embryogrowth (version 10.2)

FormatNests: 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"
)

Value

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

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.

Author

Marc Girondot

Details

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

Examples

if (FALSE) {
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)

}