Ecosyste.ms: Issues

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GitHub / chjackson/flexsurv-dev issues and pull requests

#170 - Analytic second derivatives

Issue - State: open - Opened by chjackson about 1 year ago
Labels: enhancement

#168 - faster bootstrap iterations for large data?

Issue - State: open - Opened by markdanese about 1 year ago - 3 comments

#167 - Splines not supported by standsurv without specifying newdata

Issue - State: open - Opened by markdanese about 1 year ago - 1 comment

#165 - use anyNA and outer negation

Pull Request - State: closed - Opened by ndunnewind over 1 year ago - 1 comment

#164 - Pass required values to sprintf

Pull Request - State: closed - Opened by ndunnewind over 1 year ago - 1 comment

#163 - `sim.fmsm()` different results with `tidy=TRUE` vs `tidy=FALSE`

Issue - State: open - Opened by mafed over 1 year ago - 2 comments

#162 - Inconsistent standard errors when rescaling continuous covariates

Issue - State: closed - Opened by JoshVeasy over 1 year ago - 2 comments

#160 - Fix p-value issue with tidy() and add unit test

Pull Request - State: closed - Opened by mattwarkentin over 1 year ago - 2 comments

#159 - P-values from flexsurv are wrong (half the value they should be)

Issue - State: closed - Opened by huftis over 1 year ago - 3 comments

#158 - Calibrating and validating flexsurvspline model

Issue - State: closed - Opened by lgondara over 1 year ago - 2 comments

#156 - Standsurv

Pull Request - State: closed - Opened by mikesweeting over 1 year ago - 1 comment

#155 - Update to "tidy" format for predictions

Pull Request - State: closed - Opened by hfrick over 1 year ago - 2 comments

#154 - `standsurv`: contrast time to certain quantiles of events

Issue - State: closed - Opened by hezht3 over 1 year ago - 4 comments

#153 - Expected number of visits from a `fmsm()` model

Issue - State: open - Opened by mattwarkentin over 1 year ago - 1 comment
Labels: enhancement

#152 - allow conditional sampling in 'sim.fmsm()' ?

Issue - State: open - Opened by kkmann over 1 year ago - 4 comments

#151 - unified documentation of 'start' paramter via roxygen @templates

Pull Request - State: closed - Opened by kkmann over 1 year ago - 1 comment

#150 - clarify 'start' paramter in 'simulate.flexsurvreg()'

Issue - State: closed - Opened by kkmann over 1 year ago - 2 comments

#149 - partial argument matching

Issue - State: closed - Opened by sebffischer over 1 year ago - 1 comment

#148 - Fixes for standsurv

Pull Request - State: closed - Opened by mikesweeting almost 2 years ago - 3 comments

#147 - Fix for dev purrr

Pull Request - State: closed - Opened by hadley almost 2 years ago - 2 comments

#146 - `predict.flexsurvreg()` without covariates

Issue - State: closed - Opened by ndunnewind almost 2 years ago - 3 comments

#145 - Automatically Extracting Parameters for Prediction Interval

Issue - State: closed - Opened by AustinFournierKL almost 2 years ago - 3 comments

#144 - Enable `.` in formula for `flexsurvreg()`

Pull Request - State: closed - Opened by hfrick almost 2 years ago - 1 comment

#143 - Enable `.` in formula

Issue - State: closed - Opened by hfrick almost 2 years ago - 4 comments

#142 - Missing or infinite values in "X" when fitting model?

Issue - State: closed - Opened by AustinFournierKL almost 2 years ago - 7 comments

#141 - FlexSurvMix Data Format / Model

Issue - State: closed - Opened by AustinFournierKL about 2 years ago - 4 comments

#140 - Age as the time-scale

Issue - State: closed - Opened by Xueke1001 about 2 years ago - 2 comments

#139 - Problem with flexsurvreg Weibull AFT

Issue - State: closed - Opened by AustinFournierKL about 2 years ago - 3 comments

#138 - simulate implementation

Issue - State: closed - Opened by mclements about 2 years ago - 6 comments

#137 - path detection in fmixmsm()

Issue - State: closed - Opened by kkmann about 2 years ago - 5 comments

#136 - Custom distributions using ActuDistns

Issue - State: closed - Opened by RossHamil about 2 years ago - 3 comments
Labels: help wanted

#135 - Some distribution functions return `-Inf` for `q<0` and `lower.tail = FALSE`

Issue - State: closed - Opened by ndunnewind about 2 years ago - 1 comment

#133 - Next CRAN release?

