--- author: "Michael Koohafkan" title: "Reproducing the R Journal Publication" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{Publication Reproduction} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- ```{r include = FALSE} library(knitr) opts_chunk$set(echo = TRUE, eval = FALSE) ``` This document provides the code needed to reproduce all results and figures from > Michael C. Koohafkan and Bassam A. Younis (2015). > Open-Channel Computation with R. The R Journal, 7(2), 249-262. > URL https://journal.r-project.org/archive/2015-2/koohafkan-younis.pdf The .Rnw file used to generate the full publication is hosted on the [package development repository](https://github.com/mkoohafkan/rivr/tree/master/inst/pub). ```{r the-code} ## ---- load-libs ------------------------------------------------------- library(knitr) opts_chunk$set(fig.width = 6, fig.height = 4, fig.path = "fig/", warning = FALSE, message = FALSE, error = FALSE, results = "asis", out.width = '\\textwidth', cache = TRUE, cache.path = "cache/") library(rivr) library(ggplot2) library(scales) library(RColorBrewer) library(dplyr) library(xtable) ## ---- startparams ----------------------------------------------------- plotopts = list(theme_bw(), xlab(expression(Distance~from~control~section~~(ft)))) g = 32.2 Cm = 1.486 slope = 0.001 mannings = 0.045 flow = 250 width = 100 sideslope = 0 # calculate control depth as 1ft above the normal depth depth.m1 = round(1 + normal_depth(slope, mannings, flow, 2, Cm, width, sideslope), 2) depth.m2 = round(1.1*critical_depth(flow, 1, g, width, sideslope), 2) rivdist = 3000 ## ---- restest --------------------------------------------------------- # Test sensitivity of step size stepsizes = c(500, 100, 50, 10, 1) resolution.test.m1 = list() resolution.test.m2 = list() for(r in stepsizes){ resolution.test.m1[[paste0('dx=', r)]] = compute_profile(slope, mannings, flow, depth.m1, Cm, g, width, sideslope, stepdist = r, totaldist = rivdist) resolution.test.m2[[paste0('dx=', r)]] = compute_profile(slope, mannings, flow, depth.m2, Cm, g, width, sideslope, stepdist = r, totaldist = rivdist) } resolution.plot = NULL for(lbl in names(resolution.test.m1)){ f1 = resolution.test.m1[[lbl]] f2 = resolution.test.m2[[lbl]] f1['type'] = 'M1' f2['type'] = 'M2' f = rbind(f1, f2) f['run'] = lbl f['res'] = as.numeric(substr(lbl, 4, 10L)) resolution.plot = rbind(resolution.plot, f) } resolution.plot['res'] = factor(resolution.plot$res, levels = rev(sort(stepsizes))) resolution.plot['run'] = factor(resolution.plot$run, levels = names(resolution.test.m1)) resolution.plot['type'] = factor(resolution.plot$type, levels = c('M1', 'M2')) stepsize = 10 ## ----resfig ---------------------------------------------------------- ggplot(resolution.plot, aes(x = x, y = y + z)) + plotopts + geom_line(aes(color = res, linetype = res), size = 1) + facet_wrap(~type) + ylab(expression(River~stage~~(ft))) + scale_linetype_manual("resolution (ft)", labels = levels(resolution.plot$res), values = c("solid", "longdash", "dashed", "dotdash", "dotted")) + scale_color_manual("resolution (ft)", values = brewer.pal(7, "YlGnBu")[3:7], labels = levels(resolution.plot$res)) ## ----roughness ------------------------------------------------------- roughness.test.m1 = list() roughness.test.m2 = list() roughnesses = 0.045*seq(0.5, 1.5, length = 5) for(n in roughnesses){ roughness.test.m1[[paste0('n=',n)]] = compute_profile(slope, n, flow, depth.m1, Cm, g, width, sideslope, stepdist=stepsize, totaldist=rivdist) roughness.test.m2[[paste0('n=',n)]] = compute_profile(slope, n, flow, depth.m2, Cm, g, width, sideslope, stepdist=stepsize, totaldist=rivdist) } roughness.plot = NULL for(lbl in names(roughness.test.m1)){ f1 = roughness.test.m1[[lbl]] f2 = roughness.test.m2[[lbl]] f1['type'] = 'M1' f2['type'] = 'M2' f = rbind(f1, f2) f['run'] = lbl f['mannings'] = as.numeric(substr(lbl, 4, 10L)) roughness.plot = rbind(roughness.plot, f) } roughness.plot['run'] = factor(roughness.plot$run, levels = names(roughness.test.m1)) roughness.plot['mannings'] = factor(roughness.plot$mannings, levels = sort(roughnesses)) roughness.plot['type'] = factor(roughness.plot$type, levels=c('M1', 'M2')) ## ---- roughplot ------------------------------------------------------- ggplot(roughness.plot, aes(x = x, y = y + z)) + geom_line(aes(linetype = mannings, color = mannings), size = 1) + plotopts + facet_wrap(~ type) + ylab(expression(River~stage~~(ft))) + scale_linetype_manual("Bed roughness", labels = levels(roughness.plot$mannings), values = c("solid", "longdash", "dashed", "dotdash", "dotted")) + scale_color_manual("Bed roughness", labels = levels(roughness.plot$mannings), values = brewer.pal(6, "Oranges")[2:6]) ## ---- relroughplot ---------------------------------------------------- roughness.rel.m1 = list() roughness.rel.m2 = list() for(n in roughnesses){ thisyn = normal_depth(slope, n, flow, 2, Cm, width, sideslope) roughness.rel.m1[[paste0('n=',n)]] = compute_profile(slope, n, flow, 1.25*thisyn, Cm, g, width, sideslope, stepdist=stepsize, totaldist=rivdist) roughness.rel.m2[[paste0('n=',n)]] = compute_profile(slope, n, flow, 0.75*thisyn, Cm, g, width, sideslope, stepdist=stepsize, totaldist=rivdist) roughness.rel.m1[[paste0('n=',n)]]['pd.yn'] = (roughness.rel.m1[[paste0('n=',n)]]$y - thisyn)/thisyn roughness.rel.m2[[paste0('n=',n)]]['pd.yn'] = (roughness.rel.m2[[paste0('n=',n)]]$y - thisyn)/thisyn } roughness.rel.plot = NULL for(lbl in names(roughness.rel.m1)){ f1 = roughness.rel.m1[[lbl]] f2 = roughness.rel.m2[[lbl]] f1['type'] = 'M1' f2['type'] = 'M2' f = rbind(f1, f2) f['run'] = lbl f['mannings'] = as.numeric(substr(lbl, 4, 10L)) roughness.rel.plot = rbind(roughness.rel.plot, f) } roughness.rel.plot['mannings'] = factor(roughness.plot$mannings, levels = sort(roughnesses)) roughness.rel.plot['run'] = factor(roughness.rel.plot$run, levels = names(roughness.rel.m1)) roughness.rel.plot['type'] = factor(roughness.rel.plot$type, levels = c('M1', 'M2')) ggplot(roughness.rel.plot, aes(x = x, y = pd.yn)) + geom_line(aes(linetype = mannings, color = mannings), size = 1) + plotopts + facet_wrap(~type, scales = 'free_y') + scale_y_continuous(expression(Percent~difference~from~normal~depth), labels = percent) + scale_linetype_manual("Bed roughness", labels = levels(roughness.rel.plot$mannings), values = c("solid", "longdash", "dashed", "dotdash", "dotted")) + scale_color_manual("Bed roughness", labels = levels(roughness.rel.plot$mannings), values = brewer.pal(6, "Oranges")[2:6]) ## ---- loadup-kwm ------------------------------------------------------ oldscipen = options('scipen') options(scipen = 1000) slope = 0.001 extent = 150000 mannings = 0.045 B = 100 SS = 0 Cm = 1.486 g = 32.2 iflow = 250 # keep Courant number at 0.7 to balance temporal and spatial resolution idepth = normal_depth(slope, mannings, 250, 10, 1.485, 100, SS) iarea = channel_geom(idepth, B, SS)["A"] cn = 0.7*iarea/iflow # define upstream boundary condition assuming a timestep in seconds bcfunc = function(x) ifelse(x < 9000, 250 + (750/pi)*(1 - cos(pi*x/(60*75))), 250) bctime = 76000 xnodes = extent/c(25, 50, 125, 250, 500, 1000, 2000, 5000) + 1 myxres = extent/(xnodes - 1) mytres = cn*myxres plotopts = list(theme_bw()) # run the model modtime = list() modelresults = list() for(i in seq(length(xnodes))){ numnodes = xnodes[i] xstep = myxres[i] tstep = mytres[i] bc = bcfunc(seq(0, bctime, by=tstep)) mp = c(1, as.integer(50000/xstep + 1), as.integer(100000/xstep + 1), numnodes) mt = as.integer(round(seq(1, length(bc), length.out=10)))[seq(7)] if(xstep == min(myxres)){ mt = as.integer(round(seq(1, length(bc), length.out=125))) mtslice = mt[round(seq(1, length(mt), length.out=7))] } lbl = paste0('dx=',xstep) modtime[[lbl]] <- system.time(modelresults[[lbl]] <- route_wave(slope, mannings, Cm, g, B, SS, iflow, bc, timestep=tstep, spacestep=xstep, numnodes=numnodes, monitor.nodes=mp, monitor.times=mt, engine="Kinematic")) modelresults[[lbl]]['deltax'] = xstep modelresults[[lbl]]['deltat'] = tstep modelresults[[lbl]]['computationtime'] = modtime[[lbl]][[3]] modelresults[[lbl]]['label'] = lbl } allresults = do.call(rbind.data.frame, modelresults) row.names(allresults) = NULL names(allresults)[which(names(allresults)=='flow')] = "Q" names(allresults)[which(names(allresults)=='distance')] = "x" names(allresults)[which(names(allresults)=='time')] = "t" ## ---- floodhydrograph ------------------------------------------------- floodhydro = data.frame(time = seq(15000), flow=bcfunc(seq(15000))) ggplot(floodhydro, aes(x=time/60, y=flow)) + geom_line(color="darkblue", size = 1) + plotopts + xlab(expression(time~~(minutes))) + ylab(expression(flow~~(ft^3~~s^-1))) ## ---- routeplot-kinematic --------------------------------------------- # still plot surfaces = group_by(filter(allresults, monitor.type=='timestep', deltax==min(deltax))) ggplot(filter(surfaces, step %in% mtslice[2:5]), aes(x=x, y=Q, linetype=factor(round(t/60)), color=factor(round(t/60)))) + geom_line(size = 1) + plotopts + scale_color_manual("time\n(minutes)", values = brewer.pal(7, "YlGnBu")[3:6]) + scale_linetype_manual("time\n(minutes)", values = c("solid", "dashed", "dotdash", "dotted")) + xlab(expression(distance~~downstream~~(ft))) + ylab(expression(flow~~(ft^3~~s^-1))) # animation routeylims = c(min(surfaces$Q), max(surfaces$Q)) routexlims = c(min(surfaces$x), max(surfaces$x)) thisdt = unique(surfaces$deltat) for(n in unique(surfaces$step)) print( ggplot(filter(surfaces, step==n), aes(x=x, y=Q)) + geom_line(color = "darkblue", size = 1) + plotopts + scale_linetype_discrete("time\n(minutes)") + scale_x_continuous(expression(distance~~downstream~~(ft)), limits=routexlims) + scale_y_continuous(expression(flow~~(ft^3~~s^-1)), limits=routeylims) + ggtitle(paste(format(round((n - 1)*thisdt/60), width = 4), "minutes")) ) ## ---- xsectionplot-kinematic ------------------------------------------ xsections = filter(allresults, monitor.type == "node", x %in% c(0,50000))[c("x","t","Q", "deltax")] xsections['deltax'] = factor(paste(xsections$deltax, "feet"), levels=paste(sort(unique(xsections$deltax)), "feet")) ggplot(xsections, aes(x=t/60, y=Q, linetype=factor(format(x, big.mark=",", trim=TRUE), levels = format(sort(unique(x)), big.mark=",", trim=TRUE)), color = deltax)) + geom_path(size = 1) + facet_grid(deltax~.) + plotopts + scale_y_continuous(expression(flow~~(ft^3~~s^-1)), breaks=c(300, 500,700)) + scale_linetype_manual("downstream\ndistance (ft)", values = c("solid", "dashed", "dotted")) + scale_x_continuous(expression(time~~(min)), limits=c(0,600)) + scale_color_manual(values = c("#7570B3", "#8DA0CB", "#66C2A5", "#A6D854", "#E5C494", "#E6AB02", "#FC8D62", "#E78AC3"), guide = FALSE) ## ---- peakstable-kinematic -------------------------------------------- peaks = as.data.frame(summarize(group_by(filter(allresults, x==50000, monitor.type=='node'), computationtime, deltax, deltat, monitor.type), peak.flow=max(Q), time.to.peak=t[which(Q==peak.flow)])) real.peak = max(floodhydro$flow) peaks['flow.percent.error'] = (peaks$peak.flow - real.peak)/real.peak tbld = as.data.frame(peaks[c("deltax", "deltat", "flow.percent.error", "computationtime")]) tbld["deltax"] = round(tbld$deltax) tbld["deltat"] = round(tbld$deltat, 2) tbld["flow.percent.error"] = round(100*tbld$flow.percent.error, 2) names(tbld) = c("$\\Delta x$ (ft)", "$\\Delta t$ (s)", "\\% error (peak flow)", "cost (s)") ptable = xtable(tbld[order(tbld[,1]),], digits = c(0,0,2,2,2)) print(ptable, include.rownames = FALSE, sanitize.colnames.function = identity, sanitize.text.function = function(x){x}, floating=FALSE, hline.after=NULL, add.to.row=list(pos=list(-1,0, nrow(ptable)), command=c('\\toprule ', '\\midrule ', '\\bottomrule ')), format.args = list(big.mark = ",")) ## ---- loadup-dwm ------------------------------------------------------ oldscipen = options('scipen') options(scipen = 1000) slope = 0.001 extent = 150000 mannings = 0.045 B = 100 SS = 0 g = 32.2 Cm = 1.486 iflow = 250 # define upstream boundary condition assuming a timestep in seconds idepth = normal_depth(slope, mannings, 250, 10, Cm, 100, SS) iarea = channel_geom(idepth, B, SS)[["A"]] # keep Courant number at 0.06 to balance temporal and spatial resolution cn = 0.06*iarea/250 bcfunc = function(x) ifelse(x < 9000, 250 + (750/pi)*(1 - cos(pi*x/(60*75))), 250) bctime = 76000 xnodes = extent/c(50, 125, 250, 500, 1000) + 1 myxres = extent/(xnodes - 1) mytres = cn*myxres plotopts = list(theme_bw()) # run the model modtime = list() modelresults = list() for(i in seq(length(xnodes))){ numnodes = xnodes[i] xstep = myxres[i] tstep = mytres[i] bc = bcfunc(seq(0, bctime, by=tstep)) dc = rep(-1, length(bc)) mp = c(1, as.integer(c(1000, 50000, 100000, 149000)/xstep + 1), numnodes) mt = as.integer(round(seq(1, length(bc), length.out=10)))[seq(7)] if(xstep == min(myxres)){ mt = as.integer(round(seq(1, length(bc), length.out=125))) mtslice = mt[round(seq(1, length(mt), length.out=7))] } lbl = paste0('dx=',xstep) modtime[[lbl]] <- system.time(modelresults[[lbl]] <- route_wave(slope, mannings, Cm, g, B, SS, iflow, bc, dc, timestep=tstep, spacestep=xstep, numnodes=numnodes, monitor.nodes=mp, monitor.times=mt, engine="Dynamic", boundary.type="QQ")) modelresults[[lbl]]['deltax'] = xstep