Plots of Element Concentrations, One-Way ANOVA Tables

Data Management

elwha = read.csv("ElwhaMicronutrientStudy_Data_Citron_150526.csv", header=TRUE)  #use if wd is set
#elwha = read.csv(file.choose(), header=TRUE)  #use if wd is not set

#is.numeric(elwha$N)  #True
#is.factor(elwha$texture) #True
#is.factor(elwha$site) #False.. need to convert to factor:
elwha$site <- as.factor(elwha$site) #convert to factor
is.factor(elwha$site) #True...now my ANOVA will work!

## [1] TRUE

elwha2 <- elwha[-c(29:30),] #make a data frame for ANOVAs that excludes forest site

Elements Plotted by Site

site.colors = c("bisque4","bisque4","bisque4","bisque3","bisque3","lightsalmon","lightsalmon","forestgreen") #make vector of colors for use in boxplot


####N
dfN <-data.frame(
  coarse1   = elwha$N[elwha$site == 1],
  coarse5   = elwha$N[elwha$site == 5],
  coarse6   = elwha$N[elwha$site == 6],
  prodelta3 = elwha$N[elwha$site == 3],
  prodelta4 = elwha$N[elwha$site == 4],
  fine2     = elwha$N[elwha$site == 2],
  fine7     = elwha$N[elwha$site == 7],
  forest8   = elwha$N[elwha$site == 8])

stripchart(
  dfN, col=site.colors,
  main="Leaf N", dlab="%N",glab="Site",
  pch=16, cex=1.5, vertical=TRUE, las=2)

####C
dfC <-data.frame(
  coarse1   = elwha$C[elwha$site == 1],
  coarse5   = elwha$C[elwha$site == 5],
  coarse6   = elwha$C[elwha$site == 6],
  prodelta3 = elwha$C[elwha$site == 3],
  prodelta4 = elwha$C[elwha$site == 4],
  fine2     = elwha$C[elwha$site == 2],
  fine7     = elwha$C[elwha$site == 7],
  forest8   = elwha$C[elwha$site == 8])

stripchart(
  dfC, col=site.colors,
  main="Leaf C", dlab="%C",glab="Site",
  pch=16, cex=1.5, vertical=TRUE, las=2)

####Na
dfNa <-data.frame(
  coarse1   = elwha$Na[elwha$site == 1],
  coarse5   = elwha$Na[elwha$site == 5],
  coarse6   = elwha$Na[elwha$site == 6],
  prodelta3 = elwha$Na[elwha$site == 3],
  prodelta4 = elwha$Na[elwha$site == 4],
  fine2     = elwha$Na[elwha$site == 2],
  fine7     = elwha$Na[elwha$site == 7],
  forest8   = elwha$Na[elwha$site == 8])

stripchart(
  dfNa, col=site.colors,
  main="Leaf Na", dlab="Na (ppm)",glab="Site",
  pch=16, cex=1.5, vertical=TRUE, las=2)

####Mg
dfMg <-data.frame(
  coarse1   = elwha$Mg[elwha$site == 1],
  coarse5   = elwha$Mg[elwha$site == 5],
  coarse6   = elwha$Mg[elwha$site == 6],
  prodelta3 = elwha$Mg[elwha$site == 3],
  prodelta4 = elwha$Mg[elwha$site == 4],
  fine2     = elwha$Mg[elwha$site == 2],
  fine7     = elwha$Mg[elwha$site == 7],
  forest8   = elwha$Mg[elwha$site == 8])

stripchart(
  dfMg, col=site.colors,
  main="Leaf Mg", dlab="Mg (ppm)",glab="Site",
  pch=16, cex=1.5, vertical=TRUE, las=2)

####Al
dfAl <-data.frame(
  coarse1   = elwha$Al[elwha$site == 1],
  coarse5   = elwha$Al[elwha$site == 5],
  coarse6   = elwha$Al[elwha$site == 6],
  prodelta3 = elwha$Al[elwha$site == 3],
  prodelta4 = elwha$Al[elwha$site == 4],
  fine2     = elwha$Al[elwha$site == 2],
  fine7     = elwha$Al[elwha$site == 7],
  forest8   = elwha$Al[elwha$site == 8])

stripchart(
  dfAl, col=site.colors,
  main="Leaf Al", dlab="Al (ppm)",glab="Site",
  pch=16, cex=1.5, vertical=TRUE, las=2)

####K
dfK <-data.frame(  
  coarse1   = elwha$K[elwha$site == 1],
  coarse5   = elwha$K[elwha$site == 5],
  coarse6   = elwha$K[elwha$site == 6],
  prodelta3 = elwha$K[elwha$site == 3],
  prodelta4 = elwha$K[elwha$site == 4],
  fine2     = elwha$K[elwha$site == 2],
  fine7     = elwha$K[elwha$site == 7],
  forest8   = elwha$K[elwha$site == 8])

stripchart(
  dfK, col=site.colors,
  main="Leaf K", dlab="K (ppm)",glab="Site",
  pch=16, cex=1.5, vertical=TRUE, las=2)