Issue - State: closed - Opened by hfrick over 2 years ago - 3 comments

#132 - Standsurv

Pull Request - State: closed - Opened by mikesweeting over 2 years ago

#131 - New S3 methods for fmsm objects

Issue - State: open - Opened by mattwarkentin over 2 years ago - 2 comments
Labels: enhancement

#130 - Standsurv

Pull Request - State: closed - Opened by mikesweeting over 2 years ago - 1 comment

#129 - Prediction after manually editing coefficient values

Issue - State: closed - Opened by vincentarelbundock over 2 years ago - 2 comments

#128 - Further functionality added to standsurv

Pull Request - State: closed - Opened by mikesweeting over 2 years ago

#127 - Bare minimum flexsurvreg object for making predictions

Issue - State: closed - Opened by mattwarkentin over 2 years ago - 21 comments

#126 - Allow predictions at time zero, fix list-column class

Pull Request - State: closed - Opened by mattwarkentin over 2 years ago - 1 comment

#125 - Competing risks: Joint likelihood versus cause-specific likelihoods

Issue - State: closed - Opened by mattwarkentin over 2 years ago - 2 comments

#124 - Customizing own distribution for flexsurvreg

Issue - State: closed - Opened by esther1262 over 2 years ago - 4 comments

#123 - estimate shared shape parameter with flexsurvreg and log-logistic distribution

Issue - State: closed - Opened by esther1262 over 2 years ago - 8 comments
Labels: help wanted

#122 - Clean up predict and broom functions and expand test coverage

Pull Request - State: closed - Opened by mattwarkentin over 2 years ago - 5 comments

#121 - Catching segfaults when using certain distributions with `flexsurvreg`

Issue - State: closed - Opened by mattwarkentin over 2 years ago - 2 comments

#120 - `summary.flexsurvreg(type = "hazard")` breaks for `NA` in `newdata`

Issue - State: closed - Opened by hfrick over 2 years ago - 5 comments

#119 - Clustering/incorporating shared-frailties/random-effects amongst groups

Issue - State: closed - Opened by josephjzhao over 2 years ago - 1 comment

#118 - Fix predict.flexsurvreg to work with rewrite of summary.flexsurvreg

Pull Request - State: closed - Opened by mattwarkentin over 2 years ago - 2 comments

#117 - predict might be somewhat broken with summary rewrite

Issue - State: closed - Opened by mattwarkentin over 2 years ago - 2 comments

#116 - Case weights are ignored by flexsurvspline when calculating knot locations

Issue - State: open - Opened by mikesweeting over 2 years ago - 1 comment
Labels: enhancement

#115 - Using `flexsurv` to fit a piecewise exponential model

Issue - State: open - Opened by elong0527 over 2 years ago - 4 comments
Labels: enhancement

#114 - Standsurv

Pull Request - State: closed - Opened by mikesweeting over 2 years ago - 1 comment

#113 - Negative hazard from hsurvspline

Issue - State: closed - Opened by Hark-Jin over 2 years ago - 4 comments

#112 - Include distribution functions in documentation

Pull Request - State: closed - Opened by ndunnewind over 2 years ago - 1 comment

#111 - Marginal (standardized) survival and other measures

Pull Request - State: closed - Opened by mikesweeting almost 3 years ago - 2 comments

#110 - flexsurvspline has optimization issues given LTRC data

Issue - State: closed - Opened by asondhi almost 3 years ago - 2 comments

#109 - Improve dbase.survspline performance

Pull Request - State: closed - Opened by ndunnewind almost 3 years ago - 2 comments

#108 - Fix typos in documentation

Pull Request - State: closed - Opened by ndunnewind almost 3 years ago - 1 comment

#107 - Fixed typo

Pull Request - State: closed - Opened by ellessenne almost 3 years ago - 1 comment

#106 - Fix qgeneric without args

Pull Request - State: closed - Opened by ndunnewind almost 3 years ago - 1 comment

#105 - Equation for flexible parametric survival model

Issue - State: closed - Opened by mattwarkentin almost 3 years ago - 4 comments

#104 - combining individual transition specific models fit with flexsurv

Issue - State: closed - Opened by svd09 almost 3 years ago - 2 comments

#103 - Fix tidy function to return baseline dist parameters

Pull Request - State: closed - Opened by mattwarkentin almost 3 years ago - 2 comments

#102 - Standardised survival

Issue - State: closed - Opened by mikesweeting almost 3 years ago - 2 comments

#101 - Error in calculating log-hazard under lognormal distribution (hlnorm)

Issue - State: closed - Opened by harrisonreeder about 3 years ago - 1 comment

#100 - pmatrix.fs - specifying a different starting time?

