Timestamp: Wed Dec 2 00:52:39 2020
Drafted: Francesco Maria Sabatini
Revised: Helge Bruelheide
Version: 1.1
This report documents the construction of the DT table for sPlot 3.0. It is based on dataset sPlot_3.0.2, received on 24/07/2019 from Stephan Hennekens.
Caution: Layer information is not available for all species in each plot. In case of missing information Layer is set to zero.
Changes in version 1.1
1) Added explanation of fields
2) Fixed taxon_group
of Friesodielsia
3) Only export the fields Ab_scale
and Abundance
knitr::opts_chunk$set(echo = TRUE)
library(tidyverse)
library(readr)
library(xlsx)
library(knitr)
library(kableExtra)
#save temporary files
write("TMPDIR = /data/sPlot/users/Francesco/_tmp", file=file.path(Sys.getenv('TMPDIR'), '.Renviron'))
write("R_USER = /data/sPlot/users/Francesco/_tmp", file=file.path(Sys.getenv('R_USER'), '.Renviron'))
#rasterOptions(tmpdir="/data/sPlot/users/Francesco/_tmp")
Search and replace unclosed quotation marks and escape them. Run in Linux terminal
# escape all double quotation marks. Run in Linux terminal
# sed 's/"/\\"/g' sPlot_3_0_2_species.csv > sPlot_3_0_2_species_test.csv
DT table is the species x plot matrix, in long format.
DT0 <- readr::read_delim("../sPlot_data_export/sPlot_3_0_2_species_test.csv",
delim="\t",
col_type = cols(
PlotObservationID = col_double(),
Taxonomy = col_character(),
`Taxon group` = col_character(),
`Taxon group ID` = col_double(),
`Turboveg2 concept` = col_character(),
`Matched concept` = col_character(),
Match = col_double(),
Layer = col_double(),
`Cover %` = col_double(),
`Cover code` = col_character(),
x_ = col_double()
)
)
nplots <- length(unique(DT0$PlotObservationID))
nspecies <- length(unique(DT0$`Matched concept`))
Match plots with those in header
load("../_output/header_sPlot3.0.RData")
DT0 <- DT0 %>%
filter(PlotObservationID %in% unique(header$PlotObservationID))
The DT table includes 43093474 species * plot records, across 1978589 plots. Before taxonomic resolution, there are 107676 species .
PlotObservationID | Taxonomy | Taxon group | Taxon group ID | Turboveg2 concept | Matched concept | Match | Layer | Cover % | Cover code | x_ |
---|---|---|---|---|---|---|---|---|---|---|
705955 | FR-France_sophy | Vascular plant | 1 | Aconitum napellus | Aconitum napellus | 3 | 0 | 3 | 1 | NA |
705955 | FR-France_sophy | Vascular plant | 1 | Adenostyles alliariae | Adenostyles alliariae | 3 | 0 | 88 | 5 | NA |
705955 | FR-France_sophy | Vascular plant | 1 | Arabis alpina | Arabis alpina | 3 | 0 | 2 |
|
NA |
705955 | FR-France_sophy | Vascular plant | 1 | Cirsium spinosissimum | Cirsium spinosissimum | 3 | 0 | 2 |
|
NA |
705955 | FR-France_sophy | Vascular plant | 1 | Doronicum grandiflorum | Doronicum grandiflorum | 3 | 0 | 2 |
|
NA |
705955 | FR-France_sophy | Vascular plant | 1 | Peucedanum ostruthium | Peucedanum ostruthium | 3 | 0 | 3 | 1 | NA |
705955 | FR-France_sophy | Vascular plant | 1 | Primula elatior | Primula elatior | 3 | 0 | 2 |
|
NA |
705955 | FR-France_sophy | Vascular plant | 1 | Tozzia alpina | Tozzia alpina | 3 | 0 | 3 | 1 | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Agrostis capillaris | Agrostis capillaris | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Agrostis stolonifera | Agrostis stolonifera | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Alopecurus pratensis | Alopecurus pratensis | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Anthoxanthum odoratum | Anthoxanthum odoratum | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Bellis perennis | Bellis perennis | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Moss | 3 | Brachythecium albicans | Brachythecium albicans | 1 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Moss | 3 | Brachythecium rutabulum | Brachythecium rutabulum | 1 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Moss | 3 | Bryum pseudotriquetrum var. bimum | Bryum pseudotriquetrum | 1 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Moss | 3 | Calliergonella cuspidata | Calliergonella cuspidata | 1 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Callitriche stagnalis | Callitriche stagnalis | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Caltha palustris | Caltha palustris | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Cardamine pratensis | Cardamine pratensis | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Carex disticha | Carex disticha | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Carex leporina | Carex leporina | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Carex paniculata | Carex paniculata | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Cerastium fontanum | Cerastium fontanum | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Cirsium palustre | Cirsium palustre | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Crepis capillaris | Crepis capillaris | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Cynosurus cristatus | Cynosurus cristatus | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Deschampsia cespitosa | Deschampsia cespitosa | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Epilobium obscurum | Epilobium obscurum | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Epilobium parviflorum | Epilobium parviflorum | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Equisetum fluviatile | Equisetum fluviatile | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Equisetum sylvaticum | Equisetum sylvaticum | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Festuca rubra | Festuca rubra | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Filipendula ulmaria | Filipendula ulmaria | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Galium palustre | Galium palustre | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Glyceria declinata | Glyceria declinata | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Glyceria fluitans | Glyceria fluitans | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Gnaphalium uliginosum | Gnaphalium uliginosum | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Holcus lanatus | Holcus lanatus | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Hypochaeris radicata | Hypochaeris radicata | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Isolepis setacea | Isolepis setacea | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Juncus acutiflorus | Juncus acutiflorus | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Juncus bufonius | Juncus bufonius | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Juncus bulbosus | Juncus bulbosus | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Juncus effusus | Juncus effusus | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Moss | 3 | Kindbergia praelonga | Kindbergia praelonga | 1 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Lathyrus pratensis | Lathyrus pratensis | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Leontodon autumnalis | Scorzoneroides autumnalis | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Lolium perenne | Lolium perenne | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Lotus pedunculatus | Lotus pedunculatus | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Lychnis flos-cuculi | Silene flos-cuculi | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Lythrum portula | Lythrum portula | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Lythrum salicaria | Lythrum salicaria | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Mentha aquatica | Mentha aquatica | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Persicaria maculosa | Persicaria maculosa | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Plantago lanceolata | Plantago lanceolata | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Poa annua | Ochlopoa annua | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Poa pratensis | Poa pratensis | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Potentilla palustris | Comarum palustre | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Prunella vulgaris | Prunella vulgaris | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Ranunculus acris | Ranunculus acris | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Ranunculus flammula | Ranunculus flammula | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Ranunculus repens | Ranunculus repens | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Moss | 3 | Rhytidiadelphus squarrosus | Rhytidiadelphus squarrosus | 1 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Rubus fruticosus aggr. | Rubus fruticosus aggr. | 1 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Rumex acetosa | Rumex acetosa | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Rumex obtusifolius | Rumex obtusifolius | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Sagina procumbens | Sagina procumbens | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Salix x multinervis | Salix x multinervis | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Senecio aquaticus | Jacobaea aquatica | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Senecio jacobaea | Jacobaea vulgaris | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Sonchus asper | Sonchus asper | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Stellaria uliginosa | Stellaria alsine | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Taraxacum officinale aggr. | Taraxacum sect. Taraxacum | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Trifolium pratense | Trifolium pratense | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Trifolium repens | Trifolium repens | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Ulex europaeus | Ulex europaeus | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Urtica dioica | Urtica dioica | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Valeriana officinalis | Valeriana officinalis subsp. officinalis | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Veronica scutellata | Veronica scutellata | 3 | 0 | 1 | x | NA |
968394 | IR-Ireland2008 | Vascular plant | 1 | Vicia cracca | Vicia cracca | 3 | 0 | 1 | x | NA |
1048670 | NL-Floranld_2013 | Vascular plant | 1 | Aster tripolium | Tripolium pannonicum subsp. tripolium | 3 | 0 | 10 | 01 | NA |
1048670 | NL-Floranld_2013 | Vascular plant | 1 | Atriplex littoralis | Atriplex littoralis | 3 | 0 | 1 | r | NA |
1048670 | NL-Floranld_2013 | Vascular plant | 1 | Atriplex portulacoides | Halimione portulacoides | 3 | 0 | 60 | 06 | NA |
1048670 | NL-Floranld_2013 | Vascular plant | 1 | Atriplex prostrata | Atriplex prostrata | 3 | 0 | 1 | p | NA |
1048670 | NL-Floranld_2013 | Vascular plant | 1 | Elytrigia atherica | Elytrigia atherica | 3 | 0 | 30 | 03 | NA |
1048670 | NL-Floranld_2013 | Vascular plant | 1 | Festuca rubra aggr. (incl. F. arenaria) | Festuca rubra aggr. | 1 | 0 | 1 | p | NA |
1048670 | NL-Floranld_2013 | Vascular plant | 1 | Puccinellia maritima | Puccinellia maritima | 3 | 0 | 1 | p | NA |
1048670 | NL-Floranld_2013 | Vascular plant | 1 | Spartina anglica | Spartina anglica | 3 | 0 | 1 | r | NA |
1048670 | NL-Floranld_2013 | Vascular plant | 1 | Suaeda maritima | Suaeda maritima | 3 | 0 | 1 | p | NA |
Import taxonomic backbone
load("../_output/Backbone3.0.RData")
Match to DT0, using Taxonomic concept
as matching key. This is the field that was used to build, and resolve, the Backbone.
