Observations can be pharmacokinetic observations (i.e., from the PC domain), or any other class of observation from any other SDTM domain. The 'testcd' specifies the value of the respective TESTCD field (e.g., 'PCTESTCD', 'VSTESTCD' or 'LBTESTCD') that defines the observation. Observation events can be attached to an administered drug by specifying the 'parent' field. This is required for, e.g., the time-after-dose ('TAD') and time-after-first-dose ('TAFD') time calculation.
Usage
add_observation(
nif,
sdtm,
domain,
testcd,
analyte = NULL,
parent = NULL,
metabolite = FALSE,
cmt = NULL,
subject_filter = "!ACTARMCD %in% c('SCRNFAIL', 'NOTTRT')",
observation_filter = "TRUE",
TESTCD_field = NULL,
DTC_field = NULL,
DV_field = NULL,
coding_table = NULL,
factor = 1,
NTIME_lookup = NULL,
ntime_method = NULL,
keep = NULL,
debug = FALSE,
include_day_in_ntime = FALSE,
silent = NULL,
duplicates = "stop",
duplicate_function = mean,
na.rm = TRUE
)Arguments
- nif
A nif object.
- sdtm
A sdtm object. Needs at least the 'DM' and 'VS' domains, and the domain the observations come from.
- domain
The domain as character.
- testcd
The observation variable, as character.
- analyte
The name for the analyte. Defaults to the 'testcd', if NULL.
- parent
The name of the parent analyte for the observation as character. Defaults to the value of 'analyte' if NULL.
- metabolite
Observation is a metabolite, as logical.
- cmt
The compartment for the observation as numeric.
- subject_filter
The filtering to apply to the DM domain.
- observation_filter
The filtering to apply to the observation source data.
- TESTCD_field
The xxTESTCD field. Defaults to the two-character domain name followed by 'TESTCD', if NULL.
- DTC_field
The field to use as the date-time code for the observation. Defaults to the two-character domain name followed by 'DTC', if NULL.
- DV_field
the field to use as the dependent variable. Defaults to the two-character domain name followed by 'STRESN', if NULL.
- coding_table
Coding table to translate a categorical values into numerical values, as data frame. The data frame must have at least one column that matches a column in the domain, and a numerical 'DV' column that provides the recoding result.
- factor
Multiplier for the DV field, as numeric.
- NTIME_lookup
A data frame with two columns, a column that defines the custom nominal time information in the target domain (e.g., 'PCELTM'), and 'NTIME'. This data frame is left_joined into the observation data frame to provide the NTIME field.
- ntime_method
the field to derive the nominal time from. Allowed values are "TPT" and "ELTM".Defaults to xxTPT where xx is the domain name, if NULL.
- keep
Columns to keep, as character.
- debug
Include debug fields, as logical.
- include_day_in_ntime
as logical.
- silent
Suppress messages, as logical. Defaults to nif_option setting if NULL.
- duplicates
Selection how to deal with duplicate observations with respect to the USUBJID, ANALYTE and DTC fields:
'stop': Stop execution and produce error message
'ignore': Include duplicates in the data set
'identify': Return a list of duplicate entries
'resolve': Resolve duplicates, applying the
duplicate_functionto the duplicate entries.
- duplicate_function
Function to resolve duplicate values, defaults to
mean.- na.rm
Logical indicating whether to remove NA values when applying the duplicate_function. Defaults to TRUE.
Details
Observations can be further specified with the 'observation_filter' term. The filter term can refer to any field of the respective SDTM domain.
A PK/PD model compartment can be specified with 'cmt' or will be
automatically assigned if cmt = NULL.