Ecosyste.ms: Issues

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

GitHub / NetCoupler/NetCoupler issues and pull requests

#192 - Find alternative to igraph?

Issue - State: open - Opened by lwjohnst86 almost 2 years ago - 2 comments
Labels: bug

#191 - Adding sections to the draft paper

Pull Request - State: open - Opened by lwjohnst86 over 2 years ago

#190 - Some dependencies don't exist on fresh install R version

Issue - State: open - Opened by danielwitte over 2 years ago - 2 comments
Labels: bug

#188 - Fix cph

Issue - State: closed - Opened by lwjohnst86 almost 3 years ago

#187 - Add reference to method

Issue - State: open - Opened by lwjohnst86 almost 3 years ago

#186 - Completed several tasks to prep for submission

Pull Request - State: closed - Opened by lwjohnst86 almost 3 years ago

#185 - Add documentation on using the classification options list argument

Issue - State: closed - Opened by lwjohnst86 almost 3 years ago
Labels: documentation

#184 - Re-write adjustment variable input so it can mimic writing it like in the formula

Issue - State: open - Opened by lwjohnst86 almost 3 years ago
Labels: bug, infrastructure

#181 - Provide examples for different study designs?

Issue - State: open - Opened by lwjohnst86 almost 3 years ago

#180 - Release NetCoupler 0.1.0

Issue - State: closed - Opened by lwjohnst86 almost 3 years ago - 1 comment

#179 - Content to include or consider for "description" vignette.

Issue - State: open - Opened by lwjohnst86 almost 3 years ago

#178 - Exceptions to log-transforming/standardizing?

Issue - State: open - Opened by lwjohnst86 almost 3 years ago

#176 - Try to follow rOpenSci guidelines

Issue - State: open - Opened by lwjohnst86 almost 3 years ago

#175 - Comments from review of the website

Issue - State: closed - Opened by danielibsen almost 3 years ago - 5 comments

#174 - Use lavaan to simulate data. Closes #168

Pull Request - State: closed - Opened by lwjohnst86 almost 3 years ago

#173 - Brainstorm methods paper

Issue - State: open - Opened by lwjohnst86 almost 3 years ago - 3 comments
Labels: documentation

#172 - Instead of p-values use s-values?

Issue - State: open - Opened by lwjohnst86 about 3 years ago
Labels: discussion

#170 - Add missingness directly to simulated data

Issue - State: closed - Opened by lwjohnst86 over 3 years ago - 1 comment

#169 - Look into butcher and parsnip packages to deal with speed and memory issues

Issue - State: open - Opened by lwjohnst86 over 3 years ago
Labels: infrastructure

#168 - Use lavaan instead of dagitty to simulate the DAG

Issue - State: closed - Opened by lwjohnst86 over 3 years ago
Labels: infrastructure

#167 - Use checkmate instead of assertive

Issue - State: closed - Opened by lwjohnst86 over 3 years ago - 1 comment
Labels: enhancement, infrastructure

#166 - Include all model outputs from estimation output

Issue - State: closed - Opened by lwjohnst86 over 3 years ago - 1 comment

#165 - (If needed) to extract formula variables use rhs() and lhs()

Issue - State: closed - Opened by lwjohnst86 over 3 years ago - 1 comment

#164 - Task list and discussion items for initial version release

Issue - State: closed - Opened by lwjohnst86 over 3 years ago

#163 - Brainstorm publication outlet and type

Issue - State: open - Opened by lwjohnst86 almost 4 years ago - 2 comments

#162 - Explore other methods to compare models, other than p-value

Issue - State: open - Opened by lwjohnst86 almost 4 years ago

#161 - Include documentation about using strata before hand

Issue - State: closed - Opened by lwjohnst86 almost 4 years ago - 1 comment
Labels: documentation

#160 - Adjustment variable list argument use tidyselect instead?

Issue - State: open - Opened by lwjohnst86 almost 4 years ago

#159 - Cluster within model argument list?

Issue - State: closed - Opened by lwjohnst86 almost 4 years ago
Labels: bug

#158 - Adjusting has some pattern selection problems

Issue - State: closed - Opened by lwjohnst86 almost 4 years ago - 1 comment
Labels: bug

#157 - Include manual thresholds for direct effect classification

Issue - State: closed - Opened by lwjohnst86 almost 4 years ago - 2 comments

#156 - Incorporate direct effect adjustment

Issue - State: closed - Opened by lwjohnst86 almost 4 years ago - 1 comment

#155 - Use ggdag for making plots instead of ggraph?

