Join WQP data to criteria and spatial MLSummaryRef (UNDER ACTIVE DEVELOPMENT) — TADA_Analysis_Join_WQP

Join WQP results to a criteria table by the best available key:

TADA.ComparableDataIdentifier (if present in both and non-NA in criteria)
TADA.CharacteristicName + TADA.ResultSampleFractionText + TADA.MethodSpeciationName
TADA.CharacteristicName + TADA.ResultSampleFractionText
TADA.CharacteristicName + TADA.MethodSpeciationName
TADA.CharacteristicName (or when byChar = TRUE)

Usage

TADA_Analysis_Join_WQP_Criteria(
  .data,
  criteria,
  byChar = FALSE,
  MLSummaryRef = NULL
)

Arguments

.data: A TADA data frame.
criteria: data.frame of TADA compatible criteria table for any of either TADA.ComparableDataIdentifier and a combination of TADA.CharacteristicName, TADA.ResultSampleFractionText, and TADA.MethodSpeciationName
byChar: A boolean value. If byChar = TRUE, this function will join the WQP data frame with the criteria table by only CharacteristicName, regardless of what has been filled out in the criteria table.
MLSummaryRef: An optional data frame which contains the completed spatial crosswalk to assign any unique spatial criteria to a parameter, use, waterbody or monitoring site/assessment unit. This table is populated based on the inputs from the users and their desired level of analysis. If provided the data frame must contain these columns: "ATTAINS.OrganizationIdentifier", "ATTAINS.AssessmentUnitIdentifier", "MonitoringLocationIdentifier", "MonitoringLocationTypeName", "TADA.ComparableDataIdentifier", "ATTAINS.ParameterName", "ATTAINS.UseName", "ATTAINS.WaterType", "SaltFresh", "DepthCategory", "LongitudeMeasure", "LatitudeMeasure", "IncludeOrExclude" and "UniqueSpatialCriteria".

Value

data.frame with WQP rows and matching criteria columns.

Details

For each fallback pass, rows with NA in any of the pass keys are dropped from both inputs for that pass. Left-join semantics are preserved overall.

When MLSummaryRef is provided (optional), this function first joins the WQP .data to the MLSummaryRef by MonitoringLocationIdentifier. NOTE: MLSummaryRef is in active development and joins the ref tables of the spatial summary, parameters and uses for analysis.

Examples

# load example data.frame
utils::data("Data_MT_MissoulaCounty", package = "EPATADA")
MT_data <- Data_MT_MissoulaCounty

# load example criteria table from community hub
criteria_MT <- EPATADA::TADA_GetCriteriaFile(org_id = "MTDEQ")

# join the table by best match from what is filled out from the criteria table
MT_data_criteria <- TADA_Analysis_Join_WQP_Criteria(MT_data, criteria_MT)
#> Your *user supplied* criteriaMethods data is missing 1 unique TADA.ComparableDataIdentifier(s):
#> 
#>   PH_NONE_NONE_NONE
#> 
#> without criteria information filled out. Please review if these entries are applicable to your analysis,
#> or ignore this message if they are not relevant.
#> Warning: No MLSummaryRef was provided, but spatial columns contain values in the criteria table: SaltFresh, UniqueSpatialCriteria. Cannot differentiate which monitoring location sites belong to any of these spatial columns. Please create the MLSummaryRef to define the sites that are applicable to these spatial columns.

# create the MLSummaryRef from params and uses
# first define param crosswalk
params <- TADA_ParametersForAnalysis(
  Data_MT_MissoulaCounty, org_id = "MTDEQ", auto_assign = "Org")
#> TADA_ParametersForAnalysis: auto_assign == 'Org' was selected, finding an alias ATTAINS.ParameterName match, by ATTAINS.OrganizationName, for each TADA.ComparableDataIdentifier - by WQP CharacteristicName if one is found.

# define uses crosswalk
uses <- TADA_UsesForAnalysis(Data_MT_MissoulaCounty,
 org_id = "MTDEQ", paramRef = params, auto_assign = TRUE)
#> TADA_UsesForAnalysis: auto_assign == TRUE was selected, 

#>   assigning all unique ATTAINS.UseName, by ATTAINS.OrganizationIdentifier, to any ATTAINS.ParameterName that an 

#>   organization have not done assessments for in prior ATTAINS cycle. Please review carefully and Exclude rows as needed.

mlsummary <- TADA_MLSummary(
  Data_MT_MissoulaCounty,
  org_id = "MTDEQ",
  AUMLRef = Data_MT_AUMLRef$ATTAINS_crosswalk,
  AU_UsesRef = Data_MT_AU_UsesRef_Water,
  usesRef = uses)
#> TADA_MLSummary: displayNA = FALSE was selected.

# join the table by best match, along with the MLSummaryRef
MT_data_criteria2 <- TADA_Analysis_Join_WQP_Criteria(
  MT_data,
  criteria_MT,
  MLSummaryRef = mlsummary)
#> Your *user supplied* criteriaMethods data is missing 1 unique TADA.ComparableDataIdentifier(s):
#> 
#>   PH_NONE_NONE_NONE
#> 
#> without criteria information filled out. Please review if these entries are applicable to your analysis,
#> or ignore this message if they are not relevant.
#> - Unmatched row(s) for these TADA.CharacteristicName or TADA.ComparableDataIdentifier values in the criteria table could not be joined to WQP data or MLSummaryRef. Correct any missing spatial definitions in MLSummaryRef or correct for any mismatched characteristic, fraction, speciation, or unit values in the criteria table, MLSummaryRef, or WQP data. Only matching values can be analyzed:
#> 
#> - TADA.ComparableDataIdentifier = ESCHERICHIA COLI_NONE_NONE_CFU/100ML for 
#>   * SECONDARY CONTACT RECREATION not found in column: 'ATTAINS.UseName'
#>   * FRESH not found in column: 'SaltFresh'
#>   * CLASSES A-1 AND A-CLOSED not found in column: 'UniqueSpatialCriteria'
#>   * CLASSES B AND C not found in column: 'UniqueSpatialCriteria'
#>   * CLASSES D, E AND F not found in column: 'UniqueSpatialCriteria'