Cultivation: Bacterial innoculation applied to grass cultivars

In SASmixed: Data sets from "SAS System for Mixed Models"

Description

The Cultivation data frame has 24 rows and 4 columns of data from an experiment on the effect on dry weight yield of three bacterial inoculation treatments applied to two grass cultivars.

Format

This data frame contains the following columns:

Block

a factor with levels 1 to 4

Cult

the cultivar factor with levels a and b

Inoc

the innoculant factor with levels con, dea and liv

drywt

a numeric vector of dry weight yields

Source

Littell, R. C., Milliken, G. A., Stroup, W. W., and Wolfinger, R. D. (1996), SAS System for Mixed Models, SAS Institute (Data Set 2.2(a)).

Littel, R. C., Freund, R. J., and Spector, P. C. (1991), SAS System for Linear Models, Third Ed., SAS Institute.

Examples

str(Cultivation)
xtabs(~Block+Cult, Cultivation)
if (require("lme4", quietly = TRUE, character = TRUE)) {
  options(contrasts = c(unordered = "contr.SAS", ordered = "contr.poly"))
  ## compare with Output 2.10, page 58
  print(fm1Cult <- lmer(drywt ~ Inoc * Cult + (1|Block) + (1|Cult),
                          Cultivation))
  print(anova(fm1Cult))
  print(fm2Cult <- lmer(drywt ~ Inoc + Cult + (1|Block) + (1|Cult),
                          Cultivation))
  print(anova(fm2Cult))
  print(fm3Cult <- lmer(drywt ~ Inoc + (1|Block) + (1|Cult), Cultivation))
  print(anova(fm3Cult))
}

Example output

'data.frame':	24 obs. of  4 variables:
 $ Block: Factor w/ 4 levels "1","2","3","4": 1 1 1 1 1 1 2 2 2 2 ...
 $ Cult : Factor w/ 2 levels "a","b": 1 1 1 2 2 2 1 1 1 2 ...
 $ Inoc : Factor w/ 3 levels "con","dea","liv": 1 2 3 1 2 3 1 2 3 1 ...
 $ drywt: num  27.4 29.7 34.5 29.4 32.5 34.4 28.9 28.7 33.4 28.7 ...
 - attr(*, "ginfo")=List of 7
  ..$ formula     :Class 'formula'  language drywt ~ 1 | Block/Cult
  .. .. ..- attr(*, ".Environment")=<environment: R_GlobalEnv> 
  ..$ order.groups:List of 2
  .. ..$ Block: logi TRUE
  .. ..$ Cult : logi TRUE
  ..$ FUN         :function (x)  
  ..$ outer       : NULL
  ..$ inner       :List of 1
  .. ..$ Cult:Class 'formula'  language ~Inoc
  .. .. .. ..- attr(*, ".Environment")=<environment: R_GlobalEnv> 
  ..$ labels      :List of 1
  .. ..$ drywt: chr "Yield"
  ..$ units       : list()
     Cult
Block a b
    1 3 3
    2 3 3
    3 3 3
    4 3 3
Linear mixed model fit by REML ['lmerMod']
Formula: drywt ~ Inoc * Cult + (1 | Block) + (1 | Cult)
   Data: Cultivation
REML criterion at convergence: 68.4874
Random effects:
 Groups   Name        Std.Dev.
 Block    (Intercept) 1.0988  
 Cult     (Intercept) 0.1606  
 Residual             1.0938  
Number of obs: 24, groups:  Block, 4; Cult, 2
Fixed Effects:
  (Intercept)        Inoccon        Inocdea          Culta  Inoccon:Culta  
       33.525         -5.500         -2.875         -0.375          0.250  
Inocdea:Culta  
       -1.025  
convergence code 0; 2 optimizer warnings; 0 lme4 warnings 
Analysis of Variance Table
          Df  Sum Sq Mean Sq F value
Inoc       2 118.176  59.088 49.3909
Cult       1   1.912   1.912  1.5981
Inoc:Cult  2   1.826   0.913  0.7631
Linear mixed model fit by REML ['lmerMod']
Formula: drywt ~ Inoc + Cult + (1 | Block) + (1 | Cult)
   Data: Cultivation
REML criterion at convergence: 73.7535
Random effects:
 Groups   Name        Std.Dev.
 Block    (Intercept) 1.1015  
 Cult     (Intercept) 0.1359  
 Residual             1.0784  
Number of obs: 24, groups:  Block, 4; Cult, 2
Fixed Effects:
(Intercept)      Inoccon      Inocdea        Culta  
    33.6542      -5.3750      -3.3875      -0.6333  
convergence code 0; 1 optimizer warnings; 0 lme4 warnings 
Analysis of Variance Table
     Df  Sum Sq Mean Sq F value
Inoc  2 118.176  59.088 50.8094
Cult  1   2.021   2.021  1.7381
Linear mixed model fit by REML ['lmerMod']
Formula: drywt ~ Inoc + (1 | Block) + (1 | Cult)
   Data: Cultivation
REML criterion at convergence: 75.6778
Random effects:
 Groups   Name        Std.Dev.
 Block    (Intercept) 1.1013  
 Cult     (Intercept) 0.3219  
 Residual             1.0784  
Number of obs: 24, groups:  Block, 4; Cult, 2
Fixed Effects:
(Intercept)      Inoccon      Inocdea  
     33.337       -5.375       -3.387  
Analysis of Variance Table
     Df Sum Sq Mean Sq F value
Inoc  2 118.18  59.088  50.807
Warning messages:
1: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  unable to evaluate scaled gradient
2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge: degenerate  Hessian with 1 negative eigenvalues
3: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
   Hessian is numerically singular: parameters are not uniquely determined

SASmixed documentation built on May 1, 2019, 9:18 p.m.