Functions that access slots of a *_ipm (including
proto_ipm). default methods correspond to *_ipm objects.
domains(object)
# S3 method for proto_ipm
domains(object)
# S3 method for default
domains(object)
vital_rate_exprs(object)
# S3 method for proto_ipm
vital_rate_exprs(object)
# S3 method for default
vital_rate_exprs(object)
vital_rate_funs(ipm)
# S3 method for ipmr_ipm
vital_rate_funs(ipm)
vital_rate_exprs(object, kernel, vital_rate) <- value
# S3 method for proto_ipm
vital_rate_exprs(object, kernel, vital_rate) <- value
new_fun_form(form)
kernel_formulae(object)
# S3 method for proto_ipm
kernel_formulae(object)
# S3 method for default
kernel_formulae(object)
kernel_formulae(object, kernel) <- value
# S3 method for proto_ipm
kernel_formulae(object, kernel) <- value
parameters(object)
# S3 method for proto_ipm
parameters(object)
# S3 method for default
parameters(object)
parameters(object, ...) <- value
# S3 method for proto_ipm
parameters(object, ...) <- value
int_mesh(ipm, full_mesh = TRUE)
# S3 method for ipmr_ipm
int_mesh(ipm, full_mesh = TRUE)
pop_state(object)
# S3 method for proto_ipm
pop_state(object)
# S3 method for default
pop_state(object)A proto_ipm or object created by make_ipm().
An object created by make_ipm(). This argument only applies to
int_mesh() and vital_rate_funs() (because these quantities don't
exist until make_ipm() is called).
The name of the kernel to insert the new vital rate expression into.
The name of the vital rate to replace. If the vital rate
doesn't already exist in the object, a new one with this name will be
created.
For parameters<-, a named list of new parameters. The new list does not need
to contain all of the parameters, just the ones to update/append. For
vital_rate_exprs<- and kernel_formulae<-, a new functional form.
The new functional form must be wrapped in a call to new_fun_form.
An expression representing the new vital rate or kernel formula to insert.
Additional arguments used in RPadrino methods.
Return the full integration mesh? Default is TRUE.
FALSE returns only unique values for each state variable.
Depending on the class of object, a list
with types numeric or character.
The *.default method corresponds to output from make_ipm(),
and the *.proto_ipm methods correspond to outputs from define_*.
When using kernel_formulae<- and vital_rates_exprs<-, the right
hand side of the expression must be wrapped in new_fun_form. See
examples.
Note that when using vital_rate_funs, unless the vital rate expression
explicitly contains an expression for integration, these functions
are not yet integrated! This is useful for things like sensitivity
and elasticity analysis, but care must be taken to not use these values
incorrectly.
data(gen_di_det_ex)
proto <- gen_di_det_ex$proto_ipm
# Create a new, iterated IPM
new_ipm <- make_ipm(proto, iterate = TRUE,
iterations = 100, return_all_envs = TRUE)
vital_rate_exprs(new_ipm)
#> g: dnorm(ht_2, g_mu, g_sd)
#> g_mu: g_int + g_slope * ht_1
#> s: inv_logit_2(s_int, s_slope, s_slope_2, ht_1)
#> f_r: inv_logit(f_r_int, f_r_slope, ht_1)
#> f_s: exp(f_s_int + f_s_slope * ht_1)
#> f_d: dnorm(ht_2, f_d_mu, f_d_sd)
kernel_formulae(new_ipm)
#> P: s * g * d_ht
#> go_discrete: f_r * f_s * g_i * d_ht
#> stay_discrete: 0
#> leave_discrete: e_p * f_d * d_ht
vital_rate_funs(new_ipm)
#> $P
#> g (not yet discretized): A 200 x 200 kernel with minimum value: 0 and maximum value: 0.0344
#> g_mu (not yet discretized): A 200 x 200 kernel with minimum value: 8.3275 and maximum value: 620.7542
#> s (not yet discretized): A 200 x 200 kernel with minimum value: 0.001 and maximum value: 1
#>
#> $go_discrete
#> f_r (not yet discretized): A 1 x 200 row vector with minimum value: 0 and maximum value: 1
#> f_s (not yet discretized): A 1 x 200 row vector with minimum value: 14.1933 and maximum value: 34141.8242
#>
#> $stay_discrete
#> No vital rates specified
#>
#> $leave_discrete
#> f_d (not yet discretized): A 200 x 1 column vector with minimum value: 0 and maximum value: 0.1948
#>
domains(new_ipm)
#> ht: lower_bound = 1.02, upper_bound = 624, n_meshpoints = 200
parameters(new_ipm)
#> g_int g_slope g_sd s_int s_slope s_slope_2 f_r_int
#> 5.781000 0.988000 20.556990 -0.352000 0.122000 -0.000213 -11.460000
#> f_r_slope f_s_int f_s_slope f_d_mu f_d_sd e_p g_i
#> 0.083500 2.620400 0.012560 5.665500 2.073400 0.150000 0.506700
# Usage is the same for proto_ipm's as *_ipm's
vital_rate_exprs(proto)
#> g: dnorm(ht_2, g_mu, g_sd)
#> g_mu: g_int + g_slope * ht_1
#> s: inv_logit_2(s_int, s_slope, s_slope_2, ht_1)
#> f_r: inv_logit(f_r_int, f_r_slope, ht_1)
#> f_s: exp(f_s_int + f_s_slope * ht_1)
#> f_d: dnorm(ht_2, f_d_mu, f_d_sd)
kernel_formulae(proto)
#> P: s * g * d_ht
#> go_discrete: f_r * f_s * g_i * d_ht
#> stay_discrete: 0
#> leave_discrete: e_p * f_d * d_ht
domains(proto)
#> ht: lower_bound = 1.02, upper_bound = 624, n_meshpoints = 200
parameters(proto)
#> g_int g_slope g_sd s_int s_slope s_slope_2 f_r_int
#> 5.781000 0.988000 20.556990 -0.352000 0.122000 -0.000213 -11.460000
#> f_r_slope f_s_int f_s_slope f_d_mu f_d_sd e_p g_i
#> 0.083500 2.620400 0.012560 5.665500 2.073400 0.150000 0.506700
int_mesh(new_ipm)
#> d_ht - 3.1149
#> ht_1 - Lower bound: 2.57745, Upper bound: 622.44255, # of Meshpoints: 200
#> ht_2 - Lower bound: 2.57745, Upper bound: 622.44255, # of Meshpoints: 200
# Setting new parameters, vital rate expressions, and kernel formulae
# only works on proto_ipm's.
# This replaces the "g_int" parameter and leaves the rest untouched
parameters(proto) <- list(g_int = 1.5)
# This creates a new g_z parameter and leaves the rest of parameters untouched
parameters(proto) <- list(g_z = 2.2)
# setting a new vital rate or kernel expression requires wrapping the
# right-hand side in a call to new_fun_form(). new_fun_form uses expressions
# with the same format as ... in define_kernel()
vital_rate_exprs(proto,
kernel = "P",
vital_rate = "g_mu") <- new_fun_form(g_int + g_z + g_slope * ht_1)
kernel_formulae(proto, kernel = "stay_discrete") <- new_fun_form(g_z * d_ht)