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Example 1: NVIS Plant Growth Forms Occurrence Matrix,' Presence/Absence' scoring metric.

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# ====================================================
# PLANT GROWTH FORM DATA: 'growth_form_table' function
# ====================================================

# NVIS Plant Growth Forms Occurrence Matrix,' Presence/Absence' scoring metric
# ============================================================================
AP.data.PGF.PA = growth_form_table(AP.data$veg.PI, m_kind="PA")
class(AP.data.PGF.PA)

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## [1] "data.frame"

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dim(AP.data.PGF.PA)

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## [1] 653  20

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head(AP.data.PGF.PA)

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##                  Aquatic Bryophyte Chenopod Cycad Epiphyte Fern Forb
## NSABBS0005-58582       0         0        0     0        1    0    1
## NSABBS0006-58557       0         0        0     0        1    0    1
## NSABHC0001-53596       0         0        0     0        0    0    1
## NSABHC0002-53597       0         0        1     0        0    0    1
## NSABHC0003-53598       0         0        0     0        0    0    1
## NSABHC0004-53599       0         0        0     0        0    0    1
##                  Fungus Grass.tree Heath.shrub Hummock.grass NC Rush Sedge
## NSABBS0005-58582      0          0           1             0  0    0     0
## NSABBS0006-58557      0          0           0             0  0    0     0
## NSABHC0001-53596      0          0           0             0  0    0     0
## NSABHC0002-53597      0          0           0             0  0    0     0
## NSABHC0003-53598      0          0           0             0  0    0     0
## NSABHC0004-53599      0          0           0             0  0    0     0
##                  Shrub Shrub.Mallee Tree.Mallee Tree.Palm Tussock.grass
## NSABBS0005-58582     1            0           0         1             1
## NSABBS0006-58557     1            0           0         1             1
## NSABHC0001-53596     1            0           0         0             1
## NSABHC0002-53597     1            0           0         0             1
## NSABHC0003-53598     1            0           0         0             1
## NSABHC0004-53599     1            0           0         0             1
##                  Vine
## NSABBS0005-58582    0
## NSABBS0006-58557    0
## NSABHC0001-53596    0
## NSABHC0002-53597    0
## NSABHC0003-53598    0
## NSABHC0004-53599    0

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summary(AP.data.PGF.PA)

