[R] [FORGED] Error occurring in "emmeans" package for the two data sets I used. Please help.

[Lenth, Russell V]

This seems to be an entirely new question.

The ‘plot.emmGrid()’ function returns a graphic object of class “ggplot” (by default) or “lattice” (if called with ‘engine = “lattice”’). You should use the provisions in those respective packages (ggplot2 or lattice) to control the details of the plot. In the case of lattice, additional arguments are passed via ‘...’ in the call. In the case of ggplot, one may “add” other ggplot:: functions to modify the plot.

Russ

Russell V. Lenth  -  Professor Emeritus
Department of Statistics and Actuarial Science   
The University of Iowa  -  Iowa City, IA 52242  USA   
Voice (319)335-0712 (Dept. office)  -  FAX (319)335-3017




From: Akhilesh Singh [mailto:akhileshsingh.igkv at gmail.com] 
Sent: Wednesday, January 10, 2018 12:45 AM
To: Sal Mangiafico <salvatore.s.mangiafico at gmail.com>
Cc: Rolf Turner <r.turner at auckland.ac.nz>; r-help mailing list <r-help at r-project.org>; Lenth, Russell V <russell-lenth at uiowa.edu>
Subject: Re: [R] [FORGED] Error occurring in "emmeans" package for the two data sets I used. Please help.

Thanks for your kind reply. Problem is solved. However, it's "confidence interval / treatment comparison plot" is not taking main title. And the fonts of axes labels can not be changed using 'cex' parameter. I will appreciate if you could help in this matter too.

Dr. A. K. Singh

On 09-Jan-2018 8:18 PM, "Sal Mangiafico" <mailto:salvatore.s.mangiafico at gmail.com> wrote:
One way to avoid this error is to create the aov without using the with function, but instead use the data= option in the aov function.
That is,
medley2 = aov(diversity ~ zinc, data=medley.clementis)
emmeans::emmeans(medley2, "zinc")
You can see the difference in the calls:
medley2$call
medley.clementis.aov$call
This works for the other data set as well, e.g.
keough2 = aov(serpulid.ln ~ biofilm, data=keough.raimondi.ln)
~ Sal Mangiafico

On 1/8/2018 4:44 PM, Rolf Turner wrote:

On 07/01/18 02:19, Akhilesh Singh wrote: 


I am a Professor of Statistics at Indira Gandhi Krishi Vishwavidyalaya, 
Raipur, India. While teaching in class about analysis of variance using R, 
I was doing a one-way analysis for the two data-sets given below in the 
R-class. I got a typical error in "emmeans" package, please help: 

Data-set-1: 
-------------- 
Medley and Clements (1998) investigated the impact of zinc contamination 
(and other heavy metals) on the diversity of diatom species in the USA 
Rocky Mountains. The diversity of diatoms (number of species) and degree of 
zinc contamination (categorized as either of high, medium, low or natural 
background level) were recorded from between four and six sampling stations 
within each of six streams known to be polluted, as given below: 

stream=c("Eagle", "Eagle", "Eagle", "Eagle", "Blue", "Blue", 
          "Blue", "Blue", "Blue", "Blue", "Blue", "Snake", "Snake", 
          "Snake", "Snake", "Snake", "Arkan", "Arkan", "Arkan", 
          "Arkan", "Arkan", "Arkan", "Arkan", "Chalk", "Chalk", 
          "Chalk", "Chalk", "Chalk", "Splat", "Splat", "Splat", 
          "Splat", "Splat", "Splat") 

zinc=c("BACK", "HIGH", "HIGH", "MED", "BACK", "HIGH", "BACK", "BACK", 
        "HIGH", "MED", "MED", "BACK", "MED", "HIGH", "HIGH", "HIGH", 
        "LOW", "LOW", "LOW", "LOW", "MED", "MED", "LOW", "LOW", 
        "HIGH", "HIGH", "MED", "LOW", "BACK", "BACK", "MED", "LOW", 
        "MED", "BACK") 

diversity=c(2.27, 1.25, 1.15, 1.62, 1.7, 0.63, 2.05, 1.98, 1.04, 
             2.19, 2.1, 2.2, 2.06, 1.9, 1.88, 0.85, 1.4, 2.18, 1.83, 
             1.88, 2.02, 1.94, 2.1, 2.38, 1.43, 1.37, 1.75, 2.83, 
             1.53, 0.76, 0.8, 1.66, 0.98, 1.89) 

medley.clementis=data.frame(stream,zinc,diversity) 

