Timestamp: Wed Dec 2 01:59:24 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
Mapania polystachya Mapania polystachya NA T Mapania polystachya 192413 0.5 Mapania genus 0.5 NA http://www.theplantlist.org/tpl1.1/search?q=Mapania;http://plants.usda.gov/java/profile?symbol=MAPAN NA NA NA NA Cyperaceae Mapania 1 NA NA NA NA NA NA NA NA NA polystachya Accepted Mapania NA genus http://www.theplantlist.org/tpl1.1/search?q=Mapania;http://plants.usda.gov/java/profile?symbol=MAPAN NA Cyperaceae FALSE tpl;usda [Partial match] NA Accepted Mapania Mapania genus Cyperaceae Mapania Tracheophyta TRUE Vascular plant
Paraphlomis lanceolata Paraphlomis lanceolata NA T Paraphlomis lanceolata 225021 1.0 Paraphlomis lanceolata species 1.0 Hand.-Mazz. http://www.theplantlist.org/tpl1.1/record/kew-147658;http://www.tropicos.org/Name/17606449 NA NA NA NA Lamiaceae Paraphlomis 1 lanceolata 1 NA NA NA NA NA NA NA NA Accepted Paraphlomis lanceolata Hand.-Mazz. species http://www.theplantlist.org/tpl1.1/record/kew-147658;http://www.tropicos.org/Name/17606449 Paraphlomis lanceolata Lamiaceae TRUE tpl;tropicos NA NA Accepted Paraphlomis lanceolata Paraphlomis species Lamiaceae Paraphlomis lanceolata Tracheophyta TRUE Vascular plant
Wendlandia nobilis Wendlandia nobilis NA T Wendlandia nobilis 329004 1.0 Wendlandia nobilis species 1.0 Geddes http://www.theplantlist.org/tpl1.1/record/kew-214475 NA NA NA NA Rubiaceae Wendlandia 1 nobilis 1 NA NA NA NA NA NA NA NA Accepted Wendlandia nobilis Geddes species http://www.theplantlist.org/tpl1.1/record/kew-214475 Wendlandia nobilis Rubiaceae TRUE tpl NA NA Accepted Wendlandia nobilis Wendlandia species Rubiaceae Wendlandia nobilis Tracheophyta TRUE Vascular plant
Pentapanax sp Pentapanax NA T Pentapanax 230473 1.0 Pentapanax genus 1.0 NA http://www.theplantlist.org/tpl1.1/search?q=Pentapanax NA NA NA NA Araliaceae Pentapanax 1 NA NA NA NA NA NA NA NA NA NA Accepted Pentapanax NA genus http://www.theplantlist.org/tpl1.1/search?q=Pentapanax NA Araliaceae TRUE tpl NA NA Accepted Pentapanax Pentapanax genus Araliaceae Pentapanax Tracheophyta TRUE Vascular plant
Casearia aequilateralis Casearia aequilateralis NA T Casearia aequilateralis 59914 1.0 Casearia aequilateralis species 1.0 Merr. http://www.theplantlist.org/tpl1.1/record/kew-4701965 NA NA NA NA Salicaceae Casearia 1 aequilateralis 1 NA NA NA NA NA NA NA NA Accepted Casearia aequilateralis Merr. species http://www.theplantlist.org/tpl1.1/record/kew-4701965 Casearia aequilateralis Salicaceae TRUE tpl NA NA Accepted Casearia aequilateralis Casearia species Salicaceae Casearia aequilateralis Tracheophyta TRUE Vascular plant
Symplocos nigridentata Symplocos nigridentata NA T Symplocos nigridentata 302916 1.0 Symplocos nigridentata species 1.0 P.W. Fritsch http://www.theplantlist.org/tpl1.1/record/tro-100352281;http://www.tropicos.org/Name/100352281 NA NA NA NA Symplocaceae Symplocos 1 nigridentata 1 NA NA NA NA NA NA NA NA No opinion NA NA NA ; NA NA TRUE tpl;tropicos NA NA Other Symplocos nigridentata Symplocos species Symplocaceae Symplocos nigridentata Tracheophyta TRUE Vascular plant
Cyperus subumbellatus Cyperus subumbellatus NA T Cyperus subumbellatus 91576 1.0 Cyperus subumbellatus species 1.0 Kük. http://www.theplantlist.org/tpl1.1/record/kew-238712 NA NA NA NA Cyperaceae Cyperus 1 subumbellatus 1 NA NA NA NA NA NA NA NA Synonym Cyperus cyperoides (L.) Kuntze species http://www.theplantlist.org/tpl1.1/record/kew-236243 Cyperus cyperoides Cyperaceae TRUE tpl NA NA Synonym Cyperus cyperoides Cyperus species Cyperaceae Cyperus cyperoides Tracheophyta TRUE Vascular plant
Vaccinium elvirae Vaccinium elvirae NA T Vaccinium elvirae 321400 1.0 Vaccinium elvirae species 1.0 Luteyn http://www.theplantlist.org/tpl1.1/record/tro-12302852;http://www.tropicos.org/Name/12302852 NA NA NA NA Ericaceae Vaccinium 1 elvirae 1 NA NA NA NA NA NA NA NA Accepted Vaccinium elvirae Luteyn species http://www.theplantlist.org/tpl1.1/record/tro-12302852;http://www.tropicos.org/Name/12302852 Vaccinium elvirae Ericaceae TRUE tpl;tropicos NA NA Accepted Vaccinium elvirae Vaccinium species Ericaceae Vaccinium elvirae Tracheophyta TRUE Vascular plant
