Timestamp: Tue Dec 1 19:44:01 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Mezoneuron baudouinii | Mezoneuron baudouinii | NA | S | Mezoneuron baudouinii | 198503 | 0.98 | Mezoneuron baudouini | species | 0.98 | Guillaumin | http://www.theplantlist.org/tpl1.1/record/tro-13051937;http://www.tropicos.org/Name/13051937 | NA | NA | NA | NA | Fabaceae | Mezoneuron | 1 | baudouini | 0.9 | NA | NA | NA | NA | NA | NA | NA | NA | No opinion | NA | NA | NA | ; | NA | NA | TRUE | tpl;tropicos | NA | NA | Other | Mezoneuron baudouini | Mezoneuron | species | NA | Mezoneuron baudouini | NA | NA | Unknown |
Odontochilus uniflorus | Odontochilus uniflorus | NA | T | Odontochilus uniflorus | 214361 | 1.00 | Odontochilus uniflorus | species | 1.00 | (Blume) H.A.Pedersen & Ormerod | http://www.theplantlist.org/tpl1.1/record/kew-463737 | NA | NA | NA | NA | Orchidaceae | Odontochilus | 1 | uniflorus | 1.0 | NA | NA | NA | NA | NA | NA | NA | NA | Accepted | Odontochilus uniflorus | (Blume) H.A.Pedersen & Ormerod | species | http://www.theplantlist.org/tpl1.1/record/kew-463737 | Odontochilus uniflorus | Orchidaceae | TRUE | tpl | NA | NA | Accepted | Odontochilus uniflorus | Odontochilus | species | Orchidaceae | Odontochilus uniflorus | Tracheophyta | TRUE | Vascular plant |
Olearia oliganthema | Olearia oliganthema | NA | T | Olearia oliganthema | 215273 | 1.00 | Olearia oliganthema | species | 1.00 | (F.Muell.) F.Muell. ex Benth. | http://dixon.iplantcollaborative.org/CompositaeWeb/default.aspx?Page=NameDetails&TabNum=0&NameId=9AF64F1F-FAFA-4C5B-9989-F250058F515C | NA | NA | NA | NA | Asteraceae | Olearia | 1 | oliganthema | 1.0 | NA | NA | NA | NA | NA | NA | NA | NA | Accepted | Olearia oliganthema | (F.Muell.) F.Muell. ex Benth. | species | http://dixon.iplantcollaborative.org/CompositaeWeb/default.aspx?Page=NameDetails&TabNum=0&NameId=9AF64F1F-FAFA-4C5B-9989-F250058F515C | Olearia oliganthema | Asteraceae | TRUE | gcc | NA | urn:lsid:compositae.org:names:9AF64F1F-FAFA-4C5B-9989-F250058F515C | Accepted | Olearia oliganthema | Olearia | species | Compositae | Olearia oliganthema | Tracheophyta | TRUE | Vascular plant |
Trifolium hybridum var. elegans | Trifolium hybridum var. elegans | NA | S | Trifolium hybridum var. elegans | 316897 | 1.00 | Trifolium hybridum var. elegans | variety | 1.00 | (Savi)Boiss. | http://www.ildis.org/LegumeWeb?version~10.01&genus~Trifolium&species~hybridum | NA | NA | NA | NA | Fabaceae | Trifolium | 1 | hybridum | 1.0 | var. | elegans | 1.00 | NA | NA | NA | NA | NA | Synonym | Trifolium hybridum subsp. elegans | (Savi)Asch. & Graebn. | subspecies | http://www.ildis.org/LegumeWeb?version~10.01&genus~Trifolium&species~hybridum | Trifolium hybridum | Fabaceae | TRUE | ildis | NA | NA | Synonym | Trifolium hybridum subsp. elegans | Trifolium | variety | Leguminosae | Trifolium hybridum | Tracheophyta | TRUE | Vascular plant |
Cymbaria dahurica | Cymbaria dahurica | NA | ST | Cymbaria dahurica | NA | NA | NA | NA | NA | NA | kew-2750578 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | Accepted | Cymbaria daurica | L. | species | kew-2750578 | Cymbaria daurica | Orobanchaceae | TRUE | tpl 1.1 | NA | NA | Accepted | Cymbaria daurica | Cymbaria | higher | Orobanchaceae | Cymbaria daurica | Tracheophyta | TRUE | Vascular plant |
Calyptranthes pileata | Calyptranthes pileata | NA | ST | Calyptranthes pileata | 53635 | 1.00 | Calyptranthes pileata | species | 1.00 | D.Legrand | http://www.theplantlist.org/tpl1.1/record/kew-32532 | NA | NA | NA | NA | Myrtaceae | Calyptranthes | 1 | pileata | 1.0 | NA | NA | NA | NA | NA | NA | NA | NA | Accepted | Calyptranthes pileata | D.Legrand | species | http://www.theplantlist.org/tpl1.1/record/kew-32532 | Calyptranthes pileata | Myrtaceae | TRUE | tpl | NA | NA | Accepted | Calyptranthes pileata | Calyptranthes | species | Myrtaceae | Calyptranthes pileata | Tracheophyta | TRUE | Vascular plant |
Tupistra albiflora | Tupistra albiflora | NA | T | Tupistra albiflora | 319161 | 1.00 | Tupistra albiflora | species | 1.00 | K.Larsen | http://www.theplantlist.org/tpl1.1/record/kew-290071 | NA | NA | NA | NA | Asparagaceae | Tupistra | 1 | albiflora | 1.0 | NA | NA | NA | NA | NA | NA | NA | NA | Synonym | Tupistra muricata | (Gagnep.) N.Tanaka | species | http://www.theplantlist.org/tpl1.1/record/kew-289950 | Tupistra muricata | Asparagaceae | TRUE | tpl | NA | NA | Synonym | Tupistra muricata | Tupistra | species | Asparagaceae | Tupistra muricata | Tracheophyta | TRUE | Vascular plant |
Sapium integerrimum | Sapium integerrimum | NA | T | Sapium integerrimum | 276000 | 1.00 | Sapium integerrimum | species | 1.00 | (Hochst.) J.Léonard | http://www.theplantlist.org/tpl1.1/record/kew-184364 | NA | NA | NA | NA | Euphorbiaceae | Sapium | 1 | integerrimum | 1.0 | NA | NA | NA | NA | NA | NA | NA | NA | Synonym | Sclerocroton integerrimus | Hochst. | species | http://www.theplantlist.org/tpl1.1/record/kew-188722 | Sclerocroton integerrimus | Euphorbiaceae | TRUE | tpl | NA | NA | Synonym | Sclerocroton integerrimus | Sclerocroton | species | Euphorbiaceae | Sclerocroton integerrimus | Tracheophyta | TRUE | Vascular plant |
