scripts/Neves_et_al_2020/generate_param_space.R
In xieshu95/robustness: Test the Robustness of DAISIE to Geodynamics
# Generate preliminary paramter space for anaysis #
# Oceanic ontogeny --------------------------------------------------------
## Maui Nui ---------------------------------------------------------------
time <- 2.55
M <- 1000
lac <- c(0.0001, 0.0002, 0.0003)
mu_min <- c(1, 2)
mu_p <- c(50, 100)
K <- c(0.001, 0.01, Inf)
gam <- c(0.01, 0.02, 0.03)
laa <- c(1, 2)
island_ontogeny <- "beta"
sea_level <- "const"
max_area <- 13500
peak_time <- 0.53
sharpness <- 1
total_island_age <- 2.864
sea_level_amplitude <- 0
sea_level_frequency <- 0
island_gradient_angle <- 0
extcutoff <- 1000
x_s <- 0
x_nonend <- 0
maui_parameter_set <- expand.grid(
time = time,
M = M,
lac = lac,
mu_min = mu_min,
mu_p = mu_p,
K = K,
gam = gam,
laa = laa,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
max_area = max_area,
peak_time = peak_time,
sharpness = sharpness,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle,
extcutoff = extcutoff,
x_s = x_s,
x_nonend = x_nonend,
stringsAsFactors = FALSE
)
## Kauai ------------------------------------------------------------------
time <- 6.15
M <- 1000
lac <- c(0.0001, 0.0002, 0.0003)
mu_min <- c(1, 2)
mu_p <- c(50, 100)
K <- c(0.001, 0.01, Inf)
gam <- c(0.01, 0.02, 0.03)
laa <- c(1, 2)
island_ontogeny <- "beta"
sea_level <- "const"
max_area <- 3787
peak_time <- 0.27
sharpness <- 1
total_island_age <- 8.473
sea_level_amplitude <- 0
sea_level_frequency <- 0
island_gradient_angle <- 0
extcutoff <- 1000
x_s <- 0
x_nonend <- 0
kauai_parameter_set <- expand.grid(
time = time,
M = M,
lac = lac,
mu_min = mu_min,
mu_p = mu_p,
K = K,
gam = gam,
laa = laa,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
max_area = max_area,
peak_time = peak_time,
sharpness = sharpness,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle,
extcutoff = extcutoff,
x_s = x_s,
x_nonend = x_nonend,
stringsAsFactors = FALSE
)
# Complete ontogeny paramter set ------------------------------------------
oceanic_ontogeny <- rbind(maui_parameter_set, kauai_parameter_set)
write.csv2(oceanic_ontogeny, "data/oceanic_ontogeny.csv", row.names = FALSE)
# Sea level ---------------------------------------------------------------
## Maui Nui ---------------------------------------------------------------
time <- 2.55
M <- 1000
lac <- c(0.0001, 0.0002, 0.0003)
mu_min <- c(1, 2)
mu_p <- c(50, 100)
K <- c(0.001, 0.01, Inf)
gam <- c(0.01, 0.02, 0.03)
laa <- c(1, 2)
island_ontogeny <- "const"
sea_level <- "sine"
max_area <- 13500
peak_time <- 0
sharpness <- 0
total_island_age <- 2.55
sea_level_amplitude <- 60
sea_level_frequency <- 2.55 * 10
island_gradient_angle <- c(75, 85)
extcutoff <- 1000
x_s <- 0
x_nonend <- 0
maui_oceanic_sea_level <- expand.grid(
time = time,
M = M,
lac = lac,
mu_min = mu_min,
mu_p = mu_p,
K = K,
gam = gam,
laa = laa,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
max_area = max_area,
peak_time = peak_time,
sharpness = sharpness,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle,
extcutoff = extcutoff,
x_s = x_s,
x_nonend = x_nonend,
stringsAsFactors = FALSE
)
## Kauai ------------------------------------------------------------------
time <- 6.15
M <- 1000
lac <- c(0.0001, 0.0002, 0.0003)
mu_min <- c(1, 2)
mu_p <- c(50, 100)
K <- c(0.001, 0.01, Inf)
gam <- c(0.01, 0.02, 0.03)
laa <- c(1, 2)
island_ontogeny <- "const"
sea_level <- "sine"
max_area <- 3787
peak_time <- 0
sharpness <- 0
total_island_age <- 6.15
sea_level_amplitude <- 60
sea_level_frequency <- 6.15 * 10
island_gradient_angle <- c(75, 85)
extcutoff <- 1000
x_s <- 0
x_nonend <- 0
kauai_oceanic_sea_level <- expand.grid(
time = time,
M = M,
lac = lac,
mu_min = mu_min,
mu_p = mu_p,
K = K,
gam = gam,
laa = laa,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
max_area = max_area,
peak_time = peak_time,
sharpness = sharpness,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle,
extcutoff = extcutoff,
x_s = x_s,
x_nonend = x_nonend,
stringsAsFactors = FALSE
)
# Complete oceanic sea level paramter set ---------------------------------
oceanic_sea_level <- rbind(maui_oceanic_sea_level, kauai_oceanic_sea_level)
write.csv2(oceanic_sea_level, "data/oceanic_sea_level.csv", row.names = FALSE)
# Oceanic ontogeny sea level ----------------------------------------------
## Maui Nui ---------------------------------------------------------------
time <- 2.55
M <- 1000
lac <- c(0.0001, 0.0002, 0.0003)
mu_min <- c(1, 2)
mu_p <- c(50, 100)
K <- c(0.001, 0.01, Inf)
gam <- c(0.01, 0.02, 0.03)
laa <- c(1, 2)
island_ontogeny <- "beta"
sea_level <- "sine"
max_area <- 13500
peak_time <- 0.53
sharpness <- 1
total_island_age <- 2.864
sea_level_amplitude <- 60
sea_level_frequency <- 2.55 * 10
