`sim_rescomp()`

`R/spec_rescomp.R`

`spec_rescomp.Rd`

Generate list of parameters for a consumer-resource model to be
passed to `sim_rescomp()`

```
spec_rescomp(
spnum = 1,
resnum = 1,
mumatrix,
kmatrix,
qmatrix,
effmatrix = NULL,
funcresp = "type1",
essential = FALSE,
chemo = TRUE,
mort = 0.03,
resspeed = 0.03,
resconc = 1,
respulse = 0,
mortpulse = 0,
pulsefreq = 0,
batchtrans = FALSE,
timepars = FALSE,
totaltime = 1000,
timeparfreq = 0,
tpinterp = "inst",
cinit = 10,
rinit = NULL,
introseq = NULL,
verbose = TRUE
)
```

- spnum
Integer vector of length 1 for the number of consumers

- resnum
Integer vector of length 1 for the number of resources

- mumatrix
Numeric matrix or list of matrices, the elements of which give the maximum growth rates (type 2 or 3) or resource consumption rate constants (type 1, or type 2 when parameterised using conversion efficiencies with

`effmatrix`

as opposed to resource quotas with`qmatrix`

). The number of rows and columns should be equal to`spnum`

and`resnum`

respectively. For time dependent parameters (with`timepars`

= TRUE), expects a list of length 2.- kmatrix
Numeric matrix or list of matrices, the elements of which give the of half saturation constants (type 2 or type 3, ignored if funcresp = "type1"). The number of rows and columns should be equal to

`spnum`

and`resnum`

respectively. For time dependent parameters (with`timepars`

= TRUE), expects a list of length 2.- qmatrix
Numeric matrix or list of matrices, the elements of which give the resource quotas. The number of rows and columns should be equal to

`spnum`

and`resnum`

respectively. For time dependent parameters (with`timepars`

= TRUE), expects a list of length 2. Default = 0.001 for all consumers.- effmatrix
Numeric matrix of resource conversion efficiencies. The number of rows should be equal to

`spnum`

and`resnum`

respectively. NB. Incompatible with specification of resource quotas. Function will throw an error if both specified.- funcresp
Character vector of length 1 or length equal to

`spnum`

. Options include "type1", 'type2", or "type3".- essential
Logical vector of length 1. If FALSE resources are substitutable.

- chemo
Logical. Default is resources supplied continuously (chemostat). If FALSE resources grow logistically.

- mort
Numeric vector or list of vectors of length 1 or length =

`spnum`

, specifying density independent mortality rates. For time dependent parameters (with`timepars`

= TRUE), expects a list of length 2.- resspeed
Numeric vector of length 1 specifying resource intrinsic rate of increase (if chemo = FALSE), or otherwise chemostat dilution rate. Set to zero for pulsing only. For continuous dilution of resource without resource supply,

`resspeed`

should be non-zero with`resconc`

set to zero.- resconc
Numeric vector of length 1 or length =

`resnum`

specifying resource carrying capacity (if chemo = FALSE), or otherwise chemostat supply concentration- respulse
Resource pulse size.

- mortpulse
Consumer mortality fraction if non-constant mortality (e.g. serial-batch transfer).

- pulsefreq
Frequency of resource pulsing and/or intermittent mortality.

- batchtrans
If TRUE, both resource is also fractionally sampled (see vignette).

- timepars
If TRUE, time dependent parameters required.

- totaltime
Total simulation time

- timeparfreq
Frequency of parameter switching if timepars = TRUE.

- tpinterp
Either "inst" (default), "lin" or "sine" interpolation of time dependent parameters. If "inst", parameters switch instantaneously with frequency given by

`timeparfreq`

. If "lin" or "sine", parameters are interpolated linearly or sinusoidaly, respectively, with period 2x`timeparfreq`

.- cinit
Numeric vector of length 1 or length =

`spnum`

specifying initialconsumer state values (densities). Defaults to 10 for all consumers.- rinit
Numeric vector of length 1 or length =

`resnum`

specifying initial resource state values (concentrations). Defaults to value given in`resconc`

.- introseq
Time sequence as a vector for consumer introductions. Vector length must equal spnum.

- verbose
If TRUE (default) prints model and simulation summary specs.

S3 object of class `rescomp`

.

```
# Single type I consumer on a single logistically growing resource
spec_rescomp()
#> Model properties
#> * 1 consumer(s) and 1 resource(s)
#> * Consumers have type 1 functional responses
#> * Resource supply is continuous (e.g. chemostat)
#> * Mortality is continuous
#>
#> Simulation properties
#> * Simulation time: 1000 time steps
#> * Init state: consumer(s) = [10], resource(s) = [1]
# Two type II consumers and two substitutable resources in a chemostat
pars <- spec_rescomp(
spnum = 2,
resnum = 2,
funcresp = "type2",
mumatrix = matrix(c(
0.7, 0.3,
0.4, 0.5
),
nrow = 2,
ncol = 2,
byrow = TRUE
),
resspeed = 3,
resconc = 1,
chemo = TRUE,
essential = FALSE
)
#> Model properties
#> * 2 consumer(s) and 2 resource(s)
#> * Consumers have type 2 functional responses
#> * Resources are substitutable
#> * Resource supply is continuous (e.g. chemostat)
#> * Mortality is continuous
#>
#> Simulation properties
#> * Simulation time: 1000 time steps
#> * Init state: consumer(s) = [10, 10], resource(s) = [1, 1]
```