Senecio pentapterus Senecio pentapterus NA T Senecio pentapterus 284849 1.0 Senecio pentapterus species 1.0 Cabrera http://dixon.iplantcollaborative.org/CompositaeWeb/default.aspx?Page=NameDetails&TabNum=0&NameId=468E380E-8583-4930-AF37-251B67F40F22;http://www.tropicos.org/Name/2733758 NA NA NA NA Asteraceae Senecio 1 pentapterus 1 NA NA NA NA NA NA NA NA Accepted Senecio pentapterus Cabrera species http://dixon.iplantcollaborative.org/CompositaeWeb/default.aspx?Page=NameDetails&TabNum=0&NameId=468E380E-8583-4930-AF37-251B67F40F22;http://www.tropicos.org/Name/2733758 Senecio pentapterus Asteraceae TRUE gcc;tropicos NA urn:lsid:compositae.org:names:468E380E-8583-4930-AF37-251B67F40F22 Accepted Senecio pentapterus Senecio species Compositae Senecio pentapterus Tracheophyta TRUE Vascular plant
Orchis x loreziana Orchis loreziana NA T Orchis loreziana 217361 1.0 Orchis loreziana species 1.0 Brügger http://www.theplantlist.org/tpl1.1/record/kew-142792 NA NA NA NA Orchidaceae Orchis 1 loreziana 1 NA NA NA NA NA NA NA NA Accepted Orchis x loreziana Brügger species http://www.theplantlist.org/tpl1.1/record/kew-142792 Orchis x loreziana Orchidaceae TRUE tpl NA NA Accepted Orchis x loreziana Orchis species Orchidaceae Orchis loreziana Tracheophyta TRUE Vascular plant
Bossiaea simulata Bossiaea simulata NA T Bossiaea simulata 44174 1.0 Bossiaea simulata species 1.0 J.H.Ross http://www.theplantlist.org/tpl1.1/record/kew-2680529 NA NA NA NA Fabaceae Bossiaea 1 simulata 1 NA NA NA NA NA NA NA NA No opinion NA NA NA NA NA NA TRUE tpl NA NA Other Bossiaea simulata Bossiaea species Leguminosae Bossiaea simulata Tracheophyta TRUE Vascular plant
Dichaea brevicaulis Dichaea brevicaulis NA T Dichaea brevicaulis 97956 1.0 Dichaea brevicaulis species 1.0 Cogn. http://www.theplantlist.org/tpl1.1/record/kew-61182;http://www.tropicos.org/Name/23519556 NA NA NA NA Orchidaceae Dichaea 1 brevicaulis 1 NA NA NA NA NA NA NA NA Accepted Dichaea brevicaulis Cogn. species http://www.theplantlist.org/tpl1.1/record/kew-61182;http://www.tropicos.org/Name/23519556 Dichaea brevicaulis Orchidaceae TRUE tpl;tropicos NA NA Accepted Dichaea brevicaulis Dichaea species Orchidaceae Dichaea brevicaulis Tracheophyta TRUE Vascular plant
Leontodon hyoseroides subsp. pseudocrispus Leontodon hyoseroides subsp. pseudocrispus NA S Leontodon hyoseroides subsp. pseudocrispus 175815 1.0 Leontodon hyoseroides subsp. pseudocrispus subspecies 1.0 (Bisch.) Greuter http://dixon.iplantcollaborative.org/CompositaeWeb/default.aspx?Page=NameDetails&TabNum=0&NameId=A3D51CCA-53A4-402C-BA0C-1EAA9378A1C7 NA NA NA NA Asteraceae Leontodon 1 hyoseroides 1 subsp. pseudocrispus 1 NA NA NA NA NA Accepted Leontodon hyoseroides subsp. pseudocrispus (Bisch.) Greuter subspecies http://dixon.iplantcollaborative.org/CompositaeWeb/default.aspx?Page=NameDetails&TabNum=0&NameId=A3D51CCA-53A4-402C-BA0C-1EAA9378A1C7 Leontodon hyoseroides Asteraceae TRUE gcc NA urn:lsid:compositae.org:names:A3D51CCA-53A4-402C-BA0C-1EAA9378A1C7 Accepted Leontodon hyoseroides subsp. pseudocrispus Leontodon subspecies Compositae Leontodon hyoseroides Tracheophyta TRUE Vascular plant
Boisduvalia subulata Boisduvalia subulata NA T Boisduvalia subulata 43313 1.0 Boisduvalia subulata species 1.0 (Ruiz & Pav.) Raim. http://www.theplantlist.org/tpl1.1/record/kew-2678879 NA NA NA NA Onagraceae Boisduvalia 1 subulata 1 NA NA NA NA NA NA NA NA Accepted Boisduvalia subulata (Ruiz & Pav.) Raim. species http://www.theplantlist.org/tpl1.1/record/kew-2678879 Boisduvalia subulata Onagraceae TRUE tpl NA NA Accepted Boisduvalia subulata Boisduvalia species Onagraceae Boisduvalia subulata Tracheophyta TRUE Vascular plant
Carica candicans Carica candicans NA T Carica candicans 59277 1.0 Carica candicans species 1.0 A.Gray http://www.theplantlist.org/tpl1.1/record/kew-2700865 NA NA NA NA Caricaceae Carica 1 candicans 1 NA NA NA NA NA NA NA NA Accepted Carica candicans A.Gray species http://www.theplantlist.org/tpl1.1/record/kew-2700865 Carica candicans Caricaceae TRUE tpl NA NA Accepted Carica candicans Carica species Caricaceae Carica candicans Tracheophyta TRUE Vascular plant
