Wrong printing of lme4 objects

[GillesSanMartin]

Hello

I have encountered a very strange behavior of knitr that appears only in very specific conditions. It seems that there is something wrong with the internal knit from spin function.

Consider the following R script example :

library(lme4)
m <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
summary(m)
print(m, cor=FALSE)

If I use spin("myscript.R", report=FALSE) I obtain 2 files : myscript.md and myscript.Rmd.

The md file does not print correctly the results :

m <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
summary(m)

## Length  Class   Mode 
##      1    mer     S4

print(m, cor = FALSE)

## <S4 Type Object>
## attr(,"env")
## <environment: 0x8f89a80>
## attr(,"nlmodel")
## I(x)
## attr(,"frame")
##     Reaction Days Subject
## 1      249.6    0     308
## 2      258.7    1     308
## 3      250.8    2     308
## 4      321.4    3     308
## 5      356.9    4     308
## 6      414.7    5     308
## 7      382.2    6     308
## 8      290.1    7     308

etc... ( 1000+ additionnal lines)

But if I knit the Rmd file generated by spin knit("myscript.Rmd"), the resulting md file is correct :

library(lme4)
m <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
summary(m)

## Linear mixed model fit by REML 
## Formula: Reaction ~ Days + (Days | Subject) 
##    Data: sleepstudy 
##   AIC  BIC logLik deviance REMLdev
##  1756 1775   -872     1752    1744
## Random effects:
##  Groups   Name        Variance Std.Dev. Corr  
##  Subject  (Intercept) 612.1    24.74          
##           Days         35.1     5.92    0.066 
##  Residual             654.9    25.59          
## Number of obs: 180, groups: Subject, 18
## 
## Fixed effects:
##             Estimate Std. Error t value
## (Intercept)   251.41       6.82    36.8
## Days           10.47       1.55     6.8
## 
## Correlation of Fixed Effects:
##      (Intr)
## Days -0.138

print(m, cor = FALSE)

## Linear mixed model fit by REML 
## Formula: Reaction ~ Days + (Days | Subject) 
##    Data: sleepstudy 
##   AIC  BIC logLik deviance REMLdev
##  1756 1775   -872     1752    1744
## Random effects:
##  Groups   Name        Variance Std.Dev. Corr  
##  Subject  (Intercept) 612.1    24.74          
##           Days         35.1     5.92    0.066 
##  Residual             654.9    25.59          
## Number of obs: 180, groups: Subject, 18
## 
## Fixed effects:
##             Estimate Std. Error t value
## (Intercept)   251.41       6.82    36.8
## Days           10.47       1.55     6.8

if I use print(m) instead of print(m, cor = FALSE), the output fo this part is correct.
And if I use the compile HTML notebook button from Rstudio(0.97.332) using spin the output is correct too.
Really strange...

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=fr_BE.UTF-8       LC_NUMERIC=C               LC_TIME=fr_BE.UTF-8       
 [4] LC_COLLATE=fr_BE.UTF-8     LC_MONETARY=fr_BE.UTF-8    LC_MESSAGES=fr_BE.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=fr_BE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] lme4_0.999999-2 Matrix_1.0-12   lattice_0.20-15 knitr_1.2      

loaded via a namespace (and not attached):
[1] digest_0.6.3   evaluate_0.4.3 formatR_0.7    grid_3.0.1     markdown_0.5.4 nlme_3.1-109  
[7] stats4_3.0.1   stringr_0.6.2  tools_3.0.1  

[yihui]

It is an environment issue. I have fixed it now. Thanks for the report!

[GillesSanMartin]

Great ! Thanks to you for developing these wonders !

[github-actions]

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