Struct bio::stats::probs::LogProb

pub struct LogProb(pub f64);

A newtype for log-scale probabilities. For performance reasons, we use an approximation of the exp method implemented in bio::utils::FastExp. This can lead to slight errors, but should not matter given that most of the probability differences are reflected within the integer part of the log probability.

Example

#[macro_use]
extern crate approx;
use bio::stats::{LogProb, Prob};

// convert from probability
let p = LogProb::from(Prob(0.5));
// convert manually
let q = LogProb(0.2f64.ln());
// obtain zero probability in log-space
let o = LogProb::ln_one();

assert_relative_eq!(*Prob::from(p.ln_add_exp(q) + o), *Prob(0.7), epsilon=0.000001);

Tuple Fields

0: f64

Implementations

impl LogProb

pub fn is_valid(&self) -> bool

pub fn ln_zero() -> LogProb

Log-space representation of Pr=0

pub fn ln_one() -> LogProb

Log-space representation of Pr=1

pub fn cap_numerical_overshoot(&self, epsilon: f64) -> LogProb

sums of LogProbs, e.g. with ln_sum_exp() can end up slightly above the maximum of LogProb <= 0 due to numerical imprecisions – this function can rescue such values before panics due to asserts in other functions handling LogProbs, e.g. ln_1m_exp

pub fn ln_one_minus_exp(&self) -> LogProb

Numerically stable calculation of 1 - p in log-space.

pub fn ln_sum_exp(probs: &[LogProb]) -> LogProb

Numerically stable sum of probabilities in log-space.

pub fn ln_add_exp(self, other: LogProb) -> LogProb

Numerically stable addition of probabilities in log-space.

pub fn ln_sub_exp(self, other: LogProb) -> LogProb

Numerically stable subtraction of probabilities in log-space.

pub fn ln_cumsum_exp<I: IntoIterator<Item = LogProb>>(probs: I) -> ScanIter<I>

Calculate the cumulative sum of the given probabilities in a numerically stable way (Durbin 1998).

pub fn ln_trapezoidal_integrate_exp<T, D>(
    density: D,
    a: T,
    b: T,
    n: usize
) -> LogProb where
    T: Copy + Add<Output = T> + Sub<Output = T> + Div<Output = T> + Mul<Output = T> + Float,
    D: FnMut(usize, T) -> LogProb,
    f64: From<T>, 

Integrate numerically stable over given log-space density in the interval [a, b]. Uses the trapezoidal rule with n grid points.

pub fn ln_simpsons_integrate_exp<T, D>(
    density: D,
    a: T,
    b: T,
    n: usize
) -> LogProb where
    T: Copy + Add<Output = T> + Sub<Output = T> + Div<Output = T> + Mul<Output = T> + Float,
    D: FnMut(usize, T) -> LogProb,
    f64: From<T>, 

Integrate numerically stable over given log-space density in the interval [a, b]. Uses Simpson’s rule with n (odd) grid points.

pub fn ln_trapezoidal_integrate_grid_exp<T, D>(
    density: D,
    grid: &[T]
) -> LogProb where
    T: Copy + Add<Output = T> + Sub<Output = T> + Div<Output = T> + Mul<Output = T> + Float,
    D: FnMut(usize, T) -> LogProb,
    f64: From<T>, 

Integrate numerically stable over given log-space density and grid points. Uses the trapezoidal rule.

Trait Implementations

impl<'a> Add<&'a LogProb> for &'a LogProb

type Output = LogProb

The resulting type after applying the + operator.

fn add(self, rhs: Self) -> LogProb

Performs the + operation.

impl<'a> Add<&'a LogProb> for LogProb

type Output = LogProb

The resulting type after applying the + operator.

fn add(self, rhs: &'a LogProb) -> LogProb

Performs the + operation.

impl Add<LogProb> for LogProb

type Output = LogProb

The resulting type after applying the + operator.

fn add(self, rhs: Self) -> LogProb

Performs the + operation.

impl<'a> Add<LogProb> for &'a LogProb

type Output = LogProb

The resulting type after applying the + operator.

