# In Vitro Toxicokinetic Data Processing and Analysis Pipeline

## Documentation for package ‘invitroTKstats’ version 0.0.13

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

.check_all_miss_cols | Check if all the data is missing for specified columns.
.check_char_cols | Check the character columns are correctly of character class.
.check_no_miss_cols | Check there is no missing data for specified columns.
.check_num_cols | Check the numeric columns are correctly of numeric class.
.check_std_colnames_in_data | Check the standard column names are in the data.
build_mydata_clint | Build Data Object for Intrinsic Hepatic Clearance (Clint) Bayesian Model
build_mydata_fup_red | Build Data Object for Fup RED Bayesian Model
build_mydata_fup_uc | Build Data Object for Fup UC Bayesian Model
caco2_cheminfo | Caco-2 Chemical Information Example Data set
caco2_L0 | Caco-2 Level-0 Example Data set
caco2_L1 | Caco-2 Level-1 Example Data set
caco2_L2 | Caco-2 Level-2 Example Data set
caco2_L3 | Caco-2 Level-3 Example Data set
calc_caco2_point | Calculate a Point Estimate of Apparent Membrane Permeability (Papp) from Caco-2 data (Level-3)
calc_clint | Calculate Intrinsic Hepatic Clearance (Clint) with Bayesian Modeling (Level-4)
calc_clint_point | Calculate a Point Estimate of Intrinsic Hepatic Clearance (Clint) (Level-3)
calc_fup_red | Calculate Fraction Unbound in Plasma (Fup) from Rapid Equilibrium Dialysis (RED) Data with Bayesian Modeling (Level-4)
calc_fup_red_point | Calculate Point Estimates of Fraction Unbound in Plasma (Fup) with Rapid Equilibrium Dialysis (RED) Data (Level-3)
calc_fup_uc | Calculate Fraction Unbound in Plasma (Fup) from Ultracentrifugation (UC) Data with Bayesian Modeling (Level-4)
calc_fup_uc_point | Calculate Point Estimates of Fraction Unbound in Plasma (Fup) with Ultracentrifugation (UC) Data (Level-3)
check_catalog | Function to Check Level 0 Data Catalog
clint_cheminfo | Clint Chemical Information Example Data set
clint_L0 | Clint Level-0 Example Data set
clint_L1 | Clint Level-1 Example Data set
clint_L2 | Clint Level-2 Example Data set
clint_L2_heldout | Clint Level-2 Heldout Example Data set
clint_L3 | Clint Level-3 Example Data set
clint_L4 | Clint Level-4 Example Data set
clint_PREJAGS | Clint Level-4 PREJAGS arguments
create_catalog | Function to create a catalog of level 0 files to be merged.
create_chem_table | Creates a Standardized Data Table of Chemical Identities
create_method_table | Creates a Standardized Data Table for Chemical Analysis Methods
extract_level1_fup_uc | Extract level 1 ultracentrifugation (Redgrave et al. 1975) data from wide level 0 file
format_caco2 | Creates a Standardized Data Frame with Caco-2 Data (Level-1)
format_clint | Creates a Standardized Data Frame with Hepatocyte Clearance Data (Level-1)
format_fup_red | Creates a Standardized Data Frame with Rapid Equilibrium Dialysis (RED) Plasma Protein Binding (PPB) Data (Level-1)
format_fup_uc | Creates a Standardized Data Frame with Ultracentrifugation (UC) Plasma Protein Binding (PPB) Data (Level-1)
fup_red_cheminfo | Fup RED Chemical Information Example Data set
fup_red_L0 | Fup RED Level-0 Example Data set
fup_red_L1 | Fup RED Level-1 Example Data set
fup_red_L2 | Fup RED Level-2 Example Data set
fup_red_L2_heldout | Fup RED Level-2 Heldout Example Data set
fup_red_L3 | Fup RED Level-3 Example Data set
fup_red_L4 | Fup RED Level-4 Example Data set
fup_red_PREJAGS | Fup RED Level-4 PREJAGS arguments
fup_uc_cheminfo | Fup UC Chemical Information Example Data set
fup_uc_L0 | Fup UC Level-0 Example Data set
fup_uc_L1 | Fup UC Level-1 Example Data set
fup_uc_L2 | Fup UC Level-2 Example Data set
fup_uc_L2_heldout | Fup UC Level-2 Heldout Example Data set
fup_uc_L3 | Fup UC Level-3 Example Data set
fup_uc_L4 | Fup UC Level-4 Example Data set
fup_uc_PREJAGS | Fup UC Level-4 PREJAGS arguments
Heaviside | Heaviside
initfunction_clint | Set Initial Values for Intrinsic Hepatic Clearance (Clint) Bayesian Model
initfunction_fup_red | Set Initial Values for Fup RED Bayesian Model
initfunction_fup_uc | Set Initial Values for Fup UC Bayesian Model
L1.common.col | Common Columns in Level-1
L1.common.cols | Common Columns in Level-1
merge_level0 | Merge Multiple Level-0 files into a Single Table for Processing
plot_clint | Plot Mass Spectrometry Responses from Measurements of Intrinsic Hepatic Clearance
plot_fup_uc | Plot Mass Spectrometry Responses for Fraction Unbound in Plasma Data from Ultracentrifugation (UC)
round_output | Round Numeric Data (Any Level and Assay)
runjagsdata.to.list | Convert a runjags-class object to a list
sample_verification | Add Sample Verification Column (Level-2)
scientific_10 | Formatting function for X-axis in log10-scale
std.catcols | Standard Data Catalog (Data Guide) Columns
summarize_table | Creates a Summary Table of Mass-Spectrometry (MS) Data