Timestamp: Mon Nov 30 13:39:58 2020
Drafted: Francesco Maria Sabatini
Revised:
version: 1.0

This reports describes and provides a basic summary of the objects composing the working version of sPlot 3.0.

library(tidyverse)
library(knitr)
library(kableExtra)

1 Taxonomic Backbone

The taxonomic backbone is a resolved list of species names from either sPlot or TRY, which allows to:
1) Match functional traits to species in sPlot, based on a common nomenclature.
2) Resolve synonyms and correct spelling mistakes in species names, so to allow matching species across the datasets constituting sPlot.
The construction of the Backbone is documented at https://git.idiv.de/fs40gaho/splot3_build/-/blob/master/public/03_TaxonomicBackbone.html (download needed)

load("../_output/Backbone3.0.RData")

1.1 Show output

Example of Backbone (only 20 randomly selected taxa shown)
Name_sPlot_TRY Name_string_corr1 Name_string_corr2 sPlot_TRY Name_submitted Name_number Overall_score Name_matched Name_matched_rank Name_score Name_matched_author Name_matched_url Author_matched Author_score Family_matched Family_score Name_matched_accepted_family Genus_matched Genus_score Specific_epithet_matched Specific_epithet_score Infraspecific_rank Infraspecific_epithet_matched Infraspecific_epithet_score Infraspecific_rank_2 Infraspecific_epithet_2_matched Infraspecific_epithet_2_score Annotations Unmatched_terms Taxonomic_status Accepted_name Accepted_name_author Accepted_name_rank Accepted_name_url Accepted_name_species Accepted_name_family Selected Source Warnings Accepted_name_lsid Status_correct Name_correct Genus_correct Rank_correct Family_correct Name_short phylum is_vascular_species Taxon group
Chusquea nobilis Chusquea nobilis NA T Chusquea nobilis 69697 1 Chusquea nobilis species 1 (Munro) L.G.Clark http://www.theplantlist.org/tpl1.1/record/kew-462686 NA NA NA NA Poaceae Chusquea 1 nobilis 1 NA NA NA NA NA NA NA NA Accepted Chusquea nobilis (Munro) L.G.Clark species http://www.theplantlist.org/tpl1.1/record/kew-462686 Chusquea nobilis Poaceae TRUE tpl NA NA Accepted Chusquea nobilis Chusquea species Poaceae Chusquea nobilis Tracheophyta TRUE Vascular plant
Spiradiclis cylindrica Spiradiclis cylindrica NA T Spiradiclis cylindrica 295068 1 Spiradiclis cylindrica species 1 Wall. ex Hook.f. http://www.theplantlist.org/tpl1.1/record/kew-194144 NA NA NA NA Rubiaceae Spiradiclis 1 cylindrica 1 NA NA NA NA NA NA NA NA Accepted Spiradiclis cylindrica Wall. ex Hook.f. species http://www.theplantlist.org/tpl1.1/record/kew-194144 Spiradiclis cylindrica Rubiaceae TRUE tpl NA NA Accepted Spiradiclis cylindrica Spiradiclis species Rubiaceae Spiradiclis cylindrica Tracheophyta TRUE Vascular plant
Euphorbia neogillettii Euphorbia neogillettii NA T Euphorbia neogillettii 125794 1 Euphorbia neogillettii species 1 Bruyns http://www.theplantlist.org/tpl1.1/record/kew-344111 NA NA NA NA Euphorbiaceae Euphorbia 1 neogillettii 1 NA NA NA NA NA NA NA NA Accepted Euphorbia neogillettii Bruyns species http://www.theplantlist.org/tpl1.1/record/kew-344111 Euphorbia neogillettii Euphorbiaceae TRUE tpl NA NA Accepted Euphorbia neogillettii Euphorbia species Euphorbiaceae Euphorbia neogillettii Tracheophyta TRUE Vascular plant
Salsola minkvitziae Salsola minkvitziae NA T Salsola minkvitziae 274467 1 Salsola minkvitziae species 1 Korovin http://www.theplantlist.org/tpl1.1/record/kew-2481258;http://www.tropicos.org/Name/100366776 NA NA NA NA Amaranthaceae Salsola 1 minkvitziae 1 NA NA NA NA NA NA NA NA No opinion Climacoptera minkvitziae (Korovin) Botsch. species http://www.theplantlist.org/tpl1.1/record/kew-2727875;http://www.theplantlist.org/tpl1.1/record/kew-2727875 Climacoptera minkvitziae Amaranthaceae TRUE tpl;tropicos NA NA Other Climacoptera minkvitziae Climacoptera species Amaranthaceae Climacoptera minkvitziae Tracheophyta TRUE Vascular plant
Eritrichium echinocaryum Eritrichium echinocaryum NA T Eritrichium echinocaryum 119421 1 Eritrichium echinocaryum species 1 (I.M.Johnst.) Y.S.Lian & J.Q.Wang http://www.theplantlist.org/tpl1.1/record/kew-2797735 NA NA NA NA Boraginaceae Eritrichium 1 echinocaryum 1 NA NA NA NA NA NA NA NA Accepted Eritrichium echinocaryum (I.M.Johnst.) Y.S.Lian & J.Q.Wang species http://www.theplantlist.org/tpl1.1/record/kew-2797735 Eritrichium echinocaryum Boraginaceae TRUE tpl NA NA Accepted Eritrichium echinocaryum Eritrichium species Boraginaceae Eritrichium echinocaryum Tracheophyta TRUE Vascular plant
Centrolepis banksii Centrolepis banksii NA T Centrolepis banksii 63376 1 Centrolepis banksii species 1 (R.Br.) Roem. & Schult. http://www.theplantlist.org/tpl1.1/record/kew-232580 NA NA NA NA Centrolepidaceae Centrolepis 1 banksii 1 NA NA NA NA NA NA NA NA Accepted Centrolepis banksii (R.Br.) Roem. & Schult. species http://www.theplantlist.org/tpl1.1/record/kew-232580 Centrolepis banksii Centrolepidaceae TRUE tpl NA NA Accepted Centrolepis banksii Centrolepis species Centrolepidaceae Centrolepis banksii NA TRUE Vascular plant
Lophanthus chinensis Lophanthus chinensis NA ST Lophanthus chinensis 184941 1 Lophanthus chinensis species 1 Benth. http://www.theplantlist.org/tpl1.1/record/kew-115110;http://www.tropicos.org/Name/17604016 NA NA NA NA Lamiaceae Lophanthus 1 chinensis 1 NA NA NA NA NA NA NA NA Accepted Lophanthus chinensis Benth. species http://www.theplantlist.org/tpl1.1/record/kew-115110;http://www.tropicos.org/Name/17604016 Lophanthus chinensis Lamiaceae TRUE tpl;tropicos NA NA Accepted Lophanthus chinensis Lophanthus species Lamiaceae Lophanthus chinensis Tracheophyta TRUE Vascular plant
Cinnamomum pedatinervium Cinnamomum pedatinervium NA T Cinnamomum pedatinervium 70347 1 Cinnamomum pedatinervium species 1 Meisn. http://www.theplantlist.org/tpl1.1/record/kew-2721519 NA NA NA NA Lauraceae Cinnamomum 1 pedatinervium 1 NA NA NA NA NA NA NA NA Accepted Cinnamomum pedatinervium Meisn. species http://www.theplantlist.org/tpl1.1/record/kew-2721519 Cinnamomum pedatinervium Lauraceae TRUE tpl NA NA Accepted Cinnamomum pedatinervium Cinnamomum species Lauraceae Cinnamomum pedatinervium Tracheophyta TRUE Vascular plant
