Simple Tree Simulations
jhmarcus
2019-04-14
Last updated: 2019-04-15
Checks: 5 1
Knit directory: drift-workflow/analysis/
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Introduction
Here I explore FLASH applied to simulations under a simple population tree, as described in Pickrell et al 2012. Specifically I use a multivariate normal approximation to allele frequencies under a fixed tree and generate genotype data given these allele frequencies. Here is a figure from Pickrell and Pritchard 2012 that shows the parameterization of the tree:
Import
Here I import the some required packages:
library(ggplot2)
library(dplyr)
library(tidyr)
library(flashier)Functions
Here are a couple functions to help with the simulations and plotting:
#' @title Simple Graph Simulation
#'
#' @description Simulates genotypes under a simple population
#' tree as described in Pickrell and Pritchard 2012:
#'
#' https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002967
#'
#' @param n_per_pop number of individuals per population
#' @param p number of SNPs
#' @param w admixture weight from population 2 --> 3
#' @param c1 branch length 1
#' @param c2 branch length 2
#' @param c3 branch length 3
#' @param c4 branch length 4
#' @param c5 branch length 5
#' @param c6 branch length 6
#' @param c7 branch length 7
#' @param mu_a mean allele frequency of the ancestral population
#' @sigma_e std. deviation of the allele frequency
#' in the ancestral population
#'
#' @return list of matrix genotypes and allele frequencies
#' allele frequencies in the ancestral population
#'
simple_graph_simulation = function(n_per_pop=10,
p=1000,
w=0.0,
c1=.1,
c2=.1,
c3=.1,
c4=.1,
c5=.05,
c6=.1,
c7=.05,
mu_a=.5,
sigma_e=.05){
# number of populations
n_pops = 4
# simulate ancestral allele freqeuncy
p_a = mu_a + rnorm(p, 0, sigma_e)
# ancestral variance
sigma_a = p_a * (1.0 - p_a)
# covariance matrix specified by the tree
V = matrix(NA, nrow=4, ncol=4)
V[1, 1] = c2 + c6
V[2, 1] = c2
V[2, 2] = c2 + c5 + c7
V[3, 1] = w * c2
V[3, 2] = w * (c2 + c5)
V[3, 3] = (w^2 * (c2 + c5)) + ((1 - w)^2 * (c1 + c3))
V[4, 1] = 0.0
V[4, 2] = 0.0
V[4, 3] = (1.0 - w) * c1
V[4, 4] = c1 + c4
# make symmetric
V[upper.tri(V)] = V[lower.tri(V)]
# simulate allele frequencies
P = matrix(NA, nrow=p, ncol=n_pops)
for(j in 1:p){
# simulate from truncated multivariate normal
P[j, ] = tmvtnorm::rtmvnorm(1, rep(p_a[j], n_pops), sigma_a[j] * V,
lower=rep(1e-4, n_pops),
upper=rep(1.0-1e-4, n_pops)
)
}
# simulate genotypes
Y = matrix(rbinom(n_per_pop * p, 2, P[,1]), nrow=p, ncol=n_per_pop)
for(i in 2:n_pops){
Y_i = matrix(rbinom(n_per_pop * p, 2, P[,i]), nrow=p, ncol=n_per_pop)
Y = cbind(Y, Y_i)
}
return(list(Y=t(Y), P=t(P), p_a=p_a))
}
plot_flash_loadings = function(flash_fit, n_per_pop){
l_df = as.data.frame(flash_fit$loadings$normalized.loadings[[1]])
colnames(l_df) = paste0("K", 1:ncol(l_df))
l_df$iid = 1:nrow(l_df)
l_df$pop = c(rep("Pop1", n_per_pop), rep("Pop2", n_per_pop),
rep("Pop3", n_per_pop), rep("Pop4", n_per_pop))
gath_l_df = l_df %>% gather(K, value, -iid, -pop)
p = ggplot(gath_l_df, aes(x=iid, y=value, color=pop)) +
geom_point() +
facet_wrap(K~., scale="free") +
theme_bw()
return(p)
}Tree Simulation
Here I simulate under a tree model by setting the admixture weight \(w=0.0\). I simulate 10 individuals per population and 10000 SNPs.
