FormatNests: Create a dataset of class Nests to be used with searchR

In embryogrowth: Tools to Analyze the Thermal Reaction Norm of Embryo Growth

Create a dataset of class Nests to be used with searchR

Description

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.

Usage

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.

Details

FormatNests creates a dataset of class "Nests" to be used with searchR

Value

A list with all the nests formated to be used with searchR.

Author(s)

Marc Girondot [e-mail]

Examples

## 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)

embryogrowth documentation built on Aug. 24, 2026, 5:07 p.m.