Plot metadata
The following fields are downloaded when you select “download plot metadata”. These fields contain information pertaining to entire plots, such as locality, climate, soil, and methodology. Please pay particular attention to the field observation_type: values in this field affect intepretation of fields downloaded as plot data (from the PlotObservations table). See discussion below. Values from this table can be linked to the plot data (see next table) either using PLOT_ID or plot_code. PLOT_ID is preferable, however, as plot_code may repeat among different projects.
| Field_name |
Data_type |
Value_list |
Can be null? |
Standardized_by_SALVIAS? |
Comments |
| PLOT_ID |
Integer |
Autoincrement |
No | Added by database |
Primary key; unique number for each plot |
| plot_code |
Text |
No |
Yes (original codes supplied by user may be modified to avoid naming conflicts with other data sets) |
Short code for plot; combination of project+plot_code is unique, but plot_code may repeat among different projects |
|
| major_geo |
Text |
Closed pick list (see Comments) |
No |
Yes |
Values as follows: “South America”, “Europe”, “Africa”,
“Trop.Asia, Oceania”, “North America”, “Central America” (includes Mexico),
“Caribbean”, “Temperate Asia”. Based on values in Missouri Botanical Garden
version of the “Alwyn Gentry 0.1 ha Transect Dataset” |
| country |
Text |
Closed pick list |
No |
Yes |
Modified to correspond to names in SALVIAS lookup tables |
| pol1 |
Text |
Yes |
No |
Next political division below country; i.e., state,
province, or department. As provided by original data provider, but may be
modified to correspond to names in SALVIAS lookup tables |
|
| pol2 |
Text |
Yes |
No |
Next political division below pol1, i.e., county,
district, municipio, depending on country. As provided by original data provider,
but may be modified to correspond to names in SALVIAS lookup tables |
|
| locality_description |
Text |
Yes |
No |
Detailed description of locality |
|
| lat_decimal |
Decimal |
Yes |
Yes |
Latitude, in decimal degrees; may be parsed and converted if original value is text field and/or in different units |
|
| long_decimal |
Decimal |
Yes |
Yes |
Longitude, in decimal degrees; conversions as for lat_decimal |
|
| elev_m |
Decimal |
Yes |
Yes |
Elevation in meters; this and following two fields
are parsed and converted if original data is text field, range, and/or non-metric |
|
| elev_max_m |
Decimal |
Yes |
Yes |
Maximum elevation in meters, if a range |
|
| elev_min_m |
Decimal |
Yes |
Yes |
Minimum elevation in meters, if a range |
|
| temp_c |
Decimal |
Yes |
No |
Mean annual temperature, in centrigrade |
|
| precip_mm |
Decimal |
Yes |
No |
Total annual precipitation, in mm |
|
| slope_aspect |
Decimal |
Yes |
No |
Aspect (compass direction) of slope, in degrees |
|
| slope_gradient |
Decimal |
Yes |
No |
Steepness of slope, in degrees |
|
| clay_percent |
Decimal |
Yes |
No |
||
| silt_percent |
Decimal |
Yes |
No |
||
| sand_percent |
Decimal |
Yes |
No |
||
| soil_pH |
Decimal |
Yes |
No |
||
| holdridge_life_zone |
Text |
Closed pick list |
Yes |
Yes |
Long description of classification within Holdridge Life Zone system |
| life_zone_code |
Text |
Closed pick list |
Yes |
Yes |
Short code for Holdridge Life Zone |
| observation_type |
Text |
Closed pick list: “individuals”; “species (individuals)”; “species (stems)” ; “species (percent cover)”; “species (line_intercept)”; “species (presence)” |
Yes |
Yes |
Important! The value in this field affects interpretation
of other fields in the plot data. Values as follows: “individuals”: all records
in plot data with same OBSERVATION_ID correspond to a single individual;
“species (individuals)”: all values in plot data with same OBSERVATION_ID
represent a record of a single species, with total numbers of individuals
recorded in the no_of_individuals field; “species (stems)”: as with
preceding, but may have one or more stem values for each species records,
and stems do not map onto specific individuals (this format is unique to
the Gentry transect dataset); “species (percent cover)”: all values in plot
data with same OBSERVATION_ID represent a record of a single species, with
proportional coverage of plot area recorded in the cover_percent field; “species
(line_intercept)”: all values in plot data with same OBSERVATION_ID represent
a record of a single species, with linear coverage along a center transect
line in cm recorded in the field intercept_cm. “species (presence)”:
all values in plot data with same OBSERVATION_ID represent a record of a
single species, with no abundance data provided. |
| plot_methodology |
Text |
Open pick list |
Yes |
Partially; user may select from list of standard descriptions, or supply new |
“free form” summary of several aspects of methodology;
typically a combined description of plot area, plot dimensions, size cufoff
(if any), growth forms included or omitted, |
| plot_area_ha |
Decimal |
Yes |
Yes |
Will be NULL if sampling method is dimension less or linear |
|
| recensused |
Text |
“Yes”, “No” |
Yes |
Yes |
If yes, then multiple censuses are available in plot data |
| date_start |
Text |
Yes |
No
|
||
| date_finish |
Text |
Yes |
No |
Plot data
Below are the fields downloaded when you select “download plot data”. The downloaded table is a single flat file derived principally from two source tables: PlotObservations (containing either species- or individual-level observations, depending on the observation_type; see Plot metadata for more details), and Stems, containing stem-level attributes. The downloaded table is thus in one-observation-per-stem format. PlotObservations is linked one-to-many with the Stems table; thus values from field in the PlotObservations table will repeat if more than one record in exists in the Stems table for a given observation in the PlotObservations table. Use OBSERVATION_ID field to group stem values for individuals. In interpreting taxonomy, please pay careful attention to the species_name_status field.
