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)
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")
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.
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).
The header object contains all plot-level information, including source and location. The description of its construction can be found at: https://git.idiv.de/fs40gaho/splot3_build/-/blob/master/public/04_buildHeader.html (download needed).
Import data
load("../_output/header_sPlot3.0.RData")
PlotObservationID | Dataset | GIVD ID | TV2 relevé number | ORIG_NUM | GUID | Longitude | Latitude | Location uncertainty (m) | Country | CONTINENT | sBiome | sBiomeID | Ecoregion | EcoregionID | Locality | Relevé area (m²) | Cover abundance scale | Date of recording | Plants recorded | Herbs identified (y/n) | Mosses identified (y/n) | Lichens identified (y/n) | elevation_dem | Altitude (m) | Aspect (°) | Slope (°) | Forest | Shrubland | Grassland | Wetland | Sparse.vegetation | Naturalness | ESY | is.forest | is.non.forest | Cover total (%) | Cover tree layer (%) | Cover shrub layer (%) | Cover herb layer (%) | Cover moss layer (%) | Cover lichen layer (%) | Cover algae layer (%) | Cover litter layer (%) | Cover open water (%) | Cover bare rock (%) | Height (highest) trees (m) | Height lowest trees (m) | Height (highest) shrubs (m) | Height lowest shrubs (m) | Aver. height (high) herbs (cm) | Aver. height lowest herbs (cm) | Maximum height herbs (cm) | Maximum height cryptogams (mm) |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
757864 | France_SOPHY | EU-FR-003 | 205552 | NA | A56EFB64-2473-4D59-86F3-AE9C5C774E8B | 6.991129 | 47.72160 | 2 | France | EU | Temperate midlatitudes | 6 | Western European broadleaf forests | 80445 | PETITEFONTAINE, LES CLOSSELOTS | NA | Braun/Blanquet (old) | 2005-01-01 | NA | NA | NA | NA | 406 | 405 | NA | NA | 0 | 0 | 1 | 0 | 0 | NA | E | FALSE | TRUE | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
1337110 | Romania Grassland Database | EU-RO-008 | 9978 | NA | D9444CEB-428F-4F2A-8983-0811FFC84FEE | 23.872752 | 45.29904 | 2200 | Romania | EU | Temperate midlatitudes | 6 | Carpathian montane forests | 80504 | Upper basin of Luncavat river (Valcea county), Balota Mt | 100 | Braun/Blanquet (old) | 2004-07-20 | NA | NA | NA | NA | 1611 | 1920 | NA | NA | 0 | 0 | 1 | 0 | 0 | 1 | E43b | FALSE | TRUE | 100 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
650065 | France_SOPHY | EU-FR-003 | 94816 | NA | 71BF61A1-8EFC-4461-A6C3-983542172E76 | 6.981229 | 48.02490 | -10 | France | EU | Temperate midlatitudes | 6 | Western European broadleaf forests | 80445 | FAIGNES DE LA LANDE | NA | Braun/Blanquet (old) | 1985-01-01 | NA | NA | NA | NA | 1199 | 1045 | NA | NA | 0 | 0 | 0 | 1 | 0 | 1 | D11 | FALSE | TRUE | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
1594901 | Turkey Forest Database | 00-TR-001 | 5755 | NA | 05187236-2D5B-41C0-BCC9-2533A8009C75 | 36.000000 | 39.00000 | 823744 | Turkey | EU | Dry midlatitudes | 7 | Central Anatolian steppe and woodlands | 80410 | Paţaini deresi kuzydođusu | 400 | Braun/Blanquet (old) | 1984-01-01 | NA | NA | NA | NA | NA | 960 | NA | 5 | 1 | 0 | 0 | 0 | 0 | 1 | G21 | TRUE | FALSE | 100 | NA | 100 | 20 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
817848 | Germany_gvrd | EU-DE-014 | 91050 | NA | 44A89728-C154-435B-83B4-97A760609ED5 | 8.529960 | 51.65718 | -10 | Germany | EU | Temperate midlatitudes | 6 | Atlantic mixed forests | 80402 | Nordrhein-Westfalen, Geseke/Kreis Soest | NA | Percentage (%) | 1977-07-25 | NA | NA | NA | NA | 94 | 96 | NA | 0 | 0 | 0 | 1 | 0 | 0 | 3 | E21 | FALSE | TRUE | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
1336488 | Romania Grassland Database | EU-RO-008 | 9348 | NA | 06110CAF-FED2-49F2-A175-0B41357DEEE1 | 26.379670 | 47.64381 | 100 | Romania | EU | Temperate midlatitudes | 6 | Central European mixed forests | 80412 | Salcea | 100 | Braun/Blanquet (old) | 2003-08-11 | NA | NA | NA | NA | 302 | 320 | 45 | 15 | 0 | 0 | 1 | 0 | 0 | 1 | E12b | FALSE | TRUE | 85 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
