nbTransmission (version 1.1.2)

nbResults: Dataset with results of nbProbabilities

Description

A ordered dataset created from pairData of the outbreak of 100 individuals including the relative transmission probabilities for each pair estimated using the function nbProbabilities. The code to recreate this dataset from pairData is shown below.

Usage

nbResults

Format

A data frame with 9900 rows and 24 variables:

pairID

A pair-level ID variable (the individual IDs separated by an '_').

label

The label for the run, here "SNPs".

pAvg

The mean transmission probability for the pair over all runs.

pSD

The standard deviation of the transmission probability for the pair over all runs.

pScaled

The mean relative transmission probability for the pair over all runs: pAvg scaled so that the probabilities for all infectors per infectee add to 1.

pRank

The rank of the probability of the the pair out of all pairs for that infectee (in case of ties all values have the minimum rank of the group).

nSamples

The number of probability estimates that contributed to pAvg. This represents the number of prediction datasets this pair was included in over the 10x1 cross prediction repeated 50 times.

individualID.1

The ID of the potential "infector".

individualID.2

The ID of the potential "infectee".

transmission

Did individual.1 truly infect individual.2?

snpDist

The number of SNPs between the individuals.

infectionDate.1

The date and time of infection of individualID.1.

infectionDate.2

The date and time of infection of individualID.2.

sampleDate.1

The date and time of sampling of individualID.1.

sampleDate.2

The date and time of sampling of individualID.2.

sampleDiff

The number of days between sampleDate.1 and sampleDate.2.

infectionDiff

The number of days between infectionDate.1 and infectionDate.2.

infectionDiffY

The number of years between infectionDate.1 and infectionDate.2.

timeCat

A categorical representation of infectionDiff: <1y, 1-2y, 2-3y, 3-4y, 4-5y, >5y.

Z1

Pair-level covariate derived from X1: 1 if match, 0 if not match.

Z2

Pair-level covariate derived from X2: 1 if match, 0 if not match.

Z3

Pair-level covariate derived from X3: 1 if a-a, 2 if b-b, 3 if a-b, 4 if b-a.

Z4

Pair-level covariate derived from X4: 1 if match, 2 if adjacent, 2 otherwise.

snpClose

Logical value indicating if a pair is a probable link. TRUE if the pair has fewer than 3 SNPs, FALSE if the pair has more than 12 SNPs, NA otherwise

Examples

# ## NOT RUN ##
# ## This is the code used to create this dataset ##
# orderedPair <- pairData[pairData$infectionDiff > 0, ]
# orderedPair$snpClose <- ifelse(orderedPair$snpDist < 3, TRUE,
#                         ifelse(orderedPair$snpDist > 12, FALSE, NA))
# set.seed(0)
# covariates = c("Z1", "Z2", "Z3", "Z4", "timeCat")
# resGen <- nbProbabilities(orderedPair = orderedPair,
#                             indIDVar = "individualID",
#                             pairIDVar = "pairID",
#                             goldStdVar = "snpClose",
#                             covariates = covariates,
#                             label = "SNPs", l = 1,
#                             n = 10, m = 1, nReps = 50)
# nbResults <- merge(resGen[[1]], orderedPair, by = "pairID", all = TRUE)