milk_subset: Milk production (subset)

In tslumley/svylme: Linear Mixed Models for Complex Survey Data

Milk production (subset)

Description

A subset of a dataset from the pedigreemm package, created as an example for the lme4qtl package. The original data had records of the milk production of 3397 lactations from first through fifty parity Holsteins. These were 1,359 cows, daughters of 38 sires in 57 herds. The data was downloaded from the USDA internet site. All lactation records represent cows with at least 100 days in milk, with an average of 347 days. Milk yield ranged from 4,065 to 19,345 kg estimated for 305 days, averaging 11,636 kg. There were 1,314, 1,006, 640, 334 and 103 records were from first thorough fifth lactation animals. The subset is of cows from 3 sires.

Usage

data("milk_subset")

Format

A data frame with 316 observations on the following 13 variables.

id

numeric identifier of cow

lact

number of lactation for which production is measured

herd

a factor indicating the herd

sire

a factor indicating the sire

dim

number of days in milk for that lactation

milk

milk production estimated at 305 days

fat

fat production estimated at 305 days

prot

protein production estimated at 305 days

scs

the somatic cell score

sdMilk

milk scaled by cow-specific standard deviation

herd_id

a character vector indicating the herd

one

a vector of 1s for convenience in weighting

one2

another vector of 1s for convenience in weighting

Details

This data example gives noticeably different results for full likelihood and pairwise likelihood because the model is misspecified. The best fitting linear model for the large herd 89 is different, and that herd gets relatively more weight in the pairwise analysis (because it has more pairs).

Source

Constructed at https://github.com/variani/lme4qtl/blob/master/vignettes/pedigreemm.Rmd

References

2010. A.I. Vazquez, D.M. Bates, G.J.M. Rosa, D. Gianola and K.A. Weigel. Technical Note: An R package for fitting generalized linear mixed models in animal breeding. Journal of Animal Science, 88:497-504.

Examples

data(milk_subset)
herd_des<- svydesign(id = ~herd + id, prob = ~one + one2, data = milk_subset)
lm(sdMilk ~ lact + log(dim),data=milk_subset,subset=herd==89)
lm(sdMilk ~ lact + log(dim),data=milk_subset,subset=herd!=89)
svy2lme(sdMilk ~ lact + log(dim) + (1|herd), design=herd_des,method="nested")
svy2lme(sdMilk ~ lact + log(dim) + (1|herd), design=herd_des,method="general")

## pairwise result is closer to herd 89 than to remainder
lme4::lmer(sdMilk ~ lact + log(dim) + (1|herd), data=milk_subset)
svy2relmer(sdMilk ~ lact + log(dim) + (1|id) + (1|herd), design=herd_des,
    relmat = list(id = A_gen))

## compare to all pairs
svy2lme(sdMilk ~ lact + log(dim) + (1|herd),
design=herd_des,method="general", all.pairs=TRUE)
svy2lme(sdMilk ~ lact + log(dim) + (1|herd),
design=herd_des,method="general", all.pairs=TRUE, subtract.margins=TRUE)

tslumley/svylme documentation built on Feb. 10, 2024, 11:01 p.m.