From 9566d9d8761e86d0828cef189387f900a08f528d Mon Sep 17 00:00:00 2001 From: Dhihram <105160118+Dhihram@users.noreply.github.com> Date: Wed, 27 Nov 2024 14:59:02 +0700 Subject: [PATCH] add beast function tree and data --- DESCRIPTION | 11 ++- NAMESPACE | 7 ++ R/beastclus.R | 142 ++++++++++++++++++++++++++++++ inst/extdata/metadata_samp.csv | 61 +++++++++++++ inst/extdata/pox_strict_comb.tree | 121 +++++++++++++++++++++++++ inst/extdata/random_tree.nwk | 1 + man/beastclus.Rd | 41 +++++++++ tests/testthat.R | 12 +++ tests/testthat/test-beastclus.R | 16 ++++ 9 files changed, 408 insertions(+), 4 deletions(-) create mode 100644 R/beastclus.R create mode 100644 inst/extdata/metadata_samp.csv create mode 100644 inst/extdata/pox_strict_comb.tree create mode 100644 inst/extdata/random_tree.nwk create mode 100644 man/beastclus.Rd create mode 100644 tests/testthat.R create mode 100644 tests/testthat/test-beastclus.R diff --git a/DESCRIPTION b/DESCRIPTION index c1dab23..e3bd252 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -5,7 +5,7 @@ Version: 0.1.3 Author: Dhihram Tenrisau, Stéphane Hué Maintainer: Dhihram Tenrisau Description: This package is used to find the cluster-based tree and metadata. The cluster-based tree is built based on the clusters in the data. The metadata contains information about the data used to build the tree. -License: file LICENSE +License: MIT + file LICENSE Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) @@ -14,12 +14,15 @@ Imports: ape, dplyr, stringr, - progress + progress, + ggtree, + treeio, + tidyr Suggests: knitr, rmarkdown, - ggtree, tidyverse, - treeio + testthat (>= 3.0.0) VignetteBuilder: knitr Year: 2024 +Config/testthat/edition: 3 diff --git a/NAMESPACE b/NAMESPACE index c2ef08f..f463832 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,5 +1,6 @@ # Generated by roxygen2: do not edit by hand +export(beastclus) export(genclus) importFrom(ape,extract.clade) importFrom(ape,getMRCA) @@ -11,9 +12,15 @@ importFrom(dplyr,filter) importFrom(dplyr,group_by) importFrom(dplyr,inner_join) importFrom(dplyr,mutate) +importFrom(dplyr,rename) importFrom(dplyr,rowwise) importFrom(dplyr,select) importFrom(dplyr,slice) +importFrom(dplyr,summarize) importFrom(dplyr,ungroup) +importFrom(ggtree,geom_range) +importFrom(ggtree,ggtree) +importFrom(ggtree,theme_tree2) importFrom(progress,progress_bar) importFrom(stringr,str_split) +importFrom(tidyr,separate_rows) diff --git a/R/beastclus.R b/R/beastclus.R new file mode 100644 index 0000000..278b0a1 --- /dev/null +++ b/R/beastclus.R @@ -0,0 +1,142 @@ +#' Extract Clusters from a BEAST Phylogenetic Tree +#' +#' @param beast_tree A BEAST tree object of class `phylo4d` or similar. +#' @param metadata A metadata dataframe containing columns `label`, `location`, and `date`. +#' @param post_threshold Numeric value specifying the posterior probability threshold for including a cluster (default = 0.70). +#' @param date_range Numeric value specifying the maximum allowable date range (in days) within clusters (default = 90). +#' @param samearea Logical value indicating whether clusters must originate from the same geographic area (default = FALSE). +#' +#' @return A dataframe summarizing the clusters, including labels, posterior probabilities, areas, date ranges, and the number of tips. +#' @importFrom dplyr group_by summarize ungroup filter select arrange rename mutate inner_join +#' @importFrom tidyr separate_rows +#' @importFrom ggtree ggtree theme_tree2 geom_range +#' @importFrom progress progress_bar +#' @export +#' @examples +#' # Example usage: +#' # Assuming `beast_tree` is a BEAST tree object and `metadata` is a dataframe +#' data_csv <- system.file("extdata", "metadata_samp.csv", package = "caIRA") +#' metadata<-read.csv(data_csv) +#' data_beast <- system.file("extdata", "pox_strict_comb.tree", package = "caIRA") +#' beast_tree <- treeio::read.beast(data_beast) +#' # with