Last updated: 2021-03-05

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Knit directory: fastTopics-experiments/analysis/

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File Version Author Date Message
Rmd d0db5de Peter Carbonetto 2021-03-05 workflowr::wflow_publish(“smallsim.Rmd”)
Rmd 275fb51 Peter Carbonetto 2021-03-05 Implemented functions simulate_sizes and simulate_factors.

Add text here.

Load the packages used in the analysis below, as well as additional functions that we will use to simulate the data.

library(fastTopics)
library(ggplot2)
library(cowplot)
source("../code/smallsim_functions.R")

Independent topics scenario

Add text here.

n <- 100
m <- 400
k <- 6
S <- matrix(-2,k,k) + 13*diag(k)
F <- simulate_factors(n,k)
s <- simulate_sizes(n)

Correlated topics scenario


sessionInfo()
# R version 3.6.2 (2019-12-12)
# Platform: x86_64-apple-darwin15.6.0 (64-bit)
# Running under: macOS Catalina 10.15.7
# 
# Matrix products: default
# BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
# LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.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] cowplot_1.0.0     ggplot2_3.3.0     fastTopics_0.5-24
# 
# loaded via a namespace (and not attached):
#  [1] ggrepel_0.9.0        Rcpp_1.0.5           invgamma_1.1        
#  [4] lattice_0.20-38      tidyr_1.0.0          prettyunits_1.1.1   
#  [7] assertthat_0.2.1     zeallot_0.1.0        rprojroot_1.3-2     
# [10] digest_0.6.23        truncnorm_1.0-8      R6_2.4.1            
# [13] backports_1.1.5      MatrixModels_0.4-1   evaluate_0.14       
# [16] coda_0.19-3          httr_1.4.2           pillar_1.4.3        
# [19] progress_1.2.2       rlang_0.4.5          lazyeval_0.2.2      
# [22] data.table_1.12.8    irlba_2.3.3          SparseM_1.78        
# [25] whisker_0.4          Matrix_1.2-18        rmarkdown_2.3       
# [28] Rtsne_0.15           stringr_1.4.0        htmlwidgets_1.5.1   
# [31] munsell_0.5.0        mixsqp_0.3-44        compiler_3.6.2      
# [34] httpuv_1.5.2         xfun_0.11            pkgconfig_2.0.3     
# [37] SQUAREM_2017.10-1    mcmc_0.9-6           htmltools_0.4.0     
# [40] tidyselect_0.2.5     tibble_2.1.3         workflowr_1.6.2.9000
# [43] quadprog_1.5-8       viridisLite_0.3.0    withr_2.1.2         
# [46] crayon_1.3.4         dplyr_0.8.3          later_1.0.0         
# [49] MASS_7.3-51.4        grid_3.6.2           jsonlite_1.6        
# [52] gtable_0.3.0         lifecycle_0.1.0      git2r_0.26.1        
# [55] magrittr_1.5         scales_1.1.0         RcppParallel_4.4.2  
# [58] stringi_1.4.3        fs_1.3.1             promises_1.1.0      
# [61] vctrs_0.2.1          tools_3.6.2          glue_1.3.1          
# [64] purrr_0.3.3          hms_0.5.2            yaml_2.2.0          
# [67] colorspace_1.4-1     ashr_2.2-51          plotly_4.9.2        
# [70] knitr_1.26           quantreg_5.54        MCMCpack_1.4-5