The code below can be used to create and save the different matrix graphics for reporting purposes. A couple things to note when using this code:
~/Desktop/fig.png. This can be changed as needed.png()
function, in inches and dots per inch. The current dimensions are
approximations that will likely need to be changed depending on intended
use.dev.off() after
png() for each figure. Otherwise the figures won’t save
correctly.alpha argument.txtsz argument for each plot can be used to modify
the size of the text in the cells for each figure. This may need to be
changed depending on the overall dimensions.# setup -------------------------------------------------------------------
# # install peptools, only do if the package is updated
# install.packages('remotes')
# remotes::install_github('tbep-tech/peptools')
library(peptools)
# update data to most recent ----------------------------------------------
# wq data, replace path with manually downloaded file
path <- system.file("extdata", "currentdata.xlsx", package="peptools")
rawdat <- read_pepwq(path)
# do data, takes a few minutes and make sure the date in endDate is updated
dodat <- read_pepdo(
site = c("01304562", "01304200", "01304650"),
nms = c("Peconic River", "Orient Harbor", "Shelter Island"),
startDate = "2013-01-01",
endDate = "2023-12-31"
)
# pathogen data
entdat <- read_pepent()
# secchi matrix -----------------------------------------------------------
p <- show_wqmatrixpep(rawdat, param = 'sd', txtsz = 3, alpha = 0.5)
png('~/Desktop/sdmatrix.png', height = 7, width = 3, res = 300, units = 'in')
print(p)
dev.off()
# chl matrix --------------------------------------------------------------
p <- show_wqmatrixpep(rawdat, param = 'chl', txtsz = 3, alpha = 0.5)
png('~/Desktop/chlmatrix.png', height = 7, width = 3, res = 300, units = 'in')
print(p)
dev.off()
# wq matrix ---------------------------------------------------------------
p <- show_matrixpep(rawdat, txtsz = 3)
png('~/Desktop/wqmatrix.png', height = 7, width = 3, res = 300, units = 'in')
print(p)
dev.off()
# do matrix ---------------------------------------------------------------
p1 <- show_domatrix(dodat, site = 'Peconic River', thr = 4.8, txtsz = 3)
p2 <- show_domatrix(dodat, site = 'Orient Harbor', thr = 4.8, txtsz = 3)
p3 <- show_domatrix(dodat, site = 'Shelter Island', thr = 4.8, txtsz = 3)
png('~/Desktop/domatrix1.png', height = 3, width = 5, res = 300, units = 'in')
print(p1)
dev.off()
png('~/Desktop/domatrix2.png', height = 3, width = 5, res = 300, units = 'in')
print(p2)
dev.off()
png('~/Desktop/domatrix3.png', height = 3, width = 5, res = 300, units = 'in')
print(p3)
dev.off()
# pathogen matrix ---------------------------------------------------------
p <- show_entmatrix(entdat, thr = 104, txtsz = 2)
png('~/Desktop/entmatrix.png', height = 6, width = 7, res = 300, units = 'in')
print(p)
dev.off()