{
  "_id": "6a102343acfb0bcc41c8d543",
  "Package": "fitnmr",
  "Version": "1.1",
  "Title": "Multidimensional Nuclear Magnetic Resonance Peak Fitting and\nAnalysis",
  "Authors@R": "c(person(\"Colin\", \"Smith\", role=c(\"aut\", \"cre\"),\nemail = \"colin.smith@wesleyan.edu\"))",
  "Description": "Tools for fitting and analyzing 1D-4D nuclear magnetic\nresonance spectra with analytical models of peak shapes and\npeak groups. The package reads spectra in 'NMRPipe' format,\nbuilds constrained parameter structures for chemical shifts,\nline widths, scalar couplings, volumes, and phases, and\nperforms nonlinear least-squares optimization for iterative\npeak discovery or simultaneous fits across multiple spectra. It\nalso provides methods for visualization, preprocessing, and\nkinetic analysis of 1D time-series data, including automated\nphase optimization, solvent suppression, time-domain correction\nfor frequency shifts and line broadening, modeling spectra as\nlinear combinations of two component spectra, and exponential\nrate fitting.",
  "License": "GPL-3",
  "URL": "https://github.com/smith-group/fitnmr/,\nhttps://smith-group.github.io/fitnmr/",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Repository": "https://smith-group.r-universe.dev",
  "Date/Publication": "2026-05-13 15:17:15 UTC",
  "RemoteUrl": "https://github.com/smith-group/fitnmr",
  "RemoteRef": "HEAD",
  "RemoteSha": "3e9bb7d758c8b5b9f00b77d3bcd579088475466c",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-13 17:38:18 UTC",
    "User": "root"
  },
  "Author": "Colin Smith [aut, cre]",
  "Maintainer": "Colin Smith <colin.smith@wesleyan.edu>",
  "MD5sum": "ae1fa2f34c0e088eb0f4ecaf54b05b7c",
  "_user": "smith-group",
  "_type": "src",
  "_file": "fitnmr_1.1.tar.gz",
  "_fileid": "206ccee47a43d0d06f0fc87a860a2ebd08acdaac7df386bba5b10101a3d1101b",
  "_filesize": 6266239,
  "_sha256": "206ccee47a43d0d06f0fc87a860a2ebd08acdaac7df386bba5b10101a3d1101b",
  "_created": "2026-05-13T17:38:18.000Z",
  "_published": "2026-05-22T09:34:59.282Z",
  "_distro": "noble",
  "_jobs": [
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      "job": 77353762266,
      "time": 162,
      "config": "linux-devel-x86_64",
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      "check": "OK",
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  ],
  "_buildurl": "https://github.com/r-universe/smith-group/actions/runs/25815674991",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/smith-group/fitnmr",
  "_commit": {
    "id": "3e9bb7d758c8b5b9f00b77d3bcd579088475466c",
    "author": "Colin Smith <colin.smith@wesleyan.edu>",
    "committer": "Colin Smith <colin.smith@wesleyan.edu>",
    "message": "Handle degenerate peak ranges in assignments\n\nGuard height assignment scaling against zero-width dimensions and preserve array shape in the 2D assignment script.\n",
    "time": 1778685435
  },
  "_maintainer": {
    "name": "Colin Smith",
    "email": "colin.smith@wesleyan.edu",
    "login": "colinasmith",
    "uuid": 1170378
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "minpack.lm",
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    },
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      "package": "abind",
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      "package": "Matrix",
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      "package": "R6",
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      "package": "knitr",
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      "package": "rmarkdown",
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  "_owner": "smith-group",
  "_selfowned": true,
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  "_updates": [
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  "_tags": [],
  "_stars": 2,
  "_contributors": [
    {
      "user": "colinasmith",
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    {
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  "_userbio": {
    "uuid": 33662178,
    "type": "organization",
    "name": "Smith Group"
  },
  "_downloads": {
    "count": 488,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/fitnmr"
  },
  "_devurl": "https://github.com/smith-group/fitnmr",
  "_pkgdown": "https://smith-group.github.io/fitnmr/",
  "_searchresults": 5,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/fitnmr.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/smith-group/fitnmr",
  "_realowner": "smith-group",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0",
      "date": "2026-03-19"
    }
  ],
  "_exports": [
