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

[Akhilesh Singh]

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. Thanking in
advance.


Dr. A.K. Singh
Professor and Head
Department of Agricultural Statistics
Indira Gandhi Krishi Vishwavidyalaya
Raipur-492012, Chhattisgarh, India
Mob: +918770625795
Email: akhileshsingh.igkv at gmail.com
WhatsApp: +919039202968

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