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

[Sal Mangiafico]

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
>


	[[alternative HTML version deleted]]