Iris kuschakewiczii | Iris kuschakewiczii | NA | T | Iris kuschakewiczii | 164738 | 1.00 | Iris kuschakewiczii | species | 1.00 | B.Fedtsch. | http://www.theplantlist.org/tpl1.1/record/kew-322022 | NA | NA | NA | NA | Iridaceae | Iris | 1 | kuschakewiczii | 1.0 | NA | NA | NA | NA | NA | NA | NA | NA | Accepted | Iris kuschakewiczii | B.Fedtsch. | species | http://www.theplantlist.org/tpl1.1/record/kew-322022 | Iris kuschakewiczii | Iridaceae | TRUE | tpl | NA | NA | Accepted | Iris kuschakewiczii | Iris | species | Iridaceae | Iris kuschakewiczii | Tracheophyta | TRUE | Vascular plant |
Rudgea longiflora | Rudgea longiflora | NA | T | Rudgea longiflora | 271470 | 1.00 | Rudgea longiflora | species | 1.00 | Benth. | http://www.theplantlist.org/tpl1.1/record/kew-180597;http://www.tropicos.org/Name/50137936 | NA | NA | NA | NA | Rubiaceae | Rudgea | 1 | longiflora | 1.0 | NA | NA | NA | NA | NA | NA | NA | NA | Accepted | Rudgea longiflora | Benth. | species | http://www.theplantlist.org/tpl1.1/record/kew-180597;http://www.tropicos.org/Name/50137936 | Rudgea longiflora | Rubiaceae | TRUE | tpl;tropicos | NA | NA | Accepted | Rudgea longiflora | Rudgea | species | Rubiaceae | Rudgea longiflora | Tracheophyta | TRUE | Vascular plant |
Lecidea cascadensis | Lecidea cascadensis | NA | T | Lecidea cascadensis | 175001 | 1.00 | Lecidea cascadensis | species | 1.00 | H. Magn. | http://plants.usda.gov/java/profile?symbol=LECA34 | NA | NA | NA | NA | Lecideaceae | Lecidea | 1 | cascadensis | 1.0 | NA | NA | NA | NA | NA | NA | NA | NA | Accepted | Lecidea cascadensis | H. Magn. | species | http://plants.usda.gov/java/profile?symbol=LECA34 | Lecidea cascadensis | Lecideaceae | TRUE | usda | NA | NA | Accepted | Lecidea cascadensis | Lecidea | species | Lecideaceae | Lecidea cascadensis | NA | FALSE | Lichen |
Indigastrum parviflorum subsp. occidentalis | Indigastrum parviflorum subsp. occidentalis | NA | S | Indigastrum parviflorum subsp. occidentalis | 162654 | 0.98 | Indigastrum parviflorum subsp. occidentale | subspecies | 0.98 | (J.B. Gillett) Schrire | http://www.theplantlist.org/tpl1.1/record/tro-13076810;http://www.tropicos.org/Name/13076810 | NA | NA | NA | NA | Fabaceae | Indigastrum | 1 | parviflorum | 1.0 | subsp. | occidentale | 0.83 | NA | NA | NA | NA | NA | Accepted | Indigastrum parviflorum subsp. occidentale | (J.B. Gillett) Schrire | subspecies | http://www.theplantlist.org/tpl1.1/record/tro-13076810;http://www.tropicos.org/Name/13076810 | Indigastrum parviflorum | Fabaceae | TRUE | tpl;tropicos | NA | NA | Accepted | Indigastrum parviflorum subsp. occidentale | Indigastrum | subspecies | Leguminosae | Indigastrum parviflorum | Tracheophyta | TRUE | Vascular plant |
Chascanum hanningtonii | Chascanum hanningtonii | NA | T | Chascanum hanningtonii | 66468 | 1.00 | Chascanum hanningtonii | species | 1.00 | (Oliv.) Moldenke | http://www.theplantlist.org/tpl1.1/record/kew-38396;http://www.tropicos.org/Name/33702929 | NA | NA | NA | NA | Verbenaceae | Chascanum | 1 | hanningtonii | 1.0 | NA | NA | NA | NA | NA | NA | NA | NA | Accepted | Chascanum hanningtonii | (Oliv.) Moldenke | species | http://www.theplantlist.org/tpl1.1/record/kew-38396;http://www.tropicos.org/Name/33702929 | Chascanum hanningtonii | Verbenaceae | TRUE | tpl;tropicos | NA | NA | Accepted | Chascanum hanningtonii | Chascanum | species | Verbenaceae | Chascanum hanningtonii | Tracheophyta | TRUE | Vascular plant |
Echinocereus poselgeri | Echinocereus poselgeri | NA | T | Echinocereus poselgeri | 108405 | 1.00 | Echinocereus poselgeri | species | 1.00 | Lem. | http://www.theplantlist.org/tpl1.1/record/kew-2782770;http://www.tropicos.org/Name/5102181;http://plants.usda.gov/java/profile?symbol=ECPO4 | NA | NA | NA | NA | Cactaceae | Echinocereus | 1 | poselgeri | 1.0 | NA | NA | NA | NA | NA | NA | NA | NA | Accepted | Echinocereus poselgeri | Lem. | species | http://www.theplantlist.org/tpl1.1/record/kew-2782770;http://www.tropicos.org/Name/5102181;http://plants.usda.gov/java/profile?symbol=ECPO4 | Echinocereus poselgeri | Cactaceae | TRUE | tpl;tropicos;usda | NA | NA | Accepted | Echinocereus poselgeri | Echinocereus | species | Cactaceae | Echinocereus poselgeri | Tracheophyta | TRUE | Vascular plant |
Herniaria argaea | Herniaria argaea | NA | S | Herniaria argaea | 153033 | 1.00 | Herniaria argaea | species | 1.00 | Boiss. | http://www.theplantlist.org/tpl1.1/record/kew-2846886 | NA | NA | NA | NA | Caryophyllaceae | Herniaria | 1 | argaea | 1.0 | NA | NA | NA | NA | NA | NA | NA | NA | No opinion | NA | NA | NA | NA | NA | NA | TRUE | tpl | NA | NA | Other | Herniaria argaea | Herniaria | species | Caryophyllaceae | Herniaria argaea | Tracheophyta | TRUE | Vascular plant |