Gethyllis ciliaris Gethyllis ciliaris NA T Gethyllis ciliaris 139216 1 Gethyllis ciliaris species 1 (Thunb.) Thunb. http://www.theplantlist.org/tpl1.1/record/kew-307906;http://www.tropicos.org/Name/100197552 NA NA NA NA Amaryllidaceae Gethyllis 1 ciliaris 1 NA NA NA NA NA NA NA NA Accepted Gethyllis ciliaris (Thunb.) Thunb. species http://www.theplantlist.org/tpl1.1/record/kew-307906;http://www.tropicos.org/Name/100197552 Gethyllis ciliaris Amaryllidaceae TRUE tpl;tropicos NA NA Accepted Gethyllis ciliaris Gethyllis species Amaryllidaceae Gethyllis ciliaris Tracheophyta TRUE Vascular plant
Anginon difforme Anginon difforme NA ST Anginon difforme 18686 1 Anginon difforme species 1 (L.) B.L.Burtt http://www.theplantlist.org/tpl1.1/record/kew-2639389 NA NA NA NA Apiaceae Anginon 1 difforme 1 NA NA NA NA NA NA NA NA Accepted Anginon difforme (L.) B.L.Burtt species http://www.theplantlist.org/tpl1.1/record/kew-2639389 Anginon difforme Apiaceae TRUE tpl NA NA Accepted Anginon difforme Anginon species Apiaceae Anginon difforme Tracheophyta TRUE Vascular plant
Gentiana affinis Gentiana affinis NA ST Gentiana affinis 137719 1 Gentiana affinis species 1 Griseb. http://www.theplantlist.org/tpl1.1/record/kew-2819836;http://www.tropicos.org/Name/13801007;http://plants.usda.gov/java/profile?symbol=GEAF NA NA NA NA Gentianaceae Gentiana 1 affinis 1 NA NA NA NA NA NA NA NA Accepted Gentiana affinis Griseb. species http://www.theplantlist.org/tpl1.1/record/kew-2819836;http://www.tropicos.org/Name/13801007;http://plants.usda.gov/java/profile?symbol=GEAF Gentiana affinis Gentianaceae TRUE tpl;tropicos;usda NA NA Accepted Gentiana affinis Gentiana species Gentianaceae Gentiana affinis Tracheophyta TRUE Vascular plant
Macrolobium 1 Macrolobium NA S Macrolobium 189274 1 Macrolobium genus 1 NA http://www.ildis.org/LegumeWeb?version~10.01&genus~Macrolobium NA NA NA NA Fabaceae Macrolobium 1 NA NA NA NA NA NA NA NA NA NA No opinion NA NA genus http://www.theplantlist.org/tpl1.1/search?q=Macrolobium NA Fabaceae FALSE ildis NA NA Other Macrolobium Macrolobium genus Leguminosae Macrolobium Tracheophyta TRUE Vascular plant
Woodfordia Woodfordia NA T Woodfordia 329540 1 Woodfordia genus 1 NA http://www.theplantlist.org/tpl1.1/search?q=Woodfordia NA NA NA NA Lythraceae Woodfordia 1 NA NA NA NA NA NA NA NA NA NA Accepted Woodfordia NA genus http://www.theplantlist.org/tpl1.1/search?q=Woodfordia NA Lythraceae TRUE tpl NA NA Accepted Woodfordia Woodfordia genus Lythraceae Woodfordia Tracheophyta TRUE Vascular plant
Sorbus pohuashanensis Sorbus pohuashanensis NA T Sorbus pohuashanensis 293219 1 Sorbus pohuashanensis species 1 (Hance) Hedl. http://www.theplantlist.org/tpl1.1/record/rjp-6906 NA NA NA NA Rosaceae Sorbus 1 pohuashanensis 1 NA NA NA NA NA NA NA NA Synonym Sorbus aucuparia L. species http://www.theplantlist.org/tpl1.1/record/rjp-68 Sorbus aucuparia Rosaceae TRUE tpl [Ambiguous match] NA Synonym Sorbus aucuparia Sorbus species Rosaceae Sorbus aucuparia Tracheophyta TRUE Vascular plant
Nepeta concolor Nepeta concolor NA T Nepeta concolor 210472 1 Nepeta concolor species 1 Boiss. & Heldr. ex Benth. http://www.theplantlist.org/tpl1.1/record/kew-134530 NA NA NA NA Lamiaceae Nepeta 1 concolor 1 NA NA NA NA NA NA NA NA Accepted Nepeta concolor Boiss. & Heldr. ex Benth. species http://www.theplantlist.org/tpl1.1/record/kew-134530 Nepeta concolor Lamiaceae TRUE tpl NA NA Accepted Nepeta concolor Nepeta species Lamiaceae Nepeta concolor Tracheophyta TRUE Vascular plant
Racosperma aneurum var. majus Racosperma aneurum var. majus NA T Racosperma aneurum var. majus 261333 1 Racosperma aneurum var. majus variety 1 (Pedley) Pedley http://www.tropicos.org/Name/50246453 NA NA NA NA Fabaceae Racosperma 1 aneurum 1 var. majus 1 NA NA NA NA NA Accepted Racosperma aneurum var. majus (Pedley) Pedley variety http://www.tropicos.org/Name/50246453 Racosperma aneurum Fabaceae TRUE tropicos NA NA Accepted Racosperma aneurum var. majus Racosperma variety Leguminosae Racosperma aneurum Tracheophyta TRUE Vascular plant
Periballia minuta Periballia minuta NA ST Periballia minuta 231948 1 Periballia minuta species 1 (L.) Asch. & Graebn. http://www.theplantlist.org/tpl1.1/record/kew-433269 NA NA NA NA Poaceae Periballia 1 minuta 1 NA NA NA NA NA NA NA NA Accepted Periballia minuta (L.) Asch. & Graebn. species http://www.theplantlist.org/tpl1.1/record/kew-433269 Periballia minuta Poaceae TRUE tpl NA NA Accepted Periballia minuta Periballia species Poaceae Periballia minuta Tracheophyta TRUE Vascular plant
Stelis violacea Stelis violacea NA T Stelis violacea 297253 1 Stelis violacea species 1 Garay http://www.theplantlist.org/tpl1.1/record/kew-196915;http://www.tropicos.org/Name/23508733 NA NA NA NA Orchidaceae Stelis 1 violacea 1 NA NA NA NA NA NA NA NA Accepted Stelis violacea Garay species http://www.theplantlist.org/tpl1.1/record/kew-196915;http://www.tropicos.org/Name/23508733 Stelis violacea Orchidaceae TRUE tpl;tropicos NA NA Accepted Stelis violacea Stelis species Orchidaceae Stelis violacea Tracheophyta TRUE Vascular plant
Verbesina glabrata Verbesina glabrata NA T Verbesina glabrata 323534 1 Verbesina glabrata species 1 Hook. & Arn. http://www.tropicos.org/Name/2717925 NA NA NA NA Asteraceae Verbesina 1 glabrata 1 NA NA NA NA NA NA NA NA Accepted Verbesina glabrata Hook. & Arn. species http://www.tropicos.org/Name/2717925 Verbesina glabrata Asteraceae TRUE tropicos NA NA Accepted Verbesina glabrata Verbesina species Compositae Verbesina glabrata Tracheophyta TRUE Vascular plant
Telitoxicum minutiflorum Telitoxicum minutiflorum NA ST Telitoxicum minutiflorum 307598 1 Telitoxicum minutiflorum species 1 (Diels) Moldenke http://www.theplantlist.org/tpl1.1/record/tro-20600371;http://www.tropicos.org/Name/20600371 NA NA NA NA Menispermaceae Telitoxicum 1 minutiflorum 1 NA NA NA NA NA NA NA NA Accepted Telitoxicum minutiflorum (Diels) Moldenke species http://www.theplantlist.org/tpl1.1/record/tro-20600371;http://www.tropicos.org/Name/20600371 Telitoxicum minutiflorum Menispermaceae TRUE tpl;tropicos NA NA Accepted Telitoxicum minutiflorum Telitoxicum species Menispermaceae Telitoxicum minutiflorum Tracheophyta TRUE Vascular plant

The Backbone contains 346392 taxon names. Of these, 43715 derive from sPlot.

