Extension of Package `hyperSpec` and Various Convenience Functions

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 |

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.... |

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 |

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