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dilp_outliers() is called internally by dilp(). However, it can be used on its own to flag specimens that may have been reported, measured, or prepared incorrectly. dilp_outliers() returns a data frame listing specimens that have unusually high or low values for the four key parameters used in DiLP analyses. This includes whether a specimen is an outlier in the entire dataset, or among other specimens in the same morphotype. If flagged, we suggest looking at the raw measurements and prepped specimen and evaluating if the data is in error or is correct. If in error, the specimen will need to be reprepared and/or remeasured, and the updated datasheet re-read back into R.

Usage

dilp_outliers(specimen_data)

Arguments

specimen_data

Processed specimen level leaf physiognomic data. The structure should match the structure of the output from dilp_processing()

Value

A 4 by X data frame. Each row represents one of the DiLP parameters, and the specimens that are outliers for that parameter.

Examples

# Check for outliers in the provided McAbeeExample dataset. Each
# of these outliers has been manually re-examined and was found acceptable.
dilp_dataset <- dilp_processing(McAbeeExample)
dilp_outliers <- dilp_outliers(dilp_dataset)
#> Warning: Outliers found. Please evaluate $outliers for possible wrong measurements
dilp_outliers
#>         site specimen_number morphotype         outlier         within
#> 1  McAbee H1     BU-712-1117         M8           tc_ip entire dataset
#> 2  McAbee H1    BU-712-1169A         M8           tc_ip entire dataset
#> 3  McAbee H1    BU-712-1176A         M8           tc_ip entire dataset
#> 4  McAbee H2    BU-712-2173A        M18       leaf_area entire dataset
#> 5  McAbee H2    BU-712-2105A        M47       leaf_area entire dataset
#> 6  McAbee H2     BU-712-2124        M94       leaf_area entire dataset
#> 7  McAbee H1      M-2015-1-1        M24 perimeter_ratio entire dataset
#> 8  McAbee H1    BU-712-1073A        M28 perimeter_ratio entire dataset
#> 9  McAbee H1     BU-712-1165        M28 perimeter_ratio entire dataset
#> 10 McAbee H1     M-2015-1-62        M28 perimeter_ratio entire dataset
#> 11 McAbee H1    BU-712-1182A         M5           tc_ip     morphotype
#> 12 McAbee H1      M-2015-1-3         M5           tc_ip     morphotype
#> 13 McAbee H1    BU-712-1182A         M5 perimeter_ratio     morphotype
#> 14 McAbee H1    M-2015-1-122         M5 perimeter_ratio     morphotype
#> 15 McAbee H1      M-2015-1-3         M5 perimeter_ratio     morphotype
#> 16 McAbee H1     M-2015-1-40         M5 perimeter_ratio     morphotype
#> 17 McAbee H1     BU-712-1117         M8           tc_ip     morphotype
#> 18 McAbee H1    BU-712-1169A         M8           tc_ip     morphotype
#> 19 McAbee H1    BU-712-1176A         M8           tc_ip     morphotype
#> 20 McAbee H1     M-2015-1-69         M8 perimeter_ratio     morphotype
#> 21 McAbee H1      M-2015-1-7        M19           tc_ip     morphotype
#> 22 McAbee H2     M-2015-2-15        M19           tc_ip     morphotype
#> 23 McAbee H2     M-2015-2-84        M19           tc_ip     morphotype
#> 24 McAbee H2     BU-712-2197        M19 perimeter_ratio     morphotype
#> 25 McAbee H1      M-2015-1-1        M24 perimeter_ratio     morphotype
#> 26 McAbee H1     M-2015-1-17        M28 perimeter_ratio     morphotype
#> 27 McAbee H1     M-2015-1-62        M28 perimeter_ratio     morphotype