island_gradient_angle <- c(75, 85)
extcutoff <- 1000
x_s <- 0
x_nonend <- 0
oceanic_ontogeny_sea_level_maui <- expand.grid(
time = time,
M = M,
lac = lac,
mu_min = mu_min,
mu_p = mu_p,
K = K,
gam = gam,
laa = laa,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
max_area = max_area,
peak_time = peak_time,
sharpness = sharpness,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle,
extcutoff = extcutoff,
x_s = x_s,
x_nonend = x_nonend,
stringsAsFactors = FALSE
)
## Kauai -------------------------------------------------------------------
time <- 6.15
M <- 1000
lac <- c(0.0001, 0.0002, 0.0003)
mu_min <- c(1, 2)
mu_p <- c(50, 100)
K <- c(0.001, 0.01, Inf)
gam <- c(0.01, 0.02, 0.03)
laa <- c(1, 2)
island_ontogeny <- "beta"
sea_level <- "sine"
max_area <- 3787
peak_time <- 0.27
sharpness <- 1
total_island_age <- 8.473
sea_level_amplitude <- 60
sea_level_frequency <- 6.15 * 10
island_gradient_angle <- c(75, 85)
extcutoff <- 1000
x_s <- 0
x_nonend <- 0
oceanic_ontogeny_sea_level_kauai <- expand.grid(
time = time,
M = M,
lac = lac,
mu_min = mu_min,
mu_p = mu_p,
K = K,
gam = gam,
laa = laa,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
max_area = max_area,
peak_time = peak_time,
sharpness = sharpness,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle,
extcutoff = extcutoff,
x_s = x_s,
x_nonend = x_nonend,
stringsAsFactors = FALSE
)
# Complete ontogeny sea level paramter set -------------------------------
oceanic_ontogeny_sea_level <- rbind(
oceanic_ontogeny_sea_level_maui,
oceanic_ontogeny_sea_level_kauai
)
write.csv2(
oceanic_ontogeny_sea_level,
"data/oceanic_ontogeny_sea_level.csv",
row.names = FALSE
)
# Nonoceanic Maui Nui -------------------------------------------------------------
time <- 2.55
M <- 1000
lac <- c(0.5, 1, 2)
mu <- c(0.5, 1, 2)
K <- c(10, 40, Inf)
gam <- c(0.01, 0.05, 0.1)
laa <- c(1, 2)
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
nonoceanic_maui <- expand.grid(
time = time,
M = M,
lac = lac,
mu = mu,
K = K,
gam = gam,
laa = laa,
x_s = x_s,
x_nonend = x_nonend,
stringsAsFactors = FALSE
)
# Nonoceanic Kauai -------------------------------------------------------------
time <- 6.15
M <- 1000
lac <- c(0.5, 1, 2)
mu <- c(0.5, 1, 2)
K <- c(10, 40, Inf)
gam <- c(0.01, 0.05, 0.1)
laa <- c(1, 2)
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
nonoceanic_kauai <- expand.grid(
time = time,
M = M,
lac = lac,
mu = mu,
K = K,
gam = gam,
laa = laa,
x_s = x_s,
x_nonend = x_nonend,
stringsAsFactors = FALSE
)
# Complete nonoceanic paramter set -------------------------------
nonoceanic <- rbind(
nonoceanic_maui,
nonoceanic_kauai
)
write.csv2(
nonoceanic,
"data/nonoceanic.csv",
row.names = FALSE
)
# Nonoceanic sea level Maui Nui -----------------------------------------------
time <- 2.55
M <- 1000
lac <- c(0.0001, 0.0002, 0.0003)
mu_min <- c(1, 2)
mu_p <- c(50, 100)
K <- c(0.001, 0.01, Inf)
gam <- c(0.01, 0.02, 0.03)
laa <- c(1, 2)
island_ontogeny <- "const"
sea_level <- "sine"
max_area <- 13500
peak_time <- 0
sharpness <- 0
total_island_age <- 2.55
sea_level_amplitude <- 60
sea_level_frequency <- 2.55 * 10
island_gradient_angle <- c(75, 85)
extcutoff <- 1000
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
nonoceanic_sea_level_maui <- expand.grid(
time = time,
M = M,
lac = lac,
mu_min = mu_min,
mu_p = mu_p,
K = K,
gam = gam,
laa = laa,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
max_area = max_area,
peak_time = peak_time,
sharpness = sharpness,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle,
extcutoff = extcutoff,
x_s = x_s,
x_nonend = x_nonend,
stringsAsFactors = FALSE
)
# Nonoceanic sea level Kauai -----------------------------------------------
time <- 6.15
M <- 1000
lac <- c(0.0001, 0.0002, 0.0003)
mu_min <- c(1, 2)
mu_p <- c(50, 100)
K <- c(0.001, 0.01, Inf)
gam <- c(0.01, 0.02, 0.03)
laa <- c(1, 2)
island_ontogeny <- "const"
sea_level <- "sine"
max_area <- 3787
peak_time <- 0
sharpness <- 0
total_island_age <- 6.15
sea_level_amplitude <- 60
sea_level_frequency <- 6.15 * 10
island_gradient_angle <- c(75, 85)
extcutoff <- 1000
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
nonoceanic_sea_level_kauai <- expand.grid(
time = time,
M = M,
lac = lac,
mu_min = mu_min,
mu_p = mu_p,
K = K,
gam = gam,
laa = laa,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
max_area = max_area,
peak_time = peak_time,
sharpness = sharpness,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle,
extcutoff = extcutoff,
x_s = x_s,
x_nonend = x_nonend,
stringsAsFactors = FALSE
)
# Complete nonoceanic sea level paramter set -------------------------------
nonoceanic_sea_level <- rbind(
nonoceanic_sea_level_maui,
nonoceanic_sea_level_kauai
)
write.csv2(
nonoceanic_sea_level,
