| aes_sp | Default aesthetics for plotting a hyperSpec object with... |
| alr | [!] Additive logratio transformation |
| apt | [!]Additive planar transform |
| binning | [!] Signal binning |
| boot_ci_mean | Bootstrapped mean and its confidence interval |
| calculate_performance | Calculate best berformance measure |
| center_subtracted_centers | [!] Calculate common center subtracted group centers of... |
| class_add | Add an additional S3 class label to an object |
| clr | [!] Centered logratio transformation |
| colRatios | [!] Calculate ratios between values of every column pair. |
| count_spectra | Summary statistics of factor variable in a hypecSpec object... |
| cpt | [!] Centered planar transform |
| createFoldsBS | DEPRECATED! |
| cvo_n_folds | DEPRECATED! |
| DataSet1 | [+] Dataset: a data frame for illustrations |
| Datasets-sp | [+] Datasets of simulated spectroscopic data |
| deprecated | Deprecated functions |
| doALS2 | [!.] Wrapper function for alternating least squares... |
| expr2text | [.] Convert 'expression' and 'call' to text and remove quotes |
| file | [!] Read header lines of OOI Base32 file |
| gapDer | [!] Gap-Segment Derivative |
| GaussAmp | [+] Generate Gaussian curves (GaussAmp). |
| get_LOF_by_class | Calculate lack_of_fit (LOF) for spectroscopic data by class |
| getScores | [+] Calculate amplitudes of spectroscopic components (a.k.a.... |
| gg_crosstab2 | [!] Plot crosstab for 2 variables in hyperSpec object |
| has_enough_IDs | Get names of groups that has enough unique cases. |
| has_too_few_IDs | Get names of groups that has to few unique cases. |
| hy2mat | Extract matrix from either 'hyperSpec' object or a matrix |
| hyAdd | [!] Add a variable to 'hyperSpec' object |
| hyAdd_color | [+!] Add a variable with color names to 'hyperSpec' object |
| hyAdd_Labels_PAP_PD_2014 | [+] Add labels to "PAP_PD_2014" and transform the dataset |
| hyAdd_Labels_TD2009 | [+] Add labels to "TD_2009" dataset |
| hyAdd_Label_wl | [!] Add a standardised label for x-axis in 'hyperSpec' object |
| hyDrop_NA | [+] Remove variables of 'hyperSpec' object that contain only... |
| hyGet_palette | [+] Get color palette used to create variable'.color' |
| hyperSpec | Initialize new hyperSpec object |
| hy_spc2df | Return transposed matrix of spectra in hyperSpec object |
| ilr | [!] Isometric logratio transformation |
| ilrBase | [!] 'ilrBase' method for 'hyperSpec' object |
| infoDim | Calculate information dimension of a matix |
| ipt | [!] Isometric planar transformation |
| IQR_outliers | Outlier detection with IQR based distances (limits) |
| ldf | [!] As long data frame |
| mad_outliers | Outlier detection with MAD based distances (limits) |
| make_table | [Internal] Make table (from prediction object) |
| mean_Nsd | [!] Find spectra that represent mean +/- n standard deiations |
| measure_bac | Balanced accuracy (for 2 or more groups) |
| measure_bac_2gr | Balanced accuracy (for binary classification) |
| measure_kappa_tmp | [Internal] measure_kappa_tmp |
| measure_tn | Calculate number of true negatives |
| measure_tp | Calculate number of true positives |
| measure_tpr | Rate of correctly identified values in a certain group |
| median_CI | Confidence interval for median |
| median_Nmad | [!] Find spectra that represent median +/- n median absolute... |
| merge | [!!!] Merge a hyperSpec object and a data frame |
| Mode | [.] Compute a mode (most frequent value) |
| na.replace | Mask NA values with other symbol |
| nID_nSp | [+!] Calculate number and percentage of unique IDs and... |
| normal_var_CI | Confidence interval for variance (parameter sigma squared) of... |
| palette_PAP | [+] Color palette |
| parser_1 | [!] Parse a filename |
| parser_TD2015 | [!] Parse a filename |
| parse_string | Parse a string and extract information to a dataframe. |
| percent2probs | Converts percentage to perobabilities |
| performance0 | [.] Cusstomizable function 'performance0': function to create... |
| performance_measures | Performance measures for ROCR::prediction object |
| plot_3D | [.] Plot 3D scatterplot |
| plot_colors | [!] Vizualize colors |
| plot_hyPalette | [!] Plot the color palette used in a hyperSpec object |