set.seed(1990)
# number of individuals per pop
n_per_pop = 20
# set w = 0.0 to just simulate from a tree
sim = simple_graph_simulation(w=0.0, p=10000, n_per_pop=n_per_pop)
# data matrix
Y = sim$Y
# centered data matrix
Y_c = scale(Y, center=TRUE, scale=FALSE)
# centered scaled data matrix
Y_cs = scale(Y, center=TRUE, scale=TRUE)
# number of individuals
n = nrow(Y)
# number of SNPs
p = ncol(Y)
# number of factors
K = 20PCA
Here I apply PCA to the centered and scaled genotype matrix:
svd_fit = lfa:::trunc.svd(Y_cs, K)
lamb = svd_fit$d^2
p = qplot(1:K, lamb / sum(lamb)) +
xlab("PC") +
ylab("PVE") +
theme_bw()
p
From the PVE plot we can see there is a large drop off after the first 3 PCs so lets just visualize them:
l_df = data.frame(svd_fit$u[,1:3])
colnames(l_df) = paste0("PC", 1:3)
l_df$iid = 1:n
l_df$pop = c(rep("Pop1", n_per_pop), rep("Pop2", n_per_pop),
rep("Pop3", n_per_pop), rep("Pop4", n_per_pop))
gath_l_df = l_df %>% gather(PC, value, -iid, -pop)
p = ggplot(gath_l_df, aes(x=iid, y=value, color=pop)) +
geom_point() +
facet_wrap(PC~., scale="free") +
theme_bw()
p
It looks like PC1 represents the first split on the tree. PC2 and PC3 represent the subsequent splits.
FLASH (Drift)
Here I apply Empirical Bayes matrix factorization with non-negative loadings and unconstrained factors:
Fix Loadings Greedy
Here I fix the first loadings vector to the 1 vector and only run the greedy algorithm:
flash_fit = flashier::flashier(Y,
greedy.Kmax=K,
prior.type=c("nonnegative", "normal.mixture"),
var.type=0,
fix.dim=list(1),
fix.idx=list(1:n),
fix.vals=list(rep(1, n)))Initializing flash object...
Adding factor 1 to flash object...
Adding factor 2 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Adding factor 3 to flash object...
Adding factor 4 to flash object...
Adding factor 5 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Adding factor 6 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Adding factor 7 to flash object...
Adding factor 8 to flash object...
Adding factor 9 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Factor doesn't increase objective and won't be added.
Nullchecking 7 factors...
Factor 6 removed, increasing objective by 3.860e+02.
Adding factor 9 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Factor doesn't increase objective and won't be added.
Nullchecking 7 factors...
Wrapping up...
Done.plot_flash_loadings(flash_fit, n_per_pop)
Very cool … K2,K3 represent the internal nodes of the tree and K4,K5,K6,K7 represent the leaves i.e. population specific factors.
Fix Loadings Final Backfit
Here I fix the first loadings vector to the 1 vector, run the greedy algorithm to pick out \(K\) from the data and then run a final backfit to clean up the greedy solution:
flash_fit = flashier::flashier(Y,
greedy.Kmax=K,
prior.type=c("nonnegative", "normal.mixture"),
var.type=0,
fix.dim=list(1),
fix.idx=list(1:n),
fix.vals=list(rep(1, n)),
backfit = "final",
backfit.order = "dropout",
backfit.reltol = 10)Initializing flash object...
Adding factor 1 to flash object...
Adding factor 2 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Adding factor 3 to flash object...
Adding factor 4 to flash object...
Adding factor 5 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Adding factor 6 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Adding factor 7 to flash object...
Adding factor 8 to flash object...
Adding factor 9 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Factor doesn't increase objective and won't be added.
Backfitting 8 factors...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
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Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
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Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
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Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
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Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Nullchecking 7 factors...
Factor 2 removed, increasing objective by 3.208e-04.
Factor 3 removed, increasing objective by 2.884e-04.
Adding factor 9 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Factor doesn't increase objective and won't be added.
Backfitting 8 factors...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Nullchecking 7 factors...
Factor 6 removed, increasing objective by 4.651e-03.
Adding factor 9 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Factor doesn't increase objective and won't be added.
Backfitting 8 factors...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Nullchecking 7 factors...
Wrapping up...
