Pharmacokinetic and Pharmacodynamic Data Management Functions


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Documentation for package ‘PKPDmisc’ version 2.1.1

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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