| Field name |
Data type |
Value list |
Can be null? |
Standardized by SALVIAS? |
Comments |
| OBSERVATION_ID |
Integer |
Autoincrement |
No |
Added by database |
Primary
key for main raw data table (PlotObservations); IMPORTANT: stem measurement
are stored in a separate table linked many-to-one with the PlotObservations
table; thus, OBSERVATION_ID will repeat if multiple stem values exist for
a given individual. |
| PLOT_ID |
Integer |
No |
see PlotMetadata table, above |
Foreign key, links to PlotMetadata table (table containing plot descriptions); unique number for each plot |
|
| plot_code |
Text |
see PlotMetadata table, above |
Short
code for plot; combination of project+plot_code is unique, but plot_code
may repeat among different projects. May function as foreign key, but
PLOT_ID is safest. |
||
| census_no |
Integer |
Yes |
Yes |
1
is default; most plots are not recensused. Different censuses for same plot
can be distinguished by unique combination of plot_code + census_no |
|
| census_date |
Text |
Yes |
No |
Date of census, if provided |
|
| subplot |
Text |
Yes |
No |
Code for subplot, line, or any other subsample or subdivision of plot |
|
| individual_code |
Text |
Yes |
No |
Any code for individual, other than tag numbers (see tag1 and tag2, below) provided in original data. |
|
| ind_id |
Text |
Yes |
Yes, if not supplied with original data for plots with observation_type = individuals |
If
observation_type=individuals (see data dictionary for PlotMetadata) this
value uniquely identifies each individual. Different records with same
value of ind_id are separate stems for same individual. If not supplied
with original data, this field will be added by SALVIAS upon import to database.
|
|
| tag1 |
Text |
Yes |
No |
Original tree tag number |
|
| tag2 |
Text |
Yes |
No |
Most recent tree tag number; if this value is not null, indicates original tag was lost; |
|
| x_position |
Decimal |
Yes |
No |
x coordinate in meters |
|
| y_position |
Decimal |
Yes |
No |
y coordinate in meters |
|
| voucher_string |
Text |
Yes |
No |
Text string for collector name and collector number of voucher specimen, if any, exactly as supplied in source data |
|
| coll_number |
Text |
Yes |
Yes. |
Collection number as parsed by SALVIAS from voucher_string |
|
| collector_code |
Text |
Yes |
Yes. |
Unique
short code for collector, assigned by SALVIAS. (this field may not be populated
for all datasets, if original data provider did not provide “key” to abbreviations
in original voucher_string) |
|
| coll_lastname |
Text |
Yes |
Yes. |
Collector’s
last name (or names) as parsed by SALVIAS from voucher_string. Or will
be same as original if already stored separately in source database. (this
field may not be populated for all datasets, if original data provider did
not provide “key” to abbreviations in original voucher_string) |
|
| coll_firstname |
Text |
Open pick list |
Yes |
Yes |
Senior
collector’s first name, as parsed by SALVIAS (this field may not be populated
for all datasets, if original data provider did not provide “key” to abbreviations
in original voucher_string) |
| det_type |
Text |
Closed pick list: “direct”, “indirect”, “unvouchered”, “default” |
Yes |
Yes |
Important!
States how reference specimen has been associated with this individual.
Permits each record to be associated with a specimen voucher, and determinations
to be updated automatically via herbarium specimens. “direct” = specimen is collection of this individual; “indirect” = individual was referenced by data provider to specific collection of a different individual; “default” = individual is connected by shared morphospecies name to voucher specimen of a different individual; “unvouchered” = no specimen vouchers (direct or otherwise) for this individual; species was never collected, and determination is presented as-is. |
| fam_status |
Integer |
Closed list: 0, 1 |
No |
Yes |
Status of family. 0 = “non-standard”; does not match any family in TROPICOS or IPNI
databases.
1 = “standard”; matches to family in TROPICOS and/or IPNI. |
| gen_status |
Integer |
Closed list: 0, 1 |
No |
Yes |
Status of genus. 0 = “non-standard”; does not match any genus in TROPICOS or IPNI
databases.
1 = “standard”; matches to genus in TROPICOS and/or IPNI. |
| species_status |
Integer |
Closed pick list: 0, 1, 2, or 3 |
Yes |
Yes |
Important!
