Nothing
author: r params$set_author
date: r format(Sys.time(), "%a %b %d %X %Y")
r params$set_file
knitr::opts_chunk$set(echo = FALSE, comment = NA, message = FALSE, warning = FALSE, fig.width = 11, fig.asp = 0.8, error = TRUE, fig.align = 'center') library(knitr) ## library(kableExtra) library(readr) library(dplyr) library(ggplot2) library(tidyr) library(tibble) library(purrr) library(forcats) theme_set(theme_bw(base_size = 14))
res <- result()
This is an autogenerated report from genogeographer
version r packageVersion("genogeographer")
.
The report contains outputs from meta and specific populations. The analysed genotype is in the appendix.
error_bar_plot(res$meta)
res_ <- res$meta if(is.null(input[[paste0("lr_", input$meta)]])) res_ <- res_ %>% mutate(LR_listing = "No") if(!is.null(input[[paste0("lr_", input$meta)]])) res_ <- res_ %>% mutate(LR_listing = ifelse(.[[1]] %in% input[[paste0("lr_",input$meta)]], "Yes", "No")) res_ <- filter(res_, !(is.na(lat) | is.na(lon))) ## Discard pops with no location map_plot(res_)
result_table(res$meta, flat = (params$set_output != "HTML"))
accepted_ <- if(is.null(input$LR_accept)) FALSE else (input$tilt == "allow") LR_list(result = res$meta, lr_pops = input$lr_meta, CI = input$CI/100, accepted = accepted_, flat = (params$set_output != "HTML"))
error_bar_plot(res$pop)
res_ <- res$pop if(is.null(input[[paste0("lr_", input$meta)]])) res_ <- res_ %>% mutate(LR_listing = "No") if(!is.null(input[[paste0("lr_", input$meta)]])) res_ <- res_ %>% mutate(LR_listing = ifelse(.[[1]] %in% input[[paste0("lr_",input$meta)]], "Yes", "No")) res_ <- filter(res_, !(is.na(lat) | is.na(lon))) ## Discard pops with no location map_plot(res_)
result_table(res$pop, flat = (params$set_output != "HTML"))
LR_list(result = res$pop, lr_pops = input$lr_pop, CI = input$CI/100, accepted = accepted_, flat = (params$set_output != "HTML"))
profile <- Profile() %>% mutate(genotype = paste0(A1, A2)) %>% select(locus, genotype) if(params$set_output == "HTML") profile %>% DT::datatable() if(params$set_output != "HTML") profile %>% kable()
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