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)

1 Taxonomic Backbone

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

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

1.1 Show output

Example of Backbone (only 20 randomly selected taxa shown)
Name_sPlot_TRY Name_string_corr1 Name_string_corr2 sPlot_TRY Name_submitted Name_number Overall_score Name_matched Name_matched_rank Name_score Name_matched_author Name_matched_url Author_matched Author_score Family_matched Family_score Name_matched_accepted_family Genus_matched Genus_score Specific_epithet_matched Specific_epithet_score Infraspecific_rank Infraspecific_epithet_matched Infraspecific_epithet_score Infraspecific_rank_2 Infraspecific_epithet_2_matched Infraspecific_epithet_2_score Annotations Unmatched_terms Taxonomic_status Accepted_name Accepted_name_author Accepted_name_rank Accepted_name_url Accepted_name_species Accepted_name_family Selected Source Warnings Accepted_name_lsid Status_correct Name_correct Genus_correct Rank_correct Family_correct Name_short phylum is_vascular_species Taxon group
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.

1.2 Description of fields

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

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

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

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


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

3 DT Table

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

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

3.1 Show output

Example of DT table (only species from three randomly selected plots shown)
PlotObservationID Species Species_original Rank_correct Taxon_group Layer Cover_code Ab_scale Abundance Relative_cover
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
The DT table contains 43093257 entries, from 76912 species.

3.2 Description of fields

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

4 Functional Traits and Community Weighted Means\Variances

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

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

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

4.1 Show output

Object try.combined.means.
Example of trait table of TRY species (only 10 randomly selected species shown)
Taxon_name Rank_correct n StemDens_mean RootingDepth_mean SLA_mean LeafC.perdrymass_mean LeafN_mean LeafP_mean PlantHeight_mean StemDiam_mean SeedMass_mean Seed.length_mean LeafThickness_mean LDMC_mean LeafNperArea_mean LeafDryMass.single_mean Leaf.delta.15N_mean SeedGerminationRate_mean Seed.num.rep.unit_mean LeafLength_mean LeafWidth_mean LeafCN.ratio_mean Leaffreshmass_mean Stem.cond.dens_mean Chromosome.n_mean Chromosome.cDNAcont_mean Disp.unit.leng_mean StemConduitDiameter_mean Wood.vessel.length_mean WoodFiberLength_mean SpecificRootLength_mean LeafArea.leaf.undef_mean LeafArea.leaflet.undef_mean LeafArea.undef.undef_mean LeafWaterCont_mean StemDens_sd RootingDepth_sd SLA_sd LeafC.perdrymass_sd LeafN_sd LeafP_sd PlantHeight_sd StemDiam_sd SeedMass_sd Seed.length_sd LeafThickness_sd LDMC_sd LeafNperArea_sd LeafDryMass.single_sd Leaf.delta.15N_sd SeedGerminationRate_sd Seed.num.rep.unit_sd LeafLength_sd LeafWidth_sd LeafCN.ratio_sd Leaffreshmass_sd Stem.cond.dens_sd Chromosome.n_sd Chromosome.cDNAcont_sd Disp.unit.leng_sd StemConduitDiameter_sd Wood.vessel.length_sd WoodFiberLength_sd SpecificRootLength_sd LeafArea.leaf.undef_sd LeafArea.leaflet.undef_sd LeafArea.undef.undef_sd LeafWaterCont_sd
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.

Object sPlot.traits.
Example of trait table of sPlot species (only 10 randomly selected species shown)
Species GrowthForm is.tree.or.tall.shrub n StemDens_mean RootingDepth_mean SLA_mean LeafC.perdrymass_mean LeafN_mean LeafP_mean PlantHeight_mean StemDiam_mean SeedMass_mean Seed.length_mean LeafThickness_mean LDMC_mean LeafNperArea_mean LeafDryMass.single_mean Leaf.delta.15N_mean SeedGerminationRate_mean Seed.num.rep.unit_mean LeafLength_mean LeafWidth_mean LeafCN.ratio_mean Leaffreshmass_mean Stem.cond.dens_mean Chromosome.n_mean Chromosome.cDNAcont_mean Disp.unit.leng_mean StemConduitDiameter_mean Wood.vessel.length_mean WoodFiberLength_mean SpecificRootLength_mean LeafArea.leaf.undef_mean LeafArea.leaflet.undef_mean LeafArea.undef.undef_mean LeafWaterCont_mean StemDens_sd RootingDepth_sd SLA_sd LeafC.perdrymass_sd LeafN_sd LeafP_sd PlantHeight_sd StemDiam_sd SeedMass_sd Seed.length_sd LeafThickness_sd LDMC_sd LeafNperArea_sd LeafDryMass.single_sd Leaf.delta.15N_sd SeedGerminationRate_sd Seed.num.rep.unit_sd LeafLength_sd LeafWidth_sd LeafCN.ratio_sd Leaffreshmass_sd Stem.cond.dens_sd Chromosome.n_sd Chromosome.cDNAcont_sd Disp.unit.leng_sd StemConduitDiameter_sd Wood.vessel.length_sd WoodFiberLength_sd SpecificRootLength_sd LeafArea.leaf.undef_sd LeafArea.leaflet.undef_sd LeafArea.undef.undef_sd LeafWaterCont_sd
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.


Object CWM.
Example of CWM table (only 10 randomly selected plots shown)
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.

4.2 Description of fields

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

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


List of Fields

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

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


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

5 Environmental variables

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

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

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

5.1 Show output

Example of dataframe soilclim.
Example of environmental information on 10 randomly selected plots
PlotObservationID Elevation_median Elevation_q2.5 Elevation_q97.5 Elevation_DEM.res bio01 bio02 bio03 bio04 bio05 bio06 bio07 bio08 bio09 bio10 bio11 bio12 bio13 bio14 bio15 bio16 bio17 bio18 bio19 bio01sd bio02sd bio03sd bio04sd bio05sd bio06sd bio07sd bio08sd bio09sd bio10sd bio11sd bio12sd bio13sd bio14sd bio15sd bio16sd bio17sd bio18sd bio19sd BLDFIE CECSOL CLYPPT CRFVOL ORCDRC PHIHOX SLTPPT SNDPPT BLDFIEsd CECSOLsd CLYPPTsd CRFVOLsd ORCDRCsd PHIHOXsd SLTPPTsd SNDPPTsd
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

5.2 Description of fields

  1. PlotObservationID: Plot ID, as in header.

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

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

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

6 SessionInfo

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