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inst/doc/traitdataform.R
In traitdataform: Formatting and Harmonizing Ecological Trait-Data
## ---- echo = FALSE, warning= FALSE, message=FALSE-----------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
library(traitdataform)
## ---- eval = FALSE, warning=FALSE, error=FALSE--------------------------------
# carabids <- read.table("../../data/carabid traits final.txt", header = TRUE)
## ---- eval = FALSE, warning=FALSE, error=FALSE--------------------------------
# # pulling data from van der Plas F, van Klink R, Manning P, Olff H, Fischer M (2017) Sensitivity of functional diversity metrics to sampling intensity. Methods in Ecology and Evolution 8(9): 1072-1080. https://doi.org/10.1111/2041-210x.12728
#
# carabids <- read.delim("https://datadryad.org/stash/downloads/file_stream/23901", stringsAsFactors = FALSE)
#
## ---- warning=FALSE, error=FALSE----------------------------------------------
dataset1 <- as.traitdata(carabids,
taxa = "name_correct",
traits = c("body_length",
"antenna_length",
"metafemur_length",
"eyewidth_corr"),
units = "mm"
)
head(dataset1)
## ---- eval = FALSE, warning=FALSE, error=FALSE-------------------------------
# #
# # heteroptera_raw
# #
# # dataset included in package traitdataform
# #
# # Data publication: M. Gossner, Martin; K. Simons, Nadja; Hoeck, Leonhard; W.
# # Weisser, Wolfgang (2016): Morphometric measures of Heteroptera sampled in
# # grasslands across three regions of Germany. figshare.
# # https://doi.org/10.6084/m9.figshare.c.3307611.v1
#
#
# dataset2 <- as.traitdata(heteroptera_raw,
# traits = c("Body_length", "Body_width", "Body_height", "Thorax_length",
# "Thorax_width", "Head_width", "Eye_width", "Antenna_Seg1",
# "Antenna_Seg2", "Antenna_Seg3", "Antenna_Seg4", "Antenna_Seg5",
# "Front.Tibia_length", "Mid.Tibia_length", "Hind.Tibia_length",
# "Front.Femur_length", "Hind.Femur_length", "Front.Femur_width",
# "Hind.Femur_width", "Rostrum_length", "Rostrum_width",
# "Wing_length", "Wing_width"),
# taxa = "SpeciesID",
# occurrences = "ID"
# )
#
# # show different trait measurements for same occurrence/individual
# subset(dataset2, occurrenceID == "5" )
## ---- warning=FALSE, error=FALSE----------------------------------------------
dataset2 <- as.traitdata(heteroptera_raw,
traits = c("Body_length", "Body_width", "Body_height", "Thorax_length",
"Thorax_width", "Head_width", "Eye_width", "Antenna_Seg1",
"Antenna_Seg2", "Antenna_Seg3", "Antenna_Seg4", "Antenna_Seg5",
"Front.Tibia_length", "Mid.Tibia_length", "Hind.Tibia_length",
"Front.Femur_length", "Hind.Femur_length", "Front.Femur_width",
"Hind.Femur_width", "Rostrum_length", "Rostrum_width",
"Wing_length", "Wing_width"),
taxa = "SpeciesID",
occurrences = "ID",
keep = c("Sex")
)
head(dataset2)
## ---- warning=FALSE, error=FALSE----------------------------------------------
dataset2 <- as.traitdata(heteroptera_raw,
traits = c("Body_length", "Body_width", "Body_height", "Thorax_length",
"Thorax_width", "Head_width", "Eye_width", "Antenna_Seg1",
"Antenna_Seg2", "Antenna_Seg3", "Antenna_Seg4", "Antenna_Seg5",
"Front.Tibia_length", "Mid.Tibia_length", "Hind.Tibia_length",
"Front.Femur_length", "Hind.Femur_length", "Front.Femur_width",
"Hind.Femur_width", "Rostrum_length", "Rostrum_width",
"Wing_length", "Wing_width"),
taxa = "SpeciesID",
occurrences = "ID",
units = "mm",
keep = c(order = "Order", family = "Family",
sex = "Sex", lifeStage = "Wing_development",
basisOfRecordDescription = "Source",
verbatimLocality = "Center_Sampling_region",
references = "Voucher_ID" )
)
head(dataset2)
## ---- warning=FALSE, error=FALSE----------------------------------------------
dataset2 <- mutate.traitdata(dataset2,
Body_shape = Body_length/Body_width,
Body_volume = Body_length*Body_width*Body_height,
Wingload = Wing_length*Wing_width/Body_volume)
head(dataset2[dataset2$verbatimTraitName %in% c("Body_shape", "Body_volume", "Wingload"),])
## ---- warning=FALSE, error=FALSE----------------------------------------------
as.trait("body_length",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "The known longest dimension of the physical structure of organisms",
identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Body_length",
author = "Maggenti and Maggenti, 2005",
broaderTerm = c("http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Body_dimension"),
narrowerTerm = c("http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Female_body_length",
"http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Male_body_length")
)
## ---- warning=FALSE, error=FALSE----------------------------------------------
thesaurus1 <- as.thesaurus(
body_length = as.trait("body_length",
expectedUnit = "mm", valueType = "numeric",
identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Body_length"),
antenna_length = as.trait("antenna_length",
expectedUnit = "mm", valueType = "numeric",
identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Antenna_length"),
metafemur_length = as.trait("femur_length",
expectedUnit = "mm", valueType = "numeric",
identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Femur_length"),
eyewidth_corr = as.trait("eye_diameter",
expectedUnit = "mm", valueType = "numeric",
identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Eye_diameter")
)
## ---- warning=FALSE, error=FALSE----------------------------------------------
thesaurus1 <- as.thesaurus(data.frame(
trait = c("body_length", "antenna_length", "metafemur_length", "eyewidth_corr"),
identifier = paste0("http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=",
c("Body_length", "Antenna_length", "Femur_length", "Eye_diameter")),
valueType = c("numeric"),
expectedUnit = "mm")
)
## ---- message=FALSE, warning=FALSE--------------------------------------------
dataset1Std <- standardize_traits(dataset1, thesaurus1)
head(dataset1Std)
## ---- warning=FALSE, error=FALSE----------------------------------------------
# M. Gossner, Martin; K. Simons, Nadja; Hoeck, Leonhard; W. Weisser, Wolfgang
# (2016): Morphometric measures of Heteroptera sampled in grasslands across
# three regions of Germany. figshare.
# https://doi.org/10.6084/m9.figshare.c.3307611.v1
# following the definitions in data publication
# http://www.esapubs.org/archive/ecol/E096/102/metadata.php
thesaurus2 <- as.thesaurus(
Body_length = as.trait("Body_length", identifier = "t1",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "From the tip of the head to the end of the abdomen"),
Body_width = as.trait("Body_width", identifier = "t2",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Widest part of the body"),
Body_height = as.trait("Body_height",identifier = "t3",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Thickest part of the body"),
Thorax_length = as.trait("Thorax_length", identifier = "t4",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Longest part of the pronotum"),
Thorax_width = as.trait("Thorax_width", identifier = "t5",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Widest part of the pronotum"),
Head_width = as.trait("Head_width", identifier = "t6",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Widest part of the head including eyes"),
Eye_width = as.trait("Eye_width", identifier = "t7",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Widest part of the left eye"),
Antenna_Seg1 = as.trait("Antenna_Seg1", identifier = "t8",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Length of first antenna segment",
broaderTerm = "http://ecologicaltraitdata.github.io/TraitDataList/Antenna_length"),
Antenna_Seg2 = as.trait("Antenna_Seg2", identifier = "t9",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Length of second antenna segment",
broaderTerm = "http://ecologicaltraitdata.github.io/TraitDataList/Antenna_length"),
Antenna_Seg3 = as.trait("Antenna_Seg3", identifier = "t10",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Length of third antenna segment",
broaderTerm = "http://ecologicaltraitdata.github.io/TraitDataList/Antenna_length"),
Antenna_Seg4 = as.trait("Antenna_Seg4", identifier = "t11",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Length of fourth antenna segment",
broaderTerm = "http://ecologicaltraitdata.github.io/TraitDataList/Antenna_length"),
Antenna_Seg5 = as.trait("Antenna_Seg5", identifier = "t12",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Length of fifth antenna segment (only Pentatomoidea)",