I did the one-way anova: 
------------------------------- 

medley.clementis.aov=with(medley.clementis, aov(diversity ~ zinc)) 

anova(medley.clementis) 

Then, I tried to do post hoc analysis using "emmeans" package following 
command: 
----------------------------------------------------------------------------------------------- 

emmeans::emmeans(medley.clementis.aov, "zinc") 


This gives following error: 
---------------------------------- 
Error in recover_data.call(fcall, delete.response(terms(object)), 
object$na.action,  : 
   object 'possibly.random' not found 
Error in ref_grid(object, ...) : 
   Perhaps a 'data' or 'params' argument is needed 



Data-set-2: 
--------------- 
Keough and Raimondi (1995) examined the effects of four biofilm types (SL: 
sterile unfilmed substrate, NL: netted laboratory biofilms, UL: unnetted 
laboratory biofilms and F: netted field biofilms) on the recruitment of 
serpulid larvae. Substrates treated with one of the four biofilm types were 
left in shallow marine waters for one week after which the number of newly 
recruited serpulid worms were counted, as given below: 

biofilm=c("SL", "SL", "SL", "SL", "SL", "SL", "SL", "UL", "UL", "UL", 
           "UL", "UL", "UL", "UL", "NL", "NL", "NL", "NL", "NL", "NL", 
           "NL", "F", "F", "F", "F", "F", "F", "F") 

serpulid=c(61, 113, 123, 75, 75, 83, 95, 143, 81, 101, 155, 156, 193, 
            163, 203, 159, 139, 161, 179, 97, 157, 128.5, 204.5, 
            108.5, 116.5, 140.5, 160.5, 87.5) 

keough.raimondi=data.frame(biofilm,serpulid) 

Applied log-transformation: 
------------------------------------------- 
keough.raimondi.ln=transform(keough.raimondi, serpulid.ln=log(serpulid)) 

I did the one-way anova, with contrasts defined below: 
------------------------------------------------------------------------ 
contrasts(keough.raimondi.ln$biofilm) <- cbind(c(0, 1, 0, -1), 
                             c(2, -1, 0, -1), c(-1, -1, 3, -1)) 
keough.raimondi.ln$biofilm 

keough.contr.list <- list(biofilm = list('NL vs UL' = 1, 
               'F vs (NL & UL)' = 2, 'SL vs (F & NL & UL)' = 3)) 
keough.contr.list 

One-way anova: 
---------------------- 
keough.raimondi.ln.aov=with(keough.raimondi.ln, aov(serpulid.ln ~ biofilm)) 

summary(keough.raimondi.ln.aov,split=keough.contr.list) 


Then, I tried to do post hoc analysis using "emmeans" package following 
command: 
----------------------------------------------------------------------------------------------- 

emmeans(keough.raimondi.ln.aov, ~ biofilm) 


This gives following error: 
---------------------------------- 
Error in recover_data.call(fcall, delete.response(terms(object)), 
object$na.action,  : 
   object 'possibly.random' not found 
Error in ref_grid(object, ...) : 
   Perhaps a 'data' or 'params' argument is needed 


Help Needed: 
------------------ 
On many other data sets and data frame I successfully used "emmeans" 
package using the help available in R. 

But, for the above two data-sets, I consistently got the same error as 
described above. 

I do not know what is amiss. Where I am missing or whatever is wrong, I 
request the entire R-team to help me to solve above problem. 

Well, you don't need the *entire* R-team!!! It probably (in some sense) includes millions of people. :-) 


Thanking in advance. 

Thanks for your thorough and well set out description of the problem. 
Your reproducible examples were flawless. 

I am not *completely* certain, but this looks to me like a bug in emmeans. 

I have therefore taken the liberty of cc-ing this reply to Russell Lenth (the maintainer of emmeans) to get his take on the issue. 

cheers, 

Rolf Turner