troyhill’s gists

troyhill / script_flowVsStage_20200803.R

Created August 3, 2020 13:38

Flow through S333 by headwater stage category, WY2006-2019

	### calculate total flow through S333 below and above 9.2' from WY 2006-2019.

	if(!"devtools" %in% installed.packages()) install.packages("devtools", repos='http://cran.us.r-project.org')
	if(!"SFNRC" %in% installed.packages()) devtools::install_github("troyhill/SFNRC")

	library(SFNRC)
	theme_set(theme_bw())

troyhill / shrimp_mortality.R

Last active May 31, 2019 13:47

recreates pink shrimp survival rate calculations from Browder et al. 2002



	### function to calculate equations 4, 3, and 5 from Browder et al. 2002
	sv.rate <- function(salinity, temperature, daily = FALSE) {
	LP <- -4.6019 + (0.7039 * temperature) + (0.2186 * salinity) +
	(-0.0250 * temperature^2) + (-0.0077 * salinity^2) +
	(0.0115 * temperature * salinity) # equation 4, using survival rate coefficients from Table 1
	ifelse(daily == TRUE,
	M1 <- -log(exp(LP)) * (exp(LP) + 1)^-1 / 28, # daily survival # equation 3
	M1 <- -log(exp(LP)) * (exp(LP) + 1)^-1 # 28-day survival

troyhill / rainfall_formula.R

Created February 22, 2019 20:15

rainfall formula exploration

	# script to explore the SFWMD's rainfall formula


	a <- list.files("C:/RDATA/rainfall_formula/", pattern = "\\.txt$", full.names = TRUE)

	rain <- read.delim(a[4], skip = 1)
	head(rain)

	pet <- read.delim(a[3], skip = 1)
	head(pet)

troyhill / crontab_fireHydro_20190221.R

Last active June 4, 2019 14:12

fireHydro crontab 20190221


	### may be necessary: install dev version of curl for google drive
	# install.packages("https://github.com/jeroenooms/curl/archive/master.tar.gz", repos = NULL)

	pkgs.used <- c("devtools", "sf", "ggplot2", "gmailr", "googledrive")
	pkgs.to.install <- pkgs.used[!pkgs.used %in% installed.packages()]
	if (length(pkgs.to.install) > 0) {
	install.packages(pkgs.to.install)
	}
	if (!"fireHydro" %in% installed.packages()) {

troyhill / tests.sh

Created December 20, 2018 14:22

tests for Jed

	###
	discharge_section_join.sh L67_L30 > /home/thill/RDATA/dataForEver/data_L67_L30_flow.csv

	###


	#!/bin/bash
	# Script pulls coordinates for all stations in DataForEver database
	# Usage: ./bash/dataForEver_getCoords.sh

troyhill / addtoPath.sh

Created December 19, 2018 22:02

add files to PATH


	export PATH=$PATH:/opt/physical/appaserver/src_waterquality:/opt/physical/appaserver/src_appaserver:/opt/physical/appaserver/utility:/opt/physical/appaserver/src_hydrology:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:.:/home/thill/bash:.:/opt/physical/appaserver/utility:/opt/physical/appaserver/src_appaserver:/opt/physical/appaserver/src_waterquality:/opt/physical/appaserver/src_hydrology:/opt/physical/sql:/opt/physical/util/

	source ~/.profile

troyhill / example.R

Created December 19, 2018 19:03

Example download script for Jed

	### script to download and summarize DataForEver hydro data for a set of stations

	### install.packages("devtools") # install devtools package, if it's not installed already
	devtools::install_github("troyhill/SFNRC")

	library(SFNRC)
	library(plyr)
	library(ggplot2)

	### stations can be defined manually

troyhill / gfh.R

Created December 18, 2018 22:16

getFireHydro test



	getFireHydro(EDEN_date = "20181018", dataToPlot = "WF_Use", output_shapefile = NULL,
	imageExport = "output_WFuse_20181018.png")
	# beepr::beep(2)

	getFireHydro(EDEN_date = "20170630", dataToPlot = "WL_des", output_shapefile = NULL,
	imageExport = "output_WLdes_20170630.png")
	# beepr::beep(2)

troyhill / WRTDS.R

Last active December 17, 2018 20:14

WRTDS implementation using DataForEver data

	### Weighted regression using time, discharge, and season
	### Application of EGRET tools to DataForEver data
	library(plyr)
	library(SFNRC)



	# Meta-analysis -----------------------------------------------------------

	targStns <- c("S333", "S12A", "S12B", "S12C", "S12D") #, "S151", "S343", "S332")

troyhill / assignTides.R

Created November 13, 2018 22:20

identifies higher and lower high/low tides


	assignTide <- function(data, timeCol = "time", levelCol = "level", tideCol = "tide") {
	### this works well with output from HL()
	### arguments:
	### data = the data frame
	### timeCol = name of column with time stamp data, in format "YYYY-MM-DD ..."
	### levelCol = name of column with water level data (numeric)
	### tideCol = name of column with tide indicator (H/L) - this is tailored to HL() output

	data[, "day"] <- substr(data[, timeCol], 1, 10) # weak point - assumes YYYY-MM-DD format

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