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The 'single_cover_value' function in the 'auplotsR' package calculates Vegetation Cover Values for particular Growth Form Types and/or Height Thresholds per Site from Raw AusPlots Vegetation Point Intercept data. The 'growth_form_table' function can also be used to calculate Cover Values for all Vegetation Growth Form Types; however, 'single_cover_value' can perform these computations for:

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Examples of the use of the 'single_cover_value' function to compute Cover Values for particular Vegetation Growth Form Types and/or Height Thresholds per Site are presented below. Examples of how to manipulate, display, and use the data generated by the 'single_cover_value' function can be found in TERN’s DSDP ‘ECOSYSTEM SURVEILLANCE (AusPlots) TUTORIAL: UNDERSTANDING AND USING THE ‘ausplotsR’ PACKAGE AND AusPlots DATA’ Tutorial. Cover values (for particular vegetation growth form types and/or height thersholds) are computed for the full set of vegetation point intersect data currently available at AusPlots. The list of data frames containing information for all currently available AusPlots sites (i.e. the 'AP.data' list) was previously created using the `get_ausplots` function (see the 'Obtaining AusPlots data: 'get_ausplots' function' Step-by-Step Guide; we use the list created in Example 4). The resulting 'Vegetation Cover (by Growth Form Type and/or Height)' data frames can be enriched with additional information as seen in the 'Manipulating AusPlots data II: Merging data frames' Step-by-Step Guide. The examples presented below cover different scenarios for sub-setting the input vegetation point intercept data frame prior to the calculation of the required vegetation cover values. Specifically, we explore how compute cover values: (1) sub-setting only by Height, (2) sub-setting only by Taxonomy, and (3) sub-setting by both Height and Taxonomy. We Combine the outputs of a single type (i.e. Height or Growth Form) into a Single Data Frame.

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Vegetation Cover of any Growth Form Type higher than 0 meters

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# ====================================================
# VEGETATION COVER DATA: 'single_cover_value' function
# ====================================================

# Vegetation Cover data, sub-setting only by Height
# =================================================

# Vegetation Cover of any Growth Form > 0m
# ----------------------------------------
AP.data.VC.gt0 = single_cover_value(AP.data$veg.PI, by.growth_form=FALSE, min.height=0)
class(AP.data.VC.gt0)

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## [1] "data.frame"

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dim(AP.data.VC.gt0)

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## [1] 653   2

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head(AP.data.VC.gt0)

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##        site_unique percentCover
## 1 NSABBS0005-58582        59.50
## 2 NSABBS0006-58557        64.06
## 3 NSABHC0001-53596        26.51
## 4 NSABHC0002-53597        30.10
## 5 NSABHC0003-53598        25.29
## 6 NSABHC0004-53599        36.73

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summary(AP.data.VC.gt0)

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##            site_unique   percentCover  
##  NSABBS0005-58582:  1   Min.   : 0.10  
##  NSABBS0006-58557:  1   1st Qu.:23.86  
##  NSABHC0001-53596:  1   Median :38.81  
##  NSABHC0002-53597:  1   Mean   :41.52  
##  NSABHC0003-53598:  1   3rd Qu.:56.53  
##  NSABHC0004-53599:  1   Max.   :98.02  
##  (Other)         :647

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Vegetation Cover of any Growth Form Type higher than 2 meters

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# Vegetation Cover of any Growth Form > 2m
# ----------------------------------------
AP.data.VC.gt2 = single_cover_value(AP.data$veg.PI, by.growth_form=FALSE, min.height=2)
#class(AP.data.VC.gt0)
#dim(AP.data.VC.gt0)
head(AP.data.VC.gt0)

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##        site_unique percentCover
## 1 NSABBS0005-58582        59.50
## 2 NSABBS0006-58557        64.06
## 3 NSABHC0001-53596        26.51
## 4 NSABHC0002-53597        30.10
## 5 NSABHC0003-53598        25.29
## 6 NSABHC0004-53599        36.73

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summary(AP.data.VC.gt0)

