An interesting observation. Please note that I have absolutely no idea about why this happens. (at least not at the time of first writing this)
In our datalab, ingeniuously named “Datalab” (the one at KUB-North, because contrary to the labs at the libraries for social sciences, and for the humanities, we are not allowed to have a name), we were visited by at student.
She wanted to make a dose-response plot. Something about the concentration of something, giving some clotting of some blood. Or something…
Anyway, she wanted to do a 4-parameter logistic model. Thats nice, I had never heard about that before, but that is the adventure of running a datalab, and what makes it fun.
Of course there is a package for it, dr4pl. After an introduction to the wonderful world of dplyr, we set out to actually fit the model. This is a minimal working example of what happened:
library(tidyverse)
library(dr4pl)
data <- tibble(dose= 1:10, response = 2:11)
dr4pl(data, dose, response)
## Error in dr4pl.default(dose = dose, response = response, init.parm = init.parm, : Both doses and responses should be numeric.
WTF? “Both doses and responses should be numeric”?. But they are!
is.numeric(data$dose)
## [1] TRUE
is.numeric(data$response)
## [1] TRUE
The error is thrown by these lines in the source:
if(!is.numeric(dose)||!is.numeric(response)) {
stop("Both doses and responses should be numeric.")
}
Lets try:
if(!is.numeric(data$dose)||!is.numeric(data$response)) {
stop("Both doses and responses should be numeric.")
} else {
print("Where did the problem go?")
}
## [1] "Where did the problem go?"
No idea. Did it disappear? No:
dr4pl(data, dose, response)
## Error in dr4pl.default(dose = dose, response = response, init.parm = init.parm, : Both doses and responses should be numeric.
Looking at the data might give us an idea of the source:
str(data)
## Classes 'tbl_df', 'tbl' and 'data.frame': 10 obs. of 2 variables: ## $ dose : int 1 2 3 4 5 6 7 8 9 10 ## $ response: int 2 3 4 5 6 7 8 9 10 11
Both dose and response are integers. Might that be the problem?
data <- tibble(dose= (1:10)*1.1, response = (2:11)*1.1)
dr4pl(data, dose, response)
## Error in dr4pl.default(dose = dose, response = response, init.parm = init.parm, : Both doses and responses should be numeric.
Nope. Both dose and response are now definitely numeric:
str(data)
## Classes 'tbl_df', 'tbl' and 'data.frame': 10 obs. of 2 variables: ## $ dose : num 1.1 2.2 3.3 4.4 5.5 6.6 7.7 8.8 9.9 11 ## $ response: num 2.2 3.3 4.4 5.5 6.6 7.7 8.8 9.9 11 12.1
But the problem persists.
Might this be the reason?
head(data,2)
## # A tibble: 2 x 2 ## dose response ## <dbl> <dbl> ## 1 1.1 2.2 ## 2 2.2 3.3
It is a tibble. And the variables are reported to be doubles.
But according to the documentation:
“numeric is identical to double (and real)”
That should not be a problem then.
However. In desperation, I tried this:
c <- data %>%
as.data.frame() %>%
dr4pl(dose, response)
And it works!
Why? Absolutely no idea!
Or do i?
The problem is that subsetting a tibble returns a new tibble. Well, subsetting a dataframe returns a dataframe as well?
It does. Unless you subset out a single variable or observation.
In a dataframe, df$var returns a vektor, containing the values of var in df.
If, however, df is a tibble, df$var will return a tibble, with just one variable.
