SMHS DataSimulation

Scientific Methods for Health Sciences - Data Simulation

Importing observed data for exploratory analytics

Using the SOCR Health Evaluation and Linkage to Primary (HELP) Care Dataset we can extract some sample data (00_Tiny_SOCR_HELP_Data_Simmulation.csv).

# data_1 <- read.csv('00_Tiny_SOCR_HELP_Data_Simmulation.csv',as.is=T, header=T)
# data_1 = read.csv(file.choose( ))
# data_1 <- read.table('00_Tiny_SOCR_HELP_Data_Simmulation.csv', header=TRUE,   sep=",", row.names="ID")

attach(data_1)  
# to ensure all variables are accessible within R, e.g., using age instead of data_1$$age
# i2 maximum number of drinks (standard units) consumed per day (in the past 30 days range 0–184) see also i1
# treat randomization group (0=usual care, 1=HELP clinic)
# pcs SF-36 Physical Component Score (range 14-75)
# mcs SF-36 Mental Component Score(range 7-62)
# cesd Center for Epidemiologic Studies Depression scale (range 0–60)
# indtot Inventory of Drug Use Con-sequences (InDUC) total score (range 4–45)
# pss_fr perceived social supports (friends, range 0–14) see also dayslink
# drugrisk Risk-Assessment Battery(RAB) drug risk score (range0–21)
# satreat any BSAS substance abuse treatment at baseline (0=no,1=yes)

Fragment of the data

ID	i2	age	treat	homeless	pcs	mcs	cesd	indtot	pss_fr	drugrisk	sexrisk	satreat	female	substance	racegrp
1	0	25	0	0	49	7	46	37	0	1	6	0	0	cocaine	black
2	18	31	0	0	48	34	17	48	0	0	11	0	0	alcohol	white
3	39	36	0	0	76	9	33	41	12	19	4	0	0	heroin	black
…
100	81	22	0	0	37	17	19	30	3	0	10	0	0	alcohol	other

Testing section

summary(data_1)

x.norm <- rnorm(n=200, m=10, sd=20)
hist(x.norm, main="N(10,20) Histogram")
hist(x.norm, main="N(10,20) Histogram")
mean(data_1$age)
sd(data_1$age)

Simulate new data to match the properties/characteristics of observed data

i2 [0: 184]
age m=34,sd=12
treat {0,1}
homeless {0,1}
pcs 14-75
mcs 7-62
cesd 0–60
indtot 4-45
pss_fr 0-14
drugrisk 0-21
sexrisk
satreat (0=no,1=yes)
female (0=no,1=yes)
racegrp (black, white, other)

# Demographics variables

Sex <- ifelse(runif(NumSubj)<.5,0,1)

Weight <- as.integer(rnorm(NumSubj, 80,10))

Age <- as.integer(rnorm(NumSubj, 62,10))

 

# Diagnosis:

Dx <- c(rep("PD", 100), rep("HC", 100), rep("SWEDD", 82))

 

# Genetics

chr12_rs34637584_GT <- c(ifelse(runif(100)<.3,0,1), ifelse(runif(100)<.6,0,1), ifelse(runif(82)<.4,0,1))                              # NumSubj Bernoulli trials

chr17_rs11868035_GT <- c(ifelse(runif(100)<.7,0,1), ifelse(runif(100)<.4,0,1), ifelse(runif(82)<.5,0,1))                              # NumSubj Bernoulli trials

 

# Clinical          # rpois(NumSubj, 15) + rpois(NumSubj, 6)

UPDRS_part_I <- c( ifelse(runif(100)<.7,0,1)+ifelse(runif(100)<.7,0,1),

ifelse(runif(100)<.6,0,1)+ ifelse(runif(100)<.6,0,1),

ifelse(runif(82)<.4,0,1)+ ifelse(runif(82)<.4,0,1) )

UPDRS_part_II <- c(sample.int(20, 100, replace=T), sample.int(14, 100, replace=T),

sample.int(18, 82, replace=T) )

UPDRS_part_III <- c(sample.int(30, 100, replace=T), sample.int(20, 100, replace=T),

           sample.int(25, 82, replace=T) )
 

# Time: VisitTime – done automatically below in aggregator

# Data (putting all components together)

sim_PD_Data <- cbind(

         rep(Cases, each= NumTime),                                      # Cases

                                         rep(L_caudate_ComputeArea, each= NumTime), # Imaging

                                         rep(Sex, each= NumTime),                                          # Demographics

rep(Weight, each= NumTime),

rep(Age, each= NumTime),

                                         rep(Dx, each= NumTime),                                                           # Dx

                                         rep(chr12_rs34637584_GT, each= NumTime),                      # Genetics

                                         rep(chr17_rs11868035_GT, each= NumTime),
                                               
                                         rep(UPDRS_part_I, each= NumTime),                       # Clinical

rep(UPDRS_part_II, each= NumTime),

rep(UPDRS_part_III, each= NumTime),

 rep(c(0,6,12,18), NumSubj)                                         # Time

)


# Assign the column names

colnames(sim_PD_Data) <- c(
"Cases",
"L_caudate_ComputeArea",
"Sex", "Weight", "Age",
"Dx", "chr12_rs34637584_GT", "chr17_rs11868035_GT",
"UPDRS_part_I", "UPDRS_part_II", "UPDRS_part_III",
"Time"
)

 

# some QC

summary(sim_PD_Data)

dim(sim_PD_Data)

head(sim_PD_Data)

.....

....

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• SOCR Home page: http://www.socr.umich.edu

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