embryogrowth (version 5.1)

info.nests: Calculte statistics about nests

Description

Calculate statistics about nests 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 series can be indicated as the name of the series, its number or TRUE or FALSE. "all" indicates that all series must be printed.

Usage

info.nests(x, parameters = NULL, fixed.parameters = NULL, SE = NULL,
  temperatures = NULL, derivate = NULL, test = NULL, stopattest = FALSE,
  M0 = NULL, series = "all", TSP.borders = c(21, 26), progress = TRUE,
  embryo.stages = "Caretta caretta", replicate.CI = 100, ref.stage = TRUE)

Arguments

x

A result file generated by searchR

parameters

A set of parameters if result is not provided.

fixed.parameters

Another set of parameters if result is not provided.

SE

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

stopattest

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

M0

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.

TSP.borders

The limits of TSP

progress

If FALSE, the progress bar is not shown (useful for use with Sweave)

embryo.stages

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

replicate.CI

Number of randomizations to estimate CI

ref.stage

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

Value

• A list with informations about thermosensitive period length for the series of nests analyzed

Details

Calculate statistics about nests

Examples

library(embryogrowth)
data(resultNest_4p)
info.nests(resultNest_4p, series=1,
	SE=c(DHA=1.396525, DHH=4.101217, T12H=0.04330405, Rho25=1.00479))
# to get info for all nests at the same time, use
infoall <- info.nests(resultNest_4p, series="all")
# it is easier to use after dataframe conversion
infoall.df <- as.data.frame(infoall$summary)