phyrmeta
: Client to Handle Phylometa Output
remotes::install_github("sckott/phyrmeta")
library('phyrmeta')
Get an example file
file <- system.file("examples/example_one_group.txt", package = "phyrmeta")
cat(readLines(file)[1:10], sep = "\n")
#> metaPhylo ANALYSIS FROM: 640_tree.txt and 640_data.txt
#>
#> RESULTS SECTION A. Traditional meta-analysis.
#> --------------------------------------------------------------------------------
#>
#> TABLE 1. Summary of fit statistics.
#> ------------------------------------------
#> Source Q df p
#> ------------------------------------------
#> Between groups 0.00 1 1.0000
Parse the file
phylometa_process(file, groups = 1)
#> $traditional_summary_fit
#> Source Q df P
#> 1 Between groups 0 1 1
#> 2 Within groups 0 19 1
#> 3 Within group 0 0 19 1
#> 4 Total 0 -9999 -9999
#> 5 random-effects 0 1 1
#>
#> $traditional_summary_pooled_effects
#> Group k effsize var CI_low CI_high Z df P
#> 1 All studies 20 0.041 0.05 -0.397 0.479 0.03 1 0.8548
#> 2 Group 0 20 0.041 0.05 -0.397 0.479 0.03 1 0.8548
#> 3 All studies 20 0.041 0.05 -0.397 0.479 0.03 1 0.8548
#> 4 Group 0 20 0.041 0.05 -0.397 0.479 0.03 1 0.8548
#>
#> $phylogenetic_summary_fit
#> Source Q df P df_polytadj P_polytadj
#> 1 Between groups 0.00 1 1 -9999 -9999
#> 2 Within groups 0.01 19 1 19 1
#> 3 Within group 0 0.01 19 1 19 1
#> 4 Total 0.01 -9999 -9999 -9999 -9999
#> 5 random-effects 0.00 1 1 -9999 -9999
#>
#> $phylogenetic_summary_pooled_effects
#> Group k effsize var CI_low CI_high Z df P
#> 1 All studies 20 0.041 0.4478 -1.271 1.352 0 1 0.9514
#> 2 Group 0 20 0.041 0.4478 -1.271 1.352 0 1 0.9514
#> 3 All studies 20 0.041 0.4478 -1.271 1.352 0 1 0.9514
#> 4 Group 0 20 0.041 0.4478 -1.271 1.352 0 1 0.9514
#>
#> $traditional_vs_phylogenetic
#> Analysis AIC_fixed AIC_random
#> 1 Traditional -114.45 -114.45
#> 2 Phylogenetically-independent -102.83 -102.83
And so on for N groups. Change the groups
parameter to the number of groups
in your output file.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.