Add new datasets

data/amniota.R

@@ -2,17 +2,149 @@
 amniota <- utils::read.csv("http://esapubs.org/archive/ecol/E096/269/Data_Files/Amniote_Database_Aug_2015.csv",
                            fileEncoding = "UTF-8")
 
-attr(amniota, 'citeAs') <- utils::bibentry(
-  bibtype = "Article",
-  title = "An amniote life-history database to perform comparative analyses with birds, mammals, and reptiles",
-  journal = "Ecology",
-  volume = 96,
-  issue = 5,
-  pages = 3109,
-  author = c(utils::person(given = "Nathan P.", family = "Myhrvold" , email = "nathanm@intven.com"), utils::as.person(c("Elita Baldridge", "Benjamin Chan", "Dhileep Sivam", "Daniel L. Freeman", "S. K. Morgan Ernest")) 
-             ),
-  year = 2015,
-  doi = "10.1890/15-0846.1"
+amniota$taxa <- paste(amniota$genus, amniota$species)
+
+#replace -999 with NA
+amniota[amniota == -999] <- NA
+
+attr(amniota, 'metadata') <- traitdataform::as.metadata(
+  datasetName = "Amniote life-history traits",
+  datasetID = "amniota",
+  bibliographicCitation =  utils::bibentry(
+    bibtype = "Article",
+    title = "An amniote life-history database to perform comparative analyses with birds, mammals, and reptiles",
+    journal = "Ecology",
+    author = c(utils::as.person("Nathan P. Myhrvold, Elita Baldridge, Benjamin CHan, Dhileep Sivam, 
+                                Daniel L. Freeman, S.K. Morgan Ernest")),
+    year = 2015,
+    doi = "10.1890/15-0846.1"
+  ),
+  author = "Nathan P. Myhrvold",
+  license = "http://creativecommons.org/publicdomain/zero/1.0/"
 )
-print({cat("loading dataset 'amniota' from original data source! \n When using this data, please cite the original publication: \n") 
-  (attributes(amniota)$citeAs) })
+
+attr(amniota, 'thesaurus') <-  traitdataform::as.thesaurus(
+  female_maturity_d = traitdataform::as.trait("female_maturity_d",
+                                        expectedUnit = "d", valueType = "numeric",
+                                        identifier = "http://ecologicaltraitdata.github.io/TraitDataList/#Development"),
+
+  litter_or_clutch_size_n = traitdataform::as.trait("litter_or_clutch_size_n",
+                                              valueType = "numeric",
+                                              identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Clutch_length"),
+
+  litters_or_clutches_per_y = traitdataform::as.trait("litters_or_clutches_per_y",
+                                                    valueType = "numeric",
+                                                    identifier = NA),
+
+  adult_body_mass_g = traitdataform::as.trait("adult_body_mass_g",
+                                              expectedUnit = "g", valueType = "numeric",
+                                              identifier = "http://purl.obolibrary.org/obo/VT_0001259"),
+
+  maximum_longevity_y = traitdataform::as.trait("maximum_longevity_y",
+                                              expectedUnit = "a", valueType = "numeric",
+                                              identifier = "http://ecologicaltraitdata.github.io/TraitDataList/#Life_span_potential"),
+
+  gestation_d = traitdataform::as.trait("gestation_d",
+                                        expectedUnit = "d", valueType = "numeric",
+                                        identifier = NA),
+
+  weaning_d = traitdataform::as.trait("weaning_d",
+                                        expectedUnit = "d", valueType = "numeric",
+                                        identifier = NA),
+
+  birth_or_hatching_weight_g = traitdataform::as.trait("birth_or_hatching_weight_g",
+                                      expectedUnit = "g", valueType = "numeric",
+                                      identifier = "http://purl.obolibrary.org/obo/VT_0001259"),
+
+  weaning_weight_g = traitdataform::as.trait("weaning_weight_g",
+                                             expectedUnit = "g", valueType = "numeric",
+                                             identifier = "http://purl.obolibrary.org/obo/VT_0001259"),
+
+  egg_mass_g = traitdataform::as.trait("egg_mass_g",
+                                       expectedUnit = "g", valueType = "numeric",
+                                       identifier = "http://ecologicaltraitdata.github.io/TraitDataList/#Egg_biomass"),
+
+  incubation_d = traitdataform::as.trait("incubation_d",
+                                         expectedUnit = "d", valueType = "numeric",
+                                         identifier = "https://ecologicaltraitdata.github.io/TraitDataList/#egg_development_time"),
+
+  fledging_age_d = traitdataform::as.trait("fledging_age_d",
+                                         expectedUnit = "d", valueType = "numeric",