broaderTerm = "http://ecologicaltraitdata.github.io/TraitDataList/Antenna_length"),
Front.Tibia_length = as.trait("Front.Tibia_length", identifier = "t13",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Length of the tibia of the foreleg"),
Mid.Tibia_length = as.trait("Mid.Tibia_length", identifier = "t14",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Length of the tibia of the mid leg",
broaderTerm = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Tibia_length"),
Hind.Tibia_length = as.trait("Hind.Tibia_length", identifier = "t15",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Length of the tibia of the hind leg",
broaderTerm = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Tibia_length"),
Front.Femur_length = as.trait("Front.Femur_length", identifier = "t16",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Length of the femur of the foreleg",
broaderTerm = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Femur_length"),
Hind.Femur_length = as.trait("Hind.Femur_length", identifier = "t17",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Length of the femur of the hind leg",
broaderTerm = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Femur_length"),
Front.Femur_width = as.trait("Front.Femur_width", identifier = "t18",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Width of the femur of the foreleg"),
Hind.Femur_width = as.trait("Hind.Femur_width", identifier = "t18",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Width of the femur of the hind leg"),
Rostrum_length = as.trait("Rostrum_length", identifier = "t19",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Length of the rostrum including all segments"),
Rostrum_width = as.trait("Rostrum_width", identifier = "t20",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Widest part of the rostrum"),
Wing_length = as.trait("Wing_length", identifier = "t21",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Longest part of the forewing",
broaderTerm = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Wing"),
Wing_width = as.trait("Wing_width", identifier = "t22",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Widest part of the forewing",
broaderTerm = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Wing")
)
## ---- message=FALSE, warning=FALSE--------------------------------------------
dataset2Std <- standardize_traits(dataset2, thesaurus2)
subset(dataset2Std, occurrenceID == 2)
attributes(dataset2Std)$traits[,c("trait", "identifier","traitDescription","expectedUnit")]
## ---- message=FALSE, warning=FALSE--------------------------------------------
dataset1Std <- standardize_taxa(dataset1)
head(dataset1Std)
## ---- eval = FALSE------------------------------------------------------------
# # dataset by Jule Mangels et al.
#
# moths <- read.service(21247, dec = ",")
#
# dataset5 <- as.traitdata(moths, taxa = "species", traits = c(body_mass =
# "weight", wing_length = "wing_length", wing_width = "wing_width", wing_area =
# "wing_area", wing_loading = "wing_loading"),
# keep = c(locationID = "plot"))
#
# dataset5Std <- standardize.exploratories(dataset1)
#
# head(dataset5Std)
## ---- message = FALSE, warning=FALSE, eval=FALSE------------------------------
# dataset1Std <- standardize(carabids,
# thesaurus = thesaurus1,
# taxa = "name_correct",
# units = "mm",
# keep = c(measurementDeterminedBy = "source_measurement")
# )
## ---- eval = FALSE, warning=FALSE, error=FALSE--------------------------------
# newdata <- rbind(dataset1Std, dataset2Std,
# datasetID = c("vanderplas15", "gossner15")
# )
## ---- warning=FALSE, error=FALSE----------------------------------------------
metadata1 <- as.metadata(
datasetName = "Carabid traits",
datasetID = "carabids",
bibliographicCitation = bibentry(
bibtype = "Article",
title = "Sensitivity of functional diversity metrics to sampling intensity",
journal = "Methods in Ecology and Evolution",
author = c(as.person("Fons van der Plas, Roel van Klink, Pete Manning, Han Olff, Markus Fischer")
),
year = 2017,
doi = "10.1111/2041-210x.12728"
),
author = "Fons van der Plas",
license = "http://creativecommons.org/publicdomain/zero/1.0/"
