMed-1.0.6/cTMed/man/MCMedStd.Rd | 2 cTMed-1.0.6/cTMed/man/MCPhi.Rd | 2 cTMed-1.0.6/cTMed/man/MCPhiSigma.Rd | 2 cTMed-1.0.6/cTMed/man/MCTotalCentral.Rd | 2 cTMed-1.0.6/cTMed/man/Med.Rd | 2 cTMed-1.0.6/cTMed/man/MedStd.Rd | 2 cTMed-1.0.6/cTMed/man/PosteriorBeta.Rd | 2 cTMed-1.0.6/cTMed/man/PosteriorIndirectCentral.Rd | 2 cTMed-1.0.6/cTMed/man/PosteriorMed.Rd | 2 cTMed-1.0.6/cTMed/man/PosteriorTotalCentral.Rd | 2 cTMed-1.0.6/cTMed/man/Total.Rd | 2 cTMed-1.0.6/cTMed/man/TotalCentral.Rd | 2 cTMed-1.0.6/cTMed/man/TotalStd.Rd | 18 cTMed-1.0.6/cTMed/man/Trajectory.Rd | 2 cTMed-1.0.6/cTMed/src/RcppExports.cpp | 28 - cTMed-1.0.6/cTMed/src/source.cpp | 275 +++-------- cTMed-1.0.6/cTMed/tests/testthat/test-cTMed-boot-beta-std.R | 18 cTMed-1.0.6/cTMed/tests/testthat/test-cTMed-boot-med-std.R | 12 cTMed-1.0.6/cTMed/tests/testthat/test-cTMed-delta-beta-std.R | 18 cTMed-1.0.6/cTMed/tests/testthat/test-cTMed-delta-med-std.R | 12 cTMed-1.0.6/cTMed/tests/testthat/test-cTMed-direct-std.R | 6 cTMed-1.0.6/cTMed/tests/testthat/test-cTMed-indirect-std.R | 6 cTMed-1.0.6/cTMed/tests/testthat/test-cTMed-mc-beta-std.R | 18 cTMed-1.0.6/cTMed/tests/testthat/test-cTMed-mc-med-std.R | 12 cTMed-1.0.6/cTMed/tests/testthat/test-cTMed-total-std.R | 86 --- 73 files changed, 310 insertions(+), 593 deletions(-)
Title: Easily Create Production-Ready Rich Text Format (RTF) Tables and
Figures
Description: Create production-ready Rich Text Format (RTF) tables and figures
with flexible format.
Author: Yilong Zhang [aut],
Siruo Wang [aut],
Simiao Ye [aut],
Fansen Kong [aut],
Brian Lang [aut],
Benjamin Wang [aut, cre],
Nan Xiao [ctb],
Madhusudhan Ginnaram [ctb],
Ruchitbhai Patel [ctb],
Huei-Ling Chen [ctb],
Peikun Wu [ctb],
Uday Preetham Palukuru [c [...truncated...]
Maintainer: Benjamin Wang <benjamin.wang@merck.com>
Diff between r2rtf versions 1.1.1 dated 2023-10-25 and 1.1.2 dated 2025-02-21
r2rtf-1.1.1/r2rtf/R/sysdata.rda |only r2rtf-1.1.2/r2rtf/DESCRIPTION | 21 ++-- r2rtf-1.1.2/r2rtf/MD5 | 39 ++++--- r2rtf-1.1.2/r2rtf/NEWS.md | 14 ++ r2rtf-1.1.2/r2rtf/R/conversion.R | 13 +- r2rtf-1.1.2/r2rtf/R/rtf_convert_format.R | 1 r2rtf-1.1.2/r2rtf/R/unicode_latex.R |only r2rtf-1.1.2/r2rtf/R/utils.R |only r2rtf-1.1.2/r2rtf/R/zzz.R | 2 r2rtf-1.1.2/r2rtf/README.md | 8 - r2rtf-1.1.2/r2rtf/inst/CITATION | 2 r2rtf-1.1.2/r2rtf/inst/doc/r2rtf-cran.R | 16 +-- r2rtf-1.1.2/r2rtf/inst/doc/r2rtf-cran.html | 14 +- r2rtf-1.1.2/r2rtf/tests/testthat.R | 2 r2rtf-1.1.2/r2rtf/tests/testthat/test-independent-testing-as_rtf_pageby.R | 30 ++---- r2rtf-1.1.2/r2rtf/tests/testthat/test-independent-testing-as_rtf_table.R | 12 +- r2rtf-1.1.2/r2rtf/tests/testthat/test-independent-testing-assemble.R | 50 +++++----- r2rtf-1.1.2/r2rtf/tests/testthat/test-independent-testing-rtf_body.R | 8 - r2rtf-1.1.2/r2rtf/tests/testthat/test-independent-testing-rtf_encode_table.R | 26 ++--- r2rtf-1.1.2/r2rtf/tests/testthat/test-independent-testing-rtf_nrow.R | 3 r2rtf-1.1.2/r2rtf/tests/testthat/test-independent-testing-rtf_pageby.R | 14 +- r2rtf-1.1.2/r2rtf/tests/testthat/test-independent-testing-rtf_read_figure.R | 1 22 files changed, 139 insertions(+), 137 deletions(-)
Title: Matching Adjusted Indirect Comparison
Description: Facilitates performing matching adjusted indirect comparison
(MAIC) analysis where the endpoint of interest is either time-to-event
(e.g. overall survival) or binary (e.g. objective tumor response). The method
is described by Signorovitch et al (2012) <doi:10.1016/j.jval.2012.05.004>.
Author: Gregory Chen [aut],
Michael Seo [aut],
Isaac Gravestock [aut, cre],
Miranta Antoniou [ctb],
Chrysostomos Kalyvas [ctb],
MSD, Inc. [cph, fnd],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Isaac Gravestock <isaac.gravestock@roche.com>
Diff between maicplus versions 0.1.1 dated 2024-11-22 and 0.1.2 dated 2025-02-21
DESCRIPTION | 9 MD5 | 77 +-- NAMESPACE | 2 NEWS.md | 9 R/binary-helper.R | 2 R/maic_anchored.R | 18 R/maic_unanchored.R | 18 R/maicplus-package.R | 1 R/matching.R | 31 - build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 53 -- inst/doc/anchored_binary.R | 72 +-- inst/doc/anchored_binary.Rmd | 2 inst/doc/anchored_binary.html | 58 +- inst/doc/anchored_survival.R | 94 ++-- inst/doc/anchored_survival.Rmd | 2 inst/doc/anchored_survival.html | 49 +- inst/doc/calculating_weights.html | 11 inst/doc/introduction.html | 4 inst/doc/kaplan_meier_plots.html | 21 - inst/doc/unanchored_binary.R | 64 +-- inst/doc/unanchored_binary.Rmd | 4 inst/doc/unanchored_binary.html | 64 ++- inst/doc/unanchored_survival.R | 72 +-- inst/doc/unanchored_survival.Rmd | 4 inst/doc/unanchored_survival.html | 47 ++ man/check_weights.Rd | 8 tests/testthat/_snaps/maic_anchored.md | 630 ++++++++++++++++++++++--------- tests/testthat/_snaps/maic_unanchored.md | 400 ++++++++++++++----- tests/testthat/_snaps/matching.md |only tests/testthat/test-maic_anchored.R | 62 ++- tests/testthat/test-maic_unanchored.R | 110 ++++- tests/testthat/test-matching.R | 61 ++- tests/testthat/test-plot_km2.R | 30 - vignettes/anchored_binary.Rmd | 2 vignettes/anchored_survival.Rmd | 2 vignettes/references.bib | 13 vignettes/unanchored_binary.Rmd | 4 vignettes/unanchored_survival.Rmd | 4 40 files changed, 1413 insertions(+), 701 deletions(-)
Title: Tools Developed by the Long Term Ecological Research Community
Description: Set of the data science tools created by various members of the Long Term
Ecological Research (LTER) community. These functions were initially written largely
as standalone operations and have later been aggregated into this package.
