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Rich Shepard

2015-Apr-30 20:56 UTC

[R] Results Differ in Ternary Plot Matrix of Compositional Response Variables

After hours of looking for the reason why one data set plots correctly and
another one does not I am still not seeing the reason. The only differences
I see between the two data sets is the number of discrete variables (one has
6 years, the other 7 years) and one contains zeros. I wonder if the number
of discrete variables is the issue.

   I'm sure that more experienced eyes will see the reason for the different
results and will point it out to me.

   The following data and code produce a matrix of ternary plots with the
other continuous variables represented by a dot above the top point of the
triangle:

<filename = snow-regression.dat>
"Year","NO3","SO4","pH","Fi","Ga","Gr","Pr","Sh"
"2005",0.60,816,7.87,0.0556,0.5370,0.1667,0.1667,0.0741
"2006",0.40,224,7.59,0.0435,0.6739,0.0870,0.1522,0.0435
"2010",0.10,571,7.81,0.0735,0.4706,0.1029,0.1912,0.1618
"2011",0.52,130,7.42,0.0462,0.5692,0.0769,0.2462,0.0615
"2012",0.42,363,7.79,0.0548,0.5205,0.0548,0.2466,0.1233
"2013",0.42,363,7.79,0.0484,0.5323,0.1129,0.2419,0.0645

<snow-ternary-plot.R>
# Create matrix of ternary plots of FFGs as dependent variables.
# Follows 'Analyzing Compositional Data with R' sec. 5.3; pp 122 ff
# Change stream name as necessary.
# load package from library
require(compositions)
# read in raw data
SnowRegr <- read.csv('snow-regression.dat', header=T)
# extract response variables
SnowY <- acomp(SnowRegr[,5:9])
# column headings; variables
names(SnowRegr)
# continuous explanatory co-variables
SnowCovars <-
SnowRegr[,c("Year","NO3","SO4","pH")]
# first continuous co-variable
SnowX1 <- SnowCovars$NO3
# second continuous co-variable
SnowX2 <- SnowCovars$SO4
# third continuous co-variable
SnowX3 <- SnowCovars$pH
# discrete co-variable
SnowX4 <- 
factor(SnowCovars$Year,c("2005","2006","2010","2011","2012","2013"),ordered=T)
# for the discrete co-var, ANOVA not specified in unique way so contrasts must 
be specified; use the
#   treatment contrasts.
contrasts(SnowX4) <- "contr.treatment"
# save figure parameters
opar <- par(xpd=NA,no.readonly=T)
# ternary plot matrix
plot(SnowY, pch=as.numeric(SnowX4), col=c("red","dark
green","dark blue","dark
goldenrod","dark orange","dark grey")[SnowX4])
# add legend
legend(x=0.83, y=-0.165, abbreviate(levels(SnowX4), 
minlength=1),pch=as.numeric(SnowX4), col=c("red","dark
green","dark blue","dark
goldenrod","dark orange","dark grey"), ncol=2, xpd=T,
bty="n", yjust=0)
# reset plot parameters
par(opar)
# unload the package
detach('package:compositions')

   This data set with eqivalent code produces plots with the other continuous
variables as bars with colors on the top points of the triangles:

<filename = jerritt-regression.dat>
"Year","NO3","SO4","pH","Fi","Ga","Gr","Pr","Sh"
"2004",1.70,2200,8.70,0.0444,0.6889,0.0222,0.2222,0.0222
"2005",2.50,5000,8.43,0.0182,0.5636,0.0909,0.3091,0.0182
"2006",1.80,6670,8.57,0.0370,0.6173,0.0741,0.2469,0.0247
"2010",0.54,4000,8.00,0.0870,0.6087,0.0870,0.2174,0.0000
"2011",2.70,4300,8.47,0.0449,0.5256,0.0897,0.2949,0.0449
"2012",0.76,595,8.21,0.0000,0.4231,0.0769,0.5000,0.0000
"2013",0.76,595,8.21,0.0000,0.4545,0.0455,0.4545,0.0455

