Bee colony modeling

🐝 pybeepop+

Python interface for BeePop+, the EPA/USDA honey bee colony simulation model.

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For more information about BeePop+ see Garber et al. 2022, Ecologies.
For more information about pybeepop+ see Minucci 2025, Journal of Open Research Software.

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Note: All values in the input file are text strings. The "Type" column below indicates the internal type the string is converted to. Integer fields must be whole numbers. Values outside the listed Min/Max range are rejected with an error.
Exposed Variable Name Type Min Max Default Units Notes Interpretation
WeatherFileName String N/A N/A Absolute file path Location of weather file
SimStart Date 1/1/100 12/31/9999 Date String - MM/DD/YYYY Sets the start date of the simulation. Must be within dates contained in weather file
SimEnd Date 1/1/100 12/31/9999 Date String - MM/DD/YYYY Sets the end date of the simulation. Must be within dates contained in weather file
ICDroneAdults Integer 0 0 # of individuals Initial Conditions for simulation - # of drone adults
ICWorkerAdults Integer 0 15000 # of individuals Initial Conditions for simulation - # of worker adults
ICDroneBrood Integer 0 0 # of individuals Initial Conditions for simulation - # of drone brood
ICWorkerBrood Integer 0 10000 # of individuals Initial Conditions for simulation - # of worker brood
ICDroneLarvae Integer 0 0 # of individuals Initial Conditions for simulation - # of drone larvae
ICWorkerLarvae Integer 0 5000 # of individuals Initial Conditions for simulation - # of worker larvae
ICDroneEggs Integer 0 0 # of eggs Initial Conditions for simulation - # of drone eggs
ICWorkerEggs Integer 0 2000 # of eggs Initial Conditions for simulation - # of worker eggs
ICQueenStrength Float 1 5 4 1-5 scale Initial Conditions for simulation - initial queen strength. 1=weak, 5=strong
ICForagerLifespan Integer 4 16 10 days Initial Conditions for simulation - forager lifespan in days
ICDroneAdultInfest Float 0 100 0 % Initial Conditions for simulation - % adult drones infested with Varroa mites
ICDroneBroodInfest Float 0 100 0 % Initial Conditions for simulation - % drone brood infested with Varroa mites
ICDroneMiteOffspring Float 0 0 mites per infesting mite Initial Conditions for simulation - number of mite offspring per infesting mite
ICDroneMiteSurvivorship Float 0 100 0 % Initial Conditions for simulation - % of mites surviving and emerging from capped drone brood
ICWorkerAdultInfest Float 0 100 0 % Initial Conditions for simulation - % adult workers infested with Varroa mites
ICWorkerBroodInfest Float 0 100 0 % Initial Conditions for simulation - % worker brood infested with Varroa mites
ICWorkerMiteOffspring Float 0 0 mites per infesting mite Initial Conditions for simulation - number of mite offspring per infesting mite
ICWorkerMiteSurvivorship Float 0 100 0 % Initial Conditions for simulation - % of mites surviving and emerging from capped worker brood
ImmType String N/A N/A Valid strings are: None, Sine, Cosine, Tangent, Exponential, Logarithmic, Polynomial Time series profile of daily immigration of mites over the ImmStart to ImmEnd time period.
PctImmMitesResistant Float 0 100 0 % Percentage of immigrating mites that are resistant to Varroa treatment. Resistant mites survive treatments.
TotalImmMites Integer 0 0 # of mites Total mites immigrating across the ImmStart to ImmEnd window, distributed by ImmType. Mites only immigrate on forage days, so fewer may arrive.
ImmStart Date 1/1/100 12/31/9999 Date String - MM/DD/YYYY Start Immigration
ImmEnd Date 1/1/100 12/31/9999 Date String - MM/DD/YYYY End Immigration
ImmEnabled Boolean N/A N/A FALSE true, false Enables or disables immigration
RQEggLayDelay Integer 0 10 days Delay in days after a requeening before the new queen begins laying eggs.
RQReQueenDate Date 1/1/100 12/31/9999 Date String - MM/DD/YYYY Sets the date of requeening, active when RQScheduled = true
RQEnableReQueen Boolean N/A N/A TRUE true, false Enables or disables requeening
RQScheduled Boolean N/A N/A FALSE true, false Either establishes Scheduled (true) or Automatic (false) requeening. Automatic requeening occurs from April-September if drone eggs exceed 15% of eggs laid due to sperm depletion. RQEnableReQueen must also be set to true.
RQQueenStrength Float 1 5 5 1-5 scale Sets the strength of the requeened queen
RQOnce Boolean N/A N/A FALSE true, false Either establishes a single requeening (true) or requeening every year on this date(false)
