## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----eval = FALSE-------------------------------------------------------------
# install.packages("refuginator")

## ----eval = FALSE-------------------------------------------------------------
# library(refuginator)
# launchRefuginator()

## ----eval = FALSE-------------------------------------------------------------
# refuginator::launchRefuginator()

## ----echo=FALSE, out.width = "90%", fig.cap = cap-----------------------------
knitr::include_graphics("Figures/Fig01_LandingPage.png")
cap = "**Figure 1**. Refuginator landing page."

## ----echo=FALSE, out.width = "90%", fig.cap = cap-----------------------------
knitr::include_graphics("Figures/Fig02_UploadData.png")
cap = "**Figure 2**. Agreeing to the Usage Policy allows users to upload their data."

## ----echo=FALSE, out.width = "90%", fig.cap = cap-----------------------------
knitr::include_graphics("Figures/Fig03_DataExampleNoID.png")
cap = "**Figure 3**. Example dataset with the *sitename*, *latitude*, and *longitude* columns."

## ----echo=FALSE, out.width = "90%", fig.cap = cap-----------------------------
knitr::include_graphics("Figures/Fig04_DataExampleWithID.png")
cap = "**Figure 4**. Example dataset including the *siteid* and *datasetid* columns."

## ----echo=FALSE, out.width = "90%", fig.cap = cap-----------------------------
knitr::include_graphics("Figures/Fig05_AnalyzeButton.png")
cap = "**Figure 5**. Once the data is uploaded, the Analyze button will appear."

## ----echo=FALSE, out.width = "90%", fig.cap = cap-----------------------------
knitr::include_graphics("Figures/Fig06_RegionalPresencePlot.png")
cap = "**Figure 6**. At the top of the main panel in the Regional Analysis tab is the Regional Presence Plot."

## ----echo=FALSE, out.width = "90%", fig.cap = cap-----------------------------
knitr::include_graphics("Figures/Fig07_DataInteraction.png")
cap = "**Figure 7**. Users can interact with the data using the toolbar in the upper right corner of the plot."

## ----echo=FALSE, out.width = "90%", fig.cap = cap-----------------------------
knitr::include_graphics("Figures/Fig08_AnimatedHeatMap.png")
cap = "**Figure 8**. At the bottom of the main panel in the Regional Analysis tab is Animated Heat Map."

## ----echo=FALSE, out.width = "90%", fig.cap = cap-----------------------------
knitr::include_graphics("Figures/Fig09_HeatMapInteractions.png")
cap = "**Figure 9**. The buttons beneath the heat map allow the user to interact with it."

## ----echo=FALSE, out.width = "90%", fig.cap = cap-----------------------------
knitr::include_graphics("Figures/Fig10_MonteCarloSidebar.png")
cap = "**Figure 10**. The sidebar of the Regional Analysis tab contains the inputs for the Monte Carlo Analysis."

## ----echo=FALSE, out.width = "90%", fig.cap = cap-----------------------------
knitr::include_graphics("Figures/Fig11_PValue.png")
cap = "**Figure 11**. After inputting all of the values, clicking the Calculate button will show the realized p-value."

## ----echo=FALSE, out.width = "90%", fig.cap = cap-----------------------------
knitr::include_graphics("Figures/Fig12_NeotomaTab.png")
cap = "**Figure 12**. Default Neotoma Pollen Database tab"

## ----echo=FALSE, out.width = "90%", fig.cap = cap-----------------------------
knitr::include_graphics("Figures/Fig13_NeotomaPreview.png")
cap = "**Figure 13**. After clicking the Search button, users will be shown a preview of the selected sites."

## ----echo=FALSE, out.width = "90%", fig.cap = cap-----------------------------
knitr::include_graphics("Figures/Fig14_NeotomaDownload.png")
cap = "**Figure 14**. After clicking the Proceed with Download button, users will be given a preview of the data, filtered according to their inputs. Pressing the Download Data button will download a CSV file onto the user's machine that can be uploaded on the [Upload Data] tab."