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First take at point-wise mutual info
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ncondits3 committed Dec 24, 2023
1 parent 0265607 commit bf0136f
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Showing 11 changed files with 103 additions and 72 deletions.
36 changes: 19 additions & 17 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,9 @@ S3method(chord,default)
S3method(chord,humdrumR)
S3method(context,default)
S3method(context,humdrumR)
S3method(count,default)
S3method(count,humdrumR)
S3method(count,table)
S3method(deg,default)
S3method(deg,humdrumR)
S3method(degree,default)
Expand Down Expand Up @@ -51,6 +54,8 @@ S3method(entropy,probability)
S3method(expandPaths,humdrumR)
S3method(figuredBass,default)
S3method(figuredBass,humdrumR)
S3method(filter,distribution)
S3method(filter,humdrumR)
S3method(format,struct)
S3method(format,token)
S3method(freq,default)
Expand All @@ -60,8 +65,10 @@ S3method(fromgrid,integer)
S3method(fromgrid,logical)
S3method(fromgrid,matrix)
S3method(fromgrid,numeric)
S3method(ggplot,humdrumR)
S3method(grid,default)
S3method(grid,humdrumR)
S3method(group_by,humdrumR)
S3method(harm,default)
S3method(harm,humdrumR)
S3method(helmholtz,default)
Expand Down Expand Up @@ -89,6 +96,7 @@ S3method(kern,humdrumR)
S3method(lag,data.frame)
S3method(lag,default)
S3method(lag,matrix)
S3method(like,data.frame)
S3method(lilypond,default)
S3method(lilypond,humdrumR)
S3method(measure,"NULL")
Expand All @@ -106,6 +114,7 @@ S3method(mint,default)
S3method(mint,humdrumR)
S3method(ms,default)
S3method(ms,humdrumR)
S3method(mutate,humdrumR)
S3method(mutualInfo,default)
S3method(mutualInfo,probability)
S3method(names,humdrumR)
Expand All @@ -120,9 +129,12 @@ S3method(pdist,count)
S3method(pdist,data.frame)
S3method(pdist,default)
S3method(pdist,humdrumR)
S3method(pdist,probability)
S3method(pdist,table)
S3method(pitch,default)
S3method(pitch,humdrumR)
S3method(pivot_longer,humdrumR)
S3method(pivot_wider,humdrumR)
S3method(print,Excluder)
S3method(print,distribution)
S3method(print,fraction)
Expand All @@ -133,6 +145,7 @@ S3method(print,humSpines)
S3method(print,humdrumDispatch)
S3method(print,humdrumR)
S3method(print,humdrumRmethod)
S3method(pull,humdrumR)
S3method(quarters,default)
S3method(quarters,humdrumR)
S3method(rbind,humdrumR.table)
Expand All @@ -142,6 +155,7 @@ S3method(recip,default)
S3method(recip,humdrumR)
S3method(reference,character)
S3method(reference,humdrumR)
S3method(reframe,humdrumR)
S3method(rep,token)
S3method(rhythmInterval,"NULL")
S3method(rhythmInterval,character)
Expand All @@ -152,8 +166,10 @@ S3method(rhythmInterval,numeric)
S3method(rhythmInterval,token)
S3method(roman,default)
S3method(roman,humdrumR)
S3method(scale_type,token)
S3method(seconds,default)
S3method(seconds,humdrumR)
S3method(select,humdrumR)
S3method(semits,default)
S3method(semits,humdrumR)
S3method(sigma,default)
Expand All @@ -165,6 +181,7 @@ S3method(solfg,humdrumR)
S3method(subset,humdrumR)
S3method(sumTies,default)
S3method(sumTies,humdrumR)
S3method(summarise,humdrumR)
S3method(summary,humdrumR)
S3method(tactus,"NULL")
S3method(tactus,character)
Expand Down Expand Up @@ -203,6 +220,7 @@ S3method(transpose,factor)
S3method(transpose,numeric)
S3method(transpose,token)
S3method(transpose,tonalInterval)
S3method(ungroup,humdrumR)
S3method(unique,struct)
S3method(unique,token)
S3method(with,humdrumR)
Expand Down Expand Up @@ -308,9 +326,6 @@ export(combineFields)
export(complement)
export(context)
export(count)
export(count.default)
export(count.humdrumR)
export(count.table)
export(d1)
export(d10)
export(d11)
Expand Down Expand Up @@ -359,8 +374,6 @@ export(expandPaths)
export(fields)
export(figuredBass)
export(filter)
export(filter.distribution)
export(filter.humdrumR)
export(findHumdrum)
export(fraction)
export(freq)
Expand All @@ -369,10 +382,8 @@ export(gamut)
export(getHumtab)
export(getRE)
export(getREexclusive)
export(ggplot.humdrumR)
export(grid)
export(group_by)
export(group_by.humdrumR)
export(groups)
export(harm)
export(helmholtz)
Expand Down Expand Up @@ -409,7 +420,7 @@ export(key)
export(knownInterpretations)
export(lag)
export(lead)
export(likely)
export(like)
export(lilypond)
export(m10)
export(m13)
Expand All @@ -435,7 +446,6 @@ export(mint)
export(ms)
export(ms2bpm)
export(mutate)
export(mutate.humdrumR)
export(mutualInfo)
export(namesSubcorpora)
export(nbeats)
Expand All @@ -455,11 +465,8 @@ export(order.tonalInterval)
export(pc)
export(pdist)
export(pitch)
export(pivot_longer.humdrumR)
export(pivot_wider.humdrumR)
export(printSilbeFormat)
export(pull)
export(pull.humdrumR)
export(pull_data.frame)
export(pull_data.table)
export(pull_tibble)
Expand All @@ -471,7 +478,6 @@ export(recip)
export(recordDuration)
export(reference)
export(reframe)
export(reframe.humdrumR)
export(removeEmptyFiles)
export(removeEmptyPaths)
export(removeEmptyPieces)
Expand All @@ -484,14 +490,12 @@ export(rhythmInterval)
export(roman)
export(romanKey)
export(rootPosition)
export(scale_type.token)
export(scale_x_token)
export(sec2bpm)
export(seconds)
export(sections)
export(segments)
export(select)
export(select.humdrumR)
export(selectedFields)
export(semits)
export(sigma)
Expand All @@ -505,7 +509,6 @@ export(step)
export(subpos)
export(sumTies)
export(summarise)
export(summarise.humdrumR)
export(summarize)
export(syncopation)
export(table)
Expand All @@ -529,7 +532,6 @@ export(uncontext)
export(unfilter)
export(unfoldStops)
export(ungroup)
export(ungroup.humdrumR)
export(unison)
export(validateHumdrum)
export(varnames)
Expand Down
78 changes: 61 additions & 17 deletions R/Distributions.R
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Original file line number Diff line number Diff line change
Expand Up @@ -290,6 +290,7 @@ setMethod('[', c('distribution', 'ANY', 'missing'),
function(x, i, drop = FALSE) {

