Package index

Data I/O

Reading and writing of data

Data input

read_data()

read external data with logging of results

Data output

output_data()

export R data for NONMEM modeling

Other

make_readonly()

Sets the read-only attribute for all files available within a folder

Data manipulation

General data manipulations, calculation of new variables, etc.

wrapper dplyr functions

left_joinr()

Perform a left join of two data frames with logging of results

filterr()

Filter data with logging of results

NONMEM specific functions

time_calc()

Create time variables for usage in NONMEM analyses

Dosing functions

create_addl()

Create ADDL data item and deletes unnecessary amount lines

expand_addl_ii()

Expand rows in case ADDL and II variables are present

fill_dates()

Fills down dates within a data frame that include a start and end date

impute_dose()

Imputes dose records using ADDL and II by looking forward and backwards

Covariate functions

egfr()

Calculates EGFR values based on different types of formulas

weight_height()

Calculates different weight variables

impute_covar()

Imputute missing covariates

num_lump()

Perform lumping of numerical values

flag_outliers()

Creates a flag for outlying values

Meta data

Handle meta data (data attributes)

attr_add()

Add attributes from a list to a dataframe

attr_extract()

Reads in attributes from an external excel file

attr_factor()

Create factors for variables within a data frame using the format attribute

attr_xls()

Reads in attributes from an external excel file

Documentation

Documentation of the data management process

Scripting functions

cmnt()

Add comment to environment to present in documentation

cmnt_print()

Function that prints the comments given by cmnt

get_log()

Retrieve log objects

filterr()

Filter data with logging of results

left_joinr()

Perform a left join of two data frames with logging of results

srce()

Add source information to environment to present in documentation

Tables and data frames

general_tbl()

General table wrapper for documentation functions

counts_df()

Create counts and frequencies within in data frame

stats_df()

Calculate basic statistics on data frame

contents_df()

Create information for multiple data frames

define_tbl()

Create define PDF file for submission of pharmacometric data files

log_df()

Create information for all functions that log actions

check_nmdata()

Checks nonmem dataset for common errors/mistakes

session_tbl()

Create information for R session

Other

plot_vars()

Creates different kind of plots for variables within a dataset using ggplot2

Misceleneous

Helper functions worth to mention

get_script()

Get the current script name (either interactive Rstudio, markdown or batch script)

check_cat()

Create an overview of the available categories