DT1 <- DT0 %>%
left_join(Backbone %>%
dplyr::select(Name_sPlot_TRY, Name_short, `Taxon group`, Rank_correct) %>%
rename(`Matched concept`=Name_sPlot_TRY,
Taxongroup_BB=`Taxon group`),
by="Matched concept") %>%
# Simplify Rank_correct
mutate(Rank_correct=fct_collapse(Rank_correct,
lower=c("subspecies", "variety", "infraspecies", "race", "forma"))) %>%
mutate(Rank_correct=fct_explicit_na(Rank_correct, "No_match")) %>%
mutate(Name_short=replace(Name_short,
list=Name_short=="No suitable",
values=NA))
Select species entries that changed after taxonomic standardization, as a way to check the backbone.
name.check <- DT1 %>%
dplyr::select(`Turboveg2 concept`:`Matched concept`, Name_short) %>%
rename(Name_TNRS=Name_short) %>%
distinct() %>%
mutate(Matched_short=word(`Matched concept`, start = 1L, end=2L)) %>%
filter(is.na(Name_TNRS) | Matched_short != Name_TNRS) %>%
dplyr::select(-Matched_short) %>%
arrange(Name_TNRS)
Turboveg2 concept | Matched concept | Name_TNRS |
---|---|---|
Listera caurina | Listera caurina | Neottia banksiana |
Strychnos darienensis | Strychnos darienensis | Strychnos bredemeyeri |
Ageratum conyzoides | Ageratum conyzoides | Ageratum |
Valerianella species | Valerianella species | Valerianella |
Ilex sp1_CUCSUR1 | Ilex sp1_CUCSUR1 | Ilex |
Dendrobium ruppianum f. ruppianum | Dendrobium ruppianum f. ruppianum | Dendrobium jonesii |
Scenedesmus quadrispina | Scenedesmus quadrispina | Scenedesmus |
Ocotea species #11 | Ocotea species #11 | Ocotea |
Sumpfgladiole haarig 135607 | Sumpfgladiole haarig 135607 | Gladiolus |
Schizaea species | Schizaea species | Schizaea |
Plectranthus Rupestris | Plectranthus Rupestris | Plectranthus hadiensis |
Dichanthelium leibergii | Dichanthelium leibergii | Panicum leibergii |
Melastomataceae species #16 | Melastomataceae species #16 | Melastomataceae |
Linealblatt krgst 155502 | Linealblatt krgst 155502 | NA |
Elaeocarpus cf. | Elaeocarpus cf. | Elaeocarpus |
Asteraceae Bl dickfleischig B gelb 134183 | Asteraceae Bl dickfleischig B gelb 134183 | Compositae |
Lycopodium complanatum var. chamaecyparissus | Lycopodium complanatum var. chamaecyparissus | Lycopodium tristachyum |
Glycosmis pentaphylla | Glycosmis pentaphylla | Glycosmis |
Acacia drummond subsp. elegans Porongu var. (R.J. Cumming 938) | Acacia drummond subsp. elegans Porongu var. (R.J. Cumming 938) | Acacia drummondii |
Klimmer orange 132257 | Klimmer orange 132257 | NA |
Freycinetia williamsii | Freycinetia williamsii | Freycinetia formosana |
Lauraceae species [CMG 2805] | Lauraceae species [CMG 2805] | Lauraceae |
Taraxacum sinicum128 | Taraxacum sinicum128 | Taraxacum sinicum |
Ochrolechia species | Ochrolechia species | Ochrolechia |
Enemion_biternatum species | Enemion_biternatum species | Enemion biternatum |
Elymus andinus | Elymus andinus | Elymus angulatus |
Dryopteris x mantoniae | Dryopteris x mantoniae | Dryopteris mantoniae |
Uapaca species [M1] | Uapaca species [M1] | Uapaca |
Lanzettblatt Fr. rot (Munkudi) 136374 | Lanzettblatt Fr. rot (Munkudi) 136374 | NA |
Juncus cognatus | Juncus cognatus | Juncus dichotomus |
Check the most common species names from DT after matching to backbone
name.check.freq <- DT1 %>%
dplyr::select(`Turboveg2 concept`:`Matched concept`, Name_short) %>%
rename(Name_TNRS=Name_short) %>%
group_by(`Turboveg2 concept`, `Matched concept`, Name_TNRS) %>%
summarize(n=n()) %>%
mutate(Matched_short=word(`Matched concept`, start = 1L, end=2L)) %>%
filter(is.na(Name_TNRS) | Matched_short != Name_TNRS) %>%
dplyr::select(-Matched_short) %>%
ungroup() %>%
arrange(desc(n))
## `summarise()` regrouping output by 'Turboveg2 concept', 'Matched concept' (override with `.groups` argument)
Turboveg2 concept | Matched concept | Name_TNRS | n |
---|---|---|---|
Deschampsia flexuosa | Avenella flexuosa | Deschampsia flexuosa | 126514 |
Festuca pratensis | Schedonorus pratensis | Festuca pratensis | 84008 |
Elymus repens | Elytrigia repens | Elymus repens | 82891 |
Phalaris arundinacea | Phalaroides arundinacea | Phalaris arundinacea | 75296 |
Bryophyta species | Bryophyta species | NA | 74393 |