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##     Aquatic           Bryophyte          Chenopod          Cycad         
##  Min.   :0.000000   Min.   :0.00000   Min.   :0.0000   Min.   :0.000000  
##  1st Qu.:0.000000   1st Qu.:0.00000   1st Qu.:0.0000   1st Qu.:0.000000  
##  Median :0.000000   Median :0.00000   Median :0.0000   Median :0.000000  
##  Mean   :0.001531   Mean   :0.01378   Mean   :0.4916   Mean   :0.003063  
##  3rd Qu.:0.000000   3rd Qu.:0.00000   3rd Qu.:1.0000   3rd Qu.:0.000000  
##  Max.   :1.000000   Max.   :1.00000   Max.   :1.0000   Max.   :1.000000  
##     Epiphyte            Fern             Forb            Fungus        
##  Min.   :0.00000   Min.   :0.0000   Min.   :0.0000   Min.   :0.000000  
##  1st Qu.:0.00000   1st Qu.:0.0000   1st Qu.:1.0000   1st Qu.:0.000000  
##  Median :0.00000   Median :0.0000   Median :1.0000   Median :0.000000  
##  Mean   :0.08882   Mean   :0.1103   Mean   :0.9173   Mean   :0.007657  
##  3rd Qu.:0.00000   3rd Qu.:0.0000   3rd Qu.:1.0000   3rd Qu.:0.000000  
##  Max.   :1.00000   Max.   :1.0000   Max.   :1.0000   Max.   :1.000000  
##    Grass.tree       Heath.shrub      Hummock.grass          NC        
##  Min.   :0.00000   Min.   :0.00000   Min.   :0.0000   Min.   :0.0000  
##  1st Qu.:0.00000   1st Qu.:0.00000   1st Qu.:0.0000   1st Qu.:0.0000  
##  Median :0.00000   Median :0.00000   Median :0.0000   Median :0.0000  
##  Mean   :0.03216   Mean   :0.07198   Mean   :0.2711   Mean   :0.0245  
##  3rd Qu.:0.00000   3rd Qu.:0.00000   3rd Qu.:1.0000   3rd Qu.:0.0000  
##  Max.   :1.00000   Max.   :1.00000   Max.   :1.0000   Max.   :1.0000  
##       Rush             Sedge            Shrub         Shrub.Mallee    
##  Min.   :0.00000   Min.   :0.0000   Min.   :0.0000   Min.   :0.00000  
##  1st Qu.:0.00000   1st Qu.:0.0000   1st Qu.:1.0000   1st Qu.:0.00000  
##  Median :0.00000   Median :0.0000   Median :1.0000   Median :0.00000  
##  Mean   :0.06126   Mean   :0.3308   Mean   :0.8652   Mean   :0.09035  
##  3rd Qu.:0.00000   3rd Qu.:1.0000   3rd Qu.:1.0000   3rd Qu.:0.00000  
##  Max.   :1.00000   Max.   :1.0000   Max.   :1.0000   Max.   :1.00000  
##   Tree.Mallee       Tree.Palm      Tussock.grass         Vine       
##  Min.   :0.0000   Min.   :0.0000   Min.   :0.0000   Min.   :0.0000  
##  1st Qu.:0.0000   1st Qu.:0.0000   1st Qu.:1.0000   1st Qu.:0.0000  
##  Median :0.0000   Median :1.0000   Median :1.0000   Median :0.0000  
##  Mean   :0.1593   Mean   :0.6279   Mean   :0.8407   Mean   :0.2496  
##  3rd Qu.:0.0000   3rd Qu.:1.0000   3rd Qu.:1.0000   3rd Qu.:0.0000  
##  Max.   :1.0000   Max.   :1.0000   Max.   :1.0000   Max.   :1.0000

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Example 2A: NVIS Plant Growth Forms Occurrence Matrix, 'Percentage Cover' scoring metric with 'Projected Foliage Cover' (PFC) option.

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# NVIS Plant Growth Forms Occurrence Matrix, 'Percentage Cover' scoring metric with 'Projected Foliage Cover' option
# ==================================================================================================================
AP.data.PGF.PC.PFC = growth_form_table(AP.data$veg.PI, m_kind="percent_cover", cover_type="PFC")
#class(AP.data.PGF.PC.PFC)
#dim(AP.data.PGF.PC.PFC)
head(AP.data.PGF.PC.PFC)

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##                  Aquatic Bryophyte Chenopod Cycad  Epiphyte Fern
## NSABBS0005-58582       0         0  0.00000     0 0.3289474    0
## NSABBS0006-58557       0         0  0.00000     0 0.1543210    0
## NSABHC0001-53596       0         0  0.00000     0 0.0000000    0
## NSABHC0002-53597       0         0 40.46053     0 0.0000000    0
## NSABHC0003-53598       0         0  0.00000     0 0.0000000    0
## NSABHC0004-53599       0         0  0.00000     0 0.0000000    0
##                        Forb Fungus Grass.tree Heath.shrub Hummock.grass NC
## NSABBS0005-58582  0.1644737      0          0    2.138158             0  0
## NSABBS0006-58557  0.6172840      0          0    0.000000             0  0
## NSABHC0001-53596 26.8656716      0          0    0.000000             0  0
## NSABHC0002-53597 40.1315789      0          0    0.000000             0  0
## NSABHC0003-53598  4.6511628      0          0    0.000000             0  0
## NSABHC0004-53599 29.6495957      0          0    0.000000             0  0
##                  Rush Sedge      Shrub Shrub.Mallee Tree.Mallee Tree.Palm
## NSABBS0005-58582    0     0 25.9868421            0           0  103.1250
## NSABBS0006-58557    0     0 17.2839506            0           0  114.9691
## NSABHC0001-53596    0     0 61.5671642            0           0    0.0000
## NSABHC0002-53597    0     0  0.6578947            0           0    0.0000
## NSABHC0003-53598    0     0 92.6356589            0           0    0.0000
## NSABHC0004-53599    0     0 38.0053908            0           0    0.0000
##                  Tussock.grass Vine
## NSABBS0005-58582     0.1644737    0
## NSABBS0006-58557     0.6172840    0
## NSABHC0001-53596    12.6865672    0
## NSABHC0002-53597    21.7105263    0
## NSABHC0003-53598     2.7131783    0
## NSABHC0004-53599    32.3450135    0