1.2 Description of fields

The bulk of the taxonomic standardization was done using TNRS or TPL, accessed using the package taxonstand. Below, the list of fields comprised in the Backbone output.

1. Name_sPlot_TRY: Taxon names, as derived from the Turboveg version of the original datasets.
2. Name_string_corr1: Taxon name after a first round of manual cleaning (e.g., some types, abbreviations).
3. Name_string_corr2: Taxon name after a second round of manual cleaning.
4. sPlot_TRY: Origin of the taxon name (S = sPlot, T = TRY, A = Alpine dataset, see Testolin et al. 2020).

The fields below derive from the output of TNRS (or TPL) - See here for additional information.
5. Name_submitted: Taxon name, as submitted to the services of taxonomic resolution, either TNRS or TPL.
6. Name_number: Order of submission to TNRS or TPL.
7. Overall_score: Level of matching in TNRS or TPL (1=perfect match).
8. Name_matched: Scientific name with the highest match score. May be an exact match or a fuzzy match. This score does not include the author score.
9. Name_matched_rank: The lowest taxonomic rank for the name matched.
10. Name_score: Overall score for the name matched based on the TNRS ranking algorithm.
11. Name_matched_author: Standard authority for the matched name.
12. Name_matched_url: Web link for the matched name (where applicable).
13. Author_matched: Standard authority of the name with the highest match score name.
14. Author_score: Score assigned by the TNRS to indicate the level of similarity to the author submitted (where applicable). This field will be blank if the user did not submit an author with the name.
15. Family_matched:The closest matching family in the TNRS database to the family submitted. This field will be blank if you did not submit a family, or the family could not be matched.
16. Family_score: Score assigned by the TNRS to indicate the level of similarity to the family submitted (where applicable).
17. Name_matched_accepted_family: Family of the accepted name.
18. Genus_matched: The closest matching genus in the TNRS database to the genus submitted. This field will be blank if the genus submitted could not be matched.
19. Genus_score: Score assigned by the TNRS to indicate the level of similarity to the genus submitted.
20. Specific_epithet_matched: The specific epithet of closest matching species in the TNRS database to the species submitted. This field will be blank if the species submitted could not be matched.
21. Specific_epithet_score: Score assigned by the TNRS to indicate the level of similarity to the species submitted.
22. Infraspecific_rank: If an infraspecific taxon was submitted (subspecies, variety, etc.), this field provides the standardized rank abbreviation for that taxon (subspecies, variety, etc.).
23. Infraspecific_epithet_matched: The infraspecific epithet of closet matching subspecies or variety in the TNRS database to the subspecies or variety submitted. This field will be blank if no infraspecific taxon was submitted, or if the subspecies or variety could not be matched.
24. Infraspecific_epithet_score: Score assigned by the TNRS to indicate the level of similarity to the infraspecific taxon submitted.
25. Infraspecific_rank_2: If a quadrinomal taxon name was submitted, this field provides the standardized rank abbreviation for that taxon. For example, “Poa annua var. purpurea forma minima” would return “fo.”.
26. Infraspecific_epithet_2_matched: The final epithet of closest matching quadrinomial infraspecific taxon in the TNRS database to the quadrinomial infraspecific taxon, for example “Poa annua var. purpurea forma minima”. This field will be blank if a quadrinomial was not submitted or if the final epithet could not be matched.
27. Infraspecific_epithet_2_score: Score assigned by the TNRS to indicate the level of similarity to the lower infraspecific taxon (quadrinomial) submitted. This field will be blank if a quadrinomial was not submitted, or if the final epithet of the quadrinomial could not be matched.
28. Annotations: Any standardized botanical annotations of uncertainty embedded within the name, such as “cf.” or “aff.”, are removed and stored here.
29. Unmatched_terms: The complete trailing portion of the name not matched by the TNRS, minus any annotations.
30. Taxonomic_status: Where the submitted name is Accepted, Synonym, or not know (e.g., No opinion, Invalid, Illegitimate, Misapplied, Unresolved).
31. Accepted_name: The accepted (correct) scientific name of the name matched by the TNRS, according to the taxonomic source used. If the name matched is an accepted name, or if the TNRS indicated “No opinion” for the name matched, then acceptedName will be the same as Name_matched. If Name_matched is a synonymy, then Accepted_name will be different.
32. Accepted_name_author: Standard authority of the Accepted_name.
33. Accepted_name_rank: Taxonomic rank of the accepted Accepted_name.
34. Accepted_name_url: Web link for the accepted name (where applicable).
35. Accepted_name_species: The genus+species portion only of the Accepted_name. If the rank of the Accepted_name is species, then Accepted_species will be the same as Accepted_name. If the rank of the Accepted_name is higher than species, for example, if the Accepted_name is a genus, then this field will be blank.
36. Accepted_name_family: The accepted familial classification of the accepted name for the name matched by the TNRS.
37. Selected: Denotes the best match according to either taxonomic or maximum score.
38. Source: Source used for the resolution (for TNRS sources see ).
39. Warnings: If TNRS is unable to uncategorically resolve your submitted name to one best matched name in our database, a red warning flag will appear next to the submitted name.
40. Accepted_name_lsid: As exported by TNRS.

Below columns added specifically for this backbone - These fields represent the actual output.
41. Status_correct: Simplification of Taxonomic_status.
42. Name_correct: If Accepted_name is non-null, otherwise returns Name_matched. This field represent the union of accepted + matched name.
43. Genus_correct: Genus derived from Name_correct, but only when Accepted_name_rank is lower than family.
44. Rank_correct: Simplification of Accepted_name_rank.
45. Family_correct: Family of Name_correct. Complements Accepted_name_family with multiple sources.
46. Name_short: First two words of Name_correct.
47. phylum: As derived from The Catalogue of Life.
48. is_vascular_species: TRUE if the species is a vascular plant. It is derived based on selection of phylum from The Catalogue of Life.
49. Taxon group: Taxon group, as in Turboveg. Five possible entries. Alga, Lichen, Moss, Vascular plant or Unknown.


The object Backbone3.0.RData also contains two ancillary vectors, which were use to refine the Backbone. These are: lichen.genera - a list of genera for lichen species contained in the Backbone; mushroom - a list of genera for mushroom species spotted in sPlot species list (and excluded); mushroom.families - a list of family names for mushroom spotted in sPlot (and excluded).

