Project

General

Profile

« Previous | Next » 

Revision 4785

Added by Aaron Marcuse-Kubitza over 12 years ago

inputs/*/*/map.csv: Remapped intercept_cm to new intercept_cm so that units match

View differences:

inputs/SALVIAS-CSV/Organism/map.csv
3 3 
PLOT_ID,locationID,,
4 4 
plot_code,plotName,,
5 5 
census_no,censusNumber,,"Brad: Assigned by SALVIAS. 1 for first plot, then 2, 3, etc. I can't recall if we even have repeat censuses in SALVIAS. Probably not."
6 
census_date,eventDate,,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:
7 
-----
8 
SELECT ""PLOT_ID"", subplot, count(DISTINCT census_date) AS census_date_count
9 
FROM ""SALVIAS-CSV"".organisms
10 
WHERE subplot IS NOT NULL AND census_date IS NOT NULL
11 
GROUP BY ""PLOT_ID"", subplot
12 
HAVING count(DISTINCT census_date) > 1
6 
census_date,eventDate,,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:
7 
-----
8 
SELECT ""PLOT_ID"", subplot, count(DISTINCT census_date) AS census_date_count
9 
FROM ""SALVIAS-CSV"".organisms
10 
WHERE subplot IS NOT NULL AND census_date IS NOT NULL
11 
GROUP BY ""PLOT_ID"", subplot
12 
HAVING count(DISTINCT census_date) > 1
13 13 
-----"
14 14 
subplot,subplot,,
15 15 
individual_code,recordNumber,,"Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
......
38 38 
habit,verbatimGrowthForm,,"Brad: This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
39 39 
no_of_individuals,individualCount,,"Brad: This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."
40 40 
cover_percent,coverPercent,,
41 
intercept_cm,intercept_m,,"Brad: This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
41 
intercept_cm,intercept_cm,,"Brad: This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
42 42 
height_m,height,/_alt/2,
43 43 
ht_first_branch_m,heightFirstBranch,,
44 44 
stem_tag1,tag,/_alt/2,"Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems."
inputs/SALVIAS-CSV/Organism/VegBIEN.csv
12 12 
subplot,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists/_first/2",
13 13 
plot_code,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/then/parent_id/locationevent/*_id/location/authorlocationcode",
14 14 
PLOT_ID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode",
15 
census_date,/location/locationevent/obsenddate/_*/date/_alt/2/_dateRangeEnd/value,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:
16 
-----
17 
SELECT ""PLOT_ID"", subplot, count(DISTINCT census_date) AS census_date_count
18 
FROM ""SALVIAS-CSV"".organisms
19 
WHERE subplot IS NOT NULL AND census_date IS NOT NULL
20 
GROUP BY ""PLOT_ID"", subplot
21 
HAVING count(DISTINCT census_date) > 1
15 
census_date,/location/locationevent/obsenddate/_*/date/_alt/2/_dateRangeEnd/value,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:
16 
-----
17 
SELECT ""PLOT_ID"", subplot, count(DISTINCT census_date) AS census_date_count
18 
FROM ""SALVIAS-CSV"".organisms
19 
WHERE subplot IS NOT NULL AND census_date IS NOT NULL
20 
GROUP BY ""PLOT_ID"", subplot
21 
HAVING count(DISTINCT census_date) > 1
22 22 
-----"
23 
census_date,/location/locationevent/obsstartdate/_*/date/_alt/2/_dateRangeStart/value,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:
24 
-----
25 
SELECT ""PLOT_ID"", subplot, count(DISTINCT census_date) AS census_date_count
26 
FROM ""SALVIAS-CSV"".organisms
27 
WHERE subplot IS NOT NULL AND census_date IS NOT NULL
28 
GROUP BY ""PLOT_ID"", subplot
29 
HAVING count(DISTINCT census_date) > 1
23 
census_date,/location/locationevent/obsstartdate/_*/date/_alt/2/_dateRangeStart/value,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:
24 
-----
25 
SELECT ""PLOT_ID"", subplot, count(DISTINCT census_date) AS census_date_count
26 
FROM ""SALVIAS-CSV"".organisms
27 
WHERE subplot IS NOT NULL AND census_date IS NOT NULL
28 
GROUP BY ""PLOT_ID"", subplot
29 
HAVING count(DISTINCT census_date) > 1
30 30 
-----"
31 31 
no_of_individuals,/location/locationevent/taxonoccurrence/aggregateoccurrence/count,"Brad: This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."
32 32 
cover_percent,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover_frac/_pct_to_frac/value,
33 33 
census_no,"/location/locationevent/taxonoccurrence/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=censusNo]]:[@fkey=tablerecord_id]/definedvalue","Brad: Assigned by SALVIAS. 1 for first plot, then 2, 3, etc. I can't recall if we even have repeat censuses in SALVIAS. Probably not."
34 
intercept_cm,/location/locationevent/taxonoccurrence/aggregateoccurrence/linecover_m,"Brad: This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
34 
intercept_cm,/location/locationevent/taxonoccurrence/aggregateoccurrence/linecover_m/_cm_to_m/value,"Brad: This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
