Fits Toxicokinetic Models to In Vivo PK Data Sets

Documentation for package ‘invivoPKfit’ version 2.0.0

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-- A --

AAFE	AAFE()
AAFE.default	Default method for AAFE()
AAFE.pk	Calculate absolute average fold error (AAFE)
add_pk	Add various 'pkproto' objects to a 'pk' object
AFE	AFE()
AFE.default	Default method for AFE()
AFE.pk	Calculate average fold error
AIC.pk	Akaike information criterion
auc_1comp	Analytic AUC for 1-compartment model
auc_1comp_cl	Analytic AUC for 1-compartment model with specific clearance
auc_2comp	Analytical AUC for the 2-compartment model
auc_flat	AUC for flat model
auto_units	Automatically select new time units

-- B --

BIC.pk

Bayesian information criterion

-- C --

calc_hessian	Calculate Hessian
calc_nca	Non-compartmental analysis
calc_rmse	Calculate RMSE (root mean squared error)
calc_rsq	Calculate r-squared for observed vs. predicted values
calc_sds_alerts	Calculate parameter SDs
check_method	Check methods
check_model	Check models
check_newdata	Check new data
check_params_1comp	Check 1-compartment model parameters
check_params_1comp_cl	Check 1-compartment model parameters
check_params_2comp	Check 2-compartment model parameters
check_params_flat	Check flat model parameters
check_required_status	Check required status
check_required_status.default	Default method for checking required status
check_required_status.pk	Check required status
coef.pk	Get coefficients
coef_sd	Coefficient standard deviations
coef_sd.default	Coefficient standard deviation default
coef_sd.pk	Get coefficient standard deviations
combined_sd	Combined standard deviation
compare_models	Model comparison
compare_models.default	Default method for compare_models()
compare_models.pk	Model comparison for [pk()] objects
conc_scale_use	Get concentration scalings
convert_summary_to_log10	Convert sample mean and SD to log10-scale
convert_time	Helper function to convert time units
cp_1comp	Analytical 1-compartment model
cp_1comp_cl	Analytical 1-compartment model with specific clearance
cp_2comp	Analytical 2-compartment model
cp_2comp_dt	Time derivative of analytical 2-compartment model
cp_flat	Flat model
cvt	CvTdb data
cvt_date	CvTdb download date

-- D --

data_summary	data_summary()
data_summary.default	Default method for data_summary()
data_summary.pk	Data summary for a 'pk' object
dlnorm_summary	Log-normal distribution density function for summary data
dnorm_summary	Normal distribution density function for summary data
do_data_info	do_data_info generic
do_data_info.default	do_data_info default method
do_data_info.pk	calculate summary data info
do_fit	Fitting
do_fit.default	do_fit default method
do_fit.pk	Do fitting
do_prefit	Prefitting
do_prefit.default	do_prefit default method
do_prefit.pk	Do pre-fitting
do_preprocess	Preprocess data generic
do_preprocess.default	do_preprocess default method
do_preprocess.pk	Do pre-processing

-- E --

eval_tkstats	eval_tkstats()
eval_tkstats.default	Default method for eval_tkstats()
eval_tkstats.pk	Evaluate TK statistics

-- F --

facet_data	Facet a PK fit
fill_params_1comp	Fill parameters for 1-compartment model
fill_params_1comp_cl	Fill parameters for 1-compartment model with specific clearance
fill_params_2comp	Fill parameters for 2-compartment model
fill_params_flat	Fill parameters for flat model
fit_group	Fit a single group of data
fold_error	Fold error
fold_error.default	fold_error default method
fold_error.pk	Fold errors

-- G --

get_data	get_data()
get_data.default	Default method for get_data()
get_data.pk	Get data
get_data_group	get_data_group()
get_data_group.default	Default method for get_data_group()
get_data_group.pk	Get data grouping
get_data_info	get_data_info()
get_data_info.default	Default method for get_data_info()
get_data_info.pk	Get data_info
get_data_original	get_data_original()
get_data_original.default	Default method for get_data_original()
get_data_original.pk	Get data_original
get_data_sigma_group	get_data_sigma_group()
get_data_sigma_group.default	Default method for get_data_sigma_group()
get_data_sigma_group.pk	Get data_sigma_group
get_data_summary	get_data_summary()
get_data_summary.default	Default method for get_data_summary()
get_elbow	Get an elbow point
get_error_group	get_error_group()
get_error_group.default	Default method for get_error_group()
get_error_group.pk	Get error group
get_fit	get_fit()
get_fit.default	Default method for get_fit()
get_fit.pk	Get fits from a 'pk' object
get_hessian	get_hessian()
get_hessian.default	Default method for get_hessian()
get_hessian.pk	Get Hessian matrixes
get_mapping	get_mapping()
get_mapping.default	Default method for get_mapping()
get_mapping.pk	Get mapping
get_nca	get_nca()
get_nca.default	Default method for get_nca()
get_nca.pk	Get NCA
get_params_1comp	Get parameters for 1-compartment model
get_params_1comp_cl	Get parameters for 1-compartment model with clearance assumption
get_params_1comp_fup	Get parameters for 1-compartment model with clearance assumption
get_params_2comp	Get parameters for 2-compartment model
get_params_flat	Get parameters to be optimized for flat model
get_peak	Find the peak of a data series
get_prefit	get_prefit()
get_prefit.default	Default method for get_prefit()
get_prefit.pk	Get prefit
get_scale_conc	get_scale_conc()
get_scale_conc.default	Default method for get_scale_conc()
get_scale_conc.pk	Get scale_conc
get_scale_time	get_scale_time()
get_scale_time.default	Default method for get_scale_time()
get_scale_time.pk	Get scale_time
get_settings_data_info	get_settings_data_info()
get_settings_data_info.default	Default method for get_settings_data_info()
get_settings_data_info.pk	Get settings_data_info
get_settings_optimx	get_settings_optimx()
get_settings_optimx.default	Default method for get_settings_optimx()
get_settings_optimx.pk	Get settings_optimx
get_settings_preprocess	get_settings_preprocess()
get_settings_preprocess.default	Default method for get_settings_preprocess()
get_settings_preprocess.pk	Get settings_preprocess
get_starts_1comp	Get starting values for 1-compartment model
get_starts_1comp_cl	Get starting values for 1-compartment model with specific clearance
get_starts_1comp_fup	Get starting values for 1-compartment model with specific clearance
get_starts_2comp	Get starting values for 2-compartment model
get_starts_flat	Get starting values for flat model
get_status	Get status
get_status.default	Default method for getting status
get_status.pk	Check status of a 'pk' object
get_stat_error_model	get_stat_error_model()
get_stat_error_model.default	Default method for get_stat_error_model()
get_stat_error_model.pk	Get stat_error_model
get_stat_model	get_stat_model()
get_stat_model.default	Default method for get_stat_model()
get_stat_model.pk	Get stat_model
get_tkstats	Get TK stats
get_tkstats.default	Default method for get_tkstats()
get_tkstats.pk	Get TK stats
get_winning_model	get_winning_model()
get_winning_model.default	Default method for get_winning_model()
get_winning_model.pk	Get winning model

