Title: Seamless 'Nonmem' Simulation Platform
Description: A complete and seamless 'Nonmem' simulation interface within R. Turns 'Nonmem' control streams into simulation control streams, executes them with specified simulation input data and returns the results. The simulation is performed by 'Nonmem', eliminating manual work and risks of re-implementation of models in other tools.
Author: Philip Delff [aut, cre],
Brian Reilly [ctb],
Sanaya Shroff [ctb]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMsim versions 0.1.3 dated 2024-08-26 and 0.1.4 dated 2024-11-01
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Title: A Stochastic Weather Generator with Seasonality
Description: A weather generator to simulate precipitation and temperature for regions with seasonality. Users input training data containing precipitation, temperature, and seasonality (up to 26 seasons). Including weather season as a training variable allows users to explore the effects of potential changes in season duration as well as average start- and end-time dates due to phenomena like climate change. Data for training should be a single time series but can originate from station data, basin averages, grid cells, etc.
Bearup, L., Gangopadhyay, S., & Mikkelson, K. (2021). "Hydroclimate Analysis Lower Santa Cruz River Basin Study (Technical Memorandum No ENV-2020-056)." Bureau of Reclamation.
Gangopadhyay, S., Bearup, L. A., Verdin, A., Pruitt, T., Halper, E., & Shamir, E. (2019, December 1). "A collaborative stochastic weather generator for climate impacts assessment in the Lower Santa Cruz River Basin, Arizona." Fall Meeting 2019, American Geophysical Union. <https://ui.adsabs.ha [...truncated...]
Author: Subhrendu Gangopadhyay [aut],
Lindsay Bearup [aut],
David Woodson [aut, cre],
Marketa McGuire [aut],
Andrew Verdin [aut],
Eylon Shamir [aut],
Eve Halper [aut]
Maintainer: David Woodson <dwoodson@usbr.gov>
Diff between wxgenR versions 1.4.1 dated 2024-07-16 and 1.4.2 dated 2024-11-01
wxgenR-1.4.1/wxgenR/inst/doc/Vignette_paperCode_inSample.R |only wxgenR-1.4.1/wxgenR/inst/doc/Vignette_paperCode_inSample.Rmd |only wxgenR-1.4.1/wxgenR/inst/doc/Vignette_paperCode_inSample.html |only wxgenR-1.4.1/wxgenR/vignettes/Vignette_paperCode_inSample.Rmd |only wxgenR-1.4.2/wxgenR/DESCRIPTION | 6 wxgenR-1.4.2/wxgenR/MD5 | 46 +- wxgenR-1.4.2/wxgenR/R/getDatesInWindow.R | 62 +++ wxgenR-1.4.2/wxgenR/R/getPtpm.R | 6 wxgenR-1.4.2/wxgenR/R/getTpars.R | 33 +- wxgenR-1.4.2/wxgenR/R/lib.R | 29 + wxgenR-1.4.2/wxgenR/R/prepData.R | 57 +++ wxgenR-1.4.2/wxgenR/R/simPamt.R | 110 +++++-- wxgenR-1.4.2/wxgenR/R/simTPocc.R | 104 +++++- wxgenR-1.4.2/wxgenR/R/wx.R | 66 +--- wxgenR-1.4.2/wxgenR/build/vignette.rds |binary wxgenR-1.4.2/wxgenR/data/stationData.rda |binary wxgenR-1.4.2/wxgenR/inst/doc/Vignette_BlacksburgVA.R | 5 wxgenR-1.4.2/wxgenR/inst/doc/Vignette_BlacksburgVA.Rmd | 5 wxgenR-1.4.2/wxgenR/inst/doc/Vignette_BlacksburgVA.html | 156 ++++------ wxgenR-1.4.2/wxgenR/inst/doc/Vignette_LowerSantaCruzRiverBasinAZ.R | 6 wxgenR-1.4.2/wxgenR/inst/doc/Vignette_LowerSantaCruzRiverBasinAZ.Rmd | 6 wxgenR-1.4.2/wxgenR/inst/doc/Vignette_LowerSantaCruzRiverBasinAZ.html | 87 ++--- wxgenR-1.4.2/wxgenR/man/getDatesInWindow.Rd | 13 wxgenR-1.4.2/wxgenR/man/wx.Rd | 12 wxgenR-1.4.2/wxgenR/vignettes/Vignette_BlacksburgVA.Rmd | 5 wxgenR-1.4.2/wxgenR/vignettes/Vignette_LowerSantaCruzRiverBasinAZ.Rmd | 6 26 files changed, 527 insertions(+), 293 deletions(-)
Title: Pakistan Population Census 2023
Description: Provides data sets and functions for exploration of Pakistan Population Census 2023 (<https://www.pbs.gov.pk/>).
Author: Muhammad Yaseen [aut, cre, cph]
,
Muhammad Arfan Dilber [ctb],
Zahid Asghar [ctb]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between PakPC2023 versions 0.1.0 dated 2023-08-15 and 0.2.0 dated 2024-11-01
PakPC2023-0.1.0/PakPC2023/build |only PakPC2023-0.1.0/PakPC2023/inst/doc |only PakPC2023-0.1.0/PakPC2023/vignettes |only PakPC2023-0.2.0/PakPC2023/DESCRIPTION | 32 ++-- PakPC2023-0.2.0/PakPC2023/MD5 | 94 +++++++++--- PakPC2023-0.2.0/PakPC2023/NEWS.md | 14 + PakPC2023-0.2.0/PakPC2023/R/TABLE_01.R |only PakPC2023-0.2.0/PakPC2023/R/TABLE_02.R |only PakPC2023-0.2.0/PakPC2023/R/TABLE_03.R |only PakPC2023-0.2.0/PakPC2023/R/TABLE_04.R |only PakPC2023-0.2.0/PakPC2023/R/TABLE_05.R |only PakPC2023-0.2.0/PakPC2023/R/TABLE_06.R |only PakPC2023-0.2.0/PakPC2023/R/TABLE_07.R |only PakPC2023-0.2.0/PakPC2023/R/TABLE_08.R |only PakPC2023-0.2.0/PakPC2023/R/TABLE_09.R |only PakPC2023-0.2.0/PakPC2023/R/TABLE_10.R |only PakPC2023-0.2.0/PakPC2023/R/TABLE_11.R |only PakPC2023-0.2.0/PakPC2023/R/TABLE_12.R |only PakPC2023-0.2.0/PakPC2023/R/TABLE_13A.R |only PakPC2023-0.2.0/PakPC2023/R/TABLE_13B.R |only PakPC2023-0.2.0/PakPC2023/R/TABLE_16.R |only PakPC2023-0.2.0/PakPC2023/R/TABLE_17.R |only PakPC2023-0.2.0/PakPC2023/R/TABLE_20.R |only PakPC2023-0.2.0/PakPC2023/R/TABLE_21.R |only PakPC2023-0.2.0/PakPC2023/R/TABLE_22.R |only PakPC2023-0.2.0/PakPC2023/R/TABLE_23.R |only PakPC2023-0.2.0/PakPC2023/R/TABLE_24.R |only PakPC2023-0.2.0/PakPC2023/R/TABLE_25.R |only PakPC2023-0.2.0/PakPC2023/R/TABLE_26.R |only PakPC2023-0.2.0/PakPC2023/README.md | 190 ++++++++++++------------- PakPC2023-0.2.0/PakPC2023/data/TABLE_01.RData |only PakPC2023-0.2.0/PakPC2023/data/TABLE_02.RData |only PakPC2023-0.2.0/PakPC2023/data/TABLE_03.RData |only PakPC2023-0.2.0/PakPC2023/data/TABLE_04.RData |only PakPC2023-0.2.0/PakPC2023/data/TABLE_05.RData |only PakPC2023-0.2.0/PakPC2023/data/TABLE_06.RData |only PakPC2023-0.2.0/PakPC2023/data/TABLE_07.RData |only PakPC2023-0.2.0/PakPC2023/data/TABLE_08.RData |only PakPC2023-0.2.0/PakPC2023/data/TABLE_09.RData |only PakPC2023-0.2.0/PakPC2023/data/TABLE_10.RData |only PakPC2023-0.2.0/PakPC2023/data/TABLE_11.RData |only PakPC2023-0.2.0/PakPC2023/data/TABLE_12.RData |only PakPC2023-0.2.0/PakPC2023/data/TABLE_13A.RData |only PakPC2023-0.2.0/PakPC2023/data/TABLE_13B.RData |only PakPC2023-0.2.0/PakPC2023/data/TABLE_16.RData |only PakPC2023-0.2.0/PakPC2023/data/TABLE_17.RData |only PakPC2023-0.2.0/PakPC2023/data/TABLE_20.RData |only PakPC2023-0.2.0/PakPC2023/data/TABLE_21.RData |only PakPC2023-0.2.0/PakPC2023/data/TABLE_22.RData |only PakPC2023-0.2.0/PakPC2023/data/TABLE_23.RData |only PakPC2023-0.2.0/PakPC2023/data/TABLE_24.RData |only PakPC2023-0.2.0/PakPC2023/data/TABLE_25.RData |only PakPC2023-0.2.0/PakPC2023/data/TABLE_26.RData |only PakPC2023-0.2.0/PakPC2023/man/TABLE_01.Rd |only PakPC2023-0.2.0/PakPC2023/man/TABLE_02.Rd |only PakPC2023-0.2.0/PakPC2023/man/TABLE_03.Rd |only PakPC2023-0.2.0/PakPC2023/man/TABLE_04.Rd |only PakPC2023-0.2.0/PakPC2023/man/TABLE_05.Rd |only PakPC2023-0.2.0/PakPC2023/man/TABLE_06.Rd |only PakPC2023-0.2.0/PakPC2023/man/TABLE_07.Rd |only PakPC2023-0.2.0/PakPC2023/man/TABLE_08.Rd |only PakPC2023-0.2.0/PakPC2023/man/TABLE_09.Rd |only PakPC2023-0.2.0/PakPC2023/man/TABLE_10.Rd |only PakPC2023-0.2.0/PakPC2023/man/TABLE_11.Rd |only PakPC2023-0.2.0/PakPC2023/man/TABLE_12.Rd |only PakPC2023-0.2.0/PakPC2023/man/TABLE_13A.Rd |only PakPC2023-0.2.0/PakPC2023/man/TABLE_13B.Rd |only PakPC2023-0.2.0/PakPC2023/man/TABLE_16.Rd |only PakPC2023-0.2.0/PakPC2023/man/TABLE_17.Rd |only PakPC2023-0.2.0/PakPC2023/man/TABLE_20.Rd |only PakPC2023-0.2.0/PakPC2023/man/TABLE_21.Rd |only PakPC2023-0.2.0/PakPC2023/man/TABLE_22.Rd |only PakPC2023-0.2.0/PakPC2023/man/TABLE_23.Rd |only PakPC2023-0.2.0/PakPC2023/man/TABLE_24.Rd |only PakPC2023-0.2.0/PakPC2023/man/TABLE_25.Rd |only PakPC2023-0.2.0/PakPC2023/man/TABLE_26.Rd |only 76 files changed, 192 insertions(+), 138 deletions(-)
Title: Identification of Cell Types, Inference of Lineage Trees, and
Prediction of Noise Dynamics from Single-Cell RNA-Seq Data
Description: Application of 'RaceID' allows inference of cell types and prediction of lineage trees by the 'StemID2' algorithm (Herman, J.S., Sagar, Grun D. (2018) <DOI:10.1038/nmeth.4662>). 'VarID2' is part of this package and allows quantification of biological gene expression noise at single-cell resolution (Rosales-Alvarez, R.E., Rettkowski, J., Herman, J.S., Dumbovic, G., Cabezas-Wallscheid, N., Grun, D. (2023) <DOI:10.1186/s13059-023-02974-1>).
Author: Dominic Gruen [aut, cre]
Maintainer: Dominic Gruen <dominic.gruen@gmail.com>
Diff between RaceID versions 0.3.6 dated 2024-10-26 and 0.3.7 dated 2024-11-01
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/VarID_functions.R | 5 +++-- inst/doc/RaceID.html | 4 ++-- 4 files changed, 12 insertions(+), 11 deletions(-)
Title: Intracluster Correlation Coefficient (ICC) in Clustered
Categorical Data
Description: Assists in generating categorical clustered outcome data, estimating the Intracluster Correlation Coefficient (ICC) for nominal or ordinal data with 2+ categories under the resampling and method of moments (MoM) methods, with confidence intervals.
Author: Nicole Solomon [aut, cre, cph]
Maintainer: Nicole Solomon <nicole.solomon@duke.edu>
Diff between iccmult versions 1.0.0 dated 2024-10-22 and 1.0.1 dated 2024-11-01
DESCRIPTION | 9 - MD5 | 8 NEWS.md | 2 R/rccat.R | 519 ++++++++++++++++++++++++++++++------------------------------ README.md | 9 + 5 files changed, 281 insertions(+), 266 deletions(-)
Title: Categorical Landscape Simulation Facility
Description: Simulates categorical maps on actual geographical realms, starting from either empty landscapes or landscapes provided by the user (e.g. land use maps). Allows to tweak or create landscapes while retaining a high degree of control on its features, without the hassle of specifying each location attribute. In this it differs from other tools which generate null or neutral landscapes in a theoretical space. The basic algorithm currently implemented uses a simple agent style/cellular automata growth model, with no rules (apart from areas of exclusion) and von Neumann neighbourhood (four cells, aka Rook case). Outputs are raster dataset exportable to any common GIS format.
Author: Dario Masante [aut, cre],
Lora Murphy [ctb]
Maintainer: Dario Masante <dario.masante@gmail.com>
Diff between landscapeR versions 1.2 dated 2017-07-08 and 1.3 dated 2024-11-01
landscapeR-1.2/landscapeR/src/init.c |only landscapeR-1.3/landscapeR/DESCRIPTION | 29 landscapeR-1.3/landscapeR/MD5 | 58 + landscapeR-1.3/landscapeR/NEWS.md | 14 landscapeR-1.3/landscapeR/R/RcppExports.R | 6 landscapeR-1.3/landscapeR/R/expandClass.R | 22 landscapeR-1.3/landscapeR/R/landscapeR-package.R | 3 landscapeR-1.3/landscapeR/R/makeClass.R | 36 - landscapeR-1.3/landscapeR/R/makeLine.R | 19 landscapeR-1.3/landscapeR/R/makePatch.R | 28 landscapeR-1.3/landscapeR/R/rmSingle.R | 9 landscapeR-1.3/landscapeR/R/zzz.R | 4 landscapeR-1.3/landscapeR/build/vignette.rds |binary landscapeR-1.3/landscapeR/inst/CITATION |only landscapeR-1.3/landscapeR/inst/doc/landscapeR.R | 44 - landscapeR-1.3/landscapeR/inst/doc/landscapeR.Rmd | 30 landscapeR-1.3/landscapeR/inst/doc/landscapeR.html | 428 +++++++------ landscapeR-1.3/landscapeR/man/expandClass.Rd | 12 landscapeR-1.3/landscapeR/man/landscapeR-package.Rd | 3 landscapeR-1.3/landscapeR/man/makeClass.Rd | 26 landscapeR-1.3/landscapeR/man/makeLine.Rd | 24 landscapeR-1.3/landscapeR/man/makePatch.Rd | 27 landscapeR-1.3/landscapeR/man/rmSingle.Rd | 5 landscapeR-1.3/landscapeR/src/RcppExports.cpp | 23 landscapeR-1.3/landscapeR/vignettes/landscapeR.Rmd | 30 landscapeR-1.3/landscapeR/vignettes/unnamed-chunk-10-1.png |only landscapeR-1.3/landscapeR/vignettes/unnamed-chunk-11-1.png |only landscapeR-1.3/landscapeR/vignettes/unnamed-chunk-12-1.png |only landscapeR-1.3/landscapeR/vignettes/unnamed-chunk-13-1.png |only landscapeR-1.3/landscapeR/vignettes/unnamed-chunk-14-1.png |only landscapeR-1.3/landscapeR/vignettes/unnamed-chunk-15-1.png |only landscapeR-1.3/landscapeR/vignettes/unnamed-chunk-3-1.png |only landscapeR-1.3/landscapeR/vignettes/unnamed-chunk-4-1.png |only landscapeR-1.3/landscapeR/vignettes/unnamed-chunk-5-1.png |only landscapeR-1.3/landscapeR/vignettes/unnamed-chunk-6-1.png |only landscapeR-1.3/landscapeR/vignettes/unnamed-chunk-8-1.png |only landscapeR-1.3/landscapeR/vignettes/unnamed-chunk-9-1.png |only 37 files changed, 535 insertions(+), 345 deletions(-)
Title: Identifying Infection with Machine Intelligence
Description: A novel machine learning method for plant viruses diagnostic using
genome sequencing data. This package includes three different machine
learning models, random forest, XGBoost, and elastic net, to train and
predict mapped genome samples. Mappability profile and unreliable regions
are introduced to the algorithm, and users can build a mappability profile
from scratch with functions included in the package. Plotting mapped sample
coverage information is provided.
