nbResults {nbTransmission} | R Documentation |
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)