VTEnable Boolean N/A N/A FALSE true, false Enables varroa treatments as scheduled with VTData.
VTData String N/A N/A Schedules a Varroa Treatment using start_date,duration_weeks,mortality% Schedules a Varroa Treatment. Pass more than one VTData entry to set up multiple treatments. Format: start_date,duration_weeks,mortality%. e.g. 6/2/2015,6,75. Mortality applies to treatment-susceptible free (running) mites only; mites in capped brood are unaffected. Use VTData=Clear to reset. Date string must be MM/DD/YYYY.
InitMitePctResistant Float 0 100 0 % Percentage of the initial mite population that is resistant to Varroa treatment.
AIAdultSlope Float 0 <20 4 dimensionless Typical range: 1 to 9 Slope parameter for the adult oral dose-response curve, which is a two-parameter Hill (log-logistic) model.
AIAdultLD50 Float >0 999 ug/bee Oral median lethal dose for Adults, in ug/bee
AIAdultSlopeContact Float 0 <20 4 dimensionless Typical range: 1 to 9 Slope parameter for the adult contact dose-response curve, which is a two-parameter Hill (log-logistic) model.
AIAdultLD50Contact Float >0 999 ug/bee Contact median lethal dose for Adults, in ug/bee
AILarvaSlope Float 0 <20 4 dimensionless Typical range: 1 to 9 Slope parameter for the larval oral dose-response curve, which is a two-parameter Hill (log-logistic) model.
AILarvaLD50 Float >0 999 ug/bee Oral median lethal dose for Larvae, in ug/bee
AIKOW Float >0 2.718282 dimensionless Octanol/water partition coefficient used to compute transpiration stream concentration factor and root concentration factor. Only used when SoilEnabled=true.
AIKOC Float >0 300 mL/g organic carbon Organic carbon partition coefficient used in the soil contamination pathway soil-water partition term. Only used when SoilEnabled=true.
AIHalfLife Float >0 15 days Active ingredient half-life used to decay foliar exposure after application. Only used when FoliarEnable=true.
AIContactFactor Float 0 2.7 dimensionless Factor used with EAppRate to convert foliar application rate into forager contact dose. Only used when FoliarEnabled=true.
CL4Pollen Float 0 1.8 mg/day Daily Pollen Consumption by age 4 Larvae (mg/day)
CL4Nectar Float 0 60 mg/day Daily Nectar Consumption by age 4 Larvae (mg/day)
CL5Pollen Float 0 3.6 mg/day Daily Pollen Consumption by age 5 Larvae (mg/day)
CL5Nectar Float 0 120 mg/day Daily Nectar Consumption by age 5 Larvae (mg/day)
CLDPollen Float 0 3.6 mg/day Daily Pollen Consumption by Drone Larvae (mg/day)
CLDNectar Float 0 130 mg/day Daily Nectar Consumption by Drone Larvae (mg/day)
CA13Pollen Float 0 6.65 mg/day Daily Pollen Consumption by age 1-3 Adult Workers (mg/day)
CA13Nectar Float 0 60 mg/day Daily Nectar Consumption by age 1-3 Adult Workers (mg/day)
CA410Pollen Float 0 9.6 mg/day Daily Pollen Consumption by age 4-10 Adult Workers (mg/day)
CA410Nectar Float 0 140 mg/day Daily Nectar Consumption by age 4-10 Adult Workers (mg/day)
CA1120Pollen Float 0 1.7 mg/day Daily Pollen Consumption by age 11-20 Adult Workers (mg/day)
CA1120Nectar Float 0 60 mg/day Daily Nectar Consumption by age 11-20 Adult Workers (mg/day)
CADPollen Float 0 0.0002 mg/day Daily Pollen Consumption by Drone Adults (mg/day)
CADNectar Float 0 235 mg/day Daily Nectar Consumption by Drone Adults (mg/day)
CForagerPollen Float 0 0.041 mg/day Daily Pollen Consumption by Foragers (mg/day)
CForagerNectar Float 0 292 mg/day Daily Nectar Consumption by Foragers (mg/day)
IPollenTrips Integer 0 3 trips/day Daily Pollen trips per Forager
INectarTrips Integer 0 17 trips/day Daily Nectar trips per Forager
IPercentNectarForagers Float 0 100 80 % Percent of all Foragers collecting Nectar
IPollenLoad Float 0 26 mg/trip/bee mg Pollen per forage trip per bee
INectarLoad Float 0 45 mg/trip/bee mg Nectar per forager trip per bee
FoliarEnabled Boolean N/A N/A FALSE true, false If true, enables pesticide exposure in foliar spray mode.
SoilEnabled Boolean N/A N/A FALSE true, false If true, enables pesticide exposure in soil application mode.
SeedEnabled Boolean N/A N/A FALSE true, false If true, enables pesticide exposure in seed treatment mode.
EAppRate Float 0 0 lb ai/acre Foliar application rate used to compute foliar contact dose and incoming foliar nectar/pollen concentration.
ESoilTheta Float 0 1 0.25 cm3 water/cm3 soil Typical range: 0 to 0.6 Volumetric soil water content. Used to estimate plant uptake from soil. Only used when SoilEnabled=true
ESoilP Float >0 1.4 g/cm3 Typical range: 1.0 to 1.8 Soil bulk density. Used to estimate plant uptake from soil. Only used when SoilEnabled=true
ESoilFoc Float >0 1 0.02 g organic carbon/g dry soil Typical range: 0.005 to 0.05 Fraction of bulk soil mass that is organic carbon. Used to estimate plant uptake from soil. Only used when SoilEnabled=true