Poa annua | Ochlopoa annua | Poa annua | 67460 |
Potentilla anserina | Argentina anserina | Potentilla anserina | 63786 |
Taraxacum sect. Ruderalia | Taraxacum sect. Taraxacum | Taraxacum | 58429 |
Taraxacum species | Taraxacum species | Taraxacum | 57167 |
Cornus sanguinea | Cornus sanguinea | Cornus controversa | 52651 |
Elytrigia repens | Elytrigia repens | Elymus repens | 51670 |
Taraxacum officinale | Taraxacum sect. Taraxacum | Taraxacum | 50502 |
Weinmannia racemosa | Weinmannia racemosa | Leiospermum racemosum | 38269 |
Bromus erectus | Bromopsis erecta | Bromus erectus | 33765 |
Cladonia species | Cladonia species | Cladonia | 32464 |
Avenella flexuosa | Avenella flexuosa | Deschampsia flexuosa | 30787 |
Rubus sect. Rubus | Rubus sect. Rubus | Rubus | 28684 |
Festuca arundinacea | Schedonorus arundinaceus | Festuca arundinacea | 26124 |
Trientalis europaea | Trientalis europaea | Lysimachia europaea | 25940 |
Rubus fruticosus aggr. | Rubus fruticosus aggr. | Rubus vestitus | 23669 |
Glaux maritima | Glaux maritima | Lysimachia maritima | 23305 |
Taraxacum officinale aggr. | Taraxacum sect. Taraxacum | Taraxacum | 22837 |
Rubus species | Rubus species | Rubus | 22098 |
Festuca gigantea | Schedonorus giganteus | Festuca gigantea | 20917 |
Taraxacum sectie Ruderalia | Taraxacum sect. Taraxacum | Taraxacum | 20888 |
Lophozonia menziesii | Lophozonia menziesii | Lophozonia | 20249 |
Juncus gerardi | Juncus gerardi | Juncus gerardii | 19094 |
Sphagnum species | Sphagnum species | Sphagnum | 18293 |
Festuca rupicola | Festuca stricta subsp. sulcata | Festuca rupicola | 18010 |
Rosa species | Rosa species | Rosa | 16657 |
Podocarpus laetus | Podocarpus laetus | Podocarpus spinulosus | 16356 |
Bromus tectorum | Anisantha tectorum | Bromus tectorum | 16302 |
Carex species | Carex species | Carex | 15744 |
Ripogonum scandens | Ripogonum scandens | Rhipogonum | 14984 |
Rubus hirtus | Rubus hirtus aggr. | Rubus proiectus | 14191 |
Avenula pubescens | Avenula pubescens | Helictotrichon pubescens | 13490 |
Notogrammitis billardierei | Notogrammitis billardierei | NA | 13117 |
Crataegus species | Crataegus species | Crataegus | 13072 |
Helictotrichon pubescens | Avenula pubescens | Helictotrichon pubescens | 12941 |
Erophila verna | Draba verna | Erophila verna | 12646 |
taxon group
Taxon group
information is only available for 35699079 entries, but absent for 7394395. To improve the completeness of this field, we derive additional info from the Backbone
, and merge it with the data already present in DT
.
table(DT1$`Taxon group`, exclude=NULL)
##
## Alga Lichen Moss Mushroom Stonewort
## 9497 324002 2034938 513 12166
## Unknown Vascular plant
## 7394395 33317963
DT1 <- DT1 %>%
mutate(`Taxon group`=ifelse(`Taxon group`=="Unknown", NA, `Taxon group`)) %>%
mutate(Taxongroup_BB=ifelse(Taxongroup_BB=="Unknown", NA, Taxongroup_BB)) %>%
mutate(`Taxon group`=coalesce(`Taxon group`, Taxongroup_BB)) %>%
dplyr::select(-Taxongroup_BB)
table(DT1$`Taxon group`, exclude=NULL)
##
## Alga Lichen Moss Mushroom Stonewort
## 9991 366919 2090925 513 12166
## Vascular plant <NA>
## 40522355 90605
Those taxa for which a measures of Basal Area exists can be safely assumed to belong to vascular plants
DT1 <- DT1 %>%
mutate(`Taxon group`=replace(`Taxon group`,
list=`Cover code`=="x_BA",
values="Vascular plant"))
Cross-complement Taxon group
information. This means that, whenever a taxon is marked to belong to one group, then assign the same taxon to that group throughout the DT
table.
DT1 <- DT1 %>%
left_join(DT1 %>%
filter(!is.na(Name_short)) %>%
filter(`Taxon group` != "Unknown") %>%
dplyr::select(Name_short, `Taxon group`) %>%
distinct(Name_short, .keep_all=T) %>%
rename(TaxonGroup_compl=`Taxon group`),
by="Name_short") %>%
mutate(`Taxon group`=coalesce(`Taxon group`, TaxonGroup_compl)) %>%
dplyr::select(-TaxonGroup_compl)
table(DT1$`Taxon group`, exclude=NULL)
##
## Alga Lichen Moss Mushroom Stonewort
## 9994 367508 2100558 513 12193
## Vascular plant <NA>
## 40523933 78775
Check species with conflicting Taxon group
information and fix manually.
