Re: How to fit a Hill model using braidrm package?
Luigi Marongiu <[email protected]>
| Newsgroups | gmane.comp.lang.r.general |
|---|---|
| Message-ID | <CAMk+s2T_zR_t7=b_36HyYiy3JA82mC8-CANWOeL2Cd1JFt9Dig@mail.gmail.com> |
Hello,
it was an assembler problem of the machine. I now managed to install
the package, I tried to fit a 4 or 5 parameters model but the fitting
is not good:
```
df = data.frame(Response = c(890.72, 890.94, 880.16,
895.46, 890.8, 884.15,
895.63, 887.22, 879.57, 894.72,
888.91, 878.89,
895.49, 890.83, 882.27, 893.59,
889.92, 881.59,
892.53, 891.76, 880.98, 895.06,
890.32, 881.45,
897.21, 886.35, 876.19, 889.27,
878.11, 868.32,
876.05, 866.57, 859.16, 850.53,
857.96, 859.34,
862.02, 859.04, 859.73, 858.36,
863.64, 861.19),
Dose = c(0.0000000015, 0.0000000015,
0.0000000015, 0.000000003,
0.000000003, 0.000000003, 0.000000006,
0.000000006,
0.000000006, 0.000000012, 0.000000012,
0.000000012,
0.000000024, 0.000000024, 0.000000024,
0.000000048,
0.000000048, 0.000000048, 0.000000095,
0.000000095,
0.000000095, 0.00000018, 0.00000018,
0.00000018, 0.00000038,
0.00000038, 0.00000038, 0.00000078,
0.00000078, 0.00000078,
0.0000015, 0.0000015, 0.0000015,
0.000007, 0.000007,
0.000007, 0.000025, 0.000025,
0.000025, 0.00005, 0.00005, 0.00005)
)
plot(Response~log10(Dose), df)
library(drc)
mod = drm(Response~Dose, data = df, fct=L.4())
plot(mod)
```
How can I set a Hill function with `drm`?
Thank you
On Thu, Sep 25, 2025 at 1:01 PM varin sacha <[email protected]> wrote:
>
> Hi,
>
> What about directly calling the model function with basicdrm library ?
>
> library(basicdrm)
>
> # Fit Hill model
> m <- drm(Response ~ Dose, data = df, fct = hillfct())
>
> summary(m)
>
> # Predict & plot
> plot(m, log = "x")
>
> Best,
> SV
>
> > Le 25 sept. 2025 à 10:12, varin sacha via R-help <[email protected]> a écrit :
> >
> >
> > Hi,
> > Could you paste me the exact error message you’re getting when trying install.packages("drc")
> >
> >
> >> Le 25 sept. 2025 à 09:02, Luigi Marongiu <[email protected]> a écrit :
> >>
> >> I got the same errors:
> >> ```
> >>> library(basicdrm)
> >>> findBestHill(Response~Dose, df)
> >> Error in findBestHill(Response ~ Dose, df) :
> >> could not find function "findBestHill"
> >>> evalHillEqn(Response~Dose, df)
> >> Error in evalHillEqn(Response ~ Dose, df) :
> >> could not find function "evalHillEqn"
> >> ```
> >>
> >>>> On Wed, Sep 24, 2025 at 1:47 PM peter dalgaard <[email protected]> wrote:
> >>>
> >>> They're in basicdrm, not braidrm...
> >>>
> >>> -pd
> >>>
> >>>>> On 24 Sep 2025, at 11:52 , Luigi Marongiu <[email protected]> wrote:
> >>>>
> >>>> Hello,
> >>>> I have a set of data coming from a dissociation experiment
> >>>> (protein/ligand). Since the data is required to calculate the constant
> >>>> of dissociation (Kd) of this pair, I am looking for a way of fitting a
> >>>> Hill function to the data.
> >>>> I have seen that the package braidrm
> >>>> (https://cran.r-project.org/web/packages/braidrm/index.html) provides
> >>>> this function, but when I launch the function `evalHillEqn`,
> >>>> `findBestHill` and so forth I get the error of function not found.
> >>>> Yet, the package is given as properly installed by the system.
> >>>> How can I run this package?
> >>>> Is there an alternative way to fit a Hill function to these data?
> >>>> Thank you
> >>>>
> >>>> ```
> >>>> df = data.frame(Response = c(890.72, 895.46, 895.63,
> >>>> 894.72, 895.49, 893.59,
> >>>> 892.53, 895.06, 897.21, 889.27, 876.05,
> >>>> 857.96, 862.02, 858.36,
> >>>> 890.94, 890.8, 887.22, 888.91, 890.83,
> >>>> 889.92, 891.76, 890.32,
> >>>> 886.35, 878.11, 866.57, 859.04, 863.64,
> >>>> 880.16, 884.15, 879.57,
> >>>> 878.89, 882.27, 881.59, 880.98, 881.45,
> >>>> 876.19, 868.32, 859.16,
> >>>> 850.53, 853.21, 859.34, 859.73, 861.19),
> >>>> Dose = c(0.0000000015, 0.000000003,
> >>>> 0.000000006, 0.000000012,
> >>>> 0.000000024, 0.000000048, 0.000000095,
> >>>> 0.00000018,
> >>>> 0.00000038, 0.00000078, 0.0000015,
> >>>> 0.000013, 0.000025,
> >>>> 0.00005, 0.0000000015, 0.000000003,
> >>>> 0.000000006,
> >>>> 0.000000012, 0.000000024, 0.000000048,
> >>>> 0.000000095,
> >>>> 0.00000018, 0.00000038, 0.00000078,
> >>>> 0.0000015, 0.000025,
> >>>> 0.00005, 0.0000000015, 0.000000003,
> >>>> 0.000000006,
> >>>> 0.000000012, 0.000000024, 0.000000048,
> >>>> 0.000000095,
> >>>> 0.00000018, 0.00000038, 0.00000078,
> >>>> 0.0000015, 0.000003,
> >>>> 0.000006, 0.000013, 0.000025, 0.00005)
> >>>> )
> >>>> plot(Response~log10(Dose), df)
> >>>> library(braidrm)
> >>>> evalHillEqn(Response~Dose, df)
> >>>> findBestHill(Response~Dose, df)
> >>>> ```
> >>>>
> >>>> ______________________________________________
> >>>> [email protected] mailing list -- To UNSUBSCRIBE and more, see
> >>>> https://stat.ethz.ch/mailman/listinfo/r-help
> >>>> PLEASE do read the posting guide https://www.R-project.org/posting-guide.html
> >>>> and provide commented, minimal, self-contained, reproducible code.
> >>>
> >>> --
> >>> Peter Dalgaard, Professor,
> >>> Center for Statistics, Copenhagen Business School
> >>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> >>> Phone: (+45)38153501
> >>> Office: A 4.23
> >>> Email: [email protected] Priv: [email protected]
> >>>
> >>
> >>
> >> --
> >> Best regards,
> >> Luigi
> >>
> >> ______________________________________________
> >> [email protected] mailing list -- To UNSUBSCRIBE and more, see
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide https://www.R-project.org/posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > [email protected] mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide https://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
--
Best regards,
Luigi