SwampThingPaul

# Functions from a seperate python script
# Calendar to Julian Days
cal2jd=function(date){
  year=as.numeric(format(date,"%Y"))
  month=as.numeric(format(date,"%m"))
  day=as.numeric(format(date,"%d"))
  
  a = (14 - month)/12
  y = year + 4800 - a
  m = month + 12*a - 3

SwampThingPaul

## Code was compiled by Paul Julian
## contact info: pauljulianphd@gmail.com

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

# projection

SwampThingPaul

## A series of functions to extract and display model summary tables 
## Generalized Additive Models

## Code was compiled by Paul Julian
## contact info: pauljulianphd@gmail.com

## libraries
library(mgcv)
library(flextable)
library(magrittr)

SwampThingPaul

library(jpeg)

# Custom function similar to print.palette(...)
RenderPal <- function(x,name){
  
  if ((missing(x)) || (missing(name))){
    stop("Internal error, please troubleshoot")
  }
  n <- length(x)
  old <- graphics::par(mar = c(0.5, 0.5, 0.5, 0.5))

SwampThingPaul

## A working example with data of ggridges
# Libraries ---------------------------------------------------------------
if(!require(ggplot2)) { install.packages('ggplot2') } ;  library(ggplot2) 
if(!require(ggridges)) { install.packages('ggridges') } ;  library(ggridges)

# Data --------------------------------------------------------------------
dat=data.frame(FedWY=c(1979, 1979, 1979, 1979, 1979, 1979, 1979, 1979, 1979, 
                       1979, 1979, 1979, 1979, 1979, 1979, 1979, 1979, 1979, 1979, 1979, 
                       1979, 1979, 1979, 1979, 1979, 1979, 1980, 1980, 1980, 1980, 1980, 
                       1980, 1980, 1980, 1980, 1980, 1980, 1980, 1980, 1980, 1980, 1980, 

SwampThingPaul

# From 
## Strobl, R.O., Robillard, P.D., 2008. Network design for water 
## quality monitoring of surface freshwaters: A review. Journal 
## of Environmental Management, Microbial and Nutrient Contaminants 
## of Fresh and Coastal Waters 87, 639–648. 
## https://doi.org/10.1016/j.jenvman.2007.03.001

#devtools::install_github("SwampThingPaul/AnalystHelper")
library(AnalystHelper)

SwampThingPaul

## quick bar and line plot in base 

data=data.frame(value=c(3,4,6,2),value2=c(10,12,20,9))

par(oma=c(3,2,0.5,3),mar=c(2,3,0.25,2))
barplot(data$value,ylim=c(0,12),las=2,space=c(0.5))
mtext(side=2,line=2,"Value")
par(new=T);x=barplot(data$value2,ylim=c(0,25),axes=F,col=NA,border=NA,space=c(0.5))
lines(x,data$value2,lwd=3)
axis(4,las=2)

SwampThingPaul

## Function to check and install packages 
## If package is installed, then the function moves to the next.

check.packages <- function(pkg){
  new.pkg <- pkg[!(pkg %in% installed.packages()[, "Package"])]
  if (length(new.pkg)) 
    install.packages(new.pkg, dependencies = TRUE)
  sapply(pkg, require, character.only = TRUE)
}

SwampThingPaul

## Data from Reckhow, K.H., K Kepford and W.W. Hicks. 1993
### Methods for the Analysis of Lake Water Quality
### EPA 841-R-93-003

## Code was compiled by Paul Julian
## contact info: paul.julian@floridadep.gov

SwampThingPaul

# Base curly brackets adapted from https://stackoverflow.com/a/9310002/5213091

CurlyBraces <- function(x, y, min.val,max.val, pos = 1, direction = 1 ,b=c(0,.2,.28,.7,.8),a=c(1,2,3,48,50)) {
  # a set flexion point for spline
  # b set depth for spline flexion point
  curve <- spline(a, b, n = 50, method = "natural")$y / 2 
  curve <- c(curve,rev(curve))
  
  a_sequence <- rep(x,100)