Issue - State: open - Opened by lwjohnst86 about 4 years ago

#154 - Remove dots on args and internal functions

Pull Request - State: closed - Opened by lwjohnst86 about 4 years ago - 1 comment

#153 - Compare standardize unlogged vs logged results

Issue - State: open - Opened by lwjohnst86 about 4 years ago

#152 - Simulate another dataset using real variable names

Issue - State: open - Opened by lwjohnst86 about 4 years ago - 2 comments

#151 - Reconsider adjusting for DE afterward

Issue - State: closed - Opened by lwjohnst86 over 4 years ago - 1 comment

#149 - Strip out data processing steps in plotting functions

Issue - State: open - Opened by lwjohnst86 over 4 years ago

#147 - Missing values not allowed in ppcor::pcor

Issue - State: closed - Opened by lwjohnst86 over 4 years ago - 1 comment
Labels: bug

#146 - Speed improvements ideas

Issue - State: open - Opened by lwjohnst86 over 4 years ago

#145 - Split out adjacency matrix from plot. Have as lone function

Issue - State: closed - Opened by lwjohnst86 over 4 years ago

#144 - Regressing on in standardize doesn't seem to like character/factor vars

Issue - State: closed - Opened by lwjohnst86 over 4 years ago
Labels: bug

#143 - Lots of updates to code for performance, checks, etc

Pull Request - State: closed - Opened by lwjohnst86 over 4 years ago

#141 - Parallelize code at long running sections

Issue - State: closed - Opened by lwjohnst86 over 4 years ago - 3 comments
Labels: enhancement

#140 - Include progress bar in model estimate function

Issue - State: open - Opened by lwjohnst86 over 4 years ago
Labels: enhancement

#139 - Adjust for DE for each iteration

Issue - State: closed - Opened by lwjohnst86 over 4 years ago - 1 comment
Labels: bug

#138 - Use data.table for internal processing?

Issue - State: closed - Opened by lwjohnst86 over 4 years ago - 1 comment
Labels: discussion, infrastructure

#137 - Speed up unit tests a bit

Pull Request - State: closed - Opened by lwjohnst86 over 4 years ago - 1 comment
Labels: infrastructure

#136 - Remove dependency on survival package

Pull Request - State: closed - Opened by lwjohnst86 over 4 years ago
Labels: infrastructure

#134 - Have help examples be in one location, and reference to that

Issue - State: closed - Opened by lwjohnst86 over 4 years ago
Labels: documentation

#133 - Function to run cross-validation on network estimation

Issue - State: open - Opened by lwjohnst86 over 4 years ago
Labels: enhancement

#132 - Function to compare edges between multiple networks and NC output

Issue - State: open - Opened by lwjohnst86 over 4 years ago
Labels: enhancement

#131 - Fix bug related to rounding.

Pull Request - State: closed - Opened by lwjohnst86 over 4 years ago

#130 - Design functions to fit with philosophy or general structure of tidymodels

Issue - State: closed - Opened by lwjohnst86 almost 5 years ago - 1 comment
Labels: enhancement, discussion

#124 - Better to show full range of weight and respective color scale in legend?

Issue - State: closed - Opened by feichel almost 5 years ago
Labels: enhancement

#121 - Create an article that describes how to use with different types of models

Issue - State: closed - Opened by lwjohnst86 almost 5 years ago - 1 comment
Labels: documentation

#120 - Remove dependency on survival and only document its use

Issue - State: closed - Opened by lwjohnst86 almost 5 years ago
Labels: infrastructure

#119 - Add documentation on using package with Cytoscape to make visualizations

Issue - State: open - Opened by lwjohnst86 almost 5 years ago
Labels: documentation

#117 - Function to make edge table

Issue - State: closed - Opened by lwjohnst86 almost 5 years ago
Labels: enhancement

#116 - Extract the code from packages if only one or two functions are used

Issue - State: open - Opened by lwjohnst86 almost 5 years ago
Labels: infrastructure

#112 - Remove use of pipes and use more intermediate objects to help with profiling

Issue - State: closed - Opened by lwjohnst86 almost 5 years ago - 1 comment
Labels: enhancement

#111 - Include variable selection and standardization within the nc_create_network function

Issue - State: closed - Opened by lwjohnst86 almost 5 years ago - 1 comment
Labels: discussion

#106 - Run estimation functions on larger datasets and identify places to improve speed

Issue - State: open - Opened by lwjohnst86 almost 5 years ago
Labels: enhancement

#102 - Refactor unit tests to process faster, esp for estimation tests

Issue - State: closed - Opened by lwjohnst86 almost 5 years ago
Labels: enhancement

#99 - Make function to create model template function?