Senecio neoviscosus | Senecio neoviscosus | NA | T | Senecio neoviscosus | 284740 | 1.00 | Senecio neoviscosus | species | 1.00 | Cuatrec. | http://www.tropicos.org/Name/2707936 | NA | NA | NA | NA | Asteraceae | Senecio | 1 | neoviscosus | 1.0 | NA | NA | NA | NA | NA | NA | NA | NA | Accepted | Senecio neoviscosus | Cuatrec. | species | http://www.tropicos.org/Name/2707936 | Senecio neoviscosus | Asteraceae | TRUE | tropicos | NA | NA | Accepted | Senecio neoviscosus | Senecio | species | Compositae | Senecio neoviscosus | Tracheophyta | TRUE | Vascular plant |
Allium lacunosum var. kernense | Allium lacunosum var. kernense | NA | T | Allium lacunosum var. kernense | 12192 | 1.00 | Allium lacunosum var. kernense | variety | 1.00 | McNeal & Ownbey | http://plants.usda.gov/java/profile?symbol=ALLAK | NA | NA | NA | NA | Amaryllidaceae | Allium | 1 | lacunosum | 1.0 | var. | kernense | 1.00 | NA | NA | NA | NA | NA | Accepted | Allium lacunosum var. kernense | McNeal & Ownbey | variety | http://plants.usda.gov/java/profile?symbol=ALLAK | Allium lacunosum | Amaryllidaceae | TRUE | usda | NA | NA | Accepted | Allium lacunosum var. kernense | Allium | variety | Amaryllidaceae | Allium lacunosum | Tracheophyta | TRUE | Vascular plant |
Sideroxylon capuronii | Sideroxylon capuronii | NA | T | Sideroxylon capuronii | 287808 | 1.00 | Sideroxylon capuronii | species | 1.00 | Aubrév. | http://www.theplantlist.org/tpl1.1/record/kew-191831;http://www.tropicos.org/Name/28700073 | NA | NA | NA | NA | Sapotaceae | Sideroxylon | 1 | capuronii | 1.0 | NA | NA | NA | NA | NA | NA | NA | NA | Accepted | Sideroxylon capuronii | Aubrév. | species | http://www.theplantlist.org/tpl1.1/record/kew-191831;http://www.tropicos.org/Name/28700073 | Sideroxylon capuronii | Sapotaceae | TRUE | tpl;tropicos | NA | NA | Accepted | Sideroxylon capuronii | Sideroxylon | species | Sapotaceae | Sideroxylon capuronii | Tracheophyta | TRUE | Vascular plant |
Pometia macrocarpa | Pometia macrocarpa | NA | T | Pometia macrocarpa | 249622 | 1.00 | Pometia macrocarpa | species | 1.00 | Kurz | http://www.theplantlist.org/tpl1.1/record/kew-2543548 | NA | NA | NA | NA | Sapindaceae | Pometia | 1 | macrocarpa | 1.0 | NA | NA | NA | NA | NA | NA | NA | NA | No opinion | NA | NA | NA | NA | NA | NA | TRUE | tpl | NA | NA | Other | Pometia macrocarpa | Pometia | species | Sapindaceae | Pometia macrocarpa | Tracheophyta | TRUE | Vascular plant |
Bridelia stipularis | Bridelia stipularis | NA | T | Bridelia stipularis | 46141 | 1.00 | Bridelia stipularis | species | 1.00 | (L.) Blume | http://www.theplantlist.org/tpl1.1/record/kew-24660;http://www.tropicos.org/Name/50056540 | NA | NA | NA | NA | Phyllanthaceae | Bridelia | 1 | stipularis | 1.0 | NA | NA | NA | NA | NA | NA | NA | NA | Accepted | Bridelia stipularis | (L.) Blume | species | http://www.theplantlist.org/tpl1.1/record/kew-24660;http://www.tropicos.org/Name/50056540 | Bridelia stipularis | Phyllanthaceae | TRUE | tpl;tropicos | NA | NA | Accepted | Bridelia stipularis | Bridelia | species | Phyllanthaceae | Bridelia stipularis | 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) |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1650005 | Ukraine_onyshchenko | EU-UA-006 | 2548 | NA | 25925B82-2D30-4627-9F08-E4FFE0CD9D31 | 34.966386 | 45.77437 | 100 | Ukraine | EU | Dry midlatitudes | 7 | Pontic steppe | 80814 | Crimea, Lenine district, Arabatska Strilka spit | 100.0 | Percentage (%) | 2003-08-07 | NA | NA | NA | NA | 2 | 3 | 80 | 3 | 0 | 0 | 1 | 0 | 0 | NA | E | FALSE | TRUE | NA | NA | NA | 50 | 5 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
748199 | France_SOPHY | EU-FR-003 | 195156 | NA | FF22275E-59ED-4FE7-81C6-7AF0A11A829D | 7.675129 | 48.24180 | -10 | France | EU | Temperate midlatitudes | 6 | Western European broadleaf forests | 80445 | VIEUX RHIN, KM 252.2 | NA | Braun/Blanquet (old) | 2004-01-01 | NA | NA | NA | NA | 161 | 166 | NA | NA | 0 | 0 | 0 | 1 | 0 | 1 | C23 | FALSE | TRUE | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
331215 | Denmark | EU-DK-002 | 1381 | NA | 35304DA6-7DD7-4BE5-980A-C3D88AD3D5DB | 10.621386 | 55.58818 | 15 | Denmark | EU | Temperate midlatitudes | 6 | Baltic mixed forests | 80405 | NA | 78.5 | Presence/Absence | 2006-01-01 | NA | NA | NA | NA | 2 | 1 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
967605 | Ireland_nvd | EU-IE-001 | 33419 | NA | F2FF08A0-A6D4-47B2-9EE7-8E9513D5ADE3 | -7.763136 | 53.54469 | 100 | Ireland | EU | Temperate midlatitudes | 6 | Celtic broadleaf forests | 80409 | Keel Deer Park | 4.0 | Domin | 2009-06-08 | NA | NA | NA | NA | 50 | 50 | NA | NA | 0 | 0 | 1 | 0 | 0 | 3 | E21 | FALSE | TRUE | NA | NA | NA | NA | 4 | NA | NA | 4 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
1871500 | Siberia | AS-RU-002 | 2824 | NA | B16B3B2C-5470-4637-A105-79C25CAD4ADC | 107.501760 | 51.23694 | 10 | Russian Federation | EU | Boreal zone | 8 | Daurian forest steppe | 80804 | NA | 100.0 | Percentage (%) | 2013-08-07 | NA | NA | NA | NA | 893 | 895 | 130 | 15 | 0 | 0 | 1 | 0 | 0 | 2 | NA | FALSE | TRUE | NA | NA | NA | 50 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
