The 'fractional_cover' function in the 'auscoverR' package calculates fractional cover from AusPlots point intercept (PI) data (as generated by 'get_ausplots'). Fractional cover refers to the proportions of green vegetation, dead vegetation and bare substrate cover. Cover fractions are assigned as follows: . ‘Green’ or ‘photosynthetic vegetation’: is living vascular plant cover. . ‘Brown’ or ‘non-photosynthetic vegetation’: is either vascular plant cover scored as ‘dead’, or substrate scored as litter, coarse woody debris or cryptogam (see below) that has no other veg cover. . ‘Bare’ or ‘bare ground’: is rock, outcrop, gravel or bare soil with no veg cover substrate.
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Example 1: 'Regular' Fractional Cover, only for Substrate
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AP.data.FC.RFC.Substrate = fractional_cover(AP.data$veg.PI, ground_fractional="FALSE", in_canopy_sky="FALSE")
class(AP.data.FC.RFC.Substrate)
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## [1] "data.frame"
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dim(AP.data.FC.RFC.Substrate)
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## [1] 653 5
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head(AP.data.FC.RFC.Substrate)
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## site_unique bare brown green NA.
## NSABBS0005-58582 NSABBS0005-58582 1.09 39.60 59.31 0.0
## NSABBS0006-58557 NSABBS0006-58557 3.17 32.67 64.06 0.1
## NSABHC0001-53596 NSABHC0001-53596 31.26 42.24 26.51 0.0
## NSABHC0002-53597 NSABHC0002-53597 0.00 0.00 30.10 69.9
## NSABHC0003-53598 NSABHC0003-53598 46.57 28.14 25.29 0.0
## NSABHC0004-53599 NSABHC0004-53599 26.63 36.63 36.73 0.0
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summary(AP.data.FC.RFC.Substrate)
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## site_unique bare brown green
## Length:653 Min. : 0.00 Min. : 0.00 Min. : 0.10
## Class :character 1st Qu.: 9.90 1st Qu.:20.69 1st Qu.:22.99
## Mode :character Median :22.48 Median :29.91 Median :38.51
## Mean :27.76 Mean :30.86 Mean :41.12
## 3rd Qu.:42.38 3rd Qu.:40.00 3rd Qu.:55.74
## Max. :98.71 Max. :77.82 Max. :97.92
## NA.
## Min. : 0.0000
## 1st Qu.: 0.0000
## Median : 0.0000
## Mean : 0.2667
## 3rd Qu.: 0.0000
## Max. :69.9000
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Example 2: 'Regular' Fractional Cover, including Trees
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AP.data.FC.RFC.Trees = fractional_cover(AP.data$veg.PI, ground_fractional="FALSE", in_canopy_sky="TRUE")
head(AP.data.FC.RFC.Trees)
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## site_unique bare brown green NA.
## NSABBS0005-58582 NSABBS0005-58582 1.09 36.53 62.38 0.0
## NSABBS0006-58557 NSABBS0006-58557 2.77 27.33 69.80 0.1
## NSABHC0001-53596 NSABHC0001-53596 31.26 42.24 26.51 0.0
## NSABHC0002-53597 NSABHC0002-53597 0.00 0.00 30.10 69.9
## NSABHC0003-53598 NSABHC0003-53598 46.57 28.14 25.29 0.0
## NSABHC0004-53599 NSABHC0004-53599 26.63 36.63 36.73 0.0
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summary(AP.data.FC.RFC.Trees)
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## site_unique bare brown green
## Length:653 Min. : 0.00 Min. : 0.00 Min. : 0.10
## Class :character 1st Qu.: 9.31 1st Qu.:19.22 1st Qu.:25.05
## Mode :character Median :22.08 Median :28.22 Median :40.89
## Mean :27.41 Mean :29.20 Mean :43.13
## 3rd Qu.:41.78 3rd Qu.:38.12 3rd Qu.:59.80
## Max. :98.71 Max. :72.67 Max. :97.92
## NA.
## Min. : 0.0000
## 1st Qu.: 0.0000
## Median : 0.0000
## Mean : 0.2634
## 3rd Qu.: 0.0000
## Max. :69.9000
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Example 3: Fractional Ground Cover
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AP.data.FC.RFC.Trees = fractional_cover(AP.data$veg.PI, ground_fractional="TRUE")
head(AP.data.FC.RFC.Trees)
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## site_unique bare brown green NA.
## NSABBS0005-58582 NSABBS0005-58582 1.58 98.42 0.00 0.00
## NSABBS0006-58557 NSABBS0006-58557 5.35 94.36 0.20 0.10
## NSABHC0001-53596 NSABHC0001-53596 33.73 55.98 10.29 0.00
## NSABHC0002-53597 NSABHC0002-53597 0.00 0.00 17.92 82.08
## NSABHC0003-53598 NSABHC0003-53598 54.02 44.12 1.86 0.00
## NSABHC0004-53599 NSABHC0004-53599 28.42 48.81 22.77 0.00
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summary(AP.data.FC.RFC.Trees)
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## site_unique bare brown green
## Length:653 Min. : 0.00 Min. : 0.00 Min. : 0.00
## Class :character 1st Qu.:13.86 1st Qu.:33.60 1st Qu.: 3.76
## Mode :character Median :26.83 Median :49.70 Median :12.18
## Mean :30.98 Mean :51.37 Mean :17.27
## 3rd Qu.:46.58 3rd Qu.:70.59 3rd Qu.:25.64
## Max. :99.60 Max. :98.42 Max. :97.92
## NA.
## Min. : 0.0000
## 1st Qu.: 0.0000
## Median : 0.0000
## Mean : 0.3838
## 3rd Qu.: 0.0000
## Max. :82.0800
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