metric.values - required fields (more than described in help)

[leppott]

Describe the bug
The function metric.values doesn't work unless have more fields than specified in help file.

To Reproduce
Steps to reproduce the behavior:

1. Use only the columns specified in the help file as your data input for metric.values.

col.help <- c("SAMPLEID, "TAXAID", "N_TAXA", "EXCLUDE", "SITE_TYPE", "NONTARGET", "PHYLUM", "CLASS", "ORDER", "FAMILY", "SUBFAMILY", "GENUS", "FFG", "HABIT", "LIFE_CYCLE", "TOLVAL", "BCG_ATTR")

2. Will keep getting errors about missing fields until add the following.

col.needed <- c("INDEX_NAME", "SITE_TYPE", "THERMAL_INDICATOR", "SUBPHYLUM", "TRIBE").

Expected behavior
Would be beneficial to:

1. check for all required fields in the function and return an error code if missing.

2. Have all required fields stated in the help file.

Screenshots

Desktop (please complete the following information):

[leppott]

Possible code fix.

• Check for required fields.

• Present to user the missing fields. Ask for user input to continue (Y/N). Warn user of dangers of continuing (i.e., some metric values will be inaccurate, e.g., habit metrics if don't have the habit field).

• If continue add the missing fields with zero or NA values.

[leppott]

col.req <- c("SAMPLEID, "TAXAID", "N_TAXA", "EXCLUDE", "INDEX_NAME", "SITE_TYPE", "NONTARGET", "PHYLUM", "SUBPHYLUM", "CLASS", "ORDER", "FAMILY", "SUBFAMILY", "TRIBE", "GENUS", "FFG", "HABIT", "LIFE_CYCLE", "TOLVAL", "BCG_ATTR", "THERMAL_INDICATOR")

[leppott]

Add QC check for missing fields. Used "utils::menu" to prompt user. Added missing fields if continue but have warning message if continue with missing fields.

Renamed "FAMILY" to "FAMILYY" to showcase error new error checking (screenshots below).

[leppott]

Still have to update Vignette.