Adesmia tomentosa Adesmia tomentosa NA T Adesmia tomentosa 6184 1.0 Adesmia tomentosa species 1.0 Meyen http://www.ildis.org/LegumeWeb?version~10.01&genus~Adesmia&species~tomentosa;http://www.tropicos.org/Name/13024785 NA NA NA NA Fabaceae Adesmia 1 tomentosa 1 NA NA NA NA NA NA NA NA Accepted Adesmia tomentosa Meyen species http://www.ildis.org/LegumeWeb?version~10.01&genus~Adesmia&species~tomentosa;http://www.tropicos.org/Name/13024785 Adesmia tomentosa Fabaceae TRUE ildis;tropicos NA NA Accepted Adesmia tomentosa Adesmia species Leguminosae Adesmia tomentosa Tracheophyta TRUE Vascular plant
Taraxacum latisectum Taraxacum latisectum NA T Taraxacum latisectum 306390 1.0 Taraxacum latisectum species 1.0 H.Lindb. http://dixon.iplantcollaborative.org/CompositaeWeb/default.aspx?Page=NameDetails&TabNum=0&NameId=CBC3F979-2CC3-49C2-B5D2-9EF5214A939E NA NA NA NA Asteraceae Taraxacum 1 latisectum 1 NA NA NA NA NA NA NA NA Accepted Taraxacum latisectum H.Lindb. species http://dixon.iplantcollaborative.org/CompositaeWeb/default.aspx?Page=NameDetails&TabNum=0&NameId=CBC3F979-2CC3-49C2-B5D2-9EF5214A939E Taraxacum latisectum Asteraceae TRUE gcc NA urn:lsid:compositae.org:names:CBC3F979-2CC3-49C2-B5D2-9EF5214A939E Accepted Taraxacum latisectum Taraxacum species Compositae Taraxacum latisectum Tracheophyta TRUE Vascular plant
Notogrammitis givenii Notogrammitis givenii Notogrammitis givenii S Notogrammitis givenii NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA No suitable matches found. NA NA higher NA NA NA NA Unknown
Cyperus swartzii Cyperus swartzii NA T Cyperus swartzii 91580 1.0 Cyperus swartzii species 1.0 (A.Dietr.) Boeckeler ex Kük. http://www.theplantlist.org/tpl1.1/record/kew-238727 NA NA NA NA Cyperaceae Cyperus 1 swartzii 1 NA NA NA NA NA NA NA NA Accepted Cyperus swartzii (A.Dietr.) Boeckeler ex Kük. species http://www.theplantlist.org/tpl1.1/record/kew-238727 Cyperus swartzii Cyperaceae TRUE tpl NA NA Accepted Cyperus swartzii Cyperus species Cyperaceae Cyperus swartzii Tracheophyta TRUE Vascular plant
Pelexia olivacea Pelexia olivacea NA T Pelexia olivacea 229221 1.0 Pelexia olivacea species 1.0 Rolfe http://www.theplantlist.org/tpl1.1/record/kew-149658;http://www.tropicos.org/Name/23510329 NA NA NA NA Orchidaceae Pelexia 1 olivacea 1 NA NA NA NA NA NA NA NA Accepted Pelexia olivacea Rolfe species http://www.theplantlist.org/tpl1.1/record/kew-149658;http://www.tropicos.org/Name/23510329 Pelexia olivacea Orchidaceae TRUE tpl;tropicos NA NA Accepted Pelexia olivacea Pelexia species Orchidaceae Pelexia olivacea 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
157145 Helictochloa pratensis Avenula pratensis species Vascular plant 6 1 CoverPerc 2 0.0273973
157145 Helictotrichon pubescens Avenula pubescens species Vascular plant 6 1 CoverPerc 2 0.0273973
157145 Briza media Briza media species Vascular plant 6 1 CoverPerc 2 0.0273973
157145 Cirsium acaulon Cirsium acaule species Vascular plant 6 1 CoverPerc 2 0.0273973
157145 Dicranum scoparium Dicranum scoparium species Moss 9 3 CoverPerc 4 0.0547945
157145 Festuca ovina Festuca ovina species Vascular plant 6 4 CoverPerc 13 0.1780822
157145 Galium verum Galium verum species Vascular plant 6 6 CoverPerc 29 0.3972603
157145 Pilosella officinarum Hieracium pilosella subsp. s. species Vascular plant 6 3 CoverPerc 4 0.0547945
157145 Koeleria macrantha Koeleria macrantha species Vascular plant 6 1 CoverPerc 2 0.0273973
157145 Leontodon hispidus Leontodon hispidus species Vascular plant 6 3 CoverPerc 4 0.0547945
157145 Lotus corniculatus Lotus corniculatus species Vascular plant 6 3 CoverPerc 4 0.0547945
157145 Pseudoscleropodium purum Pseudoscleropodium purum species Moss 9 2 CoverPerc 3 0.0410959
157145 Thymus praecox Thymus praecox arcticus lower Vascular plant 6 1 CoverPerc 2 0.0273973
210150 Acer campestre Acer campestre species Vascular plant 4
CoverPerc 2 0.0057307
210150 Acer platanoides Acer platanoides species Vascular plant 4
