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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summary(AP.data)
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## Length Class Mode
## site.info 43 data.frame list
## struct.summ 15 data.frame list
## soil.subsites 12 data.frame list
## soil.bulk 15 data.frame list
## soil.char 34 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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str(AP.data)
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## List of 9
## $ site.info :'data.frame': 4 obs. of 43 variables:
## ..$ site_location_name : chr [1:4] "QDAMGD0022" "SATFLB0004" "SATFLB0004" "NTASTU0002"
## ..$ established_date : chr [1:4] "2013-06-04T00:00:00" "2012-09-18T00:00:00" "2012-09-18T00:00:00" "2016-05-01T16:58:00"
## ..$ description : chr [1:4] "Mackunda Downs Station, 500m east of homestead. 26km west of Middleton." "Brachina Gorge Heysen Range Lower. 63km North North East of Adelaide" "Brachina Gorge Heysen Range Lower. 63km North North East of Adelaide" "Maryfield Station, 7.6km north north west of homestead. 27.5km south east of Larrimah"
## ..$ bioregion_name : chr [1:4] "MGD" "FLB" "FLB" "STU"
## ..$ landform_pattern : chr [1:4] "ALP" "MOU" "MOU" "PLA"
## ..$ landform_element : chr [1:4] "PLA" "HSL" "HSL" "PLA"
## ..$ site_slope : chr [1:4] "1" "17" "17" "0"
## ..$ site_aspect : chr [1:4] "180" "225" "225" NA
## ..$ comments : chr [1:4] "Astrebla pectinata / Cenchrus ciliaris / Astrebla elymoides low open tussock grassland on alluvial plain adjoin"| __truncated__ "Grazing impact high- goat tracks and droppings. Rabbit droppings also.
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Example 2: Default data for a particular Geographic Extent
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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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Example 3: 'Default data' + 'basal.wedge' + 'structural_summaries' for the genus Eucalyptus
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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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Example 4: 'site_info', 'veg.PI', and 'basal.wedge' data for all sites
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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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## Time difference of 1.126162 mins
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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$site.info)
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## [1] 662 43
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names(AP.data$site.info)
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## [1] "site_location_name" "established_date"
## [3] "description" "bioregion_name"
## [5] "landform_pattern" "landform_element"
## [7] "site_slope" "site_aspect"
## [9] "comments" "outcrop_lithology"
## [11] "other_outcrop_lithology" "plot_dimensions"
## [13] "site_location_visit_id" "visit_start_date"
## [15] "visit_end_date" "visit_notes"
## [17] "location_description" "erosion_type"
## [19] "erosion_abundance" "erosion_state"
## [21] "microrelief" "drainage_type"
## [23] "disturbance" "climatic_condition"
## [25] "vegetation_condition" "observer_veg"
## [27] "observer_soil" "described_by"
## [29] "pit_marker_easting" "pit_marker_northing"
## [31] "pit_marker_mga_zones" "pit_marker_datum"
## [33] "pit_marker_location_method" "soil_observation_type"
## [35] "a_s_c" "plot_is_100m_by_100m"
## [37] "plot_is_aligned_to_grid" "plot_is_permanently_marked"
## [39] "latitude" "longitude"
## [41] "point" "state"
## [43] "site_unique"
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head(AP.data$site.info)
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## site_location_name established_date
## 1 WAANUL0007 2014-09-06T15:24:41
## 2 NTAFIN0031 2012-10-25T00:00:00
## 3 QDAMUL0003 2013-04-26T00:00:00
## 4 NTAFIN0004 2011-10-06T00:00:00
## 5 NTAFIN0004 2011-10-06T00:00:00
## 6 SASMDD0002 2012-09-23T00:00:00
## description
## 1 Great Victoria Desert Nature Reserve, 102.2km south east of Tjuntjuntjara
## 2 Umbeara Station 26.5km South East of Umbeara Homestead. 11km North of SA/Not Border
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dim(AP.data$veg.PI)
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## [1] 734464 13
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names(AP.data$veg.PI)
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## [1] "site_location_name" "site_location_visit_id"
## [3] "transect" "point_number"
## [5] "veg_barcode" "herbarium_determination"
## [7] "substrate" "in_canopy_sky"
## [9] "dead" "growth_form"
## [11] "height" "hits_unique"
## [13] "site_unique"
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head(AP.data$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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