The 'growth_form_table' function in the 'ausplotR' package can be used to generate occurrence matrices for plant growth forms in the AusPlots plots. The plant growth forms considered are those in the National Vegetation Information System (NVIS; Executive Steering Committee for Australian Vegetation Information, 2003).
The input for the 'growth_form_table' function is a data frame of raw AusPlots point intercept data generated using the 'get_ausplots function'. Three metrics can be selected to score species growth form:
- Presence/Absence: Set by the argument 'm_kind = “PA”'.
- Percent Cover: Based on total frequency of hits. Set by the argument 'm_kind = “percent_cover”'. This is the most useful and commonly used metric. It can be subsequently used in statistical analyses (e.g. MANOVA, Ordination, Classification, etc.) at continental scale where species turnover is too high for some methods to provide meaningful results.
- Species Richness: Set by the argument 'm_kind = “richness”'. Note that when ‘m_kind’ is set to “richness” the rowSums of the occurrence matrix can be higher than the observed SR because in some occasions the same species is recorded with different growth forms in a plot and therefore the same species can count towards the weights for multiple growth forms.
Whe Percent Cover is used two types of cover type can be selected:
- Projected Foliage Cover (PFC): Hits scored as ‘in canopy sky’ are removed. Set by the argument 'cover_type = "PFC"'.
- Opaque Canopy Cover (OCC): Hits scored as ‘in canopy sky’ are retained. Set by the argument 'cover_type = "OCC"'.
The output of the 'growth_form_table' function is a data frame. In this output data frame rows correspond to unique sites, columns to NVIS plant growth forms, and cell values are either Presence/Absences, Percent Cover, or Species Richness depending on the option chosen for the ‘m_kind’ argument.
REFERENCES
- National Vegetation Information System, Version 6.0
Executive Steering Committee for Australian Vegetation Information (ESCAVI)
Department of the Environment and Heritage, 2003
ISBN 0 642 54953 2
EXAMPLES
Examples of the use of the 'growth_form_table' funtion are presented below. In the examples growth form ocurrences are computed using different scoring metrics (i.e. Presence/Absence, Percentage Cover, and Species Richness) by varying the argument values (see above). Growth form types occurrences 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 'Fractional Cover' data frames can be eriched with addional information as seen in the 'Manipulating AusPlots data II: Merging data frames' Step-by-Step Guide.
Boxes with grey background contain code snippets, and boxes with white background containt code (text) outputs.
Example 1: NVIS Plant Growth Forms Occurrence Matrix,' Presence/Absence' scoring metric.
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AP.data.PGF.PA = growth_form_table(AP.data$veg.PI, m_kind="PA")
class(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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## 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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AP.data.PGF.PC.PFC = growth_form_table(AP.data$veg.PI, m_kind="percent_cover", cover_type="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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AP.data.PGF.PC = growth_form_table(AP.data$veg.PI, m_kind="percent_cover", cover_type="OCC")
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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## 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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AP.data.PGF.SR = growth_form_table(AP.data$veg.PI, m_kind="richness")
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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## 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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