Package index • nif

All functions

GeomAdmin: GeomAdmin ggproto object
adam(): adam object class constructor
add_administration(): Add administration events
add_ae_observation() experimental: Add AE observation
add_baseline(): Add a baseline covariate
add_bl_crcl(): Add baseline creatinine clearance field.
add_bl_creat(): Add baseline creatinine
add_bl_lbm(): Add baseline lean body mass (LBM)
add_bl_odwg(): Add baseline hepatic function class
add_bl_renal(): Add baseline renal function class
add_cfb() deprecated: Add baseline and change from baseline fields
add_covariate(): Add time-varying covariate
add_dd(): Add Field definition to Data Definition Table
add_dose_level(): Add dose level (DL) column
add_ntile(): Add quantiles for a subject-level covariate
add_obs_per_dosing_interval(): Add the number of observations per dosing interval
add_observation(): Add observation events to nif
add_time_deviation() experimental: Calculate time deviations for observations
add_time_window_flag() experimental: Flag time window violations
add_trtdy(): Add treatment day ('TRTDY') column
administration_summary(): Administration summary
ae_summary(): AE summary
analyte_overview(): Analyte overview
analytes(): Analytes within a NIF or SDTM object
bintime_plot() experimental: BINTIME plot
bsa_dubois(): Body surface area (Du Bois formula)
bsa_mosteller(): Body surface area (Mosteller formula)
cdiscpilot01_nif: Pharmaverse sample nif object
cdiscpilot01_sdtm: Pharmaverse sample SDTM data
check(): Check nif or sdtm object
cmt_mapping() deprecated: Analyte-to-compartment mapping
compartments(): Compartments used in a nif object
correlate_obs() experimental: Correlate observations
covariate_barplot(): Generic covariate barplot
covariate_hist(): Generic covariate distribution histogram
crea_mdrd(): Serum creatinine estimation from eGFR (MDRD)
dataset(): Retrieve dataset from adam object
ddt(): Data definition table for nif object
derive_baseline(): Extract the individual baseline value for an analyte
derive_cfb(): Calculate change from baseline
derive_cfb_analyte(): Derive a new analyte with change from baseline from an existing analyte
derive_rtb(): Calculate ratio to baseline
derive_sld() experimental: Calculate SLD for SDTM.TR domain
disposition_summary(): Subject disposition overview
domain(): Return a specific domain from a sdtm object
domain_model: SDTM Domain Model variables
dose_levels(): Dose levels within a NIF object
dose_lin() experimental: Test for dose linearity
dose_red_sbs(): Subjects with dose reduction
doses(): Doses in a nif or sdtm object
edish_plot(): Drug-induced serious hepatotoxicity (eDISH) plot
egfr_cg(): Glomerular filtration rate estimation from serum creatinine (Cockcroft-Gault)
egfr_mdrd(): Glomerular filtration rate estimation from serum creatinine (MDRD)
egfr_raynaud(): Glomerular filtration rate estimation from serum creatinine (Raynaud method)
examplinib_fe: Synthetic SDTM data from a fictional clinical food effect study for 'examplinib'.
examplinib_fe_nif: Synthetic NIF data from a fictional clinical food effect study for 'examplinib'.
examplinib_iv: Synthetic SDTM data from a fictional clinical iv administraiton study for 'examplinib'.
examplinib_poc: Synthetic SDTM data from a fictional clinical single-arm study with rich and sparse pk sampling.
examplinib_poc_min_nif: Synthetic NIF data from a fictional clinical single-arm study with rich and sparse pk sampling. Reduced to the minimally required fields.
examplinib_poc_nif: Synthetic NIF data from a fictional clinical single-arm study with rich and sparse pk sampling.
examplinib_sad: Synthetic SDTM data from a fictional clinical SAD FIH study with rich PK sampling
examplinib_sad_min_nif: Synthetic NIF data from a fictional clinical SAD FIH study with rich PK sampling. Reduced to the minimally required fields.
examplinib_sad_nif: Synthetic NIF data from a fictional clinical SAD FIH study with rich PK sampling
filter_subject(): Keep only selected USUBJID in the data set
gather_duplicates() experimental: Consolidate multiplicate observations in a nif object
geom_admin(): Administration geom layer for ggplot
hash(): XXH128 hash
import_from_connection(): Import nif object from connection
import_nif(): Import nif file
import_observation() experimental: Add observation from non-SDTM-formatted data table
imputation_rules_1: Alternative imputation rule set 1
imputation_rules_minimal: Minimal imputation rule set
imputation_rules_standard: Standard imputation rule set
imputation_rules_void: Void imputation rule set
imputation_summary(): Summary of imputations in nif object
index_dosing_interval(): Index dosing intervals
index_rich_sampling_intervals(): Identify and index rich PK sampling intervals
last_dtc(): Last recorded date-time
lbm_boer(): Lean body mass (Boer formula)
lbm_hume(): Lean body mass (Hume formula)
lbm_peters(): Lean body mass (Peters formula)
limit(): Subset nif to rows with DTC before the last individual or global observation
make_time(): Calculate time fields based on DTC
max_admin_time(): Maximal administration time
max_observation_time(): Maximal observation time
max_time(): Maximal time in nif object
n_administrations(): Number of administrations per subject
nca() experimental: Non-compartmental analysis of NIF data
nca_from_pp(): Generate NCA table from the SDTM.PP domain
nca_power_model() experimental: Power fit for PK parameters
nca_summary(): PK parameter summary statistics by dose
nca_summary_table(): PK parameter summary statistics table by dose
new_nif() deprecated: nif class constructor
new_sdtm() deprecated: SDTM class constructor, creating a sdtm object from a set of SDTM domains
nif(): nif class constructor
nif_auto() experimental: Auto-generate nif from sdtm object
nif_disclaimer(): Disclaimer statement
nif_option(): Set or get global options
nif_pinboard(): Get or set pinboard path
nif_viewer(): NIF viewer
obs_per_dose_level(): Observations per dose level
pb_list_nif() experimental: List nif objects in pinboard
pb_list_sdtm() experimental: List sdtm objects in pinboard
pb_read_nif() experimental: Read nif object from pinboard
pb_read_sdtm() experimental: Read sdtm object from pinboard
pb_write() experimental: Generic pin_write function
plot(<domain>): Plot domain object
plot(<nif>): Plot NIF object.
plot(<sdtm>): Plot SDTM object
race_coding: Race coding table
read_adam(): Load ADaM data sets from disk
read_sdtm(): Read SDTM data
recode_race(): Recode RACE columns in nif object
rich_sampling_sbs(): Identify subjects with rich sampling
sdtm(): SDTM class constructor
sdtm_missing_times(): Number of DTC entries with missing time information
standardize_date_format(): Convert date fields to POSIX format
stat_admin(): ggplot stat for treatment administrations
studies(): Studies within a nif object
subject_info(): Baseline details for specific subjects
subjects(): Unique subjects within a data set
subs_per_dose_level(): Subjects per dose level
suggest(): Suggest data programming steps to generate a nif object from an sdtm object
summary(<adam>): Summary method for adam objects
testcd(): Extract TESTCD fields by domain from a sdtm object
treatments(): Treatments in a nif or sdtm object
trial_dco(): Cut-off date
trial_title(): Trial title
usubjid(): Get the USUBJID of subject
watermark(): Add a watermark annotation layer for a ggplot2 object
write_monolix(): Write as comma-separated file, complying with the format used by Monolix
write_nonmem(): Write NONMEM input formatted nif object to file