Quoting smooth random terms mccv::gam

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Quoting smooth random terms mccv::gam

magic_kingdom
Dear All,

I have a mgcv::gam model of the form:

m1 <- gam(Y ~ A + s(B, bs = "re"), data = dataframe, family = gaussian, method = "REML")

The random term is quoted in summary(m1) as, for example,

Approximate significance of smooth terms:
           # edf Ref.df      F p-value
s(B)  4.486      5 97.195 6.7e-08 ***

My question is, how would I quote this result (statistic and P value) in a formal document?

For example, one possibility is F[4.486,5] = 97.195, P = 6.7e-08. However, arguing against this, “reverse engineering” of the result using

pf(q= 97.195, df1= 4.486, df2= 5, lower.tail=FALSE)

gives an incorrect p value:

[1] 0.1435508

I would be very grateful for your advice. Many thanks for your help!

________________________________

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Re: Quoting smooth random terms mccv::gam

Simon Wood
I would quote the p-value, but not the statistic (as it is not a
standard F stat). The actual statistic is given here:

https://academic.oup.com/biomet/article-pdf/100/4/1005/566200/ast038.pdf

On 14/12/2018 04:33, Smith, Desmond wrote:

> Dear All,
>
> I have a mgcv::gam model of the form:
>
> m1 <- gam(Y ~ A + s(B, bs = "re"), data = dataframe, family = gaussian, method = "REML")
>
> The random term is quoted in summary(m1) as, for example,
>
> Approximate significance of smooth terms:
>             # edf Ref.df      F p-value
> s(B)  4.486      5 97.195 6.7e-08 ***
>
> My question is, how would I quote this result (statistic and P value) in a formal document?
>
> For example, one possibility is F[4.486,5] = 97.195, P = 6.7e-08. However, arguing against this, “reverse engineering” of the result using
>
> pf(q= 97.195, df1= 4.486, df2= 5, lower.tail=FALSE)
>
> gives an incorrect p value:
>
> [1] 0.1435508
>
> I would be very grateful for your advice. Many thanks for your help!
>
> ________________________________
>
> UCLA HEALTH SCIENCES IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: Quoting smooth random terms mccv::gam

magic_kingdom
Thanks very much, Simon!

On 12/17/18, 8:23 AM, "Simon Wood" <[hidden email]> wrote:

    I would quote the p-value, but not the statistic (as it is not a
    standard F stat). The actual statistic is given here:
   
    https://urldefense.proofpoint.com/v2/url?u=https-3A__academic.oup.com_biomet_article-2Dpdf_100_4_1005_566200_ast038.pdf&d=DwIDaQ&c=UXmaowRpu5bLSLEQRunJ2z-YIUZuUoa9Rw_x449Hd_Y&r=y6YM-SSv8WOxR70LMzwwFohC41WMNU4ZGFcHpTmGWLo&m=CqMTgm500nmgBrPfC2cLIc45sZ6h0I2odVPYT8qCmYA&s=epymthgL8_opS9pITmfKRJnH_uzCCzEWTYU9qEwQ_q0&e=
   
    On 14/12/2018 04:33, Smith, Desmond wrote:
    > Dear All,
    >
    > I have a mgcv::gam model of the form:
    >
    > m1 <- gam(Y ~ A + s(B, bs = "re"), data = dataframe, family = gaussian, method = "REML")
    >
    > The random term is quoted in summary(m1) as, for example,
    >
    > Approximate significance of smooth terms:
    >             # edf Ref.df      F p-value
    > s(B)  4.486      5 97.195 6.7e-08 ***
    >
    > My question is, how would I quote this result (statistic and P value) in a formal document?
    >
    > For example, one possibility is F[4.486,5] = 97.195, P = 6.7e-08. However, arguing against this, “reverse engineering” of the result using
    >
    > pf(q= 97.195, df1= 4.486, df2= 5, lower.tail=FALSE)
    >
    > gives an incorrect p value:
    >
    > [1] 0.1435508
    >
    > I would be very grateful for your advice. Many thanks for your help!
    >
    > ________________________________
    >
    > UCLA HEALTH SCIENCES IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.
    >
    > [[alternative HTML version deleted]]
    >
    > ______________________________________________
    > [hidden email] mailing list -- To UNSUBSCRIBE and more, see
    > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dhelp&d=DwIDaQ&c=UXmaowRpu5bLSLEQRunJ2z-YIUZuUoa9Rw_x449Hd_Y&r=y6YM-SSv8WOxR70LMzwwFohC41WMNU4ZGFcHpTmGWLo&m=CqMTgm500nmgBrPfC2cLIc45sZ6h0I2odVPYT8qCmYA&s=XCgKsfTTCyRoegz5hqMvtEt9m0KRm-qD0HtpXGYdxzg&e=
    > PLEASE do read the posting guide https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject.org_posting-2Dguide.html&d=DwIDaQ&c=UXmaowRpu5bLSLEQRunJ2z-YIUZuUoa9Rw_x449Hd_Y&r=y6YM-SSv8WOxR70LMzwwFohC41WMNU4ZGFcHpTmGWLo&m=CqMTgm500nmgBrPfC2cLIc45sZ6h0I2odVPYT8qCmYA&s=hyi1_CVKTW4c_7lyb3TlmtPnSpsQfnI7BhRjVOLhXdI&e=
    > and provide commented, minimal, self-contained, reproducible code.
   

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