Movatterモバイル変換

install.packages("kfre")

# install.packages("remotes")remotes::install_github("lshpaner/kfre_r")

toy<-data.frame(age =c(55,72),sex_txt =c("male","female"),eGFR =c(45,28),uACR =c(120,800),dm =c(1,0),htn =c(1,1),albumin =c(4.2,3.4),phosphorous =c(3.3,4.6),bicarbonate =c(24,22),calcium =c(9.1,9.8),stringsAsFactors =FALSE)cols<-list(age ="age",sex ="sex_txt",eGFR ="eGFR",uACR ="uACR",dm ="dm",htn ="htn",albumin ="albumin",phosphorous ="phosphorous",bicarbonate ="bicarbonate",calcium ="calcium")

rp<- RiskPredictor$new(df = toy,columns = cols)# 4-variable KFRE (2-year), North America constantsp4_2y<- rp$predict_kfre(years =2,is_north_american =TRUE,use_extra_vars =FALSE,num_vars =4)# 6-variable KFRE (5-year)p6_5y<- rp$predict_kfre(years =5,is_north_american =TRUE,use_extra_vars =TRUE,num_vars =6)# 8-variable KFRE (2-year)p8_2y<- rp$predict_kfre(years =2,is_north_american =TRUE,use_extra_vars =TRUE,num_vars =8)p4_2yp6_5yp8_2y

# Male, 55yo, 2-year risk (4-var)rp$kfre_person(age =55,is_male =TRUE,eGFR =45,uACR =120,is_north_american =TRUE,years =2)# Female, 72yo, 5-year risk (6-var)rp$kfre_person(age =72,is_male =FALSE,eGFR =28,uACR =800,is_north_american =TRUE,years =5,dm =0,htn =1)# Female, 72yo, 2-year risk (8-var)rp$kfre_person(age =72,is_male =FALSE,eGFR =28,uACR =800,is_north_american =TRUE,years =2,albumin =3.4,phosphorous =4.6,bicarbonate =22,calcium =9.8)

toy_kfre<-add_kfre_risk_col(df = toy,age_col ="age",sex_col ="sex_txt",eGFR_col ="eGFR",uACR_col ="uACR",dm_col ="dm",htn_col ="htn",albumin_col ="albumin",phosphorous_col ="phosphorous",bicarbonate_col ="bicarbonate",calcium_col ="calcium",num_vars =c(4,6,8),years =c(2,5),is_north_american =TRUE,copy =TRUE)names(toy_kfre)head(toy_kfre)# Adds:# kfre_4var_2year, kfre_4var_5year,# kfre_6var_2year, kfre_6var_5year,# kfre_8var_2year, kfre_8var_5year

# ESRD outcome within 2 years (duration is in days → converted to years)out<-data.frame(eGFR =c(95,25),ESRD_flag =c(1,1),followup_days =c(200,1000))out<-class_esrd_outcome(df = out,col ="ESRD_flag",years =2,duration_col ="followup_days",prefix ="esrd",create_years_col =TRUE)# Adds: ESRD_duration_years and esrd_2_year_outcome# CKD stage labelsout<-class_ckd_stages(df = out,egfr_col ="eGFR",stage_col ="stage",combined_stage_col ="stage_combined")table(out$stage)table(out$stage_combined)

df_pcr<-data.frame(sex =c("female","male","female"),dm  =c(1,0,1),htn =c(1,1,0),pcr =c(150,600,50))acr<-upcr_uacr(  df_pcr,sex_col ="sex",diabetes_col ="dm",hypertension_col ="htn",upcr_col ="pcr",female_str ="female")acr

met<-eval_kfre_metrics(df = toy_kfre,# must contain truth + prediction columnsn_var_list =c(4,6,8),outcome_years =c(2,5),decimal_places =4)met# Rows: Metrics; Cols: "{2_year|5_year}_{4|6|8}_var_kfre"

# Basic: compute & plot both ROC and PR (no files written)plot_kfre_metrics(df = toy_kfre,num_vars =c(4,6,8),plot_type ="all_plots",mode ="both",# compute + plotshow_years =c(2,5))# Save to disk (PNG/SVG)plot_kfre_metrics(df = toy_kfre,num_vars =c(4,6),plot_type ="auc_roc",mode ="both",show_years =c(2,5),save_plots =TRUE,image_path_png ="plots",image_prefix ="kfre")

library(devtools)devtools::load_all(".")devtools::test()