embryogrowth (version 9.5)

info.nests: Calculte statistics about nests

Description

This function calculates many statistics about 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 as compared to the final size.
Series can be indicated as the name of the series, their numbers or series or succession 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.
If one parameter is named "pipping_emergence" it is used as the number of days between pipping and emergence to calculate the 1/3 and 2/3 of incubation.
The summary object is a data.frame composed of these elements with the suffix .mean, .se or .quantile_x with x from the parameter probs.

• Temperature.max Maximum temperature recorded during incubation

• TimeWeighted.temperature Average temperature during all incubation

• GrowthWeighted.temperature Average temperature weighted by the actual growth during all incubation

• TimeWeighted.GrowthRateWeighted.temperature Average temperature weighted by the growth rate during all incubation

• TSP.TimeWeighted.temperature Average temperature during the TSP

• TSP.GrowthWeighted.temperature Average temperature weighted by the actual growth during the TSP

• TSP.TimeWeighted.GrowthRateWeighted.temperature Average temperature weighted by the growth rate during the TSP

• TSP.TimeWeighted.STRNWeighted.temperature Average temperature weighted by the thermal reaction norm of sexualization during the TSP

• TSP.GrowthWeighted.STRNWeighted.temperature Average temperature weighted by actual growth and the thermal reaction norm of sexualization during the TSP

• TSP.TimeWeighted.GrowthRateWeighted.STRNWeighted.temperature Average temperature weighted by growth rate and the thermal reaction norm of sexualization during the TSP

• TSP.length TSP duration

• TSP.begin Beginning of the TSP

• TSP.end End of the TSP

• TSP.PM.GrowthWeighted Average of male probability for each temperature weighted by actual growth during the TSP

• TSP.PM.TimeWeighted.GrowthRateWeighted Average of male probability for each temperature weighted by growth rate during the TSP

• TSP.PM.TimeWeighted Average of male probability for each temperature during the TSP

• Incubation.length Incubation length duration

• MiddleThird.length Middle third incubation duration

• MiddleThird.begin Beginning of the middle third incubation duration

• MiddleThird.end End of the middle third incubation duration

• MiddleThird.TimeWeighted.temperature Average temperature during the middle third incubation

• MiddleThird.GrowthWeighted.temperature Average temperature weighted by the actual growth during the middle third incubation

• MiddleThird.TimeWeighted.GrowthRateWeighted.temperature Average temperature weighted by the growth rate during the middle third incubation

• TSP.TimeWeighted.sexratio Sex ratio based on average temperature during the TSP

• TSP.GrowthWeighted.sexratio Sex ratio based on average temperature weighted by the actual growth during the TSP

• TSP.TimeWeighted.GrowthRateWeighted.sexratio Sex ratio based on average temperature weighted by the growth rate during the TSP

• TSP.TimeWeighted.STRNWeighted.sexratio Sex ratio based on average temperature weighted by the thermal reaction norm of sexualization during the TSP

• TSP.GrowthWeighted.STRNWeighted.sexratio Sex ratio based on average temperature weighted by the actual growth and thermal reaction norm of sexualization during the TSP

• TSP.TimeWeighted.GrowthRateWeighted.STRNWeighted.sexratio Sex ratio based on average temperature weighted by the growth rate and the thermal reaction norm of sexualization during the TSP

• MiddleThird.TimeWeighted.sexratio Sex ratio based on average temperature during the middle third incubation

• MiddleThird.GrowthWeighted.sexratio Sex ratio based on average temperature weighted by actual growth during the middle third incubation

• MiddleThird.TimeWeighted.GrowthRateWeighted.sexratio Sex ratio based on average temperature weighted by growth rate during the middle third incubation

• TimeWeighted.sexratio Sex ratio based on average temperature during all incubation

• GrowthWeighted.sexratio Sex ratio based on average temperature weighted by actual growth during all incubation

• TimeWeighted.GrowthRateWeighted.sexratio Sex ratio based on average temperature weighted by growth rate during all incubation

If out is equal to summary, the return is a list with:

• summary is a data.frame with statistics for each nest.

