# Detecting Environmental Outliers in Data Analysis Pipelines

## Documentation for package ‘specleanr’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

abdata | Alburnoides bipunctatus species data from GBIF and iNaturalist
adjustboxplots | Adjust the boxplots bounding fences using medcouple to flag suspicious outliers.
bestmethod | Identifies the best method for outlier detection for a single species.
boots | To implement bootstrapping procedures. Sampling with replacement.
broad_classify | Outlier detection method broad classification.
check.exclude | indicate excluded columns.
checks | Post checks for PCA and bootstrapping
check_names | Check species names for inconsistencies
check_packages | Check for packages to install and respond to use
classify_data | Extract final clean data using either absolute or best method generated outliers.
cosine | Cosine similarity index based on (Gautam & Kulkarni 2014; Joy & Renumol 2020)
datacleaner-class | Outlier detection class for multiple methods
distboxplot | Distribution boxplot
ecological_ranges | Check for environmental outliers using species optimal ranges.
efidata | EFIPLUS data used to develop ecological sensitivity parameters for riverine species in European streams and rivers.
eif | Computes the empirical influence function for each values in the dataset
extentvalues | To check for a bounding box
extractMethods | List of outlier detection methods implemented in this package.
extractoutliers | Extract outliers for a one species
extract_clean_data | Extract final clean data using either absolute or best method generated outliers.
geo_ranges | Checks for geographic ranges from FishBase
getdata | Download species records from online database.
getdiff | get dataframe from the large dataframe.
ggenvironmentalspace | Title Plotting to show the quality controlled data in environmental space.
ggoutlieraccum | Identify if enough methods are selected for the outlier detection.
ggoutliers | Visualize the outliers identified by each method
hamming | Identify best outlier detection method using Hamming distance.
hampel | Flag suspicious outliers based on the Hampel filter method..
handle_true_errors | Catch errors during methods implementation.
interquartile | Computes interquartile range to flag environmental outliers
isoforest | Identify outliers using isolation forest model.
jaccard | Identifies the best outlier detection method using Jaccard coefficient.
jdsdata | Joint Danube Survey Data
jknife | Identifies outliers using Reverse Jackknifing method based on Chapman et al., (2005).
kdat | Sequential fences constants
logboxplot | Log boxplot based for outlier detection.
mahal | Flags outliers based on Mahalanobis distance matrix for all records.
match.argc | Customized match function
match_datasets | Data harmonizing for offline data based on Darwin Core terms .
medianrule | Median rule method
mixediqr | Mixed Interquartile range and semiInterquartile range 'Walker et al., 2018'
mth | mth datasets with constant at each confidence interval levels.
multiabsolute | Identifies absolute outliers for multiple species.
multibestmethod | Identify best method for outlier removal for multiple species using majority votes.
multidetect | Ensemble multiple outlier detection methods.
ocindex | Identifies absolute outliers and their proportions for a single species.
onesvm | Identify outliers using One Class Support Vector Machines
optimal_threshold | Optimize threshold for clean data extraction.
overlap | Identifies best outlier detection method using Overlap coefficient.
pca | Implement principal component analysis for dimension reduction
pcboot | To package both principal component analysis and bootstrapping.
pred_extract | Preliminary data cleaning including removing duplicates, records outside a particular basin, and NAs.
search_threshold | Determine the threshold using Locally estimated or weighted Scatterplot Smoothing.
semiIQR | Computes semi-interquantile range to flag suspicious outliers
seqfences | Sequential fences method
show-method | set method for displaying output details after outlier detection.
smc | Identify best outlier detection method using simple matching coefficient.
sorensen | Identifies best outlier detection method suing Sorensen Similarity Index.
thermal_ranges | Collates minimum, maximum, and preferable temperatures from FishBase.
ttdata | Thymallus thymallus species data from GBIF and iNaturalist
xglosh | Global-Local Outlier Score from Hierarchies
xkmeans | Flags outliers using kmeans clustering method
xknn | k-nearest neighbors for outlier detection
xlof | Flags suspicious using the local outlier factor or Density-Based Spatial Clustering of Applications with Noise.
zscore | Computes z-scores to flag environmental outliers.