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

[Akhilesh Singh]

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" <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

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