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##            site_unique   percentCover  
##  NSABBS0005-58582:  1   Min.   : 0.10  
##  NSABBS0006-58557:  1   1st Qu.:23.86  
##  NSABHC0001-53596:  1   Median :38.81  
##  NSABHC0002-53597:  1   Mean   :41.52  
##  NSABHC0003-53598:  1   3rd Qu.:56.53  
##  NSABHC0004-53599:  1   Max.   :98.02  
##  (Other)         :647

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Combine Height Results (> 0m, > 2m, and 0 to 2m) in a Sigle Data Frame

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# Results (> 0m, > 2m, and 0 to 2m) combined in a single Data Frame
# -----------------------------------------------------------------
AP.data.VC.Height = data.frame(site_unique=AP.data.VC.gt0$site_unique, 
                               VCF.gt0=AP.data.VC.gt0$percentCover, 
                               VCF.gt2=AP.data.VC.gt2$percentCover, 
                               VCG.0to2=(AP.data.VC.gt0$percentCover-AP.data.VC.gt2$percentCover))
head(AP.data.VC.Height)

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##        site_unique VCF.gt0 VCF.gt2 VCG.0to2
## 1 NSABBS0005-58582   59.50   51.88     7.62
## 2 NSABBS0006-58557   64.06   59.70     4.36
## 3 NSABHC0001-53596   26.51    0.00    26.51
## 4 NSABHC0002-53597   30.10    0.00    30.10
## 5 NSABHC0003-53598   25.29    0.00    25.29
## 6 NSABHC0004-53599   36.73    0.00    36.73

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summary(AP.data.VC.Height)

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##            site_unique     VCF.gt0         VCF.gt2         VCG.0to2    
##  NSABBS0005-58582:  1   Min.   : 0.10   Min.   : 0.00   Min.   : 0.10  
##  NSABBS0006-58557:  1   1st Qu.:23.86   1st Qu.: 0.20   1st Qu.:13.17  
##  NSABHC0001-53596:  1   Median :38.81   Median : 8.00   Median :22.97  
##  NSABHC0002-53597:  1   Mean   :41.52   Mean   :14.37   Mean   :27.15  
##  NSABHC0003-53598:  1   3rd Qu.:56.53   3rd Qu.:23.07   3rd Qu.:38.20  
##  NSABHC0004-53599:  1   Max.   :98.02   Max.   :91.09   Max.   :98.02  
##  (Other)         :647

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Example 2: Vegetation Cover data, sub-setting only by Taxonomy

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Trees ("Tree/Palm" + "Tree Mallee", which is the default)

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# Vegetation Cover data, sub-setting only by Taxonomy
# ===================================================

# Trees (my.growth_forms=c("Tree/Palm", "Tree Mallee"), which is the default)
# ---------------------------------------------------------------------------
AP.data.VC.trees = single_cover_value(AP.data$veg.PI, min.height=0)
#class(AP.data.VC.trees)
#dim(AP.data.VC.trees)
head(AP.data.VC.trees)

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##        site_unique percentCover
## 1 NSABBS0005-58582        49.50
## 2 NSABBS0006-58557        58.81
## 3 NSABHC0001-53596         0.00
## 4 NSABHC0002-53597         0.00
## 5 NSABHC0003-53598         0.00
## 6 NSABHC0004-53599         0.00

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summary(AP.data.VC.trees)

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##            site_unique   percentCover  
##  NSABBS0005-58582:  1   Min.   : 0.00  
##  NSABBS0006-58557:  1   1st Qu.: 0.00  
##  NSABHC0001-53596:  1   Median : 3.27  
##  NSABHC0002-53597:  1   Mean   :11.60  
##  NSABHC0003-53598:  1   3rd Qu.:17.92  
##  NSABHC0004-53599:  1   Max.   :79.54  
##  (Other)         :647

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Grasses ("Hummock grass" + "Tussock grass")

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# Grasses (my.growth_forms=c("Hummock.grass", "Tussock.grass"))
# ------------------------------------------------------------------
AP.data.VC.grass = single_cover_value(AP.data$veg.PI, my.growth_forms=c("Hummock grass", "Tussock grass"), min.height=0)
#class(AP.data.VC.grass)
#dim(AP.data.VC.grass)
head(AP.data.VC.grass)