Done.plot_flash_loadings(flash_fit, n_per_pop)
Hmm it seems like the final backfit removes the nice signal we had in the greedy run and it zeros out some of the factors.
Fix Loadings Alternating Backfit
Here I fix the first loadings vector to the 1 vector and run a scheme where backfitting is performed after greedily adding each factor:
flash_fit = flashier::flashier(Y,
greedy.Kmax=K,
prior.type=c("nonnegative", "normal.mixture"),
var.type=0,
fix.dim=list(1),
fix.idx=list(1:n),
fix.vals=list(rep(1, n)),
backfit = "alternating",
backfit.order = "dropout",
backfit.reltol = 10)Initializing flash object...
Adding factor 1 to flash object...
Adding factor 2 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Backfitting 2 factors...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Adding factor 3 to flash object...
Backfitting 3 factors...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Adding factor 4 to flash object...
Backfitting 4 factors...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Adding factor 5 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Factor doesn't increase objective and won't be added.
Nullchecking 3 factors...
Wrapping up...
Done.plot_flash_loadings(flash_fit, n_per_pop)
Again this leads to an odd solution with only two population specific factors and its not obvious what K2 represents.
Mean Center Greedy
Here I don’t fix the first loadings vector and just mean center the data matrix before running greedy FLASH (Drift):
flash_fit = flashier::flashier(Y_c,
greedy.Kmax=K,
prior.type=c("nonnegative", "normal.mixture"),
var.type=0)Initializing flash object...
Adding factor 1 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Adding factor 2 to flash object...
Adding factor 3 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Adding factor 4 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Adding factor 5 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Adding factor 6 to flash object...
Adding factor 7 to flash object...
Adding factor 8 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Factor doesn't increase objective and won't be added.
Nullchecking 7 factors...
Factor 3 removed, increasing objective by 4.883e+02.
Adding factor 8 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Factor doesn't increase objective and won't be added.
Nullchecking 7 factors...
Wrapping up...
Done.plot_flash_loadings(flash_fit, n_per_pop)
Mean centering gives a similar solution to fixing the factors.
Mean Center Final Backfit
Here I don’t fix the first loadings vector and just mean center the data matrix before running greedy FLASH (Drift) with a final backfit:
flash_fit = flashier::flashier(Y_c,
greedy.Kmax=K,
prior.type=c("nonnegative", "normal.mixture"),
var.type=0,
backfit = "final",
backfit.order = "dropout",
backfit.reltol = 10)Initializing flash object...
Adding factor 1 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Adding factor 2 to flash object...
Adding factor 3 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Adding factor 4 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Adding factor 5 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Adding factor 6 to flash object...
Adding factor 7 to flash object...
Adding factor 8 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Factor doesn't increase objective and won't be added.
Backfitting 7 factors...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Nullchecking 7 factors...
Factor 2 removed, increasing objective by 1.556e-04.
Factor 3 removed, increasing objective by 2.671e-03.
Factor 7 removed, increasing objective by 7.662e-04.
Adding factor 8 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Factor doesn't increase objective and won't be added.
Backfitting 7 factors...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Nullchecking 7 factors...
Wrapping up...
Done.plot_flash_loadings(flash_fit, n_per_pop)
Now we only see the population specific factors.
Mean Center Alternating Backfit
Here I don’t fix the first loadings vector and just mean center the data matrix before running greedy FLASH (Drift) with alternating backfits:
flash_fit = flashier::flashier(Y_c,
greedy.Kmax=K,
prior.type=c("nonnegative", "normal.mixture"),
var.type=0,
backfit = "alternating",
backfit.order = "dropout",
backfit.reltol = 10)Initializing flash object...
Adding factor 1 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Adding factor 2 to flash object...
Backfitting 2 factors...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Adding factor 3 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Backfitting 3 factors...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Adding factor 4 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Backfitting 4 factors...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Adding factor 5 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Factor doesn't increase objective and won't be added.
Nullchecking 4 factors...
Wrapping up...
Done.plot_flash_loadings(flash_fit, n_per_pop)
Again we see only population specific factors but not shared factors.
FLASH
Here I run FLASH with no sign constraints on the loadings or factors:
Mean Center Greedy
Here I mean center the data matrix before running greedy FLASH:
flash_fit = flashier::flashier(Y_c,
greedy.Kmax=K,
prior.type=c("normal.mixture", "normal.mixture"),
var.type=0)Initializing flash object...
