As HEC-EFM considers ecosystem dynamics according to the percentage of years or percentage of time that a flow or ecological event occurs, no conceptual reason compels an analysis to be stopped due to missing data within a flow regime. Via the “Edit” menu, the software offers a check option entitled “Handle Missing Data”, which instructs HEC-EFM to work around any missing data, and a menu option called “Missing Data Identifiers…”, which opens an interface where users can specify the numeric values to be treated as missing data (Figure 19). Blanks and non-numbers are automatically identified as missing values.

Figure 19. The Missing Data Identifiers interface is used to specify values to be treated as missing.
When the “Handle Missing Data” option is active and missing data are encountered, the software simply omits the water year with missing data from the relationship’s calculations. The number of valid years (i.e., years that have all required data) associated with rankings, frequencies, and plotting positions are adjusted accordingly. As season is set for each relationship, each flow regime is screened for missing data for each relationship.
HEC-EFM also generates a report that lists water years omitted due to missing data. To view the report, use the "File – Data Summary" menu option (Figure 20).

Figure 20. Excerpt from Data Summary report, which details periods of record, water year range, missing data, and number of valid years for each pairing of flow regime and relationship analyzed.