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Hospital Dirtiness scoring - final for GitHub.R
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Hospital Dirtiness scoring - final for GitHub.R
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library(dplyr)
##read into R "Raw scores" csv file exported from the tab with the same name in the
#"Hospital Dirtiness scoring - final for GitHub.xlsx" file
frac<-read.csv("Raw scores.csv")
dim(frac)
####
#### plot groups
#####
#### plotting by room and contamination material
#### type of contamination material
#"shavings", "hay/straw", "feces","fur","other organic","moisture"
##room:
####MH main hallway
#"MH_S", "MH_HS", "MH_F", "MH_Fur", "MH_OO", "MH_M",
####StR student rounds room
#"StR._S", "StR_HS", "StR_F", "StR_Fur", "StR_OO", "StR_M"
####SH short hallway
#"SH._S", "SH_HS", "SH._F", "SH._Fur", "SH_OO", "SH._M"
####BP bullpen
#"BP._S", "BP_HS", "BP._F", "BP_Fur", "BP_OO", "BP_M"
####UL unloading
#"UL._S", "UL_HS", "UL._F", "UL_Fur", "UL_OO", "UL_M"
##other variables but all zero: , "UL_Mcab", "UL_Ocab")
####Tx treatment room
#"Tx_S", "Tx_HS", "Tx_F", "Tx_Fur", "Tx_OO", "Tx_M"
##other variables but all zero: , "Tx_Mcab", "Tx_Ocab", "Tx_Mcomp", "Tx_Ocomp")
####Close close hallway
#"Close._S", "Close_HS", "Close._F", "Close._Fur", "Close_OO", "Close_M"
####Far far hallway
#"Far._S", "Far_HS", "Far._F", "Far._Fur", "Far_OO", "Far_M"
####SR small ruminant room
#"SR._S", "SR_HS", "SR._F", "SR._Fur", "SR_OO", "SR._M"
##other variables but all zero: , "SR._Mcab", "SR._Ocab")
frac1<-data.frame(frac)
####################################################################
########### summary statistics across multiple materials or rooms
##########################################################################
###far hallway overall dirtiness
S<-c("Far._S", "Far_HS", "Far._F", "Far._Fur", "Far_OO", "Far_M")
Far<-data.frame(x=unlist (frac1[,S]))
summary(Far)
###small ruminant overall dirtiness
S<-c("SR._S", "SR_HS", "SR._F", "SR._Fur", "SR_OO", "SR._M")
SR<-data.frame(x=unlist (frac1[,S]))
summary(SR)
###student rounds overall dirtiness
S<-c("StR._S", "StR_HS", "StR_F", "StR_Fur", "StR_OO", "StR_M")
StR<-data.frame(x=unlist (frac1[,S]))
summary(StR)
###MH main hallway
S<-c("MH_S", "MH_HS", "MH_F", "MH_Fur", "MH_OO", "MH_M")
mh<-data.frame(x=unlist (frac1[,S]))
summary(mh)
###SH short hallway
S<-c("SH._S", "SH_HS", "SH._F", "SH._Fur", "SH_OO", "SH._M")
sh<-data.frame(x=unlist (frac1[,S]))
summary(sh)
###BP bullpen
S<-c("BP._S", "BP_HS", "BP._F", "BP_Fur", "BP_OO", "BP_M")
bp<-data.frame(x=unlist (frac1[,S]))
summary(bp)
####UL unloading
S<-c("UL._S", "UL_HS", "UL._F", "UL_Fur", "UL_OO", "UL_M")
ul<-data.frame(x=unlist (frac1[,S]))
summary(ul)
####Tx treatment room
S<-c("Tx_S", "Tx_HS", "Tx_F", "Tx_Fur", "Tx_OO", "Tx_M")
tx<-data.frame(x=unlist (frac1[,S]))
summary(tx)
####Close close hallway
S<-c("Close._S", "Close_HS", "Close._F", "Close._Fur", "Close_OO", "Close_M")
ch<-data.frame(x=unlist (frac1[,S]))
summary(ch)