Adding factor 1 to flash object...
Adding factor 2 to flash object...
Adding factor 3 to flash object...
Adding factor 4 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Factor doesn't increase objective and won't be added.
Nullchecking 3 factors...
Wrapping up...
Done.plot_flash_loadings(flash_fit, n_per_pop)
Here we get a pretty nice solution similar to PCA but with a more interpretable sparsity pattern. K1 cleanly represents the first split in the tree and K2 and K3 cleanly represent the subsequent splits.
Mean Center Final Backfit
Here I mean center the data matrix before running greedy FLASH with a final backfit:
flash_fit = flashier::flashier(Y_c,
greedy.Kmax=K,
prior.type=c("normal.mixture", "normal.mixture"),
var.type=0,
backfit = "final",
backfit.order = "dropout",
backfit.reltol = 10)Initializing flash object...
Adding factor 1 to flash object...
Adding factor 2 to flash object...
Adding factor 3 to flash object...
Adding factor 4 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Factor doesn't increase objective and won't be added.
Backfitting 3 factors...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Nullchecking 3 factors...
Wrapping up...
Done.plot_flash_loadings(flash_fit, n_per_pop)
This solution looks very similar to the greedy solution.
Mean Center Alternating Backfit
Here I mean center the data matrix before running greedy FLASH with alternating backfits:
flash_fit = flashier::flashier(Y_c,
greedy.Kmax=K,
prior.type=c("normal.mixture", "normal.mixture"),
var.type=0,
backfit = "alternating",
backfit.order = "dropout",
backfit.reltol = 10)Initializing flash object...
Adding factor 1 to flash object...
Adding factor 2 to flash object...
Backfitting 2 factors...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Adding factor 3 to flash object...
Backfitting 3 factors...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Adding factor 4 to flash object...Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.
Warning in estimate_mixprop(data, g, prior, optmethod = optmethod, control
= control, : Optimization failed to converge. Results may be unreliable.
Try increasing maxiter and rerunning.Factor doesn't increase objective and won't be added.
Nullchecking 3 factors...
Wrapping up...
Done.plot_flash_loadings(flash_fit, n_per_pop)
sessionInfo()R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS 10.14.2
Matrix products: default
BLAS/LAPACK: /Users/jhmarcus/miniconda3/lib/R/lib/libRblas.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] flashier_0.1.1 tidyr_0.8.2 dplyr_0.8.0.1 ggplot2_3.1.0
loaded via a namespace (and not attached):
[1] zoo_1.8-4 tidyselect_0.2.5 xfun_0.4
[4] purrr_0.3.0 ashr_2.2-32 lattice_0.20-38
[7] gmm_1.6-2 colorspace_1.4-0 htmltools_0.3.6
[10] stats4_3.5.1 yaml_2.2.0 rlang_0.3.1
[13] mixsqp_0.1-109 pillar_1.3.1 glue_1.3.0
[16] withr_2.1.2 foreach_1.4.4 plyr_1.8.4
[19] stringr_1.4.0 munsell_0.5.0 gtable_0.2.0
[22] workflowr_1.2.0 mvtnorm_1.0-10 lfa_1.12.0
[25] codetools_0.2-16 evaluate_0.12 labeling_0.3
[28] knitr_1.21 doParallel_1.0.14 pscl_1.5.2
[31] parallel_3.5.1 Rcpp_1.0.0 corpcor_1.6.9
[34] scales_1.0.0 backports_1.1.3 tmvtnorm_1.4-10
[37] truncnorm_1.0-8 fs_1.2.6 digest_0.6.18
[40] stringi_1.2.4 grid_3.5.1 rprojroot_1.3-2
[43] tools_3.5.1 sandwich_2.5-1 magrittr_1.5
[46] lazyeval_0.2.1 tibble_2.0.1 crayon_1.3.4
[49] pkgconfig_2.0.2 MASS_7.3-51.1 Matrix_1.2-15
[52] SQUAREM_2017.10-1 assertthat_0.2.0 rmarkdown_1.11
[55] iterators_1.0.10 R6_2.4.0 git2r_0.23.0
[58] compiler_3.5.1