• dynamic.metric object is a list composed of data.frames with the dynamics of growth for each nest. It showed only temperatures from original dataset.

• summary.dynamic.metric is a data.frame with the following columns with the suffix .mean, .se or .quantile_x with x from the parameter probs.

If out is equal to details, the return is a list with:

• The statistics for each replicate for each nest (one per element of the list)

If out is equal to metric, the return is a list with:

• dynamic.metric object is a list composed of data.frames with the dynamics of growth for each nest

• indices.dynamic.metric is a data.frame with the following columns.

The object summary.dynamic.metric or indices.dynamic.metric is a data.frame with the following columns:

• series Name of the series

• metric.begin.tsp Metric at the beginning of TSP

• metric.end.tsp Metric at the end of TSP

• hatchling.metric.mean Average expected size of hatchlings

• hatchling.metric.sd standard deviation of expected size of hatchlings

• time.begin.tsp Time at the beginning of TSP

• time.end.tsp Time at the end of TSP

• time.begin.middlethird Time at the beginning of the middle third incubation

• time.end.middlethird Time at the end of the middle third incubation

• stop.at.hatchling.metric Take the value of NA if stop.at.hatchling.metric was FALSE. TRUE if at least one incubation series was longer than hatchling size and FALSE at contrary

• stop.at.hatchling.metric Take the value of NA if stop.at.hatchling.metric was FALSE. TRUE if at least one incubation series was longer than hatchling size and FALSE at contrary

• stop.at.hatchling.metric Take the value of NA if stop.at.hatchling.metric was FALSE. TRUE if at least one incubation series was longer than hatchling size and FALSE at contrary

• stop.at.hatchling.metric Take the value of NA if stop.at.hatchling.metric was FALSE. TRUE if at least one incubation series was longer than hatchling size and FALSE at contrary

• stop.at.hatchling.metric Take the value of NA if stop.at.hatchling.metric was FALSE. TRUE if at least one incubation series was longer than hatchling size and FALSE at contrary

• stop.at.hatchling.metric Take the value of NA if stop.at.hatchling.metric 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 hatchling.metric values.
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

But remember that mass is not the best proxy to describe the growth of an embryo because it can decrease if the substrate becomes dry.
The progress bar is based on both replicates and timeseries progress. It necessitates the pbapply package.
If replicate.CI is null or 0, only maximum likelihood is used and no confidence interval is calculated.
If replicate.CI is 1, one random value for the parameters is used but no confidence interval is calculated.
In other cases, replicate.CI random samples are used to estimate confidence interval.

Usage

info.nests(
  x = NULL,
  parameters = NULL,
  NestsResult = NULL,
  resultmcmc = NULL,
  hessian = NULL,
  GTRN.CI = NULL,
  fixed.parameters = NULL,
  SE = NULL,
  temperatures = NULL,
  integral = NULL,
  derivate = NULL,
  hatchling.metric = NULL,
  stop.at.hatchling.metric = FALSE,
  M0 = NULL,
  series = "all",
  TSP.borders = NULL,
  embryo.stages = NULL,
  TSP.begin = 0,
  TSP.end = 0.5,
  replicate.CI = 0,
  weight = NULL,
  out = "likelihood",
  fill = NULL,
  probs = c(0.025, 0.5, 0.975),
  SexualisationTRN = NULL,
  SexualisationTRN.mcmc = NULL,
  SexualisationTRN.CI = NULL,
  metric.end.incubation = "observed",
  metabolic.heating = 0,
  temperature.heterogeneity = 0,
  progressbar = FALSE,
  warnings = TRUE,
  parallel = TRUE,
  tsd = NULL,
  tsd.CI = NULL,
  tsd.mcmc = NULL,
  zero = 1e-09,
  verbose = FALSE
)

Value

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

Arguments

x

A set of parameters to model the embryo growth thermal reaction norm or a NestsResult object.

parameters

A set of parameters to model the embryo growth thermal reaction norm. It will replace the parameters included in NestsResult (same as x).