+                                         identifier = NA),
+
+  longevity_y = traitdataform::as.trait("longevity_y",
+                                        expectedUnit = "a", valueType = "numeric",
+                                        identifier = "http://purl.obolibrary.org/obo/VT_0001661"),
+
+  male_maturity_d = traitdataform::as.trait("male_maturity_d",
+                                        expectedUnit = "d", valueType = "numeric",
+                                        identifier = "http://ecologicaltraitdata.github.io/TraitDataList/#Development"),
+
+  inter_litter_or_interbirth_interval_y = traitdataform::as.trait("inter_litter_or_interbirth_interval_y",
+                                            expectedUnit = "a", valueType = "numeric",
+                                            identifier = NA),
+
+  female_body_mass_g = traitdataform::as.trait("female_body_mass_g",
+                                            expectedUnit = "g", valueType = "numeric",
+                                            identifier = "http://purl.obolibrary.org/obo/VT_0001259"),
+
+  male_body_mass_g = traitdataform::as.trait("male_body_mass_g",
+                                               expectedUnit = "g", valueType = "numeric",
+                                               identifier = "http://purl.obolibrary.org/obo/VT_0001259"),
+
+  no_sex_body_mass_g = traitdataform::as.trait("no_sex_body_mass_g",
+                                               expectedUnit = "g", valueType = "numeric",
+                                               identifier = "http://purl.obolibrary.org/obo/VT_0001259"),
+
+  egg_width_mm = traitdataform::as.trait("egg_width_mm",
+                                               expectedUnit = "mm", valueType = "numeric",
+                                               identifier = "http://ecologicaltraitdata.github.io/TraitDataList/#Egg_size"),
+
+  egg_length_mm = traitdataform::as.trait("egg_length_mm",
+                                               expectedUnit = "mm", valueType = "numeric",
+                                               identifier = "http://ecologicaltraitdata.github.io/TraitDataList/#Egg_size"),
+
+  fledging_mass_g = traitdataform::as.trait("fledging_mass_g",
+                                               expectedUnit = "g", valueType = "numeric",
+                                               identifier = "http://purl.obolibrary.org/obo/VT_0001259"),
+
+  adult_svl_cm = traitdataform::as.trait("adult_svl_cm",
+                                               expectedUnit = "cm", valueType = "numeric",
+                                               identifier = "http://purl.obolibrary.org/obo/VT_0100005"),
+
+  male_svl_cm = traitdataform::as.trait("male_svl_cm",
+                                               expectedUnit = "cm", valueType = "numeric",
+                                               identifier = "http://purl.obolibrary.org/obo/VT_0100005"),
+
+  female_svl_cm = traitdataform::as.trait("female_svl_cm",
+                                        expectedUnit = "cm", valueType = "numeric",
+                                        identifier = "http://purl.obolibrary.org/obo/VT_0100005"),
+
+  birth_or_hatching_svl_cm = traitdataform::as.trait("birth_or_hatching_svl_cm",
+                                        expectedUnit = "cm", valueType = "numeric",
+                                        identifier = "http://purl.obolibrary.org/obo/VT_0100005"),
+
+  female_svl_at_maturity_cm = traitdataform::as.trait("female_svl_at_maturity_cm",
+                                        expectedUnit = "cm", valueType = "numeric",
+                                        identifier = "http://purl.obolibrary.org/obo/VT_0100005"),
+
+  female_body_mass_at_maturity_g = traitdataform::as.trait("female_body_mass_at_maturity_g",
+                                        expectedUnit = "g", valueType = "numeric",
+                                        identifier = "http://purl.obolibrary.org/obo/VT_0001259"),
+
+  no_sex_svl_cm = traitdataform::as.trait("no_sex_svl_cm",
+                                        expectedUnit = "cm", valueType = "numeric",
+                                        identifier = "http://purl.obolibrary.org/obo/VT_0100005"),
+
+  no_sex_maturity_d = traitdataform::as.trait("no_sex_maturity_d",
+                                        expectedUnit = "d", valueType = "numeric",
+                                        identifier = "http://ecologicaltraitdata.github.io/TraitDataList/#Development")
+)
+
+attr(amniota, 'taxa') <- "taxa"
+
+
+print(attributes(amniota)$metadata)
+
+
+

data/amphibio.R

@@ -5,18 +5,131 @@ utils::unzip(temp, files = "AmphiBIO_v1.csv", exdir = ".")
 unlink(temp)
 rm(temp)
 