"data/nonoceanic_sea_level.csv",
row.names = FALSE
)
# Nonoceanic 1 short land bridge DI Maui Nui
time <- 2.55
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- Inf
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(1.225, 1.325)))
maui_nui_1_short_lb_di <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
maui_nui_1_short_lb_di <- cbind(maui_nui_1_short_lb_di,
lac_2 = maui_nui_1_short_lb_di[, 3] / 2,
mu_2 = maui_nui_1_short_lb_di[, 4] / 2,
K_2 = K_1,
gam_2 = maui_nui_1_short_lb_di[, 6] * 2,
laa_2 = 0)
# Nonoceanic 1 long land bridge DI Maui Nui
time <- 2.55
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- Inf
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(1.175, 1.375)))
maui_nui_1_long_lb_di <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
maui_nui_1_long_lb_di <- cbind(maui_nui_1_long_lb_di,
lac_2 = maui_nui_1_long_lb_di[, 3] / 2,
mu_2 = maui_nui_1_long_lb_di[, 4] / 2,
K_2 = K_1,
gam_2 = maui_nui_1_long_lb_di[, 6] * 2,
laa_2 = 0)
# Nonoceanic 3 short land bridge DI Maui Nui
time <- 2.55
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- Inf
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(0.5875, 0.6875, 1.225, 1.325, 1.8625, 1.9625)))
maui_nui_3_short_lb_di <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
maui_nui_3_short_lb_di <- cbind(maui_nui_3_short_lb_di,
lac_2 = maui_nui_3_short_lb_di[, 3] / 2,
mu_2 = maui_nui_3_short_lb_di[, 4] / 2,
K_2 = K_1,
gam_2 = maui_nui_3_short_lb_di[, 6] * 2,
laa_2 = 0)
# Nonoceanic 3 long land bridge DI Maui Nui
time <- 2.55
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- Inf
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(0.5375, 0.7375, 1.175, 1.375, 1.8125, 2.0125)))
maui_nui_3_long_lb_di <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
maui_nui_3_long_lb_di <- cbind(maui_nui_3_long_lb_di,
lac_2 = maui_nui_3_long_lb_di[, 3] / 2,
mu_2 = maui_nui_3_long_lb_di[, 4] / 2,
K_2 = K_1,
gam_2 = maui_nui_3_long_lb_di[, 6] * 2,
laa_2 = 0)
# Nonoceanic 1 short land bridge DD Maui Nui
time <- 2.55
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- 10
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(1.225, 1.325)))
maui_nui_1_short_lb_dd <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
maui_nui_1_short_lb_dd <- cbind(maui_nui_1_short_lb_dd,
lac_2 = maui_nui_1_short_lb_dd[, 3] / 2,
mu_2 = maui_nui_1_short_lb_dd[, 4] / 2,
K_2 = K_1,
gam_2 = maui_nui_1_short_lb_dd[, 6] * 2,
laa_2 = 0)
# Nonoceanic 1 long land bridge DD Maui Nui
time <- 2.55
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- 10
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(1.175, 1.375)))
maui_nui_1_long_lb_dd <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
maui_nui_1_long_lb_dd <- cbind(maui_nui_1_long_lb_dd,
lac_2 = maui_nui_1_long_lb_dd[, 3] / 2,
mu_2 = maui_nui_1_long_lb_dd[, 4] / 2,
K_2 = K_1,
gam_2 = maui_nui_1_long_lb_dd[, 6] * 2,
laa_2 = 0)
# Nonoceanic 3 short land bridge DD Maui Nui
time <- 2.55
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- 10
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(0.5875, 0.6875, 1.225, 1.325, 1.8625, 1.9625)))
maui_nui_3_short_lb_dd <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
maui_nui_3_short_lb_dd <- cbind(maui_nui_3_short_lb_dd,
lac_2 = maui_nui_3_short_lb_dd[, 3] / 2,
mu_2 = maui_nui_3_short_lb_dd[, 4] / 2,
K_2 = K_1,
gam_2 = maui_nui_3_short_lb_dd[, 6] * 2,
laa_2 = 0)
# Nonoceanic 3 long land bridge DD Maui Nui
time <- 2.55
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- 10
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(0.5375, 0.7375, 1.175, 1.375, 1.8125, 2.0125)))
maui_nui_3_long_lb_dd <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
maui_nui_3_long_lb_dd <- cbind(maui_nui_3_long_lb_dd,
lac_2 = maui_nui_3_long_lb_dd[, 3] / 2,
mu_2 = maui_nui_3_long_lb_dd[, 4] / 2,
K_2 = K_1,
gam_2 = maui_nui_3_long_lb_dd[, 6] * 2,
laa_2 = 0)
# Nonoceanic 1 short land bridge DI Kauai
time <- 6.15
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- Inf
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(3.025, 3.125)))
kauai_1_short_lb_di <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
kauai_1_short_lb_di <- cbind(kauai_1_short_lb_di,
lac_2 = kauai_1_short_lb_di[, 3] / 2,
mu_2 = kauai_1_short_lb_di[, 4] / 2,
K_2 = K_1,
gam_2 = kauai_1_short_lb_di[, 6] * 2,
laa_2 = 0)
# Nonoceanic 1 long land bridge DI Kauai
time <- 6.15
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- Inf
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(2.975, 3.175)))
kauai_1_long_lb_di <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
kauai_1_long_lb_di <- cbind(kauai_1_long_lb_di,
lac_2 = kauai_1_long_lb_di[, 3] / 2,
mu_2 = kauai_1_long_lb_di[, 4] / 2,
K_2 = K_1,
gam_2 = kauai_1_long_lb_di[, 6] * 2,
laa_2 = 0)