Issue - State: closed - Opened by lwjohnst86 almost 5 years ago - 3 comments
Labels: enhancement, discussion

#97 - Construct simulated data so metabolite with outcome association is more obvious

Issue - State: closed - Opened by lwjohnst86 almost 5 years ago
Labels: enhancement

#96 - Function to check if model arg list contains appropriate args?

Issue - State: closed - Opened by lwjohnst86 almost 5 years ago - 2 comments
Labels: enhancement, question

#95 - Test results against actual simulated betas (for outcome)

Issue - State: closed - Opened by lwjohnst86 almost 5 years ago - 2 comments
Labels: enhancement

#92 - Include MuMIn threshold option

Issue - State: closed - Opened by lwjohnst86 almost 5 years ago - 1 comment
Labels: discussion

#90 - Create function to save plots as svg to modify in other programs

Issue - State: open - Opened by lwjohnst86 almost 5 years ago
Labels: discussion

#87 - Need to use MuMIn? Or just brute force iterate on all combinations of formula?

Issue - State: closed - Opened by lwjohnst86 about 5 years ago - 2 comments
Labels: discussion

#86 - Does MuMIn models use same sample size (e.g. drops all missing values)?

Issue - State: closed - Opened by lwjohnst86 about 5 years ago - 1 comment
Labels: discussion

#84 - Incorporate estimate distribution information in output results?

Issue - State: open - Opened by lwjohnst86 about 5 years ago
Labels: enhancement, discussion

#79 - Allow using multiple outcomes/exposures

Issue - State: open - Opened by lwjohnst86 about 5 years ago
Labels: enhancement, discussion

#78 - Convert model id that is generated into number format, rather than original SHA

Issue - State: open - Opened by lwjohnst86 about 5 years ago - 1 comment
Labels: enhancement, discussion

#77 - Add progress bar to _estimates() functions?

Issue - State: open - Opened by lwjohnst86 about 5 years ago
Labels: enhancement, discussion

#74 - Include formula interface with functions

Issue - State: open - Opened by lwjohnst86 about 5 years ago
Labels: enhancement, discussion

#72 - Function to plot exposure and outcome side estimation

Issue - State: closed - Opened by lwjohnst86 about 5 years ago
Labels: enhancement

#70 - Expand and refine vignettes

Pull Request - State: closed - Opened by lwjohnst86 about 5 years ago - 1 comment
Labels: documentation, work in progress

#67 - Allow model functions to be passed as arg that have already been built

Issue - State: closed - Opened by lwjohnst86 about 5 years ago - 2 comments
Labels: enhancement, discussion, documentation

#64 - Write function to summarise model results and run p-value adjustment

Issue - State: closed - Opened by lwjohnst86 about 5 years ago - 1 comment
Labels: enhancement

#63 - Write tests that check if results are expected.

Issue - State: closed - Opened by lwjohnst86 about 5 years ago

#62 - Make use of tidyselect when selecting variables

Issue - State: closed - Opened by lwjohnst86 about 5 years ago - 1 comment
Labels: discussion

#58 - Include limit on number of nodes/metabolites to use

Issue - State: open - Opened by lwjohnst86 about 5 years ago
Labels: discussion

#43 - Remove dependency on pcalg? Or make better installation instructions.

Issue - State: closed - Opened by lwjohnst86 over 5 years ago - 1 comment
Labels: discussion, documentation

#40 - Make generic, base template function for creating network

Issue - State: open - Opened by lwjohnst86 almost 6 years ago
Labels: enhancement

#33 - Submit abstract to useR conference?

Issue - State: closed - Opened by lwjohnst86 about 6 years ago
Labels: discussion, onhold

#26 - Submit idea/method outline to RIO Journal?

Issue - State: closed - Opened by lwjohnst86 over 6 years ago
Labels: discussion

#16 - Agenda and minutes for meetings

Issue - State: open - Opened by lwjohnst86 over 6 years ago - 11 comments

#13 - Idea for a "hex sticker" or "logo"

Issue - State: open - Opened by lwjohnst86 over 6 years ago
Labels: discussion

#8 - Tasks to complete for final package setup

Issue - State: closed - Opened by lwjohnst86 over 6 years ago - 2 comments