'apa_print' doesn't work for object of class "afex_aov"

[alexholcombe]

Describe the bug
"No applicable method for 'apa_print' applied to an object of class "afex_aov"" even though it's mentioned in the manual here: https://crsh.github.io/papaja_man/reporting.html

To Reproduce

mtcar<- mtcars %>% mutate(rownum = row_number())

mt_anova <- afex::aov_ez(
  data = mtcar
  , dv = "mpg"
  , id = "rownum" #subj
  , between = c("cyl")
)
#This doesn't work even though it's mentioned in the manual here https://crsh.github.io/papaja_man/reporting.html
apa_anova <- papaja::apa_print(mt_anova)

Error in UseMethod("apa_print", x) : no applicable method for 'apa_print' applied to an object of class "afex_aov"

Expected behavior
Print object

[crsh]

Hi Alex, I can reproduce this and I'll have to take a closer look when I find some time. It appears this is somehow related to the S3 method dispatch. It works for me when I either first load papaja or call the S3 method directly:

apa_anova <- papaja::apa_print.afex_aov(mt_anova) 

[mariusbarth]

Hi guys, I just figured out what the problem is: roxygen2 seems to have problems disambiguating S3 methods for apa_print(), which results in creating an erroneous NAMESPACE file, with the methods exported as separate functions. I'm just testing a possible solution, will keep you posted.

See also hadley Wickham's recent addition to his book mentioning this problem.

[crsh]

Related: #250

[shirdekel]

I'm still getting the same error as @alexholcombe (when using his reprex), even after installing from the development branch. However, the following works (as per @mariusbarth's comment):

apa_anova <- papaja:::apa_print.afex_aov(mt_anova)

Session Info

─ Session info ────────────────────────────
 setting  value                       
 version  R version 3.5.3 (2019-03-11)
 os       macOS Mojave 10.14.6        
 system   x86_64, darwin15.6.0        
 ui       RStudio                     
 language (EN)                        
 collate  en_AU.UTF-8                 
 ctype    en_AU.UTF-8                 
 tz       Australia/Sydney            
 date     2020-06-08  

RStudio version: 1.3.300

[mariusbarth]

Hi @shirdekel, thanks for reporting this!.
With R 3.5,, you would have to use the syntax papaja::apa_print.afex_aov(mt_anova). However, I think it's better to update R, because otherwise your code will break as soon as you update later.
Would be great if you could try updating R and tell me whether it works then.

[crsh]

In my opinion, the best approach to avoid any of these problems is to load papaja via library("papaja") rather than calling apa_print via :: or :::.

[mariusbarth]

I'm right there with you!

[shirdekel]

@crsh, at the moment, even loading papaja first doesn't fix it for me. Will upgrade R, as @mariusbarth suggested and see if that helps.

[shirdekel]

Upgraded to R 4.0.1, and it works fine now. Thanks everyone!

[mariusbarth]

Perfect, thanks for your efforts!

[crsh]

Thanks @shirdekel, I have updated the R dependency to >= 3.6 on the devel branch.

[intanwardhani]

Hello @crsh ! I'm new to papaja, so I used the example file from ECVP 2019 tutorial to see how it worked. I ran it on R 4.0.2, but I still got the aforementioned error. Below is the error message. I wonder where that went wrong.

Quitting from lines 319-375 (manuscript-v1.rmd) Error in UseMethod("apa_print", x) : no applicable method for 'apa_print' applied to an object of class "afex_aov"

[crsh]

Are you using the current development version (remotes::install_github("crsh/papaja@devel"))?

[intanwardhani]

Oops, my bad! It works with the current development version. The pdf rendering works well, but the word rendering looks a bit awkward (as already addressed as a limitation) and always opens via Skype, for some reason... I wonder if that also happens to others and a new issue should be opened? Thanks for your prompt response!

[alexholcombe]

Mine also always opens via Skype. Someone else also mentioned somewhere that it doesn't open in Word for them, either. Not sure if this is a bug in papaja, but still, changing papaja somehow might remedy this. In the meantime, in case you're having trouble with a workaround: once the file opens in Skype, I send it within Skype to a family member, who knows to ignore the attachments. Then I can download it from the Skype conversation. Alex

…

On Thu, Jun 25, 2020 at 2:50 AM intanwardhani ***@***.***> wrote: Oops, my bad! It works with the current development version. The pdf rendering works well, but the word rendering looks a bit awkward (as already addressed as a limitation) and always opens via Skype, for some reason... I wonder if that also happens to others and a new issue should be opened? Thanks for your prompt response! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#361 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGYKTTWUU5JULOAWXDYKA3RYIVEVANCNFSM4MKNKBOA> .

-- Alex Holcombe | Professor School of Psychology | Faculty of Science The University of Sydney Web <https://sydney.edu.au/science/people/alex.holcombe.php>, Twitter <https://twitter.com/ceptional>, Map <http://openwetware.org/wiki/Holcombe:Location>

[alexholcombe]

The Skype thing is definitely not related to papaja, I believe, as I also have the problem when knitting other RMarkdown documents.

[crsh]

Thanks for confirming this. So this is either a more general issue with rmarkdown/knitr or pandoc. If you want to get to the bottom of this, you could try directly converting a Markdown document to Word with pandoc.

[hcp4715]

Hi, there,

I had an error when using 'apa_print.afex_aov()', but without problem when using apa_print().

I dowloaded the latest version of papaja, see below, and reproduced @alexholcombe 's code.

Session info:

 version  R version 4.0.3 (2020-10-10)
 os       Ubuntu 20.04.1 LTS          
 system   x86_64, linux-gnu           
 ui       RStudio                     
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8  
papaja         * 0.1.0.9997 2021-01-25 [1] Github (crsh/papaja@ef14546)    

The results were:

> apa_anova <- papaja::apa_print(mt_anova)
> apa_anova
$estimate
$estimate$cyl
[1] "$\\hat{\\eta}^2_G = .732$"


$statistic
$statistic$cyl
[1] "$F(2, 29) = 39.70$, $\\mathit{MSE} = 10.39$, $p < .001$"


$full_result
$full_result$cyl
[1] "$F(2, 29) = 39.70$, $\\mathit{MSE} = 10.39$, $p < .001$, $\\hat{\\eta}^2_G = .732$"


$table
A data.frame with 7 labelled columns:

  term estimate statistic df df.residual   mse p.value
1  Cyl     .732     39.70  2          29 10.39  < .001

term       : Effect 
estimate   : $\\hat{\\eta}^2_G$ 
statistic  : $F$ 
df         : $\\mathit{df}$ 
df.residual: $\\mathit{df}_{\\mathrm{res}}$ 
... (2 more labels)
attr(,"class")
[1] "apa_results" "list"       
> apa_anova <- papaja::apa_print.afex_aov(mt_anova)
Error: 'apa_print.afex_aov' is not an exported object from 'namespace:papaja'
> library(papaja)
> apa_anova <- apa_print.afex_aov(mt_anova)
Error in apa_print.afex_aov(mt_anova) : 
  could not find function "apa_print.afex_aov"

[mariusbarth]

Hi @hcp4715,

calling methods directly via papaja::apa_print.afex_aov() is not intended to work, you should just use apa_print(). See here for an explanation and more details.

[hcp4715]

Hi, @mariusbarth ,

thanks for your quick response!
good to know that using apa_print() it's the right way.