fn add(self, rhs: LogProb) -> LogProb

Performs the + operation.

impl AddAssign<LogProb> for LogProb

fn add_assign(&mut self, other: LogProb)

Performs the += operation.

impl Clone for LogProb

fn clone(&self) -> LogProb

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for LogProb

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Default for LogProb

fn default() -> LogProb

Returns the “default value” for a type.

impl Deref for LogProb

type Target = f64

The resulting type after dereferencing.

fn deref(&self) -> &Self::Target

Dereferences the value.

impl<'de> Deserialize<'de> for LogProb

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error> where
    __D: Deserializer<'de>, 

Deserialize this value from the given Serde deserializer.

impl From<LogProb> for f64

fn from(v: LogProb) -> Self

Performs the conversion.

impl From<LogProb> for NotNan<f64>

fn from(p: LogProb) -> NotNan<f64>

Performs the conversion.

impl From<LogProb> for Prob

fn from(p: LogProb) -> Prob

Performs the conversion.

impl From<LogProb> for PHREDProb

fn from(p: LogProb) -> PHREDProb

Performs the conversion.

impl From<NotNan<f64>> for LogProb

fn from(p: NotNan<f64>) -> LogProb

Performs the conversion.

impl From<PHREDProb> for LogProb

fn from(p: PHREDProb) -> LogProb

Performs the conversion.

impl From<Prob> for LogProb

fn from(p: Prob) -> LogProb

Performs the conversion.

impl From<f64> for LogProb

fn from(v: f64) -> Self

Performs the conversion.

impl PartialEq<LogProb> for LogProb

fn eq(&self, other: &LogProb) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &LogProb) -> bool

This method tests for !=.

impl PartialOrd<LogProb> for LogProb

fn partial_cmp(&self, other: &LogProb) -> Option<Ordering>

This method returns an ordering between self and other values if one exists.

fn lt(&self, other: &Rhs) -> bool

This method tests less than (for self and other) and is used by the < operator.

fn le(&self, other: &Rhs) -> bool

This method tests less than or equal to (for self and other) and is used by the <= operator.

fn gt(&self, other: &Rhs) -> bool

This method tests greater than (for self and other) and is used by the > operator.

fn ge(&self, other: &Rhs) -> bool

This method tests greater than or equal to (for self and other) and is used by the >= operator.

impl Serialize for LogProb

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error> where
    __S: Serializer, 

Serialize this value into the given Serde serializer.

impl<'a> Sub<&'a LogProb> for &'a LogProb

type Output = LogProb

The resulting type after applying the - operator.

fn sub(self, rhs: Self) -> LogProb

Performs the - operation.

impl<'a> Sub<&'a LogProb> for LogProb

type Output = LogProb

The resulting type after applying the - operator.

fn sub(self, rhs: &'a LogProb) -> LogProb

Performs the - operation.

impl Sub<LogProb> for LogProb

type Output = LogProb

The resulting type after applying the - operator.

fn sub(self, rhs: Self) -> LogProb

Performs the - operation.

impl<'a> Sub<LogProb> for &'a LogProb

type Output = LogProb

The resulting type after applying the - operator.

fn sub(self, rhs: LogProb) -> LogProb

Performs the - operation.

impl SubAssign<LogProb> for LogProb

fn sub_assign(&mut self, other: LogProb)

Performs the -= operation.

impl<'a> Sum<&'a LogProb> for LogProb

fn sum<I: Iterator<Item = &'a LogProb>>(iter: I) -> Self

Method which takes an iterator and generates Self from the elements by “summing up” the items.

impl<'a> Sum<LogProb> for LogProb

fn sum<I: Iterator<Item = LogProb>>(iter: I) -> Self

Method which takes an iterator and generates Self from the elements by “summing up” the items.

impl Zero for LogProb

fn zero() -> Self

Returns the additive identity element of Self, 0.

fn is_zero(&self) -> bool

Returns true if self is equal to the additive identity.

fn set_zero(&mut self)

Sets self to the additive identity element of Self, 0.

impl Copy for LogProb

impl StructuralPartialEq for LogProb