使用发布包将 Cox 回归结果导出到 excel 或 word

如何解决使用发布包将 Cox 回归结果导出到 excel 或 word

看下面的代码

library(pec)
data(GBSG2,package="pec")
setDT(GBSG2)
GBSG2

library(survival)
library(prodlim)
library(Publish)

cox_lung <- coxph(Surv(time,cens)~tgrade+age+strata(menostat)+tsize+pnodes+progrec+estrec,data=GBSG2)
publish(cox_lung,org=TRUE)

输出:

> publish(cox_GBSG2,org=TRUE)
|  Variable | Units | HazardRatio |       CI.95 |   p-value |
|-----------+-------+-------------+-------------+-----------|
|    tgrade |     I |         Ref |             |           |
|           |    II |        1.86 | [1.14;3.03] |   0.01276 |
|           |   III |        2.24 | [1.32;3.78] |   0.00263 |
|       age |       |        0.99 | [0.97;1.01] |   0.27167 |
|     tsize |       |        1.01 | [1.00;1.01] |   0.06029 |
|    pnodes |       |        1.05 | [1.04;1.07] |   < 0.001 |
|   progrec |       |        1.00 | [1.00;1.00] |   < 0.001 |
|    estrec |       |        1.00 | [1.00;1.00] |   0.70522 |

我想知道是否有一种简单的方法可以将上述输出导出为 CSV、word 或 excel 文件。

解决方法

这是一种使用 capture.outputgsub 获取 csv 文件的方法。我也在展示中间步骤:

cox_out <- capture.output( publish(cox_lung,org=TRUE) )

# Demonstration of intermediates (don't need to do these

gsub("[|]",",cox_out)   # Change "|" to commas
 [1] ",Variable,Units,HazardRatio,CI.95,p-value,"
 [2] ",-----------+-------+-------------+-------------+-----------,"
 [3] ",tgrade,I,Ref,"
 [4] ",II,1.86,[1.14;3.03],0.01276,"
 [5] ",III,2.24,[1.32;3.78],0.00263,"
 [6] ",age,0.99,[0.97;1.01],0.27167,"
 [7] ",tsize,1.01,[1.00;1.01],0.06029,"
 [8] ",pnodes,1.05,[1.04;1.07],< 0.001,"
 [9] ",progrec,1.00,[1.00;1.00],"
[10] ",estrec,0.70522,"
[11] ""                                                             
gsub("[|]",cox_out)[-2]   # Remove second line
 [1] ","
[10] ""                                                             
gsub( "^,|,$","",gsub("[|]",cox_out)[-2] ) # wrap second gsub to take out leading and trailing commas
 [1] "  Variable,p-value "
 [2] "    tgrade,0.01276 "
 [4] ",0.00263 "
 [5] "       age,0.27167 "
 [6] "     tsize,0.06029 "
 [7] "    pnodes,< 0.001 "
 [8] "   progrec,< 0.001 "
 [9] "    estrec,0.70522 "
[10] ""                                
#                         
cat( paste( gsub( "^,cox_out)[-2] ),collapse="\n"),# need paste( ...,colapse="\n") to append linefeeds at each line.
     file="cox_out.csv" )

与使用 cat 相比,使用 write.table 可能会更干净(因为它避免了需要“手动”添加换行符):

cox_out <- capture.output( publish(cox_lung,org=TRUE) )
write.table( gsub( "^,file="cox_out.csv" )

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