inst/riojaPlot/www/riojaPlot.md

title: "riojaPlot Version 1.0" output: html_document: default pdf_document: default

Steve Juggins Oct 2020

Introduction

riojaPlot is a web app for plotting stratigraphic data found in micropalaeontological or palaeoecological studies. It can plot multiple biological and non-biological proxies against depth or age and allows trends to be visualized using a range of plot types.

Input data

Data should be in an Excel spreadsheet, with a single row of column names. These names will be used to label the x-variables so choose them carefully. Any variables starting with the words "Depth" or "Age" will be used as y-variables. For example, "Depth_in_m"" or "AgeBP" are fine, "Years BP" or "core depth" are not. This allows one to plot the data using different age models by labelling the columns "Age01", "Age02" etc. If you do not include a Depth or Age variable samples data be plotted against sample number. A column starting with the word "Label" can contain text that will be used to label samples on the the y-axis. All other columns should be numeric and are used as x-variables. Data are plotted 'as is' and in the order they appear in the file. If you want to plot a diagram of microfossil counts expressed as relative abundances you should supply percentage data with columns in correct the order. Zonation is not available is the data contain missing values. An example spreadsheet containing pollen stratigraphic data from Birks & Mathews (1978) can be downloaded from the Help tab. A screenshot of the data is listed at the end of this help file.

Getting started

Upload a Excel file and select the worksheet to use, or check the box Use example dataset. If your data look like biostratigraphic data with row sums in the range 50-150 riojaPlot will assume they are percentages and scale each curve appropriately, and de-select any variables with a maximum value less than 2%. If not, each curve will have equal width and be scaled from min-max data values (option Scale for % under the Settings tab). If you have more than 50 variables on the first 50 will be selected. You can change this selection on the Variables tab.

Options

Variables

Select a variable for the Y axis (if you have included more than one Depth, Age or Label columns). riojaPlot will try to guess the type of data you have. If the data look like biological counts transformed to percentages then variables with a maximum value of less than 2.0 will be de-selected to avoid over-crowding. Use Select X variables this option to remove or add variables to the diagram. Use the Scale for % checkbox to force riojaPlot to plot the data as percentage (or not).

Auto Select X vars can be used with % scaling to automatically select variables. riojaPlot calculates the maximum value of each variable and selects those variables whose maximum falls between the min / max cutoff. This is useful for quickly de-selecting rare taxa in large datasets.

Settings

Colours

Select colour for lines, bars, silhouettes, symbols, zones and exaggeration.

Sizes

Adjust axis, label font size and label rotation.

Zonation

Add a zonation (constrained clustering) to the diagram using CONISS (Grimm 1987). Optional show zones on the diagram with the number of zones determined automatically using a broken-stick model (Bennett 1996) or chosen manually. Data can be transformed prior to calculation of dissimilarities. Sqrt is good for biological data expressed as percentage relative abundance (Legendre & Gallagher, 2001). Scale scales each variable to zero mean and unit standard deviation and is good for non-biological data with different units of measurement.

Groups

Assign each variable to a group and plot silhouettes in a different colour for each group.

Save the plot

Save the plot as a pdf, png or svg file. Scalable vector graphics (svg) format is good for importing into Powerpoint or Word.

Details

riojaPlot is powered by the function strat.plot in the R package rioja. The web interface is built using shiny and shinydashboard.

Example dataset

Pollen stratigraphic data from the Abernethy Forest, Scotland, spanning approximately 5500 - 12100 BP (from Birks & Mathews 1978).

Abernethy Forest Pollen Stratigraphic data (from Birks & Matthews, 1978)

Contact

Bug reports and suggestions for improvement to Steve Juggins: Stephen.Juggins@ncl.ac.uk.

References

Bennett, K (1996) Determination of the number of zones in a biostratigraphic sequence. New Phytologist, 132, 155-170.

Birks, HH & Mathews, RW (1978) Studies in the vegetational history of Scotland V. Late Devensian and early Flandrian macrofossil stratigraphy at Abernethy Forest, Invernessshire. New Phytologist, 80, 455-84.

Grimm, EC (1987) CONISS: A FORTRAN 77 program for stratigraphically constrained cluster analysis by the method of incremental sum of squares. Computers & Geosciences, 13, 13-35.

Legendre, P & Gallagher E (2001) Ecologically meaningful transformations for ordination of species data. Oecologia, 129, 271-280.



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rioja documentation built on Oct. 28, 2020, 5:07 p.m.