Loading NAMESPACE +1 −0 Original line number Diff line number Diff line Loading @@ -17,6 +17,7 @@ export(collapse_counts) export(compute_I2) export(compute_hash) export(correct_counts) export(fit_model.presto) export(genemeans.presto) export(glmm_uni) export(nnzeroGroups) Loading R/glmm.R +2 −1 Original line number Diff line number Diff line Loading @@ -44,7 +44,7 @@ glmm_uni <- function(feature, formula, design, response, family, nsim, has_offse ## prior distributions for random effects ## CAUTION: Residuals are dropped for lmer without as.data.frame prior_sd <- as.numeric(as.data.frame(lme4::VarCorr(model))$vcov) prior_sd <- as.numeric(as.data.frame(lme4::VarCorr(model))$sdcor) if (isGLMM(model)) { ## for GLMMs, use SD of pearson residuals prior_sd <- c(prior_sd, sd(residuals(model, 'pearson'))) Loading @@ -57,6 +57,7 @@ glmm_uni <- function(feature, formula, design, response, family, nsim, has_offse }) } #' @export fit_model.presto <- function(formula, design, response, feature, family) { ## initialize model on one feature if (family == 'nb') { Loading Loading
NAMESPACE +1 −0 Original line number Diff line number Diff line Loading @@ -17,6 +17,7 @@ export(collapse_counts) export(compute_I2) export(compute_hash) export(correct_counts) export(fit_model.presto) export(genemeans.presto) export(glmm_uni) export(nnzeroGroups) Loading
R/glmm.R +2 −1 Original line number Diff line number Diff line Loading @@ -44,7 +44,7 @@ glmm_uni <- function(feature, formula, design, response, family, nsim, has_offse ## prior distributions for random effects ## CAUTION: Residuals are dropped for lmer without as.data.frame prior_sd <- as.numeric(as.data.frame(lme4::VarCorr(model))$vcov) prior_sd <- as.numeric(as.data.frame(lme4::VarCorr(model))$sdcor) if (isGLMM(model)) { ## for GLMMs, use SD of pearson residuals prior_sd <- c(prior_sd, sd(residuals(model, 'pearson'))) Loading @@ -57,6 +57,7 @@ glmm_uni <- function(feature, formula, design, response, family, nsim, has_offse }) } #' @export fit_model.presto <- function(formula, design, response, feature, family) { ## initialize model on one feature if (family == 'nb') { Loading
