embryogrowth (version 6.1.1)

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, their numbers or series of TRUE or FALSE. "all" indicates that all series must be analyzed. The likelihood object is just the total likelihood of the data in the model. The summary object is a data.frame composed of these elements:

• TimeWeighted.temperature.meanAverage temperature weigthed by the time at each temperature
• TimeWeighted.temperature.seStandard error for the average temperature weigthed by the time at each temperature
• TSP.TimeWeighted.temperature.meanAverage temperature during the TSP weigthed by the time at each temperature
• TSP.TimeWeighted.temperature.seStandard error for the average temperature during the TSP weigthed by the time at each temperature
• TSP.MassWeighted.temperature.meanAverage temperature during the TSP weigthed by the mass increase at each temperature
• TSP.MassWeighted.temperature.seStandard error for the average temperature during the TSP weigthed by the mass increase at each temperature
• TSP.STRNWeighted.temperature.meanAveraged temperature during the TSP weighted by sexualisation thermal reaction norm
• TSP.STRNWeighted.temperature.seStandard error for temperature during the TSP weighted by sexualisation thermal reaction norm
• TSP.MassWeighted.STRNWeighted.temperature.meanAveraged temperature during the TSP weighted by sexualisation thermal reaction norm and embryo growth
• TSP.MassWeighted.STRNWeighted.temperature.seStandard error for temperature during the TSP weighted by sexualisation thermal reaction norm and embryo growth
• TSP.length.meanAverage length of the TSP
• TSP.length.seStandard error for length of the TSP
• TSP.begin.meanAverage time of the beginning of the TSP
• TSP.begin.seStandard error for the beginning of the TSP
• TSP.end.meanAverage time of the endd of the TSP
• TSP.end.seStandard error for the end of the TSP
• Incubation.length.meanAverage number of days for the incubation length
• Incubation.length.seStandard error for number of days for the incubation length
• Middlethird.begin.meanAverage day at which the middle third incubation begins
• Middlethird.begin.seStandard error for day at which the middle third incubation begins
• Middlethird.end.meanAverage day at which the middle third incubation ends
• Middlethird.end.seStandard error at which the middle third incubation ends
• Middlethird.length.meanAverage days for second third of incubation
• Middlethird.length.seStandard error for second third of incubation
• MiddleThird.TimeWeighted.temperature.meanAverage temperature during the middle third of incubation
• MiddleThird.TimeWeighted.temperature.seStandard error for the temperature during the middle third of incubation
• MiddleThird.MassWeighted.temperature.meanAverage temperature during the middle third of incubation weight by embryo growth
• MiddleThird.MassWeighted.temperature.seStandard error for temperature during the middle third of incubation weight by embryo growth

The metric object is a list composed of data.frames which have the following attributes for each element of the list:

• time.begin.tspAverage time at the beginning of TSP
• time.end.tspAverage time at the end of TSP
• time.begin.middlethirdAverage time at the beginning of the middle third of incubation
• time.begin.middlethirdAverage time at the end of the middle third of incubation
• time.begin.tsp.seStandard error for the time at the beginning of TSP
• time.end.tsp.seStandard error for the time at the end of TSP
• time.begin.middlethird.seStandard error for the time at the beginning of the middle third of incubation
• time.end.middlethird.seStandard error for the time at the end of the middle third of incubation
• stopattestNA if stopattest was false, TRUE if at least one incubation series was longer than hatchling size and FALSE at contrary

If you indicate new set of temperatures, you must probably also indicate new test values. Note: two species have predefined embryo stages. embryo.stages parameter can take the values:

• Caretta caretta.SCL
• Emys orbicularis.SCL
• Emys orbicularis.mass

The progress bar is based on replicates.

Usage

info.nests(NestsResult = NULL, parameters = NULL, fixed.parameters = NULL,
  SE = NULL, temperatures = NULL, derivate = NULL, test = NULL,
  stopattest = FALSE, M0 = NULL, series = "all", TSP.borders = NULL,
  embryo.stages = "Caretta caretta.SCL", replicate.CI = 1, weight = NULL,
  out = "Likelihood", fill = NULL, SexualisationTRN = NULL,
  metric.end.incubation = NULL, progress = TRUE, warnings = TRUE)

Arguments

NestsResult

A NestsResult 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, 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.

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. If TRUE, the model stops when proxy of size reached 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 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.

replicate.CI

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

weight

Weights of the different nests to estimate likelihood

out

Can take the values of likelihood or metric or summary. metric and summary can be combined: c("metric", "summary")

fill

Number of minutes between two records. Create new one if they do not exist. NULL does not change the time of temperature recordings.

SexualisationTRN

A set of parameters used to model thermal reaction norm during TSP

metric.end.incubation

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

progress

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

warnings

if FALSE, does not show warnings

Value

• Return or the total likelihood or a list with $metric and $summary depending on out parameter

Details

Calculate statistics about nests

Examples

library(embryogrowth)
data(resultNest_4p)
summary.nests <- info.nests(resultNest_4p, out="summary", replicate.CI=20,
  SE=c(DHA=17.7357362231266, DHH=55.2002231419364,
  T12H=0.850237694629938, Rho25=8.47868153136681))
  # Result is in summary.nests$summary
infoall <- info.nests(resultNest_4p)
  # Result is a value
infoall.df <- info.nests(resultNest_4p, out="metric", replicate.CI=20,
  SE=c(DHA=17.7357362231266, DHH=55.2002231419364,
  T12H=0.850237694629938, Rho25=8.47868153136681)))
# Result is in summary.nests$metric
infoall.both <- info.nests(resultNest_4p, out=c("metric", summary), replicate.CI=20,
  SE=c(DHA=17.7357362231266, DHH=55.2002231419364,
  T12H=0.850237694629938, Rho25=8.47868153136681)))
# Result is in summary.nests$summary and in summary.nests$metric