[R-meta] Specifying variable names in metafor::vec2mat()

Thank you, Wolfgang. I figured something out for `coef(res)` order. But
should `vcov(res)` also follow/match the changes that happen in the order
of `coef(res)`, if the user wants to eventually use both as input in
`matreg()`?

# EXAMPLE:
dat <- dat.craft2003
dat$var1.var2 <- apply(dat[c("var1","var2")],1,paste0,collapse=".")

res <- rma(ri~var1.var2+0, 1, data=dat)

rs <- coef(res)[c(3,5,6,1,2,4)] # vs.  rs <- coef(res)

r_mat = vec2mat(rs, dimnames=c("perf","acog","asom","conf")) # vs.
c("acog","asom","conf","perf")

v_mat = vcov(res) ## How should this change if: rs <- coef(res)?

matreg(4, 2:3, R=r_mat, V=v_mat)

Many thanks for your knowledge,
Yuhang

On Tue, Sep 12, 2023 at 9:20?AM Viechtbauer, Wolfgang (NP) <
wolfgang.viechtbauer at maastrichtuniversity.nl> wrote:

Given the ordering of the coefficients in coef(res), this won't be
possible. Look at:

print(res, num=TRUE)

Note that coefficients 1-6 and 18 all pertain to the correlation between
L2DA and the other 7 variables. These should all be together in the same
column, but

vec2mat(coef(res))

doesn't know that and so coefficient 18 ends up in the wrong place. This
is what I tried to explain in my previous post. First, you need to ensure
that the ordering of the coefficients is such that filling them in
(columnwise) into the matrix makes sense.

So you first need to rearrange the coefficients so that the first set
pertains to L2DA (there are 7 of those), then the second set contains the
remaining coefficients that pertain to say variable L2DF (there are 6 of
those), and so on. Within each set, the order of the variables also needs
to be consistent, so if you start with L2DA.L2DF, L2DA.L2G, L2DA.L2L, ...,
in the first set, then the second set must start with L2DF.L2G, L2DF.L2L,
..., and so on.

Once you understand this, then setting the appropriate dimension names is
obvious.

Best,
Wolfgang

-----Original Message-----
From: Yuhang Hu [mailto:yh342 at nau.edu]
Sent: Tuesday, 12 September, 2023 17:36
To: Viechtbauer, Wolfgang (NP)
Cc: R Special Interest Group for Meta-Analysis
Subject: Re: [R-meta] Specifying variable names in metafor::vec2mat()

Thank you, Wolfgang. When you say "it depends on the ordering of the

values in

coef(res)", could you please elaborate on how exactly the user should

follow that

ordering when specifying the "dimnames=" esp. when the number of

variables is

larger?

For example, below, I have 8 variables with their names being `c("L2R",

"L2DA",

"L2DF", "L2V", "L2G", "L2P", "L2M", "L2L")`. But I wonder how to order

them

correctly in "dimnames="?

In fact, I think I'm getting the order for 7 of them right `c("L2DA",

"L2DF",

"L2G", "L2L", "L2M", "L2P", "L2V")` but don't know where to put "L2R" in

that

mix?

dat <- read.csv("https://raw.githubusercontent.com/ilzl/i/master/j.csv")

dat1 <- escalc("COR", ri = ri, ni = N, data = dat)

dat2 <-

transform(dat1,var1.var2=apply(dat1[c("var1","var2")],1,paste0,collapse="."))

res <- rma(yi~var1.var2+0, 1, data=dat2)

vec2mat(coef(res), dimnames = ????)
Many thanks for your expertise,
Yuhang

On Tue, Sep 12, 2023 at 1:06?AM Viechtbauer, Wolfgang (NP)
<wolfgang.viechtbauer at maastrichtuniversity.nl> wrote:
Dear Yuhang,

Since coef(res) is of length 6, vec2mat() will put these values (i.e.,

the

estimated average correlations) into a 4x4 (correlation) matrix. Given

the

ordering of the values in coef(res), the appropriate dimension names

would be

something like this:

vec2mat(coef(res), dimnames=c("acog","asom","conf","perf"))

However, there is no general rule for this, as it depends on the

ordering of the

values in coef(res).

I have tried to make various functions in metafor behave in a consistent

manner

when it comes to ordering certain elements, but in this case, it is

really up to

the user to check that adding dimension names even makes sense for the

resulting

matrix. For example:

vec2mat(sample(coef(res)))

is perfectly fine in principle (albeit a bit weird), but it no longer

makes sense

to say that all values in the first column/row pertain to the

correlations

between one of the four variables and the other three variables (unless

you get

lucky) and so on.

But say the coefficients had been ordered like this:

coef(res)[c(3,5,6,1,2,4)]

Then the appropriate dimension names would be:

vec2mat(coef(res)[c(3,5,6,1,2,4)],

dimnames=c("perf","acog","asom","conf"))

Best,
Wolfgang

-----Original Message-----
From: R-sig-meta-analysis [mailto:

r-sig-meta-analysis-bounces at r-project.org] On

Behalf Of Yuhang Hu via R-sig-meta-analysis
Sent: Monday, 11 September, 2023 5:32
To: R meta
Cc: Yuhang Hu
Subject: [R-meta] Specifying variable names in metafor::vec2mat()

Hello Everyone,

I'm using the metafor::vec2mat() as shown in the toy example below.
However, I wonder how I should specify the order of the variables' names
defined in "dimnames=" when converting the vector of coefficients to a
correlation matrix using metafor::vec2mat()?

Is there generally a rule or a technique to order the variables' names
correctly in "vec2mat()", especially if there are many variable names?

Thanks,
Yuhang

# EXAMPLE:
tmp <- rcalc(ri ~ var1 + var2 | study, ni=ni, data=dat.craft2003)
V <- tmp$V
dat <- tmp$dat

res <- rma.mv(yi~ var1.var2 - 1, V,
             random = ~  var1.var2| study, struct = "UN",
             data=dat)

vec2mat(coef(res), dimnames= ??????)