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climate_offset_trajectories.R
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climate_offset_trajectories.R
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######################################################################
#
# Climate offset strategies (PLOTLY for 3D visualization):
# emission avoidances and silvicultural interventions
# required to stabilize community compositions
#
# Method: trace on NPMR surface in 3+ dimensions
#
# Rob Smith, phytomosaic@gmail.com, 27 Oct 2020
#
## GNU General Public License, Version 3.0 ###################
### Climate offset trajectories:
# N avoidance and stand silvicultural modification as
# pathways to climate adaptation
# With CE Ellis and LH Geiser and Jill McMurray
# Use FIA data and the Root airscores model
# 3-D regression surface, ball and arrow trajectories
# Need stand info: hardwood ratio, total BA, canopy cover, etc
### preamble
require(plotly) # for interactive 3D surface plots
# require(shiny) # for hosting app
### data preparation
rm(list=ls())
# setwd('/home/rob/prj/trajectories/')
d <- read.csv('./n_west_contour.csv', header=T)
names(d) <- c('Step','x','y','z')
d$z[d$z < 0] <- NA
d <- d[d$x < 7.1,] # remove a slew of NA at high N dep
# rounding (may reduce filesize, from 2.6 MB to 1.2 MB)
d[,2:4] <- sapply(d[,2:4], round, digits=2)
`reshape_w` <- function (data, ...) {
if (!is.data.frame(data))
stop('must be dataframe')
if (ncol(data) != 3)
stop('must have 3-column format')
x <- data[, 1]
y <- data[, 2]
z <- data[, 3]
fx <- as.factor(x)
fy <- as.factor(y)
m <- matrix(NA, nrow = nlevels(fx), ncol = nlevels(fy),
dimnames = list(levels(fx), levels(fy)))
m[cbind(fx, fy)] <- z
list(x = sort(unique(x)), y = sort(unique(y)), z = m)
}
w <- reshape_w(d[,-1])
x <- w$x
y <- w$y
z <- w$z
# ### EXPERIMENTAL: roughen the surface to see more texture
# set.seed(88)
# z <- z + rnorm(prod(dim(z)), 0, 0.02)
### axis labels setup
# xlb <- expression(Nitrogen~(kg~N~ha^{-1}~y^{-1}))
xlb <- 'N deposition'
ylb <- 'Max Aug Temp (\u00B0C)'
# zlb <- 'Airscores'
zlb <- '<b>Dirty/warm</b> \u2190 Airscores \u2192 <b>Clean/cool</b>'
### function definitions
`make_trace` <- function(vvx, vvy) {
n <- 9 # interpolation steps
vx <- c(sapply(1:(length(vvx)-1), function(i) {seq(vvx[i], vvx[i+1], len=n)}))
vy <- c(sapply(1:(length(vvy)-1), function(i) {seq(vvy[i], vvy[i+1], len=n)}))
vz <- sapply(1:length(vx), function(k) { # get target z locations from surface
z[which.min(abs(x - vx[k])), which.min(abs(y - vy[k]))]})
isna <- is.na(vz) # smooth right over NA values (TODO...)
vz[!isna] <- predict(smooth.spline(vz[!isna] ))$y # smoothing
return(list(vx=vx, vy=vy, vz=vz))