###wood shavings across all rooms
S<-c("MH_S", "StR._S", "SH._S", "BP._S", "UL._S", "Tx_S", "Close._S", "Far._S", "SR._S")
ws<-data.frame(x=unlist (frac1[,S]))
summary(ws)
###hay and straw across all rooms
S<-c("MH_HS", "StR_HS", "SH_HS", "BP_HS", "UL_HS", "Tx_HS", "Close_HS", "Far_HS", "SR_HS")
h<-data.frame(x=unlist (frac1[,S]))
summary(h)
###moisture across all rooms
S<-c("MH_M", "StR_M", "SH._M", "BP_M", "UL_M", "Tx_M", "Close_M" , "Far_M" , "SR._M")
m<-data.frame(x=unlist (frac1[,S]))
summary(m)
###feces across all rooms
S<-c("MH_F", "StR_F", "SH._F", "BP._F", "UL._F", "Tx_F", "Close._F", "Far._F", "SR._F")
f<-data.frame(x=unlist (frac1[,S]))
summary(f)
###fur across all rooms
S<-c("MH_Fur","StR_Fur","SH._Fur","BP_Fur", "UL_Fur", "Tx_Fur", "Close._Fur", "Far._Fur", "SR._Fur")
fu<-data.frame(x=unlist (frac1[,S]))
summary(fu)
###other organic across all rooms
S<-c("MH_OO", "StR_OO", "SH_OO", "BP_OO", "UL_OO", "Tx_OO", "Close_OO", "Far_OO", "SR_OO")
oo<-data.frame(x=unlist (frac1[,S]))
summary(oo)
###all organic matter across all rooms
S<-c("MH_S", "StR._S", "SH._S", "BP._S", "UL._S", "Tx_S", "Close._S", "Far._S", "SR._S",
"MH_HS", "StR_HS", "SH_HS", "BP_HS", "UL_HS", "Tx_HS", "Close_HS", "Far_HS", "SR_HS",
"MH_F", "StR_F", "SH._F", "BP._F", "UL._F", "Tx_F", "Close._F", "Far._F", "SR._F",
"MH_Fur","StR_Fur","SH._Fur","BP_Fur", "UL_Fur", "Tx_Fur", "Close._Fur", "Far._Fur", "SR._Fur",
"MH_OO", "StR_OO", "SH_OO", "BP_OO", "UL_OO", "Tx_OO", "Close_OO", "Far_OO", "SR_OO")
allo<-data.frame(x=unlist (frac1[,S]))
summary(allo)
##### organic matter without moisture
###far hallway overall organic matter
S<-c("Far._S", "Far_HS", "Far._F", "Far._Fur", "Far_OO")
Far<-data.frame(x=unlist (frac1[,S]))
summary(Far)
###small ruminant overall organic matter
S<-c("SR._S", "SR_HS", "SR._F", "SR._Fur", "SR_OO")
SR<-data.frame(x=unlist (frac1[,S]))
summary(SR)
###student rounds overall organic matter
S<-c("StR._S", "StR_HS", "StR_F", "StR_Fur", "StR_OO")
StR<-data.frame(x=unlist (frac1[,S]))
summary(StR)
###MH main hallway overall organic matter
S<-c("MH_S", "MH_HS", "MH_F", "MH_Fur", "MH_OO")
mh<-data.frame(x=unlist (frac1[,S]))
summary(mh)
###SH short hallway overall organic matter
S<-c("SH._S", "SH_HS", "SH._F", "SH._Fur", "SH_OO")
sh<-data.frame(x=unlist (frac1[,S]))
summary(sh)
###BP bullpen overall organic matter
S<-c("BP._S", "BP_HS", "BP._F", "BP_Fur", "BP_OO")
bp<-data.frame(x=unlist (frac1[,S]))
summary(bp)
####UL unloading overall organic matter
S<-c("UL._S", "UL_HS", "UL._F", "UL_Fur", "UL_OO")
ul<-data.frame(x=unlist (frac1[,S]))
summary(ul)
####Tx treatment room overall organic matter
S<-c("Tx_S", "Tx_HS", "Tx_F", "Tx_Fur", "Tx_OO")
tx<-data.frame(x=unlist (frac1[,S]))
summary(tx)
####Close close hallway overall organic matter
S<-c("Close._S", "Close_HS", "Close._F", "Close._Fur", "Close_OO")
ch<-data.frame(x=unlist (frac1[,S]))
summary(ch)
#######################################
### plot dirtiness by material and room (Figure 3)
#############################################