#check for conflicts in attribution of genera to Taxon groups
DT1 %>%
filter(!is.na(Name_short)) %>%
filter(!is.na(`Taxon group`)) %>%
distinct(Name_short, `Taxon group`) %>%
mutate(Genus=word(Name_short,1)) %>%
dplyr::select(Genus, `Taxon group`) %>%
distinct() %>%
group_by(Genus) %>%
summarize(n=n()) %>%
filter(n>1) %>%
arrange(desc(n))
## `summarise()` ungrouping output (override with `.groups` argument)
## # A tibble: 15 x 2
## Genus n
## <chr> <int>
## 1 Brachytheciastrum 2
## 2 Brachythecium 2
## 3 Chara 2
## 4 Characeae 2
## 5 Hepatica 2
## 6 Hypericum 2
## 7 Hypnum 2
## 8 Leptorhaphis 2
## 9 Lychnothamnus 2
## 10 Nitella 2
## 11 Oxymitra 2
## 12 Pancovia 2
## 13 Peltaria 2
## 14 Tonina 2
## 15 Zygodon 2
Manually fix some known problems in Taxon group
attribution. Some lists of taxa (e.g., lichen.genera
, mushroom.genera
) were defined when building the Backbone
.
#Attach genus info
DT1 <- DT1 %>%
left_join(Backbone %>%
dplyr::select(Name_sPlot_TRY, Name_short) %>%
mutate(Genus=word(Name_short, 1, 1)) %>%
dplyr::select(-Name_short) %>%
rename(`Matched concept`=Name_sPlot_TRY),
by="Matched concept") %>%
mutate(`Taxon group`=fct_collapse(`Taxon group`,
Alga_Stonewort=c("Alga", "Stonewort")))
#manually fix some known problems
mosses.gen <- c("Hypnum", "Brachytheciastrum","Brachythecium","Hypnum",
"Zygodon", "Oxymitra", "Bryophyta", "Musci", '\\\"Moos\\\"')
vascular.gen <- c("Polystichum", "Hypericum", "Peltaria", "Pancovia", "Calythrix", "Ripogonum",
"Notogrammitis", "Fuscospora", "Lophozonia", "Rostellularia",
"Hesperostipa", "Microsorium", "Angiosperm","Dicotyledonae", "Spermatophy",
"Oxymitra", "Friesodielsia")
alga.gen <- c("Chara", "Characeae", "Tonina", "Nostoc", "Entermorpha", "Hydrocoleum" )
DT1 <- DT1 %>%
mutate(`Taxon group`=replace(`Taxon group`,
list=Genus %in% mosses.gen,
values="Moss")) %>%
mutate(`Taxon group`=replace(`Taxon group`,
list=Genus %in% vascular.gen,
values="Vascular plant")) %>%
mutate(`Taxon group`=replace(`Taxon group`,
list=Genus %in% alga.gen,
values="Alga_Stonewort")) %>%
mutate(`Taxon group`=replace(`Taxon group`,
list=Genus %in% c(lichen.genera, "Lichenes"),
values="Lichen")) %>%
mutate(`Taxon group`=replace(`Taxon group`,
list=Genus %in% mushroom,
values="Mushroom"))
table(DT1$`Taxon group`, exclude=NULL)
##
## Alga_Stonewort Lichen Moss Mushroom Vascular plant
## 23098 367509 2100635 513 40525774
## <NA>
## 75945
Delete all records of fungi, and use lists of genera to fix additional problems. While in the previous round the matching was done on the resolved Genus name, here the match is based on unresolved Genus names.
DT1 <- DT1 %>%
dplyr::select(-Genus) %>%
left_join(DT1 %>%
distinct(`Matched concept`) %>%
mutate(Genus=word(`Matched concept`, 1)),
by="Matched concept") %>%
mutate(`Taxon group`=replace(`Taxon group`,
list=Genus %in% mushroom,
values = "Mushroom")) %>%
mutate(`Taxon group`=replace(`Taxon group`,
list=Genus %in% lichen.genera,
values="Lichen")) %>%
mutate(`Taxon group`=replace(`Taxon group`,
list=Genus %in% mosses.gen,
values="Moss")) %>%
mutate(`Taxon group`=replace(`Taxon group`,
list=Genus %in% vascular.gen,
values="Vascular plant")) %>%
mutate(`Taxon group` = fct_explicit_na(`Taxon group`, "Unknown")) %>%
filter(`Taxon group`!="Mushroom") %>%
mutate(`Taxon group`=factor(`Taxon group`))
#dplyr::select(-Genus)
table(DT1$`Taxon group`, exclude=NULL)
##
## Alga_Stonewort Lichen Moss Vascular plant Unknown
## 23098 367855 2103292 40563071 35721
After cross-checking all sources of information, the number of taxa not having Taxon group
information decreased to 35721 entries
Species abundance information varies across datasets and plots. While for the large majority of plots abundance values are returned as percentage cover, there is a subset where abundance is returned with different scales. These are marked in the column Cover code
as follows:
x_BA - Basal Area
x_IC - Individual count
x_SC - Stem count
x_IV - Relative Importance
x_RF - Relative Frequency
x - Presence absence
Still, it’s not really intuitive that in case Cover code
belongs to one of the classes above, then the actual abundance value is stored in the x_
column. This stems from the way this data is stored in TURBOVEG
.
