Basal Area data: 'basal_area' function
- Bernardo Blanco-Martin
The 'basal_area' function in the 'ausplotsR' package calculates the Basal Area or Mean Number of Basal Wedge Hits of plots using the raw basal wedge data returned by the 'get_ausplots' function also in the 'ausplotsR' package.
The basal_area function has the following arguments:
- 'veg.basal': Name of the data frame containing the Raw Basal Wedge Data generated by the 'get_ausplots' function in the 'ausplotsR' package.
- 'by.spp': Whether Basal Wedge values are computed by Plot or Individual Species. This argument can take two values:
- 'FALSE': The function returns combined values per plot. This is the default value for the argument.
- 'TRUE': Returns values for individual species
- 'by.hits': Whether the Basal Wedge values are computed as Basal Area or Mean Number of Individual Basal Wedge Hits. This argument can take two values:
- 'FALSE': The function returns the Basal Area (in m2/ha). This is the default value for the argument.
- 'TRUE': Returns the Mean Number of Individual Basal Wedge Hits.
This function returns a data frame with two columns. In this data frame rows correspond to representing Plots (or species by plots), the first column contains the unique sites names and the second column contains the Basal Area or Hit Scores depending on the value assigned to the 'by.hits' argument.
EXAMPLES
Examples of the use of the 'basal_area' function to compute the Basal Area or Mean Number of Basal Wedge Hits of individual plots from raw basal wedge data (as returned by the 'get_ausplots' function) are presented below. Basal areas (or mean number of /wedge hits) are computed for the full set of basal wedge 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 Basal Areas or Mean Number of Wedge Hits data frames can be enriched with additional information as seen as seen in the 'Manipulating AusPlots data II: Merging data frames' Step-by-Step Guide. The examples below cover all possible combinations of argument values in the 'basal_area 'function.
Boxes with grey background contain code snippets, and boxes with white background containt code (text) outputs.
Example 1: Basal Area (m2/ha) per Plot (the default argument values)
# ======================================
# Basal Area data: 'basal_area' function
# ======================================
# The default arguments are: 'by.spp=FALSE' and 'by.hits=FALSE'
# Basal Area (m2/ha) per Plot (the default argument values)
# =========================================================
AP.data.BAperPlot = basal_area(AP.data$veg.basal)
class(AP.data.BAperPlot)## [1] "data.frame"dim(AP.data.BAperPlot)## [1] 354 2head(AP.data.BAperPlot)## site_unique basal_area_m2_ha
## 1 NSABBS0005-58582 26.805556
## 2 NSABBS0006-58557 22.577778
## 3 NSABHC0028-58027 11.588889
## 4 NSABHC0029-58028 26.905556
## 5 NSACHC0002-58558 4.616667
## 6 NSACHC0003-58575 9.437500summary(AP.data.BAperPlot)## site_unique basal_area_m2_ha
## Length:354 Min. : 0.050
## Class :character 1st Qu.: 2.282
## Mode :character Median : 4.811
## Mean : 7.601
## 3rd Qu.:10.189
## Max. :43.094Example 2: Basal Area (m2/ha) per Individual Species
# Basal Area (m2/ha) per Individual Species
# ==========================================
AP.data.BAperSpp = basal_area(AP.data$veg.basal, by.spp=TRUE)
#class(AP.data.BAperSpp)
#dim(AP.data.BAperSpp)
head(AP.data.BAperSpp)## site_unique herbarium_determination basal_area_m2_ha
## 1 WAAGES0003-58025 Acacia acuminata 0.350000
## 2 NSAMDD0027-57087 Acacia aneura 6.416667
## 3 NSAMUL0004-58560 Acacia aneura 5.843750
## 4 NTABRT0001-53616 Acacia aneura 0.800000
## 5 NTABRT0002-53617 Acacia aneura 0.612500
## 6 NTAFIN0004-58010 Acacia aneura 1.422222summary(AP.data.BAperSpp)## site_unique herbarium_determination basal_area_m2_ha
## Length:1613 Length:1613 Min. :-0.4000
## Class :character Class :character 1st Qu.: 0.3000
## Mode :character Mode :character Median : 0.7333
## Mean : 1.9947
## 3rd Qu.: 2.0278
## Max. :40.2500Example 3: Mean Number of Basal Wedge Hits per Plot
# Mean Number of Basal Wedge Hits per Plot
# ========================================
AP.data.BWHperPlot = basal_area(AP.data$veg.basal, by.hits=TRUE)
#class(AP.data.BWHperPlot)
#dim(AP.data.BWHperPlot)
head(AP.data.BWHperPlot)## site_unique mean_hits
## 1 NSABBS0005-58582 24.77778
## 2 NSABBS0006-58557 25.11111
## 3 NSABHC0028-58027 20.44444
## 4 NSABHC0029-58028 16.88889
## 5 NSACHC0002-58558 10.11111
## 6 NSACHC0003-58575 8.87500summary(AP.data.BWHperPlot)## site_unique mean_hits
## Length:354 Min. : 1.00
## Class :character 1st Qu.:11.44
## Mode :character Median :16.83
## Mean :18.01
## 3rd Qu.:22.52
## Max. :62.78Example 4: Mean Number of Basal Wedge Hits per Individual Species
# Mean Number of Basal Wedge Hits per Individual Species
# ======================================================
AP.data.BWHperSpp = basal_area(AP.data$veg.basal, by.spp=TRUE, by.hits=TRUE)
#class(AP.data.BWHperSpp)
#dim(AP.data.BWHperSpp)
head(AP.data.BWHperSpp)## site_unique herbarium_determination mean_hits
## 1 WAAGES0003-58025 Acacia acuminata 3.500000
## 2 NSAMDD0027-57087 Acacia aneura 9.888889
## 3 NSAMUL0004-58560 Acacia aneura 10.875000
## 4 NTABRT0001-53616 Acacia aneura 8.000000
## 5 NTABRT0002-53617 Acacia aneura 6.125000
## 6 NTAFIN0004-58010 Acacia aneura 14.222222summary(AP.data.BWHperSpp)## site_unique herbarium_determination mean_hits
## Length:1613 Length:1613 Min. : 0.6667
## Class :character Class :character 1st Qu.: 2.0000
## Mode :character Mode :character Median : 4.2500
## Mean : 5.3265
## 3rd Qu.: 7.7500
## Max. :38.7778