Author: Nicholas Lyon [aut, cre] ,
Angel Chen [aut] ,
Miguel C. Leon [ctb] ,
National Science Foundation [fnd] ,
University of California, Santa Barbara [cph]
Maintainer: Nicholas Lyon <lyon@nceas.ucsb.edu>
Diff between ltertools versions 1.1.0 dated 2024-09-20 and 1.2.0 dated 2025-02-21
DESCRIPTION | 8 +- MD5 | 19 +++--- NAMESPACE | 1 NEWS.md | 6 + R/expand_key.R |only README.md | 4 + inst/doc/ltertools.R | 22 +++++-- inst/doc/ltertools.Rmd | 31 +++++++--- inst/doc/ltertools.html | 118 +++++++++++++++++++++++---------------- man/expand_key.Rd |only tests/testthat/test-expand_key.R |only vignettes/ltertools.Rmd | 31 +++++++--- 12 files changed, 158 insertions(+), 82 deletions(-)
Title: Flexible Non-Linear Least Square Model Fitting
Description: Provides tools for flexible non-linear least squares model fitting using general-purpose optimization techniques. The package supports a variety of optimization algorithms, including those provided by the 'optimx' package, making it suitable for handling complex non-linear models. Features include parallel processing support via the 'future' and 'foreach' packages, comprehensive model diagnostics, and visualization capabilities. Implements methods described in Nash and Varadhan (2011, <doi:10.18637/jss.v043.i09>).
Author: Johan Aparicio [cre, aut],
Jeffrey Endelman [aut],
University of Wisconsin Madison [cph]
Maintainer: Johan Aparicio <aparicioarce@wisc.edu>
Diff between flexFitR versions 1.0.0 dated 2025-01-20 and 1.1.0 dated 2025-02-21
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Title: Classifying DNA Sequences to Taxonomic Groupings
Description: Classification based analysis of DNA sequences to taxonomic groupings. This package primarily implements Naive Bayesian Classifier from the Ribosomal Database Project. This approach has traditionally been used to classify 16S rRNA gene sequences to bacterial taxonomic outlines; however, it can be used for any type of gene sequence. The method was originally described by Wang, Garrity, Tiedje, and Cole in Applied and Environmental Microbiology 73(16):5261-7 <doi:10.1128/AEM.00062-07>. The package also provides functions to read in 'FASTA'-formatted sequence data.
Author: Pat Schloss [aut, cre, cph]
Maintainer: Pat Schloss <pschloss@umich.edu>
Diff between phylotypr versions 0.1.0 dated 2024-10-14 and 0.1.1 dated 2025-02-21
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Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence
dating data analysis. This includes, amongst others, data import, export,
application of age models, curve deconvolution, sequence analysis and
plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre, dtc]
,
Christoph Burow [aut, trl, dtc]
,
Michael Dietze [aut] ,
Margret C. Fuchs [aut] ,
Christoph Schmidt [aut] ,
Manfred Fischer [aut, trl],
Johannes Friedrich [aut] ,
Norbert Mercier [aut] ,
Rachel K. Smedley [ct [...truncated...]
Maintainer: Sebastian Kreutzer <maintainer_luminescence@r-luminescence.org>
Diff between Luminescence versions 0.9.26 dated 2024-11-18 and 1.0.0 dated 2025-02-21
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Luminescence-1.0.0/Luminescence/man/calc_HomogeneityTest.Rd | 8 Luminescence-1.0.0/Luminescence/man/calc_Huntley2006.Rd | 32 Luminescence-1.0.0/Luminescence/man/calc_IEU.Rd | 7 Luminescence-1.0.0/Luminescence/man/calc_Lamothe2003.Rd | 30 Luminescence-1.0.0/Luminescence/man/calc_MaxDose.Rd | 6 Luminescence-1.0.0/Luminescence/man/calc_MinDose.Rd | 65 Luminescence-1.0.0/Luminescence/man/calc_MoransI.Rd |only Luminescence-1.0.0/Luminescence/man/calc_OSLLxTxDecomposed.Rd | 12 Luminescence-1.0.0/Luminescence/man/calc_OSLLxTxRatio.Rd | 16 Luminescence-1.0.0/Luminescence/man/calc_SourceDoseRate.Rd | 38 Luminescence-1.0.0/Luminescence/man/calc_Statistics.Rd | 12 Luminescence-1.0.0/Luminescence/man/calc_TLLxTxRatio.Rd | 2 Luminescence-1.0.0/Luminescence/man/calc_ThermalLifetime.Rd | 13 Luminescence-1.0.0/Luminescence/man/calc_WodaFuchs2008.Rd | 4 Luminescence-1.0.0/Luminescence/man/calc_gSGC.Rd | 14 Luminescence-1.0.0/Luminescence/man/calc_gSGC_feldspar.Rd | 4 Luminescence-1.0.0/Luminescence/man/combine_De_Dr.Rd | 11 Luminescence-1.0.0/Luminescence/man/convert_Activity2Concentration.Rd | 6 Luminescence-1.0.0/Luminescence/man/convert_BIN2CSV.Rd | 2 Luminescence-1.0.0/Luminescence/man/convert_CW2pHMi.Rd |only Luminescence-1.0.0/Luminescence/man/convert_CW2pLM.Rd |only Luminescence-1.0.0/Luminescence/man/convert_CW2pLMi.Rd |only Luminescence-1.0.0/Luminescence/man/convert_CW2pPMi.Rd |only Luminescence-1.0.0/Luminescence/man/convert_Concentration2DoseRate.Rd | 2 Luminescence-1.0.0/Luminescence/man/convert_Daybreak2CSV.Rd | 2 Luminescence-1.0.0/Luminescence/man/convert_PSL2CSV.Rd | 2 Luminescence-1.0.0/Luminescence/man/convert_PSL2Risoe.BINfileData.Rd |only Luminescence-1.0.0/Luminescence/man/convert_RLum2Risoe.BINfileData.Rd | 20 Luminescence-1.0.0/Luminescence/man/convert_SG2MG.Rd | 5 Luminescence-1.0.0/Luminescence/man/convert_Second2Gray.Rd |only Luminescence-1.0.0/Luminescence/man/convert_Wavelength2Energy.Rd | 11 Luminescence-1.0.0/Luminescence/man/convert_XSYG2CSV.Rd | 2 Luminescence-1.0.0/Luminescence/man/extract_IrradiationTimes.Rd | 8 Luminescence-1.0.0/Luminescence/man/extract_ROI.Rd | 13 Luminescence-1.0.0/Luminescence/man/fit_CWCurve.Rd | 59 Luminescence-1.0.0/Luminescence/man/fit_DoseResponseCurve.Rd |only Luminescence-1.0.0/Luminescence/man/fit_EmissionSpectra.Rd | 46 Luminescence-1.0.0/Luminescence/man/fit_LMCurve.Rd | 29 Luminescence-1.0.0/Luminescence/man/fit_OSLLifeTimes.Rd | 26 Luminescence-1.0.0/Luminescence/man/fit_SurfaceExposure.Rd | 4 Luminescence-1.0.0/Luminescence/man/fit_ThermalQuenching.Rd | 18 Luminescence-1.0.0/Luminescence/man/get_Layout.Rd | 5 Luminescence-1.0.0/Luminescence/man/get_Quote.Rd | 2 Luminescence-1.0.0/Luminescence/man/get_RLum.Rd | 41 Luminescence-1.0.0/Luminescence/man/get_Risoe.BINfileData.Rd | 21 Luminescence-1.0.0/Luminescence/man/get_rightAnswer.Rd | 2 Luminescence-1.0.0/Luminescence/man/import_Data.Rd | 18 Luminescence-1.0.0/Luminescence/man/length_RLum.Rd | 16 Luminescence-1.0.0/Luminescence/man/melt_RLum.Rd |only Luminescence-1.0.0/Luminescence/man/merge_RLum.Analysis.Rd | 2 Luminescence-1.0.0/Luminescence/man/merge_RLum.Data.Curve.Rd | 31 Luminescence-1.0.0/Luminescence/man/merge_RLum.Data.Spectrum.Rd |only Luminescence-1.0.0/Luminescence/man/merge_RLum.Rd | 2 Luminescence-1.0.0/Luminescence/man/merge_RLum.Results.Rd | 2 Luminescence-1.0.0/Luminescence/man/merge_Risoe.BINfileData.Rd | 2 Luminescence-1.0.0/Luminescence/man/metadata.Rd |only Luminescence-1.0.0/Luminescence/man/methods_RLum.Rd | 21 Luminescence-1.0.0/Luminescence/man/names_RLum.Rd | 19 Luminescence-1.0.0/Luminescence/man/plot_AbanicoPlot.Rd | 38 Luminescence-1.0.0/Luminescence/man/plot_DRCSummary.Rd | 50 Luminescence-1.0.0/Luminescence/man/plot_DRTResults.Rd | 8 Luminescence-1.0.0/Luminescence/man/plot_DetPlot.Rd | 21 Luminescence-1.0.0/Luminescence/man/plot_DoseResponseCurve.Rd |only Luminescence-1.0.0/Luminescence/man/plot_FilterCombinations.Rd | 13 Luminescence-1.0.0/Luminescence/man/plot_GrowthCurve.Rd | 249 - Luminescence-1.0.0/Luminescence/man/plot_Histogram.Rd | 6 Luminescence-1.0.0/Luminescence/man/plot_KDE.Rd | 10 Luminescence-1.0.0/Luminescence/man/plot_MoranScatterplot.Rd |only Luminescence-1.0.0/Luminescence/man/plot_NRt.Rd | 16 Luminescence-1.0.0/Luminescence/man/plot_OSLAgeSummary.Rd | 5 Luminescence-1.0.0/Luminescence/man/plot_RLum.Analysis.Rd | 15 Luminescence-1.0.0/Luminescence/man/plot_RLum.Data.Curve.Rd | 12 Luminescence-1.0.0/Luminescence/man/plot_RLum.Data.Image.Rd | 2 Luminescence-1.0.0/Luminescence/man/plot_RLum.Data.Spectrum.Rd | 27 Luminescence-1.0.0/Luminescence/man/plot_RLum.Rd | 2 Luminescence-1.0.0/Luminescence/man/plot_RLum.Results.Rd | 2 