prediction_score {aphylo} | R Documentation |
Calculate prediction score (quality of prediction)
Description
Calculate prediction score (quality of prediction)
Usage
prediction_score(x, expected, alpha0 = NULL, alpha1 = NULL, W = NULL, ...)
## Default S3 method:
prediction_score(x, expected, alpha0 = NULL, alpha1 = NULL, W = NULL, ...)
## S3 method for class 'aphylo_estimates'
prediction_score(
x,
expected = NULL,
alpha0 = NULL,
alpha1 = NULL,
W = NULL,
loo = TRUE,
...
)
## S3 method for class 'aphylo_prediction_score'
print(x, ...)
Arguments
x |
An object of class aphylo_estimates or a numeric matrix. |
expected |
Integer vector of length |
alpha0 , alpha1 |
Probability of observing a zero an a one, respectively. |
W |
A square matrix. Must have as many rows as genes in |
... |
Further arguments passed to predict.aphylo_estimates |
loo |
Logical scalar. When |
Details
In the case of prediction_score
, ...
are passed to
predict.aphylo_estimates
.
In the case of the method for aphylo estimates, the function takes as a reference using alpha equal to the proportion of observed tip annotations that are equal to 1, this is:
mean(x$dat$tip.annotation[x$dat$tip.annotation != 9L], na.rm = TRUE)
Value
A list of class aphylo_prediction_score
:
obs : Observed 1 - MAE.
obs_raw : Unnormalized (raw) scores.
random_raw: Unnormalized (raw) scores.
worse_raw : Unnormalized (raw) scores.
pval : Computed p-value.
worse : Reference of worse case.
predicted : Numeric matrix with observed predictions.
expected : Integer matrix with expected annotations.
random : Random score (null).
alpha0 : The passed alpha parameters.
alpha1 : The passed alpha parameters.
auc : An object of class
aphylo_auc
.obs.ids : Indices of the ids.
leaf.ids : IDs of the leafs (if present).
tree : Of class
phylo
.
Examples
# Example with prediction_score ---------------------------------------------
set.seed(11552)
ap <- raphylo(
50, P = 1,
Pi = 0,
mu_d = c(.8,.2),
mu_s = c(0.1,0.1),
psi = c(0,0)
)
ans <- aphylo_mcmc(
ap ~ mu_d + mu_s + Pi,
control = list(nsteps=2e3, thin=20, burnin = 500),
priors = bprior(c(9, 1, 1, 1, 5), c(1, 9, 9, 9, 5))
)
(pr <- prediction_score(ans, loo = TRUE))
plot(pr)