使用lapply创建t-test表

时间：2015-07-17 03:53:26

标签： r extract lapply

我希望在两个人群之间进行t检验（治疗组内外（分别在下面的样本数据中为1或0），并且在不同的研究中，所有这些都在相同的数据帧。在下面的示例数据中，我想为1/0治疗组之间的所有变量（样本数据：Age，Dollars，DiseaseCnt）生成t检验。我希望按程序运行这些t检验，而不是跨群体运行。我有生成t检验的逻辑。但是，我需要帮助完成从功能和提取中获取适当部分的最后步骤。创造易于消化的东西。

最终，我想要的是：一个t-stats表，p值，执行t-test的变量，以及测试变量的程序。

DT<-data.frame(
               Treated=sample(0:1,1000,replace=T)
              ,Program=c('Program A','Program B','Program C','Program D')
              ,Age=as.integer(rnorm(1000,mean=65,sd=15))
              ,Dollars=as.integer(rpois(1000,lambda=1000))
              ,DiseaseCnt=as.integer(rnorm(1000,mean=5,sd=2)) )

progs<-unique(DT$Program) # Pull program names
vars<-names(DT)[3:5] # pull variables to run t tests

test<-lapply(progs, function(i)
          tt<-lapply(vars, function(j) {t.test( DT[DT$Treated==1 & DT$Program == i,names(DT)==j] 
                                                ,DT[DT$Treated==0 & DT$Program == i,names(DT)==j]
                                                ,alternative = 'two.sided'  ) 
              list(j,tt$statistic,tt$p.value)  }
                 ) ) 
  # nested lapply produces results in list format that can be binded, but complete output w/ both lapply's is erroneous

3 个答案:

答案 0 :(得分：5)

您应该先将其转换为data.table。 （在我的代码中，我称之为原始表DF）：

DT <- as.data.table(DF)
DT[, t.test(data=.SD, Age ~ Treated), by=Program]
   Program  statistic parameter   p.value   conf.int estimate null.value alternative
1: Program A -0.6286875  247.8390 0.5301326 -4.8110579 65.26667          0   two.sided
2: Program A -0.6286875  247.8390 0.5301326  2.4828527 66.43077          0   two.sided
3: Program B  1.4758524  230.5380 0.1413480 -0.9069634 67.15315          0   two.sided
4: Program B  1.4758524  230.5380 0.1413480  6.3211834 64.44604          0   two.sided
5: Program C  0.1994182  246.9302 0.8420998 -3.3560930 63.56557          0   two.sided
6: Program C  0.1994182  246.9302 0.8420998  4.1122406 63.18750          0   two.sided
7: Program D -1.1321569  246.0086 0.2586708 -6.1855837 62.31707          0   two.sided
8: Program D -1.1321569  246.0086 0.2586708  1.6701237 64.57480          0   two.sided
                method      data.name
1: Welch Two Sample t-test Age by Treated
2: Welch Two Sample t-test Age by Treated
3: Welch Two Sample t-test Age by Treated
4: Welch Two Sample t-test Age by Treated
5: Welch Two Sample t-test Age by Treated
6: Welch Two Sample t-test Age by Treated
7: Welch Two Sample t-test Age by Treated
8: Welch Two Sample t-test Age by Treated

采用这种格式，对于每个Program，statistic对于两者都相同且等于t，parameter此处为df，对于conf.int，它（按顺序）低于上限（因此对于Program A，置信区间为(-4.8110579, 2.4828527)，对于estimate，它将为group 0然后是group 1（因此对于Program A，Treated == 0的平均值为65.26667等。

这是我能提出的最快的解决方案，你可以循环vars，或者可能有更简单的方法。

编辑：我只使用以下代码确认Program A和Age：

DT[Program == 'Program A', t.test(Age ~ Treated)]
    Welch Two Sample t-test

data:  Age by Treated
t = -0.62869, df = 247.84, p-value = 0.5301
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 -4.811058  2.482853
sample estimates:
mean in group 0 mean in group 1
       65.26667        66.43077

编辑2：这是循环遍历变量的代码，rbind将它们放在一起：

do.call(rbind, lapply(vars, function(x) DT[, t.test(data=.SD, eval(parse(text=x)) ~ Treated), by=Program]))

