Description

This repository contains:

1. The complete Python code for a population dynamics model of Bemisia tabaci under the influence of transgenic plants. The model applies transgenic-induced mortality effects to different insect life stages and incorporates transgenic plants within an otherwise non-transgenic agricultural field.
2. The data used for all field temperatures.
3. An excel file containing all the parameters we used for the matrix population model for all temperatures. It also includes the calculations that lead us to the final matrices.

Authorship

The code was written by Oren Hasson and Adam Lampert,
Institute of Environmental Sciences,
Robert H. Smith Faculty of Agriculture, Food and Environment,
The Hebrew University of Jerusalem, Israel.

Installation

Running the model requires an installation of Python, version 3.12.4 or a compatible version, Jupyter Notebook, and the following Python packages: pandas, numpy, scipy, matplotlib, openpyxl.

The code file, 'Bemisia_Tabbaci_Population_Eradication_Dynamics.ipynb' should be saved at the same directory with the temperatures data file, 'Field_Temps_17-18.xlsx'

Running the Code

1. Open the project file 'Bemisia_Tabbaci_Population_Eradication_Dynamics.ipynb' using Jupyter Notebook editor.
2. Run all cells in the notebook and wait for the execution to complete.

Description of the Data Files

The data files include:

• 'Field_Temps_17-18.xlsx': An Excel workbook containing temperature data spanning 409 days, organized into two worksheets:

  • Sheet 1: temperature_15min:

    • 'Date and Time' – Date and time of each 15-minute temperature measurement.
    • Temperature – Air temperature (°C) recorded at each 15-minute interval.

  • Sheet 2: daily_average_temperature:

    • Date – Calendar date corresponding to each daily mean calculation.
    • Average temperature – Daily mean temperature (°C), calculated as the arithmetic mean of all 15-minute measurements recorded on the corresponding date.

    Daily mean temperatures were derived from the 15-minute temperature records and used as inputs for temperature-dependent parameterization of the population model.

• 'Bemisia_matrix_model_data.xlsx': An Excel workbook containing the calculations and temperature-dependent transition matrices used in the matrix population model.The workbook includes estimates of daily probabilities of survival, development, reproduction, and mortality for five discrete temperature regimes.
  The file includes transition matrices for five temperature conditions (16°C, 20°C, 24°C, 28°C, and 32°C). Each matrix represents daily stage-to-stage transitions among the following life stages:
  e – eggs
  l – larvae
  p – pupae
  a – adults
  Matrix entries represent the probabilities of surviving, developing, reproducing, or remaining within a life stage during a single time-step (one day), with transitions occurring from one life stage (columns) to another (rows). Diagonal elements represent stage-specific daily survival probabilities. Off-diagonal elements represent development to the next life stage.

  All worksheets contain Excel formulas used to derive developmental, survival, mortality, and reproduction parameters from experimentally measured values, except for the final worksheet, “Final Matrices,” which contains the finalized transition matrices used directly in the population model.

  The formulas convert stage-level developmental durations and experimentally measured survival percentages into daily transition parameters required for matrix population modeling.

  • Worksheet: “Egg to 1st Instar”:
    This worksheet contains calculations used to estimate daily transition probabilities from the egg stage to the first larval instar stage under different temperature conditions.

    Raw input data in this worksheet include:

    • median developmental time (days)
    • stage survival (%)

    Calculated outputs include:

    • daily mortality probabilities
    • daily developmental transition probabilities
    • daily survival probabilities

  • Worksheets "1st Instar to 2nd", "2nd Instar to 3rd", "3rd Instar to 4th":

    These worksheets contain calculations used to estimate daily transition probabilities between larval instar stages under different temperature conditions, using the same calculation framework described above.

    Each worksheet corresponds to one larval developmental sub-phase and includes calculations of:

    • daily survival probabilities
    • daily mortality probabilities
    • daily developmental transition probabilities

  • Worksheet: "Larva to Pupae":

    This worksheet integrates the developmental and survival parameters from all larval instar sub-phases into a combined larval-stage representation used in the population model.

    The three lower tables summarize calculations derived from the individual larval instar worksheets:

    • “1st Instar to 2nd”
    • “2nd Instar to 3rd”
    • “3rd Instar to 4th”

    The upper table contains the final combined larval-stage transition parameters used for construction of the temperature-dependent population matrices.

    In the final population matrices, the four larval instar sub-phases are aggregated into a single larval-stage compartment used in the simulation model.

  • Worksheet "Pupae to Adult":

    Contains calculations used to estimate daily transition probabilities from the pupal stage to the adult stage under different temperature conditions, using the same calculation framework described above.

  • Worksheet "Adult Survival+Reproduction":

    Contains calculations of adult survival and temperature-dependent reproductive output used to parameterize adult contributions to the egg stage in the population matrices. 

    Raw input data in this worksheet include:

    • median developmental time (days)
    • stage survival (%)
    • mean oviposition (eggs per female)
    • median oviposition time (days)

    Calculated outputs include:

    • daily mortality probabilities

    • daily developmental transition probabilities

    • daily survival probabilities

    • number of eggs laid per day

      The adult row includes reproduction terms contributing to the egg stage. Mortality is implicitly represented as the remaining probability not accounted for by survival or development transitions.

  • Worksheet "Final Matrices":

    Contains the finalized temperature-specific population projection matrices used directly in the simulation model. This worksheet contains finalized numerical matrices only and does not contain formulas. Each projection matrix represents transitions occurring over a single daily timestep.

    Matrices are provided for the following constant temperature conditions:
    16°C, 20°C, 24°C, 28°C, 32°C.