Re: How to fit a Hill model using braidrm package?
varin sacha via R-help <[email protected]>
| Newsgroups | gmane.comp.lang.r.general |
|---|---|
| Message-ID | <[email protected]> |
Hi, I would say : • The Hill function is parameterized directly in terms of EC50 and Hill slope. • The LL.4/LL.5 models are mathematically very close, but parameterized on the log-dose scale and designed for dose–response data. Best, > Le 25 sept. 2025 à 13:45, Luigi Marongiu <[email protected]> a écrit : > > ADDENDUM: I managed though with the LL4 and LL5 algorithms: > ``` > mod = drm(Response~Dose, data = df, fct=LL.4()) > plot(mod) > ``` > what would be the difference with the Hill function? > Thank you > >> On Thu, Sep 25, 2025 at 1:41 PM Luigi Marongiu <[email protected]> wrote: >> >> 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 > > > > -- > Best regards, > Luigi [[alternative HTML version deleted]]