valentinitnelav

# Load library
library(XML)

# -----------------------
# Read the web page
# -----------------------
link <- "http://www.adirondacklakessurvey.org/alscrpt.inc.php?alscpond=020225B&pname=ALLEGANY%20BROOK%20POND"
# NOTE: is ethical to store the page and not read it unnecessarily too many times, 
# overloading their server
link.scrap <- htmlParse(link)

valentinitnelav

# Load library
library(rvest)

# -----------------------
# Read the web page
# -----------------------
link <- "http://www.adirondacklakessurvey.org/alscrpt.inc.php?alscpond=020225B&pname=ALLEGANY%20BROOK%20POND"
# NOTE: is ethical to store the page and not read it unnecessarily too many times, 
# overloading their server
link.scrap <- read_html(link)

valentinitnelav

# ================================
# helper script for species counts (lakes for Leana)
# ================================
library(data.table)

# read data
lake_data <- fread("links_extract_dt.csv")

# count unique species by combination of `Pond Name`, Town, County
# skip or add column in the "by" section if needed

valentinitnelav

# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Script to read list of lake links and parse through them
# for Leana
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
library(XML)
library(stringr)
library(data.table)

#####################################################
#####################################################

valentinitnelav

# ==========================================================================
# Example of plot for publication with inwards ticks in ggplot
# ==========================================================================

library(ggplot2)

# ==================================
# create some data
# ==================================
set.seed(1)

valentinitnelav

# ==========================================================================
# Example of plot for publication in base R with inwards ticks
# ==========================================================================

# ==================================
# create some data
# ==================================
set.seed(1)
DF <- data.frame(year = c(2000:2020),
                 mean = rnorm(n=21, mean=100, sd=10))

valentinitnelav

# ==========================================================================
# Dotplot with CI/error bars for publication - ggplot
# see also: http://www.cookbook-r.com/Graphs/Plotting_means_and_error_bars_(ggplot2)/
# ==========================================================================

library(ggplot2)

# ==================================
# create some data
# ==================================

valentinitnelav

# ==========================================================================
# Barplot with CI/error bars for publication - ggplot
# see more at: http://www.cookbook-r.com/Graphs/Plotting_means_and_error_bars_(ggplot2)/
# ==========================================================================

library(ggplot2)

# ==================================
# create some data
# ==================================

valentinitnelav

# ======================================================================================
# Color case.
# Confidence bands and setting order of line types in legend based on group - ggplot.
# The lower and upper values could be computed through bootstrapping.
# ======================================================================================

library(ggplot2)

# create some data
x=seq(from=0, to=2*pi, by=0.1)

valentinitnelav

# ======================================================================================
# Color case.
# Confidence lines and setting order of line types in legend based on group - ggplot.
# ======================================================================================

library(ggplot2)

# create some data
x=seq(from=0, to=2*pi, by=0.1)
my.data <- data.frame(x        = rep(x,2),