flight_curve Compute the annual flight curve from butterfly count data collated across sites.

flight_curve Compute the annual flight curve from butterfly count data collated across sites.

Usage

flight_curve(
  ts_season_count,
  NbrSample = 100,
  MinVisit = 3,
  MinOccur = 2,
  MinNbrSite = 1,
  MaxTrial = 3,
  GamFamily = "poisson",
  CompltSeason = TRUE,
  SelectYear = NULL,
  SpeedGam = TRUE,
  OptiGam = TRUE,
  KeepModel = TRUE,
  KeepModelData = TRUE,
  TimeUnit = "d",
  MultiVisit = "mean",
  weekday = 3,
  mod_form = NULL,
  tp_col = NULL,
  parallel = FALSE,
  n_cores = NULL,
  verbose = TRUE,
  ...
)

Arguments

ts_season_count

data.table Time-series of counts and season information returned by ts_monit_count_site

NbrSample

integer The maximum number of sites to use for computing the flight curve, default=100.

MinVisit

integer The minimum number of visits required for a site to be included, default=3.

MinOccur

integer The minimum number of positive records (e.g. >= 1) required in one year for a site to be included, default=2.

MinNbrSite

integer The minimum number of sites required to compute a flight curve, default=1.

MaxTrial

integer The maximum number of trials for model convergence, default=3.

GamFamily

string The distribution of the error term used in the GAM, default='poisson', but can be the negative-binomial 'nb' or 'quasipoisson'.

CompltSeason

Logical to restrict computation of flight curve for years where the complete season has been sampled, default=TRUE.

SelectYear

integer Select a specific year to compute the flight curve, default=NULL.

SpeedGam

Logical Set if the bam method should be used, default instead of the default gam method.

OptiGam

Logical Set the use of the bam method when data are larger than 200 and gam for smaller datasets

KeepModel

Logical to keep model output in a list object named flight_curve_model.

KeepModelData

Logical to keep the data used for the GAM.

TimeUnit

character The time-step for which the spline should be computed, 'd' day or 'w' week.

MultiVisit

string Function to apply for summarising multiple counts within a time unit, 'max' or 'mean' (default).

weekday

Integer for selected day of the week for weekly summary, default is 3 (Wednesday). [1-7] where 1 = Monday.

mod_form

string with formula to be passed to the gam model, default null.

tp_col

string or vector of string with additional variable used in the gam model, default null.

parallel

logical Fit the flight curves of the years in parallel, default FALSE. Useful with many years and large data; with small data, starting the workers can take longer than the fit. The workers load the installed rbms package. The random streams of the workers (sampling of NbrSample sites) are seeded from the session, so the result is reproducible with set.seed(), but can differ from the sequential fit when sites are sampled.

n_cores

integer Number of cores used with parallel = TRUE, default NULL (all available cores minus one, at most one per year).

verbose

a logical indicating if some “progress report” should be given.

...

Additional parameters passed to gam or bam function from the gam package.

Value

A list with three objects, i) **pheno**: a vector with annual flight curves f_pheno with expected relative abundance, normalize to sum to one over a full season, ii) **model**: a list of the resulting gam models f_model fitted on the count data for each year and iii) **data**: a data.table with the data used to fit the GAM model.

See also

fit_gam

gam

bam

Author

Reto Schmucki - retoshm@ceh.ac.uk