1253264 | Poland | EU-PL-001 | 8492 | NA | 7D0C57BA-336C-4F08-A2B2-96F3875F3681 | 17.172500 | 54.66556 | NA | Poland | EU | Temperate midlatitudes | 6 | Baltic mixed forests | 80405 | Smoldzino | 10 | Braun/Blanquet (old) | 2001-06-29 | NA | NA | NA | NA | NA | NA | NA | NA | 0 | 0 | 1 | 0 | 0 | 2 | E22 | FALSE | TRUE | NA | NA | NA | 100 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
910359 | Germany_vegmv | EU-DE-001 | 58158 | NA | 50DB7373-8AB3-467F-9A3D-B8358A902B7A | 11.290227 | 53.12349 | 3939 | Germany | EU | Temperate midlatitudes | 6 | Atlantic mixed forests | 80402 | Dömitz | 150 | Braun/Blanquet (new) | 2000-09-05 | NA | NA | Y | Y | 12 | 12 | NA | NA | NA | NA | NA | NA | NA | NA | ? | FALSE | TRUE | 90 | NA | NA | 90 | 5 | NA | NA | NA | NA | NA | NA | NA | NA | NA | 100 | NA | 200 | 10 |
1548318 | Spain_sivim_sclerophyllous_pinus | EU-00-004f | 9773 | NA | 9D33F657-4D6F-4B04-8D86-EF6F0CD0AFFC | 1.111440 | 42.57185 | 10000 | Spain | EU | Subtropics with winter rain | 4 | Pyrenees conifer and mixed forests | 80433 | barranc dels Estanyets | 100 | Braun/Blanquet (old) | NA | NA | NA | NA | NA | 1671 | NA | 270 | NA | 1 | 0 | 0 | 0 | 0 | 1 | G32 | TRUE | FALSE | NA | 40 | NA | 90 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
587639 | France_SOPHY | EU-FR-003 | 29592 | NA | 803922EE-4923-4AA5-A5C0-48CB2EED258A | -1.881971 | 49.53780 | -10 | France | EU | Temperate midlatitudes | 6 | Atlantic mixed forests | 80402 | LE CAP DE FLAMANVILLE | NA | Braun/Blanquet (old) | 1977-01-01 | NA | NA | NA | NA | NA | 20 | NA | NA | 0 | 0 | 1 | 0 | 0 | 2 | IE1E | FALSE | TRUE | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
sPlot 3.0 contains 1977637 Plots.
PlotObservationID
: Identificator provided by Turboveg 3, unique for each plot.Dataset
: Name of source dataset.GIVD ID
: GIVD code of source dataset.TV2 relevé number
: Original number in the Turboveg 2 version of the source dataset.ORIG_NUM
: Original number of the plot in the source dataset.GUID
: GUID identifier, as created in Turboveg 2.Longitude
: Degrees, WGS85.Latitude
: Degrees, WGS85.Location uncertainty (m)
: Uncertainty of geographic coordinates. Negative if estimated, instead of measured.Country
: Original country name in Turboveg 3.CONTINENT
: Continent.sBiome
: Biome, as defined in Bruelheide et al. 2019 - JVS.sBiomeID
: Biome ID, as defined in Bruelheide et al. 2019 - JVS (see Appendix 5).Ecoregion
: WWF EcoregionEcoregionID
: WWF ecoreigon ID.Locality
: As reported in the original data.Relevé area (m²)
: Size of the sampling plot.Cover abundance scale
: Cover\abundance scale used in the field.Date of recording
: Date of sampling.Plants recorded
: Group of plants recorded in the field: e.g., “All vascular plants”, “Woody plants with DBH > 10cm”. In case of NA, it is mostly safe to assume that all vascular plants were recorded.Herbs identified (y/n)
: Y if herbs were identified (as opposed to woody species). In case of NA, it is mostly safe to assume that herbs were sampled and identified.Mosses identified (y/n)
: Y if mosses were identified. In case of NA, it is safe to assume that Mosses were NOT sampled.Lichens identified (y/n)
: Y if lichens were identified. In case of NA, it is safe to assume that lichens were NOT sampled.elevation_dem
: Elevation of plot, as derived from geographic coordinates (and averaged based on location uncertainty).Altitude (m)
: Elevation of plot, as measured in the field.Aspect (°)
: Topographical aspect of plot (in degrees).Slope (°)
: Topographical slope of plot (in degrees).Forest
: TRUE (=1) or Fals (=0).Shrubland
: TRUE (=1) or Fals (=0).Grassland
: TRUE (=1) or Fals (=0).Wetland
: TRUE (=1) or Fals (=0).Sparse.vegetation
: TRUE (=1) or Fals (=0).Naturalness
