[R] Knitr/Lattice/Lyx [was: Trellis Plots: translating lattice xyplot() to ggplot()]

[Rich Shepard]

On Sat, 11 Jul 2015, Rich Shepard wrote:

>  Attached are the .RData file from the cwd, the test.lyx file (lyx-2.1.3),
> and the two test files from /tmp/.../lyx_tmpbuf3/.

   The .RData and .lyx files were stripped off. I'll try sending them again.

Rich
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#LyX 2.1 created this file. For more info see http://www.lyx.org/
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load('.RData')
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echo=FALSE
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\begin_layout Standard
Some text in here; separating knitr chunks.
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carlin <- read.csv("./carlin.csv", header = TRUE, sep = ",", stringsAsFactors
 = F)
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Next paragraph of text.
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carlin$sampdate <- as.Date(carlin$sampdate)
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str(carlin)
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Another paragraph or two of text.
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summary(carlin)
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Plots of these distributions are the next step ...
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carlin.1 <- subset(carlin, select = siteid:CO3)
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carlin.2 <- subset(carlin, select = c(siteid, sampdate, Alk:Ca))
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carlin.3 <- subset(carlin, select = c(siteid, sampdate, Mg:Cr))
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carlin.4 <- subset(carlin, select = c(siteid, sampdate, Co:Hg))
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To plot each chemical constituent's concentration as a function of collection
 date the data format needs to be reshaped from wide to long:
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library(reshape2)
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carlin.1.melt <- melt(carlin.1, na.rm = F, id.vars = c('siteid', 'sampdate'))
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carlin.2.melt <- melt(carlin.2, na.rm = F, id.vars = c('siteid', 'sampdate'))
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carlin.3.melt <- melt(carlin.3, na.rm = F, id.vars = c('siteid', 'sampdate'))
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carlin.4.melt <- melt(carlin.4, na.rm = F, id.vars = c('siteid', 'sampdate'))
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The scatter (X-Y) plots use only measured data; missing data are not included.
 These plots show the measured values over time for each measured constituent.
 For example, Figure 
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reference "fig: scatter-plot group 1"

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 shows that most chemical constitent concentrations are low and have low
 variability.
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library(lattice)
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xyplot(value ~ sampdate | variable, data=carlin.1.melt, rm.na = T, ylab = 'Measured
 Value', xlab = 'Date')
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name "fig: scatter-plot group 1"

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Variability of measured values in group 1 constituents over the period of
 record at the Carlin station.
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Because river discharge (in cubic feet per second) spiked at about 8,000
 cfs in the mis-1980s the Y-axis for all panels in the figure have the save
 range.
 This compresses low values yet any single constituent can be plotted by
 itself and the details of its variability over time easily seen.
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The second group of constituents (Figure 
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reference "fig: scatter-plot group 2"

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)
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xyplot(value ~ sampdate | variable, data=carlin.2.melt, rm.na = T, ylab = 'Measured
 Value', xlab = 'Date'
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LatexCommand label
name "fig: scatter-plot group 2"

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Variability of measured values in group 2 constituents over the period of
 record at the Carlin station.
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 reveals that nutrients (the nitrogen compounds, phosphate, and organic
 carbon) are all consistenly low with low variability while total dissolved
 solids (TDS) concentrations are very highly variable both within years
 (as shown by the different concentrations at the same date) and across
 the period of observations.
 Alkalinity and hardness are also quite variable at both time scales.
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