Prepare, Analyze, and Visualize Covid-19 Wastewater Data

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Documentation for package ‘Covid19Wastewater’ version 1.0.1

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Covid19Wastewater-package Covid19Wastewater: A package for running Covid19 wastewater concentration analysis
Aux_info_data Auxiliary data
bagging Bootstrap aggregating of dataset gen a list of dataframes using row resampling and column downsizing
buildCaseAnalysisDF Prep case data into right format
buildRegressionEstimateTable Run DHS analysis at a top level
buildWasteAnalysisDF Convert wastewater_data data to workset4 shape
Case_data Case data
classifyCaseRegression Create Case Flags based on regression slope
classifyQuantileFlagRegression Classify FlagRegression with rolling Quantile info
classifyRegressionAnalysis classifyRegressionAnalysis
computeJumps compute first difference Jumps for N1 and N2
computeRankQuantiles computeRankQuantiles
countFlags Create counts of flag data
Covariants_data Covariants data
Covid19Wastewater Covid19Wastewater: A package for running Covid19 wastewater concentration analysis
createCaseFlag Create Case flags
Data_Description Data Description This package contains a lot of data with many column names, here is a list of them all: [](
date_distance_calc date_distance_calc
date_distance_clamp remove distances above threshold
date_distance_remove remove distances above threshold
DF_date_vector DF_date_vector
Example_data Example data
expand_formula Expand formula for increased info takes a formula with shape A ~ B | C and convert . to its real representation
expSmoothMod expSmoothMod Add a column of the smoothed values using exponential smoothing
factorVecByVec Get ordering for ploting based on factoring vector
flagOutliers Create column with Boolean based on a threshold
Flag_From_Trend Flag values as outliers based on error from estimated trend This function can be done within group if the data fed into it was grouped
gen_INCMSE get increased mean square error for each column
gen_OOB_pred get OOB predictions of the training dataset returns the predictions of each row of the input data using only trees not trained on the row
heatmapcorfunc Outputs a heatmap where the color is the r squared of wastewater data and center day + x many future days and y many past days Helps inform Offset Analysis
HFGCase_data High frequency case data
HFGWaste_data High frequency Waste data
InterceptorCase_data Madison interceptor case data
loessSmoothMod loessSmoothMod Add a column of the smoothed values using Loess
makeQuantileColumns Add many combo of rolling quantile columns to dataframe have info for each quant window combo
OffsetDFMaker Returns a dataframe with the multiple ways to analyze how offset the Wastewater is from cases data
OffsetDF_Plot Given output from OffsetDFMaker returns a 2x3 grid of all the plots with highlighted values
OffsetHeatmap Outputs a heatmap of the offset for variant / time windows and population size / region
OOB_MSE_num_trees get OOB MSE vs number of forest in trees
Pop_data Sewer shed population data
predict-method predict new data from random_linear_forest models
random_linear_forest Fitting linear random forest
random_linear_forest-class random_linear_forest model class using a random forest of linear forest models
rankJumps rankJumps
removeOutliers Add column with NA values where the data was flagged
sgolaySmoothMod sgolaySmoothMod Add a column of the smoothed values using sgolayfilt
show-method display form for random_linear_forest class
summary-method summary method for linear forest class
VariantPlot Shows each variant in proportion to the others in 2 week time periods
WasteWater_data Wastewater data set