}
# # isoline (walk along contour, strategy for NO CHANGE in airscores)
# `make_isoline` <- function(zq=3.7) {
# n <- 9
# dev <- abs(z - zq)
# iso <- which(dev < quantile(dev, prob=0.01, na.rm=T), arr.ind=T)
# vvx <- x[iso[,1]]
# vvy <- y[iso[,2]]
# vx <- c(sapply(1:(length(vvx)-1), function(i) {seq(vvx[i], vvx[i+1], len=n)}))
# vy <- c(sapply(1:(length(vvy)-1), function(i) {seq(vvy[i], vvy[i+1], len=n)}))
# isnax <- is.na(vx) # smooth right over NA values (TODO...)
# isnay <- is.na(vy) # smooth right over NA values (TODO...)
# vx[!isnax] <- predict(smooth.spline(vx[!isnax] ))$y # smoothing
# vy[!isnay] <- predict(smooth.spline(vy[!isnay] ))$y # smoothing
# data.frame(vx=vx, vy=vy)
# }
# `trans3d` <- function (x, y, z, pmat) {
# tr <- cbind(x, y, z, 1, deparse.level = 0L) %*% pmat
# list(x = tr[, 1]/tr[, 4], y = tr[, 2]/tr[, 4])
# }
# `surfcol` <- function (x, ngrid, alpha = 0.9, begin = 0.1, end = 0.85, dir = 1,
# pal, ...) {
# if (missing(pal)) {
# pal <- viridis::viridis(n = ngrid, alpha = alpha, begin = begin,
# end = end, direction = dir)
# }
# xavg <- (x[-1, -1] + x[-1, -(ncol(x) - 1)] + x[-(nrow(x) -
# 1), -1] + x[-(nrow(x) - 1), -(ncol(x) - 1)])/4
# pal[cut(xavg, breaks = length(pal), include.lowest = T)]
# }
# `persp_trace` <- function(vx, vy, vz, theta=-35, ...) {
# p <- persp(x, y, z, theta = theta, phi = 30,
# col = surfcol(z, prod(dim(z)), pal=viridis::viridis(99)),
# shade = 0.01, border = '#0000001A',
# ticktype = 'detailed', xaxs = 'i',
# xlab = xlb, ylab = ylb, zlab = 'Airscores')
# path <- trans3d(vx, vy, vz, pmat = p)
# lines(path, col=2, lwd=3)
# }
`plty_trace` <- function(vx, vy, vz, showscale=FALSE, tracecol='red',
tracename='tracenm', xlb, ylb, zlb) {
plot_ly(z=t(z), x=x, y=y, hoverinfo = 'none') %>%
# add regression surface
add_surface(showscale=showscale,
colorbar = list(title = 'Airscores')) %>%
# add contours to regression surface
add_surface(
contours = list(
z = list(show = TRUE, highlight = FALSE,
project=list(z=TRUE), start=0, end=99,
size=0.5)),
showscale=FALSE) %>%
# add trace of trajectories to surface
add_trace(x = vx, y = vy, z = vz+0.05,
showlegend=T, name=tracename,
type ='scatter3d', mode = 'lines',
line = list(color=tracecol, width=4)) %>%
layout(scene = list(
# aspectratio=list(x=0.9, y=1, z=0.8),
camera = list(
center = list(x=0.1, y=0.1, z=-0.35),
eye = list(x=-1.75, y=-0.5, z=0)),
xaxis = list(title = xlb, type='linear'),
yaxis = list(title = ylb, type='linear'),
zaxis = list(title = zlb, type='linear')))
}
