add.significance.stars output

[kofm]

Hi,
when using the options add.significance.stars in pander() mehod the output is not well interpreted by pandoc that recognizes the asterisks as markup code for bold and italic fonts.
Here's a minimal example:

> ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
> trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
> group <- gl(2, 10, 20, labels = c("Ctl","Trt"))
> weight <- c(ctl, trt)
> lm.D9 <- lm(weight ~ group)
> lm.D90 <- lm(weight ~ group - 1) # omitting intercept
> 
> anova(lm.D9)
Analysis of Variance Table

Response: weight
          Df Sum Sq Mean Sq F value Pr(>F)
group      1 0.6882 0.68820  1.4191  0.249
Residuals 18 8.7292 0.48496               
> pander(anova(lm.D9),add.significance.stars = T)

----------------------------------------------------------
    &nbsp;       Df   Sum Sq   Mean Sq   F value   Pr(>F) 
--------------- ---- -------- --------- --------- --------
   **group**     1    0.6882   0.6882     1.419           

 **Residuals**   18   8.729     0.485      NA        NA   
----------------------------------------------------------

Table: Analysis of Variance Table

Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

The last string ("Signif. codes") does not render well in PDF output as you can see here:

If i manually copy&paste pander() output and escape the asterisks like this:

Codici sign.:  0 '\*\*\*' 0.001 '\*\*' 0.01 '\*' 0.05 '\.' 0.1 ' ' 1 

then it renders well from md to pdf with pandoc.

Thanks

[daroczig]

Sorry for the long delay with my reply -- thanks for reporting this, I hope the above commit resolves the issue. Looking forward to any feedback. Thanks, Gergely

[kofm]

Thanks for the fix!
It appears to still have some problems.

> pander(anova(model),add.significance.stars=T,missing="",caption="Risultati ANOVA")

--------------------------------------------------------------
            Df   Sum Sq   Mean Sq   F value   Pr(>F)     
--------------- ---- -------- --------- --------- --------- --
 **treatment**   2    0.2317   0.1158     2.28     0.1036     

  **variety**    83   22.31    0.2688     5.291   1.077e-30   

 **Residuals**  418   21.24    0.05081                        
--------------------------------------------------------------

Table: Risultati ANOVA

Signif. codes:  0 '\*\*\*' 0.001 '\*\*' 0.01 '\*' 0.05 '.' 0.1 ' ' 1

Significance stars are not added anymore to the table and it also add another not needed empty column after Pr(>F).
Here's how the same output should be (imho):

----------------------------------------------------------
            Df   Sum Sq   Mean Sq   F value   Pr(>F) 
--------------- ---- -------- --------- --------- --------
 **treatment**   2    0.2317   0.1158     2.28            

  **variety**    83   22.31    0.2688     5.291    * * *  

 **Residuals**  418   21.24    0.05081                    
----------------------------------------------------------

Table: Risultati ANOVA

Signif. codes:  0 '\*\*\*' 0.001 '\*\*' 0.01 '\*' 0.05 '.' 0.1 ' ' 1

Thanks again

[daroczig]

Ah, right -- sorry for the above typo, it should be fixed now. Please note that the add.signigicance.stars feature does not replace the P values with stars, but instead adds a new column including the stars. Please let me know how it works for you.

[kofm]

Works like a charm!
Thank you very much for your awesome work

d> pander(anova(model),add.significance.stars = T,missing="")

-----------------------------------------------------------------
            Df   Sum Sq   Mean Sq   F value   Pr(>F)        
--------------- ---- -------- --------- --------- --------- -----
  **variety**    83   8.309    0.1001     5.051   5.914e-29 * * *

 **treatment**   2    0.1377   0.06885    3.474    0.0319     *  

 **Residuals**  418   8.285    0.01982                           
-----------------------------------------------------------------

Table: Analysis of Variance Table

Signif. codes:  0 '\*\*\*' 0.001 '\*\*' 0.01 '\*' 0.05 '.' 0.1 ' ' 1