# Nonoceanic 3 short land bridge DI Kauai
time <- 6.15
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- Inf
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(1.4875, 1.5875, 3.025, 3.125, 4.5625, 4.6625)))
kauai_3_short_lb_di <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
kauai_3_short_lb_di <- cbind(kauai_3_short_lb_di,
lac_2 = kauai_3_short_lb_di[, 3] / 2,
mu_2 = kauai_3_short_lb_di[, 4] / 2,
K_2 = K_1,
gam_2 = kauai_3_short_lb_di[, 6] * 2,
laa_2 = 0)
# Nonoceanic 3 long land bridge DI Kauai
time <- 6.15
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- Inf
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(1.4375, 1.6375, 2.975, 3.175, 4.5125, 4.7125)))
kauai_3_long_lb_di <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
kauai_3_long_lb_di <- cbind(kauai_3_long_lb_di,
lac_2 = kauai_3_long_lb_di[, 3] / 2,
mu_2 = kauai_3_long_lb_di[, 4] / 2,
K_2 = K_1,
gam_2 = kauai_3_long_lb_di[, 6] * 2,
laa_2 = 0)
# Nonoceanic 1 short land bridge DD Kauai
time <- 6.15
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- 10
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(3.025, 3.125)))
kauai_1_short_lb_dd <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
kauai_1_short_lb_dd <- cbind(kauai_1_short_lb_dd,
lac_2 = kauai_1_short_lb_dd[, 3] / 2,
mu_2 = kauai_1_short_lb_dd[, 4] / 2,
K_2 = K_1,
gam_2 = kauai_1_short_lb_dd[, 6] * 2,
laa_2 = 0)
# Nonoceanic 1 long land bridge DD Kauai
time <- 6.15
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- 10
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(2.975, 3.175)))
kauai_1_long_lb_dd <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
kauai_1_long_lb_dd <- cbind(kauai_1_long_lb_dd,
lac_2 = kauai_1_long_lb_dd[, 3] / 2,
mu_2 = kauai_1_long_lb_dd[, 4] / 2,
K_2 = K_1,
gam_2 = kauai_1_long_lb_dd[, 6] * 2,
laa_2 = 0)
# Nonoceanic 3 short land bridge DD Kauai
time <- 6.15
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- 10
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(1.4875, 1.5875, 3.025, 3.125, 4.5625, 4.6625)))
kauai_3_short_lb_dd <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
kauai_3_short_lb_dd <- cbind(kauai_3_short_lb_dd,
lac_2 = kauai_3_short_lb_dd[, 3] / 2,
mu_2 = kauai_3_short_lb_dd[, 4] / 2,
K_2 = K_1,
gam_2 = kauai_3_short_lb_dd[, 6] * 2,
laa_2 = 0)
# Nonoceanic 3 long land bridge DD Kauai
time <- 6.15
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- 10
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(1.4375, 1.6375, 2.975, 3.175, 4.5125, 4.7125)))
kauai_3_long_lb_dd <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
kauai_3_long_lb_dd <- cbind(kauai_3_long_lb_dd,
lac_2 = kauai_3_long_lb_dd[, 3] / 2,
mu_2 = kauai_3_long_lb_dd[, 4] / 2,
K_2 = K_1,
gam_2 = kauai_3_long_lb_dd[, 6] * 2,
laa_2 = 0)
# Complete nonoceanic land bridge paramter set -------------------------------
nonoceanic_land_bridge <- rbind(
maui_nui_1_short_lb_di,
maui_nui_1_long_lb_di,
maui_nui_3_short_lb_di,
maui_nui_3_long_lb_di,
maui_nui_1_short_lb_dd,
maui_nui_1_long_lb_dd,
maui_nui_3_short_lb_dd,
maui_nui_3_long_lb_dd,
kauai_1_short_lb_di,
kauai_1_long_lb_di,
kauai_3_short_lb_di,
kauai_3_long_lb_di,
kauai_1_short_lb_dd,
kauai_1_long_lb_dd,
kauai_3_short_lb_dd,
kauai_3_long_lb_dd
)
write.csv2(
nonoceanic_land_bridge,
"data/nonoceanic_land_bridge.csv",
row.names = FALSE
)
# Trait dependent rates Maui Nui
time <- 2.55
Mtotal <- 1000
M <- c(Mtotal * 0.1, Mtotal * 0.5, Mtotal)
lac <- c(0.5, 1, 2)
mu <- c(0.5, 1, 2)
K <- c(10, Inf)
gam <- c(0.01, 0.05, 0.1)
laa <- 1
trans <- c(0, 0.5)
trans2 <- c(0, 0.1, 0.5)
trait_maui_nui <- expand.grid(time = time,
M = M,
lac = lac,
mu = mu,
K = K,
gam = gam,
laa = laa,
trans = trans,
trans2 = trans2)
trait_maui_nui <- cbind(trait_maui_nui,
M2 = Mtotal - trait_maui_nui[, 2],
lac2 = trait_maui_nui[, 3] / 2,
mu2 = trait_maui_nui[, 4] / 2,
gam2 = trait_maui_nui[, 6] * 2,
laa2 = trait_maui_nui[, 7] * 2)
# Trait dependent rates kauai
time <- 6.15
Mtotal <- 1000
M <- c(Mtotal * 0.1, Mtotal * 0.5, Mtotal)
lac <- c(0.5, 1, 2)
mu <- c(0.5, 1, 2)
K <- c(10, Inf)
gam <- c(0.01, 0.05, 0.1)
laa <- 1
trans <- c(0, 0.5)
trans2 <- c(0, 0.1, 0.5)
trait_kauai <- expand.grid(time = time,
M = M,
lac = lac,
mu = mu,
K = K,
gam = gam,
laa = laa,
trans = trans,
trans2 = trans2)
trait_kauai <- cbind(trait_kauai,
M2 = Mtotal - trait_kauai[, 2],
lac2 = trait_kauai[, 3] / 2,
mu2 = trait_kauai[, 4] / 2,
gam2 = trait_kauai[, 6] * 2,
laa2 = trait_kauai[, 7] * 2)
# Complete trait dependent paramter set -----------------------------------
trait <- rbind(
trait_maui_nui,
trait_kauai
)
write.csv2(
trait,
"data/trait.csv",
row.names = FALSE
)
xieshu95/robustness documentation built on April 13, 2020, 1 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
