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library(greta.dynamics)Loading required package: greta
Attaching package: 'greta'The following objects are masked from 'package:stats':
binomial, cov2cor, poissonThe following objects are masked from 'package:base':
%*%, apply, backsolve, beta, chol2inv, colMeans, colSums, diag,
eigen, forwardsolve, gamma, identity, rowMeans, rowSums, sweep,
tapplygreta_sitrep()ℹ checking if python available✔ python (version 3.7) availableℹ checking if TensorFlow available✔ TensorFlow (version 1.14.0) availableℹ checking if TensorFlow Probability available✔ TensorFlow Probability (version 0.7.0) availableℹ checking if greta conda environment available✔ greta conda environment availableℹ greta is ready to use!# simulate from a probabilistic 4-stage transition matrix model
k <- 4
# component variables
# survival probability for all stages
survival <- uniform(0, 1, dim = k)
# conditional (on survival) probability of staying in a stage
stasis <- c(uniform(0, 1, dim = k - 1), 1)
# marginal probability of staying/progressing
stay <- survival * stasis
progress <- (survival * (1 - stay))[1:(k - 1)]
# recruitment rate for the largest two stages
recruit <- exponential(c(3, 5))# combine into a matrix:
tmat <- zeros(k, k)
diag(tmat) <- stay
progress_idx <- row(tmat) - col(tmat) == 1
tmat[progress_idx] <- progress
tmat[1, k - (1:0)] <- recruit# analyse this to get the intrinsic growth rate and stable state
iterations <- iterate_matrix(tmat)
iterations$lambdagreta array (operation)
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[4,] ? ? # Can also do this simultaneously for a collection of transition matrices
k <- 2
n <- 10
survival <- uniform(0, 1, dim = c(n, k))
stasis <- cbind(uniform(0, 1, dim = n), rep(1, n))
stay <- survival * stasis
progress <- (survival * (1 - stasis))[, 1]
recruit_rate <- 1 / seq(0.1, 5, length.out = n)
recruit <- exponential(recruit_rate, dim = n)
tmats <- zeros(10, 2, 2)
tmats[, 1, 1] <- stasis[, 1]
tmats[, 2, 2] <- stasis[, 2]
tmats[, 2, 1] <- progress
tmats[, 1, 2] <- recruititerations <- iterate_matrix(tmats)
iterations$lambdagreta array (operation)
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[10,] ? ? These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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