project/01_0_install_R_packages.ipynb

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    "methods = 'KNN_IMPUTE,msImpute'"
   ]
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   "source": [
    "# options(\"install.lock\"=FALSE)\n",
    "\n",
    "packages_base_R <-\n",
    "  c(\"BiocManager\", \"reshape2\", \"data.table\", \"readr\", \"tibble\")\n",
    "\n",
    "install_rpackage  <- function(pkg) {\n",
    "  # If not installed, install the package\n",
    "  if (!require(pkg, character.only = TRUE)) {\n",
    "    install.packages(pkg)\n",
    "    library(pkg, character.only = TRUE)\n",
    "  }\n",
    "  \n",
    "}\n",
    "\n",
    "# used in the large imputation function for two packages\n",
    "install_bioconductor  <- function(pkg) {\n",
    "  # If not installed, install the package\n",
    "  if (!require(pkg, character.only = TRUE)) {\n",
    "    BiocManager::install(pkg)\n",
    "    library(pkg, character.only = TRUE)\n",
    "  }\n",
    "  \n",
    "}\n",
    "\n",
    "\n",
    "nafunctions <- function(method = \"zero\") {\n",
    "  method <- tolower(method)\n",
    "  if (method == \"zero\") {\n",
    "  }\n",
    "  else if (method == \"minimum\") {\n",
    "  }\n",
    "  else if (method == \"colmedian\") {\n",
    "    install_rpackage('e1071')\n",
    "  }\n",
    "  else if (method == \"rowmedian\") {\n",
    "    install_rpackage('e1071')\n",
    "  }\n",
    "  else if (method == \"knn_impute\") {\n",
    "    install_bioconductor('impute')\n",
    "  }\n",
    "  else if (method == \"seqknn\") {\n",
    "    if (!require(SeqKnn)) {\n",
    "      install.packages(\"src/R_NAGuideR/SeqKnn_1.0.1.tar.gz\",\n",
    "                       repos = NULL,\n",
    "                       type = \"source\")\n",
    "    }\n",
    "  }\n",
    "  else if (method == \"bpca\") {\n",
    "    install_bioconductor('pcaMethods')\n",
    "  }\n",
    "  else if (method == \"svdmethod\") {\n",
    "    install_bioconductor('pcaMethods')\n",
    "  }\n",
    "  else if (method == \"lls\") {\n",
    "    install_bioconductor('pcaMethods')\n",
    "  }\n",
    "  else if (method == \"mle\") {\n",
    "    install_rpackage('norm')\n",
    "  }\n",
    "  else if (method == \"qrilc\") {\n",
    "    install_bioconductor(\"impute\")\n",
    "    install_bioconductor(\"pcaMethods\")\n",
    "    install_rpackage('gmm')\n",
    "    install_rpackage('imputeLCMD')\n",
    "  }\n",
    "  else if (method == \"mindet\") {\n",
    "    install_bioconductor(\"impute\")\n",
    "    install_bioconductor(\"pcaMethods\")\n",
    "    install_rpackage('gmm')\n",
    "    install_rpackage('imputeLCMD')\n",
    "  }\n",
    "  else if (method == \"minprob\") {\n",
    "    install_bioconductor(\"impute\")\n",
    "    install_bioconductor(\"pcaMethods\")\n",
    "    install_rpackage('gmm')\n",
    "    install_rpackage('imputeLCMD')\n",
    "  }\n",
    "  else if (method == \"irm\") {\n",
    "    install_rpackage('VIM')\n",
    "  }\n",
    "  else if (method == \"impseq\") {\n",
    "    install_rpackage('rrcovNA')\n",
    "  }\n",
    "  else if (method == \"impseqrob\") {\n",
    "    install_rpackage('rrcovNA')\n",
    "  }\n",
    "  else if (method == \"mice-norm\") {\n",
    "    install_rpackage('mice')\n",
    "  }\n",
    "  else if (method == \"mice-cart\") {\n",
    "    install_rpackage('mice')\n",
    "  }\n",
    "  else if (method == \"trknn\") {\n",
    "    source('src/R_NAGuideR/Imput_funcs.r')\n",
    "  }\n",
    "  else if (method == \"rf\") {\n",
    "    install_rpackage(\"missForest\")\n",
    "  }\n",
    "  else if (method == \"pi\") {\n",
    "  }\n",
    "  # else if(method==\"grr\"){\n",
    "  #   library(DreamAI)\n",
    "  #   df<-impute.RegImpute(data=as.matrix(df1), fillmethod = \"row_mean\", maxiter_RegImpute = 10,conv_nrmse = 1e-03)\n",
    "  # }\n",
    "  else if (method == \"gms\") {\n",
    "    # install.packages('GMSimpute')\n",
    "    if (!require(GMSimpute)) {\n",
    "      install.packages(\n",
    "        \"src/R_NAGuideR/GMSimpute_0.0.1.1.tar.gz\",\n",
    "        repos = NULL,\n",
    "        type = \"source\"\n",
    "      )\n",
    "      }\n",
    "  }\n",
    "  else if (method == \"msimpute\") {\n",
    "    install_bioconductor(\"msImpute\")\n",
    "  }\n",
    "  else if (method == \"msimpute_mnar\") {\n",
    "    install_bioconductor(\"msImpute\")\n",
    "  }\n",
    "  else if (method == \"gsimp\") {\n",
    "    options(stringsAsFactors = F)\n",
    "    # dependencies parly for sourced file\n",
    "    \n",
    "    install_bioconductor(\"impute\")\n",
    "    install_bioconductor(\"pcaMethods\")\n",
    "    install_rpackage('gmm')\n",
    "    install_rpackage('imputeLCMD')\n",
    "    install_rpackage(\"magrittr\")\n",
    "    install_rpackage(\"glmnet\")\n",
    "    install_rpackage(\"abind\")\n",
    "    install_rpackage(\"foreach\")\n",
    "    install_rpackage(\"doParallel\")\n",
    "    source('src/R_NAGuideR/GSimp.R')\n",
    "    \n",
    "    } \n",
    "  else{\n",
    "    stop(paste(\"Unspported methods so far: \", method))\n",
    "  }\n",
    "  df <- as.data.frame(df)\n",
    "  df\n",
    "}\n",
    "\n",
    "\n",
    "for (package in packages_base_R) {\n",
    "  # Check if the package is already installed\n",
    "  install_rpackage(pkg = package)\n",
    "}\n",
    "\n",
    "if (!require(\"BiocManager\", quietly = TRUE))\n",
    "    install.packages(\"BiocManager\")"
   ]
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   "source": [
    "methods = unlist(strsplit(methods, split = \",\"))\n",
    "for (package in methods) {\n",
    "  # Check if the package is already installed, otherwise install\n",
    "  nafunctions(method = package)\n",
    "}\n"
   ]
  }
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