# Generate preliminary paramter space for anaysis #
# Oceanic ontogeny --------------------------------------------------------
## Maui Nui ---------------------------------------------------------------
time <- 2.55
M <- 1000
lac <- c(0.0001, 0.0002, 0.0003)
mu_min <- c(1, 2)
mu_p <- c(50, 100)
K <- c(0.001, 0.01, Inf)
gam <- c(0.01, 0.02, 0.03)
laa <- c(1, 2)
island_ontogeny <- "beta"
sea_level <- "const"
max_area <- 13500
peak_time <- 0.53
sharpness <- 1
total_island_age <- 2.864
sea_level_amplitude <- 0
sea_level_frequency <- 0
island_gradient_angle <- 0
extcutoff <- 1000
x_s <- 0
x_nonend <- 0
maui_parameter_set <- expand.grid(
time = time,
M = M,
lac = lac,
mu_min = mu_min,
mu_p = mu_p,
K = K,
gam = gam,
laa = laa,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
max_area = max_area,
peak_time = peak_time,
sharpness = sharpness,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle,
extcutoff = extcutoff,
x_s = x_s,
x_nonend = x_nonend,
stringsAsFactors = FALSE
)
## Kauai ------------------------------------------------------------------
time <- 6.15
M <- 1000
lac <- c(0.0001, 0.0002, 0.0003)
mu_min <- c(1, 2)
mu_p <- c(50, 100)
K <- c(0.001, 0.01, Inf)
gam <- c(0.01, 0.02, 0.03)
laa <- c(1, 2)
island_ontogeny <- "beta"
sea_level <- "const"
max_area <- 3787
peak_time <- 0.27
sharpness <- 1
total_island_age <- 8.473
sea_level_amplitude <- 0
sea_level_frequency <- 0
island_gradient_angle <- 0
extcutoff <- 1000
x_s <- 0
x_nonend <- 0
kauai_parameter_set <- expand.grid(
time = time,
M = M,
lac = lac,
mu_min = mu_min,
mu_p = mu_p,
K = K,
gam = gam,
laa = laa,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
max_area = max_area,
peak_time = peak_time,
sharpness = sharpness,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle,
extcutoff = extcutoff,
x_s = x_s,
x_nonend = x_nonend,
stringsAsFactors = FALSE
)
# Complete ontogeny paramter set ------------------------------------------
oceanic_ontogeny <- rbind(maui_parameter_set, kauai_parameter_set)
write.csv2(oceanic_ontogeny, "data/oceanic_ontogeny.csv", row.names = FALSE)
# Sea level ---------------------------------------------------------------
## Maui Nui ---------------------------------------------------------------
time <- 2.55
M <- 1000
lac <- c(0.0001, 0.0002, 0.0003)
mu_min <- c(1, 2)
mu_p <- c(50, 100)
K <- c(0.001, 0.01, Inf)
gam <- c(0.01, 0.02, 0.03)
laa <- c(1, 2)
island_ontogeny <- "const"
sea_level <- "sine"
max_area <- 13500
peak_time <- 0
sharpness <- 0
total_island_age <- 2.55
sea_level_amplitude <- 60
sea_level_frequency <- 2.55 * 10
island_gradient_angle <- c(75, 85)
extcutoff <- 1000
x_s <- 0
x_nonend <- 0
maui_oceanic_sea_level <- expand.grid(
time = time,
M = M,
lac = lac,
mu_min = mu_min,
mu_p = mu_p,
K = K,
gam = gam,
laa = laa,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
max_area = max_area,
peak_time = peak_time,
sharpness = sharpness,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle,
extcutoff = extcutoff,
x_s = x_s,
x_nonend = x_nonend,
stringsAsFactors = FALSE
)
## Kauai ------------------------------------------------------------------
time <- 6.15
M <- 1000
lac <- c(0.0001, 0.0002, 0.0003)
mu_min <- c(1, 2)
mu_p <- c(50, 100)
K <- c(0.001, 0.01, Inf)
gam <- c(0.01, 0.02, 0.03)
laa <- c(1, 2)
island_ontogeny <- "const"
sea_level <- "sine"
max_area <- 3787
peak_time <- 0
sharpness <- 0
total_island_age <- 6.15
sea_level_amplitude <- 60
sea_level_frequency <- 6.15 * 10
island_gradient_angle <- c(75, 85)
extcutoff <- 1000
x_s <- 0
x_nonend <- 0
kauai_oceanic_sea_level <- expand.grid(
time = time,
M = M,
lac = lac,
mu_min = mu_min,
mu_p = mu_p,
K = K,
gam = gam,
laa = laa,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
max_area = max_area,
peak_time = peak_time,
sharpness = sharpness,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle,
extcutoff = extcutoff,
x_s = x_s,
x_nonend = x_nonend,
stringsAsFactors = FALSE
)
# Complete oceanic sea level paramter set ---------------------------------
oceanic_sea_level <- rbind(maui_oceanic_sea_level, kauai_oceanic_sea_level)
write.csv2(oceanic_sea_level, "data/oceanic_sea_level.csv", row.names = FALSE)
# Oceanic ontogeny sea level ----------------------------------------------
## Maui Nui ---------------------------------------------------------------
time <- 2.55
M <- 1000
lac <- c(0.0001, 0.0002, 0.0003)
mu_min <- c(1, 2)
mu_p <- c(50, 100)
K <- c(0.001, 0.01, Inf)
gam <- c(0.01, 0.02, 0.03)
laa <- c(1, 2)
island_ontogeny <- "beta"
sea_level <- "sine"
max_area <- 13500
peak_time <- 0.53
sharpness <- 1
total_island_age <- 2.864
sea_level_amplitude <- 60
sea_level_frequency <- 2.55 * 10
island_gradient_angle <- c(75, 85)
extcutoff <- 1000
x_s <- 0
x_nonend <- 0