)
dataset1 <- as.traitdata(carabids,
taxa = "name_correct",
thesaurus = thesaurus1,
units = "mm",
keep = c(datasetID = "source_measurement", measurementRemark = "note"),
metadata = metadata1
)
head(dataset1)
## ---- warning=FALSE, error=FALSE----------------------------------------------
metadata2 <- as.metadata(
datasetName = "Heteroptera morphometry traits",
datasetID = "heteroptera",
bibliographicCitation = bibentry(
bibtype = "Article",
title = "Morphometric measures of Heteroptera sampled in grasslands across three regions of Germany",
journal = "Ecology",
volume = 96,
issue = 4,
pages = 1154,
author = c(as.person("Martin M. Gossner , Nadja K. Simons, Leonhard Hoeck, Wolfgang W. Weisser")),
year = 2015,
doi = "10.1890/14-2159.1"
),
author = "Martin M. Gossner",
license = "http://creativecommons.org/publicdomain/zero/1.0/"
)
dataset2 <- as.traitdata(heteroptera_raw,
taxa = "SpeciesID",
thesaurus = thesaurus2,
units = "mm",
keep = c(sex = "Sex", references = "Source", lifestage = "Wing_development"),
metadata = metadata2
)
database <- rbind(dataset1, dataset2,
datasetID = c("vanderplas17", "gossner15"),
metadata_as_columns = TRUE
)
head(database)
## ---- warning=FALSE, error=FALSE----------------------------------------------
attributes(dataset1)$metadata$bibliographicCitation
## ---- eval = FALSE, warning=FALSE, error=FALSE--------------------------------
# carabids <- utils::read.delim(url("https://datadryad.org/stash/downloads/file_stream/24267",
# encoding = "UTF-8")
# )
#
# attr(carabids, 'metadata') <- traitdataform::as.metadata(
# datasetName = "Carabid traits",
# datasetID = "carabids",
# bibliographicCitation = utils::bibentry(
# bibtype = "Article",
# title = "Sensitivity of functional diversity metrics to sampling intensity",
# journal = "Methods in Ecology and Evolution",
# author = c(utils::as.person("Fons van der Plas, Roel van Klink, Pete Manning, Han Olff, Markus Fischer")
# ),
# year = 2017,
# doi = "10.1111/2041-210x.12728"
# ),
# author = "Fons van der Plas",
# license = "http://creativecommons.org/publicdomain/zero/1.0/"
# )
#
# attr(carabids, 'thesaurus') <- traitdataform:::as.thesaurus(
# body_length = traitdataform:::as.trait("body_length",
# expectedUnit = "mm", valueType = "numeric",
# identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Body_length"),
# antenna_length = traitdataform:::as.trait("antenna_length",
# expectedUnit = "mm", valueType = "numeric",
# identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Antenna_length"),
# metafemur_length = traitdataform:::as.trait("femur_length",
# expectedUnit = "mm", valueType = "numeric",
# identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Femur_length"),
# eyewidth_corr = traitdataform:::as.trait("eye_diameter",
# expectedUnit = "mm", valueType = "numeric",
# identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Eye_diameter")
# )
#
# attr(carabids, 'taxa') <- "name_correct"
# attr(carabids, 'units') <- "mm"
# attr(carabids, 'keep') <- c(measurementDeterminedBy = "source_measurement", measurementRemarks = "note")
#
## -----------------------------------------------------------------------------
#example for adding metadata as a table
## ---- eval = FALSE------------------------------------------------------------
#
# head(dataset3)
#
# dataset3wide <- cast.traitdata(dataset3)
#
# head(dataset3wide)
#
## ---- eval = FALSE, warning=FALSE, error=FALSE--------------------------------
# write.table(dataset1Std, file = "carabids_std.csv",
# sep = ",", dec = ".", quote = TRUE, eol = "\r", row.names = FALSE)
## ---- eval = FALSE, warning=FALSE, error=FALSE--------------------------------
# capture.output(attributes(dataset1Std)$metadata, file = "metadata.txt")
#
# write.table(attributes(dataset1Std)$traits, file = "traits.csv",
# sep = ",", dec = ".", quote = TRUE, eol = "\r", row.names = FALSE)
# write.table(attributes(dataset1Std)$taxonomy, file = "taxa.csv",
# sep = ",", dec = ".", quote = TRUE, eol = "\r", row.names = FALSE)
## ---- eval = FALSE, warning=FALSE, error=FALSE--------------------------------
# zip("carabids_std.zip", c("carabids_std.csv", "metadata.txt", "traits.csv", "taxa.csv") )
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## ---- echo = FALSE, warning= FALSE, message=FALSE-----------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