the required columns: +#' beastclus(beast_tree, metadata, post_threshold = 0.50, date_range = 90, samearea = TRUE) +beastclus <- function(beast_tree, metadata, post_threshold = 0.70, date_range = 90, samearea = FALSE) { + library(treeio) + library(ape) + library(ggtree) + library(dplyr) + library(tidyr) + + # Calculate the total number of iterations for progress tracking + tip_count <- length(beast_tree@phylo$tip.label) + total_iterations <- (tip_count * (tip_count - 1)) / 2 + + # Set up the progress bar + pb <- progress_bar$new( + format = "(:spin) [:bar] :percent [Elapsed time: :elapsedfull || Estimated time remaining: :eta]", + total = total_iterations, + complete = "=", # Completion bar character + incomplete = "-", # Incomplete bar character + current = ">", # Current bar character + clear = FALSE, # If TRUE, clears the bar when finish + width = 100 # Width of the progress bar + ) + # Number of tips in the tree (leaf nodes) + tree <- beast_tree@phylo + num_tips <- length(tree$tip.label) + + # Extract internal node numbers using the edge matrix (parent-child relationships) + internal_nodes <- unique(tree$edge[, 1][tree$edge[, 1] > num_tips]) + + # Create an empty list to store clades and their leaf nodes + clade_leaf_nodes <- list() + + # Loop through each internal node and extract the clade + for (i in internal_nodes) { + # Extract the clade rooted at the current internal node + clade <- extract.clade(tree, node = i) + + # Get the leaf (tip) names for the clade + leaf_nodes <- clade$tip.label + + # Store the clade and its leaf nodes in the list + clade_leaf_nodes[[as.character(i)]] <- leaf_nodes # Assign node number as the name + } + + # Convert the list to a data frame for easier visualization + clade_df <- data.frame( + nodes = rep(names(clade_leaf_nodes), sapply(clade_leaf_nodes, length)), + label = unlist(clade_leaf_nodes) + ) + + # Merging posterior probability from tree data + tre <- ggtree(beast_tree, mrsd = min(metadata$date)) + + theme_tree2() + geom_range(range = 'length_0.95_HPD', color = 'red', alpha = .6, size = 2) + post_dat <- tre$data + post_dat <- select(post_dat, node, posterior, x) + + clade_df <- merge(clade_df, post_dat, by.x = "nodes", by.y = "node", all.x = TRUE) + + # Merging metadata + metadata_2 <- select(metadata, label, location, date) + clade_df <- merge(clade_df, metadata_2, by.x = "label", by.y = "label", all.x = TRUE) + + # Summarize data + summary_df <- clade_df %>% + group_by(nodes) %>% + summarize( + label = paste(label, collapse = ", "), # Merge all labels for the group + Posterior = round(mean(posterior, na.rm = TRUE), 2), # Use mean posterior (or adjust as needed) + AreaName = ifelse(length(unique(location)) > 1, # Check the number of unique locations + paste(unique(location), collapse = ", "), + unique(location)), # Use single location if only one + min_date = min(as.Date(date)), # Minimum date in the group + max_date = max(as.Date(date)), # Maximum date in the group + NumTips = n(), # Count of label entries + .groups = "drop" # Avoid grouping in the output + ) + + summary_df$dif <- as.numeric(summary_df$max_date - summary_df$min_date) + summary_df = rename(summary_df, c('ParentNode' = 'nodes')) + + # Filtering the data based on the posterior and date range criteria + filtered_df <- summary_df %>% + filter(Posterior > post_threshold, + dif <= date_range, + (samearea == TRUE & !grepl(",", AreaName)) | samearea == FALSE) + + # Separate the label into different rows based on ',' separator + filtered_df <- filtered_df %>% + separate_rows(label, sep = ", ") # Use ", " as separator to split the label + + # Remove duplicate labels, keeping the one with the maximum NumTips + filtered_df <- filtered_df %>% + group_by(label) %>% + filter(NumTips == max(NumTips)) %>% + ungroup() + + # Merge the `label` values with a comma separator + final_df <- filtered_df %>% + group_by(ParentNode) %>% + summarize( + label = paste(label, collapse = ", "), # Merge labels with a comma separator + Posterior = first(Posterior), # Keep the first value of `Posterior` + AreaName = first(AreaName), # Keep the first value of `AreaName` + min_date = min(min_date), # Get the minimum date + max_date = max(max_date), # Get the maximum date + NumTips = first(NumTips), # Sum NumTips (if needed) + dif = max(dif), # Get the maximum difference + .groups = "drop" # Remove the grouping after summarizing + ) + + # Convert ParentNode to numeric + final_df$ParentNode <- as.numeric(final_df$ParentNode) + + #order date + final_df <- final_df[order(final_df$min_date),] + + return(final_df) +} + +utils::globalVariables(c("node", "posterior", "label", "location", "n")) diff --git a/inst/extdata/metadata_samp.csv b/inst/extdata/metadata_samp.csv new file mode 100644 index 0000000..83053d4 --- /dev/null +++ b/inst/extdata/metadata_samp.csv @@ -0,0 +1,61 @@ +"","label","Sex","Age","Passage.details.history","Accession.ID","date","Submission.Date","Length","Location","location","Submitting.lab","id" +"1","hMpxV/Indonesia/JK-NIHRD-MP0024/2022","M",27,"Original","EPI_ISL_14615579",2022-08-18,"2022-08-25","197,204","Asia / Indonesia / Jakarta","Jabodetabek","National Institute of Health Research and Development","C1" +"2","hMpxV/Indonesia/JK-NIHRD-MP005/2023","M",26,"Original","EPI_ISL_18436040",2023-10-12,"2023-10-26","197,199","Asia / Indonesia / DKI Jakarta / Jakarta Selatan","Jabodetabek","National Institute of Health Research and Development","C2" +"3","hMpxV/Indonesia/JK-NIHRD-MP010/2023","M",30,"Original","EPI_ISL_18436041",2023-10-20,"2023-10-26","197,196","Asia / Indonesia / DKI Jakarta / Jakarta Timur","Jabodetabek","National Institute of Health Research and Development","C3" +"4","hMpxV/Indonesia/JK-NIHRD-MP008/2023","M",28,"Original","EPI_ISL_18463158",2023-10-18,"2023-11-03","197,199","Asia / Indonesia / DKI Jakarta / Jakarta Barat","Jabodetabek","National Institute of Health Research and Development","C4" +"5","hMpxV/Indonesia/JK-NIHRD-MP017/2023","M",30,"Original","EPI_ISL_18463161",2023-10-21,"2023-11-03","197,199","Asia / Indonesia / DKI Jakarta / Jakarta Barat","Jabodetabek","National Institute of Health Research and Development","C5" +"6","hMpxV/Indonesia/JK-NIHRD-MP015/2023","M",31,"Original","EPI_ISL_18463160",2023-10-20,"2023-11-03","197,199","Asia / Indonesia / DKI Jakarta / Jakarta Pusat","Jabodetabek","National Institute of Health Research and Development","C6" +"7","hMpxV/Indonesia/JK-NIHRD-MP012/2023","M",31,"Original","EPI_ISL_18463159",2023-10-20,"2023-11-03","197,192","Asia / Indonesia / DKI Jakarta / Jakarta Selatan","Jabodetabek","National Institute of Health Research and Development","C7" +"8","hMpxV/Indonesia/BT-NIHRD-MP059/2023","C",NA,"Original","EPI_ISL_18467794",2023-10-27,"2023-11-06","197,199","Asia / Indonesia / Banten / Tangerang Selatan","Jabodetabek","National Institute of Health Research and Development","C8" +"9","hMpxV/Indonesia/JK-NIHRD-MP023/2023","M",26,"Original","EPI_ISL_18467795",2023-10-23,"2023-11-06","197,199","Asia / Indonesia / DKI Jakarta / Jakarta Barat","Jabodetabek","National Institute of Health Research and Development","C9" +"10","hMpxV/Indonesia/JK-NIHRD-MP081/2023","M",24,"Original","EPI_ISL_18467798",2023-10-27,"2023-11-06","197,199","Asia / Indonesia / DKI Jakarta / Jakarta Barat","Jabodetabek","National Institute of Health Research and Development","C10" +"11","hMpxV/Indonesia/JK-NIHRD-MP025/2023","M",30,"Original","EPI_ISL_18467796",2023-10-23,"2023-11-06","197,199","Asia / Indonesia / DKI Jakarta / Jakarta Barat","Jabodetabek","National Institute of Health Research and Development","C11" +"12","hMpxV/Indonesia/JK-NIHRD-MP055/2023","M",23,"Original","EPI_ISL_18467797",2023-10-27,"2023-11-06","197,199","Asia / Indonesia / DKI Jakarta / Jakarta Barat","Jabodetabek","National Institute of