Hi,
I am trying to optimise a categorical resistance surface, which contains landcover data with pre-assigned resistance values from the literature. I would like to optimise this to identify which landcovers are important for gene flow in my study area.
I ratify the categorical variables following the tutorial, and make a conductance surface using the below code:
surface_gsp <- conductance_surface(covariates = stack(Region_rat), coords = Coords, directions = 4)
I then make a Euclidean genetic distance matrix using dist() in adegenet between all samples.
I then try to fit mlpe using the below code:
fit_mlpe_cat <- radish(Genetic_dist ~ Region_Mosaic, data = surface_gsp,
conductance_model = radish::loglinear_conductance,
measurement_model = radish::mlpe)
However I get the error code below almost immediately:
Projected Newton-Raphson with Hager-Zhang line search
Error in radish_algorithm(f = conductance_model, g = measurement_model, :
length(s$demes) == nrow(S) is not TRUE
What is s$demes and nrow(S) referring to? I would greatly appreciate any guidance on how to get this to work.
Hi, I am trying to optimise a categorical resistance surface, which contains landcover data with pre-assigned resistance values from the literature. I would like to optimise this to identify which landcovers are important for gene flow in my study area.
I ratify the categorical variables following the tutorial, and make a conductance surface using the below code: surface_gsp <- conductance_surface(covariates = stack(Region_rat), coords = Coords, directions = 4)
I then make a Euclidean genetic distance matrix using dist() in adegenet between all samples.
I then try to fit mlpe using the below code: fit_mlpe_cat <- radish(Genetic_dist ~ Region_Mosaic, data = surface_gsp, conductance_model = radish::loglinear_conductance, measurement_model = radish::mlpe)
However I get the error code below almost immediately: Projected Newton-Raphson with Hager-Zhang line search Error in radish_algorithm(f = conductance_model, g = measurement_model, : length(s$demes) == nrow(S) is not TRUE
What is s$demes and nrow(S) referring to? I would greatly appreciate any guidance on how to get this to work.
Many thanks