: 1=Natural, 2=Semi-natural, 3=Anthropogenic.ESY
: EUNIS Habitat Classification Expert system, as described in Chytrý et al. (2020).Cover total (%)
: Total cover of vegetation.Cover tree layer (%)
: Total cover of tree layer.Cover shrub layer (%)
: Total cover of shrub layer.Cover herb layer (%)
: Total cover of herb layer.Cover moss layer (%)
: Total cover of moss layer.Cover lichen layer (%)
: Total cover of lichen layer.Cover algae layer (%)
: Total cover of algae layer.Cover litter layer (%)
: Total cover of litter layer.Cover open water (%)
: Total cover of open water.Cover bare rock (%)
: Total cover of bare rocks.Height (highest) trees (m)
: Height of the highest tree layer.Height lowest trees (m)
: Height of the lowest tree layer.Height (highest) shrubs (m)
: Height of the highest shrub layer.Height lowest shrubs (m)
: Height of the lowest shrub layer.Aver. height (high) herbs (cm)
: Average height of highest herb layer.Aver. height lowest herbs (cm)
: Average height of the lowest herb layer.Maximum height herbs (cm)
: Maximum height of herbs.Maximum height cryptogams (mm)
: Maximum height of cryptogams.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")
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 |
PlotObservationID
: Plot ID (as in Header).Species
: Resolved species name (as derived from the field name_short
in the Backbone).Species_original
: Original species name (before resolution, as in the field name_sPlot_TRY
in the Backbone).Rank_correct
: Taxonomic rank of the corrected name (as in the homonymous field in the Backbone).Taxon_group
: Taxon group (as in the homonymous field in the Backbone).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.Cover_code
: Cover\abundance code in original data, before transformation to quantitative value or percentage cover.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.Abundance
: Abundance value, in original value, or as transformed from original Cover code
to quantitative values.Relative_cover
: Abundance\Cover of each species after being normalized to 1 in each plot.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")
try.combined.means
.
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.
sPlot.traits
.
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.
CWM
.
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.
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.
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:
soilclim
.
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 |
PlotObservationID
: Plot ID, as in header
.Elevation_median
: Median elevation in a circle centered on plot location, having a radius of the plot’s location uncertainty
(NA if >50km).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).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).Elevation_DEM.res
: Resolution of Digital Elevation Model used (in m).bio01
: Annual Mean Temperaturebio02
: Mean Diurnal Rangebio03
: Isothermalitybio04
: Temperature Seasonalitybio05
: Max Temperature of Warmest Monthbio06
: Min Temperature of Coldest Monthbio07
: Temperature Annual Rangebio08
: Mean Temperature of Wettest Quarterbio09
: Mean Temperature of Driest Quarterbio10
: Mean Temperature of Warmest Quarterbio11
: Mean Temperature of Coldest Quarterbio12
: Annual Precipitationbio13
: Precipitation of Wettest Monthbio14
: Precipitation of Driest Monthbio15
: Precipitation Seasonalitybio16
: Precipitation of Wettest Quarterbio17
: Precipitation of Driest Quarterbio18
: Precipitation of Warmest Quarterbio19
: Precipitation of Coldest QuarterBLDFIE
: Bulk Density (fine earth) in kg/m3CECSOL
: Cation Exchange capacity of soilCLYPPT
: Clay mass fraction in %CRFVOL
: Coarse fragments volumetric in %ORCDRC
: Soil Organic Carbon Content in g/kgPHIHOX
: Soil pH x 10 in H20SLTPPT
: Silt mass fraction in %SNDPPT
: Sand mass fraction in %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