To make the cover data more user friendly, I simplify the way cover it is stored, so that there are only two columns:
Ab_scale
- to report the type of scale used
Abundance
- to coalesce the cover\abundance values previously in the columns Cover %
and x_
.
# Create Ab_scale field
DT1 <- DT1 %>%
mutate(Ab_scale = ifelse(`Cover code` %in%
c("x_BA", "x_IC", "x_SC", "x_IV", "x_RF") & !is.na(x_),
`Cover code`,
"CoverPerc"))
Fix some errors. There are some plots where all species have zeros in the field Cover %
. Some of them are marked as p\a (Cover code=="x"
), but other not. Consider all this plots as presence\absence and transform Cover %
to 1.
allzeroes <- DT1 %>%
group_by(PlotObservationID) %>%
summarize(allzero=all(`Cover %`==0) ) %>%
filter(allzero==T) %>%
pull(PlotObservationID)
## `summarise()` ungrouping output (override with `.groups` argument)
DT1 <- DT1 %>%
mutate(`Cover %`=replace(`Cover %`,
list=(PlotObservationID %in% allzeroes),
values=1)) %>%
mutate(`Cover code`=replace(`Cover code`,
list=(PlotObservationID %in% allzeroes),
values="x"))
Consider all plot-layer combinations where Cover code=="x"
, and all the entries of the field Cover % == 1
as presence\absence data, and transform Ab_scale
to “pa”. This is done to avoid confusion with plots where Cover code=="x"
but “x” has to be intended as a class in the cover scale used. For p\a plots, replace the field Cover %
with NA, and assign the value 1 to the field x_
.
#plots with at least one entry in Cover code=="x"
sel <- DT1 %>%
filter(`Cover code`=="x") %>%
distinct(PlotObservationID) %>%
pull(PlotObservationID)
DT1 <- DT1 %>%
left_join(DT1 %>%
filter(PlotObservationID %in% sel) %>%
group_by(PlotObservationID, Layer) %>%
mutate(to.pa= all(`Cover %`==1 & `Cover code`=="x")) %>%
distinct(PlotObservationID, Layer, to.pa),
by=c("PlotObservationID", "Layer")) %>%
replace_na(list(to.pa=F)) %>%
mutate(Ab_scale=ifelse(to.pa==T, "pa", Ab_scale)) %>%
mutate(`Cover %`=ifelse(to.pa==T, NA, `Cover %`)) %>%
mutate(x_=ifelse(to.pa==T, 1, x_)) %>%
dplyr::select(-to.pa)
There are also some plots having different cover scales in the same layer. They are not many, and I will reduce their cover value to p\a.
Find these plots first:
mixed <- DT1 %>%
distinct(PlotObservationID, Ab_scale, Layer) %>%
group_by(PlotObservationID, Layer) %>%
summarize(n=n()) %>%
filter(n>1) %>%
pull(PlotObservationID) %>%
unique()
## `summarise()` regrouping output by 'PlotObservationID' (override with `.groups` argument)
length(mixed)
## [1] 335
Transform these plots to p\a and correct field Ab_scale
. Note: the column Abundance
is only created here.
DT1 <- DT1 %>%
mutate(Ab_scale=replace(Ab_scale,
list=PlotObservationID %in% mixed,
values="mixed")) %>%
mutate(`Cover %`=replace(`Cover %`,
list=Ab_scale=="mixed",
values=NA)) %>%
mutate(x_=replace(x_, list=Ab_scale=="mixed", values=1)) %>%
mutate(Ab_scale=replace(Ab_scale, list=Ab_scale=="mixed", values="pa")) %>%
#Create additional field Abundance to avoid overwriting original data
mutate(Abundance =ifelse(Ab_scale %in% c("x_BA", "x_IC", "x_SC", "x_IV", "x_RF", "pa"),
x_, `Cover %`)) %>%
mutate(Abundance=replace(Abundance,
list=PlotObservationID %in% mixed,
values=1))
Double check and summarize Ab_scales
scale_check <- DT1 %>%
distinct(PlotObservationID, Layer, Ab_scale) %>%
group_by(PlotObservationID) %>%
summarise(Ab_scale_combined=ifelse(length(unique(Ab_scale))==1,
unique(Ab_scale),
"Multiple_scales"))
## `summarise()` ungrouping output (override with `.groups` argument)
nrow(scale_check)== length(unique(DT1$PlotObservationID))
## [1] TRUE
table(scale_check$Ab_scale_combined)
##
## CoverPerc Multiple_scales pa x_BA x_IC
## 1690405 2084 271057 6293 2092
## x_IV x_RF x_SC
## 146 585 4878
Transform abundances to relative abundance. For consistency with the previous version of sPlot, this field is called Relative_cover
.
Watch out - Even plots with p\a information are transformed to relative cover.
