remove non-parametric fitting method

[jasmineirx]

While debugging some install messages, I noticed we were getting the following log during PKPDmap install:

Note: possible error in 'np_fit_wrapper(obj = obj, ': unused argument (lagtime = lagtime)

I thought this was an odd but easy fix, so I tried adding the argument to the function, since it can be passed on to PKPDsim within the function easily enough.

When doing that fix, I realized there were some other issues. We were also using a variable called error but not passing it onto the function, and so calling np_fit_wrapper would have been erroring anyways due to a variable not being found in scope. I then tried adding that argument too (easily available within PKPDmap::get_map_estimates), and I added a unit test.

However, upon trying to write a meaningful unit test, I learned that np_fit_wrapper silently only supported models parameterized by CL and V, in that order (example hardcoding:

PKPDmap/R/get_np_estimates.R

Line 25 in ce1f15e

par_tmp <- list(CL = parameter_grid[i, 1], V = parameter_grid[i, 2])

), and not lagtime. At this point I figured the entire feature of NP fitting was neither operational nor close to being operational, and has not been for a long time, and I think it is better to therefore remove it entirely rather than spend time fixing something that isn't being used or having a bunch of dead code around.

However, if we want to start extending it into something useful again, my original fixes are in this branch: https://github.com/InsightRX/PKPDmap/tree/np_fit_fix1.

[Copilot]

Pull request overview

This PR removes the non-parametric (NP) fitting feature set from PKPDmap, including the hybrid NP pathway, related helpers, exports, and documentation, to avoid carrying non-operational/dead code.

Changes:

• Removed NP estimation implementation files (np_fit_wrapper, get_np_estimates, grid creation, default NP settings) and their generated man pages.
• Updated get_map_estimates() to drop the np_settings argument and remove the np_hybrid execution path.
• Updated NAMESPACE + documentation (README/man/CLAUDE) to stop advertising NP methods.

Reviewed changes

Copilot reviewed 12 out of 18 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
README.md	Removed NP method bullets from the estimation-method list.
R/np_settings_default.R	Deleted NP default settings object.
R/np_fit_wrapper.R	Deleted NP wrapper used by hybrid estimation.
R/get_np_estimates.R	Deleted NP grid-based estimator implementation.
R/get_map_estimates.R	Removed np_settings arg and np_hybrid branch from main API.
R/create_grid_around_parameters.R	Deleted grid helper used by NP estimation.
NAMESPACE	Removed exports for NP-related functions/objects.
man/parse_weights.Rd	Updated wording to remove NP mention.
man/parse_residuals_from_predictions.Rd	Updated wording to remove NP mention.
man/np_settings_default.Rd	Deleted generated docs for np_settings_default.
man/np_fit_wrapper.Rd	Deleted generated docs for np_fit_wrapper.
man/ll_func_PKPDsim.Rd	Updated wording to remove NP mention.
man/get_np_estimates.Rd	Deleted generated docs for get_np_estimates.
man/get_map_estimates.Rd	Removed np_settings and NP-related type options from docs.
man/create_grid_around_parameters.Rd	Deleted generated docs for grid helper.
man/check_inputs.Rd	Updated type option wording to remove NP mention.
man/calc_residuals.Rd	Updated wording to remove NP mention.
CLAUDE.md	Removed NP method bullets and pipeline references, but retains NP mention in overview text.

Files not reviewed (6)

• man/calc_residuals.Rd: Generated file
• man/check_inputs.Rd: Generated file
• man/get_map_estimates.Rd: Generated file
• man/ll_func_PKPDsim.Rd: Generated file
• man/parse_residuals_from_predictions.Rd: Generated file
• man/parse_weights.Rd: Generated file

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[mccarthy-m-g]

Nice catch! Changes look good to me. Will leave final judgement on whether to remove or fix to @roninsightrx