Quickly import NONMEM output tables into R. This function automatically detects the optimal settings to import the tables from nonmem.
read_nm_tables(
file = NULL,
dir = NULL,
combined = TRUE,
rm_duplicates = TRUE,
quiet = FALSE,
simtab = NULL,
ziptab = TRUE,
...
)
A character vector of path to the files or a nm_table_list
object created with list_nm_tables
.
Location of the model files.
Logical value indicating whether multiple tables should be combined into a single one. If the number of rows does not match an error will be returned.
Logical value indicating whether duplicated columns should be removed.
Logical, if FALSE
messages are printed to the console.
If TRUE
only reads in simulation tables, if FALSE
only reads estimation tables.
Default NULL
reads all tables.
If TRUE
search for the tables that have been compressed and renamed ´<file>.zip'.
Additional arguments to be passed to the read_table
or read_csv
functions.
When using read_nm_tables
with the combined
argument set to FALSE
an ID
column
must be present in all data tables. When combined
is set to TRUE
instead an ID
column must be
present in at least one table for each problem and for each `firstonly` category. ID
columns are required
to properly combine/merge tables and removing NA
records. If the ID
column is missing from a table and
combined = FALSE
read_nm_tables
will return the following warning: Unknown variables: `ID`
. While
the data is returned beware that NA
records might be left in the data and the output should be checked carefully.
If combined = TRUE
read_nm_tables
xpose is more strict and will return the following warning instead:
Dropped `<tablenames>` due to missing required `ID` column.
.
if (FALSE) {
# Import tables manually and return them as a list of individual tables
nm_tables <- read_nm_tables(file = c('sdtab001', 'patab001'),
dir = 'models', combined = FALSE)
# Import tables manually and return them as a single merged table
nm_tables <- read_nm_tables(file = c('sdtab001', 'patab001'),
dir = 'models', combined = TRUE)
# Import tables automatically (used internally by xpose_data())
nm_tables <- read_nm_model(file = 'run001.lst', dir = 'models') %>%
list_nm_tables() %>%
read_nm_tables()
# Passing arguments to readr via `...`
# (e.g. import columns as character and only first 10 rows)
nm_tables <- read_nm_tables(file = 'sdtab001', dir = 'models',
col_type = readr::cols(.default = 'c'),
n_max = 10)
}