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

[Yuhang Hu]

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("perf", c("acog","asom"), R=r_mat, V=v_mat)

Many thanks for your knowledge,
Yuhang

On Wed, Sep 13, 2023 at 1:40 PM Yuhang Hu <yh342 using nau.edu> wrote:

> 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 using 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 using 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 using 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 using 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= ??????)
>>
>
>

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