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summary(AP.data.PGF.PC.PFC)

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##     Aquatic            Bryophyte          Chenopod          Cycad         
##  Min.   :0.0000000   Min.   : 0.0000   Min.   :  0.00   Min.   :0.000000  
##  1st Qu.:0.0000000   1st Qu.: 0.0000   1st Qu.:  0.00   1st Qu.:0.000000  
##  Median :0.0000000   Median : 0.0000   Median :  0.00   Median :0.000000  
##  Mean   :0.0006053   Mean   : 0.1331   Mean   : 10.79   Mean   :0.004358  
##  3rd Qu.:0.0000000   3rd Qu.: 0.0000   3rd Qu.: 12.25   3rd Qu.:0.000000  
##  Max.   :0.3952569   Max.   :66.2047   Max.   :100.00   Max.   :2.540107  
##     Epiphyte             Fern              Forb            Fungus        
##  Min.   : 0.00000   Min.   : 0.0000   Min.   : 0.000   Min.   :0.000000  
##  1st Qu.: 0.00000   1st Qu.: 0.0000   1st Qu.: 1.569   1st Qu.:0.000000  
##  Median : 0.00000   Median : 0.0000   Median : 5.983   Median :0.000000  
##  Mean   : 0.08855   Mean   : 0.3525   Mean   :13.398   Mean   :0.004604  
##  3rd Qu.: 0.00000   3rd Qu.: 0.0000   3rd Qu.:17.319   3rd Qu.:0.000000  
##  Max.   :14.28571   Max.   :54.3062   Max.   :94.268   Max.   :2.042901  
##    Grass.tree     Heath.shrub     Hummock.grass            NC          
##  Min.   : 0.00   Min.   : 0.000   Min.   :  0.0000   Min.   : 0.00000  
##  1st Qu.: 0.00   1st Qu.: 0.000   1st Qu.:  0.0000   1st Qu.: 0.00000  
##  Median : 0.00   Median : 0.000   Median :  0.0000   Median : 0.00000  
##  Mean   : 0.46   Mean   : 1.142   Mean   :  8.7219   Mean   : 0.04686  
##  3rd Qu.: 0.00   3rd Qu.: 0.000   3rd Qu.:  0.6061   3rd Qu.: 0.00000  
##  Max.   :50.18   Max.   :93.555   Max.   :183.8565   Max.   :14.09836  
##       Rush             Sedge             Shrub          Shrub.Mallee    
##  Min.   : 0.0000   Min.   : 0.0000   Min.   :  0.000   Min.   : 0.0000  
##  1st Qu.: 0.0000   1st Qu.: 0.0000   1st Qu.:  2.296   1st Qu.: 0.0000  
##  Median : 0.0000   Median : 0.0000   Median : 14.358   Median : 0.0000  
##  Mean   : 0.1527   Mean   : 2.8579   Mean   : 24.832   Mean   : 0.5343  
##  3rd Qu.: 0.0000   3rd Qu.: 0.8929   3rd Qu.: 37.944   3rd Qu.: 0.0000  
##  Max.   :12.3487   Max.   :76.2029   Max.   :139.655   Max.   :37.7863  
##   Tree.Mallee       Tree.Palm       Tussock.grass          Vine        
##  Min.   : 0.000   Min.   :  0.000   Min.   :  0.000   Min.   : 0.0000  
##  1st Qu.: 0.000   1st Qu.:  0.000   1st Qu.:  1.066   1st Qu.: 0.0000  
##  Median : 0.000   Median :  2.974   Median : 15.842   Median : 0.0000  
##  Mean   : 3.863   Mean   : 20.984   Mean   : 28.872   Mean   : 0.6741  
##  3rd Qu.: 0.000   3rd Qu.: 37.524   3rd Qu.: 52.174   3rd Qu.: 0.0000  
##  Max.   :91.979   Max.   :144.211   Max.   :116.019   Max.   :62.4561

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Example 2B: NVIS Plant Growth Forms Occurrence Matrix, 'Percentage Cover' scoring metric with 'Opaque Canopy Cover' (OCC) option.

