dclab 0.62.11__cp39-cp39-macosx_11_0_arm64.whl → 2.18.0__cp39-cp39-macosx_11_0_arm64.whl

dclab/lme4/lme4_template.R

@@ -1,94 +0,0 @@
-require(stats);
-require(lme4);
-
-model_name <- "<MODEL_NAME>"
-cat("OUTPUT model:", model_name, "#*#\n")
-
-func_model <- "feature ~ group + (1 + group | repetition)"
-func_nullmodel <- "feature ~ (1 + group | repetition)"
-
-# These are the feature, group, and repetition arrays that are set by dclab
-# via templates.
-feature <- c(<FEATURES>)
-group <- c(<GROUPS>)
-repetition <- c(<REPETITIONS>)
-
-data <- data.frame(feature, group, repetition)
-
-if (model_name == "glmer+loglink") {
-    Model <- glmer(func_model, data, family=Gamma(link='log'))
-    NullModel <- glmer(func_nullmodel, data, family=Gamma(link='log'))
-} else if (model_name == "lmer") {
-    Model <- lmer(func_model, data)
-    NullModel <- lmer(func_nullmodel, data)
-} else {
-    stop("Invalid model_name:", model_name)
-}
-
-# Anova analysis (increase verbosity by making models global)
-# Using anova is a very conservative way of determining
-# p values.
-res_anova <- anova(Model, NullModel)
-cat("OUTPUT r anova: ")
-res_anova
-cat("#*#\n")
-
-pvalue <- res_anova$"Pr(>Chisq)"[2]
-cat("OUTPUT anova p-value:", pvalue, "#*#\n")
-
-model_summary <- summary(Model)
-cat("OUTPUT r model summary:")
-model_summary
-cat("#*#\n")
-
-model_coefficients <- coef(Model)
-cat("OUTPUT r model coefficients:")
-model_coefficients
-cat("#*#\n")
-
-fe_reps <- model_coefficients$repetition
-
-effects <- data.frame(coef(model_summary))
-
-fe_icept <- effects$Estimate[1]
-
-fe_treat <- effects$Estimate[2]
-
-if (model_name == "glmer+loglink") {
-    # transform back from log
-    fe_treat <- exp(fe_icept + fe_treat) - exp(fe_icept)
-    fe_icept <- exp(fe_icept)
-    fe_reps[, 2] = exp(fe_reps[, 1] + fe_reps[, 2]) - exp(fe_reps[, 1])
-    fe_reps[, 1] = exp(fe_reps[, 1])
-}
-
-cat("OUTPUT fixed effects intercept:", fe_icept, "#*#\n")
-cat("OUTPUT fixed effects treatment:", fe_treat, "#*#\n")
-cat("OUTPUT fixed effects repetitions:")
-fe_reps
-cat("#*#\n")
-
-# convergence
-
-# convergence warnings in lme4
-is_warning_generated <- function(m) {
-  df <- summary(m)
-  !is.null(df$optinfo$conv$lme4$messages) &&
-           grepl('failed to converge', df$optinfo$conv$lme4$messages)
-}
-lme4_not_converged <- is_warning_generated(Model)
-
-# convergence code by the optimizer
-lme4l <- model_summary$optinfo$conv$lme4
-if (length(lme4l) == 0) {
-    # the optimizer probably does not know
-    conv_code <- 0
-} else if (is.null(lme4l$code)) {
-    # NULL means 0
-    conv_code <- 0
-} else {
-    conv_code <- lme4l$code
-}
-
-cat("OUTPUT model converged:", (conv_code == 0) && !lme4_not_converged, "#*#\n")
-cat("OUTPUT lme4 messages:", lme4l$optinfo$conv$lme4$messages, "#*#\n")