Update grid summary => new headers and round numbers

Author: Marco Chiapello

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: Ramf
 Type: Package
 Title: Arbuscular Mycorrhizal colonization calculation
-Version: 0.4
-Authors@R: person("Marco", "Chiapello", email = "mc983.cam@gmail.com", role = c("aut", "cre"))
+Version: 0.5
+Author: Marco Chiapello
 Maintainer: Marco Chiapello <mc983@cam.ac.uk>
 Description: The package reads data from trouvelot quantification files or grid
 	system quantification files, compute the colonization rate according to the

R/functions.R

@@ -6,11 +6,11 @@ grid_summary <- function(x){
 	# Create summary table
 	y <- x %>% 
 			group_by(samples, replicates) %>%
-			summarise(Total = mean(Total, na.rm = TRUE),
-					  Hyphopodia = mean(Hyphopodia, na.rm = TRUE),
-					  IntrHyphae = mean(IntrHyphae, na.rm = TRUE),
-					  Arbuscule = mean(Arbuscule, na.rm = TRUE),
-					  Vesicles = mean(Vesicles, na.rm = TRUE)) %>%
+			summarise(Total = round(mean(Total, na.rm = TRUE), 2),
+					  Hyphopodia = round(mean(Hyphopodia, na.rm = TRUE), 2),
+					  IntrHyphae = round(mean(IntrHyphae, na.rm = TRUE), 2),
+					  Arbuscule = round(mean(Arbuscule, na.rm = TRUE), 2),
+					  Vesicles = round(mean(Vesicles, na.rm = TRUE),2)) %>%
 			ungroup
 	y <- y %>% arrange(factor(samples, levels = unique(x$samples)), replicates)
 	return(y)

R/methods-grid.R

@@ -6,16 +6,16 @@ am_summary.grid <- function(x){
 	final <- tmp %>%
 	mutate(num = n()) %>%
 	group_by(samples) %>%
-	summarise(mean_Total = mean(Total, na.rm = TRUE),
-			  se_Total = sd(Total, na.rm = TRUE) / sqrt(mean(num, na.rm = TRUE)),
-			  mean_Hyphopodia = mean(Hyphopodia, na.rm = TRUE),
-			  se_Hyphopodia = sd(Hyphopodia, na.rm = TRUE) / sqrt(mean(num, na.rm = TRUE)),
-			  mean_IntrHyphae = mean(IntrHyphae, na.rm = TRUE),
-			  se_IntrHyphae = sd(IntrHyphae, na.rm = TRUE) / sqrt(mean(num, na.rm = TRUE)),
-			  mean_Arbuscule = mean(Arbuscule, na.rm = TRUE),
-			  se_Arbuscule = sd(Arbuscule, na.rm = TRUE) / sqrt(mean(num, na.rm = TRUE)),
-			  mean_Vesicles = mean(Vesicles, na.rm = TRUE),
-			  se_Vesicles = sd(Vesicles, na.rm = TRUE) / sqrt(mean(num, na.rm = TRUE))
+	summarise(`Mean Total` = round(mean(Total, na.rm = TRUE), 2),
+			  `Standard error Total` = round(sd(Total, na.rm = TRUE) / sqrt(mean(num, na.rm = TRUE)), 2),
+			  `Mean Hyphopodia` = round(mean(Hyphopodia, na.rm = TRUE), 2),
+			  `Standard error Hyphopodia` = round(sd(Hyphopodia, na.rm = TRUE) / sqrt(mean(num, na.rm = TRUE)), 2),
+			  `Mean IntrHyphae` = round(mean(IntrHyphae, na.rm = TRUE), 2),
+			  `Standard error IntrHyphae` = round(sd(IntrHyphae, na.rm = TRUE) / sqrt(mean(num, na.rm = TRUE)), 2),
+			  `Mean Arbuscule` = round(mean(Arbuscule, na.rm = TRUE), 2),
+			  `Standard error Arbuscule` = round(sd(Arbuscule, na.rm = TRUE) / sqrt(mean(num, na.rm = TRUE)), 2),
+			  `Mean Vesicles` = round(mean(Vesicles, na.rm = TRUE), 2),
+			  `Standard error Vesicles` = round(sd(Vesicles, na.rm = TRUE) / sqrt(mean(num, na.rm = TRUE)), 2)
 			  )
 	final <- final[match(unique(x$samples), final$samples), ]
 	l <- list(tmp, final)