1539531 | Spain_sivim_sclerophyllous_pinus | EU-00-004f | 499 | NA | A6001CF9-BEDC-40FA-8821-56DE70DEDD5C | 0.529760 | 40.76404 | 1000 | Spain | EU | Subtropics with winter rain | 4 | Northeastern Spain and Southern France Mediterranean forests | 81215 | Barranc de Pasqualet prop del mas del Racó | 40.0 | Braun/Blanquet (old) | 2003-03-27 | NA | NA | NA | NA | 14 | 21 | 180 | NA | 0 | 0 | 1 | 0 | 0 | NA | E | FALSE | TRUE | 75 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 1 | NA | NA | NA | NA | NA |
381504 | Denmark | EU-DK-002 | 61438 | NA | 2021121A-C4A5-4AD8-BD37-9B1B9F270979 | 9.544908 | 56.94567 | 15 | Denmark | EU | Temperate midlatitudes | 6 | Baltic mixed forests | 80405 | NA | 78.5 | Presence/Absence | 2009-01-01 | NA | NA | NA | NA | 1 | 1 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
1099756 | Netherlands | EU-NL-001 | 354151 | NA | 277368FE-D802-4CF2-9320-34126A13A7E6 | 5.586538 | 52.33894 | 10 | Netherlands | EU | Temperate midlatitudes | 6 | Atlantic mixed forests | 80402 | NA | NA | Ordinale scale (1-9) | 1991-01-01 | NA | NA | NA | NA | -3 | -2 | NA | NA | 0 | 0 | 0 | 1 | 0 | 1 | C23 | FALSE | TRUE | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
146483 | European Boreal Forest Database | EU-00-027 | 2142 | NA | 18ED64A2-A010-4D50-BF5B-67C492B3CA32 | 44.876383 | 58.21260 | -10 | Russian Federation | EU | Boreal zone | 8 | Scandinavian and Russian taiga | 80608 | Manturovsky leshoz, Manturovskoye lesnichestvo, v 100 m na V ot op. D-18 | 100.0 | Braun/Blanquet (old) | 2004-07-07 | NA | NA | NA | NA | 123 | NA | 45 | 1 | 1 | 0 | 0 | 0 | 0 | NA | G | TRUE | FALSE | NA | NA | 20 | 50 | 80 | 5 | NA | NA | NA | NA | NA | NA | 12 | NA | 40 | NA | NA | NA |
824142 | Germany_gvrd | EU-DE-014 | 97364 | NA | 2282B367-6439-4D7F-B0AD-1018E55FA5D7 | 11.419217 | 48.96722 | 254927 | Germany | EU | Temperate midlatitudes | 6 | Western European broadleaf forests | 80445 | NA | 314.0 | Braun/Blanquet (new) | 1995-07-01 | NA | NA | NA | NA | NA | 0 | 315 | 14 | 1 | 0 | 0 | 0 | 0 | NA | G | TRUE | FALSE | NA | 25 | 25 | 45 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
sPlot 3.0 contains 1977654 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 |
---|---|---|---|---|---|---|---|---|---|
517177 | Bryum pseudotriquetrum | Bryum pseudotriquetrum | species | Moss | 9 | 5 | CoverPerc | 1 | 0.0833333 |
517177 | Calamagrostis stricta | Calamagrostis stricta | species | Vascular plant | 6 | 3- | CoverPerc | 1 | 0.0833333 |
517177 | Calliergon giganteum | Calliergon giganteum | species | Moss | 9 | 5 | CoverPerc | 1 | 0.0833333 |
517177 | Carex aquatilis | Carex aquatilis | species | Vascular plant | 6 | 6+ | CoverPerc | 1 | 0.0833333 |
517177 | Cinclidium stygium | Cinclidium stygium | species | Moss | 9 | 5 | CoverPerc | 1 | 0.0833333 |
517177 | Limprichtia cossonii | Drepanocladus revolvens var. intermedius | lower | Moss | 9 | 5 | CoverPerc | 1 | 0.0833333 |
517177 | Equisetum fluviatile | Equisetum fluviatile | species | Vascular plant | 6 | 5 | CoverPerc | 1 | 0.0833333 |
517177 | Eriophorum angustifolium | Eriophorum angustifolium | species | Vascular plant | 6 | 4 | CoverPerc | 1 | 0.0833333 |
517177 | Pedicularis palustris | Pedicularis palustris | species | Vascular plant | 6 | 5- | CoverPerc | 1 | 0.0833333 |
517177 | Comarum palustre | Potentilla palustris | species | Vascular plant | 6 | 5 | CoverPerc | 1 | 0.0833333 |
517177 | Scorpidium scorpioides | Scorpidium scorpioides | species | Moss | 9 | 7 | CoverPerc | 1 | 0.0833333 |
517177 | Triglochin palustris | Triglochin palustris | species | Vascular plant | 6 | 5 | CoverPerc | 1 | 0.0833333 |
602531 | Alchemilla hoppeana | Alchemilla hoppeana | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0434783 |
602531 | Asperula cynanchica | Asperula cynanchica | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0434783 |
602531 | Asplenium ruta-muraria | Asplenium ruta-muraria | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0434783 |
602531 | Asplenium trichomanes | Asplenium trichomanes | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0434783 |
602531 | Bupleurum angulosum | Bupleurum angulosum | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0434783 |
602531 | Clinopodium alpinum | Calamintha alpina | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0434783 |
602531 | Campanula rotundifolia | Campanula rotundifolia | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0434783 |
602531 | Chaenorhinum origanifolium | Chaenorrhinum origanifolium | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0434783 |
602531 | Dethawia splendens | Dethawia tenuifolia | species | Vascular plant | 0 | 1 | CoverPerc | 3 | 0.0652174 |
602531 | Erinus alpinus | Erinus alpinus | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0434783 |
602531 | Globularia repens | Globularia cordifolia subsp. nana | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0434783 |
602531 | Hieracium lawsonii | Hieracium lawsonii | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0434783 |
