Question

I am trying to simulate three small datasets, which contains x1,x2,x3,x4, trt and IND.

However, when I try to split simulated data by IND using “split” in R I get Warning messages and outputs are correct. Could someone please give me a hint what I did wrong in my R code?

# Step 2: simulate data
Alpha = 0.05
S = 3 # number of replicates
x = 8 # number of covariates
G = 3 # number of treatment groups
N = 50 # number of subjects per dataset
tot = S*N # total subjects for a simulation run

# True parameters
alpha = c(0.5, 0.8) # intercepts
b1 = c(0.1,0.2,0.3,0.4) # for pi_1 of trt A
b2 = c(0.15,0.25,0.35,0.45) # for pi_2 of trt B
b = c(1.1,1.2,1.3,1.4);
##############################################################################
# Scenario 1: all covariates are independent standard normally distributed   #
##############################################################################
set.seed(12)
x1 = rnorm(n=tot, mean=0, sd=1);x2 = rnorm(n=tot, mean=0, sd=1);
x3 = rnorm(n=tot, mean=0, sd=1);x4 = rnorm(n=tot, mean=0, sd=1);
###############################################################################

p1 = exp(alpha[1]+b1[1]*x1+b1[2]*x2+b1[3]*x3+b1[4]*x4)/
             (1+exp(alpha[1]+b1[1]*x1+b1[2]*x2+b1[3]*x3+b1[4]*x4) +
                exp(alpha[2]+b2[1]*x1+b2[2]*x2+b2[3]*x3+b2[4]*x4))

p2 = exp(alpha[2]+b2[1]*x1+b2[2]*x2+b2[3]*x3+b2[4]*x4)/
             (1+exp(alpha[1]+b1[1]*x1+b1[2]*x2+b1[3]*x3+b1[4]*x4) +
                exp(alpha[2]+b2[1]*x1+b2[2]*x2+b2[3]*x3+b2[4]*x4))

p3 = 1/(1+exp(alpha[1]+b1[1]*x1+b1[2]*x2+b1[3]*x3+b1[4]*x4) +
          exp(alpha[2]+b2[1]*x1+b2[2]*x2+b2[3]*x3+b2[4]*x4))

# To assign subjects to one of treatment groups based on response probabilities
tmp = function(x){sample(c("A","B","C"), 1, prob=x, replace=TRUE)}
trt = apply(cbind(p1,p2,p3),1,tmp)

IND=rep(1:S,each=N) #create an indicator for split simulated data
sim=data.frame(x1,x2,x3,x4,trt, IND)

Aset = subset(sim, trt=="A")
Bset = subset(sim, trt=="B")
Cset = subset(sim, trt=="C")

Anew = split(Aset, f = IND)
Bnew = split(Bset, f = IND)
Cnew = split(Cset, f = IND)

The warning message:

> Anew = split(Aset, f = IND)
Warning message:
In split.default(x = seq_len(nrow(x)), f = f, drop = drop, ...) :
  data length is not a multiple of split variable

and the output becomes

$`2`
            x1          x2          x3         x4 trt IND
141  1.0894068  0.09765185 -0.46702047  0.4049424   A   3
145 -1.2953113 -1.94291045  0.09926239 -0.5338715   A   3
148  0.0274979  0.72971804  0.47194731 -0.1963896   A   3

$`3`
[1] x1  x2  x3  x4  trt IND
<0 rows> (or 0-length row.names)

I have checked my R code several times however, I can’t figure out what I did wrong. Many thanks in advance

Answer 1

IND is the global variable for the full data, sim. You want to use the specific one for the subset, eg

Anew <- split(Aset, f = Aset$IND)