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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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# Obtain the data ('site_info', 'veg.vouchers', and 'veg.PI' are retraived by default)
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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# Explore retrieved data
class(AP.data)

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## [1] "list"

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# 'site_info', 'veg.vouchers', and 'veg.PI' data retrived for Brisbane (27.4698S, 153.0251E) and its sourrounding area
AP.data = get_ausplots(bounding_box=c(152.5, 153.5, -28, -27))

# Explore retrieved data
#class(AP.data)   # As in Example 1 (can run uncommented if curious) 
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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# Default data frames ('site_info', 'veg.vouchers', and 'veg.PI') + 'basal.wedge' + structural_summaries data frames for the genus Eucalyptus
AP.data = get_ausplots(basal.wedge=TRUE, structural_summaries=TRUE, species_name_search="Eucalyptus") 

# Explore retrieved data
#class(AP.data)   # As in Example 1 (can run uncommented if curious) 
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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#str(AP.data)   # Similar to Example 1 (can run uncommented if curious) 

# Explore species contained in each data frame
head(AP.data$veg.vouch) # Includes Records that match 'eucalyptus'

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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)  # Includes Plots where 'eucalyptus' occurs

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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) # Includes Records that match 'eucalyptus'

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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)  # Includes Plots where 'eucalyptus' occurs

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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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# Retreive data
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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# Explore 
#class(AP.data) # As in Example 1 (can run uncommented if curious) 
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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# Explore 'site_info' data
dim(AP.data$site.info)

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## [1] 662  43

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# Explore 'veg_PI' data
dim(AP.data$veg.PI)

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## [1] 734464     13

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