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>.

Install the latest version of this package by entering the following in R:
install.packages("fullfact")
AuthorAimee Lee Houde [aut, cre], Trevor Pitcher [aut]
Date of publication2017-04-12 13:43:07 UTC
MaintainerAimee Lee Houde <aimee.lee.houde@gmail.com>
LicenseGPL (>= 2)
Version1.2
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

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

Functions

barMANA Man page
boxMANA Man page
buildBinary Man page
buildMulti Man page
chinook_bootL Man page
chinook_bootS Man page
chinook_jackL Man page
chinook_length Man page
chinook_resampL Man page
chinook_resampS Man page
chinook_survival Man page
ciJack Man page
ciJack2 Man page
ciJack3 Man page
ciMANA Man page
ciMANA2 Man page
ciMANA3 Man page
fixedGlmer Man page
fixedLmer Man page
JackGlmer Man page
JackGlmer2 Man page
JackGlmer3 Man page
JackLmer Man page
JackLmer2 Man page
JackLmer3 Man page
observGlmer Man page
observGlmer2 Man page
observGlmer3 Man page
observLmer Man page
observLmer2 Man page
observLmer3 Man page
powerGlmer Man page
powerGlmer2 Man page
powerGlmer3 Man page
powerLmer Man page
powerLmer2 Man page
powerLmer3 Man page
randGlmer Man page
randLmer Man page
resampFamily Man page
resampGlmer Man page
resampGlmer2 Man page
resampGlmer3 Man page
resampLmer Man page
resampLmer2 Man page
resampLmer3 Man page
resampRepli Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.