Troy Hill troyhill
troyhill
/ script_flowVsStage_20200803.R
Created
August 3, 2020 13:38
Flow through S333 by headwater stage category, WY2006-2019
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| ### 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
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| ### 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 |
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| # script to explore the SFWMD's rainfall formula | |
| a <- list.files("C:/RDATA/rainfall_formula/", pattern = "\\.txt$", full.names = TRUE) | |
| rain <- read.delim(a[4], skip = 1) | |
| head(rain) | |
| pet <- read.delim(a[3], skip = 1) | |
| head(pet) |
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| ### may be necessary: install dev version of curl for google drive | |
| # install.packages("https://github.com/jeroenooms/curl/archive/master.tar.gz", repos = NULL) | |
| pkgs.used <- c("devtools", "sf", "ggplot2", "gmailr", "googledrive") | |
| pkgs.to.install <- pkgs.used[!pkgs.used %in% installed.packages()] | |
| if (length(pkgs.to.install) > 0) { | |
| install.packages(pkgs.to.install) | |
| } | |
| if (!"fireHydro" %in% installed.packages()) { |
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| ### | |
| discharge_section_join.sh L67_L30 > /home/thill/RDATA/dataForEver/data_L67_L30_flow.csv | |
| ### | |
| #!/bin/bash | |
| # Script pulls coordinates for all stations in DataForEver database | |
| # Usage: ./bash/dataForEver_getCoords.sh |
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| export PATH=$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 |
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| ### 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 |
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| 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) |
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| ### 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") |
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| 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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