Fits Toxicokinetic Models to In Vivo PK Data Sets


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Documentation for package ‘invivoPKfit’ version 2.0.2

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A B C D E F G H I L M N P R S T misc

-- 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
adjust_model_name Sets the 'name' element for models to the 'pk_model' object name in the environment
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_2comp Analytical AUC for the 2-compartment model
auc_flat AUC for flat model
auc_httk_gas_pbtk Calculates AUC for 'httk''s 'gas_pbtk' PBPK 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_group_hierarchy Checking data, error, and summary group hierarchical structure
check_method Check methods
check_model Check models
check_newdata Check new data
check_params_1comp 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_2comp Analytical 2-compartment model
cp_2comp_dt Time derivative of analytical 2-compartment model
cp_flat Flat model
cp_httk_gas_pbtk Calculates plasma concentration for 'httk''s 'gas_pbtk' model
cvt CvTdb data
cvtdb_original SQL query result (current)
cvt_2.0.0 CvTdb data for invivoPKfit 2.0.0 release (old)
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_2comp Fill parameters for 2-compartment model
fill_params_flat Fill parameters for flat model
fit_group Fit a single group of data
fit_sigma.pk Hyperparameter fitting
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_nca_group get_nca_group()
get_nca_group.default Default method for get_nca_group()
get_nca_group.pk Get nca_group
get_params_1comp Get parameters for 1-compartment model
get_params_2comp Get parameters for 2-compartment model
get_params_flat Get parameters to be optimized for flat model
get_params_httk_gas_pbtk Get parameters to fit 'httk''s 'gas_pbtk' PBPK 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_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_2comp Get starting values for 2-compartment model
get_starts_flat Get starting values for flat model
get_starts_httk_gas_pbtk Get starting values for httk 'gas_pbtk' model with specific clearance
get_status Get status
get_status.default Default method for getting status
get_status.pk Check status of a 'pk' object
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_model Checks whether object is of class 'pk_model'
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_2comp 2-compartment model
model_flat Flat model
model_httk_gas_pbtk Gas pbtk 'httk' 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_loq_group Add loq_group
pk_add.pk_nca_group Add a 'pk_nca_group' object.
pk_add.pk_scales Add a 'pk_scales' object to a 'pk' object.
pk_add.pk_sd_group Add sd_group
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.
post_name_value Creates a [cli::cli_fmt()] output for the pattern "name(x), length = "
predict.pk Get predictions
print.pk Print a user-friendly version of a 'pk' object
pseudo_cvt Creating a simple test CvT dataset

-- R --

recalculate_httk_pbtk_params Recalculating parameters for 'httk''s pbtk or gas_pbtk model
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_optimx 'optimx' optimizer settings
settings_preprocess Data preprocessing settings
set_params_optimize Set model parameters to optimize
set_params_starts Set model parameter starts
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_loq_group LOQ Group
stat_model Add PK model(s) to be fitted
stat_nca_group NCA group
stat_sd_group SD Group
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_2comp Toxicokinetic statistics for 1-compartment model
tkstats_flat TK stats for flat model
tkstats_httk_gas_pbtk TK stats for gas_pbtk model fit with inivivoPKfit
toggle_clearance_mode Switch between model parameters to optimize
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