Movatterモバイル変換

Marcus W. Beck,marcusb@sccwrp.org; Susanna Theroux,susannat@sccwrp.org; Robert Butler (maintainer),robertb@sccwrp.org; Quynh-Thi Ho,qthi.ho@gmail.com

R package materials to calculate the Algal Stream Condition Index (ASCI) based on predictive MMI scores using diatom, soft-bodied algae, or a hybrid appproach.

Installation

Install the package as follows:

install.packages('devtools')library(devtools)install_github('SCCWRP/ASCI')library(ASCI)

Usage

The sample filesdemo_algae_tax anddemo_station are included to demonstrate the correct formats for the input data. Thedemo_algae_tax file is adata.frame of taxonomic data in long format (one row per sample). Thedemo_station file is adata.frame of GIS predictors in wide format, one row per station. See the help files for more information (e.g.,?demo_algae_tax). Also see the help file forchkinp() andcalcgis() for requirements of each file to work with the ASCI.

head(demo_algae_tax)

## # A tibble: 6 x 7##   StationCode SampleDate          Replicate SampleTypeCode BAResult  Result##   <chr>       <dttm>                  <dbl> <chr>             <dbl>   <dbl>## 1 909M24937   2016-06-22 00:00:00         1 Macroalgae           NA  1.21e9## 2 909M24937   2016-06-22 00:00:00         1 Epiphyte             15 NA## 3 909M24937   2016-06-22 00:00:00         1 Epiphyte             83 NA## 4 909M24937   2016-06-22 00:00:00         1 Epiphyte              2 NA## 5 909M24937   2016-06-22 00:00:00         1 Integrated            5 NA## 6 909M24937   2016-06-22 00:00:00         1 Integrated           53 NA## # … with 1 more variable: FinalID <chr>

head(demo_station)

## # A tibble: 3 x 26##   StationCode CondQR50 SITE_ELEV TEMP_00_09 KFCT_AVE  AtmCa PPT_00_09##   <chr>          <int>     <int>      <int>    <dbl>  <dbl>     <dbl>## 1 404M07357         NA       199       2456    0.278 0.0554    55570.## 2 801M16916         NA       197       2685    0.185 0.0652    25406.## 3 909M24937         NA       582       2442    0.202 0.106     37972.## # … with 19 more variables: MAX_ELEV <int>, CaO_Mean <dbl>,## #   MgO_Mean <dbl>, S_Mean <dbl>, UCS_Mean <dbl>, LPREM_mean <dbl>,## #   AtmMg <dbl>, AtmSO4 <dbl>, MINP_WS <dbl>, MEANP_WS <dbl>,## #   SumAve_P <dbl>, TMAX_WS <dbl>, XWD_WS <dbl>, MAXWD_WS <dbl>,## #   LST32AVE <dbl>, BDH_AVE <dbl>, PRMH_AVE <dbl>, PSA6C <chr>,## #   XerMtn <lgl>

The output is in a wide format.

demo_results<-ASCI(demo_algae_tax,demo_station)demo_results

## # A tibble: 3 x 55##   SampleID StationCode SampleDate          Replicate SampleType##   <chr>    <chr>       <dttm>                  <int> <chr>## 1 404M073… 404M07357   2016-06-13 00:00:00         1 Integrate…## 2 801M169… 801M16916   2016-05-25 00:00:00         1 Microalga…## 3 909M249… 909M24937   2016-06-22 00:00:00         1 Macroalga…## # … with 50 more variables: D_ValveCount <int>, S_EntityCount <int>,## #   S_Biovolume <dbl>, D_NumberTaxa <dbl>, S_NumberTaxa <dbl>,## #   H_NumberTaxa <dbl>, UnrecognizedTaxa <chr>, D_ASCI <dbl>,## #   S_ASCI <dbl>, H_ASCI <dbl>, D_pct_att_prp_spp_BCG12 <dbl>,## #   D_pct_att_prp_spp_OxRq_DO100_75 <dbl>,## #   D_pct_att_prp_spp_Salinity_BF <dbl>,## #   D_pct_att_prp_spp_Trophic_E <dbl>, D_prp_spp_BCG12_mod <dbl>,## #   D_prp_spp_BCG12_mod_scr <dbl>, D_prp_spp_BCG12_pred <dbl>,## #   D_prp_spp_OxRq_DO100_75_raw <dbl>,## #   D_prp_spp_OxRq_DO100_75_raw_scr <dbl>,## #   D_prp_spp_Salinity_BF_mod <dbl>, D_prp_spp_Salinity_BF_mod_scr <dbl>,## #   D_prp_spp_Salinity_BF_pred <dbl>, D_prp_spp_Trophic_E_mod <dbl>,## #   D_prp_spp_Trophic_E_mod_scr <dbl>, D_prp_spp_Trophic_E_pred <dbl>,## #   H_OxRd_DO_30_richness_mod <dbl>, H_OxRd_DO_30_richness_mod_scr <dbl>,## #   H_OxRd_DO_30_richness_pred <dbl>, H_pct_att_OxRd_DO_30_richness <dbl>,## #   H_pct_att_prp_spp_BCG4 <dbl>, H_pct_att_prp_spp_IC_DOC_high <dbl>,## #   H_pct_att_Salinity_BF_richness <dbl>, H_prp_spp_BCG4_mod <dbl>,## #   H_prp_spp_BCG4_mod_scr <dbl>, H_prp_spp_BCG4_pred <dbl>,## #   H_prp_spp_IC_DOC_high_raw <dbl>, H_prp_spp_IC_DOC_high_raw_scr <dbl>,## #   H_Salinity_BF_richness_mod <dbl>,## #   H_Salinity_BF_richness_mod_scr <dbl>,## #   H_Salinity_BF_richness_pred <dbl>, S_cnt_spp_IC_DOC_high_raw <dbl>,## #   S_cnt_spp_IC_DOC_high_raw_scr <dbl>,## #   S_pct_att_cnt_spp_IC_DOC_high <dbl>, S_pct_att_prp_spp_BCG45 <dbl>,## #   S_pct_att_prp_spp_Green <dbl>, S_prp_spp_BCG45_raw <dbl>,## #   S_prp_spp_BCG45_raw_scr <dbl>, S_prp_spp_Green_raw <dbl>,## #   S_prp_spp_Green_raw_scr <dbl>, Comments <chr>