602531 | Hypericum nummularium | Hypericum nummularium | species | Vascular plant | 0 | 1 | CoverPerc | 3 | 0.0652174 |
602531 | Laserpitium siler | Laserpitium siler | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0434783 |
602531 | Potentilla alchimilloides | Potentilla alchimilloides | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0434783 |
602531 | Rhamnus alpina | Rhamnus alpina | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0434783 |
602531 | Salix pyrenaica | Salix pyrenaica | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0434783 |
602531 | Saxifraga paniculata | Saxifraga aizoon | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0434783 |
602531 | Sedum dasyphyllum | Sedum dasyphyllum | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0434783 |
602531 | Sempervivum tectorum | Sempervivum tectorum | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0434783 |
602531 | Silene saxifraga | Silene saxifraga | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0434783 |
602531 | Thymelaea dioica | Thymelaea dioica | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0434783 |
642792 | Brachypodium pinnatum | Brachypodium pinnatum | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0206186 |
642792 | Calluna vulgaris | Calluna vulgaris | species | Vascular plant | 0 | 4 | CoverPerc | 68 | 0.7010309 |
642792 | Erica arborea | Erica arborea | species | Vascular plant | 0 | 2 | CoverPerc | 13 | 0.1340206 |
642792 | Filipendula vulgaris | Filipendula hexapetala | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0206186 |
642792 | Fraxinus ornus | Fraxinus ornus | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0206186 |
642792 | Genista germanica | Genista germanica | species | Vascular plant | 0 | 1 | CoverPerc | 3 | 0.0309278 |
642792 | Genista pilosa | Genista pilosa | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0206186 |
642792 | Pteridium aquilinum | Pteridium aquilinum | species | Vascular plant | 0 | 1 | CoverPerc | 3 | 0.0309278 |
642792 | Quercus petraea | Quercus sessiliflora | lower | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0206186 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Vatairea guianensis | species | 8 | 0.6722159 | 2.7797016 | 12.525344 | 482.4938 | 18.46591 | 0.8018833 | 11.0628212 | 0.2602396 | 379.4035820 | 9.5311951 | 0.2056143 | 0.4063768 | 1.5387119 | 302.88476 | 1.118710 | 93.83952 | 74.29787 | 47.12289 | 1.7882276 | 25.55010 | 0.7297503 | 15.79152 | 20.70242 | 2.299487 | 12.253839 | 43.56165 | 347.2080 | 853.4776 | 1238.2091 | 3296.4645 | 2295.1041 | 2874.9363 | 2.211670 | 0.0565956 | 0.1885776 | 0.3639127 | 1.2848536 | 0.3645544 | 0.0374935 | 0.4137487 | 0.0306235 | 14.2669305 | 0.3402057 | 0.0015678 | 0.0038958 | 0.0354565 | 8.2952800 | 0.0748858 | 0.2590640 | 15.040658 | 3.4695883 | 0.0676247 | 0.7849064 | 0.0163645 | 0.5326662 | 0.3648002 | 0.0431242 | 0.4982434 | 1.1135193 | 5.601424 | 11.682894 | 63.02109 | 96.13970 | 103.87224 | 100.91769 | 0.0620986 |
Margaritaria nobilis | species | 40 | 0.5993023 | 1.5537653 | 18.466311 | 477.2751 | 24.72803 | 1.1678184 | 16.6453056 | 0.2107132 | 11.6734939 | 5.9838651 | 0.2124410 | 0.3161126 | 1.4204863 | 214.79447 | 6.803236 | 87.87249 | 10590.62666 | 48.68189 | 2.2395557 | 20.99614 | 0.7392856 | 29.27085 | 38.05340 | 2.869246 | 6.573622 | 66.18166 | 642.9324 | 1648.2597 | 4666.3020 | 3357.1332 | 3207.3254 | 4332.4171 | 3.477996 | 0.0587574 | 0.1691138 | 3.3082034 | 4.9062931 | 1.5151420 | 0.0602008 | 1.8489183 | 0.0486448 | 1.0350642 | 0.2543133 | 0.0161508 | 0.0130944 | 0.2069211 | 69.6159406 | 0.1879278 | 0.5966915 | 2144.262327 | 6.9903980 | 0.3413702 | 1.1812389 | 0.2243943 | 1.4884228 | 0.9514486 | 0.0639922 | 0.3252025 | 2.4227549 | 24.214544 | 46.773579 | 416.82937 | 847.47317 | 627.81196 | 1113.05809 | 0.2265792 |
Lyonia ferruginea | species | 87 | 0.6400153 | 0.2399927 | 6.690179 | 476.8079 | 11.19432 | 0.6896101 | 1.9432441 | 0.0472154 | 0.3183684 | 1.4826902 | 0.1786788 | 0.4055247 | 1.7106733 | 101.12063 | -2.308281 | 69.71591 | 3091.29348 | 47.96378 | 2.4530686 | 41.86658 | 0.2352875 | 153.41107 | 34.93723 | 2.609818 | 1.470244 | 52.65022 | 663.1614 | 1019.7598 | 4339.8605 | 628.4237 | 617.7565 | 1175.7141 | 2.144294 | 0.0053745 | 0.0191243 | 0.8012776 | 1.3254882 | 0.4199479 | 0.0252266 | 0.1271815 | 0.0038214 | 0.0180788 | 0.0438777 | 0.0086333 | 0.0110886 | 0.1379272 | 24.0866318 | 0.1453524 | 0.5100642 | 578.893961 | 5.2878449 | 0.3514646 | 1.2938295 | 0.0551677 | 11.0475458 | 0.6651824 | 0.0466308 | 0.0475863 | 2.3995974 | 43.549965 | 40.903721 | 308.53495 | 164.45151 | 121.13990 | 252.57982 | 0.1125458 |