3 DT Table

The DT table, contains information on which species was recorded in what plot, and with what abundance. The construction of the object DT_sPlot3.0 is documented at https://git.idiv.de/fs40gaho/splot3_build/-/blob/master/public/06_buildDT.html (download needed).

load("../_output/DT_sPlot3.0.RData")

3.1 Show output

Example of DT table (only species from three randomly selected plots shown)
PlotObservationID Species Species_original Rank_correct Taxon_group Layer Cover_code Ab_scale Abundance Relative_cover
641829 Atriplex glabriuscula Atriplex babingtonii var. prostrata species Vascular plant 0
CoverPerc 2 0.0235294
641829 Cotula coronopifolia Cotula coronopifolia species Vascular plant 0
CoverPerc 2 0.0235294
641829 Crypsis aculeata Crypsis aculeata species Vascular plant 0 2 CoverPerc 13 0.1529412
641829 Bolboschoenus maritimus Scirpus maritimus species Vascular plant 0 4 CoverPerc 68 0.8000000
1127960 Achillea millefolium Achillea millefolium species Vascular plant 0
CoverPerc 2 0.0092166
1127960 Agrostis capillaris Agrostis capillaris species Vascular plant 0 3 CoverPerc 38 0.1751152
1127960 Aulacomnium androgynum Aulacomnium androgynum species Moss 0
CoverPerc 2 0.0092166
1127960 Berberis vulgaris Berberis vulgaris species Vascular plant 0 r CoverPerc 1 0.0046083
1127960 Bryonia cretica Bryonia dioica species Vascular plant 0 r CoverPerc 1 0.0046083
1127960 Calamagrostis epigejos Calamagrostis epigejos species Vascular plant 0 2b CoverPerc 18 0.0829493
1127960 Carex arenaria Carex arenaria species Vascular plant 0 3 CoverPerc 38 0.1751152
1127960 Cerastium arvense Cerastium arvense species Vascular plant 0
CoverPerc 2 0.0092166
1127960 Crataegus monogyna Crataegus monogyna species Vascular plant 0 2a CoverPerc 8 0.0368664
1127960 Dicranum scoparium Dicranum scoparium species Moss 0 2m CoverPerc 4 0.0184332
1127960 Kindbergia praelonga Eurhynchium praelongum species Moss 0 2m CoverPerc 4 0.0184332
1127960 Festuca filiformis Festuca filiformis species Vascular plant 0 1 CoverPerc 3 0.0138249
1127960 Galeopsis tetrahit Galeopsis tetrahit species Vascular plant 0
CoverPerc 2 0.0092166
1127960 Galium verum Galium verum species Vascular plant 0
CoverPerc 2 0.0092166
1127960 Hypnum jutlandicum Hypnum jutlandicum species Moss 0 2m CoverPerc 4 0.0184332
1127960 Lonicera periclymenum Lonicera periclymenum species Vascular plant 0 1 CoverPerc 3 0.0138249
1127960 Luzula campestris Luzula campestris species Vascular plant 0
CoverPerc 2 0.0092166
1127960 Moehringia trinervia Moehringia trinervia species Vascular plant 0 2a CoverPerc 8 0.0368664
1127960 Pimpinella saxifraga Pimpinella saxifraga species Vascular plant 0 r CoverPerc 1 0.0046083
1127960 Plagiomnium affine Plagiomnium affine species Moss 0 2m CoverPerc 4 0.0184332
1127960 Pseudoscleropodium purum Pseudoscleropodium purum species Moss 0 2m CoverPerc 4 0.0184332
1127960 Quercus robur Quercus robur species Vascular plant 0 3 CoverPerc 38 0.1751152
1127960 Rhamnus cathartica Rhamnus cathartica species Vascular plant 0 r CoverPerc 1 0.0046083
1127960 Rosa canina Rosa canina species Vascular plant 0 r CoverPerc 1 0.0046083
1127960 Rubus caesius Rubus caesius species Vascular plant 0 2a CoverPerc 8 0.0368664
1127960 Rumex acetosella Rumex acetosella species Vascular plant 0
CoverPerc 2 0.0092166
1127960 Sambucus nigra Sambucus nigra species Vascular plant 0
CoverPerc 2 0.0092166
1127960 Jacobaea vulgaris Senecio jacobaea species Vascular plant 0
CoverPerc 2 0.0092166
1127960 Senecio sylvaticus Senecio sylvaticus species Vascular plant 0 1 CoverPerc 3 0.0138249
1127960 Silene dioica Silene dioica species Vascular plant 0
CoverPerc 2 0.0092166
1127960 Teucrium scorodonia Teucrium scorodonia species Vascular plant 0
CoverPerc 2 0.0092166
1127960 Urtica dioica Urtica dioica species Vascular plant 0
CoverPerc 2 0.0092166
1127960 Veronica officinalis Veronica officinalis species Vascular plant 0
CoverPerc 2 0.0092166
1127960 Viola riviniana Viola riviniana species Vascular plant 0 r CoverPerc 1 0.0046083
1515499 Adiantum capillus-veneris Adiantum capillus-veneris species Vascular plant 0
CoverPerc 2 0.0232558
1515499 Aristolochia baetica Aristolochia baetica species Vascular plant 0
CoverPerc 2 0.0232558
1515499 Arum italicum Arum italicum species Vascular plant 0
CoverPerc 2 0.0232558
1515499 Arundo donax Arundo donax species Vascular plant 0 1 CoverPerc 3 0.0348837
1515499 Brachypodium sylvaticum Brachypodium sylvaticum subsp. sylvaticum higher Vascular plant 0
CoverPerc 2 0.0232558
1515499 Cyperus longus Cyperus longus species Vascular plant 0
CoverPerc 2 0.0232558
1515499 Nerium oleander Nerium oleander subsp. oleander species Vascular plant 0
CoverPerc 2 0.0232558
1515499 Olea europaea Olea europaea subsp. sylvestris lower Vascular plant 0 1 CoverPerc 3 0.0348837
1515499 Populus alba Populus alba species Vascular plant 0 3 CoverPerc 38 0.4418605
1515499 Potentilla reptans Potentilla reptans species Vascular plant 0
CoverPerc 2 0.0232558
1515499 Rubus ulmifolius Rubus ulmifolius species Vascular plant 0 2 CoverPerc 13 0.1511628
1515499 Salix secalliana Salix x secalliana species Vascular plant 0
CoverPerc 2 0.0232558
1515499 Smilax aspera Smilax aspera species Vascular plant 0 2 CoverPerc 13 0.1511628
The DT table contains 43102856 entries, from 76912 species.

3.2 Description of fields

  1. PlotObservationID: Plot ID (as in Header).
  2. Species: Resolved species name (as derived from the field name_short in the Backbone).
  3. Species_original: Original species name (before resolution, as in the field name_sPlot_TRY in the Backbone).
  4. Rank_correct: Taxonomic rank of the corrected name (as in the homonymous field in the Backbone).
  5. Taxon_group: Taxon group (as in the homonymous field in the Backbone).
  6. Layer: Vegetation layer, as specified in Turboveg: 0: No layer specified, 1: Upper tree layer, 2: Middle tree layer, 3: Lower tree layer, 4: Upper shrub layer, 5: Lower shrub layer, 6: Herb layer, 7: Juvenile, 8: Seedling, 9: Moss layer.
  7. Cover_code: Cover\abundance code in original data, before transformation to quantitative value or percentage cover.
  8. Ab_scale: Abundance scale in original data. Possible values are: CoverPerc: Cover Percentage, pa: Presence absence, x_BA: Basal Area, x_IC: Individual count, x_SC: Stem count, x_IV: Relative Importance, x_RF: Relative Frequency.
  9. Abundance: Abundance value, in original value, or as transformed from original Cover code to quantitative values.
  10. Relative_cover: Abundance\Cover of each species after being normalized to 1 in each plot.

