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hurlbertlab / dietdatabase

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clean_all_names() error #83

Closed pwinner1 closed 6 years ago

pwinner1 commented 6 years ago

When I use clean_all_names, this error appears

clean = clean_all_names(dietdb)

[1] "1 out of 1"

Retrieving data for taxon 'Heteroptera'

Error in $<-.data.frame(*tmp*, "Prey_Name_Status", value = c(NA, NA, : replacement has 178 rows, data has 180

  1. stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), N, nrows), domain = NA)

  2. $<-.data.frame(*tmp*, "Prey_Name_Status", value = c(NA, NA, NA, NA, NA, NA, NA, "103358", NA, NA, NA, NA, NA, NA, NA, NA, NA, "103358", NA, NA, NA, NA, NA, NA, NA, NA, NA, "103358", NA, NA, NA, NA, NA, NA, NA, NA, NA, "103358", NA, NA, NA, NA, NA, ... at prey_name_cleaning.R#168

  3. $<-(*tmp*, "Prey_Name_Status", value = c(NA, NA, NA, NA, NA, NA, NA, "103358", NA, NA, NA, NA, NA, NA, NA, NA, NA, "103358", NA, NA, NA, NA, NA, NA, NA, NA, NA, "103358", NA, NA, NA, NA, NA, NA, NA, NA, NA, "103358", NA, NA, NA, NA, NA, NA, NA, NA, ... at prey_name_cleaning.R#168

  4. clean_names("Suborder", clean_fam$diet, all = TRUE, problemNames = clean_fam$badnames) at database_error_checking.R#323

  5. clean_all_names(dietdb)

ahhurlbert commented 6 years ago

This was occurring because there was a reference to "Prey_Name_Status" field which no longer exists. All code now references the "Prey_Name_ITIS_ID" field instead.

I also made sure the problematic names were propagating properly (say that 3 times fast).

The clean_all_names function should work now on the Cooper_1993 datafile.