[R-meta] May I ask a question about how to extract specific values from summary(netmeta) output?

[Yan LUO]

Dear Guido,

Thank you so much for your detailed explanations.

I have tried them all, and all solved my problem perfectly. It is really
very helpful.
With the reference to your codes, I will try to create and decorate my
plots based on my needs, as a way of studying. At the same time waiting for
your update of netmeta package!

Thanks again for the great work of your group, for this netmeta package :)

Best wishes,
Yan

Guido Schwarzer <sc using imbi.uni-freiburg.de> 于2019年9月30日周一 下午9:06写道：

> Am 27.09.19 um 17:26 schrieb Yan LUO:
>
> [...]
> I am considering of constructing a "2-dimensional figure" to show the
> results of a network meta-analysis, which means using the x-axis to the
> indicate efficacy ORs for a group of drugs and y-axis to indicate safety
> ORs for the same group of drugs. I selected drug A as conference for both
> efficacy and safety networks. In order to draw the scatter plot, I need to
> extract information from 2 network meta-analyses. The output of
> summary(netmeta)  function (if set ref=drug A) displays all the ORs
> compared to drug A (which I need), however this result is not included in
> the returned list. If it were in the returned list then it would be not
> hard to extract, but since it cannot be found there, how can I extract
> these ORs values from the output? Besides, I am wondering why the displayed
> results are different from the returned list?
>
> Dear Yan,
>
> You do not directly find the odds ratios in an R object created with
> netmeta() as the log odds ratio is stored. Furthermore, instead of only
> containing comparisons with the reference treatment, all network estimates
> are stored in the list elements 'TE.fixed' and 'TE.random'.
> These matrices contain the network estimates comparing the treatment in
> the row with the treatment in the column. For a netmeta object net1, for
> example, you can extract the log odds ratio of treatment comparisons with
> the reference treatment using the following commands:
> net1$TE.fixed[, net1$reference.group]
> net1$TE.random[, net1$reference.group]
>
> Similar matrices are stored in a netmeta object containing the standard
> errors, lower and upper confidence limits as well as z- and p-values (see
> help page of netmeta).
>
> Concerning a scatter plot of an efficacy and safety outcome, I wrote some
> R code (see attached file) which does the job. This will probably be the
> basis for a new plotting function in R package *netmeta* to easily create
> such scatter plots.
>
>
> By the way, I have another question about the netgraph function. It seems
> not to be a defaulted selection of drawing a netgraph with the size of
> nodes proportional to the randomized number of patients (sample size), but
> can I manage to do it by some ways?
>
> The number of randomized patients per treatment is stored in list element
> 'n.trts' which can be used to determine the node size in a network graph.
> E.g.,
>
> example(smokingcessation)
> netgraph(net1, plastic = FALSE, points = TRUE, adj = 0.5,
>          cex.points = 15 * sqrt(n.trts / max(n.trts)))
>
> Best wishes, Guido
>
> P.S. Some additional remarks:
>
> - R function netleague() can be used to create a league table for an
> efficacy and safety outcome. E.g., netleague(net.efficacy, net.safety)
>
> - R functions netbind() and forest.netbind() can be used to combine / bind
> results of several networks and to generate a corresponding forest plot
>
> - R functions netposet() and plot.netposet() can be used to generate a
> scatter plot of P-scores for two outcomes (to partially order / rank
> treatments based on two outcomes)
>
> --
> Dr. Guido Schwarzer
> Institute of Medical Biometry and Statistics,
> Faculty of Medicine and Medical Center - University of Freiburg
>
> Postal address: Stefan-Meier-Str. 26, D-79104 Freiburg
>
> Phone: +49/761/203-6668
> Mail: sc using imbi.uni-freiburg.de
> Homepage: http://www.imbi.uni-freiburg.de
>
> ORCID iD: https://orcid.org/0000-0001-6214-9087
> R-book: https://www.springer.com/gp/book/9783319214153
>
>

-- 
Yan LUO, M.D., PhD candidate
Department of Health Promotion and Human Behavior
School of Public Health, Graduate School of Medicine
Kyoto University
Email: luo.yan.66a using kyoto-u.jp, lilacluo using gmail.com

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