Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / pbs-assess/sdmTMB issues and pull requests

#235 - Fix ELPD

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

#227 - Does an extra_time argument still exist?

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

#225 - Fix mixture scaling for mixture families

Issue - State: closed - Opened by ericward-noaa over 1 year ago - 6 comments

#224 - Improve tidy() handing of range with anisotropy

Issue - State: open - Opened by seananderson over 1 year ago

#208 - error handling / factors and chars

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

#207 - Add more handling for binomial factors

Issue - State: open - Opened by ericward-noaa over 1 year ago - 1 comment

#206 - Add time-varying effects to tidy()

Issue - State: open - Opened by seananderson over 1 year ago - 1 comment

#200 - Add support for spatial DLM

Issue - State: open - Opened by ericward-noaa over 1 year ago

#199 - fix(plot_anisotropy*): Returns NULL if no H

Pull Request - State: closed - Opened by kellijohnson-NOAA over 1 year ago

#198 - `plot_anisotropy()` fails when `sdmTMB(anisotropy = FALSE)`

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

#197 - Spatial trend vignette should add fixed effect + zeta_s

Issue - State: closed - Opened by seananderson over 1 year ago

#194 - Release sdmTMB 0.4.0

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

#193 - Look into waywiser compatibility

Issue - State: open - Opened by seananderson over 1 year ago

#191 - Fix aniso print

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

#190 - Issue # 184

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

#186 - Check poisson-link delta models

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

#184 - Fix handling of factors

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

#182 - Use additional Newton optimization by default

Issue - State: closed - Opened by seananderson almost 2 years ago

#176 - `print()` should check `sanity()` and warn if something looks off

Issue - State: closed - Opened by seananderson almost 2 years ago
Labels: enhancement, good first issue

#174 - Allow standard errors on overall predictions from delta models

Issue - State: closed - Opened by seananderson almost 2 years ago - 1 comment
Labels: enhancement

#172 - Visreg Error: Specified time column is missing from data

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

#170 - Warn in `make_mesh()` if a mesh looks overly complex

Issue - State: closed - Opened by seananderson almost 2 years ago
Labels: enhancement, good first issue

#169 - Release sdmTMB 0.3.0

Issue - State: closed - Opened by seananderson almost 2 years ago

#166 - Add sub-regions to get_index()

Issue - State: closed - Opened by ericward-noaa almost 2 years ago - 2 comments

#165 - sdmTMB_cv: object not found w/ offset

Issue - State: closed - Opened by CamFreshwater almost 2 years ago - 4 comments
Labels: bug

#164 - Release sdmTMB 0.2.2

Issue - State: closed - Opened by seananderson almost 2 years ago

#163 - Add error message to predict() when `re_form_iid` is not specified but new levels in newdata

Issue - State: closed - Opened by seananderson almost 2 years ago
Labels: bug, good first issue

#162 - Recognize time as non-numeric?

Issue - State: closed - Opened by ericward-noaa almost 2 years ago - 4 comments
Labels: bug

#160 - combined predictions from delta/hurdle model not working as described

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

#159 - Add variable meshes by time step

Issue - State: open - Opened by ericward-noaa almost 2 years ago - 3 comments
Labels: enhancement

#158 - Fix 'Additional issues' CRAN checks

Issue - State: closed - Opened by seananderson almost 2 years ago - 4 comments
Labels: bug

#157 - Add anisotropy to model print()

Issue - State: closed - Opened by ecophilina almost 2 years ago

#156 - Expand sdmTMB_cv to also include leave future out cross validation

Pull Request - State: closed - Opened by ericward-noaa almost 2 years ago

#155 - Add LFOCV to cross validation sdmTMB_cv

Issue - State: closed - Opened by ericward-noaa almost 2 years ago
Labels: enhancement

#154 - Fix quadratic summary stats with delta models

Pull Request - State: open - Opened by ericward-noaa almost 2 years ago

#153 - class of `delta_*()` families is `"list"` not `"family"`

Issue - State: closed - Opened by kellijohnson-NOAA almost 2 years ago - 1 comment

#152 - Add type of spatiotemporal field to print output

Issue - State: closed - Opened by seananderson almost 2 years ago - 1 comment
Labels: enhancement, good first issue

#149 - Improve reporting of range with anisotropic models

Issue - State: closed - Opened by seananderson almost 2 years ago - 2 comments
Labels: enhancement, good first issue

#148 - Develop wiki/vignette/chapter of user guide on mesh guidance

Issue - State: open - Opened by seananderson almost 2 years ago
Labels: enhancement, help wanted

#147 - Add Metabolic Index features

Issue - State: open - Opened by jindivero almost 2 years ago
Labels: enhancement

#146 - Add std normal

Issue - State: open - Opened by ericward-noaa almost 2 years ago - 4 comments
Labels: enhancement

#141 - Ece mixtures

Pull Request - State: closed - Opened by ericward-noaa about 2 years ago - 5 comments

#140 - predict(...., type= "response", se_fit = T) gives both est and se as link

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

#135 - Add 2 more tests: d() argument in t2, and factor smooths (bs = "fs")

