SwampThingPaul

library(sp)
library(rgeos)
library(rworldmap)


# epsg.io
wgs=CRS("+init=epsg:4326")

map_dat=getMap()
map_dat=spTransform(map_dat,wgs)

SwampThingPaul

# This is a very general script to perform gif animations from 
# space-time Generalized Additive Model predictions

# GIS libraries 
library(rgdal)
library(rgeos)
library(raster)
library(tmap)

# GAM libraries

SwampThingPaul

# GIS libraries 
library(sp)
library(rgdal)
library(rgeos)
library(raster)
library(mapmisc)

## defines the coordinate reference system
utm17=CRS("+init=epsg:26917")

SwampThingPaul

using DelimitedFiles
using DataFrames

# HTML Path for data
dat_path="http://recondata.sccf.org/cgi-data/nph-data.cgi?x=utc_date&y=salinity,temperature&min_date=20210101&max_date=20220301&node=11&data_format=text"

# Just to read the data as a tab delimited file
recon_data=readdlm(download(dat_path),'\t',skipstart=1,header=true)

## From what I can find on how to change the file 

SwampThingPaul

# Load Library
library(mblm); # For trend line

# Commented out - added function in script
# devtools::install_github("SwampThingPaul/AnalystHelper")
# library(AnalystHelper); # some plotting helper functions like axis_fun(...), pt_lines(...), etc

## axis function from AnalystHelper package
axis_fun=function (side, at, at2, labels, cex.axis = 1, line = -0.25, 
                   lwd = 1, maj.tcl = -0.6, min.tcl = -0.3, las = 1, axisLine = 0, 

SwampThingPaul

## Using as.Date with an arbitrary year you can define each peirod
pre.emg.period=seq(as.Date("2021-03-01"),as.Date("2021-03-20"),"1 days")
emg.period=seq(as.Date("2021-03-21"),as.Date("2021-04-14"),"1 days")
mate.period=seq(as.Date("2021-04-15"),as.Date("2021-05-15"),"1 days")
gest.period=seq(as.Date("2021-05-16"),as.Date("2021-08-23"),"1 days")
post.part.period=seq(as.Date("2021-08-24"),as.Date("2021-10-31"),"1 days")

# fake data
dat=data.frame(Date=seq(as.Date("2019-01-01"),as.Date("2022-12-31"),"1 days"))
dat$Yr=as.numeric(format(dat$Date,'%Y'))

SwampThingPaul

b2=seq(-100,500,20)
pal2=c(colorRampPalette(c("blue","grey90"))(length(b2[b2<0])),
       colorRampPalette(c("grey90",'red'))(length(b2[b2>0])))

plot(1:length(pal2),pch=21,cex=2,bg=pal2)
       

SwampThingPaul

library(zoo)

# Read data and set up ----------------------------------------------------
dat=read.csv("ex_dat_S79_NA25.csv")
dat$Date=as.Date(dat$Date)
dat$S79.14d=with(dat,rollapply(S79,width=14,FUN=function(x)mean(x,na.rm=T),fill=NA,align="right"))
dat$CRE.low=with(dat,ifelse(S79.14d<750,1,0)) # RECOVER Low flow envelope

# Helper functions for 14-day periods
dat$period.14=c(0,rep(1:(nrow(dat)-1))%/%14)+1

SwampThingPaul

# date.fun from personal AnalystHelper package
date.fun=function (x, tz = "EST", form = "%F"){as.POSIXct(strptime(x, form), tz = tz)}

# Example dataset
example=c("19-AUG-53 12.00.00.000000000 AM", "26-AUG-53 12.00.00.000000000 AM",
          "26-AUG-53 12.00.00.000000000 AM", "26-AUG-53 12.00.00.000000000 AM", 
          "26-AUG-53 12.00.00.000000000 AM", "26-AUG-53 12.00.00.000000000 AM",
          "01-APR-02 05.45.00.000000000 PM", "01-APR-02 12.00.00.000000000 AM", 
          "01-APR-02 12.00.00.000000000 AM", "01-APR-02 12.00.00.000000000 AM", 
          "01-APR-02 12.00.00.000000000 AM", "01-APR-02 12.00.00.000000000 AM")

SwampThingPaul

##
## LOK MFL 18 month period exploration and learning
##
## Code was compiled by Paul Julian
## contact info: pjulian@sccf.org

# Libraries
import datetime as dt

#