    "contour_pipe",
    "coupling_param_idx",
    "fit_peak_iter",
    "get_spec_int",
    "HamiltonianMultiplet",
    "height_assign",
    "limit_omega0_by_r2",
    "make_fit_input",
    "make_map",
    "make_param_list",
    "nmr_pipe",
    "nmrpipe_ft",
    "nmrpipe_fti",
    "nmrpipe_ps",
    "nmrpipe_sp",
    "nmrpipe_zf",
    "noise_estimate",
    "omega0_param_idx",
    "param_list_to_arg_list",
    "param_list_to_peak_df",
    "param_list_to_tables",
    "param_values",
    "param_values<-",
    "peak_df_to_fit_input",
    "peak_df_to_param_list",
    "perform_fit",
    "plot_fit_1d",
    "plot_fit_2d",
    "plot_peak_df",
    "plot_resonances_1d",
    "plot_resonances_2d",
    "plot_resonances_3d",
    "plot_sparse_1d",
    "plot_sparse_2d",
    "ppm_to_pts",
    "read_nmrdraw_peak_tab",
    "read_nmrpipe",
    "read_resonance_tables",
    "sim_time_nd",
    "tables_to_param_list",
    "update_fit_bounds",
    "write_nmrdraw_peak_tab"
  ],
  "_help": [
    {
      "page": "fitnmr-package",
      "title": "fitnmr Package Overview",
      "topics": [
        "fitnmr-package",
        "fitnmr"
      ]
    },
    {
      "page": "abind_list",
      "title": "Combine multi-dimensional arrays with lists",
      "topics": [
        "abind_list"
      ]
    },
    {
      "page": "collapse_na",
      "title": "Collapse strings of repeated NAs in a vector with numeric names",
      "topics": [
        "collapse_na"
      ]
    },
    {
      "page": "collapse_na_array",
      "title": "Collapse blocks of NAs in an array with numeric dimension names",
      "topics": [
        "collapse_na_array"
      ]
    },
    {
      "page": "comb_vec_to_param_array",
      "title": "Determine array of destination parameters from a source vector",
      "topics": [
        "comb_vec_to_param_array"
      ]
    },
    {
      "page": "contour_pipe",
      "title": "Plot Spectra Contours",
      "topics": [
        "contour_pipe"
      ]
    },
    {
      "page": "coupling_param_idx",
      "title": "Get a list of logical arrays indicating which parameters correspond to scalar couplings",
      "topics": [
        "coupling_param_idx"
      ]
    },
    {
      "page": "extract_params",
      "title": "Extract parameters from fit object for use with make_fit_input",
      "topics": [
        "extract_params"
      ]
    },
    {
      "page": "fit_footprint",
      "title": "Determine the region of a spectrum containing the majority of the fit peaks",
      "topics": [
        "fit_footprint"
      ]
    },
    {
      "page": "fit_peak_cluster",
      "title": "Fit a cluster of nearby peaks starting from a seed table of chemical shifts",
      "topics": [
        "fit_peak_cluster"
      ]
    },
    {
      "page": "fit_peak_iter",
      "title": "Iterative Peak Fitting",
      "topics": [
        "fit_peak_iter"
      ]
    },
    {
      "page": "fit_peaks",
      "title": "Fit peaks from a table of chemical shifts",
      "topics": [
        "fit_peaks"
      ]
    },
    {
      "page": "get_spec_int",
      "title": "Get arrays of spectral intensities for input, starting parameters, and fit peaks",
      "topics": [
        "get_spec_int"
      ]
    },
    {
      "page": "get_spec_peak_int",
      "title": "Get spectra for individual peaks",
      "topics": [
        "get_spec_peak_int"
      ]
    },
    {
      "page": "HamiltonianMultiplet",
      "title": "HamiltonianMultiplet R6 class",
      "topics": [
        "HamiltonianMultiplet"
      ]
    },
    {
      "page": "height_assign",
      "title": "Calculate mapping from assigned peak list onto an unknown peak list",
      "topics": [
        "height_assign"
      ]
    },
    {
      "page": "infer_acquisition_time",
      "title": "Infer acquisition time for each dimension",
      "topics": [
        "infer_acquisition_time"
      ]
    },
    {
      "page": "infer_aliasing",
      "title": "Infer which dimension was directly acquired",
      "topics": [
        "infer_aliasing"
      ]
    },
    {
      "page": "infer_direct",
      "title": "Infer which dimension was directly acquired",
      "topics": [
        "infer_direct"
      ]
    },
    {
      "page": "infer_sweep_width",
      "title": "Infer original sweep width for each dimension",
      "topics": [
        "infer_sweep_width"
      ]
    },
    {
      "page": "limit_omega0_by_r2",
      "title": "Add upper/lower limits based on the r2 value",
      "topics": [
        "limit_omega0_by_r2"
      ]
    },
    {
      "page": "make_coupling_mat",