Author: Haochen Ning [aut],
Ian Boyes [aut],
Ibrahim Numanagic [aut] ,
Michael Rott [aut],
Li Xing [aut] ,
Xuekui Zhang [aut, cre]
Maintainer: Xuekui Zhang <xuekui@uvic.ca>
Diff between iimi versions 1.1.1 dated 2024-07-26 and 1.2.1 dated 2024-11-01
iimi-1.1.1/iimi/data/virus_segments.rda |only iimi-1.1.1/iimi/man/virus_segments.Rd |only iimi-1.2.1/iimi/DESCRIPTION | 17 iimi-1.2.1/iimi/MD5 | 68 +-- iimi-1.2.1/iimi/R/convert_bam_to_rle.R | 118 +++--- iimi-1.2.1/iimi/R/convert_rle_to_df.R | 334 +++++++++--------- iimi-1.2.1/iimi/R/create_high_nucleotide_content.R | 193 +++++----- iimi-1.2.1/iimi/R/create_mappability_profile.R | 45 ++ iimi-1.2.1/iimi/R/data.R | 20 - iimi-1.2.1/iimi/R/globals.R | 3 iimi-1.2.1/iimi/R/plot_cov.R | 16 iimi-1.2.1/iimi/R/predict_iimi.R | 3 iimi-1.2.1/iimi/R/train_iimi.R | 215 +++++------ iimi-1.2.1/iimi/data/example_cov.rda |binary iimi-1.2.1/iimi/data/example_diag.rda |binary iimi-1.2.1/iimi/data/nucleotide_info.rda |binary iimi-1.2.1/iimi/data/trained_en.rda |binary iimi-1.2.1/iimi/data/trained_rf.rda |binary iimi-1.2.1/iimi/data/trained_xgb.rda |binary iimi-1.2.1/iimi/data/unreliable_regions.rda |binary iimi-1.2.1/iimi/inst/REFERENCES/reference.bib | 10 iimi-1.2.1/iimi/inst/doc/package_vignette.R | 22 - iimi-1.2.1/iimi/inst/doc/package_vignette.Rmd | 29 - iimi-1.2.1/iimi/inst/doc/package_vignette.html | 66 +-- iimi-1.2.1/iimi/man/convert_bam_to_rle.Rd | 60 +-- iimi-1.2.1/iimi/man/convert_rle_to_df.Rd | 100 ++--- iimi-1.2.1/iimi/man/create_high_nucleotide_content.Rd | 4 iimi-1.2.1/iimi/man/create_mappability_profile.Rd | 81 ++-- iimi-1.2.1/iimi/man/example_diag.Rd | 8 iimi-1.2.1/iimi/man/nucleotide_info.Rd | 2 iimi-1.2.1/iimi/man/plot_cov.Rd | 7 iimi-1.2.1/iimi/man/train_iimi.Rd | 13 iimi-1.2.1/iimi/man/trained_rf.Rd | 2 iimi-1.2.1/iimi/man/trained_xgb.Rd | 32 - iimi-1.2.1/iimi/man/unreliable_regions.Rd | 56 +-- iimi-1.2.1/iimi/vignettes/package_vignette.Rmd | 29 - 36 files changed, 839 insertions(+), 714 deletions(-)
Title: Sum of Ranking Differences Statistical Test
Description: We provide an implementation for Sum of Ranking Differences (SRD),
a novel statistical test introduced by Héberger (2010)
<doi:10.1016/j.trac.2009.09.009>. The test allows the comparison of
different solutions through a reference by first performing a rank
transformation on the input, then calculating and comparing the distances
between the solutions and the reference - the latter is measured in the
L1 norm. The reference can be an external benchmark (e.g. an established
gold standard) or can be aggregated from the data. The calculated distances,
called SRD scores, are validated in two ways, see Héberger and Kollár-Hunek
(2011) <doi:10.1002/cem.1320>. A randomization test (also called permutation
test) compares the SRD scores of the solutions to the SRD scores of randomly
generated rankings. The second validation option is cross-validation that
checks whether the rankings generated from the solutions come from the same
distribution or not. For a detailed analysis about the [...truncated...]
Author: Jochen Staudacher [aut, cph, cre]
,
Balazs R. Sziklai [aut, cph] ,
Linus Olsson [aut, cph],
Dennis Horn [ctb],
Alexander Pothmann [ctb],
Ali Tugay Sen [ctb],
Attila Gere [ctb] ,
Karoly Hebeger [ctb]
Maintainer: Jochen Staudacher <jochen.staudacher@hs-kempten.de>
Diff between rSRD versions 0.1.7 dated 2023-02-08 and 0.1.8 dated 2024-11-01
DESCRIPTION | 63 +++++++++++++++++++++++++------------ MD5 | 20 ++++++------ R/SRD_utility.R | 45 ++++++++++++++++++--------- R/heatmap.R | 10 ++++-- man/plotHeatmapSRD.Rd | 9 ++++- man/utilsCalculateDistance.Rd | 5 +-- man/utilsCalculateRank.Rd | 68 ++++++++++++++++++++--------------------- man/utilsColorPalette.Rd | 44 +++++++++++++------------- man/utilsDetailedSRD.Rd | 2 - man/utilsDetailedSRDNoChars.Rd | 5 +-- src/Cross_Validation.cpp | 13 ++++++- 11 files changed, 173 insertions(+), 111 deletions(-)
Title: Generalized Dissimilarity Modeling
Description: A toolkit with functions to fit, plot, summarize, and apply Generalized Dissimilarity Models. Mokany K, Ware C, Woolley SNC, Ferrier S, Fitzpatrick MC (2022) <doi:10.1111/geb.13459> Ferrier S, Manion G, Elith J, Richardson K (2007) <doi:10.1111/j.1472-4642.2007.00341.x>.
Author: Matt Fitzpatrick [aut, cre] ,
Karel Mokany [aut] ,
Glenn Manion [aut],
Diego Nieto-Lugilde [aut] ,
Simon Ferrier [aut] ,
Roozbeh Valavi [ctb],
Matthew Lisk [ctb],
Chris Ware [ctb],
Skip Woolley [ctb],
Tom Harwood [ctb]
Maintainer: Matt Fitzpatrick <mfitzpatrick@umces.edu>
Diff between gdm versions 1.6.0-2 dated 2024-09-27 and 1.6.0-3 dated 2024-11-01
DESCRIPTION | 8 ++-- MD5 | 26 +++++++------- NEWS.md | 7 ++-- R/gdm.predict.R | 36 +++++++++----------- R/gdm.transform.R | 54 +++++++++++++++---------------- README.md | 22 ++++-------- inst/tinytest/test_gdm.R | 9 ++++- man/figures/README-extractSplines-1.png |binary man/figures/README-plotGDM-1.png |binary man/figures/README-predictSpaceGDM-1.png |binary man/figures/README-predictTimeGDM-1.png |binary man/figures/README-transformGDM-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/gdm.transform.Rd | 11 ++---- 14 files changed, 82 insertions(+), 91 deletions(-)
Title: Reliability Growth Analysis
Description: Modeling and plotting functions for Reliability Growth Analysis (RGA). Models include the Duane (1962) <doi:10.1109/TA.1964.4319640>, Non-Homogeneous Poisson Process (NHPP) by Crow (1975) <https://apps.dtic.mil/sti/citations/ADA020296>, Piecewise Weibull NHPP by Guo et al. (2010) <doi:10.1109/RAMS.2010.5448029>, and Piecewise Weibull NHPP with Change Point Detection based on the 'segmented' package by Muggeo (2024) <https://cran.r-project.org/package=segmented>.
