Reptile Development Database

Source Notebook

This data measures the plasticity of some reptile phenotypic traits under changes in environmental conditions during development

Details

This database allows to identify how the environment, particularly the thermal environment, experienced by embryos can influence phenotypic variation, including sex ratio, phenology and survival

Available properties include:

"TaxonomicSpecies"

scientific name of the specie

"EggDesign"

reflecting how eggs were allocated to each incubation treatment

"TraitCatategory"

categories into which each trait is assigned

"Trait"

name of the traits

"EggEmbryoHatchling"

specification of the life stage at which the phenotypic trait was measured

"Age"

days post-hatching at which the trait was measured

"Sex"

sex of the individuals in the sample

"ConstFluct"

incubation temperature design

"Temperature"

mean temperature of the incubation treatment

"TemperatureFluctuation"

range of temperature of the incubation treatment This column can be used to treat temperature fluctuations on a continuous scale or classify experimental designs (as is done in const_fluct) in a user specific way.

"WaterPotential"

water potential of treatment.

"TraitValue"

trait value

Examples

Basic Examples (6)

Getting the database:

In[1]:=

$rdd = ResourceData[\!$\* TagBox["\"\<Reptile Development Database\>\"", #& , BoxID -> "ResourceTag-Reptile Development Database-Input", AutoDelete->True]$]$

Out[1]=

Categories of the measured traits and their sizes (i.e., number of times reported in database):

In[2]:=

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Traits by category and their sizes (i.e., number of times reported in database):

In[3]:=

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Variations for GrowthRateHeadLength for the same specie and under different temperatures values:

In[4]:=

data = ({Sequence @@ (Union /@ #[[{1, 2, 3, 4, 5, 6, 8, 9, 10, 11}]]),
Thread[#[[7]] -> #[[12]]]} &@Transpose[#]) & /@ Values[Normal[
rdd[GatherBy[#, {#[[DeleteCases[Range[1, 11, 1], 7]]]} &] &]]];
data[[1]]

Out[5]=

Average variance of traits by category under the same treatment conditions:

In[6]:=

$Dataset[<|"Category" -> #[[1, 1, 1]], "AverageVariance" -> Mean[#[[All, 2]]], "MinMaxVariance" -> MinMax[#[[All, 2]]]|> & /@ GatherBy[ DeleteCases[{Sequence @@ #[[-3 ;; -2]], If[Length[#[[-1, All, 2]]] > 1, Variance[(#[[-1, All, 2]] /. Quantity[x_, _] :> x)], Missing["NotAvailable"]]} & /@ data, {__, Missing["NotAvailable"]}], First][[All, All, {1, -1}]]]$

Out[6]=

Average variance of traits under the same treatment conditions:

In[7]:=

$Dataset[<|"Category" -> #[[1, 1, 1]], "Trait" -> #[[1, 2, 1]], "AverageVariance" -> Mean[#[[All, -1]]], "MinMaxVariance" -> MinMax[#[[All, -1]]]|> & /@ SortBy[#, First] &@ GatherBy[ DeleteCases[{Sequence @@ #[[-3 ;; -2]], If[Length[#[[-1, All, 2]]] > 1, Variance[(#[[-1, All, 2]] /. Quantity[x_, _] :> x)], Missing["NotAvailable"]]} & /@ data, {__, Missing["NotAvailable"]}], #[[2]] &]]$

Out[7]=

Scope & Additional Elements (1)

Get the definitions of the values of some properties:

In[8]:=

$rddDefinitions = ResourceData[\!$\* TagBox["\"\<Reptile Development Database\>\"", #& , BoxID -> "ResourceTag-Reptile Development Database-Input", AutoDelete->True]$, "Definitions"]$

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Visualizations (1)

Get an histogram of variances in the value of some trait when a treatment condition is changed (i.e., variable) and the other variables are keep equal:

In[9]:=

In[10]:=

$traits = Union@Normal@rdd[All, 11]; conditions = #[[1]] -> #[[2, 1]] & /@ DeleteElements[ Normal@PositionIndex@Keys@Normal@rdd[1], {"TraitValue" -> _, "TraitCategory" -> _, "Trait" -> _}]; raw = Values[Normal[rdd[GatherBy[#, {#[[Range[1, 11, 1]]]} &] &]]];$

In[11]:=

$Manipulate[ traitSelected = ({Sequence @@ (Union /@ Transpose[#[[All, 1 ;; -2]]]), Mean[#[[All, -1]]]}) & /@ DeleteCases[ Select[#, StringContainsQ[#[[-2]], trait] &] & /@ raw, {}]; If[MatchQ[Union[#[[All, -1]]], {Missing["NotAvailable"]}], "There is not enough data to estimate the variance", Histogram[#[[All, -1]], 10]] &@({Sequence @@ #[[1, 1 ;; -2]], If[Length[#[[All, -1]]] > 1, Variance[(#[[All, -1]] /. Quantity[x_, _] :> x)], Missing["NotAvailable"]]} & /@ GatherBy[ traitSelected, #[[ DeleteCases[Range[1, 9, 1], variable /. conditions]]] &]) , {trait, traits}, {variable, conditions[[All, 1]]}]$

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External Links

Bibliographic Citation

Lina Marcela, "Reptile Development Database" from the Wolfram Data Repository (2024)

License Information

Free

Data Resource History

Date Created: 9 February 2024

Source Metadata

Title: A comprehensive database of thermal developmental plasticity in reptiles: Reptile Development Database
Creator: Noble, D.W.A et al.
Publisher: Scientific Data
Date: 2018
Language: English
Citation:
- Noble, D.W.A, Stenhouse, V., Riley, J.E., Warner, D.A., While, G.M., Du, W.-G., Uller, T. and Schwanz, L.E. (2018) A comprehensive database of thermal developmental plasticity in reptiles: Reptile Development Database. Scientific Data, in press.

Data Downloads

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Publisher Information

Prepared for the Wolfram Data Repository By: Lina Marcela Ruiz Galvis and Keiko Hirayama
Publisher of Record: Lina Marcela