ESoilConcentration Float 0 0 ug/g soil Soil concentration input for the soil exposure pathway. Used to estimate plant uptake from soil. Only used when SoilEnabled=true
ESeedAppRate Float 0 0 mg ai/seed Application rate of seed treatment active ingredient, in mg a.i./seed. During the seed forage window, incoming pollen residue is set to AppRate x 18 ng a.i./g and incoming nectar residue to AppRate x 45 ng a.i./g.
FoliarAppDate Date 1/1/100 12/31/9999 Date String - MM/DD/YYYY Foliar application date.
FoliarForageBegin Date 1/1/100 12/31/9999 Date String - MM/DD/YYYY Start date of the foliar foraging exposure window.
FoliarForageEnd Date 1/1/100 12/31/9999 Date String - MM/DD/YYYY End date of the foliar foraging exposure window.
SoilForageBegin Date 1/1/100 12/31/9999 Date String - MM/DD/YYYY Start date of the soil foraging exposure window.
SoilForageEnd Date 1/1/100 12/31/9999 Date String - MM/DD/YYYY End date of the soil foraging exposure window.
SeedForageBegin Date 1/1/100 12/31/9999 Date String - MM/DD/YYYY Start date of the seed-treatment foraging exposure window.
SeedForageEnd Date 1/1/100 12/31/9999 Date String - MM/DD/YYYY End date of the seed-treatment foraging exposure window.
NecPolFileEnable Boolean N/A N/A FALSE true, false If true, enables the Nectar/Pollen Contamination file for direct specification of daily residue levels in pollen and nectar.
NecPolFileName String N/A N/A Absolute file path Name of the Nectar/Pollen Contamination file
InitColNectar Float 0 20000 grams Mass (grams) of colony nectar resources at start of simulation
InitColPollen Float 0 10000 grams Mass (grams) of colony pollen resources at start of simulation
MaxColNectar Float 0 100000 grams Maximum mass (grams) of nectar resources contained in colony during simulation
MaxColPollen Float 0 60000 grams Maximum mass (grams) of pollen resources contained in colony during simulation
SupPollenEnable Boolean N/A N/A FALSE true, false If true, enables supplemental pollen feeding
SupPollenAmount Float 0 0 grams Amount (grams) of pollen supplemental feed
SupPollenBegin Date 1/1/100 12/31/9999 Date String - MM/DD/YYYY Start date of pollen supplemental feeding
SupPollenEnd Date 1/1/100 12/31/9999 Date String - MM/DD/YYYY End date of pollen suppemental feeding
SupNectarEnable Boolean N/A N/A FALSE true, false If true, enables supplemental nectar feeding
SupNectarAmount Float 0 0 grams Amount (grams) of nectar supplemental feed
SupNectarBegin Date 1/1/100 12/31/9999 Date String - MM/DD/YYYY Start date of nectar supplemental feeding
SupNectarEnd Date 1/1/100 12/31/9999 Date String - MM/DD/YYYY End date of nectar suppemental feeding
ForagerMaxProp Float 0 1 0.3 proportion Max proportion of total adult worker population that can be active foragers
NeedResourcesToLive Boolean N/A N/A FALSE true, false If true, colony dies when pollen or nectar mass reaches 0
Latitude Float -90 90 decimal degrees Latitude in decimal degrees for calculating day length. Day length beyond +/-65 degrees is calculated as at +/-65 degrees.
EtoLXitionEn Boolean N/A N/A FALSE true, false Enable Eggs to Larvae transition survival rate variable?
LtoBXitionEn Boolean N/A N/A FALSE true, false Enable Larave to Pupae transition survival rate variable?
BtoAXitionEn Boolean N/A N/A FALSE true, false Enable Pupae to Adult transition survival rate variable?
AtoFXitionEn Boolean N/A N/A FALSE true, false Enable Adult to Forager transition survival rate variable?
EtoLXition String N/A N/A In the format StartDate, EndDate, float. Date string must be MM/DD/YYYY. Sets the survival rate (%) for the Eggs to Larvae Transition for the period between StartDate and EndDate. Example: "07/05/2016, 04/13/2017, 75.0"
LtoBXition String N/A N/A In the format StartDate, EndDate, float. Date string must be MM/DD/YYYY. Sets the survival rate (%) for the Larvae to Pupae Transition for the period between StartDate and EndDate. Example: "07/05/2016, 04/13/2017, 75.0"
BtoAXition String N/A N/A In the format StartDate, EndDate, float. Date string must be MM/DD/YYYY. Sets the survival rate (%) for the Pupae to AdultTransition for the period between StartDate and EndDate. Example: "07/05/2016, 04/13/2017, 75.0"
AtoFXition String N/A N/A In the format StartDate, EndDate, float. Date string must be MM/DD/YYYY. Sets the survival rate (%) for the Adult to Forager Transition for the period between StartDate and EndDate. Example: "07/05/2016, 04/13/2017, 75.0"

For the full list and latest details, see BeePop_exposed_parameters.csv on GitHub.