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Example 1. Scoring metric; Presence/Absence ('m_kind = "PA")

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# ===========================================================================
# SPECIES-LEVEL DATA: 'species_table' function and species occurence matrices
# ===========================================================================

# Scoring metric: Presence/Absence
# ================================
AP.data.SppbySites.PA = species_table(AP.data$veg.PI, m_kind="PA")
class(AP.data.SppbySites.PA)

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## [1] "data.frame"

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dim(AP.data.SppbySites.PA) # Number of rows and columns in the matrix: Sites x Species

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## [1]  653 3665

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AP.data.SppbySites.PA[1:5, 1:5]

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##                  Abutilon.fraseri Abutilon.halophilum Abutilon.hannii
## NSABBS0005-58582                0                   0               0
## NSABBS0006-58557                0                   0               0
## NSABHC0001-53596                0                   0               0
## NSABHC0002-53597                0                   0               0
## NSABHC0003-53598                0                   0               0
##                  Abutilon.hannii.subsp..prostrate..p.k.latz.427.
## NSABBS0005-58582                                               0
## NSABBS0006-58557                                               0
## NSABHC0001-53596                                               0
## NSABHC0002-53597                                               0
## NSABHC0003-53598                                               0
##                  Abutilon.leucopetalum
## NSABBS0005-58582                     0
## NSABBS0006-58557                     0
## NSABHC0001-53596                     0
## NSABHC0002-53597                     0
## NSABHC0003-53598                     0

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summary(AP.data.SppbySites.PA[,1:3])

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##  Abutilon.fraseri  Abutilon.halophilum Abutilon.hannii   
##  Min.   :0.00000   Min.   :0.000000    Min.   :0.000000  
##  1st Qu.:0.00000   1st Qu.:0.000000    1st Qu.:0.000000  
##  Median :0.00000   Median :0.000000    Median :0.000000  
##  Mean   :0.01072   Mean   :0.007657    Mean   :0.001531  
##  3rd Qu.:0.00000   3rd Qu.:0.000000    3rd Qu.:0.000000  
##  Max.   :1.00000   Max.   :1.000000    Max.   :1.000000

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Example 2A. Scoring metric; Percent Cover (m_kind = "percent_cover"), Cover Type: Prejected Foliage Cover (cover_type="PFC")

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# Scoring metric: Percent Cover
# =============================

# Cover Type: Projected foliage cover (PFC)
# -----------------------------------------
# Hits scoered as 'in canopy sky' are removed
AP.data.SppbySites.PcC.PFC = species_table(AP.data$veg.PI, m_kind="percent_cover", cover_type="PFC")
#class(AP.data.SppbySites.PcC.PFC)
#dim(AP.data.SppbySites.PcC.PFC) # Number of rows and columns in the matrix: Sites x Species
#AP.data.SppbySites.PcC.PFC[1:5, 1:5]
summary(AP.data.SppbySites.PcC.PFC[,1:3])

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##  Abutilon.fraseri   Abutilon.halophilum Abutilon.hannii    
##  Min.   :0.000000   Min.   :0.000000    Min.   :0.0000000  
##  1st Qu.:0.000000   1st Qu.:0.000000    1st Qu.:0.0000000  
##  Median :0.000000   Median :0.000000    Median :0.0000000  
##  Mean   :0.001516   Mean   :0.005307    Mean   :0.0003033  
##  3rd Qu.:0.000000   3rd Qu.:0.000000    3rd Qu.:0.0000000  
##  Max.   :0.297030   Max.   :1.980198    Max.   :0.1980198

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Example 2B. Scoring metric; Percent Cover (m_kind = "percent_cover"), Cover Type: Opaque Canopy Cover (cover_type="OCC")

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# Cover Type: Opaque Canopy Cover (OCC)
# -------------------------------------
# Hits scoered as 'in canopy sky' are retained
AP.data.SppbySites.PcC.OCC = species_table(AP.data$veg.PI, m_kind="percent_cover", cover_type="OCC")
#class(AP.data.SppbySites.PcC.OCC)
#dim(AP.data.SppbySites.PcC.OCC) # Number of rows and columns in the matrix: Sites x Species
#AP.data.SppbySites.PcC.OCC[1:5, 1:5]
summary(AP.data.SppbySites.PcC.OCC[,1:3])