Luminescence-1.0.0/Luminescence/man/plot_ROI.Rd | 7 Luminescence-1.0.0/Luminescence/man/plot_RadialPlot.Rd | 4 Luminescence-1.0.0/Luminescence/man/plot_Risoe.BINfileData.Rd | 23 Luminescence-1.0.0/Luminescence/man/plot_SingleGrainDisc.Rd |only Luminescence-1.0.0/Luminescence/man/plot_ViolinPlot.Rd | 14 Luminescence-1.0.0/Luminescence/man/read_BIN2R.Rd | 17 Luminescence-1.0.0/Luminescence/man/read_Daybreak2R.Rd | 8 Luminescence-1.0.0/Luminescence/man/read_HeliosOSL2R.Rd | 5 Luminescence-1.0.0/Luminescence/man/read_PSL2R.Rd | 6 Luminescence-1.0.0/Luminescence/man/read_RF2R.Rd | 12 Luminescence-1.0.0/Luminescence/man/read_SPE2R.Rd | 7 Luminescence-1.0.0/Luminescence/man/read_TIFF2R.Rd | 7 Luminescence-1.0.0/Luminescence/man/read_XSYG2R.Rd | 19 Luminescence-1.0.0/Luminescence/man/replicate_RLum.Rd | 9 Luminescence-1.0.0/Luminescence/man/report_RLum.Rd | 2 Luminescence-1.0.0/Luminescence/man/sTeve.Rd | 2 Luminescence-1.0.0/Luminescence/man/scale_GammaDose.Rd | 18 Luminescence-1.0.0/Luminescence/man/set_RLum.Rd | 35 Luminescence-1.0.0/Luminescence/man/set_Risoe.BINfileData.Rd | 15 Luminescence-1.0.0/Luminescence/man/smooth_RLum.Rd | 23 Luminescence-1.0.0/Luminescence/man/sort_RLum.Rd |only Luminescence-1.0.0/Luminescence/man/structure_RLum.Rd | 24 Luminescence-1.0.0/Luminescence/man/subset_SingleGrainData.Rd | 2 Luminescence-1.0.0/Luminescence/man/template_DRAC.Rd | 10 Luminescence-1.0.0/Luminescence/man/trim_RLum.Data.Rd | 31 Luminescence-1.0.0/Luminescence/man/tune_Data.Rd | 2 Luminescence-1.0.0/Luminescence/man/use_DRAC.Rd | 16 Luminescence-1.0.0/Luminescence/man/verify_SingleGrainData.Rd | 19 Luminescence-1.0.0/Luminescence/man/view.Rd |only Luminescence-1.0.0/Luminescence/man/write_R2BIN.Rd | 10 Luminescence-1.0.0/Luminescence/man/write_R2TIFF.Rd | 2 Luminescence-1.0.0/Luminescence/man/write_RLum2CSV.Rd | 19 Luminescence-1.0.0/Luminescence/src/RcppExports.cpp | 15 Luminescence-1.0.0/Luminescence/src/src_EED_Calc_Overall_StatUncertainty.cpp |only Luminescence-1.0.0/Luminescence/src/src_analyse_IRSARRF_SRS.cpp | 128 Luminescence-1.0.0/Luminescence/tests/testthat/_data/CLBR.xlsx |only Luminescence-1.0.0/Luminescence/tests/testthat/_data/CLBR_IR100.csv |only Luminescence-1.0.0/Luminescence/tests/testthat/_data/CLBR_IR150.csv |only Luminescence-1.0.0/Luminescence/tests/testthat/_data/CLBR_IR225.csv |only Luminescence-1.0.0/Luminescence/tests/testthat/_data/CLBR_IR50.csv |only Luminescence-1.0.0/Luminescence/tests/testthat/_data/bin-tests |only Luminescence-1.0.0/Luminescence/tests/testthat/_data/xsyg-tests |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/RLum.Analysis-class.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/Risoe.BINfileData-class.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/analyse_Al2O3C_CrossTalk.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/analyse_IRSAR.RF.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/analyse_SAR.CWOSL.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/analyse_baSAR.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/apply_Crosstalk.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/calc_AliquotSize.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/calc_AverageDose.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/calc_CentralDose.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/calc_CobbleDoseRate.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/calc_CommonDose.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/calc_CosmicDoseRate.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/calc_FadingCorr.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/calc_Huntley2006.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/calc_IEU.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/calc_MoransI.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/calc_OSLLxTxDecomposed.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/calc_OSLLxTxRatio.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/calc_Statistics.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/convert_CW2pX.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/convert_Second2Gray.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/fit_DoseResponseCurve.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/fit_LMCurve.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/fit_OSLLifeTimes.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/internals_Thermochronometry.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/merge_RLum.Data.Curve.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/merge_RLum.Data.Spectrum.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/plot_AbanicoPlot |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/plot_NRt.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/read_BIN2R.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/read_SPE2R.md |only Luminescence-1.0.0/Luminescence/tests/testthat/_snaps/smooth_RLum.md |only Luminescence-1.0.0/Luminescence/tests/testthat/setup.R | 72 Luminescence-1.0.0/Luminescence/tests/testthat/test_Analyse_SAROSLdata.R | 15 Luminescence-1.0.0/Luminescence/tests/testthat/test_RLum.Analysis-class.R | 58 Luminescence-1.0.0/Luminescence/tests/testthat/test_RLum.Data.Curve.R | 25 Luminescence-1.0.0/Luminescence/tests/testthat/test_RLum.Data.Image.R | 9 Luminescence-1.0.0/Luminescence/tests/testthat/test_RLum.Data.Spectrum.R | 21 Luminescence-1.0.0/Luminescence/tests/testthat/test_RLum.Results-class.R | 12 Luminescence-1.0.0/Luminescence/tests/testthat/test_Risoe.BINfileData-class.R |only Luminescence-1.0.0/Luminescence/tests/testthat/test_Risoe.BINfileData2RLum.Analysis.R | 26 Luminescence-1.0.0/Luminescence/tests/testthat/test_analyse_Al2O3C_CrossTalk.R | 66 Luminescence-1.0.0/Luminescence/tests/testthat/test_analyse_Al2O3C_ITC.R | 6 Luminescence-1.0.0/Luminescence/tests/testthat/test_analyse_Al2O3C_Measurement.R | 67 Luminescence-1.0.0/Luminescence/tests/testthat/test_analyse_FadingMeasurement.R | 119 Luminescence-1.0.0/Luminescence/tests/testthat/test_analyse_IRSAR.RF.R | 209 Luminescence-1.0.0/Luminescence/tests/testthat/test_analyse_SAR.CWOSL.R | 289 - Luminescence-1.0.0/Luminescence/tests/testthat/test_analyse_SAR.TL.R | 41 Luminescence-1.0.0/Luminescence/tests/testthat/test_analyse_ThermochronometryData.R |only Luminescence-1.0.0/Luminescence/tests/testthat/test_analyse_baSAR.R | 308 + Luminescence-1.0.0/Luminescence/tests/testthat/test_analyse_pIRIRSequence.R | 89 Luminescence-1.0.0/Luminescence/tests/testthat/test_analyse_portableOSL.R | 34 Luminescence-1.0.0/Luminescence/tests/testthat/test_apply_CosmicRayRemoval.R | 32 Luminescence-1.0.0/Luminescence/tests/testthat/test_apply_Crosstalk.R |only Luminescence-1.0.0/Luminescence/tests/testthat/test_apply_EfficiencyCorrection.R | 16 Luminescence-1.0.0/Luminescence/tests/testthat/test_as_latex_table.R | 5 Luminescence-1.0.0/Luminescence/tests/testthat/test_bin_RLumData.R | 24 Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_AliquotSize.R | 74 Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_AverageDose.R | 53 Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_CentralDose.R | 58 Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_CobbleDoseRate.R | 51 Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_CommonDose.R | 38 Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_CosmicDoseRate.R | 63 Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_EED_Model.R |only Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_FadingCorr.R | 84 Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_FastRatio.R | 92 Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_FiniteMixture.R | 48 Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_FuchsLang2001.R | 18 Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_HomogeneityTest.R | 15 Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_Huntley2006.R | 166 Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_IEU.R | 113 Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_Lamothe2003.R | 75 Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_MinDose.R | 17 Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_MoransI.R |only Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_OSLLxTxDecomposed.R | 18 Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_OSLLxTxRatio.R | 144 Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_SourceDoseRate.R | 30 Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_Statistics.R | 93 Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_TLLxTxRatio.R | 14 Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_ThermalLifetime.R | 21 Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_WodaFuchs2008.R | 4 Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_gSGC.R | 20 Luminescence-1.0.0/Luminescence/tests/testthat/test_calc_gSGC_feldspar.R | 8 Luminescence-1.0.0/Luminescence/tests/testthat/test_combine_De_Dr.R | 25 Luminescence-1.0.0/Luminescence/tests/testthat/test_convert_Activity2Concentration.R | 8 Luminescence-1.0.0/Luminescence/tests/testthat/test_convert_BIN2CSV.R |only Luminescence-1.0.0/Luminescence/tests/testthat/test_convert_CW2pX.R |only Luminescence-1.0.0/Luminescence/tests/testthat/test_convert_Concentration2DoseRate.R | 13 Luminescence-1.0.0/Luminescence/tests/testthat/test_convert_Daybreak2CSV.R | 6 Luminescence-1.0.0/Luminescence/tests/testthat/test_convert_PSL2CSV.R | 46 Luminescence-1.0.0/Luminescence/tests/testthat/test_convert_PSL2RisoeBINfiledata.R |only Luminescence-1.0.0/Luminescence/tests/testthat/test_convert_RLum2Risoe.BINfileData.R | 23 Luminescence-1.0.0/Luminescence/tests/testthat/test_convert_SG2MG.R | 11 Luminescence-1.0.0/Luminescence/tests/testthat/test_convert_Second2Gray.R |only Luminescence-1.0.0/Luminescence/tests/testthat/test_convert_Wavelength2Energy.R | 25 Luminescence-1.0.0/Luminescence/tests/testthat/test_convert_XSYG2CSV.R | 28 Luminescence-1.0.0/Luminescence/tests/testthat/test_extract_IrradiationTimes.R | 34 Luminescence-1.0.0/Luminescence/tests/testthat/test_extract_ROI.R | 46 Luminescence-1.0.0/Luminescence/tests/testthat/test_fit_CWCurve.R | 56 Luminescence-1.0.0/Luminescence/tests/testthat/test_fit_DoseResponseCurve.R |only Luminescence-1.0.0/Luminescence/tests/testthat/test_fit_EmissionSpectra.R | 74 Luminescence-1.0.0/Luminescence/tests/testthat/test_fit_IsothermalHolding.R |only Luminescence-1.0.0/Luminescence/tests/testthat/test_fit_LMCurve.R | 126 Luminescence-1.0.0/Luminescence/tests/testthat/test_fit_OSLLifeTimes.R | 72 Luminescence-1.0.0/Luminescence/tests/testthat/test_fit_SurfaceExposure.R | 22 Luminescence-1.0.0/Luminescence/tests/testthat/test_fit_ThermalQuenching.R | 28 Luminescence-1.0.0/Luminescence/tests/testthat/test_github.R | 22 Luminescence-1.0.0/Luminescence/tests/testthat/test_import_Data.R | 42 Luminescence-1.0.0/Luminescence/tests/testthat/test_internals.R | 313 + Luminescence-1.0.0/Luminescence/tests/testthat/test_internals_Thermochronometry.R |only Luminescence-1.0.0/Luminescence/tests/testthat/test_merge_RLum.Analysis.R | 10 Luminescence-1.0.0/Luminescence/tests/testthat/test_merge_RLum.Data.Curve.R | 141 Luminescence-1.0.0/Luminescence/tests/testthat/test_merge_RLum.Data.Spectrum.R |only Luminescence-1.0.0/Luminescence/tests/testthat/test_merge_RLum.R | 15 Luminescence-1.0.0/Luminescence/tests/testthat/test_merge_RLum.Results.R | 12 Luminescence-1.0.0/Luminescence/tests/testthat/test_merge_Risoe.BINfileData.R | 4 Luminescence-1.0.0/Luminescence/tests/testthat/test_metadata.R |only Luminescence-1.0.0/Luminescence/tests/testthat/test_methods_DRAC.R | 45 Luminescence-1.0.0/Luminescence/tests/testthat/test_methods_S3.R | 9 Luminescence-1.0.0/Luminescence/tests/testthat/test_names_RLum.R | 6 Luminescence-1.0.0/Luminescence/tests/testthat/test_plot_AbanicoPlot.R | 110 Luminescence-1.0.0/Luminescence/tests/testthat/test_plot_DRCSummary.R | 7 Luminescence-1.0.0/Luminescence/tests/testthat/test_plot_DRTResults.R | 19 Luminescence-1.0.0/Luminescence/tests/testthat/test_plot_DetPlot.R | 22 Luminescence-1.0.0/Luminescence/tests/testthat/test_plot_DoseResponseCurve.R |only Luminescence-1.0.0/Luminescence/tests/testthat/test_plot_FilterCombinations.R | 6 Luminescence-1.0.0/Luminescence/tests/testthat/test_plot_GrowthCurve.R | 610 -- Luminescence-1.0.0/Luminescence/tests/testthat/test_plot_Histogram.R | 10 Luminescence-1.0.0/Luminescence/tests/testthat/test_plot_KDE.R | 24 Luminescence-1.0.0/Luminescence/tests/testthat/test_plot_MoranScatterplot.R |only Luminescence-1.0.0/Luminescence/tests/testthat/test_plot_NRt.R | 31 Luminescence-1.0.0/Luminescence/tests/testthat/test_plot_OSLAgeSummary.R | 19 Luminescence-1.0.0/Luminescence/tests/testthat/test_plot_RLum.Analysis.R | 57 Luminescence-1.0.0/Luminescence/tests/testthat/test_plot_RLum.Data.Curve.R | 28 Luminescence-1.0.0/Luminescence/tests/testthat/test_plot_RLum.Data.Image.R | 26 Luminescence-1.0.0/Luminescence/tests/testthat/test_plot_RLum.Data.Spectrum.R | 75 Luminescence-1.0.0/Luminescence/tests/testthat/test_plot_RLum.R | 12 Luminescence-1.0.0/Luminescence/tests/testthat/test_plot_RLum.Results.R | 29 Luminescence-1.0.0/Luminescence/tests/testthat/test_plot_ROI.R | 24 Luminescence-1.0.0/Luminescence/tests/testthat/test_plot_RadialPlot.R | 18 Luminescence-1.0.0/Luminescence/tests/testthat/test_plot_Risoe.BINfileData.R | 18 Luminescence-1.0.0/Luminescence/tests/testthat/test_plot_SingleGrainDisc.R |only Luminescence-1.0.0/Luminescence/tests/testthat/test_plot_ViolinPlot.R | 27 Luminescence-1.0.0/Luminescence/tests/testthat/test_read_BIN2R.R | 170 Luminescence-1.0.0/Luminescence/tests/testthat/test_read_Daybreak2R.R | 20 Luminescence-1.0.0/Luminescence/tests/testthat/test_read_HeliosOSL2R.R | 32 Luminescence-1.0.0/Luminescence/tests/testthat/test_read_PSL2R.R | 15 Luminescence-1.0.0/Luminescence/tests/testthat/test_read_RF2R.R | 30 Luminescence-1.0.0/Luminescence/tests/testthat/test_read_SPE2R.R | 31 Luminescence-1.0.0/Luminescence/tests/testthat/test_read_TIFF2R.R | 19 Luminescence-1.0.0/Luminescence/tests/testthat/test_read_XSYG2R.R | 70 Luminescence-1.0.0/Luminescence/tests/testthat/test_report_RLum.R | 14 Luminescence-1.0.0/Luminescence/tests/testthat/test_scale_GammaDose.R | 79 Luminescence-1.0.0/Luminescence/tests/testthat/test_smooth_RLum.R | 12 Luminescence-1.0.0/Luminescence/tests/testthat/test_structure_RLum.R | 6 Luminescence-1.0.0/Luminescence/tests/testthat/test_subset_SingleGrainData.R | 6 Luminescence-1.0.0/Luminescence/tests/testthat/test_template_DRAC.R | 23 Luminescence-1.0.0/Luminescence/tests/testthat/test_trim_RLum.Data.R | 55 Luminescence-1.0.0/Luminescence/tests/testthat/test_use_DRAC.R | 64 Luminescence-1.0.0/Luminescence/tests/testthat/test_utils_DRAC.R |only Luminescence-1.0.0/Luminescence/tests/testthat/test_verify_SingleGrainData.R | 61 Luminescence-1.0.0/Luminescence/tests/testthat/test_view.R |only Luminescence-1.0.0/Luminescence/tests/testthat/test_write_R2BIN.R | 105 Luminescence-1.0.0/Luminescence/tests/testthat/test_write_R2TIFF.R | 26 Luminescence-1.0.0/Luminescence/tests/testthat/test_write_RLum2CSV.R | 37 Luminescence-1.0.0/Luminescence/tests/testthat/test_zzz.R | 4 Luminescence-1.0.0/Luminescence/vignettes/crosstalk.Rmd |only 513 files changed, 13979 insertions(+), 14308 deletions(-)
Title: Semiparametric Spatial Filtering with Eigenvectors in
(Generalized) Linear Models
Description: Tools to decompose (transformed) spatial connectivity matrices and perform supervised or unsupervised semiparametric spatial filtering in a regression framework. The package supports unsupervised spatial filtering in standard linear as well as some generalized linear regression models.