####Ca
dfCa <-data.frame(
  coarse1   = elwha$Ca[elwha$site == 1],
  coarse5   = elwha$Ca[elwha$site == 5],
  coarse6   = elwha$Ca[elwha$site == 6],
  prodelta3 = elwha$Ca[elwha$site == 3],
  prodelta4 = elwha$Ca[elwha$site == 4],
  fine2     = elwha$Ca[elwha$site == 2],
  fine7     = elwha$Ca[elwha$site == 7],
  forest8   = elwha$Ca[elwha$site == 8])

stripchart(
  dfCa, col=site.colors,
  main="Leaf Ca", dlab="Ca (ppm)",glab="Site",
  pch=16, cex=1.5, vertical=TRUE, las=2)

####V
dfV <-data.frame(
  coarse1   = elwha$V[elwha$site == 1],
  coarse5   = elwha$V[elwha$site == 5],
  coarse6   = elwha$V[elwha$site == 6],
  prodelta3 = elwha$V[elwha$site == 3],
  prodelta4 = elwha$V[elwha$site == 4],
  fine2     = elwha$V[elwha$site == 2],
  fine7     = elwha$V[elwha$site == 7],
  forest8   = elwha$V[elwha$site == 8])

stripchart(
  dfV, col=site.colors,
  main="Leaf V", dlab="V (ppm)",glab="Site",
  pch=16, cex=1.5, vertical=TRUE, las=2)

####Cr
dfCr <-data.frame(
  coarse1   = elwha$Cr[elwha$site == 1],
  coarse5   = elwha$Cr[elwha$site == 5],
  coarse6   = elwha$Cr[elwha$site == 6],
  prodelta3 = elwha$Cr[elwha$site == 3],
  prodelta4 = elwha$Cr[elwha$site == 4],
  fine2     = elwha$Cr[elwha$site == 2],
  fine7     = elwha$Cr[elwha$site == 7],
  forest8   = elwha$Cr[elwha$site == 8])

stripchart(
  dfCr, col=site.colors,
  main="Leaf Cr", dlab="Cr (ppm)",glab="Site",
  pch=16, cex=1.5, vertical=TRUE, las=2)

####Mn
dfMn <-data.frame(
  coarse1   = elwha$Mn[elwha$site == 1],
  coarse5   = elwha$Mn[elwha$site == 5],
  coarse6   = elwha$Mn[elwha$site == 6],
  prodelta3 = elwha$Mn[elwha$site == 3],
  prodelta4 = elwha$Mn[elwha$site == 4],
  fine2     = elwha$Mn[elwha$site == 2],
  fine7     = elwha$Mn[elwha$site == 7],
  forest8   = elwha$Mn[elwha$site == 8])

stripchart(
  dfMn, col=site.colors,
  main="Leaf Mn", dlab="Mn (ppm)",glab="Site",
  pch=16, cex=1.5, vertical=TRUE, las=2)

####Fe
dfFe <-data.frame(
  coarse1   = elwha$Fe[elwha$site == 1],
  coarse5   = elwha$Fe[elwha$site == 5],
  coarse6   = elwha$Fe[elwha$site == 6],
  prodelta3 = elwha$Fe[elwha$site == 3],
  prodelta4 = elwha$Fe[elwha$site == 4],
  fine2     = elwha$Fe[elwha$site == 2],
  fine7     = elwha$Fe[elwha$site == 7],
  forest8   = elwha$Fe[elwha$site == 8])

stripchart(
  dfFe, col=site.colors,
  main="Leaf Fe", dlab="Fe (ppm)",glab="Site",
  pch=16, cex=1.5, vertical=TRUE, las=2)

####Co
dfCo <-data.frame(
  coarse1   = elwha$Co[elwha$site == 1],
  coarse5   = elwha$Co[elwha$site == 5],
  coarse6   = elwha$Co[elwha$site == 6],
  prodelta3 = elwha$Co[elwha$site == 3],
  prodelta4 = elwha$Co[elwha$site == 4],
  fine2     = elwha$Co[elwha$site == 2],
  fine7     = elwha$Co[elwha$site == 7],
  forest8   = elwha$Co[elwha$site == 8])

stripchart(
  dfCo, col=site.colors,
  main="Leaf Co", dlab="Co (ppm)",glab="Site",
  pch=16, cex=1.5, vertical=TRUE, las=2)

####Ni
dfNi <-data.frame(
  coarse1   = elwha$Ni[elwha$site == 1],
  coarse5   = elwha$Ni[elwha$site == 5],
  coarse6   = elwha$Ni[elwha$site == 6],
  prodelta3 = elwha$Ni[elwha$site == 3],
  prodelta4 = elwha$Ni[elwha$site == 4],
  fine2     = elwha$Ni[elwha$site == 2],
  fine7     = elwha$Ni[elwha$site == 7],
  forest8   = elwha$Ni[elwha$site == 8])

stripchart(
  dfNi, col=site.colors,
  main="Leaf Ni", dlab="Ni (ppm)",glab="Site",
  pch=16, cex=1.5, vertical=TRUE, las=2)