modelresults[[lbl]]['deltat'] = tstep modelresults[[lbl]]['computationtime'] = modtime[[lbl]][[3]] modelresults[[lbl]]['label'] = lbl } # combine results allresults = do.call(rbind.data.frame, modelresults) row.names(allresults) = NULL names(allresults)[which(names(allresults)=='flow')] = "Q" names(allresults)[which(names(allresults)=='distance')] = "x" names(allresults)[which(names(allresults)=='time')] = "t" allresults['t'] = (allresults$step - 1)*allresults$deltat allresults['x'] = (allresults$node - 1)*allresults$deltax ## ---- routeplot-characteristic ---------------------------------------- # still plot surfaces = filter(allresults, monitor.type=='timestep', deltax==min(deltax)) ggplot(filter(surfaces, step %in% mtslice[2:5]), aes(x=x, y=Q, linetype=factor(round(t/60)), color=factor(round(t/60)))) + geom_line(size = 1) + plotopts + scale_color_manual("time\n(minutes)", values = brewer.pal(7, "YlGnBu")[3:6]) + scale_linetype_manual("time\n(minutes)", values = c("solid", "dashed", "dotdash", "dotted")) + xlab(expression(distance~~downstream~~(ft))) + ylab(expression(flow~~(ft^3~~s^-1))) # animation routeylims = c(min(surfaces$Q), max(surfaces$Q)) routexlims = c(min(surfaces$x), max(surfaces$x)) thisdt = unique(surfaces$deltat) for(n in unique(surfaces$step)) print( ggplot(filter(surfaces, step==n), aes(x=x, y=Q)) + geom_line(color = "darkblue", size = 1) + plotopts + scale_linetype_discrete("time\n(minutes)") + scale_x_continuous(expression(distance~~downstream~~(ft)), limits=routexlims) + scale_y_continuous(expression(flow~~(ft^3~~s^-1)), limits = routeylims) + ggtitle(paste(format(round((n - 1)*thisdt/60), width = 4), "minutes")) ) ## ---- xsectionplot-characteristic ------------------------------------- xsections = filter(allresults, monitor.type == "node", x %in% c(0, 50000, 150000))[c("x","t","Q", "deltax")] xsections['deltax'] = factor(paste(xsections$deltax, "feet"), levels=paste(sort(unique(xsections$deltax)), "feet")) data(waterolympics) realdat = NULL for(x in unique(xsections$deltax)){ thisdat = waterolympics[waterolympics$t > 200*60,] thisdat['deltax'] = x realdat = rbind(realdat, thisdat) } realdat['deltax'] = factor(realdat$deltax) ggplot(xsections, aes(x=t/60, y=Q, linetype=factor(format(x, big.mark=",", trim=TRUE), levels = format(sort(unique(x)), big.mark=",", trim=TRUE)), color = deltax)) + geom_path(size = 1) + geom_point(data = realdat[realdat$t > 200*60,], color = "black") + facet_grid(deltax~.) +scale_y_continuous(expression(flow~~(ft^3~~s^-1)), breaks=c(300, 500,700)) + scale_linetype_manual("downstream\ndistance (ft)", values = c("solid", "dashed", "dotted")) + plotopts + scale_x_continuous(expression(time~~(min)), limits=c(0,1250)) + scale_color_manual(values = c("#8DA0CB", "#66C2A5", "#A6D854", "#E5C494", "#E6AB02"), guide = FALSE) ## ---- peakstable-characteristic --------------------------------------- peaks = as.data.frame(summarize(group_by(filter(allresults, x==50000, monitor.type=='node'), computationtime, deltax, deltat, monitor.type), peak.flow=max(Q), time.to.peak=t[which(Q==peak.flow)])) real.peak.flow = max(waterolympics$Q) real.time.to.peak = waterolympics$t[which(waterolympics$Q==real.peak.flow)][1] peaks['flow.percent.error'] = (peaks$peak.flow - real.peak.flow)/real.peak.flow