Author: Sebastian Juhl [aut, cre]
Maintainer: Sebastian Juhl <sebastian.juhl@t-online.de>
Diff between spfilteR versions 2.0.0 dated 2025-01-22 and 2.1.0 dated 2025-02-21
DESCRIPTION | 6 +-- MD5 | 26 ++++++------- NEWS.md | 16 +++++++- R/MI.decomp.R | 79 +++++++++++++++++++++------------------- R/MI.resid.R | 29 +++++++++++--- R/MI.vec.R | 60 +++++++++++++++++------------- R/utils.R | 4 +- R/vp.R | 2 - inst/doc/spfilteR_vignette.R | 5 ++ inst/doc/spfilteR_vignette.Rmd | 7 +++ inst/doc/spfilteR_vignette.html | 40 ++++++++++++-------- man/MI.resid.Rd | 11 +++++ tests/testthat/testing.R | 46 +++++++++++++++++++---- vignettes/spfilteR_vignette.Rmd | 7 +++ 14 files changed, 224 insertions(+), 114 deletions(-)
Title: Relational Data Modeler
Description: The aim of this package is to manipulate relational
data models in R.
It provides functions to create, modify and export data models
in json format.
It also allows importing models created
with 'MySQL Workbench' (<https://www.mysql.com/products/workbench/>).
These functions are accessible through a graphical user
interface made with 'shiny'.
Constraints such as types, keys, uniqueness and mandatory fields are
automatically checked and corrected when editing a model.
Finally, real data can be confronted to a model to check their compatibility.
Author: Patrice Godard [aut, cre, cph],
Kai Lin [ctb]
Maintainer: Patrice Godard <patrice.godard@gmail.com>
Diff between ReDaMoR versions 0.7.6 dated 2024-07-07 and 0.8.2 dated 2025-02-21
DESCRIPTION | 6 +- MD5 | 28 ++++++----- NAMESPACE | 2 R/df_to_model.R | 109 +++++++++++++++++++++++++++++++++++++++++++++ R/model_relational_data.R | 2 R/namespace.R | 2 build/vignette.rds |binary inst/doc/ReDaMoR.R | 26 ++++++---- inst/doc/ReDaMoR.Rmd | 42 +++++++++-------- inst/doc/ReDaMoR.html | 90 +++++++++++++++++++++++-------------- inst/examples/ex_from_df.R | 5 +- inst/pkgdown.yml | 7 +- man/df_to_model.Rd | 5 +- man/figures |only man/guess_constraints.Rd |only vignettes/ReDaMoR.Rmd | 42 +++++++++-------- 16 files changed, 263 insertions(+), 103 deletions(-)
Title: Analyzing and Visualizing Multidimensional Plant Traits
Description: Implements analytical methods for multidimensional plant traits, including Competitors-Stress tolerators-Ruderals strategy analysis using leaf traits, Leaf-Height-Seed strategy analysis, Niche Periodicity Table analysis, and Trait Network analysis. Provides functions for data analysis, visualization, and network metrics calculation. Methods are based on Grime (1974) <doi:10.1038/250026a0>, Pierce et al. (2017) <doi:10.1111/1365-2435.12882>, Westoby (1998) <doi:10.1023/A:1004327224729>, Yang et al. (2022) <doi:10.1016/j.foreco.2022.120540>, Winemiller et al. (2015) <doi:10.1111/ele.12462>, He et al. (2020) <doi:10.1016/j.tree.2020.06.003>.
Author: Yan He [aut, cre],
Zhaogang Liu [aut],
Jiangshan Lai [aut],
Lingfeng Mao [aut]
Maintainer: Yan He <heyan@njfu.edu.cn>
Diff between MultiTraits versions 0.2.0 dated 2024-12-21 and 0.3.0 dated 2025-02-21
DESCRIPTION | 15 +++++++++------ MD5 | 14 ++++++++++---- NEWS.md | 23 +++++++++++++++++++++++ R/NPT.R | 3 +-- inst/doc/MultiTraits_tutorial.html | 22 +++++++++++----------- tests |only 6 files changed, 54 insertions(+), 23 deletions(-)
Title: m-Out-of-n Bootstrap Functions
Description: Functions and examples based on the m-out-of-n bootstrap suggested by
Politis, D.N. and Romano, J.P. (1994) <doi:10.1214/aos/1176325770>.
Additionally there are functions to estimate the scaling factor tau
and the subsampling size m. For a detailed description and a full list
of references, see Dalitz, C. and Lögler, F. (2024)
<doi:10.48550/arXiv.2412.05032>.
Author: Christoph Dalitz [aut, cre],
Felix Loegler [aut]
Maintainer: Christoph Dalitz <christoph.dalitz@hs-niederrhein.de>
Diff between moonboot versions 0.9.1 dated 2024-12-10 and 1.0.1 dated 2025-02-21
Changelog |only DESCRIPTION | 12 +++---- MD5 | 24 +++++++------- R/distpower.R | 3 + R/moonboot.R | 87 ++++++++++++++++++++++++++++++++-------------------- R/shorth.R | 5 +- README.md | 16 ++++++++- build |only man/distPower.Rd | 3 + man/estimate.m.Rd | 4 +- man/estimate.tau.Rd | 4 +- man/mboot.Rd | 14 ++++---- man/mboot.ci.Rd | 34 ++++++++++++++------ man/shorth.Rd | 5 +- 14 files changed, 136 insertions(+), 75 deletions(-)
Title: Model Evaluation and Analysis
Description: Analyses species distribution models and evaluates their performance. It includes functions for variation partitioning, extracting variable importance, computing several metrics of model discrimination and calibration performance, optimizing prediction thresholds based on a number of criteria, performing multivariate environmental similarity surface (MESS) analysis, and displaying various analytical plots. Initially described in Barbosa et al. (2013) <doi:10.1111/ddi.12100>.
Author: A. Marcia Barbosa [aut, cre],
Jennifer A. Brown [aut],
Alberto Jimenez-Valverde [aut],
Raimundo Real [aut],
Oswald van Ginkel [ctb],
Jurica Levatic [ctb],
Victoria Formoso-Freire [ctb],
Andres Baselga [ctb],
Carola Gomez-Rodriguez [ctb],
Jose Carlos [...truncated...]
