From 9d500a0499c5bf98195f336ead8cc6f81ff7bc5f Mon Sep 17 00:00:00 2001
From: Mika Braginsky <mikabr@stanford.edu>
Date: Fri, 28 Oct 2016 15:40:20 -0400
Subject: [PATCH] missing imports from stats

---
 R/ggcorplot.R |  6 +++---
 R/multiboot.R | 12 ++++++------
 R/util.R      |  6 +++---
 3 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/R/ggcorplot.R b/R/ggcorplot.R
index 7de4ea4..c98397b 100644
--- a/R/ggcorplot.R
+++ b/R/ggcorplot.R
@@ -67,9 +67,9 @@ ggcorplot <- function(data,
       y <- data[,j]
       x_mid <- min(x) + diff(range(x)) / 2
       y_mid <- min(y) + diff(range(y)) / 2
-      this_cor <- cor(x,y)
+      this_cor <- stats::cor(x,y)
       this_cor.test <- 0
-      this_cor.test <- cor.test(x, y)
+      this_cor.test <- stats::cor.test(x, y)
       this_col <- ifelse(this_cor.test$p.value < .05, "<.05", ">.05")
       this_size <- (this_cor) ^ 2
       cor_text <- ifelse(this_cor > 0,
@@ -152,7 +152,7 @@ ggcorplot <- function(data,
 #' ezLev(x, c(3,1,2))
 ezLev <- function(x, new_order){
   for (i in rev(new_order)) {
-    x <- relevel(x, ref = i)
+    x <- stats::relevel(x, ref = i)
   }
   return(x)
 }
diff --git a/R/multiboot.R b/R/multiboot.R
index f77a19c..71c7154 100644
--- a/R/multiboot.R
+++ b/R/multiboot.R
@@ -43,7 +43,7 @@ multi_boot.numeric <- function(data,
   
   if (length(statistics_functions) == 1) {
     all_samples <- all_samples %>%
-      dplyr::rename_(.dots = setNames("sample", statistics_functions))
+      dplyr::rename_(.dots = stats::setNames("sample", statistics_functions))
   }
   
   return(all_samples)
@@ -140,7 +140,7 @@ multi_boot.data.frame <- function(data,
                                           fun = as.name(summary_function),
                                           arg = as.name(column)))
     call_summary_function <- function(df) {
-      dplyr::summarise_(df, .dots = setNames(summary_dots, "summary"))
+      dplyr::summarise_(df, .dots = stats::setNames(summary_dots, "summary"))
     }
   }
   
@@ -184,8 +184,8 @@ multi_boot.data.frame <- function(data,
   if (typeof(statistics_functions) == "character" &
       length(statistics_functions) == 1) {
     booted_vals <- dplyr::rename_(booted_vals,
-                                  .dots = setNames("summary",
-                                                   statistics_functions))
+                                  .dots = stats::setNames("summary",
+                                                          statistics_functions))
   }
   
   return(booted_vals)
@@ -251,7 +251,7 @@ multi_boot_standard <- function(data, column, na.rm = NULL,
   }
   
   call_empirical_function <- function(df) {
-    dplyr::summarise_(df, .dots = setNames(empirical_dots, "summary")) 
+    dplyr::summarise_(df, .dots = stats::setNames(empirical_dots, "summary")) 
   }
   
   booted_data <- multi_boot(data, summary_function = call_empirical_function, 
@@ -260,7 +260,7 @@ multi_boot_standard <- function(data, column, na.rm = NULL,
   
   call_empirical_function(data) %>%
     dplyr::left_join(booted_data) %>%
-    dplyr::rename_(.dots = setNames("summary", empirical_function))
+    dplyr::rename_(.dots = stats::setNames("summary", empirical_function))
 }
 
 #' Non-parametric bootstrap with multiple sample statistics
diff --git a/R/util.R b/R/util.R
index cdd791a..42180e2 100644
--- a/R/util.R
+++ b/R/util.R
@@ -16,7 +16,7 @@ sem <- function(x, na.rm = FALSE) {
   } else {
     n <- length(x)
   }
-  sd(x, na.rm = na.rm) / sqrt(n)
+  stats::sd(x, na.rm = na.rm) / sqrt(n)
 }
 
 #' Confidence interval (lower)
@@ -32,7 +32,7 @@ sem <- function(x, na.rm = FALSE) {
 #' ci_lower(x)
 #' @export
 ci_lower <- function(x, na.rm = FALSE) {
-  quantile(x, 0.025, na.rm)
+  stats::quantile(x, 0.025, na.rm)
 }
 
 #' Confidence interval (upper)
@@ -48,7 +48,7 @@ ci_lower <- function(x, na.rm = FALSE) {
 #' ci_upper(x)
 #' @export
 ci_upper <- function(x, na.rm = FALSE) {
-  quantile(x, 0.975, na.rm)
+  stats::quantile(x, 0.975, na.rm)
 }
 
 #' Significance stars