DT1 <- DT1 %>%
left_join(x=.,
y={.} %>%
group_by(PlotObservationID) %>%
summarize(tot.abundance=sum(Abundance)),
by=c("PlotObservationID")) %>%
mutate(Relative.cover=Abundance/tot.abundance)
## `summarise()` ungrouping output (override with `.groups` argument)
# check: there should be no plot where the sum of all relative covers !=0
DT1 %>%
group_by(PlotObservationID) %>%
summarize(tot.cover=sum(Relative.cover),
num.layers=sum(unique(Layer))) %>%
filter(tot.cover != num.layers) %>%
nrow()
## `summarise()` ungrouping output (override with `.groups` argument)
## [1] 1957767
DT2 <- DT1 %>%
dplyr::select(PlotObservationID, Name_short, `Turboveg2 concept`, Rank_correct, `Taxon group`, Layer:x_, Ab_scale, Abundance, Relative.cover ) %>%
rename(Species_original=`Turboveg2 concept`,
Species=Name_short,
Taxon_group=`Taxon group`,
Cover_perc=`Cover %`,
Cover_code=`Cover code`,
Relative_cover=Relative.cover) %>%
## change in Version 1.1.
dplyr::select(-x_, -Cover_perc)
The output of the DT table contains 43093037 records, over 1977540 plots. The total number of taxa is 116256 and 0, before and after standardization, respectively. Information on the Taxon group
is available for 76548 standardized species.
PlotObservationID | Species | Species_original | Rank_correct | Taxon_group | Layer | Cover_code | Ab_scale | Abundance | Relative_cover |
---|---|---|---|---|---|---|---|---|---|
705955 | Aconitum napellus | Aconitum napellus | species | Vascular plant | 0 | 1 | CoverPerc | 3 | 0.0285714 |
705955 | Adenostyles alliariae | Adenostyles alliariae | species | Vascular plant | 0 | 5 | CoverPerc | 88 | 0.8380952 |
705955 | Arabis alpina | Arabis alpina | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0190476 |
705955 | Cirsium spinosissimum | Cirsium spinosissimum | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0190476 |
705955 | Doronicum grandiflorum | Doronicum grandiflorum | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0190476 |
705955 | Peucedanum ostruthium | Peucedanum ostruthium | species | Vascular plant | 0 | 1 | CoverPerc | 3 | 0.0285714 |
705955 | Primula elatior | Primula elatior | species | Vascular plant | 0 |
|
CoverPerc | 2 | 0.0190476 |
705955 | Tozzia alpina | Tozzia alpina | species | Vascular plant | 0 | 1 | CoverPerc | 3 | 0.0285714 |
968394 | Agrostis capillaris | Agrostis capillaris | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Agrostis stolonifera | Agrostis stolonifera | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Alopecurus pratensis | Alopecurus pratensis | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Anthoxanthum odoratum | Anthoxanthum odoratum | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Bellis perennis | Bellis perennis | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Brachythecium albicans | Brachythecium albicans | species | Moss | 0 | x | pa | 1 | 0.0136986 |
968394 | Brachythecium rutabulum | Brachythecium rutabulum | species | Moss | 0 | x | pa | 1 | 0.0136986 |
968394 | Bryum pseudotriquetrum | Bryum pseudotriquetrum var. bimum | species | Moss | 0 | x | pa | 1 | 0.0136986 |
968394 | Calliergonella cuspidata | Calliergonella cuspidata | species | Moss | 0 | x | pa | 1 | 0.0136986 |
968394 | Callitriche stagnalis | Callitriche stagnalis | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Caltha palustris | Caltha palustris | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Cardamine pratensis | Cardamine pratensis | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Carex disticha | Carex disticha | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Carex leporina | Carex leporina | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Carex paniculata | Carex paniculata | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Cerastium fontanum | Cerastium fontanum | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Cirsium palustre | Cirsium palustre | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Crepis capillaris | Crepis capillaris | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Cynosurus cristatus | Cynosurus cristatus | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Deschampsia cespitosa | Deschampsia cespitosa | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Epilobium obscurum | Epilobium obscurum | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Epilobium parviflorum | Epilobium parviflorum | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Equisetum fluviatile | Equisetum fluviatile | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Equisetum sylvaticum | Equisetum sylvaticum | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Festuca rubra | Festuca rubra | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Filipendula ulmaria | Filipendula ulmaria | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Galium palustre | Galium palustre | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Glyceria declinata | Glyceria declinata | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Glyceria fluitans | Glyceria fluitans | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Gnaphalium uliginosum | Gnaphalium uliginosum | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Holcus lanatus | Holcus lanatus | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Hypochaeris radicata | Hypochaeris radicata | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Isolepis setacea | Isolepis setacea | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Juncus acutiflorus | Juncus acutiflorus | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Juncus bufonius | Juncus bufonius | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Juncus bulbosus | Juncus bulbosus | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Juncus effusus | Juncus effusus | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Kindbergia praelonga | Kindbergia praelonga | species | Moss | 0 | x | pa | 1 | 0.0136986 |