答案 1 :(得分：2)

您可以从回归中获得相同的t检验;如果您认为不同程序的治疗效果不同，您应该包括互动。您还可以指定多个响应。 

> m <- lm(cbind(Age,Dollars,DiseaseCnt)~Treated * Program - Treated - 1, DT)
> lapply(summary(m), `[[`, "coefficients")
$`Response Age`
                              Estimate  Std. Error       t value         Pr(>|t|)
ProgramProgram A         63.0875912409 1.294086510 48.7506752932 1.355786133e-265
ProgramProgram B         65.3846153846 1.400330869 46.6922616771 1.207761156e-252
ProgramProgram C         66.0695652174 1.412455172 46.7763979425 3.534894216e-253
ProgramProgram D         66.6691729323 1.313402302 50.7606640010 5.038015651e-278
Treated:ProgramProgram A  2.8593114140 1.924837595  1.4854819032  1.377339219e-01
Treated:ProgramProgram B -0.9786003470 1.919883369 -0.5097186438  6.103619649e-01
Treated:ProgramProgram C -0.5066022544 1.922108032 -0.2635659631  7.921691261e-01
Treated:ProgramProgram D -2.8657541289 1.919883369 -1.4926709484  1.358412980e-01

$`Response Dollars`
                                Estimate  Std. Error        t value     Pr(>|t|)
ProgramProgram A          998.5474452555 2.681598120 372.3702808887 0.0000000000
ProgramProgram B          997.4188034188 2.901757030 343.7292623810 0.0000000000
ProgramProgram C         1001.6869565217 2.926880936 342.2370019265 0.0000000000
ProgramProgram D         1001.2180451128 2.721624185 367.8752013053 0.0000000000
Treated:ProgramProgram A   -0.9899231316 3.988636646  -0.2481858388 0.8040419882
Treated:ProgramProgram B    2.5060086113 3.978370529   0.6299082986 0.5288996396
Treated:ProgramProgram C   -5.4721417069 3.982980462  -1.3738811324 0.1697889454
Treated:ProgramProgram D   -4.0043698991 3.978370529  -1.0065351806 0.3144036460

$`Response DiseaseCnt`
                               Estimate   Std. Error        t value         Pr(>|t|)
ProgramProgram A          4.53284671533 0.1793523653 25.27341475576 3.409326912e-109
ProgramProgram B          4.56410256410 0.1940771747 23.51694665775  1.515736580e-97
ProgramProgram C          4.25217391304 0.1957575279 21.72163675698  6.839384262e-86
ProgramProgram D          4.60150375940 0.1820294143 25.27890219412 3.133081901e-109
Treated:ProgramProgram A  0.13087009883 0.2667705543  0.49057175444  6.238378600e-01
Treated:ProgramProgram B -0.02274918064 0.2660839292 -0.08549625944  9.318841210e-01
Treated:ProgramProgram C  0.47375201288 0.2663922537  1.77840010867  7.564438017e-02
Treated:ProgramProgram D -0.31090546880 0.2660839292 -1.16844887901  2.429064705e-01

您特别关注回归表的Treated:Program条目。

答案 2 :(得分：1)

您正在尝试从 tt$statistic的 tt内的中访问results <- lapply(progs, function (i) { DS = subset(DT, Program == i) o <- lapply(vars, function (i) { frm <- formula(paste0(i, '~ Treated')) tt <- t.test(frm, DS) data.frame(Variable=i, T=tt$statistic, P=tt$p.value) }) o <- do.call(rbind, o) o$Program <- i o }) do.call(rbind, results) ，从而导致出现错误。一些包围问题。

以下是按照您的版本

执行此操作的一种方法 
rbind

或者你可以使用（例如）ddply来代替library(plyr) combinations <- expand.grid(Program=progs, Y=vars) ddply(combinations, .(Program, Y), function (x) { # x is a dataframe with the program and variable; # just do the t-test and add the statistic & p-val to it frm <- formula(paste0(x$Y, '~ Treated')) tt <- t.test(frm, subset(DT, Program == x$Program)) x$T <- tt$statistic x$P <- tt$p.value x }) - 我认为rbinding仍然会发生，只是在幕后）：

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