Package 'TrackTrap'

Calculate a simple-average degree-day index for trap observations

Description

Calculate a simple-average degree-day index for trap observations

Usage

calc_pest_phenology(
  trap_data,
  pest = NULL,
  lat = NULL,
  lon = NULL,
  weather_source = "open_meteo",
  cimis_csv_path = NULL,
  custom_lower = NULL,
  custom_upper = NULL,
  custom_thermal_requirement = NULL,
  custom_flight_interval = NULL,
  custom_pest_label = NULL,
  upper_cutoff = c("explicit", "none", "horizontal"),
  weather_data = NULL,
  weather_provenance = NULL,
  timezone = "auto",
  open_meteo_model = "era5_land",
  database = NULL
)

Arguments

trap_data	Data frame with date and trap_counts, one row per date.
pest	Optional database code.
lat, lon	Weather coordinates.
weather_source	open_meteo, daymet, cimis_csv, or supplied.
cimis_csv_path	Path to CIMIS Fahrenheit daily report.
custom_lower, custom_upper	Optional Fahrenheit threshold overrides.
custom_thermal_requirement	Optional user-defined thermal marker (Fahrenheit DD).
custom_flight_interval	Deprecated alias for custom_thermal_requirement.
custom_pest_label	Optional plot label.
upper_cutoff	"explicit", "none", or "horizontal". Missing database upper thresholds require an explicit "none" choice or a supplied upper.
weather_data	Optional daily Date, tmin, tmax data in Fahrenheit.
weather_provenance	Description of provided temperatures/station/time convention.
timezone, open_meteo_model	Open-Meteo settings.
database	Optional database; defaults to TrackTrap::pest_thresholds.

Details

Biofix is always the first positive trap count; its DD is excluded. Daily DD is max(min(mean temperature, upper) - lower, 0), or no upper cap.

Value

Original data frame.

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Fetch daily historical Open-Meteo temperatures in Fahrenheit

Description

Fetch daily historical Open-Meteo temperatures in Fahrenheit

Usage

fetch_open_meteo(
  lat,
  lon,
  start_date,
  end_date = as.character(Sys.Date()),
  timezone = "auto",
  model = "era5_land"
)

Arguments

lat, lon	Coordinates.
start_date, end_date	Requested dates, inclusive.
timezone	IANA timezone or "auto"
model	Explicit archive model identifier.

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Pest temperature thresholds and thermal reference values

Description

Reference parameters and source information for 90 pest records. Missing parameters are stored as NA. Inclusion does not imply that a complete or independently validated phenology model is available.

Usage

pest_thresholds

Format

A data frame with 90 rows and 10 variables:

pest_code

Unique pest identifier.

pest_name

Common name.

scientific_name

Scientific name.

lower_thresh

Lower temperature threshold in degrees Fahrenheit.

upper_thresh

Upper temperature threshold in degrees Fahrenheit, where available.

thermal_requirement_dd

Thermal reference value in Fahrenheit degree-days for the stated endpoint; not necessarily a flight interval.

lower_source

Reference supporting the lower threshold.

upper_source

Reference supporting the upper threshold.

thermal_requirement_source

Reference for the thermal value.

thermal_requirement_endpoint

Developmental or phenological endpoint associated with the thermal value.

Details

Parameter sources and model compatibility require assessment before application. Seasonal event thresholds and developmental requirements are not interchangeable.

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Plot trap catches against the calculated DD index

Description

Plot trap catches against the calculated DD index

Usage

plot_trap_phenology(
  pheno_data,
  pest = NULL,
  year = NULL,
  lat = NULL,
  lon = NULL,
  custom_thermal_requirement = NULL,
  repeat_markers = FALSE,
  custom_flight_interval = NULL,
  custom_pest_label = NULL
)

Arguments

pheno_data	Output of calc_pest_phenology().
pest	Optional label only; never used to retrieve marker intervals.
year, lat, lon	Optional title settings.
custom_thermal_requirement	Optional user-defined marker in Fahrenheit DD.
repeat_markers	If TRUE, show user-defined multiples; default FALSE.
custom_flight_interval	Deprecated alias for custom_thermal_requirement.
custom_pest_label	Optional title label.

Details

When a thermal marker is selected, the subtitle displays its value. A matching database reference supplies the developmental endpoint; otherwise the endpoint is reported as unspecified. The caption explains the reference and distinguishes first-capture multiples from observed generations. Database requirements are not automatically selected as markers.

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