In mkoohafkan/rremat: Russian River Estuary data collected by the Largier Lab

Visualizing Russian River Estuary Data

library(rremat)
library(ggplot2)
library(scales)
library(knitr)
opts_chunk$set(fig.width = 12, fig.height = 8, echo = FALSE)

CTD data

data(ctd)

baseplot = function(p) 
  ggplot(p, aes(x = depth, color = id)) + scale_x_reverse() + coord_flip() +
  scale_y_continuous(breaks = pretty_breaks()) +  facet_wrap(~ dist, nrow = 1)

lyrs = list(
  ta = geom_line(aes(y = ta)),
  sa = geom_line(aes(y = sa)),
  fl = geom_line(aes(y = fl)),
  oa = geom_line(aes(y = oa)),
  sat = geom_line(aes(y = sat)),
  da = geom_line(aes(y = fl)),
  bt = geom_line(aes(y = bt))
)

dates = unique(ctd$date)
names(dates) = paste(dates)

ctd.plots = vector("list", length = length(lyrs))
names(ctd.plots) = names(lyrs)
for(n in names(ctd.plots)){
  ctd.plots[[n]] = vector("list", length = length(dates))
  names(ctd.plots[[n]]) = paste(dates)
  for(d in names(dates))
    ctd.plots[[n]][[d]] = baseplot(subset(ctd, date == dates[[d]])) + 
      lyrs[[n]] + ggtitle(d)
}

Temperature

for(p in ctd.plots$ta)
  print(p)

Salinity

for(p in ctd.plots$sa){
  print(p)
}

Dissolved Oxygen

for(p in ctd.plots$oa)
  print(p)

Interpolated CTD grids

data(grids)

baseplot = function(p) 
  ggplot(p, aes(x = dist, y = elev)) + xlim(min(grids$dist), max(grids$dist)) +
    ylim(min(grids$elev), max(grids$elev)) + facet_wrap(~ id)
lyrs = list(
  ta = geom_raster(aes(fill = ta)),
  sa = geom_raster(aes(fill = sa)),
  fl = geom_raster(aes(fill = fl)),
  oa = geom_raster(aes(fill = oa)),
  sat = geom_raster(aes(fill = sat)),
  da = geom_raster(aes(fill = fl)),
  bt = geom_raster(aes(fill = bt))
)

dates = unique(grids$date)
names(dates) = paste(dates)

grids.plots = vector("list", length = length(lyrs))
names(grids.plots) = names(lyrs)
for(n in names(grids.plots)){
  grids.plots[[n]] = vector("list", length = length(dates))
  names(grids.plots[[n]]) = paste(dates)
  for(d in names(dates))
    grids.plots[[n]][[d]] = baseplot(na.omit(subset(grids, 
    date== dates[[d]]))) + lyrs[[n]] + ggtitle(d)
}

Temperature

for(p in grids.plots$ta)
  print(p + scale_fill_gradientn(colours = rev(c("#A50026", "#D73027", 
    "#F46D43", "#FDAE61", "#FEE090", "#E0F3F8", "#ABD9E9", "#74ADD1", 
    "#4575B4", "#313695"))))

Salinity

for(p in grids.plots$sa)
  print(p  + scale_fill_gradientn(colours = rev(c("#A50026", "#D73027", 
    "#F46D43", "#FDAE61", "#FEE090", "#E0F3F8", "#ABD9E9", "#74ADD1", 
    "#4575B4", "#313695"))) )

Dissolved Oxygen

for(p in grids.plots$oa)
  print(p + scale_fill_gradientn(colours = c("#A50026", "#D73027", "#F46D43", 
    "#FDAE61", "#FEE090", "#E0F3F8", "#ABD9E9", "#74ADD1", "#4575B4", 
    "#313695")) )

WLL Data

data(wll)

Water Depth

ggplot(wll, aes(x = mtime, y = depth)) + geom_line() + 
  facet_wrap(~ site, ncol = 1)

Water Temperature

ggplot(wll, aes(x = mtime, y = temp)) + geom_line() + 
  facet_wrap(~ site, ncol = 1)

mkoohafkan/rremat documentation built on July 3, 2021, 12:06 p.m.