oceanic_ontogeny_sea_level_maui <- expand.grid(
time = time,
M = M,
lac = lac,
mu_min = mu_min,
mu_p = mu_p,
K = K,
gam = gam,
laa = laa,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
max_area = max_area,
peak_time = peak_time,
sharpness = sharpness,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle,
extcutoff = extcutoff,
x_s = x_s,
x_nonend = x_nonend,
stringsAsFactors = FALSE
)
## Kauai -------------------------------------------------------------------
time <- 6.15
M <- 1000
lac <- c(0.0001, 0.0002, 0.0003)
mu_min <- c(1, 2)
mu_p <- c(50, 100)
K <- c(0.001, 0.01, Inf)
gam <- c(0.01, 0.02, 0.03)
laa <- c(1, 2)
island_ontogeny <- "beta"
sea_level <- "sine"
max_area <- 3787
peak_time <- 0.27
sharpness <- 1
total_island_age <- 8.473
sea_level_amplitude <- 60
sea_level_frequency <- 6.15 * 10
island_gradient_angle <- c(75, 85)
extcutoff <- 1000
x_s <- 0
x_nonend <- 0
oceanic_ontogeny_sea_level_kauai <- expand.grid(
time = time,
M = M,
lac = lac,
mu_min = mu_min,
mu_p = mu_p,
K = K,
gam = gam,
laa = laa,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
max_area = max_area,
peak_time = peak_time,
sharpness = sharpness,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle,
extcutoff = extcutoff,
x_s = x_s,
x_nonend = x_nonend,
stringsAsFactors = FALSE
)
# Complete ontogeny sea level paramter set -------------------------------
oceanic_ontogeny_sea_level <- rbind(
oceanic_ontogeny_sea_level_maui,
oceanic_ontogeny_sea_level_kauai
)
write.csv2(
oceanic_ontogeny_sea_level,
"data/oceanic_ontogeny_sea_level.csv",
row.names = FALSE
)
# Nonoceanic Maui Nui -------------------------------------------------------------
time <- 2.55
M <- 1000
lac <- c(0.5, 1, 2)
mu <- c(0.5, 1, 2)
K <- c(10, 40, Inf)
gam <- c(0.01, 0.05, 0.1)
laa <- c(1, 2)
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
nonoceanic_maui <- expand.grid(
time = time,
M = M,
lac = lac,
mu = mu,
K = K,
gam = gam,
laa = laa,
x_s = x_s,
x_nonend = x_nonend,
stringsAsFactors = FALSE
)
# Nonoceanic Kauai -------------------------------------------------------------
time <- 6.15
M <- 1000
lac <- c(0.5, 1, 2)
mu <- c(0.5, 1, 2)
K <- c(10, 40, Inf)
gam <- c(0.01, 0.05, 0.1)
laa <- c(1, 2)
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
nonoceanic_kauai <- expand.grid(
time = time,
M = M,
lac = lac,
mu = mu,
K = K,
gam = gam,
laa = laa,
x_s = x_s,
x_nonend = x_nonend,
stringsAsFactors = FALSE
)
# Complete nonoceanic paramter set -------------------------------
nonoceanic <- rbind(
nonoceanic_maui,
nonoceanic_kauai
)
write.csv2(
nonoceanic,
"data/nonoceanic.csv",
row.names = FALSE
)
# Nonoceanic sea level Maui Nui -----------------------------------------------
time <- 2.55
M <- 1000
lac <- c(0.0001, 0.0002, 0.0003)
mu_min <- c(1, 2)
mu_p <- c(50, 100)
K <- c(0.001, 0.01, Inf)
gam <- c(0.01, 0.02, 0.03)
laa <- c(1, 2)
island_ontogeny <- "const"
sea_level <- "sine"
max_area <- 13500
peak_time <- 0
sharpness <- 0
total_island_age <- 2.55
sea_level_amplitude <- 60
sea_level_frequency <- 2.55 * 10
island_gradient_angle <- c(75, 85)
extcutoff <- 1000
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
nonoceanic_sea_level_maui <- expand.grid(
time = time,
M = M,
lac = lac,
mu_min = mu_min,
mu_p = mu_p,
K = K,
gam = gam,
laa = laa,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
max_area = max_area,
peak_time = peak_time,
sharpness = sharpness,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle,
extcutoff = extcutoff,
x_s = x_s,
x_nonend = x_nonend,
stringsAsFactors = FALSE
)
# Nonoceanic sea level Kauai -----------------------------------------------
time <- 6.15
M <- 1000
lac <- c(0.0001, 0.0002, 0.0003)
mu_min <- c(1, 2)
mu_p <- c(50, 100)
K <- c(0.001, 0.01, Inf)
gam <- c(0.01, 0.02, 0.03)
laa <- c(1, 2)
island_ontogeny <- "const"
sea_level <- "sine"
max_area <- 3787
peak_time <- 0
sharpness <- 0
total_island_age <- 6.15
sea_level_amplitude <- 60
sea_level_frequency <- 6.15 * 10
island_gradient_angle <- c(75, 85)
extcutoff <- 1000
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
nonoceanic_sea_level_kauai <- expand.grid(
time = time,
M = M,
lac = lac,
mu_min = mu_min,
mu_p = mu_p,
K = K,
gam = gam,
laa = laa,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
max_area = max_area,
peak_time = peak_time,
sharpness = sharpness,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle,
extcutoff = extcutoff,
x_s = x_s,
x_nonend = x_nonend,
stringsAsFactors = FALSE
)
# Complete nonoceanic sea level paramter set -------------------------------
nonoceanic_sea_level <- rbind(
nonoceanic_sea_level_maui,
nonoceanic_sea_level_kauai
)
write.csv2(
nonoceanic_sea_level,
"data/nonoceanic_sea_level.csv",
row.names = FALSE
)
# Nonoceanic 1 short land bridge DI Maui Nui
time <- 2.55
