phenology (version 10.1)

TableECFOCF: Format a CMR dataset into a file that fitCF can use.

Description

This function formats a CMR dataset to a file that fitCF can use.
If date0 is not null, a 3D TableECFOCF is generated.
3D table (ECF, OCF, period) has two attributes:

• table with 5 elements:
  begin, end are the first and last elements with counts
  final is the last period with information
  min and max are the first and last period where a nest could have been laid based on MaxNests value
  

• characteristics with 5 elements:
  MinimumDaysBetween2Nest, MeanDaysBetween2Nest MaxNests, date0, length_season
  p parameter can be setup to +Inf until begin and after end

Usage

TableECFOCF(
  data = stop("A dataframe with a column 'ID' and a column 'Date'"),
  columnID = "ID",
  columnDate = "Date",
  MinimumDaysBetween2Nest = 7,
  MeanDaysBetween2Nest = 9.8,
  MaxNests = 15,
  date0 = NULL,
  length_season = floor(365/MeanDaysBetween2Nest) + 1
)

Value

Return a matrix with counts for all OCF and ECF combinations.

Arguments

data

CMR file.

columnID

Name of the column in data for unique identifier of females.

columnDate

Name of the column in data for morning date when female has been seen on the beach.

MinimumDaysBetween2Nest

Number of minimum days between two nests.

MeanDaysBetween2Nest

Average number of days between two nests.

MaxNests

Maximum number of nests by a female.

date0

Date for the ordinal day 0.

length_season

The total length of season based on groups of interclutch intervals.

Author

Marc Girondot

Details

TableECFOCF formats a CMR dataset into a file that fitCF can use.

See Also

Other Model of Clutch Frequency: ECFOCF_f(), ECFOCF_full(), fitCF(), fitCF_MHmcmc(), fitCF_MHmcmc_p(), generateCF(), lnLCF(), logLik.ECFOCF(), plot.ECFOCF(), plot.TableECFOCF()

Examples

if (FALSE) {
library(phenology)
# Example
data(MarineTurtles_2002)
ECFOCF_2002 <- TableECFOCF(MarineTurtles_2002)
plot(ECFOCF_2002)
ECFOCF_2002 <- TableECFOCF(MarineTurtles_2002, date0=as.Date("2002-01-01"))
plot(ECFOCF_2002, period=11)
}