-- H --

hess_sd1	Inverse diagonal, method 1
hess_sd2	Inverse diagonal, method 2

-- I --

ignore_unused_imports	Ignore unused imports
is.pk	Check whether an object is of class 'pk'
is.pkproto	Is an object pkproto?
is.pk_faceted	Check whether an object is of class 'pk_faceted'
is.pk_scales	Is an object class 'pk_scales'?

-- L --

logLik.pk	Log-likelihood
log_likelihood	Log-likelihood

-- M --

mapping	New mapping
midpt_log10	Log10-scaled midpoint
model_1comp	1-compartment model
model_1comp_cl_nonrest	1-compartment model that assumes non-restrictive clearance
model_1comp_cl_rest	1-compartment model that assumes restrictive clearance
model_1comp_fup	1-compartment model that assumes restrictive clearance optimizes Fup
model_2comp	2-compartment model
model_flat	Flat model

-- N --

nca	nca()
nca.default	Default method for nca()
nca.pk	NCA for a 'pk' object

-- P --

pk	Create a new 'pk' object
pkdataset_nheerlcleaned	Toxicokinetic data from the "Concentration vs. Time Database"
pk_add	Add a 'pkproto' object to a 'pk' object
pk_add.default	Add pkproto object default method
pk_add.pk_facet_data	Add facet_data()
pk_add.pk_scales	Add a 'pk_scales' object to a 'pk' object.
pk_add.pk_settings_data_info	Add a 'pk_settings_data_info' object.
pk_add.pk_settings_optimx	Add a 'pk_settings_optimx' object.
pk_add.pk_settings_preprocess	Add a 'pk_settings_preprocess' object.
pk_add.pk_stat_error_model	Add a 'pk_stat_error_model' object.
pk_add.pk_stat_model	Add a 'pk_stat_model' object.
pk_add.uneval	Add an 'uneval' object
pk_model	Create a new 'pk_model' object
pk_subtract	Subtract a 'pkproto' object from a 'pk' object
pk_subtract.default	Subtract pkproto object default method
pk_subtract.pk_stat_model	Subtract a 'pk_stat_model' object.
plot.pk	Plot a [pk()] object.
predict.pk	Get predictions
print.pk	Print a user-friendly version of a 'pk' object

-- R --

rename2_cvt	Convert invivoPKfit output table names to the CvTdb names
residuals.pk	Get residuals
rmse	Root mean squared error (RMSE)
rmse.default	Root mean squared error (RMSE) default method
rmse.pk	Root mean squared error
rowwise_calc_percentages	Helper function for calculating percentages of count data, by row
rsq	rsq()
rsq.default	Default method for rsq()
rsq.pk	Calculate R-squared for observed vs. predicted values

-- S --

scale_conc	Scale concentrations
scale_time	Scale times
settings_data_info	Data info settings
settings_optimx	'optimx' optimizer settings
settings_preprocess	Data preprocessing settings
status_data_info	Status ID for data summary info
status_fit	Status ID for fitting
status_init	Status ID for initialization
status_prefit	Status ID for pre-fitting
status_preprocess	Status ID for preprocessing
stat_error_model	Error model
stat_model	Add PK model(s) to be fitted
subtract_pk	Subtract various 'pkproto' objects from a 'pk' object
summary.pk	Print summary of a 'pk' object

-- T --

time_conversions	Time conversion table
time_units	Allowable time units
tkstats_1comp	Toxicokinetic statistics for 1-compartment model
tkstats_1comp_cl	Toxicokinetic statistics for 1-compartment model with specific clearance
tkstats_2comp	Toxicokinetic statistics for 1-compartment model
tkstats_flat	TK stats for flat model
transformed_params_2comp	Transformed parameters for 2-compartment model
twofold_test	twofold_test()
twofold_test.default	Default method for twofold_test()
twofold_test.pk	Evaluate whether data and predictions are within two-fold of mean or concentration, respectively

-- misc --

+.pk	Add a 'pkproto' object to a 'pk' object
-.pk	Subtract a pkproto object from a pk object