Reads a text configuration file (KEY = value), merges values with package defaults, validates options, resolves gradient specifications into a tidy table, materialises quadrat sizes, and sets the random seed. This is the only supported public entry point for reading configs; low-level parsing is handled internally.
Value
A named list P with fully-resolved parameters used by the
simulator (including a tidy P$GRADIENT tibble and P$QUADRAT_SIZE).
Details
Supported value forms:
Scalars:
300,TRUE,0.15,"#22223b".Comma vectors:
A,B,Cor0.1, 0.2, 0.3.R-style character vectors for inline edgelists: e.g.
INTERACTIONS_EDGELIST = c("A,B-D,0.8", "C,A,1.2", "E,*,0.95").Named entries:
A:0.55,temperature:0.12.
You may specify INTERACTIONS_FILE = "path/to/interactions.txt" to point to
a separate interactions config, or embed rules directly with
INTERACTIONS_EDGELIST = c("A,B-D,0.8", "C,A,1.2"). If neither is provided,
interactions default to neutral (all 1.0) with INTERACTION_RADIUS = 0.
Gradient keys can be arbitrary driver names (legacy defaults:
temperature, elevation, rainfall). Use
GRADIENT_SPECIES, GRADIENT_ASSIGNMENTS, plus either
GRADIENT_OPTIMA and GRADIENT_TOLERANCE as scalar, per-species
named, or per-gradient named values.
Model-family presets:
manual: no high-level preset.niche_filtering: baseline Poisson placement plus gradient filtering.neutral_csr: neutral SAD baseline with CSR placement.neutral_hubbell_like: sequential neutral recruitment with immigration/speciation and dispersal.hybrid: neutral recruitment with environmental sorting during recruitment.
Constrained landscape options:
DOMAIN_TYPE = "network"or"coastline"enables a linearized coordinate for recruitment and distance-decay summaries.DISTANCE_METRIC = "along_path"uses along-coordinate distance.ENV_COVARIATES_FILEcan supply external section/node covariates (CSV withx,y, and environmental columns).