Owing to increased complexity and more diverse applications, recursive
rec_cncpt) may specify callback functions
to be called on corresponding data objects and perform post-processing
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pafi( ..., match_win = hours(2L), mode = c("match_vals", "extreme_vals", "fill_gaps"), fix_na_fio2 = TRUE, interval = NULL ) safi( ..., match_win = hours(2L), mode = c("match_vals", "extreme_vals", "fill_gaps"), fix_na_fio2 = TRUE, interval = NULL ) vent_dur(..., match_win = hours(6L), min_length = mins(30L), interval = NULL) vent_ind(..., interval = NULL) sed(..., interval = NULL) gcs( ..., valid_win = hours(6L), set_sed_max = TRUE, set_na_max = TRUE, interval = NULL ) urine24( ..., min_win = hours(12L), limits = NULL, start_var = "start", end_var = "end", interval = NULL ) vaso60(..., max_gap = mins(5L), interval = NULL) vaso_ind(..., interval = NULL) supp_o2(..., interval = NULL) avpu(..., interval = NULL) bmi(..., interval = NULL) norepi_equiv(..., interval = NULL)
Data input used for concept calculation
Time-span during which matching of values is allowed
Method for matching PaO2 and FiO2 values
Logical flag indicating whether to impute missing FiO2 values with 21
Expected time series step size (determined from data if
Minimal time span between a ventilation start and end time
Maximal time window for which a GCS value is valid if no newer measurement is available
Logical flag for considering sedation
Logical flag controlling imputation of missing GCS values with the respective maximum values
Minimal time span required for calculation of urine/24h
Maximum time gap between administration windows that are merged (can be negative).
Several concept callback functions are exported, mainly for documenting their arguments, as default values oftentimes represent somewhat arbitrary choices and passing non-default values might be of interest for investigating stability with respect to such choices. Furthermore, default values might not be ideal for some datasets and/or analysis tasks.
In order to calculate the PaO2/FiO2 (or Horowitz index), for a given time point, both a PaO2 and a FiO2 measurement is required. As the two are often not measured at the same time, some form of imputation or matching procedure is required. Several options are available:
match_vals allows for a time difference of maximally
between two measurements for calculating their ratio
extreme_vals uses the worst PaO2 and a
FiO2 values within the time window spanned by
fill_gaps represents a variation of
extreme_vals, where ratios are
evaluated at every time-point as specified by
intervalas opposed to
only the time points where either a PaO2 or a
FiO2 measurement is available
fix_na_fio2 imputes all remaining missing FiO2 with 21,
the percentage (by volume) of oxygen in (tropospheric) air.
Building on the atomic concepts
determines time windows during which patients are mechanically ventilated
by combining start and end events that are separated by at most
and at least
min_length. Durations can be converted into an indicator
variable represented by
vent_ind, where time-points (as determined by
interval) that fall into such ventilation windows are set to
while missingness (
FALSE indicate no mechanical ventilation.
Currently, no clear distinction between invasive an non-invasive
ventilation is made.
In order to construct an indicator for patient sedation, information from
the two concepts
rass is pooled: A patient is considered
sedated if intubated or has less or equal to -2 on the Richmond
Aggregating components of the Glasgow Coma Scale into a total score
(whenever the total score
tgcs is not already available) requires
coinciding availability of an eye (
egcs), verbal (
vgcs) and motor
mgcs) score. In order to match values, a last observation carry forward
imputation scheme over the time span specified by
valid_win is performed.
set_sed_max will assume maximal points for
time steps where the patient is sedated (as indicated by
sed) and passing
set_na_max will assume maximal points for missing values (after
matching and potentially applying
Single urine output events are aggregated into a 24 hour moving window sum.
At default value of
limits = NULL, moving window evaluation begins with
the first and ends with the last available measurement. This can however be
extended by passing an
id_tbl object, such as for example returned by
stay_windows() to full stay windows. In order to provide data earlier
than 24 hours before the evaluation start point,
min_win specifies the
minimally required data window and the evaluation scheme is adjusted for
shorter than 24 hour windows.
Building on concepts for drug administration rate and drug administration
durations, administration events are filtered if they do not fall into
administrations windows of at least 1h. The
max_gap argument can be used
to control how far apart windows can be in order to be merged (negative
times are possible as well, meaning that even overlapping windows can be
considered as individual windows).
ts_tbl depending on the type of concept.
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