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- Inf
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(1.225, 1.325)))
maui_nui_1_short_lb_di <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
maui_nui_1_short_lb_di <- cbind(maui_nui_1_short_lb_di,
lac_2 = maui_nui_1_short_lb_di[, 3] / 2,
mu_2 = maui_nui_1_short_lb_di[, 4] / 2,
K_2 = K_1,
gam_2 = maui_nui_1_short_lb_di[, 6] * 2,
laa_2 = 0)
# Nonoceanic 1 long land bridge DI Maui Nui
time <- 2.55
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- Inf
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(1.175, 1.375)))
maui_nui_1_long_lb_di <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
maui_nui_1_long_lb_di <- cbind(maui_nui_1_long_lb_di,
lac_2 = maui_nui_1_long_lb_di[, 3] / 2,
mu_2 = maui_nui_1_long_lb_di[, 4] / 2,
K_2 = K_1,
gam_2 = maui_nui_1_long_lb_di[, 6] * 2,
laa_2 = 0)
# Nonoceanic 3 short land bridge DI Maui Nui
time <- 2.55
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- Inf
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(0.5875, 0.6875, 1.225, 1.325, 1.8625, 1.9625)))
maui_nui_3_short_lb_di <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
maui_nui_3_short_lb_di <- cbind(maui_nui_3_short_lb_di,
lac_2 = maui_nui_3_short_lb_di[, 3] / 2,
mu_2 = maui_nui_3_short_lb_di[, 4] / 2,
K_2 = K_1,
gam_2 = maui_nui_3_short_lb_di[, 6] * 2,
laa_2 = 0)
# Nonoceanic 3 long land bridge DI Maui Nui
time <- 2.55
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- Inf
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(0.5375, 0.7375, 1.175, 1.375, 1.8125, 2.0125)))
maui_nui_3_long_lb_di <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
maui_nui_3_long_lb_di <- cbind(maui_nui_3_long_lb_di,
lac_2 = maui_nui_3_long_lb_di[, 3] / 2,
mu_2 = maui_nui_3_long_lb_di[, 4] / 2,
K_2 = K_1,
gam_2 = maui_nui_3_long_lb_di[, 6] * 2,
laa_2 = 0)
# Nonoceanic 1 short land bridge DD Maui Nui
time <- 2.55
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- 10
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(1.225, 1.325)))
maui_nui_1_short_lb_dd <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
maui_nui_1_short_lb_dd <- cbind(maui_nui_1_short_lb_dd,
lac_2 = maui_nui_1_short_lb_dd[, 3] / 2,
mu_2 = maui_nui_1_short_lb_dd[, 4] / 2,
K_2 = K_1,
gam_2 = maui_nui_1_short_lb_dd[, 6] * 2,
laa_2 = 0)
# Nonoceanic 1 long land bridge DD Maui Nui
time <- 2.55
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- 10
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(1.175, 1.375)))
maui_nui_1_long_lb_dd <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
maui_nui_1_long_lb_dd <- cbind(maui_nui_1_long_lb_dd,
lac_2 = maui_nui_1_long_lb_dd[, 3] / 2,
mu_2 = maui_nui_1_long_lb_dd[, 4] / 2,
K_2 = K_1,
gam_2 = maui_nui_1_long_lb_dd[, 6] * 2,
laa_2 = 0)
# Nonoceanic 3 short land bridge DD Maui Nui
time <- 2.55
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- 10
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(0.5875, 0.6875, 1.225, 1.325, 1.8625, 1.9625)))
maui_nui_3_short_lb_dd <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
maui_nui_3_short_lb_dd <- cbind(maui_nui_3_short_lb_dd,
lac_2 = maui_nui_3_short_lb_dd[, 3] / 2,
mu_2 = maui_nui_3_short_lb_dd[, 4] / 2,
K_2 = K_1,
gam_2 = maui_nui_3_short_lb_dd[, 6] * 2,
laa_2 = 0)
# Nonoceanic 3 long land bridge DD Maui Nui
time <- 2.55
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- 10
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(0.5375, 0.7375, 1.175, 1.375, 1.8125, 2.0125)))
maui_nui_3_long_lb_dd <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
maui_nui_3_long_lb_dd <- cbind(maui_nui_3_long_lb_dd,
lac_2 = maui_nui_3_long_lb_dd[, 3] / 2,
mu_2 = maui_nui_3_long_lb_dd[, 4] / 2,
K_2 = K_1,
gam_2 = maui_nui_3_long_lb_dd[, 6] * 2,
laa_2 = 0)
# Nonoceanic 1 short land bridge DI Kauai
time <- 6.15
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- Inf
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(3.025, 3.125)))
kauai_1_short_lb_di <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
kauai_1_short_lb_di <- cbind(kauai_1_short_lb_di,
lac_2 = kauai_1_short_lb_di[, 3] / 2,
mu_2 = kauai_1_short_lb_di[, 4] / 2,
K_2 = K_1,
gam_2 = kauai_1_short_lb_di[, 6] * 2,
laa_2 = 0)
# Nonoceanic 1 long land bridge DI Kauai
time <- 6.15
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- Inf
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(2.975, 3.175)))
kauai_1_long_lb_di <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
kauai_1_long_lb_di <- cbind(kauai_1_long_lb_di,
lac_2 = kauai_1_long_lb_di[, 3] / 2,
mu_2 = kauai_1_long_lb_di[, 4] / 2,
K_2 = K_1,
gam_2 = kauai_1_long_lb_di[, 6] * 2,
laa_2 = 0)
# Nonoceanic 3 short land bridge DI Kauai
time <- 6.15
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- Inf