4 Functional Traits and Community Weighted Means\Variances

The object Traits_CWMs_sPlot3.RData contains three data.frames:
1) data.frame try.combined.means - Mean and s.d. of gap-filled functional traits of all species in TRY 5.0.
2) data.frame sPlot.traits - Mean and s.d. of gap-filled functional traits of all species in sPlot.
3) data.frame CWM - Plot Community Weighted means and variances.

A detailed description of the construction of this object is available at: https://git.idiv.de/fs40gaho/splot3_build/-/blob/master/public/07_buildCWMs.html (download needed)

load("../_output/Traits_CWMs_sPlot3.RData")

4.1 Show output

Object try.combined.means.
Example of trait table of TRY species (only 10 randomly selected species shown)
Taxon_name Rank_correct n StemDens_mean RootingDepth_mean SLA_mean LeafC.perdrymass_mean LeafN_mean LeafP_mean PlantHeight_mean StemDiam_mean SeedMass_mean Seed.length_mean LeafThickness_mean LDMC_mean LeafNperArea_mean LeafDryMass.single_mean Leaf.delta.15N_mean SeedGerminationRate_mean Seed.num.rep.unit_mean LeafLength_mean LeafWidth_mean LeafCN.ratio_mean Leaffreshmass_mean Stem.cond.dens_mean Chromosome.n_mean Chromosome.cDNAcont_mean Disp.unit.leng_mean StemConduitDiameter_mean Wood.vessel.length_mean WoodFiberLength_mean SpecificRootLength_mean LeafArea.leaf.undef_mean LeafArea.leaflet.undef_mean LeafArea.undef.undef_mean LeafWaterCont_mean StemDens_sd RootingDepth_sd SLA_sd LeafC.perdrymass_sd LeafN_sd LeafP_sd PlantHeight_sd StemDiam_sd SeedMass_sd Seed.length_sd LeafThickness_sd LDMC_sd LeafNperArea_sd LeafDryMass.single_sd Leaf.delta.15N_sd SeedGerminationRate_sd Seed.num.rep.unit_sd LeafLength_sd LeafWidth_sd LeafCN.ratio_sd Leaffreshmass_sd Stem.cond.dens_sd Chromosome.n_sd Chromosome.cDNAcont_sd Disp.unit.leng_sd StemConduitDiameter_sd Wood.vessel.length_sd WoodFiberLength_sd SpecificRootLength_sd LeafArea.leaf.undef_sd LeafArea.leaflet.undef_sd LeafArea.undef.undef_sd LeafWaterCont_sd
Cryptocarya natalensis species 1 0.5751702 2.5326360 10.425681 493.2546 15.11499 0.9388697 10.6950543 0.1209285 457.804656 12.989073 0.3112685 0.3560181 1.479780 298.27651 0.6206322 112.53326 113.217312 56.57014 2.802918 32.91668 0.8092815 47.18446 22.96402 5.419259 13.924957 37.69650 515.9514 863.6061 1947.776 811.3117 2348.1398 2194.8650 2.792570 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Bocoa alterna species 1 0.9125905 1.1339245 10.518535 509.9198 24.33333 0.7045276 11.9729104 0.1504608 33.720315 5.142241 0.2171166 0.3949078 2.401758 401.12982 1.7795199 83.71626 92.279192 60.20606 5.637404 22.20116 0.9789514 19.08332 23.95259 1.981819 4.145950 54.02743 438.7304 1116.2937 1308.088 3846.4499 2495.7900 3174.8976 2.443792 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Bennettiodendron brevipes species 1 0.5781547 0.8435309 14.360997 471.4161 22.91266 1.5456854 5.9635009 0.1179603 2.213717 1.990114 0.1891193 0.3637583 1.675917 141.30015 -0.9310381 94.42429 758.940295 57.18425 3.086715 21.92293 0.3750499 89.83075 43.04883 1.493224 3.250831 45.72194 367.5357 619.4289 3277.570 1718.2817 1494.2554 2464.9919 2.712138 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Scolopia saeva species 2 0.7899502 3.1822886 9.027328 457.1123 16.04483 0.9764401 18.4433954 0.2947169 20.533128 3.342978 0.2309048 0.4206842 1.864172 201.48475 -0.0841129 95.38262 330.132271 59.10071 3.039186 33.44951 0.4218930 42.31889 34.92623 1.569432 4.770587 40.72187 301.2944 676.3618 1855.663 1287.6262 1397.6839 2234.2578 1.990111 0.0519314 0.2872102 0.2181785 0.5197153 0.0774819 0.0371150 1.3861640 0.0002931 0.7399860 0.0252650 0.0035401 0.0042215 0.0418106 7.9826763 0.0648714 0.6657861 43.625004 2.518151 0.0786960 0.2160075 0.0073534 0.1466821 0.1514306 0.0495655 0.0206792 0.5698272 5.1412382 3.775272 9.929002 19.31647 44.04323 61.55722 0.0375625
Vatica curtisii species 1 0.7194836 1.9853486 11.527575 497.6605 18.75709 0.9971404 16.9726573 0.2181583 173.213606 9.039822 0.1727677 0.4350126 1.698477 402.06116 1.2596487 87.89654 8.840748 81.82680 5.546836 27.36905 0.8717038 11.11344 14.20389 1.797976 9.037071 36.87050 319.7365 835.2874 1018.786 3477.0242 1504.5839 4114.1738 1.884152 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Ranunculus amphitricha species 1 0.4020374 0.1225216 21.112912 443.8196 24.68358 1.9810207 0.2308111 0.0035119 1.289509 2.573498 0.2502646 0.1960809 1.228664 29.00105 1.1583751 87.43866 181.860963 59.54537 1.416366 19.19464 0.1537919 78.32043 26.11825 12.217823 2.769810 22.34653 581.9661 1079.0724 8146.454 611.4105 611.3839 625.9909 5.768824 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Machilus fukienensis species 1 0.4884060 1.1628463 11.679418 486.2174 15.93420 0.9767168 5.0179899 0.0760557 244.386632 10.149695 0.2595631 0.3894300 1.368160 203.59721 -1.9834892 91.96203 6.481295 82.88210 2.312889 34.10576 0.5261823 18.62376 19.56246 2.702459 15.325680 31.48919 291.7998 719.6984 1546.158 2098.2663 1471.4240 1942.5019 2.268804 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Pavonia triloba species 3 0.5120897 0.7818407 10.834469 467.5585 21.60702 1.3101960 0.8717291 0.0937987 5.025609 2.185744 0.3267239 0.3287125 2.163640 189.32822 2.0569963 94.78500 70.392131 35.59508 2.476686 25.06726 0.5885133 27.92908 37.68935 3.484783 2.624127 41.81412 575.4631 851.3510 1336.604 1788.3632 686.7844 1967.7456 2.872966 0.0031441 0.0446174 0.2224161 2.1799127 0.3918129 0.0196044 0.0367559 0.0010029 0.2018370 0.0498766 0.0026000 0.0016838 0.0301100 6.9541572 0.1948813 5.2829529 3.812206 3.712947 0.1310660 0.5153179 0.0251107 1.6703587 0.2465976 0.0244086 0.0496105 2.9796639 15.0878606 42.414195 21.304214 84.16093 10.11728 98.35451 0.0390276
Colutea orientalis species 3 0.6424158 2.6198239 14.400063 482.8484 23.31427 1.7001040 2.1076911 0.1807712 12.680219 2.578731 0.2017130 0.2811712 1.833895 36.27834 2.4344224 98.88317 81.774844 30.58707 0.842056 21.07510 0.1175464 25.65415 17.18773 1.628289 3.786408 30.38306 147.0151 440.3090 3492.938 462.6028 814.3348 363.9224 3.978484 0.0063975 0.0339844 0.4518514 0.9837510 0.2853458 0.0236740 0.3085389 0.0018823 0.7410762 0.0842644 0.0027163 0.0023933 0.0530173 0.9469016 0.1201782 0.3237740 11.086449 1.558648 0.0396399 0.3734227 0.0033726 0.3392473 0.1936004 0.0038318 0.1133477 0.1664452 0.7900182 4.439983 165.466575 23.27069 27.46112 16.07298 0.0764919
Macroscepis diademata species 1 0.5680507 0.8830066 15.631220 472.2120 19.45698 1.3175519 3.2246353 0.0516895 9.646357 4.375631 0.2145493 0.2883040 1.323244 156.96433 1.4300267 87.42576 86.095968 63.22982 3.258888 28.86790 0.5660702 29.86252 35.88395 1.939692 4.307702 61.24330 474.9934 970.4987 1754.126 2024.5715 1936.2448 2741.2378 4.016610 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

