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"Title": "An Interface to the Reptile Database",
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"Description": "Provides tools to retrieve and summarize taxonomic\ninformation and synonymy data for reptile species using data\nscraped from The Reptile Database website\n(). Outputs include\nclean and structured data frames useful for ecological,\nevolutionary, and conservation research.",
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"reptCompare",
"reptRefs",
"reptSearch",
"reptSpecies",
"reptSplitCheck",
"reptStats",
"reptSync",
"reptSynonyms",
"reptTidySyn"
],
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{
"name": "allReptiles",
"title": "Example dataset: allReptiles",
"object": "allReptiles",
"class": [
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],
"fields": [
"species",
"order",
"suborder",
"family",
"genus",
"year",
"author",
"url"
],
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{
"name": "allSynonyms",
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],
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"species",
"synonyms"
],
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"table": true,
"tojson": true
},
{
"name": "allSynonymsRef",
"title": "Example dataset: allSynonymsRef",
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"data.frame"
],
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"species",
"synonyms",
"ref"
],
"rows": 112626,
"table": true,
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},
{
"name": "br_snakes_atlas",
"title": "Example dataset: br_snakes_atlas",
"object": "br_snakes_atlas",
"class": [
"spec_tbl_df",
"tbl_df",
"tbl",
"data.frame"
],
"fields": [
"species",
"latitude",
"longitude"
],
"rows": 411,
"table": true,
"tojson": true
},
{
"name": "letsRept_ReptTraits",
"title": "Example dataset: letsRept_ReptTraits",
"object": "letsRept_ReptTraits",
"class": [
"data.frame"
],
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"species",
"RDB",
"nomenclature.status",
"order",
"suborder",
"family",
"genus",
"Description.author.s",
"Description.year",
"Subspecies",
"Main.biogeographic.region",
"Microhabitat",
"Habitat.type",
"Minimal.elevation..m.",
"Maximum.elevation..m.",
"Mean.Annual.Temperature...C.",
"Temperature.Seasonality..standard.deviation.100.",
"Seasonality.Precipitation..coefficient.of.variation...100.",
"Insular.endemic..yes.or.no.",
"Venomous..yes.or.no.",
"Diet",
"Diet..comments",
"Active.time",
"Dorsal.colour",
"Dorsal.pattern",
"Foraging.mode",
"Pupil.Shape",
"Fangs",
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"Maximum.body.mass..g.",
"Maximum.total.length...TL...mm.",
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"Maximum.female.length...SVL...mm..straight.carapace.length.for.turtles...SCL...mm.",
"Maximum.male.length...SVL...mm..straight.carapace.length.for.turtles...SCL...mm.",
"Maximum.juvenile.length...SVL...mm..straight.carapace.length.for.turtles...SCL...mm.",
"Hatchling.neonate.mass..g.",
"Reproductive.mode",
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"Mean.number.of.offspring.per.litter.or.number.of.eggs.per.clutch",
"Smallest.clutch.size",
"Largest.clutch.size",
"Number.of.litters.or.clutches.produced.per.year",
"Egg.length..mm.",
"Egg.width..mm.",
"Mean.Tb",
"Minimum.Tb",
"Maximum.Tb",
"Genetic.data..yes.or.not.",
"IUCN.redlist.assessment",
"IUCN.population.trend"
],
"rows": 12060,
"table": true,
"tojson": true
},
{
"name": "letsRept_SquamBase",
"title": "Example dataset: letsRept_SquamBase",
"object": "letsRept_SquamBase",
"class": [
"data.frame"
],
"fields": [
"species",
"RDB",
"nomenclature.status",
"sub.order",
"infraorder",
"family",
"description.year",
"synonyms",
"Sources..general.",
"maximum.total.length..mm.",
"mean.female.total.length..mm.",
"hatchling.neonate.total.length..mm.",
"maximum.SVL..mm.",
"mean.female.SVL..mm.",
"hatchling.neonate.SVL..mm.",
"mean.female.mass..g.",
"hatchling.neonate.mass..g.",
"maximum.mass..derived.from.allometric.equations..in.log10..g.",
"mean.female.mass..derived.from.allometric.equations..in.log10..g.",
"mean.hatchling.neonate.mass..derived.from.allometric.equations..in.log10..g.",
"mass_equation..from.Feldman.et.al..2016.unless.stated.",
"size.metadata",
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"Minimum.elevation..m.",
"Maximum.elevation..m.",
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"substrate",
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"Diet",
