[R-meta] Calculation of p values in selmodel

[Viechtbauer, Wolfgang (NP)]

Did you actually install the devel version as instructed under the link I posted? When you do library(metafor), which version is being loaded? If it is 4.4-0, then you are not using the devel version (which has version 4.5-x).

> -----Original Message-----
> From: R-sig-meta-analysis <r-sig-meta-analysis-bounces using r-project.org> On Behalf
> Of Will Hopkins via R-sig-meta-analysis
> Sent: Thursday, March 21, 2024 00:34
> To: 'R Special Interest Group for Meta-Analysis' <r-sig-meta-analysis using r-
> project.org>
> Cc: Will Hopkins <willthekiwi using gmail.com>
> Subject: Re: [R-meta] Calculation of p values in selmodel
>
> Thank you! Unfortunately I still get the warning...
>  Extra argument ('pval') disregarded.
> ...with every invocation of selmodel.
>
> Here’s the line of code involving pval:
>     result <- metafor::selmodel(x,  type="step", steps=(0.025),
> pval=meta_data$pValue)
>
> It's reading the variable meta_data$pValue OK, because if I make it
> meta_data$junk, I get this:
> There were 50 or more warnings (use warnings() to see the first 50)
> Browse[1]> Q
> > warnings()
> Warning messages:
> 1: Unknown or uninitialised column: `junk`.
> 2: Extra argument ('pval') disregarded.
> etc.
>
> I closed R and reopened it, but still no joy. I had already restarted R prior to
> install.
>
> -----Original Message-----
> From: R-sig-meta-analysis <r-sig-meta-analysis-bounces using r-project.org> On Behalf
> Of Viechtbauer, Wolfgang (NP) via R-sig-meta-analysis
> Sent: Thursday, March 21, 2024 11:34 AM
> To: R Special Interest Group for Meta-Analysis <r-sig-meta-analysis using r-
> project.org>
> Cc: Viechtbauer, Wolfgang (NP) <wolfgang.viechtbauer using maastrichtuniversity.nl>
> Subject: Re: [R-meta] Calculation of p values in selmodel
>
> See: https://www.metafor-project.org/doku.php/installation#development_version
>
> > -----Original Message-----
> > From: R-sig-meta-analysis <r-sig-meta-analysis-bounces using r-project.org>
> > On Behalf Of Will Hopkins via R-sig-meta-analysis
> > Sent: Wednesday, March 20, 2024 23:01
> > To: 'R Special Interest Group for Meta-Analysis'
> > <r-sig-meta-analysis using r- project.org>
> > Cc: Will Hopkins <willthekiwi using gmail.com>
> > Subject: Re: [R-meta] Calculation of p values in selmodel
> >
> > Wolfgang, I figured that I might be able to implement your
> > selmodel(...,
> > pval=dat$pValue) by reverting to for-loop processing. I solved the
> > previous problems I had with this approach by stripping out the NULLs
> > from the list objects, so the simulations are running nicely.
> >
> > However, it appears that the latest version of metafor, which I have
> > just installed, does not have the pval functionality yet, because I
> > get this warning with every invocation of selmodel:
> > Extra argument ('pval') disregarded.
> >
> > I am still a newbie with R, so I may have done something wrong with
> > the update process. I got this warning, and nine others like it, but I
> > presume this doesn't apply to metafor:
> > Warning: package 'boot' in library 'C:/Program
> > Files/R/R-4.3.2/library' will not be updated.
> >
> > I then got this, again presumably irrelevant:
> > Warning: cannot remove prior installation of package ‘lattice’
> > Warning: restored ‘lattice’
> >
> > The only warning for loading metafor was this:
> > package ‘Matrix’ was built under R version 4.3.3
> >
> > The other possibility is that my for-loop processing has some kind of
> > mistake, but it seems to be OK. Each loop produces a meta-analysis
> > object resultmeta from invocation of ram.uni with a dataset meta_data
> > (the i-th subset of my full dataset). I then apply selmodel to
> > resultmeta within a function, where the x is
> > resultmeta:
> > result <- metafor::selmodel(x,  type="step", steps=(0.025),
> > pval=meta_data$pValue)
> >
> > I give up. Help, please!
> >
> > Will