From 671ce79dd0c3cc12e5fe4089a60225fd7beec63e Mon Sep 17 00:00:00 2001 From: Beaudette Date: Mon, 8 Apr 2024 12:48:30 -0700 Subject: [PATCH] update, ensuring this still works #81 --- misc/sandbox/slice-wise-Tukey-HSD.R | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/misc/sandbox/slice-wise-Tukey-HSD.R b/misc/sandbox/slice-wise-Tukey-HSD.R index d3f62a3c2..b095d1ace 100644 --- a/misc/sandbox/slice-wise-Tukey-HSD.R +++ b/misc/sandbox/slice-wise-Tukey-HSD.R @@ -3,11 +3,11 @@ library(aqp) library(soilDB) library(lattice) library(latticeExtra) -library(viridis) +library(tactile) library(grid) # define plotting style -tps <- list(superpose.line=list(col=c('RoyalBlue', 'DarkRed', 'DarkGreen'), lwd=2)) +tps <- tactile.theme(superpose.line=list(col=c('RoyalBlue', 'DarkRed', 'DarkGreen'), lwd=2)) # get multiple series' worth of data # TODO: add code to deal with those series that return 0 records @@ -72,7 +72,7 @@ ck <- list( # standard output from slab() -p.1 <- xyplot(top ~ p.q50 | variable, groups=taxonname, data=HSD$agg, ylab='Depth', +p.1 <- xyplot(top ~ p.q50 | variable, groups=taxonname, data=HSD$agg, ylab='Depth (cm)', xlab='median bounded by 25th and 75th percentiles', lower=HSD$agg$p.q25, upper=HSD$agg$p.q75, ylim=c(105, -5), panel=panel.depth_function, alpha=0.25, sync.colors=TRUE, @@ -94,7 +94,7 @@ p.1 <- xyplot(top ~ p.q50 | variable, groups=taxonname, data=HSD$agg, ylab='Dept # experimental HSD viz p.2 <- segplot( hzn_top ~ lwr + upr, centers = diff, level = p.adj, data = HSD$HSD, - col.regions = viridis, ylim = c(105, -5), + col.regions = hcl.colors, ylim = c(105, -5), xlab = 'HSD', at = col.at, colorkey = ck, @@ -178,7 +178,7 @@ z <- z[idx, vars] dd <- datadist(z) options(datadist="dd") -# GLS: I've used this before to parametrize correlation sturcture +# GLS: I've used this before to parametrize correlation structure (m.gls <- Gls(wmpd ~ rcs(mid) * group, data = z, correlation = corAR1(form = ~ mid | sliceID))) plot(Predict(m.gls))