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Revision 4069

inputs/SALVIAS-CSV/maps/VegCSV.organisms.csv: Added _alt to height_m, stem_height_m to choose between them when both are specified (rather than having bin/map choose their priority order based on their order in the map). Note that when both of the heights are specified, they are always either the same, or height_m is invalid (see <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/SALVIAS_issues#Some-organisms-have-one-stem-but-different-heights-in-the-organisms-and-stems-tables&gt;).

View differences:

inputs/SALVIAS-CSV/test/import.organisms.xml.ref
101 101
                            <diameterbreastheight>$stem_dbh</diameterbreastheight>
102 102
                            <height>
103 103
                                <_alt>
104
                                    <0>$height_m</0>
105 104
                                    <1>$stem_height_m</1>
105
                                    <2>$height_m</2>
106 106
                                </_alt>
107 107
                            </height>
108 108
                            <heightfirstbranch>
inputs/SALVIAS-CSV/maps/VegCSV.organisms.csv
39 39
no_of_individuals,individualCount,"Brad: Incorrect for VegX. 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 41
intercept_cm,volumeCanopy,"Brad: Incorrect for VegBank 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
height_m,height,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
42
height_m,height/_alt/2,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
43 43
ht_first_branch_m,heightFirstBranch,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
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."
45 45
stem_tag2,previousTag/_alt/2,Brad: see above
46 46
stem_dbh,diameterBreastHeight,
47 47
basal_diam,basalDiameter,
48
stem_height_m,height,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."
48
stem_height_m,height/_alt/1,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."
49 49
stem_height_first_branch_m,heightFirstBranch,"Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."
50 50
stem_canopy_form,canopyForm,Brad: Should also be userDefined for VegBank. 
51 51
stem_canopy_position,canopyPosition,Brad: Should also be userDefined for VegBank. 
inputs/SALVIAS-CSV/maps/VegCSV.organisms.full.csv
15 15
stem_dbh,diameterBreastHeight,
16 16
orig_family,family,Brad: OMIT
17 17
habit,"growthForm/_map:[./{T,Arbol,palm}=tree,./{H,""Hemiepífito""}=hemiepiphyte,./{L,l,""L?"",Liana}=liana,E=epiphyte,S=shrub,Hb=herb,""vine-herbaceous""=vine,graminoid=grass,rosette=forb,*=]/value","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
18
height_m,height,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
19
stem_height_m,height,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."
18
stem_height_m,height/_alt/1,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."
19
height_m,height/_alt/2,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
20 20
ht_first_branch_m,heightFirstBranch,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
21 21
stem_height_first_branch_m,heightFirstBranch,"Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."
22 22
cf_aff,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."
inputs/SALVIAS-CSV/maps/VegBIEN.organisms.csv
27 27
stem_liana_infestation,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=lianaInfestation]]:[@fkey=tablerecord_id]/definedvalue",Brad: Should also be userDefined for VegBank. 
28 28
notes,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=notes]]:[@fkey=tablerecord_id]/definedvalue",
29 29
stem_dbh,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight,
30
height_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
31
stem_height_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."
30
stem_height_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height/_alt/1,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."
31
height_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height/_alt/2,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
32 32
ht_first_branch_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/heightfirstbranch,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
33 33
stem_height_first_branch_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/heightfirstbranch,"Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."
34 34
tag1,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag/_alt/1","Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once.; Quotes sort it before tag2"

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