Description
Simulation of Bird Flight Range.
Description
Functions for range estimation in birds based on Pennycuick (2008) and Pennycuick (1975), 'Flight' program which compliments Pennycuick (2008) requires manual entry of birds which can be tedious when there are thousands of birds to estimate. Implemented are two ODE methods discussed in Pennycuick (1975) and time-marching computation method "constant muscle mass" as in Pennycuick (1998). See Pennycuick (1975, ISBN:978-0-12-249405-5), Pennycuick (1998) <doi:10.1006/jtbi.1997.0572>, and Pennycuick (2008, ISBN:9780080557816).
README.md
flying
The package provides methods for predicting flight range of birds based on their physiological characteristics. This is an R implementation of Flight program provided by Pennycuick.
Installation
Install the development version from GitHub with:
# install.packages("devtools")
devtools::install_github("BMasinde/flight")
Examples
Time-Marching computation
library(flying)
#> Welcome to package flying
## basic example code
## birds comes with the package
data("birds")
simulation <- migrate(data = birds, method = "cmm", settings = list(airDensity = 0.905))
simulation$range
#> Anser anser Hydrobates pelagicus Pachyptila desolata
#> 3099.512 2711.612 3728.924
#> Regulus regulus Calidris canutus Aegypius monachus
#> 1134.909 3845.427 3523.496
#> Limosa lapponica Anas crecca Hirundo rustica
#> 11488.486 3406.054 2987.473
#> Cygnus cygnus Sylvia borin Luscinia luscinia
#> 3097.141 2281.368 1892.490
#> Corvus monedula Anas penelope Fregata magnificens
#> 2051.622 5206.999 9954.016
#> Larus ridibundus Diomedea exulans Phalacrocorax carbo
#> 5359.893 5519.687 2613.821
#> Gyps rueppellii Torgos tracheliotus Ardeotis kori
#> 6443.840 5800.438 3918.554
#> Sturnus vulgaris Fringilla coelebs Carduelis spinus
#> 3603.239 2420.191 2262.704
#> Turdus philomelos Calidris tenuirostris Buteo swainsoni M
#> 2712.934 5689.756 5102.483
#> Buteo swainsoni F
#> 6459.878
The function also returns the mechanical and chemical power during the simulation
Range estimation based on ODE
This function estimates the range based on Pennycuick (1975) Mechanics of Flight where Breguet set of equations are used.
## when estimating range of a single bird
birds_range <- flysim(data = birds, settings = list(airDensity = 0.905))
birds_range$range
#> Anser anser Hydrobates pelagicus Pachyptila desolata
#> 3193.8 3252.9 4192.0
#> Regulus regulus Calidris canutus Aegypius monachus
#> 1521.6 4240.6 3951.6
#> Limosa lapponica Anas crecca Hirundo rustica
#> 11209.3 3797.8 3898.0
#> Cygnus cygnus Sylvia borin Luscinia luscinia
#> 3296.0 2801.7 2301.9
#> Corvus monedula Anas penelope Fregata magnificens
#> 2452.7 5428.0 10527.4
#> Larus ridibundus Diomedea exulans Phalacrocorax carbo
#> 6113.1 5436.8 2918.8
#> Gyps rueppellii Torgos tracheliotus Ardeotis kori
#> 6808.3 6334.7 4211.5
#> Sturnus vulgaris Fringilla coelebs Carduelis spinus
#> 4197.4 3036.6 2926.6
#> Turdus philomelos Calidris tenuirostris Buteo swainsoni M
#> 3243.8 6053.5 5671.6
#> Buteo swainsoni F
#> 6994.8
The data
birds definitions pulled from Flight program in-built datasets and fat mass randomly generated where initially zero. In addition, by default muscle mass was derived as 0.17 fraction of the all-up mass. Users's data should have columns named appropriately. The package looks for columns named id, name or species.name, bodymass or allupmass, wingspan, ws, wingarea, ordo, order (which is a factored column with levels 1 or 2 passerines and non-passerines respectively) fatmass, fat.mass, fat_mass and lastly muscle_mass.
birds
#> Scientific.name Empty.mass Wing.span Fat.mass Order Wing.area
#> 1 Anser anser 3.77000 1.600 0.84641 2 0.33100
#> 2 Hydrobates pelagicus 0.02580 0.355 0.00591 2 0.01610
#> 3 Pachyptila desolata 0.15500 0.637 0.03886 2 0.04710
#> 4 Regulus regulus 0.00542 0.156 0.00112 1 0.00525
#> 5 Calidris canutus 0.12700 0.538 0.03500 2 0.03320
#> 6 Aegypius monachus 9.90000 3.040 2.02565 2 1.40000
#> 7 Limosa lapponica 0.36700 0.748 0.20112 2 0.05680
#> 8 Anas crecca 0.23500 0.582 0.06562 2 0.04580
#> 9 Hirundo rustica 0.01900 0.318 0.00570 1 0.01320
#> 10 Cygnus cygnus 12.50000 2.560 2.50000 2 0.75600
#> 11 Sylvia borin 0.02200 0.240 0.00660 1 0.01100
#> 12 Luscinia luscinia 0.02700 0.263 0.00675 1 0.01300
#> 13 Corvus monedula 0.18100 0.600 0.03620 1 0.06180
#> 14 Anas penelope 0.77000 0.822 0.28607 2 0.08290
#> 15 Fregata magnificens 1.67000 2.140 0.55799 2 0.37200
#> 16 Larus ridibundus 0.28500 0.967 0.07881 2 0.09920
#> 17 Diomedea exulans 9.57000 3.060 2.12836 2 0.64400
#> 18 Phalacrocorax carbo 2.56000 1.350 0.50768 2 0.22400
#> 19 Gyps rueppellii 7.30000 2.500 2.52588 2 0.89200
#> 20 Torgos tracheliotus 6.60000 2.640 2.01454 2 1.03000
#> 21 Ardeotis kori 11.90000 2.470 3.45889 2 1.06000
#> 22 Sturnus vulgaris 0.08190 0.384 0.02973 1 0.02530
#> 23 Fringilla coelebs 0.02300 0.264 0.00690 1 0.01310
#> 24 Carduelis spinus 0.01120 0.212 0.00336 1 0.00785
#> 25 Turdus philomelos 0.07160 0.361 0.02148 1 0.02250
#> 26 Calidris tenuirostris 0.23300 0.587 0.08970 2 0.03960
#> 27 Buteo swainsoni M 0.77500 1.250 0.22248 2 0.21000
#> 28 Buteo swainsoni F 1.06000 1.330 0.37117 2 0.24000
#> Muscle.mass
#> 1 0.6409000
#> 2 0.0043860
#> 3 0.0263500
#> 4 0.0009214
#> 5 0.0215900
#> 6 1.6829999
#> 7 0.0623900
#> 8 0.0399500
#> 9 0.0032300
#> 10 2.1250000
#> 11 0.0037400
#> 12 0.0045900
#> 13 0.0307700
#> 14 0.1309000
#> 15 0.2839000
#> 16 0.0484500
#> 17 1.6268999
#> 18 0.4352000
#> 19 1.2410000
#> 20 1.1220000
#> 21 2.0229999
#> 22 0.0139230
#> 23 0.0039100
#> 24 0.0019040
#> 25 0.0121720
#> 26 0.0396100
#> 27 0.1317500
#> 28 0.1802000