jpeg(file="all rooms-all materials_300dpi.jpeg", units="in", width=7.2, height=10.2, res=300)
par(mfrow=c(9,6),mai = c(0.15, 0.6, 0.3, 0.1))
####MH main hallway
#"MH_S", "MH_HS", "MH_F", "MH_Fur", "MH_OO", "MH_M",
boxplot(frac1[,"MH_S"], col = c("red"), main = "shavings", ylab="main halway", ylim=c(0,3),cex.lab = 1.4, cex.main=1.4)
boxplot(frac1[,"MH_HS"], col = c("red"), main = "hay/straw", ylim=c(0,3), cex.main=1.4)
boxplot(frac1[,"MH_F"], col = c("red"), main = "feces", ylim=c(0,3), cex.main=1.4)
boxplot(frac1[,"MH_Fur"], col = c("red"), main = "fur", ylim=c(0,3), cex.main=1.4)
boxplot(frac1[,"MH_OO"], col = c("red"), main = "organic", ylim=c(0,3), cex.main=1.4)
boxplot(frac1[,"MH_M"], col = c("red"), main = "moisture", ylim=c(0,3), cex.main=1.4)
####StR student rounds room
#"StR._S", "StR_HS", "StR_F", "StR_Fur", "StR_OO", "StR_M"
boxplot(frac1[,"StR._S"], col = c("red"), ylab="student rounds", ylim=c(0,3),cex.lab = 1.4)
boxplot(frac1[,"StR_HS"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"StR_F"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"StR_Fur"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"StR_OO"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"StR_M"], col = c("red"), ylim=c(0,3))
####SH short hallway
#"SH._S", "SH_HS", "SH._F", "SH._Fur", "SH_OO", "SH._M"
boxplot(frac1[,"SH._S"], col = c("red"), ylab="short hallway", ylim=c(0,3),cex.lab = 1.4)
boxplot(frac1[,"SH_HS"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"SH._F"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"SH._Fur"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"SH_OO"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"SH._M"], col = c("red"), ylim=c(0,3))
####BP bullpen
#"BP._S", "BP_HS", "BP._F", "BP_Fur", "BP_OO", "BP_M"
boxplot(frac1[,"BP._S"], col = c("red"), ylab="bullpen", ylim=c(0,3),cex.lab = 1.4)
boxplot(frac1[,"BP_HS"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"BP._F"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"BP_Fur"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"BP_OO"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"BP_M"], col = c("red"), ylim=c(0,3))
####UL unloading
#"UL._S", "UL_HS", "UL._F", "UL_Fur", "UL_OO", "UL_M"
##other variables but all zero: , "UL_Mcab", "UL_Ocab")
boxplot(frac1[,"UL._S"], col = c("red"), ylab="unloading", ylim=c(0,3),cex.lab = 1.4)
boxplot(frac1[,"UL_HS"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"UL._F"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"UL_Fur"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"UL_OO"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"UL_M"], col = c("red"), ylim=c(0,3))
####Tx treatment room
#"Tx_S", "Tx_HS", "Tx_F", "Tx_Fur", "Tx_OO", "Tx_M"
##other variables but all zero: , "Tx_Mcab", "Tx_Ocab", "Tx_Mcomp", "Tx_Ocomp")
boxplot(frac1[,"Tx_S"], col = c("red"), ylab="treatment", ylim=c(0,3),cex.lab = 1.4)