Panicum dichotomiflorum | species | 27 | 0.4059287 | 0.4359736 | 23.571384 | 403.1738 | 19.66168 | 2.6043284 | 1.2465636 | 0.0124930 | 0.7296375 | 2.0653552 | 0.1664591 | 0.2201341 | 0.8964605 | 379.09704 | 4.267982 | 81.61515 | 3346.88608 | 268.70892 | 3.4902659 | 20.63088 | 1.6941180 | 39.72366 | 51.90559 | 3.510563 | 2.578718 | 67.92478 | 708.7898 | 1271.1449 | 9842.3613 | 7451.8230 | 4220.6560 | 7801.4471 | 5.600981 | 0.0044038 | 0.0246653 | 1.9623561 | 1.6244233 | 0.4290883 | 0.0668692 | 0.1496899 | 0.0012612 | 0.1019641 | 0.1174036 | 0.0063154 | 0.0139840 | 0.0558758 | 118.7710476 | 0.1391440 | 0.4055841 | 477.131299 | 30.3026706 | 0.5409015 | 0.4323524 | 0.5729647 | 2.3290410 | 0.9727910 | 0.0587627 | 0.1902446 | 2.7469026 | 19.414616 | 33.149771 | 496.01369 | 2018.54248 | 928.03982 | 2000.97191 | 0.3212448 |
Siparuna | genus | 272 | 0.5864524 | 1.3055412 | 17.561570 | 457.8918 | 25.90621 | 0.6553297 | 12.0367827 | 0.1092103 | 13.4312673 | 3.0122804 | 0.2641140 | 0.2428260 | 1.5765823 | 856.73718 | 3.499448 | 95.86484 | 757.05999 | 56.13095 | 10.2830389 | 21.10720 | 3.7492430 | 11.33537 | 28.09510 | 1.934749 | 2.002132 | 48.29942 | 461.5262 | 882.5998 | 1249.6767 | 12463.7054 | 10766.8889 | 10993.9539 | 5.494656 | 0.0726384 | 0.4800029 | 4.4459762 | 9.1313018 | 3.1834821 | 0.1318165 | 3.3421098 | 0.0292040 | 2.0373690 | 0.1974227 | 0.0533452 | 0.0326744 | 0.3633497 | 1106.0557364 | 1.1712826 | 2.1549495 | 343.540502 | 17.9219671 | 4.4403416 | 1.8544555 | 4.1989000 | 1.8983721 | 1.5002411 | 0.0779665 | 0.1798266 | 7.7172258 | 55.272916 | 156.454307 | 261.03092 | 10822.62248 | 7947.98875 | 7695.55901 | 1.0678063 |
Calceolaria ascendens | species | 1 | 0.4447722 | 1.3601926 | 6.347353 | 510.3746 | 21.75669 | 1.5720155 | 0.0428175 | 0.2466362 | 0.0203332 | 0.3749964 | 0.5472826 | 0.2326140 | 4.6886615 | 519.59897 | -1.792459 | 88.11839 | 64.95110 | 44.38752 | 2.3135643 | 32.00758 | 1.6476915 | 114.82585 | 109.60774 | 3.800072 | 1.036005 | 80.61037 | 827.4609 | 676.9891 | 1323.1818 | 1825.0987 | 342.1614 | 415.8707 | 3.511569 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
Pinus heldreichii | species | 28 | 0.5178953 | 2.2539728 | 3.035730 | 499.8060 | 10.32942 | 0.8665113 | 23.2948582 | 0.6353712 | 22.9025100 | 7.0107313 | 1.3297759 | 0.4300700 | 3.5790837 | 56.96435 | -2.466553 | 74.39418 | 32316.01218 | 73.74505 | 0.2294704 | 55.15549 | 0.1260591 | 219.05671 | 28.84489 | 45.913610 | 13.299355 | 10.67479 | 761.1557 | 1545.9367 | 973.7049 | 139.5551 | 353.2741 | 192.6266 | 2.212363 | 0.0038475 | 0.1293572 | 0.0726053 | 1.0905367 | 0.1067092 | 0.0122529 | 6.1332782 | 0.0731602 | 2.2844592 | 0.3745275 | 0.0334996 | 0.0037914 | 0.0739657 | 4.9463990 | 0.0727970 | 0.4827775 | 5608.088123 | 5.3478132 | 0.0179995 | 0.6355534 | 0.0101801 | 10.7763495 | 0.3755246 | 0.8703276 | 0.6054345 | 0.2348116 | 10.894686 | 29.032838 | 33.87290 | 12.33229 | 30.15243 | 17.21768 | 0.0310121 |
Plectritis macrocera | species | 3 | 0.4080781 | 0.1760720 | 30.348698 | 447.7354 | 20.29953 | 1.7475233 | 0.5690021 | 0.0106863 | 0.4171745 | 1.9543881 | 0.1631470 | 0.1580604 | 0.7418369 | 28.99839 | -1.948937 | 87.25034 | 757.70197 | 64.70594 | 2.4486339 | 24.16146 | 0.1675290 | 129.64781 | 21.08783 | 4.706707 | 2.816474 | 25.09128 | 506.9501 | 816.2272 | 7006.4302 | 802.7997 | 764.1667 | 760.9637 | 6.317764 | 0.0017195 | 0.0066200 | 0.0949752 | 0.9659482 | 0.1739723 | 0.0204453 | 0.0063019 | 0.0000635 | 0.0121886 | 0.0213697 | 0.0008300 | 0.0027907 | 0.0089611 | 0.5048533 | 0.0853765 | 0.2341677 | 62.040826 | 0.4910093 | 0.0234829 | 0.1549764 | 0.0042817 | 4.4867440 | 0.2168985 | 0.0102219 | 0.0041514 | 0.2249483 | 3.109494 | 9.404808 | 48.56302 | 15.69051 | 18.93648 | 21.43769 | 0.0579898 |
Oxycoccus macrocarpos | species | 1 | 0.6035942 | 0.1636927 | 9.316208 | 490.1482 | 12.59416 | 0.8165591 | 0.9922413 | 0.0733816 | 0.3771482 | 1.4337547 | 0.2531170 | 0.3979453 | 1.4467550 | 15.85061 | -2.969219 | 85.81865 | 255.19846 | 23.64796 | 0.7751801 | 40.94049 | 0.0400045 | 134.80812 | 31.92064 | 2.222710 | 1.758093 | 27.19607 | 489.2154 | 709.0878 | 1631.4581 | 132.7401 | 122.0543 | 145.3374 | 2.373835 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
Leidesia procumbens | species | 5 | 0.5593456 | 0.7914904 | 16.098304 | 452.6199 | 23.69874 | 1.4363048 | 0.3421095 | 0.0357829 | 12.3938525 | 2.0233259 | 0.2004298 | 0.2997918 | 1.6921532 | 109.50815 | 2.274450 | 91.60527 | 21.85357 | 27.53842 | 1.8078170 | 23.73503 | 0.3615321 | 26.35735 | 29.65715 | 3.647588 | 2.345868 | 43.84997 | 352.0058 | 677.4410 | 2685.9820 | 1245.0791 | 1654.7699 | 1760.0227 | 3.375736 | 0.0071851 | 0.0471449 | 0.1885470 | 1.7500842 | 0.4706820 | 0.0228739 | 0.0440011 | 0.0026347 | 0.5498201 | 0.0740992 | 0.0021000 | 0.0020124 | 0.0212530 | 30.1326768 | 0.0866579 | 0.9643899 | 4.864554 | 11.8142117 | 0.7780635 | 0.3660885 | 0.0972223 | 0.7987999 | 0.8028841 | 0.1309149 | 0.0796371 | 1.3132401 | 12.620701 | 22.177161 | 95.53994 | 320.20868 | 397.83301 | 651.61422 | 0.0475394 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Baeckea elderiana | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
