Prepare, Analyze, and Visualize Covid-19 Wastewater Data

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Documentation for package ‘Covid19Wastewater’ version 1.0.1

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

Help Pages

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: [https://github.com/UW-Madison-DSI/Covid19Wastewater/blob/main/docs/data/data_columns_discription.md](https://github.com/UW-Madison-DSI/Covid19Wastewater/blob/main/docs/data/data_columns_discription.md)
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