# ### TEST render
# n <- 7
# tr <- make_trace(seq(2, 3, len=n), seq(22,30,len=n))
# plty_trace(tr$vx, tr$vy, tr$vz, showscale=F,
# tracecol='red', 'Increase N dep', xlb, ylb, zlb)
# ### plot single SCENARIO
# # target xy locations
# tr <- make_trace(vvx=seq(2, 6, len=7), vvy=c(15, 16.5, 17.5, 20, 30, 32, 32.5))
# # persp
# set_par_mercury(1)
# persp_trace(tr$vx, tr$vy, tr$vz)
# # plotly
# plty_trace(tr$vx, tr$vy, tr$vz, T, '#DF536B', 'tracename', xlb, ylb, zlb)
### set up 5 different SCENARIOS
# # strategy that yields NO CHANGE in airscores (isoline contour walk)
# iso <- make_isoline(zq=3.7)
# iso <- iso[iso$vy > 22 & iso$vy < 30 & iso$vx > 1 & iso$vx < 2,]
# po <- plty_trace(iso$vx, iso$vy, 3.7, showscale=F,
# tracecol='darkblue', 'Iso-trajectory', xlb, ylb, zlb)
# increasing N-dep, 8 degrees warming
n <- 7
tr <- make_trace(seq(2, 3, len=n), seq(22,30,len=n))
p0 <- plty_trace(tr$vx, tr$vy, tr$vz, showscale=FALSE,
tracecol='red',
'<b>Worse:</b> increase N dep, 1 kg ha<sup>-1</sup> y<sup>-1</sup>',
# 'Increase N dep',
xlb, ylb, zlb)
# constant N-dep, 8 degrees warming
tr <- make_trace(rep(2, n), seq(22,30,len=n))
p1 <- plty_trace(tr$vx, tr$vy, tr$vz, showscale=F,
tracecol='firebrick',
'<b>Neutral:</b> business as usual',
xlb, ylb, zlb)
# declining N-dep, 8 degrees warming
tr <- make_trace(seq(2, 1, len=n), seq(22,30,len=n))
p2 <- plty_trace(tr$vx, tr$vy, tr$vz, showscale=F,
tracecol='purple',
# 'Mitigate N dep',
'<b>Better:</b> mitigate N dep, 1 kg ha<sup>-1</sup> y<sup>-1</sup>',
xlb, ylb, zlb)
# declining N-dep, 4 degrees warming
tr <- make_trace(seq(2, 1, len=n), seq(22,26,len=n))
p3 <- plty_trace(tr$vx, tr$vy, tr$vz, showscale=F,
tracecol='cyan', '<b>Best:</b> mitigate N+GHG emissions',
xlb, ylb, zlb)
# overplot them
p <- subplot(p0, p1, p2, p3)
# annotate the origin, and make the gradient steeper
a <- list(list(x=tr$vx[1], y=tr$vy[1], z=tr$vz[1],
arrowsize = 1.5, arrowwidth = 0.95, arrowhead = 3,
ax = 20, ay=20, textangle = 0, arrowcolor = 'gold',
text = 'Start',
font = list(color='gold', size=12),
xanchor='left', yanchor='bottom'))
p <- p %>%
layout(scene = list(annotations = a,
aspectratio = list(x=0.9, y=1, z=1))) %>%
config(displayModeBar = FALSE) %>%
toWebGL() %>% # for faster rendering in browser
partial_bundle() %>% # for smaller filesize and faster load time
layout(legend = list(
title = list(text='<b> Mitigation scenario </b>'),
font = list(size = 12),
bgcolor = '#BFBFBF',
bordercolor = '#000000',
borderwidth = 1))
# ### OPTION 1 --- render as interactive plotly object
# p
# ### OPTION 2 --- save it locally as HTML
# # htmlwidgets::saveWidget(as_widget(p), file = './index.html',
# # title='Mitigation trajectories')
# p$dependencies[[5]]
htmlwidgets::saveWidget(as_widget(p),
file = './index.html',
selfcontained = FALSE,
libdir = 'lib',
title='Mitigation trajectories')