library(traitdataform)
## ---- eval = FALSE, warning=FALSE, error=FALSE--------------------------------
# carabids <- read.table("../../data/carabid traits final.txt", header = TRUE)
## ---- eval = FALSE, warning=FALSE, error=FALSE--------------------------------
# # pulling data from van der Plas F, van Klink R, Manning P, Olff H, Fischer M (2017) Sensitivity of functional diversity metrics to sampling intensity. Methods in Ecology and Evolution 8(9): 1072-1080. https://doi.org/10.1111/2041-210x.12728
#
# carabids <- read.delim("https://datadryad.org/stash/downloads/file_stream/23901", stringsAsFactors = FALSE)
#
## ---- warning=FALSE, error=FALSE----------------------------------------------
dataset1 <- as.traitdata(carabids,
taxa = "name_correct",
traits = c("body_length",
"antenna_length",
"metafemur_length",
"eyewidth_corr"),
units = "mm"
)
head(dataset1)
## ---- eval = FALSE, warning=FALSE, error=FALSE-------------------------------
# #
# # heteroptera_raw
# #
# # dataset included in package traitdataform
# #
# # Data publication: M. Gossner, Martin; K. Simons, Nadja; Hoeck, Leonhard; W.
# # Weisser, Wolfgang (2016): Morphometric measures of Heteroptera sampled in
# # grasslands across three regions of Germany. figshare.
# # https://doi.org/10.6084/m9.figshare.c.3307611.v1
#
#
# dataset2 <- as.traitdata(heteroptera_raw,
# traits = c("Body_length", "Body_width", "Body_height", "Thorax_length",
# "Thorax_width", "Head_width", "Eye_width", "Antenna_Seg1",
# "Antenna_Seg2", "Antenna_Seg3", "Antenna_Seg4", "Antenna_Seg5",
# "Front.Tibia_length", "Mid.Tibia_length", "Hind.Tibia_length",
# "Front.Femur_length", "Hind.Femur_length", "Front.Femur_width",
# "Hind.Femur_width", "Rostrum_length", "Rostrum_width",
# "Wing_length", "Wing_width"),
# taxa = "SpeciesID",
# occurrences = "ID"
# )
#
# # show different trait measurements for same occurrence/individual
# subset(dataset2, occurrenceID == "5" )
## ---- warning=FALSE, error=FALSE----------------------------------------------
dataset2 <- as.traitdata(heteroptera_raw,
traits = c("Body_length", "Body_width", "Body_height", "Thorax_length",
"Thorax_width", "Head_width", "Eye_width", "Antenna_Seg1",
"Antenna_Seg2", "Antenna_Seg3", "Antenna_Seg4", "Antenna_Seg5",
"Front.Tibia_length", "Mid.Tibia_length", "Hind.Tibia_length",
"Front.Femur_length", "Hind.Femur_length", "Front.Femur_width",
"Hind.Femur_width", "Rostrum_length", "Rostrum_width",
"Wing_length", "Wing_width"),
taxa = "SpeciesID",
occurrences = "ID",
keep = c("Sex")
)
head(dataset2)
## ---- warning=FALSE, error=FALSE----------------------------------------------
dataset2 <- as.traitdata(heteroptera_raw,
traits = c("Body_length", "Body_width", "Body_height", "Thorax_length",
"Thorax_width", "Head_width", "Eye_width", "Antenna_Seg1",
"Antenna_Seg2", "Antenna_Seg3", "Antenna_Seg4", "Antenna_Seg5",
"Front.Tibia_length", "Mid.Tibia_length", "Hind.Tibia_length",
"Front.Femur_length", "Hind.Femur_length", "Front.Femur_width",
"Hind.Femur_width", "Rostrum_length", "Rostrum_width",
"Wing_length", "Wing_width"),
taxa = "SpeciesID",
occurrences = "ID",
units = "mm",
keep = c(order = "Order", family = "Family",
sex = "Sex", lifeStage = "Wing_development",
basisOfRecordDescription = "Source",
verbatimLocality = "Center_Sampling_region",
references = "Voucher_ID" )
)
head(dataset2)
## ---- warning=FALSE, error=FALSE----------------------------------------------
dataset2 <- mutate.traitdata(dataset2,
Body_shape = Body_length/Body_width,
Body_volume = Body_length*Body_width*Body_height,
Wingload = Wing_length*Wing_width/Body_volume)
head(dataset2[dataset2$verbatimTraitName %in% c("Body_shape", "Body_volume", "Wingload"),])
## ---- warning=FALSE, error=FALSE----------------------------------------------
as.trait("body_length",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "The known longest dimension of the physical structure of organisms",
identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Body_length",
