fullfact: Full Factorial Breeding Analysis

We facilitate the analysis of full factorial mating designs with mixed-effects models. The observed data functions extract the variance explained by random and fixed effects and provide their significance. We then calculate the additive genetic, nonadditive genetic, and maternal variance components explaining the phenotype. In particular, we integrate nonnormal error structures for estimating these components for nonnormal data types. The resampled data functions are used to produce bootstrap confidence intervals, which can then be plotted using a simple function. This package will facilitate the analyses of full factorial mating designs in R, especially for the analysis of binary, proportion, and/or count data types and for the ability to incorporate additional random and fixed effects and power analyses. The paper associated with the package including worked examples is: Houde ALS, Pitcher TE (2016) <doi:10.1002/ece3.1943>.

AuthorAimee Lee Houde [aut, cre], Trevor Pitcher [aut]
Date of publication2016-12-17 22:38:52
MaintainerAimee Lee Houde <aimee.lee.houde@gmail.com>
LicenseGPL (>= 2)
Version1.1
https://www.r-project.org

View on CRAN

Man pages

barMANA: Bargraph of confidence intervals

boxMANA: Boxplot of resampled results

buildBinary: Convert to a binary data frame

buildMulti: Convert to a multinomial frame

chinook_bootL: Chinook salmon length, bootstrap calculations

chinook_bootS: Chinook salmon survival, bootstrap data

chinook_jackL: Chinook salmon length, jackknife data

chinook_length: Chinook salmon length, raw data

chinook_resampL: Chinook salmon length, bootstrap resampled

chinook_resampS: Chinook salmon survival, bootstrap resampled

chinook_survival: Chinook salmon survival, raw data

ciJack: Jackknife confidence intervals

ciJack2: Jackknife confidence intervals 2

ciJack3: Jackknife confidence intervals 3

ciMANA: Bootstrap confidence intervals

ciMANA2: Bootstrap confidence intervals 2

ciMANA3: Bootstrap confidence intervals 3

fullfact-internal: Internal fullfact functions

fullfact-package: Full Factorial Breeding Analysis

JackGlmer: Jackknife components for non-normal data

JackGlmer2: Jackknife components for non-normal data 2

JackGlmer3: Jackknife components for non-normal data 3

JackLmer: Jackknife components for normal data

JackLmer2: Jackknife components for normal data 2

JackLmer3: Jackknife components for normal data 3

observGlmer: Variance components for non-normal data

observGlmer2: Variance components for non-normal data 2

observGlmer3: Variance components for non-normal data 3

observLmer: Variance components for normal data

observLmer2: Variance components for normal data 2

observLmer3: Variance components for normal data 3

powerGlmer: Power analysis for non-normal data

powerGlmer2: Power analysis for non-normal data 2

powerGlmer3: Power analysis for non-normal data 3

powerLmer: Power analysis for normal data

powerLmer2: Power analysis for normal data 2

powerLmer3: Power analysis for normal data 3

resampFamily: Bootstrap resample within families

resampGlmer: Bootstrap components for non-normal data

resampGlmer2: Bootstrap components for non-normal data 2

resampGlmer3: Bootstrap components for non-normal data 3

resampLmer: Bootstrap components for normal data

resampLmer2: Bootstrap components for normal data 2

resampLmer3: Bootstrap components for normal data 3

resampRepli: Bootstrap resample within replicates

Files in this package

fullfact
fullfact/NAMESPACE
fullfact/data
fullfact/data/chinook_jackL.rda
fullfact/data/chinook_bootS.rda
fullfact/data/chinook_resampL.rda
fullfact/data/chinook_survival.rda
fullfact/data/chinook_resampS.rda
fullfact/data/chinook_bootL.rda
fullfact/data/chinook_length.rda
fullfact/R
fullfact/R/observGlmer2.R fullfact/R/resampLmer2.R fullfact/R/resampGlmer3.R fullfact/R/JackLmer3.R fullfact/R/buildBinary.R fullfact/R/observGlmer.R fullfact/R/powerGlmer2.R fullfact/R/resampRepli.R fullfact/R/barMANA.R fullfact/R/powerLmer2.R fullfact/R/JackGlmer2.R fullfact/R/observGlmer3.R fullfact/R/observLmer2.R fullfact/R/JackLmer2.R fullfact/R/powerGlmer.R fullfact/R/buildMulti.R fullfact/R/ciMANA.R fullfact/R/ciJack2.R fullfact/R/powerGlmer3.R fullfact/R/resampGlmer2.R fullfact/R/fixedLmer.R fullfact/R/observLmer3.R fullfact/R/powerLmer3.R fullfact/R/JackGlmer3.R fullfact/R/resampFamily.R fullfact/R/ciMANA3.R fullfact/R/randLmer.R fullfact/R/observLmer.R fullfact/R/ciJack.R fullfact/R/resampLmer3.R fullfact/R/JackLmer.R fullfact/R/randGlmer.R fullfact/R/powerLmer.R fullfact/R/resampGlmer.R fullfact/R/ciJack3.R fullfact/R/ciMANA2.R fullfact/R/JackGlmer.R fullfact/R/boxMANA.R fullfact/R/fixedGlmer.R fullfact/R/resampLmer.R
fullfact/MD5
fullfact/build
fullfact/build/partial.rdb
fullfact/DESCRIPTION
fullfact/man
fullfact/man/JackLmer.Rd fullfact/man/ciJack2.Rd fullfact/man/powerGlmer2.Rd fullfact/man/chinook_survival.Rd fullfact/man/ciMANA3.Rd fullfact/man/chinook_bootS.Rd fullfact/man/observGlmer3.Rd fullfact/man/resampGlmer.Rd fullfact/man/resampRepli.Rd fullfact/man/fullfact-package.Rd fullfact/man/observLmer.Rd fullfact/man/buildBinary.Rd fullfact/man/resampLmer.Rd fullfact/man/JackGlmer2.Rd fullfact/man/powerLmer.Rd fullfact/man/JackGlmer3.Rd fullfact/man/ciMANA2.Rd fullfact/man/chinook_resampS.Rd fullfact/man/resampLmer3.Rd fullfact/man/fullfact-internal.Rd fullfact/man/chinook_jackL.Rd fullfact/man/chinook_bootL.Rd fullfact/man/powerLmer2.Rd fullfact/man/resampGlmer3.Rd fullfact/man/observGlmer2.Rd fullfact/man/barMANA.Rd fullfact/man/resampLmer2.Rd fullfact/man/resampFamily.Rd fullfact/man/powerGlmer3.Rd fullfact/man/JackGlmer.Rd fullfact/man/ciJack.Rd fullfact/man/chinook_length.Rd fullfact/man/observLmer3.Rd fullfact/man/chinook_resampL.Rd fullfact/man/resampGlmer2.Rd fullfact/man/boxMANA.Rd fullfact/man/ciJack3.Rd fullfact/man/ciMANA.Rd fullfact/man/buildMulti.Rd fullfact/man/observGlmer.Rd fullfact/man/powerLmer3.Rd fullfact/man/observLmer2.Rd fullfact/man/powerGlmer.Rd fullfact/man/JackLmer2.Rd fullfact/man/JackLmer3.Rd

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