NestsResult

A NestsResult object generated by searchR to model the embryo growth thermal reaction

resultmcmc

A mcmc result for embryo growth thermal reaction norm

hessian

An hessian matrix for embryo growth thermal reaction norm. It will replace the hessian matrix included in NestResult object.

GTRN.CI

How to estimate CI for embryo growth thermal reaction norm; can be NULL, "SE", "MCMC", or "Hessian".

fixed.parameters

A set of fixed parameters to model the embryo growth thermal reaction norm. It will replace the fixed parameters included in NestsResult.

SE

Standard error for each parameter. It will replace the SE in NestsResult. Use SE=NA to remove SE from NestResult

temperatures

Timeseries of temperatures formatted using formatNests(). It will replace the one in NestsResult.

integral

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

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. It will replace the one in NestsResult.

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. It will replace the one in NestsResult.

series

The name or number of the series to be estimated.

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.

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. See description

weight

Weights of the different nests to estimate likelihood. It will replace the ones in NestsResult.

out

Can take the values of "likelihood", "summary", "details", "metric" or "dynamic".

fill

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

probs

Probabilities for metric quantiles.

SexualisationTRN

A set of parameters used to model sexualisation thermal reaction norm during TSP or a result of STRN()

SexualisationTRN.mcmc

A mcmc object obtained from STRN_MHmcmc() to generate variability for sexualisation thermal reaction norm during TSP

SexualisationTRN.CI

How to estimate CI of sexualisation thermal reaction norm. Can be NULL, "SE", "MCMC", or "Hessian".

metric.end.incubation

The metric at the end of incubation used to calibrate TSP size. Can be "hatchling.metric", or "observed".

metabolic.heating

Degrees Celsius to be added at the end of incubation due to metabolic heating.

temperature.heterogeneity

SD of heterogeneity of temperatures. Can be 2 values, sd_low and sd_high and then HelpersMG::r2norm() is used.

progressbar

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

warnings

If FALSE, does not show warnings

parallel

If TRUE use parallel version for nests estimation

tsd

A object from tsd() that describe the thermal react norm of sex ratio at constant temperatures

tsd.CI

How to estimate CI for sex ratio thermal reaction norm; Can be NULL, "SE", "MCMC", or "Hessian".

tsd.mcmc

A object from tsd_MHmcmc() .

zero

Value to replace 0 or 1.

verbose

If TRUE, show more information.

Author

Marc Girondot

Details

Calculate statistics about nests

References

9039embryogrowth
10871embryogrowth
8566embryogrowth
10620embryogrowth

Examples

if (FALSE) {
library(embryogrowth)
data(resultNest_4p_SSM)
# Some basic calculations to show the advantage of parallel computing
system.time(summary.nests <- info.nests(x=resultNest_4p_SSM, out="summary", 
  embryo.stages="Caretta caretta.SCL", replicate.CI=0, parallel=FALSE))
system.time(summary.nests <- info.nests(x=resultNest_4p_SSM, out="summary", 
  embryo.stages="Caretta caretta.SCL", replicate.CI=0, parallel=TRUE))
system.time(summary.nests <- info.nests(x=resultNest_4p_SSM, out="summary", 
  embryo.stages="Caretta caretta.SCL", replicate.CI=0, parallel=TRUE, progressbar=TRUE))
system.time(summary.nests <- info.nests(x=resultNest_4p_SSM, out="likelihood", 
  embryo.stages="Caretta caretta.SCL", replicate.CI=0, parallel=TRUE, progressbar=FALSE))
  