Issue - State: closed - Opened by eiriksko about 3 years ago - 2 comments

#99 - Migrate to GitHub Actions

Pull Request - State: closed - Opened by mattwarkentin about 3 years ago - 1 comment

#98 - Added start parameter to predict.flexsurvreg

Pull Request - State: closed - Opened by mattwarkentin over 3 years ago - 4 comments

#97 - Add start argument to predict.flexsurvreg method

Issue - State: closed - Opened by mattwarkentin over 3 years ago - 1 comment

#96 - Discrepant results between flexsurvreg and flexsurvspline

Issue - State: closed - Opened by mattwarkentin over 3 years ago

#95 - Can't Tidy Exponential Model

Issue - State: closed - Opened by ApexHeel over 3 years ago - 1 comment

#94 - Extend the ability of hgengamma with simple change to how hgengamma is calculated

Issue - State: closed - Opened by swihart over 3 years ago - 1 comment

#93 - Flexible parametric competing risks models

Issue - State: open - Opened by mattwarkentin over 3 years ago - 1 comment
Labels: enhancement

#92 - parametrization of gamma AFT model

Issue - State: closed - Opened by FBartos over 3 years ago - 2 comments

#91 - Warnings during model fitting

Issue - State: open - Opened by chjackson over 3 years ago - 2 comments

#90 - Cumulative incidence function from cause-specific flexsurv models

Issue - State: closed - Opened by mattwarkentin over 3 years ago - 14 comments

#89 - "initial value in 'vmmin' is not finite" error for flexsurvspline

Issue - State: closed - Opened by Erikwjoh almost 4 years ago - 3 comments

#88 - Parameter output from non-convergent models?

Issue - State: closed - Opened by sbae almost 4 years ago - 2 comments

#87 - [ready to review] switching to numDeriv::hessian by default for flexsurvmix

Pull Request - State: closed - Opened by kkmann about 4 years ago - 1 comment

#86 - activate bash strict mode for CI

Issue - State: closed - Opened by kkmann about 4 years ago - 4 comments

#84 - [WIP] replace solve( with chol2inv(chol for hessian -> covariance matrix

Pull Request - State: closed - Opened by kkmann about 4 years ago - 3 comments

#83 - [WIP] fix "number of items to replace is not a multiple of replacement length" for sim.fmsm

Pull Request - State: closed - Opened by kkmann about 4 years ago - 2 comments

#82 - bugfix sim.fmsm

Pull Request - State: closed - Opened by kkmann about 4 years ago - 1 comment

#81 - Account for case weights in survival and cumulative hazard KM plots

Pull Request - State: closed - Opened by andbe about 4 years ago - 1 comment

#80 - Does `sim.fmsm` take into account coefficient uncertainty?

Issue - State: closed - Opened by sdaza about 4 years ago - 4 comments

#79 - Cumulative baseline hazard for relative survival models

Issue - State: closed - Opened by heor-robyoung over 4 years ago - 13 comments

#78 - More methods needed for residuals.flexsurvreg

Issue - State: open - Opened by chjackson over 4 years ago - 8 comments
Labels: enhancement

#77 - added S3 methods for predict, residuals, and broom funs

Pull Request - State: closed - Opened by mattwarkentin over 4 years ago - 16 comments

#76 - Add S3 method for anova generic

Issue - State: closed - Opened by mattwarkentin over 4 years ago - 4 comments

#75 - Develop out S3 methods for predict and broom generics

Issue - State: closed - Opened by mattwarkentin over 4 years ago - 24 comments

#74 - Log logistic and Gompertz - warning messages (not converging)

Issue - State: closed - Opened by tku23 over 4 years ago - 2 comments
Labels: help wanted

#73 - Cannot call pmatrix.simfs from inside a function

Issue - State: closed - Opened by nskourlis over 4 years ago - 1 comment

#71 - support for broom

Issue - State: closed - Opened by kkmann over 4 years ago - 3 comments

#70 - No 'nobs' method for flexsurvreg

Issue - State: closed - Opened by Chris-Angell over 4 years ago - 3 comments