Update function calls and environment

[johanna0321]

Description of your changes

Update file paths and package calls to reduce errors
Make an renv.lock file for environment reproducibility

Issue ticket number and link

#3

Type of change

• Bug fix
• New feature
  • Backwards Incompatible?
• Refactoring / code clean-up
• Documentation add / update
• Automated Test
• Other (please specify)

(If applicable) How has this been tested?

[Copilot]

Pull request overview

This PR updates DIMS/HABC lipidomics code to remove clamr::-qualified calls, add default_tg_is_ms3 loading/usage, adjust figure scripts for repository-relative paths, and introduce an renv.lock for environment reproducibility.

Changes:

• Replaced several namespaced clamr:: calls with local function references and added default_tg_is_ms3 loading/parameter passing.
• Updated figure Rmd setup chunks by removing unused libraries and using here::here().
• Added a new renv.lock intended to pin package versions.

Reviewed changes

Copilot reviewed 9 out of 10 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
renv.lock	Adds an R environment lockfile.
R/habc4_lipids.R	Loads default_tg_is_ms3 and switches MS3/helper calls to local references.
R/habc_lipids.R	Loads default_tg_is_ms3 and switches HABC helper/search calls to local references.
R/docr_lipids.R	Renames/updates DOCR processing function and passes MS3 IS library as an argument.
R/direct_infusion.R	Updates documentation and local helper call references.
inst/scripts/lipidomics-dims-script.R	Loads/passes default_tg_is_ms3 into positive-mode DOCR processing.
inst/figures/Figure_5.Rmd	Removes unused library imports.
inst/figures/Figure_4.Rmd	Removes unused imports and uses here::here() for the local path.
inst/figures/Figure_3.Rmd	Removes unused imports, uses here::here(), and updates extdata paths.
inst/figures/Figure_1_2.Rmd	Removes unused imports and uses here::here() for the local path.

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[Copilot]

Pull request overview

Copilot reviewed 10 out of 11 changed files in this pull request and generated 4 comments.