# Create a dataset of class Nests to be used with searchR Will create a dataset of class Nests to be used with searchR FormatNests(nest, previous=x) with x being a previously formated data. The raw data must be organized being: First column is the time in minutes since the beginning of incubation Each column next is the trace of temperatures, one column for each nest. For example, for two nests: Time Nest1 Nest2 0 29.8 27.6 90 30.2 28.8 120 30.4 30.7 180 31.2 32.6 ... 65800 30.8 32.6 65890 30.2 65950 30.4 The Nest1 ends incubation at 65800 minutes whereas Nest2 ends incubation at 65950 (last row with temperature for each). The parameter Weight is a vector: weight=c(Nest1=1, Nest2=1.2). The parameter LayingTime is also a vector of POSIXct time or POSIXlt time. It can be used to format database already formated with old format; in this case, just use data=xxx with xxx being the old format database. The UnitTime should be "seconds", "minutes", "hours", or "days" to be understood by plot function. ```r FormatNests( data = stop("A dataset must be provided !"), Time.Format = NULL, Time.Zone = NULL, previous = NULL, LayingTime = NULL, UnitTime = "minutes", Longitude = NULL, Latitude = NULL, Informations = NULL, Males = NULL, Females = NULL, usemiddletime = FALSE, simplify = TRUE, weight = NULL, hatchling.metric.mean = NULL, hatchling.metric.sd = NULL, col.Time = "Time" ) ``` ## Arguments - `data`: Data to be newly formated. - `Time.Format`: Format of time. See description. If NULL, no time conversion is done. - `Time.Zone`: The format of time zone as obtained by OlsonNames(). See description. - `previous`: Data already formated. - `LayingTime`: Named POSIXct or POSIXlt time for each nest in data. - `UnitTime`: The units for time as a named list or vector - `Longitude`: The longitude of the nests as a named list or vector - `Latitude`: The latitude of the nests as a named list or vector - `Informations`: Some textual information about the nests as a named list or vector - `Males`: Number of sexed eggs being males - `Females`: Number of sexed eggs being females - `usemiddletime`: If TRUE, suppose that recorded temperatures are those at middle segment. - `simplify`: If TRUE, simply the time series by removing identical time series of temperatures. - `weight`: Named vector with weight used to estimate likelihood. - `hatchling.metric.mean`: The average size of hatchlings - `hatchling.metric.sd`: The standard deviation of size of hatchlings - `col.Time`: Name of the column with time. ## Returns A list with all the nests formated to be used with searchR. ## Details FormatNests creates a dataset of class "Nests" to be used with searchR ## Examples ```r ## Not run: library(embryogrowth) data(nest) formated <- FormatNests(data=nest, previous=NULL, col.Time="Time") # If I try to add the same nest, I have an error formated <- FormatNests(data=nest, previous=formated, col.Time="Time") # I duplicate the database and change the names nest_duplicate <- nest colnames(nest_duplicate) <- paste0(colnames(nest_duplicate), "_essai") formated <- FormatNests(data=nest_duplicate, previous=formated, col.Time="Time_essai") # It is possible to add information about these nests formated <- FormatNests(data=nest, previous=NULL, col.Time="Time") formated <- UpdateNests(data=formated, Males=c(DY.1=10), Females=c(DY.1=2)) #################### Laying.Time <- matrix(c("DY.1", "15/05/2010", "DY.17", "24/05/2010", "DY.16", "24/05/2010", "DY.18", "25/05/2010", "DY.20", "25/05/2010", "DY.21", "26/05/2010", "DY.22", "26/05/2010", "DY.23", "26/05/2010", "DY.24", "27/05/2010", "DY.25", "27/05/2010", "DY.28", "28/05/2010", "DY.26", "28/05/2010", "DY.27", "28/05/2010", "DY.146", "20/06/2010", "DY.147", "20/06/2010", "DY.172", "24/06/2010", "DY.175", "24/06/2010", "DY.170", "24/06/2010", "DY.260", "06/07/2010", "DY.282", "12/07/2010", "DY.310", "18/07/2010", "DY.309", "18/07/2010", "DY.328", "25/07/2010", "DY.331", "26/07/2010"), byrow=TRUE, ncol=2) tz <- OlsonNames()[grepl("Asia/Istanbul", OlsonNames())] Laying.Time_f <- setNames(as.POSIXlt.character(Laying.Time[, 2], format = "%d/%m/%Y", tz=tz), Laying.Time[, 1]) formated <- FormatNests(data=nest, previous=NULL, col.Time="Time", LayingTime=Laying.Time_f) #################### # Now when the data are with absolute dates that are already formatted nest_ec <- data.frame(Time=as.POSIXlt("24/05/2010", format="%d/%m/%Y")+ nest[, 1]*60, DY.1.x=nest[, 2]) formated <- FormatNests(data=nest_ec, previous=NULL, col.Time="Time") #################### # Now when the data are with absolute date that are in text format for example after # reading a csv format nest_ec <- data.frame(Time=format(as.POSIXlt("24/05/2010", format="%d/%m/%Y")+ nest[, 1]*60, format = "%d/%m/%Y %H:%M:%S"), DY.1.x=nest[, 2]) formated <- FormatNests(data=nest_ec, previous=NULL, col.Time="Time", Time.Format="%d/%m/%Y %H:%M:%S", Time.Zone=OlsonNames()[grepl("Asia/Istanbul", OlsonNames())], hatchling.metric.mean=39.33, hatchling.metric.sd=1.92) ## End(Not run) ``` ## Author(s) Marc Girondot marc.girondot@gmail.com

FormatNests function