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amova.h
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amova.h
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/**
* @file amova.h
* @brief header file for amova.cpp
* @details contains functions for performing Analysis of Molecular Variance (AMOVA)
*/
#ifndef __AMOVA_H__
#define __AMOVA_H__
/* INCLUDES ----------------------------------------------------------------- */
#include "shared.h"
/* END-OF-INCLUDES ---------------------------------------------------------- */
/* FORWARD-DECLARATIONS ----------------------------------------------------- */
typedef struct metadata_t metadata_t;
typedef struct argStruct argStruct;
typedef struct dmat_t dmat_t;
typedef struct outfile_t outfile_t;
typedef struct amova_t amova_t;
typedef struct strArray strArray;
/* END-OF-FORWARD-DECLARATIONS ---------------------------------------------- */
/* MACROS ------------------------------------------------------------------- */
/* END-OF-MACROS ------------------------------------------------------------ */
/* TYPEDEF-STRUCTS ---------------------------------------------------------- */
/**
* @brief amova - struct for storing AMOVA results
* @note if isShared==FALSE; then the arrays are allocated for each bootstrap replicate
* and the first array always stores the original data
*/
struct amova_t {
/// ------------------------------------------///
/// -> shared between bootstrap replicates <- ///
/// @var metadata - pointer to metadata to be used in AMOVA
metadata_t* metadata;
/// @var df - array of degrees of freedom
/// @note size = nLevels
/// df[i] = df for i-th level within the (i-1)-th level
/// [bootstrap] isShared = TRUE
int* df;
/// @var df_total - total degrees of freedom
/// [bootstrap] isShared = TRUE
int df_total;
/// @var vmat - used in the calculation of cmat
/// @note size = (nLevels * (nLevels+1)) / 2
/// upper triangular matrix of v_ij elements used in calculation of variance coefficients
/// [bootstrap] isShared = TRUE
double* vmat;
/// @var cmat - upper triangular matrix of variance coefficients
/// @note size = (nLevels * (nLevels+1)) / 2
/// in classical amova permutation test, this is isShared = FALSE
/// in bootstrapping, this is isShared = TRUE since ninds are not permuted
/// [bootstrap] isShared = TRUE
double* cmat;
/// @var lmat - inverse of cmat
/// @note size = (nLevels * (nLevels+1)) / 2
/// [bootstrap] isShared = TRUE
double* lmat;
/// ------------------------------------------///
/// -> unique to each bootstrap replicate <- ///
size_t nRuns;
/// @var ss - array of sum of squares within (SS^(w))
/// @note size = [nRuns][nLevels]
/// ss[i] = SS within the i-th level
/// ss[nLevels-1] = SS within individuals (currently unused! set to 0.0)
/// [bootstrap] isShared = FALSE
double** ss;
/// @var ss_total - total sum of squares
/// @note size = nRuns
/// [bootstrap] isShared = FALSE
double* ss_total;
/// @var ssd - array of sum of squared deviations (SSD)
/// @note size = [nRuns][nLevels]
/// [bootstrap] isShared = FALSE
double** ssd;
/// @var ssd_total - total sum of squared deviations (SSD)
/// @note size = nRuns
/// [bootstrap] isShared = FALSE
double* ssd_total;
/// @var msd - array of mean squared deviations
/// @note size = [nRuns][nLevels]
/// [bootstrap] isShared = FALSE
double** msd;
/// @var msd_total - total mean squared deviation
/// @note size = nRuns
/// [bootstrap] isShared = FALSE
double* msd_total;
/// @var sigmasq - array of variance components
/// @note size = [nRuns][nLevels]
/// sigmasq[r][i] = variance component for i-th level (for r-th run)
/// [bootstrap] isShared = FALSE
double** sigmasq;
/// @var sigmasq_total - sum of all variance components
/// @note size = nRuns
/// [bootstrap] isShared = FALSE
double* sigmasq_total;
/// @var phi_xt - array of phi_xt statistics
/// @note size = [nRuns][nLevels-1]
/// [bootstrap] isShared = FALSE
double** phi_xt;
/// @var phi_xy - array of phi_xy statistics
/// @note size = [nRuns][nLevels-2]
/// phi_xy[r][i] = Phi_{i(i-1)}^{*(r)} (r-th run)
/// [bootstrap] isShared = FALSE
double** phi_xy;
/// @note *_adj: allocated iff adjustment is needed (found a negative variance component)
/// @var sigmasq_adj - array of adjusted variance components
/// @note size = [nRuns][nLevels]
/// sigmasq_adj[r][i] = adjusted variance component for i-th level (for r-th run)
/// [bootstrap] isShared = FALSE
double** sigmasq_adj;
/// @var sigmasq_total_adj - sum of all adjusted variance components
/// @note size = [nRuns]
double* sigmasq_total_adj;
/// @var phi_xt_adj - array of adjusted phi_xt statistics
/// @note size = [nRuns][nLevels-1]
/// [bootstrap] isShared = FALSE
double** phi_xt_adj;
/// @var phi_xy_adj - array of adjusted phi_xy statistics
/// @note size = [nRuns][nLevels-2]
/// [bootstrap] isShared = FALSE
double** phi_xy_adj;
};
/* END-OF-TYPEDEF-STRUCTS --------------------------------------------------- */
/* FUNCTION-DECLARATIONS ----------------------------------------------------- */
amova_t* amova_get(dmat_t* dmat, metadata_t* mtd);
void amova_destroy(amova_t* amv);
/* END-OF-FUNCTION-DECLARATIONS ---------------------------------------------- */
// #endif // __X_H__
/* ========================================================================== */
#endif // __AMOVA_H__