Author: Paul Govan [aut, cre, cph]
Maintainer: Paul Govan <paul.govan2@gmail.com>
Diff between ReliaGrowR versions 0.1.0 dated 2024-09-19 and 0.1.1 dated 2024-11-01
ReliaGrowR-0.1.0/ReliaGrowR/inst/doc/rga.R |only ReliaGrowR-0.1.0/ReliaGrowR/inst/doc/rga.Rmd |only ReliaGrowR-0.1.0/ReliaGrowR/inst/doc/rga.html |only ReliaGrowR-0.1.0/ReliaGrowR/vignettes/rga.Rmd |only ReliaGrowR-0.1.1/ReliaGrowR/DESCRIPTION | 6 +-- ReliaGrowR-0.1.1/ReliaGrowR/MD5 | 30 +++++++++--------- ReliaGrowR-0.1.1/ReliaGrowR/NEWS.md | 9 ++++- ReliaGrowR-0.1.1/ReliaGrowR/R/duane_plot.R | 13 ++++++- ReliaGrowR-0.1.1/ReliaGrowR/R/rga.R | 8 ++++ ReliaGrowR-0.1.1/ReliaGrowR/README.md | 18 ++++++---- ReliaGrowR-0.1.1/ReliaGrowR/build/vignette.rds |binary ReliaGrowR-0.1.1/ReliaGrowR/inst/CITATION | 11 +++--- ReliaGrowR-0.1.1/ReliaGrowR/inst/doc/RGA.R |only ReliaGrowR-0.1.1/ReliaGrowR/inst/doc/RGA.Rmd |only ReliaGrowR-0.1.1/ReliaGrowR/inst/doc/RGA.html |only ReliaGrowR-0.1.1/ReliaGrowR/man/duane_plot.Rd | 1 ReliaGrowR-0.1.1/ReliaGrowR/man/rga.Rd | 2 - ReliaGrowR-0.1.1/ReliaGrowR/tests/testthat/Rplots.pdf |binary ReliaGrowR-0.1.1/ReliaGrowR/tests/testthat/test-rga.R | 8 ++-- ReliaGrowR-0.1.1/ReliaGrowR/vignettes/RGA.Rmd |only 20 files changed, 65 insertions(+), 41 deletions(-)
Title: R Object-Oriented Programming with or without References
Description: Methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers. The package has been developed since 2001 and is now considered very stable. This is a cross-platform package implemented in pure R that defines standard S3 classes without any tricks.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.oo versions 1.26.0 dated 2024-01-24 and 1.27.0 dated 2024-11-01
DESCRIPTION | 6 +++--- MD5 | 32 ++++++++++++++++---------------- NAMESPACE | 8 ++++++-- NEWS.md | 33 +++++++++++++++++++++------------ R/006.fixVarArgs.R | 6 +++++- R/060.Class.R | 11 +++++++---- R/BasicObject.R | 18 +++++++++--------- man/BasicObject.Rd | 8 ++++---- man/DOLLAR.BasicObject.Rd | 4 ++-- man/DOLLAR.Class.Rd | 4 ++-- man/DOLLARLT_-.BasicObject.Rd | 4 ++-- man/DOLLARLT_-.Class.Rd | 4 ++-- man/attach.BasicObject.Rd | 4 ++-- man/detach.BasicObject.Rd | 4 ++-- man/extend.BasicObject.Rd | 2 +- man/getFields.BasicObject.Rd | 4 ++-- man/print.BasicObject.Rd | 2 +- 17 files changed, 87 insertions(+), 67 deletions(-)
Title: Hidden Markov Models for Multivariate Panel Data
Description: Estimates hidden Markov models from the family of Cholesky-decomposed Gaussian hidden Markov models (CDGHMM) under various missingness schemes. This family improves upon estimation of traditional Gaussian HMMs by introducing parsimony, as well as, controlling for dropped out observations and non-random missingness. See Neal, Sochaniwsky and McNicholas (2024) <DOI:10.1007/s11222-024-10462-0>.
Author: Mackenzie R. Neal [aut, cre] ,
Alexa A. Sochaniwsky [aut],
Paul D. McNicholas [aut]
Maintainer: Mackenzie R. Neal <nealm6@mcmaster.ca>
Diff between CDGHMM versions 0.1.0 dated 2024-05-16 and 0.1.1 dated 2024-11-01
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/cdghmm.R | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: PX-Web Data by API
Description: Function to read PX-Web data into R via API. The example code reads data from the three national statistical institutes, Statistics Norway, Statistics Sweden and Statistics Finland.
Author: Oeyvind Langsrud [aut, cre],
Jan Bruusgaard [aut],
Solveig Bjoerkholt [ctb],
Susie Jentoft [ctb]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between PxWebApiData versions 0.9.0 dated 2024-01-29 and 1.0.0 dated 2024-11-01
DESCRIPTION | 17 +- LICENSE | 193 --------------------------------- MD5 | 20 +-- NEWS.md | 12 ++ R/ApiData.R | 5 R/fromJSONstatExtra.R | 212 ++++++++++++++++++------------------- inst/doc/Introduction.R | 29 +++-- inst/doc/Introduction.Rmd | 29 +++-- inst/doc/Introduction.html | 257 +++++++++++++++++++++++++-------------------- man/ApiData.Rd | 5 vignettes/Introduction.Rmd | 29 +++-- 11 files changed, 356 insertions(+), 452 deletions(-)
Title: Helper Functions to Install and Maintain TeX Live, and Compile
LaTeX Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] ,
Posit Software, PBC [cph, fnd],
Christophe Dervieux [ctb] ,
Devon Ryan [ctb] ,
Ethan Heinzen [ctb],
Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.53 dated 2024-09-15 and 0.54 dated 2024-11-01
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/install.R | 36 +++++++++++++++++++++++++++++++++--- R/latex.R | 10 +--------- 4 files changed, 41 insertions(+), 19 deletions(-)
Title: Breeding Program Simulations
Description: The successor to the 'AlphaSim' software for breeding program
simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>].
Used for stochastic simulations of breeding programs to the level of DNA
sequence for every individual. Contained is a wide range of functions for
modeling common tasks in a breeding program, such as selection and crossing.
These functions allow for constructing simulations of highly complex plant and
animal breeding programs via scripting in the R software environment. Such
simulations can be used to evaluate overall breeding program performance and
conduct research into breeding program design, such as implementation of
genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS')
for fast simulation of biallelic sequences according to a population
demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].
