DatabaseTSD {embryogrowth} | R Documentation |
Database of TSD information for reptiles
Description
Database of TSD information for reptiles
The columns are:
-
Species
: Name of the species in binominal nommenclature -
Subspecies
: Name of the subspecies -
Country
: From which country the eggs come from -
Area
: Name of the beach or region the eggs come from -
RMU.2010
: For marine turtles, name of the RMU for this population; see Wallace, B.P., DiMatteo, A.D., Hurley, B.J., Finkbeiner, E.M., Bolten, A.B., Chaloupka, M.Y., Hutchinson, B.J., Abreu-Grobois, F.A., Amorocho, D., Bjorndal, K.A., Bourjea, J., Bowen, B.W., Duenas, R.B., Casale, P., Choudhury, B.C., Costa, A., Dutton, P.H., Fallabrino, A., Girard, A., Girondot, M., Godfrey, M.H., Hamann, M., Lopez-Mendilaharsu, M., Marcovaldi, M.A., Mortimer, J.A., Musick, J.A., Nel, R., Seminoff, J.A., Troeng, S., Witherington, B., Mast, R.B., 2010. Regional management units for marine turtles: a novel framework for prioritizing conservation and research across multiple scales. Plos One 5, e15465. -
RMU.2023
: For marine turtles, name of the RMU for this population; see Wallace BP, Posnik ZA, Hurley BJ, DiMatteo AD, Bandimere A, Rodriguez I, Maxwell SM, Meyer L, Brenner H, Jensen MP, LaCasella E, Shamblin BM, Abreu Abreu-Grobois FA, Stewart KR, Dutton PH, Barrios-Garrido H, Dalleau M, Dell’amico F, Eckert KL, FitzSimmons NN, Garcia-Cruz M, Hays GC, Kelez S, Lagueux CJ, Madden Hof CA, Marco A, Martins SLT, Mobaraki A, Mortimer JA, Nel R, Phillott AD, Pilcher NJ, Putman NF, Rees AF, Rguez-Baron JM, Seminoff JA, Swaminathan A, Turkozan O, Vargas SM, Vernet PD, Vilaça S, Whiting SD, Hutchinson BJ, Casale P, Mast RB (2023) Marine turtle regional management units 2.0: an updated framework for conservation and research of wide-ranging megafauna species. Endangered Species Research 52:209-223. -
Incubation.temperature.set
: Nominal incubation temperature -
Incubation.temperature.recorded
: Nominal or real (if available) incubation temperature -
Duplicated.data
: TRUE if these data are duplicated in database -
Duplicate
: Unique code for the duplicate -
Incubation.temperature.Constant
: Does the incubation temperature was set as constant or CTE was reported -
Incubation.temperature.Accuracy
: What is the accuracy of the measure of temperature -
Incubation.temperature.SD
: Experimental SD of incubation temperatures -
Incubation.temperature.Amplitude
: How much the temperature could fluctuate around nominal temperature -
Correction.factor
: Difference between the incubator temperature and the eggs temperature -
IP.min
: Shorter incubation period -
IP.max
: Longer incubation period -
IP.mean
: Mean incubation periods -
IP.SD
: Standard deviation for incubation periods -
Total
: Total number of eggs incubated -
Hatched
: Number of hatchlings -
NotHatched
: Number of embryos with development visible but dead during incubation -
Undeveloped
: Number of embryos showing no development -
Intersexes
: Number of individuals intersexes or ambiguous for sex phenotype -
Males
: Number of individuals indentified as males -
Females
: Number of individuals indentified as females -
Sexed
: Number of sexed individuals -
Box
: Identity of the condition incubation -
Clutch
: Identity or number of clutches -
Reference
: Bibliographic reference -
Note
: Diverse information for this incubation -
Digital_Identifier
: A unique digital identifier -
Version
: Date of the last modification for each record
The Incubation.temperature records are the incubation temperature of the incubator. If a correction factor was substracted in the publication to represent the temperature of the egg itself, it has been added here.
Usage
DatabaseTSD
Format
A dataframe with raw data.
Details
Database of TSD information for marine turtles
Author(s)
Marc Girondot marc.girondot@universite-paris-saclay.fr
See Also
Other Functions for temperature-dependent sex determination:
DatabaseTSD.version()
,
P_TRT()
,
ROSIE
,
ROSIE.version()
,
TSP.list
,
plot.tsd()
,
predict.tsd()
,
stages
,
tsd()
,
tsd_MHmcmc()
,
tsd_MHmcmc_p()
Examples
## Not run:
library(embryogrowth)
data(DatabaseTSD)
DatabaseTSD.version()
totalIncubation_Lo <- subset(DatabaseTSD,
Species=="Lepidochelys olivacea" & (!is.na(Sexed) & Sexed!=0),
select=c("Males", "Females", "Incubation.temperature"))
tot_Lo <- with(totalIncubation_Lo, tsd(males=Males, females=Females,
temperatures=Incubation.temperature), parameters.initial = c(P=30.5, S=-0.4))
predict(tot_Lo)
## End(Not run)