Maintainer: A. Marcia Barbosa <ana.marcia.barbosa@gmail.com>
Diff between modEvA versions 3.29 dated 2025-02-16 and 3.30 dated 2025-02-21
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS | 10 ++++++++++ R/AUC.R | 6 +++--- R/Boyce.R | 6 +++--- R/lollipop.R | 6 +++--- R/optiPair.R | 6 +++--- man/modEvA-package.Rd | 4 ++-- 8 files changed, 35 insertions(+), 25 deletions(-)
Title: Analyzing Dendrometer Data
Description: Various functions to import, verify, process and plot
high-resolution dendrometer data using daily and stem-cycle approaches
as described in Deslauriers et al, 2007 <doi:10.1016/j.dendro.2007.05.003>.
For more details about the package please see:
Van der Maaten et al. 2016 <doi:10.1016/j.dendro.2016.06.001>.
Author: Olivier Bouriaud [aut],
Ernst van der Maaten [aut],
Marieke van der Maaten-Theunissen [aut],
Marko Smiljanic [aut, cre]
Maintainer: Marko Smiljanic <marko.smiljanic313@gmail.com>
Diff between dendrometeR versions 1.1.0 dated 2024-10-14 and 1.1.1 dated 2025-02-21
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/phase_def.R | 8 ++++++-- inst/doc/data_import.R | 36 ++++++++++++++++++------------------ 4 files changed, 30 insertions(+), 26 deletions(-)
Title: Causal Analysis of Observational Time-to-Event Data
Description: Implements target trial emulation methods to apply randomized
clinical trial design and analysis in an observational setting. Using
marginal structural models, it can estimate intention-to-treat and
per-protocol effects in emulated trials using electronic health
records. A description and application of the method can be found in
Danaei et al (2013) <doi:10.1177/0962280211403603>.
Author: Isaac Gravestock [aut, cre] ,
Li Su [aut],
Roonak Rezvani [aut] ,
Julia Moesch [aut],
Medical Research Council [fnd],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Isaac Gravestock <isaac.gravestock@roche.com>
Diff between TrialEmulation versions 0.0.4.0 dated 2024-11-29 and 0.0.4.2 dated 2025-02-21
DESCRIPTION | 6 MD5 | 28 ++-- NEWS.md | 4 R/generics.R | 2 R/trial_sequence.R | 3 build/vignette.rds |binary inst/WORDLIST | 36 ----- inst/doc/Getting-Started.Rmd | 4 inst/doc/Getting-Started.html | 198 +++++++++++++++--------------- inst/doc/new-interface.R | 40 +++--- inst/doc/new-interface.html | 17 +- man/calculate_weights.Rd | 3 man/fit_outcome_model.Rd | 3 tests/testthat/test-te_datastore_duckdb.R | 34 +++-- vignettes/Getting-Started.Rmd | 4 15 files changed, 189 insertions(+), 193 deletions(-)
More information about TrialEmulation at CRAN
Permanent link
Title: Custom Inputs Widgets for Shiny
Description: Collection of custom input controls and user interface components for 'Shiny' applications.
Give your applications a unique and colorful style !
Author: Victor Perrier [aut, cre, cph],
Fanny Meyer [aut],
David Granjon [aut],
Ian Fellows [ctb] ,
Wil Davis [ctb] ,
Spencer Matthews [ctb] ,
JavaScript and CSS libraries authors [ctb, cph]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between shinyWidgets versions 0.8.7 dated 2024-09-23 and 0.9.0 dated 2025-02-21
DESCRIPTION | 6 MD5 | 70 + NAMESPACE | 2 NEWS.md | 11 R/calendar-pro-input.R |only R/color-pickr.R | 10 R/dependencies.R | 1073 ++++++++++++++---------------- R/input-icon.R | 637 ++++++++--------- R/input-knob.R | 5 R/input-pretty.R | 42 - R/input-search.R | 355 +++++---- R/input-switch.R | 683 +++++++++---------- R/onLoad.R | 208 +++-- R/sw-dropdown.R | 32 R/utils.R | 26 R/virtual-select.R | 2 inst/assets/sw-dropdown/sw-dropdown.js | 296 ++++---- inst/examples/calendar-pro |only inst/packer/WinBox.js | 2 inst/packer/air-datepicker.js | 2 inst/packer/autonumeric.js | 2 inst/packer/buttons-group.js | 2 inst/packer/calendar-pro.js |only inst/packer/calendar-pro.js.LICENSE.txt |only inst/packer/colorpickr.js | 3 inst/packer/multi.js | 2 inst/packer/nouislider.js | 2 inst/packer/slim-select.js | 2 inst/packer/tree.js | 2 inst/packer/virtual-select.js | 2 inst/packer/virtual-select.js.LICENSE.txt | 2 man/calendarProInput.Rd |only man/colorPickr.Rd | 18 man/figures/lifecycle-deprecated.svg |only man/knobInput.Rd | 3 man/searchInput.Rd | 4 man/switchInput.Rd | 3 man/textInputIcon.Rd | 4 man/updateCalendarPro.Rd |only 39 files changed, 1832 insertions(+), 1681 deletions(-)
Title: Tools for Reading and Writing ISO/OGC Geographic Metadata
Description: Provides facilities to read, write and validate geographic metadata
defined with ISO TC211 / OGC ISO geographic information metadata standards, and
encoded using the ISO 19139 and ISO 19115-3 (XML) standard technical specifications.
This includes ISO 19110 (Feature cataloguing), 19115 (dataset metadata), 19119 (service metadata)
and 19136 (GML). Other interoperable schemas from the OGC are progressively supported
as well, such as the Sensor Web Enablement (SWE) Common Data Model, the OGC GML
Coverage Implementation Schema (GMLCOV), or the OGC GML Referenceable Grid (GMLRGRID).
Author: Emmanuel Blondel [aut, cre] ,
R Consortium [fnd]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between geometa versions 0.9 dated 2025-01-29 and 0.9.1 dated 2025-02-21
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/ISOAbstractObject.R | 1 - README.md | 2 +- 4 files changed, 8 insertions(+), 9 deletions(-)
Title: Fast Alternatives to 'tidyverse' Functions
Description: A full set of fast data manipulation tools with a tidy
front-end and a fast back-end using 'collapse' and 'cheapr'.
Author: Nick Christofides [aut, cre]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>
Diff between fastplyr versions 0.5.0 dated 2024-12-02 and 0.5.1 dated 2025-02-21
DESCRIPTION | 8 - LICENSE | 4 MD5 | 24 +-- NEWS.md | 7 + R/f_nest_by.R | 134 ++++++++++----------- R/f_summarise.R | 4 R/f_tibble.R | 228 ++++++++++++++++++------------------- R/reconstruct.R | 194 +++++++++++++++---------------- R/utils-pipe.R | 28 ++-- man/desc.Rd | 38 +++--- man/f_filter.Rd | 44 +++---- man/pipe.Rd | 40 +++--- tests/testthat/test-f_duplicates.R | 118 +++++++++---------- 13 files changed, 439 insertions(+), 432 deletions(-)
Title: Explore and Visualize Your Data Interactively
Description: A 'shiny' gadget to create 'ggplot2' figures interactively with drag-and-drop to map your variables to different aesthetics.
You can quickly visualize your data accordingly to their type, export in various formats,
and retrieve the code to reproduce the plot.
Author: Fanny Meyer [aut],
Victor Perrier [aut, cre],
Ian Carroll [ctb] ,
Xiangnan Dang [ctb] ,
Nicolas Bevacqua [cph] ,
Daybrush [cph] ,
Zeno Rocha [cph]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between esquisse versions 2.0.1 dated 2024-09-18 and 2.1.0 dated 2025-02-21
DESCRIPTION | 8 MD5 | 70 - NAMESPACE | 6 NEWS.md | 442 +++++------ R/esquisse-server.R | 7 R/esquisse-ui.R | 9 R/export-history.R |only R/export.R | 14 R/geometries.R | 618 +++++++-------- R/ggcall.R | 354 ++++----- R/ggplot_to_ppt.R | 12 R/mapping.R | 136 +-- R/module-controls.R | 2 R/module-select-aes.R | 300 +++---- R/module-select-geom-aes.R | 332 ++++---- R/onLoad.R | 36 R/safe_ggplot.R | 154 +-- R/settings.R | 130 +-- R/utils-shiny.R | 11 build/vignette.rds |binary inst/assets/dragula/dragula-bindings.js | 380 ++++----- inst/assets/esquisse/js/shiny-utils.js | 8 inst/doc/get-started.R | 56 - inst/doc/get-started.Rmd | 340 ++++---- inst/doc/get-started.html | 974 ++++++++++++------------ inst/doc/shiny-usage.R | 456 +++++------ inst/doc/shiny-usage.Rmd | 646 ++++++++-------- inst/doc/shiny-usage.html | 1256 ++++++++++++++++---------------- inst/geomIcon/iconGeom.R | 758 +++++++++---------- man/esquisse-module.Rd | 18 man/save-ggplot-module.Rd | 2 man/save-ggplot-multi-module.Rd |only tests/testthat/Rplots.pdf |binary tests/testthat/test-geoms.R | 122 +-- tests/testthat/test-safe_ggplot.R | 58 - vignettes/get-started.Rmd | 340 ++++---- vignettes/shiny-usage.Rmd | 646 ++++++++-------- 37 files changed, 4385 insertions(+), 4316 deletions(-)
Title: Estimate Disease Severity and Case Ascertainment
Description: Estimate the severity of a disease and ascertainment of
cases, as discussed in Nishiura et al. (2009)
<doi:10.1371/journal.pone.0006852>.
