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reshape.R
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reshape.R
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### R code from vignette source 'reshape.Rnw'
###################################################
### code chunk number 1: load_data
###################################################
library(reshape)
library(Hmisc)
load("mtx.RData")
################################################################################
# [1] "patid" "visitid" "dob"
# [4] "trt_age" "sex" "height"
# [7] "weight" "ibw" "adjust_bw"
#[10] "bsa" "dosing_bsa" "dx"
#[13] "pleural_effusion" "ascites" "mtxlvl_0"
#[16] "mtx_mgm2" "infuse_timeh" "infuse_timecode"
#[19] "mtx_startdt" "mtx_starttm" "leu_init_dose"
#[22] "leu_init_freq" "leu_route" "keppra"
#[25] "keppra_dose" "keppra_freq" "num_inter_meds"
#[28] "hydrate_fluids" "hydrate_fluids_rate" "mtx_startdt_base"
#[31] "mtx_starttm_base" "urine_0" "scr_0"
#[34] "crclwt_0" "crcl_0" "ast_0"
#[37] "alt_0" "labdt_24" "labtm_24"
#[40] "urine_24" "scr_24" "crcl_24"
#[43] "mtxlvl_24" "delaymtx_24" "labdt_48"
#[46] "labtm_48" "urine_48" "scr_48"
#[49] "crcl_48" "mtxlvl_48" "delaymtx_48"
#[52] "labdt_72" "labtm_72" "urine_72"
#[55] "scr_72" "crcl_72" "mtxlvl_72"
#[58] "delaymtx_72" "labdtadd_1" "labtmadd_1"
#[61] "urineadd_1" "scradd_1" "crcladd_1"
#[64] "mtxlvladd_1" "labdtadd_2" "labtmadd_2"
#[67] "urineadd_2" "scradd_2" "crcladd_2"
#[70] "mtxlvladd_2" "labdtadd_3" "labtmadd_3"
#[73] "urineadd_3" "scradd_3" "crcladd_3"
#[76] "mtxlvladd_3" "delaymtx_any" "nontoxic_mtx_tm"
#[79] "urine_add3" "mtx_lvl_add1" "mtx_lvl_24h"
#[82] "delaymtx2_any"
################################################################################
mtx_both <- mtx_dt[,c("patid","visitid","keppra","trt_age","mtxlvl_24","scr_24","mtxlvl_48","scr_48","mtxlvl_72","scr_72")]
names(mtx_both)[5:10] <- c("mtxlvl.24","scr.24","mtxlvl.48","scr.48","mtxlvl.72","scr.72")
mtx.mltf <- melt(mtx_both, id=c("patid","visitid","keppra","trt_age"), variable_name="lab.var")
mtx.mltf.srt <- with(mtx.mltf, mtx.mltf[order(patid,visitid),])
mtx.mltf.lab <- cbind(mtx.mltf.srt, colsplit(mtx.mltf.srt$lab.var, names=c("lab","time"), split="\\."))
mtx.mtxlvl <- mtx_dt[,c("patid","visitid","keppra","trt_age","mtxlvl_24","mtxlvl_48","mtxlvl_72")]
names(mtx.mtxlvl)[5:7] <- c("mtxlvl.24","mtxlvl.48","mtxlvl.72")
mtx.mlt1 <- melt(mtx.mtxlvl, id=c("patid","visitid","keppra","trt_age"), measured=c("mtxlvl.24","mtxlvl.48","mtxlvl.72"), variable_name="lab.var")
mtx.mlt1.srt <- with(mtx.mlt1, mtx.mlt1[order(patid,visitid),])
mtx.mlt1.lab <- cbind(mtx.mlt1.srt, colsplit(mtx.mlt1.srt$lab.var, names=c("lab","time"), split="\\."))
###################################################
### code chunk number 2: mtxraw
###################################################
latex(mtx.mtxlvl[1:5,c(1:3,5:7)],file="",rowname=NULL)
###################################################
### code chunk number 3: mtxmelt
###################################################
latex(mtx.mlt1.srt[1:6,c(1:3,5:6)], file="", rowname=NULL)
###################################################
### code chunk number 4: mlttrt
###################################################
latex(mtx.mlt1.lab[1:3,c(1:3,6:8)], file="", rowname=NULL)
###################################################
### code chunk number 5: meas2
###################################################
latex(head(mtx.mltf.lab[1:6,c(1:3,5:6)]), file="", rowname=NULL)
###################################################
### code chunk number 6: mltmeas2
###################################################
latex(head(mtx.mltf.lab[1:6,c(1:3,5:8)]), file="", rowname=NULL)
###################################################
### code chunk number 7: castit
###################################################
latex(head(cast(mtx.mlt1.srt, patid+visitid~lab.var)), file="", rowname=NULL)
###################################################
### code chunk number 8: castit2
###################################################
mtx.castf.lab <- cast(mtx.mltf.lab, patid+visitid+keppra+time~lab)
latex(head(mtx.castf.lab), file="", rowname=NULL)
###################################################
### code chunk number 9: castag
###################################################
latex(cast(mtx.mltf.lab, keppra~lab, mean, na.rm=TRUE), file="", rowname=NULL, digits=2)
#cast(mtx.mltf.lab, keppra+time~lab, mean, na.rm=TRUE, margins="keppra")
#cast(mtx.mltf.lab, keppra~lab, mean, na.rm=TRUE, margins="grand_col")
#cast(mtx.mltf.lab, keppra~lab, mean, na.rm=TRUE, margins="grand_row")
#cast(mtx.mltf.lab, keppra~lab, mean, na.rm=TRUE, margins=TRUE)
###################################################
### code chunk number 10: castag2
###################################################
latex(cast(mtx.mltf.lab, lab~., quantile, c(0.25,0.5,0.75),na.rm=TRUE), file="", rowname=NULL)
###################################################
### code chunk number 11: castag3
###################################################
latex(cast(mtx.mltf.lab, time+keppra~lab, mean, na.rm=TRUE), file="", rowname=NULL, digits=2)
###################################################
### code chunk number 12: castag4
###################################################
latex(cast(mtx.mltf.lab, time+keppra~lab, mean, na.rm=TRUE, margins="time"), file="", rowname=NULL, digits=2)