## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(fig.width=6, fig.height=4.5) # Set the width and height ## ----eval=FALSE--------------------------------------------------------------- # install.packages("csmpv") ## ----eval=FALSE--------------------------------------------------------------- # # Install devtools package if not already installed # options(repos = c(CRAN = "https://cloud.r-project.org")) # install.packages("devtools") # # # Install csmpv package from GitHub # devtools::install_github("ajiangsfu/csmpv",force = TRUE) # # Using force = TRUE will ensure the installation, overriding any existing versions ## ----eval=FALSE--------------------------------------------------------------- # # Install remotes package if not already installed # install.packages("remotes") # # Install csmpv package from GitHub # remotes::install_github("ajiangsfu/csmpv",force = TRUE) # # Using force = TRUE will ensure the installation, overriding any existing versions ## ----------------------------------------------------------------------------- library(csmpv) data("datlist", package = "csmpv") tdat = datlist$training dim(tdat) vdat = datlist$validation dim(vdat) ## ----------------------------------------------------------------------------- Xvars = c("B.Symptoms","MYC.IHC","BCL2.IHC", "CD10.IHC","BCL6.IHC", "MUM1.IHC","Male","AgeOver60", "stage3_4","PS1","LDH.Ratio1", "Extranodal1","Bulk10cm","HANS_GCB", "DTI") ## ----------------------------------------------------------------------------- AgeXvars = setdiff(Xvars, "AgeOver60") ## ----------------------------------------------------------------------------- set.seed(12345) ## ----------------------------------------------------------------------------- temp_dir = tempdir() knitr::opts_knit$set(root.dir = temp_dir) ## ----echo=FALSE--------------------------------------------------------------- options(warn = -1) ## ----results = 'hide',message=FALSE, warnings=FALSE--------------------------- bconfirm = confirmVars(data = tdat, biomks = Xvars, Y = "DZsig", outfile = "confirmBinary") ## ----------------------------------------------------------------------------- print(bconfirm$fit) bconfirm$allplot[[2]] ## ----results = 'hide',message=FALSE, warnings=FALSE--------------------------- cconfirm = confirmVars(data = tdat, biomks = AgeXvars, Y = "Age", outcomeType = "continuous", outfile = "confirmContinuous") ## ----------------------------------------------------------------------------- print(cconfirm$fit) cconfirm$allplot[[2]] ## ----results = 'hide',message=FALSE, warnings=FALSE--------------------------- tconfirm = confirmVars(data = tdat, biomks = Xvars, time = "FFP..Years.", event = "Code.FFP", outcomeType = "time-to-event", outfile = "confirmSurvival") ## ----------------------------------------------------------------------------- print(tconfirm$fit) tconfirm$allplot[[2]] ## ----------------------------------------------------------------------------- bl = LASSO2(data = tdat, biomks = Xvars, Y = "DZsig", outfile = "binaryLASSO2") ## ----------------------------------------------------------------------------- bl$coefs ## ----------------------------------------------------------------------------- cl = LASSO2(data = tdat, biomks = AgeXvars, outcomeType = "continuous", Y = "Age", outfile = "continuousLASSO2") ## ----------------------------------------------------------------------------- cl$coefs ## ----------------------------------------------------------------------------- tl = LASSO2(data = tdat, biomks = Xvars, outcomeType = "time-to-event", time = "FFP..Years.",event = "Code.FFP", outfile = "survivalLASSO2") ## ----------------------------------------------------------------------------- tl$coefs ## ----------------------------------------------------------------------------- b2fit = LASSO2plus(data = tdat, biomks = Xvars, Y = "DZsig", outfile = "binaryLASSO2plus") b2fit$fit$coefficients ## ----------------------------------------------------------------------------- c2fit = LASSO2plus(data = tdat, biomks = AgeXvars, outcomeType = "continuous", Y = "Age", outfile = "continuousLASSO2plus") c2fit$fit$coefficients ## ----------------------------------------------------------------------------- t2fit = LASSO2plus(data = tdat, biomks = Xvars, outcomeType = "time-to-event", time = "FFP..Years.",event = "Code.FFP", outfile = "survivalLASSO2plus") t2fit$fit$coefficients ## ----------------------------------------------------------------------------- bfit = LASSO_plus(data = tdat, biomks = Xvars, Y = "DZsig", outfile = "binaryLASSO_plus", topN = 5) bfit$fit$coefficients ## ----------------------------------------------------------------------------- cfit = LASSO_plus(data = tdat, biomks = AgeXvars, outcomeType = "continuous", Y = "Age", outfile = "continuousLASSO_plus", topN = 5) cfit$fit$coefficients ## ----------------------------------------------------------------------------- tfit = LASSO_plus(data = tdat, biomks = Xvars, outcomeType = "time-to-event", time = "FFP..Years.",event = "Code.FFP", outfile = "survivalLASSO_plus", topN = 5) tfit$fit$coefficients ## ----results = 'hide',message=FALSE, warnings=FALSE--------------------------- blr = LASSO2_reg(data = tdat, biomks = Xvars, Y = "DZsig", outfile = "binaryLASSO2_reg") ## ----------------------------------------------------------------------------- blr$fit$coefficients ## ----results = 'hide',message=FALSE, warnings=FALSE--------------------------- clr = LASSO2_reg(data = tdat, biomks = AgeXvars, outcomeType = "continuous", Y = "Age", outfile = "continuousLASSO2_reg") ## ----------------------------------------------------------------------------- clr$fit$coefficients ## ----results = 'hide',message=FALSE, warnings=FALSE--------------------------- tlr = LASSO2_reg(data = tdat, biomks = Xvars, outcomeType = "time-to-event", time = "FFP..Years.",event = "Code.FFP", outfile = "survivalLASSO2_reg") ## ----------------------------------------------------------------------------- tlr$fit$coefficients ## ----------------------------------------------------------------------------- bxfit = XGBtraining(data = tdat, biomks = Xvars, Y = "DZsig", outfile = "binary_XGBoost") head(bxfit$XGBoost_score) ## ----------------------------------------------------------------------------- cxfit = XGBtraining(data = tdat, biomks = AgeXvars, outcomeType = "continuous", Y = "Age", outfile = "continuous_XGBoost") head(cxfit$XGBoost_score) ## ----------------------------------------------------------------------------- txfit = XGBtraining(data = tdat, biomks = Xvars, outcomeType = "time-to-event", time = "FFP..Years.",event = "Code.FFP", outfile = "survival_XGBoost") head(txfit$XGBoost_score) ## ----------------------------------------------------------------------------- blxfit = LASSO2_XGBtraining(data = tdat, biomks = Xvars, Y = "DZsig", outfile = "binary_LASSO2_XGBoost") head(blxfit$XGBoost_score) ## ----------------------------------------------------------------------------- clxfit = LASSO2_XGBtraining(data = tdat, biomks = AgeXvars, outcomeType = "continuous", Y = "Age", outfile = "continuous_LASSO2_XGBoost") head(clxfit$XGBoost_score) ## ----------------------------------------------------------------------------- tlxfit = LASSO2_XGBtraining(data = tdat, biomks = Xvars, outcomeType = "time-to-event", time = "FFP..Years.",event = "Code.FFP", outfile = "survival_LASSO2_XGBoost") head(tlxfit$XGBoost_score) ## ----warning=FALSE------------------------------------------------------------ blpxfit = LASSO_plus_XGBtraining(data = tdat, biomks = Xvars, Y = "DZsig", topN = 5,outfile = "binary_LASSO_plus_XGBoost") head(blpxfit$XGBoost_score) ## ----warning=FALSE------------------------------------------------------------ clpxfit = LASSO_plus_XGBtraining(data = tdat, biomks = AgeXvars, outcomeType = "continuous", Y = "Age", topN = 5,outfile = "continuous_LASSO_plus_XGBoost") head(clpxfit$XGBoost_score) ## ----warning=FALSE------------------------------------------------------------ tlpxfit = LASSO_plus_XGBtraining(data = tdat, biomks = Xvars, outcomeType = "time-to-event", time = "FFP..Years.",event = "Code.FFP", topN = 5,outfile = "survival_LASSO_plus_XGBoost") head(tlpxfit$XGBoost_score) ## ----warning=FALSE------------------------------------------------------------ bl2xfit = LASSO2plus_XGBtraining(data = tdat, biomks = Xvars, Y = "DZsig", outfile = "binary_LASSO2plus_XGBoost") head(bl2xfit$XGBoost_score) ## ----warning=FALSE------------------------------------------------------------ cl2xfit = LASSO2plus_XGBtraining(data = tdat, biomks = AgeXvars, outcomeType = "continuous", Y = "Age", outfile = "continuous_LASSO2plus_XGBoost") head(cl2xfit$XGBoost_score) ## ----warning=FALSE------------------------------------------------------------ tl2xfit = LASSO2plus_XGBtraining(data = tdat, biomks = Xvars, outcomeType = "time-to-event", time = "FFP..Years.", event = "Code.FFP", outfile = "survival_LASSO2plus_XGBoost") head(tl2xfit$XGBoost_score) ## ----------------------------------------------------------------------------- pbl = LASSO2_predict(bl, newdata = vdat, outfile = "pred_LASSO2_binary") head(pbl) ## ----------------------------------------------------------------------------- pcl = LASSO2_predict(cl, newdata = vdat, outfile = "pred_LASSO2_cont") head(pbl) ## ----------------------------------------------------------------------------- ptl = LASSO2_predict(tl, newdata = vdat, outfile = "pred_LASSO2_time_to_event") head(pbl) ## ----------------------------------------------------------------------------- pblr = rms_model(blr$fit, newdata = vdat, outfile = "pred_LASSO2reg_binary") head(pblr) ## ----------------------------------------------------------------------------- pclr = rms_model(clr$fit, newdata = vdat, outfile = "pred_LASSO2reg_continuous") head(pclr) ## ----------------------------------------------------------------------------- ptlr = rms_model(tlr$fit, data = tdat, newdata = vdat, outfile = "pred_LASSO2reg_time_to_event") head(ptlr) ## ----------------------------------------------------------------------------- pbfit = rms_model(bfit$fit, newdata = vdat, outfile = "pred_LASSOplus_binary") ## ----------------------------------------------------------------------------- pcfit = rms_model(cfit$fit, newdata = vdat, outfile = "pred_LASSOplus_continuous") ## ----------------------------------------------------------------------------- ptfit = rms_model(tfit$fit, data = tdat, newdata = vdat, outfile = "pred_LASSOplus_time_to_event") ## ----------------------------------------------------------------------------- p2bfit = rms_model(b2fit$fit, newdata = vdat, outfile = "pred_LASSO2plus_binary") ## ----------------------------------------------------------------------------- p2cfit = rms_model(c2fit$fit, newdata = vdat, outfile = "pred_LASSO2plus_continuous") ## ----------------------------------------------------------------------------- p2tfit = rms_model(t2fit$fit, data = tdat, newdata = vdat, outfile = "pred_LASSO2plus_time_to_event") ## ----------------------------------------------------------------------------- pbxfit = XGBtraining_predict(bxfit, newdata = vdat, outfile = "pred_XGBoost_binary") ## ----------------------------------------------------------------------------- pcxfit = XGBtraining_predict(cxfit, newdata = vdat, outfile = "pred_XGBoost_cont") ## ----------------------------------------------------------------------------- ptxfit = XGBtraining_predict(txfit, newdata = vdat, outfile = "pred_XGBoost_time_to_event") ## ----------------------------------------------------------------------------- pblxfit = XGBtraining_predict(blxfit, newdata = vdat, outfile = "pred_LXGBoost_binary") ## ----------------------------------------------------------------------------- pclxfit = XGBtraining_predict(clxfit, newdata = vdat, outfile = "pred_LXGBoost_cont") ## ----------------------------------------------------------------------------- ptlxfit = XGBtraining_predict(tlxfit, newdata = vdat, outfile = "pred_LXGBoost_time_to_event") ## ----------------------------------------------------------------------------- pblpxfit = XGBtraining_predict(blpxfit, newdata = vdat, outfile = "pred_LpXGBoost_binary") ## ----------------------------------------------------------------------------- pclpxfit = XGBtraining_predict(clpxfit, newdata = vdat, outfile = "pred_LpXGBoost_cont") ## ----------------------------------------------------------------------------- ptlpxfit = XGBtraining_predict(tlpxfit, newdata = vdat, outfile = "pred_LpXGBoost_time_to_event") ## ----------------------------------------------------------------------------- pbl2xfit = XGBtraining_predict(bl2xfit, newdata = vdat, outfile = "pred_L2XGBoost_binary") ## ----------------------------------------------------------------------------- pcl2xfit = XGBtraining_predict(cl2xfit, newdata = vdat, outfile = "pred_L2XGBoost_cont") ## ----------------------------------------------------------------------------- ptl2xfit = XGBtraining_predict(tl2xfit, newdata = vdat, outfile = "pred_L2XGBoost_time_to_event") ## ----------------------------------------------------------------------------- vbl = LASSO2_predict(bl, newdata = vdat, newY = TRUE, outfile = "valid_LASSO2_binary") ## ----------------------------------------------------------------------------- vcl = LASSO2_predict(cl, newdata = vdat, newY = TRUE, outfile = "valid_LASSO2_cont") ## ----------------------------------------------------------------------------- vtl = LASSO2_predict(tl, newdata = vdat, newY = TRUE, outfile = "valid_LASSO2_time_to_event") ## ----------------------------------------------------------------------------- vblr = rms_model(blr$fit, newdata = vdat, newY = TRUE, outfile = "valid_LASSO2reg_binary") ## ----------------------------------------------------------------------------- vclr = rms_model(clr$fit, newdata = vdat, newY = TRUE, outfile = "valid_LASSO2reg_continuous") ## ----------------------------------------------------------------------------- vtlr = rms_model(tlr$fit, data = tdat, newdata = vdat, newY = TRUE, outfile = "valid_LASSO2reg_time_to_event") ## ----------------------------------------------------------------------------- vbfit = rms_model(bfit$fit, newdata = vdat, newY = TRUE, outfile = "valid_LASSOplus_binary") ## ----------------------------------------------------------------------------- vcfit = rms_model(cfit$fit, newdata = vdat, newY = TRUE, outfile = "valid_LASSOplus_continuous") ## ----------------------------------------------------------------------------- vtfit = rms_model(tfit$fit, data = tdat, newdata = vdat, newY = TRUE, outfile = "valid_LASSOplus_time_to_event") ## ----------------------------------------------------------------------------- v2bfit = rms_model(b2fit$fit, newdata = vdat, newY = TRUE, outfile = "valid_LASSO2plus_binary") ## ----------------------------------------------------------------------------- v2cfit = rms_model(c2fit$fit, newdata = vdat, newY = TRUE, outfile = "valid_LASSO2plus_continuous") ## ----------------------------------------------------------------------------- v2tfit = rms_model(t2fit$fit, data = tdat, newdata = vdat, newY = TRUE, outfile = "valid_LASSO2plus_time_to_event") ## ----------------------------------------------------------------------------- vbxfit = XGBtraining_predict(bxfit, newdata = vdat, newY = TRUE, outfile = "valid_XGBoost_binary") ## ----------------------------------------------------------------------------- vcxfit = XGBtraining_predict(cxfit, newdata = vdat, newY = TRUE, outfile = "valid_XGBoost_cont") ## ----------------------------------------------------------------------------- vtxfit = XGBtraining_predict(txfit, newdata = vdat, newY = TRUE, outfile = "valid_XGBoost_time_to_event") ## ----------------------------------------------------------------------------- vblxfit = XGBtraining_predict(blxfit, newdata = vdat, newY = TRUE, outfile = "valid_LXGBoost_binary") ## ----------------------------------------------------------------------------- vclxfit = XGBtraining_predict(clxfit, newdata = vdat, newY = TRUE, outfile = "valid_LXGBoost_cont") ## ----------------------------------------------------------------------------- vtlxfit = XGBtraining_predict(tlxfit, newdata = vdat, newY = TRUE, outfile = "valid_LXGBoost_time_to_event") ## ----------------------------------------------------------------------------- vblpxfit = XGBtraining_predict(blpxfit, newdata = vdat, newY = TRUE, outfile = "valid_LpXGBoost_binary") ## ----------------------------------------------------------------------------- vclpxfit = XGBtraining_predict(clpxfit, newdata = vdat, newY = TRUE, outfile = "valid_LpXGBoost_cont") ## ----------------------------------------------------------------------------- vtlpxfit = XGBtraining_predict(tlpxfit, newdata = vdat, newY = TRUE, outfile = "valid_LpXGBoost_time_to_event") ## ----------------------------------------------------------------------------- vbl2xfit = XGBtraining_predict(bl2xfit, newdata = vdat, newY = TRUE, outfile = "valid_L2XGBoost_binary") ## ----------------------------------------------------------------------------- vcl2xfit = XGBtraining_predict(cl2xfit, newdata = vdat, newY = TRUE, outfile = "valid_L2XGBoost_cont") ## ----------------------------------------------------------------------------- vtl2xfit = XGBtraining_predict(tl2xfit, newdata = vdat, newY = TRUE, outfile = "valid_L2XGBoost_time_to_event") ## ----eval = FALSE------------------------------------------------------------- # modelout = csmpvModelling(tdat = tdat, vdat = vdat, # Ybinary = "DZsig", varsBinary = Xvars, # Ycont = "Age", varsCont = AgeXvars, # time = "FFP..Years.", event = "Code.FFP", # varsSurvival = Xvars, # outfileName= "all_in_one") ## ----warning=FALSE------------------------------------------------------------ DZlassoreg = csmpvModelling(tdat = tdat, vdat = vdat, Ybinary = "DZsig", varsBinary = Xvars, methods = "LASSO2_reg", outfileName= "just_one") ## ----results = 'hide',message=FALSE, warnings=FALSE--------------------------- xgobj = XGpred(data = tdat, varsIn = Xvars, selection = TRUE, vsMethod = "LASSO_plus", topN = 5, time = "FFP..Years.", event = "Code.FFP", outfile = "XGpred") ## ----results = 'hide',message=FALSE, warnings=FALSE--------------------------- xgobj3 = XGpred(data = tdat, varsIn = Xvars, time = "FFP..Years.", event = "Code.FFP", selection = TRUE, vsMethod = "LASSO_plus", topN = 5, nclass = 3, outfile = "XGpred") ## ----results = 'hide',message=FALSE, warnings=FALSE--------------------------- tdat$XGpred_class2 = xgobj$XGpred_prob_class training_risk_confirm2 = confirmVars(data = tdat, biomks = "XGpred_class2", time = "FFP..Years.", event = "Code.FFP", outfile = "training2grps_riskSurvival", outcomeType = "time-to-event") training_risk_confirm2[[3]] tdat$XGpred_class3 = xgobj3$XGpred_prob_class training_risk_confirm3 = confirmVars(data = tdat, biomks = "XGpred_class3", time = "FFP..Years.", event = "Code.FFP", outfile = "training3grps_riskSurvival", outcomeType = "time-to-event") training_risk_confirm3[[3]] ## ----------------------------------------------------------------------------- xgNew = XGpred_predict(newdat = vdat, XGpredObj = xgobj) xgNew3 = XGpred_predict(newdat = vdat, XGpredObj = xgobj3) ## ----results = 'hide',message=FALSE, warnings=FALSE--------------------------- vdat$XGpred_class2 = xgNew$XGpred_prob_class risk_confirm2 = confirmVars(data = vdat, biomks = "XGpred_class2", time = "FFP..Years.", event = "Code.FFP", outfile = "riskSurvival2grps", outcomeType = "time-to-event") risk_confirm2[[3]] vdat$XGpred_class3 = xgNew3$XGpred_prob_class risk_confirm3 = confirmVars(data = vdat, biomks = "XGpred_class3", time = "FFP..Years.", event = "Code.FFP", outfile = "riskSurvival3grps", outcomeType = "time-to-event") risk_confirm3[[3]] ## ----------------------------------------------------------------------------- devtools::session_info()