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"Mean.population.density..minimum...ha..1.",
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"Length.of.Activity.Season..minimum..months.",
"Length.of.Activity.Season..maximum..months.",
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"Averge.body.temperature..minimum..during.activity..in.nature..in..C",
"Averge.body.temperature..maximum..during.activity..in.nature..in..C",
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"Preferred.temperature.metadata",
"youngest.age.at.first.breeding..female..months.",
"oldest.age.at.first.breeding..female..months.",
"breeding.age..metadata.",
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"smallest.brood",
"largest.brood",
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"maximum.mean.brood.size",
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"Yearly.broods..maximum.",
"Yearly.broods.metadata",
"Major.Biome..GARD.1.7.",
"Major.Realm..Falaschi.et.al..2023.designation.",
"Geographic.range.size..GARD.1.7..Caetano.et.al..2023..km.2.",
"Geographic.range.size.range.size..IUCN..August.2022..km.2.",
"Extinct.",
"Threat.status..IUCN..October.2023.",
"Population.trend..IUCN..October.2023.",
"IUCN.threat.criteria..October.2023.",
"year.assessed.by.the.IUCN",
"name.in.Tonini.et.al...2016.",
"name.in.Zheng.and.Wiens..2016.",
"name.in.the.IUCN.redlist",
"GARD.id",
"Reptile.database.id",
"in.the.reptile.database..October.2023.release."
],
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"_help": [
{
"page": "allReptiles",
"title": "Example dataset: allReptiles",
"topics": [
"allReptiles"
]
},
{
"page": "allSynonyms",
"title": "Example dataset: allSynonyms",
"topics": [
"allSynonyms"
]
},
{
"page": "allSynonymsRef",
"title": "Example dataset: allSynonymsRef",
"topics": [
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]
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{
"page": "br_snakes_atlas",
"title": "Example dataset: br_snakes_atlas",
"topics": [
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]
},
{
"page": "letsRept_ReptTraits",
"title": "Example dataset: letsRept_ReptTraits",
"topics": [
"letsRept_ReptTraits"
]
},
{
"page": "letsRept_SquamBase",
"title": "Example dataset: letsRept_SquamBase",
"topics": [
"letsRept_SquamBase"
]
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{
"page": "reptAdvancedSearch",
"title": "Search The Reptile Database website (RDB): Advanced",
"topics": [
"reptAdvancedSearch"
]
},
{
"page": "reptCompare",
"title": "Compare species nomenclature between datasets or with Reptile Database Data",
"topics": [
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]
},
{
"page": "reptRefs",
"title": "Extract references from the Reptile Database",
"topics": [
"reptRefs"
]
},
{
"page": "reptSearch",
"title": "Search for a Single Reptile Species in The Reptile Database (RDB)",
"topics": [
"reptSearch"
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},
{
"page": "reptSpecies",
"title": "Retrieve Reptile Species and Taxonomic Information from RDB",
"topics": [
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]
},
{
"page": "reptSplitCheck",
"title": "Check for potential taxonomic splits in a query",
"topics": [
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]
},
{
"page": "reptStats",
"title": "Summarize Taxonomic Composition",
"topics": [
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]
},
{
"page": "reptSync",
"title": "Synchronize Species Names Using The Reptile Database",
"topics": [
"reptSync"
]
},
{
"page": "reptSynonyms",
"title": "Retrieve Synonyms for Reptile Species from RDB",
"topics": [
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]
},
{
"page": "reptTidySyn",
"title": "Printing reptSync and reptSplitCheck outcomes in a tidy way",
"topics": [
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]
}
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"title": "Case Study: Using letsRept to harmonize reptile species nomenclature",
"author": "João Paulo dos Santos Vieira-Alencar",
"engine": "knitr::rmarkdown",
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"References"
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"title": "letsRept: An Interface to the Reptile Database",
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"List of functions and examples",
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"Function reptRefs:",
"Function reptAdvancedSearch:",
"Function reptSpecies:",
"Function `reptStats``:",
"Function reptSynonyms:",
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