Detecting Environmental Outliers in Data Analysis Pipelines

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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.