R/ui_model-building.R
add_covariates.Rd
Note that new global parameters are not given any default prior.
add_covariates(nm, ..., use_regexpr = TRUE)
A networkModel
object.
One or several formulas defining the covariates.
Boolean, use regular expression to match the parameters affected by the formulas?
A networkModel
object.
# Using a subset of the topology from the Trinidad case study
m <- new_networkModel() %>%
set_topo("NH4, NO3 -> epi, FBOM", "epi -> petro, pseph")
#> Using default distribution family for proportions ("gamma_cv").
#> (eta is the coefficient of variation of gamma distributions.)
#> Using default distribution family for sizes ("normal_cv").
#> (zeta is the coefficient of variation of normal distributions.)
# Taking initial condtions from the 'lalaja' dataset at t=0
# Grouping by transect id
inits <- lalaja[lalaja[["time.days"]] == 0, ]
inits
#> # A tibble: 24 × 6
#> # Groups: stream, transect [3]
#> stream transect compartment mgN.per.m2 prop15N time.days
#> <chr> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 UL transect.1 NH4 0.300 0.0240 0
#> 2 UL transect.1 NO3 31.5 0.00397 0
#> 3 UL transect.2 NH4 0.300 0.0140 0
#> 4 UL transect.2 NO3 31.5 0.00407 0
#> 5 UL transect.3 NH4 0.300 0.00694 0
#> 6 UL transect.3 NO3 31.5 0.00413 0
#> 7 UL transect.1 arg 2.31 0.00366 0
#> 8 UL transect.2 arg 2.31 0.00366 0
#> 9 UL transect.3 arg 2.31 0.00366 0
#> 10 UL transect.1 epi 329. 0.00366 0
#> # ℹ 14 more rows
m <- set_init(m, inits, comp = "compartment", size = "mgN.per.m2",
prop = "prop15N", group_by = "transect")
#> Some compartments are not present in the network topology and are
#> removed from the initial data:
#> - arg
#> - tricor
m
#> # A tibble: 3 × 5
#> topology initial observations parameters group
#> <list> <list> <list> <list> <list>
#> 1 <topology [6 × 6]> <tibble [6 × 3]> <NULL> <tibble [14 × 2]> <chr [1]>
#> 2 <topology [6 × 6]> <tibble [6 × 3]> <NULL> <tibble [14 × 2]> <chr [1]>
#> 3 <topology [6 × 6]> <tibble [6 × 3]> <NULL> <tibble [14 × 2]> <chr [1]>
# Default model
params(m, simplify = TRUE)
#> [1] "eta" "lambda_FBOM" "lambda_NH4"
#> [4] "lambda_NO3" "lambda_epi" "lambda_petro"
#> [7] "lambda_pseph" "upsilon_NH4_to_FBOM" "upsilon_NH4_to_epi"
#> [10] "upsilon_NO3_to_FBOM" "upsilon_NO3_to_epi" "upsilon_epi_to_petro"
#> [13] "upsilon_epi_to_pseph" "zeta"
# Adding an effect of the "transect" covariate on some parameters
m <- add_covariates(m, upsilon_epi_to_pseph ~ transect)
params(m, simplify = TRUE)
#> [1] "eta" "lambda_FBOM"
#> [3] "lambda_NH4" "lambda_NO3"
#> [5] "lambda_epi" "lambda_petro"
#> [7] "lambda_pseph" "upsilon_NH4_to_FBOM"
#> [9] "upsilon_NH4_to_epi" "upsilon_NO3_to_FBOM"
#> [11] "upsilon_NO3_to_epi" "upsilon_epi_to_petro"
#> [13] "upsilon_epi_to_pseph|transect.1" "upsilon_epi_to_pseph|transect.2"
#> [15] "upsilon_epi_to_pseph|transect.3" "zeta"