Plotting results - mtop/speciesgeocoder GitHub Wiki

If the plotting flag is switched on, a set of output graphics and tables will be produced and saved in the working directory:

Barchart_per_polygon.pdf

This is a multi-page file containing one bar chart for each input polygon per page. It shows the total number of occurrences for each species in this polygon. The title of each plot indicates the polygon name, the y axis shows the number of occurrences of each species in this polygon. Only species with at least 1 occurrence are shown. This means that the x-axis is likely to differ between the plots. barchart_per_polgon speciesgeocoder output

Barchart_per_species.pdf

This is a multi-page file containing one barchart per species per page, showing the relative number of occurrences in each input polygon. The title indicates the species, the x-axis shows all input polygons and the y-axis shows the percent of the species' occurrences per polygon. "barchart per species" speciesgeocoder output plot

Heatplot_coexistence.pdf

This file contains a heat plot showing the co-existence pattern of all species in the analysis. The plot indicates which percentage of the species in each row co-occur with at least one individual of the species in the respective column. heatplot species coexistence speciesgeocoder plot output

Map_samples_overview.pdf

This file contains two graphs. The first is an overview map of all samples and all polygons used for the speciesgeocoder run (see figure below). The second is a map of all samples that did not fall in any of the input polygons (indicated in red). "map sample overview" speciesgeocoder plot output

Map_samples_per_polygon.pdf

This is a multi-page file containing on map for each input-polygon. All sample points falling in the respective polygon are shown, color-coded per species. The title indicates the polygon. speciesgeocoder output samples per polygon

Map_samples_per_species.pdf

This is a multi-page file containing one graph per species in the input file. All occurrences of the respective species are shown. Samples classified to any polygon are shown in blue, unclassified samples are shown in red. speciesgeocoder output samples per species

Number_of_species_per_polygon.pdf

This file contains a plot showing the absolute number of species for all input polygons. The x-axis shows all input-polygons and the y-axis shows the number of species. speciesgeocoder output species number per polygon

Sample_classification_to_polygon.txt

This is a summary table showing the classification for each sample point. ###Species_occurrence_per_polygon.txt This is a summary table showing the presence or absence of every species in the input polygons. ###Species_number_per_polygon.txt This is a table summarizing the number of species for each polygon. ###Unclassified_samples.txt This file contains a map showing all samples that could not be classified to any of the input polygons.