The object try.combined.means contains the average and standard deviation of the gap-filled trait values of 57869 taxa (species or genera) from TRY 5.0.

Object sPlot.traits.
Example of trait table of sPlot species (only 10 randomly selected species shown)
Species GrowthForm is.tree.or.tall.shrub n StemDens_mean RootingDepth_mean SLA_mean LeafC.perdrymass_mean LeafN_mean LeafP_mean PlantHeight_mean StemDiam_mean SeedMass_mean Seed.length_mean LeafThickness_mean LDMC_mean LeafNperArea_mean LeafDryMass.single_mean Leaf.delta.15N_mean SeedGerminationRate_mean Seed.num.rep.unit_mean LeafLength_mean LeafWidth_mean LeafCN.ratio_mean Leaffreshmass_mean Stem.cond.dens_mean Chromosome.n_mean Chromosome.cDNAcont_mean Disp.unit.leng_mean StemConduitDiameter_mean Wood.vessel.length_mean WoodFiberLength_mean SpecificRootLength_mean LeafArea.leaf.undef_mean LeafArea.leaflet.undef_mean LeafArea.undef.undef_mean LeafWaterCont_mean StemDens_sd RootingDepth_sd SLA_sd LeafC.perdrymass_sd LeafN_sd LeafP_sd PlantHeight_sd StemDiam_sd SeedMass_sd Seed.length_sd LeafThickness_sd LDMC_sd LeafNperArea_sd LeafDryMass.single_sd Leaf.delta.15N_sd SeedGerminationRate_sd Seed.num.rep.unit_sd LeafLength_sd LeafWidth_sd LeafCN.ratio_sd Leaffreshmass_sd Stem.cond.dens_sd Chromosome.n_sd Chromosome.cDNAcont_sd Disp.unit.leng_sd StemConduitDiameter_sd Wood.vessel.length_sd WoodFiberLength_sd SpecificRootLength_sd LeafArea.leaf.undef_sd LeafArea.leaflet.undef_sd LeafArea.undef.undef_sd LeafWaterCont_sd
Cullen balsamicum shrub FALSE 1 0.7658141 1.1357731 14.574205 470.7908 24.79413 1.0757493 0.7632617 0.0803196 10.1953783 2.4795811 0.1927224 0.3463087 1.907615 44.962733 1.2294652 88.70267 32.70424 11.29050 0.6326952 22.57503 0.1346718 20.03144 21.42409 2.382236 2.7979452 40.80183 291.5052 728.8761 1505.746 662.69302 477.97997 493.71686 2.637198 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Asplenium gracillimum NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Chaptalia cordata herb FALSE NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Juncus usitatus herb FALSE 1 0.4091928 0.3306955 4.059129 455.9002 13.55613 1.2942317 0.7075022 0.0212076 0.0106495 0.5648196 0.7184515 0.3620511 3.246347 27.831492 -0.7344482 89.62360 2363.18814 66.17733 0.5378561 34.43963 0.0768512 98.93933 50.59446 2.859040 0.5616332 29.32984 392.2232 639.4656 3757.660 123.09508 160.02641 141.78844 3.220099 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Ternstroemia acrodantha tree TRUE NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Rumex pictus herb FALSE 7 0.3578154 0.9648497 13.962281 454.9639 13.68960 0.6793454 0.4425787 0.0138313 0.7740556 2.1233639 0.3309167 0.2200303 1.018417 34.620120 -2.1866605 79.01673 520.93105 36.63076 1.5339184 33.15975 0.1702470 199.15830 28.08642 4.827151 2.1713416 34.38641 508.9707 683.2313 2371.522 472.56574 1193.14005 1048.83968 6.642336 0.0044673 0.1030289 0.1980500 2.6128162 0.4108824 0.0371299 0.0433507 0.0014053 0.0378214 0.0378566 0.0084461 0.0025655 0.0218695 1.7637077 0.2851467 11.681253 87.011303 4.234934 0.1363528 1.160389 0.0090686 19.27375 0.3512609 0.0520653 0.0363208 4.4999466 18.25610 64.20648 101.3928 27.195039 62.15051 54.04355 0.1413085
Cinchonopsis amazonica tree TRUE NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Ferula grigoriewii NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Centaurea melanocephala NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Crossotoma spinescens shrub FALSE 8 0.8014587 0.0838612 6.048407 421.9298 13.67867 0.7690420 0.4821147 0.2013032 9.5823304 2.8344815 0.2753666 0.3836693 2.686704 4.199538 1.4836421 83.46168 21.55450 34.49594 0.8690264 35.95583 0.0101748 176.32695 20.98942 1.517257 5.3409227 12.57043 301.2933 826.8403 2216.018 28.78313 23.62365 55.48094 2.330571 0.0047632 0.0055335 0.7318927 0.9680828 0.5231827 0.0342816 0.1960718 0.0314662 1.4528715 0.1835786 0.0144772 0.0103723 0.2212469 0.7488502 0.1774395 0.631457 4.486621 5.094522 0.1549661 1.397549 0.0017404 12.48717 0.1362215 0.0371624 0.3081829 0.3744928 7.02001 23.64030 116.5048 5.703395 4.84936 11.32248 0.1134490

The object sPlot.traits contains the average and standard deviation of the gap-filled trait values for 32201 taxa (species or genera), out of 76912 in sPlot. It also contains growth form information for 45587 species.


Object CWM.
Example of CWM table (only 10 randomly selected plots shown)
PlotObservationID variable sp.richness prop.sp.with.trait trait.coverage CWM CWV
693027 LeafP_mean 13 0.9230769 0.9467213 1.740370e+00 1.707564e-01
1339398 LeafLength_mean 8 0.6250000 0.5227273 2.165635e+01 3.033668e+02
692278 LeafP_mean 20 0.7000000 0.5355517 2.332146e+00 7.008663e-01
1729372 LeafWidth_mean 7 0.8571429 0.7904762 1.453743e+00 2.909174e-01
502174 StemDens_mean 29 0.7586207 0.4222222 3.868366e-01 1.125460e-02
1095140 Seed.length_mean 18 0.8888889 0.9600000 1.776557e+00 4.106242e-01
1178622 LeafThickness_mean 21 0.6666667 0.8346457 1.664092e-01 4.295500e-03
857064 Seed.length_mean 24 0.9166667 0.6666667 1.757482e+00 3.281443e-01
143848 SpecificRootLength_mean 25 0.4800000 0.4899320 5.883528e+07 4.706267e+16
1078481 LeafC.perdrymass_mean 9 1.0000000 1.0000000 4.368949e+02 1.265754e+02

The CWM table contains 56284833 entries, i.e., the combination between 1705601 unique plots, and 33.

