Merge branch 'main' into dev

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: scLANE
 Type: Package
 Title: Model gene expression dynamics with spline-based NB GLMs, GEEs, & GLMMs
-Version: 0.7.9
+Version: 0.8.0
 Authors@R: c(person(given = "Jack", family = "Leary", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0009-0004-8821-3269")), 
              person(given = "Rhonda", family = "Bacher", email = "[email protected]", role = c("ctb", "fnd"), comment = c(ORCID = "0000-0001-5787-476X")))
 Description: scLANE uses truncated power basis spline models to build flexible, interpretable models of single cell gene expression over pseudotime or latent time. 

R/fitGLMM.R

@@ -161,8 +161,8 @@ fitGLMM <- function(X_pred = NULL,
     }
   }
   # set up results
-  marge_style_names <- c("B_finalIntercept", marge_style_names)
-  coef_names <- c("Intercept", coef_names)
+  marge_style_names <- c("B_finalIntercept", marge_style_names[nonzero_coefs])
+  coef_names <- c("Intercept", coef_names[nonzero_coefs])
   res <- list(final_mod = glmm_mod,
               basis_mtx = NULL,
               WIC_mtx = NULL,  # only used in GLM / GEE models

R/stat_out_score_gee_null.R

@@ -41,7 +41,7 @@ stat_out_score_gee_null <- function(Y = NULL,
   alpha_est <- ests$alpha
   sigma_est <- ests$phi
   mu_est <- as.matrix(stats::fitted.values(ests))
-  V_est <- mu_est * (1 + mu_est * sigma_est)  # Type I NB variance = mu (1 + mu * sigma); sigma = 1 / theta
+  V_est <- mu_est * (1 + mu_est * sigma_est)  # Type I NB variance = mu (1 + mu * sigma); sigma = 1 / phi
   n_vec1 <- c(0, n_vec)
   VS_est_list <- AWA_est_list <- J2_list <- Sigma2_list <- vector("list", length = N)
   J11 <- Sigma11 <- matrix(0, ncol(B_null), ncol(B_null))
@@ -52,7 +52,8 @@ stat_out_score_gee_null <- function(Y = NULL,
     if (cor.structure == "independence") {
       R_alpha <- diag(1, n_vec[i], n_vec[i])
     } else if (cor.structure == "exchangeable") {
-      R_alpha <- matrix(alpha_est, n_vec[i], n_vec[i]) + diag(c(1 - alpha_est), n_vec[i], n_vec[i])
+      R_alpha <- matrix(alpha_est, nrow = n_vec[i], ncol = n_vec[i])
+      R_alpha <- R_alpha + diag(c(1 - alpha_est), nrow = n_vec[i], ncol = n_vec[i])
     } else if (cor.structure == "ar1") {
       R_alpha <- alpha_est^outer(seq(n_vec[i]), seq(n_vec[i]), \(x, y) abs(x - y))
     } else {