Add RMSE to output diagnostics

[bpbond]

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

[wilsonsj100]

[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 @wilsonsj100<https://github.com/wilsonsj100> request this PR adds RMSE<https://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: #73 Commit Summary * 1514cc2<1514cc2> Add RMSE to output diagnostics File Changes (3 files<https://github.com/COMPASS-DOE/fluxfinder/pull/73/files>) * M R/models.R<https://github.com/COMPASS-DOE/fluxfinder/pull/73/files#diff-f3f37c58b4cfc2367699d9b16ab0b014e3f9189f15008358dc0f04207f48cdc7> (26) * M man/ffi_fit_models.Rd<https://github.com/COMPASS-DOE/fluxfinder/pull/73/files#diff-d1af02ae038bb0bbc25524af482e297398983fd834a80e49e595eb012aa116d4> (2) * M vignettes/intro-to-fluxfinder.Rmd<https://github.com/COMPASS-DOE/fluxfinder/pull/73/files#diff-5784b982b06628457573b505cb6e76caf21392bc20834a7fc7be266fe51e45be> (3) Patch Links: * https://github.com/COMPASS-DOE/fluxfinder/pull/73.patch * https://github.com/COMPASS-DOE/fluxfinder/pull/73.diff — Reply to this email directly, view it on GitHub<#73>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A5E7565KHM363BPW2VF7BL3ZWAI2JAVCNFSM6AAAAABOATIMYGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGUYTSMRXGI3DCMY>. You are receiving this because you were mentioned.Message ID: ***@***.***>