mastitis: Mastitis cases in dairy cattle

In pedigreemm: Pedigree-based mixed-effects models

Description

Records of the number of cases of clinical mastitis during the first lactation of 1,675 cows, primarily Holsteins. Cows belonged to 41 herds and were daughters of 38 sires. There were 1,491 healthy cows, 134 had only one case of mastitis, 36 had 2 cases, and 14 had between 4 and cases. Overall, mastitis incidence was 0.11. Calving years for these records were from 2000 through 2005. The sire, herd and days in milk are also recorded for each cow.

Format

A data frame with 1675 observations on the following 8 variables.

id

Identifier of the animal.

sire

Identifier of the animal's sire.

birth

year of birth of the animal (as a factor).

herd

herd id number (as a factor).

calvingYear

year of calving for this lactation.

DIM

total number of days in milk for the lactation.

mastitis

a factor indicating if the cow had any incidents of clinical mastitis during the lactation.

NCM

An ordered factor giving the number of clinical mastitis cases for the cow during this lactation.

Details

The pedigree of the sires is given in the companion pedSires data set.

Source

Vazquez, A.I. 2007. Analysis of number of episodes of clinical mastitis in Norwegian Red and Holstein cows with Poisson and categorical data mixed models. Master of Science Thesis. University of Wisconsin - Madison. 162 pp.

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.

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.

See Also

pedSires, pedigree

Examples

str(mastitis)
summary(mastitis, maxsum = 10)

Example output

Loading required package: lme4
Loading required package: Matrix
'data.frame':	1675 obs. of  8 variables:
 $ id         : Factor w/ 1675 levels "62","105","671",..: 1617 1618 1619 1620 1621 1622 1623 1624 1625 1626 ...
 $ sire       : Factor w/ 352 levels "1","2","3","4",..: 2 2 2 2 2 2 2 2 2 2 ...
 $ birth      : Ord.factor w/ 10 levels "1989"<"1990"<..: 1 1 2 2 2 2 2 2 1 1 ...
 $ herd       : Factor w/ 41 levels "1","2","4","5",..: 40 40 40 40 40 40 40 40 40 40 ...
 $ calvingYear: Ord.factor w/ 6 levels "2000"<"2001"<..: 5 5 5 5 5 5 5 5 5 5 ...
 $ DIM        : int  286 281 305 281 305 305 305 330 305 273 ...
 $ mastitis   : Factor w/ 2 levels "N","Y": 1 1 1 1 1 1 1 1 1 1 ...
 $ NCM        : num  0 0 0 0 0 0 0 0 0 0 ...
       id            sire       birth          herd      calvingYear
 62     :   1   343    :  68   1989: 33   89     : 106   2000: 17   
 105    :   1   327    :  62   1990: 16   14     : 104   2001:106   
 671    :   1   348    :  58   1996:  3   2      :  91   2002:333   
 692    :   1   329    :  53   1997: 17   23     :  75   2003:561   
 726    :   1   3      :  51   1998: 68   69     :  72   2004:594   
 894    :   1   2      :  49   1999:149   59     :  61   2005: 64   
 896    :   1   319    :  49   2000:353   90     :  57              
 897    :   1   326    :  49   2001:532   45     :  52              
 899    :   1   328    :  49   2002:454   68     :  50              
 (Other):1666   (Other):1187   2003: 50   (Other):1007              
      DIM        mastitis      NCM        
 Min.   : 15.0   N:1491   Min.   :0.0000  
 1st Qu.:303.0   Y: 184   1st Qu.:0.0000  
 Median :330.0            Median :0.0000  
 Mean   :346.3            Mean   :0.1552  
 3rd Qu.:374.0            3rd Qu.:0.0000  
 Max.   :989.0            Max.   :6.0000  
                                          
                                          
                                          
                                          

pedigreemm documentation built on May 2, 2019, 5:19 p.m.