fix plot diag

DESCRIPTION

@@ -44,4 +44,4 @@ VignetteBuilder: knitr
 License: GPL-3 | file LICENSE
 LazyData: true
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

NAMESPACE

@@ -77,6 +77,7 @@ importFrom(shiny,runGadget)
 importFrom(stats,anova)
 importFrom(stats,aov)
 importFrom(stats,as.formula)
+importFrom(stats,density)
 importFrom(stats,fitted)
 importFrom(stats,lm)
 importFrom(stats,median)

NEWS.md

@@ -9,7 +9,8 @@
 # inti 0.6.6
 
 - Package
-  - Update function to remove outliers => "`remove_outliers`"
+  - Update function to outliers_remove => "`remove_outliers`"
+  - Update function `plot_diag()` 
 
 - Rticles
   - Fix Tables and Figures order in final document

R/gdoc2qmd.R

@@ -114,11 +114,11 @@ gdoc2qmd <- function(file
 
   tab <- txt %>% 
     dplyr::filter(grepl("^\\|", .data$value) | grepl("#tbl", .data$value)) %>% 
-    ungroup() %>% 
-    mutate(group = case_when(
+    dplyr::ungroup() %>% 
+    dplyr::mutate(group = case_when(
       grepl("#tbl", .data$value) ~ .data$name
     )) %>% 
-    tidyr::fill(., group, .direction = "up") %>% 
+    tidyr::fill(., .data$group, .direction = "up") %>% 
     split(.$group) %>% 
     purrr::map_dfr(~ slice(.data = ., c(n(),  1:(n()-1)))) %>% 
     split(.$group) %>% 

R/plot_diag.R

@@ -7,17 +7,19 @@
 #'
 #' @return plots
 #' 
+#' @importFrom stats density
+#' 
 #' @export
 #' 
 #' @examples
 #' 
 #' \dontrun{
 #' 
-#' dt <- potato
+#' library(inti)
 #' 
-#' lm <- aov(stemdw ~ bloque + geno*treat, dt)
+#' lm <- aov(stemdw ~ bloque + geno*treat, data = potato)
 #' 
-#' #lm <- lme4::lmer(stemdw ~ bloque + (1|geno:treat), dt)
+#' #lm <- lme4::lmer(stemdw ~ bloque + (1|geno:treat), data = potato)
 #'  
 #' plot(lm, which = 1)
 #' plot_diag(lm)[3]
@@ -52,7 +54,7 @@ plot_diag <- function( model, title = NA) {
 
   # Histogram
   p1 <- ggplot(dt , aes(.data$.resid)) +
-    geom_histogram(aes(y = after_stat(density)), 
+    geom_histogram(aes(y = ggplot2::after_stat(density)), 
                    color = "black", fill = "grey82", bins = 30) + 
     stat_function(fun = stats::dnorm, color = "blue", args = list(mean = 0, sd = sd(dt$.resid))) +
     theme_bw() +

R/remove_outliers.R

@@ -3,9 +3,9 @@
 #' Function to remove outliers in MET experiments
 #'
 #' @param data Experimental design data frame with the factors and traits.
-#' @param trait Name of the trait.
-#' @param model The fixed or random effects in the model.
+#' @param formula mixed model formula.
 #' @param drop_na drop NA values from the data.frame
+#' @param plot_diag Diagnostic plot based in the raw and clean data
 #'
 #' @description
 #'
@@ -30,11 +30,10 @@
 #'
 #' library(inti)
 #'
-#' rmout <- remove_outliers(
-#'   data = potato
-#'   , formula = stemdw ~ 0 + (1|bloque) + treat*geno  + geno
+#' rmout <- remove_outliers(data = potato
+#'   , formula = stemdw ~ 0 + (1|bloque) + treat*geno
 #'   , drop_na = FALSE
-#'   , plot_diag = TRUE 
+#'   , plot_diag = FALSE 
 #'   )
 #' 
 #' rmout
@@ -47,7 +46,7 @@ remove_outliers <- function(data
                             ) {
 
   # data = potato; drop_na = TRUE; plot_diag = TRUE
-  # formula = stemdw ~ 0  + (1|bloque) + treat*geno+ geno
+  # formula = stemdw ~ 0  + (1|bloque) + treat*geno
 
   out_flag <- bholm <- NULL