Package: CPTtools 0.8-4

CPTtools: Tools for Creating Conditional Probability Tables

Provides support parameterized tables for Bayesian networks, particularly the IRT-like DiBello tables. Also, provides some tools for visualing the networks.

Authors:Russell Almond

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CPTtools.pdf |CPTtools.html✨
CPTtools/json (API)

# Install 'CPTtools' in R:

install.packages('CPTtools', repos = c('https://ralmond.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ralmond/cpttools/issues

Datasets:

ACED.QEM - Data from ACED field trial
ACED.Qmatrix - Data from ACED field trial
ACED.items - Data from ACED field trial
ACED.posttest - Data from ACED field trial
ACED.prePost - Data from ACED field trial
ACED.pretest - Data from ACED field trial
ACED.scores - Data from ACED field trial
ACED.skillNames - Data from ACED field trial
ACED.splitHalves - Data from ACED field trial
ACED.taskNames - Data from ACED field trial
Language_exp - Accuracy and Expected Accuracy Matrixes for Langauge Test.
Language_modal - Accuracy and Expected Accuracy Matrixes for Langauge Test.
MathGrades - Grades on 5 mathematics tests from Mardia, Kent and Bibby
language16 - Accuracy and Expected Accuracy Matrixes for Langauge Test.
language24 - Accuracy and Expected Accuracy Matrixes for Langauge Test.

On CRAN:

bayesian-network statistics

5.03 score 1 stars 4 packages 20 scripts 100 exports 24 dependencies

Last updated 2 months agofrom:c3b8e8383a. Checks:1 OK, 6 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 23 2025
R-4.5-win	NOTE	Jan 23 2025
R-4.5-linux	NOTE	Jan 23 2025
R-4.4-win	NOTE	Jan 23 2025
R-4.4-mac	NOTE	Jan 23 2025
R-4.3-win	NOTE	Jan 23 2025
R-4.3-mac	NOTE	Jan 23 2025

Exports:accuracy areaProbs as.CPA as.CPF barchart.CPF betaci build2FactorTab buildFactorTab buildMarginTab buildParentList buildRegressions buildRegressionTables calcDDFrame calcDDTable calcDNFrame calcDNllike calcDNTable calcDPCFrame calcDPCTable calcDSFrame calcDSllike calcDSTable calcNoisyAndFrame calcNoisyAndTable calcNoisyOrFrame calcNoisyOrTable catTable ciTest colorspread compareBars compareBars2 Compensatory Conjunctive cptChi2 cptG2 cptKL dataTable defaultAlphas defaultBetas Disjunctive EAPBal effectiveThetas eThetaFrame ewoe.CPF expTable factorPart fcKappa getOffsetRules getTableParents getTableStates gkGamma gkLambda gradedResponse is.CPA is.CPF isDecreasing isIncreasing isMonotonic isNondecreasing isNonincreasing isOffsetRule localDepTest mapDPC marginTab mcSearch mutualInformation normalize normalize.array normalize.CPA normalize.CPF normalize.data.frame normalize.default normalize.matrix normalizeTable normalLink numericPart OCP OCP.CPF OCP2 OCP2.CPF OffsetConjunctive OffsetDisjunctive parseProbVec partialCredit plotsimplex proflevelci pvecTable pvecToCutpoints pvecToMidpoints readHistory rescaleTable scaleMatrix scaleTable setOffsetRules simplex_vertex_projection stackedBarplot stackedBars structMatrix woeBal woeHist

Dependencies:cli cpp11 dplyr einsum fansi generics glue lifecycle magrittr mathjaxr pillar pkgconfig purrr R6 Rcpp rlang stringi stringr tibble tidyr tidyselect utf8 vctrs withr

Building Bayesian networks using regression

Rendered fromRegression.Rmdusingknitr::rmarkdownon Jan 23 2025.

Last update: 2023-07-18
Started: 2023-04-11

Conditional Probability Frames and Arrays

Rendered fromCPF.Rmdusingknitr::rmarkdownon Jan 23 2025.

Last update: 2023-07-18
Started: 2023-04-11

Discrete Partial Credit Models

Rendered fromDPCmodels.Rmdusingknitr::rmarkdownon Jan 23 2025.

Last update: 2023-04-11
Started: 2021-05-23

Graphing Discrete Bayesian Networks

Rendered fromgraphing.Rmdusingknitr::rmarkdownon Jan 23 2025.

Last update: 2023-07-18
Started: 2023-04-11

Measues of Agreement

Rendered fromMeasuringAgreement.Rmdusingknitr::rmarkdownon Jan 23 2025.

Last update: 2024-12-24
Started: 2024-12-24

Parameter Estimation

Rendered fromParemeterEstimation.Rmdusingknitr::rmarkdownon Jan 23 2025.

Last update: 2024-12-24
Started: 2024-12-24

Reference Distributions

Rendered fromRefDist.Rmdusingknitr::rmarkdownon Jan 23 2025.

Last update: 2024-12-24
Started: 2024-12-24

Statistical Summaries of Conditional Probability Tables

Rendered fromStatistics.Rmdusingknitr::rmarkdownon Jan 23 2025.

Last update: 2023-04-11
Started: 2023-04-11

Tracking Scores Over Time

Rendered fromTimeSeries.Rmdusingknitr::rmarkdownon Jan 23 2025.