Author: Chris Gaynor [aut, cre] ,
Gregor Gorjanc [ctb] ,
John Hickey [ctb] ,
Daniel Money [ctb] ,
David Wilson [ctb],
Thiago Oliveira [ctb] ,
Audrey Martin [ctb] ,
Philip Greenspoon [ctb]
Maintainer: Chris Gaynor <gaynor.robert@hotmail.com>
Diff between AlphaSimR versions 1.6.0 dated 2024-08-17 and 1.6.1 dated 2024-11-01
DESCRIPTION | 8 LICENSE | 2 MD5 | 363 +- NAMESPACE | 320 - NEWS.md | 836 ++--- R/AlphaSimR.R | 58 R/Class-HybridPop.R | 256 - R/Class-LociMap.R | 752 ++-- R/Class-Pop.R | 2096 ++++++------- R/Class-RRsol.R | 54 R/Class-SimParam.R | 5136 ++++++++++++++++---------------- R/GS.R | 3052 +++++++++---------- R/RcppExports.R | 742 ++-- R/crossing.R | 1796 +++++------ R/founderPop.R | 1222 +++---- R/hybrids.R | 862 ++--- R/importData.R | 592 +-- R/mergePops.R | 388 +- R/misc.R | 1314 ++++---- R/phenotypes.R | 528 +-- R/polyploids.R | 614 +-- R/popSummary.R | 1412 ++++---- R/pullGeno.R | 2251 +++++++------- R/selection.R | 1122 +++--- R/writePlink.R | 278 - R/writeRecords.R | 212 - README.md | 62 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 22 inst/REFERENCES.bib | 342 +- inst/doc/intro.R | 110 inst/doc/intro.Rmd | 274 - inst/doc/intro.html | 1196 +++---- inst/doc/traits.Rmd | 372 +- inst/doc/traits.pdf |binary man/AlphaSimR-package.Rd | 100 man/HybridPop-class.Rd | 122 man/LociMap-class.Rd | 42 man/MapPop-class.Rd | 102 man/MultiPop-class.Rd | 112 man/NamedMapPop-class.Rd | 96 man/Pop-class.Rd | 181 - man/RRBLUP.Rd | 132 man/RRBLUP2.Rd | 224 - man/RRBLUPMemUse.Rd | 56 man/RRBLUP_D.Rd | 134 man/RRBLUP_D2.Rd | 178 - man/RRBLUP_GCA.Rd | 136 man/RRBLUP_GCA2.Rd | 176 - man/RRBLUP_SCA.Rd | 134 man/RRBLUP_SCA2.Rd | 184 - man/RRsol-class.Rd | 52 man/RawPop-class.Rd | 122 man/SimParam.Rd | 3896 ++++++++++++------------ man/TraitA-class.Rd | 36 man/TraitA2-class.Rd | 34 man/TraitA2D-class.Rd | 32 man/TraitAD-class.Rd | 32 man/TraitADE-class.Rd | 32 man/TraitADEG-class.Rd | 40 man/TraitADG-class.Rd | 40 man/TraitAE-class.Rd | 32 man/TraitAEG-class.Rd | 40 man/TraitAG-class.Rd | 40 man/aa.Rd | 64 man/addSegSite.Rd | 80 man/attrition.Rd | 74 man/bv.Rd | 62 man/cChr.Rd | 54 man/calcGCA.Rd | 74 man/dd.Rd | 62 man/dot-newPop.Rd | 108 man/doubleGenome.Rd | 80 man/ebv.Rd | 60 man/editGenome.Rd | 98 man/editGenomeTopQtl.Rd | 90 man/fastRRBLUP.Rd | 156 man/genParam.Rd | 134 man/genicVarA.Rd | 62 man/genicVarAA.Rd | 64 man/genicVarD.Rd | 62 man/genicVarG.Rd | 62 man/getGenMap.Rd | 80 man/getNumThreads.Rd | 38 man/getPed.Rd | 66 man/getQtlMap.Rd | 88 man/getSnpMap.Rd | 90 man/gv.Rd | 58 man/hybridCross.Rd | 102 man/importGenMap.Rd | 64 man/importHaplo.Rd | 124 man/importInbredGeno.Rd | 122 man/isFemale.Rd | 76 man/isPop.Rd | 56 man/makeCross.Rd | 84 man/makeCross2.Rd | 88 man/makeDH.Rd | 86 man/mapLoci.Rd |only man/meanG.Rd | 58 man/meanP.Rd | 58 man/mergeGenome.Rd | 86 man/mergePops.Rd | 72 man/mutate.Rd | 94 man/nInd.Rd | 58 man/newEmptyPop.Rd | 68 man/newMapPop.Rd | 106 man/newMultiPop.Rd | 68 man/newPop.Rd | 110 man/pedigreeCross.Rd | 158 man/pheno.Rd | 58 man/popVar.Rd | 40 man/pullIbdHaplo.Rd | 82 man/pullMarkerGeno.Rd | 90 man/pullMarkerHaplo.Rd | 100 man/pullQtlGeno.Rd | 84 man/pullQtlHaplo.Rd | 106 man/pullSegSiteGeno.Rd | 80 man/pullSegSiteHaplo.Rd | 102 man/pullSnpGeno.Rd | 84 man/pullSnpHaplo.Rd | 106 man/quickHaplo.Rd | 70 man/randCross.Rd | 108 man/randCross2.Rd | 126 man/reduceGenome.Rd | 110 man/resetPop.Rd | 72 man/runMacs.Rd | 160 man/runMacs2.Rd | 190 - man/sampleHaplo.Rd | 66 man/selIndex.Rd | 92 man/selInt.Rd | 36 man/selectCross.Rd | 176 - man/selectFam.Rd | 180 - man/selectInd.Rd | 214 - man/selectOP.Rd | 170 - man/selectWithinFam.Rd | 182 - man/self.Rd | 84 man/setEBV.Rd | 134 man/setMarkerHaplo.Rd | 100 man/setPheno.Rd | 222 - man/setPhenoGCA.Rd | 166 - man/setPhenoProgTest.Rd | 184 - man/smithHazel.Rd | 60 man/solveMKM.Rd | 48 man/solveMVM.Rd | 48 man/solveRRBLUP.Rd | 36 man/solveRRBLUPMK.Rd | 40 man/solveRRBLUPMV.Rd | 44 man/solveRRBLUP_EM.Rd | 60 man/solveRRBLUP_EM2.Rd | 68 man/solveRRBLUP_EM3.Rd | 76 man/solveUVM.Rd | 40 man/transMat.Rd | 98 man/usefulness.Rd | 124 man/varA.Rd | 62 man/varAA.Rd | 64 man/varD.Rd | 62 man/varG.Rd | 58 man/varP.Rd | 58 man/writePlink.Rd | 140 man/writeRecords.Rd | 80 src/algorithm.cpp | 2 src/simulator.cpp | 4 tests/testthat.R | 8 tests/testthat/test-addTrait.R | 228 - tests/testthat/test-crossing.R | 272 - tests/testthat/test-editGenome.R | 32 tests/testthat/test-hybrids.R | 132 tests/testthat/test-importData.R | 96 tests/testthat/test-misc.R | 102 tests/testthat/test-selection.R | 74 tests/testthat/test-statistics.R | 60 vignettes/AlphaSimR.bib | 288 - vignettes/articles/AlphaSimR.Rmd | 50 vignettes/articles/DataImport.Rmd | 42 vignettes/articles/Genome.Rmd | 52 vignettes/articles/GenomicSelection.Rmd | 78 vignettes/articles/Meiosis.Rmd | 86 vignettes/articles/Misc.Rmd | 62 vignettes/articles/QuantGen.Rmd | 64 vignettes/articles/Traits.Rmd | 70 vignettes/intro.Rmd | 274 - vignettes/traits.Rmd | 372 +- 183 files changed, 23162 insertions(+), 23111 deletions(-)
Title: Accessing Spatial Basemaps in R
Description: A lightweight package to access spatial basemaps from open sources such as 'OpenStreetMap', 'Carto', 'Mapbox' and others in R.
Author: Jakob Schwalb-Willmann [aut, cre]
Maintainer: Jakob Schwalb-Willmann <dev@schwalb-willmann.de>
Diff between basemaps versions 0.0.7 dated 2024-04-16 and 0.0.8 dated 2024-11-01
DESCRIPTION | 8 ++-- MD5 | 20 +++++------ NEWS.md | 17 +++++++++ R/basemap.R | 7 ++- R/get_maptypes.R | 4 +- R/internal.R | 49 +++++++++++++++++++++------ R/plot.R | 4 +- README.md | 66 ++++++++++++++++++++++++++----------- tests/testthat/helper-vars.R | 3 + tests/testthat/test-basemap.R | 6 ++- tests/testthat/test-get_maptypes.R | 4 +- 11 files changed, 135 insertions(+), 53 deletions(-)
Title: Interactive Maps with 'Mapbox GL JS' and 'MapLibre GL JS'
Description: Provides an interface to the 'Mapbox GL JS' (<https://docs.mapbox.com/mapbox-gl-js/guides>)
and the 'MapLibre GL JS' (<https://maplibre.org/maplibre-gl-js/docs/>) interactive mapping libraries to help users
create custom interactive maps in R. Users can create interactive globe visualizations; layer 'sf' objects to create
filled maps, circle maps, 'heatmaps', and three-dimensional graphics; and customize map styles and views. The package
also includes utilities to use 'Mapbox' and 'MapLibre' maps in 'Shiny' web applications.