boxplot(frac1[,"Tx_HS"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"Tx_F"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"Tx_Fur"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"Tx_OO"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"Tx_M"], col = c("red"), ylim=c(0,3))
####Close close hallway
#"Close._S", "Close_HS", "Close._F", "Close._Fur", "Close_OO", "Close_M"
boxplot(frac1[,"Close._S"], col = c("red"), ylab="close hallway", ylim=c(0,3),cex.lab = 1.4)
boxplot(frac1[,"Close_HS"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"Close._F"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"Close._Fur"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"Close_OO"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"Close_M"], col = c("red"), ylim=c(0,3))
####Far far hallway
#"Far._S", "Far_HS", "Far._F", "Far._Fur", "Far_OO", "Far_M"
boxplot(frac1[,"Far._S"], col = c("red"), ylab="far hallway", ylim=c(0,3),cex.lab = 1.4)
boxplot(frac1[,"Far_HS"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"Far._F"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"Far._Fur"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"Far_OO"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"Far_M"], col = c("red"), ylim=c(0,3))
####SR small ruminant room
#"SR._S", "SR_HS", "SR._F", "SR._Fur", "SR_OO", "SR._M"
##other variables but all zero: , "SR._Mcab", "SR._Ocab")
boxplot(frac1[,"SR._S"], col = c("red"), ylab="small ruminant", ylim=c(0,3),cex.lab = 1.4)
boxplot(frac1[,"SR_HS"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"SR._F"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"SR._Fur"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"SR_OO"], col = c("red"), ylim=c(0,3))
boxplot(frac1[,"SR._M"], col = c("red"), ylim=c(0,3))
dev.off()
#####################################
##############################################################
##################################################################
# summary statistics for each variable (Table 1) ######
####################################################################
###################################################################
orig.cols <- colnames(frac)
orig.cols
V<-orig.cols
B<-matrix(,length(V),7)
rownames(B)<-V
colnames(B)<-c("all-Min", "all-25%","all-50%","all-Mean", "all-75%", "all-Max", "Missing")
for (i in (1:length(V))){ B[i,]<-c(summary(frac[,V[i]])[1:6],sum(is.na(frac[,V[i]]))) }
B
write.csv(B,file="all data summary.csv")
###############################################
####
#### plot groups
#####
#############################################
#### ploting by room
#MH main hallway
V<-c("MH_S", "MH_HS", "MH_F", "MH_Fur", "MH_OO", "MH_M")
L<-c("shavings", "hay/straw", "feces","fur","other organic","moisture")
x11(); par(mfrow=c(1,6))
for (i in (1:length(V))){ boxplot(frac[,V[i]], col = c("red"), main = paste(L[i]), ylim=c(0,3),cex=2, cex.main=2, cex.axis=2) }
#StR student rounds room
V<-c("StR._S", "StR_HS", "StR_F", "StR_Fur", "StR_OO", "StR_M")
#other variables but all zero: , "StR_Mdoor", "StR_Odoor", "StR._Mcab", "StR._Ocabs", "StR_Mcomp", "StR_Ocomp")
