| Name this damn pattern. | |
| \binom{N}{0}, \binom{N}{1}, \binom{N}{2}, ..., \binom{N}{floor(N/2)}, ... N! |
| # Replacing multilocus lineages with one representative sample | |
| library(poppr) | |
| data(monpop) | |
| mlg.filter(monpop) <- 0 + .Machine$double.eps | |
| mondf <- genind2df(monpop, usepop = FALSE) | |
| mid <- mlg.id(monpop) | |
| orders <- unlist(mid, use.names = FALSE) | |
| monpop <- monpop[orders, ] | |
| mondif <- mondf[orders, ] | |
| n <- vapply(mid, length, integer(1)) |
| # poppr.plot.phylo definition: | |
| # https://github.com/grunwaldlab/poppr/blob/9170398f6552f27ab69b294172c97c8ee7a97ce0/R/internal.r#L1529-L1545 | |
| # You can also get it by simply typing poppr:::poppr.plot.phylo in your R console | |
| library("ape") | |
| library("phangorn") | |
| poppr.plot.phylo <- function(tree, type = "nj", root = FALSE){ | |
| barlen <- min(median(tree$edge.length), 0.1) | |
| if (barlen < 0.1) barlen <- 0.01 | |
| if (!root && type != "upgma"){ | |
| tree <- ladderize(tree) |
| library('rjson') | |
| library('wordcloud') | |
| library('viridis') | |
| library('magrittr') | |
| library('purrr') | |
| library('svglite') | |
| # Download JSON data ------------------------------------------------------ |
| library('cranlogs') | |
| library('ggplot2') | |
| library('ggthemes') | |
| library('lubridate') | |
| library('dplyr') | |
| releases <- tibble::tribble( | |
| ~version, ~date, ~size, | |
| "1.0.0", lubridate::ymd("2013-04-26"), "2.5M", | |
| "1.0.1", lubridate::ymd("2013-07-03"), "2.5M", |
| library("poppr") | |
| library("dplyr") | |
| library("tidyr") | |
| library("ggplot2") | |
| library("reshape2") | |
| data(Pinf) | |
| x <- diversity_ci(Pinf, n = 100L) | |
| CI <- melt(x[[3]]) %>% spread(CI, value) %>% rename(lb = `2.5 %`, ub = `97.5 %`) | |
| obs <- melt(x[[1]]) %>% rename(observed = value) |
This is an example of how to use google sheets and infuser to create dossiers from the output of googlesheets surveys. This method is used in https://github.com/zkamvar/InspirationDisseminationSchedule.
Notes:
lookup = TRUE to authenticate yourselfcat()
| @misc{ref1, | |
| author = {AuthorA}, | |
| title = {Title of a web resource}, | |
| howpublished = {\url{http://url/of/resource/}}, | |
| year = {2007} | |
| } | |
| @article{ref2, | |
| author = {AuthorC}, | |
| journal = {Journal name}, |
| "INRA63.167","INRA63.171","INRA63.173","INRA63.175","INRA63.177","INRA63.179","INRA63.181","INRA63.183","INRA63.185","INRA5.137","INRA5.139","INRA5.141","INRA5.143","INRA5.145","INRA5.147","INRA5.149","ETH225.137","ETH225.139","ETH225.141","ETH225.143","ETH225.145","ETH225.147","ETH225.149","ETH225.151","ETH225.153","ETH225.155","ETH225.157","ETH225.159","ILSTS5.182","ILSTS5.184","ILSTS5.186","ILSTS5.190","ILSTS5.194","HEL5.149","HEL5.151","HEL5.153","HEL5.155","HEL5.157","HEL5.159","HEL5.161","HEL5.163","HEL5.165","HEL5.167","HEL5.169","HEL1.101","HEL1.103","HEL1.105","HEL1.107","HEL1.109","HEL1.111","HEL1.113","HEL1.115","HEL1.117","INRA35.102","INRA35.104","INRA35.106","INRA35.108","INRA35.110","INRA35.114","INRA35.120","ETH152.181","ETH152.187","ETH152.191","ETH152.193","ETH152.195","ETH152.197","ETH152.199","ETH152.201","ETH152.203","ETH152.205","ETH152.207","ETH152.209","INRA23.193","INRA23.197","INRA23.199","INRA23.201","INRA23.203","INRA23.205","INRA23.207","INRA23.209","INRA23.211","INRA23.213","INRA |
| # 2015-12-06 10:55:45 PST ---------------------------------- | |
| # This script will allow you to update your fork of the | |
| # NESCent popgenInfo page without having to interact with | |
| # the command line. Note: you do not need to install git | |
| # for this particular script to work, but it is necessary | |
| # to use pull/commit/push through Rstudio. | |
| library("git2r") | |
| # Do this once and then open the Rproject file ------------ | |
| # clone(url = "", |