4.2 Description of fields

Legend of traits used in the data.frame sPlot.traits and try.combined.means. The number represents the code in TRY dictionary. The abbreviation used is reported after the trait description.

4 Stem specific density (SSD) or wood density (stem dry mass per stem fresh volume)_g/cm3 - StemDens
6 Root rooting depth_m - RootingDepth
11 Leaf area per leaf dry mass (specific leaf area, SLA or 1/LMA) - SLA
13 Leaf carbon (C) content per leaf dry mass_mg/g - LeafC.perdrymass
14 Leaf nitrogen (N) content per leaf dry mass_mg/g - LeafN
15 Leaf phosphorus (P) content per leaf dry mass_mg/g - LeafP
18 Plant height (vegetative + generative) - PlantHeight
21 Stem diameter_m - StemDiam
26 Seed dry mass_mg - SeedMass
27 Seed length_mm - Seed.length
46 Leaf thickness_mm - LeafThickness
47 Leaf dry mass per leaf fresh mass (leaf dry matter content, LDMC)_g g-1 - LDMC
50 Leaf nitrogen (N) content per leaf area_g m-2 - LeafNperArea
55 Leaf dry mass (single leaf)_mg - LeafDryMass.single
78 Leaf nitrogen (N) isotope signature (delta 15N)_per - Leaf.delta.15N
95 Seed germination rate (germination efficiency) % - SeedGerminationRate
138 Seed number per reproducton unit_number - Seed.num.rep.unit
144 Leaf length_mm - LeafLength
145 Leaf width_cm - LeafWidth
146 Leaf carbon/nitrogen (C/N) ratio_g/cm3 - LeafCN.ratio
163 Leaf fresh mass_g - Leaffreshmass
169 Stem conduit density (vessels and tracheids)_mm-2 - Stem.cond.dens
223 Species genotype: chromosome number_dimensionless - Chromosome.n
224 Species genotype: chromosome cDNA content_pg - Chromosome.cDNAcont
237 Dispersal unit length_mm - Disp.unit.leng
281 Stem conduit diameter (vessels, tracheids)_micro m - StemConduitDiameter
282 Wood vessel element length; stem conduit (vessel and tracheids) element length_micro m - Wood.vessel.length
289 Wood fiber lengths_micro m - WoodFiberLength
1080 Root length per root dry mass (specific root length, SRL)_cm/g - SpecificRootLength
3112 Leaf area (in case of compound leaves: leaf, undefined if petiole in- or excluded)_mm2 - LeafArea.leaf.undef
3113 Leaf area (in case of compound leaves: leaflet, undefined if petiole is in- or excluded)_mm2 - LeafArea.leaflet.undef
3114 Leaf area (in case of compound leaves undefined if leaf or leaflet, undefined if petiole is in- or excluded)_mm2 - LeafArea.undef.undef
3120 Leaf water content per leaf dry mass (not saturated)_g(W)/g(DM) - LeafWaterCont


List of Fields

Object sPlot.traits
1. Species: Species name, as in the field Species of DT2.
2. GrowthForm: Possible values: herb , herb/shrub , herb/shrub/tree , other , shrub , shrub/tree , tree.
3. is.tree.or.tall.shrub: TRUE\FALSE - Defines as tree of tall shrub if Growth Form contains is equal to ‘tree’, ‘shrub/tree’ or ‘shrub’, or if Height > 10 m.
4. n: Number of individual gap-filled entries used for calculating mean and s.d. of the taxon.
5-37. Functional traits means
38-70. Functional traits standard deviations

Object try.combined.means
1. Taxon_name: Species name, as in the field Species of DT2.
2. Rank_correct: Rank of taxon name (either “Species”, or “Genus”), used for calculating the mean and s.d. of trait values.
3. n: Number of individual gap-filled entries used for calculating mean and s.d. of the taxon.
4-36. Functional trait means
37-69. Functional trait standard deviations


Object CWM
1. PlotObservationID: Plot ID, as in header.
2. variable: Functional trait.
3. sp.richness: Number of species in plot.
4. prop.sp.with.trait: Proportion of species with trait information.
5. trait.coverage: Proportion of the species’ relative cover for which functional trait is available.
6. CWM: Community Weighted Mean.
7. CWV: Community Weighted Variance.

5 Environmental variables

load("../_output/SoilClim_sPlot3.RData")

The object SoilClim_sPlot3 contains data on the environmental conditions of plots, as derived from matching Plots’ coordinates with global-scale layers of topography, climate and soil data. Its construction is documented at: https://git.idiv.de/fs40gaho/splot3_build/-/blob/master/public/05_ExtractEnvironment.html (download needed).
Environmental data derive from three sources:

  1. Bioclimatic variables (bio01-bio19) derive from CHELSA.
  2. Soil variables (5 cm depth) derive from the ISRIC dataset, downloaded at 250-m resolution.
  3. DEM derive from package elevatr, which uses the Terrain Tiles on Amazon Web Services.

