R help - Aug 2019 - Code that works when run as straight code, but that fails when run as a function

I have code that works perfectly when run as in-line code, but that fails when
the code is put into a function with the following message:
Error in contest1D.lmerModLmerTest(model, ll, rhs = rhs, ddf = ddf, confint =
confint, :
length(L) == length(model at beta) is not TRUE

Why does moving the code to a function lead to an error? What can I do to avoid
the error?
Thank you,
John

In-line code:
fit2aCort <-
lmer(SBP~age+jFStage+AHIgt5+jFStage*AHIgt5+(1|patid),data=alldata)

c1 <-c(1,  5.99,  1, 0,   0,  1, 0 )
c2 <-c(1,  5.99,  0, 1,   0,  0, 1 )

model <- fit2aCort
s1a <- contest(model,L=c1,joint=FALSE)
s1as1E <- s1a$Estimate

s2a <- contest(model,L=c2,joint=FALSE)
s2E <- s2a$Estimate

Time <- c(1,2)
SBP  <- c(s1E,s2E)
plot(Time,SBP)
title("Predicted Sys SBP, age 5.99 yr (SS 524 obs with BP 190mmHg
removed)")
plotCI(Time,SBP,uiw=1.96*c(s1a$"Std. Error",s2a$"Std.
Error"))


Code put into a function that fails:
plotit <- function(c1,c2,model)
{
s1a <- contest(model,L=c1,joint=FALSE)
s1as1E <- s1a$Estimate

s2a <- contest(model,L=c2,joint=FALSE)
s2E <- s2a$Estimate

Time <- c(1,2)
SBP  <- c(s1E,s2E)
plot(Time,SBP)
title("Predicted Sys SBP, age 5.99 yr (SS 524 obs with BP 190mmHg
removed)")
plotCI(Time,SBP,uiw=1.96*c(s1a$"Std. Error",s2a$"Std.
Error"))
}

fit2aCort <-
lmer(SBP~age+jFStage+AHIgt5+jFStage*AHIgt5+(1|patid),data=alldata)

c1 <-c(1,  5.99,  1, 0,   0,  1, 0 )
c2 <-c(1,  5.99,  0, 1,   0,  0, 1 )
plotit(c1,c2,fit2aCort)

	[[alternative HTML version deleted]]

Since this isn't reproducible, my first guess would be that alldata,
which is required for your model, is not visible within the
environment of the function.

Or something similar: that kind of problem is almost always a scoping issue.

Sarah

On Fri, Aug 23, 2019 at 3:46 PM Sorkin, John <jsorkin at
som.umaryland.edu> wrote:
>
> I have code that works perfectly when run as in-line code, but that fails
when the code is put into a function with the following message:
> Error in contest1D.lmerModLmerTest(model, ll, rhs = rhs, ddf = ddf, confint
= confint, :
> length(L) == length(model at beta) is not TRUE
>
> Why does moving the code to a function lead to an error? What can I do to
avoid the error?
> Thank you,
> John
>
> In-line code:
> fit2aCort <-
lmer(SBP~age+jFStage+AHIgt5+jFStage*AHIgt5+(1|patid),data=alldata)
>
> c1 <-c(1,  5.99,  1, 0,   0,  1, 0 )
> c2 <-c(1,  5.99,  0, 1,   0,  0, 1 )
>
> model <- fit2aCort
> s1a <- contest(model,L=c1,joint=FALSE)
> s1as1E <- s1a$Estimate
>
> s2a <- contest(model,L=c2,joint=FALSE)
> s2E <- s2a$Estimate
>
> Time <- c(1,2)
> SBP  <- c(s1E,s2E)
> plot(Time,SBP)
> title("Predicted Sys SBP, age 5.99 yr (SS 524 obs with BP 190mmHg
removed)")
> plotCI(Time,SBP,uiw=1.96*c(s1a$"Std. Error",s2a$"Std.
Error"))
>
>
> Code put into a function that fails:
> plotit <- function(c1,c2,model)
> {
> s1a <- contest(model,L=c1,joint=FALSE)
> s1as1E <- s1a$Estimate
>
> s2a <- contest(model,L=c2,joint=FALSE)
> s2E <- s2a$Estimate
>
> Time <- c(1,2)
> SBP  <- c(s1E,s2E)
> plot(Time,SBP)
> title("Predicted Sys SBP, age 5.99 yr (SS 524 obs with BP 190mmHg
removed)")
> plotCI(Time,SBP,uiw=1.96*c(s1a$"Std. Error",s2a$"Std.
Error"))
> }
>
> fit2aCort <-
lmer(SBP~age+jFStage+AHIgt5+jFStage*AHIgt5+(1|patid),data=alldata)
>
> c1 <-c(1,  5.99,  1, 0,   0,  1, 0 )
> c2 <-c(1,  5.99,  0, 1,   0,  0, 1 )
> plotit(c1,c2,fit2aCort)
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.


-- 
Sarah Goslee (she/her)
http://www.numberwright.com

Hello,

Inline.

?s 20:45 de 23/08/19, Sorkin, John escreveu:
> I have code that works perfectly when run as in-line code, but that fails
when the code is put into a function with the following message:
> Error in contest1D.lmerModLmerTest(model, ll, rhs = rhs, ddf = ddf, confint
= confint, :
> length(L) == length(model at beta) is not TRUE
> 
> Why does moving the code to a function lead to an error? What can I do to
avoid the error?
> Thank you,
> John
> 
> In-line code:
> fit2aCort <-
lmer(SBP~age+jFStage+AHIgt5+jFStage*AHIgt5+(1|patid),data=alldata)
> 
> c1 <-c(1,  5.99,  1, 0,   0,  1, 0 )
> c2 <-c(1,  5.99,  0, 1,   0,  0, 1 )
> 
> model <- fit2aCort
> s1a <- contest(model,L=c1,joint=FALSE)
> s1as1E <- s1a$Estimate
> 
> s2a <- contest(model,L=c2,joint=FALSE)
> s2E <- s2a$Estimate
> 
> Time <- c(1,2)
> SBP  <- c(s1E,s2E)
> plot(Time,SBP)
> title("Predicted Sys SBP, age 5.99 yr (SS 524 obs with BP 190mmHg
removed)")
> plotCI(Time,SBP,uiw=1.96*c(s1a$"Std. Error",s2a$"Std.
Error"))
> 
> 
> Code put into a function that fails:
> plotit <- function(c1,c2,model)
> {
> s1a <- contest(model,L=c1,joint=FALSE)
> s1as1E <- s1a$Estimate
> 
> s2a <- contest(model,L=c2,joint=FALSE)
> s2E <- s2a$Estimate
Is s1as1E a typo? The way you define and use s2E suggests that it should be

s1E <- s1a$Estimate


Hope this helps,

Rui Barradas
> 
> Time <- c(1,2)
> SBP  <- c(s1E,s2E)
> plot(Time,SBP)
> title("Predicted Sys SBP, age 5.99 yr (SS 524 obs with BP 190mmHg
removed)")
> plotCI(Time,SBP,uiw=1.96*c(s1a$"Std. Error",s2a$"Std.
Error"))
> }
> 
> fit2aCort <-
lmer(SBP~age+jFStage+AHIgt5+jFStage*AHIgt5+(1|patid),data=alldata)
> 
> c1 <-c(1,  5.99,  1, 0,   0,  1, 0 )
> c2 <-c(1,  5.99,  0, 1,   0,  0, 1 )
> plotit(c1,c2,fit2aCort)
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>