df <- as.data.frame(x)[i , , drop = FALSE]

if (drop) df else distribution(df, x)
})
#
Expand Down Expand Up @@ -322,9 +323,11 @@ setMethod('[', c('distribution', 'ANY', 'ANY'),
})

setMethod('[', c('distribution', 'matrix'),
function(x, i, j, cartesian = FALSE, drop = FALSE) {
function(x, i, j, cartesian = TRUE, drop = FALSE) {

i <- as.data.frame(i)
names(i) <- NULL

i <- as.list(i)
do.call('[[', c(list(x, cartesian = cartesian, drop = drop), i))

})
Expand All @@ -342,6 +345,11 @@ setMethod('[[', 'distribution',
missing <- sapply(args, rlang::is_missing)
args[!missing] <- lapply(args[!missing], rlang::eval_tidy)

if (missing[2] && length(args) == 2L) {
args <- args[1L]
missing <- missing[1L]
}


levels <- getLevels(x)
if (length(args) > length(levels)) .stop("This distribution only has {num2print(length(levels))} dimensions to index.",
Expand Down Expand Up @@ -801,7 +809,7 @@ pdist.count <- function(x, ..., condition = NULL, na.rm = FALSE, sort = FALSE,

dist <- distribution(x, 'p', N = n)

if (!is.null(condition)) dist <- conditionalize(dist, condition = condition)
if (!is.null(condition)) dist <- conditional(dist, condition = condition)

if (sort) dist <- sort(dist, decreasing = sort > 0L)