-amphibio <- utils::read.csv("AmphiBIO_v1.csv")
+amphibio <- utils::read.csv("AmphiBIO_v1.csv", fileEncoding = "latin1")
 file.remove("AmphiBIO_v1.csv")
 
-attr(amphibio, 'citeAs') <- utils::bibentry(
-  bibtype = "Article",
-  title = "AmphiBIO, a global database for amphibian ecological traits",
-  journal = "Scientific Data",
-  volume = 4,
-  pages = 170123,
-  author = utils::as.person("Brunno Freire Oliveira, Vinícius Avelar São-Pedro, Georgina Santos-Barrera, Caterina Penone, and Gabriel C. Costa"),
-  year = 2017,
-  doi = "10.1038/sdata.2017.123"
+attr(amphibio, 'metadata') <- traitdataform::as.metadata(
+  datasetName = "AmphiBIO",
+  datasetID = "amphibio",
+  bibliographicCitation =    utils::bibentry(
+    bibtype = "Article",
+    title = "AmphiBIO, a global database for amphibian ecological traits",
+    journal = "Scientific Data",
+    volume = 4,
+    pages = 170123,
+    author = utils::as.person("Brunno Freire Oliveira, Vinícius Avelar São-Pedro, 
+                              Georgina Santos-Barrera, Caterina Penone, and Gabriel C. Costa"),
+    year = 2017,
+    doi = "10.1038/sdata.2017.123"
+  ),
+  author = "Brunno Freire Oliveira",
+  license = "http://creativecommons.org/publicdomain/zero/1.0/"
 )
-print({cat("loading dataset 'amphibio' from original data source! \n When using this data, please cite the original publication: \n") 
-  (attributes(amphibio)$citeAs) })
+
+attr(amphibio, 'thesaurus') <-  traitdataform::as.thesaurus(
+  Fos = traitdataform::as.trait("Fossorial",
+                                expectedUnit = NA, valueType = "logical",
+                                identifier = NA),
+  Ter = traitdataform::as.trait("Terrestrial",
+                                expectedUnit = NA, valueType = "logical",
+                                identifier = NA),
+  Aqu = traitdataform::as.trait("Aquatic",
+                                expectedUnit = NA, valueType = "logical",
+                                identifier = NA),
+  Arb = traitdataform::as.trait("Arboreal",
+                                expectedUnit = NA, valueType = "logical",
+                                identifier = NA),
+
+  Leaves = traitdataform::as.trait("Leaves",
+                                expectedUnit = NA, valueType = "logical",
+                                identifier = NA),
+  Flowers = traitdataform::as.trait("Flowers",
+                                expectedUnit = NA, valueType = "logical",
+                                identifier = NA),
+  Seeds = traitdataform::as.trait("Seeds",
+                                expectedUnit = NA, valueType = "logical",
+                                identifier = NA),
+  Fruits = traitdataform::as.trait("Fruits",
+                                expectedUnit = NA, valueType = "logical",
+                                identifier = NA),
+  Arthro = traitdataform::as.trait("Arthro",
+                                expectedUnit = NA, valueType = "logical",
+                                identifier = NA),
+
+  Diu = traitdataform::as.trait("Diurnal",
+                                expectedUnit = NA, valueType = "logical",
+                                identifier = "http://purl.obolibrary.org/obo/VT_0001502"),
+  Noc = traitdataform::as.trait("Nocturnal",
+                                expectedUnit = NA, valueType = "logical",
+                                identifier = "http://purl.obolibrary.org/obo/VT_0001502"),
+  Crepu = traitdataform::as.trait("Crepuscular",
+                                expectedUnit = NA, valueType = "logical",
+                                identifier = "http://purl.obolibrary.org/obo/VT_0001502"),
+
+  Wet_warm = traitdataform::as.trait("Wet_warm_season",
+                                expectedUnit = NA, valueType = "logical",
+                                identifier = NA),
+  Wet_cold = traitdataform::as.trait("Wet_cold_season",
+                                expectedUnit = NA, valueType = "logical",
+                                identifier = NA),
+  Dry_warm = traitdataform::as.trait("Dry_warm_season",
+                                expectedUnit = NA, valueType = "logical",
