The transplantr package provides a set of vectorised functions for audit and clinical research in solid organ transplantation. These are particularly intended to work well with multiple datapoints in large series of data, where manual calculations would be particularly tedious.
The functions provided fall into three groups:
Although the package was built with unit tests, inaccuracies cannot be completely excluded. it is not a medical device and should not be used for making clinical decisions.
transplantr can be installed from CRAN:
# install transplantr
install.packages("transplantr")
# load transplantr once installed
library(transplantr)The development version can be installed from GitHub, if you want all the latest features, together with all the latest bugs and errors. Installing from CRAN is the best option for most users as the submitted packages have to pass some very pedantic automated tests before they can be hosted on CRAN. If you do want the caveat emptor, you have been warned version, this is how:
# install from GitHub
devtools::install_packages("johnasher/transplantr")As vectorised functions, the functions can be applied across a whole dataset fairly rapidly. I find that the easiest way to do this is using a “pipe” of functions from the dplyr package. dplyr can be installed on its own or, as I would recommend, by installing the whole tidyverse family of packages - a family which includes the legendary ggplot2 graphing package.
# install whole tidyverse
install.packages("tidyverse")
# install just dplyr
install.packages("dplyr")Although recommended, dplyr is not necessary for most
transplantr functions to work. dplyr is needed for the
EPTS and KDPI functions, and additionally stringr is needed for
the hla_mm_level_str() function and also for the
chi2dob() function, one unlikely to be needed by anyone
working outside Scotland!
By default, all the functions work with the units most commonly used
in the UK, which for creatinine and bilirubin is µmol/l, but each
function using either of these can be used with mg/dl instead by
changing an optional units parameter to "US"
or by calling a wrapper function suffixed with _US();
e.g. when calculating eGFR, the ckd_epi_US() function calls
ckd_epi() using creatinine in mg/dl.
Albumin is generally reported in g/l in the UK, but more commonly as
g/dl in the US. The few functions using albumin default to g/l but
change to g/dl if the units parameter is set to
"US" or the _US() wrapper function is
called.
Which is the best option to use? Calling the wrapper function uses fewer keystrokes so is quicker to type, but as it is a function calling another function, there is a slight increase in computational overhead.
Let’s say you want to calculate MELD scores for a series of liver
transplant candidates. OK, you probably actually want MELD-Na, but let’s
go with MELD as it has fewer variables! The data is in a dataframe or
tibble called “oltx.assessments” and the relevant variables are
Patient.INR, Patient.Bilirubin, Patient.Creatinine and Patient.Dialysed.
To add a new Patient.MELD variable to the dataframe, you would use a
dplyr pipe with the mutate() verb:
oltx.assessments <- oltx.assessments %>%
mutate(Patient.MELD = meld(INR = Patient.INR, bili = Patient.Bilirubin,
creat = Patient.Creatinine, dialysis = Patient.Dialysed, units = "SI"))The units = "SI" can be left out provided that
creatinine and bilirubin are both in µmol/l. To switch to mg/dl, use
units = "US" or call meld_US() instead.
Although I think dplyr makes life much easier when
organising data, I concede that some people prefer to use base R
functions instead. Using a vectorised function with multiple vector
inputs is not easy in base R but can be done with the
mapply(), or more easily with the pmap_dbl()
from the purrr package.
# attach oltx.assessments to save a lot of typing!
attach(oltx.assessments)
# method using pmap_dbl()
oltx.assessments$Patient.MELD = pmap_dbl(list(Patient.INR, Patient.Bilirubin,
Patient.Creatinine, Patient.Dialysed),
meld, units = "SI")
# alternative method using mapply()
oltx.assessments$Patient.MELD = mapply(FUN = meld, Patient.INR, Patient.Bilirubin,
Patient.Creatinine, Patient.Dialysed,
MoreArgs = list(units = "SI"),
SIMPLIFY = TRUE)
# detach oltx.assessments to avoid namespace errors
detach(oltx.assessments)The advantage of using a dplyr pipe, apart from easier code,
is speed. Benchmarking on a basic Linux laptop showed that the median
time to perform vectorised calculation of 100,000 MELD scores was 115
milliseconds, compared with 6007 milliseconds using
`pmap_dbl() and 6484 with mapply().
Although vectorised functions for multiple calculations are one of the best features of R, you might just want to collect data on a single case. This is very straightforward:
# using µmol/l
meld(INR = 2.1, bili = 34, creat = 201, dialysis = 0)
# using mg/dl
meld(INR = 2.1, bili = 2.0, creat = 2.3, dialysis = 0, units = "US")
# using mg/dl with wrapper function
meld_US(INR = 2.1, bili = 2.0, creat = 2.3, dialysis = 0)For more information, function documentation and usage vignettes, visit transplantr.txtools.net.