From f79047db94d1cf9589dadc55f5354e4800b9d058 Mon Sep 17 00:00:00 2001
From: Flavio Lozano Isla <flozano@lamolina.edu.pe>
Date: Sat, 6 Jul 2024 16:17:22 -0500
Subject: [PATCH] fix plot diag

---
 DESCRIPTION            |  2 +-
 NAMESPACE              |  1 +
 NEWS.md                |  3 ++-
 R/gdoc2qmd.R           |  6 +++---
 R/plot_diag.R          | 10 ++++++----
 R/remove_outliers.R    | 13 ++++++-------
 man/plot_diag.Rd       |  6 +++---
 man/remove_outliers.Rd | 13 ++++++-------
 8 files changed, 28 insertions(+), 26 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 3733422f..69e4e505 100644
--- a/DESCRIPTION
+++ b/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
diff --git a/NAMESPACE b/NAMESPACE
index 5d61f2f9..70380290 100644
--- a/NAMESPACE
+++ b/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)
diff --git a/NEWS.md b/NEWS.md
index 0ca20880..267e9aaa 100644
--- a/NEWS.md
+++ b/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
diff --git a/R/gdoc2qmd.R b/R/gdoc2qmd.R
index c7215af9..e39a0f32 100644
--- a/R/gdoc2qmd.R
+++ b/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) %>% 
diff --git a/R/plot_diag.R b/R/plot_diag.R
index 1e2b3fb0..8bad7f15 100644
--- a/R/plot_diag.R
+++ b/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() +
diff --git a/R/remove_outliers.R b/R/remove_outliers.R
index e6ad7fe0..52b192c8 100644
--- a/R/remove_outliers.R
+++ b/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
 
diff --git a/man/plot_diag.Rd b/man/plot_diag.Rd
index 80923a2b..8bc6cb3d 100644
--- a/man/plot_diag.Rd
+++ b/man/plot_diag.Rd
@@ -21,11 +21,11 @@ Function to plot the diagnostic of models
 
 \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]
diff --git a/man/remove_outliers.Rd b/man/remove_outliers.Rd
index 8be156ba..4de38b20 100644
--- a/man/remove_outliers.Rd
+++ b/man/remove_outliers.Rd
@@ -9,11 +9,11 @@ remove_outliers(data, formula, drop_na = TRUE, plot_diag = FALSE)
 \arguments{
 \item{data}{Experimental design data frame with the factors and traits.}
 
-\item{drop_na}{drop NA values from the data.frame}
+\item{formula}{mixed model formula.}
 
-\item{trait}{Name of the trait.}
+\item{drop_na}{drop NA values from the data.frame}
 
-\item{model}{The fixed or random effects in the model.}
+\item{plot_diag}{Diagnostic plot based in the raw and clean data}
 }
 \value{
 list. 1. Table with date without outliers. 2. The outliers in the
@@ -30,11 +30,10 @@ Function to remove outliers in MET experiments
 
 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