Author: Kyle Walker [aut, cre]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between mapgl versions 0.1.3 dated 2024-09-04 and 0.1.4 dated 2024-11-01
DESCRIPTION | 10 MD5 | 76 - NAMESPACE | 4 NEWS.md | 10 R/controls.R | 572 +++++++----- R/image.R |only R/layers.R | 97 +- R/legends.R | 243 ++--- R/plugins.R | 73 + R/shiny.R | 219 ++-- R/style_helpers.R | 342 +++---- R/terrain.R | 26 inst/htmlwidgets/lib/freehand-mode/freehand-mode.js | 96 +- inst/htmlwidgets/lib/mapbox-gl-draw |only inst/htmlwidgets/lib/mapbox-gl-globe-minimap |only inst/htmlwidgets/lib/maplibre-gl-geocoder |only inst/htmlwidgets/lib/maplibre-gl/maplibre-gl.js | 8 inst/htmlwidgets/mapboxgl.js | 460 ++++++++-- inst/htmlwidgets/mapboxgl.yaml | 63 - inst/htmlwidgets/mapboxgl_compare.js | 894 +++++++++++--------- inst/htmlwidgets/maplibregl.js | 317 ++++++- inst/htmlwidgets/maplibregl.yaml | 59 - inst/htmlwidgets/maplibregl_compare.js | 890 +++++++++++-------- man/add_categorical_legend.Rd | 23 man/add_continuous_legend.Rd | 8 man/add_draw_control.Rd | 16 man/add_fill_layer.Rd | 3 man/add_geolocate_control.Rd |only man/add_globe_minimap.Rd |only man/add_image.Rd |only man/add_legend.Rd | 8 man/add_line_layer.Rd | 70 + man/add_navigation_control.Rd | 5 man/add_symbol_layer.Rd | 9 man/cluster_options.Rd | 5 man/interpolate.Rd | 10 man/mapgl-package.Rd | 2 man/match_expr.Rd | 8 man/move_layer.Rd |only man/set_style.Rd | 12 man/set_terrain.Rd | 26 man/step_expr.Rd | 8 42 files changed, 2940 insertions(+), 1732 deletions(-)
Title: Prior Diagnostics and Sensitivity Analysis
Description: Provides functions for prior and likelihood sensitivity analysis in Bayesian models. Currently it implements methods to determine the sensitivity of the posterior to power-scaling perturbations of the prior and likelihood.
Author: Noa Kallioinen [aut, cre, cph],
Topi Paananen [aut],
Paul-Christian Buerkner [aut],
Aki Vehtari [aut],
Frank Weber [ctb]
Maintainer: Noa Kallioinen <noa.kallioinen@aalto.fi>
Diff between priorsense versions 1.0.3 dated 2024-10-01 and 1.0.4 dated 2024-11-01
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/powerscale_gradients.R | 13 +++++++------ inst/doc/powerscaling.html | 4 ++-- 5 files changed, 21 insertions(+), 15 deletions(-)
Title: Create Useful .gitignore Files for your Project
Description: Simple interface to query gitignore.io to fetch
gitignore templates that can be included in the .gitignore file. More
than 450 templates are currently available.
Author: Philippe Massicotte [aut, cre]
,
Amanda Dobbyn [rev],
Mauro Lepore [rev]
Maintainer: Philippe Massicotte <pmassicotte@hotmail.com>
Diff between gitignore versions 0.1.7 dated 2024-07-08 and 0.1.8 dated 2024-11-01
gitignore-0.1.7/gitignore/tests/testthat/test_gi_fetch_templates.R |only gitignore-0.1.7/gitignore/tests/testthat/test_gi_write_gitignore.R |only gitignore-0.1.8/gitignore/DESCRIPTION | 11 ++-- gitignore-0.1.8/gitignore/MD5 | 23 +++++----- gitignore-0.1.8/gitignore/NEWS.md | 6 ++ gitignore-0.1.8/gitignore/R/gi_available_templates.R | 10 ++-- gitignore-0.1.8/gitignore/R/gi_fetch_templates.R | 21 ++++----- gitignore-0.1.8/gitignore/R/gi_write_gitignore.R | 19 ++++---- gitignore-0.1.8/gitignore/inst/WORDLIST | 7 ++- gitignore-0.1.8/gitignore/man/gi_available_templates.Rd | 2 gitignore-0.1.8/gitignore/man/gi_fetch_templates.Rd | 2 gitignore-0.1.8/gitignore/tests/testthat.R | 8 +++ gitignore-0.1.8/gitignore/tests/testthat/test-gi_available_templates.R |only gitignore-0.1.8/gitignore/tests/testthat/test-gi_fetch_templates.R |only gitignore-0.1.8/gitignore/tests/testthat/test-gi_write_gitignore.R |only 15 files changed, 69 insertions(+), 40 deletions(-)
Title: Causal Inference with Continuous (Multiple Time Point)
Interventions
Description: Estimation of counterfactual outcomes for multiple values of continuous interventions at different time points, and plotting of causal dose-response curves. Details are given in Schomaker, McIlleron, Denti, Diaz (2024) <doi:10.48550/arXiv.2305.06645>.
Author: Michael Schomaker [aut, cre]
Maintainer: Michael Schomaker <michael.schomaker@stat.uni-muenchen.de>
Diff between CICI versions 0.9.2 dated 2024-10-22 and 0.9.3 dated 2024-11-01
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/custom.measure.r | 9 ++++++++- R/gformula.r | 29 +++++++++++++++++------------ R/plot.gformula.r | 8 ++++++-- man/CICI-package.Rd | 4 ++-- 6 files changed, 42 insertions(+), 26 deletions(-)
Title: Crosstables for Descriptive Analyses
Description: Create descriptive tables for continuous and categorical variables.
Apply summary statistics and counting function, with or without a grouping variable, and create beautiful reports using 'rmarkdown' or 'officer'.
You can also compute effect sizes and statistical tests if needed.
Author: Dan Chaltiel [aut, cre] ,
David Hajage [ccp]
Maintainer: Dan Chaltiel <dan.chaltiel@gmail.com>
Diff between crosstable versions 0.8.0 dated 2024-09-30 and 0.8.1 dated 2024-11-01
DESCRIPTION | 6 +- MD5 | 20 ++++----- NEWS.md | 25 +++++++++++- R/compact.R | 25 +++++++----- inst/doc/crosstable-report.html | 4 - inst/doc/crosstable-selection.html | 30 +++++++------- inst/doc/crosstable.html | 24 +++++------ inst/doc/percent_pattern.html | 10 ++-- man/ct_compact.Rd | 9 +++- tests/testthat/_snaps/compact.md | 76 +++++++++++++++++++------------------ tests/testthat/test-compact.R | 23 +++++++++++ 11 files changed, 156 insertions(+), 96 deletions(-)
Title: Spatial and Environmental Blocking for K-Fold and LOO
Cross-Validation
Description: Creating spatially or environmentally separated folds for cross-validation to provide a robust error estimation in spatially structured environments; Investigating and visualising the effective range of spatial autocorrelation in continuous raster covariates and point samples to find an initial realistic distance band to separate training and testing datasets spatially described in Valavi, R. et al. (2019) <doi:10.1111/2041-210X.13107>.
Author: Roozbeh Valavi [aut, cre] ,
Jane Elith [aut],
Jose Lahoz-Monfort [aut],
Ian Flint [aut],
Gurutzeta Guillera-Arroita [aut]
Maintainer: Roozbeh Valavi <valavi.r@gmail.com>
Diff between blockCV versions 3.1-4 dated 2024-05-23 and 3.1-5 dated 2024-11-01
DESCRIPTION | 10 - MD5 | 10 - R/cv_plot.R | 452 +++++++++++++++++++++++------------------------ build/vignette.rds |binary inst/doc/tutorial_1.html | 24 +- inst/doc/tutorial_2.html | 6 6 files changed, 253 insertions(+), 249 deletions(-)
Title: Generalized Linear Regression Models on Network-Linked Data with
Statistical Inference
Description: Linear regression model and generalized linear models with nonparametric network effects on network-linked observations. The model is originally proposed by Le and Li (2022) <doi:10.48550/arXiv.2007.00803> and is assumed on observations that are connected by a network or similar relational data structure. A more recent work by Wang, Le and Li (2024) <doi:10.48550/arXiv.2410.01163> further extends the framework to generalized linear models. All these models are implemented in the current package. The model does not assume that the relational data or network structure to be precisely observed; thus, the method is provably robust to a certain level of perturbation of the network structure. The package contains the estimation and inference function for the model.