Expand All @@ -815,7 +823,7 @@ pdist.probability <- function(x, ..., condition = NULL, na.rm = FALSE, sort = F
exprs <- rlang::enexprs(...)
if (length(exprs)) condition <- pexprs(exprs, colnames(x), condition)$Condition %||% condition

if (!is.null(condition)) conditionalize(x, condition) else x
if (!is.null(condition)) conditional(x, condition) else x

}

Expand Down Expand Up @@ -924,7 +932,7 @@ pdist.table <- function(x, ..., condition = NULL, na.rm = FALSE, sort = FALSE, b



conditionalize <- function(pdist, condition) {
conditional <- function(pdist, condition) {
varnames <- varnames(pdist)
if (any(!condition %in% varnames)) .stop("We can only calculate a conditional probability across an existing dimension/factor.",
"The <conditions|condition> {harvard(setdiff(varnames, condition), 'and')} are not dimensions of the given",
Expand Down Expand Up @@ -1009,14 +1017,49 @@ pexprs <- function(exprs, colnames, condition) {

## Likelihoods ----

###likelihood() ----
### like() ----

#' @export
setGeneric('likely', function(x, log, ...) standardGeneric('likely'))
like <- function(..., distribution) UseMethod('like')

#' @export
ic <- function(..., distribution, base = 2) -log(like(..., distribution = distribution), base = base)

#' @export
like.default <- function(..., distribution) {
like.data.frame(data.frame(...), distribution = distribution)
}

#' @export
like.data.frame <- function(df, ..., distribution) {

if (missing(distribution)) distribution <- do.call('pdist', list(df, ...))

colnames <- colnames(df)
varnames <- varnames(distribution)

if (!setequal(colnames, varnames)) .stop("To calculate likelihoods, the expected distribution must have the same variables as the observed variables.")

distribution[as.matrix(df), , drop = TRUE]$p

}


#' @rdname entropy
#' @export
setGeneric('ic', function(x, ...) standardGeneric('ic'))
pMI <- function(..., distribution, base = 2) {
df <- data.frame(...)

if (missing(distribution)) distribution <- do.call('pdist', df)

independent <- Reduce('*', lapply(varnames(distribution), \(j) distribution[ , j]))

ic_observed <- ic(df, distribution = distribution, base = base)
ic_independent <- ic(df, distribution = independent, base = base)

ic_independent - ic_observed

}


## Distributional ----

Expand Down Expand Up @@ -1071,7 +1114,7 @@ H <- entropy
#' @rdname entropy
#' @export
entropy.probability <- function(q, p, condition = NULL, base = 2) {
if (!is.null(condition)) q <- conditionalize(q, condition)
if (!is.null(condition)) q <- conditional(q, condition)

if (missing(p) || !inherits(p, 'probability')) {
expected <- unconditional(q)$p
Expand Down Expand Up @@ -1173,18 +1216,19 @@ mutualInfo <- function(..., base = 2) {
#' @export
mutualInfo.probability <- function(x, base = 2) {
varnames <- varnames(x)
if (length(varnames) != 2L) .stop("Can't calculate mutual information of a single variable.")
if (length(varnames) < 2L) .stop("Can't calculate mutual information of a single variable.")

x <- unconditional(x)

observed <- setNames(x$p, do.call('paste', c(getLevels(x), list(sep = '.'))))

expected <- (x[ , 1] * x[ , 2])
expected <- setNames(expected$p, do.call('paste', c(getLevels(expected), list(sep = '.'))))
independent <- Reduce('*', lapply(varnames, \(j) x[ , j]))
# expected <- (x[ , 1] * x[ , 2])
independent <- setNames(independent$p, do.call('paste', c(getLevels(independent), list(sep = '.'))))

expected <- expected[names(observed)]
independent <- independent[names(observed)]

ratio <- observed / expected
ratio <- observed / independent
logratio <- ifelse(ratio == 0 | ratio == Inf, 0, log(ratio, base = base))

equation <- Pequation(x, 'I', ';')
Expand All @@ -1207,9 +1251,9 @@ mutualInfo.default <- function(..., base = 2) {



###################################################
##################################################-
# table() extensions for humdrumR ---- ###########
##################################################
##################################################-



Expand Down
6 changes: 1 addition & 5 deletions man/cleave.Rd
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