<jerritt-ternary-plot.R>
# Create matrix of ternary plots of FFGs as dependent variables.
# Follows 'Analyzing Compositional Data with R' sec. 5.3; pp 122 ff
# Change stream name as necessary.
# load package from library
require(compositions)
# read in raw data
JerrittRegr <- read.csv('jerritt-regression.dat', header=T)
# extract response variables
JerrittY <- acomp(JerrittRegr[,5:9])
# column headings; variables
names(JerrittRegr)
# continuous explanatory co-variables
JerrittCovars <-
JerrittRegr[,c("Year","NO3","SO4","pH")]
# first continuous co-variable
JerrittX1 <- JerrittCovars$NO3
# second continuous co-variable
JerrittX2 <- JerrittCovars$SO4
# third continuous co-variable
JerrittX3 <- JerrittCovars$pH
# discrete co-variable
JerrittX4 <- 
factor(JerrittCovars$Year,c("2004","2005","2006","2010","2011","2012","2013"),ordered=T)
# for the discrete co-var, ANOVA not specified in unique way so contrasts must 
be specified; use the
#   treatment contrasts.
contrasts(JerrittX4) <- "contr.treatment"
# save figure parameters
opar <- par(xpd=NA,no.readonly=T)
# ternary plot matrix
plot(JerrittY, pch=as.numeric(JerrittX4),
col=c("black","red","dark
green","dark blue","dark goldenrod","dark
orange","dark grey")[JerrittX4])
# add legend
legend(x=0.83, y=-0.165, abbreviate(levels(JerrittX4), 
minlength=1),pch=as.numeric(JerrittX4),
col=c("black","red","dark green","dark
blue","dark goldenrod","dark orange","dark
grey"), ncol=2, xpd=T, bty="n",
yjust=0)
# reset plot parameters
par(opar)
# unload the package
detach('package:compositions')

Thanks in advance,

Rich

David L Carlson

2015-May-01 15:54 UTC

head link

[R] Results Differ in Ternary Plot Matrix of Compositional Response Variables

Add plotMissings=FALSE to the second plot and see the plot.acomp manual page
description of this argument:

plot(JerrittY, pch=as.numeric(JerrittX4),
col=c("black","red", "dark green",
     "dark blue","dark goldenrod","dark
orange","dark grey")[JerrittX4],
      plotMissings=FALSE)


-------------------------------------
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77840-4352

-----Original Message-----
From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Rich Shepard
Sent: Thursday, April 30, 2015 3:57 PM
To: r-help at r-project.org
Subject: [R] Results Differ in Ternary Plot Matrix of Compositional Response
Variables

   After hours of looking for the reason why one data set plots correctly and
another one does not I am still not seeing the reason. The only differences
I see between the two data sets is the number of discrete variables (one has
6 years, the other 7 years) and one contains zeros. I wonder if the number
of discrete variables is the issue.

   I'm sure that more experienced eyes will see the reason for the different
results and will point it out to me.

   The following data and code produce a matrix of ternary plots with the
other continuous variables represented by a dot above the top point of the
triangle:

<filename = snow-regression.dat>
"Year","NO3","SO4","pH","Fi","Ga","Gr","Pr","Sh"
"2005",0.60,816,7.87,0.0556,0.5370,0.1667,0.1667,0.0741
"2006",0.40,224,7.59,0.0435,0.6739,0.0870,0.1522,0.0435
"2010",0.10,571,7.81,0.0735,0.4706,0.1029,0.1912,0.1618
"2011",0.52,130,7.42,0.0462,0.5692,0.0769,0.2462,0.0615
"2012",0.42,363,7.79,0.0548,0.5205,0.0548,0.2466,0.1233
"2013",0.42,363,7.79,0.0484,0.5323,0.1129,0.2419,0.0645

<snow-ternary-plot.R>
# Create matrix of ternary plots of FFGs as dependent variables.
# Follows 'Analyzing Compositional Data with R' sec. 5.3; pp 122 ff
# Change stream name as necessary.
# load package from library
require(compositions)
# read in raw data
SnowRegr <- read.csv('snow-regression.dat', header=T)
# extract response variables
SnowY <- acomp(SnowRegr[,5:9])
# column headings; variables
names(SnowRegr)
# continuous explanatory co-variables
SnowCovars <-
SnowRegr[,c("Year","NO3","SO4","pH")]
# first continuous co-variable
SnowX1 <- SnowCovars$NO3
# second continuous co-variable
SnowX2 <- SnowCovars$SO4
# third continuous co-variable
SnowX3 <- SnowCovars$pH
# discrete co-variable
SnowX4 <- 
factor(SnowCovars$Year,c("2005","2006","2010","2011","2012","2013"),ordered=T)
# for the discrete co-var, ANOVA not specified in unique way so contrasts must 
be specified; use the
#   treatment contrasts.
contrasts(SnowX4) <- "contr.treatment"
# save figure parameters
opar <- par(xpd=NA,no.readonly=T)
# ternary plot matrix
plot(SnowY, pch=as.numeric(SnowX4), col=c("red","dark
green","dark blue","dark
goldenrod","dark orange","dark grey")[SnowX4])
# add legend
legend(x=0.83, y=-0.165, abbreviate(levels(SnowX4), 
minlength=1),pch=as.numeric(SnowX4), col=c("red","dark
green","dark blue","dark
goldenrod","dark orange","dark grey"), ncol=2, xpd=T,
bty="n", yjust=0)
# reset plot parameters
par(opar)
# unload the package
detach('package:compositions')