35 35 
individual_code,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,"Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
36 36 
OBSERVATION_ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
37 37 
det_type,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left","Brad: A SALVIAS value referring to the relationship between the voucher specimen and the observation. Affect how the identification of the specimen(latin name) is transferred to the observation. 'direct'=voucher specimen was collected from this same tree; they are one and the same individual. 'indirect'=voucher specimen was collected for a different individual, but the original data provider confirmed that this is the same species. 'default'=basically same as 'indirect'. 'uncollected'=no voucher specimen, data provider  asserted that this was the name but was unable to collect. The main different is that with 'direct', 'indirect', and 'default', the scientific name can be updated automatically based on the name attached to the specimen voucher (assuming you have a link to that data, presumably from a herbarium database. Whereas, if det_type='uncollected', the name can never change because there is no specimen."
inputs/SALVIAS-CSV/Organism/test.xml.ref
27 27 
                                </userdefined_id>
28 28 
                                <definedvalue>$census_no</definedvalue>
29 29 
                            </definedvalue>
30 
                            <linecover_m>$intercept_cm</linecover_m>
30 
                            <linecover_m><_cm_to_m><value>$intercept_cm</value></_cm_to_m></linecover_m>
31 31 
                            <plantobservation>
32 32 
                                <collectionnumber>$individual_code</collectionnumber>
33 33 
                                <sourceaccessioncode>$OBSERVATION_ID</sourceaccessioncode>
inputs/SALVIAS-CSV/Organism/new_terms.csv
17 17 
infra_ep_1
18 18 
cf_aff
19 19 
no_of_individuals
20 
intercept_cm
21 20 
height_m
22 21 
ht_first_branch_m
23 22 
stem_tag1
inputs/SALVIAS/plotObservations/map.csv
51 51 
ht_first_branch_m,heightFirstBranch,,
52 52 
NoInd,individualCount,,"Brad: This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."
53 53 
cover_percent,coverPercent,,
54 
intercept_cm,intercept_m,,"Brad: This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
54 
intercept_cm,intercept_cm,,"Brad: This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
55 55 
cfaff,identificationQualifier,,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank."
56 56 
other_annotations,other_annotations,,
57 57 
morphocf,morphocf,,
inputs/SALVIAS/plotObservations/VegBIEN.csv
31 31 
NoInd,/location/locationevent/taxonoccurrence/aggregateoccurrence/count,"Brad: This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."
32 32 
cover_percent,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover_frac/_pct_to_frac/value,
33 33 
census_no,"/location/locationevent/taxonoccurrence/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=censusNo]]:[@fkey=tablerecord_id]/definedvalue","Brad: Assigned by SALVIAS. 1 for first plot, then 2, 3, etc. I can't recall if we even have repeat censuses in SALVIAS. Probably not."
34 
intercept_cm,/location/locationevent/taxonoccurrence/aggregateoccurrence/linecover_m,"Brad: This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
34 
intercept_cm,/location/locationevent/taxonoccurrence/aggregateoccurrence/linecover_m/_cm_to_m/value,"Brad: This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
35 35 
Notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes,
36 36 
Ind,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,"Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
37 37 
PlotObsID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
inputs/SALVIAS/plotObservations/test.xml.ref
27 27 
                                </userdefined_id>
28 28 
                                <definedvalue>$census_no</definedvalue>
29 29 
                            </definedvalue>
30 
                            <linecover_m>$intercept_cm</linecover_m>
30 
                            <linecover_m><_cm_to_m><value>$intercept_cm</value></_cm_to_m></linecover_m>
31 31 
                            <notes>$Notes</notes>
32 32 
                            <plantobservation>
33 33 
                                <collectionnumber>$Ind</collectionnumber>
inputs/SALVIAS/plotObservations/new_terms.csv
19 19 
height_m
20 20 
ht_first_branch_m
21 21 
NoInd
22 
intercept_cm
23 22 
cfaff
24 23 
OrigFamily
25 24 
OrigGenus

Also available in: Unified diff