ROSIE: Database of TSD information for turtles
In embryogrowth: Tools to Analyze the Thermal Reaction Norm of Embryo Growth

ROSIE

R Documentation

Database of TSD information for turtles

Description

Database of incubation information with sex ratio for turtles

Usage

ROSIE

Format

A dataframe with raw data.

Details

Database of TSD information for turtles

Author(s)

Caleb Krueger kruegeca@gmail.com

References

\insertRef

12889embryogrowth

Examples

## Not run: 
library(embryogrowth)
data(ROSIE)
ROSIE.version()
ROSIE <- cbind(ROSIE, RMU.2023=NA)
ROSIE[(ROSIE$Species == "Lepidochelys_olivacea") & 
      (grepl("Orissa", ROSIE$Location)), 
      "RMU.2023"] <- "Northeast Indian"
ROSIE[(ROSIE$Species == "Lepidochelys_olivacea") & 
      (grepl("Oaxaca", ROSIE$Location) | grepl("Nancite", ROSIE$Location) | 
      grepl("Destiladeras", ROSIE$Location) | grepl("Baja California", ROSIE$Location) | 
      grepl("Sinaloa", ROSIE$Location) | grepl("Chocó, Colombia", ROSIE$Location) | 
      grepl("Jalisco, Mexico", ROSIE$Location)), 
      "RMU.2023"] <- "East Pacific"
ROSIE[(ROSIE$Species == "Lepidochelys_olivacea") & 
      (grepl("Brazil", ROSIE$Location)), 
      "RMU.2023"] <- "West Atlantic"
      
ROSIE[(ROSIE$Species == "Dermochelys_coriacea") & 
      (grepl("Suriname", ROSIE$Location) | grepl("French Guiana", ROSIE$Location)), 
      "RMU.2023"] <- "Northwest Atlantic"
ROSIE[(ROSIE$Species == "Dermochelys_coriacea") & 
      (grepl("Playa Grande", ROSIE$Location)), 
      "RMU.2023"] <- "East Pacific"
ROSIE[(ROSIE$Species == "Dermochelys_coriacea") & 
      (grepl("Malaysia", ROSIE$Location)), 
      "RMU.2023"] <- "West Pacific"
      
ROSIE[(ROSIE$Species == "Eretmochelys_imbricata") & 
      (grepl("Florida", ROSIE$Location) | grepl("Antigua", ROSIE$Location) | 
      grepl("Virgin Islands", ROSIE$Location) | grepl("Puerto Rico", ROSIE$Location) | 
      grepl("Campeche", ROSIE$Location) | grepl("Yucatán", ROSIE$Location) | 
      grepl("St. Kitts and Nevis", ROSIE$Location)), 
      "RMU.2023"] <- "Northwest Atlantic"
ROSIE[(ROSIE$Species == "Eretmochelys_imbricata") & 
      (grepl("Queensland", ROSIE$Location)), 
      "RMU.2023"] <- "Southwest Pacific"
ROSIE[(ROSIE$Species == "Eretmochelys_imbricata") & 
      (grepl("Brazil", ROSIE$Location)), 
      "RMU.2023"] <- "Southwest Atlantic"
      
      
ROSIE[(ROSIE$Species == "Caretta_caretta") & 
      (grepl("Georgia", ROSIE$Location) | grepl("South Carolina", ROSIE$Location) | 
      grepl("North Carolina", ROSIE$Location) | grepl("Florida", ROSIE$Location) | 
      grepl("Texas", ROSIE$Location)), 
      "RMU.2023"] <- "Northwest Atlantic"
ROSIE[(ROSIE$Species == "Caretta_caretta") & 
      (grepl("Cyprus", ROSIE$Location) | grepl("Greece", ROSIE$Location) | 
      grepl("Turkey", ROSIE$Location)), 
      "RMU.2023"] <- "Mediterranean"
ROSIE[(ROSIE$Species == "Caretta_caretta") & 
      (grepl("Queensland", ROSIE$Location)), 
      "RMU.2023"] <- "South Pacific"
ROSIE[(ROSIE$Species == "Caretta_caretta") & 
      (grepl("Western Australia", ROSIE$Location)), 
      "RMU.2023"] <- "Southeast Indian"
ROSIE[(ROSIE$Species == "Caretta_caretta") & 
      (grepl("South Africa", ROSIE$Location)), 
      "RMU.2023"] <- "Southwest Indian"
ROSIE[(ROSIE$Species == "Caretta_caretta") & 
      (grepl("Japan", ROSIE$Location)), 
      "RMU.2023"] <- "North Pacific"
ROSIE[(ROSIE$Species == "Caretta_caretta") & 
      (grepl("Brazil", ROSIE$Location)), 
      "RMU.2023"] <- "Southwest Atlantic"
      
