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Multi state#244

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adibender wants to merge 85 commits intomasteradibender/pammtools:masterfrom multi-stateadibender/pammtools:multi-stateCopy head branch name to clipboard

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Commits

Commits on Jan 8, 2024

• Add additional test for multistate. So far only example

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Commits on Jan 9, 2024

• Add temporary folder to upload debugging files, can be deleted when finished

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• Added split-data.R functions to debug

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Commits on Jan 10, 2024

• Fix error 'get_cut applied to an object of class list' by specifying get_cut.list

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• seperate debugging file in functions and script

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Commits on Jan 15, 2024

• Added dimensionality tests for as_ped_multistate

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Commits on Feb 26, 2024

• initial version of add_trans_prob

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• pammtools comparison with beyersmann example

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Commits on Feb 28, 2024

• update add_trans_prob and run scripts so that make_newdata with groups other than transition works. not final yet. Add abstract example mgus2 run script

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Commits on Mar 1, 2024

• add run script of survival package example. excessive runtime for fitting gam

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• include scam class in warn_about_time_points to accept scam splines

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• fix type in warning

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• add x-make.scam for scam objects2

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• add object class scam

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• Bugfix of hard coded dimensions

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• add all calculated examples

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• add some comments

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Commits on Mar 11, 2024

• update picture of hgb spline for iwsm abstract

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• update transition probability picture

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Commits on Mar 12, 2024

• rename plots with different effects: contour, groups

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• push up-to-date code for sample calculation

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• add comment

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Commits on Mar 14, 2024

• add new figure for iwsm abstract with contour lines

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• update code to calculate example

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Commits on Mar 18, 2024

• add iwsm files

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• add debugging file of fct trans_prob: improve performance, debugging, and commenting

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Commits on Mar 21, 2024

• Performance update transition matrices, testing on large dataset ndata

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• initial simulation file for debugging transition probability code

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Commits on Apr 25, 2024

• initial simulation codes for msm

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Commits on May 13, 2024

• added new simulations and extended beyersmann example calculations for sanity checks of add_transition_probabilities

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Commits on May 22, 2024

• add comparison of mvna results and pammtools for multistate with time dependent 1-2 hazard

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• up-to-date-code

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• up-to-date files

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• re-organize simulations

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• re-name

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• add basic example

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• throw out simulation code from beyersmann msm example

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Commits on Jun 3, 2024

• bugfixes and minor changes

  johannespiller

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Commits on Jun 4, 2024

• initial comparison example to cox with recurrent events and multistate

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Commits on Jun 17, 2024

• update examples used for IWSM Mini Paper for poster session

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Commits on Jun 27, 2024

• add add_trans_prob

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• update simulation and example codes

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• add further simulation results

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• add further example figures for iwsm and useR

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Commits on Jul 9, 2024

• add_trans_prob: wrapper w/o ci

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• include lines of code to debug wrapper

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Commits on Jul 10, 2024

• debugging and building of confidence intervals

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Commits on Jul 11, 2024

• add add_trans_ci function

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Commits on Jul 12, 2024

• include add_trans_ci in add_functions

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• initial version for multistate vignette with prothr example from workshop

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Commits on Jul 30, 2024

• add keyword to use get_sim_cumu

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Commits on Aug 1, 2024

• optimize add_trans_ci code to reduce data storage

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• include AJ estimator

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• update docu

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• Merge remote-tracking branch 'origin/master' into multi-state

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Commits on Aug 6, 2024

• push tmp folder

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• merge conflict man

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• merge conflict

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• resolve descr and namespace

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• multi state helpers

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• include add_trans_ci in add_trans_prob

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Commits on Aug 7, 2024

• resolve error

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• commit all changes due to errors loading the package

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• remove .Rdata

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Commits on Aug 8, 2024

• push most current multi state version

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Commits on Aug 12, 2024

• comparision of transition probabilities are added

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• change colors of plots

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• correct wrong data table test

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• delete print statements

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• most current version

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Commits on Aug 30, 2024

• include minimax fct to overcome well-definedness issues as a quick fix

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• include test for add_trans_prob fct

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Commits on Sep 12, 2024

• adapt split-data.R to work with variable cut. Include event time points when needed

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• save debugging file for next weekly

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Commits on Sep 17, 2024

• debug split-data max_time. now working for multi state data as well

  johannespiller

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• fix error message of tests: outcome var was not defined in cut-points.R

  johannespiller

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• fix error message: include mstate package to load prothr data for testthat

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• fix error message: include multi-state vignette in pkgdown

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Commits on Sep 18, 2024

• fix error with geom_stepribbon: no manual found, copied code from master

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• add manuals which have been missing, created using devtools::document()

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• update namespace and documentation with missing fcts

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• debugging error messages in from package

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• Fix headline and exclude tidyverse lib

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• add msm and mvna library to website

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Commits on Jan 15, 2025

• msm vignette current version

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