plot.NestsResult: Plot the embryo growth

In embryogrowth: Tools to Analyze the Thermal Reaction Norm of Embryo Growth

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 class '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
)

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

Details

plot.NestsResult Plot the embryo growth

Value

Nothing

Author(s)

Marc Girondot [e-mail]

Examples

## Not run: 
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)
     }

## End(Not run)

embryogrowth documentation built on Oct. 24, 2023, 5:07 p.m.