Package {TrackTrap}

TrackTrap: Calculate and Visualize Degree-Days for Pest Monitoring

Description

Combines pest trap observations with daily temperatures to calculate and visualize cumulative degree-days. Temperature inputs include 'Daymet' https://daymet.ornl.gov, 'Open-Meteo' https://open-meteo.com/, reports from the California Irrigation Management Information System ('CIMIS') https://cimis.water.ca.gov, and user-supplied daily weather data. Degree-days are calculated using the simple-average method with either an upper threshold applied to the daily mean or an explicitly selected calculation without an upper cutoff. The first positive trap count defines the biofix for every pest, with accumulation beginning on the following day. Negative daily degree-day values are set to zero. Users can provide temperature thresholds and optional thermal reference values. Thermal reference markers and their multiples do not independently establish flight or generation identities. Complete daily calculations and weather provenance are retained with the output to support reproducibility.

Author(s)

Maintainer: Santosh Bhandari santoshbhandari4556@gmail.com

Authors:

• Santosh Bhandari santoshbhandari4556@gmail.com

• Lalit Kharel klalitkharel@gmail.com

• Mahesh Ghimire maesghimire@gmail.com

Pipe operator

Description

See magrittr::%>% for details.

Usage

lhs %>% rhs

Arguments

Value

The result of calling rhs(lhs).

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

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.

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

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.

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

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.