Author: Jianxiang Wang [aut, cre],
Tianxi Li [aut],
Can M. Le [aut]
Maintainer: Jianxiang Wang <jw1881@scarletmail.rutgers.edu>
Diff between NetworkReg versions 1.1 dated 2024-02-08 and 2.0 dated 2024-11-01
NetworkReg-1.1/NetworkReg/man/NetReg-package.Rd |only NetworkReg-2.0/NetworkReg/DESCRIPTION | 25 NetworkReg-2.0/NetworkReg/MD5 | 12 NetworkReg-2.0/NetworkReg/NAMESPACE | 9 NetworkReg-2.0/NetworkReg/R/SP_Inf.R | 637 ++++++++++++-------- NetworkReg-2.0/NetworkReg/man/NetworkReg-package.Rd |only NetworkReg-2.0/NetworkReg/man/SP.Inf.Rd | 226 ++----- NetworkReg-2.0/NetworkReg/man/net.gen.from.P.Rd | 35 - 8 files changed, 529 insertions(+), 415 deletions(-)
Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates graphics with
details from statistical tests included in the plots themselves. It
provides an easier syntax to generate information-rich plots for
statistical analysis of continuous (violin plots, scatterplots,
histograms, dot plots, dot-and-whisker plots) or categorical (pie and
bar charts) data. Currently, it supports the most common types of
statistical approaches and tests: parametric, nonparametric, robust,
and Bayesian versions of t-test/ANOVA, correlation analyses,
contingency table analysis, meta-analysis, and regression analyses.
References: Patil (2021) <doi:10.21105/joss.03236>.
Author: Indrajeet Patil [cre, aut, cph]
,
Chuck Powell [ctb]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between ggstatsplot versions 0.12.4 dated 2024-07-06 and 0.12.5 dated 2024-11-01
ggstatsplot-0.12.4/ggstatsplot/data/bugs_wide.rdata |only ggstatsplot-0.12.4/ggstatsplot/man/bugs_wide.Rd |only ggstatsplot-0.12.5/ggstatsplot/DESCRIPTION | 28 ggstatsplot-0.12.5/ggstatsplot/MD5 | 148 +-- ggstatsplot-0.12.5/ggstatsplot/NEWS.md | 31 ggstatsplot-0.12.5/ggstatsplot/R/combine-plots.R | 8 ggstatsplot-0.12.5/ggstatsplot/R/data.R | 42 - ggstatsplot-0.12.5/ggstatsplot/R/extract-stats.R | 49 - ggstatsplot-0.12.5/ggstatsplot/R/ggbarstats.R | 6 ggstatsplot-0.12.5/ggstatsplot/R/ggbetweenstats-helpers.R | 2 ggstatsplot-0.12.5/ggstatsplot/R/ggbetweenstats.R | 26 ggstatsplot-0.12.5/ggstatsplot/R/ggcoefstats.R | 94 +- ggstatsplot-0.12.5/ggstatsplot/R/ggcorrmat.R | 12 ggstatsplot-0.12.5/ggstatsplot/R/ggdotplotstats.R | 3 ggstatsplot-0.12.5/ggstatsplot/R/gghistostats.R | 4 ggstatsplot-0.12.5/ggstatsplot/R/ggpiestats-ggbarstats-helpers.R | 45 - ggstatsplot-0.12.5/ggstatsplot/R/ggpiestats.R | 18 ggstatsplot-0.12.5/ggstatsplot/R/ggscatterstats.R | 17 ggstatsplot-0.12.5/ggstatsplot/R/ggstatsplot-package.R | 2 ggstatsplot-0.12.5/ggstatsplot/R/ggwithinstats.R | 4 ggstatsplot-0.12.5/ggstatsplot/R/theme-ggstatsplot.R | 6 ggstatsplot-0.12.5/ggstatsplot/README.md | 11 ggstatsplot-0.12.5/ggstatsplot/inst/WORDLIST | 6 ggstatsplot-0.12.5/ggstatsplot/man/bugs_long.Rd | 9 ggstatsplot-0.12.5/ggstatsplot/man/combine_plots.Rd | 8 ggstatsplot-0.12.5/ggstatsplot/man/dot-grouped_list.Rd | 2 ggstatsplot-0.12.5/ggstatsplot/man/extract_stats.Rd | 11 ggstatsplot-0.12.5/ggstatsplot/man/ggbarstats.Rd | 42 - ggstatsplot-0.12.5/ggstatsplot/man/ggbetweenstats.Rd | 34 ggstatsplot-0.12.5/ggstatsplot/man/ggcoefstats.Rd | 40 ggstatsplot-0.12.5/ggstatsplot/man/ggcorrmat.Rd | 30 ggstatsplot-0.12.5/ggstatsplot/man/ggdotplotstats.Rd | 28 ggstatsplot-0.12.5/ggstatsplot/man/gghistostats.Rd | 24 ggstatsplot-0.12.5/ggstatsplot/man/ggpiestats.Rd | 42 - ggstatsplot-0.12.5/ggstatsplot/man/ggscatterstats.Rd | 34 ggstatsplot-0.12.5/ggstatsplot/man/ggstatsplot-package.Rd | 4 ggstatsplot-0.12.5/ggstatsplot/man/ggwithinstats.Rd | 38 ggstatsplot-0.12.5/ggstatsplot/man/grouped_ggbarstats.Rd | 46 - ggstatsplot-0.12.5/ggstatsplot/man/grouped_ggbetweenstats.Rd | 38 ggstatsplot-0.12.5/ggstatsplot/man/grouped_ggcorrmat.Rd | 30 ggstatsplot-0.12.5/ggstatsplot/man/grouped_ggdotplotstats.Rd | 32 ggstatsplot-0.12.5/ggstatsplot/man/grouped_gghistostats.Rd | 28 ggstatsplot-0.12.5/ggstatsplot/man/grouped_ggpiestats.Rd | 46 - ggstatsplot-0.12.5/ggstatsplot/man/grouped_ggscatterstats.Rd | 38 ggstatsplot-0.12.5/ggstatsplot/man/grouped_ggwithinstats.Rd | 42 - ggstatsplot-0.12.5/ggstatsplot/man/iris_long.Rd | 3 ggstatsplot-0.12.5/ggstatsplot/man/movies_long.Rd | 2 ggstatsplot-0.12.5/ggstatsplot/man/theme_ggstatsplot.Rd | 6 ggstatsplot-0.12.5/ggstatsplot/tests/testthat/_snaps/combine-plots/defaults-work-as-expected.svg | 20 ggstatsplot-0.12.5/ggstatsplot/tests/testthat/_snaps/extract-stats.md | 24 ggstatsplot-0.12.5/ggstatsplot/tests/testthat/_snaps/ggbarstats/checking-paired-two-way-table-without-na.svg | 4 ggstatsplot-0.12.5/ggstatsplot/tests/testthat/_snaps/ggbarstats/checking-unpaired-two-way-table-without-na.svg | 103 +- ggstatsplot-0.12.5/ggstatsplot/tests/testthat/_snaps/ggbarstats/common-legend-when-levels-are-dropped.svg | 110 -- ggstatsplot-0.12.5/ggstatsplot/tests/testthat/_snaps/ggbarstats/grouped-ggbarstats-with-two-way-table.svg | 114 -- ggstatsplot-0.12.5/ggstatsplot/tests/testthat/_snaps/ggbetweenstats/default-plot-as-expected.svg | 20 ggstatsplot-0.12.5/ggstatsplot/tests/testthat/_snaps/ggbetweenstats/plot-with-outliers-as-expected.svg | 20 ggstatsplot-0.12.5/ggstatsplot/tests/testthat/_snaps/ggcorrmat/with-nas.svg | 60 - ggstatsplot-0.12.5/ggstatsplot/tests/testthat/_snaps/ggcorrmat/without-nas.svg | 40 ggstatsplot-0.12.5/ggstatsplot/tests/testthat/_snaps/ggdotplotstats/defaults-work-as-expected.svg | 40 ggstatsplot-0.12.5/ggstatsplot/tests/testthat/_snaps/ggdotplotstats/further-modification-with-ggplot-works.svg | 40 ggstatsplot-0.12.5/ggstatsplot/tests/testthat/_snaps/gghistostats/defaults-as-expected.svg | 60 - ggstatsplot-0.12.5/ggstatsplot/tests/testthat/_snaps/gghistostats/modification-with-ggplot2-works.svg | 60 - ggstatsplot-0.12.5/ggstatsplot/tests/testthat/_snaps/ggpiestats/checking-one-way-table-without-na.svg | 10 ggstatsplot-0.12.5/ggstatsplot/tests/testthat/_snaps/ggpiestats/checking-paired-two-way-table-without-na.svg | 48 - ggstatsplot-0.12.5/ggstatsplot/tests/testthat/_snaps/ggpiestats/checking-unpaired-two-way-table-without-na.svg | 401 ++++------ ggstatsplot-0.12.5/ggstatsplot/tests/testthat/_snaps/ggpiestats/common-legend-when-levels-are-dropped.svg | 110 -- ggstatsplot-0.12.5/ggstatsplot/tests/testthat/_snaps/ggpiestats/grouped-ggpiestats-with-one-way-table.svg | 73 - ggstatsplot-0.12.5/ggstatsplot/tests/testthat/_snaps/ggpiestats/grouped-ggpiestats-with-two-way-table.svg | 114 -- ggstatsplot-0.12.5/ggstatsplot/tests/testthat/_snaps/ggscatterstats/aesthetic-modifications-work.svg | 60 - ggstatsplot-0.12.5/ggstatsplot/tests/testthat/_snaps/ggscatterstats/defaults-work-as-expected.svg | 40 ggstatsplot-0.12.5/ggstatsplot/tests/testthat/_snaps/ggwithinstats/grouped-plots-default.svg | 20 ggstatsplot-0.12.5/ggstatsplot/tests/testthat/test-extract-stats.R | 20 ggstatsplot-0.12.5/ggstatsplot/tests/testthat/test-ggbarstats.R | 6 ggstatsplot-0.12.5/ggstatsplot/tests/testthat/test-gghistostats.R | 9 ggstatsplot-0.12.5/ggstatsplot/tests/testthat/test-ggpiestats.R | 8 ggstatsplot-0.12.5/ggstatsplot/tests/testthat/test-ggscatterstats.R | 14 76 files changed, 1222 insertions(+), 1645 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-10-17 0.1.0
Title: Structural Modeling for Multiple Latent Class Variables
Description: Provides comprehensive tools for the implementation of Structural Latent Class Models (SLCM), including
Latent Transition Analysis (LTA; Linda M. Collins and Stephanie T. Lanza, 2009) <doi:10.1002/9780470567333>,
Latent Class Profile Analysis (LCPA; Hwan Chung et al., 2010) <doi:10.1111/j.1467-985x.2010.00674.x>, and
Joint Latent Class Analysis (JLCA; Saebom Jeon et al., 2017) <doi:10.1080/10705511.2017.1340844>, and
any other extended models involving multiple latent class variables.