author = "Maggenti and Maggenti, 2005",
broaderTerm = c("http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Body_dimension"),
narrowerTerm = c("http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Female_body_length",
"http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Male_body_length")
)
## ---- warning=FALSE, error=FALSE----------------------------------------------
thesaurus1 <- as.thesaurus(
body_length = as.trait("body_length",
expectedUnit = "mm", valueType = "numeric",
identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Body_length"),
antenna_length = as.trait("antenna_length",
expectedUnit = "mm", valueType = "numeric",
identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Antenna_length"),
metafemur_length = as.trait("femur_length",
expectedUnit = "mm", valueType = "numeric",
identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Femur_length"),
eyewidth_corr = as.trait("eye_diameter",
expectedUnit = "mm", valueType = "numeric",
identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Eye_diameter")
)
## ---- warning=FALSE, error=FALSE----------------------------------------------
thesaurus1 <- as.thesaurus(data.frame(
trait = c("body_length", "antenna_length", "metafemur_length", "eyewidth_corr"),
identifier = paste0("http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=",
c("Body_length", "Antenna_length", "Femur_length", "Eye_diameter")),
valueType = c("numeric"),
expectedUnit = "mm")
)
## ---- message=FALSE, warning=FALSE--------------------------------------------
dataset1Std <- standardize_traits(dataset1, thesaurus1)
head(dataset1Std)
## ---- warning=FALSE, error=FALSE----------------------------------------------
# M. Gossner, Martin; K. Simons, Nadja; Hoeck, Leonhard; W. Weisser, Wolfgang
# (2016): Morphometric measures of Heteroptera sampled in grasslands across
# three regions of Germany. figshare.
# https://doi.org/10.6084/m9.figshare.c.3307611.v1
# following the definitions in data publication
# http://www.esapubs.org/archive/ecol/E096/102/metadata.php
thesaurus2 <- as.thesaurus(
Body_length = as.trait("Body_length", identifier = "t1",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "From the tip of the head to the end of the abdomen"),
Body_width = as.trait("Body_width", identifier = "t2",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Widest part of the body"),
Body_height = as.trait("Body_height",identifier = "t3",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Thickest part of the body"),
Thorax_length = as.trait("Thorax_length", identifier = "t4",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Longest part of the pronotum"),
Thorax_width = as.trait("Thorax_width", identifier = "t5",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Widest part of the pronotum"),
Head_width = as.trait("Head_width", identifier = "t6",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Widest part of the head including eyes"),
Eye_width = as.trait("Eye_width", identifier = "t7",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Widest part of the left eye"),
Antenna_Seg1 = as.trait("Antenna_Seg1", identifier = "t8",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Length of first antenna segment",
broaderTerm = "http://ecologicaltraitdata.github.io/TraitDataList/Antenna_length"),
Antenna_Seg2 = as.trait("Antenna_Seg2", identifier = "t9",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Length of second antenna segment",
broaderTerm = "http://ecologicaltraitdata.github.io/TraitDataList/Antenna_length"),
Antenna_Seg3 = as.trait("Antenna_Seg3", identifier = "t10",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Length of third antenna segment",
broaderTerm = "http://ecologicaltraitdata.github.io/TraitDataList/Antenna_length"),
Antenna_Seg4 = as.trait("Antenna_Seg4", identifier = "t11",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Length of fourth antenna segment",
broaderTerm = "http://ecologicaltraitdata.github.io/TraitDataList/Antenna_length"),
Antenna_Seg5 = as.trait("Antenna_Seg5", identifier = "t12",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Length of fifth antenna segment (only Pentatomoidea)",