Gives status of species name (binomial), as determined by SALVIAS TaxonScrubber. If NULL,
name was loaded as-is to database; either not “scrubbed”, or scrubbed by
status not confirmed by inspection. 0 = “non-standard binomial”; does not match any name within TROPICOS or IPNI database, but apparently a latin binomial; in absence of evidence to contrary, should be assumed to be same species as all other individuals bearing same Genus+species string 1 = “standard binomial”; matches to name in TROPICOS and/or IPNI database. Does not mean names is “correct”, simply that it exists in taxonomic database. User must determine validity of name; 2 = “indet”, undetermined to species and is *not* a morphospecies, therefore does not necesarily match to other individuals bearing the same species string; 3 = “morphospecies”; has not been identified to a standard name, but original determiner asserts that all individuals bearing this species string represent to the same species within a given plot. |
| family |
Text |
Yes |
Yes |
Family name from TROPICOS database; matched by SALVIAS TaxonScrubber based on genus |
|
| genus |
Text |
Yes |
Yes |
Corrected genus name from SALVIAS TaxonScrubber; may or may not correspond to Genus portion of orig_species |
|
| specific_epithet |
Text |
Yes |
Yes |
Corrected specific epithet from SALVIAS TaxonScrubber; may or may not correspond to specific epithet in orig_species |
|
| specific_authority |
Text |
Yes |
Yes |
Corrected authority from SALVIAS
TaxonScrubber; this field is usually only populated if original data (see
orig_species field) contains authority |
|
| infra_rank_1 |
Text |
Yes |
Yes |
Rank of determination below level of species, if any, as parsed by SALVIAS TaxonScrubber |
|
| infra_ep_1 |
Text |
Yes |
Yes |
Epithet of determination below level of species, if any, as parsed by SALVIAS TaxonScrubber |
|
| cf_aff |
Text |
“cf.”, “aff.” |
Yes |
Yes |
“cf.” or “aff.” annotations |
| habit |
Text |
Closed pick list; T = tree, H = hemiepiphyte, L = Liana, E = epiphyte, S = shrub, Hb = herb |
Yes |
Yes |
Growth form. May be null, depending on information provided in original data. Note that many data sets lump S under T. |
| no_of_individuals |
Integer |
Yes if observation_type = “individuals”, “species (individuals)”, or “species (stems)”; otherwise No |
Partially; see Comments |
Important! Number of individuals.
Can sum by plot_code, OBSERVATION_ID, or taxon to obtain counts of individuals.
For observation_type =”species-individuals”, equals total individuals
for that species within the subplot; if have multiple stem records for each
species (Gentry data only) then equals total individuals for first stem record
only; for other stem records = 0. For observation_type = “individuals”
will be 1 for first stem for that individual, 0 for remaining stems of same
individual. For all other observation_type, will be NULL; see data
dictionary for PlotMetadata. |
|
| cover_percent |
Decimal |
Yes |
No |
Percent cover (for observation_type=”species (percent cover)” only; see data dictionary for PlotMetadata) |
|
| intercept_cm |
Decimal |
Yes |
No |
Intercept along center line, in cm (for observation_type=”species (point intercept)” only; see data dictionary for PlotMetadata) |
|
| height_m |
Decimal |
Yes |
No |
Total height of individual, in meters |
|
| ht_first_branch_m |
Decimal |
Yes |
No |
Height to first branch, in meters |
|
| stem_tag1 |
Text |
Yes |
No | Original stem tag number (if tags provided for individual stems, as opposed to entire tree) |
|
| stem_tag2 |
Text |
Yes |
No |
Most recent stem tag number; if this value is not null, indicates original tag was lost |
|
| stem_dbh |
Decimal |
Yes |
No |
Diameter at breast height of this stem (usually taken at 1.3 meters, but may vary; see metadata files for this dataset) |
|
| basal_diam |
Decimal |
Yes |
No |
Diameter at ground level for this stem |
|
| stem_height_m |
Decimal |
Yes |
No |
Total height of this stem only, in meters. for this stem only. |
|
| stem_height_first_ branch_m |
Decimal |
Yes |
No |
Height to first branch, in meters. For this stem only. |
|
| stem_canopy_form |
Text |
Open pick list |
Yes |
No |
See
accompanying documents for particular dataset. Codes are specific to particular
dataset, therefore no standardization enforced. Stem-level attribute. |
| stem_canopy_position |
Text |
Open pick list |
Yes |
No |
See
accompanying documents for particular dataset. Codes are specific to particular
dataset, therefore no standardization enforced. Stem-level attribute. |
| stem_liana_infestation |
Text |
Open pick list |
Yes |
No |
See
accompanying documents for particular dataset. Codes are specific to particular
dataset, therefore no standardization enforced. Stem-level attribute |
| notes |
Text |
Yes |
No |
Miscellaneous comments, relevant to this record |
|
| orig_family |
Text |
Yes |
No |
Original,
unaltered text string of family from original data set, for comparison.
This field may be null if original dataset consisted of species name only |
|
| orig_species |
Text |
Yes |
No |
Original
text string of species name from original dataset. If Genus, specific epithet,
and/or authority were in separate fields in original dataset, these will
appear concatenated in this field. Provided for comparison. |
