Man pages for TheAlexBarth/EcotaxaTools
Data wrangling and post-validation processing programs
| add_col | add_col |
| add_count_zeros | Inside function for force bins option |
| add_custom_trim | Call this function to edit vectorSelect |
| add_par_zeros | Add particle zeros |
| add_range | add_range |
| add_zeros | add_zeros |
| add_zoo | Add column to all zooplankton files |
| all_taxa | Get all taxa |
| any_in | Any In |
| area_to_esd | Convert Area to ESD |
| as_ecopart_obj | Set classes |
| as_par_df | set class for par_pdf |
| assign_etx_class | Assign an etx class |
| assign_spectra_bins | Make size bins in a cut style vector |
| as_zoo_df | Set class for zoo_df |
| average_casts | Average uvp concentrations across similar casts |
| avg_casts | Inside averaging |
| bin_by | bin_by - a function to make easy cuts by default |
| bin_by_df | bin_by_df - returns a data frame for counts by bin |
| bin_format | Format Bins |
| bin_format_check | bin_format_check returns true if all character of the vector... |
| bin_format_depth | Legacy in interior for bin format |
| bin_format_general | Interior for bin format |
| bin_par_plot | Plot a size-binned particle plot |
| bin_taxa | Bin observations by taxa according to some common factor This... |
| biovolume | Get vignette biovolume |
| bru_dat | Single merger function |
| calc_ellps_vol | Calculate the ellipsoid volume of a vignette |
| calc_par_conc | inner particle concentration calculator |
| calc_par_conc_bin | Inside calculation for particle counts by bin |
| calc_par_db_spectra | Split par_calc |
| calc_sph_vol | Calculate Spherical Volume of vignette |
| cast_assign | Inside function to assign casts for lapply |
| check_custom | check_custom - a function to check the custom range input |
| chk_input | chk_input - helper to check input against known values |
| count_size_classes | Count he number of observations in each size bin |
| create_log_size_classes | Generate size limits based on a log scale |
| create_width_size_classes | Generate size limits based on a fixed width |
| descent_plot | Plot Descent |
| ecopart_example | ecopart_example |
| ecopart_file_check | Warning message for unmatched PAR and ZOO files |
| ecopart_import | Read in files from a folder of ecopart raw export |
| ecopart_vol_bin | Ecopart Volume Binning |
| force_bins_switch | Force bins will add zeros to bins that don't have any... |
| force_par_zeros | Force 0's to the particle concentrations |
| format_header | format_header - a function to format headers |
| get_all | Get all for some column |
| get_bin_limits | get_bin_limits This function pulls bin limits from the... |
| get_col_name | get_col_name |
| get_ecopart_vol | Get Volumes from Par files |
| getTime | formatting plugs into timeOfDay |
| get_zoo_df_features | Get major and minor axis from zoo_df |
| gg_cbb_col | Colorblind friendly pallete |
| gg_color_hue | ggplot color selection |
| integrate_all | Integrate all taxa in a group |
| integration_matcher | Match df to integrate |
| intg_to_tib | Switch integration list to a dataframe |
| is.etx_class | Check classes of objects |
| lin_interp | Linear interpolation between sets of points |
| list_to_tib | Make a tibble from a list - with names as a new column |
| merge_casts | Merge casts into one file |
| mod_zoo | Modify a list of ecotaxa tsv dfs |
| multi_manager | multi_manager - a tool to re-label vignettes with multiple... |
| name_match | Find a match to list |
| names_drop | Drop certain names from the ecotaxa dataframe |
| names_keep | Keep only names from the ecotaxa dataframe |
| names_to | Assign names based on taxo hierarchy |
| nearest | nearest |
| numeric_spectra | Calculate the numeric particle spectra |
| order_bins | order_bins - a function to order bins correctly |
| par_df_spectra | Calculate numeric spectra in depth bins of par_df |
| particle_plot | Plot a particle diagram |
| pool_casts | Inside cast pooling |
| raw_bru_import | Read in raw bru files |
| raw_dat_import | Read in raw dat files |
| raw_merge_brudat | Merge raw_dat and raw_bru files |
| read_etx | read_etx - a function to read tsv from ecotaxa |
| read_raw_bru | Interior bru reader |
| read_raw_datfile | Read raw dat |
| rel_abundance | Get the percent contribution of taxa |
| rel_taxa | Get the percent contribution of taxa |
| single_par_plot | Plot a single particle diagram - total concentration |
| split_ecopart_obj | Split an ecopart object based on some meta_data |
| timeOfDay | Calculate the time of day as day, twilight, buffer |
| trap_integrate | Trapezoidal integration |
| trim_ecopart_depth | Trim an ecopart object by depth |
| trim_par | Trim par_list |
| trim_par_inner | Inside par trimmer |
| trim_zoo | Trim zoo_list |
| trim_zoo_inner | Inside zoo_list trimmer A simple function to trim par list... |
| tsv_trim | tsv_trim - an automated trimming tool for ecotaxa tsv's |
| uvp_conc | Calculate UVP Concentration from Ecopart Object |
| uvp_par_conc | Calculate particle concentration |
| uvp_par_spectra | Number Size Spectra by bins |
| uvp_split_par | Split par file based on depth bins |
| uvp_zoo_conc | Calculate UVP Zooplankton Concentration from an Ecopart... |
| vector_select | vector_select - background mechanism for storing trim factors |
| vol_sampled | vol_sampled - get the volume sampled from a UVP cast |