Health Research and Development","C12" +"13","hMpxV/Indonesia/JK-NIHRD-MP085/2023","M",31,"Original","EPI_ISL_18467803",2023-10-30,"2023-11-06","197,199","Asia / Indonesia / DKI Jakarta / Jakarta Selatan","Jabodetabek","National Institute of Health Research and Development","C13" +"14","hMpxV/Indonesia/JK-NIHRD-MP022/2023","M",28,"Original","EPI_ISL_18467799",2023-10-23,"2023-11-06","197,199","Asia / Indonesia / DKI Jakarta / Jakarta Selatan","Jabodetabek","National Institute of Health Research and Development","C14" +"15","hMpxV/Indonesia/JK-NIHRD-MP036/2023","M",32,"Original","EPI_ISL_18467800",2023-10-25,"2023-11-06","197,199","Asia / Indonesia / DKI Jakarta / Jakarta Selatan","Jabodetabek","National Institute of Health Research and Development","C15" +"16","hMpxV/Indonesia/JK-NIHRD-MP061/2023","M",31,"Original","EPI_ISL_18467802",2023-10-27,"2023-11-06","197,095","Asia / Indonesia / DKI Jakarta / Jakarta Selatan","Jabodetabek","National Institute of Health Research and Development","C16" +"17","hMpxV/Indonesia/JK-NIHRD-MP039/2023","M",20,"Original","EPI_ISL_18467801",2023-10-25,"2023-11-06","197,199","Asia / Indonesia / DKI Jakarta / Jakarta Selatan","Jabodetabek","National Institute of Health Research and Development","C17" +"18","hMpxV/Indonesia/JK-NIHRD-MP044/2023","M",48,"Original","EPI_ISL_18467805",2023-10-25,"2023-11-06","197,183","Asia / Indonesia / DKI Jakarta / Jakarta Timur","Jabodetabek","National Institute of Health Research and Development","C18" +"19","hMpxV/Indonesia/JK-NIHRD-MP035/2023","M",28,"Original","EPI_ISL_18467804",2023-10-25,"2023-11-06","197,181","Asia / Indonesia / DKI Jakarta / Jakarta Timur","Jabodetabek","National Institute of Health Research and Development","C19" +"20","hMpxV/Indonesia/JK-NIHRD-MP080/2023","M",38,"Original","EPI_ISL_18467806",2023-10-28,"2023-11-06","197,199","Asia / Indonesia / DKI Jakarta / Jakarta Utara","Jabodetabek","National Institute of Health Research and Development","C20" +"21","hMpxV/Indonesia/JK-NIHRD-MP088/2023","M",21,"Original","EPI_ISL_18467807",2023-10-30,"2023-11-06","197,199","Asia / Indonesia / DKI Jakarta / Jakarta Utara","Jabodetabek","National Institute of Health Research and Development","C21" +"22","hMpxV/Indonesia/JB-NIHRD-MP041/2023","M",36,"Original","EPI_ISL_18467808",2023-10-25,"2023-11-06","197,199","Asia / Indonesia / Jawa Barat / Bandung","Bandung","National Institute of Health Research and Development","C22" +"23","hMpxV/Indonesia/BT-NIHRD-MP231/2023","C",NA,"Original","EPI_ISL_18642365",2023-11-16,"2023-12-18","197,204","Asia / Indonesia / Banten / Tangerang Selatan","Jabodetabek","National Institute of Health Research and Development","C23" +"24","hMpxV/Indonesia/JK-NIHRD-MP109/2023","M",32,"Original","EPI_ISL_18642356",2023-10-31,"2023-12-18","197,196","Asia / Indonesia / DKI Jakarta / Jakarta Pusat","Jabodetabek","National Institute of Health Research and Development","C24" +"25","hMpxV/Indonesia/JK-NIHRD-MP209/2023","M",34,"Original","EPI_ISL_18642363",2023-11-13,"2023-12-18","197,196","Asia / Indonesia / DKI Jakarta / Jakarta Selatan","Jabodetabek","National Institute of Health Research and Development","C25" +"26","hMpxV/Indonesia/JK-NIHRD-MP177/2023","M",37,"Original","EPI_ISL_18642361",2023-11-08,"2023-12-18","197,195","Asia / Indonesia / DKI Jakarta / Jakarta Selatan","Jabodetabek","National Institute of Health Research and Development","C26" +"27","hMpxV/Indonesia/JK-NIHRD-MP218/2023","M",28,"Original","EPI_ISL_18642364",2023-11-14,"2023-12-18","197,199","Asia / Indonesia / DKI Jakarta / Jakarta Selatan","Jabodetabek","National Institute of Health Research and Development","C27" +"28","hMpxV/Indonesia/JK-NIHRD-MP156/2023","M",38,"Original","EPI_ISL_18642360",2023-11-04,"2023-12-18","197,200","Asia / Indonesia / DKI Jakarta / Jakarta Selatan","Jabodetabek","National Institute of Health Research and