inputs/GBIF/raw_occurrence_record/: renamed to raw_occurrence_record_plants because it's actually only the plants in raw_occurrence_record, not all of raw_occurrence_record. also, this will allow us to create a separate raw_occurrence_record_plants view whose name matches the folder and does not collide with the raw_occurrence_record table.

inputs/GBIF/raw_occurrence_record/run: herbaria_filter/make(): added runtime, which is ~0 since it just needs to do CSV import and index scans

inputs/GBIF/raw_occurrence_record/run: herbaria_filter/make(): time the population of herbaria_filter

inputs/GBIF/raw_occurrence_record/run: plant_fraction/make(): updated runtime. added rows affected count to runtime so if the number of rows it's related to (in this case, institution_code) changes, the runtime can be expected to change accordingly.

inputs/.TNRS/schema.sql: tnrs_populate_fields(): documented runtime (17 min)

bugfix: inputs/GBIF/raw_occurrence_record/run: plant_fraction/make(): plant_fraction column: COUNT counts non-NULL rather than true values (which counter-intuitively includes false, because it's non-NULL), so need to add NULLIF around the boolean expression to turn it into a NULL-or-not expression. see http://vegpath.org/wiki/2013-06-06_conference_call#GBIF-subsetting-fix-plant_fraction-SQL-bug .

inputs/.TNRS/schema.sql: tnrs_populate_fields(): documented that when changing this function, you must regenerate the derived cols using `UPDATE tnrs SET "Name_submitted" = "Name_submitted"`

inputs/.TNRS/schema.sql: tnrs_populate_fields(): Is_plant: must match family as Family_score = 1 (as discussed during conference call vegpath.org/wiki/2013-05-30_conference_call#postprocess-TNRS-results-to-exclude-animals-with-genus-homonyms) instead of as Family_matched IS NOT NULL (as listed in Brad's formula at vegpath.org/wiki/Result_filtering#TNRS-results) because TNRS transforms animal to plant families via fuzzy matching, necessitating a Family_score check to ensure an exact match to a plant family that was not transformed from an animal family

inputs/.TNRS/schema.sql: added Is_plant derived field, which is populated using the formula at vegpath.org/wiki/Result_filtering#TNRS-results . note that the homonym filtering is currently excluded until we determine whether we can get direct access to the IRMNG homonyms database (http://www.cmar.csiro.au/datacentre/irmng/homonyms.htm). note also that changes to the TNRS schema cannot be fully tested until any TNRS client bugs are fixed, because the data.sql updater requires a working TNRS client to regenerate the sample data.

inputs/.TNRS/schema.sql: updated for current TSV schema: renamed Accepted_species->Accepted_name_species, Accepted_family->Accepted_name_family