include_reference doesn't work for pscl models
#1134
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Summary of Changes
Hello @strengejacke, I'm Gemini Code Assist1! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!
This pull request delivers a targeted bug fix to improve the compatibility and correctness of the include_reference feature when used with statistical models from the pscl package, particularly zeroinfl and hurdle models. The changes adapt the parameter and reference level handling to align with the specific naming conventions employed by these models, ensuring accurate processing and display.
Highlights
- Bug Fix: Addresses an issue where the
include_referencefunctionality did not work correctly for models generated by thepsclpackage, specificallyzeroinflandhurdlemodels. This resolves the problem described in issue #1130. - Parameter Matching for
psclModels: Introduced logic to correctly identify and match factor parameters forpsclmodels. This involves prependingcount_andzero_prefixes to factor names when checking against the model's internal parameter representation, as these models use such prefixes for their different components. - Reference Level Formatting: Ensures that once a reference level is identified, any
count_orzero_prefixes (which were added for internal matching) are removed from thereference_levelstring before it is used, ensuring correct and clean display.
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Code Review
The pull request addresses issue #1130 by fixing the include_reference functionality for pscl models. The changes involve adding prefixes to factor names and removing them from reference levels to ensure correct matching of parameters. The review suggests adding comments to explain the purpose of these changes for better code maintainability.
| # for models from pscl, we have "count_" and "zero_" prefixes, which | ||
| # we need to add to "f" names, so that we can match them with the parameters | ||
| if (inherits(model, c("zeroinfl", "hurdle"))) { | ||
| f <- c(paste0("count_", f), paste0("zero_", f)) | ||
| } |
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It would be beneficial to add a comment explaining why these prefixes are necessary for pscl models. This enhances code understanding and maintainability.
# for models from pscl, we have "count_" and "zero_" prefixes,
# which we need to add to "f" names, so that we can match them with the parameters
# (pscl models require these prefixes for parameter identification)
if (inherits(model, c("zeroinfl", "hurdle"))) {| reference_level <- f[!f %in% names(pretty_names)] | ||
| reference_level <- gsub("^(count_|zero_)", "", reference_level, fixed = TRUE) |
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Consider adding a comment explaining why this gsub call is necessary. What potential issues does it resolve?
# Remove the count_ or zero_ prefix from the reference level
reference_level <- gsub("^(count_|zero_)", "", reference_level, fixed = TRUE)
Fixes #1130