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(1.4875, 1.5875, 3.025, 3.125, 4.5625, 4.6625)))
kauai_3_short_lb_di <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
kauai_3_short_lb_di <- cbind(kauai_3_short_lb_di,
lac_2 = kauai_3_short_lb_di[, 3] / 2,
mu_2 = kauai_3_short_lb_di[, 4] / 2,
K_2 = K_1,
gam_2 = kauai_3_short_lb_di[, 6] * 2,
laa_2 = 0)
# Nonoceanic 3 long land bridge DI Kauai
time <- 6.15
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- Inf
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(1.4375, 1.6375, 2.975, 3.175, 4.5125, 4.7125)))
kauai_3_long_lb_di <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
kauai_3_long_lb_di <- cbind(kauai_3_long_lb_di,
lac_2 = kauai_3_long_lb_di[, 3] / 2,
mu_2 = kauai_3_long_lb_di[, 4] / 2,
K_2 = K_1,
gam_2 = kauai_3_long_lb_di[, 6] * 2,
laa_2 = 0)
# Nonoceanic 1 short land bridge DD Kauai
time <- 6.15
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- 10
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(3.025, 3.125)))
kauai_1_short_lb_dd <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
kauai_1_short_lb_dd <- cbind(kauai_1_short_lb_dd,
lac_2 = kauai_1_short_lb_dd[, 3] / 2,
mu_2 = kauai_1_short_lb_dd[, 4] / 2,
K_2 = K_1,
gam_2 = kauai_1_short_lb_dd[, 6] * 2,
laa_2 = 0)
# Nonoceanic 1 long land bridge DD Kauai
time <- 6.15
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- 10
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(2.975, 3.175)))
kauai_1_long_lb_dd <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
kauai_1_long_lb_dd <- cbind(kauai_1_long_lb_dd,
lac_2 = kauai_1_long_lb_dd[, 3] / 2,
mu_2 = kauai_1_long_lb_dd[, 4] / 2,
K_2 = K_1,
gam_2 = kauai_1_long_lb_dd[, 6] * 2,
laa_2 = 0)
# Nonoceanic 3 short land bridge DD Kauai
time <- 6.15
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- 10
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(1.4875, 1.5875, 3.025, 3.125, 4.5625, 4.6625)))
kauai_3_short_lb_dd <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
kauai_3_short_lb_dd <- cbind(kauai_3_short_lb_dd,
lac_2 = kauai_3_short_lb_dd[, 3] / 2,
mu_2 = kauai_3_short_lb_dd[, 4] / 2,
K_2 = K_1,
gam_2 = kauai_3_short_lb_dd[, 6] * 2,
laa_2 = 0)
# Nonoceanic 3 long land bridge DD Kauai
time <- 6.15
M <- 1000
lac_1 <- c(0.5, 1, 2)
mu_1 <- c(0.5, 1, 2)
K_1 <- 10
gam_1 <- c(0.01, 0.05, 0.1)
laa_1 <- 1
x_s <- c(0.05, 0.1)
x_nonend <- c(0.1, 0.9)
shift_times <- I(list(c(1.4375, 1.6375, 2.975, 3.175, 4.5125, 4.7125)))
kauai_3_long_lb_dd <- expand.grid(time = time,
M = M,
lac_1 = lac_1,
mu_1 = mu_1,
K_1 = K_1,
gam_1 = gam_1,
laa_1 = laa_1,
x_s = x_s,
x_nonend = x_nonend,
shift_times = shift_times)
kauai_3_long_lb_dd <- cbind(kauai_3_long_lb_dd,
lac_2 = kauai_3_long_lb_dd[, 3] / 2,
mu_2 = kauai_3_long_lb_dd[, 4] / 2,
K_2 = K_1,
gam_2 = kauai_3_long_lb_dd[, 6] * 2,
laa_2 = 0)
# Complete nonoceanic land bridge paramter set -------------------------------
nonoceanic_land_bridge <- rbind(
maui_nui_1_short_lb_di,
maui_nui_1_long_lb_di,
maui_nui_3_short_lb_di,
maui_nui_3_long_lb_di,
maui_nui_1_short_lb_dd,
maui_nui_1_long_lb_dd,
maui_nui_3_short_lb_dd,
maui_nui_3_long_lb_dd,
kauai_1_short_lb_di,
kauai_1_long_lb_di,
kauai_3_short_lb_di,
kauai_3_long_lb_di,
kauai_1_short_lb_dd,
kauai_1_long_lb_dd,
kauai_3_short_lb_dd,
kauai_3_long_lb_dd
)
write.csv2(
nonoceanic_land_bridge,
"data/nonoceanic_land_bridge.csv",
row.names = FALSE
)
# Trait dependent rates Maui Nui
time <- 2.55
Mtotal <- 1000
M <- c(Mtotal * 0.1, Mtotal * 0.5, Mtotal)
lac <- c(0.5, 1, 2)
mu <- c(0.5, 1, 2)
K <- c(10, Inf)
gam <- c(0.01, 0.05, 0.1)
laa <- 1
trans <- c(0, 0.5)
trans2 <- c(0, 0.1, 0.5)
trait_maui_nui <- expand.grid(time = time,
M = M,
lac = lac,
mu = mu,
K = K,
gam = gam,
laa = laa,
trans = trans,
trans2 = trans2)
trait_maui_nui <- cbind(trait_maui_nui,
M2 = Mtotal - trait_maui_nui[, 2],
lac2 = trait_maui_nui[, 3] / 2,
mu2 = trait_maui_nui[, 4] / 2,
gam2 = trait_maui_nui[, 6] * 2,
laa2 = trait_maui_nui[, 7] * 2)
# Trait dependent rates kauai
time <- 6.15
Mtotal <- 1000
M <- c(Mtotal * 0.1, Mtotal * 0.5, Mtotal)
lac <- c(0.5, 1, 2)
mu <- c(0.5, 1, 2)
K <- c(10, Inf)
gam <- c(0.01, 0.05, 0.1)
laa <- 1
trans <- c(0, 0.5)
trans2 <- c(0, 0.1, 0.5)
trait_kauai <- expand.grid(time = time,
M = M,
lac = lac,
mu = mu,
K = K,
gam = gam,
laa = laa,
trans = trans,
trans2 = trans2)
trait_kauai <- cbind(trait_kauai,
M2 = Mtotal - trait_kauai[, 2],
lac2 = trait_kauai[, 3] / 2,
mu2 = trait_kauai[, 4] / 2,
gam2 = trait_kauai[, 6] * 2,
laa2 = trait_kauai[, 7] * 2)
# Complete trait dependent paramter set -----------------------------------
trait <- rbind(
trait_maui_nui,
trait_kauai
)
write.csv2(
trait,
"data/trait.csv",
row.names = FALSE
)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.