CoverPerc 2 0.0057307
210150 Actaea spicata Actaea spicata species Vascular plant 6 1 CoverPerc 3 0.0085960
210150 Ajuga reptans Ajuga reptans species Vascular plant 6
CoverPerc 2 0.0057307
210150 Arctium lappa Arctium lappa species Vascular plant 6
CoverPerc 2 0.0057307
210150 Athyrium filix-femina Athyrium filix-femina species Vascular plant 6 1 CoverPerc 3 0.0085960
210150 Atrichum undulatum Atrichum undulatum species Moss 9
CoverPerc 2 0.0057307
210150 Atropa bella-donna Atropa bella-donna species Vascular plant 6
CoverPerc 2 0.0057307
210150 Campanula patula Campanula patula species Vascular plant 6
CoverPerc 2 0.0057307
210150 Campanula persicifolia Campanula persicifolia species Vascular plant 6
CoverPerc 2 0.0057307
210150 Cardamine impatiens Cardamine impatiens species Vascular plant 6
CoverPerc 2 0.0057307
210150 Cardamine kitaibelii Cardamine kitaibelli species Vascular plant 6 3 CoverPerc 38 0.1088825
210150 Carex digitata Carex digitata species Vascular plant 6
CoverPerc 2 0.0057307
210150 Carex divulsa Carex divulsa species Vascular plant 6
CoverPerc 2 0.0057307
210150 Carex sylvatica Carex sylvatica species Vascular plant 6 1 CoverPerc 3 0.0085960
210150 Carpinus betulus Carpinus betulus species Vascular plant 4
CoverPerc 2 0.0057307
210150 Castanea sativa Castanea sativa species Vascular plant 1 1 CoverPerc 3 0.0085960
210150 Castanea sativa Castanea sativa species Vascular plant 4
CoverPerc 2 0.0057307
210150 Cephalanthera longifolia Cephalanthera longifolia species Vascular plant 6
CoverPerc 2 0.0057307
210150 Chelidonium majus Chelidonium majus species Vascular plant 6
CoverPerc 2 0.0057307
210150 Circaea lutetiana Circaea lutetiana species Vascular plant 6 2 CoverPerc 13 0.0372493
210150 Cirsium Cirsium species genus Vascular plant 6
CoverPerc 2 0.0057307
210150 Corylus avellana Corylus avellana species Vascular plant 4
CoverPerc 2 0.0057307
210150 Cardamine bulbifera Dentaria bulbifera species Vascular plant 6 3 CoverPerc 38 0.1088825
210150 Dicranella heteromalla Dicranella heteromalla species Moss 9
CoverPerc 2 0.0057307
210150 Dryopteris carthusiana Dryopteris carthusiana species Vascular plant 6
CoverPerc 2 0.0057307
210150 Dryopteris filix-mas Dryopteris filix-mas species Vascular plant 6
CoverPerc 2 0.0057307
210150 Erigeron annuus Erigeron annuus species Vascular plant 6
CoverPerc 2 0.0057307
210150 Eupatorium cannabinum Eupatorium cannabinum species Vascular plant 6
CoverPerc 2 0.0057307
210150 Euphorbia amygdaloides Euphorbia amygdaloides species Vascular plant 6
CoverPerc 2 0.0057307
210150 Fagus sylvatica Fagus sylvatica species Vascular plant 1 4 CoverPerc 68 0.1948424
210150 Fagus sylvatica Fagus sylvatica species Vascular plant 4 1 CoverPerc 3 0.0085960
210150 Festuca drymeja Festuca drymeia species Vascular plant 6
CoverPerc 2 0.0057307
210150 Fraxinus ornus Fraxinus ornus species Vascular plant 4
CoverPerc 2 0.0057307
210150 Galeopsis speciosa Galeopsis speciosa species Vascular plant 6 2 CoverPerc 13 0.0372493
210150 Galium odoratum Galium odoratum species Vascular plant 6 3 CoverPerc 38 0.1088825
210150 Genista tinctoria Genista tinctoria species Vascular plant 4
CoverPerc 2 0.0057307
210150 Geranium robertianum Geranium robertianum species Vascular plant 6
CoverPerc 2 0.0057307
210150 Glechoma hirsuta Glechoma hirsuta species Vascular plant 6
CoverPerc 2 0.0057307
210150 Hedera helix Hedera helix species Vascular plant 6
CoverPerc 2 0.0057307
210150 Hypericum androsaemum Hypericum androsaemum species Vascular plant 6
CoverPerc 2 0.0057307
210150 Hypericum montanum Hypericum montanum species Vascular plant 6
CoverPerc 2 0.0057307
210150 Hypnum cupressiforme Hypnum cupressiforme species Moss 9
CoverPerc 2 0.0057307
210150 Lamium galeobdolon Lamiastrum galeobdolon s.s. species Vascular plant 6 1 CoverPerc 3 0.0085960
210150 Lathyrus vernus Lathyrus vernus species Vascular plant 6
CoverPerc 2 0.0057307
210150 Luzula forsteri Luzula forsteri species Vascular plant 6
CoverPerc 2 0.0057307
210150 Luzula luzuloides Luzula luzuloides species Vascular plant 6
