embryogrowth (version 9.5)

plot.NestsResult: Plot the embryo growth

Description

Plot the embryo growth from one or several nests.
The embryo.stages is a named vector with relative size as compared to final size at the beginning of the stage. Names are the stages.
For example for SCL in Caretta caretta:
embryo.stages=structure(c(8.4, 9.4, 13.6, 13.8, 18.9, 23.5, 32.2, 35.2, 35.5, 38.5)/39.33),
.Names = c("21", "22", "23", "24", "25", "26", "27", "28", "29", "30", "31"))
indicates that the stages 21 begins at the relative size of 8.4/39.33.
Series can be indicated as the name of the series, its number or succesion of TRUE or FALSE. "all" indicates that all series must be printed.
show.fioritures parameter does not affect show.hatchling.metric option.
Note: Four species have predefined embryo stages. embryo.stages parameter can take the values:

• Caretta caretta.SCL

• Chelonia mydas.SCL

• Emys orbicularis.SCL

• Emys orbicularis.mass

• Podocnemis expansa.SCL

• Lepidochelys olivacea.SCL

• Generic.ProportionDevelopment

Usage

# S3 method for NestsResult
plot(
  x,
  ...,
  parameters = NULL,
  fixed.parameters = NULL,
  resultmcmc = NULL,
  hessian = NULL,
  SE = NULL,
  temperatures = NULL,
  integral = NULL,
  derivate = NULL,
  hatchling.metric = NULL,
  stop.at.hatchling.metric = FALSE,
  M0 = NULL,
  weight = NULL,
  series = "all",
  TSP.borders = NULL,
  embryo.stages = NULL,
  STRN = NULL,
  TSP.begin = 0,
  TSP.end = 0.5,
  replicate.CI = 100,
  metric.end.incubation = "observed",
  col.stages = "blue",
  col.PT = "red",
  col.TSP = "gray",
  col.temperatures = "green",
  col.S = "black",
  lty.temperatures = 1,
  lwd.temperatures = 2,
  ylimT = NULL,
  ylimS = NULL,
  xlim = NULL,
  show.stages = TRUE,
  show.TSP = TRUE,
  show.third = TRUE,
  GTRN.CI = NULL,
  show.metric = TRUE,
  show.fioritures = TRUE,
  show.temperatures = TRUE,
  show.PT = TRUE,
  PT = c(mean = NA, SE = NA),
  show.hatchling.metric = TRUE,
  add = FALSE,
  lab.third = "2nd third of incubation",
  at.lab.third = 10,
  lab.PT = "PT",
  lab.stages = "Stages",
  at.lab.TSP = 8,
  lab.TSP = "TSP",
  mar = c(4, 5, 4, 5) + 0.3,
  xlab = "Days of incubation",
  ylabT = expression("Temperature in " * degree * "C"),
  ylabS = "Embryo metric",
  progress = TRUE,
  parallel = TRUE
)

Value

Nothing

Arguments

x

A result file generated by searchR

...

Parameters for plot()

parameters

A set of parameters if result is not provided.

fixed.parameters

Another set of parameters if result is not provided.

resultmcmc

A mcmc result. Will be used rather than SE if provided.

hessian

An Hessian matrix.

SE

Standard error for each parameter if result is not provided, or replace the one in NestsResult. Use SE=NA to remove SE from NestResult

temperatures

Timeseries of temperatures formatted using formatNests(). Will replace the one in result.

integral

Function used to fit embryo growth: integral.Gompertz, integral.exponential or integral.linear

derivate

Function used to fit embryo growth: dydt.Gompertz, dydt.exponential or dydt.linear. It will replace the one in NestsResult.

hatchling.metric

Mean and SD of size of hatchlings

stop.at.hatchling.metric

TRUE or FALSE. If TRUE, the model stops when proxy of size reached the mean hatchling.metric size.

M0

Measure of hatchling size proxi at laying date

weight

Weights of the different nests to estimate likelihood

series

The name or number of the series to be displayed. Only one series can be displayed at a time.

TSP.borders

The limits of TSP in stages. See embryo.stages parameter.

embryo.stages

The embryo stages. At least TSP.borders stages must be provided to estimate TSP borders. See note.

STRN

An object obtained from STRN()

TSP.begin

Where TSP begin during the stage of beginning? In relative proportion of the stage.