      "title": "Make a multiplet matrix with weights and scalar coupling coefficients",
      "topics": [
        "make_coupling_mat"
      ]
    },
    {
      "page": "make_fit_input",
      "title": "Prepare input data structure for peak fitting",
      "topics": [
        "make_fit_input"
      ]
    },
    {
      "page": "make_map",
      "title": "Create a sparse axis map",
      "topics": [
        "make_map"
      ]
    },
    {
      "page": "make_param_list",
      "title": "Make a parameter list for a set of spectra and chemical shifts",
      "topics": [
        "make_param_list"
      ]
    },
    {
      "page": "nmr_pipe",
      "title": "Process an FID with NMRPipe",
      "topics": [
        "nmr_pipe"
      ]
    },
    {
      "page": "nmrpipe_ft",
      "title": "Fourier transform a 1D FID",
      "topics": [
        "nmrpipe_ft"
      ]
    },
    {
      "page": "nmrpipe_fti",
      "title": "Inverse Fourier transform a 1D spectrum",
      "topics": [
        "nmrpipe_fti"
      ]
    },
    {
      "page": "nmrpipe_ps",
      "title": "Change phases of a 1D spectrum",
      "topics": [
        "nmrpipe_ps"
      ]
    },
    {
      "page": "nmrpipe_sp",
      "title": "Apply sine-based window function to a 1D FID",
      "topics": [
        "nmrpipe_sp"
      ]
    },
    {
      "page": "nmrpipe_zf",
      "title": "Apply zero filling to a 1D FID",
      "topics": [
        "nmrpipe_zf"
      ]
    },
    {
      "page": "noise_estimate",
      "title": "Estimate Noise",
      "topics": [
        "noise_estimate"
      ]
    },
    {
      "page": "omega0_comb_source_idx",
      "title": "Get the first index in the omega0 array corresponding to each TRUE value in omega0_idx",
      "topics": [
        "omega0_comb_source_idx"
      ]
    },
    {
      "page": "omega0_param_idx",
      "title": "Get a list of logical arrays indicating which parameters correspond to peak positions",
      "topics": [
        "omega0_param_idx"
      ]
    },
    {
      "page": "param_array_to_comb_vec",
      "title": "Determine vector of source parameters from destination array via least squares",
      "topics": [
        "param_array_to_comb_vec"
      ]
    },
    {
      "page": "param_list_to_arg_list",
      "title": "Convert a list of parameters for use with make_fit_input",
      "topics": [
        "param_list_to_arg_list"
      ]
    },
    {
      "page": "param_list_to_peak_df",
      "title": "Convert Fit to Data Frame",
      "topics": [
        "param_list_to_peak_df"
      ]
    },
    {
      "page": "param_list_to_tables",
      "title": "Convert a parameter list into a set of tables with resonance/nuclei/couplings",
      "topics": [
        "param_list_to_tables"
      ]
    },
    {
      "page": "param_values",
      "title": "Get/set a subset of fitting parameters specified by a list of logical vectors",
      "topics": [
        "param_values",
        "param_values<-"
      ]
    },
    {
      "page": "peak_bind",
      "title": "Combine parameter lists referring to different peaks",
      "topics": [
        "peak_bind"
      ]
    },
    {
      "page": "peak_df_to_fit_input",
      "title": "Convert a peak data frame to fit input",
      "topics": [
        "peak_df_to_fit_input"
      ]
    },
    {
      "page": "peak_df_to_param_list",
      "title": "Convert a peak data frame to a parameter list",
      "topics": [
        "peak_df_to_param_list"
      ]
    },
    {
      "page": "perform_fit",
      "title": "Perform a fit with an input data structure",
      "topics": [
        "perform_fit"
      ]
    },
    {
      "page": "plot_fit_1d",
      "title": "Plot a one dimensional peak fit",
      "topics": [
        "plot_fit_1d"
      ]
    },
    {
      "page": "plot_fit_2d",
      "title": "Plot a two dimensional peak fit",
      "topics": [
        "plot_fit_2d"
      ]
    },
    {
      "page": "plot_peak_df",
      "title": "Plot Peaks from a Peak Table",
      "topics": [
        "plot_peak_df"
      ]
    },
    {
      "page": "plot_resonances_1d",
      "title": "Plot resonances from 1D fit",
      "topics": [
        "plot_resonances_1d"
      ]
    },
    {
      "page": "plot_resonances_2d",
      "title": "Plot resonances from 2D fit",
      "topics": [
        "plot_resonances_2d"
      ]
    },
    {
      "page": "plot_resonances_3d",
      "title": "Plot resonances from 3D fit",
      "topics": [
        "plot_resonances_3d"
      ]
    },
    {
      "page": "plot_sparse_1d",
      "title": "Plot spectrum from 1D fit",
      "topics": [
        "plot_sparse_1d"
      ]