CoverPerc 2 0.0057307
210150 Melittis melissophyllum Melittis melissophyllum species Vascular plant 6
CoverPerc 2 0.0057307
210150 Moehringia trinervia Moehringia trinervia species Vascular plant 6
CoverPerc 2 0.0057307
210150 Lactuca muralis Mycelis muralis species Vascular plant 6 1 CoverPerc 3 0.0085960
210150 Neottia nidus-avis Neottia nidus-avis species Vascular plant 6
CoverPerc 2 0.0057307
210150 Polystichum setiferum Polystichum setiferum species Vascular plant 6 1 CoverPerc 3 0.0085960
210150 Potentilla micrantha Potentilla micrantha species Vascular plant 6
CoverPerc 2 0.0057307
210150 Pteridium aquilinum Pteridium aquilinum species Vascular plant 6
CoverPerc 2 0.0057307
210150 Pulmonaria officinalis Pulmonaria officinalis species Vascular plant 6
CoverPerc 2 0.0057307
210150 Quercus petraea Quercus petraea species Vascular plant 1 1 CoverPerc 3 0.0085960
210150 Quercus petraea Quercus petraea species Vascular plant 4
CoverPerc 2 0.0057307
210150 Quercus petraea Quercus petraea species Vascular plant 6
CoverPerc 2 0.0057307
210150 Rubus proiectus Rubus hirtus higher Vascular plant 6 1 CoverPerc 3 0.0085960
210150 Salvia glutinosa Salvia glutinosa species Vascular plant 6
CoverPerc 2 0.0057307
210150 Sanicula europaea Sanicula europaea species Vascular plant 6
CoverPerc 2 0.0057307
210150 Scrophularia nodosa Scrophularia nodosa species Vascular plant 6 1 CoverPerc 3 0.0085960
210150 Stachys sylvatica Stachys sylvatica species Vascular plant 6
CoverPerc 2 0.0057307
210150 Stellaria media Stellaria media species Vascular plant 6
CoverPerc 2 0.0057307
210150 Symphytum tuberosum Symphytum tuberosum species Vascular plant 6
CoverPerc 2 0.0057307
210150 Dioscorea communis Tamus communis species Vascular plant 6
CoverPerc 2 0.0057307
210150 Tilia tomentosa Tilia tomentosa species Vascular plant 4
CoverPerc 2 0.0057307
210150 Ulmus glabra Ulmus glabra species Vascular plant 4
CoverPerc 2 0.0057307
210150 Urtica dioica Urtica dioica species Vascular plant 6
CoverPerc 2 0.0057307
210150 Veronica chamaedrys Veronica chamaedrys species Vascular plant 6
CoverPerc 2 0.0057307
210150 Veronica officinalis Veronica officinalis species Vascular plant 6
CoverPerc 2 0.0057307
1751900 Artemisia indica Artemisia indica species Vascular plant 0 x pa 1 0.1250000
1751900 Equisetum arvense Equisetum arvense species Vascular plant 0 x pa 1 0.1250000
1751900 Eupatorium makinoi Eupatorium makinoi species Vascular plant 0 x pa 1 0.1250000
1751900 Miscanthus sinensis Miscanthus sinensis species Vascular plant 0 x pa 1 0.1250000
1751900 Paederia foetida Paederia scandens species Vascular plant 0 x pa 1 0.1250000
1751900 Pleioblastus argenteostriatus Pleioblastus chino species Vascular plant 0 x pa 1 0.1250000
1751900 Brucea javanica Rhus javanica species Vascular plant 0 x pa 1 0.1250000
1751900 Wisteria floribunda Wisteria floribunda species Vascular plant 0 x pa 1 0.1250000
The DT table contains 43093037 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
Drepanostachyum genus 1 0.4057230 0.9014529 15.359283 453.5450 17.35274 1.4004084 4.9855991 0.0262101 2.1730591 3.306315 0.1818327 0.3510744 1.1551053 56.044604 1.5797527 87.94684 2810.6109237 85.347057 0.9031270 25.17220 0.1654503 34.233100 30.30769 5.935070 4.123685 47.76709 483.9390 1104.1283 8025.0729 790.38872 795.92675 1007.19179 2.546621 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Ceiba aesculifolia species 6 0.4820417 2.3001887 16.011447 404.8469 22.25432 1.8693660 12.2755495 0.2879955 67.8687272 7.509337 0.2379996 0.4085606 1.3747399 545.362008 6.9506290 82.15171 20.1401894 199.336935 8.3741034 20.09306 1.4079830 5.461869 28.68927 3.211683 7.747220 35.25949 618.8141 1196.3740 707.5558 8368.96242 3080.02547 4640.36638 2.107640 0.0043806 0.1205091 0.5049096 2.7714176 0.1761799 0.0367398 0.4420985 0.0122740 9.2983184 0.3744325 0.0034008 0.0032446 0.0326732 24.636029 0.0872883 1.9062724 1.610926 4.488380 0.1865971 0.3013615 0.0481286 0.0904663 0.1939685 0.0312121 0.3852789 1.1679678 10.50207 23.31146 18.65997 199.28309 88.54442 102.16978 0.0328329
