# Pharmacokinetic and Pharmacodynamic Data Management Functions

## Documentation for package ‘PKPDmisc’ version 2.1.1

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

## Help Pages

as_numeric | convert to numeric passing through character for safety
auc_inf | Calculate AUCt-inf
auc_partial | Calculate partial AUC
auc_partial_cpp | calculate partial AUC
basename_sans_ext | get the basename of a filepath, minus any extensions
base_theme | A theme with better default values for pharmacometric plots, especially conc-time
bring_to_front | bring select columns to the front of a dataframe
calculate_wam | internal WAM function
capitalize_names | capitalize all names for a dataframe
capture_groups | wrapper to capture groups from a grouped data frame
char_to_numeric | convert all columns to numeric
chunk | split IDs into groups to use for subsequent plotting
chunk_df | chunk dataframes so easy to split for parallel processing
chunk_grp | split IDs into groups to use for subsequent plotting
chunk_grp_list | split IDs into groups to use for subsequent plotting
chunk_list | split IDs into groups to use for subsequent plotting
color_pallete | design-quality color palletes to use in ggplot2
cols_to_factor | convert column to type factor
cols_to_numeric | convert column to type numeric
cor_to_cov | correlation to covariance matrix
cov_to_cor | covariance to correlation
dapa_IV_oral | IV and oral pharmacokinetic data for daptomycin
file_rows | count number of rows in a file without needing to read file into R
fill_backward | given NA values fill them with the next non-na value
fill_forward | given NA values fill them with the final non-na value
has_ext | check for if the passed name has a file extension
ids_per_plot | split IDs into groups to use for subsequent plotting
is_dir | detect if a filepath is for a directory
jprint | print multiple values joined together
lowercase_names | lowercase all names for a dataframe
max_through | give the max value up to that point
min_through | give the min value up to that point
NCA | calculate basic NCA parameters t1/2 Cl, Cmax etc
nca | calculate basic NCA parameters t1/2 Cl, Cmax etc
new_report | a better new rmd template for reports
nm_description | show description output from .mod file
nm_notes | show notes output from .mod file
nonmem_report | create basic folder structure for a nonmem report
ordinal_to_binary_ | convert a column of categorical covariates into a number of columns with a binary flag for each category
pad_left | add left padding to a vector of values
peek | peek at the results in a dplyr pipeline
phx_report | create basic folder structure for a phoenix report
print_plots | create a list of plots cleanly with extra pdf functionality
read_nonmem | read nonmem files easily
read_phx | to more easily read data with a 2nd row with units common to phx data
rename_table_pattern | simple table name replacement for a given pattern
replace_dots | Convert '.' values into missing values.
replace_empty | Convert empty strings into missing values.
replace_from_template | replace values from a template file
replace_list_elements | replace list elements by name
replace_values | replace symbols or other character flags
resample_df | resampling
rf51_factory | factory to create read fort51 file
round_columns | round columns
sd_oral_richpk | One-compartment pharmacokinetic data given single oral dose
set_bins | given a set of bin ranges, assign each value to a bin
set_bins_cpp | given a set of bin ranges, assign each value to a bin
set_bins_df | given a set of bin ranges, assign each value to a bin and provide the label
set_groups | set groups
strip_attributes | strip additional attributes that make dplyr fail
strip_curves | basic curve stripping to get initial estimates
s_pauc | summarize paucs
s_pauc_ | summarize paucs
s_quantiles | summarize quantiles for a column
s_quantiles_ | summarize quantiles for a column
unique_non_numerics | find all unique non-numeric values
view_creator | create view commands that save rds files to where a shiny app is listening for them
wam | wam function
write_nonmem | easily write a csv file compatible with nonmem