broaderTerm = "http://ecologicaltraitdata.github.io/TraitDataList/Antenna_length"),
Front.Tibia_length = as.trait("Front.Tibia_length", identifier = "t13",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Length of the tibia of the foreleg"),
Mid.Tibia_length = as.trait("Mid.Tibia_length", identifier = "t14",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Length of the tibia of the mid leg",
broaderTerm = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Tibia_length"),
Hind.Tibia_length = as.trait("Hind.Tibia_length", identifier = "t15",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Length of the tibia of the hind leg",
broaderTerm = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Tibia_length"),
Front.Femur_length = as.trait("Front.Femur_length", identifier = "t16",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Length of the femur of the foreleg",
broaderTerm = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Femur_length"),
Hind.Femur_length = as.trait("Hind.Femur_length", identifier = "t17",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Length of the femur of the hind leg",
broaderTerm = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Femur_length"),
Front.Femur_width = as.trait("Front.Femur_width", identifier = "t18",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Width of the femur of the foreleg"),
Hind.Femur_width = as.trait("Hind.Femur_width", identifier = "t18",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Width of the femur of the hind leg"),
Rostrum_length = as.trait("Rostrum_length", identifier = "t19",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Length of the rostrum including all segments"),
Rostrum_width = as.trait("Rostrum_width", identifier = "t20",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Widest part of the rostrum"),
Wing_length = as.trait("Wing_length", identifier = "t21",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Longest part of the forewing",
broaderTerm = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Wing"),
Wing_width = as.trait("Wing_width", identifier = "t22",
expectedUnit = "mm", valueType = "numeric",
traitDescription = "Widest part of the forewing",
broaderTerm = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Wing")
)
## ---- message=FALSE, warning=FALSE--------------------------------------------
dataset2Std <- standardize_traits(dataset2, thesaurus2)
subset(dataset2Std, occurrenceID == 2)
attributes(dataset2Std)$traits[,c("trait", "identifier","traitDescription","expectedUnit")]
## ---- message=FALSE, warning=FALSE--------------------------------------------
dataset1Std <- standardize_taxa(dataset1)
head(dataset1Std)
## ---- eval = FALSE------------------------------------------------------------
# # dataset by Jule Mangels et al.
#
# moths <- read.service(21247, dec = ",")
#
# dataset5 <- as.traitdata(moths, taxa = "species", traits = c(body_mass =
# "weight", wing_length = "wing_length", wing_width = "wing_width", wing_area =
# "wing_area", wing_loading = "wing_loading"),
# keep = c(locationID = "plot"))
#
# dataset5Std <- standardize.exploratories(dataset1)
#
# head(dataset5Std)
## ---- message = FALSE, warning=FALSE, eval=FALSE------------------------------
# dataset1Std <- standardize(carabids,
# thesaurus = thesaurus1,
# taxa = "name_correct",
# units = "mm",
# keep = c(measurementDeterminedBy = "source_measurement")
# )
## ---- eval = FALSE, warning=FALSE, error=FALSE--------------------------------
# newdata <- rbind(dataset1Std, dataset2Std,
# datasetID = c("vanderplas15", "gossner15")
# )
## ---- warning=FALSE, error=FALSE----------------------------------------------
metadata1 <- as.metadata(
datasetName = "Carabid traits",
datasetID = "carabids",
bibliographicCitation = bibentry(
bibtype = "Article",
title = "Sensitivity of functional diversity metrics to sampling intensity",
journal = "Methods in Ecology and Evolution",
author = c(as.person("Fons van der Plas, Roel van Klink, Pete Manning, Han Olff, Markus Fischer")
),
year = 2017,
doi = "10.1111/2041-210x.12728"
),
author = "Fons van der Plas",
license = "http://creativecommons.org/publicdomain/zero/1.0/"
)
dataset1 <- as.traitdata(carabids,