L<-c("shavings", "hay/straw", "feces","fur","other organic","moisture")
x11(); par(mfrow=c(1,6))
for (i in (1:length(V))){ boxplot(frac[,V[i]], col = c("red"), main = paste(L[i]), ylim=c(0,3),cex=2, cex.main=2, cex.axis=2) }
#SH short hallway
V<-c("SH._S", "SH_HS", "SH._F", "SH._Fur", "SH_OO", "SH._M")
L<-c("shavings", "hay/straw", "feces","fur","other organic","moisture")
x11(); par(mfrow=c(1,6))
for (i in (1:length(V))){ boxplot(frac[,V[i]], col = c("red"), main = paste(L[i]), ylim=c(0,3),cex=2, cex.main=2, cex.axis=2) }
#BP bullpen
V<-c("BP._S", "BP_HS", "BP._F", "BP_Fur", "BP_OO", "BP_M")
##other variables but all zero: , "BP_Mcab", "BP_Ocab")
L<-c("shavings", "hay/straw", "feces","fur","other organic","moisture")
x11(); par(mfrow=c(1,6))
for (i in (1:length(V))){ boxplot(frac[,V[i]], col = c("red"), main = paste(L[i]), ylim=c(0,3),cex=2, cex.main=2, cex.axis=2) }
#UL unloading
V<-c("UL._S", "UL_HS", "UL._F", "UL_Fur", "UL_OO", "UL_M")
##other variables but all zero: , "UL_Mcab", "UL_Ocab")
L<-c("shavings", "hay/straw", "feces","fur","other organic","moisture")
x11(); par(mfrow=c(1,6))
for (i in (1:length(V))){ boxplot(frac[,V[i]], col = c("red"), main = paste(L[i]), ylim=c(0,3),cex=2, cex.main=2, cex.axis=2) }
#Tx treatment room
V<-c("Tx_S", "Tx_HS", "Tx_F", "Tx_Fur", "Tx_OO", "Tx_M")
##other variables but all zero: , "Tx_Mcab", "Tx_Ocab", "Tx_Mcomp", "Tx_Ocomp")
L<-c("shavings", "hay/straw", "feces","fur","other organic","moisture")
x11(); par(mfrow=c(1,6))
for (i in (1:length(V))){ boxplot(frac[,V[i]], col = c("red"), main = paste(L[i]), ylim=c(0,3),cex=2, cex.main=2, cex.axis=2) }
#Close close hallway
V<-c("Close._S", "Close_HS", "Close._F", "Close._Fur", "Close_OO", "Close_M")
L<-c("shavings", "hay/straw", "feces","fur","other organic","moisture")
x11(); par(mfrow=c(1,6))
for (i in (1:length(V))){ boxplot(frac[,V[i]], col = c("red"), main = paste(L[i]), ylim=c(0,3),cex=2, cex.main=2, cex.axis=2) }
#Far far hallway
V<-c("Far._S", "Far_HS", "Far._F", "Far._Fur", "Far_OO", "Far_M")
L<-c("shavings", "hay/straw", "feces","fur","other organic","moisture")
x11(); par(mfrow=c(1,6))
for (i in (1:length(V))){ boxplot(frac[,V[i]], col = c("red"), main = paste(L[i]), ylim=c(0,3),cex=2, cex.main=2, cex.axis=2) }
#SR small ruminant room
V<-c("SR._S", "SR_HS", "SR._F", "SR._Fur", "SR_OO", "SR._M")
##other variables but all zero: , "SR._Mcab", "SR._Ocab")
L<-c("shavings", "hay/straw", "feces","fur","other organic","moisture")
x11(); par(mfrow=c(1,6))
for (i in (1:length(V))){ boxplot(frac[,V[i]], col = c("red"), main = paste(L[i]), ylim=c(0,3),cex=2, cex.main=2, cex.axis=2) }
#### ploting people animals and feces
#people
V<-c("MH_Ppl", "StR_Ppl", "SH_Ppl", "BP_Ppl", "UL_Ppl", "Tx_Ppl", "Close_Ppl", "Far_Ppl", "SR_Ppl")
L<-c("main hallway", "student rounds room", "short hallway","bullpen","unloading","treatment room","close hallway", "far hallway","small ruminant room")
x11(); par(mfrow=c(3,3))
for (i in (1:length(V))){ boxplot(frac[,V[i]], col = c("red"), main = paste(L[i]), ylim=c(0,15),cex=2, cex.main=2, cex.axis=2) }