Eremogone franklinii species 1 0.4777268 0.7845974 17.048162 441.3303 18.09457 1.6776747 0.1507854 0.0027387 0.9860844 1.277448 0.1988838 0.2825014 1.0924580 1.187687 -1.6169185 95.31555 52.9829341 7.911873 0.2505004 24.36442 0.0046409 228.135249 33.63544 1.563906 1.247657 45.48463 189.8317 335.1878 7979.1707 24.26244 21.10188 22.29988 4.992062 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Gymnanthemum myrianthum species 8 0.4843249 1.0602932 19.904655 438.1041 21.11539 1.5027133 3.0518266 0.0232179 0.9965609 2.584903 0.2587789 0.2184061 1.1452616 123.923415 0.9791606 86.94869 547.1967338 351.032994 15.8364073 29.18296 0.5415260 53.066616 23.77786 3.994287 3.188657 31.28761 454.2144 895.3490 4138.6077 2011.14546 1658.79334 3375.30020 4.912217 0.0043964 0.0761244 0.4009333 0.7248858 0.2667614 0.0338172 1.1162661 0.0033139 0.1420139 0.1963875 0.0016634 0.0042258 0.0152364 13.803818 0.0847578 0.4653637 109.608103 42.138335 2.2418511 0.2677539 0.0559799 2.7701808 0.3262487 0.0524128 0.2203419 0.8716061 10.74401 21.22127 158.02812 227.77847 181.68544 444.73263 0.0772936
Lecythis persistens species 786 0.8444539 3.0101887 7.993054 502.9715 18.94371 0.5285054 16.3480278 0.1637905 48.2675764 9.334647 0.3015469 0.3758386 2.4493050 1340.380417 2.9754123 76.95352 48.0321676 172.346012 7.7159805 26.67494 3.4074118 13.917000 19.64343 2.053875 9.430847 48.46453 374.9298 1303.0984 2342.6111 10724.54811 5600.02878 8380.29776 2.832448 0.0060686 0.3294677 1.4404938 3.9278702 0.9836505 0.0258264 1.8828083 0.0306784 3.6647746 0.3408385 0.0436337 0.0138321 0.3193915 404.293649 0.4494092 0.6561307 8.660933 21.754808 1.1830443 1.3044652 0.9639606 1.0211626 0.3681428 0.0574280 0.4007138 2.4171412 15.19263 47.66295 224.80805 2818.46505 1206.16608 1920.86496 0.1964429
Drosanthemum genus 12 0.4504954 0.2403066 8.017799 491.7139 14.55369 3.4843979 0.8711685 0.2175509 2.2647919 1.277112 0.8763993 0.2801509 2.1289854 50.162223 -1.1412305 90.45757 91.1849075 15.266775 0.5271914 37.31492 0.1853362 57.089404 19.59081 3.066388 1.439249 19.25915 496.7353 711.3360 1621.4862 243.25237 468.03985 109.29190 3.155936 0.0075172 0.0622774 0.4350621 3.1368870 0.1931800 0.1160749 0.4273108 0.0530658 3.2734668 0.6484864 0.0221589 0.0157661 0.0869887 21.532728 0.3766419 1.0916200 63.420323 4.002995 0.1822702 1.1736738 0.0703159 10.8026498 0.4238425 0.0994340 0.6761978 2.6856095 28.62041 64.03992 439.00050 93.34228 165.30110 51.66518 0.2116728
Vitis hancockii species 1 0.5162367 2.8725249 26.728791 432.8678 24.22382 2.3378588 5.0337985 0.0120384 19.9841364 5.321653 0.1409259 0.2511948 0.8089279 134.245880 -1.4858586 57.16932 0.4214558 47.736270 6.1406273 16.52038 0.6283703 28.004080 34.80672 1.162008 3.910425 78.29891 247.7974 549.3463 2070.0866 4644.76037 3960.32229 3227.88332 5.720362 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Mirbelia genus 18 0.6742776 0.9607115 10.415147 484.7987 21.08030 1.2084646 0.3373557 0.0538932 2.6231895 2.022400 0.2217971 0.3647173 2.2834145 4.972895 0.1332392 99.81520 32.3164833 8.113365 0.1708010 25.58045 0.0135887 37.442118 16.85133 2.725524 2.401474 26.13711 202.3020 522.2733 1624.1768 56.05136 63.84803 67.24825 2.495197 0.0093061 0.0971229 0.6551877 4.4747244 0.3776976 0.0388681 0.0665854 0.0050632 1.2935460 0.2811125 0.0047994 0.0105899 0.0932360 1.754205 0.2952777 0.6329611 8.760880 1.509425 0.0396620 0.6004087 0.0046681 3.7098321 0.6608809 0.0840480 0.3031331 1.7579150 5.04675 16.36762 157.42760 20.94297 24.77994 20.23081 0.0803374
Skimmia japonica species 3 0.6576795 1.2009958 10.403075 457.3350 20.47927 1.2246062 7.5283779 0.1706651 13.9450113 3.895747 0.2654632 0.3555677 2.0656173 255.804695 0.3475245 79.75481 235.8049444 71.627128 2.2939261 23.13572 0.7148209 53.463359 41.22583 7.199847 5.587908 30.24192 597.8252 1044.5640 1103.8998 2063.47398 826.65248 2223.33171 3.046468 0.0046467 0.0350884 0.1290591 0.3582027 0.0377735 0.0165186 0.2101261 0.0072744 0.1285291 0.0687470 0.0016760 0.0010976 0.0233760 22.024975 0.0811359 0.2911933 27.960827 2.178286 0.0817905 0.0936990 0.0593648 0.1089999 0.6686308 0.1438806 0.1003705 0.6127537 14.10298 19.06548 47.78941 172.37148 114.15535 150.78912 0.0151544