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##  Abutilon.fraseri   Abutilon.halophilum Abutilon.hannii    
##  Min.   :0.000000   Min.   :0.000000    Min.   :0.0000000  
##  1st Qu.:0.000000   1st Qu.:0.000000    1st Qu.:0.0000000  
##  Median :0.000000   Median :0.000000    Median :0.0000000  
##  Mean   :0.001516   Mean   :0.005307    Mean   :0.0003033  
##  3rd Qu.:0.000000   3rd Qu.:0.000000    3rd Qu.:0.0000000  
##  Max.   :0.297030   Max.   :1.980198    Max.   :0.1980198

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Example 3. Scoring metric; Frequency ('m_kind = "freq")

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# Scoring metric: Frequency
# =========================
AP.data.SppbySites.Freq = species_table(AP.data$veg.PI, m_kind="freq")
#class(AP.data.SppbySites.Freq)
#dim(AP.data.SppbySites.Freq) # Number of rows and columns in the matrix: Sites x Species
#AP.data.SppbySites.Freq[1:5, 1:5]
summary(AP.data.SppbySites.Freq[,1:3])

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##  Abutilon.fraseri   Abutilon.halophilum Abutilon.hannii    
##  Min.   :0.000000   Min.   :0.00000     Min.   :0.0000000  
##  1st Qu.:0.000000   1st Qu.:0.00000     1st Qu.:0.0000000  
##  Median :0.000000   Median :0.00000     Median :0.0000000  
##  Mean   :0.001378   Mean   :0.00245     Mean   :0.0003063  
##  3rd Qu.:0.000000   3rd Qu.:0.00000     3rd Qu.:0.0000000  
##  Max.   :0.200000   Max.   :0.80000     Max.   :0.2000000

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Example 4A. Scoring metric; IVI (m_kind = "IVI"), Cover Type: Prejected Foliage Cover (cover_type="PFC")

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# Scoring metric: IVI
# ===================

# Cover Type: Projected foliage cover (PFC)
# -----------------------------------------
# Hits scoered as 'in canopy sky' are removed
AP.data.SppbySites.IVI.PFC = species_table(AP.data$veg.PI, m_kind="IVI", cover_type="PFC")
#class(AP.data.SppbySites.IVI.PFC)
#dim(AP.data.SppbySites.IVI.PFC) # Number of rows and columns in the matrix: Sites x Species
#AP.data.SppbySites.IVI.PFC[1:5, 1:5]
summary(AP.data.SppbySites.IVI.PFC[,1:3])

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##  Abutilon.fraseri   Abutilon.halophilum Abutilon.hannii    
##  Min.   :0.000000   Min.   :0.00000     Min.   :0.0000000  
##  1st Qu.:0.000000   1st Qu.:0.00000     1st Qu.:0.0000000  
##  Median :0.000000   Median :0.00000     Median :0.0000000  
##  Mean   :0.001378   Mean   :0.00245     Mean   :0.0003063  
##  3rd Qu.:0.000000   3rd Qu.:0.00000     3rd Qu.:0.0000000  
##  Max.   :0.200000   Max.   :0.80000     Max.   :0.2000000

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Example 4B. Scoring metric; IVI (m_kind = "IVI"), Cover Type: Opaque Canopy Cover (cover_type="OCC")

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# Cover Type: Opaque Canopy Cover (OCC)
# -------------------------------------
# Hits scoered as 'in canopy sky' are retained
AP.data.SppbySites.IVI.OCC = species_table(AP.data$veg.PI, m_kind="IVI", cover_type="OCC")
#class(AP.data.SppbySites.IVI.OCC)
#dim(AP.data.SppbySites.IVI.OCC) # Number of rows and columns in the matrix: Sites x Species
#AP.data.SppbySites.IVI.OCC[1:5, 1:5]
summary(AP.data.SppbySites.IVI.OCC[,1:3])

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##  Abutilon.fraseri   Abutilon.halophilum Abutilon.hannii    
##  Min.   :0.000000   Min.   :0.00000     Min.   :0.0000000  
##  1st Qu.:0.000000   1st Qu.:0.00000     1st Qu.:0.0000000  
##  Median :0.000000   Median :0.00000     Median :0.0000000  
##  Mean   :0.001378   Mean   :0.00245     Mean   :0.0003063  
##  3rd Qu.:0.000000   3rd Qu.:0.00000     3rd Qu.:0.0000000  
##  Max.   :0.200000   Max.   :0.80000     Max.   :0.2000000

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