knitr::opts_chunk$set(fig.path='figures/', echo=TRUE, warning=FALSE, message=FALSE)
# function to convert levels to numeric or characters LtoN <- function(x) as.numeric(as.character(x)) LtoC <- function(x) as.character(x)
output=read.csv("output_cont.csv") nb=length(unique(output$path)) cat=unique(output$category) states=unique(output$state) library(plyr) #matTemp=ddply(output,"category",summarise, #frequency=length(nbYears)/nb, #years=median(nbYears), #depths=mean(nbDepths), #lakes=sum(nbLakes), #obs=sum(nbObs)) catSum=ddply(output,c("category","lvl2","lvl1","state"),summarise, frequency=length(unique(lvl1))/nb, years=median(nbYears), depths=mean(nbDepths), lakes=sum(nbLakes), obs=sum(nbObs)) lvl2Sum=ddply(catSum,c("lvl1","state"),summarise, frequency=max(frequency), years=max(years), depths=max(depths), lakes=max(lakes), obs=max(obs)) library(tidyr) heatMat <- spread(lvl2Sum[,c("lvl1","state","lakes")], state, lakes) rownames(heatMat)=heatMat$lvl1;heatMat$lvl1=NULL heatMat=heatMat[order(rowSums(heatMat),decreasing = T),]
library(plotrix) par(mar = c(0, 10, 4, 0)) #par(mar = c(0.5, 4, 3.5, 0.5)) color2D.matplot(heatMat, show.values = TRUE, axes = F, xlab = "", ylab = "", vcex = 1, vcol = "black", extremes = c("white", "red")) axis(3, at = seq_len(ncol(heatMat)) - 0.5, labels = colnames(heatMat), tick = FALSE, cex.axis = 1,las=2) axis(2, at = seq_len(nrow(heatMat)) -0.5, labels = rev(rownames(heatMat)), tick = FALSE, las = 1, cex.axis = 1)
catSub=catSum[catSum$lvl2=="Contaminants-Inorganic",] catSub=ddply(catSub,c("category","state"),summarise, frequency=max(frequency), years=max(years), depths=max(depths), lakes=max(lakes), obs=max(obs)) library(tidyr) heatMat <- spread(catSub[,c("category","state","lakes")], state, lakes) rownames(heatMat)=heatMat$category;heatMat$category=NULL heatMat=heatMat[order(rowSums(heatMat),decreasing = T),]
library(plotrix) par(mar = c(0, 10, 4, 0)) #par(mar = c(0.5, 4, 3.5, 0.5)) color2D.matplot(heatMat, show.values = TRUE, axes = F, xlab = "", ylab = "", vcex = 1, vcol = "black", extremes = c("white", "red")) axis(3, at = seq_len(ncol(heatMat)) - 0.5, labels = colnames(heatMat), tick = FALSE, cex.axis = 1,las=2) axis(2, at = seq_len(nrow(heatMat)) -0.5, labels = rev(rownames(heatMat)), tick = FALSE, las = 1, cex.axis = 1)
catSub=catSum[catSum$lvl2=="Contaminants-Inorganic",] catSub=ddply(catSub,c("category","state"),summarise, frequency=max(frequency), years=max(years), depths=max(depths), lakes=max(lakes), obs=max(obs)) library(tidyr) heatMat <- spread(catSub[,c("category","state","years")], state, years) rownames(heatMat)=heatMat$category;heatMat$category=NULL heatMat=heatMat[order(rowSums(heatMat),decreasing = T),]
library(plotrix) par(mar = c(0, 10, 4, 0)) #par(mar = c(0.5, 4, 3.5, 0.5)) color2D.matplot(heatMat, show.values = TRUE, axes = F, xlab = "", ylab = "", vcex = 1, vcol = "black", extremes = c("white", "red")) axis(3, at = seq_len(ncol(heatMat)) - 0.5, labels = colnames(heatMat), tick = FALSE, cex.axis = 1,las=2) axis(2, at = seq_len(nrow(heatMat)) -0.5, labels = rev(rownames(heatMat)), tick = FALSE, las = 1, cex.axis = 1)
catSub=catSum[catSum$lvl1=="ions",] catSub=ddply(catSub,c("category","state"),summarise, frequency=max(frequency), years=max(years), depths=max(depths), lakes=max(lakes), obs=max(obs)) library(tidyr) heatMat <- spread(catSub[,c("category","state","lakes")], state, lakes) rownames(heatMat)=heatMat$category;heatMat$category=NULL heatMat=heatMat[order(rowSums(heatMat),decreasing = T),]
library(plotrix) par(mar = c(0, 10, 4, 0)) #par(mar = c(0.5, 4, 3.5, 0.5)) color2D.matplot(heatMat, show.values = TRUE, axes = F, xlab = "", ylab = "", vcex = 1, vcol = "black", extremes = c("white", "red")) axis(3, at = seq_len(ncol(heatMat)) - 0.5, labels = colnames(heatMat), tick = FALSE, cex.axis = 1,las=2) axis(2, at = seq_len(nrow(heatMat)) -0.5, labels = rev(rownames(heatMat)), tick = FALSE, las = 1, cex.axis = 1)
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