TSP.end

Where TSP begin during the stage of ending? In relative proportion of the stage.

replicate.CI

Number of replicates to estimate CI. If 1, no CI is estimated.

metric.end.incubation

The expected metric at the end of incubation. Used to calibrate TSP size. If NULL, take the maximum Mean of the hatchling.metric parameter. If NA, use the actual final size. Can be a vector and is recycled if necessary.

col.stages

The color of the stages

col.PT

The color of the pivotal temperature

col.TSP

The color of the TSP

col.temperatures

The color of the temperatures

col.S

The color of the size or mass. Can be a vector (useful when series="all" option).

lty.temperatures

Type of line for temperatures

lwd.temperatures

Width of line for temperatures

ylimT

Range of temperatures to be displayed

ylimS

Range of size to be displayed

xlim

Range of incubation days to be displayed

show.stages

TRUE or FALSE, does the embryo stages should be displayed?

show.TSP

TRUE or FALSE, does the TSP boders should be displayed?

show.third

TRUE or FALSE, does the first and second third boders should be displayed?

GTRN.CI

How to estimate CI; can be NULL, "SE", "MCMC", or "Hessian"

show.metric

TRUE or FALSE, does the plot of embryo metric is shown?

show.fioritures

If FALSE, set show.PT, show.temperatures, show.stages, show.TSP, show.third to FALSE, GTRN.CI to NULL

show.temperatures

TRUE or FALSE, does the temperatures should be displayed?

show.PT

TRUE or FALSE, does the pivotal temperature should be displayed?

PT

Value for pivotal temperature, mean and SE

show.hatchling.metric

TRUE or FALSE, does the hatchling size should be displayed

add

If TRUE, all the curves are shown on the same graph

lab.third

Label for 2nd third of incubation

at.lab.third

Position of Label for 2nd third of incubation [default=10]; y-lim is scaled by at.lab.third

lab.PT

Label for Pivotal Temperature

lab.stages

Label for Stages

at.lab.TSP

Position of Label for TSP [default=8]; y-lim is scaled by at.lab.third

lab.TSP

Label for the TSP

mar

Parameter mar used for plot

xlab

Label for axis

ylabT

Label for temperature axis

ylabS

Label for size axis

progress

If FALSE, the progress bar is not shown (useful for use with sweave or knitr)

parallel

Should parallel computing be used ? TRUE or FALSE

NestsResult

A NestsResult file generated by searchR

Author

Marc Girondot

Details

plot.NestsResult Plot the embryo growth

Examples

if (FALSE) {
library(embryogrowth)
data(resultNest_4p_SSM)
plot(resultNest_4p_SSM, xlim=c(0,70), ylimT=c(22, 32), ylimS=c(0,45), series=1,  
	    SE=c(DHA=1.396525, DHH=4.101217, T12H=0.04330405, Rho25=1.00479), 
	    GTRN.CI = "SE", replicate.CI = 100, 
	    embryo.stages="Caretta caretta.SCL")
plot(resultNest_4p_SSM, xlim=c(0,70), ylimT=c(22, 32), ylimS=c(0,45), series=1, 
	    GTRN.CI = "Hessian", replicate.CI = 100, 
	    embryo.stages="Caretta caretta.SCL")
plot(resultNest_4p_SSM, xlim=c(0,70), ylimT=c(22, 32), ylimS=c(0,45), series=1,  
     resultmcmc = resultNest_mcmc_4p_SSM, 
	    GTRN.CI = "MCMC", replicate.CI = 100, 
     embryo.stages="Caretta caretta.SCL")
# to plot all the nest at the same time, use
plot(resultNest_4p_SSM, xlim=c(0,70), ylimT=c(22, 32), ylimS=c(0,45),  
	    series="all", show.fioritures=FALSE, add=TRUE, 
	    embryo.stages="Caretta caretta.SCL")
# to use color different for series
plot(resultNest_4p_SSM, xlim=c(0,70), ylimT=c(22, 32), ylimS=c(0,45), add=TRUE, 
	    series="all", show.fioritures=FALSE, col.S=c(rep("black", 5), rep("red", 6)), 
	    embryo.stages="Caretta caretta.SCL")
	    
# to plot all the temperature profiles

par(mar=c(4, 4, 1, 1))
plot(resultNest_4p_SSM$data[[1]][, 1]/60/24,
     resultNest_4p_SSM$data[[1]][, 2], bty="n", 
     las=1, xlab="Days of incubation", 
     ylab=expression("Temperatures in "*degree*"C"), 
     type="l", xlim=c(0,70),ylim=c(20, 35))
     
     for (i in 2:21) {
          par(new=TRUE)
          plot(resultNest_4p_SSM$data[[i]][, 1]/60/24,
          resultNest_4p_SSM$data[[i]][, 2], bty="n", 
          las=1, xlab="", ylab="", type="l", xlim=c(0,70),
          ylim=c(20, 35), axes = FALSE)
     }
}