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# NVIS Plant Growth Forms Occurrence Matrix, 'Percentage Cover' scoring metric with 'Opaque Canopy Cover' option
# ==============================================================================================================
AP.data.PGF.PC = growth_form_table(AP.data$veg.PI, m_kind="percent_cover", cover_type="OCC")
#class(AP.data.PGF.PC)
#dim(AP.data.PGF.PC)
head(AP.data.PGF.PC)

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##                  Aquatic Bryophyte Chenopod Cycad  Epiphyte Fern
## NSABBS0005-58582       0         0  0.00000     0 0.3289474    0
## NSABBS0006-58557       0         0  0.00000     0 0.1543210    0
## NSABHC0001-53596       0         0  0.00000     0 0.0000000    0
## NSABHC0002-53597       0         0 40.46053     0 0.0000000    0
## NSABHC0003-53598       0         0  0.00000     0 0.0000000    0
## NSABHC0004-53599       0         0  0.00000     0 0.0000000    0
##                        Forb Fungus Grass.tree Heath.shrub Hummock.grass NC
## NSABBS0005-58582  0.1644737      0          0    2.138158             0  0
## NSABBS0006-58557  0.6172840      0          0    0.000000             0  0
## NSABHC0001-53596 26.8656716      0          0    0.000000             0  0
## NSABHC0002-53597 40.1315789      0          0    0.000000             0  0
## NSABHC0003-53598  4.6511628      0          0    0.000000             0  0
## NSABHC0004-53599 29.6495957      0          0    0.000000             0  0
##                  Rush Sedge      Shrub Shrub.Mallee Tree.Mallee Tree.Palm
## NSABBS0005-58582    0     0 25.9868421            0           0  103.1250
## NSABBS0006-58557    0     0 17.2839506            0           0  114.9691
## NSABHC0001-53596    0     0 61.5671642            0           0    0.0000
## NSABHC0002-53597    0     0  0.6578947            0           0    0.0000
## NSABHC0003-53598    0     0 92.6356589            0           0    0.0000
## NSABHC0004-53599    0     0 38.0053908            0           0    0.0000
##                  Tussock.grass Vine
## NSABBS0005-58582     0.1644737    0
## NSABBS0006-58557     0.6172840    0
## NSABHC0001-53596    12.6865672    0
## NSABHC0002-53597    21.7105263    0
## NSABHC0003-53598     2.7131783    0
## NSABHC0004-53599    32.3450135    0

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summary(AP.data.PGF.PC)