####Cu
dfCu <-data.frame(
  coarse1   = elwha$Cu[elwha$site == 1],
  coarse5   = elwha$Cu[elwha$site == 5],
  coarse6   = elwha$Cu[elwha$site == 6],
  prodelta3 = elwha$Cu[elwha$site == 3],
  prodelta4 = elwha$Cu[elwha$site == 4],
  fine2     = elwha$Cu[elwha$site == 2],
  fine7     = elwha$Cu[elwha$site == 7],
  forest8   = elwha$Cu[elwha$site == 8])

stripchart(
  dfCu, col=site.colors,
  main="Leaf Cu", dlab="Cu (ppm)",glab="Site",
  pch=16, cex=1.5, vertical=TRUE, las=2)

####Zn
dfZn <-data.frame(
  coarse1   = elwha$Zn[elwha$site == 1],
  coarse5   = elwha$Zn[elwha$site == 5],
  coarse6   = elwha$Zn[elwha$site == 6],
  prodelta3 = elwha$Zn[elwha$site == 3],
  prodelta4 = elwha$Zn[elwha$site == 4],
  fine2     = elwha$Zn[elwha$site == 2],
  fine7     = elwha$Zn[elwha$site == 7],
  forest8   = elwha$Zn[elwha$site == 8])

stripchart(
  dfZn, col=site.colors,
  main="Leaf Zn", dlab="Zn (ppm)",glab="Site",
  pch=16, cex=1.5, vertical=TRUE, las=2)

####Ag
dfAg <-data.frame(
  coarse1   = elwha$Ag[elwha$site == 1],
  coarse5   = elwha$Ag[elwha$site == 5],
  coarse6   = elwha$Ag[elwha$site == 6],
  prodelta3 = elwha$Ag[elwha$site == 3],
  prodelta4 = elwha$Ag[elwha$site == 4],
  fine2     = elwha$Ag[elwha$site == 2],
  fine7     = elwha$Ag[elwha$site == 7],
  forest8   = elwha$Ag[elwha$site == 8])

stripchart(
  dfAg, col=site.colors,
  main="Leaf Ag", dlab="Ag (ppm)",glab="Site",
  pch=16, cex=1.5, vertical=TRUE, las=2)

####Cd
dfCd <-data.frame(  
  coarse1   = elwha$Cd[elwha$site == 1],
  coarse5   = elwha$Cd[elwha$site == 5],
  coarse6   = elwha$Cd[elwha$site == 6],
  prodelta3 = elwha$Cd[elwha$site == 3],
  prodelta4 = elwha$Cd[elwha$site == 4],
  fine2     = elwha$Cd[elwha$site == 2],
  fine7     = elwha$Cd[elwha$site == 7],
  forest8   = elwha$Cd[elwha$site == 8])

stripchart(
  dfCd, col=site.colors,
  main="Leaf Cd", dlab="Cd (ppm)",glab="Site",
  pch=16, cex=1.5, vertical=TRUE, las=2)

####Ba
dfBa <-data.frame(
  coarse1   = elwha$Ba[elwha$site == 1],
  coarse5   = elwha$Ba[elwha$site == 5],
  coarse6   = elwha$Ba[elwha$site == 6],
  prodelta3 = elwha$Ba[elwha$site == 3],
  prodelta4 = elwha$Ba[elwha$site == 4],
  fine2     = elwha$Ba[elwha$site == 2],
  fine7     = elwha$Ba[elwha$site == 7],
  forest8   = elwha$Ba[elwha$site == 8])

stripchart(
  dfBa, col=site.colors,
  main="Leaf Ba", dlab="Ba (ppm)",glab="Site",
  pch=16, cex=1.5, vertical=TRUE, las=2)

ANOVA Tables

#by site, all sites (dataframe "elwha")
#Source    Df Sum Sq Mean Sq F value Pr(>F)  
#site       7
#plant     22

#by site, forest excluded (dataframe "elwha2")
#Source    Df Sum Sq Mean Sq F value Pr(>F)   
#site       6
#plant     21

#by texture, all sites (dataframe "elwha")
#Source    Df Sum Sq Mean Sq F value Pr(>F)   
#texture    3
#plant     26

#by texture, forest excluded (dataframe "elwha2")
#Source    Df Sum Sq Mean Sq F value Pr(>F)   
#texture    2
#plant     25

#by site nested in texture, all sites (dataframe "elwha")
#Source    Df Sum Sq Mean Sq F value Pr(>F)   
#texture    3
#site       4  #(no replication, so adding the forest site doesn't affect site df)
#plant     22

#by site nested in texture, forest excluded (dataframe "elwha2")
#Source    Df Sum Sq Mean Sq F value Pr(>F)   
#texture    2
#site       4
#plant     21

Plots of Element Concentrations, One-Way ANOVA Tables

Ezra Citron

Monday, May 29, 2015

Data Management

Elements Plotted by Site

ANOVA Tables