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

In phenology: Tools to Manage a Parametric Function that Describes Phenology and More

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
)

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.

Details

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

Value

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

Author(s)

Marc Girondot

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

## Not run: 
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)

## End(Not run)

phenology documentation built on Sept. 11, 2024, 6:07 p.m.