R/globalVariables.R

In fawda123/ASCI: Calculate scores for the Algal Stream Condition Index

globalVariables(
  c(
    'STE', 'Class', 'acast', 'mmilkup', 'SampleTypeCode', 'Phylum', 'Result', 'ComboResult',
    'melt', 'value', 'specnumber', 'ddply', 'summarize', 'stations', 'diversity',
    'SampleID', 'met', 'name', 'pnorm', 
    'results', 'sd', 'taxa', 'val', '.', 'SampleID_raw', 'mets', 'rfmods', 
    'MMI', 'MMI_Percentile',
    'Replicate', 'SampleDate', 'StationCode', 'BAResult', 'RefCalMean',
    'diaind', 'variable', 'FinalIDassigned', 'StationID', 'ave', 'cls', 'data', 'fst', 'grp', 
    'ind', 'lm', 'mmi', 'prc_amg', 'prc_wth', 'psa', 'res_tst', 'rfmod', 'scr.x', 
    'scr.y', 'typ', 'metest', 'Assemblage', 'rowname', 'Metric', 'FinalID', 'Met', 'Value',
    'grouped_id', 'scores', 'D_ASCI', 'D_NumberTaxa',
    'D_ValveCount', 'H_ASCI', 'H_NumberTaxa', 'S_ASCI', 'S_Biovolume', 'S_EntityCount',
    'S_NumberTaxa', 'SampleType', 'UnrecognizedTaxa', 
    
    # traits 
    'NitrogenUptakeMetabolism',
    'OxygenRequirements', 
    'Salinity', 
    'Saprobity', 
    'TrophicState', 
    'Genus', 
    'Motility', 
    'designation', 
    'Salinity2', 
    'ZHR', 
    'CRUS', 
    'Green', 'BCG', 'BCG12', 'BCG45', 'CRUS', 'IndicatorClass_TP', 'IndicatorClass_Cu', 
    'IndicatorClass_DOC', 'IndicatorClass_Ref', 'IndicatorClass_TN', 'Heterocystous', 
    'NitrogenUptakeMetabolism2','Habitat', 
    
    # metrics 
    "cnt.spp.most.tol", "cnt.spp.most.tol_raw", "cnt.spp.most.tol_pred",
    "EpiRho.richness", "EpiRho.richness_raw", "EpiRho.richness_pred",
    "prop.spp.IndicatorClass_TN_low", "prop.spp.IndicatorClass_TN_low_raw", "prop.spp.IndicatorClass_TN_low_pred",
    "Salinity.BF.richness", "Salinity.BF.richness_raw","Salinity.BF.richness_pred",
    "cnt.spp.IndicatorClass_TP_high", "cnt.spp.IndicatorClass_TP_high_raw", "cnt.spp.IndicatorClass_TP_high_pred",
    "OxyRed.DO_30.richness", "OxyRed.DO_30.richness_raw","OxyRed.DO_30.richness_pred",
    "prop.spp.Planktonic", "prop.spp.Planktonic_raw","prop.spp.Planktonic_pred",
    "prop.spp.Trophic.E", "prop.spp.Trophic.E_raw", "prop.spp.Trophic.E_pred",
    "prop.spp.ZHR_raw",
    "Salinity.BF.richness", "Salinity.BF.richness_raw", "Salinity.BF.richness_pred",
    "prop.spp.IndicatorClass_DOC_high_raw",
    "prop.spp.IndicatorClass_NonRef_raw",
    "prop.spp.IndicatorClass_TP_high_raw",
    "prop.spp.ZHR_raw", 
    "richness",

    # GIS Predictors
    "AREA_SQKM","AtmCa","CondQR50","SITE_ELEV","TMAX_WS","XerMtn",
    "KFCT_AVE","PPT_00_09","MAX_ELEV",

    # Other various column names that show up in strings of dplyr pipes
    # and Travis wants to see them show up in this file
    "Score", "Metric", "Metric_Type", "Used for ASCI"

  )
)

#' @importFrom stats ave lm na.omit pnorm predict runif sd t.test var
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#' @importFrom utils data tail
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#' @importFrom methods .S4methods new
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