abund projections

R/RK_project_alpha_pairwise_lambdacov_global_alphacov_global.R

@@ -44,7 +44,7 @@ RK_project_alpha_pairwise_lambdacov_global_alphacov_global <- function(lambda,
 
   term <- 0 #create the denominator term for the model
   for(z in 1:length(abundance)){
-    term <- term - (alpha[z] + cov_term[[z]]) * abundance[z]  
+    term <- term - (alpha[z] + cov_term) * abundance[z]  
   }
   expected_abund <- (lambda * (num) * exp(term)) * abundance[names(lambda)]
   expected_abund

R/abundance_projection.R

@@ -16,7 +16,7 @@
 #' @param alpha_matrix square matrix with taxa names in rows and columns.
 #' @param lambda_cov optional named matrix with covariates in columns and taxa in rows,
 #' representing the effect of each covariate on the lambda parameter of each taxa.
-#' @param alpha_cov optional list. Each element of the named list represents the effects of
+#' @param alpha_cov REWRITE optional list. Each element of the named list represents the effects of
 #' a covariate over alpha values. Thus, each list element contains either 
 #' a single element (alpha_cov_form "global").
 #' or a square matrix of same dimensions as `alpha_matrix` (alpha_cov_form "pairwise").