Development","C28" +"29","hMpxV/Indonesia/JK-NIHRD-MP114/2023","M",27,"Original","EPI_ISL_18642357",2023-11-01,"2023-12-18","197,199","Asia / Indonesia / DKI Jakarta / Jakarta Timur","Jabodetabek","National Institute of Health Research and Development","C29" +"30","hMpxV/Indonesia/JK-NIHRD-MP147/2023","M",20,"Original","EPI_ISL_18642359",2023-11-03,"2023-12-18","197,200","Asia / Indonesia / DKI Jakarta / Jakarta Timur","Jabodetabek","National Institute of Health Research and Development","C30" +"31","hMpxV/Indonesia/JK-NIHRD-MP118/2023","M",41,"Original","EPI_ISL_18642358",2023-11-01,"2023-12-18","197,196","Asia / Indonesia / DKI Jakarta / Jakarta Utara","Jabodetabek","National Institute of Health Research and Development","C31" +"32","hMpxV/Indonesia/JB-NIHRD-MP205/2023","M",24,"Original","EPI_ISL_18642362",2023-11-10,"2023-12-18","197,199","Asia / Indonesia / Jawa Barat / Cirebon","Cirebon","National Institute of Health Research and Development","C32" +"33","hMpxV/Indonesia/JK-NIHRD-MP235/2023","M",28,"Original","EPI_ISL_18798836",2023-11-16,"2024-01-22","197,199","Asia / Indonesia / DKI Jakarta / Jakarta Barat","Jabodetabek","National Institute of Health Research and Development","C33" +"34","hMpxV/Indonesia/JK-NIHRD-MP252/2023","M",24,"Original","EPI_ISL_18798838",2023-11-21,"2024-01-22","197,166","Asia / Indonesia / DKI Jakarta / Jakarta Pusat","Jabodetabek","National Institute of Health Research and Development","C34" +"35","hMpxV/Indonesia/JK-NIHRD-MP279/2023","M",34,"Original","EPI_ISL_18798842",2023-11-30,"2024-01-22","197,199","Asia / Indonesia / DKI Jakarta / Jakarta Selatan","Jabodetabek","National Institute of Health Research and Development","C35" +"36","hMpxV/Indonesia/JK-NIHRD-MP246/2023","M",30,"Original","EPI_ISL_18798837",2023-11-20,"2024-01-22","197,199","Asia / Indonesia / DKI Jakarta / Jakarta Selatan","Jabodetabek","National Institute of Health Research and Development","C36" +"37","hMpxV/Indonesia/JK-NIHRD-MP225/2023","M",31,"Original","EPI_ISL_18798835",2023-11-16,"2024-01-22","197,199","Asia / Indonesia / DKI Jakarta / Jakarta Selatan","Jabodetabek","National Institute of Health Research and Development","C37" +"38","hMpxV/Indonesia/JK-NIHRD-MP159/2023","M",27,"Original","EPI_ISL_18798834",2023-11-06,"2024-01-22","197,199","Asia / Indonesia / DKI Jakarta / Jakarta Selatan","Jabodetabek","National Institute of Health Research and Development","C38" +"39","hMpxV/Indonesia/JK-NIHRD-MP276/2023","M",36,"Original","EPI_ISL_18798841",2023-11-29,"2024-01-22","197,197","Asia / Indonesia / DKI Jakarta / Jakarta Utara","Jabodetabek","National Institute of Health Research and Development","C39" +"40","hMpxV/Indonesia/JB-NIHRD-MP255/2023","M",23,"Original","EPI_ISL_18798840",2023-11-20,"2024-01-22","197,184","Asia / Indonesia / Jawa Barat / Bogor","Jabodetabek","National Institute of Health Research and Development","C40" +"41","hMpxV/Indonesia/JB-NIHRD-MP254/2023","M",39,"Original","EPI_ISL_18798839",2023-11-20,"2024-01-22","197,199","Asia / Indonesia / Jawa Barat / Bogor","Jabodetabek","","C41" +"42","hMpxV/Indonesia/BT-Biokes-MP303/2023","F",26,"Original","EPI_ISL_19159112",2023-12-12,"2024-05-23","197,199","Asia / Indonesia / Banten / Tangerang Selatan","Jabodetabek","Balai Besar Laboratorium Biologi Kesehatan","C42" +"43","hMpxV/Indonesia/JK-Biokes-MP302/2023","M",32,"Original","EPI_ISL_19159111",2023-12-12,"2024-05-23","197,181","Asia / Indonesia / DKI Jakarta / Jakarta Barat","Jabodetabek","Balai Besar Laboratorium Biologi Kesehatan","C43" +"44","hMpxV/Indonesia/JK-Biokes-MP311/2023","M",27,"Original","EPI_ISL_19159114",2023-12-15,"2024-05-23","197,209","Asia / Indonesia / DKI Jakarta / Jakarta Pusat","Jabodetabek","Balai Besar Laboratorium Biologi Kesehatan","C44" +"45","hMpxV/Indonesia/JK-Biokes-MP018/2024","M",34,"Original","EPI_ISL_19159118",2024-02-07,"2024-05-23","197,209","Asia / Indonesia / DKI Jakarta / Jakarta Pusat","Jabodetabek","Balai