R help - Jan 2018 - [FORGED] Error occurring in "emmeans" package for the two data sets I used. Please help.

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

	[[alternative HTML version deleted]]

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

-- 
Technical Editor ANZJS
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276

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]]

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

	[[alternative HTML version deleted]]

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