#animals
V<-c("Cows", "Calves", "Pigs", "Piglets", "Sheepgoats", "Lambkids")
x11(); par(mfrow=c(3,2))
for (i in (1:length(V))){ boxplot(frac[,V[i]], col = c("red"), main = paste(V[i]), ylim=c(0,7),cex=2, cex.main=2, cex.axis=2) }
#feces
V<-c("Feces_fur", "Feces_feet", "Feces_wall", "Feces_gate", "Feces_wbucket", "Feces_fbucket")
L<-c("fur", "feet", "wall", "gate", "water bucket", "feed bucket")
x11(); par(mfrow=c(3,2))
for (i in (1:length(V))){ boxplot(frac[,V[i]], col = c("red"), main = paste(L[i]), ylim=c(0,4),cex=2, cex.main=2, cex.axis=2) }
###ploting by dirt matter
#shavings
V<-c("MH_S","StR._S","SH._S","BP._S","UL._S","Tx_S","Close._S","Far._S","SR._S")
L<-c("main hallway", "student rounds room", "short hallway","bullpen","unloading","treatment room","close hallway", "far hallway","small ruminant room")
x11(); par(mfrow=c(3,3))
for (i in (1:length(V))){ boxplot(frac[,V[i]], col = c("red"), main = paste(L[i]), ylim=c(0,3),cex=2, cex.main=2, cex.axis=2) }
#hay/straw
V<-c("MH_HS","StR_HS","SH_HS","BP_HS","UL_HS","Tx_HS","Close_HS","Far_HS","SR_HS")
L<-c("main hallway", "student rounds room", "short hallway","bullpen","unloading","treatment room","close hallway", "far hallway","small ruminant room")
x11(); par(mfrow=c(3,3))
for (i in (1:length(V))){ boxplot(frac[,V[i]], col = c("red"), main = paste(L[i]), ylim=c(0,3),cex=2, cex.main=2, cex.axis=2) }
#feces
V<-c("MH_F","StR_F","SH._F","BP._F","UL._F","Tx_F","Close._F","Far._F","SR._F")
L<-c("main hallway", "student rounds room", "short hallway","bullpen","unloading","treatment room","close hallway", "far hallway","small ruminant room")
x11(); par(mfrow=c(3,3))
for (i in (1:length(V))){ boxplot(frac[,V[i]], col = c("red"), main = paste(L[i]), ylim=c(0,3),cex=2, cex.main=2, cex.axis=2) }
#fur
V<-c("MH_Fur","StR_Fur","SH._Fur","BP_Fur","UL_Fur","Tx_Fur","Close._Fur","Far._Fur","SR._Fur")
L<-c("main hallway", "student rounds room", "short hallway","bullpen","unloading","treatment room","close hallway", "far hallway","small ruminant room")
x11(); par(mfrow=c(3,3))
for (i in (1:length(V))){ boxplot(frac[,V[i]], col = c("red"), main = paste(L[i]), ylim=c(0,3),cex=2, cex.main=2, cex.axis=2) }
#other organic
V<-c("MH_OO","StR_OO","SH_OO","BP_OO","UL_OO","Tx_OO","Close_OO","Far_OO","SR_OO")
L<-c("main hallway", "student rounds room", "short hallway","bullpen","unloading","treatment room","close hallway", "far hallway","small ruminant room")
x11(); par(mfrow=c(3,3))
for (i in (1:length(V))){ boxplot(frac[,V[i]], col = c("red"), main = paste(L[i]), ylim=c(0,3),cex=2, cex.main=2, cex.axis=2) }
#moisture
V<-c("MH_M","StR_M","SH._M","BP_M","UL_M","Tx_M","Close_M","Far_M","SR._M")
L<-c("main hallway", "student rounds room", "short hallway","bullpen","unloading","treatment room","close hallway", "far hallway","small ruminant room")
x11(); par(mfrow=c(3,3))
for (i in (1:length(V))){ boxplot(frac[,V[i]], col = c("red"), main = paste(L[i]), ylim=c(0,3),cex=2, cex.main=2, cex.axis=2) }