[R] [UPDATE] grofit issues with replicates - probit or logit or glmm

[Marcelo Laia]

I done a mistake when I paste the script in the message. An update:

url.csv <-
https://dl.dropboxusercontent.com/u/34009642/cepajabo07_wide_acumulado.csv

data02 <- read.table(url.csv, header=TRUE, sep="\t", dec=",")

head(data02)

timepoints <- 1:5 # 5 days
time <- t(matrix(rep(timepoints, 120), c(5, 120))) 
                                    # 5 days and 120 experimentos
                                    # (6 iso * 4 doses
                                    # * 5 rep)
time

MyOpt1 <- grofit.control(smooth.gc = 0.5, parameter = 28, 
interactive = FALSE)

MyOpt2 <- grofit.control(smooth.gc = 0.5, parameter = 28, 
interactive = FALSE, log.x.dr = TRUE)

TestRun1 <- grofit(time, data02, TRUE, MyOpt1)
TestRun2 <- grofit(time, data02, TRUE, MyOpt2)

TestRun1$drFit
TestRun2$drFit

colData <- c("black", "cyan", "magenta", "blue")

plot(TestRun1$gcFit, opt = "s", colData = colData, colSpline = 1, 
pch = 1:4, cex = 1)

plot(TestRun2$gcFit, opt = "s", colData = colData, colSpline = 1, 
pch = 1:4, cex = 1)

plot(TestRun1$drFit$drFittedSplines[[1]], colData = colData, 
pch = 1:4, cex = 1)

plot(TestRun2$drFit$drFittedSplines[[1]], colData = colData, 
pch = 1:4, cex = 1)

Thank you very much!

Marcelo

On 12/02/15 at 12:57am, Marcelo Laia wrote:
> Hello
> 
> I tried use grofit package in our data set. We provide a subset of our
> data with X iso, and 4 doses, and insect died was count each day for
> long 5 days. We started with Y insects per dishes. When one is dead, it
> was counted and removed. Died insect is cumulative in the next days.
> i.e. day 1 died 1. day 2 no died, so, day 2 is assigned 1 died (from day
> 1).
> 
> Here is the script:
> 
> library(lattice)
> library(grofit)
> library(repmis)
> 
> url.csv <- https://dl.dropboxusercontent.com/u/34009642/cepajabo07_wide_acumulado.csv
> 
> data02 <- read.table(url.csv, header=TRUE, sep="\t", dec=",")
> 
> head(data02)
> 
> timepoints <- 1:5 # 5 days
> time <- t(matrix(rep(timepoints, 120), c(5, 120))) # 5 days and 120 experiments
>                                                    # (6 iso * 4 doses
>                                                    # * 5 rep)
> time
> 
> TestRun1$drFit
> TestRun2$drFit
> 
> colData <- c("black", "cyan", "magenta", "blue")
> 
> plot(TestRun1$gcFit, opt = "s", colData = colData, colSpline = 1, 
>      pch = 1:4, cex = 1)
> 
> plot(TestRun2$gcFit, opt = "s", colData = colData, colSpline = 1, 
>      pch = 1:4, cex = 1)
> 
> plot(TestRun1$drFit$drFittedSplines[[1]], colData = colData, 
>      pch = 1:4, cex = 1)
> 
> plot(TestRun2$drFit$drFittedSplines[[1]], colData = colData, 
>      pch = 1:4, cex = 1)
> 
> The problem: grofit didn't deal with replicates and do a curve for each
> ones.
> 
> Is it a way to get response curve with the replicates?
> 
> We are interested in LD50, and dose response curve, and graphs.
> 
> Any suggestion is very welcome!
> 
> Thank you!
> 
> -- 
> Marcelo
> 

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