Crithmum maritimum | herb | FALSE | 31 | 0.3598245 | 0.4623795 | 9.87179 | 462.6409 | 20.76717 | 1.818932 | 0.3256135 | 0.0318075 | 2.7979171 | 3.879444 | 0.3032341 | 0.1044528 | 2.2884799 | 29.032602 | 1.0110576 | 99.40896 | 4035.61311 | 58.69327 | 0.8554186 | 25.25249 | 0.1781171 | 117.01788 | 20.30854 | 5.2547393 | 5.951872 | 23.22521 | 393.1173 | 833.7714 | 3597.262 | 276.96952 | 280.32378 | 451.2584 | 9.144722 | 0.0038413 | 0.0296692 | 0.5707082 | 1.018281 | 0.3246270 | 0.0426899 | 0.0726439 | 0.0035257 | 0.4745796 | 0.2397221 | 0.0079225 | 0.0065069 | 0.1012649 | 2.521166 | 0.0934804 | 0.4656056 | 993.271726 | 3.601071 | 0.0580773 | 0.4145022 | 0.0128764 | 5.389161 | 0.2386332 | 0.0734118 | 0.3396245 | 0.6743566 | 7.967126 | 15.831094 | 170.35607 | 20.30759 | 20.36548 | 35.79330 | 0.2559365 |
Artemisia stricta | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
Genista valdes-bermejoi | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
Honkenya | NA | NA | 40 | 0.4091937 | 0.4133352 | 16.38002 | 465.1512 | 21.24890 | 2.315687 | 0.1821260 | 0.0222774 | 1.8973443 | 2.292418 | 0.2128676 | 0.2138782 | 1.4964675 | 6.420282 | -1.0345258 | 84.33356 | 98.61291 | 24.78855 | 0.4870728 | 24.99793 | 0.0291914 | 124.56430 | 31.10676 | 4.5264983 | 3.405845 | 41.41104 | 452.5658 | 741.2316 | 1851.067 | 97.51589 | 75.36323 | 257.4962 | 5.147197 | 0.0072841 | 0.0482834 | 2.6976842 | 1.878441 | 0.9209020 | 0.1211113 | 0.0398220 | 0.0030937 | 1.0047648 | 0.2929820 | 0.0137556 | 0.0267117 | 0.1572643 | 1.037782 | 0.1297828 | 0.4306473 | 40.286379 | 1.982077 | 0.0512710 | 0.9243451 | 0.0038323 | 7.454068 | 0.4103227 | 0.0917059 | 0.4095038 | 2.0367969 | 16.605210 | 22.452615 | 178.67409 | 12.34936 | 10.30276 | 31.62444 | 0.6237807 |
Bulbophyllum regnellii | other | 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 |
Rubus polyanthemus | shrub | FALSE | 4 | 0.3888007 | 0.4937079 | 19.84643 | 449.7492 | 20.65614 | 1.899736 | 0.9816003 | 0.0165019 | 1.7696248 | 2.644587 | 0.1914462 | 0.3332844 | 1.0473794 | 132.583672 | 0.1554687 | 89.50816 | 65.83166 | 88.09421 | 7.1123231 | 22.73657 | 0.4474139 | 79.75308 | 27.84558 | 0.8682862 | 2.774451 | 51.58788 | 419.4643 | 611.3399 | 3133.963 | 2604.14528 | 2390.49028 | 3337.2844 | 3.629212 | 0.0011950 | 0.0162483 | 0.2368944 | 1.297367 | 0.0917424 | 0.0609001 | 0.0505738 | 0.0008787 | 0.1188227 | 0.1009590 | 0.0031232 | 0.0034674 | 0.0120614 | 8.665769 | 0.0870896 | 0.3111570 | 9.128662 | 5.292013 | 0.3120354 | 0.2952896 | 0.0294363 | 1.365777 | 0.1753860 | 0.0141503 | 0.1954446 | 1.5339044 | 6.958913 | 14.193933 | 83.17955 | 163.02939 | 107.00082 | 209.65861 | 0.0485950 |
Trisetaria panicea | herb | FALSE | 8 | 0.3692896 | 0.2543290 | 33.41967 | 428.6107 | 17.39745 | 1.566507 | 0.1456960 | 0.0035342 | 0.0750225 | 1.014454 | 0.1525806 | 0.2365561 | 0.6227592 | 9.861193 | 0.4045322 | 94.68273 | 942.65597 | 49.03700 | 0.3735864 | 27.76907 | 0.0436304 | 59.64955 | 23.85574 | 9.3535842 | 1.579966 | 22.53872 | 384.6134 | 750.2583 | 16417.882 | 271.67078 | 311.76552 | 315.9873 | 4.435674 | 0.0102041 | 0.0310212 | 7.6821815 | 2.115690 | 1.0507764 | 0.1082438 | 0.0061670 | 0.0005251 | 0.0090930 | 0.0566146 | 0.0147142 | 0.0219960 | 0.0992812 | 1.656297 | 0.0871180 | 0.2874750 | 137.849683 | 1.384951 | 0.0203598 | 1.4514962 | 0.0036330 | 1.543279 | 0.3019474 | 0.2918524 | 0.0880394 | 0.8205240 | 8.794040 | 8.169421 | 1238.31793 | 19.97421 | 13.13648 | 11.29422 | 0.4692172 |
Kallstroemia angustifolia | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
Catapyrenium waltheri | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 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 |
---|---|---|---|---|---|---|
560875 | Stem.cond.dens_mean | 31 | 0.8064516 | 0.9267016 | 49.7518752 | 2.792975e+03 |
628539 | LeafArea.undef.undef_mean | 23 | 0.9130435 | 0.9285714 | 392.7217984 | 3.127773e+05 |
1296883 | StemConduitDiameter_mean | 8 | 1.0000000 | 1.0000000 | 44.3022001 | 2.372018e+03 |
1287621 | LeafArea.leaf.undef_mean | 22 | 0.9545455 | 0.9789474 | 292.5977563 | 9.133854e+04 |
272579 | StemDens_mean | 6 | 1.0000000 | 1.0000000 | 0.3134321 | 1.422200e-03 |
166254 | LeafArea.undef.undef_mean | 14 | 0.3571429 | 0.1940299 | 3141.2611221 | 4.594239e+07 |
1174679 | Wood.vessel.length_mean | 13 | 1.0000000 | 1.0000000 | 372.0917903 | 1.834795e+04 |
771554 | Chromosome.n_mean | 14 | 1.0000000 | 1.0000000 | 37.7696428 | 5.286600e+01 |
1642465 | StemDiam_mean | 20 | 1.0000000 | 1.0000000 | 0.0138721 | 9.650000e-05 |
1559730 | LeafDryMass.single_mean | 13 | 1.0000000 | 1.0000000 | 23.6498147 | 1.358426e+02 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1515357 | 952 | 859 | 1111 | 153 | 101.00000 | 91.00000 | 378.5000 | 5008.250 | 236.000 | -3.750000 | 240.0000 | 50.2500 | 175.500000 | 175.5000 | 37.250000 | 1024.0000 | 130.50000 | 30.25000 | 37.50000 | 384.7500 | 91.500 | 91.5000 | 360.0000 | 4.3969687 | 0.0000000 | 0.5773503 | 8.057088 | 4.396969 | 4.0311289 | 0.0000000 | 4.0311289 | 4.2031734 | 4.2031734 | 4.0311289 | 32.567878 | 4.3588989 | 0.9574271 | 0.5773503 | 12.971122 | 3.000000 | 3.000000 | 11.803954 | 967.2375 | 17.88750 | 16.425000 | 20.625000 | 73.45000 | 56.30000 | 37.98750 | 45.56250 | 60.500496 | 1.5260916 | 1.5813390 | 1.8237186 | 16.254230 | 1.4703827 | 1.2375328 | 1.9476942 |
