The 'get_ausplots' function extracts and compiles AusPlots data.
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There are several variables common to all data frames. These include 'site_location_name', 'site_location_visit_id', and 'site_unique' (a combination of the previous two). These variables can be used to merge data frames. For example, the contents of two data frames can be combined using the common variable as a link (i.e. guidance to add the merged contents in the correct row). The variable 'site_unique' is typically the best option to link data frames in a merge, as it is the most specific variable representing a single visit to a particular site and it should be used in most analyses. Otherwise, errors such including data from the wrong visit to a site can occur.
EXAMPLES
To run the examples below the 'ausplosR' library should have been installed and loaded in R, as show in 'Installing and Loading 'ausplotsR'' the Step-by-Step Guide.
Boxes with grey background contain code snippets, and boxes with white background containt code (text) outputs.
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Example 1: All available data (i.e. all data types) for 3 plots
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AP.data = get_ausplots( my.Plot_IDs=c("SATFLB0004", "QDAMGD0022", "NTASTU0002"),
structural_summaries=TRUE, basal.wedge=TRUE,
soil_subsites=TRUE, soil_bulk_density=TRUE, soil_character=TRUE )
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## User-supplied Plot_IDs located.
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class(AP.data)
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## [1] "list"
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AP.data = get_ausplots(bounding_box=c(152.5, 153.5, -28, -27))
summary(AP.data)
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## Length Class Mode
## site.info 43 data.frame list
## veg.vouch 12 data.frame list
## veg.PI 13 data.frame list
## citation 1 -none- character
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AP.data = get_ausplots(basal.wedge=TRUE, structural_summaries=TRUE, species_name_search="Eucalyptus")
summary(AP.data)
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## Length Class Mode
## site.info 43 data.frame list
## struct.summ 15 data.frame list
## veg.basal 10 data.frame list
## veg.vouch 12 data.frame list
## veg.PI 13 data.frame list
## citation 1 -none- character
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head(AP.data$veg.vouch)
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## site_location_name veg_barcode herbarium_determination
## 1 QDAMUL0003 QDA 001432 Eucalyptus crebra x e. melanophloia
## 2 SASMDD0002 SAS 000461 Eucalyptus oleosa
## 3 SASMDD0002 SAS 000462 Eucalyptus dumosa
## 4 SASMDD0002 SAS 000463 Eucalyptus socialis subsp. socialis
## 5 SASMDD0002 SAS 000038 Eucalyptus oleosa subsp. oleosa
## 6 SASMDD0002 SAS 000039 Eucalyptus dumosa
## is_uncertain_determination visit_start_date site_location_visit_id
## 1 FALSE 2013-04-26T00:00:00 53595
## 2 FALSE 2012-09-23T00:00:00 53711
## 3 FALSE 2012-09-23T00:00:00 53711
## 4 FALSE 2012-09-23T00:00:00 53711
## 5 FALSE 2012-09-23T00:00:00 53711
## 6 FALSE 2012-09-23T00:00:00 53711
## primary_gen_barcode secondary_gen_barcode_1 secondary_gen_barcode_2
## 1 <NA> <NA> <NA>
## 2 not collected <NA> <NA>
## 3 not collected <NA> <NA>
## 4 not collected <NA> <NA>
## 5 SAS 000521 SAS 000522 SAS 000523
## 6 SAS 000526 SAS 000528 SAS 000529
## secondary_gen_barcode_3 secondary_gen_barcode_4 site_unique
## 1 <NA> <NA> QDAMUL0003-53595
## 2 <NA> <NA> SASMDD0002-53711
## 3 <NA> <NA> SASMDD0002-53711
## 4 <NA> <NA> SASMDD0002-53711
## 5 SAS 000524 SAS 000525 SASMDD0002-53711
## 6 SAS 000527 <NA> SASMDD0002-53711
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head(AP.data$veg.PI)
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## site_location_name site_location_visit_id transect point_number
## 1 WAACOO0006 53438 S1-N1 0
## 2 WAACOO0006 53438 S1-N1 1
## 3 WAACOO0006 53438 S1-N1 2
## 4 WAACOO0006 53438 S1-N1 3
## 5 WAACOO0006 53438 S1-N1 4
## 6 WAACOO0006 53438 S1-N1 5
## veg_barcode herbarium_determination substrate
## 1 <NA> <NA> Crypto
## 2 <NA> <NA> Crypto
## 3 WAA 001053 Melaleuca pauperiflora subsp. fastigiata Litter
## 4 WAA 001053 Melaleuca pauperiflora subsp. fastigiata Litter
## 5 WAA 001053 Melaleuca pauperiflora subsp. fastigiata Litter
## 6 WAA 001053 Melaleuca pauperiflora subsp. fastigiata Litter
## in_canopy_sky dead growth_form height hits_unique site_unique
## 1 NA NA <NA> NA S1-N1 0 WAACOO0006-53438
## 2 NA NA <NA> NA S1-N1 1 WAACOO0006-53438
## 3 FALSE FALSE Shrub 3.5 S1-N1 2 WAACOO0006-53438
## 4 FALSE FALSE Shrub 3.5 S1-N1 3 WAACOO0006-53438
## 5 FALSE FALSE Shrub 3.7 S1-N1 4 WAACOO0006-53438
## 6 FALSE FALSE Shrub 3.5 S1-N1 5 WAACOO0006-53438
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head(AP.data$veg.basal)
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## site_location_name site_location_visit_id site_location_id point_id
## 1 WAACOO0006 53438 59857 NW
## 2 WAACOO0006 53438 59857 NW
## 3 WAACOO0006 53438 59857 NW
## 4 WAACOO0006 53438 59857 N
## 5 WAACOO0006 53438 59857 N
## 6 WAACOO0006 53438 59857 N
## herbarium_determination veg_barcode hits basal_area_factor basal_area
## 1 Eucalyptus moderata WAA 001048 1 0.1 0.10
## 2 Eucalyptus salubris WAA 001083 5 0.1 0.50
## 3 Eucalyptus salubris WAA 001093 7 0.1 0.70
## 4 Eucalyptus moderata WAA 001048 0 0.1 0.00
## 5 Eucalyptus salubris WAA 001083 2 0.1 0.15
## 6 Eucalyptus salubris WAA 001093 4 0.1 0.40
## site_unique
## 1 WAACOO0006-53438
## 2 WAACOO0006-53438
## 3 WAACOO0006-53438
## 4 WAACOO0006-53438
## 5 WAACOO0006-53438
## 6 WAACOO0006-53438
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head(AP.data$struct.summ)
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## site_location_name site_location_visit_id
## 1 QDAMUL0003 53595
## 2 SASMDD0002 53711
## 3 SASMDD0016 57000
## 4 NSAMDD0005 56969
## 5 QDAMUL0001 53594
## 6 NTAGFU0032 53679
## phenology_comment
## 1 Mulga have just finished flowering but no fruit. Tussock grasses mostly dry. Dom hibiscus in ground layer has just finished fruiting throughout the site
## 2 None
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start.time = Sys.time()
AP.data = get_ausplots(veg.vouchers=FALSE, basal.wedge=TRUE)
end.time = Sys.time()
end.time - start.time
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summary(AP.data)
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## Length Class Mode
## site.info 43 data.frame list
## veg.basal 10 data.frame list
## veg.PI 13 data.frame list
## citation 1 -none- character
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dim(AP.data$site.info)
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## [1] 662 43
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dim(AP.data$veg.PI)
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## [1] 734464 13
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