[R] Metafor and forest(); not showing 'ilab' and text

[Michael Dewey]

Comments in line

On 31/08/2015 16:08, Marco Colagrossi wrote:
> Thanks for your help,
>
> I got the mistake I was making and I managed to find a solution
> regarding those graphs; I don't want to abuse of your patience but I
> have three further questions:
>
> 1. Always regarding the forest plots, it is possible to make a
> cross-subset? I try to explain my self better; I have one dummy
> variable called pub and another variable called SIMiv that can take
> the values of "share", "loan", "number" and "duration". How can I
> subset my sample so that the forest shows only (for example) studies
> when the dummy takes the value of 1 and the SIMiv variable takes the
> values of "share" and "loan"?
> Something like this:
> forest(pc, var, ci95m, ci95p, slab = authoryear2, psize=1,
> subset=(pub==1, SIMiv=("share", "loan", "duration"))
>

Do you not want something like
(pub == 1) & (SIMIv %in% c("share", "loan", "duration"))


> 2. I have few doubts regarding the multilevel modeling;
>      rma.mv(pc, var, random = ~ 1 | author, data=codebook)
>     if I'm correct this should be a multilevel model nested at "author"
> level; what I cannot understand If it is a varying intercept
> (Y=A+BjX), a varying slope (Y=Aj+BX) or a varying intercept&slope
> model (Y=Aj+BjX). Are there the formulas for it somewhere? So far I
> only found the formulas for the estimators included in the metafor
> package.
>

I think it a random intercept but Wolfgang may correct me there.

> 3. metareg1 <- rma.mv(pc, var, random = ~ 1 | author, mods = ~ pub +
> SIMiv, data=codebook)
> Again, if I'm correct this should be a multilevel meta regression
> (correct me if I'm wrong); I have the same doubts as before.
>
> Thank you again
>
> Marco
>
> On 25 August 2015 at 19:24, Michael Dewey <lists at dewey.myzen.co.uk> wrote:
>> Dear Marco
>>
>> When you change xlim it increases the width of the forest plot in the sense
>> you describe. It does not push your text out of the way to make space for it
>> but instead overprints it. You may like to use alim to truncate your
>> confidence interval whiskers to fit within the space you see or make your
>> labels shorter.
>>
>>
>> On 25/08/2015 17:25, Marco Colagrossi wrote:
>>>
>>> I think I've not explained myself well. When I say "the width of the
>>> forest plot" I mean the region above the observed outcome, the
>>> "actual" forest plot, not the plot as a whole. Even if I change values
>>> for Xlim, cex or ilab.xpos the width of that particular region within
>>> the plot doesn't change.
>>>
>>> Best,
>>>
>>> Marco
>>>
>>> On 25 August 2015 at 18:11, Viechtbauer Wolfgang (STAT)
>>> <wolfgang.viechtbauer at maastrichtuniversity.nl> wrote:
>>>>
>>>> The 'xlim' argument does not change the actual width of the plotting
>>>> device. For that, you need to use the 'width' argument with whatever device
>>>> you are actually using. You can then use the 'xlim' argument to create
>>>> appropriate spacing to the left/right of the part of the plot that shows the
>>>> estimates and their CIs. Within that space, you can then add additional
>>>> columns with the 'ilab' argument. It's up to you to find an appropriate
>>>> combination of plotting device width, character/symbol expansion factor
>>>> ('cex' argument), 'xlim' values, and 'ilab.xpos' values to create a nice
>>>> looking plot that has no overlapping text and no excessive white space. An
>>>> example is this:
>>>>
>>>> http://www.metafor-project.org/doku.php/plots:forest_plot_with_subgroups
>>>>
>>>> Note that it took me dozens of iterations to create that plot. You just
>>>> have to start experimenting.
>>>>
>>>> Best,
>>>> Wolfgang
>>>>
>>>>> -----Original Message-----
>>>>> From: Marco Colagrossi [mailto:marco.colagrossi at gmail.com]
>>>>> Sent: Tuesday, August 25, 2015 17:59
>>>>> To: Viechtbauer Wolfgang (STAT)
>>>>> Cc: r-help at r-project.org; Michael Dewey
>>>>> Subject: Re: [R] Metafor and forest(); not showing 'ilab' and text
>>>>>
>>>>> Thanks again for your help. I'm sorry to bother you but I don't get
>>>>> how to widen the forest plot; if I try to change the values of xlim or
>>>>> the ilab.xpos values the width of the forest plot region does not
>>>>> change, but only moves on the graphs. What I'm I missing?
>>>>>
>>>>>
>>>>> forest(pc, var, ci95m, ci95p, slab = authoryear, psize=1,
>>>>> subset=(pub==1),
>>>>>          xlim = c(-16, 6),
>>>>>          ilab = data.frame(SIMdv, SIMiv),
>>>>>          ilab.xpos = c(-7.5, -5.5), cex = 0.75)
>>>>> op <- par(cex=.75, font=2)
>>>>>         text(c(-7.5, -5.5), 54, c("DV", "IV"))
>>>>>         text(-16,                54, "Author(s) and Year",     pos=4)
>>>>>         text(6,                  54, "Outcome [95% CI]", pos=2)
>>>>> par(op)
>>>>>>
>>>>>> par("usr")[1:2]
>>>>>
>>>>> [1] -16   6
>>
>>
>> --
>> Michael
>> http://www.dewey.myzen.co.uk/home.html
>

-- 
Michael
http://www.dewey.myzen.co.uk/home.html