5.1 Show output

Example of dataframe soilclim.
Example of environmental information on 10 randomly selected plots
PlotObservationID Elevation_median Elevation_q2.5 Elevation_q97.5 Elevation_DEM.res bio01 bio02 bio03 bio04 bio05 bio06 bio07 bio08 bio09 bio10 bio11 bio12 bio13 bio14 bio15 bio16 bio17 bio18 bio19 bio01sd bio02sd bio03sd bio04sd bio05sd bio06sd bio07sd bio08sd bio09sd bio10sd bio11sd bio12sd bio13sd bio14sd bio15sd bio16sd bio17sd bio18sd bio19sd BLDFIE CECSOL CLYPPT CRFVOL ORCDRC PHIHOX SLTPPT SNDPPT BLDFIEsd CECSOLsd CLYPPTsd CRFVOLsd ORCDRCsd PHIHOXsd SLTPPTsd SNDPPTsd
926871 NA NA NA NA 161.000 12.00000 82.0000 4742.000 236.0000 89.0000000 146.0000 108.00000 231.00000 231.0000 100.00000 796.0000 161.00000 1.00000 85.00000 478.0000 3.0000 3.0000 385.0000 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 1323.0000 23.80000 25.40000 18.400000 30.40000 70.20000 37.20000 38.00000 37.033768 1.095445 1.3416408 1.1401754 4.615192 0.4472136 0.4472136 1.2247449
654600 NA NA NA NA 117.482 74.00000 310.0945 5769.304 251.9301 12.5746692 239.3459 144.01323 67.82420 200.7032 43.22306 744.4877 80.23629 50.77883 12.75992 217.0870 156.0794 192.6711 183.1474 2.031047 0.000000 0.3825604 15.06149 2.215823 1.886606 0.6595651 16.9136 2.720103 2.145469 1.897805 62.95901 6.811235 4.344781 0.5814532 18.32586 13.903119 16.49924 16.215669 988.5854 16.25147 20.63628 12.025206 23.63887 62.96561 38.21720 41.12073 92.959008 2.246399 3.4595559 1.8352642 5.752081 4.4650441 3.4865659 5.6465916
1485922 NA NA NA NA 112.000 72.00000 260.0000 7125.000 256.0000 -22.0000000 279.0000 82.00000 20.00000 210.0000 16.00000 2260.0000 255.00000 131.00000 19.00000 749.0000 408.0000 536.0000 455.0000 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 847.4000 26.80000 26.60000 12.400000 78.00000 61.80000 41.20000 32.20000 16.425590 1.303840 0.5477226 2.0736441 8.602325 0.8366600 1.9235384 1.4832397
131079 NA NA NA NA 100.052 68.87348 307.4922 5434.270 222.9445 -0.3414211 223.3085 91.71231 80.18717 176.7868 28.66378 806.6915 75.59099 51.86482 10.01040 223.3778 169.9913 218.5095 186.2964 1.595589 0.332719 0.5003730 14.06297 1.347725 1.752845 0.5668633 62.1180 1.585407 1.480651 1.713292 41.57112 3.985972 2.667791 0.3534002 11.60577 9.059119 12.45340 9.849944 675.8064 13.91451 13.87350 8.424516 19.73961 62.81977 64.22330 21.87242 84.695727 1.464204 1.5854461 1.2474760 4.989717 5.4984385 8.4684489 9.3935629
1248228 NA NA NA NA 91.000 72.00000 269.0000 7079.000 236.0000 -33.0000000 269.0000 187.00000 -2.00000 187.0000 -3.00000 574.0000 79.00000 27.00000 36.00000 229.0000 83.0000 229.0000 96.0000 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 1258.0000 18.00000 17.00000 9.000000 22.00000 69.00000 34.00000 50.00000 NA NA NA NA NA NA NA NA
1574531 623 623 623 153 89.000 80.00000 288.0000 6845.000 238.0000 -42.0000000 279.0000 185.00000 3.00000 185.0000 -1.00000 1707.0000 206.00000 77.00000 31.00000 591.0000 235.0000 591.0000 248.0000 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 776.5000 27.83333 20.00000 27.500000 110.83333 57.16667 36.00000 44.50000 25.913317 3.250641 0.6324555 1.8708287 16.485347 0.4082483 1.0954451 1.0488088
455864 40 40 40 153 85.000 31.00000 160.0000 5794.000 189.0000 -5.0000000 194.0000 70.00000 52.00000 168.0000 9.00000 695.0000 72.00000 40.00000 19.00000 216.0000 127.0000 195.0000 139.0000 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 717.7500 14.25000 12.62500 7.875000 28.12500 64.75000 26.75000 60.50000 7.324128 0.462910 0.7440238 0.3535534 2.167124 0.7071068 0.4629100 0.5345225
1065857 3 3 3 153 99.000 36.00000 203.0000 4966.000 194.0000 15.0000000 179.0000 89.00000 70.00000 171.0000 33.00000 816.0000 85.00000 40.00000 22.00000 255.0000 133.0000 237.0000 166.0000 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 791.6667 18.33333 19.00000 10.333333 55.33333 68.50000 30.33333 50.33333 28.394835 1.032796 0.6324555 3.3862467 5.955390 0.5477226 1.2110601 1.0327956
690377 252 252 252 153 105.000 43.00000 276.0000 3921.000 188.0000 33.0000000 155.0000 71.00000 154.00000 162.0000 54.00000 969.0000 120.00000 52.00000 29.00000 352.0000 164.0000 176.0000 277.0000 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 699.0000 25.40000 18.40000 16.400000 140.00000 48.20000 49.40000 32.60000 39.147158 1.673320 0.5477226 0.5477226 7.035624 0.8366600 0.8944272 0.8944272
1891379 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

5.2 Description of fields

  1. PlotObservationID: Plot ID, as in header.

    Elevation data - median and s.d.
  2. Elevation_median: Median elevation in a circle centered on plot location, having a radius of the plot’s location uncertainty (NA if >50km).
  3. Elevation_q2.5: 2.5 percentile of elevation in a circle centered on plot location, having a radius of the plot’s location uncertainty (NA if >50km).
  4. Elevation_q97.5: 97.5 percentile of elevation in a circle centered on plot location, having a radius of the plot’s location uncertainty (NA if >50km).
  5. Elevation_DEM.res: Resolution of Digital Elevation Model used (in m).

    Bioclimatic Variables - Mean and s.d.
  6. bio01: Annual Mean Temperature
  7. bio02: Mean Diurnal Range
  8. bio03: Isothermality
  9. bio04: Temperature Seasonality
  10. bio05: Max Temperature of Warmest Month
  11. bio06: Min Temperature of Coldest Month
  12. bio07: Temperature Annual Range
  13. bio08: Mean Temperature of Wettest Quarter
  14. bio09: Mean Temperature of Driest Quarter
  15. bio10: Mean Temperature of Warmest Quarter
  16. bio11: Mean Temperature of Coldest Quarter
  17. bio12: Annual Precipitation
  18. bio13: Precipitation of Wettest Month
  19. bio14: Precipitation of Driest Month
  20. bio15: Precipitation Seasonality
  21. bio16: Precipitation of Wettest Quarter
  22. bio17: Precipitation of Driest Quarter
  23. bio18: Precipitation of Warmest Quarter
  24. bio19: Precipitation of Coldest Quarter
    25-43 - Same as above, but standard deviations

    Soil Variables - Mean and s.d.
  25. BLDFIE: Bulk Density (fine earth) in kg/m3
  26. CECSOL: Cation Exchange capacity of soil
  27. CLYPPT: Clay mass fraction in %
  28. CRFVOL: Coarse fragments volumetric in %
  29. ORCDRC: Soil Organic Carbon Content in g/kg
  30. PHIHOX: Soil pH x 10 in H20
  31. SLTPPT: Silt mass fraction in %
  32. SNDPPT: Sand mass fraction in %
    52-59 - Same as above, but standard deviations

6 SessionInfo

sessionInfo()
## R version 3.6.3 (2020-02-29)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.7 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/openblas-base/libblas.so.3
## LAPACK: /usr/lib/libopenblasp-r0.2.18.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] kableExtra_1.3.1 knitr_1.30       forcats_0.5.0    stringr_1.4.0   
##  [5] dplyr_1.0.2      purrr_0.3.4      readr_1.4.0      tidyr_1.1.2     
##  [9] tibble_3.0.1     ggplot2_3.3.0    tidyverse_1.3.0 
## 
## loaded via a namespace (and not attached):
##  [1] tidyselect_1.1.0  xfun_0.19         haven_2.3.1       colorspace_2.0-0 
##  [5] vctrs_0.3.5       generics_0.1.0    htmltools_0.5.0   viridisLite_0.3.0
##  [9] yaml_2.2.1        rlang_0.4.9       pillar_1.4.3      glue_1.4.2       
## [13] withr_2.3.0       DBI_1.1.0         dbplyr_2.0.0      modelr_0.1.6     
## [17] readxl_1.3.1      lifecycle_0.2.0   munsell_0.5.0     gtable_0.3.0     
## [21] cellranger_1.1.0  rvest_0.3.6       evaluate_0.14     fansi_0.4.1      
## [25] highr_0.8         broom_0.7.0       Rcpp_1.0.5        scales_1.1.1     
## [29] backports_1.2.0   webshot_0.5.2     jsonlite_1.7.1    fs_1.5.0         
## [33] hms_0.5.3         digest_0.6.25     stringi_1.5.3     grid_3.6.3       
## [37] cli_2.2.0         tools_3.6.3       magrittr_2.0.1    crayon_1.3.4     
## [41] pkgconfig_2.0.3   ellipsis_0.3.1    xml2_1.3.2        reprex_0.3.0     
## [45] lubridate_1.7.9.2 assertthat_0.2.1  rmarkdown_2.5     httr_1.4.2       
## [49] rstudioapi_0.13   R6_2.5.0          compiler_3.6.3