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##        site_unique percentCover
## 1 NSABBS0005-58582         0.10
## 2 NSABBS0006-58557         0.40
## 3 NSABHC0001-53596         3.36
## 4 NSABHC0002-53597         6.53
## 5 NSABHC0003-53598         0.69
## 6 NSABHC0004-53599        11.88

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summary(AP.data.VC.grass)

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##            site_unique   percentCover  
##  NSABBS0005-58582:  1   Min.   : 0.00  
##  NSABBS0006-58557:  1   1st Qu.: 0.69  
##  NSABHC0001-53596:  1   Median : 7.52  
##  NSABHC0002-53597:  1   Mean   :15.45  
##  NSABHC0003-53598:  1   3rd Qu.:25.94  
##  NSABHC0004-53599:  1   Max.   :88.71  
##  (Other)         :647

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Combine Growth Form Types Results (Trees & Grasses) in a Sigle Data Frame

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# Results (trees & grass) combined in a single Data Frame
# -----------------------------------------------------------------
AP.data.VC.TreesGrass = data.frame(site_unique=AP.data.VC.trees$site_unique,
                                   VCF.trees=AP.data.VC.trees$percentCover,
                                   VCF.grass=AP.data.VC.grass$percentCover)
head(AP.data.VC.TreesGrass)

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##        site_unique VCF.trees VCF.grass
## 1 NSABBS0005-58582     49.50      0.10
## 2 NSABBS0006-58557     58.81      0.40
## 3 NSABHC0001-53596      0.00      3.36
## 4 NSABHC0002-53597      0.00      6.53
## 5 NSABHC0003-53598      0.00      0.69
## 6 NSABHC0004-53599      0.00     11.88

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summary(AP.data.VC.TreesGrass)

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##            site_unique    VCF.trees       VCF.grass    
##  NSABBS0005-58582:  1   Min.   : 0.00   Min.   : 0.00  
##  NSABBS0006-58557:  1   1st Qu.: 0.00   1st Qu.: 0.69  
##  NSABHC0001-53596:  1   Median : 3.27   Median : 7.52  
##  NSABHC0002-53597:  1   Mean   :11.60   Mean   :15.45  
##  NSABHC0003-53598:  1   3rd Qu.:17.92   3rd Qu.:25.94  
##  NSABHC0004-53599:  1   Max.   :79.54   Max.   :88.71  
##  (Other)         :647

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Example 3: Vegetation Cover data, sub-setting by both Height and Taxonomy

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Trees ("Tree/Palm" + "Tree Mallee", the default) higher than 5 meters

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# Vegetation Cover data, sub-setting by both Height and Taxonomy
# ==============================================================
# Trees (my.growth_forms=c("Tree/Palm", "Tree Mallee")) > 5 m.
# 'c("Tree/Palm", "Tree Mallee")' is the default values for 'my.growth.forms',
# so it is not really necesary
AP.data.VC.Trees.gt5 = single_cover_value(AP.data$veg.PI, 
                                          my.growth_forms=c("Tree/Palm", "Tree Mallee"), min.height=5)
#class(AP.data.VC.Trees.gt5)
#dim(AP.data.VC.Trees.gt5)
head(AP.data.VC.Trees.gt5)

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##        site_unique percentCover
## 1 NSABBS0005-58582        46.24
## 2 NSABBS0006-58557        55.45
## 3 NSABHC0001-53596         0.00
## 4 NSABHC0002-53597         0.00
## 5 NSABHC0003-53598         0.00
## 6 NSABHC0004-53599         0.00

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summary(AP.data.VC.Trees.gt5)

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##            site_unique   percentCover   
##  NSABBS0005-58582:  1   Min.   : 0.000  
##  NSABBS0006-58557:  1   1st Qu.: 0.000  
##  NSABHC0001-53596:  1   Median : 0.590  
##  NSABHC0002-53597:  1   Mean   : 8.461  
##  NSABHC0003-53598:  1   3rd Qu.:10.400  
##  NSABHC0004-53599:  1   Max.   :70.000  
##  (Other)         :647

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