Pull Request - State: closed - Opened by ericward-noaa about 2 years ago - 1 comment

#130 - Allow prediction on new data with missing time elements

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

#127 - passing family as variable to sdmTMB_cv

Issue - State: closed - Opened by seanhardison1 about 2 years ago - 6 comments
Labels: bug

#112 - `Error when reading the variable: 'proj_mesh'` with TMB 1.9.1

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

#110 - predict() function issues

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

#109 - Append threshold covariates to simulated data

Issue - State: closed - Opened by ericward-noaa over 2 years ago - 1 comment
Labels: enhancement, good first issue

#108 - Nonstationary and threshold models

Pull Request - State: closed - Opened by ericward-noaa over 2 years ago - 3 comments

#107 - predict with nsim > 0 fails with multiple spatially varying terms

Issue - State: closed - Opened by Ax3man over 2 years ago - 2 comments

#106 - issues with simple example

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

#105 - Add support for logit-normal distribution

Issue - State: closed - Opened by ericward-noaa over 2 years ago - 2 comments
Labels: enhancement

#104 - Include functionality for age comp data?

Issue - State: open - Opened by ericward-noaa over 2 years ago
Labels: enhancement

#103 - Add ability to predict using stars data objects

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

#102 - Add vignette on residuals / diagnostics

Issue - State: open - Opened by ericward-noaa over 2 years ago - 1 comment
Labels: enhancement, help wanted

#101 - Add and document ggeffects ggpredict support

Issue - State: open - Opened by seananderson over 2 years ago - 6 comments
Labels: enhancement

#100 - `predict()` makes R session crash in dev branch when passing `newdata`

Issue - State: closed - Opened by kellijohnson-NOAA over 2 years ago - 15 comments

#99 - Visreg error

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

#98 - Error in getUserDLL() : Multiple TMB models loaded. Failed to guess DLL name.

Issue - State: closed - Opened by gfmg over 2 years ago - 6 comments

#97 - Add vignette on forecasting

Issue - State: open - Opened by jindivero over 2 years ago - 6 comments
Labels: enhancement

#96 - Only apply range part of PC matern prior once if range is shared

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

#95 - Add Jacobian transformations for priors

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

#94 - visreg not working for models with RW spatiotemporal fields

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

#93 - Weights argument for binomial models in sdmTMB, mgcv, glm, or glmmTMB

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

#92 - Make predict work with newdata not expanded by time

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

#90 - tidy() doesn't return coefficient estimates for the linear components of smoothers

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

#89 - presence-only-vignette

Pull Request - State: closed - Opened by jindivero over 2 years ago - 3 comments

#87 - Update delta-model vignette to use new built-in delta functionality

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

#86 - Add a function to facilitate projections using TMB simulate()

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

#85 - Add unit testing against VAST

Issue - State: open - Opened by seananderson over 2 years ago - 3 comments
Labels: enhancement

#84 - Make vignette on modelling presence-only data

Issue - State: open - Opened by seananderson over 2 years ago - 7 comments
Labels: enhancement

#83 - Add vignette on using visreg to visualize conditional effects

Issue - State: closed - Opened by seananderson over 2 years ago - 28 comments

#82 - Expand unit testing

Issue - State: closed - Opened by seananderson over 2 years ago

#81 - Doc some warning and stop messages

Pull Request - State: closed - Opened by kellijohnson-NOAA over 2 years ago - 7 comments

#76 - Changes for visreg

Pull Request - State: closed - Opened by ericward-noaa over 2 years ago - 12 comments

#75 - Stacking fold IDs

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

#74 - Parallel processing

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

#72 - sigma function?

Issue - State: open - Opened by ericward-noaa over 2 years ago
Labels: enhancement

#71 - Release sdmTMB 0.2.0

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

#70 - Add dispersion formula interface

Issue - State: open - Opened by seananderson almost 3 years ago
Labels: enhancement, help wanted

#68 - CAR model development

Issue - State: open - Opened by ericward-noaa almost 3 years ago - 9 comments
Labels: enhancement

#66 - Clean up documentation throughout

Issue - State: closed - Opened by seananderson almost 3 years ago

#65 - Allow spatial_varying to use a full model matrix

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

#64 - Make normalize = TRUE work with IID random effects and REML

Issue - State: open - Opened by ecophilina almost 3 years ago
Labels: enhancement

#62 - Consider adding 'exclude' to predict.sdmTMB

Issue - State: open - Opened by seananderson about 3 years ago
Labels: enhancement

#61 - Make something similar to plot.gam to quickly visualize smoothers

Issue - State: closed - Opened by seananderson about 3 years ago - 15 comments

#60 - Check for mgcv::s(..., bs = 're') and issue an error

Issue - State: closed - Opened by seananderson about 3 years ago

#59 - Make sdmTMB() work without a mesh if all fields are turned off

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

#52 - quantile residuals for sdmTMB_cv fit

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

#46 - Add tmbstan examples, vignette, and predict function

Issue - State: closed - Opened by seananderson over 3 years ago - 1 comment
Labels: enhancement

#45 - Implement simulation from the joint precision matrix

Issue - State: closed - Opened by seananderson over 3 years ago - 6 comments