+                                identifier = NA),
+  Dry_cold = traitdataform::as.trait("Dry_cold_season",
+                                expectedUnit = NA, valueType = "logical",
+                                identifier = NA),
+
+  Body_mass_g = traitdataform::as.trait("Body_mass_g",
+                                expectedUnit = "g", valueType = "numeric",
+                                identifier = "http://purl.obolibrary.org/obo/VT_0001259"),
+  Age_at_maturity_min_y = traitdataform::as.trait("Age_at_maturity_min_y",
+                                expectedUnit = "a", valueType = "numeric",
+                                identifier = "https://ecologicaltraitdata.github.io/TraitDataList/#Age_at_maturity"),
+  Age_at_maturity_max_y = traitdataform::as.trait("Age_at_maturity_max_y",
+                                expectedUnit = "a", valueType = "numeric",
+                                identifier = "https://ecologicaltraitdata.github.io/TraitDataList/#Age_at_maturity"),
+  Body_size_mm = traitdataform::as.trait("Body_size_mm",
+                                expectedUnit = "mm", valueType = "numeric",
+                                identifier = "http://ecologicaltraitdata.github.io/TraitDataList/#Body_length"),
+  Size_at_maturity_min_mm = traitdataform::as.trait("Size_at_maturity_min_mm",
+                                expectedUnit = "mm", valueType = "numeric",
+                                identifier = "http://ecologicaltraitdata.github.io/TraitDataList/#Body_length"),
+  Size_at_maturity_max_mm = traitdataform::as.trait("Size_at_maturity_max_mm",
+                                expectedUnit = "mm", valueType = "numeric",
+                                identifier = "http://ecologicaltraitdata.github.io/TraitDataList/#Body_length"),
+  Longevity_max_y = traitdataform::as.trait("Longevity_max_y",
+                                expectedUnit = "a", valueType = "numeric",
+                                identifier = "http://ecologicaltraitdata.github.io/TraitDataList/#Life_span_potential"),
+  Litter_size_min_n = traitdataform::as.trait("Litter_size_min_n",
+                                expectedUnit = NA, valueType = "numeric",
+                                identifier = "http://ecologicaltraitdata.github.io/TraitDataList/#Clutch_size"),
+  Litter_size_max_n = traitdataform::as.trait("Litter_size_max_n",
+                                expectedUnit = NA, valueType = "numeric",
+                                identifier = "http://ecologicaltraitdata.github.io/TraitDataList/#Clutch_size"),
+  Reproductive_output_y = traitdataform::as.trait("Reproductive_output_y",
+                                expectedUnit = "a", valueType = "numeric",
+                                identifier = "http://ecologicaltraitdata.github.io/TraitDataList/#Fecundity"),
+  Offspring_size_min_mm = traitdataform::as.trait("Offspring_size_min_mm",
+                                expectedUnit = "mm", valueType = "numeric",
+                                identifier = "http://ecologicaltraitdata.github.io/TraitDataList/#Reproduction_mode"),
+  Offspring_size_max_mm = traitdataform::as.trait("Offspring_size_max_mm",
+                                expectedUnit = "mm", valueType = "numeric",
+                                identifier = "http://ecologicaltraitdata.github.io/TraitDataList/#Reproduction_mode"),
+
+  Dir = traitdataform::as.trait("Direct_development",
+                                expectedUnit = NA, valueType = "logical",
+                                identifier = NA),
+  Lar = traitdataform::as.trait("Larval__development",
+                                expectedUnit = NA, valueType = "logical",
+                                identifier = NA),
+  Viv = traitdataform::as.trait("Viviparous_development",
+                                expectedUnit = NA, valueType = "logical",
+                                identifier = NA)
+)
+
+attr(amphibio, 'taxa') <- "Species"
+attr(amphibio, 'keep') <-  c(measurementRemarks = "OBS", basisOfRecord = "literatureData")
+
+
+print(attributes(amphibio)$metadata)
+