check_ordered: checks if states within data frame are ordered as inputted...

In skgallagher/EpiCompare: A Pipeline to Analyze and Compare Infectious Disease Epidemics

Description

This function assesses whether agents's time they enter each state is correctly ordered. The assumption is that these would be ordered in increasing values, with the allowance of NA values not effecting this decision.

Usage

check_ordered(df, states, assert_error = TRUE)

Arguments

df	data frame with individual agent information (n x p)
states	time entered state, in expected order
assert_error	boolean if we should raise error if ordering assumption is violated.

Details

If this important assumption is violated this function either raises an error or provides the user with information on what when wrong - to allow the user to how to corect the error (see assert_error to change between these states).

Value

This function returns either

• TRUE, if the states are ordered,

• an error is observed (when assert_error = TRUE), or

• a list of 2 data frames. The first, ordering_df, an (n x 3) data.frame, contains information per agent on if they violated the assumption ("error" column), and the ordering of their states ("ordering" column). The second, summary_df (k x 3) data frame contains information on the number of unique ordering ("ordering"), if they caused the assumption to be violated ("error") and the number of agents that had the ordering ("count"). Note that if an individual has NA for every states' time, then they have a NA in their "error" column (this is not the cause of the erroring).

Examples

df_not_ordered <- data.frame(group1 = 1:5,
                             group2 = c(2:5,1))
output <- check_ordered(df_not_ordered, c("group1", "group2"),
                        assert_error = FALSE)
output

skgallagher/EpiCompare documentation built on Sept. 14, 2021, 5:45 a.m.