A B C D E F G H I L M N P R S T misc
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 |
BIC.pk | Bayesian information criterion |
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 |
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 |
eval_tkstats | eval_tkstats() |
eval_tkstats.default | Default method for eval_tkstats() |
eval_tkstats.pk | Evaluate TK statistics |
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 |
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 |
hess_sd1 | Inverse diagonal, method 1 |
hess_sd2 | Inverse diagonal, method 2 |
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'? |
logLik.pk | Log-likelihood |
log_likelihood | Log-likelihood |
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 |
nca | nca() |
nca.default | Default method for nca() |
nca.pk | NCA for a 'pk' object |
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 |
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 |
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 |
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 |
+.pk | Add a 'pkproto' object to a 'pk' object |
-.pk | Subtract a pkproto object from a pk object |