Xanthophyllum stipitatum species 7 0.8002994 2.8709370 9.937829 461.9866 19.88493 1.1930254 6.4329831 0.3192731 17.7364829 4.096073 0.1757175 0.2674803 2.2683902 63.611973 4.6223292 50.11257 28.3004312 51.396400 1.0952695 24.03864 0.2121077 18.088051 40.25543 1.334190 4.260756 152.48930 299.5842 1351.6809 2744.6829 502.67996 572.69085 912.71414 3.987659 0.0180401 0.1623352 0.8623919 1.5109757 0.6986446 0.0455504 0.2156130 0.0210698 0.5707360 0.0626710 0.0061977 0.0086721 0.1228332 2.625592 0.0491308 0.4025378 4.111778 2.490378 0.0515711 0.6897274 0.0068037 0.2657108 0.4416678 0.0120337 0.0394032 3.7249708 5.20424 13.67985 111.72203 31.31742 25.16775 49.46878 0.1528217

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
Pentacalia vaccinioides 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
Persicaria hirsuta 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
Hypericum pseudopetiolatum NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Astragalus scholerianus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Ajuga relicta NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Flacourtia shrub NA 24 0.7445853 1.128381 25.321611 464.8990 24.71657 1.2722779 8.222665 0.1396927 22.98815 3.051363 0.1351468 0.3874425 1.139069 128.44961 3.533009 95.22187 1296.29746 57.233597 3.3076883 21.19824 0.3172835 35.92698 39.9458 1.323638 3.892080 96.99243 508.8097 1059.0525 3827.390 2274.7243 1789.314 3307.3191 2.152059 0.0407795 0.121354 2.10598 2.804484 0.7533088 0.0494221 2.735897 0.0351534 21.07076 0.6642014 0.0025534 0.0069559 0.1028133 29.36674 0.3852788 1.624267 709.1287 17.71392 1.056663 1.03882 0.0677041 2.283238 1.000972 0.0309349 0.8099799 5.393026 24.14255 43.23723 407.3936 483.2749 386.2956 853.5132 0.0562997
Eucalyptus mcquoidii NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Erysimum gelidum NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Acacia leucolobia shrub FALSE 1 0.7796576 3.436666 6.755453 469.2437 23.60286 0.9178626 5.707647 0.1497570 25.74604 4.889168 0.3155986 0.4396316 3.523036 53.23634 2.806156 92.82492 13.06468 8.028186 0.2452563 19.69180 0.1210850 13.96315 28.4069 2.484120 4.878471 57.44075 283.4374 915.1371 1925.323 261.5759 132.787 477.2411 1.738833 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Pedicularis mandshurica 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

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
1670682 StemConduitDiameter_mean 1 1.0000000 1.0000000 47.3510444 NA
938690 StemDiam_mean 51 0.9215686 0.8519882 0.0151319 2.785700e-03
1563420 LeafNperArea_mean 32 0.9375000 0.8943662 1.4559799 2.340808e-01
297290 RootingDepth_mean 11 1.0000000 1.0000000 0.3963494 3.272055e-01
1224545 RootingDepth_mean 12 0.6666667 0.5864198 0.1092728 3.209700e-03
1050854 LeafN_mean 20 0.9000000 0.9310345 25.0384562 2.732765e+01
1879432 StemConduitDiameter_mean 30 0.6666667 0.6605505 53.0375860 2.892897e+03
990310 LeafWidth_mean 39 0.8461538 0.9221557 0.6370811 2.211296e+00
171590 SpecificRootLength_mean 11 1.0000000 1.0000000 7761.5510095 1.763218e+07
864144 LeafWaterCont_mean 20 0.9500000 0.9884388 3.4888804 1.924490e+00

The CWM table contains 56251008 entries, i.e., the combination between 1704576 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
1249727 NA NA NA NA 90.00000 73.00000 268.0000 7132.000 235.0000 -35.0000000 271.0000 183.00000 -4.00000 186.0000 -5.00000 546.0000 86.00000 25.00000 43.00000 244.0000 75.00000 222.0000 82.0000 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 949.0000 15.00000 11.00000 7.000000 22.00000 60.00000 32.00000 58.00000 NA NA NA NA NA NA NA NA
1170931 5 5 5 153 105.00000 43.00000 233.0000 4873.000 202.0000 20.0000000 182.0000 93.00000 79.00000 175.0000 40.00000 820.0000 87.00000 43.00000 22.00000 259.0000 140.00000 241.0000 170.0000 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 576.6667 17.16667 14.50000 3.833333 62.66667 62.83333 18.50000 67.00000 29.37800 0.7527727 0.5477226 0.4082483 7.814516 2.136976 1.2247449 1.4142136