866010 | 19 | 0 | 38 | 153 | 89.40426 | 52.56383 | 232.9468 | 6165.511 | 212.234 | -13.606383 | 225.7553 | 170.4468 | 9.946808 | 176.7447 | 8.797872 | 573.8830 | 62.79787 | 31.80851 | 18.18085 | 184.0532 | 108.000 | 179.0106 | 108.0638 | 0.8715226 | 0.4985681 | 1.5336163 | 8.764229 | 1.213061 | 0.6912368 | 0.7137086 | 0.9904601 | 4.2989547 | 0.9830408 | 0.8747324 | 14.264669 | 2.2268150 | 0.7798069 | 0.9153737 | 6.651650 | 2.514474 | 5.460503 | 2.517929 | 731.0573 | 16.70785 | 11.739249 | 6.645734 | 36.63003 | 63.24710 | 27.38020 | 60.85666 | 103.466162 | 2.9802354 | 1.7845713 | 0.7923541 | 18.247267 | 2.3470348 | 4.4830606 | 4.4957401 |
1285109 | NA | NA | NA | NA | 91.00000 | 70.00000 | 264.0000 | 7086.000 | 236.000 | -30.000000 | 266.0000 | 184.0000 | -2.000000 | 187.0000 | -2.000000 | 522.0000 | 76.00000 | 26.00000 | 33.00000 | 213.0000 | 82.000 | 194.0000 | 82.0000 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 1037.0000 | 13.00000 | 9.000000 | 7.000000 | 30.00000 | 63.00000 | 22.00000 | 70.00000 | NA | NA | NA | NA | NA | NA | NA | NA |
1119017 | 14 | 14 | 14 | 153 | 103.00000 | 45.00000 | 243.0000 | 4934.000 | 203.000 | 16.000000 | 186.0000 | 91.0000 | 78.000000 | 174.0000 | 37.000000 | 856.0000 | 92.00000 | 45.00000 | 22.00000 | 274.0000 | 149.000 | 246.0000 | 178.0000 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 663.6667 | 15.50000 | 9.333333 | 5.500000 | 69.83333 | 62.16667 | 14.83333 | 75.83333 | 32.512562 | 0.5477226 | 0.8164966 | 0.8366600 | 8.863784 | 0.9831921 | 0.9831921 | 0.9831921 |
508397 | 11 | 8 | 15 | 153 | 25.00000 | 47.00000 | 155.0000 | 8770.000 | 186.000 | -119.000000 | 305.0000 | 107.0000 | -14.000000 | 149.0000 | -93.000000 | 529.0000 | 60.00000 | 29.00000 | 25.00000 | 176.0000 | 89.000 | 152.0000 | 100.0000 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 421.3750 | 28.12500 | 12.500000 | 13.125000 | 188.37500 | 45.87500 | 33.75000 | 54.00000 | 23.748308 | 2.1001701 | 2.3904572 | 1.2464235 | 12.316510 | 0.8345230 | 3.2841611 | 5.4248107 |
226093 | 264 | 257 | 271 | 153 | 91.00000 | 73.00000 | 262.0000 | 7277.000 | 238.000 | -40.000000 | 278.0000 | 186.0000 | -5.000000 | 189.0000 | -7.000000 | 667.0000 | 91.00000 | 31.00000 | 40.00000 | 271.0000 | 95.000 | 249.0000 | 100.0000 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 1034.0000 | 17.60000 | 19.000000 | 7.800000 | 28.40000 | 61.20000 | 51.00000 | 29.80000 | 54.438038 | 0.5477226 | 0.7071068 | 1.3038405 | 2.073644 | 0.4472136 | 1.0000000 | 1.6431677 |
668066 | 4 | 4 | 4 | 153 | 110.00000 | 55.00000 | 291.0000 | 4750.000 | 214.000 | 23.000000 | 191.0000 | 96.0000 | 87.000000 | 179.0000 | 48.000000 | 774.0000 | 90.00000 | 47.00000 | 21.00000 | 262.0000 | 146.000 | 181.0000 | 166.0000 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 600.6667 | 18.33333 | 16.000000 | 5.166667 | 59.66667 | 61.16667 | 27.00000 | 57.00000 | 38.655746 | 0.8164966 | 0.6324555 | 0.4082483 | 7.339391 | 0.9831921 | 1.0954451 | 1.5491933 |
769073 | -1 | -2 | 3 | 153 | 96.00000 | 37.01980 | 195.1683 | 5414.030 | 197.495 | 7.910891 | 189.6238 | 129.5248 | 68.475247 | 174.0000 | 24.445545 | 794.1089 | 81.87129 | 42.06931 | 21.86139 | 241.0495 | 138.604 | 236.3663 | 147.3069 | 0.0000000 | 1.4965306 | 5.6799108 | 19.733452 | 1.171527 | 0.8136217 | 1.8102568 | 38.9773252 | 0.5018777 | 0.0000000 | 0.4995047 | 7.094929 | 0.5415416 | 0.7246713 | 0.7075267 | 1.023487 | 2.462029 | 2.583497 | 2.331277 | 710.8170 | 21.88255 | 23.023830 | 9.617021 | 71.31489 | 66.76255 | 35.75404 | 41.24085 | 74.096958 | 3.1254018 | 5.3176230 | 3.8032600 | 25.855177 | 1.5390301 | 5.2002423 | 10.1554711 |
429725 | NA | NA | NA | NA | 85.00000 | 29.00000 | 148.0000 | 5979.000 | 191.000 | -8.000000 | 199.0000 | 171.0000 | 7.000000 | 171.0000 | 7.000000 | 576.0000 | 60.00000 | 29.00000 | 21.00000 | 179.0000 | 101.000 | 179.0000 | 101.0000 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 708.3333 | 25.33333 | 18.333333 | 9.000000 | 70.50000 | 62.50000 | 27.66667 | 54.00000 | 50.618837 | 2.6583203 | 1.2110601 | 0.8944272 | 11.878552 | 1.6431677 | 1.6329932 | 1.7888544 |
1888421 | 219 | 219 | 219 | 153 | 251.00000 | 53.00000 | 563.0000 | 856.000 | 301.000 | 208.000000 | 93.0000 | 244.0000 | 253.000000 | 262.0000 | 238.000000 | 1877.0000 | 279.00000 | 24.00000 | 50.00000 | 755.0000 | 97.000 | 374.0000 | 488.0000 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 1324.8000 | 9.00000 | 23.600000 | 30.200000 | 23.80000 | 48.00000 | 16.00000 | 60.40000 | 8.105554 | 1.0000000 | 0.5477226 | 2.7748874 | 2.049390 | 0.0000000 | 0.7071068 | 1.1401754 |
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 fansi_0.4.1
## [25] highr_0.8 broom_0.7.0 Rcpp_1.0.5 scales_1.1.1
## [29] backports_1.2.0 webshot_0.5.2 jsonlite_1.7.1 fs_1.5.0
## [33] hms_0.5.3 digest_0.6.25 stringi_1.5.3 grid_3.6.3
## [37] cli_2.2.0 tools_3.6.3 magrittr_2.0.1 crayon_1.3.4
## [41] pkgconfig_2.0.3 ellipsis_0.3.1 xml2_1.3.2 reprex_0.3.0
## [45] lubridate_1.7.9.2 assertthat_0.2.1 rmarkdown_2.5 httr_1.4.2
## [49] rstudioapi_0.13 R6_2.5.0 compiler_3.6.3