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##     Aquatic            Bryophyte          Chenopod          Cycad         
##  Min.   :0.0000000   Min.   : 0.0000   Min.   :  0.00   Min.   :0.000000  
##  1st Qu.:0.0000000   1st Qu.: 0.0000   1st Qu.:  0.00   1st Qu.:0.000000  
##  Median :0.0000000   Median : 0.0000   Median :  0.00   Median :0.000000  
##  Mean   :0.0006053   Mean   : 0.1331   Mean   : 10.79   Mean   :0.004358  
##  3rd Qu.:0.0000000   3rd Qu.: 0.0000   3rd Qu.: 12.25   3rd Qu.:0.000000  
##  Max.   :0.3952569   Max.   :66.2047   Max.   :100.00   Max.   :2.540107  
##     Epiphyte             Fern              Forb            Fungus        
##  Min.   : 0.00000   Min.   : 0.0000   Min.   : 0.000   Min.   :0.000000  
##  1st Qu.: 0.00000   1st Qu.: 0.0000   1st Qu.: 1.569   1st Qu.:0.000000  
##  Median : 0.00000   Median : 0.0000   Median : 5.983   Median :0.000000  
##  Mean   : 0.08855   Mean   : 0.3525   Mean   :13.398   Mean   :0.004604  
##  3rd Qu.: 0.00000   3rd Qu.: 0.0000   3rd Qu.:17.319   3rd Qu.:0.000000  
##  Max.   :14.28571   Max.   :54.3062   Max.   :94.268   Max.   :2.042901  
##    Grass.tree     Heath.shrub     Hummock.grass            NC          
##  Min.   : 0.00   Min.   : 0.000   Min.   :  0.0000   Min.   : 0.00000  
##  1st Qu.: 0.00   1st Qu.: 0.000   1st Qu.:  0.0000   1st Qu.: 0.00000  
##  Median : 0.00   Median : 0.000   Median :  0.0000   Median : 0.00000  
##  Mean   : 0.46   Mean   : 1.142   Mean   :  8.7219   Mean   : 0.04686  
##  3rd Qu.: 0.00   3rd Qu.: 0.000   3rd Qu.:  0.6061   3rd Qu.: 0.00000  
##  Max.   :50.18   Max.   :93.555   Max.   :183.8565   Max.   :14.09836  
##       Rush             Sedge             Shrub          Shrub.Mallee    
##  Min.   : 0.0000   Min.   : 0.0000   Min.   :  0.000   Min.   : 0.0000  
##  1st Qu.: 0.0000   1st Qu.: 0.0000   1st Qu.:  2.296   1st Qu.: 0.0000  
##  Median : 0.0000   Median : 0.0000   Median : 14.358   Median : 0.0000  
##  Mean   : 0.1527   Mean   : 2.8579   Mean   : 24.832   Mean   : 0.5343  
##  3rd Qu.: 0.0000   3rd Qu.: 0.8929   3rd Qu.: 37.944   3rd Qu.: 0.0000  
##  Max.   :12.3487   Max.   :76.2029   Max.   :139.655   Max.   :37.7863  
##   Tree.Mallee       Tree.Palm       Tussock.grass          Vine        
##  Min.   : 0.000   Min.   :  0.000   Min.   :  0.000   Min.   : 0.0000  
##  1st Qu.: 0.000   1st Qu.:  0.000   1st Qu.:  1.066   1st Qu.: 0.0000  
##  Median : 0.000   Median :  2.974   Median : 15.842   Median : 0.0000  
##  Mean   : 3.863   Mean   : 20.984   Mean   : 28.872   Mean   : 0.6741  
##  3rd Qu.: 0.000   3rd Qu.: 37.524   3rd Qu.: 52.174   3rd Qu.: 0.0000  
##  Max.   :91.979   Max.   :144.211   Max.   :116.019   Max.   :62.4561

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Example 3: NVIS Plant Growth Forms Occurrence Matrix, 'Species Richness' scoring metric.

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# NVIS Plant Growth Forms Occurrence Matrix, 'Species Richness' scoring metric
# ============================================================================
AP.data.PGF.SR = growth_form_table(AP.data$veg.PI, m_kind="richness")
#class(AP.data.PGF.SR)
#dim(AP.data.PGF.SR)
head(AP.data.PGF.SR)

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##                  Aquatic Bryophyte Chenopod Cycad Epiphyte Fern Forb
## NSABBS0005-58582       0         0        0     0        2    0    1
## NSABBS0006-58557       0         0        0     0        1    0    2
## NSABHC0001-53596       0         0        0     0        0    0    7
## NSABHC0002-53597       0         0       11     0        0    0    8
## NSABHC0003-53598       0         0        0     0        0    0    2
## NSABHC0004-53599       0         0        0     0        0    0   18
##                  Fungus Grass.tree Heath.shrub Hummock.grass NC Rush Sedge
## NSABBS0005-58582      0          0           1             0  0    0     0
## NSABBS0006-58557      0          0           0             0  0    0     0
## NSABHC0001-53596      0          0           0             0  0    0     0
## NSABHC0002-53597      0          0           0             0  0    0     0
## NSABHC0003-53598      0          0           0             0  0    0     0
## NSABHC0004-53599      0          0           0             0  0    0     0
##                  Shrub Shrub.Mallee Tree.Mallee Tree.Palm Tussock.grass
## NSABBS0005-58582     4            0           0         5             1
## NSABBS0006-58557     5            0           0         5             3
## NSABHC0001-53596    18            0           0         0             5
## NSABHC0002-53597     2            0           0         0             5
## NSABHC0003-53598    16            0           0         0             4
## NSABHC0004-53599    13            0           0         0            11
##                  Vine
## NSABBS0005-58582    0
## NSABBS0006-58557    0
## NSABHC0001-53596    0
## NSABHC0002-53597    0
## NSABHC0003-53598    0
## NSABHC0004-53599    0