# By default parallel computing is TRUE but progressbar is FALSE
# When out is "likelihood", it returns only the likelihood
# otherwise, it returns a list with 3 objects "summary", 
#        "dynamic.metric", and "summary.dynamic.metric".

summary.nests <- info.nests(resultNest_4p_SSM, out="summary", 
  embryo.stages="Caretta caretta.SCL", 
  replicate.CI=100, 
  resultmcmc=resultNest_mcmc_4p_SSM, 
  GTRN.CI="MCMC", 
  progressbar=TRUE)
  
summary.nests <- info.nests(resultNest_4p_SSM, 
  embryo.stages="Caretta caretta.SCL", 
  out="summary", replicate.CI=100, 
  GTRN.CI="Hessian", 
  progressbar=TRUE)
  
summary.nests <- info.nests(resultNest_4p_SSM, 
  series = 1, 
  embryo.stages="Caretta caretta.SCL", 
  out="summary", replicate.CI=100, 
  GTRN.CI="SE", 
  progressbar=TRUE)
  
# Example of use of embryo.stages and TSP.borders:
  summary.nests <- info.nests(resultNest_4p_SSM, out="summary", 
                            embryo.stages=c("10"=0.33, "11"=0.33, "12"=0.66, "13"=0.66), 
                            TSP.borders = c(10, 12), 
                            replicate.CI=100,
                            progressbar=TRUE)
                            
#########################################
# Sex ratio using Massey et al. method PM
#########################################

# Massey, M.D., Holt, S.M., Brooks, R.J., Rollinson, N., 2019. Measurement 
# and modelling of primary sex ratios for species with temperature-dependent 
# sex determination. J Exp Biol 222, 1-9.
  
CC_Mediterranean <- subset(DatabaseTSD, RMU=="Mediterranean" & 
Species=="Caretta caretta" & (!is.na(Sexed) & Sexed!=0))
tsdL <- with (CC_Mediterranean, tsd(males=Males, females=Females, 
                                    temperatures=Incubation.temperature, 
                                    equation="logistic", replicate.CI=NULL))
                                    
PM <- info.nests(x=resultNest_4p_SSM, 
  GTRN.CI="Hessian", tsd.CI="Hessian", 
  embryo.stages="Caretta caretta.SCL", replicate.CI=100, 
  out="summary", progressbar=TRUE, tsd=tsdL)
  

plot_errbar(x=PM$summary$TimeWeighted.temperature.mean, 
            y=PM$summary$TSP.PM.GrowthWeighted.mean, 
            y.minus=PM$summary$TSP.PM.GrowthWeighted.quantile_0.025, 
            y.plus=PM$summary$TSP.PM.GrowthWeighted.quantile_0.975, 
            xlab="CTE SCL growth", 
            ylab="PM Massey et al. 2016", xlim=c(26, 32), ylim=c(0, 1), las=1)

# Relationship between growth and growth rate

infoall.df <- info.nests(x=resultNest_4p_SSM, out="summary", 
  embryo.stages="Caretta caretta.SCL", 
  replicate.CI=100, 
  resultmcmc=resultNest_mcmc_4p_SSM, 
  GTRN.CI="MCMC", 
  progressbar=TRUE)
  
  layout(1)
plot(x=infoall.df$dynamic.metric[[1]][, "Time"], 
     y=infoall.df$dynamic.metric[[1]][, "Metric_50%"], 
     type="l", las=1, bty="n", 
     xlab="Time in minute", ylab="Growth", ylim=c(0, 39), xlim=c(0, 100000))
lines(x=infoall.df$dynamic.metric[[1]][, "Time"], 
     y=infoall.df$dynamic.metric[[1]][, "Metric_2.5%"], lty=2)
lines(x=infoall.df$dynamic.metric[[1]][, "Time"], 
     y=infoall.df$dynamic.metric[[1]][, "Metric_97.5%"], lty=2)
}