| plot_LOF_hist | Plot histogram of LOF values |
| plot_LOF_MDS | Plot MDS of LOF_obj data |
| plot_LOF_sp | Plot spectra colored by LOF values |
| plot_roc | [.] Plot ROC - sample code |
| plot_spCompare | [!] Compare 2 spectroscopic signals |
| plot_spDiff | [+] Plot difference between original and reconstructed... |
| plot_spDistribution | [!] Distribution of spectroscopoc data as percentiles |
| plot_stacked | Plot stacked spectra |
| poisson_lambda_CI | Confidence interval for parameter lambda of Poisson... |
| prediction0 | [!] Function to create prediction objects |
| prepare_PAP_RK_2014__MATLAB_failui | [+] Transform dataset "PAP_RK_2014" and add labels |
| qplot_confusion | [!+] Plot a confusion matrix (a.k.a. classification table) |
| qplot_crosstab | [!.] Plot a cross-tabulation (classification table) |
| qplot_infoDim | [+] Scree plot with indicated information dimension (ggplot2) |
| qplot_kAmp | [!+] Plot amplitudes (a.k.a scores) of spectroscopic... |
| qplot_kSp | [!+] Plot spectroscopic curves and spectral components... |
| qplot_prediction | [!!!] Proximity plot created using multi-dimensiolal scaling... |
| qplot_resamples | ggplot Function for Visualizing Resampling Results of Models... |
| qplot_spc | [!!!] Plot spectroscopic curves |
| qplot_spDistrib | [!] Plot distributions of spectroscopic data |
| qplot_spRange | [!] Plot range of spectroscopic data intensities |
| qplot_spRangeCenter | [!] Plot mean and range of spectroscopic data intensities |
| qplot_spRangeMean | [!] Plot mean and range of spectroscopic data intensities |
| qplot_spRangeMedian | [!] Plot Median and range of spectroscopic data intensities |
| qplot_spStat | [+] Plot a summary statistic of spectroscopic data by group |
| quality_of_fit | [!] Calculate quality of fit parameters (for spectroscopic... |
| quartiles | Median and quantiles |
| read3csv2hy | [+] Read spectroscopic data from 3 CSV files ("data",... |
| read.OceanView | [!v0.3] Read spectroscopic OceanView file |
| read.OceanView.header | [!] Read header lines of OceanView file |
| read.OOIBase32 | [!] Read data from OceanOptics OOI Base32 ASCII file with... |
| read_OOspectra | Read OceanOptics spectra |
| read.sp.csv2 | [!v0.1] Read spectroscopic CSV (comma separated values) file |
| reconstructSp | [+] Reconstruct spectra from loadings and scores (i.e.... |
| reexports | Objects exported from other packages |
| replace_spc | [!!!] Replace 'object$spc' and 'colnames(object$spc)' |
| rmExpr | [.] Convert expressions in 'ggplot2' object labels to strings |
| rm_stripes | [!] Remove facet stripes from 'ggplot2' plot |
| ROC_ | [.] Do ROC analysis and plot it's results (ROC_) |
| roc_extract_info | [!!!] roc_create_predictor |
| save_rds_unique | [~!~] Save object as '.RDS' with unique name (i.e., without... |
| sd_outliers | [!] Outlier detection based on standard deviations (sd) |
| simSpectra | [!] Simulate spectroscopic data |
| sortLoadings | [!+] Process (Sort, flip, name, etc.) spectra of components... |
| sp_class_perform | [.!] Compare spectra of groups at each wavelength |
| sp_data_labels | Lables for variables derived from spectroscopic data files |
| sp_filter | Filter noise form a spectroscopic signal |
| spHelper | Extension for 'hyperSpec' and convenience functions |
| sp_normalize | Normalize spectra |
| sp_normalize2 | Normalize spectra |
| sp_remove_offset | Remove offset |
| spStat | [+] Calculate summary statistic of spectroscopic data for all... |
| spStat_ci | Calculate a statistic |
| spStat_ldf | Calculate a summary statistic and return long-format data... |
| spZone | [!] Annotate x axis range in ggplot2 graphs |
| stat_chull | [+] A convex hull layer for 'ggplot2' |
| subt | [+] Add bold title and subtitle to a plot |
| summary_hyData | [!] Summary statistics of non-spectroscopic data in... |
| test_folds_BS | DEPRECATED! |
| uncall | [.] Unwrap text from 'call' object Assumption: only the... |
| unGroup | [!] Mix values of factor variable levels in equal proportions |
| unipeak | [+] Find and keep only the highest positive part of a curve |
| whichOutlier | [! DEPRECATED] Find indices of rows that contain outlier... |
| x90 | Rotate x axis tick labels |
