plot.NestsResult: Plot the information about a nest

Description

Plot the information about a nest The embryo.stages is a list with stage numbers and relative size as compared to final size at the beginning of the stage. For example embryo.stages=list(number=21:30, size=c(8.4, 9.4, 13.6, 13.8, 18.9, 23.5, 32.2, 35.2, 35.5, 38.5)/39.33) indicates that the stages 21 begins at the relative size of 8.4/39.33. The default is for the turtle "Caretta caretta". 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. The object return is an invisible list composed of two lists: $summary with the summary statistics for each nest and $traces with the change of length or mass for each nest. show.fioritures does not affect show.test option.

Usage

## S3 method for class 'NestsResult':
plot(x, ..., OutPlot = NULL, parameters = NULL,
  fixed.parameters = NULL, SE = NULL, temperatures = NULL,
  derivate = NULL, test = NULL, stopattest = FALSE, M0 = NULL,
  series = 1, col.stages = "blue", col.PT = "red", col.TSP = "gray",
  col.temperatures = "green", col.S = "black", ylimT = c(25, 35),
  ylimS = NULL, xlim = NULL, TSP.borders = c(21, 26),
  embryo.stages = "Caretta caretta", show.stages = TRUE, show.TSP = TRUE,
  show.third = TRUE, show.CI = TRUE, replicate.CI = 100,
  ref.stage = TRUE, show.fioritures = TRUE, progress = TRUE,
  show.temperatures = TRUE, show.PT = TRUE, PT = c(NA, NA),
  show.test = TRUE, lab.third = "2nd third of incubation",
  at.lab.third = 4, lab.PT = "PT", lab.stages = "Stages", mar = c(4, 5,
  4, 5) + 0.3, xlab = "Days of incubation",
  ylabT = expression("Temperatures in " * degree * "C"),
  ylabS = "Embryo metric", show.plot = TRUE)

Arguments

A result file generated by searchR

...

Parameters for plot()

OutPlot

A previous output of a plot.NestsResult() or info.nests()

parameters

A set of parameters if result is not provided.

fixed.parameters

Another set of parameters if result is not provided.

Standard error for each parameter if result is not provided.

temperatures

Timeseries of temperatures. Will replace the one in result.

derivate

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

test

Mean and SD of size of hatchlings ie test=c(Mean=xx, SD=yy)

stopattest

True or False, does the plot stops when proxi of size reaches the mean test size.

Measure of hatchling size proxi at laying date

series

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

col.stages

The color of the stages

col.temperatures

The color of the temperatures

col.TSP

The color of the TSP

col.PT

The color of the pivotal temperature

col.S

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

ylimT

Range of temperatures to be displayed

ylimS

Range of size to be displayed

xlim

Range of incubation days to be displayed

TSP.borders

The limits of TSP

embryo.stages

The embryo stages. At least TSP.borders stages must be provided if show.TSP is TRUE

ref.stage

If TRUE, the reference size for stage is the observed one in modelling. If FALSE, it is the field observed size.

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

show.CI

True or False, do the confidence intervals should be displayed

replicate.CI

Number of randomizations to estimate CI

show.temperatures

True or False, does the temperatures should be displayed

show.PT

TRUE or FALSE, does the pivotal temperature should be displayed

show.fioritures

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

Value for pivotal temperature

show.test

True or False, does the hatchling size should be displayed

lab.third

Label for 2nd third of incubation

at.lab.third

Position of Label for 2nd third of incubation [default=4]

lab.PT

Label for Pivotal Temperature

lab.stages

Label for Stages

xlab

Label for axis

ylabT

Label for temperature axis

ylabS

Label for size axis

mar

Parameter mar used for plot

show.plot

If FALSE, only the text output is shown

progress

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

Value

A list with informations about statistics for the series of nests analyzed ($summary) and exact times series of length changes for each nest ($traces)

Details

plot.NestsResult Plot the information about a nest

Examples

Run this code

library(embryogrowth)
data(resultNest_4p)
plot(resultNest_4p, 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))
# to plot all the nest at the same time, use
plot(resultNest_4p, xlim=c(0,70), ylimT=c(22, 32), ylimS=c(0,45),
	series="all", show.fioritures=FALSE)
# to use color different for series
plot(resultNest_4p, xlim=c(0,70), ylimT=c(22, 32), ylimS=c(0,45),
	series="all", show.fioritures=FALSE, col.S=c(rep("black", 5), rep("red", 6)))

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