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summary(AP.data.PGF.SR)

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##     Aquatic           Bryophyte          Chenopod          Cycad         
##  Min.   :0.000000   Min.   :0.00000   Min.   : 0.000   Min.   :0.000000  
##  1st Qu.:0.000000   1st Qu.:0.00000   1st Qu.: 0.000   1st Qu.:0.000000  
##  Median :0.000000   Median :0.00000   Median : 0.000   Median :0.000000  
##  Mean   :0.001531   Mean   :0.01531   Mean   : 2.037   Mean   :0.003063  
##  3rd Qu.:0.000000   3rd Qu.:0.00000   3rd Qu.: 3.000   3rd Qu.:0.000000  
##  Max.   :1.000000   Max.   :2.00000   Max.   :14.000   Max.   :1.000000  
##     Epiphyte            Fern             Forb            Fungus        
##  Min.   :0.00000   Min.   :0.0000   Min.   : 0.000   Min.   :0.000000  
##  1st Qu.:0.00000   1st Qu.:0.0000   1st Qu.: 2.000   1st Qu.:0.000000  
##  Median :0.00000   Median :0.0000   Median : 4.000   Median :0.000000  
##  Mean   :0.09954   Mean   :0.1179   Mean   : 6.141   Mean   :0.007657  
##  3rd Qu.:0.00000   3rd Qu.:0.0000   3rd Qu.: 8.000   3rd Qu.:0.000000  
##  Max.   :3.00000   Max.   :3.0000   Max.   :32.000   Max.   :1.000000  
##    Grass.tree       Heath.shrub    Hummock.grass          NC         
##  Min.   :0.00000   Min.   : 0.00   Min.   :0.0000   Min.   :0.00000  
##  1st Qu.:0.00000   1st Qu.: 0.00   1st Qu.:0.0000   1st Qu.:0.00000  
##  Median :0.00000   Median : 0.00   Median :0.0000   Median :0.00000  
##  Mean   :0.03216   Mean   : 0.34   Mean   :0.3109   Mean   :0.03369  
##  3rd Qu.:0.00000   3rd Qu.: 0.00   3rd Qu.:1.0000   3rd Qu.:0.00000  
##  Max.   :1.00000   Max.   :19.00   Max.   :3.0000   Max.   :2.00000  
##       Rush             Sedge            Shrub        Shrub.Mallee   
##  Min.   :0.00000   Min.   : 0.000   Min.   : 0.00   Min.   :0.0000  
##  1st Qu.:0.00000   1st Qu.: 0.000   1st Qu.: 2.00   1st Qu.:0.0000  
##  Median :0.00000   Median : 0.000   Median : 5.00   Median :0.0000  
##  Mean   :0.09188   Mean   : 0.781   Mean   : 6.25   Mean   :0.1593  
##  3rd Qu.:0.00000   3rd Qu.: 1.000   3rd Qu.: 9.00   3rd Qu.:0.0000  
##  Max.   :4.00000   Max.   :14.000   Max.   :39.00   Max.   :5.0000  
##   Tree.Mallee       Tree.Palm      Tussock.grass         Vine        
##  Min.   :0.0000   Min.   : 0.000   Min.   : 0.000   Min.   : 0.0000  
##  1st Qu.:0.0000   1st Qu.: 0.000   1st Qu.: 1.000   1st Qu.: 0.0000  
##  Median :0.0000   Median : 1.000   Median : 4.000   Median : 0.0000  
##  Mean   :0.2802   Mean   : 1.933   Mean   : 4.496   Mean   : 0.3844  
##  3rd Qu.:0.0000   3rd Qu.: 3.000   3rd Qu.: 7.000   3rd Qu.: 0.0000  
##  Max.   :5.0000   Max.   :17.000   Max.   :20.000   Max.   :12.0000

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