Author: Pratik R. Gupte [aut, cph] ,
Adam Kucharski [aut, cph, cre]
,
Tim Russell [aut, cph] ,
Joshua W. Lambert [rev] ,
Hugo Gruson [rev] ,
Tim Taylor [rev] ,
James M. Azam [rev] ,
Abdoelnaser M. Degoot [rev] ,
Sebastian Funk [rev]
Maintainer: Adam Kucharski <adam.kucharski@lshtm.ac.uk>
Diff between cfr versions 0.1.2 dated 2024-09-26 and 0.2.0 dated 2025-02-21
DESCRIPTION | 12 ++--- LICENSE | 2 MD5 | 34 ++++++++------- NEWS.md | 12 ++++- R/cfr_rolling.R | 2 R/cfr_static.R | 2 R/cfr_time_varying.R | 2 R/estimate_ascertainment.R | 3 - R/prepare_data.R | 10 +--- README.md | 2 build/vignette.rds |binary inst/WORDLIST | 61 ++++++++++++++------------- inst/doc/delay_distributions.Rmd | 6 +- inst/doc/delay_distributions.html | 9 ++- inst/doc/estimate_from_individual_data.R |only inst/doc/estimate_from_individual_data.Rmd |only inst/doc/estimate_from_individual_data.html |only inst/doc/estimate_time_varying_severity.html | 8 ++- vignettes/delay_distributions.Rmd | 6 +- vignettes/estimate_from_individual_data.Rmd |only 20 files changed, 95 insertions(+), 76 deletions(-)
Title: Bayesian Methods for Change Points Analysis
Description: Perform change points detection on univariate and multivariate time series according to the methods presented by Asael Fabian Martínez and Ramsés H. Mena (2014) <doi:10.1214/14-BA878> and Corradin, Danese and Ongaro (2022) <doi:10.1016/j.ijar.2021.12.019>. It also clusters different types of time dependent data with common change points, see "Model-based clustering of time-dependent observations with common structural changes" (Corradin,Danese,KhudaBukhsh and Ongaro, 2024) <doi:10.48550/arXiv.2410.09552> for details.
Author: Luca Danese [aut, cre, cph] ,
Riccardo Corradin [aut],
Andrea Ongaro [aut]
Maintainer: Luca Danese <l.danese1@campus.unimib.it>
Diff between BayesChange versions 1.1.1 dated 2025-02-14 and 1.1.2 dated 2025-02-21
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ src/code.cpp | 7 +++---- 4 files changed, 13 insertions(+), 10 deletions(-)
Title: Causal Inference and Prediction in Cohort-Based Analyses
Description: 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, competing events, and multi-state data. For multistate data, semi-Markov model with interval censoring may be considered, and we propose the possibility to consider the excess of mortality related to the disease compared to reference lifetime tables. 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. Finally, several functions are available to assess time-dependent ROC curves or survival curves from aggregated data.
Author: Yohann Foucher [aut, cre]
Maintainer: Yohann Foucher <Yohann.Foucher@univ-poitiers.fr>
Diff between RISCA versions 1.0.6 dated 2025-01-20 and 1.0.7 dated 2025-02-21
DESCRIPTION | 14 ++--- MD5 | 20 ++++---- R/markov.3states.rsadd.R | 94 +-------------------------------------- R/markov.4states.rsadd.R | 94 +-------------------------------------- R/semi.markov.3states.rsadd.R | 94 +-------------------------------------- R/semi.markov.4states.rsadd.R | 94 +-------------------------------------- man/markov.3states.rsadd.Rd | 2 man/markov.4states.rsadd.Rd | 2 man/roc.net.Rd | 3 - man/semi.markov.3states.rsadd.Rd | 8 --- man/semi.markov.4states.rsadd.Rd | 2 11 files changed, 32 insertions(+), 395 deletions(-)
Title: QTL Mapping and Hotspots Detection
Description: For QTL mapping, this package comprises several functions designed to execute diverse
tasks, such as simulating or analyzing data, calculating significance thresholds, and
visualizing QTL mapping results. The single-QTL or multiple-QTL method, which enables
the fitting and comparison of various statistical models, is employed to analyze the
data for estimating QTL parameters. The models encompass linear regression, permutation
tests, normal mixture models, and truncated normal mixture models. The Gaussian stochastic
process is utilized to compute significance thresholds for QTL detection on a genetic
linkage map within experimental populations. Two types of data, complete genotyping, and
selective genotyping data from various experimental populations, including backcross, F2,
recombinant inbred (RI) populations, and advanced intercrossed (AI) populations, are
considered in the QTL mapping analysis. For QTL hotspot detection, statistical methods can
be developed based on either utilizin [...truncated...]
Author: Ping-Yuan Chung [cre],
Chen-Hung Kao [aut],
Y.-T. Guo [aut],
H.-N. Ho [aut],
H.-I. Lee [aut],
P.-Y. Wu [aut],
M.-H. Yang [aut],
M.-H. Zeng [aut]
Maintainer: Ping-Yuan Chung <pychung@webmail.stat.sinica.edu.tw>
Diff between QTLEMM versions 2.1.0 dated 2024-06-25 and 3.0.0 dated 2025-02-21
QTLEMM-2.1.0/QTLEMM/R/EM.MIM2.R |only QTLEMM-2.1.0/QTLEMM/R/IM.search2.R |only QTLEMM-2.1.0/QTLEMM/R/MIM.points2.R |only QTLEMM-2.1.0/QTLEMM/R/MIM.search2.R |only QTLEMM-2.1.0/QTLEMM/man/EM.MIM2.Rd |only QTLEMM-2.1.0/QTLEMM/man/IM.search2.Rd |only QTLEMM-2.1.0/QTLEMM/man/MIM.points2.Rd |only QTLEMM-2.1.0/QTLEMM/man/MIM.search2.Rd |only QTLEMM-3.0.0/QTLEMM/DESCRIPTION | 8 QTLEMM-3.0.0/QTLEMM/MD5 | 36 - QTLEMM-3.0.0/QTLEMM/NAMESPACE | 4 QTLEMM-3.0.0/QTLEMM/R/EM.MIM.R | 719 +++++++++++++++++++++++++++------ QTLEMM-3.0.0/QTLEMM/R/EM.MIM0.R |only QTLEMM-3.0.0/QTLEMM/R/EM.MIMv.R | 133 +++++- QTLEMM-3.0.0/QTLEMM/R/IM.search.R | 216 ++++++--- QTLEMM-3.0.0/QTLEMM/R/MIM.points.R | 216 +++++++-- QTLEMM-3.0.0/QTLEMM/R/MIM.search.R | 221 +++++++--- QTLEMM-3.0.0/QTLEMM/R/methEM.R |only QTLEMM-3.0.0/QTLEMM/R/methSG.R |only QTLEMM-3.0.0/QTLEMM/R/mixprop.R |only QTLEMM-3.0.0/QTLEMM/man/EM.MIM.Rd | 133 +++++- QTLEMM-3.0.0/QTLEMM/man/EM.MIMv.Rd | 24 - QTLEMM-3.0.0/QTLEMM/man/IM.search.Rd | 72 ++- QTLEMM-3.0.0/QTLEMM/man/MIM.points.Rd | 84 +++ QTLEMM-3.0.0/QTLEMM/man/MIM.search.Rd | 83 +++ 25 files changed, 1554 insertions(+), 395 deletions(-)
Title: Microclimatic Data Processing
Description: Handling the microclimatic data in R. The 'myClim' workflow begins
at the reading data primary from microclimatic dataloggers,
but can be also reading of meteorological station data from files.
Cleaning time step, time zone settings and metadata collecting is the next step of the work flow.
