Analysis of Dose-Response Curves.
Analysis of dose-response data is made available through a suite of flexible and versatile model fitting and after-fitting functions.
Questions tagged [drc]
84 questions
10
votes
3 answers
Plotting dose response curves with ggplot2 and drc
In biology we often want to plot dose response curves. The R package 'drc' is really useful and base graphics can easily handle 'drm models'. However, I would like to add my drm curves to a ggplot2.
My dataset:
library("drc")
library("reshape2")
…
biomiha
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7
votes
0 answers
Handling error produced by drm
I am stuck with this problem and my R abilities are apparently not sufficient to solve it. Hopefully, someone can help me out.
I am currently working on a script that uses the function "drm" of the package "drc". I want to obtain the EC10, 20, and…
I Ho
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7
votes
1 answer
ggplot2 stat_summary mean_sdl not the same as mean +/- sd
I am unsure as to why the error bars generated by the mean_sdl function (from Hmisc) in ggplot2 are significantly broader than the error bars generated manually and plotting mean + sd and mean - sd. My…
biomiha
- 1,358
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6
votes
3 answers
drc:: drc plot with ggplot2
I'm trying to reproduce drc plots with ggplot2. Here is my first attempt (MWE is given below). However, my ggplot2 is little bit different from base R plot. I wonder if I am missing something here?
library(drc)
chickweed.m1 <- drm(count~start+end,…
MYaseen208
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4
votes
1 answer
Reproducing drc::plot.drc with ggplot2
I want to reproduce the following drc::plot.drc graphs with ggplot2.
df1 <-
structure(list(TempV = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L,…
MYaseen208
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3
votes
1 answer
"NaNs produced" warning when calculating absolute EC50 values with drc package
I'm trying to figure out how to calculate absolute EC50 values using the LL.3 and LL.4 (3 and 4 parameter) dose response models in the package drc, but I keep getting these errors of "Warning message:In log(exp(-tempVal/parmVec[5]) - 1) : NaNs…
Phillip Martin
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3
votes
1 answer
nonlinear regression prediction in R
I am confused by this warning message as I try to fit my data with a nonlinear regression model by using the drc package and drm function.
I have
N_obs <- c(1, 80, 80, 80, 81, 82, 83, 84, 84, 95, 102, 102, 102, 103, 104, 105, 105, 109, 111, 117,…
yearntolearn
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3
votes
1 answer
Dose-response curve plot in drc package does not show all the points
I am using drc package to plot a dose response curve using 13 points. However, when using the data below, only 6 out of the 13 points are visible in the plot. Does anyone have a solution to this problem? I suspect the duplicated X values are part…
J Miller
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3
votes
2 answers
plotting on logarithmic scale (with asymptotes) and Zero in ggplot2
I am plotting dose-response curves which have asymptotic tails. I would really like to include the vehicle (control) dosage in the plot showing 0
0 is generally calculated as a dosage of .0000000001 - a common practice in these plots.
I really like…
Arch
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2
votes
1 answer
nplr failing, unclear why
I tried to run an nplr function:
require(nplr)
b<- data.frame("Conc" = c(0.03125, 0.046875, 0.0625, 0.09375, 0.1875),"BKA" =c(1.89970905356837, 98.2543214102345, 98.0660619544754, 98.1858634263221, 98.0489474584974))
nplr(x = b$Conc, y =…
Laura
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- 3
2
votes
1 answer
Regression of multiple dose-response curves using the drc package in R
I am trying to fit regressions (4 or 5 PL) through my experimental data. I have several compounds inhibiting my enzyme of interest. Each has it's own range between 0-100% enzyme activity. All the data is in one dataframe and dinstinguished by one…
Steff
- 35
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2
votes
1 answer
Plotting both a GLM and LM of same data
I would like to plot both a linear model (LM) and non-linear (GLM) model of the same data.
The range between 16% - 84% should line up between a LM and GLM, Citation: section 3.5
I have included a more complete chunk of the code because I am not…
Arch
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2
votes
1 answer
Strange ED50 with drc
I am trying to estimate IC50 values with the drc package. Plotting the model works fine. But when I use the ED I get unreasonable results.
In my understanding the IC50 should by around the inflection point of the model. In this case I estimate…
WitheShadow
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2
votes
1 answer
Parameters and AUC and IC50 of a dose response curve
I have these dose response data:
df <- data.frame(viability=c(14,81,58,78,71,83,64,16,32,100,100,81,86,83,100,90,15,100,38,100,91,84,92,100),
…
dan
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2
votes
1 answer
drc:: optim initial value in 'vmmin' is not finite
I want to fit log-logistic regression for the following data in drc R package. However, my code throws the following error.
df1 <-
structure(list(Temp = c(15L, 15L, 15L, 15L, 15L, 15L, 15L, 15L,
15L, 20L, 20L, 20L, 20L, 20L, 20L, 25L, 25L,…
MYaseen208
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