1.10.1 Workspace

  1. It is where your R code and files are located and were all the data objects you create reside.

  2. C:/Users/marss/Documents/R_Workspace

  3. R_Workspace

  4. “knitr”“,”rmarkdown“”, “.GlobalEnv”“,”tools:rstudio“,”package:stats“,”package:graphics“,”package:grDevices“,”package:utils“,”package:datasets“,”package:methods“,”Autoloads“,”package:base"

  5. “C:/Program Files/R/R-3.5.1/library/

  6. Current objects: “Cumulative_risk_IAI”, “Cumulative_risk_IDU,”Cumulative_risk_IOI“,”Cumulative_risk_IPVI“,”Cumulative_risk_PNS“,”Cumulative_risk_RAI“,”Cumulative_risk_ROI“,”Cumulative_risk_RPVI“,”P_IAI“,”P_IDU“,”P_IOI“, P_IPVI”, “P_PNS”, “P_RAI”, “P_ROI”, “P_RPVI”

1.10.2 Math Operations

Modulus: Gives you the remainder of a division problem

10%%3
## [1] 1

Integer Divide: Gives you the quotient of a division problem

10%/%3
## [1] 3

1.10.3 Body Mass Index

Caculated BMI (did not report as requested)

1.10.4 Logarithm

curve(log(x), 0, 6)
abline(v = c(1, exp(1)), h = c(0, 1), lty = 2)

Graph is logistic, meaning as X increases it eventually begins to level out/not climb as steeply.

1.10.5 Risk and Risk Odds

curve(x/(1-x), 0, 1)

curve(log(x/(1-x)), 0, 1)

Odds at is exponential and begins at 0, however when the log of odds is taken now both ends are infinity and -infinity.

1.10.6 HIV Transmission Probabilities

Needle-sharing injection-drug use (IDU):

P_IDU <- 67/10000
P_IDU
## [1] 0.0067
Cumulative_risk_IDU <- 1-(1-P_IDU)^365
Cumulative_risk_IDU
## [1] 0.9140276

Receptive anal intercourse (RAI):

P_RAI <- 50/10000
P_RAI
## [1] 0.005
Cumulative_risk_RAI <- 1-(1-P_RAI)^365
Cumulative_risk_RAI
## [1] 0.8395187

Percutaneous needle stick (PNS):

P_PNS <- 30/10000
P_PNS
## [1] 0.003
Cumulative_risk_PNS <- 1-(1-P_PNS)^365
Cumulative_risk_PNS
## [1] 0.6660105

Receptive penile-vaginal intercourse (RPVI):

P_RPVI <- 10/10000
P_RPVI
## [1] 0.001
Cumulative_risk_RPVI <- 1-(1-P_RPVI)^365
Cumulative_risk_RPVI
## [1] 0.3059301

Insertive anal intercourse (IAI):

P_IAI <- 6.5/10000
P_IAI
## [1] 0.00065
Cumulative_risk_IAI <- 1-(1-P_IAI)^365
Cumulative_risk_IAI
## [1] 0.2112668

Insertive penile-vaginal intercourse (IPVI):

P_IPVI <- 5/10000
P_IPVI
## [1] 5e-04
Cumulative_risk_IPVI <- 1-(1-P_IPVI)^365
Cumulative_risk_IPVI
## [1] 0.1668534

Receptive oral intercourse on penis (ROI):

P_ROI <- 1/10000
P_ROI
## [1] 1e-04
Cumulative_risk_ROI <- 1-(1-P_ROI)^365
Cumulative_risk_ROI
## [1] 0.03584367

Insertive oral intercourse with penis (IOI):

P_IOI <- 0.5/10000
P_IOI
## [1] 5e-05
Cumulative_risk_IOI <- 1-(1-P_IOI)^365
Cumulative_risk_IOI
## [1] 0.01808493

The cumulative risks do make sense because each time you do the same risky action you increase your overall chance of HIV infection.

1.10.7 Sourcing Files

source("C:/Users/marss/Documents/R_Workspace/job01.R")

The code runs/reads in directly into R but no output appears.

source("C:/Users/marss/Documents/R_Workspace/job01.R", echo = TRUE)
## 
## > P_IDU <- 67/10000
## 
## > P_IDU
## [1] 0.0067
## 
## > Cumulative_risk_IDU <- 1 - (1 - P_IDU)^365
## 
## > Cumulative_risk_IDU
## [1] 0.9140276

Adding echo = TRUE made R print the actual code in found in the file.

sink("C:/Users/marss/Documents/R_Workspace/job01.log1a")
source("C:/Users/marss/Documents/R_Workspace/job01.R")
sink()
sink("C:/Users/marss/Documents/R_Workspace/job01.log1b")
source("C:/Users/marss/Documents/R_Workspace/job01.R", echo = TRUE)
## 
## > P_IDU <- 67/10000
## 
## > P_IDU
## [1] 0.0067
## 
## > Cumulative_risk_IDU <- 1 - (1 - P_IDU)^365
## 
## > Cumulative_risk_IDU
## [1] 0.9140276
sink()

Created two new files, one blank (job01.log1a) and the other(job01.log1b) with the code found in the original job01.R file.

source("C:/Users/marss/Documents/R_Workspace/job02.R", echo = TRUE)
## 
## > n <- 365
## 
## > per.act.risk <- c(0.5, 1, 5, 6.5, 10, 30, 50, 67)/10000
## 
## > risks <- 1 - (1 - per.act.risk)^n
## 
## > show(risks)
## [1] 0.01808493 0.03584367 0.16685338 0.21126678 0.30593011 0.66601052
## [7] 0.83951869 0.91402762

The code calculated the cumulative risks that I calculated earlier, except in only a few lines rather than the many I wrote to complete the same task.