Author: Youngsun Kim [aut, cre] ,
Hwan Chung [aut]
Maintainer: Youngsun Kim <yskstat@gmail.com>
Diff between slca versions 1.0.0 dated 2024-04-22 and 1.2.0 dated 2024-11-01
slca-1.0.0/slca/R/nlsy_jlcpa.R |only slca-1.2.0/slca/DESCRIPTION | 10 ++- slca-1.2.0/slca/MD5 | 84 +++++++++++++++++++----------- slca-1.2.0/slca/R/addhealth.R |only slca-1.2.0/slca/R/data_encode.R | 3 - slca-1.2.0/slca/R/diagnostic.R | 52 ++++++++++++------ slca-1.2.0/slca/R/estModel.R | 2 slca-1.2.0/slca/R/estimate.R | 18 +++--- slca-1.2.0/slca/R/gss7677.R | 2 slca-1.2.0/slca/R/methods.R | 21 ++++--- slca-1.2.0/slca/R/nlsy_fit.R |only slca-1.2.0/slca/R/plot.slca.R | 86 ++++++++++++++++++++++--------- slca-1.2.0/slca/R/regression.R | 54 +++++++++++-------- slca-1.2.0/slca/R/slcaControl.R | 17 ++---- slca-1.2.0/slca/README.md |only slca-1.2.0/slca/data/addhealth.rda |only slca-1.2.0/slca/data/gss7677.rda |binary slca-1.2.0/slca/data/nlsy97.rda |binary slca-1.2.0/slca/data/nlsy_jlcpa.rda |binary slca-1.2.0/slca/inst |only slca-1.2.0/slca/man/addhealth.Rd |only slca-1.2.0/slca/man/compare.Rd | 17 +++--- slca-1.2.0/slca/man/estimate.Rd | 13 ++-- slca-1.2.0/slca/man/examples/addhealth.R |only slca-1.2.0/slca/man/examples/diag.R | 6 +- slca-1.2.0/slca/man/examples/gss7677.R | 8 +- slca-1.2.0/slca/man/examples/nlsy97.R | 54 +++++++++---------- slca-1.2.0/slca/man/examples/plot.R |only slca-1.2.0/slca/man/examples/reg.R | 8 +- slca-1.2.0/slca/man/examples/reorder.R | 10 +-- slca-1.2.0/slca/man/figures |only slca-1.2.0/slca/man/gof.Rd | 15 +++-- slca-1.2.0/slca/man/gss7677.Rd | 10 +-- slca-1.2.0/slca/man/nlsy97.Rd | 54 +++++++++---------- slca-1.2.0/slca/man/nlsy_jlcpa.Rd | 8 +- slca-1.2.0/slca/man/param.Rd | 2 slca-1.2.0/slca/man/regress.Rd | 8 +- slca-1.2.0/slca/man/reorder.slca.Rd | 10 +-- slca-1.2.0/slca/man/slca-package.Rd | 8 ++ slca-1.2.0/slca/man/slcaControl.Rd | 18 +++--- slca-1.2.0/slca/src/estimate.cpp | 4 - slca-1.2.0/slca/tests |only 42 files changed, 356 insertions(+), 246 deletions(-)
Title: Classification with Parallel Factor Analysis
Description: Classification using Richard A. Harshman's Parallel Factor Analysis-1 (Parafac) model or Parallel Factor Analysis-2 (Parafac2) model fit to a three-way or four-way data array. See Harshman and Lundy (1994): <doi:10.1016/0167-9473(94)90132-5>. Uses component weights from one mode of a Parafac or Parafac2 model as features to tune parameters for one or more classification methods via a k-fold cross-validation procedure. Allows for constraints on different tensor modes. Supports penalized logistic regression, support vector machine, random forest, feed-forward neural network, regularized discriminant analysis, and gradient boosting machine. Supports binary and multiclass classification. Predicts class labels or class probabilities and calculates multiple classification performance measures. Implements parallel computing via the 'parallel' and 'doParallel' packages.
Author: Matthew A. Snodgress [aut, cre]
Maintainer: Matthew A. Snodgress <snodg031@umn.edu>
Diff between cpfa versions 1.1-5 dated 2024-10-01 and 1.1-6 dated 2024-11-01
DESCRIPTION | 8 ++--- MD5 | 29 ++++++++++----------- R/cpfa.R | 32 +++++++++-------------- R/kcv.gbm.R | 69 +++++++------------------------------------------- R/kcv.nn.R | 39 ---------------------------- R/kcv.plr.R | 53 +++----------------------------------- R/kcv.rda.R | 46 ++------------------------------- R/kcv.rf.R | 39 ---------------------------- R/kcv.svm.R | 45 ++------------------------------ R/kcvcheck.R |only R/plotcpfa.R | 5 ++- R/predict.tunecpfa.R | 37 ++++++++++---------------- R/print.tunecpfa.R | 55 ++++++++++----------------------------- R/tunecpfa.R | 63 +++++++++++++-------------------------------- inst/ChangeLog.txt | 16 +++++++++++ man/cpfa-internals.Rd | 1 16 files changed, 123 insertions(+), 414 deletions(-)
Title: Linkage Map Construction using the MSTmap Algorithm
Description: Functions for Accurate and Speedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred 'R/qtl' objects. This includes extremely fast linkage map clustering and optimal marker ordering using 'MSTmap' (see Wu et al.,2008).
Author: Julian Taylor [aut, cre],
David Butler. [aut]
Maintainer: Julian Taylor <julian.taylor@adelaide.edu.au>
Diff between ASMap versions 1.0-7 dated 2024-01-09 and 1.0-8 dated 2024-11-01
DESCRIPTION | 22 ++++++++++++++++------ MD5 | 22 +++++++++++----------- README.md | 4 ++++ build/vignette.rds |binary inst/doc/asmapvignette.pdf |binary man/alignCross.Rd | 2 +- man/heatMap.Rd | 2 +- src/genetic_map_DH.cpp | 39 ++++++++++++++++++++------------------- src/genetic_map_RIL.cpp | 8 ++++---- src/linkage_group_DH.cpp | 2 +- src/linkage_group_RIL.cpp | 2 +- src/sexp.cpp | 2 +- 12 files changed, 60 insertions(+), 45 deletions(-)