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 ) -> LogProbwhere 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 ) -> LogProbwhere 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] ) -> LogProbwhere 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.

Methods from Deref<Target = f64>

pub const RADIX: u32 = 2u32

pub const MANTISSA_DIGITS: u32 = 53u32

pub const DIGITS: u32 = 15u32

pub const EPSILON: f64 = 2.2204460492503131E-16f64

pub const MIN: f64 = -1.7976931348623157E+308f64

pub const MIN_POSITIVE: f64 = 2.2250738585072014E-308f64

pub const MAX: f64 = 1.7976931348623157E+308f64

pub const MIN_EXP: i32 = -1_021i32

pub const MAX_EXP: i32 = 1_024i32

pub const MIN_10_EXP: i32 = -307i32

pub const MAX_10_EXP: i32 = 308i32

pub const NAN: f64 = NaNf64

pub const INFINITY: f64 = +Inff64

pub const NEG_INFINITY: f64 = -Inff64

pub fn total_cmp(&self, other: &f64) -> Ordering

Return the ordering between self and other.

Unlike the standard partial comparison between floating point numbers, this comparison always produces an ordering in accordance to the totalOrder predicate as defined in the IEEE 754 (2008 revision) floating point standard. The values are ordered in the following sequence:

• negative quiet NaN
• negative signaling NaN
• negative infinity
• negative numbers
• negative subnormal numbers
• negative zero
• positive zero
• positive subnormal numbers
• positive numbers
• positive infinity
• positive signaling NaN
• positive quiet NaN.

The ordering established by this function does not always agree with the PartialOrd and PartialEq implementations of f64. For example, they consider negative and positive zero equal, while total_cmp doesn’t.

The interpretation of the signaling NaN bit follows the definition in the IEEE 754 standard, which may not match the interpretation by some of the older, non-conformant (e.g. MIPS) hardware implementations.

Example

struct GoodBoy {
    name: String,
    weight: f64,
}

let mut bois = vec![
    GoodBoy { name: "Pucci".to_owned(), weight: 0.1 },
    GoodBoy { name: "Woofer".to_owned(), weight: 99.0 },
    GoodBoy { name: "Yapper".to_owned(), weight: 10.0 },
    GoodBoy { name: "Chonk".to_owned(), weight: f64::INFINITY },
    GoodBoy { name: "Abs. Unit".to_owned(), weight: f64::NAN },
    GoodBoy { name: "Floaty".to_owned(), weight: -5.0 },
];

bois.sort_by(|a, b| a.weight.total_cmp(&b.weight));

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<'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 Add<LogProb> for LogProb

type Output = LogProb

The resulting type after applying the + operator.

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

fn from(p: LogProb) -> PHREDProb

Converts to this type from the input type.

impl From<LogProb> for Prob

fn from(p: LogProb) -> Prob

Converts to this type from the input type.

impl From<LogProb> for f64

fn from(v: LogProb) -> Self

Converts to this type from the input type.

impl From<NotNan<f64>> for LogProb

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

Converts to this type from the input type.

impl From<PHREDProb> for LogProb

fn from(p: PHREDProb) -> LogProb

Converts to this type from the input type.

impl From<Prob> for LogProb

fn from(p: Prob) -> LogProb

Converts to this type from the input type.

impl From<f64> for LogProb

fn from(v: f64) -> Self

Converts to this type from the input type.

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: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

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<'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 Sub<LogProb> for LogProb

type Output = LogProb

The resulting type after applying the - operator.

fn sub(self, rhs: Self) -> 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 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 TryFrom<LogProb> for NotNan<f64>

type Error = FloatIsNan

The type returned in the event of a conversion error.

fn try_from(p: LogProb) -> Result<Self, Self::Error>

Performs the conversion.

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