1299378 NA NA NA NA 89.00000 73.00000 262.0000 7276.000 235.0000 -42.0000000 277.0000 183.00000 -7.00000 186.0000 -9.00000 818.0000 113.00000 41.00000 38.00000 336.0000 125.00000 309.0000 136.0000 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 922.0000 16.00000 15.00000 9.000000 41.00000 59.00000 44.00000 42.00000 NA NA NA NA NA NA NA NA
1363121 200 162 253 153 111.00000 81.00000 265.4000 7964.000 267.0000 -37.8000000 305.0000 190.60000 42.80000 215.6000 0.80000 619.2000 80.80000 34.20000 26.40000 231.8000 105.80000 170.4000 135.0000 2.738613 0.0000000 0.5477226 16.04681 2.738613 2.489980 0.0000000 2.880972 2.588436 2.880972 2.588436 42.82172 3.033150 3.114482 1.8165902 10.89495 8.983318 5.639149 12.549900 1167.1412 23.17647 23.61176 6.235294 25.28235 65.75294 39.10588 37.35294 62.43762 1.2926207 1.1556705 1.4771841 3.119111 2.103885 1.0121115 1.6381311
1101654 -3 -3 -3 153 100.00000 57.00000 277.0000 5310.000 212.0000 4.0000000 208.0000 175.00000 77.00000 175.0000 29.00000 824.0000 85.00000 47.00000 17.00000 249.0000 153.00000 249.0000 169.0000 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
596366 1023 1023 1023 153 62.00000 77.00000 300.0000 6258.000 201.0000 -57.0000000 258.0000 -3.00000 39.00000 150.0000 -20.00000 1390.0000 149.00000 99.00000 13.00000 436.0000 302.00000 312.0000 409.0000 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 607.0000 23.83333 19.50000 18.833333 131.83333 50.83333 38.83333 41.83333 23.68122 2.1369761 2.8106939 1.4719601 11.771434 1.602082 1.8348479 4.4459720
1369058 NA NA NA NA 92.12571 81.00000 261.5886 8108.162 249.5257 -59.6590476 309.1943 196.53524 -14.49524 198.4590 -18.61524 703.7105 104.68190 32.11810 44.42286 312.8781 97.20571 259.5886 104.7276 2.914069 0.0000000 0.5613700 27.84277 3.217587 2.572598 0.9809083 3.191890 2.632460 3.142412 2.617571 59.04902 10.745306 2.802901 2.2258568 32.12494 8.680919 25.756313 9.158908 1210.3211 25.20468 27.62941 5.631213 29.61609 63.94562 43.11044 29.25078 64.50096 1.4437056 1.6489552 1.6651883 6.511977 2.285598 1.7381191 2.0988056
554558 392 189 690 153 140.40000 88.60000 312.6000 6675.600 296.0000 12.8000000 283.0000 117.00000 160.00000 238.0000 55.60000 820.4000 107.20000 39.60000 28.40000 311.6000 145.00000 155.6000 148.4000 7.861298 0.5477226 0.8944272 25.94803 8.366600 7.791021 1.0000000 8.062258 88.642541 8.366600 7.569676 66.72556 11.233877 1.816590 0.8944272 32.19161 10.931606 7.635444 14.501724 1177.0390 23.37662 25.89610 18.311688 38.11688 68.68831 37.14286 36.96104 119.51585 1.2777340 0.9945168 1.7641141 12.944186 3.313687 0.9829371 1.2611770
121756 NA NA NA NA 100.05199 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 169.99133 218.5095 186.2964 1.595589 0.3327190 0.5003730 14.06297 1.347725 1.752845 0.5668633 62.118003 1.585407 1.480651 1.713292 41.57112 3.985972 2.667791 0.3534002 11.60577 9.059119 12.453399 9.849944 675.8064 13.91451 13.87350 8.424516 19.73961 62.81977 64.22330 21.87242 84.69573 1.4642037 1.5854461 1.2474760 4.989717 5.498438 8.4684489 9.3935629
1898300 14 14 14 153 193.00000 49.00000 228.0000 5805.000 292.0000 75.0000000 217.0000 270.00000 175.00000 270.0000 113.00000 1299.0000 173.00000 60.00000 33.00000 514.0000 203.00000 514.0000 264.0000 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 1166.0000 19.25000 15.00000 1.500000 43.25000 45.25000 25.00000 60.00000 16.39105 0.5000000 0.0000000 0.5773503 2.629956 0.500000 0.8164966 0.8164966

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     ps_1.4.0         
## [25] fansi_0.4.1       highr_0.8         broom_0.7.0       Rcpp_1.0.5       
## [29] scales_1.1.1      backports_1.2.0   webshot_0.5.2     jsonlite_1.7.1   
## [33] fs_1.5.0          hms_0.5.3         digest_0.6.25     stringi_1.5.3    
## [37] grid_3.6.3        cli_2.2.0         tools_3.6.3       magrittr_2.0.1   
## [41] crayon_1.3.4      pkgconfig_2.0.3   ellipsis_0.3.1    xml2_1.3.2       
## [45] reprex_0.3.0      lubridate_1.7.9.2 assertthat_0.2.1  rmarkdown_2.5    
## [49] httr_1.4.2        rstudioapi_0.13   R6_2.5.0          compiler_3.6.3