taxa = "name_correct",
thesaurus = thesaurus1,
units = "mm",
keep = c(datasetID = "source_measurement", measurementRemark = "note"),
metadata = metadata1
)
head(dataset1)
## ---- warning=FALSE, error=FALSE----------------------------------------------
metadata2 <- as.metadata(
datasetName = "Heteroptera morphometry traits",
datasetID = "heteroptera",
bibliographicCitation = bibentry(
bibtype = "Article",
title = "Morphometric measures of Heteroptera sampled in grasslands across three regions of Germany",
journal = "Ecology",
volume = 96,
issue = 4,
pages = 1154,
author = c(as.person("Martin M. Gossner , Nadja K. Simons, Leonhard Hoeck, Wolfgang W. Weisser")),
year = 2015,
doi = "10.1890/14-2159.1"
),
author = "Martin M. Gossner",
license = "http://creativecommons.org/publicdomain/zero/1.0/"
)
dataset2 <- as.traitdata(heteroptera_raw,
taxa = "SpeciesID",
thesaurus = thesaurus2,
units = "mm",
keep = c(sex = "Sex", references = "Source", lifestage = "Wing_development"),
metadata = metadata2
)
database <- rbind(dataset1, dataset2,
datasetID = c("vanderplas17", "gossner15"),
metadata_as_columns = TRUE
)
head(database)
## ---- warning=FALSE, error=FALSE----------------------------------------------
attributes(dataset1)$metadata$bibliographicCitation
## ---- eval = FALSE, warning=FALSE, error=FALSE--------------------------------
# carabids <- utils::read.delim(url("https://datadryad.org/stash/downloads/file_stream/24267",
# encoding = "UTF-8")
# )
#
# attr(carabids, 'metadata') <- traitdataform::as.metadata(
# datasetName = "Carabid traits",
# datasetID = "carabids",
# bibliographicCitation = utils::bibentry(
# bibtype = "Article",
# title = "Sensitivity of functional diversity metrics to sampling intensity",
# journal = "Methods in Ecology and Evolution",
# author = c(utils::as.person("Fons van der Plas, Roel van Klink, Pete Manning, Han Olff, Markus Fischer")
# ),
# year = 2017,
# doi = "10.1111/2041-210x.12728"
# ),
# author = "Fons van der Plas",
# license = "http://creativecommons.org/publicdomain/zero/1.0/"
# )
#
# attr(carabids, 'thesaurus') <- traitdataform:::as.thesaurus(
# body_length = traitdataform:::as.trait("body_length",
# expectedUnit = "mm", valueType = "numeric",
# identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Body_length"),
# antenna_length = traitdataform:::as.trait("antenna_length",
# expectedUnit = "mm", valueType = "numeric",
# identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Antenna_length"),
# metafemur_length = traitdataform:::as.trait("femur_length",
# expectedUnit = "mm", valueType = "numeric",
# identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Femur_length"),
# eyewidth_corr = traitdataform:::as.trait("eye_diameter",
# expectedUnit = "mm", valueType = "numeric",
# identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Eye_diameter")
# )
#
# attr(carabids, 'taxa') <- "name_correct"
# attr(carabids, 'units') <- "mm"
# attr(carabids, 'keep') <- c(measurementDeterminedBy = "source_measurement", measurementRemarks = "note")
#
## -----------------------------------------------------------------------------
#example for adding metadata as a table
## ---- eval = FALSE------------------------------------------------------------
#
# head(dataset3)
#
# dataset3wide <- cast.traitdata(dataset3)
#
# head(dataset3wide)
#
## ---- eval = FALSE, warning=FALSE, error=FALSE--------------------------------
# write.table(dataset1Std, file = "carabids_std.csv",
# sep = ",", dec = ".", quote = TRUE, eol = "\r", row.names = FALSE)
## ---- eval = FALSE, warning=FALSE, error=FALSE--------------------------------
# capture.output(attributes(dataset1Std)$metadata, file = "metadata.txt")
#
# write.table(attributes(dataset1Std)$traits, file = "traits.csv",
# sep = ",", dec = ".", quote = TRUE, eol = "\r", row.names = FALSE)
# write.table(attributes(dataset1Std)$taxonomy, file = "taxa.csv",
# sep = ",", dec = ".", quote = TRUE, eol = "\r", row.names = FALSE)
## ---- eval = FALSE, warning=FALSE, error=FALSE--------------------------------
# zip("carabids_std.zip", c("carabids_std.csv", "metadata.txt", "traits.csv", "taxa.csv") )
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