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rauc

How to set subdivisions for the auc() function in the MESS package to prevent getting an error message?

I have time series data from several samples (wildtype (WT) vs. knockout (KO)) for calcium concentrations. In particular, I get 2 peaks for each sample and use the 2nd peak to calibrate the first peak, for this I need the AUC of both peaks. My goal is to apply a spline function to my time series data and to calculate the AUCs.

So far I used the MESS package and the auc() function and set type=spline

Time is measured in ms from 0 to 1801204 ms

df <- data

df
# A tibble: 551 x 7
    Time         KO_1     WT1           KO_2    WT2           KO_3    WT3

 1 29800            87      80            94      99           102      99
 2 30000            77      91            89      89            80     104
 3 31487           264     334           261     147           330     257
 4 31687           352     294           349     176           242     356
 5 31887           341     333           359     260           303     353
 6 32087           349     436           346     250           280     334
 7 32287           328     373           383     321           287     443
 8 32487           382     484           376     323           270     416
 9 32687           437     495           295     317           300     458
10 32887           351     542           387     378           312     422
# ... with 541 more rows


library(MESS)

auc(df$Time, df$WT1, from=min(df$Time, na.rm = TRUE), 
    to = max(df$Time, na.rm = TRUE) ,type = 'spline')

My expected result is that I get a value for AUC for WT1. But I always receive the error message:

Error in integrate(myfunction, lower = from, upper = to) : maximum number of subdivisions reached

Solution

  • The error message comes from function integrate that is used within MESS::auc.

    More precisely, it comes from the argument subdivisions (maximum number of subintervals), which is set to 100 by default. However, in your case, a higher value would probably make more sense.

    An quick and easy fix (but not a very sustainable one!), is, to copy+paste the auc function into an R script, adapt it to your needs (see below) and then source it before you use it.

    Here is how that works:

    1. Copy + paste the auc function into an R script and save it as mess_auc_adapted.R
    2. Assign the function as auc (auc <- function...).
    3. Within the auc function, change the last bit:

    res <- integrate(myfunction, lower = from, upper = to)$value

    becomes

    res <- integrate(myfunction, lower = from, upper = to, ...)$value

    1. Then use auc the following way:

    source("mess_auc_adapted.R")

    auc(x = df$Time, y = df$WT1, from=min(df$Time, na.rm = TRUE), to = max(df$Time, na.rm = TRUE) ,type = 'spline', subdivisions = WHATEVER_NUMBER_THAT_MAKES_SENSE)

    A better solution is to contact the maintainer, tell them your problem and a possible solution to it. Just open an issue here: https://github.com/ekstroem/MESS/issues. This way the problem can be addressed directly.