Add RMSE to output diagnostics

Per @wilsonsj100 request this PR adds RMSE to the output diagnostics, updating the documentation and introductory vignette to reflect this.

Linear cars data:

> ffi_fit_models(cars$speed, cars$dist)
  HM81_AIC HM81_flux.estimate HM81_p.value HM81_r.squared HM81_RMSE HM81_sigma  lin_AIC lin_flux.estimate lin_flux.std.error
1       NA                 NA           NA             NA        NA         NA 419.1569          3.932409          0.4155128
  lin_int.estimate lin_int.std.error  lin_p.value lin_r.squared lin_RMSE lin_sigma poly_AIC poly_r.squared poly_RMSE  rob_AIC
1        -17.57909           6.75844 1.489836e-12     0.6510794 15.06886  15.37959  419.885      0.6731808   14.5838 419.7356
  rob_converged rob_flux.estimate rob_flux.RMSE rob_flux.std.error rob_sigma
1          TRUE          3.773429      15.15631          0.3892199  13.28595

Nonlinear Puromycin data:

> ffi_compute_fluxes(Puromycin,
+                    group_column = NULL,
+                    time_column = "conc",
+                    gas_column = "rate")

NOTE: HM81_flux.estimate is not NA, implying nonlinear data

       conc HM81_AIC HM81_flux.estimate HM81_p.value HM81_r.squared HM81_RMSE HM81_sigma  lin_AIC lin_flux.estimate
1 0.3121739 200.9997           246.1399 9.406055e-11      0.8696062  16.77997   17.56084 223.7834           105.398
  lin_flux.std.error lin_int.estimate lin_int.std.error  lin_p.value lin_r.squared lin_RMSE lin_sigma poly_AIC poly_r.squared
1            16.9191         96.03154          7.780867 3.525876e-06     0.6488706 27.53571  28.81711  205.746      0.8653059
  poly_RMSE  rob_AIC rob_converged rob_flux.estimate rob_flux.RMSE rob_flux.std.error rob_sigma conc_min conc_max
1  17.05442 223.8119          TRUE          106.2137      27.55276           20.65072  24.79301     0.02      1.1

[heart] Wilson, Stephanie reacted to your message:

From: Ben Bond-Lamberty @.> Sent: Wednesday, September 11, 2024 10:06:28 AM To: COMPASS-DOE/fluxfinder @.> Cc: Wilson, Stephanie @.>; Mention @.> Subject: [COMPASS-DOE/fluxfinder] Add RMSE to output diagnostics (PR #73)

External Email - Exercise Caution

Per @wilsonsj100https://github.com/wilsonsj100 request this PR adds RMSEhttps://en.wikipedia.org/wiki/Root_mean_square_deviation to the output diagnostics, updating the documentation and introductory vignette to reflect this.

ffi_fit_models(cars$speed, cars$dist) HM81_AIC HM81_flux.estimate HM81_p.value HM81_r.squared HM81_RMSE HM81_sigma lin_AIC lin_flux.estimate lin_flux.std.error 1 NA NA NA NA NA NA 419.1569 3.932409 0.4155128 lin_int.estimate lin_int.std.error lin_p.value lin_r.squared lin_RMSE lin_sigma poly_AIC poly_r.squared poly_RMSE rob_AIC 1 -17.57909 6.75844 1.489836e-12 0.6510794 15.06886 15.37959 419.885 0.6731808 14.5838 419.7356 rob_converged rob_flux.estimate rob_flux.RMSE rob_flux.std.error rob_sigma 1 TRUE 3.773429 15.15631 0.3892199 13.28595

ffi_compute_fluxes(Puromycin,

group_column = NULL,

time_column = "conc",

gas_column = "rate") NOTE: HM81_flux.estimate is not NA, implying nonlinear data conc HM81_AIC HM81_flux.estimate HM81_p.value HM81_r.squared HM81_RMSE HM81_sigma lin_AIC lin_flux.estimate 1 0.3121739 200.9997 246.1399 9.406055e-11 0.8696062 16.77997 17.56084 223.7834 105.398 lin_flux.std.error lin_int.estimate lin_int.std.error lin_p.value lin_r.squared lin_RMSE lin_sigma poly_AIC poly_r.squared 1 16.9191 96.03154 7.780867 3.525876e-06 0.6488706 27.53571 28.81711 205.746 0.8653059 poly_RMSE rob_AIC rob_converged rob_flux.estimate rob_flux.RMSE rob_flux.std.error rob_sigma conc_min conc_max 1 17.05442 223.8119 TRUE 106.2137 27.55276 20.65072 24.79301 0.02 1.1

You can view, comment on, or merge this pull request online at:

https://github.com/COMPASS-DOE/fluxfinder/pull/73

Commit Summary

1514cc2https://github.com/COMPASS-DOE/fluxfinder/pull/73/commits/1514cc2f5c18ce94319549e48a21ea2ef3f7da70 Add RMSE to output diagnostics

File Changes

(3 fileshttps://github.com/COMPASS-DOE/fluxfinder/pull/73/files)

M R/models.Rhttps://github.com/COMPASS-DOE/fluxfinder/pull/73/files#diff-f3f37c58b4cfc2367699d9b16ab0b014e3f9189f15008358dc0f04207f48cdc7 (26)
M man/ffi_fit_models.Rdhttps://github.com/COMPASS-DOE/fluxfinder/pull/73/files#diff-d1af02ae038bb0bbc25524af482e297398983fd834a80e49e595eb012aa116d4 (2)
M vignettes/intro-to-fluxfinder.Rmdhttps://github.com/COMPASS-DOE/fluxfinder/pull/73/files#diff-5784b982b06628457573b505cb6e76caf21392bc20834a7fc7be266fe51e45be (3)

Patch Links:

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COMPASS-DOE / fluxfinder

Add RMSE to output diagnostics #73