Besar Laboratorium Biologi Kesehatan","C45" +"46","hMpxV/Indonesia/JK-Biokes-MP029/2024","M",33,"Original","EPI_ISL_19159120",2024-04-11,"2024-05-23","197,163","Asia / Indonesia / DKI Jakarta / Jakarta Selatan","Jabodetabek","Balai Besar Laboratorium Biologi Kesehatan","C46" +"47","hMpxV/Indonesia/JK-Biokes-MP310/2023","M",22,"Original","EPI_ISL_19159113",2023-12-15,"2024-05-23","197,199","Asia / Indonesia / DKI Jakarta / Jakarta Selatan","Jabodetabek","Balai Besar Laboratorium Biologi Kesehatan","C47" +"48","hMpxV/Indonesia/JK-Biokes-MP016/2024","M",23,"Original","EPI_ISL_19159117",2024-02-07,"2024-05-23","197,177","Asia / Indonesia / DKI Jakarta / Jakarta Selatan","Jabodetabek","Balai Besar Laboratorium Biologi Kesehatan","C48" +"49","hMpxV/Indonesia/JK-Biokes-MP020/2024","M",30,"Original","EPI_ISL_19159119",2024-02-17,"2024-05-23","197,199","Asia / Indonesia / DKI Jakarta / Jakarta Utara","Jabodetabek","Balai Besar Laboratorium Biologi Kesehatan","C49" +"50","hMpxV/Indonesia/JK-Biokes-MP239/2023","M",34,"Original","EPI_ISL_19159108",2023-11-18,"2024-05-23","197,192","Asia / Indonesia / DKI Jakarta / Jakarta Utara","Jabodetabek","Balai Besar Laboratorium Biologi Kesehatan","C50" +"51","hMpxV/Indonesia/JK-Biokes-MP010/2024","F",29,"Original","EPI_ISL_19159115",2024-01-22,"2024-05-23","197,199","Asia / Indonesia / DKI Jakarta / Jakarta Utara","Jabodetabek","Balai Besar Laboratorium Biologi Kesehatan","C51" +"52","hMpxV/Indonesia/JK-Biokes-MP011/2024","M",34,"Original","EPI_ISL_19159116",2024-01-22,"2024-05-23","197,182","Asia / Indonesia / DKI Jakarta / Jakarta Utara","Jabodetabek","Balai Besar Laboratorium Biologi Kesehatan","C52" +"53","hMpxV/Indonesia/JB-Biokes-MP295/2023","F",26,"Original","EPI_ISL_19159110",2023-12-09,"2024-05-23","197,201","Asia / Indonesia / Jawa Barat / Depok","Jabodetabek","Balai Besar Laboratorium Biologi Kesehatan","C53" +"54","hMpxV/Indonesia/JB-Biokes-MP294/2023","M",29,"Original","EPI_ISL_19159109",2023-12-07,"2024-05-23","197,182","Asia / Indonesia / Jawa Barat / Bandung","Bandung","Balai Besar Laboratorium Biologi Kesehatan","C54" +"55","hMpxV/Indonesia/CU-56/2023","C",NA,"Orginal","EPI_ISL_19255531",2023-11-04,"2024-07-10","531","Asia / Indonesia / Jakarta","Jabodetabek","Pathogen Hunter's Research Collaborative Team","C55" +"56","hMpxV/Indonesia/CU-58/2023","C",NA,"Orginal","EPI_ISL_19255530",2023-11-21,"2024-07-10","531","Asia / Indonesia / Jakarta","Jabodetabek","Pathogen Hunter's","C56" +"57","hMpxV/Indonesia/CU-42/2023","C",NA,"Orginal","EPI_ISL_19255532",2023-10-11,"2024-07-10","531","Asia / Indonesia / Jakarta","Jabodetabek","","C57" +"58","hMpxV/Indonesia/CU-45/2023","C",NA,"Orginal","EPI_ISL_19255533",2023-11-16,"2024-07-10","531","Asia / Indonesia / Jakarta","Jabodetabek","","C58" +"59","hMpxV/Indonesia/CU-29/2023","C",NA,"Orginal","EPI_ISL_19255528",2023-10-13,"2024-07-10","531","Asia / Indonesia / West Java","West Java","","C59" +"60","hMpxV/Indonesia/CU-74/2023","C",NA,"Orginal","EPI_ISL_19255529",2023-10-16,"2024-07-10","448","Asia / Indonesia / West Java","West Java","","C60" diff --git a/inst/extdata/pox_strict_comb.tree b/inst/extdata/pox_strict_comb.tree new file mode 100644 index 0000000..12ce11b --- /dev/null +++ b/inst/extdata/pox_strict_comb.tree @@ -0,0 +1,121 @@ +#NEXUS + +Begin taxa; + Dimensions ntax=54; + Taxlabels + hMpxV/Indonesia/BT-Biokes-MP303/2023 + hMpxV/Indonesia/BT-NIHRD-MP059/2023 + hMpxV/Indonesia/BT-NIHRD-MP231/2023 + hMpxV/Indonesia/JB-Biokes-MP294/2023 + hMpxV/Indonesia/JB-Biokes-MP295/2023 + hMpxV/Indonesia/JB-NIHRD-MP041/2023 + hMpxV/Indonesia/JB-NIHRD-MP205/2023 + hMpxV/Indonesia/JB-NIHRD-MP254/2023 + hMpxV/Indonesia/JB-NIHRD-MP255/2023 + hMpxV/Indonesia/JK-Biokes-MP010/2024 + hMpxV/Indonesia/JK-Biokes-MP011/2024 + hMpxV/Indonesia/JK-Biokes-MP016/2024 + hMpxV/Indonesia/JK-Biokes-MP018/2024 + hMpxV/Indonesia/JK-Biokes-MP020/2024 + hMpxV/Indonesia/JK-Biokes-MP029/2024 + hMpxV/Indonesia/JK-Biokes-MP239/2023 + hMpxV/Indonesia/JK-Biokes-MP302/2023 + hMpxV/Indonesia/JK-Biokes-MP310/2023 + hMpxV/Indonesia/JK-Biokes-MP311/2023 + hMpxV/Indonesia/JK-NIHRD-MP0024/2022 + hMpxV/Indonesia/JK-NIHRD-MP005/2023 + hMpxV/Indonesia/JK-NIHRD-MP008/2023 + hMpxV/Indonesia/JK-NIHRD-MP010/2023 + hMpxV/Indonesia/JK-NIHRD-MP012/2023 + hMpxV/Indonesia/JK-NIHRD-MP015/2023 + hMpxV/Indonesia/JK-NIHRD-MP017/2023 + hMpxV/Indonesia/JK-NIHRD-MP022/2023 + hMpxV/Indonesia/JK-NIHRD-MP023/2023 + hMpxV/Indonesia/JK-NIHRD-MP025/2023 + hMpxV/Indonesia/JK-NIHRD-MP035/2023 + hMpxV/Indonesia/JK-NIHRD-MP036/2023 + hMpxV/Indonesia/JK-NIHRD-MP039/2023 + hMpxV/Indonesia/JK-NIHRD-MP044/2023 + hMpxV/Indonesia/JK-NIHRD-MP055/2023 + hMpxV/Indonesia/JK-NIHRD-MP061/2023 + hMpxV/Indonesia/JK-NIHRD-MP080/2023 + hMpxV/Indonesia/JK-NIHRD-MP081/2023 + hMpxV/Indonesia/JK-NIHRD-MP085/2023 + hMpxV/Indonesia/JK-NIHRD-MP088/2023 + hMpxV/Indonesia/JK-NIHRD-MP109/2023 + hMpxV/Indonesia/JK-NIHRD-MP114/2023 + hMpxV/Indonesia/JK-NIHRD-MP118/2023 + hMpxV/Indonesia/JK-NIHRD-MP147/2023 + hMpxV/Indonesia/JK-NIHRD-MP156/2023 + hMpxV/Indonesia/JK-NIHRD-MP159/2023 + hMpxV/Indonesia/JK-NIHRD-MP177/2023 + hMpxV/Indonesia/JK-NIHRD-MP209/2023 + hMpxV/Indonesia/JK-NIHRD-MP218/2023 + hMpxV/Indonesia/JK-NIHRD-MP225/2023 + hMpxV/Indonesia/JK-NIHRD-MP235/2023 + hMpxV/Indonesia/JK-NIHRD-MP246/2023 + hMpxV/Indonesia/JK-NIHRD-MP252/2023 + hMpxV/Indonesia/JK-NIHRD-MP276/2023 + hMpxV/Indonesia/JK-NIHRD-MP279/2023 + ; +End; + +Begin trees; + Translate + 1 hMpxV/Indonesia/BT-Biokes-MP303/2023, + 2 hMpxV/Indonesia/BT-NIHRD-MP059/2023, + 3 hMpxV/Indonesia/BT-NIHRD-MP231/2023, + 4 hMpxV/Indonesia/JB-Biokes-MP294/2023, + 5 hMpxV/Indonesia/JB-Biokes-MP295/2023, + 6 hMpxV/Indonesia/JB-NIHRD-MP041/2023, + 7 hMpxV/Indonesia/JB-NIHRD-MP205/2023, + 8 hMpxV/Indonesia/JB-NIHRD-MP254/2023, + 9 hMpxV/Indonesia/JB-NIHRD-MP255/2023, + 10 hMpxV/Indonesia/JK-Biokes-MP010/2024, + 11 hMpxV/Indonesia/JK-Biokes-MP011/2024, + 12 hMpxV/Indonesia/JK-Biokes-MP016/2024, + 13 hMpxV/Indonesia/JK-Biokes-MP018/2024, + 14 hMpxV/Indonesia/JK-Biokes-MP020/2024, + 15 hMpxV/Indonesia/JK-Biokes-MP029/2024, + 16 hMpxV/Indonesia/JK-Biokes-MP239/2023, + 17 hMpxV/Indonesia/JK-Biokes-MP302/2023, + 18 hMpxV/Indonesia/JK-Biokes-MP310/2023, + 19 hMpxV/Indonesia/JK-Biokes-MP311/2023, + 20 hMpxV/Indonesia/JK-NIHRD-MP0024/2022, + 21 hMpxV/Indonesia/JK-NIHRD-MP005/2023, + 22 hMpxV/Indonesia/JK-NIHRD-MP008/2023, + 23 hMpxV/Indonesia/JK-NIHRD-MP010/2023, + 24 hMpxV/Indonesia/JK-NIHRD-MP012/2023, + 25 hMpxV/Indonesia/JK-NIHRD-MP015/2023, + 26 hMpxV/Indonesia/JK-NIHRD-MP017/2023, + 27 hMpxV/Indonesia/JK-NIHRD-MP022/2023, + 28 hMpxV/Indonesia/JK-NIHRD-MP023/2023, + 29 hMpxV/Indonesia/JK-NIHRD-MP025/2023, + 30 hMpxV/Indonesia/JK-NIHRD-MP035/2023, + 31 hMpxV/Indonesia/JK-NIHRD-MP036/2023, + 32 hMpxV/Indonesia/JK-NIHRD-MP039/2023, + 33 hMpxV/Indonesia/JK-NIHRD-MP044/2023, + 34 hMpxV/Indonesia/JK-NIHRD-MP055/2023, + 35 hMpxV/Indonesia/JK-NIHRD-MP061/2023, + 36 hMpxV/Indonesia/JK-NIHRD-MP080/2023, + 37 hMpxV/Indonesia/JK-NIHRD-MP081/2023, + 38 hMpxV/Indonesia/JK-NIHRD-MP085/2023, + 39 hMpxV/Indonesia/JK-NIHRD-MP088/2023, + 40 hMpxV/Indonesia/JK-NIHRD-MP109/2023, + 41 hMpxV/Indonesia/JK-NIHRD-MP114/2023, + 42 hMpxV/Indonesia/JK-NIHRD-MP118/2023, + 43 hMpxV/Indonesia/JK-NIHRD-MP147/2023, + 44 hMpxV/Indonesia/JK-NIHRD-MP156/2023, + 45 hMpxV/Indonesia/JK-NIHRD-MP159/2023, + 46 hMpxV/Indonesia/JK-NIHRD-MP177/2023, + 47 hMpxV/Indonesia/JK-NIHRD-MP209/2023, + 48 hMpxV/Indonesia/JK-NIHRD-MP218/2023, + 49 hMpxV/Indonesia/JK-NIHRD-MP225/2023, + 50 hMpxV/Indonesia/JK-NIHRD-MP235/2023, + 51 hMpxV/Indonesia/JK-NIHRD-MP246/2023, + 52 hMpxV/Indonesia/JK-NIHRD-MP252/2023, + 53 hMpxV/Indonesia/JK-NIHRD-MP276/2023, + 54 hMpxV/Indonesia/JK-NIHRD-MP279/2023 + ; +tree TREE1 = [&R] 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+End; diff --git a/inst/extdata/random_tree.nwk b/inst/extdata/random_tree.nwk new file mode 100644 index 0000000..b659482 --- /dev/null +++ b/inst/extdata/random_tree.nwk @@ -0,0 +1 @@ +((((t8:0.942455692,t5:0.9626080138)100:0.3889450287,(((t1:0.002272966085,t17:0.6089374525)93:0.53576129,t7:0.8368015594)63:0.7332459057,t4:0.7515225627)74:0.7398552792)97:0.216567311,(((t13:0.001380843576,t10:0.3556659538)55:0.5373766953,(t9:0.8289421306,(t15:0.4106351258,t12:0.5734758989)55:0.3567219994)53:0.6121330902)71:0.5357899938,(((t3:0.9192039291,t19:0.9625702936)56:0.3949730452,((t20:0.9036345251,t11:0.6034740848)67:0.7244976,(t16:0.9373858497,t6:0.8504827507)61:0.6315072989)92:0.2335235255)56:0.7196572924,t2:0.5798208991)83:0.5896783036)72:0.4527315726)87:0.2171576982,(t14:0.1137186091,t18:0.7645077587)84:0.8214039239)59; diff --git a/man/beastclus.Rd b/man/beastclus.Rd new file mode 100644 index 0000000..e1cbc5a --- /dev/null +++ b/man/beastclus.Rd @@ -0,0 +1,41 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/beastclus.R +\name{beastclus} +\alias{beastclus} +\title{Extract Clusters from a BEAST Phylogenetic Tree} +\usage{ +beastclus( + beast_tree, + metadata, + post_threshold = 0.7, + date_range = 90, + samearea = FALSE +) +} +\arguments{ +\item{beast_tree}{A BEAST tree object of class \code{phylo4d} or similar.} + +\item{metadata}{A metadata dataframe containing columns \code{label}, \code{location}, and \code{date}.} + +\item{post_threshold}{Numeric value specifying the posterior probability threshold for including a cluster (default = 0.70).} + +\item{date_range}{Numeric value specifying the maximum allowable date range (in days) within clusters (default = 90).} + +\item{samearea}{Logical value indicating whether clusters must originate from the same geographic area (default = FALSE).} +} +\value{ +A dataframe summarizing the clusters, including labels, posterior probabilities, areas, date ranges, and the number of tips. +} +\description{ +Extract Clusters from a BEAST Phylogenetic Tree +} +\examples{ +# Example usage: +# Assuming `beast_tree` is a BEAST tree object and `metadata` is a dataframe +data_csv <- system.file("extdata", "metadata_samp.csv", package = "caIRA") +metadata<-read.csv(data_csv) +data_beast <- system.file("extdata", "pox_strict_comb.tree", package = "caIRA") +beast_tree <- treeio::read.beast(data_beast) +# with the required columns: +beastclus(beast_tree, metadata, post_threshold = 0.50, date_range = 90, samearea = TRUE) +} diff --git a/tests/testthat.R b/tests/testthat.R new file mode 100644 index 0000000..4a6a75f --- /dev/null +++ b/tests/testthat.R @@ -0,0 +1,12 @@ +# This file is part of the standard setup for testthat. +# It is recommended that you do not modify it. +# +# Where should you do additional test configuration? +# Learn more about the roles of various files in: +# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview +# * https://testthat.r-lib.org/articles/special-files.html + +library(testthat) +library(caIRA) + +test_check("caIRA") diff --git a/tests/testthat/test-beastclus.R b/tests/testthat/test-beastclus.R new file mode 100644 index 0000000..a8eabcf --- /dev/null +++ b/tests/testthat/test-beastclus.R @@ -0,0 +1,16 @@ +test_that("beastclus returns expected output", { + library(treeio) + library(ggtree) + library(dplyr) + library(tidyverse) + # Example inputs + metadata<-read.csv('https://raw.githubusercontent.com/Dhihram/caIRA/refs/heads/master/data/metadata_samp.csv') + beast_tree <- read.beast('https://raw.githubusercontent.com/Dhihram/caIRA/refs/heads/master/data/pox_strict_comb.tree') + + # Run the function + result <- beastclus(beast_tree, metadata, post_threshold = 0.50, date_range = 90, samearea = TRUE) + + # Expectations + expect_s3_class(result, "data.frame") + expect_named(result, c("ParentNode", "label", "Posterior", "AreaName", "min_date", "max_date", "NumTips", "dif")) +})