   This data set with eqivalent code produces plots with the other continuous
variables as bars with colors on the top points of the triangles:

<filename = jerritt-regression.dat>
"Year","NO3","SO4","pH","Fi","Ga","Gr","Pr","Sh"
"2004",1.70,2200,8.70,0.0444,0.6889,0.0222,0.2222,0.0222
"2005",2.50,5000,8.43,0.0182,0.5636,0.0909,0.3091,0.0182
"2006",1.80,6670,8.57,0.0370,0.6173,0.0741,0.2469,0.0247
"2010",0.54,4000,8.00,0.0870,0.6087,0.0870,0.2174,0.0000
"2011",2.70,4300,8.47,0.0449,0.5256,0.0897,0.2949,0.0449
"2012",0.76,595,8.21,0.0000,0.4231,0.0769,0.5000,0.0000
"2013",0.76,595,8.21,0.0000,0.4545,0.0455,0.4545,0.0455

<jerritt-ternary-plot.R>
# Create matrix of ternary plots of FFGs as dependent variables.
# Follows 'Analyzing Compositional Data with R' sec. 5.3; pp 122 ff
# Change stream name as necessary.
# load package from library
require(compositions)
# read in raw data
JerrittRegr <- read.csv('jerritt-regression.dat', header=T)
# extract response variables
JerrittY <- acomp(JerrittRegr[,5:9])
# column headings; variables
names(JerrittRegr)
# continuous explanatory co-variables
JerrittCovars <-
JerrittRegr[,c("Year","NO3","SO4","pH")]
# first continuous co-variable
JerrittX1 <- JerrittCovars$NO3
# second continuous co-variable
JerrittX2 <- JerrittCovars$SO4
# third continuous co-variable
JerrittX3 <- JerrittCovars$pH
# discrete co-variable
JerrittX4 <- 
factor(JerrittCovars$Year,c("2004","2005","2006","2010","2011","2012","2013"),ordered=T)
# for the discrete co-var, ANOVA not specified in unique way so contrasts must 
be specified; use the
#   treatment contrasts.
contrasts(JerrittX4) <- "contr.treatment"
# save figure parameters
opar <- par(xpd=NA,no.readonly=T)
# ternary plot matrix
plot(JerrittY, pch=as.numeric(JerrittX4),
col=c("black","red","dark
green","dark blue","dark goldenrod","dark
orange","dark grey")[JerrittX4])
# add legend
legend(x=0.83, y=-0.165, abbreviate(levels(JerrittX4), 
minlength=1),pch=as.numeric(JerrittX4),
col=c("black","red","dark green","dark
blue","dark goldenrod","dark orange","dark
grey"), ncol=2, xpd=T, bty="n",
yjust=0)
# reset plot parameters
par(opar)
# unload the package
detach('package:compositions')

Thanks in advance,

Rich

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and provide commented, minimal, self-contained, reproducible code.

Rich Shepard

2015-May-01 18:32 UTC

head link

[R] Results Differ in Ternary Plot Matrix of Compositional Response Variables

On Fri, 1 May 2015, David L Carlson wrote:
> Add plotMissings=FALSE to the second plot and see the plot.acomp manual
> page description of this argument:
>
> plot(JerrittY, pch=as.numeric(JerrittX4),
col=c("black","red", "dark green",
>     "dark blue","dark goldenrod","dark
orange","dark grey")[JerrittX4],
>      plotMissings=FALSE)
David,

   Mea culpa! I overlooked the man page for plot.acomp.

   When I add plotMissings=FALSE I see no differences in the output despite
there being zeros for a comple of variables in two years.

   The horizontal bar with colors and labels on top of each ternary diagram
is what I want to eliminate and replace with the dot seen in plots with no
more than 6 rows (years) of data. There are 3 data sets with 6 rows, 1 with
7 rows (jerritt), and one with 8 rows and no missing data. The latter two
have the horizontal bars while the former three have dots.

Thanks,

Rich

R help - May 2015 - Results Differ in Ternary Plot Matrix of Compositional Response Variables

[R] Results Differ in Ternary Plot Matrix of Compositional Response Variables

[R] Results Differ in Ternary Plot Matrix of Compositional Response Variables

[R] Results Differ in Ternary Plot Matrix of Compositional Response Variables