Score samples using the ASCI tool
ASCI(taxa, stations)
| taxa |
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| stations |
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A dataframe with all metrics calculated for each provided taxa
One index for three taxonomy types are scored, MMI for diatoms, soft-bodied algae, and hybrid. If only soft-bodied algae or diatoms are present, only the respective ASCI and metrics are returned.
# calculate all ASCI(demo_algae_tax, demo_station)#> # A tibble: 3 x 109 #> SampleID StationCode SampleDate Replicate SampleType D_ValveCount #> <chr> <chr> <dttm> <dbl> <chr> <int> #> 1 404M073… 404M07357 2016-06-13 00:00:00 1 Integrate… 600 #> 2 801M169… 801M16916 2016-05-25 00:00:00 1 Microalga… 600 #> 3 909M249… 909M24937 2016-06-22 00:00:00 1 Macroalga… 600 #> # … with 103 more variables: S_EntityCount <int>, S_Biovolume <dbl>, #> # D_NumberTaxa <int>, S_NumberTaxa <int>, H_NumberTaxa <int>, #> # UnrecognizedTaxa <chr>, D_ASCI <dbl>, S_ASCI <dbl>, H_ASCI <dbl>, #> # D_cnt.spp.most.tol_mod <dbl>, D_cnt.spp.most.tol_mod_scr <dbl>, #> # D_cnt.spp.most.tol_pct_att <dbl>, D_cnt.spp.most.tol_pred <dbl>, #> # D_cnt.spp.most.tol_raw <int>, D_cnt.spp.most.tol_raw_scr <dbl>, #> # D_EpiRho.richness_mod <dbl>, D_EpiRho.richness_mod_scr <dbl>, #> # D_EpiRho.richness_pct_att <dbl>, D_EpiRho.richness_pred <dbl>, #> # D_EpiRho.richness_raw <int>, D_EpiRho.richness_raw_scr <dbl>, #> # D_prop.spp.IndicatorClass_TN_low_mod <dbl>, #> # D_prop.spp.IndicatorClass_TN_low_mod_scr <dbl>, #> # D_prop.spp.IndicatorClass_TN_low_pct_att <dbl>, #> # D_prop.spp.IndicatorClass_TN_low_pred <dbl>, #> # D_prop.spp.IndicatorClass_TN_low_raw <dbl>, #> # D_prop.spp.IndicatorClass_TN_low_raw_scr <dbl>, #> # D_prop.spp.Planktonic_mod <dbl>, D_prop.spp.Planktonic_mod_scr <dbl>, #> # D_prop.spp.Planktonic_pct_att <dbl>, D_prop.spp.Planktonic_pred <dbl>, #> # D_prop.spp.Planktonic_raw <dbl>, D_prop.spp.Planktonic_raw_scr <dbl>, #> # D_prop.spp.Trophic.E_mod <dbl>, D_prop.spp.Trophic.E_mod_scr <dbl>, #> # D_prop.spp.Trophic.E_pct_att <dbl>, D_prop.spp.Trophic.E_pred <dbl>, #> # D_prop.spp.Trophic.E_raw <dbl>, D_prop.spp.Trophic.E_raw_scr <dbl>, #> # D_Salinity.BF.richness_mod <dbl>, D_Salinity.BF.richness_mod_scr <dbl>, #> # D_Salinity.BF.richness_pct_att <dbl>, D_Salinity.BF.richness_pred <dbl>, #> # D_Salinity.BF.richness_raw <int>, D_Salinity.BF.richness_raw_scr <dbl>, #> # S_prop.spp.IndicatorClass_DOC_high_raw_pct_att <dbl>, #> # S_prop.spp.IndicatorClass_DOC_high_raw_raw <dbl>, #> # S_prop.spp.IndicatorClass_NonRef_pct_att <dbl>, #> # S_prop.spp.IndicatorClass_NonRef_raw <dbl>, #> # S_prop.spp.IndicatorClass_NonRef_raw_scr <dbl>, #> # S_prop.spp.IndicatorClass_TP_high_pct_att <dbl>, #> # S_prop.spp.IndicatorClass_TP_high_raw <dbl>, #> # S_prop.spp.IndicatorClass_TP_high_raw_scr <dbl>, #> # S_prop.spp.ZHR_pct_att <dbl>, S_prop.spp.ZHR_raw <dbl>, #> # S_prop.spp.ZHR_raw_scr <dbl>, H_cnt.spp.IndicatorClass_TP_high_mod <dbl>, #> # H_cnt.spp.IndicatorClass_TP_high_mod_scr <dbl>, #> # H_cnt.spp.IndicatorClass_TP_high_pct_att <dbl>, #> # H_cnt.spp.IndicatorClass_TP_high_pred <dbl>, #> # H_cnt.spp.IndicatorClass_TP_high_raw <int>, #> # H_cnt.spp.IndicatorClass_TP_high_raw_scr <dbl>, #> # H_cnt.spp.most.tol_mod <dbl>, H_cnt.spp.most.tol_mod_scr <dbl>, #> # H_cnt.spp.most.tol_pct_att <dbl>, H_cnt.spp.most.tol_pred <dbl>, #> # H_cnt.spp.most.tol_raw <int>, H_cnt.spp.most.tol_raw_scr <dbl>, #> # H_EpiRho.richness_mod <dbl>, H_EpiRho.richness_mod_scr <dbl>, #> # H_EpiRho.richness_pct_att <dbl>, H_EpiRho.richness_pred <dbl>, #> # H_EpiRho.richness_raw <int>, H_EpiRho.richness_raw_scr <dbl>, #> # H_OxyRed.DO_30.richness_mod <dbl>, H_OxyRed.DO_30.richness_mod_scr <dbl>, #> # H_OxyRed.DO_30.richness_pct_att <dbl>, H_OxyRed.DO_30.richness_pred <dbl>, #> # H_OxyRed.DO_30.richness_raw <int>, H_OxyRed.DO_30.richness_raw_scr <dbl>, #> # H_prop.spp.Planktonic_mod <dbl>, H_prop.spp.Planktonic_mod_scr <dbl>, #> # H_prop.spp.Planktonic_pct_att <dbl>, H_prop.spp.Planktonic_pred <dbl>, #> # H_prop.spp.Planktonic_raw <dbl>, H_prop.spp.Planktonic_raw_scr <dbl>, #> # H_prop.spp.Trophic.E_mod <dbl>, H_prop.spp.Trophic.E_mod_scr <dbl>, #> # H_prop.spp.Trophic.E_pct_att <dbl>, H_prop.spp.Trophic.E_pred <dbl>, #> # H_prop.spp.Trophic.E_raw <dbl>, H_prop.spp.Trophic.E_raw_scr <dbl>, #> # H_prop.spp.ZHR_pct_att <dbl>, H_prop.spp.ZHR_raw <dbl>, #> # H_prop.spp.ZHR_raw_scr <dbl>, H_Salinity.BF.richness_mod <dbl>, #> # H_Salinity.BF.richness_mod_scr <dbl>, H_Salinity.BF.richness_pct_att <dbl>, #> # H_Salinity.BF.richness_pred <dbl>, H_Salinity.BF.richness_raw <int>, …# works if either soft-bodied or diatoms are missing # remove diatoms from station sample 909M24937 tmp <- subset(demo_algae_tax, !(StationCode == '909M24937' & SampleTypeCode == 'Integrated')) ASCI(tmp, demo_station)#> Warning: Only diatom or soft-bodied algae present at sites: 909M24937_2016-06-22_1#> # A tibble: 2 x 109 #> SampleID StationCode SampleDate Replicate SampleType D_ValveCount #> <chr> <chr> <dttm> <dbl> <chr> <int> #> 1 404M073… 404M07357 2016-06-13 00:00:00 1 Integrate… 600 #> 2 801M169… 801M16916 2016-05-25 00:00:00 1 Microalga… 600 #> # … with 103 more variables: S_EntityCount <int>, S_Biovolume <dbl>, #> # D_NumberTaxa <int>, S_NumberTaxa <int>, H_NumberTaxa <int>, #> # UnrecognizedTaxa <chr>, D_ASCI <dbl>, S_ASCI <dbl>, H_ASCI <dbl>, #> # D_cnt.spp.most.tol_mod <dbl>, D_cnt.spp.most.tol_mod_scr <dbl>, #> # D_cnt.spp.most.tol_pct_att <dbl>, D_cnt.spp.most.tol_pred <dbl>, #> # D_cnt.spp.most.tol_raw <int>, D_cnt.spp.most.tol_raw_scr <dbl>, #> # D_EpiRho.richness_mod <dbl>, D_EpiRho.richness_mod_scr <dbl>, #> # D_EpiRho.richness_pct_att <dbl>, D_EpiRho.richness_pred <dbl>, #> # D_EpiRho.richness_raw <int>, D_EpiRho.richness_raw_scr <dbl>, #> # D_prop.spp.IndicatorClass_TN_low_mod <dbl>, #> # D_prop.spp.IndicatorClass_TN_low_mod_scr <dbl>, #> # D_prop.spp.IndicatorClass_TN_low_pct_att <dbl>, #> # D_prop.spp.IndicatorClass_TN_low_pred <dbl>, #> # D_prop.spp.IndicatorClass_TN_low_raw <dbl>, #> # D_prop.spp.IndicatorClass_TN_low_raw_scr <dbl>, #> # D_prop.spp.Planktonic_mod <dbl>, D_prop.spp.Planktonic_mod_scr <dbl>, #> # D_prop.spp.Planktonic_pct_att <dbl>, D_prop.spp.Planktonic_pred <dbl>, #> # D_prop.spp.Planktonic_raw <dbl>, D_prop.spp.Planktonic_raw_scr <dbl>, #> # D_prop.spp.Trophic.E_mod <dbl>, D_prop.spp.Trophic.E_mod_scr <dbl>, #> # D_prop.spp.Trophic.E_pct_att <dbl>, D_prop.spp.Trophic.E_pred <dbl>, #> # D_prop.spp.Trophic.E_raw <dbl>, D_prop.spp.Trophic.E_raw_scr <dbl>, #> # D_Salinity.BF.richness_mod <dbl>, D_Salinity.BF.richness_mod_scr <dbl>, #> # D_Salinity.BF.richness_pct_att <dbl>, D_Salinity.BF.richness_pred <dbl>, #> # D_Salinity.BF.richness_raw <int>, D_Salinity.BF.richness_raw_scr <dbl>, #> # S_prop.spp.IndicatorClass_DOC_high_raw_pct_att <dbl>, #> # S_prop.spp.IndicatorClass_DOC_high_raw_raw <dbl>, #> # S_prop.spp.IndicatorClass_NonRef_pct_att <dbl>, #> # S_prop.spp.IndicatorClass_NonRef_raw <dbl>, #> # S_prop.spp.IndicatorClass_NonRef_raw_scr <dbl>, #> # S_prop.spp.IndicatorClass_TP_high_pct_att <dbl>, #> # S_prop.spp.IndicatorClass_TP_high_raw <dbl>, #> # S_prop.spp.IndicatorClass_TP_high_raw_scr <dbl>, #> # S_prop.spp.ZHR_pct_att <dbl>, S_prop.spp.ZHR_raw <dbl>, #> # S_prop.spp.ZHR_raw_scr <dbl>, H_cnt.spp.IndicatorClass_TP_high_mod <dbl>, #> # H_cnt.spp.IndicatorClass_TP_high_mod_scr <dbl>, #> # H_cnt.spp.IndicatorClass_TP_high_pct_att <dbl>, #> # H_cnt.spp.IndicatorClass_TP_high_pred <dbl>, #> # H_cnt.spp.IndicatorClass_TP_high_raw <int>, #> # H_cnt.spp.IndicatorClass_TP_high_raw_scr <dbl>, #> # H_cnt.spp.most.tol_mod <dbl>, H_cnt.spp.most.tol_mod_scr <dbl>, #> # H_cnt.spp.most.tol_pct_att <dbl>, H_cnt.spp.most.tol_pred <dbl>, #> # H_cnt.spp.most.tol_raw <int>, H_cnt.spp.most.tol_raw_scr <dbl>, #> # H_EpiRho.richness_mod <dbl>, H_EpiRho.richness_mod_scr <dbl>, #> # H_EpiRho.richness_pct_att <dbl>, H_EpiRho.richness_pred <dbl>, #> # H_EpiRho.richness_raw <int>, H_EpiRho.richness_raw_scr <dbl>, #> # H_OxyRed.DO_30.richness_mod <dbl>, H_OxyRed.DO_30.richness_mod_scr <dbl>, #> # H_OxyRed.DO_30.richness_pct_att <dbl>, H_OxyRed.DO_30.richness_pred <dbl>, #> # H_OxyRed.DO_30.richness_raw <int>, H_OxyRed.DO_30.richness_raw_scr <dbl>, #> # H_prop.spp.Planktonic_mod <dbl>, H_prop.spp.Planktonic_mod_scr <dbl>, #> # H_prop.spp.Planktonic_pct_att <dbl>, H_prop.spp.Planktonic_pred <dbl>, #> # H_prop.spp.Planktonic_raw <dbl>, H_prop.spp.Planktonic_raw_scr <dbl>, #> # H_prop.spp.Trophic.E_mod <dbl>, H_prop.spp.Trophic.E_mod_scr <dbl>, #> # H_prop.spp.Trophic.E_pct_att <dbl>, H_prop.spp.Trophic.E_pred <dbl>, #> # H_prop.spp.Trophic.E_raw <dbl>, H_prop.spp.Trophic.E_raw_scr <dbl>, #> # H_prop.spp.ZHR_pct_att <dbl>, H_prop.spp.ZHR_raw <dbl>, #> # H_prop.spp.ZHR_raw_scr <dbl>, H_Salinity.BF.richness_mod <dbl>, #> # H_Salinity.BF.richness_mod_scr <dbl>, H_Salinity.BF.richness_pct_att <dbl>, #> # H_Salinity.BF.richness_pred <dbl>, H_Salinity.BF.richness_raw <int>, …# works if either soft-bodied or diatoms are missing # remove soft-bodied from station sample 801M16916 tmp <- subset(demo_algae_tax, !(StationCode == '801M16916' & SampleTypeCode != 'Integrated')) ASCI(tmp, demo_station)#> Warning: Only diatom or soft-bodied algae present at sites: 801M16916_2016-05-25_1#> # A tibble: 2 x 109 #> SampleID StationCode SampleDate Replicate SampleType D_ValveCount #> <chr> <chr> <dttm> <dbl> <chr> <int> #> 1 404M073… 404M07357 2016-06-13 00:00:00 1 Integrate… 600 #> 2 909M249… 909M24937 2016-06-22 00:00:00 1 Macroalga… 600 #> # … with 103 more variables: S_EntityCount <int>, S_Biovolume <dbl>, #> # D_NumberTaxa <int>, S_NumberTaxa <int>, H_NumberTaxa <int>, #> # UnrecognizedTaxa <chr>, D_ASCI <dbl>, S_ASCI <dbl>, H_ASCI <dbl>, #> # D_cnt.spp.most.tol_mod <dbl>, D_cnt.spp.most.tol_mod_scr <dbl>, #> # D_cnt.spp.most.tol_pct_att <dbl>, D_cnt.spp.most.tol_pred <dbl>, #> # D_cnt.spp.most.tol_raw <int>, D_cnt.spp.most.tol_raw_scr <dbl>, #> # D_EpiRho.richness_mod <dbl>, D_EpiRho.richness_mod_scr <dbl>, #> # D_EpiRho.richness_pct_att <dbl>, D_EpiRho.richness_pred <dbl>, #> # D_EpiRho.richness_raw <int>, D_EpiRho.richness_raw_scr <dbl>, #> # D_prop.spp.IndicatorClass_TN_low_mod <dbl>, #> # D_prop.spp.IndicatorClass_TN_low_mod_scr <dbl>, #> # D_prop.spp.IndicatorClass_TN_low_pct_att <dbl>, #> # D_prop.spp.IndicatorClass_TN_low_pred <dbl>, #> # D_prop.spp.IndicatorClass_TN_low_raw <dbl>, #> # D_prop.spp.IndicatorClass_TN_low_raw_scr <dbl>, #> # D_prop.spp.Planktonic_mod <dbl>, D_prop.spp.Planktonic_mod_scr <dbl>, #> # D_prop.spp.Planktonic_pct_att <dbl>, D_prop.spp.Planktonic_pred <dbl>, #> # D_prop.spp.Planktonic_raw <dbl>, D_prop.spp.Planktonic_raw_scr <dbl>, #> # D_prop.spp.Trophic.E_mod <dbl>, D_prop.spp.Trophic.E_mod_scr <dbl>, #> # D_prop.spp.Trophic.E_pct_att <dbl>, D_prop.spp.Trophic.E_pred <dbl>, #> # D_prop.spp.Trophic.E_raw <dbl>, D_prop.spp.Trophic.E_raw_scr <dbl>, #> # D_Salinity.BF.richness_mod <dbl>, D_Salinity.BF.richness_mod_scr <dbl>, #> # D_Salinity.BF.richness_pct_att <dbl>, D_Salinity.BF.richness_pred <dbl>, #> # D_Salinity.BF.richness_raw <int>, D_Salinity.BF.richness_raw_scr <dbl>, #> # S_prop.spp.IndicatorClass_DOC_high_raw_pct_att <dbl>, #> # S_prop.spp.IndicatorClass_DOC_high_raw_raw <dbl>, #> # S_prop.spp.IndicatorClass_NonRef_pct_att <dbl>, #> # S_prop.spp.IndicatorClass_NonRef_raw <dbl>, #> # S_prop.spp.IndicatorClass_NonRef_raw_scr <dbl>, #> # S_prop.spp.IndicatorClass_TP_high_pct_att <dbl>, #> # S_prop.spp.IndicatorClass_TP_high_raw <dbl>, #> # S_prop.spp.IndicatorClass_TP_high_raw_scr <dbl>, #> # S_prop.spp.ZHR_pct_att <dbl>, S_prop.spp.ZHR_raw <dbl>, #> # S_prop.spp.ZHR_raw_scr <dbl>, H_cnt.spp.IndicatorClass_TP_high_mod <dbl>, #> # H_cnt.spp.IndicatorClass_TP_high_mod_scr <dbl>, #> # H_cnt.spp.IndicatorClass_TP_high_pct_att <dbl>, #> # H_cnt.spp.IndicatorClass_TP_high_pred <dbl>, #> # H_cnt.spp.IndicatorClass_TP_high_raw <int>, #> # H_cnt.spp.IndicatorClass_TP_high_raw_scr <dbl>, #> # H_cnt.spp.most.tol_mod <dbl>, H_cnt.spp.most.tol_mod_scr <dbl>, #> # H_cnt.spp.most.tol_pct_att <dbl>, H_cnt.spp.most.tol_pred <dbl>, #> # H_cnt.spp.most.tol_raw <int>, H_cnt.spp.most.tol_raw_scr <dbl>, #> # H_EpiRho.richness_mod <dbl>, H_EpiRho.richness_mod_scr <dbl>, #> # H_EpiRho.richness_pct_att <dbl>, H_EpiRho.richness_pred <dbl>, #> # H_EpiRho.richness_raw <int>, H_EpiRho.richness_raw_scr <dbl>, #> # H_OxyRed.DO_30.richness_mod <dbl>, H_OxyRed.DO_30.richness_mod_scr <dbl>, #> # H_OxyRed.DO_30.richness_pct_att <dbl>, H_OxyRed.DO_30.richness_pred <dbl>, #> # H_OxyRed.DO_30.richness_raw <int>, H_OxyRed.DO_30.richness_raw_scr <dbl>, #> # H_prop.spp.Planktonic_mod <dbl>, H_prop.spp.Planktonic_mod_scr <dbl>, #> # H_prop.spp.Planktonic_pct_att <dbl>, H_prop.spp.Planktonic_pred <dbl>, #> # H_prop.spp.Planktonic_raw <dbl>, H_prop.spp.Planktonic_raw_scr <dbl>, #> # H_prop.spp.Trophic.E_mod <dbl>, H_prop.spp.Trophic.E_mod_scr <dbl>, #> # H_prop.spp.Trophic.E_pct_att <dbl>, H_prop.spp.Trophic.E_pred <dbl>, #> # H_prop.spp.Trophic.E_raw <dbl>, H_prop.spp.Trophic.E_raw_scr <dbl>, #> # H_prop.spp.ZHR_pct_att <dbl>, H_prop.spp.ZHR_raw <dbl>, #> # H_prop.spp.ZHR_raw_scr <dbl>, H_Salinity.BF.richness_mod <dbl>, #> # H_Salinity.BF.richness_mod_scr <dbl>, H_Salinity.BF.richness_pct_att <dbl>, #> # H_Salinity.BF.richness_pred <dbl>, H_Salinity.BF.richness_raw <int>, …