# ### OPTION 3 --- host as shiny app
# txt_desc <- paste0(
# 'Trajectories for climate and air-quality mitigation. Trajectories ',
# 'describe expected pathways of community compositional change under ',
# 'multiple global-change scenarios. Regression surface is from: '
# )
# txt_note <- paste0(
# 'Patience, takes a moment to load....'
# )
# em_cite <- em(paste0('Geiser, Root, Smith, Jovan, St. Clair, and Dillman (',
# 'unpublished, 2021).'))
# ui <- fluidPage(
# verticalLayout(
# titlePanel(title = 'Mitigation trajectories',
# windowTitle = 'Mitigation trajectories'),
# p(txt_desc, em_cite,
# 'Contact:', a('robert.smith3@usda.gov',
# href='robert.smith3@usda.gov',
# target='_blank')
# ),
# p(txt_note),
# br(),
# plotlyOutput('graph', width = '100%', height = '95vh'),
# br()
# )
# )
# server <- function(input, output, session){
# output$graph <- renderPlotly({ p })
# }
# shinyApp(ui, server) # <<------
# #############################################################################
# ### zoom in by trimming matrix
# d <- d[d$x < 3 & d$y > 20 & d$y < 32,]
# w <- reshape_w(d[,-1])
# x <- w$x
# y <- w$y
# z <- w$z
# ### strategy that yields NO CHANGE in airscores (isoline contour walk)
# iso <- make_isoline(zq=3.7)
# iso <- iso[iso$vy > 22 & iso$vy < 30 & iso$vx > 1 & iso$vx < 2,]
# po <- plty_trace(iso$vx, iso$vy, 3.7, showscale=F,
# tracecol='darkblue', 'Iso-trajectory', xlb, ylb, zlb)
# # increasing N-dep, 8 degrees warming
# n <- 7
# tr <- make_trace(seq(2, 3, len=n), seq(22,30,len=n))
# p0 <- plty_trace(tr$vx, tr$vy, tr$vz, showscale=T,
# tracecol='red', 'N increase', xlb, ylb, zlb)
# # constant N-dep, 8 degrees warming
# tr <- make_trace(rep(2, n), seq(22,30,len=n))
# p1 <- plty_trace(tr$vx, tr$vy, tr$vz, showscale=F,
# tracecol='firebrick', 'No change', xlb, ylb, zlb)
# # declining N-dep, 8 degrees warming
# tr <- make_trace(seq(2, 1, len=n), seq(22,30,len=n))
# p2 <- plty_trace(tr$vx, tr$vy, tr$vz, showscale=F,
# tracecol='purple', 'N mitigation', xlb, ylb, zlb)
# # declining N-dep, 4 degrees warming
# tr <- make_trace(seq(2, 1, len=n), seq(22,26,len=n))
# p3 <- plty_trace(tr$vx, tr$vy, tr$vz, showscale=F,
# tracecol='cyan', 'N+GHG mitigation', xlb, ylb, zlb)
# # overplot them
# p <- subplot(po, p0, p1, p2, p3)
# # annotate the origin, and make the gradient steep
# a <- list(list(x=tr$vx[1], y=tr$vy[1], z=tr$vz[1],
# arrowsize = 1.5, arrowwidth = 0.95, arrowhead = 3,
# ax = 10, textangle = 0, arrowcolor = 'gold', text = 'Start',
# font = list(color='gold', size=12), xanchor='left'))
# p <- p %>% layout(scene = list(annotations = a,
# aspectratio = list(x=0.9, y=1, z=1)))
# p
#
# # ### save it locally as HTML
# # getwd()
# # htmlwidgets::saveWidget(as_widget(p), '/home/rob/prj/orise_wildstew/wildstew/www/index.html')
#
#
#
#
#
#
#
#
# ### something like what was in the FARM team prezi:
# # png(file=paste0('./fig/z_08_npmr.png'),
# # wid=5.0, hei=3.25, unit='in', bg='transparent', res=900)
# require(ggplot2)
# zz <- data.frame(x1 = c(0,0,0.2,0.3,0.4),
# y1 = c(22,24,26,28,30),
# x2 = c(6.65,6.95,7.05,6.9,6.6),
# y2 = c(22,24,26,28,30))
# ggplot(d,aes(x,y,z=z)) +
# geom_contour_filled(breaks = seq(2,10, by=0.5)) +
# # scale_colour_viridis(option='D', direction=1, begin=0, end=.9, discrete=T, na.value=NA) +
# geom_segment(aes(x = x1, y = y1, xend = x2, yend = y2), data=zz, size=1,
# inherit.aes = F, color=viridis::inferno(5, begin=0.1, end=0.8)) +
# xlab(expression(Nitrogen ~ (kg ~ N ~ ha^{-1} ~ y^{-1}))) +
# ylab('Max Aug Temp (\u00B0C)') +
# guides(fill=guide_legend(
# title=expression(Airscores ~ (kg ~ N ~ ha^{-1} ~ y^{-1})), ticks=F,
# title.position='top', title.hjust=0.5, reverse=T) ) +
# theme_classic() +
# theme(plot.background = element_blank(),
# panel.background = element_blank(),
# legend.title = element_text(size=10),
# legend.background = element_blank(),
# legend.key = element_blank(),
# legend.key.size = unit(0.25,'line'),
# legend.text = element_text(size=6),
# title = element_text(size=14, face='bold'),
# # plot.margin=unit(c(2,1,2,0),'mm'),
# text=element_text(family='Routed Gothic', colour='black'),
# axis.text=element_text(colour='black')) +
# scale_x_continuous(breaks=0:7, #limits=c(0,7.5),
# expand = expansion(0,0)) +
# scale_y_continuous(breaks=seq(15,35,by=5), expand = expansion(0,0))
# # dev.off()
#### END ####