peaks['time.percent.error'] = (peaks$time.to.peak - real.time.to.peak)/real.time.to.peak tbld = as.data.frame(peaks[c("deltax", "deltat", "flow.percent.error", "time.percent.error", "computationtime")]) tbld["flow.percent.error"] = round(100*tbld$flow.percent.error, 2) tbld["time.percent.error"] = round(100*tbld$time.percent.error, 2) names(tbld) = c("$\\Delta x$ (ft)", "$\\Delta t$ (s)", "\\% error (peak flow)", "\\% error (time to peak)", "cost (s)") ptable = xtable(tbld[order(tbld[,1]),], digits = c(0,0,2,2,2,2)) print(ptable, include.rownames=FALSE, sanitize.colnames.function=identity, sanitize.text.function = function(x){x}, floating=FALSE, hline.after=NULL, add.to.row=list(pos=list(-1,0, nrow(ptable)), command=c('\\toprule ', '\\midrule ', '\\bottomrule ')), format.args = list(big.mark = ",")) ## ---- loadup-boundaries ----------------------------------------------- oldscipen = options('scipen') options(scipen = 1000) plotopts = list(theme_bw()) slope = 0.00008 extent = 5000 mannings = 0.013 B = 6.1 SS = 1.5 g = 9.81 Cm = 1 ic = 126 id = 5.79 ia = channel_geom(id, B, SS)[["A"]] CN = 0.9 dx = 10 dt = round(dx*CN/(ic/ia + sqrt(id*g)), 2) numnodes = extent/dx + 1 bctime = 2000 bc = rep(id, round(bctime/dt) + 1) dc = rep(0, length(bc)) dt = round(bctime/(length(bc) - 1), 2) CN = dt*(ic/ia + sqrt(id*g))/dx mp = c(1, as.integer(c(1500, 2500, 3000, 5000)/dx + 1)) mt = as.integer(round(seq(0, length(bc)-1, by=25))) + 1L mtslice = c(1, as.integer(c(500, 1000, 1500, 2000)/dt + 1)) dclose.lax = route_wave(slope, mannings, Cm, g, B, SS, ic, bc, dc, timestep=dt, spacestep=dx, numnodes=numnodes, monitor.nodes=mp, monitor.times=mt, engine="Dynamic", scheme="Lax", boundary.type="yQ") dclose.mac = route_wave(slope, mannings, Cm, g, B, SS, ic, bc, dc, timestep=dt, spacestep=dx, numnodes=numnodes, monitor.nodes=mp, monitor.times=mt, engine="Dynamic", scheme="MacCormack", boundary.type="yQ") dclose.lax['scheme'] = "Lax diffusive" dclose.mac['scheme'] = "MacCormack predictor-corrector" dclose = rbind(dclose.lax, dclose.mac) row.names(dclose) = NULL dclose["CN"] = dt*(dclose$flow/dclose$area + sqrt(dclose$depth*g))/dx ## ---- through-time ---------------------------------------------------- dclose.times = filter(dclose, monitor.type=="timestep") ggplot(filter(dclose.times, step %in% mtslice), aes(x=distance, y=depth, linetype = factor(round(time)), color = factor(round(time)))) + geom_path(size = 1) + scale_y_continuous(expression(depth~~(ft))) + facet_wrap(~scheme) + scale_x_continuous(expression(distance~~downstream~~(ft))) + plotopts + scale_color_manual("time (s)", values = brewer.pal(7, "YlGnBu")[3:7]) + scale_linetype_manual("time (s)", values = c("solid", "longdash", "dashed", "dotdash", "dotted")) # animation routeylims = c(min(dclose.times$depth), max(dclose.times$depth)) routexlims = c(min(dclose.times$distance), max(dclose.times$distance)) for(n in unique(dclose.times$step)) print( ggplot(filter(dclose.times, step==n), aes(x=distance, y=depth)) + geom_line(color = "darkblue", size = 1) + plotopts + scale_linetype_discrete("time\n(minutes)") + scale_x_continuous(expression(distance~~downstream~~(ft)), limits=routexlims) + scale_y_continuous(expression(depth~~(ft)), limits=routeylims) + ggtitle(paste(format(round((n - 1)*dt), width = 4), "seconds")) + facet_wrap(~scheme) ) ```