{
  "_id": "6a1aac081d7bb097a09d4dd0",
  "Package": "RCASPAR",
  "Type": "Package",
  "Title": "A package for survival time prediction based on a piecewise\nbaseline hazard Cox regression model.",
  "Version": "1.59.0",
  "Date": "2010-08-23",
  "Author": "Douaa Mugahid, Lars Kaderali",
  "Maintainer": "Douaa Mugahid <douaa.mugahid@gmail.com>, Lars Kaderali\n<lars.kaderali@uni-greifswald.de>",
  "Description": "The package is the R-version of the C-based software\n\\bold{CASPAR} (Kaderali,2006:\n\\url{http://bioinformatics.oxfordjournals.org/content/22/12/1495}).\nIt is meant to help predict survival times in the presence of\nhigh-dimensional explanatory covariates. The model is a\npiecewise baseline hazard Cox regression model with an Lq-norm\nbased prior that selects for the most important regression\ncoefficients, and in turn the most relevant covariates for\nsurvival analysis. It was primarily tried on gene expression\nand aCGH data, but can be used on any other type of\nhigh-dimensional data and in disciplines other than biology and\nmedicine.",
  "biocViews": "aCGH, GeneExpression, Genetics, Proteomics, Visualization",
  "License": "GPL (>=3)",
  "LazyLoad": "yes",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:35:29 UTC",
  "RemoteUrl": "https://github.com/bioc/RCASPAR",
  "RemoteRef": "HEAD",
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  "NeedsCompilation": "no",
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    "User": "root"
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777379729
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  "_maintainer": {
    "name": "Douaa Mugahid",
    "email": "lars.kaderali@uni-greifswald.de",
    "login": "dam39",
    "description": "",
    "uuid": 55767045
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  "_dependencies": [],
  "_owner": "bioc",
  "_selfowned": true,
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  "_updates": [
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    "geneexpression",
    "genetics",
    "proteomics",
    "visualization"
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  "_userbio": {
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    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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    "source": "https://www.bioconductor.org/packages/stats/bioc/RCASPAR"
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    "manual.pdf"
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  "_realowner": "bioc",
  "_cranurl": false,
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    "deriv_weight_estimator_BLH_noprior",
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    "kmplt_svrl",
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    "survivAURC",
    "survivROC",
    "trapezoid",
    "weight_estimator_BLH",
    "weight_estimator_BLH_noprior",
    "weights_BLH",
    "weights_xvBLH"
  ],
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      "name": "Bergamaschi",
      "title": "Gene expression data of 82 patients with 10 genes as covariates",
      "object": "Bergamaschi",
      "file": "Bergamaschi.RData",
      "class": [
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        "IMAGE:50794",
        "IMAGE:302190",
        "IMAGE:51408",
        "IMAGE:324901",
        "IMAGE:234856",
        "IMAGE:628529",
        "IMAGE:49464",
        "IMAGE:78294",
        "IMAGE:51328"
      ],
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      "table": true,
      "tojson": true
    },
    {
      "name": "survData",
      "title": "Survial data of 82 patients",
      "object": "survData",
      "file": "survData.RData",
      "class": [
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      ],
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        "Sample.ID.Bauke.",
        "Experiment.Jon.",
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        "Status.0.A..1.AWD..2.DOD..3.DOC",
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        "True_STs"
      ],
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      "table": true,
      "tojson": true
    }
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  "_help": [
    {
      "page": "RCASPAR-package",
      "title": "A package for survival time prediction based on a piecewise baseline hazard Cox regression model.",
      "topics": [
        "RCASPAR-package",
        "RCASPAR"
      ]
    },
    {
      "page": "Bergamaschi",
      "title": "Gene expression data of 82 patients with 10 genes as covariates",
      "topics": [
        "Bergamaschi"
      ]
    },
    {
      "page": "deriv_weight_estimator_BLH",
      "title": "A function that gives the derivative of the objective function of the model for gradient-based optimization algorithms.",
      "topics": [
        "deriv_weight_estimator_BLH"
      ]
    },
    {
      "page": "deriv_weight_estimator_BLH_noprior",
      "title": "A function that gives the derivative of the objective function of the model for gradient-based optimization algorithms without including the prior on the regression coefficients.",
      "topics": [
        "deriv_weight_estimator_BLH_noprior"
      ]
    },
    {
      "page": "kmplt",
      "title": "Plot Kaplan Meier curve",
      "topics": [
        "kmplt"
      ]
    },
    {
      "page": "kmplt_svrl",
      "title": "A function that plots the KM curves of $2-3$ patient sets in one graph.",
      "topics": [
        "kmplt_svrl"
      ]
    },
    {
      "page": "logrnk",
      "title": "Performs Log Rank test on the long and short patient sets",
      "topics": [
        "logrnk"
      ]
    },
    {
      "page": "pltgamma",
      "title": "Plotting the gamma distribution of shape parameter",
      "topics": [
        "pltgamma"
      ]
    },
    {
      "page": "pltprior",
      "title": "A function to visualize the shape of the prior on the weights with the chosen q and s parameters.",
      "topics": [
        "pltprior"
      ]
    },
    {
      "page": "simpson",
      "title": "A function that calculates the area under a curve based on the Simposon algorithm",
      "topics": [
        "simpson"
      ]
    },
    {
      "page": "STpredictor_BLH",
      "title": "Predicts the survival times of the validation set based on the regression coefficients and baseline hazards determined according to the Piecewise baseline hazard Cox regression model.",
      "topics": [
        "STpredictor_BLH"
      ]
    },
    {
      "page": "STpredictor_xvBLH",
      "title": "This function performs a cross validation on the full data set to help predict the survival times of the patients using the piecewise baseline hazard PH Cox model.",
      "topics": [
        "STpredictor_xvBLH"
      ]
    },
    {
      "page": "survData",
      "title": "Survial data of 82 patients",
      "topics": [
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      ]
    },
    {
      "page": "survivAURC",
      "title": "A function that calculates the area under a curve constructed from plotting the area under a ROC curve at the corresponding time point at which it was generated.",
      "topics": [
        "survivAURC"
      ]
    },
    {
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      "topics": [
        "survivROC"
      ]
    },
    {
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      "title": "A function that calculates the area under a curve based on the Simposon algorithm",
      "topics": [
        "trapezoid"
      ]
    },
    {
      "page": "weight_estimator_BLH",
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      "topics": [
        "weight_estimator_BLH"
      ]
    },
    {
      "page": "weight_estimator_BLH_noprior",
      "title": "Returns the value of the objective function used for optimizing for the regression parameters and baseline hazards in the model, without including the prior on the regression coefficients.",
      "topics": [
        "weight_estimator_BLH_noprior"
      ]
    },
    {
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      "title": "Optimization for the regression coefficients and baseline hazards that maximize the partial likelihood in our PW Cox PH regression model.",
      "topics": [
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      ]
    },
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      "page": "weights_xvBLH",
      "title": "A special version of STpredictor.BLH used within k-xv to predict the survival times of the kth validation group in the cross validation step.",
      "topics": [
        "weights_xvBLH"
      ]
    }
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  "_vignettes": [
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      "source": "RCASPAR.Rnw",
      "filename": "RCASPAR.pdf",
      "title": "RCASPAR: Software for high-dimentional-data driven survival time prediction",
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      "headings": [],
      "created": "2013-11-01 20:18:51",
      "modified": "2013-11-01 20:18:51",
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