Function reference • champsmortality

Reading and Validating Data

Functions for setting up, reading, and validating the datasets necessary for calculations with this package.

create_dataset_directory(): Create a dataset directory with the shell of a config.yaml file

read_and_validate_data(): Read and validate data files from a specified directory

process_data(): Process a set of CHAMPS data files

Seeing What’s In the Data

Functions for seeing what kind of.

valid_conditions(): Get a list of valid conditions found in the causal chain

valid_maternal_conditions(): Get a list of valid maternal conditions

get_site_info(): Get a list of sites and catchments with data start and end years

Getting Rates and Fractions

Functions for calculating and viewing crude and adjusted rates and fractions.

get_rates_and_fractions(): Get rate and fraction data

batch_rates_and_fractions(): Calculate rates and fraction of an input list of values.

rates_fracs_to_df(): Wrapper for get_rates_and_fractions()

Creating Outputs

Functions to create tables and figures of rate and fraction calculation results.

table_rates_fracs(): Create an overview table of results

table_adjust_decision(): Selected variables decision table

table_factor_sig_stats(): Build pretty table of factor significance and level counts

plot_rates_fracs(): Create a plot of rates or fractions

champs_web_report(): Create html outputs for a given mortality rate/fraction analysis