Package: EstimationTools 4.3.0

EstimationTools: Maximum Likelihood Estimation for Probability Functions from Data Sets

Total Time on Test plot and routines for parameter estimation of any lifetime distribution implemented in R via maximum likelihood (ML) given a data set. It is implemented thinking on parametric survival analysis, but it feasible to use in parameter estimation of probability density or mass functions in any field. The main routines 'maxlogL' and 'maxlogLreg' are wrapper functions specifically developed for ML estimation. There are included optimization procedures such as 'nlminb' and 'optim' from base package, and 'DEoptim' Mullen (2011) <doi:10.18637/jss.v040.i06>. Standard errors are estimated with 'numDeriv' Gilbert (2011) <https://CRAN.R-project.org/package=numDeriv> or the option 'Hessian = TRUE' of 'optim' function.

Authors:Jaime Mosquera [aut, cre], Freddy Hernandez [ctb]

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EstimationTools/json (API)
NEWS

# Install 'EstimationTools' in R:
install.packages('EstimationTools', repos = c('https://jaimemosg.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/jaimemosg/estimationtools/issues

Datasets:

On CRAN:

distance-samplingmaximum-likelihood-estimationttt-plot

6.07 score 4 stars 1 packages 97 scripts 341 downloads 35 exports 83 dependencies

Last updated 1 years agofrom:c3ac130027. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 16 2024
R-4.5-winNOTENov 16 2024
R-4.5-linuxNOTENov 16 2024
R-4.4-winNOTENov 16 2024
R-4.4-macNOTENov 16 2024
R-4.3-winOKNov 16 2024
R-4.3-macOKNov 16 2024

Exports:bootstrap_maxlogLcoefManycum_hazard_funcum_hazard.maxlogLexpected_valueexpected_value.maxlogLextract_fun_argsfo_and_dataformula2Survgauss_quadhalf_norm_keyhazard_funhazard_rate_keyHazard_Shapeidentityintegrationinterp.optionsis.EmpiricalTTTis.HazardShapeis.maxlogLis.optimizer.configlegend.HazardShapeloess.optionslog_linklogit_linkmaxlogLmaxlogLregNegInv_linknull_maxlogLsaturated_maxlogLset_optimizersummateTTT_hazard_shapeTTTE_Analyticaluniform_key

Dependencies:abindautoimagebackportsBBmiscBHbootbroomcarcarDatacheckmateclicodetoolscolorspacecowplotcpp11crayondata.tableDEoptimDerivdoBydotCall64dplyrfansifarverfieldsforeachFormulaGAgaussquadgenericsggplot2gluegtableisobanditeratorslabelinglatticelifecyclelme4magrittrmapprojmapsMASSMatrixMatrixModelsMBAmgcvmicrobenchmarkminqamodelrmunsellnlmenloptrnnetnumDerivorthopolynompbkrtestpillarpkgconfigpolynompurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackrlangscalesspamSparseMstringistringrsurvivaltibbletidyrtidyselectutf8vctrsviridisLitewithr

Bootstrap implementation

Jaime Mosquera

Rendered fromBootstrap_implementation.Rmdusingknitr::rmarkdownon Nov 16 2024.

Last update: 2021-03-14
Started: 2019-08-06

Estimation with maxlogL objects

Jaime Mosquera

Rendered fromExamples.Rmdusingknitr::rmarkdownon Nov 16 2024.

Last update: 2021-03-24
Started: 2020-07-31

Readme and manuals

Help Manual

Help pageTopics
Acute Lymphoblastic Leukemia, table 4.1ALL_colosimo_table_4_1
Acute Lymphoblastic Leukemia, table 4.3ALL_colosimo_table_4_3
Bootstrap computation of standard error for 'maxlogL' class objects.bootstrap_maxlogL
Extract Model Coefficients in a 'maxlogL' Fitscoef.maxlogL coefMany oefficients
Cumulative hazard functions for any distributioncum_hazard_fun
Cumuative hazard function of a 'maxlogLreg' model.cum_hazard.maxlogL
Expected value of a given function for any distributionexpected_value
Expected value of a 'maxlogLreg' model.expected_value.maxlogL
Tensile strengthsFibers
Numerical integration through Gaussian Quadraturegauss_quad
Half normal key functionhalf_norm_key
Hazard functions for any distributionhazard_fun
Hazard rate key functionhazard_rate_key
Head and neck cancerhead_neck_cancer
Integrationintegration
Configure various aspects of interpolating function in 'TTT_hazard_shape'interp.options
Is return of any object of 'EstimationTools'?is.EmpiricalTTT is.HazardShape is.maxlogL is.optimizer.config
Customize legend for 'plot.HazardShape' outputslegend.HazardShape
Configure various aspects of LOESS in 'TTT_hazard_shape'loess.options
Logarithmic link function (for estimation with 'maxlogL' object)log_link
Logit link function (for estimation with 'maxlogL' object)logit_link
Maximum Likelihood Estimation for parametric distributionsmaxlogL
Maximum Likelihood Estimation for parametric linear regression modelsmaxlogLreg
Negative inverse link function (for estimation with 'maxlogL' object)NegInv_link
Plot method for 'EmpiricalTTT' objectsplot.EmpiricalTTT
Plot of 'HazardShape' objectsplot.HazardShape
Plot Residual Diagnostics for an 'maxlogL' Objectplot.maxlogL
Predict Method for 'maxlogL' Fitspredict.maxlogL
Print method for 'HazardShape' objectsprint.HazardShape
Reduction cellsreduction_cells
Extract Residuals from 'maxlogL' model.residuals.maxlogL
Set custom optimizer in 'maxlogLreg'set_optimizer
Summarize Maximum Likelihood Estimationsummary.maxlogL
Summation of One-Dimensional Functionssummate
Hazard Shape estimation from TTT plotTTT_hazard_shape TTT_hazard_shape.EmpiricalTTT TTT_hazard_shape.formula
Empirical Total Time on Test (TTT), analytic version.TTTE_Analytical
Uniform key functionuniform_key