With 'myClim' tools one can crop, join, downscale, and convert microclimatic data formats, sort them into localities,
request descriptive characteristics and compute microclimatic variables.
Handy plotting functions are provided with smart defaults.
Author: Matej Man [aut],
Vojtech Kalcik [aut, cre],
Martin Macek [aut],
Josef Bruna [aut],
Lucia Hederova [aut],
Jan Wild [aut],
Martin Kopecky [aut],
Institute of Botany of the Czech Academy of Sciences [cph]
Maintainer: Vojtech Kalcik <Vojtech.Kalcik@ibot.cas.cz>
Diff between myClim versions 1.3.0 dated 2024-10-21 and 1.4.0 dated 2025-02-21
myClim-1.3.0/myClim/man/mc_info_join.Rd |only myClim-1.4.0/myClim/DESCRIPTION | 6 myClim-1.4.0/myClim/MD5 | 129 ++-- myClim-1.4.0/myClim/NAMESPACE | 4 myClim-1.4.0/myClim/NEWS.md | 57 + myClim-1.4.0/myClim/R/calc.R | 11 myClim-1.4.0/myClim/R/common.R | 18 myClim-1.4.0/myClim/R/info.R | 101 +-- myClim-1.4.0/myClim/R/join.R | 288 ++++++---- myClim-1.4.0/myClim/R/model.R | 12 myClim-1.4.0/myClim/R/myClim-package.R | 3 myClim-1.4.0/myClim/R/plot.R | 181 +++++- myClim-1.4.0/myClim/R/prep.R | 260 +++++---- myClim-1.4.0/myClim/R/read.R | 44 + myClim-1.4.0/myClim/R/reshape.R | 23 myClim-1.4.0/myClim/R/serialize.R | 81 ++ myClim-1.4.0/myClim/R/states.R | 254 +++++++- myClim-1.4.0/myClim/data/mc_data_example_agg.rda |binary myClim-1.4.0/myClim/data/mc_data_example_clean.rda |binary myClim-1.4.0/myClim/data/mc_data_example_raw.rda |binary myClim-1.4.0/myClim/data/mc_data_formats.rda |binary myClim-1.4.0/myClim/data/mc_data_heights.rda |binary myClim-1.4.0/myClim/data/mc_data_physical.rda |binary myClim-1.4.0/myClim/data/mc_data_sensors.rda |binary myClim-1.4.0/myClim/data/mc_data_vwc_parameters.rda |binary myClim-1.4.0/myClim/inst/doc/myclim-custom-loggers.html | 26 myClim-1.4.0/myClim/inst/doc/myclim-demo.R | 110 +-- myClim-1.4.0/myClim/man/mc_LocalityMetadata-class.Rd | 2 myClim-1.4.0/myClim/man/mc_LoggerMetadata-class.Rd | 4 myClim-1.4.0/myClim/man/mc_info_clean.Rd | 1 myClim-1.4.0/myClim/man/mc_info_logger.Rd | 2 myClim-1.4.0/myClim/man/mc_info_states.Rd | 3 myClim-1.4.0/myClim/man/mc_join.Rd | 38 - myClim-1.4.0/myClim/man/mc_load.Rd | 3 myClim-1.4.0/myClim/man/mc_plot_line.Rd | 5 myClim-1.4.0/myClim/man/mc_prep_calib_load.Rd | 2 myClim-1.4.0/myClim/man/mc_prep_clean.Rd | 46 + myClim-1.4.0/myClim/man/mc_prep_crop.Rd | 38 - myClim-1.4.0/myClim/man/mc_read_problems.Rd |only myClim-1.4.0/myClim/man/mc_reshape_wide.Rd | 13 myClim-1.4.0/myClim/man/mc_save_localities.Rd |only myClim-1.4.0/myClim/man/mc_states_insert.Rd | 5 myClim-1.4.0/myClim/man/mc_states_join.Rd |only myClim-1.4.0/myClim/man/mc_states_replace.Rd | 17 myClim-1.4.0/myClim/man/mc_states_to_sensor.Rd | 3 myClim-1.4.0/myClim/man/mc_states_update.Rd | 2 myClim-1.4.0/myClim/man/myClim-package.Rd | 3 myClim-1.4.0/myClim/tests/data/TMSoffsoil/data_93142790_0.csv |only myClim-1.4.0/myClim/tests/data/clean-conflict |only myClim-1.4.0/myClim/tests/data/crop |only myClim-1.4.0/myClim/tests/data/join_serial |only myClim-1.4.0/myClim/tests/data/join_tolerance |only myClim-1.4.0/myClim/tests/data/serialize/raw_data_1.3.2.rds |only myClim-1.4.0/myClim/tests/testthat/libtest.R | 33 + myClim-1.4.0/myClim/tests/testthat/test-agg.R | 8 myClim-1.4.0/myClim/tests/testthat/test-calc.R | 34 - myClim-1.4.0/myClim/tests/testthat/test-common.R | 18 myClim-1.4.0/myClim/tests/testthat/test-env.R | 2 myClim-1.4.0/myClim/tests/testthat/test-filter.R | 18 myClim-1.4.0/myClim/tests/testthat/test-info.R | 32 - myClim-1.4.0/myClim/tests/testthat/test-join.R | 28 myClim-1.4.0/myClim/tests/testthat/test-plot.R | 41 + myClim-1.4.0/myClim/tests/testthat/test-prep.R | 93 ++- myClim-1.4.0/myClim/tests/testthat/test-read.R | 140 ++-- myClim-1.4.0/myClim/tests/testthat/test-reshape.R | 8 myClim-1.4.0/myClim/tests/testthat/test-serialize.R | 43 + myClim-1.4.0/myClim/tests/testthat/test-states.R | 211 +++++-- 67 files changed, 1709 insertions(+), 795 deletions(-)
Title: Minimization Tool for Pharmacokinetic-Pharmacodynamic Data
Analysis
Description: This is a set of minimization tools (maximum likelihood estimation and least square fitting) to solve examples in the Johan Gabrielsson and Dan Weiner's book "Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications" 5th ed. (ISBN:9198299107). Examples include linear and nonlinear compartmental model, turn-over model, single or multiple dosing bolus/infusion/oral models, allometry, toxicokinetics, reversible metabolism, in-vitro/in-vivo extrapolation, enterohepatic circulation, metabolite modeling, Emax model, inhibitory model, tolerance model, oscillating response model, enantiomer interaction model, effect compartment model, drug-drug interaction model, receptor occupancy model, and rebound phenomena model.
Author: Kyun-Seop Bae [aut, cre, cph]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between wnl versions 0.8.1 dated 2024-05-31 and 0.8.2 dated 2025-02-21
DESCRIPTION | 9 +++++---- MD5 | 6 +++--- R/nlr.R | 18 +++++++++++------- inst/NEWS.Rd | 7 +++++++ 4 files changed, 26 insertions(+), 14 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-29 1.1.2
2020-03-12 1.1.1
2018-11-14 1.1.0
Title: Uniform Exact Functional Tests for Contingency Tables
Description: Testing whether two discrete variables have a functional
relationship under null distributions where the two variables are
statistically independent with fixed marginal counts.
The fast enumeration algorithm was based on (Nguyen et al. 2020) <doi:10.24963/ijcai.2020/372>.
Author: Yiyi Li [aut, cre] ,
Joe Song [aut]
Maintainer: Yiyi Li <gtarex@nmsu.edu>
Diff between UniExactFunTest versions 1.0.0 dated 2023-10-06 and 1.0.1 dated 2025-02-21
UniExactFunTest-1.0.0/UniExactFunTest/tests/testthat/testthat-problems.rds |only UniExactFunTest-1.0.1/UniExactFunTest/DESCRIPTION | 10 - UniExactFunTest-1.0.1/UniExactFunTest/MD5 | 15 - UniExactFunTest-1.0.1/UniExactFunTest/NEWS | 9 + UniExactFunTest-1.0.1/UniExactFunTest/R/UEFT.R | 39 +++- UniExactFunTest-1.0.1/UniExactFunTest/build/vignette.rds |binary UniExactFunTest-1.0.1/UniExactFunTest/inst/doc/Examples.R | 2 UniExactFunTest-1.0.1/UniExactFunTest/inst/doc/Examples.html | 84 ++++------ UniExactFunTest-1.0.1/UniExactFunTest/man/UEFT.Rd | 17 +- 9 files changed, 109 insertions(+), 67 deletions(-)
More information about UniExactFunTest at CRAN
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