Man pages for zsmith27/CHESSIE
Chessie BIBI
| agency_count | Agency/Program count and percentage per bioregion |
| agency_count2 | Agency/Program count and percentage per bioregion |
| agency_resolution | Test Agency/Program Standard Taxonomic Resolution |
| agency_taxa_diff | Check for Differences in the Taxa Identified by Agency |
| agency_taxa_diff2 | Agency Taxonomic Differences |
| agg_catchment_map | Aggregate scores by catchment |
| agg_catchment_map_old | Aggregate scores by catchment |
| agg_huc12_map | Aggregate scores by HUC12 |
| agg_hucs_map | Prepare HUC data to be mapped |
| agg_station_map | Aggregate scores by station |
| ag_res_output | Write csv files of Agency/Program Standard Taxonomic... |
| all_tables | All Tables |
| auto_bio | Automate Spatial Classification |
| auto_index | Combine Multiple Automation Functions to Create an Index |
| auto_metrics | Automate Metric Calculation |
| auto_plot | Automate Plots |
| auto_score | Automate Scoring |
| bibi_2011_vs_2016 | 2011 Ratings vs. 2016 Ratings |
| bibi_figures | BIBI Figures |
| bioregion_agg | Bioregion aggregation |
| category_counts | Category Counts |
| cf_score | Calculate the metrics from GLIMPSS |
| clean_char | Clean Up Character Vectors |
| clean_taxa | Clean Taxa |
| common_agency_discrepancies | Checks for common Agency/Program Discrepancies |
| common_agency_discrepancies2 | Checks for common Agency/Program Discrepancies |
| create_map | Generate BIBI Map |
| create_subdir | Create a Subdirectory for BIBI Outpt |
| glimpss | Calculate and score the metrics from GLIMPSS |
| glimpss_metrics | Calculate the metrics from GLIMPSS |
| group.me | Group Output Files |
| group.me2 | Group Me 2 |
| group.me3 | Group Me 3 |
| group.me.low.res | Group Me Low Resolution |
| group.names | Data frame of Taxa of Interest |
| hello | Hello, World! |
| identify_duplicates | Identify Duplicate Samples |
| import_msa_data | Import MS Access Data Sheets |
| index_plot2 | Index Plot |
| index_table | Index Table |
| iterate_dev | Iterative Index Development |
| jack_table | Jackknife Table |
| mac | Middle Atlantic Coastal Plain |
| mac_clean_taxa | MAC: Standarize Taxonomic Resolution |
| map_this | Map the BIBI Ratings |
| metrics_mac | Middle Atlantic Coastal Plain Metrics |
| metrics_napu | NAPU Metrics |
| metrics_nca | NCA metrics |
| metrics_pied | Piedmont metrics |
| metrics_ridges | Ridges metrics |
| metrics_sep | Southeastern Plains Metrics |
| metrics_valleys | Valleys-All metrics |
| metrics_valleys_lv | Valleys_LV metrics |
| metrics_valleys_nlv | Valleys-NLV metrics |
| metric_table | Metric Table |
| napu | NAPU |
| napu_clean_taxa | NAPU: Standarize Taxonomic Resolution |
| nca | NCA |
| nca_clean_taxa | NCA: Standarize Taxonomic Resolution |
| one_and_done | One and done |
| organize_all_event_ratings | Prep event ratings |
| output_agency_taxa_diff2 | Write csv files containing agency/program taxonomic... |
| percentile_summary | Precentile Summary |
| pied | Piedmont |
| pied_clean_taxa | Piedmont: Standarize Taxonomic Resolution |
| plot_jack | Plot Jackknife Results |
| plot.me | Import Output |
| plot.me2 | Plot Me2 |
| plot.me.old | Plot Me Old |
| prep_agency_taxa_res | Prepare data for checking taxonomic resolution discrepancies... |
| prep_bioregion | Add a Bioregion Column |
| prep_class_multi | Prepare Class Multi |
| prep_data | Merge taxa, water quality, and habitat data into one |
| prep_ecoregion | Ecoregion and Bioregion Modifications |
| prep_env | Prepare Environmental Parameters |
| prep_habitat | Prepare Habitat Data |
| prep_habitat_old | Prepare Habitat Data |
| prep_large | Large River's PREP |
| prep_mac | Middle Atlantic Coastal Plain Data PREP |
| prep_merge | Merge taxa, water quality, and habitat data into one |
| prep_napu | NAPU Data PREP |
| prep_nca | NCA Data PREP |
| prep_pied | Piedmont Data PREP |
| prep_pied_large | Piedmont Large River's PREP |
| prep_rate_stacks | Prep Rate Stacks |
| prep_ridges | Ridges Data PREP |
| prep_ridges_large | Ridges Large River's PREP |
| prep_sep | Southeastern Plains Data PREP |
| prep_subset | Prepare subset specific to BIBI |
| prep_taxa | Prepare Taxonomic Counts |
| prep_valleys | Valley's Data PREP |
| prep_valleys_large | Valleys-All Large River's PREP |
| prep_valleys_lv | Valleys_LV PREP |
| prep_valleys_nlv | Valleys_NLV PREP |
| prep_wq | Prepare Water Quality Data |
| prep_wq_old | Prepare Water Quality Data |
| random_events | Random Events |
| rate.me2 | Rate Me 2 |
| rate_stacks | Rate Stacks |
| read.me | Import Output |
| ref_sev_percentiles | Caclulate Reference and Severely Degraded percentiles |
| remove_errors | Remove Environmental Paramater Errors |
| ridge_clean_taxa | Ridge: Standarize Taxonomic Resolution |
| ridges | Ridges |
| score_1_3_5 | 1-3-5 Scoring |
| score_mac | Score Middle Atlantic Coastal Plain Metrics |
| score_napu | Score NAPU Metrics |
| score_nca | Score NCA Metrics |
| score_pied | Score Piedmont Metrics |
| score_ridges | Score Ridges Metrics |
| score_sep | Score Southeastern Plains Metrics |
| score_valleys | Score valley's Metrics |
| score_valleys_lv | Valleys_LV |
| score_valleys_nlv | Valleys NVL |
| sep | Southeastern Plains |
| sep_clean_taxa | SEP: Standarize Taxonomic Resolution |
| shrink_env | Just Important Environmental Parameters |
| site_classification | Site Classification |
| site_classification_2011 | Site Classification (2011) |
| taxa_absence | Taxa Absent from Agency/Program |
| test_id | Test Agency/Program Standard Taxonomic Resolution of Specific... |
| test_id2 | Test Agency/Program Standard Taxonomic Resolution of Specific... |
| val_clean_taxa | Valleys: Standarize Taxonomic Resolution |
| valleys | Valleys |
| valleys_lv | Valleys_LV |
| valleys_nlv | Valleys-No Limestone |
| wvsci | Calculate and score the metrics from WVSCI |
| wvsci_metrics | Calculate the metrics from WVSCI |
| year_counts_barplot | Year Counts |