    },
    {
      "page": "plot_sparse_2d",
      "title": "Plot spectrum from 2D fit",
      "topics": [
        "plot_sparse_2d"
      ]
    },
    {
      "page": "ppm_to_pts",
      "title": "Convert PPM values to points",
      "topics": [
        "ppm_to_pts"
      ]
    },
    {
      "page": "read_nmrdraw_peak_tab",
      "title": "Read an NMRDraw formatted peak table",
      "topics": [
        "read_nmrdraw_peak_tab"
      ]
    },
    {
      "page": "read_nmrpipe",
      "title": "Read NMRPipe spectrum",
      "topics": [
        "read_nmrpipe"
      ]
    },
    {
      "page": "read_resonance_tables",
      "title": "Read resonance, nuclei, coupling, and spin system tables",
      "topics": [
        "read_resonance_tables"
      ]
    },
    {
      "page": "resonance_to_param_list",
      "title": "Convert data frame of resonances into a parameter list",
      "topics": [
        "resonance_to_param_list"
      ]
    },
    {
      "page": "set_spinsystem_params",
      "title": "Update HamiltonianMultiplet parameters from input data",
      "topics": [
        "set_spinsystem_params"
      ]
    },
    {
      "page": "sim_time_nd",
      "title": "Simulate an FID using the NMRPipe SimTimeND function",
      "topics": [
        "sim_time_nd"
      ]
    },
    {
      "page": "spec_bind",
      "title": "Combine parameter lists referring to different spectra",
      "topics": [
        "spec_bind"
      ]
    },
    {
      "page": "spec_overlap_mat",
      "title": "Determine a matrix of fractional peak overlap",
      "topics": [
        "spec_overlap_mat"
      ]
    },
    {
      "page": "split_coupling_names",
      "title": "Split string of scalar coupling names",
      "topics": [
        "split_coupling_names"
      ]
    },
    {
      "page": "tables_to_param_list",
      "title": "Convert tables with resonance/nuclei/couplings to a parameter list",
      "topics": [
        "tables_to_param_list"
      ]
    },
    {
      "page": "update_fit_bounds",
      "title": "Update bounds on fitting parameters",
      "topics": [
        "update_fit_bounds"
      ]
    },
    {
      "page": "update_spinsystem_params",
      "title": "Update HamiltonianMultiplet parameters from fit data",
      "topics": [
        "update_spinsystem_params"
      ]
    },
    {
      "page": "whz_to_pts",
      "title": "Convert widths in Hz into points",
      "topics": [
        "whz_to_pts"
      ]
    },
    {
      "page": "write_nmrdraw_peak_tab",
      "title": "Write an NMRDraw formatted peak table",
      "topics": [
        "write_nmrdraw_peak_tab"
      ]
    }
  ],
  "_readme": "https://github.com/smith-group/fitnmr/raw/HEAD/README.md",
  "_rundeps": [
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    "lattice",
    "Matrix",
    "minpack.lm",
    "R6"
  ],
  "_vignettes": [
    {
      "source": "timeseries1d.Rmd",
      "filename": "timeseries1d.html",
      "title": "1D Time Series Preprocessing/Two-State Fitting",
      "author": "Katerina M. Blejec and Colin A. Smith",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1D Preprocessing",
        "Rate Fitting"
      ],
      "created": "2025-11-11 00:46:21",
      "modified": "2026-03-20 15:54:47",
      "commits": 4
    },
    {
      "source": "peak2d.Rmd",
      "filename": "peak2d.html",
      "title": "Automated 2D Peak Fitting Code",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Sample Data",
        "Reading Spectra",
        "Displaying Spectra",
        "Estimating Noise",
        "Fitting Peaks",
        "Fitting a Few Peak Clusters",
        "A Peek Inside the Algorithm",
        "Fitting the Remainder of the Peaks",
        "Fitting Peaks without Scalar Couplings",
        "Editing Fit Clusters",
        "Separating Fit Clusters",
        "Deleting Peaks",
        "Extending the Fit to Other Spectra"
      ],
      "created": "2020-01-11 16:14:39",
      "modified": "2026-03-20 15:54:47",
      "commits": 10
    },
    {
      "source": "peak2d_scripts.Rmd",
      "filename": "peak2d_scripts.html",
      "title": "Automated 2D Peak Fitting Scripts",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Fitting Initial Set of Peaks",
        "Output Files",
        "Refining the Initial Fit",
        "Extending the Fit to Other Spectra",
        "Transferring Assignments"
      ],
      "created": "2020-03-18 18:50:01",
      "modified": "2026-03-20 15:54:47",
      "commits": 10
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  "_nocasepkg": "fitnmr",
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