Last update: 2023-07-18
Started: 2023-04-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Tools for Creating Conditional Probability Tables	CPTtools-package CPTtools
Data from ACED field trial	ACED ACED.items ACED.posttest ACED.prePost ACED.pretest ACED.QEM ACED.Qmatrix ACED.scores ACED.skillNames ACED.splitHalves ACED.taskNames
Translates between normal and categorical probabilities	areaProbs pvecToCutpoints pvecToMidpoints
This function produces a plot of a conditional probability frame.	barchart.CPF
Credibility intervals for a proportion based on beta distribution	betaci
Builds probability tables from Scored Bayes net output.	build2FactorTab buildFactorTab buildMarginTab marginTab
Builds a list of parents of nodes in a graph	buildParentList
Creates a series of regressions from a covariance matrix	buildRegressions
Builds conditional probability tables from regressions	buildRegressionTables
Calculates DiBello-Dirichlet model probability and parameter tables	calcDDFrame calcDDTable
Creates the probability table for DiBello-Normal distribution	calcDNFrame calcDNTable
Creates the probability table for the discrete partial credit model	calcDPCFrame calcDPCTable
Calculates the log-likelihood for data from a DiBello-Samejima (Normal) distribution	calcDNllike calcDSllike
Creates the probability table for DiBello-Samejima distribution	calcDSFrame calcDSTable
Calculate the conditional probability table for a Noisy-And or Noisy-Min distribution	calcNoisyAndFrame calcNoisyAndTable
Calculate the conditional probability table for a Noisy-Or distribution	calcNoisyOrFrame calcNoisyOrTable
Produces an ordered palate of colours with the same hue.	colorspread
Produces comparison stacked bar charts for two sets of groups	compareBars compareBars2
DiBello-Samejima combination function	Compensatory Conjunctive Disjunctive
Representation of a conditional probability table as an array.	as.CPA CPA is.CPA
Representation of a conditional probability table as a data frame.	as.CPF CPF is.CPF
Compare and observed to an expected conditional probability table.	cptChi2 cptG2 cptKL
Constructs a table of counts from a set of discrete observations.	dataTable
Generates default values for Alpha and Beta parameters	defaultAlphas defaultBetas
Produces a graphical balance sheet for EAP or other univarate statistics.	EAPBal
Assigns effective theta levels for categorical variable	effectiveThetas
Constructs a data frame showing the effective thetas for each parent combination.	eThetaFrame
Calculates the expected weight of evidence from a conditional probability frame.	ewoe.CPF
Builds expected contingency tables.	catTable expTable pvecTable
Functions for measuring rater agreement.	accuracy fcKappa gkLambda
Gets meta data about a conditional probability table.	getTableParents getTableStates
Calculates the Goodman and Kruskal gamma measure of association.	gkGamma
A link function based on Samejima's graded response	gradedResponse
Tests to see if a sequence is ascending or descending	isDecreasing isIncreasing isMonotonic isNondecreasing isNonincreasing
Distinguishes Offset from ordinary rules.	getOffsetRules isOffsetRule setOffsetRules
Accuracy and Expected Accuracy Matrixes for Langauge Test.	language16 language24 Language_exp Language_modal
Tests for conditional independence between two variables given a third	ciTest localDepTest
Finds an MAP estimate for a discrete partial credit CPT	mapDPC
Grades on 5 mathematics tests from Mardia, Kent and Bibby	MathGrades
Orders variables using Maximum Cardinality search	mcSearch
Calculates Mutual Information for a two-way table.	mutualInformation
Normalizes a conditional probability table.	normalize normalize.array normalize.CPA normalize.CPF normalize.data.frame normalize.default normalize.matrix normalize.table
Link function using a normal regression.	normalLink
Splits a mixed data frame into a numeric matrix and a factor part.	factorPart numericPart
Observable Characteristic Plot	OCP OCP2
Plots a conditional probability distribuiton with data overlayed	OCP.CPF OCP2.CPF
Conjunctive combination function with one difficulty per parent.	OffsetConjunctive OffsetDisjunctive
Parses Probability Vector Strings	parseProbVec parseProbVecRow
A link function based on the generalized partial credit model	partialCredit
Produces a simplex plot of probability vectors.	plotsimplex simplex_vertex_projection
Produce cumulative sum credibility intervals	proflevelci
Reads a file of histories of marginal distributions.	readHistory
Rescales the numeric part of the table	normalizeTable rescaleTable
Scales a matrix to have a unit diagonal	scaleMatrix
Scales a table according to the Sum and Scale column.	scaleTable
Produces a hanging barplot	stackedBarplot
Produces a stacked, staggered barplot	stackedBars
Finds graphical structure from a covariance matrix	structMatrix
Weight of Evidence Balance Sheet	woeBal
Creates weights of evidence from a history matrix.	woeHist

Package: CPTtools 0.8-4

CPTtools: Tools for Creating Conditional Probability Tables

Building Bayesian networks using regression

Conditional Probability Frames and Arrays

Discrete Partial Credit Models

Graphing Discrete Bayesian Networks

Measues of Agreement

Parameter Estimation

Reference Distributions

Statistical Summaries of Conditional Probability Tables

Tracking Scores Over Time

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)