ROSIE[(ROSIE$Species == "Chelonia_mydas") & 
      (grepl("Queensland", ROSIE$Location)), 
      "RMU.2023"] <- "Southwest Pacific"
ROSIE[(ROSIE$Species == "Chelonia_mydas") & 
      (grepl("Tortuguero", ROSIE$Location) | grepl("British West Indies", ROSIE$Location)), 
      "RMU.2023"] <- "North Atlantic"
ROSIE[(ROSIE$Species == "Chelonia_mydas") & 
      (grepl("Suriname", ROSIE$Location) | grepl("Ascension Island", ROSIE$Location) | 
      grepl("Guinea-Bissau", ROSIE$Location)), 
      "RMU.2023"] <- "South Atlantic"
ROSIE[(ROSIE$Species == "Chelonia_mydas") & 
      (grepl("Malaysia", ROSIE$Location) | grepl("Phillipines", ROSIE$Location) | 
      grepl("China", ROSIE$Location) | grepl("Taiwan", ROSIE$Location) | 
      grepl("Western Australia", ROSIE$Location)), 
      "RMU.2023"] <- "East Indian and Southeast Asia"
ROSIE[(ROSIE$Species == "Chelonia_mydas") & 
      (grepl("Japan", ROSIE$Location)), 
      "RMU.2023"] <- "West Central Pacific"
ROSIE[(ROSIE$Species == "Chelonia_mydas") & 
      (grepl("Cyprus", ROSIE$Location) | grepl("Turkey", ROSIE$Location)), 
      "RMU.2023"] <- "Mediterranean"
ROSIE[(ROSIE$Species == "Chelonia_mydas") & 
      (grepl("Oman", ROSIE$Location)), 
      "RMU.2023"] <- "Northwest Indian"
ROSIE[(ROSIE$Species == "Chelonia_mydas") & 
      (grepl("Hawaii", ROSIE$Location)), 
      "RMU.2023"] <- "North Central Pacific"
      
ROSIE[(ROSIE$Species == "Natator_depressus"), 
      "RMU.2023"] <- "nd"
      
ROSIE[(ROSIE$Species == "Lepidochelys_kempii"), 
      "RMU.2023"] <- "Northwest Atlantic"
      
      
totalIncubation_Lo <- subset(ROSIE, 
         (Species == "Lepidochelys_olivacea") & (!is.na(Total_Sexed) & Total_Sexed!=0) & 
         (Incubation_Setup == "Constant"), 
         select=c("Males", "Females", "Mean_Temp", "Latitude", "Longitude", "Location", "RMU.2023"))
         
library(mapdata)
map()
scale <- 50
title(bquote("Species name: "*italic(.("Lepidochelys olivacea"))))
for (l in unique(totalIncubation_Lo$Location)) {
  SR_sub <- subset(totalIncubation_Lo, subset = Location == l)
  points(x=SR_sub$Longitude[1], y=SR_sub$Latitude[1], pch=19, 
  col= 1 + which(l == unique(totalIncubation_Lo$Location)), 
  cex=sum(SR_sub$Males + SR_sub$Females, na.rm = TRUE)/scale)
}

tot_Lo <- with(totalIncubation_Lo, tsd(males=Males, females=Females, 
 temperatures=Mean_Temp), parameters.initial = c(P=30.5, S=-0.4))
 plot(tot_Lo, xlim=c(20, 40))
 plot(tot_Lo, xlim=c(20, 40), use.ggplot=FALSE)
 predict(tot_Lo)

## End(Not run)

embryogrowth documentation built on Sept. 11, 2024, 8:16 p.m.