968394 | Lathyrus pratensis | Lathyrus pratensis | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Scorzoneroides autumnalis | Leontodon autumnalis | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Lolium perenne | Lolium perenne | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Lotus pedunculatus | Lotus pedunculatus | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Silene flos-cuculi | Lychnis flos-cuculi | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Lythrum portula | Lythrum portula | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Lythrum salicaria | Lythrum salicaria | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Mentha aquatica | Mentha aquatica | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Persicaria maculosa | Persicaria maculosa | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Plantago lanceolata | Plantago lanceolata | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Poa annua | Poa annua | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Poa pratensis | Poa pratensis | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Comarum palustre | Potentilla palustris | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Prunella vulgaris | Prunella vulgaris | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Ranunculus acris | Ranunculus acris | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Ranunculus flammula | Ranunculus flammula | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Ranunculus repens | Ranunculus repens | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Rhytidiadelphus squarrosus | Rhytidiadelphus squarrosus | species | Moss | 0 | x | pa | 1 | 0.0136986 |
968394 | Rubus vestitus | Rubus fruticosus aggr. | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Rumex acetosa | Rumex acetosa | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Rumex obtusifolius | Rumex obtusifolius | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Sagina procumbens | Sagina procumbens | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Salix integra | Salix x multinervis | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Jacobaea aquatica | Senecio aquaticus | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Jacobaea vulgaris | Senecio jacobaea | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Sonchus asper | Sonchus asper | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Stellaria uliginosa | Stellaria uliginosa | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Taraxacum | Taraxacum officinale aggr. | genus | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Trifolium pratense | Trifolium pratense | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Trifolium repens | Trifolium repens | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Ulex europaeus | Ulex europaeus | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Urtica dioica | Urtica dioica | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Valeriana officinalis | Valeriana officinalis | higher | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Veronica scutellata | Veronica scutellata | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
968394 | Vicia cracca | Vicia cracca | species | Vascular plant | 0 | x | pa | 1 | 0.0136986 |
1048670 | Tripolium pannonicum | Aster tripolium | lower | Vascular plant | 0 | 01 | CoverPerc | 10 | 0.0943396 |
1048670 | Atriplex littoralis | Atriplex littoralis | species | Vascular plant | 0 | r | CoverPerc | 1 | 0.0094340 |
1048670 | Atriplex portulacoides | Atriplex portulacoides | species | Vascular plant | 0 | 06 | CoverPerc | 60 | 0.5660377 |
1048670 | Atriplex prostrata | Atriplex prostrata | species | Vascular plant | 0 | p | CoverPerc | 1 | 0.0094340 |
1048670 | Elymus athericus | Elytrigia atherica | species | Vascular plant | 0 | 03 | CoverPerc | 30 | 0.2830189 |
1048670 | Festuca rubra | Festuca rubra aggr. (incl. F. arenaria) | species | Vascular plant | 0 | p | CoverPerc | 1 | 0.0094340 |
1048670 | Puccinellia maritima | Puccinellia maritima | species | Vascular plant | 0 | p | CoverPerc | 1 | 0.0094340 |
1048670 | Spartina anglica | Spartina anglica | species | Vascular plant | 0 | r | CoverPerc | 1 | 0.0094340 |
1048670 | Suaeda maritima | Suaeda maritima | species | Vascular plant | 0 | p | CoverPerc | 1 | 0.0094340 |
PlotObservationID
- Plot ID, as in header
.Species
- Resolved species name, based on taxonomic backboneSpecies_original
- Original species name, as provided by data contributor.Rank_correct
- Taxonomic rank at which Species_original
was matched.Taxon_group
- Possible entries are: Alga_Stonewort, Lichen, Moss, Vascular plant, Unknown.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 value in original data, before transformation to 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 of each species after being normalized to 1 in each plot.save(DT2, file = "../_output/DT_sPlot3.0.RData")
## 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=en_US.UTF-8
## [9] LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] kableExtra_1.3.1 knitr_1.30 xlsx_0.6.5 forcats_0.5.0
## [5] stringr_1.4.0 dplyr_1.0.2 purrr_0.3.4 readr_1.4.0
## [9] tidyr_1.1.2 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 rJava_0.9-13 haven_2.3.1
## [5] colorspace_2.0-0 vctrs_0.3.5 generics_0.1.0 viridisLite_0.3.0
## [9] htmltools_0.5.0 yaml_2.2.1 utf8_1.1.4 rlang_0.4.9
## [13] pillar_1.4.3 glue_1.4.2 withr_2.3.0 DBI_1.1.0
## [17] dbplyr_2.0.0 modelr_0.1.6 readxl_1.3.1 lifecycle_0.2.0
## [21] munsell_0.5.0 gtable_0.3.0 cellranger_1.1.0 rvest_0.3.6
## [25] evaluate_0.14 ps_1.4.0 xlsxjars_0.6.1 fansi_0.4.1
## [29] highr_0.8 broom_0.7.0 Rcpp_1.0.5 scales_1.1.1
## [33] backports_1.2.0 webshot_0.5.2 jsonlite_1.7.1 fs_1.5.0
## [37] hms_0.5.3 digest_0.6.25 stringi_1.5.3 grid_3.6.3
## [41] cli_2.2.0 tools_3.6.3 magrittr_2.0.1 crayon_1.3.4
## [45] pkgconfig_2.0.3 ellipsis_0.3.1 xml2_1.3.2 reprex_0.3.0
## [49] lubridate_1.7.9.2 assertthat_0.2.1 rmarkdown_2.5 httr_1.4.2
## [53] rstudioapi_0.13 R6_2.5.0 compiler_3.6.3