Man pages for GegznaV/spHelper
Extension of Package `hyperSpec` and Various Convenience Functions

aes_spDefault aesthetics for plotting a hyperSpec object with...
alr[!] Additive logratio transformation
apt[!]Additive planar transform
binning[!] Signal binning
boot_ci_meanBootstrapped mean and its confidence interval
calculate_performanceCalculate best berformance measure
center_subtracted_centers[!] Calculate common center subtracted group centers of...
class_addAdd an additional S3 class label to an object
clr[!] Centered logratio transformation
colRatios[!] Calculate ratios between values of every column pair.
count_spectraSummary statistics of factor variable in a hypecSpec object...
cpt[!] Centered planar transform
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_classCalculate 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_IDsGet names of groups that has enough unique cases.
has_too_few_IDsGet names of groups that has to few unique cases.
hy2matExtract 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'
hyperSpecInitialize new hyperSpec object
hy_spc2dfReturn transposed matrix of spectra in hyperSpec object
ilr[!] Isometric logratio transformation
ilrBase[!] 'ilrBase' method for 'hyperSpec' object
infoDimCalculate information dimension of a matix
ipt[!] Isometric planar transformation
IQR_outliersOutlier detection with IQR based distances (limits)
ldf[!] As long data frame
mad_outliersOutlier 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_bacBalanced accuracy (for 2 or more groups)
measure_bac_2grBalanced accuracy (for binary classification)
measure_kappa_tmp[Internal] measure_kappa_tmp
measure_tnCalculate number of true negatives
measure_tpCalculate number of true positives
measure_tprRate of correctly identified values in a certain group
median_CIConfidence 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.replaceMask NA values with other symbol
nID_nSp[+!] Calculate number and percentage of unique IDs and...
normal_var_CIConfidence interval for variance (parameter sigma squared) of...
palette_PAP[+] Color palette
parser_1[!] Parse a filename
parser_TD2015[!] Parse a filename
parse_stringParse a string and extract information to a dataframe.
percent2probsConverts percentage to perobabilities
performance0[.] Cusstomizable function 'performance0': function to create...
performance_measuresPerformance 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_histPlot histogram of LOF values
plot_LOF_MDSPlot MDS of LOF_obj data
plot_LOF_spPlot 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_stackedPlot stacked spectra
poisson_lambda_CIConfidence 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_resamplesggplot 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...
quartilesMedian 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_OOspectraRead 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_labelsLables for variables derived from spectroscopic data files
sp_filterFilter noise form a spectroscopic signal
spHelperExtension for 'hyperSpec' and convenience functions
sp_normalizeNormalize spectra
sp_normalize2Normalize spectra
sp_remove_offsetRemove offset
spStat[+] Calculate summary statistic of spectroscopic data for all...
spStat_ciCalculate a statistic
spStat_ldfCalculate 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...
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...
x90Rotate x axis tick labels
GegznaV/spHelper documentation built on Aug. 14, 2018, 11:27 p.m.