geo_ranges

Checks for geographic ranges from FishBase

A framework used to detect and handle outliers during data analysis workflows. Outlier detection is a statistical concept with applications in data analysis workflows, highlighting records that are suspiciously high or low. Outlier detection in distribution models was initiated by Chapman (1991) (available at <https://www.researchgate.net/publication/332537800_Quality_control_and_validation_of_point-sourced_environmental_resource_data>), who developed the reverse jackknifing method. The concept was further developed and incorporated into different R packages, including 'flexsdm' (Velazco et al., 2022, <doi:10.1111/2041-210X.13874>) and 'biogeo' (Robertson et al., 2016 <doi:10.1111/ecog.02118>). We compiled various outlier detection methods obtained from the literature, including those elaborated in Dastjerdy et al. (2023) <doi:10.3390/geotechnics3020022> and Liu et al. (2008) <doi:10.1109/ICDM.2008.17>. In this package, we introduced the ensembling aspect, where multiple outlier detection methods are used to flag the record as either an absolute outlier. The concept can also be applied in general data analysis, as well as during the development of species distribution models.

Anthony Basooma

specleanr

Detecting Environmental Outliers in Data Analysis Pipelines

Thomas Hein

Astrid Schmidt-Kloiber

Merret Buurman

Sami Domisch

Martin Tschikof

Florian Borgwardt

geo_ranges function

<dl><dt>data</dt>
<dd>Dataframe or vector to retrieve ranges from FishBase.</dd>
<dt>colsp</dt>
<dd>Column with species names from the data set.</dd>
<dt>verbose</dt>
<dd>TRUE and messages will show. Default FALSE:</dd>
<dt>pct</dt>
<dd>The percentage similarity of species names during standardization from FishBase.</dd>
<dt>sn</dt>
<dd>TRUE and synonyms will be generated and not accepted ones. Default is FALSE, where species accepted names will be produced.</dd>
<dt>warn</dt>
<dd>FALSE, not to generate warnings and TRUE for warnings. Default is FALSE:</dd>
<dt>synonym</dt>
<dd>A standard database for species synonym names from FishBase. See <a href="https://www.fishbase.se/">FishBase</a> for more information.</dd>
<dt>ranges</dt>
<dd>A standard database for ecological ranges from FishBase. See <a href="https://www.fishbase.se/">FishBase</a> for more information.</dd></dl>

Arguments

Checks for geographic ranges from FishBase — geo_ranges

<dl>

<dt>data</dt>
<dd>Dataframe or vector to retrieve ranges from FishBase.</dd>


<dt>colsp</dt>
<dd>Column with species names from the data set.</dd>


<dt>verbose</dt>
<dd>TRUE and messages will show. Default FALSE:</dd>


<dt>pct</dt>
<dd>The percentage similarity of species names during standardization from FishBase.</dd>


<dt>sn</dt>
<dd>TRUE and synonyms will be generated and not accepted ones. Default is FALSE, where species accepted names will be produced.</dd>


<dt>warn</dt>
<dd>FALSE, not to generate warnings and TRUE for warnings. Default is FALSE:</dd>


<dt>synonym</dt>
<dd>A standard database for species synonym names from FishBase. See <a href='https://www.fishbase.se/'>FishBase</a> for more information.</dd>


<dt>ranges</dt>
<dd>A standard database for ecological ranges from FishBase. See <a href='https://www.fishbase.se/'>FishBase</a> for more information.</dd>

</dl>

geo_ranges: Checks for geographic ranges from FishBase

Description

Usage

Value

Arguments

Examples